CiNii Books - Annual reports in computational chemistry

Annual Reports in Computational Chemistry, Volume 15, provides timely and critical reviews of important topics in computational chemistry. Topics covered in this series 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.

Contributions from: Roland Lindh Michelle Coote Shenggang Li Mingyang Chen Ryan C. Fortenberry Thomas Daniel Crawford So Hirata

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 Computational Chemistry is a 'must' for researchers and students wishing to stay up-to-date on current developments in computational chemistry.

Quantum Mechanical Methods (T.D. Crawford). Molecular Modelling Methods (C. Simmerling). Advances in QSAR/QSPR (Y. Martin). Applications of Computational Methods (H.Carlson). Chemical Education (T. Zielinski). Emerging Science (R. Wheeler).

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 Computational Chemistry is a 'must' for researchers and students wishing to stay up-to-date on current developments in computational chemistry.

Section 1: Chemical Education 1. Real World Kinetics via Simulations. Section 2: Quantum Mechanical Methods 2. Explicitly Correlated Approaches for Electronic Structure Computations. 3. Hybrid Methods: ONIOM (QM:MM) and QM/MM. 4. On the Selection of Domains and Pairs in Local Correlation Treatments. Section 3: Molecular Modeling Methods 5. Simulations of Temperature and Pressure Unfolding Peptides and Proteins with Replica Exchange Molecular Dynamics. 6. Hybrid Explicit/Implicit Solvation Methods. Section 4: Advances in QSAR/QSPR 7. Variable Selection QSAR and Model Validation. 8. Machine Learning in Computational Chemistry. 9. Molecular Similarity: Advances in Methods, Applications, and Validations in Virtual Screening and QSAR. Section 5: Applications of Computational Methods 10. Cytochrome P450 Enzymes: Computational Approaches to Substrate Prediction. 11. Recent Advances in Design of Small-Molecule Ligands to Target Protein-Protein Interactions. 12. Accelerating Conformational Transitions in Biomolecular Simulations. 13. Principal Component Analysis: A Review of its Application on Molecular Dynamics Data. 14. Solvent Effects on Organic Reactions from QM/MM Simulations. 15. Structure-Based Design of New Anti-Bacterial Agents. 16. Recent Evaluations of High Throughput Docking Methods for Pharmaceutical Lead Finding - Consensus and Caveats.

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 Computational Chemistry is a 'must' for researchers and students wishing to stay up-to-date on current developments in computational chemistry.In Volume 3, topics covered include Simulation Methodologies (Carlos Simmerling), Biological and Biophysical Applications (Heather Carlson), Chemical Education (Theresa Zielinski), Materials and Polymers (Jeffry Madura), Quantum Chemistry (T. Daniel Crawford), and Emerging Technologies (Wendy Cornell). With this volume we extend the practice of cumulative indexing of both the current and past editions in order to provide easy identification of past reports.

Simulation MethodologiesChapter 1 Molecular Simulations of pH-Mediated Biological Processes Chapter 2 Extending Atomistic Time Scale Simulations by Optimization of the ActionChapter 3 Fishing for Functional Motions with Elastic Network ModelsChapter 4 Alchemical Free Energy Calculations: Ready for Prime Time?Biological and Biophysical Chapter 5 Linear Quantitative Structure-Activity Relationships for the Interaction of Small Molecules with Human Cytochrome P450 IsoenzymesChemical Education Chapter 6 Observations on Crystallographic EducationChapter 7 Achieving a Holistic Web in the Chemistry CurriculumMaterials and PolymersChapter 8 The Role of Long-time Correlation in Dissipative Adsorbate Dynamics on Metal SurfacesQuantum ChemistryChapter 9 An Active Database Approach to Complete Rotational-Vibrational Spectra of Small MoleculesChapter 10 The Effective Fragment Potential: A General Method for Predicting Intermolecular InteractionsChapter 11 Gaussian Basis Sets Exhibiting Systematic Convergence to the Complete Basis Set LimitEmerging TechnologiesChapter 12 Principles of G-Protein Coupled Receptor Modeling for Drug Discovery

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 Computational Chemistry is a "must" for researchers and students wishing to stay up-to-date on current developments in computational chemistry.

