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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
The list of papers that were published during the duration of the Center For Complex Molecular Systems and Biomolecules 2000 - 2004 may be found here.

This is a list of 121 papers that were published during the duration of the Center for Biomolecules and Complex Molecular Systems in years 2005 - 2009.

•  Alexandrova, Z.; Starty, I.; Stara, I. et al
Synthetic studies leading to helically chiral compounds.
Chemicke listy, 99 [11] 829 (2005)
•  Alexandrova, Z.; Sehnal, P.; Stara, I. et al
Modified synthesis of heptahelicene and its resolution into single enantiomers.
Collection of Czechoslovak Chemical Communications., 71 [8] 1256 - 1264 (2006)
abstract    
•  Alpturk, O.; Rusin, O.; Fakayode, S. O. et al
Lanthanide complexes as fluorescent indicators for neutral sugars and cancer biomarkers.
Proceedings of the National Academy of Sciences of the United States of America, 103 9756 - 9760 (2006)
abstract    
•  Andronova, A.; Stara, I.; Stary, I.
Synteza noveho typu neracemickych helicenum podobnych latek se dvema chiralnimi centry.
Chemicke listy, 99 [11] 829 - 830 (2005)
•  Banas, P.; Otyepka, M.; Jerabek, P. et al
1,2,3-Trichloropropane by Mutant Haloalkane Dehalogenase Revealed by Molecular Modeling.
Journal of Computer-Aided Molecular Design, 20 [6] 375 - 383 (2006)
abstract    
•  Barratt, E. ; Bronowska, A.; Vondrasek, J. et al
Thermodynamic penalty arising from burial of a ligand polar group within a hydrophobic pocket of a protein receptor.
Journal of Molecular Biology, 362 994 - 1003 (2006)
abstract    
•  Bartova, I.; Otyepka, M.; Kriz, Z. et al
The mechanism of inhibition of the cyclin-dependent kinase-2 as revealed by the molecular dynamics study on the complex CDK2 with the peptide substrate HHASPRK.
Protein Science, 14 [2] 445 - 451 (2005)
abstract    
•  Bludsky, O.; Silhan, M.; Nachtigall, P. et al
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)
abstract    
•  Bludsky, O.; Nachtigallova, D.; Bulanek, R. et al
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, 100 [3] 385 - 389 (2005)
abstract    
•  Brown, E. C.; Mucha, M.; Jungwirth, P. et al
Structure and vibrational spectroscopy of salt water/air interfaces: Predictions from classical molecular dynamics simulations.
Journal of Physical Chemistry B, 109 [16] 7934 - 7940 (2005)
abstract    
•  Bulanek, R.; Drobna, H.; Nachtigall, P. et al
On the site-specificity of polycarbonyl complexes in Cu/zeolites: combined experimental and DFT study.
Physical Chemistry Chemical Physics, 8 5535 - 5542 (2006)
abstract    
•  Caffrey, C. R.; Placha, L.; Barinka, C. et al
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)
abstract    
•  Cerny, J.; Hobza, P.
The X3LYP extended density functional accuratelydescribes H-bonding but fails completely for stacking.
Physical Chemistry Chamical Physics, 7 [8] 1624 - 1626 (2005)
abstract    
•  Cerny, J.; Spirko, V.; Mons, M. et al
Theoretical study of the ground and excited states of 7-methyl guanine and 9-methyl guanine: comparison with experiment.
Physical Chemistry Chemical Physics, 8 3059 - 3065 (2006)
abstract    
•  Chalupsky, J.; Neese, F.; Solomon, E. I. et al
Multireference ab initio calculations on reaction intermediates of the multicopper oxidases.
Inorganic Chemistry, 45 [26] 11051 - 11059 (2006)
abstract    
•  Crews, B.; Abo-Riziq, A.; Grace, L. et al
IR-UV double resonance spectroscopy of guanine-H2O clusters.
Physical Chemistry Chemical Physics, 7 [16] 3015 - 3020 (2005)
abstract    
•  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] 204322 (2005)
abstract    
•  Dang, L. X.; Chang, T. M. ; Roeselova, M. et al
On NO3- --H2O interactions in aqueous solutions and at interfaces.
Journal of Chemical Physics. Ro?. 124, - (2006), 066101/1-066101/3 , 124 066101/1 - 066101/3 (2006)
abstract    
•  Dobes, P.; Otyepka, M. ; Strnad, M. et al
Interaction energies for the purine inhibitor roscovitine with cyclin-dependent kinase 2: Correlated ab initio quantum-chemical, DFT and empirical calculations.
