MOLECULAR INTERACTIONS Edited by Aurelia Meghea Molecular Interactions Edited by Aurelia Meghea Published by InTech Janeza Trdine 9, 51000 Rijeka, Croatia Copyright © 2012 InTech All chapters are Open Access distributed under the Creative Commons Attribution 3.0 license, which allows users to download, copy and build upon published articles even for commercial purposes, as long as the author and publisher are properly credited, which ensures maximum dissemination and a wider impact of our publications. After this work has been published by InTech, authors have the right to republish it, in whole or part, in any publication of which they are the author, and to make other personal use of the work. Any republication, referencing or personal use of the work must explicitly identify the original source. As for readers, this license allows users to download, copy and build upon published chapters even for commercial purposes, as long as the author and publisher are properly credited, which ensures maximum dissemination and a wider impact of our publications. Notice Statements and opinions expressed in the chapters are these of the individual contributors and not necessarily those of the editors or publisher. No responsibility is accepted for the accuracy of information contained in the published chapters. The publisher assumes no responsibility for any damage or injury to persons or property arising out of the use of any materials, instructions, methods or ideas contained in the book. Publishing Process Manager Daria Nahtigal Technical Editor Teodora Smiljanic Cover Designer InTech Design Team First published February, 2012 Printed in Croatia A free online edition of this book is available at www.intechopen.com Additional hard copies can be obtained from [email protected] Molecular Interactions, Edited by Aurelia Meghea p. cm. ISBN 978-953-51-0079-9 Contents Preface IX Part 1 Physico-Chemical Aspects of Molecular Interactions 1 Chapter 1 Modeling of Volumetric Properties of Organic Mixtures Based on Molecular Interactions 3 Mirjana Lj. Kijevčanin, Bojan D. Djordjević, Ivona R. Radović, Emila M. Živković, Aleksandar Ž. Tasić and Slobodan P. Šerbanović Chapter 2 Molecular Interactions in Chromatographic Retention: A Tool for QSRR/QSPR/QSAR Studies 25 Vilma Edite Fonseca Heinzen, Berenice da Silva Junkes, Carlos Alberto Kuhnen and Rosendo Augusto Yunes Chapter 3 Molecular Interactions of Some Free Base Porphyrins with - and -Acceptor Molecules 49 Abedien Zabardasti Part 2 Interactions at Interfaces, Molecular Design and Nano-Engineering of Multifunctional Materials 79 Chapter 4 Molecular Interactions at Interfaces 81 Raj Kumar Gupta and V. Manjuladevi Chapter 5 Impacts of Surface Functionalization on the Electrocatalytic Activity of Noble Metals and Nanoparticles 105 Zhi-you Zhou and Shaowei Chen Chapter 6 Cantilever – Based Optical Interfacial Force Microscopy 125 Byung I. Kim VI Contents Chapter 7 Molecular Interactions in Natural and Synthetic Self-Assembly Systems 145 Liane Gloria Raluca Stan, Rodica Mirela Nita and Aurelia Meghea Chapter 8 Nano-Engineering of Molecular Interactions in Organic Electro-Optic Materials 183 Stephanie J. Benight, Bruce H. Robinson and Larry R. Dalton Part 3 Molecular Interactions Applied in Biology and Medicine 209 Chapter 9 DNA-DNA Recognition: From Tight Contact to Fatal Attraction 211 Youri Timsit Chapter 10 In Vivo Bacterial Morphogenetic Protein Interactions 229 René van der Ploeg and Tanneke den Blaauwen Chapter 11 Towards an In Silico Approach to Personalized Pharmacokinetics 263 Akihiko Konagaya Chapter 12 New Aspect of Bone Morphogenetic Protein Signaling and Its Relationship with Wnt Signaling in Bone 283 Nobuhiro Kamiya Part 4 Molecular Dynamics Simulations 333 Chapter 13 Molecular Dynamics Simulations of Proton Transport in Proton Exchange Membranes Based on Acid-Base Complexes 335 Liuming Yan and Liqing Xie Chapter 14 General Index and Its Application in MD Simulations 361 Guangcai Zhang, Aiguo Xu and Guo Lu Preface After discovery of the electronic structure of atoms and molecules, the first part of the XXth century has been dominated by quantum chemistry of valence bonds, mainly dealing with interatomic interactions within molecules, without paying much interest on weak intermolecular interactions. Following progress in molecular biology and biophysical chemistry, a series of properties of complex molecules, such as denaturation of proteins with their secondary, tertiary and quaternary structures or double and triple helix structures of DNA and collagen could not be explained simply based on strong interactions within molecules. In this context, a huge step forward has