Volume 13, Issue 6-7

Search all Journal of Molecular Modeling articles

July 2007

International conference and workshop: Modeling and Design of Molecular Materials, 10-15 September 2006, Wrocław, Poland

Issue Editors:

W. Andrzej Sokalski,
Jaroslav V. Burda,
Jerzy Leszczynski,
Jaroslav V. Burda

26 articles in this issue

International conference and workshop: Modeling and Design of Molecular Materials (10–15 September 2006, Wrocław, Poland)
W. Andrzej Sokalski
Jaroslav V. Burda
Jerzy Leszczyński
Editorial 24 May 2007 Pages: 629 - 630
Interaction energies in non-covalently bound intermolecular complexes derived using the subsystem formulation of density functional theory
Marcin Dułak
Tomasz A. Wesołowski
Original Paper 13 March 2007 Pages: 631 - 642
Halogen bonding and the design of new materials: organic bromides, chlorides and perhaps even fluorides as donors
Peter Politzer
Jane S. Murray
Monica C. Concha
Original Paper 15 March 2007 Pages: 643 - 650
The field theoretical study of chemical interaction in terms of the Rigged QED: new reactivity indices
Paweł Szarek
Akitomo Tachibana
Original Paper 30 May 2007 Pages: 651 - 663
Localization of ligand binding site in proteins identified in silico
Michal Brylinski
Marek Kochanczyk
Irena Roterman
Original Paper 30 March 2007 Pages: 665 - 675
The molecular basis of urokinase inhibition: from the nonempirical analysis of intermolecular interactions to the prediction of binding affinity
Renata Grzywa
Edyta Dyguda-Kazimierowicz
Józef Oleksyszyn
Original Paper 20 March 2007 Pages: 677 - 683
A molecular modeling study on the enantioselectivity of aryl alkyl ketone reductions by a NADPH-dependent carbonyl reductase
Thomas R. Cundari
Adriana Dinescu
Ling Hua
Original Paper 06 February 2007 Pages: 685 - 690
Hierarchical modeling of protein interactions
Mateusz Kurcinski
Andrzej Kolinski
Original Paper 13 February 2007 Pages: 691 - 698
Ion conductance vs. pore gating and selectivity in KcsA channel: Modeling achievements and perspectives
Céline Boiteux
Sebastian Kraszewski
Claude Girardet
Original Paper 06 April 2007 Pages: 699 - 713
Locally enhanced sampling molecular dynamics study of the dioxygen transport in human cytoglobin
Slawomir Orlowski
Wieslaw Nowak
Original Paper 15 May 2007 Pages: 715 - 723
Insights into catalytic activity of industrial enzyme Co-nitrile hydratase. Docking studies of nitriles and amides
Lukasz Peplowski
Karina Kubiak
Wieslaw Nowak
Original Paper 27 February 2007 Pages: 725 - 730
Modeling the adsorption of aromatic compounds on the TiO₂/SiO₂ catalyst
Bartłomiej Szyja
Krzysztof Brodzik
Original Paper 06 March 2007 Pages: 731 - 737
Theoretical analysis of the effects of guanine oxidative damage on the properties of B-DNA telomere fragments
Piotr Cysewski
Przemysław Czeleń
Original Paper 06 March 2007 Pages: 739 - 750
Development of realistic models for Double Metal Cyanide catalyst active sites
Jacek C. Wojdeł
Stefan T. Bromley
Jacobus C. Jansen
Original Paper 13 June 2007 Pages: 751 - 756
Orbital landscapes for reductive 2e⁻ activation of dihydrogen molecule
Wojciech Grochala
Original Paper 23 March 2007 Pages: 757 - 767
Towards superconductivity in hydrides: computational studies of two hypothetical ternary compounds, \( {\text{Yb}}^{{{\text{II}}}} {\text{BeH}}_{4} \) and \( {\text{Cs}}_{3} {\text{Yb}}^{{{\text{III}}}} {\text{H}}_{6} \)
Tomasz Jaroń
Wojciech Grochala
Roald Hoffmann
Original Paper 08 March 2007 Pages: 769 - 774
Vibrational analysis of a solvated green fluorescent protein chromophore
Tadeusz Andruniów
Original Paper 23 March 2007 Pages: 775 - 783
Experimental and theoretical investigations of spectroscopic properties of azobenzene derivatives in solution
Robert Zaleśny
Katarzyna Matczyszyn
Piotr Cysewski
Original Paper 17 April 2007 Pages: 785 - 791
Theoretical study of geometrical and nonlinear optical properties of pyridinum N-phenolate betaine dyes
Wawrzyniec Niewodniczański
Wojciech Bartkowiak
Original Paper 20 April 2007 Pages: 793 - 800
Accurate gas phase acidities of carboxylic acids estimated by scaling the vibrational contribution of ab initio gibbs free energies
Piotr Cysewski
Original Paper 03 April 2007 Pages: 801 - 808
Proton transfer in some periodic molecular systems
Henryk Chojnacki
Original Paper 04 May 2007 Pages: 809 - 812
Modeling of isotopomeric cluster of the molecular ion
Andrzej J. Gorączko
Original Paper 09 May 2007 Pages: 813 - 821
Computational prediction of the regio- and diastereoselectivity in a rhodium-catalyzed hydroformylation/cyclization domino process
Giuliano Alagona
Caterina Ghio
Silvia Rocchiccioli
Original Paper 22 May 2007 Pages: 823 - 837
Non-empirical study of the phosphorylation reaction catalyzed by 4-methyl-5-β-hydroxyethylthiazole kinase: relevance of the theory of intermolecular interactions
Edyta Dyguda-Kazimierowicz
W. Andrzej Sokalski
Jerzy Leszczyński
Original Paper 24 March 2007 Pages: 839 - 849
Oxidation mechanism in the metabolism of (S)-N-[1-(3-morpholin-4-ylphenyl)ethyl]-3-phenylacrylamide on oxyferryl active site in CYP3A4 Cytochrome: DFT modeling
Abdul Rajjak Shaikh
Ewa Broclawik
Akira Miyamoto
Original Paper 27 March 2007 Pages: 851 - 860
Interaction of copper organometallic precursors with barrier layers of Ti, Ta and W and their nitrides: a first-principles molecular dynamics study
Eduardo Machado
Marcin Kaczmarski
Hansong Cheng
Original Paper 09 March 2007 Pages: 861 - 864

