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Research Center for Complex Molecular Systems and Biomolecules
Center for Biomolecules and Complex Molecular Systems   
Supported by the Ministry of Education, Czech Republic      
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Publications
This is a list of 174 papers that were published during the duration of the Center for Complex Molecular Systems and Biomolecules in years 2000 - 2004.

•  Bakker, J.M.; Compagnon, I. ; Meijer, G. et al
The mid-IR absorption spectrum of gas-phase clusters of the nucleobases guanine and cytosine.
Physical Chemistry Chemical Physics, 6 [10] 2810 - 2815 (2004)
abstract    
•  Ball, L. J.; Kuhne, R.; Hoffmann, B. et al
Dual epitope recognition by the VASP EVH1 domain modulates polyproline ligand specificity and binding affinity
EMBO Journal, 19 [18] 4903 - 4914 (2000)
abstract    
•  Benda, A.; Benes, M.; Marecek, V. et al
How to Determine Diffusion Coefficients in Planar Phospholipid Systems by Confocal Fluorescence Correlation Spectroscopy.
Langmuir , 19 [10] 4120 - 4126 (2003)
abstract    
•  Benes, M.; Hudecek, J.; Anzenbacher, P. et al
Coumarin 6, Hypericin, Resorufins, and Flavins: Suitable Chromophores for Fluorescence Correlation Spectroscopy of Biological Molecules.
Collection of Czechoslovak Chemical Communications, 66 [6] 855 - 869 (2001)
abstract    
•  Benes, M.; Hermens, W. T.; Hof, M.
Muscovite Allows for the Characterisation of Supported Bilayers by Confocal Fluorescence Correlation Spectroscopy.
Biological Chemistry, 383 [2] 33 - 341 (2002)
abstract    
•  Bludsky O.; Chocholousova J.; Vacek J. et al
Anharmonic treatment of the lowest-energy conformers of glycine: A theoretical study
Journal of Chemical Physics, 113 [11] 4629 - 4635 (2000)
abstract    
•  Bludsky, O.; Jenc, F.
Critical Evaluation of the Prediction of the Dissociation Energy and the Energy Spectrum of the Ground State of KRb by the Reduced Potential Curve Method.
Journal of Molecular Spectroscopy, 207 [1] 1 - 3 (2001)
abstract    
•  Bludsky, O.; Silhan, M.; Nachtigallova, D. et al
Calculations of Site-Specific CO Stretching Frequencies for Copper Carbonyls with the "Near Spectroscopic Accuracy": CO Interaction with Cu+/MFI.
Journal of Physical Chemistry A, 107 [48] 10381 - 10388 (2003)
abstract    
•  Bludsky, O.; Spirko, V.; Odaka, T. E. et al
A theoretical study of the MgNC/MgCN isomerization in the electronic ground state.
Journal of Molecular Structure, 695 219 - 226 (2004)
abstract    
•  Bock, H.; Havlas, Z.; Gharagozloo-Hubmann, K. et al
1,2-diphenylbenzene dianion: Alkali-metal salts with drastically spread C-6 rings.
Angewandte Chemie - International Edition 42 (36): 4385-4389 2003 , 42 [36] 4385 - 4389 (2003)
•  Bour, P.; Sychrovsky, V.; Malon, P. et al
Conformation of the dipeptide cyclo(L-Pro-L-Pro) monitored by the nuclear magnetic resonance and Raman optical activity spectra. Experimental and ab initio computational study
Journal of Physical Chemistry A, 106 [32] 7321 - 7327 (2002)
abstract    
•  Bradforth, S. E.; Jungwirth, P.
The excited states of iodide anions in water: A comparison of the electronic structure in clusters and in bulk solution.
J. Phys. Chem. A, 106 1286 - 1298 (2002)
abstract    
•  Bulanek, R.; Cicmanec, P. ; Knotek, P. et al
Localization of Cu+ sites and framework Al positions in high-silica zeolites: Combined experimental and theoretical study.
Physical Chemistry Chemical Physics, 6 [9] 2003 - 2007 (2004)
abstract    
•  Bumba, J. ; Kolafa, J.
Global phase diagrams of the van der Waals-Dieterici and the BMCSL-Dieterici equations of state.
Physical Chemistry Chemical Physics, 6 [9] 2301 - 2306 (2004)
abstract    
•  Burcl, R.; Piecuch, P.; Spirko, V. et al
Bound and quasi-bound states of the Li...FH van der Waals molecule
International Journal of Quantum Chemistry, 80 [4] 916 - 933 (2002)
abstract    
•  Burcl, R.; Piecuch, P.; Spirko, V. et al
Bound and quasi-bound states of the Li center dot center dot center dot FH van der Waals molecule: The effects of the potential energy surface and of the basis set superposition error
Journal of Molecular Structure - Theochem, 591 151 - 174 (2002)
abstract    
•  Burda, J. V.; Sponer, J.; Leszczynski, J.
The Influence of Square Planar Platinum Complexes on DNA Bases Pairing. An ab initio DFT Study.
Physical Chemistry Chemical Physics, 3 [19] 4404 - 4411 (2001)
abstract    
•  Cejchan, A.; Spirko, V.
Transforming from Internal Coordinates to Cartesian Displacements in the Eckart Frame: a Taylor Series Expansion Approach.
Journal of Molecular Spectroscopy, 217 [1] 142 - 145 (2003)
•  Chocholousova, J.; Vacek, J.; Hobza, P.
Potential energy and free energy surfaces of the formic acid dimer: Correlated ab initio calculations and molecular dynamics simulations.
Physical Chemistry Chemical Physics, 4 [11] 2119 - 2122 (2002)
abstract    
•  Chocholousova, J.; Vacek, J.; Hobza, P.
Acetic Acid Dimer in the Gas Phase, Nonpolar Solvent, Microhydrated Environment, and Dilute and Concentrated Acetic Acid: Ab Initio Quantum Chemical and Molecular Dynamics Simulations
Journal of Physical Chemistry A, 107 [17] 3086 - 3092 (2003)
abstract    
•  Chocholousova, J.; Vacek, J.; Hobza, P.
Acetic acid dimer in the gas phase, nonpolar solvent, microhydtated environment, and dilute and concentrated acetic acid: ab initio quantum chemical and molecular dynamics simulations.
