Prof. Pavel Hobza, Dr.Sc.

Email: pavel.hobza@uochb.cas.cz
Location:
Institute of Organic Chemistry and Biochemistry , Academy of Sciences of the Czech Republic,  166 10 Prague 6, Czech Republic
Phone:
(+420 )220 410 311

Tady bude neviditelný text – prázdná mezera

Tady bude neviditelný text – prázdná mezera

Tady bude neviditelný text – prázdná mezera

Professional
Born October 21, 1946 in Prerov, Czech Republic
Professor in Physical Chemistry, Charles University, Prague, Czech Republic
Professor in Physical Chemistry, Palacky University, Olomouc, Czech Republic
World Class University Professor, Postech University, Pohang, Korea

Career
Institute of Hygiene and Epidemiology
1979,1982       Postdoctoral Fellow at the Universite de Montreal, Canada
1984,1986       Visiting Professor at the Universite de Montreal, Canada
1990                Research Associate at Friedrich-Alexander-Universität Erlangen-Nürnberg, Germany and Technische Universität München, Germany
1990-1991       DFG-visiting professor, Technische Universität München, Germany
1991-2003       J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Prague
2000-2004      Research Center for Complex  Molecular Systems and Biomolecules, head
2002-now        Professor of Physical Chemistry, Charles University, Prague
2005-now        Research Center for Biomolecules and Complex Molecular Systems, head
2003-now        Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Department of Molecular Modelling, head
2005-now        Professor of Physical Chemistry, Palacký University, Olomouc

Field of Scholary Interest
Quantum chemistry and computational chemistry, non-covalent interactions, structure and dynamics of molecular and biomolecular clusters and biomolecules, hydrogen-bonding and improper, blue-shifting hydrogen-bonding, halogen bonding, drug design

Education and Training
Faculty of Technical and Nuclear Physics,  Czech Technical   University, Prague, chemistry (M.Sc.)
Institute of Physical Chemistry, Czechoslovak Academy of Sciences, Prague, C.Sc. (Ph.D.)

Awards and Honors
D.Sc. from Institute of Chemical Technology, Prague (1988)
Prize of Czech Literary Fond (1981, 1989)
Deutsche Forschung Gemeinschaft Gastprofessor, Technische Universität München (1992)
Czech Learned Society (1996), member
European Academy of Arts, Sciences and Humanities (2000),  member
Prize of Ministry of Education  of the Czech Republic (2000)
Prize of the Academy of Sciences of the Czech Republic (2003)
The Royal Society of Chemistry (2005), fellow
The Photon Science Institute, University of Manchester (2006) , fellow
Distinguish Chair, Institute of Organic Chemistry and Biochemistry (2007)
Praemium Academiae, Academy of Sciences of the Czech Republic (2007)
Ceska hlava, Goverment of the Czech Republic(2008)
World Class University Professor, Postech University, Pohang, Korea (2009)

Publication activities:
396 papers in referred journals and 3 books.

Citation index
The total number of citations (ICI) until February, 2011 is more than 17000; value of Hirsch index amounts to 70

Thesis adviser
PH directed altogether 22 PhD students, 10 Diploma students and 4 postdoctoral fellows. At present he supervises 6 PhD students, 1 Diploma students and 7  postdoctoral fellows.

Oral presentations, invited talks at world symposia and international conferences:
more than 50 pleneary and invited lectures at international conferences and leading universities in Europe, USA and Asia in the last 5 years

Funding
-Praemium Academiae, Academy of Sciences of the Czech Republic (2007-12; 25 000 000 Cz crowns),PI
-Research Center for Complex Molecular Systems and Biomolecules, Ministry of Education of the Czech Republic (2000 – 4; 85 000 000 Cz crowns), head
-Research Center for Biomolecules and Complex Molecular Systems, Ministry of Education of the Czech Republic (2005 -  11; 98 000 000 Cz crowns), head
-NSF grants   (2002-4 ; 2010-12 together with M.de Vries, University of California) PH is co-PI
-1995-present : 10 grants from Grant Agency of the Czech Republic and Grant Agency of the Academy of Sciences of the Czech Republic, PH is PI

Membership in Editorial  Boards
Chemistry – A European Journal (2005-now)
Chemical Reviews (1994-2004)
Phys. Chem. Chem. Phys. (2004-now)
Chem. Phys. Chem. (2006-now)
Chem. Phys. (2006-now)
Collection of Czechoslov. Chem. Commun.(2006-now, Chairman)

Membership in Scientific and Govermental Commitees
Scientific Council of the Academy of Sciences of the Czech Republic
Research and Development Council of the Czech Republic
Scientific Council of the Faculty of Science, Palacky University

Show publications

Publications

2011

  • [DOI] E. Munusamy, R. Sedlak, and P. Hobza, “On the Nature of the Stabilization of Benzene center dot center dot
    center dot Dihalogen and Benzene center dot center dot center dot
    Dinitrogen Complexes: CCSD(T)/CBS and DFT-SAPT Calculations,” CHEMPHYSCHEM, vol. 12, iss. 17, pp. 3253-3261, 2011.
    [Bibtex]
    @article ISI:000297693200021,
    Author = Munusamy, Elango and Sedlak, Robert and Hobza, Pavel,
    Title = On the Nature of the Stabilization of Benzene center dot center dot
       center dot Dihalogen and Benzene center dot center dot center dot
       Dinitrogen Complexes: CCSD(T)/CBS and DFT-SAPT Calculations,
    Journal = CHEMPHYSCHEM,
    Year = 2011,
    Volume = 12,
    Number = 17,
    Pages = 3253-3261,
    Month = DEC 9,
    Abstract = The structure and stabilization energies of benzene (and methylated
       benzenes)-X2 (X=F, Cl, Br, N) complexes were investigated by performing
       CCSD(T)/complete basis set limit and density functional
       theory/symmetry-adapted perturbation theory (DFT-SAPT) calculations. The
       global minimum of the benzene-dihalogen complexes corresponds to the
       T-shaped structure, whereas that of benzene-dinitrogen corresponds to
       the sandwich one. The different binding motifs of these complexes arise
       from the different quadrupole moments of dihalogens and dinitrogen. The
       different sign of the quadrupole moments of these diatomics is explained
       based on the electrostatic potential (ESP). Whereas all dihalogens,
       including difluorine, possess a positive sigma hole, such a positive
       area of the ESP is completely missing in the case of dinitrogen.
       Moreover, benzene-X(2) (X=Br, Cl) electrostatic, dispersion, induction,
       and delta(HartreeFock) energies, we recapitulate that the former
       complexes are stabilized mainly by dispersion energy, followed by
       electrostatic energy, whereas the latter complexes are stabilized mostly
       by the dispersion interaction. The charge-transfer energy of
       benzene-dibromine complexes, and surprisingly, also of methylated
       benzenes-dibromine complexes is only moderate, and thus, not responsible
       for their stabilization. Benzene-dichlorine and benzene-dibromine
       complexes can thus be characterized merely as complexes with a halogen
       bond rather than as charge-transfer complexes.,
    DOI = 10.1002/cphc.201100455,
    ISSN = 1439-4235,
    Unique-ID = ISI:000297693200021,
    
  • [DOI] J. Rezac, K. E. Riley, and P. Hobza, “Extensions of the S66 Data Set: More Accurate Interaction Energies and
    Angular-Displaced Nonequilibrium Geometries,” JOURNAL OF CHEMICAL THEORY AND COMPUTATION, vol. 7, iss. 11, pp. 3466-3470, 2011.
    [Bibtex]
    @article ISI:000296597300002,
    Author = Rezac, Jan and Riley, Kevin E. and Hobza, Pavel,
    Title = Extensions of the S66 Data Set: More Accurate Interaction Energies and
       Angular-Displaced Nonequilibrium Geometries,
    Journal = JOURNAL OF CHEMICAL THEORY AND COMPUTATION,
    Year = 2011,
    Volume = 7,
    Number = 11,
    Pages = 3466-3470,
    Month = NOV,
    Abstract = We present two extensions of the recently published S66 data set
       [Rezac, Riley, Hobza; DOI: 10.1021/ct2002946]. Interaction energies
       for the equilibrium geometry complexes have been recalculated using a
       triple-zeta basis set for the CCSD(T) term in the CCSD(T)/CBS scheme.
       This allows for the extrapolation of this term to the complete basis set
       limit, improving accuracy by almost 1 order of magnitude compared to the
       scheme previously used for the S66 set. Now, we estimate the largest
       error in the set to be about 1\%. Validation of several methods against
       the new data indicates the exceptional robustness and accuracy of the
       SCS-MI-CCSD method. The second extension improves the coverage of
       nonequilibrium geometries. We introduce a new data set, S66a8, that
       samples intermolecular angular degrees of freedom in the S66 complexes.
       For each of the 66 complexes, eight displaced geometries have been
       constructed, systematically sampling possible rotations of the monomers.
       Interaction energies in this set are calculated at the CCSD(T)/CBS level
       consistently with the earlier introduced S66x8 data set that samples the
       intermolecular distance.,
    DOI = 10.1021/ct200523a,
    ISSN = 1549-9618,
    Unique-ID = ISI:000296597300002,
    
  • [DOI] J. Granatier, P. Lazar, M. Otyepka, and P. Hobza, “The Nature of the Binding of Au, Ag, and Pd to Benzene, Coronene, and
    Graphene: From Benchmark CCSD(T) Calculations to Plane-Wave DFT
    Calculations,” JOURNAL OF CHEMICAL THEORY AND COMPUTATION, vol. 7, iss. 11, pp. 3743-3755, 2011.
    [Bibtex]
    @article ISI:000296597300030,
    Author = Granatier, Jaroslav and Lazar, Petr and Otyepka, Michal and Hobza, Pavel,
    Title = The Nature of the Binding of Au, Ag, and Pd to Benzene, Coronene, and
       Graphene: From Benchmark CCSD(T) Calculations to Plane-Wave DFT
       Calculations,
    Journal = JOURNAL OF CHEMICAL THEORY AND COMPUTATION,
    Year = 2011,
    Volume = 7,
    Number = 11,
    Pages = 3743-3755,
    Month = NOV,
    Abstract = The adsorption of Ag, Au, and Pd atoms on benzene, coronene, and
       graphene has been studied using post Hartree-Fock wave function theory
       (CCSD(T), MP2) and density functional theory (M06-2X, DFT-D3, PBE,
       vdW-DF) methods. The CCSD(T) benchmark binding energies for benzene-M (M
       = Pd, Au, Ag) complexes are 19.7, 4.2, and 2.3 kcal/mol, respectively.
       We found that the nature of binding of the three metals is different:
       While silver binds predominantly through dispersion interactions, the
       binding of palladium has a covalent character, and the binding of gold
       involves a subtle combination of charge transfer and dispersion
       interactions as well as relativistic effects. We demonstrate that the
       CCSD(T) benchmark binding energies for benzene-M complexes can be
       reproduced in plane-wave density functional theory calculations by
       including a fraction of the exact exchange and a nonempirical van der
       Waals correction (EE+vdW). Applying the EE+vdW method, we obtained
       binding energies for the graphene-M (M = Pd, Au, Ag) complexes of 17.4,
       5.6, and 4.3 kcal/mol, respectively. The trends in binding energies
       found for the benzene M complexes correspond to those in coronene and
       graphene complexes. DFT methods that use empirical corrections to
       account for the effects of vdW interactions significantly overestimate
       binding energies in some of the studied systems.,
    DOI = 10.1021/ct200625h,
    ISSN = 1549-9618,
    Unique-ID = ISI:000296597300030,
    
  • [DOI] V. Spiwok, P. Hobza, and J. Rezac, “Free-Energy Simulations of Hydrogen Bonding versus Stacking of
    Nucleobases on a Graphene Surface,” JOURNAL OF PHYSICAL CHEMISTRY C, vol. 115, iss. 40, pp. 19455-19462, 2011.
    [Bibtex]
    @article ISI:000295546100001,
    Author = Spiwok, Vojtech and Hobza, Pavel and Rezac, Jan,
    Title = Free-Energy Simulations of Hydrogen Bonding versus Stacking of
       Nucleobases on a Graphene Surface,
    Journal = JOURNAL OF PHYSICAL CHEMISTRY C,
    Year = 2011,
    Volume = 115,
    Number = 40,
    Pages = 19455-19462,
    Month = OCT 13,
    Abstract = It has been demonstrated by molecular modeling and experiments that free
       nucleic acid bases form hydrogen-bonded complexes in vacuum but prefer
       pi-pi stacking in partially and fully solvated systems. Here we show
       using molecular dynamics simulations and metadynamics that the addition
       of a surface (in this case a nanographene monolayer) reverts the
       situation from stacking back to hydrogen bonding. Watson-Crick as well
       as several non-Watson-Crick base pairs lying on a graphene surface are
       significantly more stable in a water environment than a pi-pi-pi-stacked
       graphene-base-base assembly. It illustrates that the thermodynamics of
       nucleobase interactions results from a fine balance among hydrogen
       bonding, stacking, and solvation, and that these effects must be
       considered in molecular design.,
    DOI = 10.1021/jp202491J,
    ISSN = 1932-7447,
    Unique-ID = ISI:000295546100001,
    
  • [DOI] K. E. Riley and P. Hobza, “Strength and Character of Halogen Bonds in Protein-Ligand Complexes,” CRYSTAL GROWTH & DESIGN, vol. 11, iss. 10, pp. 4272-4278, 2011.
    [Bibtex]
    @article ISI:000295488200006,
    Author = Riley, Kevin E. and Hobza, Pavel,
    Title = Strength and Character of Halogen Bonds in Protein-Ligand Complexes,
    Journal = CRYSTAL GROWTH \& DESIGN,
    Year = 2011,
    Volume = 11,
    Number = 10,
    Pages = 4272-4278,
    Month = OCT,
    Abstract = In this study we investigate the strength and character of eight halogen
       bonding interactions from six protein-ligand complexes. The halogen
       bonding complexes investigated here were selected because of their
       favorable halogen bond characteristics. Interaction energies of model
       systems derived from protein-ligand complexes are computed at the
       MP2/aug-cc-pVDZ level of theory, and the relative contributions of
       electrostatics and dispersion are estimated by computing Delta
       E(HF)/Delta E(MP2) ratios. The relationship between these ratios and
       DFT-SAPT E(elec)/E(disp) results is calibrated using smaller model
       systems in order to gain a qualitative understanding of the relative
       roles that electrostatics and dispersion play in these halogen bonds.
       Electrostatic potentials for the halogen bonding ligands are also
       generated in order to study the relationship between halogen bond
       strengths and halogen a-hole size (and charge). It is found that the
       strength and character of the protein-ligand halogen bonds investigated
       here are strongly dependent on geometric factors and a-hole
       characteristics. Many of the halogen bonds studied here, especially
       those with favorable geometric and electrostatic properties, are found
       to be of sufficient magnitude to make significant contributions to
       protein-ligand binding.,
    DOI = 10.1021/cg200882f,
    ISSN = 1528-7483,
    Unique-ID = ISI:000295488200006,
    
  • [DOI] S. Karthikeyan, R. Sedlak, and P. Hobza, “on the Nature of Stabilization in Weak, Medium, and Strong
    Charge-Transfer Complexes: CCSD(T)/CBS and SAPT Calculations,” JOURNAL OF PHYSICAL CHEMISTRY A, vol. 115, iss. 34, SI, pp. 9422-9428, 2011.
    [Bibtex]
    @article ISI:000294146400011,
    Author = Karthikeyan, S. and Sedlak, Robert and Hobza, Pavel,
    Title = on the Nature of Stabilization in Weak, Medium, and Strong
       Charge-Transfer Complexes: CCSD(T)/CBS and SAPT Calculations,
    Journal = JOURNAL OF PHYSICAL CHEMISTRY A,
    Year = 2011,
    Volume = 115,
    Number = 34, SI,
    Pages = 9422-9428,
    Month = SEP 1,
    Abstract = Weak, medium, and strong charge-transfer (CT) complexes containing
       various electron donors (C(2)H(4), C(2)H(2), NH(3), NMe(3), HCN, H(2)O)
       and acceptors (F(2), Cl(2), BH(3), SO(2)) were investigated at the
       CCSD(T)/complete basis set (CBS) limit. The nature of the stabilization
       for these CT complexes was evaluated on the basis of perturbative NBC
       calculations and DFT-SAPT/CBS calculations. The structure of all of the
       complexes was determined by the counterpoise-corrected gradient
       optimization performed at the MP2/cc-pVTZ level, and most of complexes
       possess a linear-like contact structure. The total stabilization
       energies lie between 1 and 55 kcal/mol and the strongest complexes
       contain BH3 as an electron acceptor. When ordering the electron donors
       and electron acceptors on the basis of these energies, we obtain the
       same order as that based on the perturbative E2 charge-transfer
       energies, which provides evidence that the charge-transfer term is the
       dominant energy contribution. The CCSD(T) correction term, defined as
       the difference between the CCSD(T) and MP2 interaction energies, is
       mostly small, which allows the investigation of the CT complexes of this
       type at the ``cheap'' MP2/CBS level. In the case of weak and medium CT
       complexes (with stabilization energy smaller than about 15 kcal/mol),
       the dominant stabilization originates in the electrostatic term; the
       dispersion as well as induction and delta(HF) terms covering the CT
       energy contribution are, however, important as well. For strong CT
       complexes, induction energy is the second (after electrostatic) most
       important energy term. The role of the induction and delta(HF) terms is
       unique and characteristic for CT complexes. For all CT complexes, the
       CCSD(T)/CBS and DFT-SAPT/CBS stabilization energies are comparable, and
       surprisingly, it is true even for very strong CT complexes with
       stabilization energy close to 50 kcal/mol characteristic by substantial
       charge transfer (more than 0.3 e). It is thus possible to conclude that
       perturbative DFT-SAPT analysis is robust enough to be applied even for
       dative-like complexes with substantial charge transfer.,
    DOI = 10.1021/jp1112476,
    ISSN = 1089-5639,
    Unique-ID = ISI:000294146400011,
    
  • [DOI] J. Rezac, K. E. Riley, and P. Hobza, “S66: A Well-balanced Database of Benchmark Interaction Energies Relevant
    to Biomolecular Structures,” JOURNAL OF CHEMICAL THEORY AND COMPUTATION, vol. 7, iss. 8, pp. 2427-2438, 2011.
    [Bibtex]
    @article ISI:000293662500012,
    Author = Rezac, Jan and Riley, Kevin E. and Hobza, Pavel,
    Title = S66: A Well-balanced Database of Benchmark Interaction Energies Relevant
       to Biomolecular Structures,
    Journal = JOURNAL OF CHEMICAL THEORY AND COMPUTATION,
    Year = 2011,
    Volume = 7,
    Number = 8,
    Pages = 2427-2438,
    Month = AUG,
    Abstract = With numerous new quantum chemistry methods being developed in recent
       years and the promise of even more new methods to be developed in the
       near future, it is clearly critical that highly accurate, well-balanced,
       reference data for many different atomic and molecular properties be
       available for the parametrization and validation of these methods. One
       area of research that is of particular importance in many areas of
       chemistry, biology, and material science is the study of noncovalent
       interactions. Because these interactions are often strongly influenced
       by correlation effects, it is necessary to use computationally expensive
       high-order wave function methods to describe them accurately. Here, we
       present a large new database of interaction energies calculated using an
       accurate CCSD(T)/CBS scheme. Data are presented for 66 molecular
       complexes, at their reference equilibrium geometries and at 8 points
       systematically exploring their dissociation curves; in total, the
       database contains 594 points: 66 at equilibrium geometries, and 528 in
       dissociation curves. The data set is designed to cover the most common
       types of noncovalent interactions in biomolecules, while keeping a
       balanced representation of dispersion and electrostatic contributions.
       The data set is therefore well suited for testing and development of
       methods applicable to bioorganic systems. In addition to the benchmark
       CCSD(T) results, we also provide decompositions of the interaction
       energies by means of DFT-SAPT calculations. The data set was used to
       test several correlated QM methods, including those parametrized
       specifically for noncovalent interactions. Among these, the SCS-MI-CCSD
       method outperforms all other tested methods, with a root-mean-square
       error of 0.08 kcal/mol for the S66 data set.,
    DOI = 10.1021/ct2002946,
    ISSN = 1549-9618,
    Unique-ID = ISI:000293662500012,
    
  • A. Illsley, P. Hobza, P. Wanklyn, and P. Belfield, “AUDIT OF STANDARDS OF DOCUMENTATION OF DEATH IN THE MEDICAL NOTES BEFORE
    AND AFTER THE INTRODUCTION OF A TRUSTWIDE PROFORMA,” AGE AND AGEING, vol. 40, iss. 2, pp. II17, 2011.
    [Bibtex]
    @article ISI:000293594600018,
    Author = Illsley, A. and Hobza, P. and Wanklyn, P. and Belfield, P.,
    Title = AUDIT OF STANDARDS OF DOCUMENTATION OF DEATH IN THE MEDICAL NOTES BEFORE
       AND AFTER THE INTRODUCTION OF A TRUSTWIDE PROFORMA,
    Journal = AGE AND AGEING,
    Year = 2011,
    Volume = 40,
    Number = 2,
    Pages = II17,
    Month = AUG,
    ISSN = 0002-0729,
    Unique-ID = ISI:000293594600018,
    
  • [DOI] A. M. Rijs, M. Kabelac, A. Abo-Riziq, P. Hobza, and M. S. de Vries, “Isolated Gramicidin Peptides Probed by IR Spectroscopy,” CHEMPHYSCHEM, vol. 12, iss. 10, SI, pp. 1816-1821, 2011.
    [Bibtex]
    @article ISI:000293385000008,
    Author = Rijs, Anouk M. and Kabelac, Martin and Abo-Riziq, Ali and Hobza, Pavel
       and de Vries, Mattanjah S.,
    Title = Isolated Gramicidin Peptides Probed by IR Spectroscopy,
    Journal = CHEMPHYSCHEM,
    Year = 2011,
    Volume = 12,
    Number = 10, SI,
    Pages = 1816-1821,
    Month = JUL 11,
    Abstract = We report double-resonant IR/UV ion-dip spectroscopy of neutral
       gramicidin peptides in the gas phase. The IR spectra of gramicidin A and
       C, recorded in both the 1000 cm(-1) to 1800 cm(-1) and the 2700 to 3750
       cm(-1) region, allow structural analysis. By studying this broad IR
       range, various local intramolecular interactions are probed, and
       complementary IR modes can be accessed. Ab initio quantum chemical
       calculations are used to support the interpretation of the experimental
       IR spectra. The comparison of the calculated frequencies with the
       experimental IR spectrum probed via the strong infrared absorptions of
       all the amide groups (NH stretch, C=O stretch and NH bend), shows
       evidence for a helical structure in the gas phase, which is similar to
       that in the condensed phase. Additionally, we show that to improve the
       spectral resolution when studying large neutral molecular structures of
       the size of gramicidin, the use of heavier carrier gas could be
       advantageous.,
    DOI = 10.1002/cphc.201100212,
    ISSN = 1439-4235,
    Unique-ID = ISI:000293385000008,
    
  • [DOI] P. Dobes, J. Rezac, J. Fanfrlik, M. Otyepka, and P. Hobza, “Semiempirical Quantum Mechanical Method PM6-DH2X Describes the Geometry
    and Energetics of CK2-Inhibitor Complexes Involving Halogen Bonds Well,
    While the Empirical Potential Fails,” JOURNAL OF PHYSICAL CHEMISTRY B, vol. 115, iss. 26, pp. 8581-8589, 2011.
    [Bibtex]
    @article ISI:000292281200025,
    Author = Dobes, Petr and Rezac, Jan and Fanfrlik, Jindrich and Otyepka, Michal
       and Hobza, Pavel,
    Title = Semiempirical Quantum Mechanical Method PM6-DH2X Describes the Geometry
       and Energetics of CK2-Inhibitor Complexes Involving Halogen Bonds Well,
       While the Empirical Potential Fails,
    Journal = JOURNAL OF PHYSICAL CHEMISTRY B,
    Year = 2011,
    Volume = 115,
    Number = 26,
    Pages = 8581-8589,
    Month = JUL 7,
    Abstract = In the present study, we have investigated complexes of CK2 protein
       kinase with halogenated inhibitors by means of the advanced
       semiempirical quantum mechanical (SQM) PM6 method (called PM6-DH2X),
       which describes various types of noncovalent interactions including
       halogen bonding well. The PM6-DH2X method provides reliable geometries
       of those CK2 protein kinase-inhibitor complexes involving halogen bonds
       that agree well with the X-ray crystal structures. When the Amber
       empirical potential is applied, this agreement becomes considerably
       worse. Similarly, the binding free energies determined by the PM6-DH2X
       SQM method are much closer to the experimental inhibition constants than
       those based on the Amber empirical potential.,
    DOI = 10.1021/jp202149z,
    ISSN = 1520-6106,
    Unique-ID = ISI:000292281200025,
    
  • [DOI] M. Kolar, T. Kubar, and P. Hobza, “On the Role of London Dispersion Forces in Biomolecular Structure
    Determination,” JOURNAL OF PHYSICAL CHEMISTRY B, vol. 115, iss. 24, pp. 8038-8046, 2011.
    [Bibtex]
    @article ISI:000291709500038,
    Author = Kolar, Michal and Kubar, Tomas and Hobza, Pavel,
    Title = On the Role of London Dispersion Forces in Biomolecular Structure
       Determination,
    Journal = JOURNAL OF PHYSICAL CHEMISTRY B,
    Year = 2011,
    Volume = 115,
    Number = 24,
    Pages = 8038-8046,
    Month = JUN 23,
    Abstract = A DNA dodecamer and the methyladenine... methylthymine (mA...mT) complex
       in aqueous environment have been studied by means of molecular dynamics
       simulation, with a modified force field accounting for the hypothetical
       absence of London dispersion forces. Under these conditions, the
       inA...mT complex is preserved, while the double-helical DNA oligomer
       passes via an extended, ladder-like intermediate to a collapsed
       structure. The results are interpreted in terms of stability and
       specificity of the structure of studied complexes. While the hydrophobic
       effect of the solvent accounts for the sufficient stabilization of the
       complex, the appearance of the native biomolecular conformation is
       attributed to the London dispersion forces. Thus, the London dispersion
       seems to provide the native structure of a biomolecular complex with the
       largest additional stabilization, preferring it among several (or many)
       possible aggregated structures. The observations are affected by the
       construction of the modified force field, and this effect is discussed
       thoroughly. The fundamental issues are the coupling of the components of
       the Lennard-Jones potential and the way to separate them. Based on the
       observations, the description of nonbonded interactions with the current
       biomolecular force fields is discussed. It is proposed that a novel
       force field composed of physically correct components to describe
       nonbonded interactions could exhibit more favorable performance in
       certain up-to-date applications.,
    DOI = 10.1021/jp202878d,
    ISSN = 1520-6106,
    Unique-ID = ISI:000291709500038,
    
  • [DOI] D. Nachtigallova, A. J. A. Aquino, J. J. Szymczak, M. Barbatti, P. Hobza, and H. Lischka, “Nonadiabatic Dynamics of Uracil: Population Split among Different Decay
    Mechanisms,” JOURNAL OF PHYSICAL CHEMISTRY A, vol. 115, iss. 21, pp. 5247-5255, 2011.
    [Bibtex]
    @article ISI:000290914500003,
    Author = Nachtigallova, Dana and Aquino, Adelia J. A. and Szymczak, Jaroslaw J.
       and Barbatti, Mario and Hobza, Pavel and Lischka, Hans,
    Title = Nonadiabatic Dynamics of Uracil: Population Split among Different Decay
       Mechanisms,
    Journal = JOURNAL OF PHYSICAL CHEMISTRY A,
    Year = 2011,
    Volume = 115,
    Number = 21,
    Pages = 5247-5255,
    Month = JUN 2,
    Abstract = Nonadiabatic dynamics simulations performed at the state-averaged CASSCF
       method are reported for uracil. Supporting calculations on stationary
       points and minima on the crossing seams have been performed at the
       MR-CISD and CASPT2 levels. The dominant mechanism is characterized by
       relaxation into the S(2) minimum of pi pi* character followed by the
       relaxation to the S(1) minimum of n pi* character. This mechanism
       contributes to the slower relaxation with a decay constant larger than
       1.5 ps, in good agreement with the long time constants experimentally
       observed. A minor fraction of trajectories decay to the ground state
       with a time constant of about 0.7 Ps, which should be compared to the
       experimentally observed short constant. The major part of trajectories
       decaying with this time constant follows the pi pi* channel and hops
       to the ground state via an ethylenic conical intersection. A
       contribution of the relaxation proceeding via a ring-opening conical
       intersection was also observed. The existence of these two latter
       channels together with a reduced long time constant is responsible for a
       significantly shorter lifetime of uracil compared to that of thymine.,
    DOI = 10.1021/jp201327w,
    ISSN = 1089-5639,
    Unique-ID = ISI:000290914500003,
    
  • [DOI] A. J. A. Aquino, D. Nachtigallova, P. Hobza, D. G. Truhlar, C. Haettig, and H. Lischka, “The Charge-Transfer States in a Stacked Nucleobase Dimer Complex: A
    Benchmark Study,” JOURNAL OF COMPUTATIONAL CHEMISTRY, vol. 32, iss. 7, pp. 1217-1227, 2011.
    [Bibtex]
    @article ISI:000288871100002,
    Author = Aquino, Adelia J. A. and Nachtigallova, Dana and Hobza, Pavel and
       Truhlar, Donald G. and Haettig, Christof and Lischka, Hans,
    Title = The Charge-Transfer States in a Stacked Nucleobase Dimer Complex: A
       Benchmark Study,
    Journal = JOURNAL OF COMPUTATIONAL CHEMISTRY,
    Year = 2011,
    Volume = 32,
    Number = 7,
    Pages = 1217-1227,
    Month = MAY,
    Abstract = Electronic singlet excitations of stacked adenine-thymine (AT) and
       guanine-cytosine (GC) complexes have been investigated with respect to
       local excitation and charge-transfer (CT) characters. Potential energy
       curves for rigid displacement of the nucleobases have been computed to
       establish the distance dependence of the CT states. The second-order
       algebraic diagrammatic construction [ADC(2)] method served as
       reference approach for comparison to a selected set of density
       functionals used within the time-dependent density functional theory
       (TD-DFT). Particular attention was dedicated to the performance of the
       recently developed family of M06 functionals. The calculations for the
       stacked complexes show that at the ADC(2) level, the lowest CT state is
       S(6) for the AT and as S(4) for the GC pair. At the reference geometry,
       the actual charge transferred is found to be 0.73 e for AT. In case of
       GC, this amount is much smaller (0.17 e). With increasing separation of
       the two nucleobases, the CT state is strongly destabilized. The M06-2X
       version provides a relatively good reproduction of the ADC(2) results.
       It avoids the serious overstabilization and overcrowding of the spectrum
       found with the B3LYP functional. On the other hand, M06-HF destabilizes
       the CT state too strongly. TD-DFT/M06-2X calculations in solution
       (heptane, isoquinoline, and water) using the polarizable continuum model
       show a stabilization of the CT state and an increase in CT character
       with increasing polarity of the solvent. (C) 2010 Wiley Periodicals,
       Inc. J Comput Chem 32: 1217-1227, 2011,
    DOI = 10.1002/jcc.21702,
    ISSN = 0192-8651,
    Unique-ID = ISI:000288871100002,
    
  • [DOI] M. Kolar, J. Fanfrlik, and P. Hobza, “Ligand Conformational and Solvation/Desolvation Free Energy in
    Protein-Ligand Complex Formation,” JOURNAL OF PHYSICAL CHEMISTRY B, vol. 115, iss. 16, pp. 4718-4724, 2011.
    [Bibtex]
    @article ISI:000289697300020,
    Author = Kolar, Michal and Fanfrlik, Jindrich and Hobza, Pavel,
    Title = Ligand Conformational and Solvation/Desolvation Free Energy in
       Protein-Ligand Complex Formation,
    Journal = JOURNAL OF PHYSICAL CHEMISTRY B,
    Year = 2011,
    Volume = 115,
    Number = 16,
    Pages = 4718-4724,
    Month = APR 28,
    Abstract = In this study, an extensive sampling of the conformational space of nine
       HIV-1 protease inhibitors was performed, to estimate the uncertainty
       with which a single conformation scoring scheme approximates the
       ligand-protein bin ding fret. energy. The SMD implicit
       solvation/desolvation energy and gas phase PM6-DH2 energy were
       calculated for a set of lop conformations of each ligand. The
       probability density functions of the energies were compared with the
       values obtained from the single-conformation approach and from a short
       ab initio molecular dynamics simulation. The relative uncertainty in the
       score within the set of nine inhibitors was calculated to be 3.5
       kcal.mol(-1) and 2.7 kcal.mol(-1) for the single-conformation and short
       dynamics, respectively. These results, though limited to the
       consideration of flexible ligands, provide a valuable insight into the
       precision of rigid models in the current computer-aided drug design.,
    DOI = 10.1021/jp2010265,
    ISSN = 1520-6106,
    Unique-ID = ISI:000289697300020,
    
  • [DOI] J. Rezac and P. Hobza, “A halogen-bonding correction for the semiempirical PM6 method,” CHEMICAL PHYSICS LETTERS, vol. 506, iss. 4-6, pp. 286-289, 2011.
    [Bibtex]
    @article ISI:000289505500032,
    Author = Rezac, Jan and Hobza, Pavel,
    Title = A halogen-bonding correction for the semiempirical PM6 method,
    Journal = CHEMICAL PHYSICS LETTERS,
    Year = 2011,
    Volume = 506,
    Number = 4-6,
    Pages = 286-289,
    Month = APR 20,
    Abstract = We analyse the failure of the semiempirical QM method PM6 to describe
       halogen bonds and suggest an empirical correction that remedies this
       problem. Owing to underestimated repulsion in the PM6 method, the
       halogen-bond interaction energies are dramatically exaggerated and the
       equilibrium distances are very short. This is addressed by a correction
       parametrised for all halogens capable of halogen bonding (Cl, Br, and
       I). The correction is applied on top of the dispersion correction,
       forming the PM6-D2X method. A comparison with ab initio calculations
       shows that the method is able to predict the interaction energy of
       halogen bonds with an error of 10\%. (C) 2011 Elsevier B. V. All rights
       reserved.,
    DOI = 10.1016/j.cplett.2011.03.009,
    ISSN = 0009-2614,
    Unique-ID = ISI:000289505500032,
    
  • N. Svadlenak, M. Ligare, L. E. Gulian, M. P. Callahan, Z. Gengeliczki, D. Nachtigalla, P. Hobza, and M. S. de Vries, “Spectroscopy of isolated prebiotic nucleobases,” ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, vol. 241, 2011.
    [Bibtex]
    @article ISI:000291982806825,
    Author = Svadlenak, Nathan and Ligare, Marshall and Gulian, Lisa E. and Callahan,
       Michael P. and Gengeliczki, Zsolt and Nachtigalla, Dana and Hobza, Pavel
       and de Vries, Mattanjah S.,
    Title = Spectroscopy of isolated prebiotic nucleobases,
    Journal = ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY,
    Year = 2011,
    Volume = 241,
    Month = MAR 27,
    Note = 241st National Meeting and Exposition of the American-Chemical-Society
       (ACS), Anaheim, CA, MAR 27-31, 2011,
    Organization = Amer Chem Soc,
    ISSN = 0065-7727,
    Unique-ID = ISI:000291982806825,
    
  • [DOI] P. Dobes, J. Fanfrlik, J. Rezac, M. Otyepka, and P. Hobza, “Transferable scoring function based on semiempirical quantum mechanical
    PM6-DH2 method: CDK2 with 15 structurally diverse inhibitors,” JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, vol. 25, iss. 3, pp. 223-235, 2011.
    [Bibtex]
    @article ISI:000288179000005,
    Author = Dobes, Petr and Fanfrlik, Jindrich and Rezac, Jan and Otyepka, Michal
       and Hobza, Pavel,
    Title = Transferable scoring function based on semiempirical quantum mechanical
       PM6-DH2 method: CDK2 with 15 structurally diverse inhibitors,
    Journal = JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN,
    Year = 2011,
    Volume = 25,
    Number = 3,
    Pages = 223-235,
    Month = MAR,
    Abstract = A semiempirical quantum mechanical PM6-DH2 method accurately covering
       the dispersion interaction and H-bonding was used to score fifteen
       structurally diverse CDK2 inhibitors. The geometries of all the
       complexes were taken from the X-ray structures and were reoptimised by
       the PM6-DH2 method in continuum water. The total scoring function was
       constructed as an estimate of the binding free energy, i.e., as a sum of
       the interaction enthalpy, interaction entropy and the corrections for
       the inhibitor desolvation and deformation energies. The applied scoring
       function contains a clear thermodynamical terms and does not involve any
       adjustable empirical parameter. The best correlations with the
       experimental inhibition constants (ln K (i)) were found for bare
       interaction enthalpy (r (2) = 0.87) and interaction enthalpy corrected
       for ligand desolvation and deformation energies (r (2) = 0.77); when the
       entropic term was considered, however, the correlation becomes worse but
       still acceptable (r (2) = 0.52). The resulting correlation based on the
       PM6-DH2 scoring function is better than previously published function
       based on various docking/scoring, SAR studies or advanced QM/MM
       approach, however, the robustness is limited by number of available
       experimental data used in the correlation. Since a very similar
       correlation between the experimental and theoretical results was found
       also for a different system of the HIV-1 protease, the suggested scoring
       function based on the PM6-DH2 method seems to be applicable in drug
       design, even if diverse protein-ligand complexes have to be ranked.,
    DOI = 10.1007/s10822-011-9413-5,
    ISSN = 0920-654X,
    Unique-ID = ISI:000288179000005,
    
  • [DOI] J. Rezac and P. Hobza, “Extrapolation and Scaling of the DFT-SAPT Interaction Energies toward
    the Basis Set Limit,” JOURNAL OF CHEMICAL THEORY AND COMPUTATION, vol. 7, iss. 3, pp. 685-689, 2011.
    [Bibtex]
    @article ISI:000287991300016,
    Author = Rezac, Jan and Hobza, Pavel,
    Title = Extrapolation and Scaling of the DFT-SAPT Interaction Energies toward
       the Basis Set Limit,
    Journal = JOURNAL OF CHEMICAL THEORY AND COMPUTATION,
    Year = 2011,
    Volume = 7,
    Number = 3,
    Pages = 685-689,
    Month = MAR,
    Abstract = The dispersion energy term in the symmetry-adapted perturbation theory
       based on the density functional theory (DFT-SAPT) converges rather
       slowly with basis set size. Accurate results for large complexes, where
       only calculations in small basis sets are practical, can be obtained by
       extrapolation to the complete basis set limit (CBS). In this paper, we
       propose an extrapolation scheme with the variable exponent optimized
       specifically for the DFT-SAPT calculations in correlation-consistent
       basis sets with diffuse functions. Another way to improve the accuracy
       term at no additional cost is to scale the dispersion term by a fixed
       amount. We present the scaling factors averaged over a balanced set of
       10 model complexes. The results of these schemes are compared to the
       high-quality :DFT-SAPT/CBS interaction energies in small complexes
       obtained by fitting to a series of basis sets up to aug-cc-pV5Z and to
       the CCSD(T)/CBS interaction energies. It is shown that even the cheapest
       extrapolation scheme yields results that are limited by the accuracy of
       the DFT-SAPT approach rather than by the basis set convergence. Scaling
       the dispersion term allows accurate interaction energies as well as
       their components to be obtained using just the aug-cc-pVDZ basis set;
       such a calculation can be applied to complexes consisting of up to 50
       first-row atoms.,
    DOI = 10.1021/ct200005p,
    ISSN = 1549-9618,
    Unique-ID = ISI:000287991300016,
    
  • [DOI] K. E. Riley, M. Pitonak, J. Cerny, and P. Hobza, “On the Structure and Geometry of Biomolecular Binding Motifs
    (Hydrogen-Bonding, Stacking, X-H center dot center dot center dot pi):
    WFT and DFT Calculations (vol 6, pg 66, 2010),” JOURNAL OF CHEMICAL THEORY AND COMPUTATION, vol. 7, iss. 3, pp. 807, 2011.
    [Bibtex]
    @article ISI:000287991300030,
    Author = Riley, Kevin E. and Pitonak, Michal and Cerny, Jir and Hobza, Pavel,
    Title = On the Structure and Geometry of Biomolecular Binding Motifs
       (Hydrogen-Bonding, Stacking, X-H center dot center dot center dot pi):
       WFT and DFT Calculations (vol 6, pg 66, 2010),
    Journal = JOURNAL OF CHEMICAL THEORY AND COMPUTATION,
    Year = 2011,
    Volume = 7,
    Number = 3,
    Pages = 807,
    Month = MAR,
    DOI = 10.1021/ct200019g,
    ISSN = 1549-9618,
    Unique-ID = ISI:000287991300030,
    
  • [DOI] S. Maity, N. G. Patwari, R. Sedlak, and P. Hobza, “A pi-stacked phenylacetylene dimer,” PHYSICAL CHEMISTRY CHEMICAL PHYSICS, vol. 13, iss. 37, pp. 16706-16712, 2011.
    [Bibtex]
    @article ISI:000294501700029,
    Author = Maity, Surajit and Patwari, G. Naresh and Sedlak, Robert and Hobza,
       Pavel,
    Title = A pi-stacked phenylacetylene dimer,
    Journal = PHYSICAL CHEMISTRY CHEMICAL PHYSICS,
    Year = 2011,
    Volume = 13,
    Number = 37,
    Pages = 16706-16712,
    Abstract = The structure of the phenylacetylene-dimer has been elucidated using
       IR-UV double resonance spectroscopy in combination with high level ab
       initio calculations at the CCSD(T)/CBS level. The IR spectra in the
       acetylenic and the aromatic C-H stretching regions indicate that the two
       phenylacetylene moieties are in identical environments and very similar
       to the phenylacetylene monomer. Calculated stabilization energies and
       the free energies at the CCSD(T)/CBS level favor the formation of an
       anti-parallel pi-stacked structure. The DFT-SAPT energy decomposition
       analysis points out that the anti-parallel pi-stacked structure
       maximizes electrostatic as well as the dispersion components of energy.
       The observed IR spectra are consistent with the anti-parallel pi-stacked
       structure.,
    DOI = 10.1039/c1cp20677j,
    ISSN = 1463-9076,
    Unique-ID = ISI:000294501700029,
    
  • [DOI] O. Prenosil, M. Pitonak, R. Sedlak, M. Kabelac, and P. Hobza, “H-Bonding Cooperativity Effects in Amyloids: Quantum Mechanical and
    Molecular Mechanics Study,” ZEITSCHRIFT FUR PHYSIKALISCHE CHEMIE-INTERNATIONAL JOURNAL OF RESEARCH
    IN PHYSICAL CHEMISTRY & CHEMICAL PHYSICS
    , vol. 225, iss. 5, SI, pp. 553-574, 2011.
    [Bibtex]
    @article ISI:000292526800008,
    Author = Prenosil, Ondrej and Pitonak, Michal and Sedlak, Robert and Kabelac,
       Martin and Hobza, Pavel,
    Title = H-Bonding Cooperativity Effects in Amyloids: Quantum Mechanical and
       Molecular Mechanics Study,
    Journal = ZEITSCHRIFT FUR PHYSIKALISCHE CHEMIE-INTERNATIONAL JOURNAL OF RESEARCH
       IN PHYSICAL CHEMISTRY \& CHEMICAL PHYSICS,
    Year = 2011,
    Volume = 225,
    Number = 5, SI,
    Pages = 553-574,
    Abstract = The cooperativity effects have been evaluated on three model systems,
       the formamide, (formylamino)acetamide and amyloidic-layer oligomers with
       an increasing size of the monomer units (6, 13 and 214 atoms). In the
       last model, each layer is a dimer of the amino-acid sequence GNNQQNY in
       one-letter amino-acid abbreviations. The series of oligomers for each
       model system of up to six monomers have been constructed. For the
       calculation of the strength of a particular H-bond formed between
       various sub-oligomers within an oligomer, different wave function,
       density functional and semi-empirical quantum mechanical methods as well
       as empirical force fields have been used.
       Semi-empirical methods are found to be a reasonable compromise between
       accuracy and computational cost. These methods are able to describe the
       cooperativity effects with an accuracy almost comparable to that of the
       ab initio methods. On the contrary, the empirical force-field methods
       for all of the model systems mostly failed to describe the H-bonding
       cooperativity effects properly. Based on the results obtained in this
       work, we recommend using semi-empirical methods. For the systems where
       this is impossible, we agree to use polarizable force fields with some
       reservations.
       Generally, the more flexible the oligomer chain is (the less steric the
       repulsion or rigid motifs are), the larger the cooperativity that can be
       achieved. With the increasing number of monomers in a sequence connected
       via H-bonds, the cooperativity effects appear to be growing, but
       relatively soon (at 3-4 monomer units) they tend to become saturated.,
    DOI = 10.1524/zpch.2011.0109,
    ISSN = 0942-9352,
    Unique-ID = ISI:000292526800008,
    
  • [DOI] T. Zeleny, P. Hobza, D. Nachtigallova, M. Ruckenbauer, and H. Lischka, “PHOTODYNAMICS OF THE ADENINE MODEL 4-AMINOPYRIMIDINE EMBEDDED WITHIN
    DOUBLE STRAND OF DNA,” COLLECTION OF CZECHOSLOVAK CHEMICAL COMMUNICATIONS, vol. 76, iss. 6, pp. 631-643, 2011.
    [Bibtex]
    @article ISI:000291434900001,
    Author = Zeleny, Tomas and Hobza, Pavel and Nachtigallova, Dana and Ruckenbauer,
       Matthias and Lischka, Hans,
    Title = PHOTODYNAMICS OF THE ADENINE MODEL 4-AMINOPYRIMIDINE EMBEDDED WITHIN
       DOUBLE STRAND OF DNA,
    Journal = COLLECTION OF CZECHOSLOVAK CHEMICAL COMMUNICATIONS,
    Year = 2011,
    Volume = 76,
    Number = 6,
    Pages = 631-643,
    Abstract = On-the-fly surface hopping nonadiabatic photodynamical simulations using
       hybrid quantum mechanical/molecular mechanical approach of
       4-aminopyrimidine were performed to model the relaxation mechanism of
       adenine within DNA double strand. The surrounding bases do not affect
       the overall ring-puckering relaxation mechanisms significantly, however,
       interesting hydrogen-bond dynamics is observed. First, formation of
       intra-strand hydrogen bonds is found. It is shown that this effect
       speeds up the decay process. In addition, the Watson-Crick structure is
       altered by breaking one of the inter-strand hydrogen bonds also leading
       to a decrease of the life time.,
    DOI = 10.1135/cccc2011046,
    ISSN = 0010-0765,
    Unique-ID = ISI:000291434900001,
    
  • [DOI] M. Pitonak, F. Aquilante, P. Hobza, P. Neogrady, J. Noga, and M. Urban, “PARALLELIZED IMPLEMENTATION OF THE CCSD(T) METHOD IN MOLCAS USING
    OPTIMIZED VIRTUAL ORBITALS SPACE AND CHOLESKY DECOMPOSED TWO-ELECTRON
    INTEGRALS,” COLLECTION OF CZECHOSLOVAK CHEMICAL COMMUNICATIONS, vol. 76, iss. 6, pp. 713-742, 2011.
    [Bibtex]
    @article ISI:000291434900006,
    Author = Pitonak, Michal and Aquilante, Francesco and Hobza, Pavel and Neogrady,
       Pavel and Noga, Jozef and Urban, Miroslav,
    Title = PARALLELIZED IMPLEMENTATION OF THE CCSD(T) METHOD IN MOLCAS USING
       OPTIMIZED VIRTUAL ORBITALS SPACE AND CHOLESKY DECOMPOSED TWO-ELECTRON
       INTEGRALS,
    Journal = COLLECTION OF CZECHOSLOVAK CHEMICAL COMMUNICATIONS,
    Year = 2011,
    Volume = 76,
    Number = 6,
    Pages = 713-742,
    Abstract = Parallelized implementation of the coupled cluster singles doubles with
       non-iterative triples in the MOLCAS program suite is described. The code
       benefits from the Cholesky decomposition of two-electron integrals and
       the algorithm is particularly designed for calculations using reduced
       optimized virtual orbital space. Different aspects of parallelization
       and its efficiency are discussed based on our recent successful
       calculations for medium sized molecules involving more than 1000 basis
       functions.,
    DOI = 10.1135/cccc2011048,
    ISSN = 0010-0765,
    Unique-ID = ISI:000291434900006,
    
  • [DOI] A. Pecina, O. Prenosil, J. Fanfrlik, J. Rezac, J. Granatier, P. Hobza, and M. Lepsik, “ON THE RELIABILITY OF THE CORRECTED SEMIEMPIRICAL QUANTUM CHEMICAL
    METHOD (PM6-DH2) FOR ASSIGNING THE PROTONATION STATES IN HIV-1
    PROTEASE/INHIBITOR COMPLEXES,” COLLECTION OF CZECHOSLOVAK CHEMICAL COMMUNICATIONS, vol. 76, iss. 5, pp. 457-479, 2011.
    [Bibtex]
    @article ISI:000290280100009,
    Author = Pecina, Adam and Prenosil, Ondrej and Fanfrlik, Jindrich and Rezac, Jan
       and Granatier, Jaroslav and Hobza, Pavel and Lepsik, Martin,
    Title = ON THE RELIABILITY OF THE CORRECTED SEMIEMPIRICAL QUANTUM CHEMICAL
       METHOD (PM6-DH2) FOR ASSIGNING THE PROTONATION STATES IN HIV-1
       PROTEASE/INHIBITOR COMPLEXES,
    Journal = COLLECTION OF CZECHOSLOVAK CHEMICAL COMMUNICATIONS,
    Year = 2011,
    Volume = 76,
    Number = 5,
    Pages = 457-479,
    Abstract = A novel computational protocol for determining the most probable
       protonation states in protein/ligand complexes is presented. The method
       consists in treating large parts of the enzyme using the corrected
       semiempirical quantum chemical (QM) method - PM6-D2 for optimization and
       PM6-DH2 for single-point energies - while the rest is calculated using
       molecular mechanics (MM) within a hybrid QM/MM fashion. The surrounding
       solvent is approximated by an implicit model. This approach is applied
       to two model systems, two different carboxylate pairs in one general and
       one unique HIV-1 protease/inhibitor complex. The effect of the size of
       the movable QM part is investigated in a series of several sizes, 3-,
       6-, 8-and 10-angstrom regions surrounding the inhibitor. For the
       smallest region (< 450 atoms) the computationally more costly DFT QM/MM
       optimizations are performed as a check of the correctness. Proton
       transfer (PT) phenomena occur at both the PM6-D2 and DFT levels, which
       underlines the requirement for a QM approach. The barriers of PT are
       checked in model carboxylic acid pairs using the highly accurate MP2 and
       CCSD(T) values. An important result of this study is the fine-tuning of
       the protocol which can be used in further applications; its limitations
       are also shown, pointing to future developments. The calculations reveal
       which protonation variants of the active site are the most stable. In
       conclusion, the presented protocol can also be utilized for defining
       probable isomers in biomolecular systems. It can also serve as a
       preparatory step for further interaction-energy and binding-score
       calculations.,
    DOI = 10.1135/cccc2011035,
    ISSN = 0010-0765,
    Unique-ID = ISI:000290280100009,
    
  • [DOI] W. Zierkiewicz, R. Wieczorek, P. Hobza, and D. Michalska, "Halogen bonded complexes between volatile anaesthetics (chloroform,
    halothane, enflurane, isoflurane) and formaldehyde: a theoretical study," PHYSICAL CHEMISTRY CHEMICAL PHYSICS, vol. 13, iss. 11, pp. 5105-5113, 2011.
    [Bibtex]
    @article ISI:000287930100039,
    Author = Zierkiewicz, Wiktor and Wieczorek, Robert and Hobza, Pavel and
       Michalska, Danuta,
    Title = Halogen bonded complexes between volatile anaesthetics (chloroform,
       halothane, enflurane, isoflurane) and formaldehyde: a theoretical study,
    Journal = PHYSICAL CHEMISTRY CHEMICAL PHYSICS,
    Year = 2011,
    Volume = 13,
    Number = 11,
    Pages = 5105-5113,
    Abstract = The structures and intermolecular interactions in the halogen bonded
       complexes of anaesthetics (chloroform, halothane, enflurane and
       isoflurane) with formaldehyde were studied by ab initio MP2 and CCSD(T)
       methods. The CCSD(T)/CBS calculated binding energies of these complexes
       are between -2.83 and -4.21 kcal mol(-1). The largest stabilization
       energy has been found for the C-Br center dot center dot center dot O
       bonded halothane center dot center dot center dot OCH(2) complex. In all
       complexes the C-X bond length (where X = Cl, Br) is slightly shortened,
       in comparison to a free compound, and an increase of the C-X stretching
       frequency is observed. The electrostatic interaction was excluded as
       being responsible for the C-X bond contraction. It is suggested that
       contraction of the C-X bond length can be explained in terms of the
       Pauli repulsion (the exchange overlap) between the electron pairs of
       oxygen and halogen atoms in the investigated complexes. This is
       supported by the DFT-SAPT results, which indicate that the repulsive
       exchange energy overcompensates the electrostatic one. Moreover, the
       dispersion and electrostatic contributions cover about 95\% of the total
       attraction forces, in these complexes.,
    DOI = 10.1039/c0cp02085k,
    ISSN = 1463-9076,
    Unique-ID = ISI:000287930100039,
    

