Royal Society of Chemistry Chemical Modelling: Applications and Theory Volume 5 (Specialist Periodical Reports - Chemical Modelling)

"Chemical Modelling: Applications and Theory" comprises critical literature reviews of molecular modelling, both theoretical and applied. Molecular modelling in this context refers to modelling the structure, properties and reactions of atoms, molecules & materials. Each chapter is compiled by experts in their fields and provides a selective review of recent literature, incorporating sufficient historical perspective for the non-specialist to gain an understanding. From the Back Cover Chemical Modelling: Applications and Theory comprises critical literature reviews of molecular modelling, both theoretical and applied. Molecular modelling in this context refers to modelling the structure, properties and reactions of atoms, molecules & materials. Each chapter is compiled by experts in their fields and provides a selective review of recent literature, incorporating sufficient historical perspective for the non-specialist to gain an understanding. Excerpt. © Reprinted by permission. All rights reserved. Chemical Modelling Applications and Theory Volume 5 A Review of the Literature Published Between June 2005 and May 2007 By A. Hinchliffe The Royal Society of Chemistry Copyright © 2008 The Royal Society of Chemistry All rights reserved. ISBN: 978-0-85404-248-7 Contents Preface Alan Hinchliffe, 7, Multiscale modelling of biological systems Christopher J. Woods and Adrian J. Mulholland, 13, Computer-aided drug design 2005–2007 Richard A. Lewis, 51, Solvation effects Michael Springborg, 67, The solid state E. A. Moore, 119, Density functional theory studies of alloys in heterogeneous catalysis John R. Kitchin, Spencer D. Miller and David S. Sholl, 50, Fluctuation relations, free energy calculations and irreversibility Debra J. Searles and Denis J. Evans, 182, Many-body perturbation theory and its application to the molecular tructure problem S. Wilson, 208, Experiment and theory in the determination of molecular hyperpolarizabilities in solution; pNA and MNA in dioxane David Pugh, 249, The floating spherical Gaussian orbital (FSGO) method A. H. Pakiari, 279, Advances in valence bond theory Peter B. Karadakov, 312, Numerical methods in chemistry T. E. Simos, 350, CHAPTER 1 Multiscale modelling of biological systems Christopher J. Woods and Adrian J. Mulholland DOI:10.1039/b608778g 1. Introduction At what point does a collection of molecules become a biomolecular system? At what length scale does biology begin, and chemistry end? Biological phenomena involve the flow of information across a range of length and timescales. For example, a cell may be placed under physical stress at the macroscopic level, which causes an increase in pressure within its protective membrane. This pressure has the effect of opening or closing mechanosensitive ion channels, thereby changing the flow of individual ions into the cell. This changes the ionic concentration within the cell, which then acts as the trigger for a signal sent via a protein signalling pathway. A chemist would look at this as a molecular system that was capable of converting mechanical forces into electrical signals. A biologist would however look at this as the mechanism a cell uses to adapt to stress, and thereby stay alive. Biology is full of such examples. Every thought we have involves the passage of signals between neurons, which itself requires the conversion of electrical signals into flows of ions. These ions trigger the release of neurotransmitter molecules, which cross the synaptic gap between neurons, and bind to individual receptor proteins at the synapse. This causes a change in protein conformation, which open nearby ion channels, causing ions to rush in or out of the neuron, thereby continuing the signal. Information is constantly flowing between the macroscopic world and the atomic, chemical world. Indeed it is this interplay between the chemical and macroscopic worlds that is a real beauty of biology, and it