Quantum simulations of materials and biological systems [1st International Symposium on Computational Sciences (ISCS2011) ; April 18 to April 21, 2011 in Shanghai, China

__Quantum Simulations of Materials and Biological Systems__ features contributions from leading world experts in the fields of density functional theory (DFT) and its applications to material and biological systems. The recent developments of correlation functionals, implementations of Time-dependent algorithm into DFTB+ method are presented. The applications of DFT method to large materials and biological systems such as understanding of optical and electronic properties of nanoparticles, X-ray structure refinement of proteins, the catalytic process of enzymes and photochemistry of phytochromes are detailed. In addition, the book reviews the recent developments of methods for protein design and engineering, as well as ligand-based drug design. Some insightful information about the 2011 International Symposium on Computational Sciences is also provided. __Quantum Simulations of Materials and Biological Systems__ is aimed at faculties and researchers in the fields of computational physics, chemistry and biology, as well as at the biotech and pharmaceutical industries. Quantum Simulations of Materials and Biological Systems 4 Preface 6 Contents 8 Contributors 10 Part I: Material Sciences 12 1 Towards a Greater Accuracy in DFT Calculations: From GGA to Hybrid Functionals 14 1.1 Introduction 14 1.2 The Starting Local and GGA Functionals 16 1.3 Technical Details 19 1.4 Hybrid Functionals 19 1.5 Final Remarks 24 References 26 2 Quantum Transport Simulations Based on Time Dependent Density Functional Theory 28 2.1 Introduction 28 2.2 Overview of Existing Methods and Recent Advances 30 2.2.1 Finite System Simulations 30 2.2.2 Methods Based on Open Boundary Conditions 33 2.2.3 Simulations Under Periodic Boundary Conditions 34 2.3 First-Principles Liouville-von Neumann Equation 35 2.3.1 Holographic Electron Density Theorem and Existence of First-Principles for Open Systems 35 2.3.2 First-Principles Formalism: TDDFT-NEGF-EOM for Open System 36 2.3.3 Hierarchical Equation of Motion for Reduced Single-Electron Density Matrix Based Liouville-von Neumann Equation 37 2.3.4 Adiabatic Wide-Band-Limit Approximation 39 References 41 3 Modeling Silicon Nanostructure Surface Functionalization for Biological Detections 44 3.1 Introduction 44 3.2 Propionic-Acid-Terminated Silicon Quantum Dots 45 3.3 Allylamine-Capped Silicon Quantum Dots 50 3.4 Amine-Capped Silicon Quantum Dots 55 3.5 Optimal Surface Functionalization of Silicon Quantum Dots 57 3.6 Conclusions 60 References 61 4 QM/MD Simulations of High-Temperature SWCNT Self-capping 64 4.1 Introduction 64 4.2 Computational Methodology 65 4.2.1 Model Systems 65 4.2.2 Quantum Chemical Molecular Dynamics Simulations 65 4.3 Results and Discussion 66 4.3.1 CUT Model Systems 66 4.3.2 OX Model Systems 75 4.3.3 Short-OX Model Systems 75 4.4 Summary 76 References 78 5 Graphene Oxide: Theoretical Perspectives 80 5.1 Introduction 80 5.2 Geometric Structure 81 5.2.1 First-Principles Energetics 82 5.2.2 Computational Spectroscopy 84 5.2.3 Thermodynamics Versus Kinetics 86 5.3 Electronic Structure and Other Properties 87 5.4 Oxidation and Reduction Reactions 89 5.5 Conclusions 91 References 91 Part II: Biological Systems 96 6 First Steps Towards Quantum Refinement of Protein X-Ray Structures 98 6.1 Introduction 98 6.2 Basics of Protein X-Ray Diffraction Analyses 100 6.3 Hen Egg-White Lysozyme Initial Structure 102 6.4 Choosing Adequate Quantum Chemical Techniques 105 6.4.1 Dispersion-Corrected DFT 105 6.4.2 The Choice of Adequate Density Functionals 106 6.4.3 The Choice