2010

  • [DOI] M. Barbatti, A. J. A. Aquino, J. J. Szymczak, D. Nachtigallova, P. Hobza, and H. Lischka, "Relaxation mechanisms of UV-photoexcited DNA and RNA nucleobases," PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF
    AMERICA
    , vol. 107, iss. 50, pp. 21453-21458, 2010.
    [Bibtex]
    @article ISI:000285521500044,
    Author = Barbatti, Mario and Aquino, Adelia J. A. and Szymczak, Jaroslaw J. and
       Nachtigallova, Dana and Hobza, Pavel and Lischka, Hans,
    Title = Relaxation mechanisms of UV-photoexcited DNA and RNA nucleobases,
    Journal = PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF
       AMERICA,
    Year = 2010,
    Volume = 107,
    Number = 50,
    Pages = 21453-21458,
    Month = DEC 14,
    Abstract = A comprehensive effort in photodynamical ab initio simulations of the
       ultrafast deactivation pathways for all five nucleobases adenine,
       guanine, cytosine, thymine, and uracil is reported. These simulations
       are based on a complete nonadiabatic surface-hopping approach using
       extended multiconfigurational wave functions. Even though all five
       nucleobases share the basic internal conversion mechanisms, the
       calculations show a distinct grouping into purine and pyrimidine bases
       as concerns the complexity of the photodynamics. The purine bases
       adenine and guanine represent the most simple photodeactivation
       mechanism with the dynamics leading along a diabatic pi pi* path
       directly and without barrier to the conical intersection seam with the
       ground state. In the case of the pyrimidine bases, the dynamics starts
       off in much flatter regions of the pi pi* energy surface due to
       coupling of several states. This fact prohibits a clear formation of a
       single reaction path. Thus, the photodynamics of the pyrimidine bases is
       much richer and includes also n pi* states with varying importance,
       depending on the actual nucleobase considered. Trapping in local minima
       may occur and, therefore, the deactivation time to the ground state is
       also much longer in these cases. Implications of these findings are
       discussed (i) for identifying structural possibilities where
       singlet/triplet transitions can occur because of sufficient retention
       time during the singlet dynamics and (ii) concerning the flexibility of
       finding other deactivation pathways in substituted pyrimidines serving
       as candidates for alternative nucleobases.,
    DOI = 10.1073/pnas.1014982107,
    ISSN = 0027-8424,
    Unique-ID = ISI:000285521500044,
    
  • [DOI] R. Sedlak, J. Fanfrlik, D. Hnyk, P. Hobza, and M. Lepsik, "Interactions of Boranes and Carboranes with Aromatic Systems: CCSD(T)
    Complete Basis Set Calculations and DFT-SAPT Analysis of Energy
    Components," JOURNAL OF PHYSICAL CHEMISTRY A, vol. 114, iss. 42, pp. 11304-11311, 2010.
    [Bibtex]
    @article ISI:000283106200037,
    Author = Sedlak, Robert and Fanfrlik, Jindrich and Hnyk, Drahomir and Hobza,
       Pavel and Lepsik, Martin,
    Title = Interactions of Boranes and Carboranes with Aromatic Systems: CCSD(T)
       Complete Basis Set Calculations and DFT-SAPT Analysis of Energy
       Components,
    Journal = JOURNAL OF PHYSICAL CHEMISTRY A,
    Year = 2010,
    Volume = 114,
    Number = 42,
    Pages = 11304-11311,
    Month = OCT 28,
    Abstract = The noncovalent interactions of heteroboranes with aromatic systems have
       only recently been acknowledged as a source of stabilization in
       supramolecular complexes. The physical basis of these interactions has
       been studied in several model complexes using advanced computational
       methods. The highly accurate CCSD(T)/complete basis set (CBS) value of
       the interaction energy for the model diborane center dot center dot
       center dot benzene complex in a stacking geometry exhibiting a B(2)H
       center dot center dot center dot pi hydrogen bond was calculated to be
       -4.0 kcal center dot mol(-1). The DFT-SAPT/CBS approach, which is shown
       to reproduce the CCSD(T)/CBS data reliably asserted that the major
       stabilizing component was dispersion, followed by electrostatics.
       Furthermore, the effect of the benzene heteroatom- and exosubstitutions
       was studied and found to be small. Next, when aromatic molecules were
       changed to cyclic aliphatic ones, van der Waals complexes stabilized by
       the dispersion term only were formed. As the last step, interactions of
       two larger icosahedral borane cages with benzene were explored. The
       complex of the monoanionic CB(11)H(12)(-) exhibited two minima: the
       first stacked above the plane of the benzene ring with a C-H center dot
       center dot center dot pi hydrogen bond and the second planar, in which
       the carborane cage bound to benzene via five B-H center dot center dot
       center dot H-C dihydrogen bonds. The DFT-SAPT/CBS calculations revealed
       that both of these binding motifs were stabilized by dispersion followed
       by electrostatic terms, with the planar complex being 1.4 kcal center
       dot mol(-1) more stable than the stacked one. The dianionic
       B(12)H(12)(2-) interacted with benzene only in the planar geometry,
       similarly as smaller anions do. The large stabilization energy of 11.0
       kcal center dot mol(-1) was composed of dominant attractive dispersion
       and slightly smaller electrostatic and induction terms. In summary, the
       borane/carborane center dot center dot center dot aromatic interaction
       is varied both in the complex geometries and in the stabilizing energy
       components. The detailed insight derived from high-level quantum
       chemical computations can help us understand such important processes as
       host-guest complexation or carborane center dot center dot center dot
       biomolecule interactions.,
    DOI = 10.1021/jp104411x,
    ISSN = 1089-5639,
    Unique-ID = ISI:000283106200037,
    
  • [DOI] M. Kolar, T. Kubar, and P. Hobza, "Sequence-Dependent Configurational Entropy Change of DNA upon
    Intercalation," JOURNAL OF PHYSICAL CHEMISTRY B, vol. 114, iss. 42, pp. 13446-13454, 2010.
    [Bibtex]
    @article ISI:000283110500024,
    Author = Kolar, Michal and Kubar, Tomas and Hobza, Pavel,
    Title = Sequence-Dependent Configurational Entropy Change of DNA upon
       Intercalation,
    Journal = JOURNAL OF PHYSICAL CHEMISTRY B,
    Year = 2010,
    Volume = 114,
    Number = 42,
    Pages = 13446-13454,
    Month = OCT 28,
    Abstract = We investigated the intercalation of an antitumor drug ellipticine into
       four adenine-thymine (AT) rich DNA duplexes with the focus on the
       configurational entropy, by means of molecular dynamics (MD)
       simulations. Two possible binding orientations of ellipticine in a DNA
       double helix were studied, and the orientation with the pyrrole nitrogen
       exposed into a major groove was identified as the more probable. The
       configurational entropy change of DNA is shown to contribute
       significantly to the binding free energy. The magnitude of this
       contribution depends on the exact DNA sequence. A detailed analysis
       revealed that the largest flexibility changes occurred in the
       sugar-phosphate backbone, resulting in an entropy gain in the most
       cases. The nucleobases were not involved in the changes of flexibility
       and entropy. BI/BII-like conformational transitions were observed after
       the intercalation of ellipticine, and the consequences of these
       transitions for the evaluation of entropy are discussed.,
    DOI = 10.1021/jp1019153,
    ISSN = 1520-6106,
    Unique-ID = ISI:000283110500024,
    
  • [DOI] J. Fanfrlik, A. K. Bronowska, J. Rezac, O. Prenosil, J. Konvalinka, and P. Hobza, "A Reliable Docking/Scoring Scheme Based on the Semiempirical Quantum
    Mechanical PM6-DH2 Method Accurately Covering Dispersion and H-Bonding:
    HIV-1 Protease with 22 Ligands," JOURNAL OF PHYSICAL CHEMISTRY B, vol. 114, iss. 39, pp. 12666-12678, 2010.
    [Bibtex]
    @article ISI:000282209900029,
    Author = Fanfrlik, Jindrich and Bronowska, Agnieszka K. and Rezac, Jan and
       Prenosil, Ondiej and Konvalinka, Jan and Hobza, Pavel,
    Title = A Reliable Docking/Scoring Scheme Based on the Semiempirical Quantum
       Mechanical PM6-DH2 Method Accurately Covering Dispersion and H-Bonding:
       HIV-1 Protease with 22 Ligands,
    Journal = JOURNAL OF PHYSICAL CHEMISTRY B,
    Year = 2010,
    Volume = 114,
    Number = 39,
    Pages = 12666-12678,
    Month = OCT 7,
    Abstract = In this study, we introduce a fast and reliable rescoring scheme for
       docked complexes based on a semiempirical quantum mechanical PM6-DH2
       method. The method utilizes a PM6-based Hamiltonian with corrections for
       dispersion energy and hydrogen bonds. The total score is constructed as
       the sum of the PM6-DH2 interaction enthalpy, the empirical force field
       (AMBER) interaction entropy, and the sum of the deformation (PM6-SMD)
       and the desolvation (SMD) energies of the ligand. The main advantage of
       the procedure is the fact that we do not add any empirical parameter for
       either an individual component of the total score or an individual
       protein ligand complex. This rescoring method is applied to a very
       challenging system, namely, the HIV-1 protease with a set of ligands. As
       opposed to the conventional DOCK procedure, the 13M6-DH2 rescoring based
       on all of the terms distinguishes between binders and nonbinders and
       provides a reliable correlation of the theoretical and experimental
       binding free energies. Such a dramatic improvement, resulting from the
       PM6-DH2 rescoring of all the complexes, provides a valuable yet
       inexpensive tool for rational drug discovery and de novo ligand design.,
    DOI = 10.1021/jp1032965,
    ISSN = 1520-6106,
    Unique-ID = ISI:000282209900029,
    
  • [DOI] D. Nachtigallova, M. Barbatti, J. J. Szymczak, P. Hobza, and H. Lischka, "The photodynamics of 2,4-diaminopyrimidine in comparison with
    4-aminopyrimidine: The effect of amino-substitution," CHEMICAL PHYSICS LETTERS, vol. 497, iss. 1-3, pp. 129-134, 2010.
    [Bibtex]
    @article ISI:000281526700027,
    Author = Nachtigallova, Dana and Barbatti, Mario and Szymczak, Jaroslaw J. and
       Hobza, Pavel and Lischka, Hans,
    Title = The photodynamics of 2,4-diaminopyrimidine in comparison with
       4-aminopyrimidine: The effect of amino-substitution,
    Journal = CHEMICAL PHYSICS LETTERS,
    Year = 2010,
    Volume = 497,
    Number = 1-3,
    Pages = 129-134,
    Month = SEP 10,
    Abstract = Nonadiabatic photodynamical surface hopping simulations of
       4-aminopyrimidine and 2,4-diaminopyrimidine were performed at
       multi-configurational level. Additional NH(2) substitution blocks part
       of the ring puckering modes necessary to reach ultrafast deactivation
       channels but does not affect the excited-state lifetime of
       2,4-diaminopyrimidine significantly since other pathways leading to
       ultrafast relaxation can be utilized.
       The effect of the excess energy on the relaxation mechanism of
       2,4-diaminopyrimidine was studied. It is shown that the amount of
       initial energy influences the time to reach the crossing seam and thus
       the lifetime. This study is important when interpreting the experimental
       results performed at different pump energies. (C) 2010 Elsevier B.V. All
       rights reserved.,
    DOI = 10.1016/j.cplett.2010.07.098,
    ISSN = 0009-2614,
    Unique-ID = ISI:000281526700027,
    
  • [DOI] K. E. Riley, M. Pitonak, P. Jurecka, and P. Hobza, "Stabilization and Structure Calculations for Noncovalent Interactions in
    Extended Molecular Systems Based on Wave Function and Density Functional
    Theories," CHEMICAL REVIEWS, vol. 110, iss. 9, pp. 5023-5063, 2010.
    [Bibtex]
    @article ISI:000281840400003,
    Author = Riley, Kevin E. and Pitonak, Michel and Jurecka, Petr and Hobza, Pavel,
    Title = Stabilization and Structure Calculations for Noncovalent Interactions in
       Extended Molecular Systems Based on Wave Function and Density Functional
       Theories,
    Journal = CHEMICAL REVIEWS,
    Year = 2010,
    Volume = 110,
    Number = 9,
    Pages = 5023-5063,
    Month = SEP,
    DOI = 10.1021/cr1000173,
    ISSN = 0009-2665,
    Unique-ID = ISI:000281840400003,
    
  • [DOI] M. Kolar, K. Berka, P. Jurecka, and P. Hobza, "On the Reliability of the AMBER Force Field and its Empirical Dispersion
    Contribution for the Description of Noncovalent Complexes," CHEMPHYSCHEM, vol. 11, iss. 11, pp. 2399-2408, 2010.
    [Bibtex]
    @article ISI:000281061500018,
    Author = Kolar, Michal and Berka, Karel and Jurecka, Petr and Hobza, Pavel,
    Title = On the Reliability of the AMBER Force Field and its Empirical Dispersion
       Contribution for the Description of Noncovalent Complexes,
    Journal = CHEMPHYSCHEM,
    Year = 2010,
    Volume = 11,
    Number = 11,
    Pages = 2399-2408,
    Month = AUG 2,
    Abstract = The reliability of the AMBER force field is tested by comparing the
       total interaction energy and dispersion energy with the reference data
       obtained at the density functional theory symmetry-adapted perturbation
       treatment (DFT-SAPT)/aug-cc-pVDZ level. The comparison is made for 194
       different geometries of noncovalent complexes (H-bonded, stacked, mixed,
       and dispersion-bound), at the equilibrium distances as well as at longer
       distances (up to a relative distance of two). The total interaction
       energies agree very well with the reference data and only the strength
       of H-bonded complexes is slightly underestimated. In the case of
       dispersion energy, the overall agreement is even better, with the
       exception of the stacked aromatic systems, where the empirical
       dispersion energy is overestimated. The use of AMBER interaction energy
       and AMBER dispersion energy for different types of noncovalent complexes
       at equilibrium as well as at longer distances is thus justified, except
       for, a few cases, such as the water molecule, where the dispersion
       energy is highly inaccurate.,
    DOI = 10.1002/cphc.201000109,
    ISSN = 1439-4235,
    Unique-ID = ISI:000281061500018,
    
  • [DOI] L. Grafova, M. Pitonak, J. Rezac, and P. Hobza, "Comparative Study of Selected Wave Function and Density Functional
    Methods for Noncovalent Interaction Energy Calculations Using the
    Extended S22 Data Set," JOURNAL OF CHEMICAL THEORY AND COMPUTATION, vol. 6, iss. 8, pp. 2365-2376, 2010.
    [Bibtex]
    @article ISI:000280661600010,
    Author = Grafova, Lucie and Pitonak, Michal and Rezac, Jan and Hobza, Pavel,
    Title = Comparative Study of Selected Wave Function and Density Functional
       Methods for Noncovalent Interaction Energy Calculations Using the
       Extended S22 Data Set,
    Journal = JOURNAL OF CHEMICAL THEORY AND COMPUTATION,
    Year = 2010,
    Volume = 6,
    Number = 8,
    Pages = 2365-2376,
    Month = AUG,
    Abstract = In this paper, an extension of the S22 data set of Jurecka et at
       (Jurecka, P, Sponer, J, Cerny, J; Hobza, P. Phys. Chem. Chem. Phys 2006,
       8, 1985), the data set of benchmark CCSD(T)/CBS interaction energies of
       twenty-two noncovalent complexes in equilibrium geometries, is presented
       The S22 data set has been extended by including the stretched (one
       shortened and three elongated) complex geometries of the S22 data set
       along the main noncovalent interaction coordinate The goal of this work
       is to assess the accuracy of the popular wave function methods (MP2-,
       MP3- and, CCSD-based) and density functional methods (with and without
       empirical correction for the dispersion energy) for noncovalent
       complexes based on a statistical evaluation not only in equilibrium, but
       also in nonequilibrium geometries The results obtained in this work
       provide information on whether an accurate and balanced description of
       the different interaction types and complex geometry distortions can be
       expected from the tested methods This information has an important
       implication in the calculation of large molecular complexes, where the
       number of distant interacting molecular fragments, often in far from
       equilibrium geometries, increases rapidly with the system size The best
       performing WFT methods were found to be the SCS-CCSD (spin-component
       scaled CCSD, according to Takatani, T, Hohenstein, E. G., Sherrill, C D
       J Chem. Phys 2008, 128, 124111), MP2C (dispersion-corrected MP2,
       according to Hesselmann, A J Chem. Phys 2008, 128, 144112), and MP2 5
       (scaled MP3, according to Pitonak, M., Neogrady, P., Cerny, J; Grimme,
       S., Hobza, P. ChemPhysChem 2009, 10, 282.) Since none of the OFT methods
       fulfilled the required statistical criteria proposed in this work, they
       cannot be generally recommended for large-scale calculations The DFT
       methods still have the potential to deliver accurate results for large
       molecules, but most likely on the basis of an error cancellation.,
    DOI = 10.1021/ct1002253,
    ISSN = 1549-9618,
    Unique-ID = ISI:000280661600010,
    
  • [DOI] K. Berka, R. A. Laskowski, P. Hobza, and J. Vondrasek, "Energy Matrix of Structurally Important Side-Chain/Side-Chain
    Interactions in Proteins," JOURNAL OF CHEMICAL THEORY AND COMPUTATION, vol. 6, iss. 7, pp. 2191-2203, 2010.
    [Bibtex]
    @article ISI:000279751500026,
    Author = Berka, Karel and Laskowski, Roman A. and Hobza, Pavel and Vondrasek,
       Jiri,
    Title = Energy Matrix of Structurally Important Side-Chain/Side-Chain
       Interactions in Proteins,
    Journal = JOURNAL OF CHEMICAL THEORY AND COMPUTATION,
    Year = 2010,
    Volume = 6,
    Number = 7,
    Pages = 2191-2203,
    Month = JUL,
    Abstract = The interactions between amino acid side chains in proteins are
       generally considered to be the most important stabilizing factor
       controlling the precise arrangement of the polypeptide chain into a
       well-defined spatial structure. We used the RI-DFT-D method to calculate
       the full 20 x 20 matrix of interaction energies between all pairs of
       amino acid side chains. For each pair, we used a representative 3D
       conformation extracted from an analysis of known protein structures from
       Protein Data Bank (PDB). The representative comes from the largest
       cluster of relative orientations of the two side chains. We find that
       all of the calculated interaction energies between selected pairs of
       amino acids are attractive in the gas phase with the exception of side
       chain pairs having the same total charge. We compared these data with
       those calculated by the parm03 and OPLS-AA/L force fields to investigate
       the reliability of simple methods in modeling biomolecules and their
       behavior. The force fields yield good overall interaction energies for
       our set but have problems in evaluation of some particular interactions
       which could be of principal importance for protein stability. We then
       looked in detail at the 20 side chain interactions involving tryptophan.
       The histograms of interaction energies showed that the distributions of
       the interaction energies are neither normal nor Boltzmann-like and that
       our representative geometries correspond mostly to the minimum energy
       geometry which is rather poorly populated in the whole pairwise energy
       distribution. We concluded that cluster representatives obtained by the
       clusterization algorithm based on geometry criteria cannot be considered
       as a typical interaction for the whole side chain/side chain interaction
       distribution. They seem to epitomize the strongest interactions in a
       protein and are often functionally or structurally important.,
    DOI = 10.1021/ct100007y,
    ISSN = 1549-9618,
    Unique-ID = ISI:000279751500026,
    
  • [DOI] D. Nachtigallova, T. Zeleny, M. Ruckenbauer, T. Mueller, M. Barbatti, P. Hobza, and H. Lischka, "Does Stacking Restrain the Photodynamics of Individual Nucleobases?," JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, vol. 132, iss. 24, pp. 8261+, 2010.
    [Bibtex]
    @article ISI:000278905700016,
    Author = Nachtigallova, Dana and Zeleny, Tomas and Ruckenbauer, Matthias and
       Mueller, Thomas and Barbatti, Mario and Hobza, Pavel and Lischka, Hans,
    Title = Does Stacking Restrain the Photodynamics of Individual Nucleobases?,
    Journal = JOURNAL OF THE AMERICAN CHEMICAL SOCIETY,
    Year = 2010,
    Volume = 132,
    Number = 24,
    Pages = 8261+,
    Month = JUN 23,
    Abstract = Nonadiabatic photodynamical simulations of 4-aminopyrimidine (4-APy)
       used as a model for adenine were performed by embedding it between two
       stacking methyl-guanine (mGua) molecules to determine the effect of
       spatial restrictions on the ultrafast photodeactivation mechanism of
       this nucleobase. A hybrid multiconfigurational ab initio/molecular
       mechanical approach in combination with surface hopping was used. During
       the dynamics the formation of a significant fraction of intrastrand
       hydrogen bonding from 4-APy to mGua above and below is observed. These
       findings show that this type of hydrogen bond may play an important role
       for the photodynamics within one DNA strand and that it should be of
       interest even in irregular segments of double stranded nucleic acids
       structures. The relaxation mechanism of internal conversion to the
       ground state is dominated by ring puckering, and an overall elongation
       of the lifetime of the embedded system by similar to 20\% as compared to
       the isolated 4-APy is computed.,
    DOI = 10.1021/ja1029705,
    ISSN = 0002-7863,
    Unique-ID = ISI:000278905700016,
    
  • [DOI] E. Gloaguen, H. Valdes, F. Pagliarulo, R. Pollet, B. Tardivel, P. Hobza, F. Piuzzi, and M. Mons, "Experimental and Theoretical Investigation of the Aromatic-Aromatic
    Interaction in Isolated Capped Dipeptides," JOURNAL OF PHYSICAL CHEMISTRY A, vol. 114, iss. 9, pp. 2973-2982, 2010.
    [Bibtex]
    @article ISI:000275046600004,
    Author = Gloaguen, Eric and Valdes, Haydee and Pagliarulo, Francesca and Pollet,
       Rodolphe and Tardivel, Benjamin and Hobza, Pavel and Piuzzi, Francois
       and Mons, Michel,
    Title = Experimental and Theoretical Investigation of the Aromatic-Aromatic
       Interaction in Isolated Capped Dipeptides,
    Journal = JOURNAL OF PHYSICAL CHEMISTRY A,
    Year = 2010,
    Volume = 114,
    Number = 9,
    Pages = 2973-2982,
    Month = MAR 11,
    Abstract = Among the forces responsible I'm shaping proteins, interactions between
       side chains of aromatic residues play all Important role I,, they are
       involved in the secondary and the tertiary structures of proteins
       contributing to the formation of hydrophobic domains. The purpose of
       this paper is to document this interaction in two capped dipeptides
       modeling a segment of a protein chain having two consecutive Phe
       residues, Ac-Phe-Phe-NH(2) and Ac-Phe-D-Phe-NH(2) These two molecules
       have been investigated in the gas phase by IR/UV double resonance
       Spectroscopy, and the assignment of the observed conformers has been
       done by comparison with quantum chemistry calculations. Both peptides
       ire found to adopt it beta-turn type I conformation stabilized by
       interaction between the two aromatic rings. Comparison with other
       dipeptides in the literature demonstrates the Impact of fill.,,
       aromatic-aromatic interaction oil the shape adopted by the peptide
       chain, and its role among the Other shaping forces (H-bonds, NH-pi
       interactions) is discussed As an illustration, the H-bond strength IS
       found to be Significantly lower in the beta-turn type I conformer, in
       which the two rings interact. as compared to (lie Similar conformer
       where such all interaction does not exist this structural feature clue
       to the backbone distortion induced by the interaction between the
       aromatic rings makes this system a good test for evaluating the ability
       Of computational methods to correctly account for the competition
       between these force. MP2, SCS-MP2. DFT, and DFT-D methods have been
       assessed in this respect. Comparison between geometries, energies, and
       frequency calculations illustrate their respective limitations in
       describing conformations resulting from a subtle equilibrium between the
       several interactions at play.,
    DOI = 10.1021/jp904216f,
    ISSN = 1089-5639,
    Unique-ID = ISI:000275046600004,
    
  • [DOI] D. Svozil, P. Hobza, and J. Sponer, "Comparison of Intrinsic Stacking Energies of Ten Unique Dinucleotide
    Steps in A-RNA and B-DNA Duplexes. Can We Determine Correct Order of
    Stability by Quantum-Chemical Calculations? (vol 114, pg 2547, 2010)," JOURNAL OF PHYSICAL CHEMISTRY B, vol. 114, iss. 7, pp. 2547, 2010.
    [Bibtex]
    @article ISI:000274578500028,
    Author = Svozil, Daniel and Hobza, Pavel and Sponer, Jiri,
    Title = Comparison of Intrinsic Stacking Energies of Ten Unique Dinucleotide
       Steps in A-RNA and B-DNA Duplexes. Can We Determine Correct Order of
       Stability by Quantum-Chemical Calculations? (vol 114, pg 2547, 2010),
    Journal = JOURNAL OF PHYSICAL CHEMISTRY B,
    Year = 2010,
    Volume = 114,
    Number = 7,
    Pages = 2547,
    Month = FEB 25,
    DOI = 10.1021/jp1004192,
    ISSN = 1520-6106,
    Unique-ID = ISI:000274578500028,
    
  • [DOI] D. Svozil, P. Hobza, and J. Sponer, "Comparison of Intrinsic Stacking Energies of Ten Unique Dinucleotide
    Steps in A-RNA and B-DNA Duplexes. Can We Determine Correct Order of
    Stability by Quantum-Chemical Calculations?," JOURNAL OF PHYSICAL CHEMISTRY B, vol. 114, iss. 2, pp. 1191-1203, 2010.
    [Bibtex]
    @article ISI:000273405000061,
    Author = Svozil, Daniel and Hobza, Pavel and Sponer, Jiri,
    Title = Comparison of Intrinsic Stacking Energies of Ten Unique Dinucleotide
       Steps in A-RNA and B-DNA Duplexes. Can We Determine Correct Order of
       Stability by Quantum-Chemical Calculations?,
    Journal = JOURNAL OF PHYSICAL CHEMISTRY B,
    Year = 2010,
    Volume = 114,
    Number = 2,
    Pages = 1191-1203,
    Month = JAN 21,
    Abstract = High level ab initio methods have been used to study stacking
       interactions in ten unique base pair steps both in A-RNA and in B-DNA
       duplexes. The protocol for selection of geometries based on molecular
       dynamics (MD) simulations is proposed, and its suitability is
       demonstrated by comparison with stacking in steps at fiber diffraction
       geometries. It is shown that fiber diffraction geometries are not
       sufficiently accurate for interaction energy calculations. In addition,
       the protocol for selection of geometries based on MD simulations allows
       for the evaluation of the variability of the intrinsic stacking energies
       along the MD trajectories. The uncertainty in stacking energies
       (difference between the most and least stable geometry) due to the
       dynamical nature of systems can be, in some cases, as large as 3.0 kcal
       center dot mol(-1), which is almost 50\% of the actual sequence
       dependence of base stacking energies (the energy difference between the
       most and least stable sequences). Thus, assessing the relative magnitude
       of the gas phase stacking energy using a single geometry for each
       sequence is insufficient to obtain an unambiguous order of gas phase
       stacking energies in canonical double helices. Though the ordering of
       ten unique dinucleotide steps cannot be definitive, some general
       conclusions were drawn. The stacking energies of base pair steps in
       A-RNA are more evenly separated compared to B-DNA, and their ordering is
       less sensitive to the dynamics of the system compared to be B-DNA. The
       most stable step both in B-DNA W A-RNA is the CG/CG step that is well
       separated from the second most stable step GC/GC. Also the leas/stable
       step (the CC/GG step) is well separated from the rest of the structures.
       The calculations further show that B-DNA stacking is favorable only
       marginally (on average by 1.14 kcal center dot mol(-1) per base pair
       step) over A-RNA stacking, and this difference vanishes after
       subtracting the stabilizing van der Waals effect of the thymine 5-methyl
       group that is absent in RNA. Basically, no correlation between the
       sequence dependence of gas phase stacking energies and the sequence
       dependence of Delta G degrees(37) free energies used in nearest-neighbor
       models was found either for B-DNA or for A-RNA. This reflects the
       complexity of the balance of forces that are responsible for the
       sequence dependence of thermodynamics stability of nucleic acids, which
       masks the effect of the intrinsic interactions between the stacked base
       pairs.,
    DOI = 10.1021/jp910788e,
    ISSN = 1520-6106,
    Unique-ID = ISI:000273405000061,
    
  • [DOI] J. Rezac, P. Hobza, and S. A. Harris, "Stretched DNA Investigated Using Molecular-Dynamics and
    Quantum-Mechanical Calculations," BIOPHYSICAL JOURNAL, vol. 98, iss. 1, pp. 101-110, 2010.
    [Bibtex]
    @article ISI:000273433800012,
    Author = Rezac, Jan and Hobza, Pavel and Harris, Sarah A.,
    Title = Stretched DNA Investigated Using Molecular-Dynamics and
       Quantum-Mechanical Calculations,
    Journal = BIOPHYSICAL JOURNAL,
    Year = 2010,
    Volume = 98,
    Number = 1,
    Pages = 101-110,
    Month = JAN 6,
    Abstract = We combined atomistic molecular-dynamics simulations with
       quantum-mechanical calculations to investigate the sequence dependence
       of the stretching behavior of duplex DNA. Our combined
       quantum-mechanical/molecular-mechanical approach demonstrates that
       molecular-mechanical force fields are able to describe both the backbone
       and base-base interactions within the highly distorted nucleic acid
       structures produced by stretching the DNA from the 5' ends, which
       include conformations containing disassociated basepairs, just as well
       as these force fields describe relaxed DNA conformations. The
       molecular-dynamics simulations indicate that the force-induced melting
       pathway is sequence-dependent and is influenced by the availability of
       noncanonical hydrogen-bond interactions that can assist the
       disassociation of the DNA basepairs. The biological implications of
       these results are discussed.,
    DOI = 10.1016/j.bpj.2009.08.062,
    ISSN = 0006-3495,
    Unique-ID = ISI:000273433800012,
    
  • [DOI] M. Korth, M. Pitonak, J. Rezac, and P. Hobza, "A Transferable H-Bonding Correction for Semiempirical Quantum-Chemical
    Methods," JOURNAL OF CHEMICAL THEORY AND COMPUTATION, vol. 6, iss. 1, pp. 344-352, 2010.
    [Bibtex]
    @article ISI:000274757000034,
    Author = Korth, Martin and Pitonak, Michal and Rezac, Jan and Hobza, Pavel,
    Title = A Transferable H-Bonding Correction for Semiempirical Quantum-Chemical
       Methods,
    Journal = JOURNAL OF CHEMICAL THEORY AND COMPUTATION,
    Year = 2010,
    Volume = 6,
    Number = 1,
    Pages = 344-352,
    Month = JAN,
    Abstract = Semiempirical methods could offer a feasible compromise between ab
       initio and empirical approaches for the calculation of large molecules
       with biological relevance. A key problem for attempts in this direction
       is the rather bad performance of current semiempirical methods for
       noncovalent interactions, especially hydrogen-bonding. On the basis of
       the recently introduced PM6-DH method, which includes, empirical
       corrections for dispersion (D) and hydrogen-bond (H) interactions, we
       have developed an improved and transferable H-bonding correction for
       semiempirical quantum chemical methods. The performance of the improved
       correction is evaluated for PM6, AM1, OM3, and SCC-DFTB (enhanced by
       standard empirical dispersion corrections) with several test sets for
       noncovalent interactions and is shown to reach the quality of current
       DFT-D approaches for these types of problems.,
    DOI = 10.1021/ct900541n,
    ISSN = 1549-9618,
    Unique-ID = ISI:000274757000034,
    
  • [DOI] K. E. Riley, M. Pitonak, J. Cerny, and P. Hobza, "On the Structure and Geometry of Biomolecular Binding Motifs
    (Hydrogen-Bonding, Stacking, X-H center dot center dot center dot pi):
    WFT and DFT Calculations," JOURNAL OF CHEMICAL THEORY AND COMPUTATION, vol. 6, iss. 1, pp. 66-80, 2010.
    [Bibtex]
    @article ISI:000274757000008,
    Author = Riley, Kevin E. and Pitonak, Michal and Cerny, Jiri and Hobza, Pavel,
    Title = On the Structure and Geometry of Biomolecular Binding Motifs
       (Hydrogen-Bonding, Stacking, X-H center dot center dot center dot pi):
       WFT and DFT Calculations,
    Journal = JOURNAL OF CHEMICAL THEORY AND COMPUTATION,
    Year = 2010,
    Volume = 6,
    Number = 1,
    Pages = 66-80,
    Month = JAN,
    Abstract = The strengths of noncovalent interactions are generally very sensitive
       to a number of geometric parameters. Among the most important of these
       parameters is the separation between the interacting moieties (in the
       case of an intermolecular interaction, this would be the intermolecular
       separation). Most works seeking to characterize the properties of
       intermolecular interactions are mainly concerned with binding energies
       obtained at the potential energy minimum (as determined at some
       particular level of theory). In this work, in order to extend our
       understanding of these types of noncovalent interactions, we investigate
       the distance dependence of several types of intermolecular interactions,
       these are hydrogen bonds, stacking interactions, dispersion
       interactions, and X-H center dot center dot center dot pi interactions.
       There are several methods that have traditionally been used to treat
       noncovalent interactions as well as many new methods that have emerged
       within the past three or four years. Here we obtain reference data using
       estimated CCSD(T) values at the complete basis set limit (using the
       CBS(T) method); potential energy curves are also produced using several
       other methods thought to be accurate for intermolecular interactions,
       these are MP2/cc-pVTZ, MP2/aug-cc-pVDZ, MP2/6-31G(star)(0.25),
       SCS(MI)-MP2/cc-pVTZ, estimated MP2.5/CBS, DFT-SAPT/aug-cc-pVTZ,
       DFT/M06-2X/6-311+G(2df,2p), and DFT-D/TPSS/6-311++G(3df,3pd). The basis
       set superposition error is systematically considered throughout the
       study. It is found that the MP2.5 and DFT-SAPT methods, which are both
       quite computationally intensive, produce potential energy curves that
       are in very good agreement to those of the reference method. Among the
       MP2 techniques, which can be said to be of medium computational expense,
       the best results are obtained with MP2/cc-pVTZ and SCS(MI)-MP2/cc-pVTZ.
       DFT-D/TPSS/6-311++G(3df,3pd) is the DFT-based method that can be said to
       give the most well-balanced description of intermolecular interactions.,
    DOI = 10.1021/ct900376r,
    ISSN = 1549-9618,
    Unique-ID = ISI:000274757000008,
    
  • [DOI] J. Cerny and P. Hobza, "Energy barriers between H-bonded and stacked structures of
    9-methyladenine center dot center dot center dot 1-methylthymine and
    9-methylguanine center dot center dot center dot 1-methylcytosine
    complexes," CHEMICAL COMMUNICATIONS, vol. 46, iss. 3, pp. 383-385, 2010.
    [Bibtex]
    @article ISI:000272992700004,
    Author = Cerny, Jiri and Hobza, Pavel,
    Title = Energy barriers between H-bonded and stacked structures of
       9-methyladenine center dot center dot center dot 1-methylthymine and
       9-methylguanine center dot center dot center dot 1-methylcytosine
       complexes,
    Journal = CHEMICAL COMMUNICATIONS,
    Year = 2010,
    Volume = 46,
    Number = 3,
    Pages = 383-385,
    Abstract = The transition structures (TS) between H-bonded (H) and stacked (S)
       structures of 9-methyladenine center dot center dot center dot
       1-methylthymine and 9-methylguanine center dot center dot center dot
       1-methylcytosine base pairs were localized at the DFT-D/TZVP potential
       energy surface. The energy barrier between the S and TS structures is
       considerably higher for the former pair than for the latter, which makes
       localization of the stacked structure of this pair possible.,
    DOI = 10.1039/b913209k,
    ISSN = 1359-7345,
    Unique-ID = ISI:000272992700004,
    
  • [DOI] M. Zgarbova, M. Otyepka, J. Sponer, P. Hobza, and P. Jurecka, "Large-scale compensation of errors in pairwise-additive empirical force
    fields: comparison of AMBER intermolecular terms with rigorous DFT-SAPT
    calculations," PHYSICAL CHEMISTRY CHEMICAL PHYSICS, vol. 12, iss. 35, pp. 10476-10493, 2010.
    [Bibtex]
    @article ISI:000281352300043,
    Author = Zgarbova, Marie and Otyepka, Michal and Sponer, Jiri and Hobza, Pavel
       and Jurecka, Petr,
    Title = Large-scale compensation of errors in pairwise-additive empirical force
       fields: comparison of AMBER intermolecular terms with rigorous DFT-SAPT
       calculations,
    Journal = PHYSICAL CHEMISTRY CHEMICAL PHYSICS,
    Year = 2010,
    Volume = 12,
    Number = 35,
    Pages = 10476-10493,
    Abstract = The intermolecular interaction energy components for several molecular
       complexes were calculated using force fields available in the AMBER
       suite of programs and compared with Density Functional Theory-Symmetry
       Adapted Perturbation Theory (DFT-SAPT) values. The extent to which such
       comparison is meaningful is discussed. The comparability is shown to
       depend strongly on the intermolecular distance, which means that
       comparisons made at one distance only are of limited value. At large
       distances the coulombic and van der Waals 1/r(6) empirical terms
       correspond fairly well with the DFT-SAPT electrostatics and dispersion
       terms, respectively. At the onset of electronic overlap the empirical
       values deviate from the reference values considerably. However, the
       errors in the force fields tend to cancel out in a systematic manner at
       equilibrium distances. Thus, the overall performance of the force fields
       displays errors an order of magnitude smaller than those of the
       individual interaction energy components. The repulsive 1/r(12)
       component of the van der Waals expression seems to be responsible for a
       significant part of the deviation of the force field results from the
       reference values. We suggest that further improvement of the force
       fields for intermolecular interactions would require replacement of the
       nonphysical 1/r(12) term by an exponential function. Dispersion
       anisotropy and its effects are discussed. Our analysis is intended to
       show that although comparing the empirical and non-empirical interaction
       energy components is in general problematic, it might bring insights
       useful for the construction of new force fields. Our results are
       relevant to often performed force-field-based interaction energy
       decompositions.,
    DOI = 10.1039/c002656e,
    ISSN = 1463-9076,
    Unique-ID = ISI:000281352300043,
    
  • [DOI] M. Pitonak, P. Neogrady, and P. Hobza, "Three- and four-body nonadditivities in nucleic acid tetramers: a
    CCSD(T) study," PHYSICAL CHEMISTRY CHEMICAL PHYSICS, vol. 12, iss. 6, pp. 1369-1378, 2010.
    [Bibtex]
    @article ISI:000274072900017,
    Author = Pitonak, M. and Neogrady, P. and Hobza, P.,
    Title = Three- and four-body nonadditivities in nucleic acid tetramers: a
       CCSD(T) study,
    Journal = PHYSICAL CHEMISTRY CHEMICAL PHYSICS,
    Year = 2010,
    Volume = 12,
    Number = 6,
    Pages = 1369-1378,
    Abstract = Three-and four-body nonadditivities in the uracil tetramer (in DNA-like
       geometry) and the GC step (in crystal geometry) were investigated at
       various levels of the wave-function theory: HF, MP2, MP3, L-CCD, CCSD
       and CCSD(T). All of the calculations were performed using the
       6-31G**(0.25,0.15) basis set, whereas the HF, MP2 and the MP3
       nonadditivities were, for the sake of comparison, also determined with
       the much larger aug-cc-pVDZ basis set. The HF and MP2 levels do not
       provide reliable values for many-body terms, making it necessary to go
       beyond the MP2 level. The benchmark CCSD(T) three-and four-body
       nonadditivities are reasonably well reproduced at the MP3 level, and
       almost quantitative agreement is obtained (fortuitously) either on the
       L-CCD level or as an average of the MP3 and the CCSD results. Reliable
       values of many-body terms (especially their higher-order correlation
       contributions) are obtained already when the rather small
       6-31G**(0.25,0.15) basis set is used. The four-body term is much
       smaller when compared to the three-body terms, but it is definitely not
       negligible, e. g. in the case of the GC step it represents about 16\% of
       all of the three-and four-body terms. While investigating the geometry
       dependence of many-body terms for the GG step at the
       MP3/6-31G**(0.25,0.15) level, we found that it is necessary to
       include at least three-body terms in the determination of optimal
       geometry parameters.,
    DOI = 10.1039/b919354e,
    ISSN = 1463-9076,
    Unique-ID = ISI:000274072900017,
    
  • [DOI] W. Zierkiewicz, D. Michalska, and P. Hobza, "Adenine ribbon stabilized by Watson-Crick and Hoogsteen hydrogen Bonds:
    WFT and DFT study," PHYSICAL CHEMISTRY CHEMICAL PHYSICS, vol. 12, iss. 12, pp. 2888-2894, 2010.
    [Bibtex]
    @article ISI:000275385700012,
    Author = Zierkiewicz, Wiktor and Michalska, Danuta and Hobza, Pavel,
    Title = Adenine ribbon stabilized by Watson-Crick and Hoogsteen hydrogen Bonds:
       WFT and DFT study,
    Journal = PHYSICAL CHEMISTRY CHEMICAL PHYSICS,
    Year = 2010,
    Volume = 12,
    Number = 12,
    Pages = 2888-2894,
    Abstract = The self-organized adenine ribbon is studied theoretically. The
       experimental evidence for the formation of such a ribbon has been found
       in the crystal structure of the supramolecular system [Dobrzynska and
       Jerzykiewicz, J. Am. Chem. Soc., 2004, 126, 11118], and the striking
       structural feature is the fact that both the Watson-Crick and Hoogsteen
       faces of adenine are involved in the hydrogen bonding within the ribbon.
       The structure and physical properties of the monomer and five clusters
       of adenine (Ade)(n) (where n = 2, 3, 4, 5, 6) with AA2(2) configuration
       have been studied by means of the B3LYP, RI-TPSS, RI-TPSS-D (augmented
       with the dispersion term) and RI-MP2 methods using the 6-311 + G(d,p),
       cc-pVTZ and TZVP basis sets. It is shown that among the investigated
       adenine clusters only the dimer has the planar structure. The evaluation
       of the three-body contribution to the total binding energy of adenine
       trimer has been performed at different levels of theory. All the methods
       consistently indicate that this term is positive and small (less than
       0.5 kcal mol(-1)) which corresponds to a weak anti-cooperative effect,
       in adenine trimer. The differences between the total electronic energies
       obtained at the RI-TPSS/TZVP-D and RI-TPSS/TZVP levels of theory have
       shown that the London dispersion forces stabilize the adenine cluster
       containing 12 or more molecules by about -8 kcal mol(-1) per molecule.
       The results from the DFT symmetry adapted perturbation theory analysis
       have revealed that the contribution of dispersion to the binding energy
       of the adenine ribbon is about 25\%.,
    DOI = 10.1039/b920433d,
    ISSN = 1463-9076,
    Unique-ID = ISI:000275385700012,
    
  • [DOI] C. A. Morgado, P. Jurecka, D. Svozil, P. Hobza, and J. Sponer, "Reference MP2/CBS and CCSD(T) quantum-chemical calculations on stacked
    adenine dimers. Comparison with DFT-D, MP2.5, SCS(MI)-MP2, M06-2X,
    CBS(SCS-D) and force field descriptions," PHYSICAL CHEMISTRY CHEMICAL PHYSICS, vol. 12, iss. 14, pp. 3522-3534, 2010.
    [Bibtex]
    @article ISI:000275938200021,
    Author = Morgado, Claudio A. and Jurecka, Petr and Svozil, Daniel and Hobza,
       Pavel and Sponer, Jiri,
    Title = Reference MP2/CBS and CCSD(T) quantum-chemical calculations on stacked
       adenine dimers. Comparison with DFT-D, MP2.5, SCS(MI)-MP2, M06-2X,
       CBS(SCS-D) and force field descriptions,
    Journal = PHYSICAL CHEMISTRY CHEMICAL PHYSICS,
    Year = 2010,
    Volume = 12,
    Number = 14,
    Pages = 3522-3534,
    Abstract = We have performed reference quantum-chemical calculations for about 130
       structures of adenine dimers in stacked conformations, with special
       attention given to dimers that are either vertically compressed
       (parallel structures) or contain close interatomic contacts
       (non-parallel structures). Such geometries are sampled during thermal
       fluctuations of nucleic acids and contribute to the local conformational
       variability of these systems. Their theoretical characterization
       requires a good description of interaction energies in the short-range
       repulsion region. The reference calculations have been performed with
       the CBS(T) method, i.e., MP2/CBS computations corrected for higher-order
       electron-correlation effects using the CCSD(T) method. These benchmark
       data have been used to examine the performance of the DFT-D,
       SCS(MI)-MP2, MP2.5, M06-2X and CBS(SCS-D) quantum-mechanical methods,
       and of the AMBER Cornell et al. force field. The present results, as
       well as those of our previous study on stacked uracil dimers, confirm
       that the force field severely exaggerates the repulsion at short
       intermolecular distances. This behavior complicates the use of the force
       field in scans of the stacking-energy dependence on local conformational
       parameters in nucleic acids. Compared against the previous results
       obtained in the uracil dimer study, the performance of DFT-D to describe
       stacking at short intermolecular distances has worsened, showing for the
       adenine dimers a larger exaggeration of the repulsion, especially for
       structures where the monomers are parallel to each other. Despite these
       deviations, the performance of DFT-D is still reasonably good and this
       method provides, for example, a relatively inexpensive way to monitor
       stacking energies along molecular dynamics trajectories. The best
       performers are the MP2.5, SCS(MI)-MP2, and CBS(SCS-D) methods. In
       addition, the energy profiles given by the SCS(MI)-MP2 and CBS(SCS-D)
       methods are the ones that most closely resemble the CBS(T) data.
       Interestingly, the performance of the SCS(MI)-MP2 method for stacked
       adenine dimers is better than for stacked uracil dimers, indicating that
       the quality of the description may vary with the nucleobase composition.
       Even though the SCS(MI)-MP2 method cannot match the speed of DFT-D, the
       results so far render it a promising tool to study intrinsic
       interactions in systems of moderate size. In general, for most
       applications all the QM methods tested here are of sufficient accuracy.,
    DOI = 10.1039/b924461a,
    ISSN = 1463-9076,
    Unique-ID = ISI:000275938200021,
    
  • [DOI] B. O. Crews, A. Abo-Riziq, K. Pluhackova, P. Thompson, G. Hill, P. Hobza, and M. S. de Vries, "Guanine-aspartic acid interactions probed with IR-UV resonance
    spectroscopy," PHYSICAL CHEMISTRY CHEMICAL PHYSICS, vol. 12, iss. 14, pp. 3597-3605, 2010.
    [Bibtex]
    @article ISI:000275938200030,
    Author = Crews, Bridgit O. and Abo-Riziq, Ali and Pluhackova, Kristyna and
       Thompson, Patrina and Hill, Glake and Hobza, Pavel and de Vries,
       Mattanjah S.,
    Title = Guanine-aspartic acid interactions probed with IR-UV resonance
       spectroscopy,
    Journal = PHYSICAL CHEMISTRY CHEMICAL PHYSICS,
    Year = 2010,
    Volume = 12,
    Number = 14,
    Pages = 3597-3605,
    Abstract = Double resonance spectroscopy of clusters of guanine with aspartic acid
       reveals geometries similar to patterns exhibited in DNA base pairs. In
       the spectral region of 32 800 cm(-1) to 35 500 cm(-1) we observe five
       isomers of guanine-aspartic acid clusters and assign their structures
       based on IR-UV hole-burning spectra and wave function theory
       calculations at the MP2/cc-pVDZ and MP2/cc-pVTZ levels. The calculations
       employed both harmonic and one-dimensional scan anharmonic
       approximations. Three of the isomers are similar, assigned to structures
       containing three hydrogen bonds and 9-enolguanine. We assign the fourth
       isomer to a structure containing a 9-keto tautomer of guanine and
       forming a triply bonded structure similar to a base pairing interaction.
       The fifth isomer dissociates with proton transfer upon excitation or
       ionization. This is the first set of experiments and high-level ab
       initio calculations of the isolated, microscopic interactions of an
       amino acid and a nucleobase, the building blocks of nucleic acids and
       proteins.,
    DOI = 10.1039/b925340h,
    ISSN = 1463-9076,
    Unique-ID = ISI:000275938200030,
    
  • [DOI] D. Nachtigallova, H. Lischka, J. J. Szymczak, M. Barbatti, P. Hobza, Z. Gengeliczki, G. Pino, M. P. Callahan, and M. S. de Vries, "The effect of C5 substitution on the photochemistry of uracil," PHYSICAL CHEMISTRY CHEMICAL PHYSICS, vol. 12, iss. 19, pp. 4924-4933, 2010.
    [Bibtex]
    @article ISI:000277359300005,
    Author = Nachtigallova, Dana and Lischka, Hans and Szymczak, Jaroslaw J. and
       Barbatti, Mario and Hobza, Pavel and Gengeliczki, Zsolt and Pino,
       Gustavo and Callahan, Michael P. and de Vries, Mattanjah S.,
    Title = The effect of C5 substitution on the photochemistry of uracil,
    Journal = PHYSICAL CHEMISTRY CHEMICAL PHYSICS,
    Year = 2010,
    Volume = 12,
    Number = 19,
    Pages = 4924-4933,
    Abstract = A combined experimental and theoretical study on the excited-state
       behavior of the uracil analogues, 5-OH-Ura and 5-NH(2)-Ura is reported.
       Two-photon ionization and IR/UV double-resonant spectra show that there
       is only one tautomer present for each with an excited state lifetime of
       1.8 ns for 5-OH-Ura and 12.0 ns for 5-NH(2)-Ura as determined from
       pump-probe experiments. The nature of the excited states of both species
       is investigated by means of multi-reference ab initio methods. Vertical
       excitation energies, excited state minima, minima on the crossing seam
       and reaction paths towards them are determined. Sizeable barriers on
       these paths are found that provide an explanation for the lifetimes of
       several nanoseconds observed in the experiment.,
    DOI = 10.1039/b925803p,
    ISSN = 1463-9076,
    Unique-ID = ISI:000277359300005,
    
  • [DOI] Z. Gengeliczki, M. P. Callahan, N. Svadlenak, C. I. Pongor, B. Sztaray, L. Meerts, D. Nachtigallova, P. Hobza, M. Barbatti, H. Lischka, and M. S. de Vries, "Effect of substituents on the excited-state dynamics of the modified DNA
    bases 2,4-diaminopyrimidine and 2,6-diaminopurine," PHYSICAL CHEMISTRY CHEMICAL PHYSICS, vol. 12, iss. 20, pp. 5375-5388, 2010.
    [Bibtex]
    @article ISI:000277689500020,
    Author = Gengeliczki, Zsolt and Callahan, Michael P. and Svadlenak, Nathan and
       Pongor, Csaba Istvan and Sztaray, Balint and Meerts, Leo and
       Nachtigallova, Dana and Hobza, Pavel and Barbatti, Mario and Lischka,
       Hans and de Vries, Mattanjah S.,
    Title = Effect of substituents on the excited-state dynamics of the modified DNA
       bases 2,4-diaminopyrimidine and 2,6-diaminopurine,
    Journal = PHYSICAL CHEMISTRY CHEMICAL PHYSICS,
    Year = 2010,
    Volume = 12,
    Number = 20,
    Pages = 5375-5388,
    Abstract = To explore the excited state dynamics of pyrimidine derivatives, we
       performed a combined experimental and theoretical study. We present
       resonant two-photon ionization (R2PI) and IR-UV double resonance spectra
       of 2,4-diaminopyrimidine and 2,6-diaminopurine seeded in a supersonic
       jet by laser desorption. For 2,4-diaminopyrimidine (S(0) -> S(1) 34 459
       cm(-1)), we observed only the diamino tautomer with an excited state
       lifetime bracketed between experimental limits of 10 ps and 1 ns. For
       2,6-diaminopurine, we observed two tautomers, the 9H- (S(0) -> S(1) 34
       881 cm(-1)) and 7H- (S(0) -> S(1) 32 215 cm(-1)) diamino forms, with
       excited state lifetimes of 6.3 +/- 0.4 ns and 8.7 +/- 0.8 ns,
       respectively. We investigated the nature of the excited state of
       2,4-diaminopyrimidine by means of multi-reference ab initio methods. The
       calculations of stationary points in the ground and excited states,
       minima on the S(0)/S(1) crossing seam and connecting reaction paths show
       that several paths with negligible barriers exist, allowing ultrafast
       radiationless deactivation if excited at energies slightly higher than
       the band origin. The sub-nanosecond lifetime found experimentally is in
       good agreement with this finding.,
    DOI = 10.1039/b917852j,
    ISSN = 1463-9076,
    Unique-ID = ISI:000277689500020,
    
