1. Introduction to computational chemistry [2017]
- Book
- xxii, 638 pages : illustrations ; 25 cm
- Preface to the First Edition xv Preface to the Second Edition xix Preface to the Third Edition xxi 1 Introduction 1 1.1 Fundamental Issues 2 1.2 Describing the System 3 1.3 Fundamental Forces 3 1.4 The Dynamical Equation 5 1.5 Solving the Dynamical Equation 7 1.6 Separation of Variables 8 1.7 Classical Mechanics 11 1.8 Quantum Mechanics 13 1.9 Chemistry 18 References 19 2 Force Field Methods 20 2.1 Introduction 20 2.2 The Force Field Energy 21 2.3 Force Field Parameterization 53 2.4 Differences in Atomistic Force Fields 62 2.5 Water Models 66 2.6 Coarse Grained Force Fields 67 2.7 Computational Considerations 69 2.8 Validation of Force Fields 71 2.9 Practical Considerations 73 2.10 Advantages and Limitations of Force Field Methods 73 2.11 Transition Structure Modeling 74 2.12 Hybrid Force Field Electronic Structure Methods 78 References 82 3 Hartree Fock Theory 88 3.1 The Adiabatic and Born Oppenheimer Approximations 90 3.2 Hartree FockTheory 94 3.3 The Energy of a Slater Determinant 95 3.4 Koopmans Theorem 100 3.5 The Basis Set Approximation 101 3.6 An Alternative Formulation of the Variational Problem 105 3.7 Restricted and Unrestricted Hartree Fock 106 3.8 SCF Techniques 108 3.9 Periodic Systems 119 References 121 4 Electron Correlation Methods 124 4.1 Excited Slater Determinants 125 4.2 Configuration Interaction 128 4.3 Illustrating how CI Accounts for Electron Correlation, and the RHF Dissociation Problem 135 4.4 The UHF Dissociation and the Spin Contamination Problem 138 4.5 Size Consistency and Size Extensivity 142 4.6 Multiconfiguration Self-Consistent Field 143 4.7 Multireference Configuration Interaction 148 4.8 Many-Body Perturbation Theory 148 4.9 Coupled Cluster 157 4.10 Connections between Coupled Cluster, Configuration Interaction and Perturbation Theory 162 4.11 Methods Involving the Interelectronic Distance 166 4.12 Techniques for Improving the Computational Efficiency 169 4.13 Summary of Electron Correlation Methods 174 4.14 Excited States 176 4.15 Quantum Monte Carlo Methods 183 References 185 5 Basis Sets 188 5.1 Slater- and Gaussian-Type Orbitals 189 5.2 Classification of Basis Sets 190 5.3 Construction of Basis Sets 194 5.4 Examples of Standard Basis Sets 200 5.5 Plane Wave Basis Functions 208 5.6 Grid and Wavelet Basis Sets 210 5.7 Fitting Basis Sets 211 5.8 Computational Issues 211 5.9 Basis Set Extrapolation 212 5.10 Composite Extrapolation Procedures 215 5.11 Isogyric and Isodesmic Reactions 222 5.12 Effective Core Potentials 223 5.13 Basis Set Superposition and Incompleteness Errors 226 References 228 6 Density Functional Methods 233 6.1 Orbital-Free Density Functional Theory 234 6.2 Kohn Sham Theory 235 6.3 Reduced Density Matrix and Density Cumulant Methods 237 6.4 Exchange and Correlation Holes 241 6.5 Exchange Correlation Functionals 244 6.6 Performance of Density Functional Methods 258 6.7 Computational Considerations 260 6.8 Differences between Density Functional Theory and Hartree-Fock 262 6.9 Time-Dependent Density Functional Theory (TDDFT) 263 6.10 Ensemble Density Functional Theory 268 6.11 Density Functional Theory