of Adequate Basis Sets 108 6.4.4 The Linear Scaling Procedure 110 6.5 Results and Discussion 112 6.5.1 Investigations on the Initial Structure with B Factor Refinement 112 6.5.2 Optimization of Even Numbered Residues in Well Defined Protein Regions 114 6.6 Conclusions 124 References 126 7 The Inverse Protein Folding Problem: Protein Design and Structure Prediction in the Genomic Era 132 7.1 Introduction: Structure Prediction on a Genomic Scale 132 7.2 Protein Structure: The Importance of Being Discrete 137 7.3 The Role of the Unfolded State 138 7.4 Relating Structures and Energies: A Molecular Mechanics Description of Proteins 139 7.5 A Divide-and-Conquer Method for Protein Design 140 7.6 Object-Oriented Software for Structural Biology 142 7.7 Exploring Sequence Space 143 7.8 Protein Design on the BOINC Distributed Computing Platform 144 7.9 Selected Results: Performance of the Energy Function 145 7.10 Generating Sequences for an Oncogenic Protein, the Src Homology 3 Domain 146 References 149 8 Integration of Ligand-Based and Structure-Based Approaches for Virtual Screening of Factor Xa Inhibitors 152 8.1 Introduction 152 8.2 Materials and Methods 154 8.2.1 Data Sets and Molecular Descriptors 154 8.2.2 Machine Learning Methods 154 8.2.3 Molecular Docking 155 8.2.4 Performance Evaluation 155 8.3 Results and Discussions 156 8.3.1 Dataset Diversity Analysis 156 8.3.2 Model Development 157 8.3.3 Model Validation 157 8.3.4 Ligand-Based Virtual Screening (LBVS) 159 8.3.5 Structure-Based Virtual Screening (SBVS) 162 8.4 Conclusion 162 References 163 9 Principles and Applications of Hybrid Quantum Mechanical and Molecular Mechanical Methods 166 9.1 Introduction 166 9.2 Overview of QM/MM Schemes 167 9.3 Self-consistent Charge Density Tight Binding Method (SCC-DFTB) 169 9.4 Potential of Mean Force 170 9.5 Applications to Enzymatic Catalysis 171 9.6 Concluding Remarks 177 References 177 10 A Computational Perspective on the Photochemistry of Photosensory Proteins: Phytochromes and Anabaena Sensory Rhodopsin 180 10.1 Introduction 180 10.2 Phytochromes 181 10.3 Anabaena Sensory Rhodopsin and Light-Driven Rotary Molecular Motors 183 10.4 Computational Methods for Excited States 186 10.5 Computational Studies of Phytochromes 187 10.5.1 Computational Details 187 10.5.2 Some Benchmark Calculations 188 10.5.3 Photoisomerization Paths 191 10.5.4 Modulation of the Intrinsic Photochemical Reactivity of the Bilin Chromophores 195 10.6 Computational Studies of Anabaena Sensory Rhodopsin 195 10.6.1 Computational Details 195 10.6.2 The Photocycle of ASR 197 10.7 Concluding Remarks 200 References 201 Index 206 Front Matter....Pages I-X Front Matter....Pages 1-1 Towards a Greater Accuracy in DFT Calculations: From GGA to Hybrid Functionals....Pages 3-15 Quantum Transport Simulations Based on Time Dependent Density Functional Theory....Pages 17-32 Modeling Silicon Nanostructure Surface Functionalization for Biological Detections....Pages 33-51 QM/MD Simulations of High-Temperature SWCNT Self-capping....Pages 53-68 Graphene Oxide: Theoretical Perspectives....Pages 69-84 Front Matter....Pages 85-85 First Steps Towards Quantum Refinement of Protein X-Ray Structures....Pages 87-120 The Inverse Protein Folding Problem: Protein Design and Structure Prediction in the Genomic Era....Pages 121-140 Integration of Ligand-Based and Structure-Based Approaches for Virtual Screening of Factor Xa Inhibitors....Pages 141-154 Principles and Applications of Hybrid Quantum Mechanical and Molecular Mechanical Methods....Pages 155-168 A Computational Perspective on the Photochemistry of Photosensory Proteins: Phytochromes and Anabaena Sensory Rhodopsin....Pages 169-194 Back Matter....Pages 195-197