2009
Patkowski K., Špirko V., Szalewicz K.:
On the Elusive Twelfth Vibrational State of Beryllium Dimer.
Science 326 (5958): 1382-1384, 2009.
West A. C., Kretchmer J. S., Sellner B., Park K., Hase W. L., Lischka H., Windus T. L.:
O(P-3) + C2H4 Potential Energy Surface: Study at the Multireference Level.
Journal of Physical Chemistry A 113 (45): 12663-12674, 2009.
Szymczak J. J., Barbatti M., Hoo J. T. S., Adkins J. A., Windus T. L., Nachtigallová D., Lischka H.:
Photodynamics Simulations of Thymine: Relaxation into the First Excited Singlet State.
Journal of Physical Chemistry A 113 (45): 12686-12693, 2009.
Lankaš F., Gonzalez O., Heffler L. M., Stoll G., Moakher M., Maddocks J. H.:
On the parameterization of rigid base and basepair models of DNA from molecular dynamics simulations.
Physical Chemistry Chemical Physics 11 (45): 10565-10588, 2009.
Besseová I., Otyepka M., Réblová K., Šponer J.:
Dependence of A-RNA simulations on the choice of the force field and salt strength.
Physical Chemistry Chemical Physics 11 (45): 10701-10711, 2009.
Řezáčova P., Pokorná J., Brynda J., Kožíšek M., Cígler P., Lepšík M., Fanfrlik J., Řezáč J., Šašková K. G., Sieglová I., Plešek J., Sicha V., Gruener B., Oberwinkler H., Sedlacek J., Kraeusslich H., Hobza P., Král V., Konvalinka J.:
Design of HIV Protease Inhibitors Based on Inorganic Polyhedral Metallacarboranes.
Journal of Medicinal Chemistry 52 (22): 7132-7141, 2009.
Maity S., Sedlák R., Hobza P., Patwari G. N.:
Infrared-optical double resonance spectroscopic measurements and high level ab initio calculations on a binary complex between phenylacetylene and borane-trimethylamine. Understanding the role of C-H center dot center dot center dot pi interactions.
Physical Chemistry Chemical Physics 11 (42): 9738-9743, 2009.
Pulido A., Delgado M. R., Bludský O., Rubeš M., Nachtigall P., Arean C. O.:
Combined DFT/CC and IR spectroscopic studies on carbon dioxide adsorption on the zeolite H-FER.
Energy \& Environmental Science 2 (11): 1187-1195, 2009.
Szymczak J. J., Barbatti M., Lischka H.:
Is the Photoinduced Isomerization in Retinal Protonated Schiff Bases a Single- or Double-Torsional Process?.
Journal of Physical Chemistry A 113 (43): 11907-11918, 2009.
Dedikova P., Demovic L., Pitoňák M., Neogrady P., Urban M.:
CCSD(T) calculations of the electron affinity of the uracil molecule.
Chemical Physics Letters 481 (1-3): 107-111, 2009.
Curuksu J., Šponer J., Zacharias M.:
Elbow Flexibility of the kt38 RNA Kink-Turn Motif Investigated by Free-Energy Molecular Dynamics Simulations.
Biophysical Journal 97 (7): 2004-2013, 2009.
Banas P., Jurečka P., Walter N. G., 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.
Zirbel C. L., Šponer J. E., Šponer J., Stombaugh J., Leontis N. B.:
Classification and energetics of the base-phosphate interactions in RNA.
Nucleic Acids Research 37 (15): 4898-4918, 2009.
Aquino A. J. A., Tunega D., Schaumann G. E., Haberhauer G., Gerzabek M. H., Lischka H.:
Stabilizing Capacity of Water Bridges in Nanopore Segments of Humic Substances: A Theoretical Investigation.
Journal of Physical Chemistry C 113 (37): 16468-16475, 2009.
Valdes H., Pluháčková K., Hobza P.:
Phenylalanyl-Glycyl-Phenylalanine Tripeptide: A Model System for Aromatic-Aromatic Side Chain Interactions in Proteins.
Journal of Chemical Theory and Computation 5 (9): 2248-2256, 2009.
Fadrna E., Spackova N., Sarzynska J., Koca J., Orozco M., Cheatham I., Kulinski T., Šponer J.:
Single Stranded Loops of Quadruplex DNA As Key Benchmark for Testing Nucleic Acids Force Fields.
