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Petr Jurečka

Email: petr.jurecka@upol.cz

Location: 17. listopadu 12, Olomouc

Phone: (+420) 58 563 4760

Fax: (+420) 585 634 761

Oblast výzkumu:

Intermolecular interactions

Dispersion interaction in Density functional theory

Reference QM calculations

Force field development

Kvalifikace:

Mgr.  Inorganic chemistry, Charles University, Prague

Ph.D. Physical chemistry, Charles University, Prague

Doc. (associate prof.) Physical chemistry, Palacký University, Olomouc

Show publications

Publications

2011

  • [DOI] 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,
DOI = 10.1021/jp204820b,
ISSN = 1089-5639,
Unique-ID = ISI:000295700600019,
  • [DOI] 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,
DOI = 10.1021/ct200162x,
ISSN = 1549-9618,
Unique-ID = ISI:000294790400025,

2010

  • [DOI] 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,
DOI = 10.1021/ct1004593,
ISSN = 1549-9618,
Unique-ID = ISI:000285217000018,
  • [DOI] 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,
DOI = 10.1021/ct100481h,
ISSN = 1549-9618,
Unique-ID = ISI:000285217000019,
  • [DOI] K. E. Riley, M. Pitonak, P. Jurecka, and P. Hobza, “Stabilization and Structure Calculations for Noncovalent Interactions in
    Extended Molecular Systems Based on Wave Function and Density Functional
    Theories,” CHEMICAL REVIEWS, vol. 110, iss. 9, pp. 5023-5063, 2010.
    [Bibtex] 
    @article ISI:000281840400003,
Author = Riley, Kevin E. and Pitonak, Michel and Jurecka, Petr and Hobza, Pavel,
Title = Stabilization and Structure Calculations for Noncovalent Interactions in
   Extended Molecular Systems Based on Wave Function and Density Functional
   Theories,
Journal = CHEMICAL REVIEWS,
Year = 2010,
Volume = 110,
Number = 9,
Pages = 5023-5063,
Month = SEP,
DOI = 10.1021/cr1000173,
ISSN = 0009-2665,
Unique-ID = ISI:000281840400003,
  • [DOI] M. Kolar, K. Berka, P. Jurecka, and P. Hobza, “On the Reliability of the AMBER Force Field and its Empirical Dispersion
    Contribution for the Description of Noncovalent Complexes,” CHEMPHYSCHEM, vol. 11, iss. 11, pp. 2399-2408, 2010.
    [Bibtex] 
    @article ISI:000281061500018,
Author = Kolar, Michal and Berka, Karel and Jurecka, Petr and Hobza, Pavel,
Title = On the Reliability of the AMBER Force Field and its Empirical Dispersion
   Contribution for the Description of Noncovalent Complexes,
Journal = CHEMPHYSCHEM,
Year = 2010,
Volume = 11,
Number = 11,
Pages = 2399-2408,
Month = AUG 2,
DOI = 10.1002/cphc.201000109,
ISSN = 1439-4235,
Unique-ID = ISI:000281061500018,
  • [DOI] M. Zgarbova, M. Otyepka, J. Sponer, P. Hobza, and P. Jurecka, “Large-scale compensation of errors in pairwise-additive empirical force
    fields: comparison of AMBER intermolecular terms with rigorous DFT-SAPT
    calculations,” PHYSICAL CHEMISTRY CHEMICAL PHYSICS, vol. 12, iss. 35, pp. 10476-10493, 2010.
    [Bibtex] 
    @article ISI:000281352300043,
Author = Zgarbova, Marie and Otyepka, Michal and Sponer, Jiri and Hobza, Pavel
   and Jurecka, Petr,
Title = Large-scale compensation of errors in pairwise-additive empirical force
   fields: comparison of AMBER intermolecular terms with rigorous DFT-SAPT
   calculations,
Journal = PHYSICAL CHEMISTRY CHEMICAL PHYSICS,
Year = 2010,
Volume = 12,
Number = 35,
Pages = 10476-10493,
DOI = 10.1039/c002656e,
ISSN = 1463-9076,
Unique-ID = ISI:000281352300043,
  • [DOI] C. A. Morgado, P. Jurecka, D. Svozil, P. Hobza, and J. Sponer, “Reference MP2/CBS and CCSD(T) quantum-chemical calculations on stacked
    adenine dimers. Comparison with DFT-D, MP2.5, SCS(MI)-MP2, M06-2X,
    CBS(SCS-D) and force field descriptions,” PHYSICAL CHEMISTRY CHEMICAL PHYSICS, vol. 12, iss. 14, pp. 3522-3534, 2010.
    [Bibtex] 
    @article ISI:000275938200021,
Author = Morgado, Claudio A. and Jurecka, Petr and Svozil, Daniel and Hobza,
   Pavel and Sponer, Jiri,
Title = Reference MP2/CBS and CCSD(T) quantum-chemical calculations on stacked
   adenine dimers. Comparison with DFT-D, MP2.5, SCS(MI)-MP2, M06-2X,
   CBS(SCS-D) and force field descriptions,
Journal = PHYSICAL CHEMISTRY CHEMICAL PHYSICS,
Year = 2010,
Volume = 12,
Number = 14,
Pages = 3522-3534,
DOI = 10.1039/b924461a,
ISSN = 1463-9076,
Unique-ID = ISI:000275938200021,

