Annual Reports in Computational Chemistry / Edited by Ralph A. Wheeler

Cover; Annual Reports in Computational Chemistry; Copyright; Contents; Contributors; Preface; Section 1: Simulation Methodologies; Chapter 1. Advancements in Molecular Dynamics Simulations of Biomoleculeson Graphical Processing Units; 1. Introduction; 2. An Overview of GPU Programming; 3. GPU-Based Implementations of Classical Molecular Dynamics; 4. Performance and Accuracy; 5. Applications; 6. Conclusions and Future Directions; Acknowledgments; References; Chapter 2. Quantum Chemistry on Graphics Processing Units; 1. Introduction; 2. Software Development for Graphics Processing Units

3. Kohn?Sham Density Functional and Hartree-Fock Theory4. Ab Initio Electron Correlation Methods; 5. Quantum Monte Carlo; 6. Concluding Remarks; Acknowledgments; References; Chapter 3. Computing Free-Energy Profiles Using Multidimensional Potentials of Mean Force and Polynomial Quadrature Methods; 1. Introduction; 2. Methods; 3. Polynomial Quadrature Method; 4. Multidimensional Potentials of Mean Force; 5. Conclusion; Acknowledgments; References; Chapter 4. QM/MM Alchemical Free Energy Simulations: Challenges and Recent Developments; 1. Introduction

2. Direct and Indirect Schemes for QM/MM AFE Simulations3. The Long-range Electrostatic Treatment in QM/MM AFE Simulations; 4. The Sampling Issue in QM/MM AFE Simulations; 5. Concluding Remarks and Future Perspectives; Acknowledgments; References; Section 2: Quantum Chemistry; Chapter 5. Deciphering Structural Fingerprints for Metalloproteinswith Quantum Chemical Calculations; 1. Introduction; 2. Computational Details; 3. Results and Discussion; 4. Conclusions; Acknowledgments; References; Chapter 6. Ab Initio Electron Propagator Methods: Applications to Fullerenes and Nucleic Acid Fragments

1. Introduction2. Electron Propagator Theory; 3. Applications; 4. Conclusions; Acknowledgments; References; Section 3: Chemical Education; Chapter 7. Using Density Functional Theory Methods for Modeling Inductionand Dispersion Interactions in Ligand- Protein Complexes; 1. Introduction; 2. Ligand-Protein Complexes; 3. Density Functional Theory; 4. The Correct Path to Dispersion; 5. Applications; 6. Conclusions; References; Chapter 8. Theoretical Calculations of Acid Dissociation Constants: A Review Article; 1. Introduction; 2. Background; 3. Calculating Changes in Free Energy in the Gas Phase

4. Calculating Changes in Free Energy in Solution5. Thermodynamic Cycles; 6. Concluding Remarks; References; Chapter 9. Antibiotics Targeting the Ribosome: Structure-Based Design and the Nobel Prize; 1. Introduction; 2. Ribosome Antibiotic Complexes; 3. RNA as a Drug Target; 4. Structure-Based Antibiotic Design: Case Studies; 5. Concluding Remarks; Acknowledgments; References; Section 4: Nanotechnology; Chapter 10. Insights into the Role of Conformational Transitions and Metal Ion Binding in RNA Catalysis from Molecular Simulations; 1. Introduction

2. Molecular Simulations of the Hammerhead Ribozyme

Annual Reports in Computational Chemistry is a new periodical providing 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. Each volume is organized into (thematic) sections with contributions written by experts. Focusing on the most recent literature and advances in the field, each article covers a specific topic of importance to computational chemists. Annual Reports in Computation