Chemistry European Journal, 12 [16] 4297 - 4304 (2006)
abstract    
•  Fanfrlik, J.; Rejnek, J.; Hanus, M. et al
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)
abstract    
•  Fanfrlik, J.; Lepsik, M.; Horinek, D. et al
Interaction of carboranes with biomolecules: Formation of dihydrogen bonds.
ChemPhysCHem, 7 1100 - 1105 (2006)
abstract    
•  Farnik, M.; Nahler, N. H.; Buck, U. et al
Photodissociation of HBr on the surface of Ar-n clusters at 193 nm.
Chemical Physics, 315 [1] 161 - 170 (2005)
abstract    
•  Garrone, E.; Bulanek, R.; Frolich, K. et al
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 22542 - 22550 (2006)
abstract    
•  Gilary, I.; Kapralova, P.; Moiseyev, N.
Ab initio calculation of harmonic generation spectra of helium using a time-dependent non-Hermitian formalism.
Physical Review. A., 74 052505 (2006)
abstract    
•  Gopalakrishnan, S.; Jungwirth, P.; Tobias, D. J. et al
Air-liquid interfaces of aqueous solutions containing ammonium and sulfate: Spectroscopic and molecular dynamics studies.
Journal of Physical Chemistry B, 109 [18] 8861 - 8872 (2005)
abstract    
•  Hobza, P.; Zahradnik, R.; Müller-Dethlefs, K
The world of non-covalent interactions: 2006.
Collection of Czechoslovak Chemical Communications, 71 [4] 443 - 531 (2006)
abstract    
•  Hocek, M.; Pohl, R.; Klepetarova, B.
A new modular and practical methodology for the synthesis of 4- or 3- substituted phenyl C-nucleosides.
, 21 4525 - 4528 (2005)
abstract    
•  Horn, M.; Maresova, L.; Rulisek, L. et al
Activation processing of cathepsin H impairs recognition by its propeptide.
Biological Chemistry, 386 [9] 941 - 947 (2005)
abstract    
•  Hrobarik, T.; Vrbka, L.; Jungwirth, P.
Selected biologically relevant ions at the air/water interface: A comparative molecular dynamics study.
Biophysical Chemistry, 124 238 - 242 (2006)
abstract    
•  Höfft, O.; Borodin, A.; Kahnert, U. et al
Surface segregation of dissolved salt ions
Journal of Physical Chemistry B, 110 11971 - 11976 (2006)
abstract    
•  Jin, B. B.; Kuzel, P.; Kadlec, F. et al
Terahertz surface impedance of epitaxial MgB2 thin film.
Applied Physics Letters 87, 87 [9] 092503 (2005)
abstract    
•  Jungwirth, P.; Tobias, D. J.
Specific ion effects at the air/water interface.
Chemical Reviews, 106 1259 - 1281 (2006)
abstract    
•  Jurecka, P.; Sponer, J.; Cerny, J. et al
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 1985 - 1993 (2006)
abstract    
•  Kabelac, M.; Zendlova, L.; Reha, D. et al
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)
abstract    
•  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 14515 - 14523 (2006)
abstract    
•  Kapralova, P.
Dynamical control near resonances in gedanken experiments using varying projectile flux.
Physical Review. A, 73 064703 (2006)
abstract    
•  Kapralova, P.; Lazebnicek, J.
Potential scattering with varying projectile flux near metastable levels.
Lecture Series on Computer and Computational Sciences, 7 248 - 251 (2006)
•  Kejik, Z.; Zaruba, K.; Machalik, D. et al
Optical sensing system for ATP using porphyrin-alkaloid conjugates.
Chemical Communications, 14 1533 - 1539 (2006)
abstract    
•  Kejik, Z.; Zaruba, K.; Michalik, D. et al
Optical sensing system for ATP using porphyrin-alkaloid conjugates.
Chemical Communications, 14 1533 - 1535 (2006)
abstract    
•  Klein, N.; Kadlec, F.; Kuzel, P. et al
A metal-dielectric antenna for terahertz near-field imaging.
Journal of Applied Physics, 98 [1] 014910 (2005)
abstract    
•  Kolafa, J.
Gear formalism of the always stable predictor-corrector method for the molecular dynamics of polarizable molecules.