Journal of Physical Chemistry A, 107 3086 - 3090 (2003)
abstract    
•  Chocholousova, J.; Spirko, V.; Hobza, P.
First local minimum of the formic acid exhibits simultaneously red-shifted O-H...O and improper blue-shifted C-H...O hydrogen bonds.
Physical Chemistry Chemical Physics, 6 [1] 37 - 41 (2004)
abstract    
•  Davidova, M.; Nachtigallova, D.; Bulanek, R. et al
Characterization of the Cu+ Sites in High-silica Zeolites Interacting with CO Molecule: Combined Computational and Experimental Study.
Journal of Physical Chemistry B, 107 [10] 2327 - 2332 (2003)
abstract    
•  Davidova, M.; Nachtigallova, D.; Bulanek, R. et al
Characterization of the Cu+ Sites in High- Silica Zeolites Interacting with CO Molecule: Combined Computational and Experimental Study.
Journal of Physical Chemistry B, 107 [10] 2327 - 2332 (2003)
abstract    
•  Elstner, M.; Hobza, P.; Frauenheim, T. et al
Hydrogen Bonding and Stacking Interactions of Nucleid Acid Base Pairs: A Density-Functional-Theory Based Treatment.
Journal of Chemical Physics, 114 [12] 5149 - 5155 (2001)
abstract    
•  Genzer, J.; Kolafa, J.
Molecular dynamics of potential models with polarizability: comparison of methods.
Journal of Molecular Liquids, 109 [2] 63 - 72 (2004)
abstract    
•  Hanus, M.; Ryjacek, F.; Kabelac , M. et al
Correlated Ab Initio Study of Nucleic Acid Basis nad their Tautomers in the Gas Phase, in a Mictrohydrated Enviroment and in Aqueous Solution. Guanine.
Journal of The American Chemical Society, 125 [25] 7678 - 7688 (2003)
abstract    
•  Hanus, M.; Ryjacek, F.; Kabelac, M. et al
Correlated ab initio Study of Nucleic Acid Bases and Their Tautomers in the Gas Phase, in a Microhydrated Environment and in Aqueous Solution. Part 2. Guanine. Surprising Stabilization of Rare Tautomers in Aqueous Solution.
Journal of the American Chemical Society, 125 7678 - 7682 (2003)
abstract    
•  Hanus, M.; Kabelac, M.; Rejnek, J. et al
Correlated Ab Initio Study of Nucleic Acid Basis nad their Tautomers in the Gas Phase, in a Mictrohydrated Enviroment and in Aqueous Solution. Adenine.
Journal of Physical Chemistry B 108, 2087 (2004). , 108 [6] 2087 - 2097 (2004)
abstract    
•  Havlas, Z.; Bock, H.
Enhanced long-range Si...N interactions in organosilicon cations. A theoretical study.
Collection of Czechoslovak Chemical Communications, 66 [3] 473 - 482 (2001)
abstract    
•  Havlas, Z.; Michl, J. et al
Prediction of an inverse heavy-atom effect in H-C-CH2Br: bromine substituent as a B acceptor.
Journal of the American Chemical Society, 124 [20] 5606 - 5607 (2002)
abstract    
•  Havlas, Z.; Kyvala, M.; Michl, J.
Spin-orbit coupling in biradicals. 4. Zero-field spliting in triplet nitrenes phosphinidenes and arsinidenes.
Collection of Czechoslovak Chemical Communication, 68 [12] 2335 - 2343 (2004)
abstract    
•  Hobza, P.
The H-Index Unambiguously Discriminates between Hydrogen Bonding and Improper Blue-Shifting Hydrogen Bonding.
Physical Chemistry Chemical Physics, 3 [13] 2555 - 2556 (2001)
abstract    
•  Hobza, P.
The H-Index Unambiguously Discriminates between Hydrogen Bonding and Improper Blue-Shifting Hydrogen Bonding.
Physical Chemistry Chemical Physics, 3 [13] 2555 - 2556 (2001)
abstract    
•  Hobza, P.; Havlas, Z.
Blue-Shifting Hydrogen Bonds.
Chemical Reviews, 100 [11] 4253 - 4264 (2000)
•  Hobza, P.; Sponer, J.
Towards true DNA base-stacking energies: MP2, CCSD(T), and complete basis set calculations
Journal of the American Chemical Society , 124 [39] 11802 - 11808 (2002)
abstract    
•  Hobza, P.
Improper, Blue-Shifting Hydrogen Bond: Theory and Experiment.
Strength from Weakness: Structural Consequences of Weak Interactions in Molecules, Supermolecules, and Crystals. . (Ed. A. Domenicano, I. Hargittai), Kluwer Academic, Dordrecht, 281 - 291 (2002)
•  Hobza, P.
N-H... F improper blue-shifting H-bond
International Journal of Quantum Chemistry, 90 [3] 1071 - 1074 (2002)
abstract    
•  Hobza, P.; Spirko, V.
Why is the N-1-H Stretch Vibration Frequency of Guanine Shifted upon Dimerization to the Red and the Amino N-H Stretch Vibration Frequency to the Blue?
Physical Chemistry Chemical Physics, 5 [6] 1290 - 1294 (2003)
abstract    
•  Hocek, M.; Stepnicka, P.; Ludvik, J. et al
Ferrocene-modified purines as potential electrochemical markers.
Chemistry - A European Journal, 10 [8] 2058 - 2066 (2004)
abstract    
•  Hof M.
Basics of Optical Spectroscopy. Handbook of Spectroscopy, eds. G. Gauglitz, T. Vo-Dinh
Wiley VCH Verlag, Weinheim, 39 - 47 (2003)
•  Honzicek, J.; Nachtigall, P.; Cisarova, I. et al
Synthesis, characterization and structural investigation of the first vanadocene(IV) carboxylic acid complexes prepared from the vanadocene dichloride.
Journal of Organometallic Chemistry, 689 [7] 1180 - 1187 (2004)
abstract    
•  Horka, V. ; Civis, S.; Spirko, V. et al
The infrared spectrum of CN in its ground electronic state.
Collection of Czechoslovak Chemical Communications, 69 [1] 73 - 89 (2004)
abstract    
•  Horn M.; Baudys M.; Vondrasek J. et al
Free-thiol Cys331 exposed during activation process is critical for native tetramer structure of cathepsin C (dipeptidyl peptidase I).
