2005

Abo-Riziq A., Grace L., Nir E., Kabelac M., Hobza P., De Vries M.S.:
Photochemical selectivity in guanine-cytosine base-pair structures.
Proceedings of the National Academy of Sciences of the United States of America 102 (1): 20-23, 2005.

Bludsky O., Nachtigall P., Cicmanec P., Knotek P., Bulanek R.:
Characterization of the Cu+ sites in MFI zeolites: Combined computational and experimental study.
Catalysis Today 100 (03/04/08): 385-389, 2005.

Bludsky O., Nachtigallova D., Bulanek R., Nachtigall P.:
Combined theoretical and experimental study of the site-specificity of vibrational dynamics of CO adsorbed on monovalent metal cations in zeolites.
Studies in Surface Science and Catalysis "158 A" (): 625-632, 2005.

Bludsky O., Silhan M., Nachtigall P., Bucko T., Benco L., Hafner J.:
Theoretical investigation of CO interaction with copper sites in zeolites: Periodic DFT and hybrid quantum mechanical/interatomic potential function study.
Journal of Physical Chemistry B 109 (19): 9631-9638, 2005.

Bour P., Andrushchenko V., Kabelac M., Maharaj V., Wieser H.:
Simulations of structure and vibrational spectra of deoxyoctanucleotides.
Journal of Physical Chemistry B 109 (43): 20579-20587, 2005.

Bour P., Budesinsky M., Spirko V., Kapitan J., Sebestik J., Sychrovsky V.:
A complete set of NMR chemical shifts and spin-spin coupling constants for L-alanyl-L-alanine zwitterion and analysis of its conformational behavior.
Journal of the American Chemical Society 127 (48): 17079-17089, 2005.

Brauer B., Gerber R.B., Kabelac M., Hobza P., Bakker J.M., Abo Riziq A.G., De Vries M.S.:
Vibrational spectroscopy of the G⋯C base pair: Experiment, harmonic and anharmonic calculations, and the nature of the anharmonic couplings.
Journal of Physical Chemistry A 109 (31): 6974-6984, 2005.

Caffrey C.R., Placha L., Barinka C., Hradilek M., Dostal J., Sajid M., McKerrow J.H., Majer P., Konvalinka J., Vondrasek J.:
Homology modeling and SAR analysis of Schistosoma japonicum cathepsin D (SjCD) with statin inhibitors identify a unique active site steric barrier with potential for the design of specific inhibitors.
Biological Chemistry 386 (4): 339-349, 2005.

Cerny J., Hobza P.:
The X3LYP extended density functional accurately describes H-bonding but fails completely for stacking.
Physical Chemistry Chemical Physics 7 (8): 1624-1626, 2005.

Chuang T.K., Roudbari A.J., Trocolli M., Chang Y.L., Reed G., Hatalis M., Spirko J., Klier K., Preis S., Pearson R., Najafov H., Biaggio I., Afentakis T., Voutsas A., Forsythe E., Shi J., Blomquist S.:
Active-Matrix Organic Light-Emitting Displays on flexible metal foils.
Proceedings of SPIE - The International Society for Optical Engineering 5801 (): 234-248, 2005.

Crews B., Abo-Riziq A., Grace L., Callahan M., Kabelac M., Hobza P., De Vries M.S.:
IR-UV double resonance spectroscopy of guanine-H2O clusters.
Physical Chemistry Chemical Physics 7 (16): 3015-3020, 2005.

Dabkowska I., Gonzalez H.V., Jurecka P., Hobza P.:
Stabilization energies of the hydrogen-bonded and stacked structures of nucleic acid base pairs in the crystal geometries of CG, AT, and AC DNA steps and in the NMR geometry of the 5′-d(GCGAAGC)-3′ hairpin: Complete basis set calculations at the MP2 and CCSD(T) levels.
Journal of Physical Chemistry A 109 (6): 1131-1136, 2005.

Dabkowska I., Jurecka P., Hobza P.:
On geometries of stacked and H-bonded nucleic acid base pairs determined at various DFT, MP2, and CCSD(T) levels up to the CCSD(T)/complete basis set limit level.
Journal of Chemical Physics 122 (20): 1-9, 2005.

Fanfrlik J., Rejnek J., Hanus M., Hobza P.:
Hydration Gibbs energies of nucleic acid bases determined by Gibbs energy perturbation, continuous and hybrid approaches.
Collection of Czechoslovak Chemical Communications 70 (11): 1756-1768, 2005.

Ge W., Schneider B., Olson W.K.:
Knowledge-based elastic potentials for docking drugs or proteins with nucleic acids.
Biophysical Journal 88 (2): 1166-1190, 2005.

Hanus M., Kabelac M., Nachtigallova D., Hobza P.:
Mutagenic properties of 5-halogenuracils: Correlated quantum chemical ab initio study.
Biochemistry 44 (5): 1701-1707, 2005.

Kabelac M., Zendlova L., Reha D., Hobza P.:
Potential energy surfaces of an adenine-thymine base pair and its methylated analogue in the presence of one and two water molecules: Molecular mechanics and correlated ab initio study.
Journal of Physical Chemistry B 109 (24): 12206-12213, 2005.

Krasovska M.V., Sefcikova J., Spackova N., Sponer J., Walter N.G.:
Structural dynamics of precursor and product of the RNA enzyme from the hepatitis delta virus as revealed by molecular dynamics simulations.
Journal of Molecular Biology 351 (4): 731-748, 2005.

