Multi-scale Quantum Models for Biocatalysis

Modern Techniques and Applications

  • Darrin M. York
  • Tai-Sung Lee

Part of the Challenges and Advances in Computational Chemistry and Physics book series (COCH, volume 7)

Table of contents

  1. Front Matter
    Pages I-XIV
  2. Overview of Methodologies

    1. Front Matter
      Pages 1-1
    2. Gustavo M. Seabra, Jason Swails, Adrian E. Roitberg
      Pages 3-20
    3. Marcus Lundberg, and Keiji Morokuma
      Pages 21-55
    4. Kin-Yiu Wong, Lingchun Song, Wangshen Xie, Dan T. Major, Yen-Lin Lin, Alessandro Cembran et al.
      Pages 79-101
  3. Fast Quantum Models with Empirical Treatments

    1. Front Matter
      Pages 103-103
    2. G.A. Cisneros, T.A. Darden, N. Gresh, J. Pilmé, P. Reinhardt, O. Parisel et al.
      Pages 137-172
    3. Pedro E.M. Lopes, Edward Harder, Benoît Roux, Alexander D. Mackerell Jr
      Pages 219-257
  4. Biocatalysis Applications

    1. Front Matter
      Pages 259-259
    2. Kurt A. Kistler, Spiridoula Matsika
      Pages 285-339
    3. Tai-Sung Lee, George M. Giambaşu, Adam Moser, Kwangho Nam, Carlos Silva-Lopez, Francesca Guerra et al.
      Pages 377-408
  5. Back Matter
    Pages 409-420

About this book

Introduction

Multi-scale Quantum Models for Biocatalysis: Modern Techniques and Applications explores various molecular modelling techniques and their applications in providing an understanding of the detailed mechanisms at play during biocatalysis in enzyme and ribozyme systems. These areas are reviewed by an international team of experts in theoretical, computational chemistry, and biophysics.

This book has three sections that group together different aspects of multi-scale quantum simulations. The first section consists of four chapters that describe strategies for multi-scale quantum models and present an overview of the current state-of-the-art molecular modelling methodologies most relevant to handling these complex systems with quantum mechanics and molecular simulation. With five chapters, the second section mainly focuses on the current efforts to improve the accuracy of quantum calculations using simplified empirical model forms. The last section consists of five chapters focused on the applications of important biological systems using multi-scale quantum models. This book presents detailed reviews concerning the development of various techniques, including ab initio molecular dynamics, density functional theory, combined QM/MM methods, solvation models, force field methods, and free-energy estimation techniques, as well as successful applications of multi-scale methods in the biocatalysis systems including several protein enzymes and ribozymes.

Multi-scale Quantum Models for Biocatalysis: Modern Techniques and Applications is an excellent source of information for research professionals involved in computational chemistry and physics, material science, nanotechnology, rational drug design and molecular biology. It is also likely to be of interest to graduate and undergraduate students exposed to these research areas.

Keywords

Biocatalysis Free Energy Methods Linear Scaling Techniques Path Integrals Polarizable Force Fields Potential QM/MM methods Solvent Boundries abinitio MD catalysis nanotechnology

Editors and affiliations

  • Darrin M. York
    • 1
  • Tai-Sung Lee
    • 1
  1. 1.Dept. ChemistryUniversity of MinnesotaMinneapolisUSA

Bibliographic information

  • DOI https://doi.org/10.1007/978-1-4020-9956-4
  • Copyright Information Springer Netherlands 2009
  • Publisher Name Springer, Dordrecht
  • eBook Packages Chemistry and Materials Science
  • Print ISBN 978-1-4020-9955-7
  • Online ISBN 978-1-4020-9956-4
  • About this book