Protein Science, 11 [4] 933 - 943 (2002)
abstract    
•  Huml, K.; Vondrasek, J.
Three approaches to the modelling of the structure and interactions of large molecules.
Materials Structure, 7 [1] 10 - 15 (2000)
•  Humpolickova, J.; Prochazka, K.; Hof, M. et al
Fluorescence Correlation Spectroscopy Using Octadecylrhodamine B as a Specific Micelle-Binding Fluorescent Tag, Light Scattering and Tapping Mode Atomic Force Microscopy Studies of Amphiphilic Water-Soluble Block Copolymer Micelles.
Langmuir, 19 [10] 4111 - 4119 (2003)
abstract    
•  Humpolickova, J.; Prochazka, K.; Hof, M.
Octadecylrhodamine B as A Specific Micelle-Binding Fluorescent Tag for Fluorescence Correlation Spectroscopy Studies of Amphiphilic Water-Soluble Block Copolymer Micelles. Spectroscopic Behavior in Aqueous Media
Collection of Czechoslovak Chemical Communications, 68 [10] 2105 - 2119 (2003)
abstract    
•  Hutterer, R.; Hof, M.
Anthroyloxy Fatty Acids: a Unique Set of Fluorescent Probes for the Investigation of Membrane Structure and Dynamics.
Recent Research Developments in Lipids. - (Ed. Pandalai, S. G.). - Trivandrum, Transworld Research Network, 71 - 83 (2001)
•  Hutterer, R.; Hof, M.
Probing ethanol-induced phospholipid phase transitions by the polarity sensitive fluorescence probes.
Zeitschrift fuer Physikalische Chemie, 216 333 - 346 (2002)
abstract    
•  Hutterer, R.; Hof, M.
Fluorescence Approaches for the Characterisation of the Peripheral Membrane Binding of Proteins Applied for the Blood Coagulation Protein Prothrombin
Fluorescence Spectroscopy, Imaging and Probes. (Ed. Kraayenhof, R. - Visser, A. J. W. G. - Gerritsen, H. C.), Springer, Weinheim, 225 - 239 (2002)
•  Jelínek, K. ; Uhlik, F.; Limpouchova, Z. et al
Amphiphilic Block Copolymer Micelles with Hydrobphobically Modified Shells
Molecular Simulations, 29 [10] 655 - 660 (2003)
abstract    
•  Jungwirth P.
Aerosols and the chemistry of the atmosphere (in Czech).
Vesmir, 82 196 (2003)
•  Jungwirth, P.
Chemical oscillations based on photoautocatalysis of ozone.
Chemical Physics Letters, 342 [3] 287 - 292 (2001)
abstract    ps    pdf
•  Jungwirth, P.; Krylov, A. I.
Small Doped 3He Clusters: A Systematic Quantum Chemistry Approach to Fermionic Nuclear Wave Functions and Energies.
Journal of Chemical Physics, 115 [22] 10214 - 10219 (2001)
abstract    ps    pdf
•  Jungwirth, P.; Tobias, D. J.
Molecular Structure of Salt Solutions: A New View of the Interface with Implications for Heterogeneous Atmospheric Chemistry.
Journal of Physical Chemistry. B, 105 [43] 10468 - 10472 (2001)
abstract    ps    pdf
•  Jungwirth, P.; Tobias, D. J.
Ions at the air/water interface
Journal of Physical Chemistry B , 106 [25] 6361 - 6373 (2002)
abstract    ps    pdf
•  Jungwirth, P.; Tobias, D. J.
Chloride anion on aqueous clusters, at the air-water interface, and in liquid water: Solvent effects on Cl- polarizability.
Journal Of Physical Chemistry A, 106 [2] 379 - 383 (2002)
abstract    ps    pdf
•  Jungwirth, P.; Curtis, J. E.; Tobias, D. J.
Polarizability and aqueous solvation of sulfate dianion
Chemical Physics Letters, 367 [5] 704 - 710 (2003)
abstract    
•  Jungwirth, P.
Physical properties and atmospheric reactivity of aqueous sea salt micro-aerosols. in: Water in confining geometries (Cluster Physics Series). Buch, V.; Devlin, J. P. (Eds.)
Springer Verlag, 227 (2003)
•  Jungwirth, P.
Aerosoly a chemie atmosfery - Co se deje na povrchu castic v atmosfere?
Vesmír, 82 [4] 196 - 198 (2003)
•  Jungwirth, P.; Curtis, J. E.; Tobias, D. J.
Polarizability and aqueous solvation of sulfate dianion.
Chemical Physics Letters, 367 (2003) 704., 367 [5] 704 - 710 (2003)
abstract    
•  Jurecka, P.; Nachtigall, P.; Hobza, P.
RI-MP2 Calculations with Extended Basis Sets - a Promising Tool for Study of H-bonded and Stacked DNA Base Pairs.
Physical Chemistry Chemical Physics, 3 [20] 4578 - 4582 (2001)
abstract    
•  Jurecka, P.; Hobza, P.
On the convergence of the (DeltaECCSD(T)-DeltaEMP2) term for complexes with multiple H-bonds.
Chemical Physics Letters, 365 [1] 89 - 94 (2002)
abstract    
•  Jurecka, P.; Hobza, P.
True Stabilization Energies for the Optimal Planar Hydrogen Bonded and Stacked Structures of Guanine&Cytosine, Adenine&Thymine and their 9- and 1-Methyl Derivatives: Complete Basis Set Calculations at the MP2 and CCSD(T) Levels and Comparison with Experiment.
Journal of the American Chemical Society, 125 [50] 15608 - 15613 (2003)
abstract    
•  Jurecka, P.; Sponer, J.; Hobza, P.
Potential energy surface of the cytosine dimmer: MP2 complete basis set limit interaction energies, CCSD(T) correction term, and comparison with the AMBER force field.
Journal of Physical Chemistry B, 108 [17] 5466 - 5471 (2004)
abstract    
•  Jurkiewicz, P.; Okruszek, A.; Hof, M. et al
Associating Oligonucleotides with Positively Charged Liposomes.
Cell. Mol. Biol. Lett., 8 [1] 77 - 84 (2003)
abstract    
•  Kabelac, M.; Ryjacek, F.; Hobza, P.