Volume 13, Issue 6-7

International conference and workshop: Modeling and Design of Molecular Materials (10–15 September 2006, Wrocław, Poland)

Interaction energies in non-covalently bound intermolecular complexes derived using the subsystem formulation of density functional theory

Halogen bonding and the design of new materials: organic bromides, chlorides and perhaps even fluorides as donors

The field theoretical study of chemical interaction in terms of the Rigged QED: new reactivity indices

Localization of ligand binding site in proteins identified in silico

The molecular basis of urokinase inhibition: from the nonempirical analysis of intermolecular interactions to the prediction of binding affinity

A molecular modeling study on the enantioselectivity of aryl alkyl ketone reductions by a NADPH-dependent carbonyl reductase

Hierarchical modeling of protein interactions

Ion conductance vs. pore gating and selectivity in KcsA channel: Modeling achievements and perspectives

Locally enhanced sampling molecular dynamics study of the dioxygen transport in human cytoglobin

Insights into catalytic activity of industrial enzyme Co-nitrile hydratase. Docking studies of nitriles and amides

Modeling the adsorption of aromatic compounds on the TiO₂/SiO₂ catalyst

Theoretical analysis of the effects of guanine oxidative damage on the properties of B-DNA telomere fragments

Development of realistic models for Double Metal Cyanide catalyst active sites

Orbital landscapes for reductive 2e⁻ activation of dihydrogen molecule

Towards superconductivity in hydrides: computational studies of two hypothetical ternary compounds, \( {\text{Yb}}^{{{\text{II}}}} {\text{BeH}}_{4} \) and \( {\text{Cs}}_{3} {\text{Yb}}^{{{\text{III}}}} {\text{H}}_{6} \)

Vibrational analysis of a solvated green fluorescent protein chromophore

Experimental and theoretical investigations of spectroscopic properties of azobenzene derivatives in solution

Theoretical study of geometrical and nonlinear optical properties of pyridinum N-phenolate betaine dyes

Accurate gas phase acidities of carboxylic acids estimated by scaling the vibrational contribution of ab initio gibbs free energies

Proton transfer in some periodic molecular systems

Modeling of isotopomeric cluster of the molecular ion

Computational prediction of the regio- and diastereoselectivity in a rhodium-catalyzed hydroformylation/cyclization domino process

Non-empirical study of the phosphorylation reaction catalyzed by 4-methyl-5-β-hydroxyethylthiazole kinase: relevance of the theory of intermolecular interactions

Oxidation mechanism in the metabolism of (S)-N-[1-(3-morpholin-4-ylphenyl)ethyl]-3-phenylacrylamide on oxyferryl active site in CYP3A4 Cytochrome: DFT modeling

Interaction of copper organometallic precursors with barrier layers of Ti, Ta and W and their nitrides: a first-principles molecular dynamics study

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