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The Annual Reports
in Computational Chemistry

Volume 3 - Table of Contents

Contributors

Preface

Section 1: Simulation Methodologies
Section Editor: Carlos Simmerling

1.   Molecular Simulations of pH-Mediated biological Processes
      Jana Khandogin and Charles L. Brooks

1. Introduction

2. Static Structure-Based pKa Prediction Methods

3. Molecular Dynamics Coupled with Acid-Base Titration

4. Applications of CPHMD

5. Summary and Outlook

Acknowledgements

References

2.   Extending Atomistic Time Scale Simulations by Optimization of the Action
      A.S. Clarke, S.M. Hamm and A.E. Cardenas

1. Introduction

2. Applications

3. Conclusions

Acknowledgements

References

3.   Fishing for Functional Motions with Elastic Network Models
      A.J. Rader

1. Introduction

2. Background

3. Identification of Functional Motions

4. Detailed EN Models

5. Merging EN Models and MD Simulations

6. Summary and Future Prospects

References

4.   Alchemical Free Energy Calculations: Ready for Prime Time?
      Michael R. Shirts, David L. Mobley and John D. Chodera

1. Introduction

2. Background

3. Equilibrium Methods

4. Nonequilibrium Methods

5. Intermediate States

6. Sampling

7. Applications

8. Conclusions

Acknowledgements

References

Section 2: Biological and Biophysical Applications
Section Editor: Heather Carlson

5.   Linear Quantitative Structure-Activity Relationships for the Interaction of Small Molecules with
      Human Cytochrome P450 Isoenzymes
      Thomas Fox and Jan M. Kriegl

1. Introduction

2. The Cytochrome P450 Superfamily

3. Methodological Overview

4. Applications

5. Discussion and Outlook

References

Section 3: Chemical Education
Section Editor: Theresa Zielinski

6.   Observations on Crystallographic Education
      Phillip E. Fanwick

1. Introduction

2. Objectives for Teaching Crystallography

3. Bragg's Law

4. Relating Crystallography to Chemistry

5. Creativity

6. Conclusions

References

7.   Achieving a Holistic Web in the Chemistry Curriculum
      Henry S. Rzepa

Introduction: The Impact of the Web on the Chemistry Curriculum

Background: The Trend Towards an Accumulation of Acrobat

1. The Properties of a PDF Collection

2. Formal Metadata-Based Approaches

3. The Comcept of Document Reuse

4. Data as the Intel Inside

5. Towards the Holistic Approach: The Podcast

6. The Wiki

Conclusions

References

Section 4: Materials and Polymers
Section Editor: Jeffry Madura

8.   The Role of Long-Time Correlation in Dissipative Adsorbate Dynamics on Metal Surfaces
      Jeremy M. Moix and Rigoberto Hernandez

1. Introduction

2. Classical Surface Diffusion

3. Molecular Dynamics Simulations and Projective Models

4. Summary and Conclusions

Acknowledgements

References

Section 5: Quantum Chemistry
Section Editor: T. Daniel Crawford

9.   An Active Database Approach to Complete Rotational-Vibrational Spectra of Small Molecules
      Attila G. Császár, Gábor Czakó, Tibor Furtenbacher and Edit Mátyus

1. Introduction

2. Nonadiabatic Computations - Where Theory Delivers

3. MARVEL - An Active Database Approach

4. Electronic Structure Computations

5. Variational Nuclear Motion Computations

6. Outlook

Acknowledgements

References

10.   The Effective Fragment Potential: A General Method for Predicting Intermolecular Interactions
        Mark S. Gordon, Lyudmilla Slipchenko, Hui Li and Jan H. Jensen

1. Introduction

2. EFP2 Theory

3. Example Applications

4. Summary of Future Developments

Acknowledgements

References

11.   Gaussian Basis Sets Exhibiting Systematic Convergence to the Complete Basis Set Limit
        Kirk A. Peterson

1. Introduction

2. Correlation Consistent Basis Sets: A Review

3. Recent Advances in Correlation Consistent Basis Sets

4. Conclusions

Acknowledgements

References

Section 6: Emerging Technologies
Section Editor: Wendy Cornell

12.   Principles of G-Protein Coupled Receptor Modeling for Drug Discovery
        Irache Visiers

1. Introduction

2. Homology Models of Rhodopsin-Like GPCRs

3. Ab Initio Methods

4. Modeling the Activated State

5. Conclusions

Acknowledgements

References

Index

Cummulative Index Vols 1-2




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