Tel: 58 563 4760, E-mail: petr.jurecka@upol.cz, Room: 3.006

Research interests

  • Force field development for RNA and DNA (AMBER)
  • Molecular dynamics of RNA and DNA
  • Noncovalent interactions
  • Benchmark QM calculations

Education

  • 1995 – 2000 – M.Sc. Inorganic chemistry, Charles University, Prague
  • 2000 – 2004 – Ph.D. Physical chemistry, Charles University, Prague
  • 2009 – doc. (associate prof.) Physical chemistry, Palacký University, Olomouc

Employment

  • 2002 – 2003 – Researcher, Jaroslav Heyrovsky Institute of Physical Chemistry, Prague
  • 2005 – 2009 – Researcher, Institute of Biophysics (group of prof. Šponer), Brno
  • 2007 – 2009 – Institute of Organic Chemistry and Biochemistry (group of prof. Hobza), Prague
  • 2006 – Researcher, Palacký University, Olomouc
  • 2009 – Doc. (Associate Prof.), Palacký University, Olomouc
  • 2012 – Researcher (part-time), Institute of Biophysics (group of prof. Šponer), Brno

International experience

  • 2002 – Stay at POSTECH, Pohang (prof. K. S. Kim), South Korea
  • 2005 – Stay at SISSA, Trieste, HPC Europa, Italy
  • 2005 – 2006 – Postdoc at University of Calgary (group of D.R. Salahub), Canada
  • 2009 – Stay at POSTECH, Pohang (prof. K. S. Kim), South Korea

Cooperation

  • Prof. Jiří Šponer, Institute of Biophysics, CAS, Brno – RNA simulations
  • Prof. Thomas E. Cheatham, University of Utah, USA – force field development
  • Prof. Javier F. Luque, University of Barcelona, Spain – molecular modeling
  • Prof. Pavel Hobza – Center for Biomolecules and Complex Molecular Systems, Prague, Czech Republic – benchmark calculations

Grants, projects

  • GACR – Molecules on the Surfaces of Carbon Nanostructures, 2010-2014

Supervized Ph.D. students

  • Marie Zgarbová (2007-2011)
  • Mikuláš Kocman (2009-2014)
  • Martin Pykal (2011-2016)

Publications

2021

  1. Gutten O, Jurečka P, Tehrani ZA, Budešínský M, Řezáč J, Rulíšek L: Conformational energies and equilibria of cyclic dinucleotides in vacuo and in solution: computational chemistry vs. NMR experiments dagger. Phys. Chem. Chem. Phys., 23(12), 7280-7294, 2021. (DOI)

2019

  1. Dubecký M, Jurečka P, Mitas L, Ditte M, Fanta R: Toward Accurate Hydrogen Bonds by Scalable Quantum Monte Carlo. J. Chem. Theory Comput., 15(6), 3552-3557, 2019. (DOI)

2018

  1. Li Q, Froning JP, Pykal M, Zhang S, Wang Z, Vondrák M, Banáš P, Čépe K, Jurečka P, Šponer J, Zbořil R, Dong M, Otyepka M: RNA nanopatterning on graphene. 2D Mater, 5, 031006, 2018. (DOI)
  2. Šponer J, Bussi G, Krepl M, Banáš P, Bottaro S, Cunha RA, Ley AG, Pinamonti G, Poblete S, Jurečka P, Walter NG, Otyepka M: RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview. Chem. Rev., 118(8), 4177–4338, 2018. (DOI)
  3. Zgarbová M, Jurečka P, Šponer J, Otyepka M: A- to B-DNA Transition in AMBER Force Fields and its Coupling to Sugar Pucker. J. Chem. Theory Comput., 14(1), 319–328, 2018. (DOI)