Journal of Chemical Theory and Computation 5 (9): 2514-2530, 2009.
Konvalinka J., Illnerová H., Hobza P., Hořejší V., Holý A., Jungwirth P., Pačes V., Martasek P., Zlatuska J.:
Czech bibliometric system fosters mediocre research.
Nature 460 (7259): 1079, 2009.
Georgieva I., Benco L., Tunega D., Trendafilova N., Hafner J., Lischka H.:
Multiple adsorption of NO on cobalt-exchanged chabazite, mordenite, and ferrierite zeolites: A periodic density functional theory study.
Journal of Chemical Physics 131 (5): 10.1063/1.3182850, 2009.
Yildirim I., Stern H. A., Šponer J., Spackova N., Turner D. H.:
Effects of Restrained Sampling Space and Nonplanar Amino Groups on Free-Energy Predictions for RNA with Imino and Sheared Tandem GA Base Pairs Flanked by GC, CG, iGiC or iCIG Base Pairs.
Journal of Chemical Theory and Computation 5 (8): 2088-2100, 2009.
Zendlová L., Řeha D., Hocek M., Hobza P.:
Theoretical Study of the Stability of the DNA Duplexes Modified by a Series of Hydrophobic Base Analogues.
Chemistry-a European Journal 15 (31): 7601-7610, 2009.
Otero Arean C., Turnes Palomino G., Llop Carayol M. R., Pulido A., Rubeš M., Bludský O., Nachtigall P.:
Hydrogen adsorption on the zeolite Ca-A: DFT and FT-IR investigation.
Chemical Physics Letters 477 (1-3): 139-143, 2009.
Matějíček P., Zedník J., Ušelová K., Pleštil J., Fanfrlik J., Nykanen A., Ruokolainen J., Hobza P., Procházka K.:
Stimuli-Responsive Nanoparticles Based on Interaction of Metallacarborane with Poly(ethylene oxide).
Macromolecules 42 (13): 4829-4837, 2009.
Eckert-Maksic M., Lischka H., Maksic Z. B., Vazdar M.:
The Isomerization Barrier in Cyanocyclobutadienes: An ab Initio Multireference Average Quadratic Coupled Cluster Study.
Journal of Physical Chemistry A 113 (29): 8351-8358, 2009.
Vokáčová Z., Bickelhaupt F. M., Šponer J., Sychrovský V.:
Structural Interpretation of J Coupling Constants in Guanosine and Deoxyguanosine: Modeling the Effects of Sugar Pucker, Backbone Conformation, and Base Pairing.
Journal of Physical Chemistry A 113 (29): 8379-8386, 2009.
Plasser F., Barbatti M., Aquino A. J. A., Lischka H.:
Excited-State Diproton Transfer in [2,2 `-Bipyridyl]-3,3 `-diol: the Mechanism Is Sequential, Not Concerted.
Journal of Physical Chemistry A 113 (30): 8490-8499, 2009.
Futera Z., Klenko J., Šponer J. E., Šponer J., Burda J. V.:
Interactions of the ``Piano-stool'' [Ruthenium(II)(eta(6)-arene)(en)Cl](+) Complexes With Water and Nucleobases; A initio and DFT Study.
Journal of Computational Chemistry 30 (12): 1758-1770, 2009.
Řezáč J., Fanfrlik J., Salahub D., Hobza P.:
Semiempirical Quantum Chemical PM6 Method Augmented by Dispersion and H-Bonding Correction Terms Reliably Describes Various Types of Noncovalent Complexes.
Journal of Chemical Theory and Computation 5 (7): 1749-1760, 2009.
Pitoňák M., Janowski T., Neogrady P., Pulay P., Hobza P.:
Convergence of the CCSD(T) Correction Term for the Stacked Complex Methyl Adenine-Methyl Thymine: Comparison with Lower-Cost Alternatives.
Journal of Chemical Theory and Computation 5 (7): 1761-1766, 2009.
Sellner B., Barbatti M., Lischka H.:
Dynamics starting at a conical intersection: Application to the photochemistry of pyrrole.
Journal of Chemical Physics 131 (2): 10.1063/1.3175799, 2009.
Bulanek R., Voleska I., Ivanova E., Hadjiivanov K., Nachtigall P.:
Localization and Coordination of Mg2+ Cations in Ferrierite: Combined FTIR Spectroscopic and Computation Investigation of CO Adsorption Complexes.