  • [DOI] M. Pitonak, J. Rezac, and P. Hobza, "Spin-component scaled coupled-clusters singles and doubles optimized
    towards calculation of noncovalent interactions," PHYSICAL CHEMISTRY CHEMICAL PHYSICS, vol. 12, iss. 33, pp. 9611-9614, 2010.
    [Bibtex]
    @article ISI:000281007200005,
    Author = Pitonak, Michal and Rezac, Jan and Hobza, Pavel,
    Title = Spin-component scaled coupled-clusters singles and doubles optimized
       towards calculation of noncovalent interactions,
    Journal = PHYSICAL CHEMISTRY CHEMICAL PHYSICS,
    Year = 2010,
    Volume = 12,
    Number = 33,
    Pages = 9611-9614,
    Abstract = The same- and opposite-spin scaling parameters for the SCS-CCSD method
       were reparametrized on the basis of benchmark CCSD(T)/CBS set
       interaction energies from the S22 set. New parameters were close to the
       original ones but swap between the different spin components, being 1.11
       for the opposite- and 1.28 for the same- spin component. The RMSD, and
       especially, the largest error for the S22 were significantly reduced in
       comparison with the original parametrization. These statistical factors
       were only slightly worse when the S22x5 test set, containing not only
       the equilibrium but also the non-equilibrium geometries, was used. This
       new method, named the SCS(MI)-CCSD (''MI'' stands for ``Molecular
       Interactions'') can thus be recommended for highly accurate
       calculations of interaction energies of various noncovalent interaction
       types, for which the CCSD(T)/CBS calculations are impractical.,
    DOI = 10.1039/c0cp00158a,
    ISSN = 1463-9076,
    Unique-ID = ISI:000281007200005,
    

2009

  • [DOI] P. Rezacova, J. Pokorna, J. Brynda, M. Kozisek, P. Cigler, M. Lepsik, J. Fanfrlik, J. Rezac, K. G. Saskova, I. Sieglova, J. Plesek, V. Sicha, B. Gruener, H. Oberwinkler, J. Sedlacek, H. Kraeusslich, P. Hobza, V. Kral, and J. Konvalinka, "Design of HIV Protease Inhibitors Based on Inorganic Polyhedral
    Metallacarboranes," JOURNAL OF MEDICINAL CHEMISTRY, vol. 52, iss. 22, pp. 7132-7141, 2009.
    [Bibtex]
    @article ISI:000271825600018,
    Author = Rezacova, Pavlina and Pokorna, Jana and Brynda, Jiri and Kozisek, Milan
       and Cigler, Petr and Lepsik, Martin and Fanfrlik, Jindrich and Rezac,
       Jan and Saskova, Klara Grantz and Sieglova, Irena and Plesek, Jaromir
       and Sicha, Vaclav and Gruener, Bohumir and Oberwinkler, Heike and
       Sedlacek, Juraj and Kraeusslich, Hans-Georg and Hobza, Pavel and Kral,
       Vladimir and Konvalinka, Jan,
    Title = Design of HIV Protease Inhibitors Based on Inorganic Polyhedral
       Metallacarboranes,
    Journal = JOURNAL OF MEDICINAL CHEMISTRY,
    Year = 2009,
    Volume = 52,
    Number = 22,
    Pages = 7132-7141,
    Month = NOV 26,
    Abstract = HIV protease (HIV PR) is a primary target for anti-HIV drug design. We
       have previously identified and characterized substituted
       metallacarboranes as a new class of HIV protease inhibitors. In a
       structure-guided drug design effort, we connected the two cobalt
       bis(dicarbollide) clusters with a linker to substituted ammonium group
       and obtained a set of compounds based on a lead formula
       [H(2)N-(8-(C(2)H(4)O)(2)-1,2-C(2)B(9)H(10))(1',2'-C(2)B(9)H(11))-3,3'-
       Co)(2)]Na. We explored inhibition properties of these compounds with
       various substitutions, determined the HIV PR:inhibitor crystal
       structure, and computationally explored the conformational space of the
       linker. Our results prove the capacity of linker-substituted dual-cage
       cobalt bis(dicarbollides) as lead compounds for design of more potent
       inhibitors of HIV PR.,
    DOI = 10.1021/jm9011388,
    ISSN = 0022-2623,
    Unique-ID = ISI:000271825600018,
    
  • [DOI] H. Valdes, K. Pluhackova, and P. Hobza, "Phenylalanyl-Glycyl-Phenylalanine Tripeptide: A Model System for
    Aromatic-Aromatic Side Chain Interactions in Proteins," JOURNAL OF CHEMICAL THEORY AND COMPUTATION, vol. 5, iss. 9, pp. 2248-2256, 2009.
    [Bibtex]
    @article ISI:000269488300009,
    Author = Valdes, H. and Pluhackova, K. and Hobza, P.,
    Title = Phenylalanyl-Glycyl-Phenylalanine Tripeptide: A Model System for
       Aromatic-Aromatic Side Chain Interactions in Proteins,
    Journal = JOURNAL OF CHEMICAL THEORY AND COMPUTATION,
    Year = 2009,
    Volume = 5,
    Number = 9,
    Pages = 2248-2256,
    Month = SEP,
    Abstract = The performance of a wide range of quantum chemical calculations for the
       ab initio study of realistic model systems of aromatic-aromatic side
       chain interactions in proteins (in particular those pi-pi interactions
       occurring between adjacent residues along the protein sequence) is here
       assessed on the phenylalanyl-glycyl-phenylalanine (FGF) tripeptide.
       Energies and geometries obtained at different levels of theory are
       compared with CCSD(T)/CBS benchmark energies and RI-MP2/cc-pVTZ
       benchmark geometries, respectively. Consequently, a protocol of
       calculation alternative to the very expensive CCSD(T)/CBS is proposed.
       In addition to this, the preferred orientation of the Phe aromatic side
       chains is discussed and compared with previous results on the topic.,
    DOI = 10.1021/ct900174f,
    ISSN = 1549-9618,
    Unique-ID = ISI:000269488300009,
    
  • [DOI] J. Konvalinka, H. Illnerova, P. Hobza, V. Horejsi, A. Holy, P. Jungwirth, V. Paces, P. Martasek, and J. Zlatuska, "Czech bibliometric system fosters mediocre research," NATURE, vol. 460, iss. 7259, pp. 1079, 2009.
    [Bibtex]
    @article ISI:000269314000014,
    Author = Konvalinka, Jan and Illnerova, Helena and Hobza, Pavel and Horejsi,
       Vaclav and Holy, Antonin and Jungwirth, Pavel and Paces, Vaclav and
       Martasek, Pavel and Zlatuska, Jiri,
    Title = Czech bibliometric system fosters mediocre research,
    Journal = NATURE,
    Year = 2009,
    Volume = 460,
    Number = 7259,
    Pages = 1079,
    Month = AUG 27,
    DOI = 10.1038/4601079c,
    ISSN = 0028-0836,
    Unique-ID = ISI:000269314000014,
    
  • [DOI] P. Matejicek, J. Zednik, K. Uselova, J. Plestil, J. Fanfrlik, A. Nykanen, J. Ruokolainen, P. Hobza, and K. Prochazka, "Stimuli-Responsive Nanoparticles Based on Interaction of
    Metallacarborane with Poly(ethylene oxide)," MACROMOLECULES, vol. 42, iss. 13, pp. 4829-4837, 2009.
    [Bibtex]
    @article ISI:000268138500068,
    Author = Matejicek, Pavel and Zednik, Jiri and Uselova, Katerina and Plestil,
       Josef and Fanfrlik, Jindrich and Nykanen, Antti and Ruokolainen, Janne
       and Hobza, Pavel and Prochazka, Karel,
    Title = Stimuli-Responsive Nanoparticles Based on Interaction of
       Metallacarborane with Poly(ethylene oxide),
    Journal = MACROMOLECULES,
    Year = 2009,
    Volume = 42,
    Number = 13,
    Pages = 4829-4837,
    Month = JUL 14,
    Abstract = We report the first evidence that the antiviral active (inhibitor of HIV
       protease) boron cluster [3-cobalt bis(1,2-dicarbollide)](-) anion.
       CoD(-), interacts and forms a stable complex with one of the most widely
       used polymeric components of drug delivery systems: poly(ethylene
       oxide), PEO. The metallacarborane/polymer complex is insoluble in
       aqueous solutions. The amount of the precipitate depends oil
       concentration of alkaline or earth-alkaline cations. The formation of
       insoluble complex is the result of a combination of several Factors. One
       of the decisive contributions is the formation of dihydrogen bonds
       between negatively charged hydrogen atoms attached to boron atoms and
       slightly positively charged H atoms in repealing -CH(2)-CH(2)-O- units.
       It is also important that alkaline cations interact with oxygen atoms of
       PEO. The formation of the insoluble NaCoD/PEO complex can be exploited
       ill design of water-soluble [3-cobalt
       bis(1,2-dicarbollide)]-containing nanoparticles which could offer
       applications ill medicine. We studied the boron cluster interaction with
       well-defined double hydrophilic block copolymer: poly(ethylene
       oxide)-block-poly(methacrylic acid), PEO-PMA. The interaction leads to
       it spontaneous formation of core-shell nanoparticles. The insoluble core
       contains the PEO/CoD(-) complex, while the polyanionic PMA blocks, which
       do not interact with the cobaltacarborane, form the pH-responsive
       micellar shell and stabilize the particles in aqueous media. The
       nanoparticles were studied by light and X-ray scattering, NMR
       spectroscopy, electrophoresis, and microscopy techniques like AFM and
       cryo-TEM. It was found that the cores are not completely frozen in
       aqueous media. Their composition depends oil salt concentration, and the
       metallacarborane call diffuse from/into the nanoparticle after the
       salinity change.,
    DOI = 10.1021/ma900484y,
    ISSN = 0024-9297,
    Unique-ID = ISI:000268138500068,
    
  • [DOI] J. Rezac, J. Fanfrlik, D. Salahub, and P. Hobza, "Semiempirical Quantum Chemical PM6 Method Augmented by Dispersion and
    H-Bonding Correction Terms Reliably Describes Various Types of
    Noncovalent Complexes," JOURNAL OF CHEMICAL THEORY AND COMPUTATION, vol. 5, iss. 7, pp. 1749-1760, 2009.
    [Bibtex]
    @article ISI:000268232500005,
    Author = Rezac, Jan and Fanfrlik, Jindrich and Salahub, Dennis and Hobza, Pavel,
    Title = Semiempirical Quantum Chemical PM6 Method Augmented by Dispersion and
       H-Bonding Correction Terms Reliably Describes Various Types of
       Noncovalent Complexes,
    Journal = JOURNAL OF CHEMICAL THEORY AND COMPUTATION,
    Year = 2009,
    Volume = 5,
    Number = 7,
    Pages = 1749-1760,
    Month = JUL,
    Abstract = Because of its construction and parametrization for more than 80
       elements, the semiempirical quantum chemical PM6 method is superior to
       other similar methods. Despite its advantages, however, the PM6 method
       fails for the description of noncovalent interactions, specifically the
       dispersion energy and H-bonding. Upon inclusion of correction terms for
       dispersion and H-bonding, the performance of the method was found to be
       dramatically improved. The former correction included two parameters in
       the damping function that were parametrized to reproduce the benchmark
       interaction energies [CCSD(T)/complete basis set (CBS) limit] of the
       dispersion-bonded complexes from the S22 data set. The latter correction
       was parametrized on an extended set of H-bonded stabilization energies
       determined at the MP2/cc-pVTZ level. The resulting PM6-DH method was
       tested on the S22 data set, for which chemical accuracy (error < 1
       kcal/mol) was achieved, and also on the JSCH2005 set, for which
       significant improvement over the original PM6 method was also obtained.
       Implementation of analytical gradients allows very efficient geometry
       optimization, which, for all complexes, provides better agreement with
       the benchmark data. Excellent results were also achieved for small
       peptides, and here again, chemical accuracy was obtained (i.e., the
       error with respect to CCSD(T)/CBS results was smaller than 1 kcal/mol).
       The performance of the technique was finally demonstrated on extended
       complexes, namely, the porphine dimer and various graphene models with
       DNA bases and base pairs, where the PM6-DH stabilization energies agree
       very well with available benchmark data obtained with DFT-D, SCS-MP2,
       and MP2.5 methods. The PM6-DH calculations are very efficient and can be
       routinely applied for systems of up to 1000 atoms. For nonaromatic
       systems, the use of a linear scaling version of the SCF procedure based
       on localized orbitals speeds up the method significantly and allows one
       to investigate systems with several thousand atoms. The method can thus
       replace force fields, which face basic problems for the description of
       quantum effects, in many applications.,
    DOI = 10.1021/ct9000922,
    ISSN = 1549-9618,
    Unique-ID = ISI:000268232500005,
    
  • [DOI] M. Pitonak, T. Janowski, P. Neogrady, P. Pulay, and P. Hobza, "Convergence of the CCSD(T) Correction Term for the Stacked Complex
    Methyl Adenine-Methyl Thymine: Comparison with Lower-Cost Alternatives," JOURNAL OF CHEMICAL THEORY AND COMPUTATION, vol. 5, iss. 7, pp. 1761-1766, 2009.
    [Bibtex]
    @article ISI:000268232500006,
    Author = Pitonak, M. and Janowski, T. and Neogrady, P. and Pulay, P. and Hobza,
       P.,
    Title = Convergence of the CCSD(T) Correction Term for the Stacked Complex
       Methyl Adenine-Methyl Thymine: Comparison with Lower-Cost Alternatives,
    Journal = JOURNAL OF CHEMICAL THEORY AND COMPUTATION,
    Year = 2009,
    Volume = 5,
    Number = 7,
    Pages = 1761-1766,
    Month = JUL,
    Abstract = We have performed large-scale calculations for the interaction energy of
       the stacked methyl adenine-methyl thymine complex at the
       CCSD(T)/aug-ccpVXZ (X = D,T) levels. The results can serve as benchmarks
       for the evaluation of two methods, MP2.5, introduced recently, and the
       widely used Delta CCSD(T) correction defined as the difference between
       the CCSD(T) and MP2 energies. Our results confirm that the Delta CCSD(T)
       correction converges much faster toward the complete basis set (CBS)
       limit than toward the MP2 or CCSD(T) energies. This justifies
       approximating the CBS energy by adding the Delta CCSD(T) correction
       calculated with a modest basis set to a large basis MP2 energy, The fast
       convergence of the Delta CCSD(T) correction is not obvious, as the
       individual CCSD and (T) contributions converge less rapidly than their
       sum. The MP2.5 method performs very well for this system, with results
       very close to CCSD(T). It is conjectured that using a Delta MP2.5
       correction, defined analogously to Delta CCSD(T), with large basis sets
       may yield more reliable nonbonded interaction energies than using Delta
       CCSD(T) with a smaller basis set. This would result in important
       computational savings as the MP3 scales computationally much less steep
       than CCSD(T), although higher than SCS-MP2, a similar approximation.,
    DOI = 10.1021/ct900126q,
    ISSN = 1549-9618,
    Unique-ID = ISI:000268232500006,
    
  • [DOI] R. Sedlak, P. Hobza, and N. G. Patwari, "Hydrogen-Bonded Complexes of Phenylacetylene with Water, Methanol,
    Ammonia, and Methylamine. The Origin of Methyl Group-Induced Hydrogen
    Bond Switching," JOURNAL OF PHYSICAL CHEMISTRY A, vol. 113, iss. 24, pp. 6620-6625, 2009.
    [Bibtex]
    @article ISI:000266930100014,
    Author = Sedlak, Robert and Hobza, Pavel and Patwari, G. Naresh,
    Title = Hydrogen-Bonded Complexes of Phenylacetylene with Water, Methanol,
       Ammonia, and Methylamine. The Origin of Methyl Group-Induced Hydrogen
       Bond Switching,
    Journal = JOURNAL OF PHYSICAL CHEMISTRY A,
    Year = 2009,
    Volume = 113,
    Number = 24,
    Pages = 6620-6625,
    Month = JUN 18,
    Abstract = The infrared spectra in the acetylenic C-H stretching region for the
       complexes of phenylacetylene with water, methanol, ammonia, and
       methylamine are indicative of change in the intermolecular structure
       upon substitution with a methyl group. High-level ab initio calculations
       at CCSD(T)/aug-cc-pVDZ level indicate that the observed complexes of
       water and ammonia are energetically the most favored structures, and
       electrostatics play a dominant role in stabilizing these structures. The
       ability of the pi electron density of the benzene ring to offer a larger
       cross-section for the interaction and the increased polarizability of
       the O-H and N-H groups in methanol and methylamine favor the formation
       of pi hydrogen-bonded complexes, in which dispersion is the dominant
       force. Further, the observed phenylacetylene-methylamine complex can be
       tentatively assigned to a kinetically trapped higher energy structure.
       The observed methyl group-induced hydrogen bond switching in the
       phenylacetylene complexes can be attributed to the switching of the
       dominant interaction from electrostatic to dispersion.,
    DOI = 10.1021/jp900813n,
    ISSN = 1089-5639,
    Unique-ID = ISI:000266930100014,
    
  • [DOI] C. A. Morgado, P. Jurecka, D. Svozil, P. Hobza, and J. Sponer, "Balance of Attraction and Repulsion in Nucleic-Acid Base Stacking:
    CCSD(T)/Complete-Basis-Set-Limit Calculations on Uracil Dimer and a
    Comparison with the Force-Field Description," JOURNAL OF CHEMICAL THEORY AND COMPUTATION, vol. 5, iss. 6, pp. 1524-1544, 2009.
    [Bibtex]
    @article ISI:000266865000009,
    Author = Morgado, Claudio A. and Jurecka, Petr and Svozil, Daniel and Hobza,
       Pavel and Sponer, Jiri,
    Title = Balance of Attraction and Repulsion in Nucleic-Acid Base Stacking:
       CCSD(T)/Complete-Basis-Set-Limit Calculations on Uracil Dimer and a
       Comparison with the Force-Field Description,
    Journal = JOURNAL OF CHEMICAL THEORY AND COMPUTATION,
    Year = 2009,
    Volume = 5,
    Number = 6,
    Pages = 1524-1544,
    Month = JUN,
    Abstract = We have carried out reference quantum-chemical calculations for about
       100 geometries of the uracil dimer in stacked conformations. The
       calculations have been specifically aimed at geometries with unoptimized
       distances between the monomers including geometries with mutually tilted
       monomers. Such geometries are characterized by a delicate balance
       between local steric clashes and local unstacking and had until now not
       been investigated using reference quantum-mechanics (QM) methods.
       Nonparallel stacking geometries often occur in nucleic acids and are of
       decisive importance, for example, for local conformational variations in
       B-DNA. Errors in the short-range repulsion region would have a major
       impact on potential energy scans which were often used in the past to
       investigate local geometry variations in DNA. An incorrect description
       of such geometries may also partially affect molecular dynamics (MD)
       simulations in applications when quantitative accuracy is required. The
       reference OM calculations have been carried out using the MP2 method
       extrapolated to the complete basis-set limit and corrected for
       higher-order electron-correlation contributions using CCSD(T)
       calculations with a medium-sized basis set. These reference calculations
       have been used as benchmark data to test the performance of the DFT-D,
       SCS(MI)-MP2, and DFT-SAPT QM methods and of the AMBER
       molecular-mechanics (MM) force field. The QM methods show close to
       quantitative agreement with the reference data, albeit the DFT-D method
       tends to modestly exaggerate the repulsion of steric clashes. The force
       field in general also provides a good description of base stacking for
       the systems studied here. However, for geometries with close interatomic
       contacts and clashes, the repulsion effects are rather severely
       exaggerated. The discrepancy reported here should not affect the overall
       stability of MD simulations and qualitative applications of the force
       field. However, it may affect the description of subtle quantitative
       effects such as the local conformational variations in B-DNA.
       Preliminary calculations for two H-bonded uracil base pairs, including
       one with a C-H center dot center dot center dot OH-bond, indicate
       excellent performance of the tested QM methods for all intermonomer
       distances. The force field, on the other hand, is less satisfactory,
       especially in the repulsive regions.,
    DOI = 10.1021/ct9000125,
    ISSN = 1549-9618,
    Unique-ID = ISI:000266865000009,
    
  • [DOI] J. Cerny, J. Vondrasek, and P. Hobza, "Loss of Dispersion Energy Changes the Stability and Folding/Unfolding
    Equilibrium of the Trp-Cage Protein," JOURNAL OF PHYSICAL CHEMISTRY B, vol. 113, iss. 16, pp. 5657-5660, 2009.
    [Bibtex]
    @article ISI:000265269100038,
    Author = Cerny, Jiri and Vondrasek, Jiri and Hobza, Pavel,
    Title = Loss of Dispersion Energy Changes the Stability and Folding/Unfolding
       Equilibrium of the Trp-Cage Protein,
    Journal = JOURNAL OF PHYSICAL CHEMISTRY B,
    Year = 2009,
    Volume = 113,
    Number = 16,
    Pages = 5657-5660,
    Month = APR 23,
    Abstract = The structure of proteins as well as their folding/unfolding equilibrium
       are commonly attributed to H-bonding and hydrophobic interactions. We
       have used the molecular dynamic simulations in an explicit water
       environment based on the standard empirical potential as well as more
       accurately (and thus also more reliably) on the QM/MM potential. The
       simulations where the dispersion term was suppressed have led to a
       substantial change of the tryptophan-cage protein structure (unfolded
       structure). This structure cannot fold without the dispersion energy
       term, whereas, if it is covered fully, the system finds its native
       structure relatively quickly. This implies that after such physical
       factors as temperature and pH, the dispersion energy is an important
       factor in protein structure determination as well as in the protein
       folding/unfolding equilibrium. The loss of dispersion also affected the
       a.-helical structure. On the other hand, weakening the electrostatic
       interactions (and thus H-bonding) affected the a.-helical structure only
       to a minor extent.,
    DOI = 10.1021/jp9004746,
    ISSN = 1520-6106,
    Unique-ID = ISI:000265269100038,
    
  • [DOI] J. Sponer, M. Zgarbova, P. Jurecka, K. E. Riley, J. E. Sponer, and P. Hobza, "Reference Quantum Chemical Calculations on RNA Base Pairs Directly
    Involving the 2 `-OH Group of Ribose," JOURNAL OF CHEMICAL THEORY AND COMPUTATION, vol. 5, iss. 4, pp. 1166-1179, 2009.
    [Bibtex]
    @article ISI:000265268800057,
    Author = Sponer, Jiri and Zgarbova, Marie and Jurecka, Petr and Riley, Kevin E.
       and Sponer, Judit E. and Hobza, Pavel,
    Title = Reference Quantum Chemical Calculations on RNA Base Pairs Directly
       Involving the 2 `-OH Group of Ribose,
    Journal = JOURNAL OF CHEMICAL THEORY AND COMPUTATION,
    Year = 2009,
    Volume = 5,
    Number = 4,
    Pages = 1166-1179,
    Month = APR,
    Abstract = The folded structures of RNA molecules and large ribonucleoprotein
       particles are stabilized by a wide range of base pairs that actively
       utilize the 2'-OH groups of ribose for base pairing. Such base pairing
       does not occur in DNA and is essential for functional RNAs. We report
       reference quantum chemical calculations of base pairing energies for a
       representative selection of 25 RNA base pairs utilizing the ribose
       moiety for base pairing, including structures with amino acceptor
       interactions. All base pairs are evaluated at the MP2 level with
       extrapolation to the complete basis set (CBS) of atomic orbitals.
       CCSD(T) correction terms were obtained for four base pairs. In addition,
       the base pairing is evaluated using the DFT-SAPT perturbational
       procedure along with the aug-cc-pVDZ basis set, which allows for the
       decomposition of the interaction energies into separate, physically
       meaningful, components. These calculations confirm that, compared to
       canonical base pairs, many RNA base pairs exhibit a modestly increased
       role of dispersion attraction compared to canonical base pairs. However,
       the effect is smaller than one would assume based on assessment of the
       ratio of HF and correlation components of the interaction energies.
       Interaction energies are further calculated using the SCS(MI)-MP2 and
       DFT-D methods. Finally, we estimate the effect of aqueous solvent
       screening on the base pairing stability using the continuum solvent
       approach.,
    DOI = 10.1021/ct800547k,
    ISSN = 1549-9618,
    Unique-ID = ISI:000265268800057,
    
  • [DOI] J. Ran and P. Hobza, "On the Nature of Bonding in Lone Pair center dot center dot center dot
    pi-Electron Complexes: CCSD(T)/Complete Basis Set Limit Calculations," JOURNAL OF CHEMICAL THEORY AND COMPUTATION, vol. 5, iss. 4, pp. 1180-1185, 2009.
    [Bibtex]
    @article ISI:000265268800058,
    Author = Ran, Jiong and Hobza, Pavel,
    Title = On the Nature of Bonding in Lone Pair center dot center dot center dot
       pi-Electron Complexes: CCSD(T)/Complete Basis Set Limit Calculations,
    Journal = JOURNAL OF CHEMICAL THEORY AND COMPUTATION,
    Year = 2009,
    Volume = 5,
    Number = 4,
    Pages = 1180-1185,
    Month = APR,
    Abstract = The nature of the stabilization in lone pair center dot center dot
       center dot pi-electron complexes was investigated using the highly
       accurate CCSD(T) method based on the complete basis set limit, as well
       as the DFT-SAPT perturabative method. Specifically, we studied various
       structures of benzene center dot center dot center dot water, benzene
       center dot center dot center dot dimethylether, and
       1,2,4,5-tetracyanobenzene center dot center dot center dot water
       complexes. The lone pair center dot center dot center dot pi-electron
       interactions between an unsubstituted aromatic ring and a water molecule
       are repulsive in the whole range of vertical distances. Partial
       stabilization results by rotating the water molecule by 900 (with the
       water and aromatic ring being localized in parallel planes) or by
       decreasing the negative charge at oxygen and simultaneously increasing
       the polarizability of the system, which provides stabilization even for
       genuine lone pair center dot center dot center dot pi-electron
       interactions. In these cases, a substantial part of the stabilization
       stems from dispersion energy. Substituting an aromatic ring by
       electron-withdrawing cyano groups represents the most powerful way to
       achieve a substantial stabilization of genuine lone pair center dot
       center dot center dot pi-electron interactions. This stabilization is
       comparable to quite strong H-bonding, originating in electrostatic and,
       to a slightly lesser degree, dispersion energies.,
    DOI = 10.1021/ct900036y,
    ISSN = 1549-9618,
    Unique-ID = ISI:000265268800058,
    
  • [DOI] K. Berka, R. Laskowski, K. E. Riley, P. Hobza, and J. Vondrasek, "Representative Amino Acid Side Chain Interactions in Proteins. A
    Comparison of Highly Accurate Correlated ab Initio Quantum Chemical and
    Empirical Potential Procedures," JOURNAL OF CHEMICAL THEORY AND COMPUTATION, vol. 5, iss. 4, pp. 982-992, 2009.
    [Bibtex]
    @article ISI:000265268800037,
    Author = Berka, Karel and Laskowski, Roman and Riley, Kevin E. and Hobza, Pavel
       and Vondrasek, Jiri,
    Title = Representative Amino Acid Side Chain Interactions in Proteins. A
       Comparison of Highly Accurate Correlated ab Initio Quantum Chemical and
       Empirical Potential Procedures,
    Journal = JOURNAL OF CHEMICAL THEORY AND COMPUTATION,
    Year = 2009,
    Volume = 5,
    Number = 4,
    Pages = 982-992,
    Month = APR,
    Abstract = Interactions between amino acid side chains play a crucial role both
       within a folded protein and between the interacting protein molecules.
       Here we have selected a representative set of 24 of the 400 (20 x 20)
       possible interacting side chain pairs based on data from Atlas of
       Protein Side-Chain Interactions. For each pair, we obtained its most
       favorable interaction geometry from the structural data and computed the
       interaction energy in the gas phase using several different, commonly
       used, ab initio and force field methods, namely Moller-Plesset
       perturbation theory (MP2), density functional theory combined with
       symmetry-adapted perturbation theory (DFT-SAPT), density functional
       theory empirically augmented with an empirical dispersion term (DFT-D),
       and empirical potentials using the OPLS-AA/L and Amber03 force fields.
       All the methods were compared against a reference method taken to be the
       CCSD(T) level of theory extrapolated to the complete basis set limit. We
       found a high degree of agreement between the different methods, even
       though the range of binding energies obtained was extremely large. The
       most computationally intensive methods yielded the best results. Among
       the less computationally time-consuming methods, the DFT-D method as
       well as parm03 force field provided consistently good results when
       compared to the reference values. We also tested how representative the
       chosen geometries of the side chains were and investigated the effect on
       the binding energies of the dielectric constant of the surrounding
       medium.,
    DOI = 10.1021/ct800508v,
    ISSN = 1549-9618,
    Unique-ID = ISI:000265268800037,
    
  • [DOI] J. Ran and P. Hobza, "Nature of Bonding in Nine Planar Hydrogen-Bonded Adenine center dot
    center dot center dot Thymine Base Pairs," JOURNAL OF PHYSICAL CHEMISTRY B, vol. 113, iss. 9, pp. 2933-2936, 2009.
    [Bibtex]
    @article ISI:000263732700045,
    Author = Ran, Jiong and Hobza, Pavel,
    Title = Nature of Bonding in Nine Planar Hydrogen-Bonded Adenine center dot
       center dot center dot Thymine Base Pairs,
    Journal = JOURNAL OF PHYSICAL CHEMISTRY B,
    Year = 2009,
    Volume = 113,
    Number = 9,
    Pages = 2933-2936,
    Month = MAR 5,
    Abstract = In this work, we investigate the mode of binding of all nine
       hydrogen-bonded structures of the adenine center dot center dot center
       dot thymine base pair. The planar H-bonded structures were optimized at
       the MP2/cc-pVTZ level, and the respective interaction energies,
       corrected for the basis set superposition error, were determined with
       the aug-cc-pVDZ basis set. The energy components were obtained from the
       DFT-SAPT procedure using the aug-cc-pVDZ basis set. The charge-transfer
       character of the single structures was estimated using NBO
       characteristics. It was established that dipole-dipole interaction
       itself cannot explain the preferred structure of the pair. Of the
       various energy components, first-order electrostatic energy plays the
       most important role. Second-order energy (the sum of induction and
       dispersion energies) amounts to about 56\% of the electrostatic energy.
       The delta(HF) term covering among others the charge-transfer energy is
       rather large. The importance of delta(HF) is reflected by the NBO
       characteristics and especially by the NBO charge-transfer energy. The
       sum of the second-order energy and the delta(HF) term is only slightly
       smaller than the electrostatic energy (75-77\%), which reflects the
       importance of the nonelectrostatic terms even in the case of strong
       H-bonded complexes. The WC structure, which exists in DNA, represents
       the seventh local minimum, while the three most stable structures
       utilize the N9-H proton donor group of the five-membered ring.,
    DOI = 10.1021/jp810001v,
    ISSN = 1520-6106,
    Unique-ID = ISI:000263732700045,
    
  • [DOI] K. Berka, P. Hobza, and J. Vondrasek, "Analysis of Energy Stabilization inside the Hydrophobic Core of
    Rubredoxin," CHEMPHYSCHEM, vol. 10, iss. 3, pp. 543-548, 2009.
    [Bibtex]
    @article ISI:000264229900014,
    Author = Berka, Karel and Hobza, Pavel and Vondrasek, Jiri,
    Title = Analysis of Energy Stabilization inside the Hydrophobic Core of
       Rubredoxin,
    Journal = CHEMPHYSCHEM,
    Year = 2009,
    Volume = 10,
    Number = 3,
    Pages = 543-548,
    Month = FEB 23,
    Abstract = The hydrophobic core of globular proteins is responsible for major
       stabilization of the protein tertiary structure. The prevailing amino
       acid residues in the core are of aliphatic or aromatic character and
       therefore the core in a folded protein structure is mostly stabilized by
       noncovalent interactions of van der Waals origin between the amino acid
       side chains. Herein, we present a theoretical analysis of the
       interaction energy between the amino acids of the hydrophobic core of
       the small globular protein rubredoxin (Rd) based on the symmetry-adapted
       perturbation theory (SAPT) method. The results show uniform proportions
       between the second-order dispersion and first-order electrostatic energy
       terms in favor of dispersion interaction which plays a major role in the
       stabilization of this important structural element. To demonstrate the
       contrast between systems stabilized by different mechanisms, we perform
       a SAPT analysis of the typical hydrogen bonds involved in the formation
       of protein secondary structure elements in Rd, where dispersion still
       plays a non-negligible role but electrostatic energy is the major
       stabilizing factor.,
    DOI = 10.1002/cphc.200800401,
    ISSN = 1439-4235,
    Unique-ID = ISI:000264229900014,
    
  • [DOI] M. Pitonak, P. Neogrady, J. Cerny, S. Grimme, and P. Hobza, "Scaled MP3 Non-Covalent Interaction Energies Agree Closely with Accurate
    CCSD(T) Benchmark Data," CHEMPHYSCHEM, vol. 10, iss. 1, pp. 282-289, 2009.
    [Bibtex]
    @article ISI:000262870500038,
    Author = Pitonak, Michal and Neogrady, Pavel and Cerny, Jiri and Grimme, Stefan
       and Hobza, Pavel,
    Title = Scaled MP3 Non-Covalent Interaction Energies Agree Closely with Accurate
       CCSD(T) Benchmark Data,
    Journal = CHEMPHYSCHEM,
    Year = 2009,
    Volume = 10,
    Number = 1,
    Pages = 282-289,
    Month = JAN 12,
    Abstract = Scaled MP3 interaction energies calculated as a sum of MP2/CBS (complete
       basis set limit) interaction energies and scaled third-order energy
       contributions obtained in small or medium size basis sets agree very
       closely with the estimated CCSD(T)/CBS interaction energies for the 22
       H-bonded, dispersion-controlled and mixed non-covalent complexes from
       the S22 data set. Performance of this so-called MP2.5 (third-order
       scaling factor of 0.5) method has also been tested for 33 nucleic acid
       base pairs and two stacked conformers of porphine dimer. In all the test
       cases, performance of the MP2.5 method was shown to be superior to the
       scaled spin-component MP2 based methods, e.g. SCS-MP2, SCSN-MP2 and
       SCS(MI)-MP2. In particular, a very balanced treatment of hydrogen-bonded
       compared to stacked complexes is achieved with MP2.5. The main advantage
       of the approach is that it employs only a single empirical parameter and
       is thus biased by two rigorously defined, asymptotically correct
       ob-initio methods, MP2 and MP3. The method is proposed as an accurate
       but computationally feasible alternative to CCSD(T) for the computation
       of the properties of various kinds of non-covalently bound systems.,
    DOI = 10.1002/cphc.200800718,
    ISSN = 1439-4235,
    Unique-ID = ISI:000262870500038,
    
  • [DOI] K. E. Riley, J. S. Murray, P. Politzer, M. C. Concha, and P. Hobza, "Br center dot center dot center dot O Complexes as Probes of Factors
    Affecting Halogen Bonding: Interactions of Bromobenzenes and
    Bromopyrimidines with Acetone," JOURNAL OF CHEMICAL THEORY AND COMPUTATION, vol. 5, iss. 1, pp. 155-163, 2009.
    [Bibtex]
    @article ISI:000262432000016,
    Author = Riley, Kevin E. and Murray, Jane S. and Politzer, Peter and Concha,
       Monica C. and Hobza, Pavel,
    Title = Br center dot center dot center dot O Complexes as Probes of Factors
       Affecting Halogen Bonding: Interactions of Bromobenzenes and
       Bromopyrimidines with Acetone,
    Journal = JOURNAL OF CHEMICAL THEORY AND COMPUTATION,
    Year = 2009,
    Volume = 5,
    Number = 1,
    Pages = 155-163,
    Month = JAN,
    Abstract = Halogen bonding is a unique type of noncovalent binding phenomenon in
       which a halogen atom interacts attractively with an electronegative atom
       such as oxygen or nitrogen. These types of interactions have been the
       subject of many recent investigations because of their potential in the
       development of new materials and pharmaceutical compounds. Recently, it
       was observed that most halogen bonding interactions in biological
       contexts involve close contacts between a halogen bound to an aromatic
       ring and a carbonyl oxygen on a protein's backbone structure. In this
       work we investigate interactions of substituted bromobenzenes and
       bromopyrimidines with acetone to ascertain the effects of various
       substituents; upon the strengths of these interactions. It was found
       that replacement of ring hydrogens in these systems has dramatic effects
       upon the interaction strengths of the resulting complexes, which have
       interaction energies between -1.80 and -7.11 kcal/mol. Examination of
       the electrostatic potentials of the substituted bromobenzene and
       bromopyrimidine monomers indicates that the addition of substituents has
       a large influence upon the most positive electrostatic potential on the
       surface of the interacting bromine and thus modulates these halogen
       bonding interactions. Results obtained using the symmetry-adapted
       perturbation theory (SAPT) interaction energy decomposition procedure
       also indicate that electrostatic interactions play the key role in these
       halogen bonding interactions. These results have important implications
       in drug design and crystal engineering. Halogen bonds have been a
       subject of great interest in these fields because of their unique
       noncovalent bonding characteristics.,
    DOI = 10.1021/ct8004134,
    ISSN = 1549-9618,
    Unique-ID = ISI:000262432000016,
    
  • [DOI] L. Zendlova, D. Reha, M. Hocek, and P. Hobza, "Theoretical Study of the Stability of the DNA Duplexes Modified by a
    Series of Hydrophobic Base Analogues," CHEMISTRY-A EUROPEAN JOURNAL, vol. 15, iss. 31, pp. 7601-7610, 2009.
    [Bibtex]
    @article ISI:000268845000013,
    Author = Zendlova, Lucie and Reha, David and Hocek, Michal and Hobza, Pavel,
    Title = Theoretical Study of the Stability of the DNA Duplexes Modified by a
       Series of Hydrophobic Base Analogues,
    Journal = CHEMISTRY-A EUROPEAN JOURNAL,
    Year = 2009,
    Volume = 15,
    Number = 31,
    Pages = 7601-7610,
    Abstract = The geometries of a 13 mer of a DNA double helix (5'-GCGTA-CACATGCG-3')
       were determined by molecular dynamics simulations using a Cornell et al.
       empirical force field. ne bases in the central base pair (shown in bold)
       were replaced (one or both) by a series of hydrophobic base analogues
       (phenyl, biphenyl, phenylnaphathalene, phenylanthracene and
       phenylphenanthrene). Due to the large fluctuations of the systems, an
       average geometry could not be determined. The interaction energies of
       the Model A, which consisted of three central steps of a duplex without
       a sugar phosphate backbone, taken from molecular dynamics simulations
       (geometry sampled every 1 ps), were calculated by the self-consistent
       charge density functional based tight-binding (SCC-DFTB-D) method and
       were subsequently averaged. The higher the stability of the systems the
       higher the aromaticity of the base analogues. To estimate the
       desolvation energy of the duplex, the COSMO continuum solvent model was
       used and the calculations were provided on a larger model, Model B (the
       three central steps of the duplex with a sugar phosphate backbone
       neutralised by H atoms), taken from molecular dynamics simulations
       (geometry sampled every 200 ps) and subsequently averaged. The
       selectivity of the base analogue pairs was ascertained (Model 13) by
       including the desolvation energy and the interaction energy of both
       strands, as determined by the SCC-DFTB-D method. The highest selectivity
       was found for a phenylphenanthrene. Replacing the nucleic acid bases
       with a base analogue leads to structural changes of the central pair.
       Only with the smallest base analogues (phenyl) does the central base
       pair stay planar. When passing to larger base analogues the central base
       pair is usually stacked.,
    DOI = 10.1002/chem.200802170,
    ISSN = 0947-6539,
    Unique-ID = ISI:000268845000013,
    
  • [DOI] T. Zeleny, P. Hobza, and M. Kabelac, "Microhydration of guanine center dot center dot center dot cytosine base
    pairs, a theoretical Study on the role of water in stability, structure
    and tautomeric equilibrium," PHYSICAL CHEMISTRY CHEMICAL PHYSICS, vol. 11, iss. 18, pp. 3430-3435, 2009.
    [Bibtex]
    @article ISI:000265413300010,
    Author = Zeleny, Tomas and Hobza, Pavel and Kabelac, Martin,
    Title = Microhydration of guanine center dot center dot center dot cytosine base
       pairs, a theoretical Study on the role of water in stability, structure
       and tautomeric equilibrium,
    Journal = PHYSICAL CHEMISTRY CHEMICAL PHYSICS,
    Year = 2009,
    Volume = 11,
    Number = 18,
    Pages = 3430-3435,
    Abstract = The potential energy surfaces of guanine center dot center dot center
       dot cytosine complexes and microhydrated guanine center dot center dot
       center dot cytosine (one and two water molecules) were investigated by
       the molecular dynamics/quenching method (MD/Q), using the empirical
       potential Parm94 force field, implemented in the Amber program package.
       The calculations were conducted for all the possible combinations of the
       four most stable tautomers of guanine and three of cytosine (covering
       the canonical forms in both cases). The obtained structures were sorted
       by their structural motifs into three main groups: planar
       hydrogen-bonded; stacked; and T-shaped structures. The most stable
       structures found at the empirical potential energy surfaces were fully
       reoptimised at the second-order Moller-Plesset perturbation theory as
       well as using the density functional method with an empirical dispersion
       term (DFT-D). A combination of the canonical form of guanine and
       cytosine and canonical cytosine with a guanine tautomer where the
       hydrogen is switched from position N9 to N7 are energetically preferred
       in microsolvated systems as well as those without the presence of a
       solvent. The rising number of water molecules leads to smaller
       differences between the stability of the various combinations of the
       tautomers of bases in the base pairs. For some of the tautomer
       combinations (mainly the enol-enol combination), two water molecules are
       sufficient for the preference of stacked structures over the H-bonded
       ones. The interaction energies and geometries obtained by the
       second-order Moller-Plesset perturbation theory method and the much less
       computationally demanding DFT-D method are comparable, except for
       stacked complexes, where the interaction energies are overestimated on
       average by 3 kcal mol(-1) at the MP2 level.,
    DOI = 10.1039/b819350a,
    ISSN = 1463-9076,
    Unique-ID = ISI:000265413300010,
    
  • [DOI] M. Kabelac, P. Hobza, and V. Spirko, "The structure and vibrational dynamics of the pyrrole dimmer," PHYSICAL CHEMISTRY CHEMICAL PHYSICS, vol. 11, iss. 20, pp. 3885-3891, 2009.
    [Bibtex]
    @article ISI:000266065400010,
    Author = Kabelac, Martin and Hobza, Pavel and Spirko, Vladimir,
    Title = The structure and vibrational dynamics of the pyrrole dimmer,
    Journal = PHYSICAL CHEMISTRY CHEMICAL PHYSICS,
    Year = 2009,
    Volume = 11,
    Number = 20,
    Pages = 3885-3891,
    Abstract = The energy, dynamical geometry characteristics and low frequency
       intermolecular vibrations of the pyrrole dimer have been examined at the
       MP2 and CCSD(T) levels of ab initio theory. The actual distortions of
       the pyrrole dimer from its reference (equilibrium) position were
       measured using the distance of the monomer mass centres (R), the angle
       between their planes (the mirror planes orthogonal to the molecular
       planes of both monomers were assumed to coincide) and the angle between
       the R directional vector and the proton-accepting monomer plane; the
       structures of the monomers were assumed to be unchanged by dimerisation.
       The lowest part of the potential energy function confining the probed
       motions possessed two equivalent energy pockets with the
       CCSD(T)/complete basis set limit stabilisation energy of 6.2 kcal
       mol(-1) separated by a relatively low barrier (0.8 kcal mol(-1)), thus
       raising questions concerning the classical interconversion of the
       T-shaped equilibrium structures via a C(2h) parallel-displaced transient
       structure and/or quantum mechanical tunnellings through the barrier. The
       questions have been answered unequivocally by calculating the energies
       and tunnelling splittings of the relevant vibrational levels.
       Importantly: (a) all the excited tunnelling (interconverting) states
       underwent fast geometry interconversions, hence evidencing
       conformational instability of the studied dimer under usual laboratory
       conditions; (b) the dynamical averages of the used geometry
       characteristics exhibited profound tunnelling (interconverting)
       dependences, thus advocating that they be respected in reliable
       structural studies of the pyrrole dimer and chemically similar systems;
       (c) the geometry characteristics of the ground vibrational state agreed
       quite reasonably with their experimental counterparts, evidencing the
       adequacy of the theory used and the reliability of the characteristics
       predicted for the excited vibrational states; and (d) the calculated
       dissociation barrier of the dimer exceeds its experimentally derived
       analogue by more than three times, showing the inadequacy of the
       constraining assumptions used to derive it from the experimental
       spectra.,
    DOI = 10.1039/b822764k,
    ISSN = 1463-9076,
    Unique-ID = ISI:000266065400010,
    
  • [DOI] M. Kabelac, P. Hobza, and V. Spirko, "The ab initio assigning of the vibrational probing modes of tryptophan:
    linear shifting of approximate anharmonic frequencies vs. multiplicative
    scaling of harmonic frequencies," PHYSICAL CHEMISTRY CHEMICAL PHYSICS, vol. 11, iss. 20, pp. 3921-3926, 2009.
    [Bibtex]
    @article ISI:000266065400014,
    Author = Kabelac, Martin and Hobza, Pavel and Spirko, Vladimir,
    Title = The ab initio assigning of the vibrational probing modes of tryptophan:
       linear shifting of approximate anharmonic frequencies vs. multiplicative
       scaling of harmonic frequencies,
    Journal = PHYSICAL CHEMISTRY CHEMICAL PHYSICS,
    Year = 2009,
    Volume = 11,
    Number = 20,
    Pages = 3921-3926,
    Abstract = To gain insight into the prospects for a few-dimensional ab initio
       quantum-mechanical description of the vibrational motions of
       conformationally flexible molecular systems, the NH-, NH(2)-, CO- and
       OH-stretching and COH-bending vibrations of the most stable tryptophan
       conformations have been probed using simple one- and two-dimensional
       anharmonic Hamiltonians and potential energy functions evaluated by
       means of the standard RI-MP2, CCSD(T) and DFT-D quantum chemical
       procedures. Although strongly dependent on the procedure used, the
       calculated vibrational spectral patterns have been found to be in a
       robust one-to-one harmony with their experimental counterparts, thus
       proving the adequacy of the theory used for the reliable assignment of
       the experimental data. Therefore, the approach appears to be a suitable
       tool for assigning the vibrational probing modes even of systems which
       are too large to be tractable by the standard normal-coordinate
       analysis.,
    DOI = 10.1039/b823373j,
    ISSN = 1463-9076,
    Unique-ID = ISI:000266065400014,
    
  • [DOI] S. Maity, R. Sedlak, P. Hobza, and N. G. Patwari, "Infrared-optical double resonance spectroscopic measurements and high
    level ab initio calculations on a binary complex between phenylacetylene
    and borane-trimethylamine. Understanding the role of C-H center dot
    center dot center dot pi interactions," PHYSICAL CHEMISTRY CHEMICAL PHYSICS, vol. 11, iss. 42, pp. 9738-9743, 2009.
    [Bibtex]
    @article ISI:000271033200015,
    Author = Maity, Surajit and Sedlak, Robert and Hobza, Pavel and Patwari, G.
       Naresh,
    Title = Infrared-optical double resonance spectroscopic measurements and high
       level ab initio calculations on a binary complex between phenylacetylene
       and borane-trimethylamine. Understanding the role of C-H center dot
       center dot center dot pi interactions,
    Journal = PHYSICAL CHEMISTRY CHEMICAL PHYSICS,
    Year = 2009,
    Volume = 11,
    Number = 42,
    Pages = 9738-9743,
    Abstract = The structure of the binary complex between phenylacetylene and
       borane-trimethylamine has been elucidated using IR-UV double resonance
       spectroscopy in combination with high level ab initio calculations at
       the CCSD(T) level. Borane-trimethylamine interacts primarily through
       multiple C-H center dot center dot center dot pi interactions with the p
       electron density of the benzene ring in phenylacetylene. CCSD(T) level
       calculations provide reliable estimates for the interaction energy and
       free energy, which are in accord with the experimental observations. The
       DFT-SAPT calculations point out that the dispersion interaction plays a
       major role in the formation of the experimentally observed complex,
       along with a sizable contribution from electrostatics.,
    DOI = 10.1039/b911926d,
    ISSN = 1463-9076,
    Unique-ID = ISI:000271033200015,
    

2008

  • [DOI] W. Zierkiewicz, L. Komorowski, D. Michalska, J. Cerny, and P. Hobza, "The Amino Group in Adenine: MP2 and CCSD(T) Complete Basis Set Limit
    Calculations of the Planarization Barrier and DFT/B3LYP Study of the
    Anharmonic Frequencies of Adenine," JOURNAL OF PHYSICAL CHEMISTRY B, vol. 112, iss. 51, pp. 16734-16740, 2008.
    [Bibtex]
    @article ISI:000261835100062,
    Author = Zierkiewicz, Wiktor and Komorowski, Ludwik and Michalska, Danuta and
       Cerny, Jiri and Hobza, Pavel,
    Title = The Amino Group in Adenine: MP2 and CCSD(T) Complete Basis Set Limit
       Calculations of the Planarization Barrier and DFT/B3LYP Study of the
       Anharmonic Frequencies of Adenine,
    Journal = JOURNAL OF PHYSICAL CHEMISTRY B,
    Year = 2008,
    Volume = 112,
    Number = 51,
    Pages = 16734-16740,
    Month = DEC 25,
    Abstract = The amino group in adenine plays a key role in formation of hydrogen
       bonds in nucleic acids and in other molecular systems. Thus, the
       structure of this group is of fundamental importance in the molecular
       recognition phenomena. Ab initio MP2 and density functional B3LYP
       methods with various basis sets have been used to calculate the
       optimized structure and the infrared spectrum of adenine (the N9-H
       tautomer). Calculations at the MP2 level with larger basis sets tend to
       decrease the degree of pyramidalization of the C-NH(2) group, whereas
       the B3LYP method consistently yields the planar or nearly planar
       structure of adenine. MP2 complete basis set (CBS) limit method with the
       aug-cc-pVTZ -> aug-cc-pVQZ (aTZ -> aQZ) extrapolation scheme has
       predicted very small planarization barrier of adenine, 0.015 kcal/mol,
       which is in very good agreement with the MP2-predicted planarization
       barrier of 0.020 kcal/mol, reported by S. Wang and H. F. Schaefer III,
       J. Chem. Phys. 2006, 124, 044303. Similar results were obtained in
       calculations by the coupled cluster CCSD(T) CBS method. Thus, it can be
       concluded that the amino group in adenine, in the gas phase, is very
       flexible with a small degree of nonplanarity. Extremely low
       planarization barrier implies that adenine requires very little energy
       to conform the structure of the amino group to formation of the
       complementary hydrogen bonds with other molecules. This fact is very
       important for base pairing in nucleic acids or other polymers containing
       adenine residues. The anharmonic frequencies of adenine have been
       calculated at the B3LYP/6-311++G(df, pd) level of theory. The
       theoretical results show excellent agreement with the available
       experimental data. The revised assignment of the infrared spectrum of
       adenine in Ar matrix has been made. The predicted anharmonic frequency
       of the NH(2) inversion, 181 cm(-1), is supported by the experimental
       data. It is demonstrated that the vibrational frequencies and potential
       energy distribution (PED) obtained from the B3LYP calculations are more
       reliable than those obtained at the MP2 level.,
    DOI = 10.1021/jp8058118,
    ISSN = 1520-6106,
    Unique-ID = ISI:000261835100062,
    
