Petr Jurečka

2011

• M. Zgarbova, P. Jurecka, P. Banas, M. Otyepka, J. E. Sponer, N. B. Leontis, C. L. Zirbel, and J. Sponer, “Noncanonical Hydrogen Bonding in Nucleic Acids. Benchmark Evaluation of
  Key Base-Phosphate Interactions in Folded RNA Molecules Using
  Quantum-Chemical Calculations and Molecular Dynamics Simulations,” JOURNAL OF PHYSICAL CHEMISTRY A, vol. 115, iss. 41, pp. 11277-11292, 2011.
  [Bibtex]

  @article ISI:000295700600019,
  Author = Zgarbova, Marie and Jurecka, Petr and Banas, Pavel and Otyepka, Michal
     and Sponer, Judit E. and Leontis, Neocles B. and Zirbel, Craig L. and
     Sponer, Jiri,
  Title = Noncanonical Hydrogen Bonding in Nucleic Acids. Benchmark Evaluation of
     Key Base-Phosphate Interactions in Folded RNA Molecules Using
     Quantum-Chemical Calculations and Molecular Dynamics Simulations,
  Journal = JOURNAL OF PHYSICAL CHEMISTRY A,
  Year = 2011,
  Volume = 115,
  Number = 41,
  Pages = 11277-11292,
  Month = OCT 20,
  Abstract = RNA molecules are stabilized by a wide range of non canonical
     interactions that are not present in DNA. Among them, the recently
     classified base phosphate (BPh) interactions belong to the most
     important ones. Twelve percent of nucleotides in the ribosomal crystal
     structures are involved in BPh interactions. BPh interactions are highly
     conserved and provide major constraints on RNA sequence evolution. Here
     we provide assessment of the energetics of BPh interactions using MP2
     computations extrapolated to the complete basis set of atomic orbitals
     and corrected for higher-order electron correlation effects. The
     reference computations are compared with DFT-D and DFT-D3 approaches,
     the SAPT method, and the molecular mechanics force field. The
     computations, besides providing the basic benchmark for the BPh
     interactions, allow some refinements of the original classification,
     including identification of some potential doubly bonded BPh patterns.
     The reference computations are followed by analysis of some larger RNA
     fragments that consider the context of the BPh interactions. The
     computations demonstrate the complexity of interaction patterns
     utilizing the BPh interactions in real RNA structures. The BPh
     interactions are often involved in intricate interaction networks. We
     studied BPh interactions of protonated adenine that can contribute to
     catalysis of hairpin ribozyme, the key BPh interaction in the S-turn
     motif of the sarcin ricin loop, which may predetermine the S-turn
     topology and complex BPh patterns-from the glmS riboswitch. Finally, the
     structural stability of BPh interactions in explicit solvent molecular
     dynamics simulations is assessed. The simulations well preserve key BPh
     interactions and allow dissection of structurally/functionally important
     water-meditated BPh bridges, which could not be considered in earlier
     bioinformatics classification of BPh interactions.,
  DOI = 10.1021/jp204820b,
  ISSN = 1089-5639,
  Unique-ID = ISI:000295700600019,
  

• M. Zgarbova, M. Otyepka, J. Sponer, A. Mladek, P. Banas, T. E. Cheatham III, and P. Jurecka, “Refinement of the Cornell et al. Nucleic Acids Force Field Based on
  Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles,” JOURNAL OF CHEMICAL THEORY AND COMPUTATION, vol. 7, iss. 9, pp. 2886-2902, 2011.
  [Bibtex]