2017

  1. Karlický F, Otyepková E, Lo R, Pitoňák M, Jurečka P, Pykal M, Hobza P, Otyepka M: Adsorption of Organic Molecules to van der Waals Materials: Comparison of Fluorographene and Fluorographite with Graphene and Graphite. J. Chem. Theory Comput., 13(3), 1328–1340, 2017. (DOI)
  2. Mlýnský V, Kührová P, Jurečka P, Šponer J, Otyepka M, Banáš P: Mapping the Chemical Space of the RNA Cleavage and its Implications for Ribozyme Catalysis. J. Phys. Chem. B, 121(48), 10828–10840, 2017. (DOI)
  3. Šponer J, Krepl M, Banáš P, Kührová P, Zgarbová M, Jurečka P, Havrila M, Otyepka M: How to understand atomistic molecular dynamics simulations of RNA and protein– RNA complexes? WIREs RNA, 8(3), e1405, 2017. (DOI)
  4. Zgarbová M, Jurečka P, Banáš P, Havrila M, Šponer J, Otyepka M: Noncanonical α/γ Backbone Conformations in RNA and the Accuracy of Their Description by the AMBER Force Field. J. Phys. Chem. B, 121(11), 2420–2433, 2017. (DOI)
  5. Zgarbová M, Jurečka P, Lankaš F, Cheatham TE, Šponer J, Otyepka M: Influence of BII Backbone Substates on DNA Twist: A Unified View and Comparison of Simulation and Experiment for all 136 Distinct Tetranucleotide Sequences. J. Chem. Inf. Model., 57(2), 275–287, 2017. (DOI)

2016

  1. Dršata T, Zgarbová M, Jurečka P, Šponer J, Lankaš F: On the Use of Molecular Dynamics Simulations for Probing Allostery through DNA. Biophys. J., 110(4), 874–876, 2016. (DOI)
  2. Dubecký M, Mitas L, Jurečka P: Noncovalent Interactions by Quantum Monte Carlo. Chem. Rev., 116(9), 5188–5215, 2016. (DOI)
  3. Galindo-Murillo R, Robertson JC, Zgarbová M, Šponer J, Otyepka M, Jurečka P, Cheatham TE: Assessing the current state of AMBER force field modifications for DNA. J. Chem. Theory Comput., 12(8), 4114–4127, 2016. (DOI)
  4. Pykal M, Jurečka P, Karlický F, Otyepka M: Modelling of graphene functionalization. Phys. Chem. Chem. Phys., 18(48), 6351-6372, 2016. (DOI)

2015

  1. Havrila M, Zgarbová M, Jurečka P, Banáš P, Krepl M, Otyepka M, Šponer J: Microsecond-Scale MD Simulations of HIV-1 DIS Kissing-Loop Complexes Predict Bulged-In Conformation of the Bulged Bases and Reveal Interesting Differences Between Available Variants of the AMBER RNA Force Fields. J. Phys. Chem. B, 119, 15176−15190, 2015. (DOI)
  2. Kocman M, Jurečka P, Dubecký M, Otyepka M, Cho Y, Kim KS: Choosing a density functional for modeling adsorptive hydrogen storage: reference quantum mechanical calculations and a comparison of dispersion-corrected density functionals. Phys. Chem. Chem. Phys., 17(9), 6423-6432, 2015. (DOI)
  3. Mlýnský V, Kührová P, Zgarbová M, Jurečka P, Walter NG, Otyepka M, Šponer J, Banáš P: Reactive Conformation of the Active Site in the Hairpin Ribozyme Achieved by Molecular Dynamics Simulations with $epsilon$/$zeta$ Force Field Reparametrizations. J. Phys. Chem. B., 119(11), 4220-4229, 2015. (DOI)
  4. Řezáč J, Dubecký M, Jurečka P, Hobza P: Extensions and applications of the A24 data set of accurate interaction energies. Phys. Chem. Chem. Phys., 17(29), 19268-19277, 2015. (DOI)
  5. Sovová Ž, Berka K, Otyepka M, Jurečka P: Coarse-Grain Simulations of Skin Ceramide NS with Newly Derived Parameters Clarify Structure of Melted Phase. J. Phys. Chem. B., 119(10), 3988-3998, 2015. (DOI)
  6. Zgarbová M, Rosnik AM, Luque FJ, Curutchet C, Jurečka P: Transferability and additivity of dihedral parameters in polarizable and nonpolarizable empirical force fields. J. Comput. Chem., 36(25), 1874-1884, 2015. (DOI)
  7. Zgarbová M, Šponer J, Otyepka M, Cheatham TE, Galindo-Murillo R, Jurečka P: Refinement of the Sugar-Phosphate Backbone Torsion Beta for the AMBER Force Fields Improves the Description of Z-DNA and B-DNA. J. Chem. Theory Comput., 11(12), 5723–5736, 2015. (DOI)

