Petr Kulhánek

Research Areas

• molecular mechanics and its usage for the study of biological systems
• quantum chemistry and its usage for the study of reaction mechanisms
• development and/or implementation of methods for free energy evaluation

Publications

1. Novotny, J.; Kulhánek, P.; Marek, R. Biocompatible Xanthine-Quadruplex Scaffold for Ion-Transporting DNA Channels. J. Phys. Chem. Lett. 2012, 3, 1788–1792.
2. Soliman, N. A.; Kulhánek, P.; Koca, J. Influence of stereochemistry on proton transfer in protonated tripeptide models. J. Mol. Model. 2012, 18, 871–879.
3. Mladek, A.; Sponer, J. E.; Kulhánek, P.; Lu, X.-J.; Olson, W. K.; Sponer, J. Understanding the Sequence Preference of Recurrent RNA Building Blocks Using Quantum Chemistry: The Intrastrand RNA Dinucleotide Platform. J. Chem. Theory Comput. 2012, 8, 335–347.
4. Standara, S.; Kulhánek, P.; Marek, R.; Hornicek, J.; Bour, P.; Straka, M. Simulations of (129)Xe NMR chemical shift of atomic xenon dissolved in liquid benzene. Theor. Chem. Acc. 2011, 129, 677–684.
5. Kolman, V.; Babinsky, M.; Kulhánek, P.; Marek, R.; Sindelar, V. Redistribution of electron density in pyridinium and pyrazinium guests induced by complexation with cucurbit[6]uril. New J. Chem. 2011, 35, 2854–2859.
6. Reblova, K.; Strelcova, Z.; Kulhánek, P.; Besseova, I.; Mathews, D. H.; Van Nostrand, K.; Yildirim, I.; Turner, D. H.; Sponer, J. An RNA Molecular Switch: Intrinsic Flexibility of 23S rRNA Helices 40 and 68 5’-UAA/5’-GAN Internal Loops Studied by Molecular Dynamics Methods. J. Chem. Theory Comput. 2010, 6, 910–929.
7. Kolman, V.; Kulhánek, P.; Sindelar, V. Inclusion of Carboxyl Function Inside of Cucurbiturils and its Use in Molecular Switches. Chem.-Asian J. 2010, 5, 2386–2392.
8. Solt, I; Kulhánek, P.; Simon, I.; Winfield, S.; Payne, M.C.; Csanyi, G.; Fuxreiter, M. Evaluating Boundary Dependent Errors in QM/MM Simulations. Journal of Physical Chemistry B, 2009, 113(17), 5728-5735.
9. Mones, L.; Kulhánek, P.; Simon, I.; Laio, A.; Fuxreiter, M. The Energy Gap as a Universal Reaction Coordinate for the Simulation of Chemical Reactions. J. Phys. Chem. B 2009, 113, 7867–7873.
10. Kolman, V.; Marek, R.; Strelcova, Z.; Kulhánek, P.; Necas, M.; Svec, J.; Sindelar, V. Electron Density Shift in Imidazolium Derivatives upon Complexation with Cucurbit[6]uril. Chem.-Eur. J. 2009, 15, 6926–6931.
11. Klvana, M.; Pavlova, M.; Koudelakova, T.; Chaloupkova, R.; Dvorak, P.; Prokop, Z.; Stsiapanava, A.; Kuty, M.; Kuta-Smatanova, I.; Dohnalek, J.; Kulhánek, P.; Wade, R.; Damborsky, J. Pathways and Mechanisms for Product Release in the Engineered Haloalkane Dehalogenases Explored Using Classical and Random Acceleration Molecular Dynamics Simulations. J. Mol. Biol. 2009, 392, 1339–1356.
12. Mishra, N. K.; Kulhánek, P.; Šnajdrová, L.; Petřek, M.; Imberty, A.; Koča, J. Molecular dynamics study of Pseudomonas aeruginosa lectin-II complexed with monosaccharides. Proteins-Structure Function and Bioinformatics, 2008, 72(1), 382-392.
13. Matoušek, J.; Čajan, M.; Kulhánek, P.; Koča, J. Mechanism of hydrogen-bond array isomerization in tetrahydroxycalix[4]arene and tetrahydroxythiacalix[4]arene. Journal of Physical Chemistry A, 2008, 112(5), 1076-1084.
14. Mones, L.; Kulhánek, P.; Florian, J.; Simon, I.; Fuxreiter, M. Probing the two-metal ion mechanism in the restriction endonuclease BamHI. Biochemistry, 2007, 46(50), 14514-14523.
15. Réblová, K.; Fadrná, E.; Sarzynska, J.; Kulinski, T.; Kulhánek, P.; Ennifar, E.; Koča, J. Šponer, J. Conformations of flanking bases in HIV-1 RNA DIS kissing complexes studied by molecular dynamics. Biophysical Journal, 2007, 93(11), 3932-3949.
16. Matoušek, J; Kulhánek, P.; Čajan, M.; Koča, J. Effect of Solvation on Pinched Cone-Pinched Cone Interconversion of Tetraethoxycalix[4]arene and Tetraethoxythiacalix[4]arene. Journal of Physical Chemistry A, 2006, 110, 861-867.
17. Šponer, J. E.; Špačková, N.; Kulhánek, P.; Leszczynski, J.; Šponer, J. Non-Watson-Crick base pairing in RNA. Quantum chemical analysis of the cis Watson-Crick/sugar edge base pair family. Journal of Physical Chemistry A, 2005, 109, 2292-2301.
18. Šnajdrová, L.; Kulhánek, P.; Imberty, A.; Koča, J. Molecular Dynamics Simulations of Glycosyltransferase LgtC. Carbohydrate Research, 2004, 339 (5), 995-1006.
19. Kulhánek, P.; Potáček, M.; Koča, J. Quantum-Chemical Insight into Mechanism of Combined Intra-intermolecular Cycloaddition. Collection of Czechoslovak Chemical Communications, 2004, 69, 231-241.
20. Kulhánek, P.; Schlag, E.W.; Koča, J. A Novel Mechanism of Proton Transfer in Protonated Peptides. Journal of the American Chemical Society, 2003, 125 (45), 13678-13679.
21. Kulhánek, P.; Schlag, E. W.; Koča, J. Mechanism of Proton Transfer in Short Protonated Oligopeptides. 1. N-Methylacetamide and N2-Acetyl-N1-methylglycinamide. Journal of Physical Chemistry A, 2003, 107 (30), 5789-5797.
22. Literák, J.; Relich, S.; Kulhánek, P.; Klán, P. Temperature Dependent Photochemical Cleavage of 2,5-Dimethylphenacyl Esters. Molecular Diversity, 2003, 7, 265-271.
23. Man, S.; Kulhánek, P.; Potáček, M.; Nečas, M. New fused heterocycles by combined intra-intermolecular criss-cross cycloaddition of nonsymmetrical azines. Tetrahedron Letters, 2002, 36, 6431-6433.
24. Klán, P.; Růžička, R.; Heger, D.; Literák, J.; Kulhánek, P.; Loupy, A. Temperature-sensitive photochemical aromatic substitution on 4-nitroanisole. Photochemical and Photobiological Sciences, 2002, 1, 1012-1017.