/ Structure / Chairs / Pavel Hobza / Papers / 2006

2006

Arean C.O., Palomino G.T., Garrone E., Nachtigallova D., Nachtigall P.:
Combined theoretical and FTIR spectroscopic studies on hydrogen adsorption on the zeolites Na-FER and K-FER.
Journal of Physical Chemistry B 110 (1): 395-402, 2006.

Barratt E., Bronowska A., Vondrasek J., Cerny J., Bingham R., Phillips S., Homans S.W.:
Thermodynamic Penalty Arising from Burial of a Ligand Polar Group Within a Hydrophobic Pocket of a Protein Receptor.
Journal of Molecular Biology 362 (5): 994-1003, 2006.

Bulanek R., Drobna H., Nachtigall P., Rubes M., Bludsky O.:
On the site-specificity of polycarbonyl complexes in Cu/zeolites: Combined experimental and DFT study.
Physical Chemistry Chemical Physics 8 (47): 5535-5542, 2006.

Burkhardt K., Schneider B., Ory J.:
A biocurator perspective: Annotation at the research collaboratory for structural bioinformatics protein data bank.
PLoS Computational Biology 2 (10): 1186-1189, 2006.

Cerny J., Spirko V., Mons M., Hobza P., Nachtigallova D.:
Theoretical study of the ground and excited states of 7-methyl guanine and 9-methyl guanine: Comparison with experiment.
Physical Chemistry Chemical Physics 8 (26): 3059-3065, 2006.

Chuang T.-K., Troccoli M., Kuo P.-C., Jamshidi A., Spirko J.A., Hatalis M.K., Klier K., Biaggio I., Voutsas A.T., Afentakis T., Hartzell J.W.:
Process technology for high-resolution AM-PLED displays on flexible metal foil substrates.
ECS Transactions 3 (8): 349-359, 2006.

Dobes P., Otyepka M., Strnad M., Hobza P.:
Interaction energies for the purine inhibitor roscovitine with cyclin-dependent kinase 2: Correlated ab initio quantum-chemical, DFT and empirical calculations.
Chemistry - A European Journal 12 (16): 4297-4304, 2006.

Fanfrlik J., Lepsik M., Horinek D., Havlas Z., Hobza P.:
Interaction of carboranes with biomolecules: Formation of dihydrogen bonds.
ChemPhysChem 7 (5): 1100-1105, 2006.

Frigato T., Svozil D., Jungwirth P.:
Valence- And dipole-bound anions of the thymine-water complex: Ab initio characterization of the potential energy surfaces.
Journal of Physical Chemistry A 110 (9): 2916-2923, 2006.

Garrone E., Bulanek R., Frolich K., Arean C.O., Delgado M.R., Palomino G.T., Nachtigallova D., Nachtigall P.:
Single and dual cation sites in zeolites: Theoretical calculations and FTIR spectroscopic studies on CO adsorption on K-FER.
Journal of Physical Chemistry B 110 (45): 22542-22550, 2006.

Griffiths M.L., Svozil D., Worsfold P., Hywel Evans E.:
The application of piecewise direct standardisation with variable selection to the correction of drift in inductively coupled atomic emission spectrometry.
Journal of Analytical Atomic Spectrometry 21 (10): 1045-1052, 2006.

Hirano T., Okuda R., Nagashima U., Spirko V., Jensen P.:
A theoretical study of FeNC in the 6Δ electronic ground state.
Journal of Molecular Spectroscopy 236 (2): 234-247, 2006.

Hobza P., Zahradnik R., Muller-Dethlefs K.:
The world of non-covalent interactions: 2006.
Collection of Czechoslovak Chemical Communications 71 (4): 443-531, 2006.

Jurecka P., Sponer J., Cerny J., Hobza P.:
Benchmark database of accurate (MP2 and CCSD(T) complete basis set limit) interaction energies of small model complexes, DNA base pairs, and amino acid pairs.
Physical Chemistry Chemical Physics 8 (17): 1985-1993, 2006.

