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This work covers advances in the interactions of proteins with their solvent environment and provides fundamental physical information useful for the application of proteins in biotechnology and industrial processes. It discusses in detail structure, dynamic and thermodynamic aspects of protein hydration, as well as proteins in aqueous and organic solvents as they relate to protein function, stability and folding.
Accomplishments from this work contribute toward a better understanding of solvation and solvent-mediated interactions in complicated molecular systems and will have broad impacts on both fundamental research and engineering applications.
Innovative and forward-looking, this volume focuses on recent achievements in this rapidly progressing field and looks at future potential for development. The first part provides a basic understanding of the factors governing protein-ligand interactions, followed by a comparison of key experimental methods (calorimetry, surface plasmon resonance, NMR) used in generating interaction data. The second half of the book is devoted to insilico methods of modeling and predicting molecular recognition and binding, ranging from first principles-based to approximate ones. Here, as elsewhere in the book, emphasis is placed on novel approaches and recent improvements to established methods. The final part looks at unresolved challenges, and the strategies to address them. With the content relevant for all drug classes and therapeutic fields, this is an inspiring and often-consulted guide to the complexity of protein-ligand interaction modeling and analysis for both novices and experts.
In the second part of my thesis I will focus on the influence of aqueous solvent on protein structures. Water is present in all biological systems, where it is not only a static medium of the reaction, but also an active part of the process called life, and it requires careful treatment. I compare models of implicit and explicit solvation for beta-turns, alpha-helices, and beta-sheets. I find that solvation by small water clusters can alter the molecular properties of gas phase molecules and continuous methods are not able to model all effects.
"Chemists familiar with conventional quantum mechanics will applaud and benefit greatly from this particularly instructive, thorough and clearly written exposition of density functional theory: its basis, concepts, terms, implementation, and performance in diverse applications. Users of DFT for structure, energy, and molecular property computations, as well as reaction mechanism studies, are guided to the optimum choices of the most effective methods. Well done!" Paul von Rague Schleyer "A conspicuous hole in the computational chemist's library is nicely filled by this book, which provides a wide-ranging and pragmatic view of the subject.[...It] should justifiably become the favorite text on the subject for practioneers who aim to use DFT to solve chemical problems." J. F. Stanton, J. Am. Chem. Soc. "The authors' aim is to guide the chemist through basic theoretical and related technical aspects of DFT at an easy-to-understand theoretical level. They succeed admirably." P. C. H. Mitchell, Appl. Organomet. Chem. "The authors have done an excellent service to the chemical community. [...] A Chemist's Guide to Density Functional Theory is exactly what the title suggests. It should be an invaluable source of insight and knowledge for many chemists using DFT approaches to solve chemical problems." M. Kaupp, Angew. Chem.
In September 2002, a NATO-ASI was held in Cetraro (CS), Italy on the theme of "Metal-Ligand Interactions in Molecular-, Nano-, Micro-, and Macro-systems in Complex Environments". This event has followed the previous ones held in the same place in 1991, 1994 and 1998. In the present and the previous schools a broad interdisciplinary cross-section of experimental and theoretical researchers, interested in a better understanding of metal-ligand interactions from different viewpoints, was linked together to exchange experience, to review the state-of-the-art, to indicate new techniques and methods, to explore new fields and perspectives. Particular emphasis was given to the problems related with the crossing from molecular systems to nano-, macro-and micro-scale materials and to the effects of the environment on the properties of the molecular systems. The school was organized around lectures and special research seminares given by leading experts in the following fields: • metal clusters • inorganic complexes and materials • surface phenomena • adsorption and catalysis • organic and bio-inorganic systems • ab initio theory • density functional theory • classical and quantum dynamics This volume contains the formal lectures and selected contributed papers and describes the main aspects and problems tackled during the 12 days of the event.
Reviewing statistical mechanics concepts for analysis of macromolecular structure formation processes, for graduate students and researchers in physics and biology.
Chemical modelling covers a wide range of disciplines, and this book is the first stop for any chemist, materials scientist, biochemist, or molecular physicist wishing to acquaint themselves with major developments in the applications and theory of chemical modelling. Containing both comprehensive and critical reviews, it is a convenient reference to the current literature. Coverage includes, but is not limited to, considerations towards rigorous foundations for the natural-orbital representation of molecular electronic transitions, quantum and classical embedding schemes for optical properties, machine learning for excited states, ultrafast and wave function-based electron dynamics, and attosecond chemistry.
Molecular Theory of Solvation presents the recent progress in the statistical mechanics of molecular liquids applied to the most intriguing problems in chemistry today, including chemical reactions, conformational stability of biomolecules, ion hydration, and electrode-solution interface. The continuum model of "solvation" has played a dominant role in describing chemical processes in solution during the last century. This book discards and replaces it completely with molecular theory taking proper account of chemical specificity of solvent. The main machinery employed here is the reference-interaction-site-model (RISM) theory, which is combined with other tools in theoretical chemistry and physics: the ab initio and density functional theories in quantum chemistry, the generalized Langevin theory, and the molecular simulation techniques. This book will be of benefit to graduate students and industrial scientists who are struggling to find a better way of accounting and/or predicting "solvation" properties.