Practical Aspects of Computational Chemistry: Methods, Concepts and Applications

"Practical Aspects of Computational Chemistry" presents contributions on a range of aspects of Computational Chemistry applied to a variety of research fields. The chapters focus on recent theoretical developments which have been used to investigate structures and properties of large systems with minimal computational resources. Studies include those in the gas phase, various solvents, various aspects of computational multiscale modeling, Monte Carlo simulations, chirality, the multiple minima problem for protein folding, the nature of binding in different species and dihydrogen bonds, carbon nanotubes and hydrogen storage, adsorption and decomposition of organophosphorus compounds, X-ray crystallography, proton transfer, structure-activity relationships, a description of the REACH programs of the European Union for chemical regulatory purposes, reactions of nucleic acid bases with endogenous and exogenous reactive oxygen species and different aspects of nucleic acid bases, base pairs and base tetrads. Table of Contents Cover Practical Aspects of Computational Chemistry I ISBN 9789400709188 Preface Contents Contributors Chapter 1: Models--Experiment--Computation: A History of Ideas in Structural Chemistry 1.1 Introduction 1.2 Frank Westheimer and the Origin of Molecular Mechanics 1.3 Gilbert N. Lewis's Models of Atoms and Bonding 1.4 VSEPRing an Efficient Model 1.5 Non-bonded Interactions 1.6 Origins of Experimental Molecular Structure Determination 1.7 Structural Chemistry in Molecular Biology 1.8 The Theory of Resonance and the Discovery of Alpha-Helix 1.9 Some Major Contributors to the MO Approach 1.10 Physical Content of Metric 1.11 John A. Pople's Comprehensive Program 1.12 Final Thoughts References Chapter 2: Many-Body Brillouin-Wigner Theories: Developmentand Prospects 2.1 Introduction 2.2 Brillouin-Wigner Theories 2.2.1 Brillouin-Wigner Expansions 2.2.2 Single-Reference Brillouin-Wigner Expansions 2.2.3 Multi-Reference Brillouin-Wigner Expansions 2.2.4 Rayleigh-Schrödinger and Brillouin-Wigner Perturbation Theories and A Posteriori `Many-Body' Corrections 2.3 Digression: Collaborative Virtual Environments for Many-Body Brillouin-Wigner Theories 2.4 Applications of Many-Body Brillouin-Wigner Theories 2.5 Future Directions 2.5.1 Relativistic Many-Body Brillouin-Wigner Theories 2.5.2 Fock Space Brillouin-Wigner Methods References Chapter 3: Multireference State-Specific Coupled Cluster Theory with a Complete Active Space Reference 3.1 Introduction 3.2 Multireference State-Specific Generalization of CCSD Theory 3.2.1 The CASCCD Method 3.3 Multireference State-Specific Coupled Cluster Theory with Complete Account of Single and Double Excitations: The CASCCSD Method 3.4 Automated Derivation of the CC Equations and Generation of the Computer Code for Solving Them 3.5 Numerical Results 3.6 Conclusions References Chapter 4: Relativistic Effects in Chemistry and a Two-Component Theory 4.1 Introduction 4.2 Relativistic Effects in Atoms and Molecules 4.2.1 Dissociation Energies and Strong Chemical Bonds to Gold 4.2.2 Electric Properties 4.2.3 Chemical Reactions o 4.2.3.1 Equilibrium Reaction Energies o 4.2.3.2 Hydrolysis of Group 11 and 12 Cations 4.2.4 Atomic Core Ionization Potentials 4.2.5 Molecular Core Electron Binding Energies 4.3 Basis of Relativistic Theory 4.3.1 One-Electron Dirac Equation 4.3.2 Relativistic Theory of Many-Particle Systems 4.4 Two-Component Relativistic Theories 4.4.1 Infinite Order Two-Component Method (IOTC) 4.4.2 Matrix Formulation 4.5 The Change of Picture Problem 4.6 Quasi-Relativistic or Exact Two-Component Method 4.7 Summary References Chapter 5: On the Electronic, Vibrational and Relativistic Contributions to the Linear and Nonlinear Optical Properties of Molecules 5.1 