Kabelac M., Hobza P.:
Na+, Mg2+, and Zn2+ binding to all tautomers of adenine, cytosine, and thymine and the eight most stable keto/enol tautomers of guanine: A correlated ab initio quantum chemical study.
Journal of Physical Chemistry B 110 (29): 14515-14523, 2006.

Kraemer W.P., Spirko V.:
Bound and low-lying quasi-bound rotation-vibration levels of the ground electronic state of LiH2+.
Chemical Physics 330 (01/02/08): 190-203, 2006.

Krasovska M.V., Sefcikova J., Reblova K., Schneider B., Walter N.G., Sponer J.:
Cations and hydration in catalytic RNA: Molecular dynamics of the hepatitis delta virus ribozyme.
Biophysical Journal 91 (2): 626-638, 2006.

Kubar T., Hanus M., Ryjacek F., Hobza P.:
Binding of cationic and neutral phenanthridine intercalators to a DNA oligomer is controlled by dispersion energy: Quantum chemical calculations and molecular mechanics simulations.
Chemistry - A European Journal 12 (1): 280-290, 2006.

Masa M., Maresova L., Vondrasek J., Horn M., Jezek J., Mares M.:
Cathepsin D propeptide: Mechanism and regulation of its interaction with the catalytic core.
Biochemistry 45 (51): 15474-15482, 2006.

Muchova E., Spirko V., Hobza P., Nachtigallova D.:
Theoretical study of photoacidity of HCN: The effect of complexation with water.
Physical Chemistry Chemical Physics 8 (42): 4866-4873, 2006.

Nachtigall P., Garrone E., Turnes Palomino G., Rodriguez Delgado M., Nachtigallova D., Otero Arean C.:
FTIR spectroscopic and computational studies on hydrogen adsorption on the zeolite Li-FER.
Physical Chemistry Chemical Physics 8 (19): 2286-2292, 2006.

Nachtigallova D., Bludsky O., Otero Arean C., Bulanek R., Nachtigall P.:
The vibrational dynamics of carbon monoxide in a confined space - CO in zeolites.
Physical Chemistry Chemical Physics 8 (42): 4849-4852, 2006.

Otyepka M., Sklenovsky P., Horinek D., Kubar T., Hobza P.:
How the stabilization of INK4 tumor suppressor 3D structure evaluated by quantum chemical and molecular mechanics calculations corresponds well with experimental results: Interplay of association enthalpy, entropy, and solvation effects.
Journal of Physical Chemistry B 110 (9): 4423-4429, 2006.

Pavelka M., Simanek M., Sponer J., Burda J.V.:
Copper cation interactions with biologically essential types of ligands: A computational DFT study.
Journal of Physical Chemistry A 110 (14): 4795-4809, 2006.

Prasanna M.D., Vondrasek J., Wlodawer A., Rodriguez H., Bhat T.N.:
Chemical compound navigator: A Web-based Chem-BLAST, chemical taxonomy-based search engine for browsing compounds.
Proteins: Structure, Function and Genetics 63 (4): 907-917, 2006.

Razga F., Zacharias M., Reblova K., Koca J., Sponer J.:
RNA Kink-Turns as Molecular Elbows: Hydration, Cation Binding, and Large-Scale Dynamics.
Structure 14 (5): 825-835, 2006.

Reha D., Hocek M., Hobza P.:
Exceptional thermodynamic stability of DNA duplexes modified by nonpolar base analogues is due to increased stacking interactions and favorable solvation: Correlated Ab initio calculations and molecular dynamics simulations.
Chemistry - A European Journal 12 (13): 3587-3595, 2006.

Rhodes M.M., Reblova K., Sponer J., Walter N.G.:
Trapped water molecules are essential to structural dynamics and function of a ribozyme.
Proceedings of the National Academy of Sciences of the United States of America 103 (36): 13380-13385, 2006.

Samoylova E., Smith V.R., Ritze H.-H., Radloff W., Kabelac M., Schultz T.:
Ultrafast deactivation processes in aminopyridine clusters: Excitation energy dependence and isotope effects.
Journal of the American Chemical Society 128 (49): 15652-15656, 2006.

Sedivcova T., Spirko V.:
Potential energy and transition dipole moment functions of C 2-.
Molecular Physics 104 ("13-14"): 1999-2005, 2006.

