Multi-scale Quantum Models for Biocatalysis

Modern Techniques and Applications

Editors:

ISBN: 978-1-4020-9955-7 (Print) 978-1-4020-9956-4 (Online)

Table of contents (14 chapters)

  1. Front Matter

    Pages I-XIV

  2. Overview of Methodologies

    1. Front Matter

      Pages 1-1

    2. No Access

      Chapter

      Pages 3-20

      Mixed Quantum-Classical Calculations in Biological Systems

    3. No Access

      Chapter

      Pages 21-55

      The Oniom Method and its Applications to Enzymatic Reactions

    4. No Access

      Chapter

      Pages 57-78

      Comparison Of Reaction Barriers In Energy And Free Energy For Enzyme Catalysis

    5. No Access

      Chapter

      Pages 79-101

      Quantum Mechanical Methods for Biomolecular Simulations

  3. Fast Quantum Models with Empirical Treatments

    1. Front Matter

      Pages 103-103

    2. No Access

      Chapter

      Pages 105-136

      Towards an Accurate Semi-Empirical Molecular Orbital Treatment of Covalent and Non-Covalent Biological Interactions

    3. No Access

      Chapter

      Pages 137-172

      Design Of Next Generation Force Fields From AB Initio Computations: Beyond Point Charges Electrostatics

    4. No Access

      Chapter

      Pages 173-196

      “Multi-Scale” QM/MM Methods with Self-Consistent-Charge Density-Functional-Tight-Binding (SCC-DFTB)

    5. No Access

      Chapter

      Pages 197-218

      Coarse-Grained Intermolecular Potentials Derived From The Effective Fragment Potential: Application To Water, Benzene, And Carbon Tetrachloride

    6. No Access

      Chapter

      Pages 219-257

      Formalisms for the Explicit Inclusion of Electronic Polarizability in Molecular Modeling and Dynamics Studies

  4. Biocatalysis Applications

    1. Front Matter

      Pages 259-259

    2. No Access

      Chapter

      Pages 261-284

      Modeling Protonation Equilibria In Biological Macromolecules

    3. No Access

      Chapter

      Pages 285-339

      Quantum Mechanical Studies of the Photophysics of DNA and RNA Bases

    4. No Access

      Chapter

      Pages 341-350

      Ab Initio Quantum Mechanical/Molecular Mechanical Studies of Histone Modifying Enzymes

    5. No Access

      Chapter

      Pages 351-375

      Interpreting The Observed Substrate Selectivity And The Product Regioselectivity In Orf2-Catalyzed Prenylation From X-Ray Structures

    6. No Access

      Chapter

      Pages 377-408

      Unraveling the Mechanisms of Ribozyme Catalysis with Multiscale Simulations

  5. Back Matter

    Pages 409-420