Already Two Water Molecules Change Planar H-bonded Structure of the Adenine...Thymine Base Pair to the Stacked Ones: a Molecular Dynamics Simulation Study.
Physical Chemistry Chemical Physics, 2 [21] 4906 - 4909 (2000)
abstract    
•  Kabelac, M.; Hobza, P.
At Nonzero Temperatures, Stacked Structures of Methylated Nucleic Acid Base Pairs and Microhydrated Nonmethylated Nucleic Acid Base Pairs are Favored over Planar Hydrogen-Bonded Structures; A Molecular Dynamics Simulations Study.
Chemistry European Journal, 7 [10] 2067 - 2074 (2001)
abstract    
•  Kabelac, M.; Hobza, P.
Potential Energy and Free Energy Surfaces of All Ten Canonical and Methylated Nucleic Acid Base Pairs: Molecular Dynamics and Quantum Chemical ab initio Studies.
Journal of Physical Chemistry. B, 105 [24] 5804 - 5817 (2001)
abstract    
•  Kabelac, M.; Hobza, P.
Potential energy and free energy surfaces of all ten canonical and methylated nucleic acids base pairs: molecular dynamics and quantum chemical ab initio studies.
Journal of Physical Chemistry B, 105 [24] 5804 - 5817 (2001)
abstract    
•  Kabelac, M.; Plutzer, Ch.; Kleinermanns, K. et al
Isomer selective IR experiments and correlated ab initio quantum chemical calculations support planar H-bonded structure of the 7-methyl adenine...adenine and stacked structure of the 9-methyl adenine...adenine base pairs.
Physical Chemistry Chemical Physics, 6 [10] 2781 - 2785 (2004)
abstract    
•  Kadlec, F.; Kadlec, C.; Kuzel, P. et al
Optical pump-terahertz probe spectroscopy of dyes in solutions: Probing the dynamics of liquid solvent or solid precipitate?
Journal of Chemical Physics, 120 [2] 912 - 917 (2004)
abstract    
•  Kempa, M.; Kuzel, P.; Kamba, S. et al
The ferroelectric soft mode and central mode in SrBi2Ta2O9 films, J. Phys.: Condens. Matter 15, 8095-8102 (2003).
Journal of Physics-Condensed Matter , 15 [47] 8095 - 8102 (2003)
abstract    
•  Klusak, V.; Havlas, Z.; Rulisek, L. et al
Sexual Attraction in the Silkworm Moth. Nature of Binding of Bombykol in Pheromone Binding Protein-An Ab Initio Study.
Chemistry and Biology, 10 [4] 331 - 340 (2003)
abstract    
•  Kolafa, J.; Labik, S.; Malijevsky, A.
The bridge function of hard spheres by direct inversion of computer simulation data.
Molecular Physics, 100 [16] 2629 - 2640 (2002)
abstract    
•  Kolafa, J.; Labik, S.; Malijevski, A.
Accurate equation of state of the hard sphere fluid in stable and metastable regions.
Physical Chemistry Chemical Physics, 6 [9] 2335 - 2340 (2004)
abstract    
•  Kraemer, W. P., ; Spirko, V.; Bludsky, O.
Bound and low-lying quasi-bound rotation-vibration energy levels of the ground and first excited electronic states of HeH2+.
Chemical Physics, 276 [3] 225 - 242 (2002)
abstract    
•  Kral, T.; Langner, M.; Benes, M. et al
The application of Fluorescence Correlation Spectroscopy in Detecting DNA Condensation.
Biophysical Chemistry, 95 [2] 135 - 144 (2002)
abstract    
•  Kral, T.; Hof, M.; Jurkiewicz, P. et al
Fluorescence Correlation Spectroscopy (FCS) as a tool to study DNA Condensation with hexadecyltrimethylamonium bromide (HTAB)
Cellular and Molecular Biology Letters, 7 [2] 203 - 211 (2002)
abstract    
•  Kral, T.; Hof , M.; Langner, M.
Effect of Spermine on the Plasmide Condensation and Dye Release Observed by Fluorescence Correlation Spectroscopy
Biological Chemistry, 383 [2] 331 - 335 (2002)
abstract    
•  Kucera, J.; Nachtigall, P.
Coordination of Alkali Metal Ions in ZSM-5: A Combined Quantum Mechanics/Interatomic Potential Function Study.
Physical Chemistry Chemical Physics, 5 [15] 3311 - 3317 (2003)
abstract    
•  Kucera, J.; Nachtigall, P.
Theoretical Study of Pyrrole Interaction with Alkali Metal Exchanged Zeolites: Investigation of the Reliability of Cluster and Periodic Models.
Collection of Czechosloval Chemical Communications, 68 [10] 1848 - 1860 (2003)
abstract    
•  Kucera, J.; Nachtigall, P.
Pyrrole as a probe molecule for characterization of alkali-metal-exchanged ZSM-5: a combination of a theoretical and experimental study.
Chemicke Listy, 97 1070 (2003)
abstract    
•  Labik, S.; Gabrielova, H.; Kolafa, J. et al
Calculation of elementary diagrams using a Metropolis-like simulation method .
Molecular Physics, 101 [8] 1139 - 1146 (2003)
abstract    
•  Lankas, F.; Cheatham, T.E.; Spackova, N. et al
Critical effect of the NH2 amino group on structure, dynamics and elasticity of DNA polypurine tracts.
Biophysical Journal, 82 [5] 2592 - 2609 (2002)
abstract    
•  Lankas, F.; Sponer, J.; Langowski, J. et al
DNA basepair step deformability inferred from molecular dynamics simulations.
Biophysical Journal, 85 [5] 2872 - 2883 (2003)
abstract    
•  Lee, L. L.; Malijevsky, A.
Structures and properties of hard sphere mixtures based on a self-consistent integral equation.
Journal of Chemical Physics, 114 [16] 7109 - 7117 (2001)
abstract    
•  Lepsik, M.
Strukturni a dynamicka pocitacova analyza vazby inhibitoru k protease viru HIV-1.
Chemicke Listy, 95 [5] 330 (2001)
•  Lysikova, M.; Havlas, Z.; Tucek, S.
Interactions between allosteric modulators and 4-DAMP and other antagonists at muscarinic receptors: potential significance of the distance between the N and Carboxyl C atoms in the molecules of antagonists.
