StructureChairsPavel HobzaPapers2011

2011

Munusamy E., Sedlák R., Hobza P.:
On the Nature of the Stabilization of Benzene center dot center dot center dot Dihalogen and Benzene center dot center dot center dot Dinitrogen Complexes: CCSD(T)/CBS and DFT-SAPT Calculations.
Chemphyschem 12 (17): 3253-3261, 2011.

Reshetnikov R. V., Šponer J., Rassokhina O. I., Kopylov A. M., Tsvetkov P. O., Makarov A. A., Golovin A. V.:
Cation binding to 15-TBA quadruplex DNA is a multiple-pathway cation-dependent process.
Nucleic Acids Research 39 (22): 9789-9802, 2011.

Riley K. E., Murray J. S., Fanfrlík J., Řezáč J., Sola R. J., Concha M. C., Ramos F. M., Politzer P.:
Halogen bond tunability I: the effects of aromatic fluorine substitution on the strengths of halogen-bonding interactions involving chlorine bromine and iodine.
Journal of Molecular Modeling 17 (12): 3309-3318, 2011.

Réblová K., Šponer J. E., Špačková N., Besseová I., Šponer J.:
A-Minor Tertiary Interactions in RNA Kink-Turns. Molecular Dynamics and Quantum Chemical Analysis.
Journal of Physical Chemistry B 115 (47): 13897-13910, 2011.

Mlynsky V., Banáš P., Walter N. G., Šponer J., Otyepka M.:
QM/MM Studies of Hairpin Ribozyme Self-Cleavage Suggest the Feasibility of Multiple Competing Reaction Mechanisms.
Journal of Physical Chemistry B 115 (47): 13911-13924, 2011.

Řezáč J., Riley K. E., Hobza P.:
Extensions of the S66 Data Set: More Accurate Interaction Energies and Angular-Displaced Nonequilibrium Geometries.
Journal of Chemical Theory and Computation 7 (11): 3466-3470, 2011.

Granatier J., Lazar P., Otyepka M., Hobza P.:
The Nature of the Binding of Au, Ag, and Pd to Benzene, Coronene, and Graphene: From Benchmark CCSD(T) Calculations to Plane-Wave DFT Calculations.
Journal of Chemical Theory and Computation 7 (11): 3743-3755, 2011.

Zgarbová M., Jurečka P., Banáš P., Otyepka M., Šponer J. E., Leontis N. B., Zirbel C. L., 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.
Journal of Physical Chemistry A 115 (41): 11277-11292, 2011.

Kraemer W. P., Špirko V.:
Vibrational Energies of LiH(2)(+) and LiD(2)(+) in the (A)over-tilde(1)Sigma(+) Electronic State.
Journal of Physical Chemistry A 115 (41): 11313-11320, 2011.

Kysilka J., Rubeš M., Grajciar L., Nachtigall P., Bludský O.:
Accurate Description of Argon and Water Adsorption on Surfaces of Graphene-Based Carbon Allotropes.
Journal of Physical Chemistry A 115 (41): 11387-11393, 2011.

Spiwok V., Hobza P., Řezáč J.:
Free-Energy Simulations of Hydrogen Bonding versus Stacking of Nucleobases on a Graphene Surface.
Journal of Physical Chemistry C 115 (40): 19455-19462, 2011.

Riley K. E., Hobza P.:
Strength and Character of Halogen Bonds in Protein-Ligand Complexes.
Crystal Growth \& Design 11 (10): 4272-4278, 2011.

Cang X., Šponer J., Cheatham I.:
Insight into G-DNA Structural Polymorphism and Folding from Sequence and Loop Connectivity through Free Energy Analysis.
Journal of the American Chemical Society 133 (36): 14270-14279, 2011.

Fiala R., Špačková N., Foldynova-Trantirkova S., Šponer J., Sklenar V., Trantirek L.:
NMR Cross-Correlated Relaxation Rates Reveal Ion Coordination Sites in DNA.
Journal of the American Chemical Society 133 (35): 13790-13793, 2011.

Zgarbová M., Otyepka M., Šponer J., Mládek A., Banáš P., Cheatham I., Jurečka P.:
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 7 (9): 2886-2902, 2011.

Sklenovsky P., Florova P., Banáš P., Réblová K., Lankaš F., Otyepka M., Šponer J.:
Understanding RNA Flexibility Using Explicit Solvent Simulations: The Ribosomal and Group I Intron Reverse Kink-Turn Motifs.
Journal of Chemical Theory and Computation 7 (9): 2963-2980, 2011.