Section 1: Bioinformatics (Section Editor: Wei Wang) 1. Structural Perspectives on Protein Evolution - Eric Franzosa and Yu Xia 2. Predicting Selectivity and Druggability in Drug Discovery - Alan C. Cheng Section 2: Biological Modeling (Section Editor: Nathan Barker) 3. Machine Learning for Protein Structure and Function Prediction - Robert Ezra Langlois and Hui Lu 4. Modeling Protein-Protein and Protein-Nucleic Acid Interactions: Structure, Thermodynamics, and Kinetics - Huan-Xiang Zhou, Sanbo Qin and Harianto Tjong 5. Analysing Protein NMR pH-titration Curves - Jens Erik Nielsen 6. Implicit Solvent Simulations of Biomolecules in Cellular Environments - Michael Feig, Seiichiro Tanizaki, and Maryam Sayadi Section 3: Simulation Methodologies (Section Editor: Carlos Simmerling) 7. Implicit Solvent Models in Molecular Dynamics Simulations: A Brief Overview - Alexey Onufriev 8. Comparing MD Simulations and NMR Relaxation Parameters - Vance Wong and David A. Case

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 Computational Chemistry is a "must" for researchers and students wishing to stay up-to-date on current developments in computational chemistry.

1. Free energies of lipid - lipid interactions in membranes - W.F. Drew Bennett* and D. Peter Tieleman 2. Quantifying uncertainty and sampling quality in biomolecular simulations - Alan Grossfield and Daniel M. Zuckerman 3. Methods for Monte Carlo simulations of biomacromolecules - Andreas Vitalis*, and Rohit V. Pappu 4. Accelerated Molecular Dynamics Methods: Introduction and Recent Developments -D. Perez, B. P. Uberuaga, Y. Shim, J. G. Amar and A. F. Voter 5. Recent Advances on in silico ADME Modeling -Junmei Wang and Tingjun Hou 6. Explicitly correlated coupled-cluster methods - Toru Shiozaki* Edward F. Valeev* and So Hirata 7. The Density Matrix Renormalization Group in Quantum Chemistry Garnet Kin-Lic Chan and Dominika Zgid 8. Electron Transfer in Gaseous Positively Charged Peptides - Relation to Mass Spectrometry - Jack Simons

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 Computational Chemistry is a "must" for researchers and students wishing to stay up-to-date on current developments in computational chemistry.

Section A 1. Advancements in Molecular Dynamics Simulations of Biomolecules on Graphical Processing Units Dong Xu, Mark J. Williamson, Ross C. Walker 2. Quantum Chemistry on Graphics Processing Units Andreas W. Gotz, Thorsten Wole, Ross C. Walker 3. Computing Free-Energy Profiles using Multidimensional Potentials of Mean Force and Polynomial Quadrature Methods Jonah Z. Vilseck and Orlando Acevedo 4. QM/MM Alchemical Free Energy Simulations: Challenges and Recent Developments Wei Yang, Qiang Cui, Donghong Min, and Hongzhi Li Section B 5. Deciphering Structural Fingerprints for Metalloproteins with Quantum Chemical Calculations Yan Ling and Yong Zhang 6. Ab initio Electron Propagator Methods:Applications to Fullerenes and Nucleic Acid Fragments Viatcheslav G. Zakrzewski, Olga Dolgounitcheva, Alexander V. Zakjevskii and J. V. Ortiz Section C 7. Using Density Functional Theory methods for modeling induction and dispersion interactions in ligand-protein complexes Hunter Utkov, Maura Livengood, and Mauricio Cafiero 8. Theoretical Calculations of Acid Dissociation Constants: A Review Article Kristin S. Alongi and George C. Shields 9. Antibiotics Targeting the Ribosome: Structure Based Design and the Nobel Prize Edward C. Sherer Section D 10. Insights into the role of conformational transitions and metal ion binding in RNA catalysis from molecular simulations Tai-Sung Lee, George M. Giambasu, Darrin M. York 11. Atomistic Modeling of Solid Oxide Fuel Cells C. Heath Turner, Xian Wang, Kah Chun Lau, Wei An, and Brett I. Dunlap Section E 12. Modelling signalling processes across cellular membranes using a mesoscopic approach George Khelashvili and Daniel Harries 13. Folding of conjugated proteins Dalit Shental-Bechor, Oshrit Arviv, Tzachi Hagai, and Yaakov Levy Section F 14. Mean-force scoring functions for protein-ligand binding Sheng-You Huang and Xiaoqin Zou

