Annual Reports in Computational Chemistry

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.

Klappentext

Provides critical reviews of important topics in computational chemistry as applied to various chemical disciplines. This title covers such topics as: quantum chemistry, molecular mechanics, force fields, chemical education, and applications in academic and industrial settings.

Inhalt

Contributors

Section 1: Bioinformatics Preface Potential Landscape and Flux Framework of Nonequilibrium Biological Networks

1. Introduction

2. Biochemical Oscillation

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

   Acknowledgments

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

8. Introduction

9. Energy-Based Approach to Coarse-Graining

10. Force-Matching Approach to Coarse-Graining

11. Mixed Resolution Dynamics

12. Prospective Utilization

13. Outlook and Summary

    An Overview of String-Based Path Sampling Methods

14. Introduction

15. Elastic Band Derived Methods

16. Applications

17. Conclusions and Outlook

    Constructing and Evaluating Predictive Models for Protein Biophysical Characteristics

18. Introduction

19. Characterizing the Error Distribution

20. Outliers

21. Accurate Model Parameters

22. 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

   Acknowledgment

   Advances in Scalable Computational Chemistry

5. Introduction

6. Software Design

7. Hartree-Fock and Density Functional Theory

8. Gaussian Basis Set HF and DFT

9. Plane-Wave Basis Set DFT

10. CC Methods

11. Perturbation Methods

12. Electron Transfer Methods

13. Relativistic Methods

14. Classical MD Simulation

15. Combined QM/MM

16. Conclusions

    Acknowledgments

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

   Acknowledgments

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

   Acknowledgments

   Computational Chemistry of Vision in Vertebrates and Invertebrates

5. Introduction

6. Retinal Proteins

7. Theoretical Framework

8. Spectral Tuning

9. Conclusion

   Acknowledgments

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

10. Background

11. Results and Discussion

12. Conclusions

    Notes and Acknowledgment