Karthikeyan S., Sedlák R., Hobza P.:
on the Nature of Stabilization in Weak, Medium, and Strong Charge-Transfer Complexes: CCSD(T)/CBS and SAPT Calculations.
Journal of Physical Chemistry A 115 (34, SI): 9422-9428, 2011.

Řezáč J., Riley K. E., Hobza P.:
S66: A Well-balanced Database of Benchmark Interaction Energies Relevant to Biomolecular Structures.
Journal of Chemical Theory and Computation 7 (8): 2427-2438, 2011.

Rijs A. M., Kabeláč M., Abo-Riziq A., Hobza P., de Vries M. S.:
Isolated Gramicidin Peptides Probed by IR Spectroscopy.
Chemphyschem 12 (10, SI): 1816-1821, 2011.

Dobeš P., Řezáč J., Fanfrlík J., Otyepka M., Hobza P.:
Semiempirical Quantum Mechanical Method PM6-DH2X Describes the Geometry and Energetics of CK2-Inhibitor Complexes Involving Halogen Bonds Well, While the Empirical Potential Fails.
Journal of Physical Chemistry B 115 (26): 8581-8589, 2011.

Kolář M., Kubař T., Hobza P.:
On the Role of London Dispersion Forces in Biomolecular Structure Determination.
Journal of Physical Chemistry B 115 (24): 8038-8046, 2011.

Otero Arean C., Rodriguez Delgado M., Fiol Bibiloni G., Bludský O., Nachtigall P.:
Variable-Temperature IR Spectroscopic and Theoretical Studies on CO(2) Adsorbed in Zeolite K-FER.
Chemphyschem 12 (8, SI): 1435-1443, 2011.

Cang X., Šponer J., Cheatham I.:
Explaining the varied glycosidic conformational, G-tract length and sequence preferences for anti-parallel G-quadruplexes.
Nucleic Acids Research 39 (10): 4499-4512, 2011.

Aquino A. J. A., Nachtigallová D., Hobza P., Truhlar D. G., Haettig C., Lischka H.:
The Charge-Transfer States in a Stacked Nucleobase Dimer Complex: A Benchmark Study.
Journal of Computational Chemistry 32 (7): 1217-1227, 2011.

Kolář M., Fanfrlík J., Hobza P.:
Ligand Conformational and Solvation/Desolvation Free Energy in Protein-Ligand Complex Formation.
Journal of Physical Chemistry B 115 (16): 4718-4724, 2011.

Řezáč J., Hobza P.:
A halogen-bonding correction for the semiempirical PM6 method.
Chemical Physics Letters 506 (4-6): 286-289, 2011.

de la Lande A., Řezáč J., Levy B., Sanders B. C., Salahub D. R.:
Transmission Coefficients for Chemical Reactions with Multiple States: Role of Quantum Decoherence.
Journal of the American Chemical Society 133 (11): 3883-3894, 2011.

Mládek A., Šponer J., Sumpter B. G., Fuentes-Cabrera M., Šponer J. E.:
On the Geometry and Electronic Structure of the As-DNA Backbone.
Journal of Physical Chemistry Letters 2 (5): 389-392, 2011.

Vazquez-Mayagoitia A., Horton S. R., Sumpter B. G., Šponer J., Šponer J. E., Fuentes-Cabrera M.:
On the Stabilization of Ribose by Silicate Minerals.
Astrobiology 11 (2): 115-121, 2011.

Dobeš P., Fanfrlík J., Řezáč J., Otyepka M., Hobza P.:
Transferable scoring function based on semiempirical quantum mechanical PM6-DH2 method: CDK2 with 15 structurally diverse inhibitors.
Journal of Computer-aided Molecular Design 25 (3): 223-235, 2011.

Řezáč J., Hobza P.:
Extrapolation and Scaling of the DFT-SAPT Interaction Energies toward the Basis Set Limit.
Journal of Chemical Theory and Computation 7 (3): 685-689, 2011.

Přenosil O., Pitoňák M., Sedlák R., Kabeláč M., Hobza P.:
H-Bonding Cooperativity Effects in Amyloids: Quantum Mechanical and Molecular Mechanics Study.
Zeitschrift fur Physikalische Chemie-international Journal of Research in Physical Chemistry \& Chemical Physics 225 (5, SI): 553-574, 2011.

Bludský O., Nachtigall P., Špirko V.:
VIBRATIONAL DYNAMICS OF ADSORBED CO(2): SEPARABILITY OF THE CO(2) ASYMMETRIC STRETCHING MODE.
Collection of Czechoslovak Chemical Communications 76 (6): 669-682, 2011.