Problems 269 6.12 Final Considerations 269 References 270 7 Semi-empirical Methods 275 7.1 Neglect of Diatomic Differential Overlap (NDDO) Approximation 276 7.2 Intermediate Neglect of Differential Overlap (INDO) Approximation 277 7.3 Complete Neglect of Differential Overlap (CNDO) Approximation 277 7.4 Parameterization 278 7.5 Huckel Theory 283 7.6 Tight-Binding Density Functional Theory 285 7.7 Performance of Semi-empirical Methods 287 7.8 Advantages and Limitations of Semi-empirical Methods 289 References 290 8 Valence Bond Methods 291 8.1 Classical Valence Bond Theory 292 8.2 Spin-Coupled Valence Bond Theory 293 8.3 Generalized Valence Bond Theory 297 References 298 9 Relativistic Methods 299 9.1 The Dirac Equation 300 9.2 Connections between the Dirac and Schrodinger Equations 302 9.3 Many-Particle Systems 306 9.4 Four-Component Calculations 309 9.5 Two-Component Calculations 310 9.6 Relativistic Effects 313 References 315 10 Wave Function Analysis 317 10.1 Population Analysis Based on Basis Functions 317 10.2 Population Analysis Based on the Electrostatic Potential 320 10.3 Population Analysis Based on the Electron Density 323 10.4 Localized Orbitals 329 10.5 Natural Orbitals 333 10.6 Computational Considerations 337 10.7 Examples 338 References 339 11 Molecular Properties 341 11.1 Examples of Molecular Properties 343 11.2 Perturbation Methods 347 11.3 Derivative Techniques 349 11.4 Response and Propagator Methods 351 11.5 Lagrangian Techniques 351 11.6 Wave Function Response 353 11.7 Electric Field Perturbation 357 11.8 Magnetic Field Perturbation 358 11.9 Geometry Perturbations 367 11.10 Time-Dependent Perturbations 372 11.11 Rotational and Vibrational Corrections 377 11.12 Environmental Effects 378 11.13 Relativistic Corrections 378 References 378 12 Illustrating the Concepts 380 12.1 Geometry Convergence 380 12.2 Total Energy Convergence 383 12.3 Dipole Moment Convergence 385 12.4 Vibrational Frequency Convergence 386 12.5 Bond Dissociation Curves 389 12.6 Angle Bending Curves 394 12.7 Problematic Systems 396 12.8 Relative Energies of C4H6 Isomers 399 References 402 13 Optimization Techniques 404 13.1 Optimizing Quadratic Functions 405 13.2 Optimizing General Functions: Finding Minima 407 13.3 Choice of Coordinates 415 13.4 Optimizing General Functions: Finding Saddle Points (Transition Structures) 418 13.5 Constrained Optimizations 431 13.6 Global Minimizations and Sampling 433 13.7 Molecular Docking 440 13.8 Intrinsic Reaction Coordinate Methods 441 References 444 14 Statistical Mechanics and Transition State Theory 447 14.1 Transition State Theory 447 14.2 Rice Ramsperger Kassel Marcus Theory 450 14.3 Dynamical Effects 451 14.4 StatisticalMechanics 452 14.5 The Ideal Gas, Rigid-Rotor Harmonic-Oscillator Approximation 454 14.6 Condensed Phases 464 References 468 15 Simulation Techniques 469 15.1 Monte Carlo Methods 472 15.2 Time-Dependent Methods 474 15.3 Periodic Boundary Conditions 491 15.4 Extracting Information from Simulations 494 15.5 Free Energy Methods 499 15.6 Solvation Models 502 References 511 16 Qualitative Theories 515 16.1 Frontier Molecular Orbital Theory 515 16.2 Concepts from Density Functional Theory 519 16.3 Qualitative