Journal of Physical Chemistry C 113 (25): 11066-11076, 2009.
Sedlák R., Hobza P., Patwari G. N.:
Hydrogen-Bonded Complexes of Phenylacetylene with Water, Methanol, Ammonia, and Methylamine. The Origin of Methyl Group-Induced Hydrogen Bond Switching.
Journal of Physical Chemistry A 113 (24): 6620-6625, 2009.
Morgado C. A., 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.
Journal of Chemical Theory and Computation 5 (6): 1524-1544, 2009.
Réblová K., Razga F., Li W., Gao H., Frank J., Šponer J.:
Structural Dynamics of Elbow Segment of E. coli Ribosomal A-site Finger. Comparison of Simulations with Cryo-EM Data and with Equivalent Segments in Other Species.
Journal of Biomolecular Structure \& Dynamics 26 (6): 9, 2009.
Banas P., Walter N. G., Šponer J., Otyepka M.:
Structural Insight into RNA Catalysis Revealed by Molecular Dynamics Simulations and QM/MM Calculation.
Journal of Biomolecular Structure \& Dynamics 26 (6): 50, 2009.
Zirbel C. L., Šponer J. E., Šponer J., Stombaugh J., Leontis N. B.:
Classification and Energetics of the Base-Phosphate Interactions in RNA.
Journal of Biomolecular Structure \& Dynamics 26 (6): 55, 2009.
Šponer J.:
Molecular Dynamics Simulations and Quantum Chemistry as Useful Complements to RNA Structural Bioinformatics.
Journal of Biomolecular Structure \& Dynamics 26 (6): 61, 2009.
Besseová I., Réblová K., Leontis N. B., Šponer J.:
RNA Three-Way Junctions Can Act as Flexible RNA Structural Elements in Large RNA Molecules: A Molecular Simulation Analysis.
Journal of Biomolecular Structure \& Dynamics 26 (6): 69, 2009.
Pulido A., Nachtigall P., Rodriguez Delgado M., Otero Arean C.:
Computational and Variable-Temperature Infrared Spectroscopic Studies on Carbon Monoxide Adsorption on Zeolite Ca-A.
Chemphyschem 10 (7): 1058-1065, 2009.
Jurečka P., Irnazarow I., Westphal A. H., Forlenza M., Arts J. A. J., Savelkoul H. F. J., Wiegertjes G. F.:
Allelic discrimination, three-dimensional analysis and gene expression of multiple transferrin alleles of common carp (Cyprinus carpio L.).
Fish \& Shellfish Immunology 26 (4): 573-581, 2009.
Jurečka P., Irnazarow I., Stafford J. L., Ruszczyk A., Taverne N., Belosevic M., Savelkoul H. F. J., Wiegertjes G. F.:
The induction of nitric oxide response of carp macrophages by transferrin is influenced by the allelic diversity of the molecule.
Fish \& Shellfish Immunology 26 (4): 632-638, 2009.
Kabeláč M., Hobza P., Špirko V.:
The structure and vibrational dynamics of the pyrrole dimmer.
Physical Chemistry Chemical Physics 11 (20): 3885-3891, 2009.
Kabeláč M., Hobza P., Špirko V.:
The ab initio assigning of the vibrational probing modes of tryptophan: linear shifting of approximate anharmonic frequencies vs. multiplicative scaling of harmonic frequencies.
Physical Chemistry Chemical Physics 11 (20): 3921-3926, 2009.
Rubeš M., Nachtigall P., Vondrášek J., Bludský O.:
Structure and Stability of the Water-Graphite Complexes.
Journal of Physical Chemistry C 113 (19): 8412-8419, 2009.
Zelený T., Hobza P., Kabeláč M.:
Microhydration of guanine center dot center dot center dot cytosine base pairs, a theoretical Study on the role of water in stability, structure and tautomeric equilibrium.
Physical Chemistry Chemical Physics 11 (18): 3430-3435, 2009.
Berka K., Laskowski R., Riley K. E., Hobza P., Vondrášek J.:
Representative Amino Acid Side Chain Interactions in Proteins. A Comparison of Highly Accurate Correlated ab Initio Quantum Chemical and Empirical Potential Procedures.
Journal of Chemical Theory and Computation 5 (4): 982-992, 2009.