  @article ISI:000294790400025,
  Author = Zgarbova, Marie and Otyepka, Michal and Sponer, Jiri and Mladek, Arnost
     and Banas, Pavel and Cheatham, III, Thomas E. and Jurecka, Petr,
  Title = Refinement of the Cornell et al. Nucleic Acids Force Field Based on
     Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles,
  Journal = JOURNAL OF CHEMICAL THEORY AND COMPUTATION,
  Year = 2011,
  Volume = 7,
  Number = 9,
  Pages = 2886-2902,
  Month = SEP,
  Abstract = We report a reparameterization of the glycosidic torsion chi of the
     Cornell et al. AMBER force field for RNA, chi(OL) The parameters remove
     destabilization of the anti region found in the ff99 force field and
     thus prevent formation of spurious ladder-like structural distortions in
     RNA simulations. They also improve the description of the syn region and
     the syn anti balance as well as enhance MD simulations of various RNA
     structures. Although chi(OL) can be combined with both ff99 and
     ff99bsc0, we recommend the latter. We do not recommend using chi(OL) for
     B-DNA because it does not improve upon ff99bsc0 for canonical
     structures. However, it might be useful in simulations of DNA molecules
     containing syn nucleotides. Our parametrization is based on high-level
     QM calculations and differs from conventional parametrization approaches
     in that it incorporates some previously neglected solvation-related
     effects (which appear to be essential for obtaining correct
     anti/high-anti balance). Our chi(OL) force field is compared with
     several previous glycosidic torsion parametrizations.,
  DOI = 10.1021/ct200162x,
  ISSN = 1549-9618,
  Unique-ID = ISI:000294790400025,
  

2010

• A. Mladek, J. E. Sponer, P. Jurecka, P. Banas, M. Otyepka, D. Svozil, and J. Sponer, “Conformational Energies of DNA Sugar-Phosphate Backbone: Reference QM
  Calculations and a Comparison with Density Functional Theory and
  Molecular Mechanics,” JOURNAL OF CHEMICAL THEORY AND COMPUTATION, vol. 6, iss. 12, pp. 3817-3835, 2010.
  [Bibtex]

  @article ISI:000285217000018,
  Author = Mladek, Arnost and Sponer, Judit E. and Jurecka, Petr and Banas, Pavel
     and Otyepka, Michal and Svozil, Daniel and Sponer, Jiri,
  Title = Conformational Energies of DNA Sugar-Phosphate Backbone: Reference QM
     Calculations and a Comparison with Density Functional Theory and
     Molecular Mechanics,
  Journal = JOURNAL OF CHEMICAL THEORY AND COMPUTATION,
  Year = 2010,
  Volume = 6,
  Number = 12,
  Pages = 3817-3835,
  Month = DEC,
  Abstract = The study investigates electronic structure and gas-phase energetics of
     the DNA sugar phosphate backbone via advanced quantum chemical (QM)
     methods. The analysis has been carried out on biologically relevant
     backbone conformations composed of 11 canonical BI-DNA structures, 8
     pathological structures with alpha/gamma torsion angles in the g+/t
     region, and 3 real noncanonical gamma-trans structures occurring in the
     loop region of guanine quadruplex DNA. The influence of backbone
     conformation on the intrinsic energetics was primarily studied using a
     model system consisting of two sugar moieties linked together via a
     phosphodiester bond (SPSOM model). To get the conformation of the
     studied system fully under control, for each calculation we have frozen
     majority of the dihedral angles to their target values. CCSD(T) energies
     extrapolated to the complete basis set were utilized as reference
     values. However, the calculations show that inclusion of higher-order
     electron correlation effects for this system is not crucial and complete
     basis set second-order perturbation calculations are sufficiently
     accurate. The reference QM data are used to assess performance of 10
     contemporary density functionals with the best performance delivered by
     the PBE-D/TZVPP combination along with the Grimme's dispersion
     correction, and by the TPSS-D/6-311++G(3df,3pd) augmented by Jurecka's
     dispersion term. In addition, the QM calculations are compared to
     molecular mechanics (MM) model based on the Cornell et al. force field.
     The destabilization of the pathological g+/t conformers with respect to
     the reference canonical structure and the network of intramolecular CH
     center dot center dot center dot O interactions were investigated by
     means of natural bond orbital analysis (NBO) and atoms-in-molecules
     (AIM) Bader analysis. Finally, four additional model systems of
     different sizes were assessed by comparing their energetics to that of
     the SPSOM system. Energetics of smaller MOSPM model consisting of a
     sugar moiety linked to a phosphate group and capped with methyl and
     methoxy group on the 5'- and 3'-ends, respectively, is fairly similar to
     that of SPSOM, while the role of undesired intramolecular interactions
     is diminished.,
  DOI = 10.1021/ct1004593,
  ISSN = 1549-9618,
  Unique-ID = ISI:000285217000018,
  