2014

  1. Dršata T, Špačková N, Jurečka P, Zgarbová M, Šponer J, Lankaš F: Mechanical properties of symmetric and asymmetric DNA A-tracts: implications for looping and nucleosome positioning. Nucleic Acids Res., 42(11), 7383-7394, 2014. (DOI)
  2. Dršata T, Zgarbová M, Špačková N, Jurečka P, Šponer J, Lankaš F: Mechanical Model of DNA Allostery. J. Phys. Chem. Lett., 5(21), 3831-3835, 2014. (DOI)
  3. Dubecký M, Derian R, Jurečka P, Mitas L, Hobza P, Otyepka M: Quantum Monte Carlo for noncovalent interactions: an efficient protocol attaining benchmark accuracy. Phys. Chem. Chem. Phys., 16(38), 20915-20923, 2014. (DOI)
  4. Kocman M, Pykal M, Jurečka P: Electric quadrupole moment of graphene and its effect on intermolecular interactions. Phys. Chem. Chem. Phys., 16(7), 3144-3152, 2014. (DOI)
  5. Mládek A, Banáš P, Jurečka P, Otyepka M, Zgarbová M, Šponer J: Energies and 2′-Hydroxyl Group Orientations of RNA Backbone Conformations. Benchmark CCSD(T)/CBS Database, Electronic Analysis, and Assessment of DFT Methods and MD Simulations. J. Chem. Theory Comput., 10(1), 463-480, 2014. (DOI)
  6. Šponer J, Banáš P, Jurečka P, Zgarbová M, Kührová P, Havrila M, Krepl M, Stadlbauer P, Otyepka M: Molecular Dynamics Simulations of Nucleic Acids. From Tetranucleotides to the Ribosome. J. Phys. Chem. Lett., 5(10), 1771-1782, 2014. (DOI)
  7. Zgarbová M, Otyepka M, Šponer J, Lankaš F, Jurečka P: Base Pair Fraying in Molecular Dynamics Simulations of DNA and RNA. J. Chem. Theory Comput., 10(8), 3177-3189, 2014. (DOI)

2013

  1. Dubecký M, Jurečka P, Derian R, Hobza P, Otyepka M, Mitas L: Quantum Monte Carlo Methods Describe Noncovalent Interactions with Subchemical Accuracy. J. Chem. Theory Comput., 9(10), 4287-4292, 2013. (DOI)
  2. Lazar P, Karlický F, Jurečka P, Kocman M, Otyepková E, Šafářová K, Otyepka M: Adsorption of Small Organic Molecules on Graphene. J. Am. Chem. Soc., 135(16), 6372-6377, 2013. (DOI)
  3. Mládek A, Krepl M, Svozil D, Čech P, Otyepka M, Banáš P, Zgarbová M, Jurečka P, Šponer J: Benchmark quantum-chemical calculations on a complete set of rotameric families of the DNA sugar–phosphate backbone and their comparison with modern density functional theory. Phys. Chem. Chem. Phys., 15(19), 7295-7310, 2013. (DOI)
  4. Pykal M, Šafářová K, Machalová Šišková K, Jurečka P, Bourlinos AB, Zbořil R, Otyepka M: Lipid Enhanced Exfoliation for Production of Graphene Nanosheets. J. Phys. Chem. C, 117(22), 11800-11803, 2013. (DOI)
  5. Šponer J, Šponer JE, Mládek A, Banáš P, Jurečka P, Otyepka M: How to understand quantum chemical computations on DNA and RNA systems? A practical guide for non-specialists. Methods, 64(1), 3-11, 2013. (DOI)
  6. Šponer J, Šponer JE, Mládek A, Jurečka P, Banáš P, Otyepka M: Nature and magnitude of aromatic base stacking in DNA and RNA: Quantum chemistry, molecular mechanics and experiment. Biopolymers, 99(12), 978–988, 2013. (DOI)
  7. Zgarbová M, Luque FJ, Šponer J, Cheatham TE, Otyepka M, Jurečka P: Toward Improved Description of DNA Backbone: Revisiting Epsilon and Zeta Torsion Force Field Parameters. J. Chem. Theory Comput., 9(5), 2339-2354, 2013. (DOI)

