2010
Mladek A., Šponer J. E., 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.
Journal of Chemical Theory and Computation 6 (12): 3817-3835, 2010.
Banáš P., Hollas D., Zgarbová M., Jurečka P., Orozco M., Cheatham I., Šponer J., Otyepka M.:
Performance of Molecular Mechanics Force Fields for RNA Simulations: Stability of UUCG and GNRA Hairpins.
Journal of Chemical Theory and Computation 6 (12): 3836-3849, 2010.
Šponer J., Šponer J. E., Petrov A. I., Leontis N. B.:
Quantum Chemical Studies of Nucleic Acids Can We Construct a Bridge to the RNA Structural Biology and Bioinformatics Communities?.
Journal of Physical Chemistry B 114 (48): 15723-15741, 2010.
Besseová I., Réblová K., Leontis N. B., Šponer J.:
Molecular dynamics simulations suggest that RNA three-way junctions can act as flexible RNA structural elements in the ribosome.
Nucleic Acids Research 38 (18): 6247-6264, 2010.
Kolář M., Kubař T., Hobza P.:
Sequence-Dependent Configurational Entropy Change of DNA upon Intercalation.
Journal of Physical Chemistry B 114 (42): 13446-13454, 2010.
Sedlák R., Fanfrlík J., Hnyk D., Hobza P., Lepšík M.:
Interactions of Boranes and Carboranes with Aromatic Systems: CCSD(T) Complete Basis Set Calculations and DFT-SAPT Analysis of Energy Components.
Journal of Physical Chemistry A 114 (42): 11304-11311, 2010.
Reshetnikov R., Golovin A., Spiridonova V., Kopylov A., Šponer J.:
Structural Dynamics of Thrombin-Binding DNA Aptamer d(GGTTGGTGTGGTTGG) Quadruplex DNA Studied by Large-Scale Explicit Solvent Simulations.
Journal of Chemical Theory and Computation 6 (10): 3003-3014, 2010.
Fanfrlík J., Bronowska A. K., Řezáč J., Přenosil O., Konvalinka J., Hobza P.:
A Reliable Docking/Scoring Scheme Based on the Semiempirical Quantum Mechanical PM6-DH2 Method Accurately Covering Dispersion and H-Bonding: HIV-1 Protease with 22 Ligands.
Journal of Physical Chemistry B 114 (39): 12666-12678, 2010.
Riley K. E., 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.
Chemical Reviews 110 (9): 5023-5063, 2010.
Nachtigallová D., Barbatti M., Szymczak J. J., Hobza P., Lischka H.:
The photodynamics of 2,4-diaminopyrimidine in comparison with 4-aminopyrimidine: The effect of amino-substitution.
Chemical Physics Letters 497 (1-3): 129-134, 2010.
Barbatti M., Pittner J., Pederzoli M., Werner U., Mitric R., Bonacic-Koutecky V., Lischka H.:
Non-adiabatic dynamics of pyrrole: Dependence of deactivation mechanisms on the excitation energy.
Chemical Physics 375 (1): 26-34, 2010.
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.
Physical Chemistry Chemical Physics 12 (35): 10476-10493, 2010.
Pitoňák M., Řezáč J., Hobza P.:
Spin-component scaled coupled-clusters singles and doubles optimized towards calculation of noncovalent interactions.
Physical Chemistry Chemical Physics 12 (33): 9611-9614, 2010.
Kabeláč M., Zimandl F., Fessl T., Chval Z., Lankaš F.:
A comparative study of the binding of QSY 21 and Rhodamine 6G fluorescence probes to DNA: structure and dynamics.
Physical Chemistry Chemical Physics 12 (33): 9677-9684, 2010.
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.
Špačková N., Réblová K., Šponer J.:
Structural Dynamics of the Box C/D RNA Kink-Turn and Its Complex with Proteins: The Role of the A-Minor 0 Interaction, Long-Residency Water Bridges, and Structural Ion-Binding Sites Revealed by Molecular Simulations.
Journal of Physical Chemistry B 114 (32): 10581-10593, 2010.
Grafova L., Pitoňák M., Řezáč J., Hobza P.:
Comparative Study of Selected Wave Function and Density Functional Methods for Noncovalent Interaction Energy Calculations Using the Extended S22 Data Set.
Journal of Chemical Theory and Computation 6 (8): 2365-2376, 2010.
Kraemer W. P., Špirko V.:
Statistical properties of the energies and electric dipole moments of the bound vibrational states of the system HCO+/COH+.
Chemical Physics 373 (3): 170-180, 2010.
Pasalic H., Aquino A. J. A., Tunega D., Haberhauer G., Gerzabek M. H., Georg H. C., Moraes T. F., Coutinho K., Canuto S., Lischka H.:
Thermodynamic Stabillity of Hydrogen-Bonded Systems in Polar and Nonpolar Environments.
Journal of Computational Chemistry 31 (10): 2046-2055, 2010.
