Regional Centre of Advanced Technologies and Materials > Personnel > Petr Jurečka

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.
  • [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.

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.
  • [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.
  • [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.
  • [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.
  • [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.
  • [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.

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.
  • [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.
  • [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.

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.
  • [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.

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.
  • [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.
  • [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.
  • [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.
  • [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.
  • [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.