Prof. Pavel Hobza, Dr.Sc.

2011

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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,
  

• 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