been registered at the end of the past century with the developments in nanosciences and nanotechnologies, when the variety of structures actually is the result of weak ordering because of noncovalent interactions. For self-assembly to be possible in soft materials, it is evident that forces between molecules must be much weaker than covalent bonds between the atoms of a molecule. The weak intermolecular interactions responsible for molecular ordering in soft materials include hydrogen bonds, coordination bonds in ligands and complexes, ionic and dipolar interactions, van der Waals forces, and hydrophobic interactions. Due to relatively weak interactions between molecules, transitions between structures can be readily driven by minor changes in physical-chemical conditions, like temperature, pH, solvents, etc. Such external parameters that induce phase transitions could lead to responsive materials, or coupled with an appropriate source of energy to mechanical systems. All these evolutions provide strong arguments to support the opportunity and importance of the topics approached in this book, the fundamental and applicative aspects related to molecular interactions being of large interest in both academic and innovative environments. In this context, the authors participating to the book chapters are well experienced experts in various interdisciplinary research domains, bringing own original contributions beyond state of the arts in the fields of interest. Thus, the first chapter is an introductory insight into thermodynamics of mixing of various organic solvents with alkanediols, and the deviations from ideality of binary systems are interpreted in detail based on specific molecular interactions between components. The second chapter deals with molecular interactions involved in chromatographic retention, X Preface while the chapter 3 presents spectral characteristics of some free base porphyrins with σ- and π- acceptor molecules, with special reference to electronic and NMR spectra. Chapter 4 is an illustration on how molecular principles are applied to discover and design new bio-inspired and bio-hybrid materials, by doing a parallel between natural and synthetic self-assembly systems. Chapters 5 and 6 are focused on molecular interactions at interfaces, namely the effect of amphiphilicity on Langmuir monolayers and, respectively, the impact of surface functionalization on electrolytic activity of noble metals and nanoparticles. The chapters 7 and 8 reveal applicative dimension of intermolecular interactions, one in cantilever based optical interfacial microscopy and the other for nano-engineering of molecular interactions in organic electro-optic materials. The next four chapters are devoted to applications in molecular biology and medicine. In this respect, chapter 9 is a deeper insight in approaching higher order DNA structures involved in genetic functions at cellular level. Chapter 10 develops non- invasive techniques widely used to study protein-protein interactions, chapter 11 is an in silico approach to personalized pharmacokinetics, while chapter 12 presents new aspects in signaling bone morphogenetic proteins. The last three chapters are dealing with recent theoretical aspects on atomic and molecular interactions. In this context in chapter 13 the density functional theory calculations and molecular dynamics simulations are applied to study the hydrogen bonding characteristics of acid-base complexes involving multifunctional molecules and formation of hydrogen-bond network. This approach has strong applicative potential in designing and optimizing proton exchange membrane characteristics used in fuel cells as promising energy conversion devices. Starting from similar premises furnished by density functional theory, a stochastic quenching method is developed in chapter 14 to describe the most random amorphous structures of various materials including metals and alloys. Chapter 15 closes this theoretical approach by using a general index combined with space hierarchy tree algorith applied in molecular dynamics simulations to explain connections between microscopic structures of materials and corresponding changes in macroscopic properties of materials under the influence of various external conditions. Finally, we express our sincere thanks to all our authors for their dedicated work and special contributions to complete the book in the desired shape. We expect this book to have a strong impact at various education and research training levels, for MSc and PhD students, for young and experienced researchers from both academia and industry. Aurelia Meghea University Politehnica of Bucharest, Romania