Introduction 5.2 The Correlation, Relativistic and Vibrational Contributions to the L&NLO Properties of ZnS, CdS and HgS 5.3 Vibrational Corrections by Numerov-Cooley Integration 5.4 Relativistic Corrections of the L&NLO Properties of Coinage Metal Hydrides 5.5 Cyclopropenone and Cyclopropenethione 5.6 Hyperpolarizabilities of the Hydrides of Li, Na and K 5.7 Electronic and Vibrational Contributions to Pyrrole 5.8 Linear and Nonlinear Optical Properties of Fullerene Derivatives and Endohedral Fullerenes 5.8.1 Substituted Dihydro-Fullerenes 5.8.2 Endohedral Fullerenes o 5.8.2.1 Nuclear Relaxation Contribution to the VibrationalNLO Properties 5.9 Nonlinear Optical Properties Due to Large Amplitude Vibrational Motions, with an Application to the Inversion Motion in NH3 5.10 Summary References Chapter 6: Using Chebyshev-Filtered Subspace Iteration and Windowing Methods to Solve the Kohn-Sham Problem 6.1 Introduction 6.2 Eigenvalue Problems in Density Functional Calculations 6.3 Numerical Methods for Parallel Platforms 6.4 The Nonlinear Chebyshev-Filtered Subspace Iteration 6.4.1 Chebyshev-Filtered Subspace Iteration 6.4.2 Chebyshev Filters and Estimation of Bounds 6.5 Window Filtering 6.6 Diagonalization in the First SCF Iteration 6.7 Numerical Results 6.8 Concluding Remarks References Chapter 7: Electronic Structure of Solids and Surfaces with WIEN2k 7.1 Introduction 7.2 Quantum Mechanics 7.3 The Augmented Plane Wave Based Method and WIEN2k 7.4 Properties and Applications 7.4.1 Verwey Transition in YBaFe2O5 7.4.2 Nanomesh with h-BN on a Rh(111) Surface 7.4.3 The Misfit Layer Compounds 7.4.4 Performance of Various GGA Functionals 7.5 Summary and Conclusion References Chapter 8: Model Core Potentials in the First Decade of the XXI Century 8.1 Introduction 8.1.1 Separability of the Valence and Core Spaces 8.1.2 Effective Core Potential Method 8.1.3 Model Core Potential Method o 8.1.3.1 General Formalism of Model Core Potential Method o 8.1.3.2 Versions of the Model Core Potential Method 8.1.4 Determination of the Model Core Potential Parameters 8.2 General Improvements in Parameterization and Basis Sets 8.3 New Approach to Relativistic Effects 8.3.1 Scalar-Relativistic Effect in Model Core Potential Method 8.3.2 Spin-Orbit Coupling in Model Core Potential Method o 8.3.2.1 Breit-Pauli and Douglas-Kroll Spin-Orbit-Coupling Operators o 8.3.2.2 Determination of the Model Core Potential Valence Space o 8.3.2.3 Basis Sets for the New Model Core Potentials o 8.3.2.4 Performance of the DK-SOC Adapted Model Core Potential 8.3.3 A Digression: From MCP to SOC 8.4 Model Core Potential Applications in the Last 10 Years 8.5 Summary and Outlook References Chapter 9: Practical Aspects of Quantum Monte Carlo for the Electronic Structure of Molecules 9.1 Introduction 9.2 Quantum Monte Carlo Approaches 9.2.1 Variational Monte Carlo (VMC) 9.2.2 Diffusion Monte Carlo (DMC) 9.2.3 Fixed-Node DMC (FN-DMC) 9.2.4 Self-Healing DMC (SH-DMC) 9.2.5 Auxiliary Field QMC (AF-QMC) 9.2.6 Reptation QMC (RQMC) 9.2.7 Full CI QMC (FCI-QMC) 9.2.8 Time-Dependent QMC (TD-QMC) 9.2.9 Applications 9.3 Trial Wave Functions 9.3.1 Antisymmetric Wave Functions 9.3.2 Backflow Transformed Wave Functions 9.3.3 Effective Core Potentials (ECP) 9.3.4 Jastrow Wave Functions 9.3.5 Trial Wave Function Optimization 9.4 Computational Considerations 9.4.1 Scaling Analysis 9.4.2 Molecular Orbital Evaluation 9.4.3 Correlation Function Evaluation 9.4.4 Load Balancing 9.4.5 Parallelization and Hardware Acceleration 9.5 Conclusions References Chapter 10: Relativistic Quantum Monte Carlo Method 10.1 Introduction 10.2 Qumatum Monte Carlo Method 10.2.1 Quantum Monte Carlo Foundations 10.2.2 Variational Monte Carlo Method 10.2.3 Diffusion Monte Carlo Method 10.2.4 Wave Functions and Selective Sampling in Optimization 10.2.5 Electron-Nucleus Coalescence