Journal of Chemical Physics, 122 [16] 164105 (2005)
abstract    
•  Kolafa, J.
Nonanalytical Equation of State of the Hard Sphere Fluid.
Physical Chemistry Chemical Physics, 8 464 - 468 (2006)
abstract    
•  Kolafa, J.; Labik, S.
Density expansion of the radial distribution and bridge functions of the hard sphere fluid.
Molecular Physics, 104 1915 - 1924 (2006)
abstract    
•  Koval, D.; Jiraskova, J.; Strisovsky, K. et al
Capillary electrophoresis method for the determination of D-serine and its application for monitoring of serine racemase activity.
Electrophoresis, 27 2558 - 2566 (2006)
abstract    
•  Kraemer, W. P.; Spirko, V
Bound and low-lying quasi-bound rotation-vibration levels of the ground electronic state of LiH2+.
Chemical Physics, 330 190 - 203 (2006)
abstract    
•  Kral, V. ; Lang, K.; Kralova, J. et al
Polyhydroxylated sapphyrins: multisite non-metallic catalysts for activated phosphodiester hydrolysis.
Journal of the American Chemical Society, 128 [2] 432 - 437 (2006)
abstract    
•  Kral, V.; Lang, K.; Kralova, J. et al
Polyhydroxylated Sapphyrins: Multisite Non-metallic Catalysts for Activated Phosphodiester Hydrolysis.
Journal of the American Chemical Society, 128 432 - 437 (2006)
abstract    
•  Krasovska, M.; Sefcikova, J.; Reblova, K. et al
Cations and hydration in catalytic RNA: Molecular dynamics of the hepatitis delta virus ribozyme.
Biophysical Journal, 91 626 - 638 (2006)
abstract    
•  Kubar, T.; Hanus, M.; Ryjacek, F. et al
Binding of cationic and neutral phenanthridine intercalators to a DNA oligomer is controlled by the dispersion energy. Quantum chemical calculations and molecular mechanics simulations.
Chemistry European Journal, 12 [1] 208 - 290 (2006)
abstract    
•  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, 158 917 - 924 (2005)
•  Kucera, J.; Nachtigall, P.
A simple correlation between average T-O-T angles and 27Al MAS NMR chemical shifts does not hold in high-silica zeolites.
Microporous and Mesoporous Materials, 85 [3] 279 - 283 (2005)
abstract    
•  Labik, S.; Kolafa, J.; Malijevsky, A.
Virial coefficients of hard spheres and hard disks up to the ninth.
Physical Review E, 71 [2] 021105 (2005)
abstract    
•  Malijevsky, A
Alternative Fundamentals measure theory for hard sphere mixtures
The Journal of Chemical Physics, 125 194519 (2006)
abstract    
•  Malijevsky, A.; Santos, A.
Structure of penetrable-rod fluids: Exact properities and comparison between Monte Carlo simulations and two simple theories.
The Journal of Chemical Physics, 124 074508 (2006)
abstract    
•  Malijevsky, A.; Santos A. ; Yuste S. B.
How sticky are short-range square-well fluids?
The Journal of Chemical Physics, 125 074507-1 (2006)
abstract    
•  Malijevsky, A.; Zientarski, T.; Sokolowski, S.
Structure and phase behavior of Widom-Rowlinson model calculated from a nonuniform Ornstein-Zernike equation.
The Journal of Chemical Physics, 125 [114505] 0 (2006)
abstract    
•  Matejicek, P.; Cigler, P.; Prochazka, K. et al
Molecular Assembly of Metallacarboranes in Water: Light Scattering and Microscopy Study
Langmuir, 22 [2] 575 - 581 (2006)
abstract    
•  McDowell, S. E.; Spackova, N.; Sponer, J. et al
Molecular dynamics simulations of RNA: An in silico single molecule approach.
Biopolymers, 85 [2] 169 - 184 (2006)
abstract    
•  Mics, Z.; Kadlec, F.; Kuzel, P. et al
Nonresonant ionization of oxygen molecules by femtosecond pulses: plasma dynamics studied by timeresolved terahertz spectroscopy.
Journal of Chemical Physics, 123 [10] 104310 (2005)
abstract    
•  Minofar, B.; Vrbka, L.; Mucha M. et al
Interior and interfacial aqueous solvation of benzene dicarboxylate dianions and their methylated analogues: A combined molecular dynamics and photoelectron spectroscopy study.
