2008

Banáš P., Rulíšek L., Hánošová V., Svozil D., Walter N.G., Šponer J., Otyepka M.:
General base catalysis for cleavage by the active-site cytosine of the hepatitis delta virus ribozyme: QM/MM calculations establish chemical feasibility.
Journal of Physical Chemistry B112 (35): 11177-11187, 2008.

Biedermannová L., Riley K. E., Berka K., Hobza P., Vondrášek J.:
Another role of proline: stabilization interactions in proteins and protein complexes concerning proline and tryptophane.
Physical Chemistry Chemical Physics 10 (42): 6350-6359, 2008.

Biedermannová L., Hobza P., Vondrášek J.:
Identifying stabilizing key residues in proteins using interresidue interaction energy matrix.
Proteins-Structure, Function and Bioinformatics 72 (1): 402-413, 2008.

Bludský O., Rubeš M.:
Ab initio investigation of intermolecular interactions in solid benzene.
Physical Review. B 77 092103/1-092103/4, 2008.

Bludský O., Rubeš M., Soldán, P. Nachtigall P.:
Investigation of the benzene-dimer potential energy surface: DFT/CCSD(T) correction scheme.
Journal of Chemical Physics 128 (11): 114102/1-114102/8, 2008.

Brumovská, E. Sychrovský V., Vokácová Z., Šponer J., Schneider B., Trantírek, L.:
Effect of local sugar and base geometry on 13C and 15N magnetic shielding anisotropy in DNA nucleosides.
Journal of Biomolecular NMR. 42 (3): 209-223, 2008.

Callahan, M. P. Gengeliczki, Z. Svadlenak, Valdes H., Hobza P., de Vries, M.:
Non-standard base pairing and stacked structures in methyl xanthine clusters.
Physical Chemistry Chemical Physics 10 (19): 2819-2826, 2008.

Cerný J., Kabelác M., Hobza P.:
Double-helical ladder structural transition in the B-DNA is induced by a loss of dispersion energy.
Journal of the American Chemical Society 130 (47): 16055-16059, 2008.

Cerný J., Tong, X. Hobza P., Müller-Dethlefs K.:
State of the art theoretical study and comparison to experiment for the phenol-argon complex.
Journal of Chemical Physics 128 (11): 114319/1-114319/6, 2008.

Cerný J., Tong, X., Hobza P., Müller-Dethlefs, K.:
Competition between stacking and hydrogen bonding: theoretical study of the phenol...Ar cation and neutral complex and comparison to experiment.
Physical Chemistry Chemical Physics 10 (19): 2780-2784, 2008.

Dedíková, P., Pitonák M., Neogrady P., Cernušák I., Urban, M.:
Toward more efficient CCSD(T) calculations of intermolecular interactions in model Hydrogen-bonded and stacked dimers.
Journal of Physical Chemistry A 112 (30): 7115-7123, 2008.

Fanfrlík J., Brynda J., Rezác J., Hobza P., Lepšík M.:
Interpretation of protein/ligand crystal structure using QM/MM calculations: Case of HIV-1 protease/metallacarborane complex.
Journal of Physical Chemistry B 112 (47): 15094-15102, 2008.

Chalupský J., Vondrášek J., Špirko V.:
Quasiplanarity of the peptide bond.
Journal of Physical Chemistry A 112 (4): 693-699, 2008.

Kožíšek M., Cígler P., Lepšík M., Fanfrlík J., Rezácová P., Brynda J., Pokorná J., Plešek J., Grüner B., Grantz-Šašková K., Prejdová J., Král V., Konvalinka J.:
Inorganic polyhedral metallacarborane inhibitors of HIV protease: a new approach to overcoming antiviral resistance.
Journal of Medicinal Chemistry 51 (15): 4839-4843, 2008.

Murray, J. S. Concha, M. C. Lane, P. Hobza P., Politzer, P.:
Blue shifts vs red shifts in sigma-hole bonding.
Journal of Molecular Modeling 14 (8): 699-704,2008.

Nachtigallová D., Hobza P., Špirko V.
Assigning the NH Stretches of the Guanine Tautomers Using Adiabatic Separation: CCSD(T) Benchmark Calculations.
Journal of Physical Chemistry A 112 (9): 1854-1856, 2008.

