Quantum Biochemistry

Copyright © 2010 Wiley-VCH Verlag GmbH & Co. KGaA

Quantum Biochemistry

Editor(s): Chérif F. Matta

Published Online: 25 JUN 2010

Print ISBN: 9783527323227

Online ISBN: 9783527629213

DOI: 10.1002/9783527629213

About this Book

Product Information

About The Product

Divided into five major parts, the two volumes of this ready reference cover the tailoring of theoretical methods for biochemical computations, as well as the many kinds of biomolecules, reaction and transition state elucidation, conformational flexibility determination, and drug design. Throughout, the chapters gradually build up from introductory level to comprehensive reviews of the latest research, and include all important compound classes, such as DNA, RNA, enzymes, vitamins, and heterocyclic compounds.
The result is in-depth and vital knowledge for both readers already working in the field as well as those entering it. Includes contributions by Prof. Ada Yonath (Nobel Prize in Chemistry 2009) and Prof. Jerome Karle (Nobel Prize in Chemistry 1985).

Table of contents

    1. You have free access to this content
      Front Matter (pages I–LVIII)

  2. Part One: Novel Theoretical, Computational, and Experimental Methods and Techniques

    1. Chapter 1

      Quantum Kernels and Quantum Crystallography: Applications in Biochemistry (pages 1–60)

      Lulu Huang, Lou Massa and Jerome Karle

    2. Chapter 2

      Getting the Most out of ONIOM: Guidelines and Pitfalls (pages 61–83)

      Fernando R. Clemente, Thom Vreven and Michael J. Frisch

    3. Chapter 3

      Modeling Enzymatic Reactions in Metalloenzymes and Photobiology by Quantum Mechanics (QM) and Quantum Mechanics/Molecular Mechanics (QM/MM) Calculations (pages 85–130)

      Lung Wa Chung, Xin Li and Keiji Morokuma

    4. Chapter 4

      From Molecular Electrostatic Potentials to Solvation Models and Ending with Biomolecular Photophysical Processes (pages 131–170)

      Jacopo Tomasi, Chiara Cappelli, Benedetta Mennucci and Roberto Cammi

    5. Chapter 5

      The Fast Marching Method for Determining Chemical Reaction Mechanisms in Complex Systems (pages 171–195)

      Yuli Liu, Steven K. Burger, Bijoy K. Dey, Utpal Sarkar, Marek R. Janicki and Paul W. Ayers

  3. Part Two: Nucleic Acids, Amino Acids, Peptides and Their Interactions

    1. Chapter 6

      Chemical Origin of Life: How do Five HCN Molecules Combine to form Adenine under Prebiotic and Interstellar Conditions (pages 197–217)

      Debjani Roy and Paul von Ragué Schleyer

    2. Chapter 7

      Hydrogen Bonding and Proton Transfer in ionized DNA Base Pairs, Amino Acids and Peptides (pages 219–243)

      Luis Rodríguez-Santiago, Marc Noguera, Joan Bertran and Mariona Sodupe

    3. Chapter 8

      To Nano-Biochemistry: Picture of the Interactions of DNA with Gold (pages 245–306)

      Eugene S. Kryachko

    4. Chapter 9

      Quantum Mechanical Studies of Noncovalent DNA–Protein Interactions (pages 307–336)

      Lesley R. Rutledge and Stacey D. Wetmore

    5. Chapter 10

      The Virial Field and Transferability in DNA Base-Pairing (pages 337–364)

      Richard F. W. Bader and Fernando Cortés-Guzmán

    6. Chapter 11

      An Electron Density-Based Approach to the Origin of Stacking Interactions (pages 365–387)

      Ricardo A. Mosquera, María J. González Moa, Laura Estévez, Marcos Mandado and Ana M. Graña

    7. Chapter 12

      Polarizabilities of Amino Acids: Additive Models and Ab Initio Calculations (pages 389–402)

      Noureddin El-Bakali Kassimi and Ajit J. Thakkar

    8. Chapter 13

      Methods in Biocomputational Chemistry: A Lesson from the Amino Acids (pages 403–421)