Molecular Orbital Theory 522 16.4 Energy Decomposition Analyses 524 16.5 Orbital Correlation Diagrams: TheWoodward Hoffmann Rules 526 16.6 The Bell Evans Polanyi Principle/Hammond Postulate/Marcus Theory 534 16.7 More O Ferrall Jencks Diagrams 538 References 541 17 Mathematical Methods 543 17.1 Numbers, Vectors, Matrices and Tensors 543 17.2 Change of Coordinate System 549 17.3 Coordinates, Functions, Functionals, Operators and Superoperators 560 17.3.1 Differential Operators 562 17.4 Normalization, Orthogonalization and Projection 563 17.5 Differential Equations 565 17.6 Approximating Functions 568 17.7 Fourier and Laplace Transformations 577 17.8 Surfaces 577 References 580 18 Statistics and QSAR 581 18.1 Introduction 581 18.2 Elementary Statistical Measures 583 18.3 Correlation between Two Sets of Data 585 18.4 Correlation between Many Sets of Data 588 18.5 Quantitative Structure Activity Relationships (QSAR) 595 18.6 Non-linear Correlation Methods 597 18.7 Clustering Methods 598 References 604 19 Concluding Remarks 605 Appendix A 608 Notation 608 Appendix B 614 The Variational Principle 614 The Hohenberg Kohn Theorems 615 The Adiabatic Connection Formula 616 Reference 617 Appendix C 618 Atomic Units 618 Appendix D 619 Z Matrix Construction 619 Appendix E 627 First and Second Quantization 627 References 628 Index 629.
- (source: Nielsen Book Data)9781118825990 20170327
(source: Nielsen Book Data)9781118825990 20170327
- Preface to the First Edition xv Preface to the Second Edition xix Preface to the Third Edition xxi 1 Introduction 1 1.1 Fundamental Issues 2 1.2 Describing the System 3 1.3 Fundamental Forces 3 1.4 The Dynamical Equation 5 1.5 Solving the Dynamical Equation 7 1.6 Separation of Variables 8 1.7 Classical Mechanics 11 1.8 Quantum Mechanics 13 1.9 Chemistry 18 References 19 2 Force Field Methods 20 2.1 Introduction 20 2.2 The Force Field Energy 21 2.3 Force Field Parameterization 53 2.4 Differences in Atomistic Force Fields 62 2.5 Water Models 66 2.6 Coarse Grained Force Fields 67 2.7 Computational Considerations 69 2.8 Validation of Force Fields 71 2.9 Practical Considerations 73 2.10 Advantages and Limitations of Force Field Methods 73 2.11 Transition Structure Modeling 74 2.12 Hybrid Force Field Electronic Structure Methods 78 References 82 3 Hartree Fock Theory 88 3.1 The Adiabatic and Born Oppenheimer Approximations 90 3.2 Hartree FockTheory 94 3.3 The Energy of a Slater Determinant 95 3.4 Koopmans Theorem 100 3.5 The Basis Set Approximation 101 3.6 An Alternative Formulation of the Variational Problem 105 3.7 Restricted and Unrestricted Hartree Fock 106 3.8 SCF Techniques 108 3.9 Periodic Systems 119 References 121 4 Electron Correlation Methods 124 4.1 Excited Slater Determinants 125 4.2 Configuration Interaction 128 4.3 Illustrating how CI Accounts for Electron Correlation, and the RHF Dissociation Problem 135 4.4 The UHF Dissociation and the Spin Contamination Problem 138 4.5 Size Consistency and Size Extensivity 142 4.6 Multiconfiguration Self-Consistent Field 143 4.7 Multireference Configuration Interaction 148 4.8 Many-Body Perturbation Theory 148 4.9 Coupled Cluster 157 4.10 Connections between Coupled Cluster, Configuration