  • [DOI] K. Pluhackova, S. Grimme, and P. Hobza, "On the Importance of Electron Correlation Effects for the Intramolecular
    Stacking Geometry of a Bis-Thiophene Derivative," JOURNAL OF PHYSICAL CHEMISTRY A, vol. 112, iss. 48, pp. 12469-12474, 2008.
    [Bibtex]
    @article ISI:000261218100023,
    Author = Pluhackova, Kristyna and Grimme, Stefan and Hobza, Pavel,
    Title = On the Importance of Electron Correlation Effects for the Intramolecular
       Stacking Geometry of a Bis-Thiophene Derivative,
    Journal = JOURNAL OF PHYSICAL CHEMISTRY A,
    Year = 2008,
    Volume = 112,
    Number = 48,
    Pages = 12469-12474,
    Month = DEC 4,
    Abstract = The structure of dithienobicyclo[4.4.1]undeca-3,8-diene-11-one
       ethylene glycol ketal (database code RESVAN) was determined using the
       wave function theory (WFT) as well as density functional theory (DFT)
       methods combined with various Gaussian AO basis sets. The apparently
       most accurate procedure, employing the CCSD(T)/complete basis set (CBS),
       provides an S-S distance and an angle between the two thiophene rings
       which differ considerably from experimental values. The best agreement
       with the experimental data among, all WFT methods was surprisingly
       obtained at the MP3/aug-cc-pVDZ and MP3/CBS(B) levels (the correction
       term to CBS was obtained by the aug-cc-pVDZ basis set). The very good
       results obtained by the CCSD(T)/6-31G* method are clearly a
       consequence of fortunate error compensation. MP2 calculations, even with
       a small basis set, overestimate the attraction between the thiophene
       rings, and the worst agreement with experimental data was found in full
       MP2/QZVP method optimizations (i.e., a strong distortion of the
       thiophene rings was observed). The SCS(MI)-MP2 and SCS-MP2 methods
       exhibit improvement over the MP2 procedure. All standard DFT approaches
       fail to predict reasonable S-S distances. The lack of intramolecular
       London dispersion energy results in too great distance between the
       thiophene rings. Much better agreement with experiment was obtained if
       advanced DFT methods, covering dispersion effects, were used. The best
       results were obtained at the TPSS-D/TZVP, M06-L/TZVP and
       B2PLYP-D/def2-TZVP levels. When a larger basis (LP in the case of TPSS
       functional) or more advanced versions of the new Truhlar functionals
       (M06-2X) was used, the agreement with experiment deteriorated. The
       accurate description of this molecule is highly functional/basis
       dependent and this dependence is hardly predictable. To estimate effects
       of neighboring molecules in the experimental crystal structure, an
       optimization in the electric field of the 26 closest RESVAN molecules
       was performed, which, however, leads to only moderate (<0.05 angstrom)
       changes of the S-S distance.,
    DOI = 10.1021/jp8051664,
    ISSN = 1089-5639,
    Unique-ID = ISI:000261218100023,
    
  • [DOI] J. Fanfrlik, J. Brynda, J. Rezac, P. Hobza, and M. Lepsik, "Interpretation of Protein/Ligand Crystal Structure using QM/MM
    Calculations: Case of HIV-1 Protease/Metallacarborane Complex," JOURNAL OF PHYSICAL CHEMISTRY B, vol. 112, iss. 47, pp. 15094-15102, 2008.
    [Bibtex]
    @article ISI:000261056400050,
    Author = Fanfrlik, Jindrich and Brynda, Jiri and Rezac, Jan and Hobza, Pavel and
       Lepsik, Martin,
    Title = Interpretation of Protein/Ligand Crystal Structure using QM/MM
       Calculations: Case of HIV-1 Protease/Metallacarborane Complex,
    Journal = JOURNAL OF PHYSICAL CHEMISTRY B,
    Year = 2008,
    Volume = 112,
    Number = 47,
    Pages = 15094-15102,
    Month = NOV 27,
    Abstract = Deltahedral metallacarborane compounds have recently been discovered as
       potent, specific, stable, and nontoxic inhibitors of HIV-1 protease
       (PR), the major target for AIDS therapy. The 2.15 angstrom-resolution
       X-ray structure has exhibited a nonsymmetrical binding of the parental
       compound [Co(3+)-(C(2)B(9)H(11))(2)](-) (GB-18) into PR dimer and a
       symmetrical arrangement in the crystal of two PR dimer complexes into a
       tetramer. In order to explore structural and energetic details of the
       inhibitor binding, quantum mechanics coupled with molecular mechanics
       approach was utilized. Realizing the close positioning of anionic
       inhibitors in the active site cavity, the possibility of an exchange of
       structural water molecules Wat50 and Wat128 by Na(+) counterions was
       studied. The energy profiles for the rotation of the GB - 18 molecules
       along their longitudinal axes in complex with PR were calculated. The
       results show that two Na(+) counterions are present in the active site
       cavity and provide energetically favorable and unfavorable positions for
       carbon atoms within the carborane cages. Eighty-one rotamer combinations
       of four molecules of GB-18 bound to PR out of 4 x 10(5) are predicted to
       be highly populated. These results lay ground for further calculations
       of interaction energies between GB - 18 and amino acids of PR active
       site and will make it possible to interpret computationally the binding
       of similar metallacarborane molecules to PR as well as to resistant PR
       variants. Moreover, this computational tool will allow the design of
       new, more potent metallacarborane-based HIV-1 protease inhibitors.,
    DOI = 10.1021/jp803528w,
    ISSN = 1520-6106,
    Unique-ID = ISI:000261056400050,
    
  • [DOI] J. Cerny, M. Kabelac, and P. Hobza, "Double-Helical -> Ladder Structural Transition in the B-DNA is Induced
    by a Loss of Dispersion Energy," JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, vol. 130, iss. 47, pp. 16055-16059, 2008.
    [Bibtex]
    @article ISI:000263319600064,
    Author = Cerny, Jiri and Kabelac, Martin and Hobza, Pavel,
    Title = Double-Helical -> Ladder Structural Transition in the B-DNA is Induced
       by a Loss of Dispersion Energy,
    Journal = JOURNAL OF THE AMERICAN CHEMICAL SOCIETY,
    Year = 2008,
    Volume = 130,
    Number = 47,
    Pages = 16055-16059,
    Month = NOV 26,
    Abstract = The role of the dispersion energy and electrostatic energy on the
       geometry and stability of the B-DNA helix was investigated. Both
       molecular dynamics simulations with empirical force field and hybrid
       quantum mechanical/molecular mechanics molecular dynamics simulations,
       where the dispersion or electrostatics term is suppressed/increased, on
       the one hand and an ab initio minimization procedure on the other have
       shown that the lack of the dispersion term leads to an increase of the
       vertical separation of the bases as well as to a loss of helicity, thus
       resulting in a ladder-like structure. A decrease of the electrostatic
       term produces a separation of the DNA strands. The biological
       consequences of both electrostatic and dispersion forces in DNA are
       enormous, and without either of them, DNA would become unstable and
       unable to, provide the storage and transfer of genetic information.,
    DOI = 10.1021/ja805428q,
    ISSN = 0002-7863,
    Unique-ID = ISI:000263319600064,
    
  • [DOI] M. Pitonak, P. Neogrady, J. Rezac, P. Jurecka, M. Urban, and P. Hobza, "Benzene Dimer: High-Level Wave Function and Density Functional Theory
    Calculations," JOURNAL OF CHEMICAL THEORY AND COMPUTATION, vol. 4, iss. 11, pp. 1829-1834, 2008.
    [Bibtex]
    @article ISI:000260851300003,
    Author = Pitonak, M. and Neogrady, P. and Rezac, J. and Jurecka, P. and Urban, M.
       and Hobza, P.,
    Title = Benzene Dimer: High-Level Wave Function and Density Functional Theory
       Calculations,
    Journal = JOURNAL OF CHEMICAL THEORY AND COMPUTATION,
    Year = 2008,
    Volume = 4,
    Number = 11,
    Pages = 1829-1834,
    Month = NOV,
    Abstract = High-level OVOS (optimized virtual orbital space) CCSD(T) interaction
       energy calculations (up to the aug-cc-pVQZ basis set) and various
       extrapolations toward the complete basis set (CBS) limit are presented
       for the most important structures on the benzene dimer potential energy
       surface. The geometries of these structures were obtained via an
       all-coordinate gradient geometry optimization using the DFT-D/BLYP
       method, covering the empirical dispersion correction fitted exclusively
       for this system. The fit was carried out against two estimated
       CCSD(T)/CBS potential energy curves corresponding to the distance
       variation between two benzene rings for the parallel-displaced (PD) and
       T-shaped (T) structures. The effect of the connected quadruple
       excitations on the interaction energy was estimated using the
       CCSD(TQ(f)) method in a 6-31 G*(0.25) basis set, destabilizing the T
       and T-shaped tilted (TT) structures by approximate to 0.02 kcal/mol and
       the PD structure by approximate to 0.04 kcal/mol. Our best CCSD(T)/CBS
       results show, within the error bars of the applied methodology, that the
       energetically lowest-lying structure is the TT structure, which is
       nearly 0.1 kcal/mol more stable than the almost isoenergetic PD and T
       structures. The specifically parametrized DFT-D/BLYP method leads to a
       correct energy ordering of the structures, with the errors being smaller
       by 0.2 kcal/mol with respect to the most accurate CCSD(T) values.,
    DOI = 10.1021/ct800229h,
    ISSN = 1549-9618,
    Unique-ID = ISI:000260851300003,
    
  • [DOI] J. Rezac and P. Hobza, "Benzene Dimer: Dynamic Structure and Thermodynamics Derived from
    On-the-Fly ab initio DFT-D Molecular Dynamic Simulations," JOURNAL OF CHEMICAL THEORY AND COMPUTATION, vol. 4, iss. 11, pp. 1835-1840, 2008.
    [Bibtex]
    @article ISI:000260851300004,
    Author = Rezac, Jan and Hobza, Pavel,
    Title = Benzene Dimer: Dynamic Structure and Thermodynamics Derived from
       On-the-Fly ab initio DFT-D Molecular Dynamic Simulations,
    Journal = JOURNAL OF CHEMICAL THEORY AND COMPUTATION,
    Year = 2008,
    Volume = 4,
    Number = 11,
    Pages = 1835-1840,
    Month = NOV,
    Abstract = The dynamic nature of the benzene dimer was explored by on-the-fly
       molecular dynamics simulations based on the DFT-D method covering the
       dispersion energy. An all-electron DFT was performed at the BLYP/TZVP
       level. The parameters in the dispersion correction term were fitted to
       mimic the benchmark CCSD(T)/complete basis set limit potential energy
       curves for both the parallel-displaced (PD) and T-shaped (TS) structures
       of the dimer exactly. A dynamic description is important at temperatures
       above 10 K, where interconversion between the TS and PD structures is
       possible and a mixture of these two species exists. The higher the
       temperature, the more dominant the TS structure because of a favorable
       entropic contribution to the free energy. An analysis of the TS
       structures revealed that the symmetric C-2v structure, a low-lying
       transition state, is practically not populated and that the tilted C-s
       TS structure is prevalent. This finding is in perfect agreement with
       infrared spectroscopy.,
    DOI = 10.1021/ct8002282,
    ISSN = 1549-9618,
    Unique-ID = ISI:000260851300004,
    
  • [DOI] M. Pitonak, K. E. Riley, P. Neogrady, and P. Hobza, "Highly accurate CCSD(T) and DFT-SAPT stabilization energies of H-bonded
    and stacked structures of the uracil dimer," CHEMPHYSCHEM, vol. 9, iss. 11, pp. 1636-1644, 2008.
    [Bibtex]
    @article ISI:000258368700022,
    Author = Pitonak, Michal and Riley, Kevin E. and Neogrady, Pavel and Hobza, Pavel,
    Title = Highly accurate CCSD(T) and DFT-SAPT stabilization energies of H-bonded
       and stacked structures of the uracil dimer,
    Journal = CHEMPHYSCHEM,
    Year = 2008,
    Volume = 9,
    Number = 11,
    Pages = 1636-1644,
    Month = AUG 4,
    Abstract = The CCSD(T) interaction energies for the H-bonded and Stacked structures
       of the uracil dimer are determined at the aug-cc-pVDZ and aug-cc-pVTZ
       levels. On the basis of these calculations we can construct the CCSD(T)
       interaction energies at the complete basis set (CBS) limit. The most
       accurate energies, based either on direct extrapolation of the CCSD(T)
       correlation energies obtained with the aug-cc-pVDZ and aug-cc-pVTZ basis
       sets or on the sum of extrapolated MP2 interaction energies (from
       aug-cc-pVTZ and aug-cc-pVQZ basis sets) and extrapolated Delta CCSD(T)
       correction terms [difference between CCSD(T) and MP2 interaction
       energies] differ only slightly, which demonstrates the reliability and
       robustness of both techniques. The latter values, which represent new
       standards for the H-bonding and stacking structures of the uracil dimer,
       differ from the previously published data for the S22 set by a small
       amount. This suggests that interaction energies of the S22 set are
       generated with chemical accuracy. The most accurate CCSD(T)/CBS
       interaction energies are compared with interaction energies obtained
       from various computational procedures, namely the SCS-MP2 (SCS:
       spin-component-scaled), SCS(MI)-MP2 (MI: molecular interaction), MP3,
       dispersion-augmented DFT (DFT-D), M06-2X, and DFT-SAPT (SAPT.
       symmetry-adapted perturbation theory) methods. Among these techniques,
       the best results are obtained with the SCS(MI)-MP2 method. Remarkably
       good binding energies are also obtained with the DFT-SAPT method. Both
       DFT techniques tested yield similarly good interaction energies. The
       large magnitude of the stacking energy for the uracil dimer, compared to
       that of the benzene dimer is explained by attractive electrostatic
       interactions present in the stacked uracil dimer. These interactions
       force both subsystems to approach each other and the dispersion energy
       benefits from a shorter intersystem separation.,
    DOI = 10.1002/cphc.200800286,
    ISSN = 1439-4235,
    Unique-ID = ISI:000258368700022,
    
  • [DOI] J. S. Murray, M. C. Concha, P. Lane, P. Hobza, and P. Politzer, "Blue shifts vs red shifts in sigma-hole bonding," JOURNAL OF MOLECULAR MODELING, vol. 14, iss. 8, pp. 699-704, 2008.
    [Bibtex]
    @article ISI:000257330700007,
    Author = Murray, Jane S. and Concha, Monica C. and Lane, Pat and Hobza, Pavel and
       Politzer, Peter,
    Title = Blue shifts vs red shifts in sigma-hole bonding,
    Journal = JOURNAL OF MOLECULAR MODELING,
    Year = 2008,
    Volume = 14,
    Number = 8,
    Pages = 699-704,
    Month = AUG,
    Abstract = sigma-Hole bonding is a noncovalent interaction between a region of
       positive electrostatic potential on the outer surface of a Group V, VI,
       or VII covalently-bonded atom (a sigma-hole) and a region of negative
       potential on another molecule, e.g., a lone pair of a Lewis base. We
       have investigated computationally the occurrence of increased vibration
       frequencies (blue shifts) and bond shortening vs decreased frequencies
       (red shifts) and bond lengthening for the covalent bonds to the atoms
       having the sigma-holes (the sigma-hole donors). Both are possible,
       depending upon the properties of the donor and the acceptor. Our results
       are consistent with models that were developed earlier by Hermansson and
       by Qian and Krimm in relation to blue vs red shifting in hydrogen bond
       formation. These models invoke the derivatives of the permanent and the
       induced dipole moments of the donor molecule.,
    DOI = 10.1007/s00894-008-0307-y,
    ISSN = 1610-2940,
    Unique-ID = ISI:000257330700007,
    
  • [DOI] L. Bendova-Biedermannova, P. Hobza, and J. Vondrasek, "Identifying stabilizing key residues in proteins using interresidue
    interaction energy matrix," PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, vol. 72, iss. 1, pp. 402-413, 2008.
    [Bibtex]
    @article ISI:000256609800035,
    Author = Bendova-Biedermannova, Lada and Hobza, Pavel and Vondrasek, Jiri,
    Title = Identifying stabilizing key residues in proteins using interresidue
       interaction energy matrix,
    Journal = PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS,
    Year = 2008,
    Volume = 72,
    Number = 1,
    Pages = 402-413,
    Month = JUL,
    Abstract = We are proposing an interresidue interaction energy map (IEM) - a new
       tool for protein structure analysis and protein bioinformatics. This
       approach employs the sum of pair-wise interaction energies of a
       particular residue as a measure of its structural importance. We will
       show that the IEM can serve as a means for identifying key residues
       responsible for the stability of a protein. Our method can be compared
       with the interresidue contact map but has the advantage of weighting the
       contacts by the stabilization energy content which they bring to the
       protein structure. For the theoretical adjustment of the proposed
       method, we chose the Trp-cage mini protein as a model system to compare
       a spectrum of computational methods ranging from the ab initio MP2 level
       through the DFT method to empirical force-field methods. The IEM method
       correctly identifies Tryptophane 6 as the key residue in the Trp-cage.
       The other residues with the highest stabilizing contributions correspond
       to the structurally important positions in the protein. We have further
       tested our method on the Trp-Cage miniprotein - a P12W mutant of the
       Trp-cage and on two proteins from the rubredoxin family that differ in
       their thermostability. Our method correctly identified the
       thermodynamically more stable variants in both cases and therefore can
       also be used as a tool for the relative measurement of protein
       stability. Finally, we will point out the important role played by
       dispersion energy, which contributes significantly to the total
       stabilization energy and whose role in aromatic pairs is clearly
       dominant. Surprisingly, the dispersion energy plays an even more
       important role in the interaction of prolines with aromatic systems.,
    DOI = 10.1002/prot.21938,
    ISSN = 0887-3585,
    Unique-ID = ISI:000256609800035,
    
  • [DOI] R. Vacha, L. Cwiklik, J. Rezac, P. Hobza, P. Jungwirth, K. Valsaraj, S. Bahr, and V. Kempter, "Adsorption of aromatic hydrocarbons and ozone at environmental aqueous
    surfaces," JOURNAL OF PHYSICAL CHEMISTRY A, vol. 112, iss. 22, pp. 4942-4950, 2008.
    [Bibtex]
    @article ISI:000256270500012,
    Author = Vacha, Robert and Cwiklik, Lukasz and Rezac, Jan and Hobza, Pavel and
       Jungwirth, Pavel and Valsaraj, Kalliat and Bahr, Stephan and Kempter,
       Volker,
    Title = Adsorption of aromatic hydrocarbons and ozone at environmental aqueous
       surfaces,
    Journal = JOURNAL OF PHYSICAL CHEMISTRY A,
    Year = 2008,
    Volume = 112,
    Number = 22,
    Pages = 4942-4950,
    Month = JUN 5,
    Abstract = Adsorption of environmentally important aromatic molecules on a water
       surface is studied by means of classical and ab initio molecular
       dynamics simulations and by reflection-absorption infrared spectroscopy.
       Both techniques show strong activity and orientational preference of
       these molecules at the surface. Benzene and naphthalene, which bind
       weakly to water surface with a significant contribution of dispersion
       interactions, prefer to lie flat on water but retain a large degree of
       orientational flexibility. Pyridine is more rigid at the surface. It is
       tilted with the nitrogen end having strong hydrogen bonding interactions
       with water molecules. The degree of adsorption and orientation of
       aromatic molecules on aqueous droplets has atmospheric implications for
       heterogeneous ozonolysis, for which the Langmuir-Hinshelwood kinetics
       mechanism is discussed. At higher coverages of aromatic molecules the
       incoming ozone almost doles not come into contact with the underlying
       aqueous phase. This may rationalize the experimental insensitivity of
       the ozonolysis on the chemical nature of the substrate on which the
       aromatic molecules adsorb.,
    DOI = 10.1021/jp711813p,
    ISSN = 1089-5639,
    Unique-ID = ISI:000256270500012,
    
  • [DOI] W. Wang and P. Hobza, "Theoretical study on the complexes of benzene with isoelectronic
    nitrogen-containing heterocycles," CHEMPHYSCHEM, vol. 9, iss. 7, pp. 1003-1009, 2008.
    [Bibtex]
    @article ISI:000255845500008,
    Author = Wang, Weizhou and Hobza, Pavel,
    Title = Theoretical study on the complexes of benzene with isoelectronic
       nitrogen-containing heterocycles,
    Journal = CHEMPHYSCHEM,
    Year = 2008,
    Volume = 9,
    Number = 7,
    Pages = 1003-1009,
    Month = MAY 2,
    Abstract = The pi-pi interactions between benzene and the aromatic nitrogen
       heterocycles pyridine, pyrimidine, 1,3,5-triazine, 1,2,3-triazine,
       1,2,4,5-tetrazine, and 1,2,3,4,5-pentazine are systematically
       investigated. The T-shaped structures of all complexes studied exhibit a
       contraction of the C-H bond accompanied by a rather large blue shift
       (40-52 cm(-1)) of its stretching frequency, and they ore almost
       isoenergetic with the corresponding displaced-parallel structures at
       reliable levels of theory. With increasing number of nitrogen atoms in
       the heterocycle, the geometries, frequencies, energies, percentage of s
       character at C, and the electron density in the C-H sigma antibonding
       orbital of the complexes all increase or decrease systematically.
       Decomposition analysis of the total binding energy showed that for all
       the complexes, the dispersion energy is the dominant attractive
       contribution, and a rather compensated by its exchange counterpart.,
    DOI = 10.1002/cphc.200700587,
    ISSN = 1439-4235,
    Unique-ID = ISI:000255845500008,
    
  • [DOI] W. Wang and P. Hobza, "Origin of the X-Hal (Hal = Cl, Br) bond-length change in the
    halogen-bonded complexes," JOURNAL OF PHYSICAL CHEMISTRY A, vol. 112, iss. 17, pp. 4114-4119, 2008.
    [Bibtex]
    @article ISI:000255292200043,
    Author = Wang, Weizhou and Hobza, Pavel,
    Title = Origin of the X-Hal (Hal = Cl, Br) bond-length change in the
       halogen-bonded complexes,
    Journal = JOURNAL OF PHYSICAL CHEMISTRY A,
    Year = 2008,
    Volume = 112,
    Number = 17,
    Pages = 4114-4119,
    Month = MAY 1,
    Abstract = The origin of the X-Hal bond-length change in the halogen bond of the
       X-Hal...Y type has been investigated at the MP2(full)/6-311++G(d,p)
       level of theory using a natural bond orbital analysis, atoms in
       molecules procedure, and electrostatic potential fitting methods. Our
       results have clearly shown that various theories explaining the nature
       of the hydrogen bond cannot be applied to explain the origin of the
       X-Hal bond-length change in the halogen bond. We provide a new
       explanation for this change. The elongation of the X-Hal bond length is
       caused by the electron-density transfer to the X-Hal sigma*
       antibonding orbital. For the blue-shifting halogen bond, the
       electron-density transfer to the X-Hal pi* antibonding orbital is only
       of minor importance; it is the electrostatic attractive interaction that
       causes the X-Hal bond contraction.,
    DOI = 10.1021/jp710992h,
    ISSN = 1089-5639,
    Unique-ID = ISI:000255292200043,
    
  • [DOI] H. Valdes, V. Klusak, M. Pitonak, O. Exner, I. Stary, P. Hobza, and L. Rulisek, "Evaluation of the intramolecular basis set superposition error in the
    calculations of larger molecules: [n]Helicenes and Phe-Gly-Phe
    tripeptide," JOURNAL OF COMPUTATIONAL CHEMISTRY, vol. 29, iss. 6, pp. 861-870, 2008.
    [Bibtex]
    @article ISI:000254766400002,
    Author = Valdes, Haydee and Klusak, Vojtech and Pitonak, Michal and Exner, Otto
       and Stary, Ivo and Hobza, Pavel and Rulisek, Lubomir,
    Title = Evaluation of the intramolecular basis set superposition error in the
       calculations of larger molecules: [n]Helicenes and Phe-Gly-Phe
       tripeptide,
    Journal = JOURNAL OF COMPUTATIONAL CHEMISTRY,
    Year = 2008,
    Volume = 29,
    Number = 6,
    Pages = 861-870,
    Month = APR 30,
    Abstract = Correlated ab initio calculations on large systems, such as the popular
       MP2 (or RI-MP2) method, suffer from the intramolecular basis set
       superposition error (BSSE). This error is typically manifested in
       molecules with folded structures, characterized by intramolecular
       dispersion interactions. It can dramatically affect the energy
       differences between various conformers as well as intramolecular
       stabilities, and it can even impair the accuracy of the predictions of
       the equilibrium molecular structures. In this study, we will present two
       extreme cases of intramolecular BSSE, the internal stability of
       [n]helicene molecules and the relative energies of various conformers
       of phenylalanyl-glycyl-phenylalanine tripeptide (Phe-Gly-Phe), and
       compare the calculated data with benchmark values (experimental or
       high-level theoretical data). As a practical and cheap solution to the
       accurate treatment of the systems with large anticipated value of
       intramolecular BSSE, the recently developed density functional method
       augmented with an empirical dispersion term (DFT-D) is proposed and
       shown to provide very good results in both of the above described
       representative cases. (c) 2007 Wiley Periodicals, Inc.,
    DOI = 10.1002/jcc.20841,
    ISSN = 0192-8651,
    Unique-ID = ISI:000254766400002,
    
  • [DOI] J. Cerny, X. Tong, P. Hobza, and K. Mueller-Dethlefs, "State of the art theoretical study and comparison to experiment for the
    phenol center dot center dot center dot argon complex," JOURNAL OF CHEMICAL PHYSICS, vol. 128, iss. 11, 2008.
    [Bibtex]
    @article ISI:000254292500039,
    Author = Cerny, Jiri and Tong, Xin and Hobza, Pavel and Mueller-Dethlefs, Klaus,
    Title = State of the art theoretical study and comparison to experiment for the
       phenol center dot center dot center dot argon complex,
    Journal = JOURNAL OF CHEMICAL PHYSICS,
    Year = 2008,
    Volume = 128,
    Number = 11,
    Month = MAR 21,
    Abstract = The phenol center dot center dot center dot argon complex was studied by
       means of various high level ab initio quantum mechanics methods and high
       resolution threshold ionization spectroscopy. The structure and
       stabilization energy of different conformers were determined.
       Stabilization energy of van der Waals bonded and H-bonded PhOH center
       dot center dot center dot Ar complex determined at CCSD(T) complete
       basis set (CBS) level for CP-RI-MP2/cc-pVTZ/Ar aug-cc-pVTZ geometries
       amount to 434 and 285 cm(-1). The CCSD(T)/CBS were constructed either as
       a sum of MP2/CBS interaction energy and CCSD(T) correction term
       [difference between CCSD(T) and MP2 correlation energies determined
       with medium basis set] or directly from CCSD(T)/aug-cc-pVDZ and
       aug-cc-pVTZ energies. Both schemes provide very similar values. Harmonic
       vibrational analysis revealed that the H-bonded structure does not
       represent energy minimum but first order transition structure. The
       respective imaginary vibrational mode (16 cm(-1)) connects two possible
       argon locations-above and below the phenol aromatic ring. Including the
       Delta ZPVE, we obtained stabilization enthalpy at 0 K of 389 cm(-1).
       This value is marginally higher (25-35 cm(-1), 0.07-0.10 kcal/mol) than
       the experimental value. The determination of Delta ZPVE constitutes the
       most significant error and possible improvements should come from more
       accurate evaluation of the (nonharmonic) vibrational frequencies. (c)
       2008 American Institute of Physics.,
    DOI = 10.1063/1.2838185,
    Article-Number = 114319,
    ISSN = 0021-9606,
    Unique-ID = ISI:000254292500039,
    
  • [DOI] K. E. Riley and P. Hobza, "A DFT-D investigation of the mechanisms for activation of the wild-type
    and S810L mutated mineralocorticoid receptor by steroid hormones," JOURNAL OF PHYSICAL CHEMISTRY B, vol. 112, iss. 10, pp. 3157-3163, 2008.
    [Bibtex]
    @article ISI:000253784700052,
    Author = Riley, Kevin E. and Hobza, Pavel,
    Title = A DFT-D investigation of the mechanisms for activation of the wild-type
       and S810L mutated mineralocorticoid receptor by steroid hormones,
    Journal = JOURNAL OF PHYSICAL CHEMISTRY B,
    Year = 2008,
    Volume = 112,
    Number = 10,
    Pages = 3157-3163,
    Month = MAR 13,
    Abstract = In this work; we investigate the mode of binding of several steroid
       hormones, namely aldosterone, deoxycorticosterone, and progesterone to
       the wild-type and S810L mutated mineralocorticoid (MR) receptor using
       the newly formulated density functional theory with an empirical
       dispersion term (DFT-D) molecular electronic structure method. It is
       found that the MR agonists, aldosterone and deoxycorticosterone, form
       tight hydrogen bonds with residues Thr945 and Asn770, which leads to the
       formation of hydrogen bond networks near the steroid D-ring, allowing
       for activation of this transcription factor. Progesterone, an MR
       antagonist, fails to form the necessary hydrogen bonds near the steroid
       D-ring. Progesterone is known to be an agonist of the mutated S810L MR
       receptor. Our studies indicate that this is possible because of a strong
       hydrogen bond between progesterone and Thr945 and a relatively strong
       hydrophobic interaction between progesterone and Asn770.,
    DOI = 10.1021/jp076362b,
    ISSN = 1520-6106,
    Unique-ID = ISI:000253784700052,
    
  • [DOI] D. Nachtigallova, P. Hobza, and V. Spirko, "Assigning the NH stretches of the Guanine tautomers using adiabatic
    separation: CCSD(T) benchmark calculations," JOURNAL OF PHYSICAL CHEMISTRY A, vol. 112, iss. 9, pp. 1854-1856, 2008.
    [Bibtex]
    @article ISI:000253512600002,
    Author = Nachtigallova, Dana and Hobza, Pavel and Spirko, Vladimir,
    Title = Assigning the NH stretches of the Guanine tautomers using adiabatic
       separation: CCSD(T) benchmark calculations,
    Journal = JOURNAL OF PHYSICAL CHEMISTRY A,
    Year = 2008,
    Volume = 112,
    Number = 9,
    Pages = 1854-1856,
    Month = MAR 6,
    Abstract = Using an adiabatic separation of the NH stretching vibration from the
       remaining vibrational molecular motions, the NH fundamental frequencies
       and absolute intensities of several keto/enol and 7/9NH tautomers of
       guanine are evaluated ab initio within the framework of a
       one-dimensional ``semirigid'' stretching Hamiltonian. The frequencies
       (calculated by means of the standard MP2, CCSD(T) and DFT procedures)
       are in a close one-to-one harmony with their experimental counterparts,
       thus evidencing the adequacy of the used separation for reliable
       assigning of the NH stretches in the vibrational spectra of very large
       molecular systems.,
    DOI = 10.1021/jp711151a,
    ISSN = 1089-5639,
    Unique-ID = ISI:000253512600002,
    
  • [DOI] K. E. Riley and P. Hobza, "Investigations into the nature of halogen bonding including symmetry
    adapted perturbation theory analyses," JOURNAL OF CHEMICAL THEORY AND COMPUTATION, vol. 4, iss. 2, pp. 232-242, 2008.
    [Bibtex]
    @article ISI:000253166000003,
    Author = Riley, Kevin E. and Hobza, Pavel,
    Title = Investigations into the nature of halogen bonding including symmetry
       adapted perturbation theory analyses,
    Journal = JOURNAL OF CHEMICAL THEORY AND COMPUTATION,
    Year = 2008,
    Volume = 4,
    Number = 2,
    Pages = 232-242,
    Month = FEB,
    Abstract = In recent years it has been recognized that, because of their unique
       properties, halogen bonds have tremendous potential in the development
       of new pharmaceutical compounds and materials. In this study we
       investigate the phenomenon of halogen bonding by carrying out ab initio
       calculations on the halomethane-formaldehyde complexes as well as the
       fluorine substituted F(n)H(3-n)CX center dot center dot center dot
       OCH(2) dimers, where the halogen bonding. halogens (X) are chlorine,
       bromine, and iodine. Coupled cluster (CCSD(T)/aug-cc-pVTZ) calculations
       indicate that the binding energies for these type of interactions lie in
       the range between - 1.05 kcal/mol (H(3)CCl center dot center dot center
       dot OCH(2)) and -3.72 kcal/mol (F(3)Cl center dot center dot center dot
       OCH(2)). One of the most important findings in this study is that,
       according to symmetry adapted perturbation theory (SAPT) analyses,
       halogen bonds are largely dependent on both electrostatic and dispersion
       type interactions. As the halogen atom involved in halogen bonding
       becomes larger the interaction strength for this type of interaction
       also gets larger and, interestingly, more electrostatic (and less
       dispersive) in character. Halogen bonding interactions also become
       stronger and more electrostatic upon substitution of (the very
       electronegative) fluorines onto the halomethane molecule.,
    DOI = 10.1021/ct700216w,
    ISSN = 1549-9618,
    Unique-ID = ISI:000253166000003,
    
  • [DOI] J. Rezac, P. Jurecka, K. E. Riley, J. Cerny, H. Valdes, K. Pluhackova, K. Berka, T. Rezac, M. Pitonak, J. Vondrasek, and P. Hobza, "QUANTUM CHEMICAL BENCHMARK ENERGY AND GEOMETRY DATABASE FOR MOLECULAR
    CLUSTERS AND COMPLEX MOLECULAR SYSTEMS (www.begdb.com): A USERS MANUAL
    AND EXAMPLES," COLLECTION OF CZECHOSLOVAK CHEMICAL COMMUNICATIONS, vol. 73, iss. 10, pp. 1261-1270, 2008.
    [Bibtex]
    @article ISI:000263121400003,
    Author = Rezac, Jan and Jurecka, Petr and Riley, Kevin E. and Cerny, Jiri and
       Valdes, Haydee and Pluhackova, Kristyna and Berka, Karel and Rezac,
       Tomas and Pitonak, Michal and Vondrasek, Jiri and Hobza, Pavel,
    Title = QUANTUM CHEMICAL BENCHMARK ENERGY AND GEOMETRY DATABASE FOR MOLECULAR
       CLUSTERS AND COMPLEX MOLECULAR SYSTEMS (www.begdb.com): A USERS MANUAL
       AND EXAMPLES,
    Journal = COLLECTION OF CZECHOSLOVAK CHEMICAL COMMUNICATIONS,
    Year = 2008,
    Volume = 73,
    Number = 10,
    Pages = 1261-1270,
    Abstract = Our previous benchmark CCSD(T)/ complete basis set limit calculations
       were collected into a database named begdb - Benchmark Energy and
       Geometry DataBase. Web-based interface to this database was prepared and
       is available at www.begdb.com. Users can browse, search and plot the
       data online or download structures and energy tables.,
    DOI = 10.1135/cccc20081261,
    ISSN = 0010-0765,
    Unique-ID = ISI:000263121400003,
    
  • [DOI] J. Rezac and P. Hobza, "Correlation between the thermodynamic stability of DNA duplexes and the
    interaction and solvation energies of DNA building blocks," COLLECTION OF CZECHOSLOVAK CHEMICAL COMMUNICATIONS, vol. 73, iss. 2, pp. 161-174, 2008.
    [Bibtex]
    @article ISI:000253884000003,
    Author = Rezac, Jan and Hobza, Pavel,
    Title = Correlation between the thermodynamic stability of DNA duplexes and the
       interaction and solvation energies of DNA building blocks,
    Journal = COLLECTION OF CZECHOSLOVAK CHEMICAL COMMUNICATIONS,
    Year = 2008,
    Volume = 73,
    Number = 2,
    Pages = 161-174,
    Abstract = The unwinding Gibbs energy (or duplex dissociation energy) is an
       important measure of the thermodynamic stability of DNA oligomers. This
       value can be measured experimentally or predicted by empirical models
       parametrised on experimental data. Our previously developed model based
       on accurate DFT-D calculations of interaction energies between nucleic
       acid bases corrected for solvation contribution. This work was
       successfully extended to cover variable lengths of oligomers. This model
       was further applied to oligomers containing inosine, an unnatural base.
       The results, however, are not satisfactory and it is clear that the
       model does not take into account all variables contributing to DNA
       stability. Inclusion of the backbone deformation energy did not improve
       the model. We also compared models based on DFT-D and forcefield
       calculations. Forcefield performs well in this application, because the
       systematic error in interaction energies is cancelled in the fitting
       procedure.,
    DOI = 10.1135/cccc20080161,
    ISSN = 0010-0765,
    Unique-ID = ISI:000253884000003,
    
  • [DOI] W. Wang and P. Hobza, "APPLICATION OF BERLIN'S THEOREM TO BOND-LENGTH CHANGES IN ISOLATED
    MOLECULES AND RED- AND BLUE-SHIFTING H-BONDED CLUSTERS," COLLECTION OF CZECHOSLOVAK CHEMICAL COMMUNICATIONS, vol. 73, iss. 6-7, pp. 862-872, 2008.
    [Bibtex]
    @article ISI:000260536700010,
    Author = Wang, Weizhou and Hobza, Pavel,
    Title = APPLICATION OF BERLIN'S THEOREM TO BOND-LENGTH CHANGES IN ISOLATED
       MOLECULES AND RED- AND BLUE-SHIFTING H-BONDED CLUSTERS,
    Journal = COLLECTION OF CZECHOSLOVAK CHEMICAL COMMUNICATIONS,
    Year = 2008,
    Volume = 73,
    Number = 6-7,
    Pages = 862-872,
    Abstract = The origin of the bond-length change in molecule or molecular cluster
       has been investigated at the MP2/aug-cc-pVDZ level of theory using the
       electrostatic potential or the electron density difference analysis
       method. Our results have clearly shown that the bond-length change of a
       chemical bond is determined mainly by the balance of the electrostatic
       forces exerted by electrons on the two nuclei. The factors that affect
       the balance of the electrostatic forces include four parts: ( i) The
       abstraction of the electron density from Berlin's binding region between
       the two nuclei. ( ii) The accumulation of the electron density in
       Berlin's antibinding regions. ( iii) The accumulation of the electron
       density in Berlin's binding region between the two nuclei. ( iv) The
       abstraction of the electron density from Berlin's antibinding regions.
       Using the change of the electron density around the two nuclei of a
       chemical bond, we have succeeded in explaining two important chemical
       phenomena: ( i) breakdown of bond length-bond strength correlation; (
       ii) the bond-length change in the hydrogen bond.,
    DOI = 10.1135/cccc20080862,
    ISSN = 0010-0765,
    Unique-ID = ISI:000260536700010,
    
  • [DOI] J. Rezac, K. Berka, D. Horinek, P. Hobza, and J. Vondrasek, "THE STABILIZATION ENERGY OF THE GLU-LYS SALT BRIDGE IN THE PROTEIN/WATER
    ENVIRONMENT: CORRELATED QUANTUM CHEMICAL ab initio, DFT AND EMPIRICAL
    POTENTIAL STUDIES," COLLECTION OF CZECHOSLOVAK CHEMICAL COMMUNICATIONS, vol. 73, iss. 6-7, pp. 921-936, 2008.
    [Bibtex]
    @article ISI:000260536700014,
    Author = Rezac, Jan and Berka, Karel and Horinek, Dominik and Hobza, Pavel and
       Vondrasek, Jiri,
    Title = THE STABILIZATION ENERGY OF THE GLU-LYS SALT BRIDGE IN THE PROTEIN/WATER
       ENVIRONMENT: CORRELATED QUANTUM CHEMICAL ab initio, DFT AND EMPIRICAL
       POTENTIAL STUDIES,
    Journal = COLLECTION OF CZECHOSLOVAK CHEMICAL COMMUNICATIONS,
    Year = 2008,
    Volume = 73,
    Number = 6-7,
    Pages = 921-936,
    Abstract = The stabilization energies of Glu-Lys salt bridges are calculated at the
       CCSD(T) complete basis set limit to provide a reasonable description of
       the strength of the ion-pair bond in the gas phase. The effect of the
       environment (protein with epsilon = 4 and water with epsilon = 80) on
       the stabilization energy was introduced via a modification of the
       quantum chemical DFT energy, for which the COSMO methodology was
       adopted. The other (standard) approach was based on incorporating a
       dielectric constant into the Coulomb electrostatic term of the Amber
       empirical potential function and utilizing the generalized Born model
       implemented in the Amber program. The environment affects the
       stabilization energy of the salt bridge dramatically: The protein
       reduces the energy to less than one half of the original value, whereas
       water sometimes changes stabilization to destabilization. Both
       theoretical procedures, based on completely different theoretical
       backgrounds, yield very similar results, which strongly support their
       validity. An ion pair is converted to an ion-neutral pair when its pH is
       changed. This transformation is connected with a strong reduction of the
       stabilization energy regardless of the environment. The substantial
       differences in the stabilization energies of ion pairs and ion-neutral
       pairs contradict the negligible changes of free energy detected
       experimentally. Evidently, the contribution of formation and hydration
       entropy is significant and compensates for the large stabilization
       energies.,
    DOI = 10.1135/cccc20080921,
    ISSN = 0010-0765,
    Unique-ID = ISI:000260536700014,
    
  • [DOI] H. Valdes, V. Spiwok, J. Rezac, D. Reha, A. G. Abo-Riziq, M. S. de Vries, and P. Hobza, "Potential-energy and free-energy surfaces of glycyl-phenylalanyl-alanine
    (GFA) tripeptide: Experiment and theory," CHEMISTRY-A EUROPEAN JOURNAL, vol. 14, iss. 16, pp. 4886-4898, 2008.
    [Bibtex]
    @article ISI:000256854600015,
    Author = Valdes, Haydee and Spiwok, Vojtech and Rezac, Jan and Reha, David and
       Abo-Riziq, Ali G. and de Vries, Mattanjah S. and Hobza, Pavel,
    Title = Potential-energy and free-energy surfaces of glycyl-phenylalanyl-alanine
       (GFA) tripeptide: Experiment and theory,
    Journal = CHEMISTRY-A EUROPEAN JOURNAL,
    Year = 2008,
    Volume = 14,
    Number = 16,
    Pages = 4886-4898,
    Abstract = The free-energy surface (FES) of glycyl-phenylalanyl-alanine (GFA)
       tripeptide was explored by molecular dynamics (MD) simulations in
       combination with high-level correlated ab initio quantum chemical
       calculations and metadynamics. Both the MD and metadynamics employed the
       tight-binding DFT-D method instead of the AMBER force field, which
       yielded inaccurate results. We classified the minima localised in the
       FESs as follows: a) the backbone-conformation at arrangement; and b) the
       existence of a CCOH center dot center dot center dot OC intramolecular
       H-bond (families CO2Hfree and CO2Hbonded). Comparison with experimental
       results showed that the most stable minima in the FES correspond to the
       experimentally observed structures. Remarkably, however, we did not
       observe experimentally the CO2Hbonded family (also predicted by
       metadynamics), although its stability is comparable to that of the
       CO2Hfee structures. This fact was explained by the former's short
       excitedstate lifetime. We also carried out ab initio calculations using
       DFT-D and the M06-2X functional. ne importance of the dispersion energy
       in stabilising peptide conformers is well reflected by our pioneer
       analysis using the DFT-SAPT method to explore the nature of the
       backbone/side-chain interactions.,
    DOI = 10.1002/chem.200800085,
    ISSN = 0947-6539,
    Unique-ID = ISI:000256854600015,
    
  • P. Hobza, "Non-Covalent Interactions with Participation of Hydrogen: Hydrogen Bond,
    Blue-Shifting Hydrogen Bond and Dihydrogen Bond," CHEMICKE LISTY, vol. 102, iss. 10, pp. 884-888, 2008.
    [Bibtex]
    @article ISI:000260453700005,
    Author = Hobza, Pavel,
    Title = Non-Covalent Interactions with Participation of Hydrogen: Hydrogen Bond,
       Blue-Shifting Hydrogen Bond and Dihydrogen Bond,
    Journal = CHEMICKE LISTY,
    Year = 2008,
    Volume = 102,
    Number = 10,
    Pages = 884-888,
    Abstract = Non-covalent interactions with participation of hydrogen are the
       strongest and most frequent of non-covalent interactions in nature.
       Their role in chemistry and especially in biodisciplines is unique.,
    ISSN = 0009-2770,
    Unique-ID = ISI:000260453700005,
    
  • [DOI] P. Hobza, "Stacking interactions," PHYSICAL CHEMISTRY CHEMICAL PHYSICS, vol. 10, iss. 19, pp. 2581-2583, 2008.
    [Bibtex]
    @article ISI:000255739200001,
    Author = Hobza, Pavel,
    Title = Stacking interactions,
    Journal = PHYSICAL CHEMISTRY CHEMICAL PHYSICS,
    Year = 2008,
    Volume = 10,
    Number = 19,
    Pages = 2581-2583,
    DOI = 10.1039/b805489b,
    ISSN = 1463-9076,
    Unique-ID = ISI:000255739200001,
    
  • [DOI] J. Sponer, K. E. Riley, and P. Hobza, "Nature and magnitude of aromatic stacking of nucleic acid bases," PHYSICAL CHEMISTRY CHEMICAL PHYSICS, vol. 10, iss. 19, pp. 2595-2610, 2008.
    [Bibtex]
    @article ISI:000255739200003,
    Author = Sponer, Jiri and Riley, Kevin E. and Hobza, Pavel,
    Title = Nature and magnitude of aromatic stacking of nucleic acid bases,
    Journal = PHYSICAL CHEMISTRY CHEMICAL PHYSICS,
    Year = 2008,
    Volume = 10,
    Number = 19,
    Pages = 2595-2610,
    Abstract = This review summarises recent advances in quantum chemical calculations
       of base-stacking forces in nucleic acids. We explain in detail the very
       complex relationship between the gas-phase base-stacking energies, as
       revealed by quantum chemical (QM) calculations, and the highly variable
       roles of these interactions in nucleic acids. This issue is rarely
       discussed in quantum chemical and physical chemistry literature. We
       further extensively discuss methods that are available for base-stacking
       studies, complexity of comparison of stacking calculations with gas
       phase experiments, balance of forces in stacked complexes of nucleic
       acid bases, and the relation between QM and force field descriptions. We
       also review all recent calculations on base- stacking systems, including
       details analysis of the B-DNA stacking. Specific attention is paid to
       the highest accuracy QM calculations, to the decomposition of the
       interactions, and development of dispersion-balanced DFT methods. Future
       prospects of computational studies of base stacking are discussed.,
    DOI = 10.1039/b719370j,
    ISSN = 1463-9076,
    Unique-ID = ISI:000255739200003,
    
  • [DOI] H. Valdes, K. Pluhackova, M. Pitonak, J. Rezac, and P. Hobza, "Benchmark database on isolated small peptides containing an aromatic
    side chain: comparison between wave function and density functional
    theory methods and empirical force field," PHYSICAL CHEMISTRY CHEMICAL PHYSICS, vol. 10, iss. 19, pp. 2747-2757, 2008.
    [Bibtex]
    @article ISI:000255739200018,
    Author = Valdes, Haydee and Pluhackova, Kristyna and Pitonak, Michal and Rezac,
       Jan and Hobza, Pavel,
    Title = Benchmark database on isolated small peptides containing an aromatic
       side chain: comparison between wave function and density functional
       theory methods and empirical force field,
    Journal = PHYSICAL CHEMISTRY CHEMICAL PHYSICS,
    Year = 2008,
    Volume = 10,
    Number = 19,
    Pages = 2747-2757,
    Abstract = A detailed quantum chemical study on five peptides (WG, WGG, FGG, GGF
       and GFA) containing the residues phenylalanyl (F), glycyl (G),
       tryptophyl (W) and alanyl (A) -where F and W are of aromatic character
       -is presented. When investigating isolated small peptides, the
       dispersion interaction is the dominant attractive force in the peptide
       backbone -aromatic side chain intramolecular interaction. Consequently,
       an accurate theoretical study of these systems requires the use of a
       methodology covering properly the London dispersion forces. For this
       reason we have assessed the performance of the MP2, SCS-MP2, MP3,
       TPSS-D, PBE-D, M062X, BH\&H, TPSS, B3LYP, tight-binding DFT-D methods
       and. 99 empirical force field compared to CCSD(T)/complete basis set
       (CBS) limit benchmark data. All the DFT techniques with a `-D' symbol
       have been augmented by empirical dispersion energy while the M06-2X
       functional was parameterized to cover the London dispersion energy. For
       the systems here studied we have concluded that the use of the. 99 force
       field is not recommended mainly due to problems concerning the
       assignment of reliable atomic charges. Tight-binding DFT-D is efficient
       as a screening tool providing reliable geometries. Among the DFT
       functionals, the M06-2X and TPSS-D show the best performance what is
       explained by the fact that both procedures cover the dispersion energy.
       The B3LYP and TPSS functionals -not covering this energy-fail
       systematically. Both, electronic energies and geometries obtained by
       means of the wave-function theory methods compare satisfactorily with
       the CCSD(T)/CBS benchmark data.,
    DOI = 10.1039/b719294k,
    ISSN = 1463-9076,
    Unique-ID = ISI:000255739200018,
    
  • [DOI] J. Cerny, X. Tong, P. Hobza, and K. Mueller-Dethlefs, "Competition between stacking and hydrogen bonding: theoretical study of
    the phenol center dot center dot center dot Ar cation and neutral
    complex and comparison to experiment," PHYSICAL CHEMISTRY CHEMICAL PHYSICS, vol. 10, iss. 19, pp. 2780-2784, 2008.
    [Bibtex]
    @article ISI:000255739200022,
    Author = Cerny, Jiri and Tong, Xin and Hobza, Pavel and Mueller-Dethlefs, Klaus,
    Title = Competition between stacking and hydrogen bonding: theoretical study of
       the phenol center dot center dot center dot Ar cation and neutral
       complex and comparison to experiment,
    Journal = PHYSICAL CHEMISTRY CHEMICAL PHYSICS,
    Year = 2008,
    Volume = 10,
    Number = 19,
    Pages = 2780-2784,
    Abstract = Experimental results obtained previously for vdW-bonded and H-bonded
       phenol center dot center dot center dot argon (PhOH center dot center
       dot center dot Ar) complexes in their S(0) and D(0) states are combined
       with ab initio quantum-chemical theoretical results. Such a combination
       allows us to present a ``complete'' description of the geometry,
       relative energies, interaction energies and enthalpies of PhOH center
       dot center dot center dot Ar complexes. Based on a minimum-energy-path
       study, the transition structures and barrier heights related to
       transitions between stable conformers are also presented. For the
       presented structures, the agreement between the theoretical interaction
       enthalpy at 0 K with experimentally obtained values is very good. On the
       other hand, for numerical harmonic-frequency calculations we find a very
       poor performance for the neutral PhOH center dot center dot center dot
       Ar complex and complete failure for the studied complexes in their
       cationic form.,
    DOI = 10.1039/b801460b,
    ISSN = 1463-9076,
    Unique-ID = ISI:000255739200022,
    
  • [DOI] M. P. Callahan, Z. Gengeliczki, N. Svadlenak, H. Valdes, P. Hobza, and M. S. de Vries, "Non-standard base pairing and stacked structures in methyl xanthine
    clusters," PHYSICAL CHEMISTRY CHEMICAL PHYSICS, vol. 10, iss. 19, pp. 2819-2826, 2008.
    [Bibtex]
    @article ISI:000255739200028,
    Author = Callahan, Michael P. and Gengeliczki, Zsolt and Svadlenak, Nathan and
       Valdes, Haydee and Hobza, Pavel and de Vries, Mattanjah S.,
    Title = Non-standard base pairing and stacked structures in methyl xanthine
       clusters,
    Journal = PHYSICAL CHEMISTRY CHEMICAL PHYSICS,
    Year = 2008,
    Volume = 10,
    Number = 19,
    Pages = 2819-2826,
    Abstract = We present resonant two-photon ionization and IR-UV double resonance
       spectra of methylated xanthine derivatives including 7-methylxanthine
       dimer and theobromine dimer seeded in a supersonic jet by laser
       desorption. For 7-methylxanthine, theophylline and theobromine monomer
       we assign the lowest energy tautomer based on comparison with IR-UV
       double resonance spectra and calculated IR frequencies. For the
       7-methylxanthine dimer, we observe hydrogen bonding on the N3H position
       suggesting 3 possible combinations, one that is reverse Watson-Crick
       type and two that are reverse Hoogsteen type. For the theobromine dimer,
       we observe a stacked structure. For trimethylxanthine dimers we infer a
       stacked structure as well.,
    DOI = 10.1039/b719874d,
    ISSN = 1463-9076,
    Unique-ID = ISI:000255739200028,
    