Condition 10.3 Relativistic Quantum Monte Carlo Method 10.3.1 Dirac Hamiltonian 10.3.2 Breit-Pauli Hamiltonian 10.3.3 ZORA Hamiltonian 10.3.4 Implementation of the ZORA Method into the MO Program 10.3.5 Local Energy for ZORA Hamiltonian 10.3.6 Electron-Nucleus Cusp Condition in ZORA-QMC Method 10.3.7 Cusp Correction Algorithm 10.4 R4QMC Program 10.5 Illustrative Results 10.5.1 Cusp Correction Effects 10.5.2 Cu Systems 10.6 Conclusions References Chapter 11: Computer Aided Nanomaterials Design - Self-assembly, Nanooptics, Molecular Electronics/Spintronics, and Fast DNA Sequencing 11.1 Introduction 11.2 Self-assembled Materials 11.2.1 Organic Nanotubes 11.2.2 Organic Nano-Scale Lens and Optical Properties 11.2.3 Nano-Mechanical Devices 11.3 Nano-Scale Electronic Materials 11.3.1 Theoretical Description of Nano-Scale Electronic Transport Phenomena 11.3.2 Electron Transport in 1-Dimensional Nanowire 11.3.3 Role of Electrodes in Molecular Electronics 11.3.4 Graphene Nanoribbon as a Spintronic Memory Device 11.4 Nano-Scale Molecular Sensors and DNA Sequencing 11.4.1 Ionophores/Receptors and Chemical Sensors 11.4.2 Graphene Nanoribbon as a Future DNA Sequencing Device 11.5 Concluding Remarks References Chapter 12: Computational Molecular Engineering for Nanodevices and Nanosystems 12.1 Introduction 12.1.1 Vibrational Electronics "Vibronics" 12.1.2 Molecular Electrostatic Potentials 12.1.3 Molecular Orbital Theory 12.1.4 Sensor Devices 12.2 Molecular Engineering Theory 12.2.1 Ab Initio Molecular Orbital Theory 12.2.2 Basis Sets 12.2.3 Hartree-Fock Theory 12.2.4 Density Functional Theory 12.2.5 Hybrid Functionals 12.2.6 Single Molecule Conductance 12.3 Optimum Fit Material for a Nano-Micro Interface 12.4 Graphene Based Sensors 12.5 Molecular Interface to Read Molecular Electrostatic Potentials Based Electronics 12.5.1 Graphene MEP Amplifier 12.6 Communication Between Molecular Scenarios: Single Molecule Detection Using Graphene Electrodes 12.7 Vibronics and Plasmonic Graphene Sensors 12.8 Graphene Vibronics Sensor 12.9 Plasmonic Graphene Sensors 12.10 Graphene Mixer 12.11 Conclusions - Summary References Chapter 13: Theoretical Studies of Thymine-Thymine Photodimerization: Using Ground State Dynamics to Model Photoreaction 13.1 Introduction 13.2 A Ground State Model for TT Dimerization in DNA 13.3 Model Calibration with dT20 and dA20dT20 13.3.1 Background 13.3.2 Computational Details 13.3.3 Results 13.4 Sequence Dependence of TT Dimerization in DNA Hairpins 13.4.1 Background 13.4.2 Computational Details 13.4.3 Results 13.5 Application to Locked Nucleic Acids 13.5.1 Background 13.5.2 Computational Details 13.5.3 Results 13.6 Quenching of TT Dimer Formation in Trinucleotides by Purines 13.6.1 Background 13.6.2 Computational Details 13.6.3 Results 13.7 Concluding Remarks References Chapter 14: Excited State Structural Analysis: TDDFT and Related Models 14.1 Introduction 14.2 CIS and Related RPA and TDDFT Methods 14.3 Main Structural Indices 14.4 CT and Hole-Particle Interpretation; Other Structural Indices 14.5 ESSA of Some Generic Systems 14.5.1 pp * -Transitions 14.5.2 n*p - and ss* -Transitions 14.5.3 Weakly Coupled Subsystems 14.5.4 Intramolecular Mixing of Local and CT Excitations 14.6 Some Photochemical Applications 14.7 Extension of ESSA to the General CI Case 14.8 Concluding Remarks References Chapter 15: VCD Chirality Transfer: A New Insight into the Intermolecular Interactions 15.1 Introduction 15.2 The Physical Manifestation of Optical Activity in Chiroptical Spectroscopic Methods 15.2.1 Chiroptical Methods 15.2.2 Chirality Transfer 15.2.3 Mode Robustness 15.3 Methods of Calculations of the VCD Spectra 15.3.1 The Molecular Origin of Vibrational Circular Dichroism 15.3.2 Practical Aspects of the Calculations: Methods, Basis Set, Software o 15.3.2.1 Electronic Structure Methods o 15.3.2.2 