Berka K., Laskowski R. A., Hobza P., Vondrášek J.:
Energy Matrix of Structurally Important Side-Chain/Side-Chain Interactions in Proteins.
Journal of Chemical Theory and Computation 6 (7): 2191-2203, 2010.
Banáš P., Walter N. G., Šponer J., Otyepka M.:
Protonation States of the Key Active Site Residues and Structural Dynamics of the glmS Riboswitch As Revealed by Molecular Dynamics.
Journal of Physical Chemistry B 114 (26): 8701-8712, 2010.
Nachtigallová D., Zelený T., Ruckenbauer M., Mueller T., Barbatti M., Hobza P., Lischka H.:
Does Stacking Restrain the Photodynamics of Individual Nucleobases?.
Journal of the American Chemical Society 132 (24): 8261+, 2010.
Ruckenbauer M., Barbatti M., Mueller T., Lischka H.:
Nonadiabatic Excited-State Dynamics with Hybrid ab Initio Quantum-Mechanical/Molecular-Mechanical Methods: Solvation of the Pentadieniminium Cation in Apolar Media.
Journal of Physical Chemistry A 114 (25): 6757-6765, 2010.
Rubeš M., Kysilka J., Nachtigall P., Bludský O.:
DFT/CC investigation of physical adsorption on a graphite (0001) surface.
Physical Chemistry Chemical Physics 12 (24): 6438-6444, 2010.
Dietrich M. A., Zmijewski D., Karol H., Hejmej A., Bilinska B., Jurečka P., Irnazarow I., Slowinska M., Hliwa P., Ciereszko A.:
Isolation and characterization of transferrin from common carp (Cyprinus carpio L.) seminal plasma.
Fish \& Shellfish Immunology 29 (1): 66-74, 2010.
Lankaš F., Špačková N., Moakher M., Enkhbayar P., Šponer J.:
A measure of bending in nucleic acids structures applied to A-tract DNA.
Nucleic Acids Research 38 (10): 3414-3422, 2010.
Lukes V., Solc R., Barbatti M., Lischka H., Kauffmann H.:
TORSIONAL POTENTIALS AND FULL-DIMENSIONAL SIMULATION OF ELECTRONIC ABSORPTION SPECTRA OF para-PHENYLENEVINYLENE OLIGOMERS USING SEMIEMPIRICAL HAMILTONIANS.
Journal of Theoretical \& Computational Chemistry 9 (1): 249-263, 2010.
Špirko V., Rubeš M., Bludský O.:
Ab initio vibrational dynamics of molecular hydrogen on graphene: An effective interaction potential.
Journal of Chemical Physics 132 (19): 10.1063/1.3427640, 2010.
Gengeliczki Z., Callahan M. P., Svadlenak N., Pongor C. I., Sztaray B., Meerts L., Nachtigallová D., Hobza P., Barbatti M., Lischka H., de Vries M. S.:
Effect of substituents on the excited-state dynamics of the modified DNA bases 2,4-diaminopyrimidine and 2,6-diaminopurine.
Physical Chemistry Chemical Physics 12 (20): 5375-5388, 2010.
Mlynsky V., Banáš P., Hollas D., Réblová K., Walter N. G., Šponer J., Otyepka M.:
Extensive Molecular Dynamics Simulations Showing That Canonical G8 and Protonated A38H(+) Forms Are Most Consistent with Crystal Structures of Hairpin Ribozyme.
Journal of Physical Chemistry B 114 (19): 6642-6652, 2010.
Oncak M., Lischka H., Slavíček P.:
Photostability and solvation: photodynamics of microsolvated zwitterionic glycine.
Physical Chemistry Chemical Physics 12 (19): 4906-4914, 2010.
Nachtigallová D., Lischka H., Szymczak J. J., Barbatti M., Hobza P., Gengeliczki Z., Pino G., Callahan M. P., de Vries M. S.:
The effect of C5 substitution on the photochemistry of uracil.
Physical Chemistry Chemical Physics 12 (19): 4924-4933, 2010.
Barbatti M., Aquino A. J. A., Lischka H.:
The UV absorption of nucleobases: semi-classical ab initio spectra simulations.
Physical Chemistry Chemical Physics 12 (19): 4959-4967, 2010.
Morgado C. A., 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.
Physical Chemistry Chemical Physics 12 (14): 3522-3534, 2010.
Crews B. O., Abo-Riziq A., Pluháčková K., Thompson P., Hill G., Hobza P., de Vries M. S.:
Guanine-aspartic acid interactions probed with IR-UV resonance spectroscopy.
Physical Chemistry Chemical Physics 12 (14): 3597-3605, 2010.
Šponer J. E., Vazquez-Mayagoitia A., Sumpter B. G., Leszczynski J., Šponer J., Otyepka M., Banáš P., Fuentes-Cabrera M.:
Theoretical Studies on the Intermolecular Interactions of Potentially Primordial Base-Pair Analogues.
Chemistry-a European Journal 16 (10): 3057-3065, 2010.