  • [DOI] D. Nachtigallova, P. Hobza, and H. Ritze, "Electronic splitting in the excited states of DNA base homodimers and
    -trimers: an evaluation of short-range and Coulombic interactions," PHYSICAL CHEMISTRY CHEMICAL PHYSICS, vol. 10, iss. 37, pp. 5689-5697, 2008.
    [Bibtex]
    @article ISI:000259381000004,
    Author = Nachtigallova, Dana and Hobza, Pavel and Ritze, Hans-Hermann,
    Title = Electronic splitting in the excited states of DNA base homodimers and
       -trimers: an evaluation of short-range and Coulombic interactions,
    Journal = PHYSICAL CHEMISTRY CHEMICAL PHYSICS,
    Year = 2008,
    Volume = 10,
    Number = 37,
    Pages = 5689-5697,
    Abstract = The nature of the electronic interactions of the stacked nucleic-acid
       bases (adenine, thymine, cytosine, and uracil) in homodimer and -trimer
       complexes in their electronically excited states was investigated and
       analysed in terms of orbital-overlap and Coulombic interactions. The
       mutual orientations of the adjacent bases were selected so as to
       correspond to the A-and B-DNA conformations. The extent of the
       electronic interaction is larger for the former conformation. It is
       shown that the orbital-overlap interactions at the distance of two bases
       relevant to the DNA structure do not contribute significantly to the
       overall electronic coupling. Only the states which are caused by the (pi
       -> pi*) transitions manifest an electronic coupling.,
    DOI = 10.1039/b806323k,
    ISSN = 1463-9076,
    Unique-ID = ISI:000259381000004,
    
  • [DOI] L. Biedermannova, K. E. Riley, K. Berka, P. Hobza, and J. Vondrasek, "Another role of proline: stabilization interactions in proteins and
    protein complexes concerning proline and tryptophane," PHYSICAL CHEMISTRY CHEMICAL PHYSICS, vol. 10, iss. 42, pp. 6350-6359, 2008.
    [Bibtex]
    @article ISI:000260485600002,
    Author = Biedermannova, Lada and Riley, Kevin E. and Berka, Karel and Hobza,
       Pavel and Vondrasek, Jiri,
    Title = Another role of proline: stabilization interactions in proteins and
       protein complexes concerning proline and tryptophane,
    Journal = PHYSICAL CHEMISTRY CHEMICAL PHYSICS,
    Year = 2008,
    Volume = 10,
    Number = 42,
    Pages = 6350-6359,
    Abstract = Proline-tryptophan complexes derived from experimental structures are
       investigated by quantum chemical procedures known to properly describe
       the London dispersion energy. We study two geometrical arrangements: the
       `'L-shaped'', stabilized by an H-bond, and the `'stacked-like'', where
       the two residues are in parallel orientation without any H-bond.
       Interestingly, the interaction energies in both cases are comparable and
       very large (similar to 7 kcal mol(-1)). The strength of stabilization in
       the stacked arrangement is rather surprising considering the fact that
       only one partner has an aromatic character. The interaction energy
       decomposition using the SAPT method further demonstrates the very
       important role of dispersion energy in such arrangement. To elucidate
       the structural features responsible for this unexpectedly large
       stabilization we examined the role of the nitrogen heteroatom and the
       importance of the cyclicity of the proline residue. We show that the
       electrostatic interaction due to the presence of the dipole, caused by
       the nitrogen heteroatom, contributes largely to the strength of the
       interaction. Nevertheless, the cyclic arrangement of proline, which
       allows for the largest amount of dispersive contact with the aromatic
       partner, also has a notable-effect. Geometry optimizations carried out
       for the `'stacked-like'' complexes show that the arrangements derived
       from protein structure are close to their gas phase optimum geometry,
       suggesting that the environment has only a minor effect on the geometry
       of the interaction. We conclude that the strength of proline
       non-covalent interactions, combined with this residue's rigidity, might
       be the explanation for its prominent role in protein stabilization and
       recognition processes.,
    DOI = 10.1039/b805087b,
    ISSN = 1463-9076,
    Unique-ID = ISI:000260485600002,
    
  • P. Hobza Jr., "The ``Parmenides'' and Plato's theory of ideas," FILOSOFICKY CASOPIS, vol. 56, iss. 1, pp. 45-64, 2008.
    [Bibtex]
    @article ISI:000256068800004,
    Author = Hobza, Jr., Pavel,
    Title = The ``Parmenides'' and Plato's theory of ideas,
    Journal = FILOSOFICKY CASOPIS,
    Year = 2008,
    Volume = 56,
    Number = 1,
    Pages = 45-64,
    Abstract = This study investigates Plato's so-called theory of ideas. The starting
       point of the investigation is an analysis of the first part of the
       Parmenides, where Parmenides presents a broad and thorough criticism of
       ideas. This analysis shows, firstly, that the usual rendering of the
       Greek terms eidos and idea as Idea (in a metaphysical or Platonic way)
       is misleading and that it is more appropriate to render these Greek
       terms using the phrases ``characteristic kind'' or ``generic
       nature''. In the course of a short excursion into the middle dialogues
       it is shown that Plato's ``theory of ideas'' - that is, Socrates'
       conception of independent Eide which Parmenides criticises in the
       dialogue of the same name - has two sources. (1) In the early dialogues
       the terms eidos and idea denoted the characteristic features common to a
       group of things - in particular, virtues. (2) In the middle dialogues
       ``ideas'' were conceived above all as objects of knowledge (cf. the
       doctrine of reminiscence), which accounts for the use of
       substantialising adjectives and for the qualifier ``in itself'' (cf.
       auto to kalon).,
    ISSN = 0015-1831,
    Unique-ID = ISI:000256068800004,
    

2007

  • [DOI] W. Wang, M. Pitonak, and P. Hobza, "C-H stretching vibrational shift of benzene dimer: Consistency of
    experiment and calculation," CHEMPHYSCHEM, vol. 8, iss. 14, pp. 2107-2111, 2007.
    [Bibtex]
    @article ISI:000250253500012,
    Author = Wang, Weizhou and Pitonak, Michal and Hobza, Pavel,
    Title = C-H stretching vibrational shift of benzene dimer: Consistency of
       experiment and calculation,
    Journal = CHEMPHYSCHEM,
    Year = 2007,
    Volume = 8,
    Number = 14,
    Pages = 2107-2111,
    Month = OCT 8,
    Abstract = Three low-energy structures of the benzene dimer are investigated by
       several theoretical procedures (RI-MP2, CCSD(T), RI-DFT-D, DFTIBBH\&H)
       covering London dispersion energy. The RI-DFT-D and CCSD(T) calculations
       are used to verify the DFTIBBH\&H dimer characteristics, as only at this
       level can anharmonic calculations be performed. It is ascertained that
       the T-shaped (C-2v) structure, in which the C-H stretching frequency of
       the proton donor shows a significant blue shift; is not stable at any
       level of theory. It is either a transition structure or a minimum which
       is easily transformed into a parallel-displaced structure or a T-shaped
       (C-s structure, even at low temperature. Consequently, no blue shift can
       be detected. On the other hand, the calculated anharmonic IR spectra of
       the two most stable structures of benzene dimer, namely, the T-shaped
       (C-s) and the parallel-displaced ones, give rise to a small red (and no
       blue) shift of the C-H stretching vibration. This finding is fully
       consistent with the experimental results.,
    DOI = 10.1002/cphc.200700415,
    ISSN = 1439-4235,
    Unique-ID = ISI:000250253500012,
    
  • [DOI] K. E. Riley and P. Hobza, "Assessment of the MP2 method, along with several basis sets, for the
    computation of interaction energies of biologically relevant hydrogen
    bonded and dispersion bound complexes," JOURNAL OF PHYSICAL CHEMISTRY A, vol. 111, iss. 33, pp. 8257-8263, 2007.
    [Bibtex]
    @article ISI:000248758800028,
    Author = Riley, Kevin E. and Hobza, Pavel,
    Title = Assessment of the MP2 method, along with several basis sets, for the
       computation of interaction energies of biologically relevant hydrogen
       bonded and dispersion bound complexes,
    Journal = JOURNAL OF PHYSICAL CHEMISTRY A,
    Year = 2007,
    Volume = 111,
    Number = 33,
    Pages = 8257-8263,
    Month = AUG 23,
    Abstract = In the past several years the MP2 method has been used extensively in
       studies of noncovalent interactions within biological systems such as
       proteins, DNA/RNA, and protein-ligand complexes. In this work we assess
       the performance that can be expected of this method, when paired with
       several different medium and extended basis sets, for the accurate
       computation of binding energies of hydrogen bonded and dispersion bound
       biologically derived complexes. It is found that, overall, the
       MP2/cc-pVTZ method produces the best, most well balanced, description of
       noncovalent interactions. Another interesting observation made in this
       study is that generally the MP2 technique, when paired with any basis
       set, does not yield reliable results for cyclic hydrogen bonds such as
       those found in nucleic acid base pairs.,
    DOI = 10.1021/jp073358r,
    ISSN = 1089-5639,
    Unique-ID = ISI:000248758800028,
    
  • [DOI] L. Bendova, P. Jurecka, P. Hobza, and J. Vondrasek, "Model of peptide bond-aromatic ring interaction: Correlated ab initio
    quantum chemical study," JOURNAL OF PHYSICAL CHEMISTRY B, vol. 111, iss. 33, pp. 9975-9979, 2007.
    [Bibtex]
    @article ISI:000248759000037,
    Author = Bendova, Lada and Jurecka, Petr and Hobza, Pavel and Vondrasek, Jiri,
    Title = Model of peptide bond-aromatic ring interaction: Correlated ab initio
       quantum chemical study,
    Journal = JOURNAL OF PHYSICAL CHEMISTRY B,
    Year = 2007,
    Volume = 111,
    Number = 33,
    Pages = 9975-9979,
    Month = AUG 23,
    Abstract = Aromatic ring-peptide bond interactions (modeled as benzene and
       formamide, N-methylformamide and N-methylacetamide) are studied by means
       of advanced computational chemistry methods: second-order Moller-Plesset
       (MP2), coupled-cluster single and double excitation model [CCSD(T)],
       and density functional theory with dispersion (DFT-D). The geometrical
       preferences of these interactions as well as their interaction energy
       content, in both parallel and T-shaped arrangements, are investigated.
       The stabilization energy reaches a value of over 5 kcal/mol for the
       N-methylformamide-benzene complex at the CCSD(T)/complete basis set
       (CBS) level. Decomposition of interaction energy by the
       DFT-symmetry-adapted perturbation treatment (SAPT) technique shows that
       the parallel and T-shaped arrangements, although similar in their total
       interaction energies, differ significantly in the proportion of
       electrostatic and dispersion terms.,
    DOI = 10.1021/jp072859+,
    ISSN = 1520-6106,
    Unique-ID = ISI:000248759000037,
    
  • [DOI] R. Sedlak, P. Jurecka, and P. Hobza, "Density functional theory-symmetry adapted perturbation treatment energy
    decomposition of nucleic acid base pairs taken from DNA crystal geometry," JOURNAL OF CHEMICAL PHYSICS, vol. 127, iss. 7, 2007.
    [Bibtex]
    @article ISI:000248905300036,
    Author = Sedlak, Robert and Jurecka, Petr and Hobza, Pavel,
    Title = Density functional theory-symmetry adapted perturbation treatment energy
       decomposition of nucleic acid base pairs taken from DNA crystal geometry,
    Journal = JOURNAL OF CHEMICAL PHYSICS,
    Year = 2007,
    Volume = 127,
    Number = 7,
    Month = AUG 21,
    DOI = 10.1063/1.2759207,
    Article-Number = 075104,
    ISSN = 0021-9606,
    Unique-ID = ISI:000248905300036,
    
  • [DOI] A. Abo-Riziq, B. O. Crews, I. Compagnon, J. Oomens, G. Meijer, G. Von Helden, M. Kabelac, P. Hobza, and M. S. de Vries, "The Mid-IR spectra of 9-ethyl guanine, guanosine, and 2-Deoxyguanosine," JOURNAL OF PHYSICAL CHEMISTRY A, vol. 111, iss. 31, pp. 7529-7536, 2007.
    [Bibtex]
    @article ISI:000248478700033,
    Author = Abo-Riziq, Ali and Crews, Bridgit O. and Compagnon, Isabelle and Oomens,
       Jos and Meijer, Gerard and Von Helden, Gert and Kabelac, Martin and
       Hobza, Pavel and de Vries, Mattanjah S.,
    Title = The Mid-IR spectra of 9-ethyl guanine, guanosine, and 2-Deoxyguanosine,
    Journal = JOURNAL OF PHYSICAL CHEMISTRY A,
    Year = 2007,
    Volume = 111,
    Number = 31,
    Pages = 7529-7536,
    Month = AUG 9,
    Abstract = We present the mid-IR (400-1800 cm(-1)) spectra of 9-ethyl guanine,
       guanosine, and 2-deoxyguanosine measured by IR-UV double-resonance
       spectroscopy. We compare the recorded mid-IR spectra with the spectra of
       the most stable structures obtained from RI-MP2 and RI-DFT-D
       calculations. The results confirm the enol form for all structures and
       demonstrate the efficacy of a new approach to DFT calculations that
       includes dispersion interactions.,
    DOI = 10.1021/jp072183i,
    ISSN = 1089-5639,
    Unique-ID = ISI:000248478700033,
    
  • [DOI] T. Kubar, P. Jurecka, J. Cerny, J. Rezac, M. Otyepka, H. Valdes, and P. Hobza, "Density-functional, density-functional tight-binding, and wave function
    calculations on biomolecular systems," JOURNAL OF PHYSICAL CHEMISTRY A, vol. 111, iss. 26, pp. 5642-5647, 2007.
    [Bibtex]
    @article ISI:000247573600007,
    Author = Kubar, Tomas and Jurecka, Petr and Cerny, Jiri and Rezac, Jan and
       Otyepka, Michal and Valdes, Haydee and Hobza, Pavel,
    Title = Density-functional, density-functional tight-binding, and wave function
       calculations on biomolecular systems,
    Journal = JOURNAL OF PHYSICAL CHEMISTRY A,
    Year = 2007,
    Volume = 111,
    Number = 26,
    Pages = 5642-5647,
    Month = JUL 5,
    Note = 232nd National Meeting of the American-Chemical-Society, San Francisco,
       CA, SEP 10-14, 2006,
    Organization = Amer Chem Soc,
    Abstract = Recently, two computational approaches that supply a
       density-functional-based quantum-chemical method with an empirical term
       accounting for London dispersion were introduced and found use in the
       studies of biomolecular systems, namely, DFT-D and SCC-DFTB-D. Here, we
       examine the performance and usability of these combined techniques for
       dealing with several tasks typically occurring in the research of
       biomolecules. The interaction energy of small biomolecular complexes
       agrees very well with the reference data yielded by correlated ab initio
       quantum chemical methods. In real-life studies aimed at interaction
       energy, structure, and infrared spectra, the mentioned methods provide
       results in good agreement with each other and with experiment (where
       available). The very favorable time demands of these approaches are
       discussed, and for each of them, a suitable area of use is proposed on
       the basis of the results of our analysis.,
    DOI = 10.1021/jp068858j,
    ISSN = 1089-5639,
    Unique-ID = ISI:000247573600007,
    
  • [DOI] M. Kolar and P. Hobza, "Accurate theoretical determination of the structure of aromatic
    complexes is complicated: The phenol dimer and Phenol center dot center
    dot center dot Methanol cases," JOURNAL OF PHYSICAL CHEMISTRY A, vol. 111, iss. 26, pp. 5851-5854, 2007.
    [Bibtex]
    @article ISI:000247573600034,
    Author = Kolar, Michal and Hobza, Pavel,
    Title = Accurate theoretical determination of the structure of aromatic
       complexes is complicated: The phenol dimer and Phenol center dot center
       dot center dot Methanol cases,
    Journal = JOURNAL OF PHYSICAL CHEMISTRY A,
    Year = 2007,
    Volume = 111,
    Number = 26,
    Pages = 5851-5854,
    Month = JUL 5,
    Abstract = The structure of the phenol dimer and phenol center dot center dot
       center dot methanol complexes was determined by gradient optimization
       using the Hartree-Fock (HF), MP2, DFT, and RI-DFT-D methods with various
       basis sets. Theoretical rotational constants were compared with
       experimental values and the following conclusions were made: (1) HF and
       DFT methods fail to predict cluster geometries; (2) MP2 with a medium
       basis set yields reliable cluster geometries but only because of a
       compensation for errors; (3) when the AO basis set is enlarged, the
       geometry becomes incorrect, and the theoretical geometry becomes
       reliable only when the higher correlation energy contributions (CCSD(T))
       are included; and (4) the RI-DFT-D procedure covering the dispersion
       energy provides excellent geometries.,
    DOI = 10.1021/jp071486+,
    ISSN = 1089-5639,
    Unique-ID = ISI:000247573600034,
    
  • [DOI] K. Pluhackova and P. Hobza, "On the nature of the surprisingly small (red) shift in the halothane
    ...acetone complex," CHEMPHYSCHEM, vol. 8, iss. 9, pp. 1352-1356, 2007.
    [Bibtex]
    @article ISI:000247811200014,
    Author = Pluhackova, Kristyna and Hobza, Pavel,
    Title = On the nature of the surprisingly small (red) shift in the halothane
       ...acetone complex,
    Journal = CHEMPHYSCHEM,
    Year = 2007,
    Volume = 8,
    Number = 9,
    Pages = 1352-1356,
    Month = JUN 25,
    Abstract = The halothone center dot center dot center dot acetone and fluoroform
       center dot center dot center dot acetone complexes are studied using the
       second-order Moller-Plesset (MP2) method with a cc-pVTZ basis set and
       the density functional theory (DFT) method with a TZVP basis set.
       Whereas halothone exhibits a small red shift upon complexation,
       fluoroform shows a pronounced blue shift. To explain this difference in
       behavior, we perform symmetry-adopted perturbation theory (SAPT) and
       natural bond orbital (NBO) analyses. Although the composition of the
       total stabilization energy of each complex is different, that alone does
       not provide a satisfactory explanation for the difference in the
       spectral shifts. This difference is interpreted as a result of the
       interplay of the hyperconjugation and rehybridization mechanisms. The
       small and surprising red shift of the C-H stretching frequency of
       halothane, which resulted from the complexation of this species with
       acetone,is explained by the compensation of the two above-mentioned
       mechanisms. On the other hand, the fluoroform center dot center dot
       center dot. acetone complex exhibits a blue shift of the C-H stretching
       frequency upon complexation, the most likely reason for this shift being
       a concerted occurrence of the hyperconjugation and rehybridization
       mechanisms. The calculated shift of the C-H stretching vibration
       frequencies of halothane (+27cm(-1)) agree with the experimental value
       of + 5 cm(-1).,
    DOI = 10.1002/cphc.200700153,
    ISSN = 1439-4235,
    Unique-ID = ISI:000247811200014,
    
  • [DOI] E. Muchova, P. Slavicek, A. L. Sobolewski, and P. Hobza, "Glycine in an electronically excited state: Ab initio electronic
    structure and dynamical calculations," JOURNAL OF PHYSICAL CHEMISTRY A, vol. 111, iss. 24, pp. 5259-5269, 2007.
    [Bibtex]
    @article ISI:000247216600018,
    Author = Muchova, Eva and Slavicek, Petr and Sobolewski, Andrzej L. and Hobza,
       Pavel,
    Title = Glycine in an electronically excited state: Ab initio electronic
       structure and dynamical calculations,
    Journal = JOURNAL OF PHYSICAL CHEMISTRY A,
    Year = 2007,
    Volume = 111,
    Number = 24,
    Pages = 5259-5269,
    Month = JUN 21,
    Abstract = The goal of this study is to explore the photochemical processes
       following optical excitation of the glycine molecule into its two
       low-lying excited states. We employed electronic structure methods at
       various levels to map the PES of the ground state and the two low-lying
       excited states of glycine. It follows from our calculations that the
       photochemistry of glycine can be regarded as a combination of
       photochemical behavior of amines and carboxylic acid. The first channel
       (connected to the presence of amino group) results in ultrafast decay,
       while the channels characteristic for the carboxylic group occur on a
       longer time scale. Dynamical calculations provided the branching ratio
       for these channels. We also addressed the question whether
       conformationally dependent photochemistry can be observed for glycine.
       While electronic structure calculations favor this possibility, the ab
       initio multiple spawning (AIMS) calculations showed only minor relevance
       of the reaction path resulting in conformationally dependent dynamics.,
    DOI = 10.1021/jp071483x,
    ISSN = 1089-5639,
    Unique-ID = ISI:000247216600018,
    
  • [DOI] E. C. Lee, D. Kim, P. Jurecka, P. Tarakeshwar, P. Hobza, and K. S. Kim, "Understanding of assembly phenomena by aromatic-aromatic interactions:
    Benzene dimer and the substituted systems," JOURNAL OF PHYSICAL CHEMISTRY A, vol. 111, iss. 18, pp. 3446-3457, 2007.
    [Bibtex]
    @article ISI:000246189700003,
    Author = Lee, Eun Cheol and Kim, Dongwook and Jurecka, Petr and Tarakeshwar, P.
       and Hobza, Pavel and Kim, Kwang S.,
    Title = Understanding of assembly phenomena by aromatic-aromatic interactions:
       Benzene dimer and the substituted systems,
    Journal = JOURNAL OF PHYSICAL CHEMISTRY A,
    Year = 2007,
    Volume = 111,
    Number = 18,
    Pages = 3446-3457,
    Month = MAY 10,
    Abstract = Interactions involving aromatic rings are important in
       molecular/biomolecular assembly and engineering. As a consequence, there
       have been a number of investigations on dimers involving benzene or
       other substituted pi systems. In this Feature Article, we examine the
       relevance of the magnitudes of their attractive and repulsive
       interaction energy components in governing the geometries of several
       pi-pi systems. The geometries and the associated binding energies were
       evaluated at the complete basis set (CBS) limit of coupled cluster
       theory with singles, doubles, and perturbative triples excitations
       [CCSD(T)] using a least biased scheme for the given data set. The
       results for the benzene dimer indicate that the floppy T-shaped
       structure (center-to-center distance: 4.96 angstrom, with an axial
       benzene off-centered above the facial benzene) is isoenergetic in
       zero-point-energy (ZPE) corrected binding energy (D-0) to the
       displaced-stacked structure (vertical interplanar distance: 3.54
       angstrom). However, the T-shaped structure is likely to be slightly more
       stable (D-0 approximate to 2.4-2.5 kcal/mol) if quadruple excitations
       are included in the coupled cluster calculations. The presence of
       substituents on the aromatic ring, irrespective of their electron
       withdrawing or donating nature, leads to an increase in the binding
       energy, and the displaced-stacked conformations are more stabilized than
       the T-shaped conformers. This explains the wide prevalence of displaced
       stacked structures in organic crystals. Despite that the dispersion
       energy is dominating, the substituent as well as the conformational
       effects are correlated to the electrostatic interaction. This
       electrostatic origin implies that the substituent effect would be
       reduced in polar solution, but important in apolar media, in particular,
       for assembling processes.,
    DOI = 10.1021/jp068635t,
    ISSN = 1089-5639,
    Unique-ID = ISI:000246189700003,
    
  • [DOI] M. Vrabel, M. Hocek, L. Havran, M. Fojta, I. Votruba, B. Klepetarova, R. Pohl, L. Rulisek, L. Zendlova, P. Hobza, I. Shih, E. Mabery, and R. Mackman, "Purines bearing phenanthroline or bipyridine ligands and their Ru-II
    complexes in position 8 as model compounds for electrochemical DNA
    labeling - Synthesis, crystal structure, electrochemistry, quantum
    chemical calculations, cytostatic and antiviral activity," EUROPEAN JOURNAL OF INORGANIC CHEMISTRY, iss. 12, pp. 1752-1769, 2007.
    [Bibtex]
    @article ISI:000246404900016,
    Author = Vrabel, Milan and Hocek, Michal and Havran, Ludek and Fojta, Miroslav
       and Votruba, Ivan and Klepetarova, Blanka and Pohl, Radek and Rulisek,
       Lubomir and Zendlova, Lucie and Hobza, Pavel and Shih, I-hung and
       Mabery, Eric and Mackman, Richard,
    Title = Purines bearing phenanthroline or bipyridine ligands and their Ru-II
       complexes in position 8 as model compounds for electrochemical DNA
       labeling - Synthesis, crystal structure, electrochemistry, quantum
       chemical calculations, cytostatic and antiviral activity,
    Journal = EUROPEAN JOURNAL OF INORGANIC CHEMISTRY,
    Year = 2007,
    Number = 12,
    Pages = 1752-1769,
    Month = APR,
    Abstract = A series of ethynyl- or (4-boronophenyl)bipyridines and -phenanthrolines
       were prepared as versatile building blocks for attachment of bidentate
       N-ligands to other molecules via cross-coupling reactions. Their
       complexation with Ru(bpy)(2)-Cl-2 gave the corresponding Ru-II
       complexes. 9-Benzyladenine derivatives bearing the bipyridine or
       phenanthroline complexes in position 8, attached via a conjugate
       acetylene or phenylene linker were prepared by cross-coupling reactions
       of the ethynyl- or 4-boronophenylbipyridines and -phenanthrolines with
       9-benzyl-8-bromoadenine. Their complexation with Ru(bpy)(2)Cl-2 afforded
       the corresponding Ru complexes as model compounds for electrochemical
       DNA labeling. The same compounds were also prepared directly by
       cross-coupling of 9-benzyl-8-bromoadenine with Ru complexes of the
       alkynes and boronic acids. Both approaches are compared in terms of
       potential applications for labeling of nucleic acids. The crystal
       structures of two Ru complexes were determined by X-ray diffraction. The
       electrochemistry of the model purities bearing the phenanthroline or
       bipyridine ligands and the Ru complexes was studied by means of cyclic
       or square-wave voltammetry with carbon paste and mercury electrodes. The
       experimental redox potentials of the title compounds were compared with
       quantum chemical calculations. A very good agreement between experiment
       and theory was obtained, with a standard deviation of 0.13 V. It was
       shown that theoretical calculations can be of a limited predictive power
       for new Run complexes, though it was difficult to reproduce differences
       smaller than 0.05 V Several compounds of this series exhibited a
       considerable cytostatic effect and activity against the hepatitis C
       virus (HCV). (C Wiley-VCH Verlag GmbH \& Co. KGaA, 69451 Weinheim,
       Germany, 2007).,
    DOI = 10.1002/ejic.200700030,
    ISSN = 1434-1948,
    Unique-ID = ISI:000246404900016,
    
  • [DOI] L. Zendlova, P. Hobza, and M. Kabelac, "Stability of nucleic acid base pairs in organic solvents: Molecular
    dynamics, molecular dynamics/quenching, and correlated ab initio study," JOURNAL OF PHYSICAL CHEMISTRY B, vol. 111, iss. 10, pp. 2591-2609, 2007.
    [Bibtex]
    @article ISI:000244735300027,
    Author = Zendlova, Lucie and Hobza, Pavel and Kabelac, Martin,
    Title = Stability of nucleic acid base pairs in organic solvents: Molecular
       dynamics, molecular dynamics/quenching, and correlated ab initio study,
    Journal = JOURNAL OF PHYSICAL CHEMISTRY B,
    Year = 2007,
    Volume = 111,
    Number = 10,
    Pages = 2591-2609,
    Month = MAR 15,
    Abstract = The dynamic structure and potential energy surface of adenine center dot
       center dot center dot thymine and guanine center dot center dot center
       dot cytosine base pairs and their methylated analogues interacting with
       a small number (from 1 to 16 molecules) of organic solvents (methanol,
       dimethylsulfoxide, and chloroform) were investigated by various
       theoretical approaches starting from simple empirical methods employing
       the Cornell et al. force field to highly accurate ab initio quantum
       chemical calculations (MP2 and particularly CCSD(T) methods). After the
       simple molecular dynamics simulation, the molecular dynamics in
       combination with quenching technique was also used. The molecular
       dynamics simulations presented here have confirmed previous experimental
       and theoretical results from the bulk solvents showing that, whereas in
       chloroform the base pairs create hydrogen-bonded structures, in
       methanol, stacked structures are preferred. While methanol (like water)
       can stabilize the stacked structures of the base pairs by a higher
       number of hydrogen bonds than is possible in hydrogen-bonded pairs, the
       chloroform molecule lacks such a property, and the hydrogen-bonded
       structures are preferred in this solvent. The large volume of the
       dimethylsulfoxide molecule is an obstacle for the creation of very
       stable hydrogen-bonded and stacked systems, and a preference for
       T-shaped structures, especially for complexes of methylated adenine
       center dot center dot center dot thymine base pairs, was observed. These
       results provide clear evidence that the preference of either the stacked
       or the hydrogen-bonded structures of the base pairs in the solvent is
       not determined only by bulk properties or the solvent polarity but
       rather by specific interactions of the base pair with a small number of
       the solvent molecules. These conclusions obtained at the empirical level
       were verified also by high-level ab initio correlated calculations.,
    DOI = 10.1021/jp065418j,
    ISSN = 1520-6106,
    Unique-ID = ISI:000244735300027,
    
  • [DOI] J. Cerny, P. Jurecka, P. Hobza, and H. Valdes, "Resolution of identity density functional theory augmented with an
    empirical dispersion term (RI-DFT-D): A promising tool for studying
    isolated small peptides," JOURNAL OF PHYSICAL CHEMISTRY A, vol. 111, iss. 6, pp. 1146-1154, 2007.
    [Bibtex]
    @article ISI:000244039600022,
    Author = Cerny, Jiri and Jurecka, Petr and Hobza, Pavel and Valdes, Haydee,
    Title = Resolution of identity density functional theory augmented with an
       empirical dispersion term (RI-DFT-D): A promising tool for studying
       isolated small peptides,
    Journal = JOURNAL OF PHYSICAL CHEMISTRY A,
    Year = 2007,
    Volume = 111,
    Number = 6,
    Pages = 1146-1154,
    Month = FEB 15,
    Abstract = Resolution of identity standard density functional theory augmented with
       a damped empirical dispersion term (RI-DFT-D) calculations have been
       carried out on a set of lowest energy minima of tryptophyl-glycine
       (Trp-Gly) and tryptophyl-glycyl-glycine (Trp-Gly-Gly) peptides. RI-DFT-D
       (TPSS/TZVP) results are in excellent agreement with benchmark data based
       on the CCSD(T) method. Experimental spectra could be assigned according
       to the calculated IR frequencies. Central processing unit (CPU) time
       requirements are only slightly higher than those needed for the DFT
       calculations. Consequently, RI-DFT-D theory seems to be a promising
       methodology for studying oligopeptides with accuracy comparable to ab
       initio quantum chemical calculations.,
    DOI = 10.1021/jp066504m,
    ISSN = 1089-5639,
    Unique-ID = ISI:000244039600022,
    
  • [DOI] P. Jurecka, J. Cerny, P. Hobza, and D. R. Salahub, "Density functional theory augmented with an empirical dispersion term.
    Interaction energies and geometries of 80 noncovalent complexes compared
    with ab initio quantum mechanics calculations," JOURNAL OF COMPUTATIONAL CHEMISTRY, vol. 28, iss. 2, pp. 555-569, 2007.
    [Bibtex]
    @article ISI:000243238700011,
    Author = Jurecka, Petr and Cerny, Jiri and Hobza, Pavel and Salahub, Dennis R.,
    Title = Density functional theory augmented with an empirical dispersion term.
       Interaction energies and geometries of 80 noncovalent complexes compared
       with ab initio quantum mechanics calculations,
    Journal = JOURNAL OF COMPUTATIONAL CHEMISTRY,
    Year = 2007,
    Volume = 28,
    Number = 2,
    Pages = 555-569,
    Month = JAN 30,
    Abstract = Standard density functional theory (DFT) is augmented with a damped
       empirical dispersion term. The damping function is optimized on a small,
       well balanced set of 22 van der Waals (vdW) complexes and verified on a
       validation set of 58 vdW complexes. Both sets contain biologically
       relevant molecules such as nucleic acid bases. Results are in remarkable
       agreement with reference high-level wave function data based on the
       CCSD(T) method. The geometries obtained by full gradient optimization
       are in very good agreement with the best available theoretical
       reference. In terms of the standard deviation and average errors,
       results including the empirical dispersion term are clearly superior to
       all pure density functionals investigated-B-LYP, B3-LYP, PBE, TPSS,
       TPSSh, and BH-LYP- and even surpass the MP2/cc-pVTZ method. The
       combination of empirical dispersion with the TPSS functional performs
       remarkably well. The most critical part of the empirical dispersion
       approach is the damping function. The damping parameters should be
       optimized for each density functional/basis set combination separately.
       To keep the method simple, we optimized mainly a single factor, s(R),
       scaling globally the vdW radii. For good results, a basis set of at
       least triple-zeta quality is required and diffuse functions are
       recommended, since the basis set superposition error seriously
       deteriorates the results. On average, the dispersion contribution to the
       interaction energy missing in the DFT functionals examined here is about
       15 and 100\% for the hydrogen-bonded and stacked complexes considered,
       respectively. (C) 2006 Wiley Periodicals. Inc.,
    DOI = 10.1002/jcc.20570,
    ISSN = 0192-8651,
    Unique-ID = ISI:000243238700011,
    
  • [DOI] J. Rejnek and P. Hobza, "Hydrogen-bonded nucleic acid base pairs containing unusual base
    tautomers: Complete basis set calculations at the MP2 and CCSD(T) levels," JOURNAL OF PHYSICAL CHEMISTRY B, vol. 111, iss. 3, pp. 641-645, 2007.
    [Bibtex]
    @article ISI:000243535900020,
    Author = Rejnek, Jaroslav and Hobza, Pavel,
    Title = Hydrogen-bonded nucleic acid base pairs containing unusual base
       tautomers: Complete basis set calculations at the MP2 and CCSD(T) levels,
    Journal = JOURNAL OF PHYSICAL CHEMISTRY B,
    Year = 2007,
    Volume = 111,
    Number = 3,
    Pages = 641-645,
    Month = JAN 25,
    Abstract = The total interaction energies of altogether 15 hydrogen-bonded nucleic
       acid base pairs containing unusual base tautomers were calculated. The
       geometry properties of all selected adenine-thymine and guanine-cytosine
       hydrogen-bonded base pairs enable their incorporation into DNA. Unusual
       base pairing patterns were compared with Watson-Crick H-bonded
       structures of the adenine-thymine and guanine-cytosine pairs. The
       complete basis set (CBS) limit of the MP2 interaction energy and the
       CCSD(T) correction term, determined as the difference between the
       CCSD(T) and MP2 interaction energies, was evaluated. Extrapolation to
       the MP2 CBS limit was done using the aug-cc-pVDZ and aug-cc-pVTZ
       results, and the CCSD(T) correction term was determined with the
       6-31G*(0.25) basis set. Final interaction energies were corrected
       while taking into account both tautomeric penalization determined at the
       CBS level and solvation/desolvation free energies. The situation for the
       adenine-thymine pairs is straightforward, and tautomeric pairs are
       significantly less stable than the Watson-Crick pair consisting of the
       canonical forms. In the case of the guanine-cytosine pair, the
       Watson-Crick structure made by canonical forms is again the most stable.
       The other two structures are, however, energetically rather similar (by
       5 and 6 kcal/mol), which provides a very small but non-negligible chance
       of detecting these structures in the DNA double helix (1:5000). Due to
       the fact that DNA bases and base pairs incorporated into DNA are
       solvated less favorably than in isolated systems, this probability
       represents the very upper limit. The results clearly show how precisely
       the canonical building blocks of DNA molecules were chosen and how well
       their stability is maintained.,
    DOI = 10.1021/jp0661692,
    ISSN = 1520-6106,
    Unique-ID = ISI:000243535900020,
    
  • [DOI] H. Szatylowicz, T. M. Krygowski, and P. Hobza, "How the shape of the NH2 group depends on the substituent effect and
    H-bond formation in derivatives of aniline," JOURNAL OF PHYSICAL CHEMISTRY A, vol. 111, iss. 1, pp. 170-175, 2007.
    [Bibtex]
    @article ISI:000243229000022,
    Author = Szatylowicz, Halina and Krygowski, Tadeusz M. and Hobza, Pavel,
    Title = How the shape of the NH2 group depends on the substituent effect and
       H-bond formation in derivatives of aniline,
    Journal = JOURNAL OF PHYSICAL CHEMISTRY A,
    Year = 2007,
    Volume = 111,
    Number = 1,
    Pages = 170-175,
    Month = JAN 11,
    Abstract = The geometry and electronic structure of the amino group in aniline and
       its derivatives are very sensitive to both intramolecular interactions
       such as substituent effects and intermolecular ones such as H-bonding.
       An analysis of experimental geometries retrieved from the CSD base and
       computational modeling of aniline and its derivatives and their H-bonded
       complexes by use of B3LYP/6-311+G** and MP2/aug-cc-pVDZ showed that
       the degree of pyramidalization of the amino group depends on H-bonding,
       which exists in two forms, (i) NH center dot center dot center dot B
       (base) and (ii) N center dot center dot center dot HB (Bronsted acid),
       both of which affect the shape of the NH2 group. The effect may be
       significantly enhanced by a substituent through resonance interaction
       from electron-attracting substituents. The NH center dot center dot
       center dot B interactions lead to a substantial planarization of the
       group, whereas N center dot center dot center dot HB interactions do
       not. The natural bond orbital analysis allowed the authors to show that
       the changes in occupancy of the ``lone pair'' orbital and in geometry
       parameters describing pyramidalization of the group depend on the
       substituent constants.,
    DOI = 10.1021/jp065336v,
    ISSN = 1089-5639,
    Unique-ID = ISI:000243229000022,
    
  • [DOI] R. L. T. Parreira, S. E. Galembeck, and P. Hobza, "On the origin of red and blue shifts of X-H and C-H stretching
    vibrations in formic acid (formate ion) and proton donor complexes," CHEMPHYSCHEM, vol. 8, iss. 1, pp. 87-92, 2007.
    [Bibtex]
    @article ISI:000243502800014,
    Author = Parreira, Renato Luis Tame and Galembeck, Sergio Emanuel and Hobza,
       Paevel,
    Title = On the origin of red and blue shifts of X-H and C-H stretching
       vibrations in formic acid (formate ion) and proton donor complexes,
    Journal = CHEMPHYSCHEM,
    Year = 2007,
    Volume = 8,
    Number = 1,
    Pages = 87-92,
    Month = JAN 8,
    Abstract = Complexes between formic acid formate anion and various proton donors
       (HF, H2O, NH3, and CH4) are studied by the MP2 and B3LYP methods with
       the 6-311 + + G(3df,3pd) basis set. Formation of a complex is
       characterized by electron-density transfer from electron donor to
       ligands. This transfer is much larger with the formate anion, for which
       it exceeds 0.1e. Electron-density transfer from electron lone pairs of
       the electron donor is directed into sigma* antibonding orbitals of X-H
       bonds of the electron acceptor and leads to elongation of the bond and a
       red shift of the X-H stretching frequency (standard H-bonding). However,
       pronounced electron-density transfer from electron lone pairs of the
       electron donor also leads to reorganization of the electron density in
       the electron donor, which results in changes in geometry and vibrational
       frequency. These changes are largest for the C-H bonds of formic acid
       and formate anion, which do not participate in H-bonding. The resulting
       blue shift of this stretching frequency is substantial and amounts to
       almost 35 and 170 cm(-1), respectively.,
    DOI = 10.1002/cphc.200600435,
    ISSN = 1439-4235,
    Unique-ID = ISI:000243502800014,
    
  • P. Hobza, "Calculations of the stabilization energies of the building blocks of
    biomacromolecules," in COMPUTATIONAL METHODS IN SCIENCE AND ENGINEERING VOL 1: THEORY AND
    COMPUTATION: OLD PROBLEMS AND NEW CHALLENGES
    , 2007, pp. 416-424.
    [Bibtex]
    @inproceedings ISI:000252146200033,
    Author = Hobza, Pavel,
    Editor = Maroulis, G and Simos, TE,
    Title = Calculations of the stabilization energies of the building blocks of
       biomacromolecules,
    Booktitle = COMPUTATIONAL METHODS IN SCIENCE AND ENGINEERING VOL 1: THEORY AND
       COMPUTATION: OLD PROBLEMS AND NEW CHALLENGES,
    Series = AIP CONFERENCE PROCEEDINGS,
    Year = 2007,
    Volume = 963,
    Pages = 416-424,
    Note = International Conference on Computational Methods in Science and
       Engineering, Corfu, GREECE, SEP 25-30, 2007,
    Organization = European Soc Computat Methods Sci \& Engn; Minist Natl Educ \& Religious
       Affairs; E4 Comp Engn,
    Abstract = Non-covalent interactions play an important role in chemistry, physics
       and especially in biodisciplines. They determine structure of
       biomacromolecules like DNA and proteins and are responsible for
       molecular recognition process. Theoretical evaluation of interaction
       energies is difficult and perturbation as well as variation
       (supermolecular) methods are briefly described. Accurate interaction
       energies are obtained by complete basis set limit calculations providing
       large portion of correlation energy is covered (e.g. by performing the
       CCSD(T) calculations). A role of H-bonding and stacking interactions in
       stabilization of DNA and proteins is described and an importance of
       London dispersion energy is pointed out.,
    ISSN = 0094-243X,
    ISBN = 978-0-7354-0477-9,
    Unique-ID = ISI:000252146200033,
    
  • [DOI] H. Ritze, P. Hobza, and D. Nachtigallova, "Electronic coupling in the excited electronic state of stacked DNA base
    homodimers," PHYSICAL CHEMISTRY CHEMICAL PHYSICS, vol. 9, iss. 14, pp. 1672-1675, 2007.
    [Bibtex]
    @article ISI:000245304500003,
    Author = Ritze, Hans-Hermann and Hobza, Pavel and Nachtigallova, Dana,
    Title = Electronic coupling in the excited electronic state of stacked DNA base
       homodimers,
    Journal = PHYSICAL CHEMISTRY CHEMICAL PHYSICS,
    Year = 2007,
    Volume = 9,
    Number = 14,
    Pages = 1672-1675,
    Abstract = The nature of the electronic coupling of stacked nucleic acid bases
       adenine (A), thymine (T), and cytosine (C), in A - A, T - T, and C - C
       complexes in their excited states was investigated; a different
       character of the electronic coupling for the T - T complex was shown.,
    DOI = 10.1039/b618382d,
    ISSN = 1463-9076,
    Unique-ID = ISI:000245304500003,
    
  • [DOI] J. Fanfrlik, D. Hnyk, M. Lepsik, and P. Hobza, "Interaction of heteroboranes with biomolecules - Part 2. The effect of
    various metal vertices and exo-substitutions," PHYSICAL CHEMISTRY CHEMICAL PHYSICS, vol. 9, iss. 17, pp. 2085-2093, 2007.
    [Bibtex]
    @article ISI:000246027500006,
    Author = Fanfrlik, Jindrich and Hnyk, Drahomir and Lepsik, Martin and Hobza,
       Pavel,
    Title = Interaction of heteroboranes with biomolecules - Part 2. The effect of
       various metal vertices and exo-substitutions,
    Journal = PHYSICAL CHEMISTRY CHEMICAL PHYSICS,
    Year = 2007,
    Volume = 9,
    Number = 17,
    Pages = 2085-2093,
    Abstract = Icosahedral heteroboranes and especially metallacarboranes, which have
       recently been shown to act as potent HIV-1 protease inhibitors, are a
       unique class of chemical compounds with unusual properties, one of which
       is the formation of dihydrogen bonds with biomolecules. In this study,
       we investigate the effect of various metal vertices and
       exo-substitutions on several series of heteroboranes, including
       11-vertex carborane cages [nido-7,8-C2B9Hn](n-13) (n = 11,12,13),
       closo-1-SB11H11, closo-1-NB11H12, metal bis(dicarbollides) [3,3'-M
       (1,2-C2B9H11)(2)](n) (M/n = Fe/2-, Co/1-, Ni/0) and fluoro (F), amino
       (NH2) and hydroxo (OH) derivatives of the metal bis( dicarbollides).
       Besides the properties of isolated systems (geometries, electronic
       properties and hydration), we study their interactions with a
       tetrapeptide, which models their biomolecular partner. Calculations have
       confirmed that the extra hydrogen in [nido-7,8-C2B9H12](-) forms a
       bridge, which fluctuates between two stationary states. Using
       RESP-derived charges, it was ascertained that the negative charge of
       heteroboranes is located mainly on boron-bound hydrogens. An increase of
       the negative total charge ( from 0 to - 1 or - 2) of heteroboranes
       yields an increase in the stabilisation energies of heteroborane center
       dot center dot center dot peptide complexes and also a substantial
       increase in the hydration free energies of heteroboranes. Compared to
       the substitutions of metal vertices, the exo-substitutions of
       metallacarboranes cause a larger increase in stabilisation energies and
       a smaller increase in desolvation penalties. These two terms,
       stabilisation energies and desolvation penalties, contribute in opposite
       directions to the total heteroborane - biomolecule binding energy and
       must both be taken into account when designing new HIV-1 protease
       inhibitors.,
    DOI = 10.1039/b617776j,
    ISSN = 1463-9076,
    Unique-ID = ISI:000246027500006,
    
  • [DOI] M. Kabelac, H. Valdes, E. C. Sherer, C. J. Cramer, and P. Hobza, "Benchmark RI-MP2 database of nucleic acid base trimers: performance of
    different density functional models for prediction of structures and
    binding energies," PHYSICAL CHEMISTRY CHEMICAL PHYSICS, vol. 9, iss. 36, pp. 5000-5008, 2007.
    [Bibtex]
    @article ISI:000249432000006,
    Author = Kabelac, Martin and Valdes, Haydee and Sherer, Edward C. and Cramer,
       Christopher J. and Hobza, Pavel,
    Title = Benchmark RI-MP2 database of nucleic acid base trimers: performance of
       different density functional models for prediction of structures and
       binding energies,
    Journal = PHYSICAL CHEMISTRY CHEMICAL PHYSICS,
    Year = 2007,
    Volume = 9,
    Number = 36,
    Pages = 5000-5008,
    Abstract = A new database of nucleic acid base trimers has been developed that
       includes 141 geometries and stabilization energies obtained at the
       RI-MP2 level of theory with the TZVPP basis set. Compared to previously
       compiled biologically oriented databases, this new construct includes
       considerably more complicated structures; the various intermolecular
       interactions in the trimers are quite heterogeneous and in particular
       include simultaneous hydrogen bonding and stacking interactions, which
       is similar to the situation in actual biopolymers. Validation against
       these benchmark data is therefore a more demanding task for approximate
       models, since correct descriptions of all energy terms are unlikely to
       be accomplished by fortuitous cancellations of systematic errors. The
       density functionals TPSS ( both with and without an empirical dispersion
       term), PWB6K, M05-2X, and BH\&H, and the self-consistent charge density
       functional tight binding method augmented with an empirical dispersion
       term (SCC-DFTB-D) were assessed for their abilities accurately to
       compute structures and energies. The best reproduction of the BSSE
       corrected RI-MP2 stabilization energies was achieved by the TPSS
       functional ( TZVPP basis set) combined with empirical dispersion;
       removal of the dispersion correction leads to significantly degraded
       performance. The M05-2X and PWB6K functionals performed very well in
       reproducing the RI-MP2 geometries, but showed a systematic moderate
       underestimation of the magnitude of base stacking interactions. The
       SCC-DFTB-D method predicts geometries in fair agreement with RI-MP2;
       given its computational efficiency it represents a good option for
       initial scanning of analogous biopolymeric potential energy surfaces.
       BH\&H gives geometries of comparable quality to the other functionals
       but significantly overestimates interaction energies other than
       stacking.,
    DOI = 10.1039/b707182e,
    ISSN = 1463-9076,
    Unique-ID = ISI:000249432000006,
    
  • [DOI] J. Cerny and P. Hobza, "Non-covalent interactions in biomacromolecules," PHYSICAL CHEMISTRY CHEMICAL PHYSICS, vol. 9, iss. 39, pp. 5291-5303, 2007.
    [Bibtex]
    @article ISI:000249925500010,
    Author = Cerny, Jiri and Hobza, Pavel,
    Title = Non-covalent interactions in biomacromolecules,
    Journal = PHYSICAL CHEMISTRY CHEMICAL PHYSICS,
    Year = 2007,
    Volume = 9,
    Number = 39,
    Pages = 5291-5303,
    Abstract = Non-covalent interactions play an important role in chemistry, physics
       and especially in biodisciplines. They determine the structure of
       biomacromolecules such as DNA and proteins and are responsible for the
       molecular recognition process. Theoretical evaluation of interaction
       energies is difficult; however, perturbation as well as variation
       (supermolecular) methods are briefly described. Accurate interaction
       energies can be obtained by complete basis set limit calculations
       providing a large portion of correlation energy is covered (e.g. by
       performing CCSD(T) calculations). The role of H-bonding and stacking
       interactions in the stabilisation of DNA, oligopeptides and proteins is
       described, and the importance of London dispersion energy is shown.,
    DOI = 10.1039/b704781a,
    ISSN = 1463-9076,
    Unique-ID = ISI:000249925500010,
    
  • [DOI] K. E. Riley, J. Vondrasek, and P. Hobza, "Performance of the DFT-D method, paired with the PCM implicit solvation
    model, for the computation of interaction energies of solvated complexes
    of biological interest," PHYSICAL CHEMISTRY CHEMICAL PHYSICS, vol. 9, iss. 41, pp. 5555-5560, 2007.
    [Bibtex]
    @article ISI:000250366900005,
    Author = Riley, Kevin E. and Vondrasek, Jiri and Hobza, Pavel,
    Title = Performance of the DFT-D method, paired with the PCM implicit solvation
       model, for the computation of interaction energies of solvated complexes
       of biological interest,
    Journal = PHYSICAL CHEMISTRY CHEMICAL PHYSICS,
    Year = 2007,
    Volume = 9,
    Number = 41,
    Pages = 5555-5560,
    Abstract = In this work we investigate the performance of the DFT method, augmented
       with an empirical dispersion function (DFT-D), paired with the PCM
       implicit solvation model, for the computation of noncovalent interaction
       energies of biologically-relevant, solvated model complexes. It is found
       that this method describes intermolecular interactions within water and
       ether ( protein-like) environments with roughly the same accuracy as in
       the gas phase. Another important finding is that, when environmental
       effects are taken into account, the empirical dispersion term associated
       with the DFT-D method need be modified very little ( or not at all), in
       order to obtain the optimum, most well balanced, performance.,
    DOI = 10.1039/b708089a,
    ISSN = 1463-9076,
    Unique-ID = ISI:000250366900005,
    
  • [DOI] K. Pluhackova, P. Jurecka, and P. Hobza, "Stabilisation energy of C6H6 center dot center dot center dot C6X6 (X =
    F, Cl, Br, I, CN) complexes: complete basis set limit calculations at
    MP2 and CCSD(T) levels," PHYSICAL CHEMISTRY CHEMICAL PHYSICS, vol. 9, iss. 6, pp. 755-760, 2007.
    [Bibtex]
    @article ISI:000243928300011,
    Author = Pluhackova, Kristyna and Jurecka, Petr and Hobza, Pavel,
    Title = Stabilisation energy of C6H6 center dot center dot center dot C6X6 (X =
       F, Cl, Br, I, CN) complexes: complete basis set limit calculations at
       MP2 and CCSD(T) levels,
    Journal = PHYSICAL CHEMISTRY CHEMICAL PHYSICS,
    Year = 2007,
    Volume = 9,
    Number = 6,
    Pages = 755-760,
    Abstract = Stabilisation energies of stacked structures of (C6H6C6X6)-C-... (X = F,
       Cl, Br, CN) complexes were determined at the CCSD(T) complete basis set
       (CBS) limit level. These energies were constructed from MP2/CBS
       stabilisation energies and a CCSD(T) correction term determined with a
       medium basis set (6-31G**). The former energies were extrapolated
       using the two-point formula of Helgaker et al. from aug-cc-pVDZ and
       aug-cc-pVTZ Hartree-Fock energies and MP2 correlation energies. The
       CCSD(T) correction term is systematically repulsive. The final
       CCSD(T)/CBS stabilisation energies are large, considerably larger than
       previously calculated and increase in the series as follows:
       hexafluorobenzene (6.3 kcal mol(-1)), hexachlorobenzene (8.8 kcal
       mol(-1)), hexabromobenzene (8.1 kcal mol(-1)) and hexacyanobenzene (11.0
       kcal mol(-1)). MP2/SDD** relativistic calculations performed for all
       complexes mentioned and also for benzene(...)hexaiodobenzene have
       clearly shown that due to relativistic effects the stabilisation energy
       of the hexaiodobenzene complex is lower than that of hexabromobenzene
       complex. The decomposition of the total interaction energy to physically
       defined energy components was made by using the symmetry adapted
       perturbation treatment (SAPT). The main stabilisation contribution for
       all complexes investigated is due to London dispersion energy, with the
       induction term being smaller. Electrostatic and induction terms which
       are attractive are compensated by their exchange counterparts. The
       stacked motif in the complexes studied is very stable and might thus be
       valuable as a supramolecular synthon.,
    DOI = 10.1039/b615318f,
    ISSN = 1463-9076,
    Unique-ID = ISI:000243928300011,
    