The Basis Set Requirements o 15.3.2.3 Implementation Procedure and Program Packages 15.4 Applications of VCD to Study Chirality Transfer 15.5 Perspectives References Chapter 16: Non-hydrogen-Bonding Intramolecular Interactions: Important but Often Overlooked 16.1 Noncovalent Interactions 16.2 The Electrostatic Potential 16.3 Some Noncovalent Intramolecular Interactions 16.3.1 The Nitro Group 16.3.2 The Si-O-N Linkage 16.3.3 Some 1,3 Si--O Interactions 16.3.4 Conformation Stabilization 16.4 Summary References Chapter 17: X-H...p and X-H...s Interactions - Hydrogen Bonds with Multicenter Proton Acceptors 17.1 Classification of Hydrogen Bonds According to Properties of Proton Donor and Proton Acceptor 17.2 Energies of X-H...p and X-H...s Interactions 17.3 The Use of Quantum Theory of `Atoms in Molecules' to Characterize X-H...p and X-H...s Interactions 17.4 The Case of Multicenter Proton Acceptors 17.5 Summary References Chapter 18: Computational Approaches Towards Modeling Finite Molecular Assemblies: Role of Cation-p, p-p and Hydrogen Bonding Interactions 18.1 Introduction 18.2 Noncovalent Interactions 18.2.1 Cation-p Interactions o 18.2.1.1 Computational Details o 18.2.1.2 Impact of Different Cations and Preferential Site of Binding to Aromatic Group o 18.2.1.3 s vs p Binding of Cations to Heteroaromatic Systems o 18.2.1.4 Cation-Aromatic Database o 18.2.1.5 Size of System o 18.2.1.6 Solvation 18.2.2 p-p Interactions 18.2.3 Hydrogen Bonding 18.3 Cooperativity 18.4 Correlation and Dispersion 18.5 Materials 18.6 Molecular Dynamics 18.7 Biological Relevance 18.8 Outlook References Chapter 19: Unusual Properties of Usual Molecules. Conformational Analysis of Cyclohexene, Its Derivatives and Heterocyclic Analogues 19.1 Conformational Properties of Cyclohexene 19.2 Derivatives of Cyclohexene Containing Exocyclic Double Bond 19.2.1 Derivatives of Cyclohexene with Conjugated Double Bonds 19.2.2 Derivatives of Cyclohexene with Non-conjugated Double Bonds 19.3 Tetrahydroheterocycles 19.3.1 Tetrahydroheterocycles Containing Chalcogen 19.3.2 Tetrahydroheterocycles Containing Pnictogen 19.4 Conclusions References Chapter 20: Molecular Models of the Stabilization of Bivalent Metal Cations in Zeolite Catalysts 20.1 Introduction 20.2 Structural Forms of the Stabilization of Single Bivalent Metal Ions in Cationic Positions of Zeolites 20.3 OxoBinuclear Structures of the Alkaline Earth (AE) Metal Cations 20.3.1 Reactivity of the Me2OX Clusters in the AE Zeolites o 20.3.1.1 CO Oxidation o 20.3.1.2 CO2 Interaction with the MeOXMe(MOR) Species o 20.3.1.3 AE Carbonate Interaction with Methanol 20.4 On the Feasible Ways of the Polynuclear Metal-Oxo Clusters Formation 20.5 On Possible Forms of Single Fe(II) Ion Stabilization in Fe/HZSM-5 Selective Oxidation Catalyst 20.5.1 The Electronic Structure of FeOa Centers 20.5.2 The Impact of the Radical Electronic State of FeOa on Oxidative Reactions 20.6 Outlook References Chapter 21: Towards Involvement of Interactions of Nucleic Acid Bases with Minerals in the Origin of Life: Quantum Chemical Approach 21.1 Introduction 21.2 Computational Details 21.3 Experimental Studies of Interactions of Minerals with DNA 21.4 Theoretical Studies of Nucleic Acid Bases and Their Interactions with Water, Cations and Minerals 21.4.1 Wächterhäuser Experiment 21.4.2 Interactions of Nucleic Acid Bases with Sodium Cation and Water 21.4.3 Interactions of Nucleic Acid Bases with Clay Minerals o 21.4.3.1 Geometrical Parameters and Charges of Thymine and Uracil Adsorbed on Minerals of Kaolinite Group o 21.4.3.2 Interactions of Thymine and Uracil with Hydrated Surface of Minerals of the Kaolinite Group o 21.4.3.3 Energetics of Thymine and Uracil Adsorbed on Hydrated Surface of Minerals of the Kaolinite Group o 21.4.3.4 Implication to Origin of Life 21.5 Conclusions References Index