Zierkiewicz W., Michalska D., Hobza P.:
Adenine ribbon stabilized by Watson-Crick and Hoogsteen hydrogen Bonds: WFT and DFT study.
Physical Chemistry Chemical Physics 12 (12): 2888-2894, 2010.
Réblová K., Razga F., Li W., Gao H., Frank J., Šponer J.:
Dynamics of the base of ribosomal A-site finger revealed by molecular dynamics simulations and Cryo-EM.
Nucleic Acids Research 38 (4): 1325-1340, 2010.
Sharma P., Šponer J. E., Šponer J., Sharma S., Bhattacharyya D., Mitra A.:
On the Role of the cis Hoogsteen:Sugar-Edge Family of Base Pairs in Platforms and Triplets-Quantum Chemical Insights into RNA Structural Biology.
Journal of Physical Chemistry B 114 (9): 3307-3320, 2010.
Gloaguen E., Valdes H., Pagliarulo F., Pollet R., Tardivel B., Hobza P., Piuzzi F., Mons M.:
Experimental and Theoretical Investigation of the Aromatic-Aromatic Interaction in Isolated Capped Dipeptides.
Journal of Physical Chemistry A 114 (9): 2973-2982, 2010.
Réblová K., Střelcová Z., Kulhánek P., Besseová I., Mathews D. H., Van Nostrand K., Yildirim I., Turner D. H., Šponer 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.
Journal of Chemical Theory and Computation 6 (3): 910-929, 2010.
Riley K. E., Pitoňák M., Černý J., Hobza P.:
On the Structure and Geometry of Biomolecular Binding Motifs (Hydrogen-Bonding, Stacking, X-H center dot center dot center dot pi): WFT and DFT Calculations.
Journal of Chemical Theory and Computation 6 (1): 66-80, 2010.
Řezáč J., Salahub D. R.:
Multilevel Fragment-Based Approach (MFBA): A Novel Hybrid Computational Method for the Study of Large Molecules.
Journal of Chemical Theory and Computation 6 (1): 91-99, 2010.
Pitoňák M., Hesselmann A.:
Accurate Intermolecular Interaction Energies from a Combination of MP2 and TDDFT Response Theory.
Journal of Chemical Theory and Computation 6 (1): 168-178, 2010.
Korth M., Pitoňák M., Řezáč J., Hobza P.:
A Transferable H-Bonding Correction for Semiempirical Quantum-Chemical Methods.
Journal of Chemical Theory and Computation 6 (1): 344-352, 2010.
Pitoňák M., Neogrady P., Hobza P.:
Three- and four-body nonadditivities in nucleic acid tetramers: a CCSD(T) study.
Physical Chemistry Chemical Physics 12 (6): 1369-1378, 2010.
Georgieva I., Aquino A. J. A., Trendafilova N., Santos P. S., Lischka H.:
Solvatochromic and lonochromic Effects of Iron(II)bis-(1,10-phenanthroline)dicyano: a Theoretical Study.
Inorganic Chemistry 49 (4): 1634-1646, 2010.
Ditzler M. A., Otyepka M., Šponer J., Walter N. G.:
Molecular Dynamics and Quantum Mechanics of RNA: Conformational and Chemical Change We Can Believe In.
Accounts of Chemical Research 43 (1): 40-47, 2010.
Svozil D., Hobza P., Šponer J.:
Comparison of Intrinsic Stacking Energies of Ten Unique Dinucleotide Steps in A-RNA and B-DNA Duplexes. Can We Determine Correct Order of Stability by Quantum-Chemical Calculations?.
Journal of Physical Chemistry B 114 (2): 1191-1203, 2010.
Řezáč J., Hobza P., Harris S. A.:
Stretched DNA Investigated Using Molecular-Dynamics and Quantum-Mechanical Calculations.
Biophysical Journal 98 (1): 101-110, 2010.
Lavery R., Zakrzewska K., Beveridge D., Bishop T. C., Case D. A., Cheatham I., Dixit S., Jayaram B., Lankaš F., Laughton C., Maddocks J. H., Michon A., Osman R., Orozco M., Perez A., Singh T., Špačková N., Šponer J.:
A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA.
Nucleic Acids Research 38 (1): 299-313, 2010.
Aquilante F., De Vico L., Ferre N., Ghigo G., Malmqvist P., Neogrady P., Pedersen T. B., Pitoňák M., Reiher M., Roos B. O., Serrano-Andres L., Urban M., Veryazov V., Lindh R.:
Software News and Update MOLCAS 7: The Next Generation.
Journal of Computational Chemistry 31 (1): 224-247, 2010.
Černý J., Hobza P.:
Energy barriers between H-bonded and stacked structures of 9-methyladenine center dot center dot center dot 1-methylthymine and 9-methylguanine center dot center dot center dot 1-methylcytosine complexes.
Chemical Communications 46 (3): 383-385, 2010.
Fri Feb 04 10:54:06 +0100 2011