Journal of Physical Chemistry A, 109 [23] 5042 - 5049 (2005)
abstract    
•  Minofar, B.; Vacha, R.; Wahab, A. et al
Propensity for the air/water interface and ion pairing in magnesium acetate vs magnesium nitrate solutions: Molecular dynamics simmulations and surface tension measurements.
Journal of Physical Chemistry B, 110 15939 - 15944 (2006)
abstract    
•  Misek, J.; Teply, F.; Stara, I. et al
Synthesis of helically chiral heteroaromatics: an easy access to azahelicene derivatives.
Chemicke Listy, 99 [11] 860 - 867 (2005)
•  Moravek, P.; Kolafa, J.; Hujo, T. et al
Excess volume of homonuclear diatomic mixtures.
The Journal of Molecular Liquids, 125 22 - 28 (2006)
abstract    
•  Mounaix, P.; Freysz, E.; Degert, J. et al
One-dimensional tunable photonic crystals with spin crossover material for the terahertz range.
Applied Physics Letters, 89 [17] 174105 (2006)
abstract    
•  Mrazkova, E.; Hobza, P. ; Bohl, M. et al
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)
abstract    
•  Muchova, E.; Spirko, V.; Hobza, P. et al
Theoretical Study of Photoacidity of HCN: the Effect of Complexation with Water.
Physical Chemistry Chemical Physics, 8 4866 - 4873 (2006)
abstract    
•  Nachtigall, P.; Bludsky, O.; Nachtigallova, D. et al
Characterization of the Cu+ sites in FER Zeolites. Combined Computational and Experimental TPD Study.
Studies in Surface Science and Catalysis, 158 925 - 932 (2005)
•  Nachtigall, P.; Bulanek, R.
Theoretical investigation of site-specific characteristics of CO adsorption complexes in the Li+-FER zeolite.
Applied Catalysis A, 307 118 - 127 (2006)
abstract    
•  Nachtigall, P.; Garrone, E.; Palomino, G. T. et al
FTIR spectroscopic and computational studies on hydrogen adsorption on the zeolite Li-FER.
Physical Chemistry Chemical Physics, 8 2286 - 2292 (2006)
abstract    
•  Nachtigallova, D.; Bludsky, O.; Arean, C. O. et al
The vibrational dynamics of carbon monoxide in a confined space-CO in zeolites.
Physical Chemistry Chemical Physics, 8 4849 - 4852 (2006)
abstract    
•  Otyepka, M. ; Sklenovsky, P.; Horinek, D. et al
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 4423 - 4429 (2006)
abstract    
•  Otyepka, M.; Bartova, I.; Kriz, Z. et al
Different Mechanisms of CDK5 and CDK2 Activation as Revealed by CDK5/p25 and CDK2/Cyclin A Dynamics
Journal of Biological Chemistry, 281 [11] 7271 - 7281 (2006)
abstract    
•  Petersen, P. B; Saykally, R. J. ; Mucha, M. et al
Enhanced concentration of polarizable anions at the liquid water surface: SHG spectroscopy and MD simulations of sodium thiocyanide.
Journal of Physical Chemistry B, 109 [21] 10915 - 10921 (2005)
abstract    
•  Petrek, M.; Otyepka, M.; Banas, P. et al
CAVER: a new tool to explore routes from protein clefts, pockets and cavities
BMC Bioinformatics, 7 316 (2006)
abstract    
•  Petrov, M.; Minofar, B.; Vrbka, L. et al
Aqueous ionic and complementary zwitterionic soluble surfactants: Molecular dynamics simulations and sum frequency generation spectroscopy of the surfaces.
Langmuir, 22 [6] 2498 - 2505 (2006)
abstract    
•  Pumera, M.; Rulisek, L.
Structures of inclusion complexes of halogenbenzoic acids and alpha-cyclodextrin based on AM1 calculations.
Journal of Molecular Modeling, 12 799 - 803 (2006)
abstract    
•  Razga, F.; Zacharias, M.; Reblova, K et al
RNA Kink-turns as molecular elbows: Hydration, cation binding, and large-scale dynamics.
Structure, 14 [5] 825 - 835 (2006)
abstract    
•  Reblova, K.; Lankas, F.; Razga, F. et al
Structure, dynamics, and elasticity of free 16S rRNA helix 44 studied by molecular dynamics simulations.