  • [DOI] M. Kabelac and P. Hobza, "Hydration and stability of nucleic acid bases and base pairs," PHYSICAL CHEMISTRY CHEMICAL PHYSICS, vol. 9, iss. 8, pp. 903-917, 2007.
    [Bibtex]
    @article ISI:000244253000001,
    Author = Kabelac, Martin and Hobza, Pavel,
    Title = Hydration and stability of nucleic acid bases and base pairs,
    Journal = PHYSICAL CHEMISTRY CHEMICAL PHYSICS,
    Year = 2007,
    Volume = 9,
    Number = 8,
    Pages = 903-917,
    Abstract = Empirical, quantum chemical calculations and molecular dynamics
       simulations of the role of a solvent on tautomerism of nucleic acid
       bases and structure and properties of nucleic acid base pairs are
       summarized. Attention was paid to microhydrated (by one and two water
       molecules) complexes, for which structures found by scanning of
       empirical potential surfaces were recalculated at a correlated ab initio
       level. Additionally, isolated as well as mono-and dihydrated H-bonded,
       T-shaped and stacked structures of all possible nucleic acid base pairs
       were studied at the same theoretical levels. We demonstrate the strong
       influence of a solvent on the tautomeric equilibrium between the
       tautomers of bases and on the spatial arrangement of the bases in a base
       pair. The results provide clear evidence that the prevalence of either
       the stacked or hydrogen-bonded structures of the base pairs in the
       solvent is not determined only by its bulk properties, but rather by
       specific hydrophilic interactions of the base pair with a small number
       of solvent molecules.,
    DOI = 10.1039/b614420a,
    ISSN = 1463-9076,
    Unique-ID = ISI:000244253000001,
    
  • [DOI] M. S. de Vries and P. Hobza, "Gas-phase spectroscopy of biomolecular building blocks," ANNUAL REVIEW OF PHYSICAL CHEMISTRY, vol. 58, pp. 585-612, 2007.
    [Bibtex]
    @article ISI:000246652300023,
    Author = de Vries, Mattanjah S. and Hobza, Pavel,
    Title = Gas-phase spectroscopy of biomolecular building blocks,
    Journal = ANNUAL REVIEW OF PHYSICAL CHEMISTRY,
    Series = Annual Review of Physical Chemistry,
    Year = 2007,
    Volume = 58,
    Pages = 585-612,
    Abstract = Gas-phase spectroscopy lends itself ideally to the study of isolated
       molecules and provides important data for comparison with theory. In
       recent years, we have seen enormous progress in the study of
       biomolecular building blocks in the gas phase. The motivation for such
       work is threefold: (a) It is important to distinguish between intrinsic
       molecular properties and properties that result from the biological
       environment. (b) Gas-phase spectroscopy of clusters provides insights
       into fundamental interactions and into microsolvation. (c) Gas-phase
       data support quantum-chemical calculations. This review focuses on the
       current status of (poly)amino acids and DTNA bases. Recent results help
       elucidate structure and hydrogen-bonded interactions, as well as
       showcase a successful interplay between theory and experiment.,
    DOI = 10.1146/annurev.physchem.57.032905.104722,
    ISSN = 0066-426X,
    ISBN = 978-0-8243-1058-5,
    Unique-ID = ISI:000246652300023,
    
  • [DOI] M. Kabelac, E. C. Sherer, C. J. Cramer, and P. Hobza, "DNA base trimers: Empirical and quantum chemical ab initio calculations
    versus experiment in vacuo," CHEMISTRY-A EUROPEAN JOURNAL, vol. 13, iss. 7, pp. 2067-2077, 2007.
    [Bibtex]
    @article ISI:000244914700017,
    Author = Kabelac, Martin and Sherer, Edward C. and Cramer, Christopher J. and
       Hobza, Pavel,
    Title = DNA base trimers: Empirical and quantum chemical ab initio calculations
       versus experiment in vacuo,
    Journal = CHEMISTRY-A EUROPEAN JOURNAL,
    Year = 2007,
    Volume = 13,
    Number = 7,
    Pages = 2067-2077,
    Abstract = A complete scan of the potential-energy surfaces for selected DNA base
       trimers has been performed by a molecular dynamics/quenching technique
       using the force field of Cornell et al. implemented in the AMBER7
       program. The resulting most stable/populated structures were then
       reoptimized at a correlated ab initio level by employing resolution of
       the identity, Moller-Plesset second-order perturbation theory (RI-MP2).
       A systematic study of these trimers at such a complete level of
       electronic structure theory is presented for the first time. We show
       that prior experimental and theoretical interpretations were incorrect
       in assuming that the most stable structures of the methylated trimers
       corresponded to planar systems characterized by cyclic intermolecular
       hydrogen bonding. We found that stacked structures of two bases with the
       third base in a T-shape arrangement are the global minima in all of the
       methylated systems: they are more stable than the cyclic planar
       structures by about 10 kcal mol(-1). The different behaviors of
       nonmethylated and methylated trimers is also discussed. ne high-level
       geometries and interaction energies computed for the trimers serve also
       as a reference for the testing of recently developed density functional
       theory (DFT) functionals with respect to their ability to correctly
       describe the balance between the electrostatic and dispersion
       contributions that bind these trimers together. The recently reported
       M052X functional with a polarized triple-zeta basis set predicts 11
       uracil trimer interaction energies with a root-mean-square error of 2.3
       kcal mol(-1) relative to highly correlated ab initio theoretical
       calculations.,
    DOI = 10.1002/chem.200601007,
    ISSN = 0947-6539,
    Unique-ID = ISI:000244914700017,
    
  • [DOI] J. Rezac and P. Hobza, "On the nature of DNA-duplex stability," CHEMISTRY-A EUROPEAN JOURNAL, vol. 13, iss. 10, pp. 2983-2989, 2007.
    [Bibtex]
    @article ISI:000245389700024,
    Author = Rezac, Jan and Hobza, Pavel,
    Title = On the nature of DNA-duplex stability,
    Journal = CHEMISTRY-A EUROPEAN JOURNAL,
    Year = 2007,
    Volume = 13,
    Number = 10,
    Pages = 2983-2989,
    Abstract = The unwinding free energy of 128 DNA octamers was correlated with the
       sum of interaction energies among DNA bases and their solvation
       energies. ne former energies were determined by using the recently
       developed density functional theory procedure augmented by London
       dispersion energy (RI-DFT-D) that provides accurate hydrogen-bonding and
       stacking energies highly comparable with CCSD(T)/complete basis set
       limit benchmark data. Efficient tight-binding DFT covering dispersion
       energy was also used and yielded satisfactory results. The latter method
       can be used for extended systems. The solvation energy was determined by
       using a CPCM continuum solvent at HF level calculations. Various models
       were adopted to correlate theoretical energies with experimental
       unwinding free energies. Unless all energy components (hydrogen-bonding,
       intra- and interstrand-stacking, and solvation energies) were included
       and weighted individually, no satisfactory correlation resulted. The
       most advanced model yielded very close correlation (RMSE=0.32 kcal
       mol(-1)) fully comparable with the entirely empirical correlation
       introduced in the original paper. 131 Analysis of the theoretical
       results shows the importance of inter- and intramolecular stacking
       energies, and especially the latter term plays a key role in determining
       DNA-duplex stabilization.,
    DOI = 10.1002/chem.200601120,
    ISSN = 0947-6539,
    Unique-ID = ISI:000245389700024,
    
  • [DOI] J. Vondrasek, T. Kubar, F. E. Jenney Jr., M. W. W. Adams, M. Kozisek, J. Cerny, V. Sklenar, and P. Hobza, "Dispersion interactions govern the strong thermal stability of a protein," CHEMISTRY-A EUROPEAN JOURNAL, vol. 13, iss. 32, pp. 9022-9027, 2007.
    [Bibtex]
    @article ISI:000250913900012,
    Author = Vondrasek, Jiri and Kubar, Tomas and Jenney, Jr., Francis E. and Adams,
       Michael W. W. and Kozisek, Milan and Cerny, Jiri and Sklenar, Vladimir
       and Hobza, Pavel,
    Title = Dispersion interactions govern the strong thermal stability of a protein,
    Journal = CHEMISTRY-A EUROPEAN JOURNAL,
    Year = 2007,
    Volume = 13,
    Number = 32,
    Pages = 9022-9027,
    Abstract = Rubredoxin from the hyperthermophile Pyrococcus furiosus (Pf Rd) is an
       extremely thermostable protein, which makes it an attractive subject of
       protein folding and stability studies. A fundamental question arises as
       to what the reason for such extreme stability is and how it can be
       elucidated from a complex set of interatomic interactions. We addressed
       this issue first theoretically through a computational analysis of the
       hydrophobic core of the protein and its mutants, including the
       interactions taking place inside the core. Here we show that a single
       mutation of one of phenylalanine's residues inside the protein's
       hydrophobic core results in a dramatic decrease in its thermal
       stability. The calculated unfolding Gibbs energy as well as the
       stabilization energy differences between a few core residues follows the
       same trend as the melting temperature of protein variants determined
       experimentally by microcalorimetry measurements. NMR spectroscopy
       experiments have shown that the only part of the protein affected by
       mutation is the reasonably rearranged hydrophobic core. It is hence
       concluded that stabilization energies, which are dominated by London
       dispersion, represent the main source of stability of this protein.,
    DOI = 10.1002/chem.200700428,
    ISSN = 0947-6539,
    Unique-ID = ISI:000250913900012,
    
  • J. Cerny and P. Hobza, "Forces of attraction," PHOTOCHEMICAL & PHOTOBIOLOGICAL SCIENCES, vol. 6, iss. 9, pp. B71, 2007.
    [Bibtex]
    @article ISI:000248986000008,
    Author = Cerny, Jiri and Hobza, Pavel,
    Title = Forces of attraction,
    Journal = PHOTOCHEMICAL \& PHOTOBIOLOGICAL SCIENCES,
    Year = 2007,
    Volume = 6,
    Number = 9,
    Pages = B71,
    ISSN = 1474-905X,
    Unique-ID = ISI:000248986000008,
    
  • J. Cerny and P. Hobza, "Forces of attraction," ORGANIC & BIOMOLECULAR CHEMISTRY, vol. 5, iss. 17, pp. B71, 2007.
    [Bibtex]
    @article ISI:000248731600008,
    Author = Cerny, Jiri and Hobza, Pavel,
    Title = Forces of attraction,
    Journal = ORGANIC \& BIOMOLECULAR CHEMISTRY,
    Year = 2007,
    Volume = 5,
    Number = 17,
    Pages = B71,
    ISSN = 1477-0520,
    Unique-ID = ISI:000248731600008,
    
  • M. Kabelac, H. Valdes, E. C. Sherer, C. J. Cramer, and P. Hobza, "New MP2 database of nucleic acid base trimers: How well reproduce DFT
    methods structure and binding energies?," in COMPUTATION IN MODERN SCIENCE AND ENGINEERING VOL 2, PTS A AND B, 2007, pp. 1244-1247.
    [Bibtex]
    @inproceedings ISI:000252602900306,
    Author = Kabelac, Martin and Valdes, Haydee and Sherer, Edward C. and Cramer,
       Christopher J. and Hobza, Pavel,
    Editor = Simos, TE and Maroulis, G,
    Title = New MP2 database of nucleic acid base trimers: How well reproduce DFT
       methods structure and binding energies?,
    Booktitle = COMPUTATION IN MODERN SCIENCE AND ENGINEERING VOL 2, PTS A AND B,
    Series = AIP CONFERENCE PROCEEDINGS,
    Year = 2007,
    Volume = 2,
    Number = Part a,
    Pages = 1244-1247,
    Note = International Conference on Computational Methods in Science and
       Engineering, Corfu, GREECE, SEP 25-30, 2007,
    Organization = European Soc Computat Methods Sci \& Engn; Minist Natl Educ \& Religious
       Affairs; E4 Comp Engn,
    Abstract = A new database of nucleic acid base trimers has been developed that
       includes 141 geometries and stabilization energies obtained at the
       RI-MP2 level of theory with the TZVPP basis set. Compared to other
       databases, this one includes considerably more complicated structures;
       the various intermolecular interactions in the trimers are quite
       heterogeneous and in particular include simultaneous hydrogen bonding
       and stacking interactions, which is similar to the situation in real
       biomolecules. Validation against these benchmark data is therefore a
       more demanding task for approximate models, since correct descriptions
       of all energy terms is unlikely to be accomplished by fortuitous
       cancellations of systematic errors. The density functionals TPSS (both
       with and without an empirical dispersion term), PWB6K, M05-2X, and
       BH\&H, and the self-consistent charge density functional tight binding
       method augmented with an empirical dispersion term (SCC-DFTB-D) were
       assessed for their abilities to accurately compute structures and
       energies. The best reproduction of the BSSE corrected RI-MP2
       stabilization energies was achieved by the TPSS functional (TZVPP basis
       set) combined with empirical dispersion; removal of the dispersion
       correction leads to significantly degraded performance. The M05-2X and
       PWB6K functionals performed very well in reproducing the RI-MP2
       geometries, but showed a systematic moderate underestimation of the
       magnitude of base stacking interactions. The SCC-DFTB-D method predicts
       geometries in fair agreement with RI-MP2; given its computational
       efficiency it represents a good option for initial scanning of potential
       energy surfaces of biopolymers. BH\&H gives geometries of comparable
       quality to the other functionals but significantly overestimates
       interaction energies other than stacking. The whole database of
       geometries and interaction energies of the complexes can be found on the
       web page: http://www.rsc.org/suppdata/CP/b7/b707182e/index.sht,
    ISSN = 0094-243X,
    ISBN = 978-0-7354-0476-2,
    Unique-ID = ISI:000252602900306,
    
  • K. Pluhackova and P. Hobza, "Theoretical investigation of the unexpected red shift in the halothane
    ... acetone complex," in COMPUTATION IN MODERN SCIENCE AND ENGINEERING VOL 2, PTS A AND B, 2007, pp. 1339-1342.
    [Bibtex]
    @inproceedings ISI:000252602900329,
    Author = Pluhackova, Kristyna and Hobza, Pavel,
    Editor = Simos, TE and Maroulis, G,
    Title = Theoretical investigation of the unexpected red shift in the halothane
       ... acetone complex,
    Booktitle = COMPUTATION IN MODERN SCIENCE AND ENGINEERING VOL 2, PTS A AND B,
    Series = AIP CONFERENCE PROCEEDINGS,
    Year = 2007,
    Volume = 2,
    Number = Part a,
    Pages = 1339-1342,
    Note = International Conference on Computational Methods in Science and
       Engineering, Corfu, GREECE, SEP 25-30, 2007,
    Organization = European Soc Computat Methods Sci \& Engn; Minist Natl Educ \& Religious
       Affairs; E4 Comp Engn,
    Abstract = Halothane ... acetone and fluoroform ... acetone complexes were studied
       using the MP2 method with a cc-pVTZ basis set and the DFT method with
       TPSS functional and a TZVP basis set. Whereas fluoroform shows a
       pronounced blue shift upon complexation, halothane exhibits a small and
       surprisingly red shift. To explain this we have performed the SAPT and
       NBO analyses. Although the composition of the total stabilisation energy
       of each complex gained different results it did not provide a
       satisfactory explanation for the difference in the spectral shifts. The
       origin of the difference in the shifts was interpreted to be a result of
       the interplay of the hyperconjugation and rehybridisation mechanisms.
       The blue-shift of the C-H stretch frequency upon complexation exhibited
       by fluoroform ... acetone complex was explained by concerting of the two
       above-mentioned mechanisms. On the other hand, in the halothane ...
       acetone complex the hyperconjugation and rehybridisation mechanisms
       compensate and it results in small red shift of the C-H stretch
       frequency. ne calculated shift of the C-H stretch vibration frequencies
       of halothane (+27 cm(-1)) agreed with the experimental value of +5
       cm(-1).,
    ISSN = 0094-243X,
    ISBN = 978-0-7354-0476-2,
    Unique-ID = ISI:000252602900329,
    
  • J. Cerny and P. Hobza, "Forces of attraction," CHEMICAL COMMUNICATIONS, iss. 33, pp. B71, 2007.
    [Bibtex]
    @article ISI:000248797800008,
    Author = Cerny, Jiri and Hobza, Pavel,
    Title = Forces of attraction,
    Journal = CHEMICAL COMMUNICATIONS,
    Year = 2007,
    Number = 33,
    Pages = B71,
    ISSN = 1359-7345,
    Unique-ID = ISI:000248797800008,
    
  • J. Cerny and P. Hobza, "Forces of attraction," DALTON TRANSACTIONS, iss. 33, pp. B71, 2007.
    [Bibtex]
    @article ISI:000248731300008,
    Author = Cerny, Jiri and Hobza, Pavel,
    Title = Forces of attraction,
    Journal = DALTON TRANSACTIONS,
    Year = 2007,
    Number = 33,
    Pages = B71,
    ISSN = 1477-9226,
    Unique-ID = ISI:000248731300008,
    

2006

  • P. Hobza, "Stabilization energies of DNA base pairs and aminoacid pairs: WFT, DFT
    and DFTB calculations," ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, vol. 232, pp. 96-COMP, 2006.
    [Bibtex]
    @article ISI:000207781604175,
    Author = Hobza, Pavel,
    Title = Stabilization energies of DNA base pairs and aminoacid pairs: WFT, DFT
       and DFTB calculations,
    Journal = ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY,
    Year = 2006,
    Volume = 232,
    Pages = 96-COMP,
    Month = SEP 10,
    ISSN = 0065-7727,
    Unique-ID = ISI:000207781604175,
    
  • [DOI] M. Kabelac and P. Hobza, "Na(+), Mg(2+), and Zn(2+) binding to all tautomers of adenine, cytosine,
    and thymine and the eight most stable keto/enol tautomers of guanine: A
    correlated ab initio quantum chemical study," JOURNAL OF PHYSICAL CHEMISTRY B, vol. 110, iss. 29, pp. 14515-14523, 2006.
    [Bibtex]
    @article ISI:000239141800076,
    Author = Kabelac, Martin and Hobza, Pavel,
    Title = Na(+), Mg(2+), and Zn(2+) binding to all tautomers of adenine, cytosine,
       and thymine and the eight most stable keto/enol tautomers of guanine: A
       correlated ab initio quantum chemical study,
    Journal = JOURNAL OF PHYSICAL CHEMISTRY B,
    Year = 2006,
    Volume = 110,
    Number = 29,
    Pages = 14515-14523,
    Month = JUL 27,
    Abstract = Interactions of adenine, cytosine, guanine, and thymine with Na(+),
       Mg(2+), and Zn(2+) cations were studied using an approximate resolution
       of identity correlated second- order MP2 ( RI- MP2) method with the
       TZVPP ([ 5s3p2d1f/ 3s2p1d]) basis set. All existing tautomers of
       adenine, cytosine, and thymine and the eight most stable keto/ enol
       tautomers of guanine were considered. Cations bind mostly in a bidentate
       manner, and stabilization energies of these complexes are larger than
       those in the case when cations bind in a unidentate manner. The cation
       center dot center dot center dot Y ( Y equal to N or O) distances for
       divalent metals are shorter than those for Na(+) and for Zn(2+) are
       mostly shorter than the Mg(2+), Y distance. The intermolecular distances
       between the cation and the base for complexes containing adenine and
       cytosine are systematically shorter than those for complexes containing
       guanine and thymine. Only for cytosine the canonical keto/ amino
       tautomer structure with ions represents the global minimum. For guanine,
       the metalated canonical form is again the most stable, but its
       stabilization energy is within less than 5\% of the stabilization
       energies of the two other rare tautomers, which indicates that the
       canonical form and these two rare tautomers could coexist. The canonical
       structures of adenine and thymine in the presence of ions are
       considerably less stable ( by more than 10\%) than the complexes of the
       rare tautomers. It can be concluded that the interaction of Na(+),
       Mg(2+), and Zn(2+) cations with cytosine in the gas phase will not
       induce the change of the canonical form to the rare tautomeric form. In
       the case of isolated guanine, the equilibrium of the canonical form with
       rare tautomers can be found. For isolated adenine and thymine the
       presence of rare tautomers is highly probable.,
    DOI = 10.1021/jp062249u,
    ISSN = 1520-6106,
    Unique-ID = ISI:000239141800076,
    
  • [DOI] W. Zierkiewicz, D. Michalska, J. Cerny, and P. Hobza, "Cation-pi complexes between alkali metal cation and
    para-halogenophenols. Structures, binding energies and thermodynamic
    properties: DFT study and CCSD(T) complete basis set limit calculations," MOLECULAR PHYSICS, vol. 104, iss. 13-14, pp. 2317-2325, 2006.
    [Bibtex]
    @article ISI:000238612500028,
    Author = Zierkiewicz, W and Michalska, D and Cerny, J and Hobza, P,
    Title = Cation-pi complexes between alkali metal cation and
       para-halogenophenols. Structures, binding energies and thermodynamic
       properties: DFT study and CCSD(T) complete basis set limit calculations,
    Journal = MOLECULAR PHYSICS,
    Year = 2006,
    Volume = 104,
    Number = 13-14,
    Pages = 2317-2325,
    Month = JUL 10,
    Abstract = Density functional (B3LYP) studies have been undertaken on the molecular
       structures, binding energies and thermodynamic properties of pi type
       complexes formed by alkali metal cations (Li+, Na+, K+) with phenol
       (Ph), and para-halogenophenols, p-XPh (X = F, Cl, Br). The performance
       of the DFT procedure for M+ (phenol) complexes was verified by
       performing the complete basis set limit calculations at the CCSD(T)
       level. The DFT stabilization energies for the Li+ and Na+ complexes
       agree well with earlier accurately determined energies, while those for
       K+ complexes are underestimated by about 30\%. This is explained by the
       role of electron correlation effects (mainly dispersion energy), which
       are neglected at the DFT level. The effect of the halogen
       para-substituent on the strength of cation binding to the pi face of the
       phenol ring is discussed. The calculated Gibbs free energy (Delta G) has
       revealed that all the investigated complexes are stable under standard
       conditions. Results show that the binding energies of these complexes
       vary in the range from -36.8 to -11.5 kcal/mol. Natural Bond Orbital
       (NBO) analysis has provided detailed insight into the nature of the
       electronic interactions in these systems.,
    DOI = 10.1080/00268970600652839,
    ISSN = 0026-8976,
    Unique-ID = ISI:000238612500028,
    
  • [DOI] P. Dobes, M. Otyepka, M. Strnad, and P. Hobza, "Interaction energies for the purine inhibitor roscovitine with
    cyclin-dependent kinase 2: Correlated ab initio quantum-chemical, DFT
    and empirical calculations," CHEMISTRY-A EUROPEAN JOURNAL, vol. 12, iss. 16, pp. 4297-4304, 2006.
    [Bibtex]
    @article ISI:000238032400009,
    Author = Dobes, P and Otyepka, M and Strnad, M and Hobza, P,
    Title = Interaction energies for the purine inhibitor roscovitine with
       cyclin-dependent kinase 2: Correlated ab initio quantum-chemical, DFT
       and empirical calculations,
    Journal = CHEMISTRY-A EUROPEAN JOURNAL,
    Year = 2006,
    Volume = 12,
    Number = 16,
    Pages = 4297-4304,
    Month = MAY 24,
    Abstract = The interaction between roscovitine and cyclin-dependent kinase 2 (cdk2)
       was investigated by performing correlated ab initio quantum-chemical
       calculations. The whole protein was fragmented into smaller systems
       consisting of one or a few amino acids, and the interaction energies of
       these fragments with roscovitine were determined by using the MP2 method
       with the extended aug-cc-pVDZ basis set. For selected complexes, the
       complete basis set limit MP2 interaction energies, as well as the
       coupled-cluster corrections with inclusion of single, double and
       noninteractive triples contributions [CCSD(T)], were also evaluated.
       The energies of interaction between roscovitine and small fragments and
       between roscovitine and substantial sections of protein (722 atoms) were
       also computed by using density-functional tight-binding methods covering
       dispersion energy (DFTB-D) and the Cornell empirical potential. Total
       stabilisation energy originates predominantly from dispersion energy and
       methods that do not account for the dispersion energy cannot, therefore,
       be recommended for the study of protein-inhibitor interactions. The
       Cornell empirical potential describes reasonably well the interaction
       between roscovitine and protein; therefore, this method can be applied
       in future thermodynamic calculations. A limited number of amino acid
       residues contribute significantly to the binding of roscovitine and
       cdk2, whereas a rather large number of amino acids make a negligible
       contribution.,
    DOI = 10.1002/chem.200501269,
    ISSN = 0947-6539,
    Unique-ID = ISI:000238032400009,
    
  • [DOI] J. Fanfrlik, M. Lepsik, D. Horinek, Z. Havlas, and P. Hobza, "Interaction of carboranes with biomolecules: Formation of dihydrogen
    bonds," CHEMPHYSCHEM, vol. 7, iss. 5, pp. 1100-1105, 2006.
    [Bibtex]
    @article ISI:000237836700021,
    Author = Fanfrlik, J and Lepsik, M and Horinek, D and Havlas, Z and Hobza, P,
    Title = Interaction of carboranes with biomolecules: Formation of dihydrogen
       bonds,
    Journal = CHEMPHYSCHEM,
    Year = 2006,
    Volume = 7,
    Number = 5,
    Pages = 1100-1105,
    Month = MAY 12,
    Abstract = Noncovalent interactions of the polyhedral corborone
       1-corbacloso-dodecaborone (CB11H12)(-) with building blocks of
       biomolecules, modelled by glycine (GLY), serine (SER), phenylalanine
       (PHE), glutamic acid (GLU), lysine (LYS) and arginine (ARG), were
       investigated in vacua by molecular dynamics simulations with the UFF
       empirical potential. Selected structures were further studied by
       accurate ob initio quantum chemical procedures. Interactions with a
       peptide bond (GLY-SER dipeptide) and a nucleic acid building block
       (guanine) were also considered. The RESP and NPA charges of carboranes
       and small model systems are compared and their use is discussed. The
       dominant interaction between carboranes and biomolecules is the
       formation of unconventional proton-hydride hydrogen bonds (dihydrogen
       bonds) characterized by a short distance between hydrogen atoms (as
       close as 1.8 angstrom) and on average strength in the range of 4.2-5.8
       kcal mol(-1). The total stabilization energy of complexes investigated
       is rather large, and the largest value (approximate to 15 kcal mol(-1))
       was found for the carborane complexes with ARG and the GLY-SER
       dipeptide. These interactions are ubiquitous under geometrical
       constraints influencing the strength of the interaction. The carborane
       forms dihydrogen bonds with biomolecules preferably with the hydrogen
       atoms of its lower hemisphere (i.e. the part of the cage opposite to the
       carbon atom). These two geometrical factors can be used to explain the
       specificity of inhibition of HIV protease by carborones.,
    DOI = 10.1002/cphc.200500648,
    ISSN = 1439-4235,
    Unique-ID = ISI:000237836700021,
    
  • [DOI] D. Reha, M. Hocek, and P. Hobza, "Exceptional thermodynamic stability of DNA duplexes modified by nonpolar
    base analogues is due to increased stacking interactions and favorable
    solvation: Correlated ab initio calculations and molecular dynamics
    simulations," CHEMISTRY-A EUROPEAN JOURNAL, vol. 12, iss. 13, pp. 3587-3595, 2006.
    [Bibtex]
    @article ISI:000237177800017,
    Author = Reha, D and Hocek, M and Hobza, P,
    Title = Exceptional thermodynamic stability of DNA duplexes modified by nonpolar
       base analogues is due to increased stacking interactions and favorable
       solvation: Correlated ab initio calculations and molecular dynamics
       simulations,
    Journal = CHEMISTRY-A EUROPEAN JOURNAL,
    Year = 2006,
    Volume = 12,
    Number = 13,
    Pages = 3587-3595,
    Month = APR 14,
    Abstract = The geometries of DNA hexamer (5'-GGAACC-3') and DNA 13-mer
       (5'-GCGTACACA7FGCG-3') have been determined by molecular dynamics (MD)
       simulations using an empirical force field. The central canonical base
       pair was replaced by a pair of nonpolar base analogues, 2,2'-bipyridyl
       and 3-methylisocarbostyril. The stabilization energy of the model system
       (model A) consisting of a central base pair (base-analogue pair) and two
       neighboring base pairs was determined by the RI-MP2 method using an
       extended aug-cc-pVDZ basis set. The geometry of the model was averaged
       from structures determined by MD simulations. The role of the solvent
       was covered by the COSMO continuum solvent model and calculations were
       performed for a larger model system (model 13) which also contained a
       sugar-phosphate backbone. The total stabilization energies of the
       unperturbed system and the system perturbed by a base-analogue pair
       (model A) were comparable to the stability of both duplexes
       experimentally determined. This is due to large stacking interaction
       energy of the base-analogue self-pair which compensates for the missing
       hydrogen-bonding energy of the replaced adenine...thymine base pair. The
       selectivity of the base-analogue pair was reproduced (model 13) when
       their desolvation energy was included with the interaction energy of
       both strands determined by the approximate SCC-DF-FB-D method.,
    DOI = 10.1002/chem.200501126,
    ISSN = 0947-6539,
    Unique-ID = ISI:000237177800017,
    
  • [DOI] H. Valdes, D. Reha, and P. Hobza, "Structure of isolated tryptophyl-glycine dipeptide and
    tryptophyl-glycyl-glycine tripeptide: Ab initio SCC-DFTB-D molecular
    dynamics simulations and high-level correlated ab initio quantum
    chemical calculations," JOURNAL OF PHYSICAL CHEMISTRY B, vol. 110, iss. 12, pp. 6385-6396, 2006.
    [Bibtex]
    @article ISI:000236407400075,
    Author = Valdes, H and Reha, D and Hobza, P,
    Title = Structure of isolated tryptophyl-glycine dipeptide and
       tryptophyl-glycyl-glycine tripeptide: Ab initio SCC-DFTB-D molecular
       dynamics simulations and high-level correlated ab initio quantum
       chemical calculations,
    Journal = JOURNAL OF PHYSICAL CHEMISTRY B,
    Year = 2006,
    Volume = 110,
    Number = 12,
    Pages = 6385-6396,
    Month = MAR 30,
    Abstract = The tryptophyl-glycine (Trp-Gly) and tryptophyl-glycyl-glycine
       (Trp-Gly-Gly) peptides have been studied by means of molecular dynamic
       simulations combined with high-level correlated ab initio quantum
       chemical and statistical thermodynamic calculations. The lowest energy
       conformers were localized in the free energy surface. The Structures of
       the different Trp-Gly and Trp-Gly-Gly conformers coexisting in the gas
       phase have been for the first time reported and their scaled theoretical
       IR spectra unambiguously assigned and compared with previous gas-phase
       experimental results. Common geometrical features have been
       systematically observed for the sequence Trp, Trp-Gly, and Trp-Gly-Gly.
       In addition. the peptide backbone of Trp-Gly-Gly has been compared with
       that of the previously studied Phe-Gly-Gly (Reha, D. et. al. Chem. Eur.
       J. 2005, 11, 6803). From the observed systematic Structural behavior
       between these peptide analogues, it is expected that the gas-phase
       conformers of other similar aromatic small peptides would present
       equivalent geometries. The DFT methodology failed to describe the
       potential energy surface of the studied peptides since the London
       dispersion energy (not covered in DFT) plays a significant role in the
       stabilization of most stable conformers.,
    DOI = 10.1021/jp057425y,
    ISSN = 1520-6106,
    Unique-ID = ISI:000236407400075,
    
  • [DOI] J. Sponer, P. Jurecka, I. Marchan, F. Luque, M. Orozco, and P. Hobza, "Nature of base stacking: Reference quantum-chemical stacking energies in
    ten unique B-DNA base-pair steps," CHEMISTRY-A EUROPEAN JOURNAL, vol. 12, iss. 10, pp. 2854-2865, 2006.
    [Bibtex]
    @article ISI:000236483400022,
    Author = Sponer, J and Jurecka, P and Marchan, I and Luque, FJ and Orozco, M and
       Hobza, P,
    Title = Nature of base stacking: Reference quantum-chemical stacking energies in
       ten unique B-DNA base-pair steps,
    Journal = CHEMISTRY-A EUROPEAN JOURNAL,
    Year = 2006,
    Volume = 12,
    Number = 10,
    Pages = 2854-2865,
    Month = MAR 20,
    Abstract = Base-stacking energies in ten unique B-DNA base-pair steps and some
       other arrangements were evaluated by the second-order Moller-Plesset
       (MP2) method, complete basis set (CBS) extrapolation, and correction for
       triple (T) electron-correlation contributions. The CBS(T) calculations
       were compared with decade-old MP2/6-31G*(0.25) reference data and
       AMBER force field. The new calculations show modest increases in
       stacking stabilization compared to the MP2/6-31G*(0.25) data and
       surprisingly large sequence-dependent variation of stacking energies.
       The absolute force-field values are in better agreement with the new
       reference data, while relative discrepancies between quantum-chemical
       (QM) and force-field values increase modestly. Nevertheless, the force
       field provides good qualitative description of stacking, and there is no
       need to introduce additional pair-additive electrostatic terms, such as
       distributed multipoles or out-of-plane charges. There is a rather
       surprising difference of about 0.1 angstrom between the vertical
       separation of base pairs predicted by quantum chemistry and derived from
       crystal structures. Evaluations of different local arrangements of the
       5'-CG-3' step indicate a sensitivity of the relative stacking energies
       to the level of calculation. Thus, describing quantitative relations
       between local DNA geometrical variations and stacking may be more
       complicated than usually assumed. The reference calculations are
       complemented by continuum-solvent assessment of solvent-screening
       effects.,
    DOI = 10.1002/chem.200501239,
    ISSN = 0947-6539,
    Unique-ID = ISI:000236483400022,
    
  • [DOI] V. Spirko and P. Hobza, "Theoretical investigations into the blue-shifting hydrogen bond in
    benzene complexes," CHEMPHYSCHEM, vol. 7, iss. 3, pp. 640-643, 2006.
    [Bibtex]
    @article ISI:000236300600016,
    Author = Spirko, V and Hobza, P,
    Title = Theoretical investigations into the blue-shifting hydrogen bond in
       benzene complexes,
    Journal = CHEMPHYSCHEM,
    Year = 2006,
    Volume = 7,
    Number = 3,
    Pages = 640-643,
    Month = MAR 13,
    Abstract = The benzene(...)X complexes (X=benzene, antracene, ovalene) were
       optimised at the MP2/6-31G** level with the C-2v symmetry of the
       complex and planarity of the proton acceptor being preserved. The
       resulting stabilisation energies amount to 1.2, 2.3 and 2.9 kcal
       mol(-1), and the C-H bond of the proton donor is contracted by 0.0035,
       0.0052 and 0.0055 A, respectively. The contraction is connected with a
       blue-shift of the C-H stretch vibration frequency. A two-dimensional
       anharmonic vibration treatment based on a MP2/6-31G** potential
       energy surface yields the following blue shifts for the complexes
       studied: 28, 42 and 43 cm(-1) . The dominant attraction in the complexes
       is London dispersion, while the attractive contribution from
       electrostatic quadrupole-quadrupole interactions is considerably
       smaller.,
    DOI = 10.1002/cphc.200500565,
    ISSN = 1439-4235,
    Unique-ID = ISI:000236300600016,
    
  • [DOI] M. Otyepka, P. Sklenovsky, D. Horinek, T. Kubar, and P. Hobza, "How the stabilization of INK4 tumor suppressor 3D structure evaluated by
    quantum chemical and molecular mechanics calculations corresponds well
    with experimental results: Interplay of association enthalpy, entropy,
    and solvation effects," JOURNAL OF PHYSICAL CHEMISTRY B, vol. 110, iss. 9, pp. 4423-4429, 2006.
    [Bibtex]
    @article ISI:000235944500084,
    Author = Otyepka, M and Sklenovsky, P and Horinek, D and Kubar, T and Hobza, P,
    Title = How the stabilization of INK4 tumor suppressor 3D structure evaluated by
       quantum chemical and molecular mechanics calculations corresponds well
       with experimental results: Interplay of association enthalpy, entropy,
       and solvation effects,
    Journal = JOURNAL OF PHYSICAL CHEMISTRY B,
    Year = 2006,
    Volume = 110,
    Number = 9,
    Pages = 4423-4429,
    Month = MAR 9,
    Abstract = The folding free energy of the INK4c tumor suppressor core, consisting
       of 10 helices, was determined as the sum of gas-phase interaction
       enthalpy, gas-phase interaction entropy, and dehydration and hydration
       free energy. The interaction energy and the hydration free energy were
       determined using the nonempirical density functional theory (DFT)
       method, augmented by a dispersion-energy correction term, the
       semiempirical density-functional tight-binding method covering the
       dispersion energy, and the density functional theory/conductor-like
       screening model (DFT/COSMO) procedure, whereas the interaction entropy
       was calculated with the empirical Cornell et al. force field.
       Alternatively, all contributions were evaluated consistently using
       empirical methods. All the values of the interaction energy of helix
       pairs are stabilizing, and the dominant stabilizing terms stem from the
       London dispersion energy and, in the case of charged systems, the
       electrostatic energy. The stabilization energy of the core, determined
       as the difference of the energy of the core and 10 separate helices,
       amounts to similar to 450 kcal/mol. Systematically, the difference in
       the hydration free energy of a helix pair and its separate components is
       smaller in magnitude than the interaction energy, and it is negative for
       some pairs while positive for others. The average total free energy of a
       core formation amounts to -29.6 kcal/mol (yielded by scaled
       quantum-chemical methods) and + 13.9 kcal/mol (resulting from empirical
       methods). These values are considerably smaller than their single
       components, which are dominated by the interaction energy. The
       computationally predicted interval encloses the experimental value of
       the folding free energy (-2.8 kcal/mol).,
    DOI = 10.1021/jp056890s,
    ISSN = 1520-6106,
    Unique-ID = ISI:000235944500084,
    
  • [DOI] L. Zendlova, P. Hobza, and M. Kabelac, "Potential energy surfaces of the microhydrated guanine(...)cytosine base
    pair and its methylated analogue," CHEMPHYSCHEM, vol. 7, iss. 2, pp. 439-447, 2006.
    [Bibtex]
    @article ISI:000235404300021,
    Author = Zendlova, L and Hobza, P and Kabelac, M,
    Title = Potential energy surfaces of the microhydrated guanine(...)cytosine base
       pair and its methylated analogue,
    Journal = CHEMPHYSCHEM,
    Year = 2006,
    Volume = 7,
    Number = 2,
    Pages = 439-447,
    Month = FEB 13,
    Abstract = A complete scan of the potential and free-energy surfaces of
       monohydrated and dihydrated guanine cytosine and
       9-methylguanine...7-methylcytosine base pairs was realized by the
       molecular dynomics/quenching technique using the force field of Cornell
       et al. implemented in the AMBER7 program. The most stable and populated
       structures localized were further fully reoptimized at the correlated ab
       initio level employing the resolution of identity Moller-Plesset method
       with a large basis set. A systematic study of microhydration of these
       systems using a high-level correlated ab initio approach is presented
       for the first time. The different behavior of guanine...cytosine and
       adenine...thymine complexes is also discussed. These studies of nucleic
       acid base pairs are important for finding binding sites of water
       molecules around bases and for better understanding of the influence of
       the solvent on the stability of the structure of DNA.,
    DOI = 10.1002/cphc.200500311,
    ISSN = 1439-4235,
    Unique-ID = ISI:000235404300021,
    
  • [DOI] P. Jurecka, J. Sponer, J. Cerny, and P. Hobza, "Benchmark database of accurate (MP2 and CCSD(T) complete basis set
    limit) interaction energies of small model complexes, DNA base pairs,
    and amino acid pairs," PHYSICAL CHEMISTRY CHEMICAL PHYSICS, vol. 8, iss. 17, pp. 1985-1993, 2006.
    [Bibtex]
    @article ISI:000236970300001,
    Author = Jurecka, P and Sponer, J and Cerny, J and Hobza, P,
    Title = Benchmark database of accurate (MP2 and CCSD(T) complete basis set
       limit) interaction energies of small model complexes, DNA base pairs,
       and amino acid pairs,
    Journal = PHYSICAL CHEMISTRY CHEMICAL PHYSICS,
    Year = 2006,
    Volume = 8,
    Number = 17,
    Pages = 1985-1993,
    Abstract = MP2 and CCSD(T) complete basis set (CBS) limit interaction energies and
       geometries for more than 100 DNA base pairs, amino acid pairs and model
       complexes are for the first time presented together. Extrapolation to
       the CBS limit is done by using two-point extrapolation methods and
       different basis sets (aug-cc-pVDZ-aug-cc-pVTZ, aug-cc-pVTZ-aug-cc-pVQZ,
       cc-pVTZ-ccp-VQZ) are utilized. The CCSD(T) correction term, determined
       as a difference between CCSD( T) and MP2 interaction energies, is
       evaluated with smaller basis sets (6-31G** and cc-pVDZ). Two sets of
       complex geometries were used, optimized or experimental ones. The
       JSCH-2005 benchmark set, which is now available to the chemical
       community, can be used for testing lower-level computational methods.
       For the first screening the smaller training set (S22) containing 22
       model complexes can be recommended. In this case larger basis sets were
       used for extrapolation to the CBS limit and also CCSD(T) and
       counterpoise-corrected MP2 optimized geometries were sometimes adopted.,
    DOI = 10.1039/b600027d,
    ISSN = 1463-9076,
    Unique-ID = ISI:000236970300001,
    
  • [DOI] J. Cerny, V. Spirko, M. Mons, P. Hobza, and D. Nachtigallova, "Theoretical study of the ground and excited states of 7-methyl guanine
    and 9-methyl guanine: comparison with experiment," PHYSICAL CHEMISTRY CHEMICAL PHYSICS, vol. 8, iss. 26, pp. 3059-3065, 2006.
    [Bibtex]
    @article ISI:000238617000002,
    Author = Cerny, J and Spirko, V and Mons, M and Hobza, P and Nachtigallova, D,
    Title = Theoretical study of the ground and excited states of 7-methyl guanine
       and 9-methyl guanine: comparison with experiment,
    Journal = PHYSICAL CHEMISTRY CHEMICAL PHYSICS,
    Year = 2006,
    Volume = 8,
    Number = 26,
    Pages = 3059-3065,
    Abstract = The keto-enol tautomerization of 7-methyl-guanine and 9-methyl-guanine
       in the excited state was investigated using the time-dependent DFT
       (TDDFT) method. For both species, the potential energy surfaces of the
       ground state and two lowest singlet excited states (due to pi -> pi*
       and n -> pi* transitions) have been investigated and their features
       discussed in terms of consequences on the excited state dynamics. The
       findings suggest that, for both species, the state due to the n -> pi*
       transition, suspected to be an intermediate in the excited state
       deactivation, exhibits two minima with the second minimum characterized
       by an elongated N1-H distance. This structure, intermediate between enol
       and keto tautomers, might play a role in the excited state relaxation.
       The existence of this second well, however, is observed in both 7- and
       9-methyl-guanine, which suggests that it cannot account alone for the
       different photophysical behavior of these species.,
    DOI = 10.1039/b601629d,
    ISSN = 1463-9076,
    Unique-ID = ISI:000238617000002,
    
  • [DOI] E. Muchova, V. Spirko, P. Hobza, and D. Nachtigallova, "Theoretical study of photoacidity of HCN: the effect of complexation
    with water," PHYSICAL CHEMISTRY CHEMICAL PHYSICS, vol. 8, iss. 42, pp. 4866-4873, 2006.
    [Bibtex]
    @article ISI:000241526600005,
    Author = Muchova, Eva and Spirko, Vladimir and Hobza, Pavel and Nachtigallova,
       Dana,
    Title = Theoretical study of photoacidity of HCN: the effect of complexation
       with water,
    Journal = PHYSICAL CHEMISTRY CHEMICAL PHYSICS,
    Year = 2006,
    Volume = 8,
    Number = 42,
    Pages = 4866-4873,
    Abstract = The character of the hydrogen bonding and the excited state proton
       transfer (ESPT) in the model system (HCNH2O)-H-... is investigated. The
       PES of the two lowest excited states of the (H2OHCN)-H-... complex was
       calculated using the CASPT2 method. The nonadiabatic coupling of the two
       states of the (pi -> pi *) and (pi -> sigma*) character is
       responsible for the excited state proton/hydrogen transfer. Compared to
       the ground state, the barrier for this process is significantly smaller.
       An increased number of water molecules in the complex with cyclic
       hydrogen-bonded network causes a large blue shift of the state of the
       (pi -> sigma*) character. The question of the dissociation of the
       complex in its excited state is also addressed.,
    DOI = 10.1039/b610001e,
    ISSN = 1463-9076,
    Unique-ID = ISI:000241526600005,
    
  • [DOI] P. Hobza, R. Zahradnik, and K. Muller-Dethlefs, "The world of non-covalent interactions: 2006," COLLECTION OF CZECHOSLOVAK CHEMICAL COMMUNICATIONS, vol. 71, iss. 4, pp. 443-531, 2006.
    [Bibtex]
    @article ISI:000236938200001,
    Author = Hobza, P and Zahradnik, R and Muller-Dethlefs, K,
    Title = The world of non-covalent interactions: 2006,
    Journal = COLLECTION OF CZECHOSLOVAK CHEMICAL COMMUNICATIONS,
    Year = 2006,
    Volume = 71,
    Number = 4,
    Pages = 443-531,
    Abstract = The review focusses on the fundamental importance of non-covalent
       interactions in nature by illustrating specific examples from chemistry,
       physics and the biosciences. Laser spectroscopic methods and both ab
       initio and molecular modelling procedures used for the study of
       non-covalent interactions in molecular clusters are briefly outlined.
       The role of structure and geometry, stabilization energy, potential and
       free energy surfaces for molecular clusters is extensively discussed in
       the light of the most advanced ab initio computational results for the
       CCSD(T) method, extrapolated to the CBS limit. The most important types
       of non-covalent complexes are classified and several small and medium
       size non-covalent systems, including H-bonded and improper H-bonded
       complexes, nucleic acid base pairs, and peptides and proteins are
       discussed with some detail. Finally, we evaluate the interpretation of
       experimental results in comparison with state of the art theoretical
       models: this is illustrated for phenol... Ar, the benzene dimer and
       nucleic acid base pairs. A review with 270 references.,
    DOI = 10.1135/cccc20060443,
    ISSN = 0010-0765,
    Unique-ID = ISI:000236938200001,
    
  • [DOI] T. Kubar, M. Hanus, F. Ryjacek, and P. Hobza, "Binding of cationic and neutral phenanthridine Intercalators to a DNA
    oligomer is controlled by dispersion energy: Quantum chemical
    calculations and molecular mechanics simulations," CHEMISTRY-A EUROPEAN JOURNAL, vol. 12, iss. 1, pp. 280-290, 2006.
    [Bibtex]
    @article ISI:000234236400025,
    Author = Kubar, T and Hanus, M and Ryjacek, F and Hobza, P,
    Title = Binding of cationic and neutral phenanthridine Intercalators to a DNA
       oligomer is controlled by dispersion energy: Quantum chemical
       calculations and molecular mechanics simulations,
    Journal = CHEMISTRY-A EUROPEAN JOURNAL,
    Year = 2006,
    Volume = 12,
    Number = 1,
    Pages = 280-290,
    Abstract = Correlated ab initio as well as semiempirical quantum chemical
       calculations and molecular dynamics simulations were used to study the
       intercalation of cationic ethidium, cationic
       5-ethyl-6-phenylphenanthridinium and uncharged
       3,8-diamino-6-phenylphenanthridine to DNA. The stabilization energy of
       the cationic intercalators is considerably larger than that of the
       uncharged one. The dominant energy contribution with all intercalators
       is represented by dispersion energy. In the case of the cationic
       intercalators, the electrostatic and charge-transfer terms are also
       important. The Delta G of ethidium intercalation to DNA was estimated at
       -4.5 kcal mol(-1) and this value agrees well with the experimental
       result. Of six contributions to the final free energy, the interaction
       energy value is crucial. The intercalation process is governed by the
       non-covalent stacking (including charge -transfer) interaction while the
       hydrogen bonding between the ethidium amino groups and the DNA backbone
       is less important. This is confirmed by the evaluation of the
       interaction energy as well as by the calculation of the free energy
       change. The intercalation affects the macroscopic properties of DNA in
       terms of its flexibility. This explains the easier entry of another
       intercalator molecule in the vicinity of an existing intercalation site.,
    DOI = 10.1002/chem.200500725,
    ISSN = 0947-6539,
    Unique-ID = ISI:000234236400025,
    
  • M. Kabelac, E. C. Sherer, C. J. Cramer, and P. Hobza, "Trimers of nucleic acid bases: Comparison of empirical, DFT and high
    level correlated ab initio data with experiment," in RECENT PROGRESS IN COMPUTATIONAL SCIENCES AND ENGINEERING, VOLS 7A AND
    7B
    , 2006, pp. 1493-1496.
    [Bibtex]
    @inproceedings ISI:000254378800376,
    Author = Kabelac, Martin and Sherer, Edward C. and Cramer, Christopher J. and
       Hobza, Pavel,
    Editor = Simos, T and Maroulis, G,
    Title = Trimers of nucleic acid bases: Comparison of empirical, DFT and high
       level correlated ab initio data with experiment,
    Booktitle = RECENT PROGRESS IN COMPUTATIONAL SCIENCES AND ENGINEERING, VOLS 7A AND
       7B,
    Series = LECTURE SERIES ON COMPUTER AND COMPUTATIONAL SCIENCES,
    Year = 2006,
    Volume = 7A-B,
    Pages = 1493-1496,
    Note = International Conference on Computational Methods in Science and
       Engineering, Chania, GREECE, OCT 27-NOV 01, 2006,
    Abstract = A complete scan of the potential energy surfaces for selected DNA base
       trimers has been performed by a molecular dynamics/quenching technique
       using the force field of Cornell et aL implemented in the AMBER7
       program. The resulting most stable/populated structures were then
       reoptimized at a correlated ab initio level employing Resolution of the
       Identity Moller-Plesset second-order perturbation theory (RI-MP2). We
       show that prior experimental and theoretical interpretations were
       incorrect in assuming that the most stable structures of the methylated
       trimers correspond to planar systems characterized by cyclic
       intermolecular hydrogen bonding. We found that stacked structures of two
       bases with the third base in a T-shape arrangement are the global minima
       in all of the methylated systems, The high-level geometries and
       interaction energies computed for the trimers serve also as a reference
       for the testing of recently developed DFT functionals with respect to
       their ability to describe correctly the balance between electrostatic
       and dispersion contributions that binds these trimers together. The
       recently reported M052X functional with a polarized triple-zeta basis
       set predicts 11 uracil trimer interaction energies with a
       root-mean-square error of 2.3 kcal/mol compared to our most highly
       correlated ab initio level of theory.,
    ISSN = 1573-4196,
    ISBN = 978-90-04-15542-8,
    Unique-ID = ISI:000254378800376,
    
  • K. Bohacek and P. Hobza, "Theme: pre-socratic philosophy," FILOSOFICKY CASOPIS, vol. 54, iss. 3, pp. 322-323, 2006.
    [Bibtex]
    @article ISI:000241081400001,
    Author = Bohacek, Krystof and Hobza, Pavel,
    Title = Theme: pre-socratic philosophy,
    Journal = FILOSOFICKY CASOPIS,
    Year = 2006,
    Volume = 54,
    Number = 3,
    Pages = 322-323,
    ISSN = 0015-1831,
    Unique-ID = ISI:000241081400001,
    
