Annual Reports in Computational Chemistry

Annual Reports in Computational Chemistry

1st Edition - October 10, 2011

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  • Editor: Ralph Wheeler
  • eBook ISBN: 9780444543028
  • Paperback ISBN: 9780444538352

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Annual Reports in Computational Chemistry provides timely and critical reviews of important topics in computational chemistry as applied to all chemical disciplines. Topics covered include quantum chemistry, molecular mechanics, force fields, chemical education, and applications in academic and industrial settings. Focusing on the most recent literature and advances in the field, each article covers a specific topic of importance to computational chemists.

Key Features

  • Broad coverage of computational chemistry and up-to-date information
  • Each chapter reviews the most recent literature on a specific topic of interest to computational chemists


Researchers and students interested in computational chemistry

Table of Contents

  • Contributors

    Section 1: Bioinformatics


    Potential Landscape and Flux Framework of Nonequilibrium Biological Networks

    1. Introduction

    2. Biochemical Oscillation

    3. Stem-Cell Differentiation and Development: Arrows of Time


    Section 2: Simulation Methodologies

    Predicting Structural and Functional Properties of Membrane Proteins from Protein Sequence

    1. Topologies and 3D Structures of Integral Membrane Proteins

    2. Predicting TM Helices from Sequence

    3. Predicting Structural Features of Helical TM Proteins

    4. Predicting the Exposure Status of TM Residues

    5. Topology and Exposure Status Prediction of TMB

    6. Functional Classification of GPCRs and Membrane Transporters

    7. Outlook

    A Review of Coarse-Grained Molecular Dynamics Techniques to Access Extended Spatial and Temporal Scales in Biomolecular Simulations

    1. Introduction

    2. Energy-Based Approach to Coarse-Graining

    3. Force-Matching Approach to Coarse-Graining

    4. Mixed Resolution Dynamics

    5. Prospective Utilization

    6. Outlook and Summary

    An Overview of String-Based Path Sampling Methods

    1. Introduction

    2. Elastic Band Derived Methods

    3. Applications

    4. Conclusions and Outlook

    Constructing and Evaluating Predictive Models for Protein Biophysical Characteristics

    1. Introduction

    2. Characterizing the Error Distribution

    3. Outliers

    4. Accurate Model Parameters

    5. Conclusion

    Supplementary Data

    Section 3: Biological Modeling

    Extracting Experimental Measurables from Molecular Dynamics Simulations of Membranes

    1. Introduction

    2. Bilayer Structure

    3. Bilayer Dynamics

    4. Future Direction: Escaping the Timescale Limits of All-Atom MD


    Advances in Scalable Computational Chemistry

    1. Introduction

    2. Software Design

    3. Hartree–Fock and Density Functional Theory

    4. Gaussian Basis Set HF and DFT

    5. Plane-Wave Basis Set DFT

    6. CC Methods

    7. Perturbation Methods

    8. Electron Transfer Methods

    9. Relativistic Methods

    10. Classical MD Simulation

    11. Combined QM/MM

    12. Conclusions


    Section 4: Quantum Chemistry

    The Super Instruction Architecture

    1. Introduction

    2. Productivity for Electronic Structure Science and Engineering

    3. Productivity for Method Developers

    4. Outlook


    Section 5: Chemical Education

    Electronically Excited States in Interstellar Chemistry

    1. Introduction

    2. Theoretical Details of Coupled Cluster Excited States

    3. Excited States in the ISM: Radicals, Cations, and Anions, Oh My!

    4. Conclusions


    Computational Chemistry of Vision in Vertebrates and Invertebrates

    1. Introduction

    2. Retinal Proteins

    3. Theoretical Framework

    4. Spectral Tuning

    5. Conclusion


    A Class Project Combining Organic Chemistry, Quantum Chemistry, and Statistics

    1. Background

    2. Results and Discussion

    3. Conclusions

    Notes and Acknowledgment

Product details

  • No. of pages: 288
  • Language: English
  • Copyright: © Elsevier 2011
  • Published: October 10, 2011
  • Imprint: Elsevier
  • eBook ISBN: 9780444543028
  • Paperback ISBN: 9780444538352

About the Editor

Ralph Wheeler

Affiliations and Expertise

Department of Chemistry & Biochemistry, Duquesne University, Pittsburgh, PA, USA

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