2009

  • [DOI] 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,
DOI = 10.1016/j.ymeth.2009.04.007,
ISSN = 1046-2023,
Unique-ID = ISI:000270443600015,
  • [DOI] C. A. Morgado, P. Jurecka, D. Svozil, P. Hobza, and J. Sponer, “Balance of Attraction and Repulsion in Nucleic-Acid Base Stacking:
    CCSD(T)/Complete-Basis-Set-Limit Calculations on Uracil Dimer and a
    Comparison with the Force-Field Description,” JOURNAL OF CHEMICAL THEORY AND COMPUTATION, vol. 5, iss. 6, pp. 1524-1544, 2009.
    [Bibtex] 
    @article ISI:000266865000009,
Author = Morgado, Claudio A. and Jurecka, Petr and Svozil, Daniel and Hobza,
   Pavel and Sponer, Jiri,
Title = Balance of Attraction and Repulsion in Nucleic-Acid Base Stacking:
   CCSD(T)/Complete-Basis-Set-Limit Calculations on Uracil Dimer and a
   Comparison with the Force-Field Description,
Journal = JOURNAL OF CHEMICAL THEORY AND COMPUTATION,
Year = 2009,
Volume = 5,
Number = 6,
Pages = 1524-1544,
Month = JUN,
DOI = 10.1021/ct9000125,
ISSN = 1549-9618,
Unique-ID = ISI:000266865000009,
  • [DOI] J. Sponer, M. Zgarbova, P. Jurecka, K. E. Riley, J. E. Sponer, and P. Hobza, “Reference Quantum Chemical Calculations on RNA Base Pairs Directly
    Involving the 2 `-OH Group of Ribose,” JOURNAL OF CHEMICAL THEORY AND COMPUTATION, vol. 5, iss. 4, pp. 1166-1179, 2009.
    [Bibtex] 
    @article ISI:000265268800057,
Author = Sponer, Jiri and Zgarbova, Marie and Jurecka, Petr and Riley, Kevin E.
   and Sponer, Judit E. and Hobza, Pavel,
Title = Reference Quantum Chemical Calculations on RNA Base Pairs Directly
   Involving the 2 `-OH Group of Ribose,
Journal = JOURNAL OF CHEMICAL THEORY AND COMPUTATION,
Year = 2009,
Volume = 5,
Number = 4,
Pages = 1166-1179,
Month = APR,
DOI = 10.1021/ct800547k,
ISSN = 1549-9618,
Unique-ID = ISI:000265268800057,

2008

  • [DOI] M. Pitonak, P. Neogrady, J. Rezac, P. Jurecka, M. Urban, and P. Hobza, “Benzene Dimer: High-Level Wave Function and Density Functional Theory
    Calculations,” JOURNAL OF CHEMICAL THEORY AND COMPUTATION, vol. 4, iss. 11, pp. 1829-1834, 2008.
    [Bibtex] 
    @article ISI:000260851300003,
Author = Pitonak, M. and Neogrady, P. and Rezac, J. and Jurecka, P. and Urban, M.
   and Hobza, P.,
Title = Benzene Dimer: High-Level Wave Function and Density Functional Theory
   Calculations,
Journal = JOURNAL OF CHEMICAL THEORY AND COMPUTATION,
Year = 2008,
Volume = 4,
Number = 11,
Pages = 1829-1834,
Month = NOV,
DOI = 10.1021/ct800229h,
ISSN = 1549-9618,
Unique-ID = ISI:000260851300003,
  • [DOI] J. Rezac, P. Jurecka, K. E. Riley, J. Cerny, H. Valdes, K. Pluhackova, K. Berka, T. Rezac, M. Pitonak, J. Vondrasek, and P. Hobza, “QUANTUM CHEMICAL BENCHMARK ENERGY AND GEOMETRY DATABASE FOR MOLECULAR
    CLUSTERS AND COMPLEX MOLECULAR SYSTEMS (www.begdb.com): A USERS MANUAL
    AND EXAMPLES,” COLLECTION OF CZECHOSLOVAK CHEMICAL COMMUNICATIONS, vol. 73, iss. 10, pp. 1261-1270, 2008.
    [Bibtex] 
    @article ISI:000263121400003,
Author = Rezac, Jan and Jurecka, Petr and Riley, Kevin E. and Cerny, Jiri and
   Valdes, Haydee and Pluhackova, Kristyna and Berka, Karel and Rezac,
   Tomas and Pitonak, Michal and Vondrasek, Jiri and Hobza, Pavel,
Title = QUANTUM CHEMICAL BENCHMARK ENERGY AND GEOMETRY DATABASE FOR MOLECULAR
   CLUSTERS AND COMPLEX MOLECULAR SYSTEMS (www.begdb.com): A USERS MANUAL
   AND EXAMPLES,
Journal = COLLECTION OF CZECHOSLOVAK CHEMICAL COMMUNICATIONS,
Year = 2008,
Volume = 73,
Number = 10,
Pages = 1261-1270,
DOI = 10.1135/cccc20081261,
ISSN = 0010-0765,
Unique-ID = ISI:000263121400003,