Neurochemical Research, 26 [4] 383 - 394 (2001)
abstract    
•  Madeja, F.; Havenith, M.; Nauta, K. et al
A polar isomer of formic acid dimmer in helium nano-droplets.
Journal of Chemical Physics, 120 [22] 10554 - 10560 (2004)
abstract    
•  Malijevsky, A. ; Labik, S.; Malijevsky, A.
Computer simulation of chemical potentials of ternary hard-sphere fluid mixtures.
Physical Chemistry Chemical Physics, 6 [8] 1742 - 1744 (2004)
abstract    
•  Malijevsky, A. ; Pizio, O.; Patrykiejew, A.
Phase behavior f symmetric binary mixtures with partially miscible components in spherical pores. Density functional approach.
Journal of Molecular Liquids, 112 [1] 81 - 89 (2004)
abstract    
•  Malijevsky, A. ; Malijevsky, A.; Yuste, S. B. et al
Structure of ternary additive hard-sphere fluid mixtures.
Physical Review E, 66 [6] 061203 (2002)
abstract    
•  Matejicek, P. ; Humpolickova, J.; Prochazka, K. et al
Hybrid Block Copolymer Micelles with Partly Hydrophobically Modified Polyelectrolyte Shells in Polar and Aqueous Media: Experimental Study Using Fluorescence Correlation Spectroscopy, Time-Resolved. Fluorescence, Light Scattering and Atomic Force Microscopy.
Journal of Physical Chemistry B, 107 [32] 8232 - 8240 (2003)
abstract    
•  Meca, L.; Reha, D.; Havlas, Z.
Racemization Barriers of 1,1 '-binaphthyl and 1,1 '-binaphthalene-2,2 '-diol: A DFT Study.
Journal of Organic Chemistry, 68 [14] 5677 - 5680 (2003)
abstract    
•  Meca. L.; Reha, D.; Havlas, Z.
Racemization barriers of 1,1 -binaphtyl and 1,1 -binaphtalene-2,2 -diol: A DFT study.
Journal of Organic Chemistry, 68 [14] 5677 - 5680 (2003)
abstract    
•  Mrazkova, E.; Hobza, P.
Hydration of Sulfo and Methyl Groups in Dimethyl Sulfoxide is Accompanied by the Formation of Red-shifted Hydrogen Bonds and Improper Blue-shifted Hydrogen Bonds: An Ab Initio Quantum Chemical Study.
Journal of Physical Chemistry A, 107 [7] 1032 - 1039 (2003)
abstract    
•  Mrazkova, E.; Hobza, P.
Hydration of Sulpho and Methyl Groups in Dimethyl Sulfoxide is Accompanied by Formation of Red-Shifted Hydrogen Bonds and Improper Blue-Shifted Hydrogen Bonds: An ab initio Quantum Chemical Study.
Journal of Physical Chemistry A , 107 [7] 1032 - 1039 (2003)
abstract    
•  Mrugala, F.; Spirko, V.; Kraemer, W. P.
Radiative Association of HeH2+.
Journal of Chemical Physics, 118 [23] 10547 - 10560 (2003)
abstract    
•  Mucha, M.; Jungwirth, P.
Salt Crystallization from an Evaporating Aqueous Solution by Molecular Dynamics Simulations.
Journal of Physical Chemistry B, 107 [33] 8271 - 8274 (2003)
abstract    
•  Nachtigall, P.; Davidova, M.; Silhan, M. et al
Theoretical interpretation of UV-VIS spectra of Cu- and Ag-species in zeolites: structure vs. transition energies.
Zeolites and mesoporous materials at the dawn of the 21st century. A. Galarneau, F. Di Renzo, F. Faujula and J. Védrine, Editors, Elsevier, Amsterdam. Studies in Surface Science and Catalysis., 135 14-O-03-1 - 14-O-03-8 (2001)
•  Nahler, N. H.; Baumfalk, R.; Buck, U. et al
Photodissociation of HBr in and on Arn Clusters: The Role of the Position of the Molecule.
Physical Chemistry Chemical Physics, 5 [16] 3394 - 3401 (2003)
abstract    
•  Nather, C.; Jess, I.; Havlas, Z. et al
Trimorphism of 4,4 '-Di(tert.-butyl)-biphenyl sturctural, thermodynamic and kinetic aspects.
Solid State Sciences, 4 [6] 859 - 871 (2002)
abstract    
•  Nemec, H.; Paskin, A.; Kuzel, P. et al
Carrier dynamics in low-temperature grown GaAs studied by terahertz emission spectroscopy.
Journal of Applied Physics, 90 [3] 1303 - 1306 (2001)
abstract    
•  Nemec, H.; Kadlec, F.; Kuzel, P.
Methodology of an optical pump-terahertz probe experiment: An analytical frequency-domain approach.
Journal of Chemical Physics, 117 [18] 8454 - 8466 (2002)
abstract    
•  Nemec, H.; Kadlec, F.; Kuzel, P.
Methodology of an optical pump-terahertz probe experiment: An analytical frequency-domain approach.
Journal of Chemical Physics, 117 [18] 8454 - 8466 (2002)
abstract    
•  Nemec, H.; Kuzel, P.; Garet, F. et al
Time-domain terahertz study of defect formation in one-dimensional photonic crystals.
Applied Optics, 43 [9] 1965 - 1970 (2004)
abstract    
•  Pashkin, A.; Kempa, M.; Nemec, H. et al
Phase-sensitive time-domain terahertz reflection spectroscopy.
Review of Scientific Instruments, 74 [11] 4711 - 4717 (2003)
abstract    
•  Piecuch, P.; Kucharski, S. A.; Spirko, V. et al
Can Ordinary Single-Reference Coupled-Cluster Methods Describe Potential Energy Surfaces with Nearly Spectroscopic Accuracy? The Renormalized Coupled-Cluster Study of the Vibrational Spectrum of HF.
Journal of Chemical Physics, 115 [13] 5796 - 5804 (2001)
abstract    
•  Pittner, J.; Hobza, P.
CCSDT and CCSD(T) calculations on model H-bonded and stacked complexes.
Chemical Physics Letters, 390 [4] 496 - 499 (2004)
abstract    
•  Pohle, W.; Gauger, D.R.; Bohl, M. et al
Lipid hydration: Headgroup CH moieties are involved in water binding.