Šponer J., Zgarbová M., Jurečka P., Riley K. E., Šponer J. E., Hobza P.:
Reference Quantum Chemical Calculations on RNA Base Pairs Directly Involving the 2 `-OH Group of Ribose.
Journal of Chemical Theory and Computation 5 (4): 1166-1179, 2009.
Ran J., Hobza P.:
On the Nature of Bonding in Lone Pair center dot center dot center dot pi-Electron Complexes: CCSD(T)/Complete Basis Set Limit Calculations.
Journal of Chemical Theory and Computation 5 (4): 1180-1185, 2009.
Černý J., Vondrášek J., Hobza P.:
Loss of Dispersion Energy Changes the Stability and Folding/Unfolding Equilibrium of the Trp-Cage Protein.
Journal of Physical Chemistry B 113 (16): 5657-5660, 2009.
Ditzler M. A., Šponer J., Walter N. G.:
Molecular dynamics suggest multifunctionality of an adenine imino group in acid-base catalysis of the hairpin ribozyme.
Rna-a Publication of the rna Society 15 (4): 560-575, 2009.
Berka K., Hobza P., Vondrášek J.:
Analysis of Energy Stabilization inside the Hydrophobic Core of Rubredoxin.
Chemphyschem 10 (3): 543-548, 2009.
Pittner J., Lischka H., Barbatti M.:
Optimization of mixed quantum-classical dynamics: Time-derivative coupling terms and selected couplings.
Chemical Physics 356 (1-3, Sp. Iss. SI): 147-152, 2009.
Rakus K. L., Wiegertjes G. F., Jurečka P., Walker P. D., Pilarczyk A., Irnazarow I.:
Major histocompatibility (MH) class II B gene polymorphism influences disease resistance of common carp (Cyprinus carpio L.).
Aquaculture 288 (1-2): 44-50, 2009.
Ran J., Hobza P.:
Nature of Bonding in Nine Planar Hydrogen-Bonded Adenine center dot center dot center dot Thymine Base Pairs.
Journal of Physical Chemistry B 113 (9): 2933-2936, 2009.
Pulido A., Nachtigall P., Zukal A., Dominguez I., Cejka J.:
Adsorption of CO2 on Sodium-Exchanged Ferrierites: The Bridged CO2 Complexes Formed between Two Extraframework Cations.
Journal of Physical Chemistry C 113 (7): 2928-2935, 2009.
Mladek A., Sharma P., Mitra A., Bhattacharyya D., Šponer J., Šponer J. E.:
Trans Hoogsteen/Sugar Edge Base Pairing in RNA. Structures, Energies, and Stabilities from Quantum Chemical Calculations.
Journal of Physical Chemistry B 113 (6): 1743-1755, 2009.
Pitoňák M., Neogrady P., Černý J., Grimme S., Hobza P.:
Scaled MP3 Non-Covalent Interaction Energies Agree Closely with Accurate CCSD(T) Benchmark Data.
Chemphyschem 10 (1): 282-289, 2009.
Jurečka P., Wiegertjes G. F., Rakus K. L., Pilarczyk A., Irnazarow I.:
Genetic resistance of carp (Cyprinus carpio L.) to Trypanoplasma borreli: Influence of transferrin polymorphisms.
Veterinary Immunology and Immunopathology 127 (1-2): 19-25, 2009.
Vokáčová Z., Buděšínský M., Rosenberg I., Schneider B., Šponer J., Sychrovský V.:
Structure and Dynamics of the ApA, ApC, CpA, and CpC RNA Dinucleoside Monophosphates Resolved with NMR Scalar Spin-Spin Couplings.
Journal of Physical Chemistry B 113 (4): 1182-1191, 2009.
Nachtigall P., Bludský O., Grajciar L., Nachtigallová D., Delgado M. R., Arean C. O.:
Computational and FTIR spectroscopic studies on carbon monoxide and dinitrogen adsorption on a high-silica H-FER zeolite.
Physical Chemistry Chemical Physics 11 (5): 791-802, 2009.
Riley K. E., Murray J. S., Politzer P., Concha M. C., Hobza P.:
Br center dot center dot center dot O Complexes as Probes of Factors Affecting Halogen Bonding: Interactions of Bromobenzenes and Bromopyrimidines with Acetone.
Journal of Chemical Theory and Computation 5 (1): 155-163, 2009.
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