Nachtigallová D., Hobza P., Ritze, H. H.:
Electronic splitting in the excited states of DNA base homodimers and -trimers: an evaluation of short-range and Coulombic interactions.
Physical Chemistry Chemical Physics 10 (37): 5689-5697, 2008.

Nachtigallová D., Vrbka L., Bludský O., Nachtigall P.:
Interaction of acetonitrile with Na-zeolites: adsorption modes and vibrational dynamics in the zeolite channels and cavities.
Physical Chemistry Chemical Physics 10 (28): 4189-4198, 2008.

Pérez A., Lankaš F., Lugue F. J., Orozco, M.:
Towards a molecular dynamics consensus view of B-DNA flexibility.
Nucleic Acids Research 36 (7): 2379-2394, 2008.

Pitonák M., Neogrady P., Rezác J., Jurecka P., Urban M., Hobza P.:
Benzene dimer: High-level wave function and density functional theory calculations.
Journal of Chemical Theory and Computation 4 (11): 1829-1834, 2008.

Pitonák M., Riley, Kevin E., Neogrady P., Hobza P.:
Highly Accurate CCSD(T) and DFT-SAPT Stabilization Energies of H-Bonded and Stacked Structures of the Uracil Dimer.
ChemPhysChem 9 (12): 1636-1644, 2008.

Pluhácková K., Grimme S., Hobza P.:
On the Importance of Electron Correlation Effects for the Intramolecular Stacking Geometry of a Bis-Thiophene Derivative.
Journal of Physical Chemistry A 112 (48): 12469-12474, 2008.

Prikryl J., Machácek V., Jansa P., Svobodová M., Růžicka A., Nachtigall P., Cerný A.:
Stable triazenes derived from 2-alkylaminonaphthalenes and 5-nitrobenzo[c]-1,2-thiazole-3-diazonium hydrogensulfate.
European Journal of Organic Chemistry 19 : 3272-3278, 2008.

Riley K. E., Hobza P.:
A DFT-D investigation of the mechanisms for activation of the wild-type and S810L mutated mineralocorticoid receptor by steroid hormones.
Journal of Physical Chemistry B 112 (10): 3157-3163, 2008.

Riley K. E., Hobza P.:
Investigations into the Nature of Halogen Bonding Including Symmetry Adapted Perturbation Theory Analyses.
Journal of Chemical Theory and Computation 4 (2): 232-242, 2008.

Rubeš M., Bludský O.:
Intermolecular .pi.-.pi. interactions in solids.
Physical Chemistry Chemical Physics 10 (19): 2611-2615, 2008.

Rubeš M., Bludský O., Nachtigall P.:
Investigation of the benzene-naphthalene and naphthalene-naphthalene potential energy surfaces: DFT/CCSD(T) correction scheme.
ChemPhysChem 9 (12): 1702-1708, 2008.

Rezác J., Hobza P.:
Benzene dimer: Dynamic structure and thermodynamics derived from on-the-fly ab initio DFT-D molecular dynamic simulations.
Journal of Chemical Theory and Computation 4 (11): 1835-1840, 2008.

Rezác J., Hobza P.:
Correlation between the thermodynamic stability of DNA duplexes and the interaction and solvation energies of DNA building blocks.
Collection of Czechoslovak Chemical Communications 73 (2): 161-174, 2008

Rezác J., Jurecka P., Riley K. E., Cerný J., Valdes H., Pluhácková K., Berka K., Rezác, Tomáš Pitonák M., Vondrášek J., Hobza P.:
Quantum chemical benchmark energy and geometry database for molecular clusters and complex molecular systems BEGDB: a users manual and examples.
Collection of Czechoslovak Chemical Communications 73 (10): 1261-1270, 2008.

Rezác J., Berka K., Horinek D., Hobza P., Vondrášek J.:
The stabilization energy of the Glu-Lys salt bridge in the protein/water environment: Correlated quantum chemical ab initio, DFT and empirical potential studies.
Collection of Czechoslovak Chemical Communications 73 (6/7): 921-936, 2008.

Svozil D., Šponer J., Marchan E. J., Pérez I., Cheatham III. A., Forti T. E., Luque F., Orözcö F. J., Šponer J.:
Geometrical and electronic structure variability of the sugar-phosphate backbone in nucleic acids.
Journal of Physical Chemistry B 112 (27): 8188-8197, 2208.