2012

  1. Banáš P, Mládek A, Otyepka M, Zgarbová M, Jurečka P, Svozil D, Lankaš F, Šponer J: Can We Accurately Describe the Structure of Adenine Tracts in B-DNA? Reference Quantum-Chemical Computations Reveal Overstabilization of Stacking by Molecular Mechanics. J. Chem. Theory Comput., 8(7), 2448-2460, 2012. (DOI)
  2. Krepl M, Zgarbová M, Stadlbauer P, Otyepka M, Banáš P, Koča J, Cheatham TE, Jurečka P, Šponer J: Reference Simulations of Noncanonical Nucleic Acids with Different chi Variants of the AMBER Force Field: Quadruplex DNA, Quadruplex RNA, and Z-DNA. J. Chem. Theory Comput., 8(7), 2506-2520, 2012. (DOI)
  3. Šponer J, Mládek A, Šponer JE, Svozil D, Zgarbová M, Banáš P, Jurečka P, Otyepka M: The DNA and RNA sugar–phosphate backbone emerges as the key player. An overview of quantum-chemical, structural biology and simulation studies. Phys. Chem. Chem. Phys., 14(44), 15257-15277, 2012. (DOI)
  4. Zgarbová M, Luque FJ, Šponer J, Otyepka M, Jurečka P: A Novel Approach for Deriving Force Field Torsion Angle Parameters Accounting for Conformation-Dependent Solvation Effects. J. Chem. Theory Comput., 8(9), 3232-3242, 2012. (DOI)

2011

  1. Zgarbová M, Jurečka P, Banáš P, Otyepka M, Šponer JE, Leontis NB, Zirbel CL, Šponer J: 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. J. Phys. Chem. A, 115(41), 11277-11292, 2011. (DOI)
  2. Zgarbová M, Otyepka M, Šponer J, Mládek A, Banáš P, Cheatham TE, Jurečka P: Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles. J. Chem. Theory Comput., 7(9), 2886-2902, 2011. (DOI)

2010

  1. Banáš P, Hollas D, Zgarbová M, Jurečka P, Orozco M, Cheatham TE, Šponer J, Otyepka M: Performance of Molecular Mechanics Force Fields for RNA Simulations: Stability of UUCG and GNRA Hairpins. J. Chem. Theory Comput., 6(12), 3836-3849, 2010. (DOI)
  2. Kolář M, Berka K, Jurečka P, Hobza P: On the Reliability of the AMBER Force Field and its Empirical Dispersion Contribution for the Description of Noncovalent Complexes. ChemPhysChem, 11(11), 2399-2408, 2010. (DOI)
  3. Mládek A, Šponer JE, Jurečka P, Banáš P, Otyepka M, Svozil D, Šponer J: Conformational Energies of DNA Sugar−Phosphate Backbone: Reference QM Calculations and a Comparison with Density Functional Theory and Molecular Mechanics. J. Chem. Theory Comput., 6(12), 3817-3835, 2010. (DOI)
  4. Morgado CA, Jurečka P, Svozil D, Hobza P, Šponer J: 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. Phys. Chem. Chem. Phys., 12(14), 3522-3534, 2010. (DOI)
  5. Riley KE, Pitoňák M, Jurečka P, Hobza P: Stabilization and Structure Calculations for Noncovalent Interactions in Extended Molecular Systems Based on Wave Function and Density Functional Theories. Chem. Rev., 110(9), 5023-5063, 2010. (DOI)
  6. Zgarbová M, Otyepka M, Šponer J, Hobza P, Jurečka P: Large-scale compensation of errors in pairwise-additive empirical force fields: comparison of AMBER intermolecular terms with rigorous DFT-SAPT calculations. Phys. Chem. Chem. Phys., 12(35), 10476-10493, 2010. (DOI)