Kucera J., Nachtigall P.:
27Al NMR chemical shifts do not correlate with average T-O-T angles: Theoretical study of MCM-58 zeolite.
Studies in Surface Science and Catalysis "158 A" (): 917-924, 2005.

Kucera J., Nachtigall P.:
A simple correlation between average T-O-T angles and 27Al NMR chemical shifts does not hold in high-silica zeolites.
Microporous and Mesoporous Materials 85 (3): 279-283, 2005.

Mrazkova E., Hobza P., Bohl M., Gauger D.R., Pohle W.:
Hydration-induced changes of structure and vibrational frequencies of methylphosphocholine studied as a model of biomembrane lipids.
Journal of Physical Chemistry B 109 (31): 15126-15134, 2005.

Nachtigall P.:
Applications of quantum chemical methods in zeolite science.
Studies in Surface Science and Catalysis 157 (): 243-262, 2005.

Nachtigall P., Bludsky O., Nachtigallova D., Cicmanec P., Drobna H., Bulanek R.:
Characterization of Cu+ sites in FER: Combined computational and experimental TPD study.
Studies in Surface Science and Catalysis "158 A" (): 925-932, 2005.

Perez A., Sponer J., Jurecka P., Hobza P., Luque F.J., Orozco M.:
Are the hydrogen bonds of RNA (A·U) stronger than those of DNA (A·T)? A quantum mechanics study.
Chemistry - A European Journal 11 (17): 5062-5066, 2005.

Prasanna M.D., Vondrasek J., Wlodawer A., Bhat T.N.:
Application of InChI to curate, index, and query 3-D structures.
Proteins: Structure, Function and Genetics 60 (1): 1-4, 2005.

Razga F., Koca J., Sponer J., Leontis N.B.:
Hinge-like motions in RNA Kink-turns: The role of the second A-minor motif and nominally unpaired bases.
Biophysical Journal 88 (5): 3466-3485, 2005.

Reha D., Valdes H., Vondrasek J., Hobza P., Abu-Riziq A., Crews B., De Vries M.S.:
Structure and IR spectrum of phenylalanyl-glycyl-glycine tripetide in the gas-phase: IR/UV experiments, Ab initio quantum chemical calculations, and molecular dynamic simulations.
Chemistry - A European Journal 11 (23): 6803-6817, 2005.

Rejnek J., Hanus M., Kabelac M., Ryjacek F., Hobza P.:
Correlated ab initio study of nucleic acid bases and their tautomers in the gas phase, in a microhydrated environment and in aqueous solution. Part 4. Uracil and thymine.
Physical Chemistry Chemical Physics 7 (9): 2006-2017, 2005.

Schultz M.J., Adler R.S., Zierkiewicz W., Privalov T., Sigman M.S.:
Using mechanistic and computational studies to explain ligand effects in the palladium-catalyzed aerobic oxidation of alcohols.
Journal of the American Chemical Society 127 (23): 8499-8507, 2005.

Spirko V.:
Potential energy curve of N2 in its ground electronic state.
Collection of Czechoslovak Chemical Communications 70 (6): 731-739, 2005.

Sponer J.E., Leszczynski J., Sychrovsky V., Sponer J.:
Sugar edge/sugar edge base pairs in RNA: Stabilities and structures from quantum chemical calculations.
Journal of Physical Chemistry B 109 (39): 18680-18689, 2005.

Sponer J.E., Spackova N., Kulhanek P., Leszczynski J., Sponer J.:
Non-Watson-Crick base pairing in RNA. Quantum chemical analysis of the cis Watson-Crick/sugar edge base pair family.
Journal of Physical Chemistry A 109 (10): 2292-2301, 2005.

Sponer J.E., Spackova N., Leszczynski J., Sponer J.:
Principles of RNA base pairing: Structures and energies of the trans Watson-Crick/ sugar edge base pairs.
Journal of Physical Chemistry B 109 (22): 11399-11410, 2005.

Svozil D., Frigato T., Havlas Z., Jungwirth P.:
Ab initio electronic structure of thymine anions.
Physical Chemistry Chemical Physics 7 (5): 840-845, 2005.

Sychrovsky V., Muller N., Schneider B., Smrecki V., Spirko V., Sponer J., Trantirek L.:
Sugar pucker modulates the cross-correlated relaxation rates across the glycosidic bond in DNA.
Journal of the American Chemical Society 127 (42): 14663-14667, 2005.

Vondrasek J., Bendova L., Klusak V., Hobza P.:
Unexpectedly strong energy stabilization inside the hydrophobic core of small protein rubredoxin mediated by aromatic residues: Correlated ab initio quantum chemical calculations.
Journal of the American Chemical Society 127 (8): 2615-2619, 2005.

Vondrasek J., Bendova L., Klusak V., Hobza P.:
Erratum: Unexpectedly strong energy stabilization inside the hydrophobic core of small protein rubredoxin mediated by aromatic residues: Correlated ab initio quantum chemical calculations (Journal of the American Chemical Society (2005) 127 (2615-2617)).
Journal of the American Chemical Society 127 (22): 8232-, 2005.

Zierkiewicz W., Jurecka P., Hobza P.:
On differences between hydrogen bonding and improper blue-shifting hydrogen bonding.
ChemPhysChem 6 (4): 609-617, 2005.

Zierkiewicz W., Privalov T.:
A theoretical study of the essential role of DMSO as a solvent/ligand in the Pd(OAc)2/DMSO catalyst system for aerobic oxidation.
Organometallics 24 (24): 6019-6028, 2005.