Sychrovský V., Budešínský M., Benda L., Špirko V.. Vokácová Z., Šebestík J., Bour P.:
Dependence ofthe L-alanyl-L-alanine conformation on molecular charge determined from ab initio computations and NMR spectra.
Journal of Physical Chemistry B 112 (6): 1796-1805, 2008.

Sychrovský V., Benda L., Prokop A., Blechta, Vratislav Schraml, Jan Špirko V.:
Probing the flexibility of internal rotation in silylated phenols with the NMR scalar spin-spin coupling constants.
Journal of Physical Chemistry A 112 (23): 5167-5174, 2008.

Špirko V., Bludský O., Kraemer, W. P.:
Energies and electronic dipole moments of the bound vibrational states of HN+2 and DN+2.
Collection of Czechoslovak Chemical Communications 73 (6/7): 873-897, 2008.

Špirko V.. Polák R.:
Potential energy function of CN-.
Journal of Molecular Spectroscopy 248 (1): 77-80, 2008.

Šponer J., Riley K.E., Hobza P.:
Nature and magnitude of aromatic stacking of nucleic acid bases.
Physical Chemistry Chemical Physics 10 (19): 2959-2610, 2008.

Vácha R., Cwiklik L., Rezác J., Hobza P., Jungwirth P., Valsaraj, K. Bahr, S. Kempter, V.:
Adsorption of aromatic hydrocarbons and ozone at environmental aqueous surfaces.
Journal of Physical Chemistry A 112 (22): 4942-4950, 2008. Benchmark database on isolated small peptides containing an aromatic side chain: comparison between wave function and density functional theory methods and empirical force field.

Valdes H., Pluhácková K., Pitonák M., Rezác J., Hobza P.:
Evaluation of the intramolecular basis set superposition error in the calculations of langer molecules: [n]helicenes and Phe -Gly-Phe tripeptide.
Physical Chemistry Chemical Physics 10 (19): 2747-2757, 2008.

Valdes H., Klusák V., Pitonák M., Exner O., Starý I., Hobza P., Rulíšek L.:
Evaluation of the intramolecular basis set superposition error in the calculations of larger molecules: [n]Helicenes and Phe-Gly-Phe tripeptide
Journal of Computational Chemistry 29 (6): 861-870, 2008.

Valdes H., Spiwok V., Rezác J., Reha D., Abo-Riziq, A. G. de Vries M. S., Hobza P.:
Potential-energy and free-energy surfaces of glycyl-phenylalanyl-alanine (GFA) tripeptide: Experiment and theory.
Chemistry A European Journal 14 (16): 4886-4898, 2008.

Vymetal J., Slabý I., Spahr A., Vondrášek J., Lyngstadaas S. P.:
Bioinformatic analysis and molecular modelling of human ameloblastin suggest a two-domain intrinsically unstructured calcium-binding protein.
European Journal of Oral Sciences 116 (2): 124-134, 2008.

Wang W., Hobza P.:
Application of Berlin's theorem to bond-length changes in isolated molecules and red- and blue-shifting H-bonded clusters.
Collection of Czechoslovak Chemical Communications 73 (6/7): 862-872, 2008.

Wang W., Hobza P.:
Origin of the X-Hal (Hal ) Cl, Br) Bond-Length Change in the Halogen-Bonded Complexes.
Journal of Physical Chemistry A 112 (7): 4114-4119, 2208.

Wang W., Hobza P.:
Theoretical Study on the Complexes of Benzene with Isoelectronic Nitrogen-Containing Heterocycles.
ChemPhysChem 9 (7): 1003-1009, 2008.

Yin S., Biedermannová L., Vondrášek J., Dokholyan, N. V.:
MedusaScore: An accurate force field-based scoring function for virtual drug screening.
Journal of Chemical Information and Modeling 48 (8): 1656-1662, 2008.

Zierkiewicz W., Komorowski L., Michalska D., Cerný J., Hobza P.:
The Amino Group in Adenine: MP2 and CCSD(T) Complete Basis Set Limit Calculations of the Planarization Barrier and DFT/B3LYP Study of the Anharmonic Frequencies of Adenine.
Journal of Physical Chemistry A 112 (51): 16734-16740, 2008.