Biopolymers, 74 [1] 27 - 31 (2004)
abstract    
•  Reha, D.; Kabelac, M.; Ryjacek, F. et al
Intercalators 1. Nature of Stacking Interactions between Intercalators (Ethidium, Daunomycin, Ellipticine, and 4,6-Diaminide-2-phenylindole) and DNA Base Pairs. Ab Initio Quantum Chemical, Density Functional Theory, and Empirical Potential Study.
Journal of the American Chemical Society, 124 [13] 3366 - 3376 (2002)
abstract    
•  Reimann, B.; Buchhold, K.; Vaupel, S. et al
Improper, blue-shifting hydrogen bond between fluorobenzene and fluoroform.
Journal of Physical Chemistry. A, 105 [23] 5560 - 5566 (2001)
abstract    
•  Roeselova, M.; Jungwirth, P.; Tobias, D. J. et al
Impact, Trapping, and Accommodation of Hydroxyl Radical and Ozone at Salt Aerosol Surfaces: A Molecular Dynamics Study.
Journal of Physical Chemistry B , 107 [46] 12690 - 12699 (2003)
abstract    
•  Rulisek, L.
Methods of quantum-chemical calculations of transition-metal-containing systems
Chemicke listy, 95 [12] 796 - 803 (2001)
abstract    
•  Rulisek, L.
Theoretical studies of the interactions of transition metals with biomolecules
Chemicke Listy, 96 [3] 132 - 144 (2002)
abstract    
•  Rulisek, L.; Havlas, Z.
Theoretical studies of metal ion selectivity. 2. DFT calculations of complexation energies of selected transition metal ions (Co2+, Ni2+, Cu2+, Zn2+, Cd2+, and Hg2+) in metal-binding sites of metalloproteins
Journal of Physical Chemistry A, 106 [15] 3855 - 3866 (2002)
abstract    
•  Rulisek, L.; Havlas, Z.
Theoretical studies of metal ion selectivity. 1. DFT calculations of interaction energies of amino acid side chains with selected transition metal ions (Co2+, Ni2+, Cu2+, Zn2+, Cd2+, and Hg2+)
Journal of the American Chemical Society, 122 [42] 10428 - 10439 (2000)
abstract    
•  Rulisek, L.; Sponer, J.
Outer-shell and Inner-shell Coordination of Phosphate Group to Hydrated Metal Ions (Mg2+, Cu,2+Zn2+, Cd2+) in the Presence and Absence of Nucleobase.
Journal of Physical Chemistry B, 107 [8] 1913 - 1923 (2003)
abstract    
•  Rulisek, L.; Havlas, Z.
Theoretical studies of metal ion selectivity. 3. A theoretical design of the most specific combinations of functional groups representing amino acid side chains for the selected metal ions (Co2+, Ni2+, Cu2+, Zn2+, Cd2+, and Hg2+).
Journal of Physical Chemistry B, 107 [10] 2376 - 2385 (2003)
abstract    
•  Rulisek, L.; Havlas, Z.
Using DFT methods for the prediction of the structure and energetics of metal-binding sites in metalloproteins.
International Journal of Quantum Chemistry, 91 [6] 504 - 510 (2003)
abstract    
•  Rulisek, L.; Sponer, J.
Outer-Shell and Inner-Shell Coordination of Phosphate Group to Hydrated metal Ions (Mg2+, Cu2+, Zn2+, Cd2+) in Presence and Absence of Nucleobase. The role of Non-electrostatic Effects.
Journal of Physical Chemistry B, 107 [8] 1913 - 1923 (2003)
abstract    
•  Ryjacek, F.; Kubar, T.; Hobza, P.
New Parameterization of the Cornell et al Empirical Force Field Covering Amino Group Nonplanarity in Nucleic Acid Bases.
Journal of Computational Chemistry, 24 [15] 1891 - 1901 (2003)
abstract    
•  Sablinskas, V.; Steiner, G.; Hof M.
Applications of Optical Spectroscopy, Handbook of Spectroscopy, eds. G. Gauglitz, T. Vo-Dinh
Wiley VCH Verlag, Weinheim, 89 - 168 (2003)
•  Salvador, P.; Curtis, J. E.; Tobias, D. J. et al
Polarizability of the Nitrate Anion and Its Solvation at the Air/Water Interface
Physical Chemistry Chemical Physics, 5 [17] 3752 - 3757 (2003)
abstract    
•  Sauer, J.; Nachtigallová, D.; Nachtigall, P. et al
Ab initio Simulation of Cu-Species in Zeolites: Siting, Coordination, UV-VIS Spectra and Reactivity.
Proceedings of the NATO Advanced Research Workshop on Catalysis by Unique Metal Ion Structures in Solid Matrices. - (Ed. Bell, A. T.; Centi, G.; Wichterlová, B.). - Dordrecht, Kluwer Academic, 221 - 224 (2001)
•  Schmidt, K. S.; Reedijk, J.; Weisz, K. et al
Loss of Hoogsteen pairing ability upon N1 adenine platinum binding
Inorganic Chemistry, 41 [11] 2855 - 2863 (2002)
abstract    
•  Sebera, J.; Spirko, V.; Fiser, J.
New rotation- vibration band and potential energy function of NeH+ in the ground electronic state.
Journal of Molecular Structure, 695 5 - 11 (2004)
abstract    
•  Sejbal, J.; Vondrasek, J.; Velek J. et al
Computational and NMR study of multiple antigenic glycopeptides (MAGs) with Tn antigens.
Peptides 2000, Martinez J. & Fehrentz J-A. Eds. EDK, Paris, France, ? (2001)
•  Sheynis, T. Eur. J. Biochem. 270, 4478-4487 (2003).; Sykora, J.; Benda, A. et al
Peptide-lipid Interactions and Bilayer Permeation Studied in Bio-mimetic Vesicles by Fluorescence Spectroscopy.
European Journal of Biochemistry, 270 [22] 4478 - 4487 (2003)
abstract    
•  Silhan, M.; Nachtigallova, D.; Nachtigall, P.
Characterization of Ag+ Sites in ZSM-5: A Combined Quantum Mechanics/Interatomic Potential Function Study.