Biopolymers, 82 [5] 504 - 520 (2006)
abstract    
•  Reha, D.; Valdes, H.; Vondrasek, J. et al
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 European Journal, 11 [23] 6804 - 6817 (2005)
abstract    
•  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)
abstract    
•  Rejnek, J.; Hanus, M.; 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. 4. Uracil and thymine.
Physical Chemistry Chamical Physics, 7 [9] 2006 - 2017 (2005)
abstract    
•  Rhodes, M. M.; Rebloba, K.; Sponer, J. et al
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)
abstract    
•  Rulisek, L.; Solomon, E. I.; Ryde, U.
A combined quantum and molecular mechanical study of the O2 reductive cleavage in the catalytic cycle of multicopper oxidases.
Inorganic Chemistry, 44 [16] 5612 - 5628 (2005)
abstract    
•  Rulisek, L.; Sebek, P; Havlas, Z. et al
An experimental and theoretical study of stereoselectivity of furan-maleic anhydride and furan-maleimide Diels-Alder reactions.
Journal of Organic Chemistry, 70 [16] 6295 - 6302 (2005)
abstract    
•  Rulisek, L.; Ryde, U.
Structure of reduced and oxidized manganese superoxide dismutase: A combined computational and experimental approach.
Journal of Physical Chemistry B, 110 11511 - 11518 (2006)
abstract    
•  Rulisek, L.; Jensen, K. P.; Lundgren, K. et al
The role mechanism of iron and manganese superoxide dismutases studied by theoretical calculations.
Journal of Computational Chemistry, 27 1398 - 1414 (2006)
abstract    
•  Samoylova, E.; Smith, V. R.; Ritze, H. H. et al
Ultrafast Deactivation Processes in Aminopyridine Clusters: Excitation energy dependence and isotope effects.
Journal of the American Chemical Society, 128 15652 - 15656 (2006)
abstract    
•  Sedivcova, T; Zdanska, P.; Spirko, V.
Computed lifetimes of metastable states of CO2+.
Journal of Chemical Physics, 124 214303 (2006)
abstract    
•  Sedivcova, T.; Spirko, V.
Potential energy and transition dipole moment functions of C2-.
Molecular Physics, 104 [13] 1999 - 2005 (2006)
abstract    
•  Sedivcova, T.; Spirko, V.; Fiser, J.
Theoretical study of the CS2+ dication.
Journal of Chemical Physics, 125 164308 (2006)
abstract    
•  Sehnal, P.; Stary, I.; Stara, I. et al
Diastereoselective synthesis of [11]helicene-like molecules via double [2+2+2] cycloisomerization.
Chemicke Listy, 99 [11] 867 - 868 (2005)
•  Spackova, N.; Sponer, J.
Molecular dynamics simulations of sarcin-ricin rRNA motif.
Nucleic Acids Research, 34 [2] 697 - 708 (2006)
abstract    
•  Spirko, V.; Amano, T.; Kraemer, W. P.
Vibrational predissociation of H5+.
Journal of Chemical Physics, 124 244303 (2006)
abstract    
•  Spirko, V.; Hobza, P.
Theoretical investigations into the blue-shifting hydrogen bond in benzene complexes.
ChemPhysCHem, 7 [3] 640 - 643 (2006)
abstract    
•  Sponer, J.; Jurecka, P.; Marchan, I. et al
Nature of base stacking: Reference quantum-chemical stacking energies in ten unique B-DNA base-pair steps.
Chemistry European Journal, 12 2854 - 2865 (2006)
abstract    
•  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)
abstract    
•  Stary, I.; Stara, I.; Alexandrova, Z. et al
Helicity control in the synthesis of helicenes and related compounds.
Pure and Applied Chemistry, 78 [2] 495 - 499 (2006)
abstract    
•  Strisovsky, K.; Jiraskova, J.; Mikulova, A. et al
Dual substrate and reaction specificity in mouse serine racemase: Identification of high-affinity dicarboxylate substrate and inhibitors and analysis of the beta-eliminase activity.
Biochemistry, 44 [39] 13091 - 13100 (2005)
abstract    
•  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 9194 - 9199 (2006)
abstract    
•  Sychrovsky, V.; Vokacova, Z; Sponer, J. et al
Calculation of Structural Behavior of Indirect NMR Spin-Spin Couplings in the Backbone of Nucleic Acids.
Journal of Physical Chemistry B, 110 22894 - 22903 (2006)
abstract    
•  Tocik, Z.; Barvik Jr., I.; Budesinsky, M. et al
Novel isosteric, isopolar phosphonate analogs of oligonucleotides: Preparation and properties.