Interaction and Perturbation Theory 162 4.11 Methods Involving the Interelectronic Distance 166 4.12 Techniques for Improving the Computational Efficiency 169 4.13 Summary of Electron Correlation Methods 174 4.14 Excited States 176 4.15 Quantum Monte Carlo Methods 183 References 185 5 Basis Sets 188 5.1 Slater- and Gaussian-Type Orbitals 189 5.2 Classification of Basis Sets 190 5.3 Construction of Basis Sets 194 5.4 Examples of Standard Basis Sets 200 5.5 Plane Wave Basis Functions 208 5.6 Grid and Wavelet Basis Sets 210 5.7 Fitting Basis Sets 211 5.8 Computational Issues 211 5.9 Basis Set Extrapolation 212 5.10 Composite Extrapolation Procedures 215 5.11 Isogyric and Isodesmic Reactions 222 5.12 Effective Core Potentials 223 5.13 Basis Set Superposition and Incompleteness Errors 226 References 228 6 Density Functional Methods 233 6.1 Orbital-Free Density Functional Theory 234 6.2 Kohn Sham Theory 235 6.3 Reduced Density Matrix and Density Cumulant Methods 237 6.4 Exchange and Correlation Holes 241 6.5 Exchange Correlation Functionals 244 6.6 Performance of Density Functional Methods 258 6.7 Computational Considerations 260 6.8 Differences between Density Functional Theory and Hartree-Fock 262 6.9 Time-Dependent Density Functional Theory (TDDFT) 263 6.10 Ensemble Density Functional Theory 268 6.11 Density Functional Theory Problems 269 6.12 Final Considerations 269 References 270 7 Semi-empirical Methods 275 7.1 Neglect of Diatomic Differential Overlap (NDDO) Approximation 276 7.2 Intermediate Neglect of Differential Overlap (INDO) Approximation 277 7.3 Complete Neglect of Differential Overlap (CNDO) Approximation 277 7.4 Parameterization 278 7.5 Huckel Theory 283 7.6 Tight-Binding Density Functional Theory 285 7.7 Performance of Semi-empirical Methods 287 7.8 Advantages and Limitations of Semi-empirical Methods 289 References 290 8 Valence Bond Methods 291 8.1 Classical Valence Bond Theory 292 8.2 Spin-Coupled Valence Bond Theory 293 8.3 Generalized Valence Bond Theory 297 References 298 9 Relativistic Methods 299 9.1 The Dirac Equation 300 9.2 Connections between the Dirac and Schrodinger Equations 302 9.3 Many-Particle Systems 306 9.4 Four-Component Calculations 309 9.5 Two-Component Calculations 310 9.6 Relativistic Effects 313 References 315 10 Wave Function Analysis 317 10.1 Population Analysis Based on Basis Functions 317 10.2 Population Analysis Based on the Electrostatic Potential 320 10.3 Population Analysis Based on the Electron Density 323 10.4 Localized Orbitals 329 10.5 Natural Orbitals 333 10.6 Computational Considerations 337 10.7 Examples 338 References 339 11 Molecular Properties 341 11.1 Examples of Molecular Properties 343 11.2 Perturbation Methods 347 11.3 Derivative Techniques 349 11.4 Response and Propagator Methods 351 11.5 Lagrangian Techniques 351 11.6 Wave Function Response 353 11.7 Electric Field Perturbation 357 11.8 Magnetic Field Perturbation 358 11.9 Geometry Perturbations 367 11.10 Time-Dependent Perturbations 372 11.11 Rotational and Vibrational Corrections 377 11.12 Environmental Effects 378 11.13 Relativistic Corrections 378 References 378 12 Illustrating the Concepts 380 12.1 Geometry Convergence 380 12.2 Total Energy