• P. Banas, D. Hollas, M. Zgarbova, P. Jurecka, M. Orozco, T. E. Cheatham III, J. Sponer, and M. Otyepka, “Performance of Molecular Mechanics Force Fields for RNA Simulations:
  Stability of UUCG and GNRA Hairpins,” JOURNAL OF CHEMICAL THEORY AND COMPUTATION, vol. 6, iss. 12, pp. 3836-3849, 2010.
  [Bibtex]

  @article ISI:000285217000019,
  Author = Banas, Pavel and Hollas, Daniel and Zgarbova, Marie and Jurecka, Petr
     and Orozco, Modesto and Cheatham, III, Thomas E. and Sponer, Jiri and
     Otyepka, Michal,
  Title = Performance of Molecular Mechanics Force Fields for RNA Simulations:
     Stability of UUCG and GNRA Hairpins,
  Journal = JOURNAL OF CHEMICAL THEORY AND COMPUTATION,
  Year = 2010,
  Volume = 6,
  Number = 12,
  Pages = 3836-3849,
  Month = DEC,
  Abstract = The RNA hairpin loops represent important RNA topologies with
     indispensable biological functions in RNA folding and tertiary
     interactions. 5'-UNCG-3' and 5'-GNRA-3' RNA tetraloops are the most
     important classes of RNA hairpin loops. Both tetraloops are highly
     structured with characteristic signature three-dimensional features and
     are recurrently seen in functional RNAs and ribonucleoprotein particles.
     Explicit solvent molecular dynamics (MD) simulation is a computational
     technique which can efficiently complement the experimental data and
     provide unique structural dynamics information on the atomic scale.
     Nevertheless, the outcome of simulations is often compromised by
     imperfections in the parametrization of simplified pairwise additive
     empirical potentials referred to also as force fields. We have pointed
     out in several recent studies that a force field description of
     single-stranded hairpin segments of nucleic acids may be particularly
     challenging for the force fields. In this paper, we report a critical
     assessment of a broad set of MD simulations of UUCG, GAGA, and GAAA
     tetraloops using various force fields. First, we utilized the three
     widely used variants of Cornell et al. (AMBER) force fields known as
     694, 699, and ff99bsc0. Some simulations were also carried out with
     CHARMM27. The simulations reveal several problems which show that these
     force fields are not able to retain all characteristic structural
     features (structural signature) of the studied tetraloops. Then we
     tested four recent reparameterizations of glycosidic torsion of the
     Cornell et al. force field (two of them being currently parametrized in
     our laboratories). We show that at least some of the new versions show
     an improved description of the tetraloops, mainly in the syn glycosidic
     torsion region of the UNCG tetraloop. The best performance is achieved
     in combination with the bsc0 parametrization of the alpha/gamma angles.
     Another critically important region to properly describe RNA molecules
     is the anti/high-anti region of the glycosidic torsion, where there are
     significant differences among the tested force fields. The tetraloop
     simulations are complemented by simulations of short A-RNA stems, which
     are especially sensitive to an appropriate description of the
     anti/high-anti region. While excessive accessibility of the high-anti
     region converts the A-RNA into a senseless ``ladder-like'' geometry,
     excessive penalization of the high-anti region shifts the simulated
     structures away from typical A-RNA geometry to structures with a visibly
     underestimated inclination of base pairs with respect to the helical
     axis.,
  DOI = 10.1021/ct100481h,
  ISSN = 1549-9618,
  Unique-ID = ISI:000285217000019,
  

• 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,
  

• 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,
  

• 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,
  

2009

• P. Banas, P. Jurecka, N. G. Walter, J. Sponer, and M. Otyepka, “Theoretical studies of RNA catalysis: Hybrid QM/MM methods and their
  comparison with MD and QM,” METHODS, vol. 49, iss. 2, pp. 202-216, 2009.
  [Bibtex]