Sedivcova T., Spirko V., Fiser J.:
Theoretical study of the CS2+ dication.
Journal of Chemical Physics 125 (16): -, 2006.

Sedivcova T., Zd'Anska P.R., Spirko V., Fiser J.:
Computed lifetimes of metastable states of CO2+.
Journal of Chemical Physics 124 (21): -, 2006.

Spackova N., Sponer J.:
Molecular dynamics simulations of sarcin-ricin rRNA motif.
Nucleic Acids Research 34 (2): 697-708, 2006.

Spirko V.:
Potential energy curve of Be2 in its ground electronic state.
Journal of Molecular Spectroscopy 235 (2): 268-270, 2006.

Spirko V., Amano T., Kraemer W.P.:
Vibrational predissociation of H5+.
Journal of Chemical Physics 124 (24): -, 2006.

Spirko V., Hobza P.:
Theoretical investigations into the blue-shifting hydrogen bond in benzene complexes.
ChemPhysChem 7 (3): 640-643, 2006.

Sponer J., Jurecka P., Marchan I., Luque F.J., Orozco M., Hobza P.:
Nature of base stacking: Reference quantum-chemical stacking energies in ten unique B-DNA base-pair steps.
Chemistry - A European Journal 12 (10): 2854-2865, 2006.

Sponer J.E., Leszczynski J., Sponer J.:
Mechanism of action of anticancer titanocene derivatives: An insight from quantum chemical calculations.
Journal of Physical Chemistry B 110 (39): 19632-19636, 2006.

Svozil D., Jungwirth P.:
Cluster model for the ionic product of water: Accuracy and limitations of common density functional methods.
Journal of Physical Chemistry A 110 (29): 9194-9199, 2006.

Sychrovsky V., Sponer J., Trantirek L., Schneider B.:
Indirect NMR spin-spin coupling constants 3J(P,C) and 2J(P,H) across the P-O⋯H-C link can be used for structure determination of nucleic acids.
Journal of the American Chemical Society 128 (21): 6823-6828, 2006.

Sychrovsky V., Vokacova Z., Sponer J., Spackova N., Schneider B.:
Calculation of structural behavior of indirect NMR spin-spin couplings in the backbone of nucleic acids.
Journal of Physical Chemistry B 110 (45): 22894-22902, 2006.

Troccoli M.N., Chuang T.-K., Roudbari A.J., Kuo P.-C., Spirko J.A., Hatalis M.K., Voutsas A.T., Afentakis T., Hartzell J.W.:
230 DPI high resolution AMPLED display on flexible metal foils with integrated row drivers.
ECS Transactions 3 (8): 237-247, 2006.

Valdes H., Reha D., Hobza P.:
Structure of isolated tryptophyl-glycine dipeptide and tryptophyl-glycyl- glycine tripeptide: Ab initio SCC-DFTB-D molecular dynamics simulations and high-level correlated ab initio quantum chemical calculations.
Journal of Physical Chemistry B 110 (12): 6385-6396, 2006.

Vrbka L., Vondrasek J., Jagoda-Cwiklik B., Vacha R., Jungwirth P.:
Quantification and rationalization of the higher affinity of sodium over potassium to protein surfaces.
Proceedings of the National Academy of Sciences of the United States of America 103 (42): 15440-15444, 2006.

Zendlova L., Hobza P., Kabelac M.:
Potential energy surfaces of the microhydrated guanine⋯Cytosine base pair and its methylated analogue.
ChemPhysChem 7 (2): 439-447, 2006.

Zierkiewicz W., Michalska D., Cerny J., Hobza P.:
Cation-π complexes between alkali metal cation and para -halogenophenols. Structures, binding energies and thermodynamic properties: DFT study and CCSD(T) complete basis set limit calculations.
Molecular Physics 104 ("13-14"): 2317-2325, 2006.

Zierkiewicz W., Privalov T.:
A computational study of oxidation of ruthenium porphyrins via ORu IV and ORuVIO species.
Dalton Transactions 6 (15): 1867-1874, 2006.