Physical Chemistry Chemical Physics, 3 [21] 4791 - 4795 (2001)
abstract    
•  Silhan, M.; Nachtigall, P. ; Bludsky, O.
Theoretical investigation of the vibrational dynamics of Ag+CO solvated in the Ne matrix.
Chemical Physics Letters, 375 [1] 54 - 58 (2003)
abstract    
•  Silhan, M.; Nachtigall, P.; Bludsky, O.
Theoretical Investigation of the Vibrational Dynamics of Ag+CO Solvated in the Ne Matrix.
Chemical Physics Letters, 275 [1] 54 - 58 (2003)
abstract    
•  Sindelka, M.; Spirko, V.; Jungwirth, P.
Electrons weakly bound to hydrogen bonded clusters: A pseudopotential model including dispersion interactions
Journal of Chemical Physics, 117 [11] 5113 - 5123 (2002)
abstract    ps    pdf
•  Sindelka, M.; Spirko, V.; Kraemer, W. P.
Vibrational Linestrengths for the Ground and First Excited Electronic States of HeH2+.
Theoretical Chemistry Accounts, 110 [3] 170 - 175 (2003)
abstract    
•  Sindelka, M.,; Spirko, V.; Urban J. et al
Potential energy surface and ro-vibrational energies of Ne3+ in the ground electronic state.
International Journal of Quantum Chemistry, 85 [3] 1232 - 1239 (2001)
abstract    
•  Slaninova, J.; Maletinska, L.; Vondrasek, J. et al
Magnesium and biological activity of oxytocin analogues modified on aromatic ring of amino acid in position 2.
Journal of Peptide Science, 7 413 - 424 (2001)
abstract    
•  Slavicek, P.; Roeselova, M.; Jungwirth, P. et al
Preference of Cluster Isomers as a Result of Quantum Delocalization: Potential Energy Surfaces and Intermolecular Vibrational States of Ne...HBr, Ne...HI, and HI(Ar)n (n=1-6).
Journal of Chemical Physics, 114 [4] 1539 - 1548 (2001)
abstract    ps    pdf
•  Slavicek, P.; Kalus, R.; Paska, P. et al
State of the Art Correlated Ab Initio Potential Energy Curves for Heavy Rare Gas Dimers Ar2, Kr2, Xe2.
Journal of Chemical Physics, 119 [4] 2102 - 2119 (2003)
abstract    
•  Slavicek, P.; Jungwirth, P.; Lewerenz, M. et al
Pickup and Photodissociation of Hydrogen Halides in Floppy Neon Clusters.
Journal of Physical Chemistry A, 107 [39] 7743 - 7754 (2003)
abstract    
•  Slavicek, P.,; Jungwirth, P.; Lewerenz, M. et al
Photodissociation of hydrogen iodide on the surface of large argon clusters: The orientation of the librational wave function and the scattering from the cluster cage.
Journal of Chemical Physics, 120 [9] 4498 - 4511 (2004)
abstract    
•  Spackova, N.; Cheatham, T.E.; Ryjacek, F. et al
Molecular Dynamics Simulations and Thermodynamics Analysis of DNA-drug Complexes. Minor Groove Binding between 4 ',6- diamidino-2-phenylindole and DNA Duplexes in Solution.
Journal of The American Chemical Society, 125 [7] 1759 - 1769 (2003)
abstract    
•  Spackova, N.; Cheatham, III T. E.; Ryjacek, F. et al
Molecular Dynamics Simulations and Thermodynamics Analysis of DNA - Drug Complexes. I. Minor Groove Binding between 4'',6-Diamidino-2-Phenylindole (DAPI) and DNA Duplexes in Solution.
Journal of the American Chemical Society, 125 [7] 1759 - 1769 (2003)
abstract    
•  Spirko, V.; Kraemer, W. P.
Inversion Splittings of SiH3-. An ab initio Study.
Journal of Molecular Structure. Theochem, 547 139 - 143 (2001)
abstract    
•  Spirko, V.; Sindelka, M.; Shirsat, R. N. et al
Bound and Continuum Vibrational States of the Bifluoride Anion.
Chemical Physics Letters, 376 [5] 595 - 605 (2003)
abstract    
•  Sponer, J.; Lezczynski, J.; Hobza, P.
Hydrogen Bonding, Stacking and Cation Binding of DNA Bases.
Journal of Molecular Structure. Theochem, 573 [1] 43 - 53 (2001)
abstract    
•  Sponer, J.; Leszczynski, J.; Hobza, P.
Electronic properties, H-bonding, stacking and cation binding of DNA and RNA bases.
Biopolymers, 61 [1] 3 - 31 (2002)
abstract    
•  Sponer, J.; Hobza, P.
Molecular Interactions of Nucleic Acid Bases. A Review Quantum Chemical Studies.
Collection of Czechoslovak Chemical Communication, 68 2231 - 2236 (2003)
abstract    
•  Sponer, J. E.; Glahe, F.; Leszczynski, J. et al
How Nucleobases Rotate When Bonded to a Metal Ion: Detailed View from an ab initio Quantum Chemical Study of a Cytosine Complex of trans-a2PTII.
Journal of Physical Chemistry. B, 105 [48] 12171 - 12179 (2001)
abstract    
•  Sponer, J. E.; Leszczynski, J.; Glahé, F. et al
Protonation of Platinated Adenine Nucleobases. Gas Phase vs Condensed Phase Picture.
Inorganic Chemistry, 40 [14] 3269 - 3278 (2001)
abstract    
•  Sponer, J.E.; Sychrovsky, V.; Sponer, J. et al
Interactions of hydrated divalent metal cations with nucleic acid bases. How to relate the gas phase data to solution situation and binding selectivity in nucleic acids.
Physical Chemistry Chemical Physics, 6 [10] 2772 - 2780 (2004)
abstract    
•  Spuhler, P.; Holthausen, M. C.; Nachtigallova, D. et al
On the existence of CuI pairs in ZSM-5 - A Computational Study.
Chemistry - A European Journal, 8 [9] 2099 - 2115 (2002)
abstract    
•  Stanislav, L.; Gabrielova, H.; Kolafa, J. et al
Calculation of elementary diagrams using a Metropolis-like simulation method.