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.

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 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 Acknowledgment 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 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 1. Introduction 2. Retinal Proteins 3. Theoretical Framework 4. Spectral Tuning 5. Conclusion Acknowledgments A Class Project Combining Organic Chemistry, Quantum Chemistry, and Statistics 1. Background 2. Results and Discussion 3. Conclusions Notes and Acknowledgment

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.

Section A: Quantum Chemistry (Section Editor: Gregory S. Tschumper) A Practical Guide to Reliable First Principles Computational Thermochemistry Predictions Across the Periodic Table David A. Dixon, David Feller and Kirk A. Peterson Ab Initio Composite Approaches: Potential Energy Surfaces and Excited Electronic States Wanyi Jiang and Angela K. Wilson On The Orthogonality of Orbitals in Subsystem Kohn-Sham Density Functional Theory Yuriy G. Khait and Mark R. Hoffmann Section B: Biological Modeling (Section Editor: Nathan Baker) Structural Models and Molecular Thermodynamics of Hydration of Ions and Small Molecules David M. Rogers, Dian Jiao, Lawrence R. Pratt and Susan B. Rempe A Review of Physics-Based Coarse-Grained Potentials for the Simulations of Protein Structure and Dynamics Hujun Shen, Zhen Xia, Guohui Li and Pengyu Ren Section C: Bioinformatics (Section Editor: Wei Wang) Poisson-Boltzmann Implicit Solvation Models Qin Cai, Jun Wang, Meng-Juei Hsieh, Xiang Ye and Ray Luo

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.

Section A: Quantum Chemistry (Section Editor: Gregory S. Tschumper) Ligand Steric Descriptors Jenna A. Bilbrey and Wesley D. Allen Efficient Monomer-Based Quantum Chemistry Methods for Molecular and Ionic Clusters Leif D. Jacobson, Ryan M. Richard, Ka Un Lao and John M. Herbert Section B: Bioinformatics (Section Editor: Wei Wang) Atomistic Modeling of Phospho-Peptide Recognition for Modular Domains Chia-en A. Chang and Yu-ming M. Huang

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.

Section A-Quantum Chemistry Quantum Chemistry Methods with Multiwavelet Bases on Massive Parallel Computers Alvaro Vazquez-Mayagoitia, W. Scott Thornton, Jeff R. Hammond and Robert J. Harrison On the Transferability of Three Water Models Developed by Adaptive Force Matching Hongyi Hu, Zhonghua Ma and Feng Wang Section B-Biological Applications Seeing the Forest in Lieu of the Trees: Continuum Simulations of Cell Membranes at Large Length Scales Kayla Sapp, Roie Shlomovitz and Lutz Maibaum A Microscopic View of the Mechanisms of Active Transport Across the Cellular Membrane Giray Enkavi, Jing Li, Pochao Wen, Sundarapandian Thangapandian, Mahmoud Moradi, Tao Jiang, Wei Han and Emad Tajkhorshid Monte Carlo Simulation of Electrolyte Solutions in Biology: In and Out of Equilibrium Dezso Boda Section C-Chemical Education The Development and Implementation of a Bio-Molecular Docking Exercise for the General Chemistry Laboratory Clare E. O'Grady, Peter Talpey, Timothy E. Elgren and Adam W. Van Wynsberghe

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.