  • P. Hobza Jr., "The conception of the earth in Anaximander's cosmology," FILOSOFICKY CASOPIS, vol. 54, iss. 3, pp. 381-392, 2006.
    [Bibtex]
    @article ISI:000241081400004,
    Author = Hobza, Jr., Pavel,
    Title = The conception of the earth in Anaximander's cosmology,
    Journal = FILOSOFICKY CASOPIS,
    Year = 2006,
    Volume = 54,
    Number = 3,
    Pages = 381-392,
    Abstract = In reconstructing Anaximander's cosmological opinions it is important to
       grasp how Anaximander conceives of the earth. The problem is not its
       position at the centre of the universe, but rather how it remains
       there-what holds it in place. According to Aristotle, Anaximander
       explained how it kept its place by its equal distance from the limits of
       the universe: that is, by its symmetrical or equilibrial position at the
       centre of the universe. Despite this geometrical conception being
       commonly accepted, closer analysis shows that Aristotle's report is
       really a biased interpretation and that the real reason for the
       remaining in place of Anaximander's earth is its hovering on air.
       Evidence of this is partly given by doxographic reports which speak of
       Anaximander's earth as hovering (meteoros), and partly by its shape
       being flat, since its flatness enabled it to rest on air.,
    ISSN = 0015-1831,
    Unique-ID = ISI:000241081400004,
    
  • P. Hobza Jr., "The oral character of Greek culture," FILOSOFICKY CASOPIS, vol. 54, iss. 6, pp. 905-919, 2006.
    [Bibtex]
    @article ISI:000243884500009,
    Author = Hobza, Jr., Pavel,
    Title = The oral character of Greek culture,
    Journal = FILOSOFICKY CASOPIS,
    Year = 2006,
    Volume = 54,
    Number = 6,
    Pages = 905-919,
    ISSN = 0015-1831,
    Unique-ID = ISI:000243884500009,
    

2005

  • [DOI] D. Reha, H. Valdes, J. Vondrasek, P. Hobza, A. Abu-Riziq, B. Crews, and M. de Vries, "Structure and IR spectrum of phenylalanyl-glycyl-glycine tripetide in
    the gas-phase: IR/UV experiments, ab initio quantum chemical
    calculations, and molecular dynamic Simulations," CHEMISTRY-A EUROPEAN JOURNAL, vol. 11, iss. 23, pp. 6803-6817, 2005.
    [Bibtex]
    @article ISI:000233508800002,
    Author = Reha, D and Valdes, H and Vondrasek, J and Hobza, P and Abu-Riziq, A and
       Crews, B and de Vries, MS,
    Title = Structure and IR spectrum of phenylalanyl-glycyl-glycine tripetide in
       the gas-phase: IR/UV experiments, ab initio quantum chemical
       calculations, and molecular dynamic Simulations,
    Journal = CHEMISTRY-A EUROPEAN JOURNAL,
    Year = 2005,
    Volume = 11,
    Number = 23,
    Pages = 6803-6817,
    Month = NOV 18,
    Abstract = We investigated the potential-energy surface (PES) of the
       phenylalanyl-glycyl-glycine tripeptide in the gas phase by means of
       IR/UV double-resonance spectroscopy, and quantum chemical and
       statistical thermodynamic calculations. Experimentally, we observed four
       conformational structures and we recorded their IR spectra in the
       spectral region of 3000-4000 cm(-1). Computationally, we investigated
       the PES by a combination of molecular dynamics/quenching procedures with
       high-level correlated ab initio calculations. We found that neither
       empirical potentials nor various DFT functionals provide satisfactory
       results. On the other hand, the approximative DFT method covering the
       dispersion energy yields a reliable set of the most stable structures,
       which we subsequently investigated with an accurate, correlated ab
       initio treatment. The global minimum contains three moderately strong
       intramolecular hydrogen bonds and is mainly stabilized by London
       dispersion forces between the phenyl ring, the carboxylic acid group,
       and various peptide bonds. A proper description of the last type of
       interaction requires accurate correlated ab initio calculations,
       including the complete basis set limit of the MP2 method and CCSD(T)
       correction terms. Since in our beam experiments the conformations are
       frozen by cooling from a higher temperature, it is necessary to localize
       the most stable structures on the free-energy surface rather than on the
       PES. We used two different procedures (rigid rotor/harmonic
       oscillator/ideal gas approximation based on ab initio characteristics
       and evaluation of relative populations from the molecular dynamic
       simulations using the AMBER potential) and both yield four structures,
       the global minimum and three local minima. These four structures were
       among the 15 most energetically stable structures obtained from accurate
       ab initio optimization. The calculated IR spectra for these four
       structures agree well with the experimental frequencies, which validates
       the localization procedure.,
    DOI = 10.1002/chem.200500465,
    ISSN = 0947-6539,
    Unique-ID = ISI:000233508800002,
    
  • E. Mrazkova, D. Nachtigallova, and P. Hobza, "Theoretical study of potential energy surfaces of hydrogen bonded
    complexes of HCN ... H20 in its ground and electronically excited states," ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, vol. 230, pp. 281-PHYS, 2005.
    [Bibtex]
    @article ISI:000236797305739,
    Author = Mrazkova, E and Nachtigallova, D and Hobza, P,
    Title = Theoretical study of potential energy surfaces of hydrogen bonded
       complexes of HCN ... H20 in its ground and electronically excited states,
    Journal = ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY,
    Year = 2005,
    Volume = 230,
    Pages = 281-PHYS,
    Month = AUG 28,
    Note = 230th National Meeting of the American-Chemical-Society, Washington, DC,
       AUG 28-SEP 01, 2005,
    ISSN = 0065-7727,
    Unique-ID = ISI:000236797305739,
    
  • [DOI] A. Perez, J. Sponer, P. Jurecka, P. Hobza, F. Luque, and M. Orozco, "Are the hydrogen bonds of RNA (A center dot U) stronger than those of
    DNA (A center dot T)? A quantum mechanics study," CHEMISTRY-A EUROPEAN JOURNAL, vol. 11, iss. 17, pp. 5062-5066, 2005.
    [Bibtex]
    @article ISI:000231556400021,
    Author = Perez, A and Sponer, J and Jurecka, P and Hobza, P and Luque, FJ and
       Orozco, M,
    Title = Are the hydrogen bonds of RNA (A center dot U) stronger than those of
       DNA (A center dot T)? A quantum mechanics study,
    Journal = CHEMISTRY-A EUROPEAN JOURNAL,
    Year = 2005,
    Volume = 11,
    Number = 17,
    Pages = 5062-5066,
    Month = AUG 19,
    Abstract = The intrinsic stability of Watson-Crick d(A(.)T) and r(A(.)U) hydrogen
       bonds was analyzed by employing a variety of quantum-mechanical
       techniques, such as energy calculations, determination of reactivity
       indexes, and analysis of electron density topology. The analyses were
       performed not only for equilibrium gas-phase geometries, but also on
       hundreds of conformations derived from molecular dynamics (MD) and
       database analysis. None of our results support the idea that r(A(.)U)
       hydrogen bonds are intrinsically more stable than those of d(A(.)T).
       Instead, our data are in accordance with the traditional view that the
       greater stability of RNA relative to DNA is attributable to a variety of
       effects (e.g., stacking, sugar puckering, solvation) rather than to a
       significant difference in the hydrogen bonding of DNA and RNA base
       pairs.,
    DOI = 10.1002/chem.200500255,
    ISSN = 0947-6539,
    Unique-ID = ISI:000231556400021,
    
  • [DOI] B. Brauer, R. Gerber, M. Kabelac, P. Hobza, J. Bakker, A. Riziq, and M. de Vries, "Vibrational spectroscopy of the G center dot center dot center dot C
    base pair: Experiment, harmonic and anharmonic calculations, and the
    nature of the anharmonic couplings," JOURNAL OF PHYSICAL CHEMISTRY A, vol. 109, iss. 31, pp. 6974-6984, 2005.
    [Bibtex]
    @article ISI:000231042500025,
    Author = Brauer, B and Gerber, RB and Kabelac, M and Hobza, P and Bakker, JM and
       Riziq, AGA and de Vries, MS,
    Title = Vibrational spectroscopy of the G center dot center dot center dot C
       base pair: Experiment, harmonic and anharmonic calculations, and the
       nature of the anharmonic couplings,
    Journal = JOURNAL OF PHYSICAL CHEMISTRY A,
    Year = 2005,
    Volume = 109,
    Number = 31,
    Pages = 6974-6984,
    Month = AUG 11,
    Abstract = The results of harmonic and anharmonic frequency calculations on a
       guanine-cytosine complex with an enolic structure (a tautomeric form
       with cytosine in the enol form and with a hydrogen at the 7-position on
       guanine) are presented and compared to gas-phase IR-UV double resonance
       spectral data. Harmonic frequencies were obtained at the RI-MP2/cc-pVDZ,
       RI-MP2/TZVPP, and semiempirical PM3 levels of electronic structure
       theory. Anharmonic frequencies were obtained by the CC-VSCF method with
       improved PM3 potential surfaces; the improved PM3 potential surfaces are
       obtained from standard PM3 theory by coordinate scaling such that the
       improved PM3 harmonic frequencies are the same as those computed at the
       RI-MP2/cc-pVDZ level. Comparison of the data with experimental results
       indicates that the average absolute percentage deviation for the methods
       is 2.6\% for harmonic RI-MP2/cc-pVDZ (3.0\% with the inclusion of a
       0.956 scaling factor that compensates for anharmonicity), 2.5\% for
       harmonic RI-MP2/TZVPP (2.9\% with a 0.956 anharmonicity factor
       included), and 2.3\% for adapted PM3 CC-VSCF; the empirical scaling
       factor for the ab initio harmonic calculations improves the stretching
       frequencies but decreases the accuracy of the other mode frequencies.
       The agreement with experiment supports the adequacy of the improved PM3
       potentials for describing the anharmonic force field of the G(...)C base
       pair in the spectroscopically probed region. These results may be useful
       for the prediction of the pathways of vibrational energy flow upon
       excitation of this system. The anharmonic calculations indicate that
       anharnionicity along single mode coordinates can be significant for
       simple stretching modes. For several other cases, coupling between
       different vibrational modes provides the main contribution to
       anharmonicity. Examples of strongly anharmonically coupled modes are the
       symmetric stretch and group torsion of the hydrogen-bonded NH2 group on
       guanine, the OH stretch and torsion of the enol group on cytosine, and
       the NH stretch and NH out-of-plane bend of the non-hydrogen-bonded NH
       group on guanine.,
    DOI = 10.1021/jp051767m,
    ISSN = 1089-5639,
    Unique-ID = ISI:000231042500025,
    
  • [DOI] E. Mrazkova, P. Hobza, M. Bohl, D. Gauger, and W. Pohle, "Hydration-induced changes of structure and vibrational frequencies of
    methylphosphocholine studied as a model of biomembrane lipids," JOURNAL OF PHYSICAL CHEMISTRY B, vol. 109, iss. 31, pp. 15126-15134, 2005.
    [Bibtex]
    @article ISI:000231042800052,
    Author = Mrazkova, E and Hobza, P and Bohl, M and Gauger, DR and Pohle, W,
    Title = Hydration-induced changes of structure and vibrational frequencies of
       methylphosphocholine studied as a model of biomembrane lipids,
    Journal = JOURNAL OF PHYSICAL CHEMISTRY B,
    Year = 2005,
    Volume = 109,
    Number = 31,
    Pages = 15126-15134,
    Month = AUG 11,
    Abstract = The chemical characteristics of the polar parts of phospholipids as the
       main components of biological membranes were investigated by using
       infrared (IR) spectroscopy and theoretical calculations with water as a
       probe molecule. The logical key molecule used in this study is
       methylphosphocholine (MePC) as it is not only a representative model for
       a polar lipid headgroup but itself has biological significance. Isolated
       MePC forms a compact (folded) structure which is essentially stabilized
       by two intramolecular C-H center dot center dot center dot O type
       hydrogen bonds. At lower hydration, considerable wavenumber shifts were
       revealed by IR spectroscopy: the frequencies of the (O-P-O)(-) stretches
       were strongly redshifted, whereas methyl and methylene C-H and O-P-O
       stretches shifted surprisingly to blue. The origin of both red- and
       blueshifts was rationalized, on the basis of molecular-dynamics and
       quantum-chemistry calculations. In more detail, the hydration-induced
       blueshifts of C-H stretches could be shown to arise from several
       origins: disruption of the intramolecular C-H center dot center dot
       center dot O hydrogen bonds, formation of intermolecular C-H center dot
       center dot center dot O-water H-bonds. The stepwise disruption of the
       intramolecular hydrogen bonds appeared to be the main feature that
       causes partial unfolding of the compact structure. However, the
       transition from a folded to extended MePC structure was completed only
       at high hydration. One might hypothesize that the mechanism of
       hydration-driven conformational changes as described here for MePC could
       be transferred to other zwitterions with relevant internal C-H center
       dot center dot center dot O hydrogen bonds.,
    DOI = 10.1021/jp051208f,
    ISSN = 1520-6106,
    Unique-ID = ISI:000231042800052,
    
  • [DOI] M. Kabelac, L. Zendlova, D. Reha, and P. Hobza, "Potential energy surfaces of an adenine-thymine base pair and its
    methylated analogue in the presence of one and two water molecules:
    Molecular mechanics and correlated ab initio study," JOURNAL OF PHYSICAL CHEMISTRY B, vol. 109, iss. 24, pp. 12206-12213, 2005.
    [Bibtex]
    @article ISI:000229867300050,
    Author = Kabelac, M and Zendlova, L and Reha, D and Hobza, P,
    Title = Potential energy surfaces of an adenine-thymine base pair and its
       methylated analogue in the presence of one and two water molecules:
       Molecular mechanics and correlated ab initio study,
    Journal = JOURNAL OF PHYSICAL CHEMISTRY B,
    Year = 2005,
    Volume = 109,
    Number = 24,
    Pages = 12206-12213,
    Month = JUN 23,
    Abstract = Potential energy surfaces of morlohydrated and dihydrated
       adenine-thymine and 9-methyladenine-1-methylthymine base pairs were
       examined by the molecular dynamics/quenching technique using the Cornell
       et al. force field (J. Am. Chem. Soc. 1995, 117, 5179). Long runs of
       molecular dynarnics/quenching calculations allowed us to evaluate the
       free energy surface. The most stable and populated structures found were
       fully reoptimized at the correlated ab initio level employing the
       resolution of identity Moller-Plesset method. A systematic study of the
       base pairs' microhydration using both the empirical and the high-level
       correlated ab initio approaches is presented for the first time. We show
       that the occurrence of water molecules and their gradually increasing
       number as well as the methylation of the bases favor stacked structures
       over the planar hydrogen-bonded ones. These results based on the
       correlated ab initio calculations are in the excellent agreement with
       data obtained from our previous empirical potential molecular dynamics
       study.,
    DOI = 10.1021/jp045970d,
    ISSN = 1520-6106,
    Unique-ID = ISI:000229867300050,
    
  • [DOI] J. Vondrasek, L. Bendova, V. Klusak, and P. Hobza, "Unexpectedly strong energy stabilization inside the hydrophobic core of
    small protein rubredoxin mediated by aromatic residues: Correlated ab
    initio quantum chemical calculations (vol 127, pg 2615, 2005)," JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, vol. 127, iss. 22, pp. 8232, 2005.
    [Bibtex]
    @article ISI:000229619500063,
    Author = Vondrasek, J and Bendova, L and Klusak, V and Hobza, P,
    Title = Unexpectedly strong energy stabilization inside the hydrophobic core of
       small protein rubredoxin mediated by aromatic residues: Correlated ab
       initio quantum chemical calculations (vol 127, pg 2615, 2005),
    Journal = JOURNAL OF THE AMERICAN CHEMICAL SOCIETY,
    Year = 2005,
    Volume = 127,
    Number = 22,
    Pages = 8232,
    Month = JUN 8,
    DOI = 10.1021/ja059908l,
    ISSN = 0002-7863,
    Unique-ID = ISI:000229619500063,
    
  • [DOI] I. Daabkowska, P. Jurecka, and P. Hobza, "On geometries of stacked and H-bonded nucleic acid base pairs determined
    at various DFT, MP2, and CCSD(T) levels up to the CCSD(T)/complete basis
    set limit level," JOURNAL OF CHEMICAL PHYSICS, vol. 122, iss. 20, 2005.
    [Bibtex]
    @article ISI:000229544500033,
    Author = Daabkowska, I and Jurecka, P and Hobza, P,
    Title = On geometries of stacked and H-bonded nucleic acid base pairs determined
       at various DFT, MP2, and CCSD(T) levels up to the CCSD(T)/complete basis
       set limit level,
    Journal = JOURNAL OF CHEMICAL PHYSICS,
    Year = 2005,
    Volume = 122,
    Number = 20,
    Month = MAY 22,
    Abstract = The geometries and interaction energies of stacked and hydrogen-bonded
       uracil dimers and a stacked adenine thymine pair were studied by means
       of high-level quantum chemical calculations. Specifically, standard as
       well as counterpoise-corrected optimizations were performed at
       second-order Molller-Plesset (MP2) and coupled cluster level of theory
       with single, double, and perturbative triple excitations [CCSD(T)]
       levels with various basis sets up to the complete basis set limit. The
       results can be summarized as follows: (i) standard geometry optimization
       with small basis set (e. g., 6-31G*) provides fairly reasonable
       intermolecular separation; (ii) geometry optimization with extended
       basis sets at the MP2 level underestimates the intermolecular distances
       compared to the reference CCSD(T) results, whereas the MP2/cc-pVTZ
       counterpoise-corrected optimization agrees well with the reference
       geometries and, therefore, is recommended as a next step for improving
       MP2/cc-pVTZ geometries; (iii) the stabilization energy of stacked
       nucleic acids base pairs depends considerably on the method used for
       geometry optimization, so the use of reliable geometries, such as
       counterpoise-corrected MP2/cc-pVTZ ones, is recommended; (iv) the
       density functional theory methods fail completely in locating the energy
       minima for stacked structures and when the geometries from MP2
       calculations are used, the resulting stabilization energies are strongly
       underestimated; (v) the self-consistent charges-density functional tight
       binding method, with inclusion of the empirical dispersion energy,
       accurately reproduces interaction energies and geometries of
       dispersion-bonded (stacked) complexes; this method can thus be
       recommended for prescanning the potential energy surfaces of van der
       Waals complexes. (c) 2005 American Institute of Physics.,
    DOI = 10.1063/1.1906205,
    Article-Number = 204322,
    ISSN = 0021-9606,
    Unique-ID = ISI:000229544500033,
    
  • [DOI] W. Zierkiewicz, P. Jurecka, and P. Hobza, "On differences between hydrogen bonding and improper blue-shifting
    hydrogen bonding," CHEMPHYSCHEM, vol. 6, iss. 4, pp. 609-617, 2005.
    [Bibtex]
    @article ISI:000228597800009,
    Author = Zierkiewicz, W and Jurecka, P and Hobza, P,
    Title = On differences between hydrogen bonding and improper blue-shifting
       hydrogen bonding,
    Journal = CHEMPHYSCHEM,
    Year = 2005,
    Volume = 6,
    Number = 4,
    Pages = 609-617,
    Month = APR,
    Abstract = Twenty two hydrogen-bonded and improper blue-shifting hydrogen-bonded
       complexes were studied by means of the HF MP2 and B3LYP methods using
       the 6-31G(dp) and 6-311++G(dp) basis sets. In contrast to the standard H
       bonding, the origin of the improper blue-shifting H bonding is still not
       fully understood Contrary to a frequently presented idea, the electric
       field of the Proton acceptor cannot solely explain the different
       behavior of H-bonded and improper blue-shifting H-bonded complexes.
       Compression of the hydrogen bond due to different attractive
       forces-dispersion or electrostatics-makes an important contribution as
       well. The symmetry-adapted perturbation theory (SAPT) has been utilized
       to decompose the total interaction energy into physically meaningful
       contributions. In the red-shifting complexes, the induction energy is
       mostly larger than the dispersion energy while, in the case of
       blue-shifting complexes, the situation is opposite. Dispersion as an
       attractive force increases the blue shift in the blue-shifting complexes
       as it compresses the H bond and, therefore, it increases the Pauli
       repulsion. On the other hand, dispersion in the red-shifting complexes
       increases their red shift.,
    DOI = 10.1002/cphc.200400243,
    ISSN = 1439-4235,
    Unique-ID = ISI:000228597800009,
    
  • A. Malkov, M. Bell, F. Castelluzo, L. Bendova, P. Hobza, and P. Kocovsky, "Chiral pyridine N-oxides as novel organocatalysts for the asymmetric
    allylation of aldehydes with allyltrichlorosilanes and the role of
    arene-arene interactions between the catalyst and the substrate.," ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, vol. 229, iss. Part 2, pp. 357-ORGN, 2005.
    [Bibtex]
    @article ISI:000235066601459,
    Author = Malkov, AV and Bell, M and Castelluzo, F and Bendova, L and Hobza, P and
       Kocovsky, P,
    Title = Chiral pyridine N-oxides as novel organocatalysts for the asymmetric
       allylation of aldehydes with allyltrichlorosilanes and the role of
       arene-arene interactions between the catalyst and the substrate.,
    Journal = ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY,
    Year = 2005,
    Volume = 229,
    Number = Part 2,
    Pages = 357-ORGN,
    Month = MAR 13,
    Note = 229th National Meeting of the American-Chemical-Society, San Diego, CA,
       MAR 13-17, 2005,
    Organization = Amer Chem Soc,
    ISSN = 0065-7727,
    Unique-ID = ISI:000235066601459,
    
  • [DOI] J. Vondrasek, L. Bendova, V. Klusak, and P. Hobza, "Unexpectedly strong energy stabilization inside the hydrophobic core of
    small protein rubredoxin mediated by aromatic residues: Correlated ab
    initio quantum chemical calculations," JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, vol. 127, iss. 8, pp. 2615-2619, 2005.
    [Bibtex]
    @article ISI:000227308100046,
    Author = Vondrasek, J and Bendova, L and Klusak, V and Hobza, P,
    Title = Unexpectedly strong energy stabilization inside the hydrophobic core of
       small protein rubredoxin mediated by aromatic residues: Correlated ab
       initio quantum chemical calculations,
    Journal = JOURNAL OF THE AMERICAN CHEMICAL SOCIETY,
    Year = 2005,
    Volume = 127,
    Number = 8,
    Pages = 2615-2619,
    Month = MAR 2,
    Abstract = The formation of a hydrophobic core of globular proteins is believed to
       be the consequence of exterior hydrophobic forces of entropic nature.
       This, together with the low occurrence of hydrogen bonds in the protein
       core, leads to the opinion that the energy contribution of core
       formation to protein folding and stability is negligible. We show that
       stabilization inside the hydrophobic core of a small protein,
       rubredoxin, determined by means of high-level correlated ab initio
       calculations (complete basis set limit of MP2 stabilization energy +
       CCSD(T) correction term), amounted to similar to50 kcal/mol. These
       results clearly demonstrate strong attraction inside a hydrophobic core.
       This finding may lead to substantial changes in the current view of
       protein folding. We also point out the inability of the DFT/B3LYP method
       to describe a strong attraction between studied amino acids.,
    DOI = 10.1021/ja044607h,
    ISSN = 0002-7863,
    Unique-ID = ISI:000227308100046,
    
  • [DOI] I. Dabkowska, H. Gonzalez, P. Jurecka, and P. Hobza, "Stabilization energies of the hydrogen-bonded and stacked structures of
    nucleic acid base pairs in the crystal geometries of CG, AT, and AC DNA
    steps and in the NMR geometry of the 5 `-d(GCGAAGC)-3 ` hairpin:
    Complete basis set calculations at the MP2 and CCSD(T) levels," JOURNAL OF PHYSICAL CHEMISTRY A, vol. 109, iss. 6, pp. 1131-1136, 2005.
    [Bibtex]
    @article ISI:000226955800024,
    Author = Dabkowska, I and Gonzalez, HV and Jurecka, P and Hobza, P,
    Title = Stabilization energies of the hydrogen-bonded and stacked structures of
       nucleic acid base pairs in the crystal geometries of CG, AT, and AC DNA
       steps and in the NMR geometry of the 5 `-d(GCGAAGC)-3 ` hairpin:
       Complete basis set calculations at the MP2 and CCSD(T) levels,
    Journal = JOURNAL OF PHYSICAL CHEMISTRY A,
    Year = 2005,
    Volume = 109,
    Number = 6,
    Pages = 1131-1136,
    Month = FEB 17,
    Abstract = Stabilization energies of the H-bonded and stacked structures of a DNA
       base pair were studied in the crystal structures of adenine-thymine,
       cytosine-guanine, and adenine-cytosine steps as well as in the
       5'-d(GCGAAGC)-3' hairpin (utilizing the NMR geometry). Stabilization
       energies were determined as the sum of the complete basis set (CBS)
       limit of MP2 stabilization energies and the DeltaE(CCSD(T)) -
       DeltaE(MP2) correction term evaluated with the 6-31G*(0.25) basis set.
       The CBS limit was determined by a two-point extrapolation using the
       aug-cc-pVXZ basis sets for X = D and T. While the H-bonding energies are
       comparable to those of base pairs in a crystal and a vacuum, the
       stacking energies are considerably smaller in a crystal. Despite this,
       the stacking is still important and accounts for a significant part of
       the overall stabilization. It contributes equally to the stability of
       DNA as does H-bonding for AT-rich DNAs, while in the case of GC-rich
       DNAs it forms about one-third of the total stabilization. Interstrand
       stacking reaches surprisingly large values, well comparable to the
       intrastrand ones, and thus contributes significantly to the overall
       stabilization. The hairpin structure is characterized by significant
       stacking, and both guanine(...)cytosine pairs possess stacking energies
       larger than 11.5 kcal/mol. A high portion of stabilization in the
       studied hairpin comes from stacking (similar to that found for AT-rich
       DNAs) despite the fact that it contains two GC Watson-Crick pairs having
       very large H-bonding stabilization. The DFT/B3LYP/6-31G** method
       yields satisfactory values of interaction energies for H-bonded
       structures, while it fails completely for stacking.,
    DOI = 10.1021/jp046738a,
    ISSN = 1089-5639,
    Unique-ID = ISI:000226955800024,
    
  • [DOI] M. Hanus, M. Kabelac, D. Nachtigallova, and P. Hobza, "Mutagenic properties of 5-halogenuracils: Correlated quantum chemical ab
    initio study," BIOCHEMISTRY, vol. 44, iss. 5, pp. 1701-1707, 2005.
    [Bibtex]
    @article ISI:000226802000033,
    Author = Hanus, M and Kabelac, M and Nachtigallova, D and Hobza, P,
    Title = Mutagenic properties of 5-halogenuracils: Correlated quantum chemical ab
       initio study,
    Journal = BIOCHEMISTRY,
    Year = 2005,
    Volume = 44,
    Number = 5,
    Pages = 1701-1707,
    Month = FEB 8,
    Abstract = The relative stability of all possible 5-bromouracil tautomers was
       studied theoretically in a gas phase, in a microhydrated environment
       (with one water molecule), and in bulk water. Tautomer structures were
       determined by gradient optimization at the correlated ab initio quantum
       chemical level with an extended basis set of atomic orbitals. The role
       of water was examined by using a self-consistent reaction field method.
       The relative stabilization and free energies in the gas phase, the
       microhydrated environment, and the bulk water clearly support the
       preference of the canonical keto form of 5-bromouracil in all mentioned
       environments. An increased abundance of enol tautomers when passing from
       uracil to 5-bromouracil is not supported by our calculations. Thus, the
       tautomeric model of the mutagenic activity of 5-bromouracil proposed
       previously [Hu et al. Biochemistry (2004) 43, 636 1] can be refuted.
       The validity of other mutagenic models was also discussed, and finally a
       new mechanism for explaining the mutagenic activity of halogenuracils
       based on their different behaviors in triplet excited states was
       suggested.,
    DOI = 10.1021/bi048112g,
    ISSN = 0006-2960,
    Unique-ID = ISI:000226802000033,
    
  • [DOI] A. Abo-Riziq, L. Grace, E. Nir, M. Kabelac, P. Hobza, and M. de Vries, "Photochemical selectivity in guanine-cytosine base-pair structures," PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF
    AMERICA
    , vol. 102, iss. 1, pp. 20-23, 2005.
    [Bibtex]
    @article ISI:000226216400005,
    Author = Abo-Riziq, A and Grace, L and Nir, E and Kabelac, M and Hobza, P and de
       Vries, MS,
    Title = Photochemical selectivity in guanine-cytosine base-pair structures,
    Journal = PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF
       AMERICA,
    Year = 2005,
    Volume = 102,
    Number = 1,
    Pages = 20-23,
    Month = JAN 4,
    Abstract = Prebiotic chemistry presumably took place before formation of an
       oxygen-rich atmosphere and thus under conditions of intense short
       wavelength UV irradiation. Therefore, the UV photochemical stability of
       the molecular building blocks of life may have been an important
       selective factor in determining the eventual chemical makeup of critical
       biomolecules. To investigate the role of UV irradiation in base-pairing
       we have studied guanine (G) and cytosine (C) base pairs in the absence
       of the RNA backbone. We distinguished base-pair structures by IR-UV
       hole-burning spectroscopy as well as by high-level correlated ab initio
       calculations. The Watson-Crick structure exhibits broad UV absorption,
       in stark contrast to other GC structures and other base-pair structures.
       This broad absorption may be explained by a rapid internal conversion
       that makes this specific base pair arrangement uniquely photochemically
       stable.,
    DOI = 10.1073/pnas.0408574102,
    ISSN = 0027-8424,
    Unique-ID = ISI:000226216400005,
    
  • [DOI] J. Cerny and P. Hobza, "The X3LYP extended density functional accurately describes H-bonding but
    fails completely for stacking," PHYSICAL CHEMISTRY CHEMICAL PHYSICS, vol. 7, iss. 8, pp. 1624-1626, 2005.
    [Bibtex]
    @article ISI:000228241500003,
    Author = Cerny, J and Hobza, P,
    Title = The X3LYP extended density functional accurately describes H-bonding but
       fails completely for stacking,
    Journal = PHYSICAL CHEMISTRY CHEMICAL PHYSICS,
    Year = 2005,
    Volume = 7,
    Number = 8,
    Pages = 1624-1626,
    Abstract = The performance of the recently introduced X3LYP density functional
       which was claimed to significantly improve the accuracy for H-bonded and
       van der Waals complexes was tested for extended H-bonded and stacked
       complexes (nucleic acid base pairs and amino acid pairs). In the case of
       planar H-bonded complexes (guanine ... cytosine, adenine ... thymine)
       the DFT results nicely agree with accurate correlated ab initio results.
       For the stacked pairs (uracil dimer, cytosine dimer, adenine ... thymine
       and guanine ... cytosine) the DFT fails completely and it was even not
       able to localize any minimum at the stacked subspace of the potential
       energy surface. The geometry optimization of all these stacked clusters
       leads systematically to the planar H-bonded pairs. The amino acid pairs
       were investigated in the crystal geometry. DFT again strongly
       underestimates the accurate correlated ab initio stabilization energies
       and usually it was not able to describe the stabilization of a pair. The
       X3LYP functional thus behaves similarly to other current functionals.
       Stacking of nucleic acid bases as well as interaction of amino acids was
       described satisfactorily by using the tight-binding DFT method, which
       explicitly covers the London dispersion energy.,
    DOI = 10.1039/b502769c,
    ISSN = 1463-9076,
    Unique-ID = ISI:000228241500003,
    
  • [DOI] J. Rejnek, M. Hanus, M. Labelac, F. Ryjacek, and P. Hobza, "Correlated ab initio study of nucleic acid bases and their tautomers in
    the gas phase, in a microhydrated environment and in aqueous solution.
    Part 4. Uracil and thymine," PHYSICAL CHEMISTRY CHEMICAL PHYSICS, vol. 7, iss. 9, pp. 2006-2017, 2005.
    [Bibtex]
    @article ISI:000228634500018,
    Author = Rejnek, J and Hanus, M and Labelac, M and Ryjacek, F and Hobza, P,
    Title = Correlated ab initio study of nucleic acid bases and their tautomers in
       the gas phase, in a microhydrated environment and in aqueous solution.
       Part 4. Uracil and thymine,
    Journal = PHYSICAL CHEMISTRY CHEMICAL PHYSICS,
    Year = 2005,
    Volume = 7,
    Number = 9,
    Pages = 2006-2017,
    Abstract = Altogether 13 keto and enol tautomers of uracil and 13 keto and enol
       tautomers of thymine were studied theoretically in the gas phase, in a
       microhydrated environment ( 1 and 2 water molecules) and in a water
       environment. Bulk water was described using the thermodynamic
       integration method, Conductor-like polarizable continuum model (C-PCM,
       COSMO) and hybrid model (C-PCM + 1-2 explicit water molecules). The
       structures of various tautomers were determined at the RI-MP2 level
       using the TZVPP basis set while relative energies were determined at the
       CCSD(T) level. The relative free energies at 298 K were based on the
       relative energies mentioned above and zero-point vibration energies, and
       temperature dependent enthalpy terms and entropies evaluated at the
       MP2/6-31G** level. The effect of bulk solvent on the relative
       stability of uracil and thymine tautomers was studied using molecular
       dynamics free energy calculations by means of the thermodynamic
       integration method and self-consistent reaction field. Despite the
       completely different nature of these methods they provide comparable
       solvation free energies. Besides theoretical investigation, experimental
       detection of uracil and thymine tautomers was performed by means of
       steady-state fluorescence. We conclude that it is impossible to utilize
       the method used by Suwaiyan and Morsy (M. A. Morsy, A. M. Al-Somali and
       A. Suwaiyan, J. Phys. Chem. B, 1999, 103( 50), 11205) for tautomer
       detection, even if a very sensitive fluorimeter is used. Theoretical
       relative energies and free energies for isolated uracil and thymine
       tautomers support the existence of the canonical form only. The
       microhydrated environment and bulk solvent stabilize enol forms more
       than the canonical keto one, but gas phase destabilization of these enol
       forms is too high. Population of rare enol forms of uracil and thymine
       in bulk water will thus be very low and canonical structure will also be
       dominant in this phase.,
    DOI = 10.1039/b501499a,
    ISSN = 1463-9076,
    Unique-ID = ISI:000228634500018,
    
  • [DOI] B. Crews, A. Abo-Riziq, L. Grace, M. Callahan, M. Kabelac, P. Hobza, and M. de Vries, "IR-UV double resonance spectroscopy of guanine-H2O clusters," PHYSICAL CHEMISTRY CHEMICAL PHYSICS, vol. 7, iss. 16, pp. 3015-3020, 2005.
    [Bibtex]
    @article ISI:000230931200004,
    Author = Crews, B and Abo-Riziq, A and Grace, L and Callahan, M and Kabelac, M
       and Hobza, P and de Vries, MS,
    Title = IR-UV double resonance spectroscopy of guanine-H2O clusters,
    Journal = PHYSICAL CHEMISTRY CHEMICAL PHYSICS,
    Year = 2005,
    Volume = 7,
    Number = 16,
    Pages = 3015-3020,
    Abstract = We present the IR-UV double resonance spectrum of guanine monohydrate in
       the region 3100 cm(-1) to 3800 cm(-1) along with the energies and
       frequencies of these structures calculated at the non-empirical
       correlated ab initio RI-MP2/cc-pVDZ level. We assign the structures of
       guanine-water clusters by comparing the experimental spectra with the ab
       initio calculations and with the IR spectra of the bare guanine monomer.
       We find two clusters with guanine in the enol-amino tautomeric form and
       one structure with guanine in the keto-amino form.,
    DOI = 10.1039/b506107e,
    ISSN = 1463-9076,
    Unique-ID = ISI:000230931200004,
    
  • [DOI] J. Fanfrlik, J. Rejnek, M. Hanus, and P. Hobza, "Hydration Gibbs energies of nucleic acid bases determined by Gibbs
    energy perturbation, continuous and hybrid approaches," COLLECTION OF CZECHOSLOVAK CHEMICAL COMMUNICATIONS, vol. 70, iss. 11, pp. 1756-1768, 2005.
    [Bibtex]
    @article ISI:000234236700002,
    Author = Fanfrlik, J and Rejnek, J and Hanus, M and Hobza, P,
    Title = Hydration Gibbs energies of nucleic acid bases determined by Gibbs
       energy perturbation, continuous and hybrid approaches,
    Journal = COLLECTION OF CZECHOSLOVAK CHEMICAL COMMUNICATIONS,
    Year = 2005,
    Volume = 70,
    Number = 11,
    Pages = 1756-1768,
    Abstract = The hydration Gibbs energies of adenine, cytosine, guanine, thymine,
       uracil and isoguanine are determined by the molecular
       dynamics-thermodynamic integration method (MD-TI) and using continuous
       COSMO and hybrid models. The role of solvents in the COSMO model is
       described by permittivity and by combining the permittivity and specific
       hydration of single water molecules placed on the energetically most
       probable position in the hybrid model. The hybrid model describes
       hydration similarly to the COSMO model; both the continuous methods are
       in good agreement with the MD-TI method. Differences are small and the
       use of both models can be recommended.,
    DOI = 10.1135/cccc20051756,
    ISSN = 0010-0765,
    Unique-ID = ISI:000234236700002,
    
  • P. Hobza, "Did Parmenides hold that thinking and being are identical?," FILOSOFICKY CASOPIS, vol. 53, iss. 5, pp. 703-716, 2005.
    [Bibtex]
    @article ISI:000235422000004,
    Author = Hobza, P,
    Title = Did Parmenides hold that thinking and being are identical?,
    Journal = FILOSOFICKY CASOPIS,
    Year = 2005,
    Volume = 53,
    Number = 5,
    Pages = 703-716,
    Abstract = It is usually assumed that Parmenides somehow identified thinking with
       being (entity), and the thesis of the identity of thinking and being is
       meant to be present in two verses (B 8.34 and B 3). Nevertheless, on a
       thorough analysis of both verses it is evident that the thesis of the
       identity of thinking and being cannot be attributed to Parmenides. The
       main interpretational problem of verse B 8.34 is tauton (same,
       identical), which is usually understood as a predicate; on this
       understanding then the verse expresses the identity between thinking and
       being. However, from the context (i.e. from the verse B 8.29) it follows
       that tauton is rather the subject and is intended as a synonym with eon
       (entity), which excludes the whole verse treating of the identity
       between thinking and being. Fragment B 3, the interpretation of which is
       essentially ambivalent, is evidentally a later paraphrase and not the
       authentic verse.,
    ISSN = 0015-1831,
    Unique-ID = ISI:000235422000004,
    

2004

  • [DOI] J. Langmaier, Z. Samec, E. Samcova, P. Hobza, and D. Reha, "Origin of difference between one-electron redox potentials of guanosine
    and guanine: Electrochemical and quantum chemical study," JOURNAL OF PHYSICAL CHEMISTRY B, vol. 108, iss. 40, pp. 15896-15899, 2004.
    [Bibtex]
    @article ISI:000224213500062,
    Author = Langmaier, J and Samec, Z and Samcova, E and Hobza, P and Reha, D,
    Title = Origin of difference between one-electron redox potentials of guanosine
       and guanine: Electrochemical and quantum chemical study,
    Journal = JOURNAL OF PHYSICAL CHEMISTRY B,
    Year = 2004,
    Volume = 108,
    Number = 40,
    Pages = 15896-15899,
    Month = OCT 7,
    Abstract = Cyclic voltammetry was used to measure the rates of the chemical
       oxidation of guanine (G), guanosine (Gs), 2'-deoxyguanosine (dG), and
       2'-deoxyguanosine Y-monophosphate (dGMP) by electrochemically generated
       tris(2,2'-bipyridyl)ruthenium(III). The numeric fit of voltammograms to
       an ECCCE type of mechanism provided the equilibrium and rate constants
       of the two-step chemical oxidation of the guanine species. One-electron
       redox potentials evaluated from the equilibrium constant of the first
       electron uptake follow the sequence G < Gs approximate to dG approximate
       to dGMP, indicating that guanine is oxidized most easily. This sequence
       is expressed in the rate constant, which apparently follows the expected
       driving force dependence. Ab initio molecular orbital calculations were
       carried out using the DFT/B3LYP method with 6-31G** and
       6-31++G** basis sets, and also the RI-MP2 method with the cc-pVDZ
       basis set, so as to clarify the role of various factors contributing to
       the redox potential. Theoretical results suggest that the difference
       between the one-electron redox potentials of Gs and G (ca. 0.13 V)
       originates partly from the higher energy of proton dissociation from the
       cation radical Gs(.+) and partly from the higher difference in the
       hydration energy between the deprotonated radical Gs(-H)(.) and the
       parent Gs, which compensate for the lower ionization potential of Gs
       compared to that of G.,
    DOI = 10.1021/jp0481207,
    ISSN = 1520-6106,
    Unique-ID = ISI:000224213500062,
    
  • [DOI] J. Sponer, P. Jurecka, and P. Hobza, "Accurate interaction energies of hydrogen-bonded nucleic acid base pairs," JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, vol. 126, iss. 32, pp. 10142-10151, 2004.
    [Bibtex]
    @article ISI:000223279300057,
    Author = Sponer, J and Jurecka, P and Hobza, P,
    Title = Accurate interaction energies of hydrogen-bonded nucleic acid base pairs,
    Journal = JOURNAL OF THE AMERICAN CHEMICAL SOCIETY,
    Year = 2004,
    Volume = 126,
    Number = 32,
    Pages = 10142-10151,
    Month = AUG 18,
    Abstract = Hydrogen-bonded nucleic acids base pairs substantially contribute to the
       structure and stability of nucleic acids. The study presents reference
       ab initio structures and interaction energies of selected base pairs
       with binding energies ranging from -5 to -47 kcal/mol. The molecular
       structures are obtained using the RI-MP2 (resolution of identity MP2)
       method with extended cc-pVTZ basis set of atomic orbitals. The RI-MP2
       method provides results essentially identical with the standard MP2
       method. The interaction energies are calculated using the Complete Basis
       Set (CBS) extrapolation at the RI-MP2 level. For some base pairs,
       Coupled-Cluster corrections with inclusion of noniterative triple
       contributions (CCSD(T)) are given. The calculations are compared with
       selected medium quality methods. The PW91 DFT functional with the
       6-31G(**) basis set matches well the RI-MP2/CBS absolute interaction
       energies and reproduces the relative values of base pairing energies
       with a maximum relative error of 2.6 kcal/mol when applied with
       Becke3LYP-optimized geometries. The Becke3LYP DFT functional
       underestimates the interaction energies by few kcal/mol with relative
       error of 2.2 kcal/mol. Very good performance of nonpolarizable Cornell
       et al. force field is confirmed and this indirectly supports the view
       that H-bonded base pairs are primarily stabilized by electrostatic
       interactions.,
    DOI = 10.1021/ja048436s,
    ISSN = 0002-7863,
    Unique-ID = ISI:000223279300057,
    
  • [DOI] F. Madeja, M. Havenith, K. Nauta, R. Miller, J. Chocholousova, and P. Hobza, "Polar isomer of formic acid dimers formed in helium nanodroplets," JOURNAL OF CHEMICAL PHYSICS, vol. 120, iss. 22, pp. 10554-10560, 2004.
    [Bibtex]
    @article ISI:000221538200022,
    Author = Madeja, F and Havenith, M and Nauta, K and Miller, RE and Chocholousova,
       J and Hobza, P,
    Title = Polar isomer of formic acid dimers formed in helium nanodroplets,
    Journal = JOURNAL OF CHEMICAL PHYSICS,
    Year = 2004,
    Volume = 120,
    Number = 22,
    Pages = 10554-10560,
    Month = JUN 8,
    Abstract = The infrared spectrum of formic acid dimers in helium nanodroplets has
       been observed corresponding to excitation of the ``free'' OH and CH
       stretches. The experimental results are consistent with a polar acyclic
       structure for the dimer. The formation of this structure in helium, as
       opposed to the much more stable cyclic isomer with two O-H.O hydrogen
       bonds, is attributed to the unique growth conditions that exist in
       helium droplets, at a temperature of 0.37 K. Theoretical calculations
       are also reported to aid in the interpretation of the experimental
       results. At long range the intermolecular interaction between the two
       monomers is dominated by the dipole-dipole interaction, which favors the
       formation of a polar dimer. By following the minimum-energy path, the
       calculations predict the formation of an acyclic dimer having one O-H.O
       and one C-H.O contact. This structure corresponds to a local minimum on
       the potential energy surface and differs significantly from the
       structure observed in the gas phase. (C) 2004 American Institute of
       Physics.,
    DOI = 10.1063/1.1709942,
    ISSN = 0021-9606,
    Unique-ID = ISI:000221538200022,
    
  • [DOI] J. Pittner and P. Hobza, "CCSDT and CCSD(T) calculations on model H-bonded and stacked complexes," CHEMICAL PHYSICS LETTERS, vol. 390, iss. 4-6, pp. 496-499, 2004.
    [Bibtex]
    @article ISI:000221730600035,
    Author = Pittner, J and Hobza, P,
    Title = CCSDT and CCSD(T) calculations on model H-bonded and stacked complexes,
    Journal = CHEMICAL PHYSICS LETTERS,
    Year = 2004,
    Volume = 390,
    Number = 4-6,
    Pages = 496-499,
    Month = JUN 1,
    Abstract = The CCSD(T) and CCSDT interaction energies were determined for model
       planar H-bonded complexes (formamide... form-formamide, formamidine...
       formamidine) and stacked complexes (ethylene... ethylene,
       formaldehyde... formaldehyde). Various basis sets from the
       6-31G*(0.25) to aug-cc-pVDZ were used. Difference between CCSD(T) and
       CCSDT interaction energies were small and become negligible (bellow 0.1
       kcal/mol) if the aug-cc-pVDZ (or aug-cc-pVDZ/cc-pVDZ) basis set was
       applied. This result strongly supports the use of the CCSD(T) method for
       determination of true stabilization energies of extended complexes. (C)
       2004 Published by Elsevier B.V.,
    DOI = 10.1016/j.cplett.2004.04.009,
    ISSN = 0009-2614,
    Unique-ID = ISI:000221730600035,
    
  • [DOI] J. Sponer, V. Sychrovsky, P. Hobza, and J. Sponer, "Interactions of hydrated divalent metal cations with nucleic acid bases.
    How to relate the gas phase data to solution situation and binding
    selectivity in nucleic acids," PHYSICAL CHEMISTRY CHEMICAL PHYSICS, vol. 6, iss. 10, pp. 2772-2780, 2004.
    [Bibtex]
    @article ISI:000222182100030,
    Author = Sponer, JE and Sychrovsky, V and Hobza, P and Sponer, J,
    Title = Interactions of hydrated divalent metal cations with nucleic acid bases.
       How to relate the gas phase data to solution situation and binding
       selectivity in nucleic acids,
    Journal = PHYSICAL CHEMISTRY CHEMICAL PHYSICS,
    Year = 2004,
    Volume = 6,
    Number = 10,
    Pages = 2772-2780,
    Month = MAY 21,
    Abstract = Binding modes of hydrated Zn2+ and Mg2+ cations to the N7 and O6
       positions of guanine have been characterized by state-of-the-art ab
       initio model calculations. We show how differences in the electronic
       structure of the cationic complexes, as revealed by gas-phase
       computations, translate into differences in the biological function of
       the two studied metals. The thermodynamic driving force of the metal
       binding process is estimated on the basis of interaction energies and
       total electronic energies. The computed results unambiguously reveal
       that the N7 position of guanine exhibits a greater propensity to bind
       Zn2+ than Mg2+ while both cations have a similar affinity to bind to O6.
       Contrary to the intuitive expectations, however, the computed data do
       not suggest any superiority of the N7 inner shell binding mode for Zn2+
       compared to the O6 binding. For Mg2+ the O6 inner shell binding mode is
       favored over the N7 one. The gas-phase data, when properly exrapolated,
       provide a relevant picture of many (though not all) fundamental aspects
       of the diversity of cation binding to nucleic acids.,
    DOI = 10.1039/b404306p,
    ISSN = 1463-9076,
    Unique-ID = ISI:000222182100030,
    
  • [DOI] M. Kabelac, C. Plutzer, K. Kleinermanns, and P. Hobza, "Isomer selective IR experiments and correlated ab initio quantum
    chemical calculations support planar H-bonded structure of the 7-methyl
    adenine center dot center dot center dot adenine and stacked structure
    of the 9-methyl adenine center dot center dot center dot adenine base
    pairs," PHYSICAL CHEMISTRY CHEMICAL PHYSICS, vol. 6, iss. 10, pp. 2781-2785, 2004.
    [Bibtex]
    @article ISI:000222182100031,
    Author = Kabelac, M and Plutzer, C and Kleinermanns, K and Hobza, P,
    Title = Isomer selective IR experiments and correlated ab initio quantum
       chemical calculations support planar H-bonded structure of the 7-methyl
       adenine center dot center dot center dot adenine and stacked structure
       of the 9-methyl adenine center dot center dot center dot adenine base
       pairs,
    Journal = PHYSICAL CHEMISTRY CHEMICAL PHYSICS,
    Year = 2004,
    Volume = 6,
    Number = 10,
    Pages = 2781-2785,
    Month = MAY 21,
    Abstract = In this paper we show that the stacked structures of 9-methyl adenine...
       adenine are comparably stable as the most stable hydrogen bonded
       structures and that the calculated IR pattern of the stacked structures
       is in a very good agreement with the experimental spectrum. The pair
       7-methyl adenine... adenine on the other hand shows a nearly planar
       hydrogen bond arrangement and no stacked structure was observed.,
    DOI = 10.1039/b316433k,
    ISSN = 1463-9076,
    Unique-ID = ISI:000222182100031,
    
  • [DOI] J. Bakker, I. Compagnon, G. Meijer, G. von Helden, M. Kabelac, P. Hobza, and M. de Vries, "The mid-IR absorption spectrum of gas-phase clusters of the nucleobases
    guanine and cytosine," PHYSICAL CHEMISTRY CHEMICAL PHYSICS, vol. 6, iss. 10, pp. 2810-2815, 2004.
    [Bibtex]
    @article ISI:000222182100036,
    Author = Bakker, JM and Compagnon, I and Meijer, G and von Helden, G and Kabelac,
       M and Hobza, P and de Vries, MS,
    Title = The mid-IR absorption spectrum of gas-phase clusters of the nucleobases
       guanine and cytosine,
    Journal = PHYSICAL CHEMISTRY CHEMICAL PHYSICS,
    Year = 2004,
    Volume = 6,
    Number = 10,
    Pages = 2810-2815,
    Month = MAY 21,
    Abstract = The mid-infrared (IR) absorption spectrum of jet-cooled clusters of the
       nucleobases guanine and cytosine has been recorded in the 500-1800
       cm(-1) range by ion-dip spectroscopy. Some 30 clearly separated and
       sharp resonances are observed. The combination of the experimental data
       with new high-level ab initio calculations is consistent with a previous
       structural assignment and a tentative assignment is made to the K7-1E
       structure of guanine-cytosine. These data can serve as a test of the
       method in the mid-IR regime.,
    DOI = 10.1039/b316158g,
    ISSN = 1463-9076,
    Unique-ID = ISI:000222182100036,
    
  • [DOI] W. Pohle, D. Gauger, M. Bohl, E. Mrazkova, and P. Hobza, "Lipid hydration: Headgroup CH moieties are involved in water binding," BIOPOLYMERS, vol. 74, iss. 1-2, pp. 27-31, 2004.
    [Bibtex]
    @article ISI:000221160600004,
    Author = Pohle, W and Gauger, DR and Bohl, M and Mrazkova, E and Hobza, P,
    Title = Lipid hydration: Headgroup CH moieties are involved in water binding,
    Journal = BIOPOLYMERS,
    Year = 2004,
    Volume = 74,
    Number = 1-2,
    Pages = 27-31,
    Month = MAY-JUN,
    Note = 10th European Conference on the Spectroscopy of Biological Molecules
       (ECSBM 2003), Szeged, HUNGARY, AUG 30-SEP 04, 2003,
    Abstract = To explore the interaction potential of phospholipids, we have studied
       the hydration of diacyl phosphatidylcholine (PC) and
       methylphosphocholine (MePC), a pertinent model compound, by ir
       spectroscopy. Related ab initio Hartree-Fock calculations were performed
       for MePC Water is considered ideal as a relevant probe molecule.
       Spectroscopic data for MePC reveal a strong influence of bound hydration
       water not only on the phosphate groups but also onto the putatively
       apolar CHn groups. The same could be demonstrated for deuterated
       dimyristoyl PC taken as a ``complete'' lipid molecule: both headgroup
       methyl and methylene moieties art gradually, but remarkably affected by
       hydration, as evidenced by strong wavenumber upshifts of C-H stretching
       vibration hands. These findings may originate in directed interactions
       of the CHn groups with bound water molecules, but hydration-driven
       conformational changes of PC headgroups could also occur. The results of
       the ab initio calculations rationalize the first explanation by
       predicting a substantial contribution of specific C-(HOH2)-O-...
       interactions, mainly characterized by a dramatic loss of electron
       density of the sigma* antibonding molecular orbitals of C-H bonds.
       Hence, the propensity of the lipid headgroup methyl and methylene groups
       to act as donor sites in hydrogen bonding must no longer be ignored when
       considering the interaction potential of PCs. (C) 2004 Wiley
       Periodicals, Inc.,
    DOI = 10.1002/bip.20037,
    ISSN = 0006-3525,
    Unique-ID = ISI:000221160600004,
    
