Molecular Materials with Specific Interactions - Modeling and Design Book

Preface xv

1 Theory of Intermolecular Forces: An Introductory Account Robert Moszynski 1

2 Hohenberg-Kohn-Sham Density Functional Theory Tomasz A. Wesolowski 153

3 Selected Microscopic and Mezoscopic Modelling Tools and Models - An Overview Magdalena Gruziel Piotr Kmiec Joanna Trylska Bogdan Lesyng 203

4 Modeling Chemical Reactions with First-Principle Molecular Dynamics Artur Michalak Tom Ziegler 225

5 Computational Enzymology: Insights into Enzyme Mechanism and Catalysis from Modelling Adrian J. Mulholland Ian M. Grant 275

6 Computational Determination of The Relative Free Energy of Binding - Application to Alanine Scanning Mutagenesis Irina S. Moreira Pedro A. Fernandes Maria J. Ramos 305

7 Substrate-Enzyme Interactions From Modeling and Isotope Effects Renata A. Kwiecien Andrzej Lewandowicz Piotr Paneth 341

8 From Inhibitors of Lap to Inhibitors of Pal: Lessons from Molecular Modeling and Experimental Interface Lukasz Berlicki Jolanta Grembecka Edyta Dyguda-Kazimierowicz Pawel Kafarski W. Andrzej Sokalski 365

9 Theoretical Studies of the Transition States Along The Reaction Coordinates of [Nife] Hydrogenase Hiroshi Nakano Pawel Szarek Kentaro Doi Akitomo Tachibana 399

10 Bacteriorhodopsin Energy Landscape: Current Status V. Renugopalakrishnan 433

11 Dimerization and Oligomerization of Rhodopsin and Other G Protein-Coupled Receptors SLawomir Filipek Anna Modzelewska Krystiana A. Krzysko 453

12 Molecular Dynamics Simulations of Hydrogen Adsorption in Finite and Infinite Bundles of Single Walled Carbon Nanotubes Hansong Cheng Alan C. Cooper Guido P. Pez Milen K. Kostov M. Todd Knippenberg Pamela Piotrowski Steven J. Stuart 469

13 The RemarkableCapacities of (6,0) Carbon and Carbon/Boron/Nitrogen Model Nanotubes for Tansmission of Electronic Effects Peter Politzer Jane S. Murray Pat Lane Monica C. Concha 487

14 Electronic Properties and Fragmentation Dynamics of Organic Species Deposited on Silicon Surfaces Jian-Ge Zhou Frank Hagelberg 505

15 Recent Advances in Fullerene Deposition on Semiconductor Surfaces C.G. Zhou L.C. Ning J.P. Wu S.J. Yao Z.B. Pi Y.S. Jiang H. Cheng 533

16 A Quest for Efficient Methods of Disintegration of Organophosphorus Compounds: Modeling Adsorption and Decomposition Processes Andrea Michalkova Leonid Gorb Jerzy Leszczynski 565

Index 593