Pitoňák M., Aquilante F., Hobza P., Neogrady P., Noga J., Urban M.:
PARALLELIZED IMPLEMENTATION OF THE CCSD(T) METHOD IN MOLCAS USING OPTIMIZED VIRTUAL ORBITALS SPACE AND CHOLESKY DECOMPOSED TWO-ELECTRON INTEGRALS.
Collection of Czechoslovak Chemical Communications 76 (6): 713-742, 2011.

Mládek A., Šponer J., Sumpter B. G., Fuentes-Cabrera M., Šponer J. E.:
Theoretical modeling on the kinetics of the arsenate-ester hydrolysis: implications to the stability of As-DNA.
Physical Chemistry Chemical Physics 13 (23): 10869-10871, 2011.

Špirko V., Li X., Paldus J.:
POTENTIAL ENERGY CURVE OF N(2) REVISITED.
Collection of Czechoslovak Chemical Communications 76 (4): 327-341, 2011.

Šponer J. E., Šponer J., Fuentes-Cabrera M.:
Prebiotic Routes to Nucleosides: A Quantum Chemical Insight into the Energetics of the Multistep Reaction Pathways.
Chemistry-a European Journal 17 (3): 847-854, 2011.

Arunan E., Desiraju G. R., Klein R. A., Sadlej J., Scheiner S., Alkorta I., Clary D. C., Crabtree R. H., Dannenberg J. J., Hobza P., Kjaergaard H. G., Legon A. C., Mennucci B., Nesbitt D. J.:
Defining the hydrogen bond: An account (IUPAC Technical Report).
Pure and Applied Chemistry 83 (8): 1619-1636, 2011.

Arunan E., Desiraju G. R., Klein R. A., Sadlej J., Scheiner S., Alkorta I., Clary D. C., Crabtree R. H., Dannenberg J. J., Hobza P., Kjaergaard H. G., Legon A. C., Mennucci B., Nesbitt D. J.:
Definition of the hydrogen bond (IUPAC Recommendations 2011).
Pure and Applied Chemistry 83 (8): 1637-1641, 2011.

Pecina A., Přenosil O., Fanfrlík J., Řezáč J., Granatier J., Hobza P., Lepšík M.:
ON THE RELIABILITY OF THE CORRECTED SEMIEMPIRICAL QUANTUM CHEMICAL METHOD (PM6-DH2) FOR ASSIGNING THE PROTONATION STATES IN HIV-1 PROTEASE/INHIBITOR COMPLEXES.
Collection of Czechoslovak Chemical Communications 76 (5): 457-479, 2011.

Zelený T., Hobza P., Nachtigallová D., Ruckenbauer M., Lischka H.:
PHOTODYNAMICS OF THE ADENINE MODEL 4-AMINOPYRIMIDINE EMBEDDED WITHIN DOUBLE STRAND OF DNA.
Collection of Czechoslovak Chemical Communications 76 (6): 631-643, 2011.

Maity S., Patwari G. N., Sedlák R., Hobza P.:
A pi-stacked phenylacetylene dimer.
Physical Chemistry Chemical Physics 13 (37): 16706-16712, 2011.

Puettner R., Sekushin V., Fukuzawa H., Uhlikova T., Špirko V., Asahina T., Kuze N., Kato H., Hoshino M., Tanaka H., Thomas T. D., Kukk E., Tamenori Y., Kaindl G., Ueda K.:
Metastable states in NO(2+) probed with Auger spectroscopy.
Physical Chemistry Chemical Physics 13 (41): 18436-18446, 2011.

Riley K. E., Řezáč J., Hobza P.:
MP2.X: a generalized MP2.5 method that produces improved binding energies with smaller basis sets.
Physical Chemistry Chemical Physics 13 (47): 21121-21125, 2011.

Maity S., Sedlák R., Addicoat M. A., Irle S., Hobza P., Patwari G. N.:
A pi-stacked phenylacetylene dimer (vol 13, pg 16706, 2011).
Physical Chemistry Chemical Physics 13 (48): 21651-21652, 2011.

Zierkiewicz W., Wieczorek R., Hobza P., Michalska D.:
Halogen bonded complexes between volatile anaesthetics (chloroform, halothane, enflurane, isoflurane) and formaldehyde: a theoretical study.
Physical Chemistry Chemical Physics 13 (11): 5105-5113, 2011.

Riley K. E., Hobza P.:
Noncovalent interactions in biochemistry.
Wiley Interdisciplinary Reviews-computational Molecular Science 1 (1): 3-17, 2011.

Sat Feb 04 13:05:49 +0100 2012