  • [DOI] P. Jurecka, J. Sponer, and P. Hobza, "Potential energy surface of the cytosine dimer: MP2 complete basis set
    limit interaction energies, CCSD(T) correction term, and comparison with
    the AMBER force field," JOURNAL OF PHYSICAL CHEMISTRY B, vol. 108, iss. 17, pp. 5466-5471, 2004.
    [Bibtex]
    @article ISI:000220997300048,
    Author = Jurecka, P and Sponer, J and Hobza, P,
    Title = Potential energy surface of the cytosine dimer: MP2 complete basis set
       limit interaction energies, CCSD(T) correction term, and comparison with
       the AMBER force field,
    Journal = JOURNAL OF PHYSICAL CHEMISTRY B,
    Year = 2004,
    Volume = 108,
    Number = 17,
    Pages = 5466-5471,
    Month = APR 29,
    Abstract = The complete basis set (CBS) limit of the MP2 interaction energy and the
       CCSD(T) correction term determined as the difference between the CCSD(T)
       and MP2 interaction energies were evaluated for 17 stacked and 4
       H-bonded structures of the cytosine dimer. Extrapolation to the MP2 CBS
       limit was done using the aug-cc-pVDZ and aug-cc-pVTZ results, and the
       CCSD(T) correction term was determined with the 6-31G*(0.25) basis
       set. Extrapolation to the CBS limit is essential in all parts of the
       potential energy surface and affects mainly the absolute MP2
       stabilization energy. The effect on the relative stability is smaller
       but not negligible. The CCSD(T) correction term is for stacked
       structures with large overlaps of the monomers substantially repulsive
       but not uniform. Thus, when comparing the final estimate (abbreviated as
       CBS(T)) with previously used medium-level MP2/6-31G*(0.25) data, the
       CCSD(T) correction partially compensates for the enhanced absolute MP2
       CBS stabilization but. further increases the relative differences
       between different structures. The difference between the
       MP2/6-31G*(0.25) and the new CBS(T) reference values is in the range
       of +0.3 to -2.1 kcal/mol. The difference between the parallel and
       antiparallel structures is enhanced by 2 kcal/mol. The CCSD(T)
       correction is negligible in the H-bonded structure and in stacked
       structures with a minimal overlap of bases. The new reference CBS(T)
       data are compared with the AMBER force field testing both HF and MP2
       electrostatic potential fitted atom-centered charges. The overall
       agreement of the force field with the CBS(T) data is very satisfactory.
       We nevertheless identify differences that are attributed to polarization
       and short-term effects not included in the force field. Interestingly,
       whereas MP2/6-31G*(0.25) calculations are better reproduced with the
       MP2 variant of the force field the new CBS(T) reference data are in
       better agreement with the use of HF charges in the force field,
       indicating the enhanced role of polarization.,
    DOI = 10.1021/jp049956c,
    ISSN = 1520-6106,
    Unique-ID = ISI:000220997300048,
    
  • [DOI] M. Hocek, P. Stepnicka, J. Ludvik, I. Cisarova, I. Votruba, D. Reha, and P. Hobza, "Ferrocene-modified purines as potential electrochemical markers:
    Synthesis, crystal structures, electrochemistry and cytostatic activity
    of (ferrocenylethynyl)- and (ferrocenylethyl)purines," CHEMISTRY-A EUROPEAN JOURNAL, vol. 10, iss. 8, pp. 2058-2066, 2004.
    [Bibtex]
    @article ISI:000221025200022,
    Author = Hocek, M and Stepnicka, P and Ludvik, J and Cisarova, I and Votruba, I
       and Reha, D and Hobza, P,
    Title = Ferrocene-modified purines as potential electrochemical markers:
       Synthesis, crystal structures, electrochemistry and cytostatic activity
       of (ferrocenylethynyl)- and (ferrocenylethyl)purines,
    Journal = CHEMISTRY-A EUROPEAN JOURNAL,
    Year = 2004,
    Volume = 10,
    Number = 8,
    Pages = 2058-2066,
    Month = APR 19,
    Abstract = Palladium-catalyzed Sonoga-shira cross-coupling reactions of halopurines
       9-benzyl-6-chloropurine (2a), 9-benzyl-8-bromoadenine (2b), and
       9-benzyl-2-chloroadenine (2c) with ethynylferrocene (1) gave the
       corresponding (ferrocenylethynyl)purines 3a-c in moderate to good
       yields. Catalytic hydrogenation of these alkynes over Pd/C afforded the
       respective saturated [2(ferrocenyl)ethyl]purines 4 a-c. The crystal
       structures 3a, 3b, 4a and 4b as determined by X-ray diffraction show
       interesting solid-state interactions, markedly different for purines 3a
       and 4a on one hand and adenines 3b and 4b that possess a free amino
       group on the other. Electrochemistry of electrochemically labelled
       purines 3 and 4 has been studied by voltammetry and cyclic voltammetry
       on platinum disc electrode and the experimental oxidation potentials
       were confirmed and explained by ionization potentials from theoretical
       DFT calculations. Several compounds of this series exhibited a
       considerable cytostatic effect.,
    DOI = 10.1002/chem.200305621,
    ISSN = 0947-6539,
    Unique-ID = ISI:000221025200022,
    
  • [DOI] W. Zierkiewicz, D. Michalska, and P. Hobza, "The barrier to internal rotation and electronic effects in
    para-halogenophenols: theoretical study," CHEMICAL PHYSICS LETTERS, vol. 386, iss. 1-3, pp. 95-100, 2004.
    [Bibtex]
    @article ISI:000189244300016,
    Author = Zierkiewicz, W and Michalska, D and Hobza, P,
    Title = The barrier to internal rotation and electronic effects in
       para-halogenophenols: theoretical study,
    Journal = CHEMICAL PHYSICS LETTERS,
    Year = 2004,
    Volume = 386,
    Number = 1-3,
    Pages = 95-100,
    Month = MAR 1,
    Abstract = The OH rotational barrier height in phenol and para-halogenophenols
       systematically decreases in the series Br, Cl and F, while the changes
       in the CO bond length and CO bond strength do not follow this order. On
       the basis of the NBO analysis it is suggested that lowering of the
       barrier height in p-halogenophenols is caused by the decrease of
       electron density in the sigma antibonding orbital, sigma*(CO), and a
       weak occupancy of this orbital is due to the electron delocalization
       from the sigma(CC) ring orbitals. This effect can be either reinforced
       or reduced, depending on the extent of conjugation between the p(z)-type
       lone electron pair on the oxygen atom and the pi*(CC) acceptor
       orbitals in the aromatic ring. (C) 2004 Elsevier B.V. All rights
       reserved.,
    DOI = 10.1016/j.cplett.2004.01.026,
    ISSN = 0009-2614,
    Unique-ID = ISI:000189244300016,
    
  • [DOI] M. Hanus, M. Kabelac, J. Rejnek, F. Ryjacek, and P. Hobza, "Correlated ab initio study of nucleic acid bases and their tautomers in
    the gas phase, in a microhydrated environment, and in aqueous solution.
    Part 3. Adenine," JOURNAL OF PHYSICAL CHEMISTRY B, vol. 108, iss. 6, pp. 2087-2097, 2004.
    [Bibtex]
    @article ISI:000188831700038,
    Author = Hanus, M and Kabelac, M and Rejnek, J and Ryjacek, F and Hobza, P,
    Title = Correlated ab initio study of nucleic acid bases and their tautomers in
       the gas phase, in a microhydrated environment, and in aqueous solution.
       Part 3. Adenine,
    Journal = JOURNAL OF PHYSICAL CHEMISTRY B,
    Year = 2004,
    Volume = 108,
    Number = 6,
    Pages = 2087-2097,
    Month = FEB 12,
    Abstract = Altogether, 14 amino and imino tautomers of adenine were studied
       theoretically in the gas phase, in a microhydrated environment (one and
       two water molecules), and in bulk water environment using the
       thermodynamic integration method (MD-TI), conductor-like polarizable
       continuum model (C-PCM, COSMO), and a hybrid model (C-PCM + one to three
       explicit water molecules). The structures and relative energies of
       various tautomers were determined at the RI-MP2 level using the TZVPP
       basis set. The relative enthalpies at 0 K and relative free energies at
       298 K were based on relative energies and zero-point vibration energies,
       temperature-dependent enthalpy terms, and entropies evaluated at the
       MP2/6-31G** level. The effect of bulk solvent on the relative
       stability of adenine tautomers was studied by molecular dynamics free
       energy calculations using the thermodynamic integration method and
       self-consistent reaction field. The dipole moment of the canonical form
       is rather small (2.8 D) but three rare imino tautomers have very large
       dipole moments (more than 10 D). The canonical form is the global
       minimum at all theoretical levels in the gas phase, in a microhydrated
       environment, and in the bulk water. Two unusual rare amino tautomers
       having hydrogens at N3 and N7, respectively, are less stable in the gas
       phase by more than 7 kcal/mol and represent the first and the second
       local rninimum. Microhydration, as well as bulk water, stabilizes these
       unusual tautomers, and the energy gap between them and the canonical
       form is reduced, but the canonical tautomer remains the global minimum
       in all three phases. Relative free energies (T = 298 K) of these two
       unusual tautomers in the bulk water evaluated by molecular dynamics free
       energy calculations are 2.5 and 2.8 kcal/mol, which supports their
       coexistence in this phase. The C-PCM results agree well with the MD-Tl
       data, and the agreement became close when considering not only the bare
       tautomers but their complexes with several water molecules representing
       first solvation shell. Other tautomers are considerably less stable (by
       12-45 kcal/mol), and neither a microhydrated environment nor bulk water
       can change this unfavorable tautomeric equilibrium. The theoretical data
       predicting the coexistence of the canonical form and the N3 and the N7
       tautomers in bulk water nicely agreed with experimental data obtained
       from NMR measurements of the adenine tautomers in DMSO (Laxer, A.;
       Major, D. T.; Gottlieb, H. E.; Fischer, B. J. Org. Client. 2001, 66,
       5463.).,
    DOI = 10.1021/jp036090m,
    ISSN = 1520-6106,
    Unique-ID = ISI:000188831700038,
    
  • [DOI] V. Sychrovsky, J. Sponer, and P. Hobza, "Theoretical calculation of the NMR spin-spin coupling constants and the
    NMR shifts allow distinguishability between the specific direct and the
    water-mediated binding of a divalent metal cation to guanine," JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, vol. 126, iss. 2, pp. 663-672, 2004.
    [Bibtex]
    @article ISI:000188197800061,
    Author = Sychrovsky, V and Sponer, J and Hobza, P,
    Title = Theoretical calculation of the NMR spin-spin coupling constants and the
       NMR shifts allow distinguishability between the specific direct and the
       water-mediated binding of a divalent metal cation to guanine,
    Journal = JOURNAL OF THE AMERICAN CHEMICAL SOCIETY,
    Year = 2004,
    Volume = 126,
    Number = 2,
    Pages = 663-672,
    Month = JAN 21,
    Abstract = The calculated intermolecular and intramolecular indirect NMR spin-spin
       coupling constants and NMR shifts were used for the discrimination
       between the inner-shell and the outer-shell binding motif of hydrated
       divalent cations Mg2+ or Zn2+ with a guanine base. The intermolecular
       coupling constants (1)J(X, O6) and (1)J(X, N7) (X = Mg2+, Zn2+) can be
       unambiguously assigned to the specific inner-shell binding motif of the
       hydrated cation either with oxygen O6 or with nitrogen N7 of guanine.
       The calculated coupling constants (1)J(Mg, O6) and (1)J(Zn, O6) were 6.2
       and -17.5 Hz, respectively, for the inner-shell complex of cation
       directly interacting with oxygen O6 of guanine. For the inner-shell
       coordination of the cation at nitrogen N7 the calculated coupling
       constants (1)J(Mg,N7) and (1)J(Zn,N7) were 5.6 and -36.5 Hz,
       respectively. When the binding of the cation is water-mediated, the
       coupling constant is zero. To obtain reliable shifts in NMR parameters,
       hydrated guanine was utilized as the reference state. The calculated
       change of NMR spin-spin coupling constants due to the hydration and
       coordination of the cation with guanine is caused mainly by the
       variation of Fermi-contact coupling contribution while the variation of
       diamagnetic spin-orbit, paramagnetic spin-orbit, and spin-dipolar
       coupling contributions is small. The change of s-character of guanine
       sigma bonding, sigma antibonding, and lone pair orbitals upon the
       hydration and cation coordination (calculated using the Natural Bond
       Orbital analysis) correlates with the variation of the Fermi-contact
       term. The calculated NMR shifts delta(N7) of -15.3 and -12.2 ppm upon
       the coordination of Mg2+ and Zn2+ ion are similar to the NMR shift of
       19.6 ppm toward the high field measured by Tanaka for N7 of guanine upon
       the coordination of the Cd2+ cation (Tanaka, Y.; Kojima, C.; Morita, E.
       H.; Kasai. Y.; Yamasaki, K.; Ono, A.; Kainosho, M.; Taira, K. J. Am.
       Chem. Soc. 2002, 124, 4595-4601). The present data indicate that
       measurements of NMR intermolecular coupling constants may be used to
       discriminate between the specific inner- and outer-shell binding of
       divalent cations to nucleobases in DNA and RNA.,
    DOI = 10.1021/ja036942w,
    ISSN = 0002-7863,
    Unique-ID = ISI:000188197800061,
    
  • [DOI] J. Chocholousova, V. Spirko, and P. Hobza, "First local minimum of the formic acid dimer exhibits simultaneously
    red-shifted O-H center dot center dot center dot O and improper
    blue-shifted C-H center dot center dot center dot O hydrogen bonds," PHYSICAL CHEMISTRY CHEMICAL PHYSICS, vol. 6, iss. 1, pp. 37-41, 2004.
    [Bibtex]
    @article ISI:000187438000007,
    Author = Chocholousova, J and Spirko, V and Hobza, P,
    Title = First local minimum of the formic acid dimer exhibits simultaneously
       red-shifted O-H center dot center dot center dot O and improper
       blue-shifted C-H center dot center dot center dot O hydrogen bonds,
    Journal = PHYSICAL CHEMISTRY CHEMICAL PHYSICS,
    Year = 2004,
    Volume = 6,
    Number = 1,
    Pages = 37-41,
    Abstract = The first local minimum of the formic acid dimer exhibits simultaneously
       red-shifted O-H...O and blue-shifted C-H...O hydrogen bonds. The
       improper, blue-shifted hydrogen bond was investigated by means of the
       NBO analysis, rehybridization model and optimization in the electric
       field. It was shown that the electrostatic model cannot describe the
       nature of the blue-shifted H-bond. From the NBO analysis it becomes
       evident that the formation of the O-H...O hydrogen bond and C-H...O
       improper hydrogen bond can be explained on the basis of an increase of
       electron density in the sigma* antibonding O-H orbital and a decrease
       of electron density in the sigma* antibonding C-H orbital. While the
       former effect is easily explained on the basis of hyperconjugation, the
       latter requires the existence of a new mesomeric structure characterized
       by delocalization of electron density from the C-H sigma* antibonding
       orbital to the remaining part of the complex. The rehybridization model
       explains properly the formation of both hydrogen bonds but fails to
       interpret the changes of the other bonds.,
    DOI = 10.1039/b314148a,
    ISSN = 1463-9076,
    Unique-ID = ISI:000187438000007,
    
  • [DOI] W. Zierkiewicz and P. Hobza, "The dihydrogen bond in X3C-H center dot center dot center dot H-M
    complexes (X = F, Cl, Br; M = Li, Na, K). A correlated quantum chemical
    ab initio and density functional theory study," PHYSICAL CHEMISTRY CHEMICAL PHYSICS, vol. 6, iss. 23, pp. 5288-5296, 2004.
    [Bibtex]
    @article ISI:000225301400004,
    Author = Zierkiewicz, W and Hobza, P,
    Title = The dihydrogen bond in X3C-H center dot center dot center dot H-M
       complexes (X = F, Cl, Br; M = Li, Na, K). A correlated quantum chemical
       ab initio and density functional theory study,
    Journal = PHYSICAL CHEMISTRY CHEMICAL PHYSICS,
    Year = 2004,
    Volume = 6,
    Number = 23,
    Pages = 5288-5296,
    Abstract = Quantum chemical calculations were performed on nine dihydrogen-bonded
       complexes with haloform (F3CH, Cl3CH and Br3CH) as a proton donor and
       alkali metal hydride (HLi, HNa and HK) as a proton acceptor.
       MP2/6-311++G(d, p) and B3LYP/6-311++G(d, p) results show that the
       stabilization energies of these complexes are large and comparable to
       the stabilization energies of standard H-bonded complexes. Elongation
       and weakening ( red shift) of the CH, HNa and HK bonds upon complexation
       were found while contraction and strengthening ( blue shift) was
       observed in HLi. The H...H bond was found to be ionic and its ionicity
       is larger than that of the H...Y bond in standard and improper H-bonds.
       The calculated free energy (DG) revealed that only potassium hydride
       complexes (F3CH...HK, Cl3CH...HK and Br3CH...HK) are stable under
       standard conditions ( T = 298.150 K and p = 101.325 N m(-2)) in the gas
       phase. To elucidate the role of the electrostatic contribution, the
       optimization of the proton donor and proton acceptor molecules in the
       electric field of a partner was performed. The HLi bond is contracted in
       the electric field of the haloform while the HM ( M = Na, K) bonds are
       elongated and the electrostatic field itself is sufficient explanation
       of these phenomena. Natural bond order (NBO) and natural resonance
       theory (NRT) analyses were performed. The NBO analysis revealed that
       significant electron density was transferred from the sigma bonding
       orbital of a proton acceptor to the antibonding sigma*(CH) orbital of
       the proton donor. Symmetry adapted perturbation theory (SAPT) was
       utilized to decompose the total interaction energy into physically
       correct contributions.,
    DOI = 10.1039/b410112j,
    ISSN = 1463-9076,
    Unique-ID = ISI:000225301400004,
    
  • K. Bohacek and P. Hobza, "Ancient philosophy - Introduction," FILOSOFICKY CASOPIS, vol. 52, iss. 6, pp. 883-885, 2004.
    [Bibtex]
    @article ISI:000227714700001,
    Author = Bohacek, K and Hobza, P,
    Title = Ancient philosophy - Introduction,
    Journal = FILOSOFICKY CASOPIS,
    Year = 2004,
    Volume = 52,
    Number = 6,
    Pages = 883-885,
    ISSN = 0015-1831,
    Unique-ID = ISI:000227714700001,
    
  • P. Hobza, "Aristotle and Theophrastus as creators of Milesian philosophy," FILOSOFICKY CASOPIS, vol. 52, iss. 6, pp. 889-924, 2004.
    [Bibtex]
    @article ISI:000227714700002,
    Author = Hobza, P,
    Title = Aristotle and Theophrastus as creators of Milesian philosophy,
    Journal = FILOSOFICKY CASOPIS,
    Year = 2004,
    Volume = 52,
    Number = 6,
    Pages = 889-924,
    Abstract = In my study I offer a new view of the thought of three Milesian
       thinkers. A critical review of the sources shows that the Milesians did
       not search for the arche (beginning, or origin) of the world. This
       viewpoint is projected onto their thought on the basis of Aristotle's
       interpretation which sees all predecessors through the prism of the
       (more or less synonomous) concepts of principle (arche), cause (aition)
       and element (stoicheion). An analysis of the sources shows that the
       concept of arche as a philosophical concept has nothing in common with
       Milesian speculation, but on the contrary enters philosophical
       terminology from the mathematics of the fifth century, through Plato up
       to Aristotle, where it is first understood as an ontological
       constituent, or more precisely, principle, of the world. However, that
       the Milesians did not search for the origin (arche) of the world throws
       an entirely new light oil their thought. A critical analysis of, for
       example, Anaximander's thought shows that the concept of the Unbounded
       (to apeiron) which is traditionally understood as the basis of his
       knowledge, is not his actual concept, but on the contrary Theophrastus'
       interpretation. Again, Anaximenes cannot be placed under a ``theory of
       physical changes'' based on gradual metamorphosis of the air as a
       principle that enables the application of the Aristotelian categories of
       dilution and compression. In summary: At the centre of Milesian
       speculation was not a search for the origin (arche) of the world as
       (Aristotelian) principles, but rather an engagement to outline the new
       cosmogonical and cosmological picture of the world.,
    ISSN = 0015-1831,
    Unique-ID = ISI:000227714700002,
    

2003

  • [DOI] P. Jurecka and P. Hobza, "True stabilization energies for the optimal planar hydrogen-bonded and
    stacked structures of guanine center dot center dot center dot cytosine,
    adenine center dot center dot center dot thymine, and their 9-and
    1-methyl derivatives: Complete basis set calculations at the MP2 and
    CCSD(T) levels and comparison with experiment," JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, vol. 125, iss. 50, pp. 15608-15613, 2003.
    [Bibtex]
    @article ISI:000187208300055,
    Author = Jurecka, P and Hobza, P,
    Title = True stabilization energies for the optimal planar hydrogen-bonded and
       stacked structures of guanine center dot center dot center dot cytosine,
       adenine center dot center dot center dot thymine, and their 9-and
       1-methyl derivatives: Complete basis set calculations at the MP2 and
       CCSD(T) levels and comparison with experiment,
    Journal = JOURNAL OF THE AMERICAN CHEMICAL SOCIETY,
    Year = 2003,
    Volume = 125,
    Number = 50,
    Pages = 15608-15613,
    Month = DEC 17,
    Abstract = Planar H-bonded and stacked structures of guanine(...)cytosine
       (G(...)C), adenine(...)thymine (A(...)T),
       9-methylguanine(...)1-methylcytosine (mG(...)mC), and
       9-methyladenine(...)1-methylthymine (mA(...)mT) were optimized at the
       RI-MP2 level using the TZVPP ([5s3p2d1f/3s2p1d]) basis set. Planar
       H-bonded structures of G(...)C, mG(...)mC, and A(...)T correspond to the
       Watson-Crick (WC) arrangement, in contrast to mA(...)mT for which the
       Hoogsteen (H) structure is found. Stabilization energies for all
       structures were determined as the sum of the complete basis set limit of
       MP2 energies and a (DeltaE(CCSD(T)) - DeltaE(MP2)) correction term
       evaluated with the cc-pVDZ(0.25,0.15) basis set. The complete basis set
       limit of MP2 energies was determined by two-point extrapolation using
       the aug-cc-pVXZ basis sets for X = D and T and X = T and Q. This
       procedure is required since the convergency of the MP2 interaction
       energy for the present complexes is rather slow, and it is thus
       important to include the extrapolation to the complete basis set limit.
       For the MP2/aug-cc-pVQZ level of theory, stabilization energies for all
       complexes studied are already very close to the complete basis set
       limit. The much cheaper D-->T extrapolation provided a complete basis
       set limit close (by less than 0.7 kcal/mol) to the more accurate T-->Q
       term, and the D-->T extrapolation can be recommended for evaluation of
       complete basis set limits of more extended complexes (e.g. larger motifs
       of DNA). The convergency of the (DeltaE(CCSD(T)) - DeltaE(MP2)) term is
       known to be faster than that of the MP2 or CCSD(T) correlation energy
       itself, and the cc-pVDZ(0.25,0.15) basis set provides reasonable values
       for planar H-bonded as well as stacked structures. Inclusion of the
       CCSD(T) correction is essential for obtaining reliable relative values
       for planar H-bonding and stacking interactions; neglecting the CCSD(T)
       correction results in very considerable errors between 2.5 and 3.4
       kcal/mol. Final stabilization energies (kcal/mol) for the base pairs
       studied are very substantial (A(...)T WC, 15.4; mA(...)mT H, 16.3;
       A(...)T stacked, 11.6; mA(...)mT stacked, 13.1; G(...)C WC, 28.8;
       mG(...)mC WC, 28.5; G(...)C stacked, 16.9; mG(...)mC stacked, 18.0),
       much larger than published previously. On the basis of comparison with
       experimental data, we conclude that our values represent the lower
       boundary of the true stabilization energies. On the basis of error
       analysis, we expect the present H-bonding energies to be fairly close to
       the true values, while stacked energies are still expected to be about
       10\% too low. The stacking energy for the mG(...)mC pair is considerably
       lower than the respective H-bonding energy, but it is larger than the
       mA(...)mT H-bonding energy. This conclusion could significantly change
       the present view on the importance of specific H-bonding interactions
       and nonspecific stacking interactions in nature, for instance, in DNA.
       Present stabilization energies for H-bonding and stacking energies
       represent the most accurate and reliable values and can be considered as
       new reference data.,
    DOI = 10.1021/ja036611j,
    ISSN = 0002-7863,
    Unique-ID = ISI:000187208300055,
    
  • [DOI] F. Ryjacek, T. Kubar, and P. Hobza, "New parameterization of the Cornell et al. empirical force field
    covering amino group nonplanarity in nucleic acid bases," JOURNAL OF COMPUTATIONAL CHEMISTRY, vol. 24, iss. 15, pp. 1891-1901, 2003.
    [Bibtex]
    @article ISI:000185991300008,
    Author = Ryjacek, F and Kubar, T and Hobza, P,
    Title = New parameterization of the Cornell et al. empirical force field
       covering amino group nonplanarity in nucleic acid bases,
    Journal = JOURNAL OF COMPUTATIONAL CHEMISTRY,
    Year = 2003,
    Volume = 24,
    Number = 15,
    Pages = 1891-1901,
    Month = NOV 30,
    Abstract = The Cornell et al. empirical potential (Cornell et al., J Am Chem Soc
       1995, 117, 5197) was modified by the introduction of nonplanarity of the
       amino group in guanine, adenine, and cytosine. Reparameterization was
       performed for 12 bond parameters of the amino group (three valence
       angles (C-N-H-1, C-N-H-2, and H-1-N-H-2) and the improper dihedral angle
       at nitrogen, four dihedral angles (X-C-N-H-1, Y-C-N-H-2, X-X-C-N,
       Y-Y-C-N), three valence angles (X-C-N, Y-C-N, X-C-Y), and the improper
       dihedral angle at the adjacent carbon), and was based on correlated ab
       initio potential energy surfaces. Calculations were performed using the
       resolution of identity MP2 (RIMP2) method with SVP (3s2p1d/2s1p), TZVP
       (5s3p1d/3s1p), TZVPP (5s3p2d1f/3s2p1d), and augTZVPP (6s4p3d2f/4s3p2d)
       basis sets. Results obtained on the latter two levels are practically
       identical with the literature reference data [MP2/6-311 + +G(2df,p)]
       and the RIMP2/augTZVPP data can be considered a new reference set. The
       potential energy surface used for reparameterization was evaluated at
       the RIMP2/SVP level because respective geometry as well as energy data
       were close to the reference ones, and the computational time was very
       favorable. The modified potential was tested for 19 H-bonded and eight
       stacked nucleic acid base pairs. Interaction energies as well as
       geometries were described by the modified potential considerably better
       than by the original one and significant improvement resulted in the
       description of the nonplanar H-bonded and stacked complexes. (C) 2003
       Wiley Periodicals, Inc.,
    DOI = 10.1002/jcc.10352,
    ISSN = 0192-8651,
    Unique-ID = ISI:000185991300008,
    
  • [DOI] P. Slavicek, R. Kalus, P. Paska, I. Odvarkova, P. Hobza, and A. Malijevsky, "State-of-the-art correlated ab initio potential energy curves for heavy
    rare gas dimers: Ar-2, Kr-2, and Xe-2," JOURNAL OF CHEMICAL PHYSICS, vol. 119, iss. 4, pp. 2102-2119, 2003.
    [Bibtex]
    @article ISI:000184103000027,
    Author = Slavicek, P and Kalus, R and Paska, P and Odvarkova, I and Hobza, P and
       Malijevsky, A,
    Title = State-of-the-art correlated ab initio potential energy curves for heavy
       rare gas dimers: Ar-2, Kr-2, and Xe-2,
    Journal = JOURNAL OF CHEMICAL PHYSICS,
    Year = 2003,
    Volume = 119,
    Number = 4,
    Pages = 2102-2119,
    Month = JUL 22,
    Abstract = Characteristics of the heavy rare gas dimers (Ar-2,Kr-2,Xe-2) have been
       studied by correlated ab initio calculations. All-electron CCSD(T)
       calculations were performed for Ar and Kr dimers, and calculations with
       relativistic effective core potentials were performed for Kr and Xe
       dimers. Extended basis sets (aug-cc-pVXZ, X=D, T, Q, 5, 6) were combined
       with bond functions (spd, spdfg). The use of bond functions
       significantly improves the basis set convergence. For the argon dimer,
       we have included also a CCSDT correction yielding a higher quality
       potential energy curve. This correction has been calculated using
       aug-cc-pVTZ+spd basis set. All possible sources of errors have been
       analyzed for the argon dimer [basis set saturation, correlation
       contributions going beyond CCSD(T) method, effect of core corrections
       and relativistic corrections]. In the case of the Ar dimer, the highest
       level of theory reproduces the semiempirical stabilization energy within
       1.3 cm(-1). To obtain even closer agreement with experiment it would be
       necessary to fully include quadruple and higher excitations as well as
       to account properly for the core corrections with yet unpublished core
       oriented basis sets. Further improvement of one electron basis set will
       not lead to a better agreement with experiment. In the case of the other
       two dimers, the agreement between theory and experiment is also
       acceptable but not quantitative as in the case of the Ar dimer.
       Apparently, current calculations are close to the basis set limit and
       better agreement can only be obtained by proper covering of
       contributions mentioned for the argon dimer. The newly developed ECP
       oriented aug-cc-pVXZ basis set is very effective and can be recommended
       for high level calculations of molecular clusters containing heavier
       rare gas elements. The fast DZ/TZ extrapolation technique has been
       extended so that the use of empirical parameters can be avoided. Results
       obtained by extrapolations with medium size basis sets are surprisingly
       close to the most accurate ones. Further, the MP2-CCSD(T) difference was
       shown to be much less dependent on the size of the basis set than the
       energies themselves. These two conditions allow to construct the true
       stabilization energy of extended complexes as a sum of extrapolated
       complete basis set limit of MP2 stabilization energy and [MP2-CCSD(T)]
       term determined in a smaller basis set. The ab initio pair
       intermolecular potential results have been fitted to suitably chosen
       analytical formulas, and tested on experimental data for the second
       virial coefficients, spectral characteristics, and scattering data. For
       argon, an excellent agreement between the theoretical and the
       experimental values has been found. In the case of krypton and xenon the
       agreement is not as good but still acceptable. (C) 2003 American
       Institute of Physics.,
    DOI = 10.1063/1.1582838,
    ISSN = 0021-9606,
    Unique-ID = ISI:000184103000027,
    
  • [DOI] M. Hanus, F. Ryjacek, M. Kabelac, T. Kubar, T. Bogdan, S. Trygubenko, and P. Hobza, "Correlated ab initio study of nucleic acid bases and their tautomers in
    the gas phase, in a microhydrated environment and in aqueous solution.
    Guanine: Surprising stabilization of rare tautomers in aqueous solution," JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, vol. 125, iss. 25, pp. 7678-7688, 2003.
    [Bibtex]
    @article ISI:000183646400045,
    Author = Hanus, M and Ryjacek, F and Kabelac, M and Kubar, T and Bogdan, TV and
       Trygubenko, SA and Hobza, P,
    Title = Correlated ab initio study of nucleic acid bases and their tautomers in
       the gas phase, in a microhydrated environment and in aqueous solution.
       Guanine: Surprising stabilization of rare tautomers in aqueous solution,
    Journal = JOURNAL OF THE AMERICAN CHEMICAL SOCIETY,
    Year = 2003,
    Volume = 125,
    Number = 25,
    Pages = 7678-7688,
    Month = JUN 25,
    Abstract = Altogether eight keto and enol tautomers of guanine were studied
       theoretically in the gas phase, in a microhydrated environment (1 and 2
       water molecules) and in bulk water. The structures of isolated, as well
       as mono- and dihydrated tautomers were determined by means of the
       RI-MP(2) method using the extended TZVPP (5s3p2d1f/3s2p1d) basis set.
       The relative energies of isolated tautomers included the correction to
       higher correlation energy terms evaluated at the CCSD(T)/aug-cc-pVDZ
       level. The relative enthalpies at 0 K and relative free energies at 298
       K were based on the above-mentioned relative energies and zero-point
       vibration energies, temperature-dependent enthalpy terms and entropies
       evaluated at the MP2/6-31G** level. The keto form having hydrogen
       atom at N7 is the global minimum while the canonical form having
       hydrogen atom at N9 represents the first local minimum at all
       theoretical levels in vacuo and in the presence of 1 and 2 water
       molecules. All three unusual rare tautomers having hydrogens at N3 and
       N7, at N3 and N9, and also at N9 and N7 are systematically considerably
       less stable and can be hardly detected in the gas phase. The theoretical
       predictions fully agree with existing theoretical as well as
       experimental results. The effect of bulk solvent on the relative
       stability of guanine tautomers was studied by self-consistent reaction
       field and molecular dynamics free energy calculations using the
       thermodynamic integration method. Bulk solvent, surprisingly, strongly
       favored these three rare tautomers over all remaining low-energy
       tautomers and probably only these forms can exist in water phase. The
       global minimum (tautomer with hydrogens at N3 and N7) is by 13 kcal/mol
       more stable than the canonical form (3rd local minimum). Addition of one
       or two water molecules does not change the relative stability order of
       isolated guanine tautomers but the respective trend clearly supports the
       surprising stabilization of three rare forms.,
    DOI = 10.1021/ja034245y,
    ISSN = 0002-7863,
    Unique-ID = ISI:000183646400045,
    
  • [DOI] P. Wojciechowski, W. Zierkiewicz, D. Michalska, and P. Hobza, "Electronic structures, vibrational spectra, and revised assignment of
    aniline and its radical cation: Theoretical study," JOURNAL OF CHEMICAL PHYSICS, vol. 118, iss. 24, pp. 10900-10911, 2003.
    [Bibtex]
    @article ISI:000183402200009,
    Author = Wojciechowski, PM and Zierkiewicz, W and Michalska, D and Hobza, P,
    Title = Electronic structures, vibrational spectra, and revised assignment of
       aniline and its radical cation: Theoretical study,
    Journal = JOURNAL OF CHEMICAL PHYSICS,
    Year = 2003,
    Volume = 118,
    Number = 24,
    Pages = 10900-10911,
    Month = JUN 22,
    Abstract = Comprehensive studies of the molecular and electronic structures,
       vibrational frequencies, and infrared and Raman intensities of the
       aniline radical cation, C6H5NH2+ have been performed by using the
       unrestricted density functional (UB3LYP) and second-order Moller-Plesset
       (UMP2) methods with the extended 6-311++G(df,pd) basis set. For
       comparison, analogous calculations were carried out for the closed-shell
       neutral aniline. The studies provided detailed insight into the bonding
       changes that take place in aniline upon ionization. The natural bond
       orbital (NBO) analysis has revealed that the ppi-radical conjugative
       interactions are of prime importance in stabilizing the planar,
       quinoid-type structure of the aniline radical cation. It is shown that
       the natural charges calculated for aniline are consistent with the
       chemical properties of this molecule (an ortho- and para-directing power
       of the NH2 group in electrophilic substitutions), whereas Mulliken
       charges are not reliable. The theoretical vibrational frequencies of
       aniline, calculated by the B3LYP method, show excellent agreement with
       the available experimental data. In contrast, the MP2 method is
       deficient in predicting the frequencies of several modes in aniline,
       despite the use of the extended basis set in calculations. The
       frequencies of aniline radical cation, calculated at the
       UB3LYP/6-311++G(df,pd) level, are in very good agreement with the
       recently reported experimental data from zero kinetic energy
       photoelectron and infrared depletion spectroscopic studies. The clear-
       cut assignment of the IR and Raman spectra of the investigated molecules
       has been made on the basis of the calculated potential energy
       distributions. Several bands in the spectra have been reassigned. It is
       shown that ionization of aniline can be easily identified by the
       appearance of the very strong band at about 1490 cm(-1), in the Raman
       spectrum. The redshift of the N-H stretching frequencies and the
       blueshift of the C-H stretching frequencies are observed in aniline,
       upon ionization. As revealed by NBO analysis, the frequency shifts can
       be correlated with the increase of electron density (ED) on the
       antibonding orbitals (sigma(NH)*) and decrease of ED on sigma(CH)*,
       respectively. These effects are associated with a weakening of N-H bonds
       and strengthening of C-H bonds in the aniline radical cation. The
       simulated theoretical Raman and infrared spectra of aniline and its
       radical cation, reported in this work, can be used in further
       spectroscopic studies of their van der Waals clusters and hydrogen
       bonded complexes. (C) 2003 American Institute of Physics.,
    DOI = 10.1063/1.1574788,
    ISSN = 0021-9606,
    Unique-ID = ISI:000183402200009,
    
  • [DOI] J. Braun, H. Neusser, and P. Hobza, "N-H center dot center dot center dot pi interactions in indole center
    dot center dot center dot benzene-h(6),d(6) and indole center dot center
    dot center dot benzene-h(6),d(6) radical cation complexes. Mass analyzed
    threshold ionization experiments and correlated ab initio quantum
    chemical calculations," JOURNAL OF PHYSICAL CHEMISTRY A, vol. 107, iss. 19, pp. 3918-3924, 2003.
    [Bibtex]
    @article ISI:000182893900044,
    Author = Braun, J and Neusser, HJ and Hobza, P,
    Title = N-H center dot center dot center dot pi interactions in indole center
       dot center dot center dot benzene-h(6),d(6) and indole center dot center
       dot center dot benzene-h(6),d(6) radical cation complexes. Mass analyzed
       threshold ionization experiments and correlated ab initio quantum
       chemical calculations,
    Journal = JOURNAL OF PHYSICAL CHEMISTRY A,
    Year = 2003,
    Volume = 107,
    Number = 19,
    Pages = 3918-3924,
    Month = MAY 15,
    Abstract = Indole-benzene complexes in the neutral and cationic forms were
       investigated by resonance enhanced two-photon ionization (REMPI) and
       mass analyzed threshold ionization (MATI) experiments and nonempirical
       ab initio quantum chemical methods. The experiment yields vibrational
       frequencies of the ionized complex in its ionic ground state. In
       addition, by observing the breakdown of the MATI signal at the cluster
       ion mass for a certain internal energy and its simultaneous appearance
       at the fragment mass, the dissociation energy of the ionic complex is
       found with high precision. Using a thermochemical cycle from this and
       the also measured adiabatic ionization energies of indole-benzene and
       indole, the dissociation energy of the neutral complex is found. The
       data were recently presented for indole-benzene-h(6) and are shown for
       indole-benzene-d(6) for the first time in this work. Stacked and
       N-H...pi H-bonded structures of the neutral dimer were optimized using
       the approximative resolution of identity MP2 (RI-MP2) method combined
       with extended basis. The RI-MP2 treatment showed the preferential
       stability of the stacked structure while the CCSD(T) calculations favor
       the N-H...pi H-bonded structure. The final stabilization enthalpy
       estimate (5.3 kcal/mol) agreed nicely with the experimental value of 5.2
       kcal/mol (1823 +/- 15 cm(-1)) and points clearly to a N-H...pi bounded
       structure of the complex. In the case of a radical cation, the stacked
       structure was shown not to be stable and was converted during
       optimization to the N-H...pi H-bonded structure. The final stabilization
       enthalpy estimate (12.8 kcal/mol) agreed reasonably well with the
       experimental value of 13.1 kcal/mol (4581 10 cm(-1)). The theoretical
       harmonic intermolecular stretch frequency obtained for the neutral and
       cationic complexes (78 and 105 cm(-1)) agreed fairly well with the
       experimental values (70 and 95 cm(-1)). A surprisingly large N-H...pi
       stabilization energy calculated for the benzene...indole complex
       supports speculation about the role of these interactions in the
       biological environment. The excellent agreement of the experimental and
       theoretical binding energies gives for the first time direct evidence
       that the theoretical treatment used can yield stabilization energies
       (enthalpies) of large molecular clusters differing from the experimental
       values by less than 0.5 kcal/mol.,
    DOI = 10.1021/jp027217v,
    ISSN = 1089-5639,
    Unique-ID = ISI:000182893900044,
    
  • [DOI] D. Reha, M. Kabelac, F. Ryjacek, J. Sponer, J. Sponer, M. Elstner, S. Suhai, and P. Hobza, "Intercalators. 1. Nature of stacking interactions between intercalators
    (Ethidium, Daunomycin, Ellipticine, and 4 `,6
    `-diaminide-2-phenylindole) and DNA base pairs. Ab initio quantum
    chemical, density functional theory, and empirical potential study (vol
    124, pg 3366, 2002)," JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, vol. 125, iss. 18, pp. 5581, 2003.
    [Bibtex]
    @article ISI:000182682700057,
    Author = Reha, D and Kabelac, M and Ryjacek, F and Sponer, J and Sponer, JE and
       Elstner, M and Suhai, S and Hobza, P,
    Title = Intercalators. 1. Nature of stacking interactions between intercalators
       (Ethidium, Daunomycin, Ellipticine, and 4 `,6
       `-diaminide-2-phenylindole) and DNA base pairs. Ab initio quantum
       chemical, density functional theory, and empirical potential study (vol
       124, pg 3366, 2002),
    Journal = JOURNAL OF THE AMERICAN CHEMICAL SOCIETY,
    Year = 2003,
    Volume = 125,
    Number = 18,
    Pages = 5581,
    Month = MAY 7,
    DOI = 10.1021/ja033983j,
    ISSN = 0002-7863,
    Unique-ID = ISI:000182682700057,
    
  • [DOI] J. Chocholousova, J. Vacek, and P. Hobza, "Acetic acid dimer in the gas phase, nonpolar solvent, microhydrated
    environment, and dilute and concentrated acetic acid: Ab initio quantum
    chemical and molecular dynamics simulations," JOURNAL OF PHYSICAL CHEMISTRY A, vol. 107, iss. 17, pp. 3086-3092, 2003.
    [Bibtex]
    @article ISI:000182490900014,
    Author = Chocholousova, J and Vacek, J and Hobza, P,
    Title = Acetic acid dimer in the gas phase, nonpolar solvent, microhydrated
       environment, and dilute and concentrated acetic acid: Ab initio quantum
       chemical and molecular dynamics simulations,
    Journal = JOURNAL OF PHYSICAL CHEMISTRY A,
    Year = 2003,
    Volume = 107,
    Number = 17,
    Pages = 3086-3092,
    Month = MAY 1,
    Abstract = Theoretical study of the acetic acid dimer, its microhydration and its
       behavior in water and chloroform solution was performed. To characterize
       the system, we adopted ab initio methods at the DFT and RI MP2 (the
       resolution of the identity approximation MP2) levels for the gas-phase
       calculations, PCM (polarizable continuum model) approximation using the
       polarizable conductor calculation model (COSMO) for description of
       solvent, and constant energy (NVE) and constant temperature (NVT)
       molecular dynamics simulations for gas phase and explicit solvent
       calculations, respectively. The cyclic structure of the acetic acid
       dimer is the most stable in the gas phase only. During microhydration,
       the water molecules are incorporated in the dimer leading to
       water-separated structures. This conclusion is based on ab initio
       quantum chemical calculations, as well as on molecular dynamics
       simulations. The fact that the cyclic structure does not appear in water
       solution is in agreement with previous theoretical and experimental
       results. Extending the search also on other acetic acid dimer
       structures, we concluded that acetic acid does not form any dimer
       structure in water solution. The cyclic structure is also supposed to be
       stable in chloroform solution.,
    DOI = 10.1021/jp027637k,
    ISSN = 1089-5639,
    Unique-ID = ISI:000182490900014,
    
  • [DOI] E. Mrazkova and P. Hobza, "Hydration of sulfo and methyl groups in dimethyl sulfoxide is
    accompanied by the formation of red-shifted hydrogen bonds and improper
    blue-shifted hydrogen bonds: An ab initio quantum chemical study," JOURNAL OF PHYSICAL CHEMISTRY A, vol. 107, iss. 7, pp. 1032-1039, 2003.
    [Bibtex]
    @article ISI:000181100400012,
    Author = Mrazkova, E and Hobza, P,
    Title = Hydration of sulfo and methyl groups in dimethyl sulfoxide is
       accompanied by the formation of red-shifted hydrogen bonds and improper
       blue-shifted hydrogen bonds: An ab initio quantum chemical study,
    Journal = JOURNAL OF PHYSICAL CHEMISTRY A,
    Year = 2003,
    Volume = 107,
    Number = 7,
    Pages = 1032-1039,
    Month = FEB 20,
    Abstract = In this study, the hydration of dimethyl sulfoxide was investigated by
       means of molecular dynamics (MD) simulations and quantum chemical
       correlated ab initio calculations. MD simulations show the hydration
       sites when the systems are exposed to 1, 3, 6, 16, and 32 water
       molecules. Various DMSO...(H2O)(n) (n = 1-3) complexes where waters
       hydrate sulfo and methyl groups were then reoptimized at the ab initio
       level. The hydration of DMSO leads to an elongation of the S=O bond and
       a contraction of methyl C-H bonds. Whereas the elongation of the S=O
       bond is accompanied by a red shift of the respective stretch frequency,
       the contraction of the C-H bonds gives a blue shift to the C-H stretch
       frequencies. The former effect is easily explained by the transfer of
       electron density to the antibonding orbitals of the S=O bond, yielding
       its weakening. Various mechanisms leading to the contraction of the
       methyl CH bonds were suggested. They were based on secondary geometry
       changes originating from the significant elongation of the S=O bond and
       also on the changes of the electron density in DMSO upon complexation,
       resulting in a rehybridization of the CH bonds. The influence of the
       electrostatic field of hydrating waters was also considered. Predicted
       frequency shifts fully agree with the observed data. Also, the observed
       blue shift increase occurring as a consequence of progressive hydration
       was interpreted theoretically, and the mechanisms of this phenomenon are
       suggested.,
    DOI = 10.1021/jp026895e,
    ISSN = 1089-5639,
    Unique-ID = ISI:000181100400012,
    
  • [DOI] N. Spackova, T. Cheatham, F. Ryjacek, F. Lankas, L. van Meervelt, P. Hobza, and J. Sponer, "Molecular dynamics simulations and thermodynamics analysis of DNA-drug
    complexes. Minor groove binding between 4 `,6-diamidino-2-phenylindole
    and DNA duplexes in solution," JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, vol. 125, iss. 7, pp. 1759-1769, 2003.
    [Bibtex]
    @article ISI:000181088000025,
    Author = Spackova, N and Cheatham, TE and Ryjacek, F and Lankas, F and van
       Meervelt, L and Hobza, P and Sponer, J,
    Title = Molecular dynamics simulations and thermodynamics analysis of DNA-drug
       complexes. Minor groove binding between 4 `,6-diamidino-2-phenylindole
       and DNA duplexes in solution,
    Journal = JOURNAL OF THE AMERICAN CHEMICAL SOCIETY,
    Year = 2003,
    Volume = 125,
    Number = 7,
    Pages = 1759-1769,
    Month = FEB 19,
    Abstract = An extended set of nanosecond-scale molecular dynamics simulations of
       DNA duplex sequences in explicit solvent interacting with the minor
       groove binding drug 4',6-diamidino-2-phenylindole (DAPI) are
       investigated for four different and sequence specific binding modes.
       Force fields for DAPI have been parametrized to properly reflect its
       internal nonplanarity. Sequences investigated include the binding modes
       observed experimentally, that is, (AATT) under bar in d(CGCGAATTCGCG)(2)
       and (ATTG) under bar in d(GGCCAATTGG)(2) and alternative shifted binding
       modes (ATTC) under bar and (AATT) under bar, respectively. In each case,
       stable MD simulations are obtained, well reproducing specific hydration
       patterns seen in the experiments. In contrast to the 2.4 Angstrom
       d(CGCGAATTCGCG)(2) crystal structure, the DAPI is nonplanar, consistent
       with its gas-phase geometry and the higher resolution crystal structure.
       The simulations also suggest that the DAPI molecule is able to adopt
       different conformational substates accompanied by specific hydration
       patterns that include long-residing waters. The MM-PBSA technology for
       estimating relative free energies was utilized. The most consistent free
       energy results were obtained with an approach that uses a single
       trajectory of the, DNA-DAPI complex to estimate all free energy terms.
       It is demonstrated that explicit inclusion of a subset of bound water
       molecules shifts the calculated relative binding free energies in favor
       of both crystallographically observed binding modes, underlining the
       importance of structured hydration.,
    DOI = 10.1021/ja025660d,
    ISSN = 0002-7863,
    Unique-ID = ISI:000181088000025,
    
  • [DOI] J. Sponer and P. Hobza, "Molecular interactions of nucleic acid bases. A review of
    quantum-chemical studies," COLLECTION OF CZECHOSLOVAK CHEMICAL COMMUNICATIONS, vol. 68, iss. 12, pp. 2231-2282, 2003.
    [Bibtex]
    @article ISI:000187207300001,
    Author = Sponer, J and Hobza, P,
    Title = Molecular interactions of nucleic acid bases. A review of
       quantum-chemical studies,
    Journal = COLLECTION OF CZECHOSLOVAK CHEMICAL COMMUNICATIONS,
    Year = 2003,
    Volume = 68,
    Number = 12,
    Pages = 2231-2282,
    Abstract = Ab initio quantum-chemical calculations with inclusion of electron
       correlation significantly contributed to our understanding of molecular
       interactions of DNA and RNA bases. Some of the most important findings
       are introduced in the present overview: structures and energies of
       hydrogen bonded base pairs, nature of base stacking, interactions
       between metal cations and nucleobases, nonplanarity of isolated
       nucleobases and other monomer properties, tautomeric equilibria of
       nucleobases, out-of-plane hydrogen bonds and amino acceptor
       interactions. The role of selected molecular interactions in nucleic
       acids is discussed and representative examples where these interactions
       occur are given. Also, accuracy of density functional theory,
       semiempirical methods, distributed multipole analysis and empirical
       potentials is commented on. Special attention is given to our very
       recent reference calculations on base stacking and H-bonding. Finally,
       we briefly comment on the relationship between advanced ab initio
       quantum-chemical methods and large-scale explicit solvent molecular
       dynamics simulations of nucleic acids.,
    DOI = 10.1135/cccc20032231,
    ISSN = 0010-0765,
    Unique-ID = ISI:000187207300001,
    
  • [DOI] P. Hobza and V. Spirko, "Why is the N-1-H stretch vibration frequency of guanine shifted upon
    dimerization to the red and the amino N-H stretch vibration frequency to
    the blue?," PHYSICAL CHEMISTRY CHEMICAL PHYSICS, vol. 5, iss. 6, pp. 1290-1294, 2003.
    [Bibtex]
    @article ISI:000181288700045,
    Author = Hobza, P and Spirko, V,
    Title = Why is the N-1-H stretch vibration frequency of guanine shifted upon
       dimerization to the red and the amino N-H stretch vibration frequency to
       the blue?,
    Journal = PHYSICAL CHEMISTRY CHEMICAL PHYSICS,
    Year = 2003,
    Volume = 5,
    Number = 6,
    Pages = 1290-1294,
    Abstract = Three isomers of the guanine dimer (K9K9-1, K9K7-1 and K7K7-1)
       possessing two N-H...O=C H-bonds were investigated theoretically using
       the ab initio calculations at the HF/6-31G** level. Amino groups in
       these isomers were not directly involved in H-bonding. Besides the red
       shifts of the N-H stretch vibrations (supporting the H-bonded character
       of these contacts) an unexpected