Quantum Chemistry (Section A) NMR Calculations for Paramagnetic Molecules and Metal Complexes Jochen Autschbach The Nonlocal Correlation Density Functional VV10: a Successful Attempt to Accurately Capture Noncovalent Interactions Joaquin Calbo, Enrique Orti, Juan C. Sancho-Garcia and Juan Arago Modeling Laser Induced Molecule Excitations Using Real-Time Time-Dependent Density Functional Theory Attila Bende Chemical Bonding, Reactivity and Viability of Large Boron Clusters Jules Tshishimbi Muya, Minh Tho Nguyen and Arnout Ceulemans Scattering Theory (Section B) A Computational Perspective on Multichannel Scattering Theory with Applications to Physical and Nuclear Chemistry Simone Taioli and Stefano Simonucci Theory of Liquids (Section C) Intermolecular Network Theory: A General Approach for Understanding the Structural and Dynamic Properties of Liquids and Solutions Aurora E. Clark

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.

Quantum Chemistry (Section A) 1. Prediction of Thermochemical Properties Across the Periodic Table: A Review of Correlation Consistent Composite Approach (ccCA) Strategies and Applications Charles Peterson, Deborah A. Penchoff and Angela K. Wilson 2. The Impact of Larger Basis Sets and Explicitly Correlated Coupled Cluster Theory on the Feller-Peterson-Dixon Composite Method David Feller, Kirk A. Peterson and David A. Dixon New Theories of Bonding (Section B) 3. Recoupled Pair Bonding: Unifying the Theory of Valence for the Main Group Elements Thom H. Dunning, Jr., David E. Woon, Lu. T. Xu, Tyler Y. Takeshita, Beth A. Lindquist and Jeff Leiding Geochemistry (Section C) 4. Computational Isotope Geochemistry James R. Rustad Nanoparticles (Section D) 5. Computer Simulation and Modeling Techniques in the Study of Nanoparticle-Membrane Interactions Zhenpeng Ge and Yi Wang

Annual Reports in Computational Chemistry, Volume 13 provides timely and critical reviews of important topics in computational chemistry. Topics in this new release include chapters on the Quantum Chemical Model for Molecular Properties and Processes at the Extreme High Pressure, a section on Interpreting Bonding and Spectra with Correlated, One-Electron Concepts from Electron Propagator Theory, Benchmark databases of intermolecular interaction energies: design, construction, and significance, Gaussian Accelerated Molecular Dynamics: Theory, Implementation and Applications, and Dissociation in Binary Acid/Base Clusters: An Examination of Inconsistencies Introduced into the Many-Body Expansion by Naive Fragmentation Schemes. Topics covered in this series 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.

Section A: Quantum Chemistry - Weak and Non-Bonded Interactions 1. Benchmark Databases of Intermolecular Interaction Energies: Design, Construction, and Significance Konrad Patkowski 2. Dissociation in Binary Acid/Base Clusters: An Examination of Inconsistencies Introduced Into the Many-Body Expansion by Naïve Fragmentation Schemes Gregory S. Tschumper, Thomas L. Ellington and Sarah N. Johnson 3. The Quantum Chemical Study of Chemical Reactions at Extreme High Pressure by Means of the Extreme-Pressure Polarizable Continuum Model Roberto Cammi Section B: Quantum Chemistry - Novel Approaches for Understanding Bonding 4. Interpreting Bonding and Spectra With Correlated, One-Electron Concepts From Electron Propagator Theory J. Vincent Ortiz Section C: Quantum Chemistry - Periodic Simulations 5. Plane–Wave DFT Methods for Chemistry Eric J. Bylaska Section D: Biochemical Simulations - Molecular Dynamics 6. Gaussian Accelerated Molecular Dynamics: Theory, Implementation, and Applications Yinglong Miao and J. Andrew McCammon

Annual Reports in Computational Chemistry, Volume 14, provides timely and critical reviews of important topics in computational chemistry. Topics covered in this series 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.

Contributions from: Steven Wheeler Karol Kowalski So Hirata Jindal K. Shah Kirk Peterson T. P. Straatsma

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