Convergence 383 12.3 Dipole Moment Convergence 385 12.4 Vibrational Frequency Convergence 386 12.5 Bond Dissociation Curves 389 12.6 Angle Bending Curves 394 12.7 Problematic Systems 396 12.8 Relative Energies of C4H6 Isomers 399 References 402 13 Optimization Techniques 404 13.1 Optimizing Quadratic Functions 405 13.2 Optimizing General Functions: Finding Minima 407 13.3 Choice of Coordinates 415 13.4 Optimizing General Functions: Finding Saddle Points (Transition Structures) 418 13.5 Constrained Optimizations 431 13.6 Global Minimizations and Sampling 433 13.7 Molecular Docking 440 13.8 Intrinsic Reaction Coordinate Methods 441 References 444 14 Statistical Mechanics and Transition State Theory 447 14.1 Transition State Theory 447 14.2 Rice Ramsperger Kassel Marcus Theory 450 14.3 Dynamical Effects 451 14.4 StatisticalMechanics 452 14.5 The Ideal Gas, Rigid-Rotor Harmonic-Oscillator Approximation 454 14.6 Condensed Phases 464 References 468 15 Simulation Techniques 469 15.1 Monte Carlo Methods 472 15.2 Time-Dependent Methods 474 15.3 Periodic Boundary Conditions 491 15.4 Extracting Information from Simulations 494 15.5 Free Energy Methods 499 15.6 Solvation Models 502 References 511 16 Qualitative Theories 515 16.1 Frontier Molecular Orbital Theory 515 16.2 Concepts from Density Functional Theory 519 16.3 Qualitative Molecular Orbital Theory 522 16.4 Energy Decomposition Analyses 524 16.5 Orbital Correlation Diagrams: TheWoodward Hoffmann Rules 526 16.6 The Bell Evans Polanyi Principle/Hammond Postulate/Marcus Theory 534 16.7 More O Ferrall Jencks Diagrams 538 References 541 17 Mathematical Methods 543 17.1 Numbers, Vectors, Matrices and Tensors 543 17.2 Change of Coordinate System 549 17.3 Coordinates, Functions, Functionals, Operators and Superoperators 560 17.3.1 Differential Operators 562 17.4 Normalization, Orthogonalization and Projection 563 17.5 Differential Equations 565 17.6 Approximating Functions 568 17.7 Fourier and Laplace Transformations 577 17.8 Surfaces 577 References 580 18 Statistics and QSAR 581 18.1 Introduction 581 18.2 Elementary Statistical Measures 583 18.3 Correlation between Two Sets of Data 585 18.4 Correlation between Many Sets of Data 588 18.5 Quantitative Structure Activity Relationships (QSAR) 595 18.6 Non-linear Correlation Methods 597 18.7 Clustering Methods 598 References 604 19 Concluding Remarks 605 Appendix A 608 Notation 608 Appendix B 614 The Variational Principle 614 The Hohenberg Kohn Theorems 615 The Adiabatic Connection Formula 616 Reference 617 Appendix C 618 Atomic Units 618 Appendix D 619 Z Matrix Construction 619 Appendix E 627 First and Second Quantization 627 References 628 Index 629.
- (source: Nielsen Book Data)9781118825990 20170327
(source: Nielsen Book Data)9781118825990 20170327
Science Library (Li and Ma)
Science Library (Li and Ma) | Status |
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Stacks | |
QD455.3 .E4 J46 2017 | Unknown |
QD455.3 .E4 J46 2017 | Unknown On reserve at Li and Ma Science Library 2-hour loan |
CHEM-261-01
- Course
- CHEM-261-01 -- Computational Chemistry
- Instructor(s)
- Markland, Thomas Edward
2. Computational organic chemistry [2014]
- Book
- 1 online resource.