2009

  1. Banáš P, Jurečka P, Walter NG, Šponer J, Otyepka M: Theoretical studies of RNA catalysis: Hybrid QM/MM methods and their comparison with MD and QM. Methods, 49(2), 202-216, 2009. (DOI)
  2. Morgado CA, Jurečka P, Svozil D, Hobza P, Šponer J: 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. J. Chem. Theory Comput., 5(6), 1524-1544, 2009. (DOI)
  3. Šponer J, Zgarbová M, Jurečka P, Riley KE, Šponer JE, Hobza P: Reference Quantum Chemical Calculations on RNA Base Pairs Directly Involving the 2′-OH Group of Ribose. J. Chem. Theory Comput., 5(4), 1166-1179, 2009. (DOI)

2008

  1. Pitoňák M, Neogrády P, Řezáč J, Jurečka P, Urban M, Hobza P: Benzene Dimer: High-Level Wave Function and Density Functional Theory Calculations. J. Chem. Theory Comput., 4(11), 1829-1834, 2008. (DOI)
  2. Řezáč J, Jurečka P, Riley KE, Černý J, Valdes H, Pluháčková K, Berka K, Řezáč T, Pitoňák M, Vondrášek J, Hobza P: Quantum Chemical Benchmark Energy and Geometry Database for Molecular Clusters and Complex Molecular Systems (www.begdb.com): A Users Manual and Examples. Collect. Czech. Chem. Commun., 73(10), 1261-1270, 2008. (DOI)

2007

  1. Bendová L, Jurečka P, Hobza P, Vondrášek J: Model of Peptide Bond−Aromatic Ring Interaction: Correlated Ab Initio Quantum Chemical Study. J. Phys. Chem. B, 111(33), 9975-9979, 2007. (DOI)
  2. Černý J, Jurečka P, Hobza P, Valdés H: Resolution of Identity Density Functional Theory Augmented with an Empirical Dispersion Term (RI-DFT-D): A Promising Tool for Studying Isolated Small Peptides. J. Phys. Chem. A, 111(6), 1146-1154, 2007. (DOI)
  3. Jurečka P, Černý J, Hobza P, Salahub DR: Density functional theory augmented with an empirical dispersion term. Interaction energies and geometries of 80 noncovalent complexes compared with ab initio quantum mechanics calculations. J. Comput. Chem., 28(2), 555-569, 2007. (DOI)
  4. Kubař T, Jurečka P, Černý J, Řezáč J, Otyepka M, Valdés H, Hobza P: Density-Functional, Density-Functional Tight-Binding, and Wave Function Calculations on Biomolecular Systems. J. Phys. Chem. A, 111(26), 5642-5647, 2007. (DOI)
  5. Lee EC, Kim D, Jurečka P, Tarakeshwar P, Hobza P, Kim KS: Understanding of Assembly Phenomena by Aromatic−Aromatic Interactions: Benzene Dimer and the Substituted Systems. J. Phys. Chem. A, 111(18), 3446-3457, 2007. (DOI)
  6. Meneni SR, Shell SM, Gao L, Jurečka P, Lee W, Šponer J, Zou Y, Chiarelli MP, Cho BP: Spectroscopic and Theoretical Insights into Sequence Effects of Aminofluorene-Induced Conformational Heterogeneity and Nucleotide Excision Repair. Biochemistry, 46(40), 11263-11278, 2007. (DOI)
  7. Pluháčková K, Jurečka P, Hobza P: Stabilisation energy of C 6 H 6 ⋯C 6 X 6 (X = F, Cl, Br, I, CN) complexes: complete basis set limit calculations at MP2 and CCSD(T) levels. Phys. Chem. Chem. Phys., 9(6), 755-760, 2007. (DOI)
  8. Sedlák R, Jurečka P, Hobza P: Density functional theory-symmetry adapted perturbation treatment energy decomposition of nucleic acid base pairs taken from DNA crystal geometry. J. Chem. Phys., 127(7), 075104, 2007. (DOI)