Molecular Interactions

382 Pages·2012·28.211 MB·English

by  A. Meghea

MOLECULAR
INTERACTIONS

Edited by Aurelia Meghea
Molecular Interactions
Edited by Aurelia Meghea

Published by InTech
Janeza Trdine 9, 51000 Rijeka, Croatia

Copyright © 2012 InTech
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Technical Editor Teodora Smiljanic
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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