Molecular Physics, 101 [8] 1139 - 1146 (2003)
abstract    
•  Steckel, J. A.; Phung, T. ; Jordan, K. D. et al
The Concerted Use of Slab and Cluster Models in and Ab Initio Study of Hydrogen Desorption from the Si(100) Surface,.
J. Phys. Chem. B, 105 [18] 4031 - 4038 (2001)
abstract    
•  Stepanek, M. ; Humpolickova, J.; Prochazka, K. et al
Light Scattering, Atomic Force Microscopy and Fluorescence Correlation Spectroscopy Studies of Polystyrene-block-poly(2-vinylpyridine)-block-poly(ethylene oxide) Micelles.
Collection of Czechoslovak Chemical Communications, 68 [11] 2120 - 2138 (2003)
abstract    
•  Sychrovsky, V.; Vacek, J.; Hobza, P. et al
Exploring the structure of a DNA hairpin with the help of NMR spin-spin coupling constants: An experimental and quantum chemical investigation
Journal of Physical Chemistry B, 106 [39] 1242 - 1250 (2002)
abstract    
•  Sychrovsky, V.; Schneider, B.; Hobza, P. et al
The Effect of Water on NMR Spin-spin Couplings in DNA: Improvement of Calculated Values by Application of two Solvent Models.
Physical Chemistry Chemical Physics, 5 [4] 734 - 739 (2003)
abstract    
•  Sychrovsky, V.; Sponer, J. ; Hobza, P.
Theoretical Calculation of the NMR Spin-spin Coupling Constants and the NMR Shifts Allow Distinguishability between the Specific Direct and the Water-Mediated Binding of the Divalent Metal Cation to Guanine.
Journal of the American Chemical Society, 126 [2] 663 - 672 (2004)
abstract    
•  Sykora, J; Mudogo, V.; Hutterer, R. et al
ABA-C15: A New Dye for Probing Solvent Relaxation in Phospholipid Bilayers.
Langmuir, 18 [24] 9276 - 9282 (2002)
abstract    
•  Sykora, J.; Kapusta, P.; Fidler, V. et al
On What Time-Scale Does Solvent Relaxation in Phospholipid Bilayers Happen?
Langmuir, 18 571 - 574 (2002)
abstract    
•  Sykora, J.; Hof, M.
Solvent Relaxation in Phospholipid Bilayers: Physical Understanding and Biophysical Applications.
Cellular and Molecular Biology Letters , 7 [2] 259 - 261 (2002)
•  Tobias, D. J.; Jungwirth, P. ; Parrinello, M.
Surface Solvation of Halogen Anions in Water Clusters: An ab initio Molecular Dynamics Study of the Cl-(H2O)6 Complex.
Journal of Chemical Physics, 114 [16] 7036 - 7044 (2001)
abstract    ps    pdf
•  Trygubenko, S. A.; Bogdan, T. V.; Rueda, M. et al
Correlated ab initio study of nucleic acid bases and their tautomers in the gas phase, in a microhydrated environment and in aqueous solution - Part 1. Cytosine
Physical Chemistry Chemical Physics, 4 [17] 4192 - 4203 (2002)
abstract    
•  Veken van der, B. J.; Herrebout, W. A.; Szostak, R. et al
The nature of improper, blue-shifting hydrogen bonding verified experimentally.
Journal of the American Chemical Society, 123 [49] 12290 - 12293 (2001)
abstract    
•  Vondrasek, J.; Wlodawer, A.
HIVdb: a database of the structures of human immunodeficiency virus protease.
Proteins - Structure Function and Genetics , 49 [4] 429 - 431 (2003)
•  Weber, J.; Mesters, J.; Lepsik, M. et al
Unusual binding mode of an HIV-1 protease inhibitor explains its potency against drug-resistant HIV strains.
Journal of Molecular Biology, 324 [4] 739 - 754 (2002)
abstract    
•  Weber, J.; Mesters, J. R.; Lepsik, M. et al
Unusual binding mode of an HIV-1 protease inhibitor explains its potency against multi-drug-resistant virus strains.
Journal of Molecular Biology, 324 [4] 739 - 754 (2003)
abstract    
•  Wu, R.; Vaupel, S.; Nachtigall, P. et al
Structure and hydrogen bonding of different isomers of 2-aminopyridine center dot NH3 studied by IR/R2PI spectroscopy.
Journal of Physical Chemistry A, 108 [16] 3338 - 3343 (2004)
abstract    
•  Wu, R.; Brutschy, B.; Nachtigall, P.
Structure and hydrogen bonding of 2- aminopyridine·(H2O)n (n=1,2) studied by infrared ion depletion spectroscopy.
Physical Chemistry Chemical Physics, 6 [3] 515 - 521 (2004)
abstract    
•  Yang, X.; Fu, Y.J.; Wang, X.B. et al
Solvent-mediated folding of a doubly charged anion.
Journal of the American Chemical Society, 126 [3] 876 - 883 (2004)
abstract    
•  Zamastil, J.; Spirko, V.; Cizek, J. et al
Multidimensional WKB Approximation and the Lifetime Calculation.
Physical Review. A, 64 042101.1 - 042101.11 (2001)
abstract    
•  Zdanska, P.; Nachtigallova, D.; Nachtigall, P. et al
Nonadiabatic Interactions between the Ground and Low-lying Excited Electronic States: Vibronic States of the Cl-HCl Complex.
Journal of Chemical Physics, 115 [13] 5974 - 5983 (2001)
abstract    ps    pdf
•  Zeizinger, M.; Burda, J. V.; Sponer, J. et al
A Systematic ab initio Study of the Hydration of Selected Palladium Square-Planar Complexes. A Comparison with Platinum Analogues.
Journal of Physical Chemistry A, 105 [34] 8086 - 8092 (2001)
abstract    
•  Zierkiewicz, W.; Michalska, D.; Havlas, Z. et al
Study of the nature of improper blue-shifting hydrogen bonding and standard hydrogen bonding in the X3CH center dot center dot center dot OH2 and XH center dot center dot center dot OH2 complexes (X = F, Cl, Br, I): A correlated ab initio study
ChemPhysChem, 3 [6] 511 - 518 (2002)
abstract    
•  Zierkiewicz, W.; Michalska, D.; Hobza, P.
The barrier to internal rotation and electronic effects in para-halogenphenols: theoretical study.
Chemical Physics Letters, 386 [1] 95 - 100 (2004)
abstract    
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