      Hugo J. Bohórquez, Constanza Cárdenas, Prof. Chérif F. Matta, Russell J. Boyd and Manuel E. Patarroyo

    9. Chapter 14

      From Atoms in Amino Acids to the Genetic Code and Protein Stability, and Backwards (pages 423–472)

      Prof. Chérif F. Matta

    10. Chapter 15

      Energy Richness of ATP in Terms of Atomic Energies: A First Step (pages 473–498)

      Prof. Chérif F. Matta and Alya A. Arabi

  4. Part Three: Reactivity, Enzyme Catalysis, Biochemical Reaction Paths and Mechanisms

    1. Chapter 16

      Quantum Transition State for Peptide Bond Formation in the Ribosome (pages 499–515)

      Lou Massa, Prof. Chérif F. Matta, Ada Yonath and Jerome Karle

    2. Chapter 17

      Hybrid QM/MM Simulations of Enzyme-Catalyzed DNA Repair Reactions (pages 517–535)

      Denis Bucher, Fanny Masson, J. Samuel Arey and Ursula Röthlisberger

    3. Chapter 18

      Computational Electronic Structure of Spin-Coupled Diiron-Oxo Proteins (pages 537–549)

      Jorge H. Rodriguez

    4. Chapter 19

      Accurate Description of Spin States and its Implications for Catalysis (pages 551–583)

      Marcel Swart, Mireia Güell and Miquel Solà

    5. Chapter 20

      Quantum Mechanical Approaches to Selenium Biochemistry (pages 585–603)

      Jason K. Pearson and Russell J. Boyd

    6. Chapter 21

      Catalytic Mechanism of Metallo β-Lactamases: Insights from Calculations and Experiments (pages 605–622)

      Matteo Dal Peraro, Alejandro J. Vila and Paolo Carloni

    7. Chapter 22

      Computational Simulation of the Terminal Biogenesis of Sesquiterpenes: The Case of 8-Epiconfertin (pages 623–642)

      José Enrique Barquera-Lozada and Gabriel Cuevas

    8. Chapter 23

      Mechanistics of Enzyme Catalysis: From Small to Large Active-Site Models (pages 643–666)

      Jorge Llano and James W. Gauld

  5. Part Four: From Quantum Biochemistry to Quantum Pharmacology, Therapeutics, and Drug Design

    1. Chapter 24

      Developing Quantum Topological Molecular Similarity (QTMS) (pages 667–691)

      Paul L. A. Popelier

    2. Chapter 25

      Quantum-Chemical Descriptors in QSAR/QSPR Modeling: Achievements, Perspectives and Trends (pages 693–721)

      Anna V. Gubskaya

    3. Chapter 26

      Platinum Complexes as Anti-Cancer Drugs: Modeling of Structure, Activation and Function (pages 723–742)

      Konstantinos Gkionis, Mark Hicks, Arturo Robertazzi, J. Grant Hill and James A. Platts

    4. Chapter 27

      Protein Misfolding: The Quantum Biochemical Search for a Solution to Alzheimer's Disease (pages 743–755)

      Donald F. Weaver

    5. Chapter 28

      Targeting Butyrylcholinesterase for Alzheimer's Disease Therapy (pages 757–780)

      Katherine V. Darvesh, Ian R. Pottie, Robert S. McDonald, Earl Martin and Sultan Darvesh

    6. Chapter 29

      Reduction Potentials of Peptide-Bound Copper (II) – Relevance for Alzheimer's Disease and Prion Diseases (pages 781–804)

      Arvi Rauk

    7. Chapter 30

      Theoretical Investigation of NSAID Photodegradation Mechanisms (pages 805–834)

      Klefah A. K. Musa and Leif A. Eriksson

  6. Part Five: Biochemical Signature of Quantum Indeterminism

    1. Chapter 31

      Quantum Indeterminism, Mutation, Natural Selection, and the Meaning of Life (pages 835–871)

      David N. Stamos

    2. Chapter 32

      Molecular Orbitals: Dispositions or Predictive Structures? (pages 873–895)

      Jean-Pierre Llored and Michel Bitbol

    1. You have free access to this content
      Index (pages 897–920)

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