2007

  • [DOI] 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,
DOI = 10.1021/bi700858s,
ISSN = 0006-2960,
Unique-ID = ISI:000249926300005,
  • [DOI] L. Bendova, P. Jurecka, P. Hobza, and J. Vondrasek, “Model of peptide bond-aromatic ring interaction: Correlated ab initio
    quantum chemical study,” JOURNAL OF PHYSICAL CHEMISTRY B, vol. 111, iss. 33, pp. 9975-9979, 2007.
    [Bibtex] 
    @article ISI:000248759000037,
Author = Bendova, Lada and Jurecka, Petr and Hobza, Pavel and Vondrasek, Jiri,
Title = Model of peptide bond-aromatic ring interaction: Correlated ab initio
   quantum chemical study,
Journal = JOURNAL OF PHYSICAL CHEMISTRY B,
Year = 2007,
Volume = 111,
Number = 33,
Pages = 9975-9979,
Month = AUG 23,
DOI = 10.1021/jp072859+,
ISSN = 1520-6106,
Unique-ID = ISI:000248759000037,
  • [DOI] R. Sedlak, P. Jurecka, and P. Hobza, “Density functional theory-symmetry adapted perturbation treatment energy
    decomposition of nucleic acid base pairs taken from DNA crystal geometry,” JOURNAL OF CHEMICAL PHYSICS, vol. 127, iss. 7, 2007.
    [Bibtex] 
    @article ISI:000248905300036,
Author = Sedlak, Robert and Jurecka, Petr and Hobza, Pavel,
Title = Density functional theory-symmetry adapted perturbation treatment energy
   decomposition of nucleic acid base pairs taken from DNA crystal geometry,
Journal = JOURNAL OF CHEMICAL PHYSICS,
Year = 2007,
Volume = 127,
Number = 7,
Month = AUG 21,
DOI = 10.1063/1.2759207,
Article-Number = 075104,
ISSN = 0021-9606,
Unique-ID = ISI:000248905300036,
  • [DOI] 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,
DOI = 10.1021/jp066504m,
ISSN = 1089-5639,
Unique-ID = ISI:000244039600022,
  • [DOI] P. Jurecka, J. Cerny, P. Hobza, and D. R. Salahub, “Density functional theory augmented with an empirical dispersion term.
    Interaction energies and geometries of 80 noncovalent complexes compared
    with ab initio quantum mechanics calculations,” JOURNAL OF COMPUTATIONAL CHEMISTRY, vol. 28, iss. 2, pp. 555-569, 2007.
    [Bibtex] 
    @article ISI:000243238700011,
Author = Jurecka, Petr and Cerny, Jiri and Hobza, Pavel and Salahub, Dennis R.,
Title = Density functional theory augmented with an empirical dispersion term.
   Interaction energies and geometries of 80 noncovalent complexes compared
   with ab initio quantum mechanics calculations,
Journal = JOURNAL OF COMPUTATIONAL CHEMISTRY,
Year = 2007,
Volume = 28,
Number = 2,
Pages = 555-569,
Month = JAN 30,
DOI = 10.1002/jcc.20570,
ISSN = 0192-8651,
Unique-ID = ISI:000243238700011,
  • [DOI] K. Pluhackova, P. Jurecka, and P. Hobza, “Stabilisation energy of C6H6 center dot center dot center dot C6X6 (X =
    F, Cl, Br, I, CN) complexes: complete basis set limit calculations at
    MP2 and CCSD(T) levels,” PHYSICAL CHEMISTRY CHEMICAL PHYSICS, vol. 9, iss. 6, pp. 755-760, 2007.
    [Bibtex] 
    @article ISI:000243928300011,
Author = Pluhackova, Kristyna and Jurecka, Petr and Hobza, Pavel,
Title = Stabilisation energy of C6H6 center dot center dot center dot C6X6 (X =
   F, Cl, Br, I, CN) complexes: complete basis set limit calculations at
   MP2 and CCSD(T) levels,
Journal = PHYSICAL CHEMISTRY CHEMICAL PHYSICS,
Year = 2007,
Volume = 9,
Number = 6,
Pages = 755-760,
DOI = 10.1039/b615318f,
ISSN = 1463-9076,
Unique-ID = ISI:000243928300011,