Biopolymers, 83 400 - 413 (2006)
abstract    
•  Tuma, L; Jenicek, D.; Jungwirth, P.
Propensity of heavier halides for the water/vapor interface revisited using the Amoeba force field.
Chemical Physics Letters, 411 [1] 70 - 74 (2005)
abstract    
•  Urban, M.; Pohl, R. ; Klepetarova, B. et al
New modular and efficient approach to 6-substituted pyridin-2-yl C-nucleosides.
Journal of Organic Chemistry, 71 [19] 7322 - 7328 (2006)
abstract    
•  Vacha, R.; Jungwirth, P.; Chen, J. et al
Adsorption of polycyclic aromatic hydrocarbons at the air-water interface: Molecular dynamics simulations and experimental atmospheric observations
Physical Chemistry Chemical Physics, 8 [38] 4461 - 4467 (2006)
abstract    
•  Valdez, 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 6385 - 6396 (2006)
abstract    
•  Valik, M.; Malina, J.; Palivec, L. et al
Troger's base scaffold in racemic and chiral fashion as a spacer for bisdistamycin formation. Synthesis and DNA binding study
Tetrahedron, 62 8591 - 8600 (2006)
abstract    
•  Vieceli, J.; Roeselova, M. ; Potter, N. et al
Molecular dynamics simulations of atmospheric oxidants at the air-water interface: Solvation and accommodation of OH and O3.
Journal of Physical Chemistry B, 109 [33] 15876 - 15892 (2005)
abstract    
•  Vrbka, L; Jungwirth, P.
Homogeneous freezing of water starts in the subsurface.
Journal of Physical Chemistry B, 110 18126 - 18129 (2006)
abstract    
•  Vrbka, L.; Jungwirth, P.
Brine rejection from freezing salt solutions: A molecular dynamics study.
Physical Review Letters, 95 [14] 148501 (2005)
abstract    
•  Vrbka, L.; Jungwirth, P.; Bauduin, P. et al
Specific ion effects at protein surfaces: A molecular dynamics study of bovine pancreatic trypsin inhibitor and horseradish peroxidase in selected salt solutions.
Journal of Physical Chemistry B, 110 7036 - 7043 (2006)
abstract    
•  Vrbka, L.; Vondrasek, J.; Cwiklik B. J. et al
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)
abstract    
•  Wagner, T.; Gutwirth, J.; Bezdicka, P. et al
Optically induced crystallization in amorphous Ag-x(Sb0.33S0.67)(100-x) films.
Journal of Non-Crystalline Solids, 352 [6] 578 - 583 (2006)
abstract    
•  Wahab, A.; Mahiuddin, S.; Hefter, G. et al
Ultrasonic velocities, densities, viscosities, electrical conductivities, Raman spectra, and molecular dynamics simmulations of aqueous solutions of Mg(OAc)2 and Mg(NO3)2: Hofmeister effects and ion pair formation.
Journal of Physical Chemistry B, 109 [50] 24108 - 24120 (2005)
abstract    
•  Wang, X. B.; Woo, H. K.; Wang, L. S. et al
Determination of the electron affinity of the acetyloxyl radical (CH3COO) by low-temperature anion photoelectron spectroscopy and ab initio calculations.
Journal of Physical Chemistry. A, 110 5047 - 5050 (2006)
abstract    
•  Wang, X. B.; Woo, H. K.; Cwiklik, B. J. et al
First steps towards dissolution of NaSO4- by water.
Physical Chemistry Chemical Physics, 8 [36] 4294 - 4296 (2006)
abstract    
•  Winter, B.; Weber, R.; Hertel, I. V. et al
Electron binding energies of aqueous alkali and halide ions: EUV photoelectron spectroscopy of liquid solutions and combined ab initio and molecular dynamics calculations.
Journal of the American Chemical Society, 127 [19] 7203 - 7214 (2005)
abstract    
•  Winter, B.; Weber, R.; Hertel, I. V. et al
Effect of bromide on the interfacial structure of aqueous tetrabutylammonium iodide: Photoelectron spectroscopy and molecular dynamics simulations.
Chemical Physics Letters, 410 [4] 222 - 227 (2005)
abstract    
•  Winter, B.; Faubel, M.; Hertel, I. V. et al
First steps towards dissolution of NaSO4- by water.
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abstract    
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abstract    
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Decorative element