  @article ISI:000270443600015,
  Author = Banas, Pavel and Jurecka, Petr and Walter, Nils G. and Sponer, Jiri and
     Otyepka, Michal,
  Title = Theoretical studies of RNA catalysis: Hybrid QM/MM methods and their
     comparison with MD and QM,
  Journal = METHODS,
  Year = 2009,
  Volume = 49,
  Number = 2,
  Pages = 202-216,
  Month = OCT,
  Abstract = Hybrid QM/MM methods combine the rigor of quantum mechanical (QM)
     calculations with the low computational cost of empirical molecular
     mechanical (MM) treatment allowing to capture dynamic properties to
     probe critical atomistic details of enzyme reactions. Catalysis by RNA
     enzymes (ribozymes) has only recently begun to be addressed with QM/MM
     approaches and is thus still a field under development. This review
     surveys methodology as well as recent advances in QM/MM applications to
     RNA mechanisms, including those of the HDV, hairpin, and hammerhead
     ribozymes, as well as the ribosome. We compare and correlate QM/MM
     results with those from QM and/or molecular dynamics (MD) simulations,
     and discuss scope and limitations with a critical eye on current
     shortcomings in available methodologies and computer resources. We thus
     hope to foster mutual appreciation and facilitate collaboration between
     experimentalists and theorists to jointly advance our understanding of
     RNA catalysis at an atomistic level. (c) 2009 Elsevier Inc. All rights
     reserved.,
  DOI = 10.1016/j.ymeth.2009.04.007,
  ISSN = 1046-2023,
  Unique-ID = ISI:000270443600015,
  

• 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. 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,
  

2008

• 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, 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,
  

2007

• S. R. Meneni, S. M. Shell, L. Gao, P. Jurecka, W. Lee, J. Sponer, Y. Zou, P. M. Chiarelli, and B. P. Cho, “Spectroscopic and theoretical insights into sequence effects of
  aminofluorene-induced conformational heterogeneity and nucleotide
  excision repair,” BIOCHEMISTRY, vol. 46, iss. 40, pp. 11263-11278, 2007.
  [Bibtex]

  @article ISI:000249926300005,
  Author = Meneni, Srinivasa Rao and Shell, Steven M. and Gao, Lan and Jurecka,
     Petr and Lee, Wang and Sponer, Jiri and Zou, Yue and Chiarelli, M. Paul
     and Cho, Bongsup P.,
  Title = Spectroscopic and theoretical insights into sequence effects of
     aminofluorene-induced conformational heterogeneity and nucleotide
     excision repair,
  Journal = BIOCHEMISTRY,
  Year = 2007,
  Volume = 46,
  Number = 40,
  Pages = 11263-11278,
  Month = OCT 9,
  Abstract = A systematic spectroscopic and computational study was conducted in
     order to probe the influence of base sequences on stacked (S) versus
     B-type (13) conformational heterogeneity induced by the major dG adduct
     derived from the model carcinogen 7-fluoro-2-antinofluorene (FAF). We
     prepared and characterized eight 12-mer DNA duplexes (-AG*N-series,
     d[CTTCTAG*NCCTC]; -CG*N-series, d[CTTCTCG*NCCTC]), in which
     the central guanines (G*) were site-specifically modified with FAF
     with varying flanking bases (N = G, A, C, T). S/B heterogeneity was
     examined by CD, UV, and dynamic F-19 NMR spectroscopy. All the modified
     duplexes studied followed a typical dynamic exchange between the S and B
     conformers in a sequence dependent manner. Specifically, purine bases at
     the 3'-flanking site promoted the S conformation (G > A > C > T).
     Simulation analysis showed that the S/B energy barriers were in the
     14-16 kcal/mol range. The correlation time's (iota = l/k) were found to
     be in the millisecond range at 20 degrees C. The van der Waals energy
     force field calculations indicated the importance of the stacking
     interaction between the carcinogen and neighboring base pairs. Quantum
     mechanics calculations showed the existence of correlations between the
     total interaction energies (including electrostatic and solvation
     effects) and the S/B population ratios. The S/B equilibrium seems to
     modulate the efficiency of Escherichia coli UvrABC-based nucleotide
     excision repair in a conformation-specific manner: i.e., greater repair
     susceptibility for the S over B conformation and for the -AG*N- over
     the -CG*N- series. The results indicate a novel structure-function
     relationship, which provides insights into how bulky DNA adducts are
     accommodated by UvrABC proteins.,
  DOI = 10.1021/bi700858s,
  ISSN = 0006-2960,
  Unique-ID = ISI:000249926300005,
  

• 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,
  

• 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,
  

• 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,