- Preface xv Acknowledgments xxi 1. Quantum Mechanics for Organic Chemistry 1 1.1 Approximations to the Schrodinger Equation TheHartree Fock Method 2 1.1.1 Nonrelativistic Mechanics 2 1.1.2 The Born Oppenheimer Approximation 3 1.1.3 The One-Electron Wavefunction and the Hartree FockMethod 3 1.1.4 Linear Combination of Atomic Orbitals (LCAO) Approximation4 1.1.5 Hartree Fock Roothaan Procedure 5 1.1.6 Restricted Versus Unrestricted Wavefunctions 7 1.1.7 The Variational Principle 7 1.1.8 Basis Sets 8 1.1.8.1 Basis Set Superposition Error 12 1.2 Electron Correlation Post-Hartree Fock Methods13 1.2.1 Configuration Interaction (CI) 14 1.2.2 Size Consistency 16 1.2.3 Perturbation Theory 16 1.2.4 Coupled-Cluster Theory 17 1.2.5 Multiconfiguration SCF (MCSCF) Theory and Complete ActiveSpace SCF (CASSCF) Theory 18 1.2.6 Composite Energy Methods 20 1.3 Density Functional Theory (DFT) 22 1.3.1 The Exchange-Correlation Functionals: ClimbingJacob s Ladder 24 1.3.1.1 Double Hybrid Functionals 26 1.3.2 Dispersion-Corrected DFT 26 1.3.3 Functional Selection 28 1.4 Computational Approaches to Solvation 28 1.4.1 Microsolvation 28 1.4.2 Implicit Solvent Models 29 1.4.3 Hybrid Solvation Models 34 1.5 Hybrid QM/MM Methods 35 1.5.1 Molecular Mechanics 36 1.5.2 QM/MM Theory 38 1.5.3 ONIOM 39 1.6 Potential Energy Surfaces 40 1.6.1 Geometry Optimization 42 1.7 Population Analysis 45 1.7.1 Orbital-Based Population Methods 46 1.7.2 Topological Electron Density Analysis 47 1.8 Interview: Stefan Grimme 48 References 51 2. Computed Spectral Properties and Structure Identification61 2.1 Computed Bond Lengths and Angles 61 2.2 IR Spectroscopy 62 2.3 Nuclear Magnetic Resonance 66 2.3.1 General Considerations 68 2.3.2 Scaling Chemical Shift Values 69 2.3.3 Customized Density Functionals and Basis Sets 71 2.3.4 Methods for Structure Prediction 73 2.3.5 Statistical Approaches to Computed Chemical Shifts 74 2.3.6 Computed Coupling Constants 76 2.3.7 Case Studies 77 2.3.7.1 Hexacyclinol 77 2.3.7.2 Maitotoxin 79 2.3.7.3 Vannusal B 80 2.3.7.4 Conicasterol F 81 2.3.7.5 1-Adamantyl Cation 81 2.4 Optical Rotation, Optical Rotatory Dispersion, ElectronicCircular Dichroism, and Vibrational Circular Dichroism 82 2.4.1 Case Studies 85 2.4.1.1 Solvent Effect 85 2.4.1.2 Chiral Solvent Imprinting 86 2.4.1.3 Plumericin and Prismatomerin 87 2.4.1.4 2,3-Hexadiene 88 2.4.1.5 Multilayered Paracyclophane 89 2.4.1.6 Optical Activity of an Octaphyrin 90 2.5 Interview: Jonathan Goodman 90 References 93 3. Fundamentals of Organic Chemistry 99 3.1 Bond Dissociation Enthalpy 99 3.1.1 Case Study of BDE: Trends in the R X BDE 102 3.2 Acidity 104 3.2.1 Case Studies of Acidity 107 3.2.1.1 Carbon Acidity of Strained Hydrocarbons 107 3.2.1.2 Origin of the Acidity of Carboxylic Acids 113 3.2.1.3 Acidity of the Amino Acids 116 3.3 Isomerism and Problems With DFT 119 3.3.1 Conformational Isomerism 119 3.3.2 Conformations of Amino Acids 121 3.3.3 Alkane Isomerism and DFT Errors 123 3.3.3.1 Chemical Consequences of Dispersion 131 3.4 Ring Strain Energy 132 3.4.1 RSE of Cyclopropane (28) and Cylcobutane (29) 138 3.5 Aromaticity 144 3.5.1 Aromatic Stabilization Energy (ASE) 145 3.5.2 Nucleus-Independent Chemical Shift (NICS) 150 3.5.3 Case Studies of Aromatic Compounds 155 3.5.3.1 [n]Annulenes 155 3.5.3.2 The Mills Nixon Effect 166 3.5.3.3 Aromaticity Versus Strain 171 3.5.4 Stacking 173 3.6 Interview: Professor Paul Von RagueSchleyer 177 References 180 4. Pericyclic Reactions 197 4.1 The Diels Alder Reaction 198 4.1.1 The Concerted Reaction of 1,3-Butadiene with Ethylene199 4.1.2 The Nonconcerted Reaction of 1,3-Butadiene with Ethylene207 4.1.3 Kinetic Isotope Effects and the Nature of theDiels Alder Transition State 209 4.1.4 Transition State Distortion Energy 214 4.2 The Cope Rearrangement 215 4.2.1 Theoretical Considerations 217 4.2.2 Computational Results 219 4.2.3 Chameleons and Centaurs 227 4.3 The Bergman Cyclization 233 4.3.1 Theoretical Considerations 237 4.3.2 Activation and Reaction Energies of the Parent BergmanCyclization 239 4.3.3 The cd Criteria and Cyclic Enediynes 244 4.3.4 Myers Saito and Schmittel Cyclization 249 4.4 Bispericyclic Reactions 256 4.5 Pseudopericyclic Reactions 260 4.6 Torquoselectivity 267 4.7 Interview: Professor Weston Thatcher Borden 278 References 282 5. Diradicals and Carbenes 297 5.1 Methylene 298 5.1.1 Theoretical Considerations of Methylene 298 5.1.2 The H C H Angle in Triplet Methylene 299 5.1.3 The Methylene and Dichloromethylene Singlet TripletEnergy Gap 300 5.2 Phenylnitrene and Phenylcarbene 304 5.2.1 The Low Lying States of Phenylnitrene and Phenylcarbene305 5.2.2 Ring Expansion of Phenylnitrene and Phenylcarbene 312 5.2.3 Substituent Effects on the Rearrangement of Phenylnitrene317 5.3 Tetramethyleneethane 324 5.3.1 Theoretical Considerations of Tetramethyleneethane 326 5.3.2 Is TME a Ground-State Singlet or Triplet? 326 5.4 Oxyallyl Diradical 330 5.5 Benzynes 333 5.5.1 Theoretical Considerations of Benzyne 333 5.5.2 Relative Energies of the Benzynes 336 5.5.3 Structure of m-Benzyne 341 5.5.4 The Singlet Triplet Gap and Reactivity of theBenzynes 345 5.6 Tunneling of Carbenes 349 5.6.1 Tunneling control 353 5.7 Interview: Professor Henry Fritz Schaefer355 5.8 Interview: Professor Peter R. Schreiner 357 References 360 6. Organic Reactions of Anions 373 6.1 Substitution Reactions 373 6.1.1 The Gas Phase SN2 Reaction 374 6.1.2 Effects of Solvent on SN2 Reactions 385 6.2 Asymmetric Induction Via 1,2-Addition to Carbonyl Compounds391 6.3 Asymmetric Organocatalysis of Aldol Reactions 404 6.3.1 Mechanism of Amine-Catalyzed Intermolecular AldolReactions 409 6.3.2 Mechanism of Proline-Catalyzed Intramolecular AldolReactions 417 6.3.3 Comparison with the Mannich Reaction 421 6.3.4 Catalysis of the Aldol Reaction in Water 426 6.3.5 Another Organocatalysis Example The ClaisenRearrangement 429 6.4 Interview: Professor Kendall N. Houk 432 References 435 7. Solution-Phase Organic Chemistry 445 7.1 Aqueous Diels Alder Reactions 446 7.2 Glucose 452 7.2.1 Models Compounds: Ethylene Glycol and Glycerol 453 7.2.1.1 Ethylene Glycol 453 7.2.1.2 Glycerol 458 7.2.2 Solvation Studies of Glucose 460 7.3 Nucleic Acids 468 7.3.1 Nucleic Acid Bases 469 7.3.1.1 Cytosine 469 7.3.1.2 Guanine 473 7.3.1.3 Adenine 475 7.3.1.4 Uracil and Thymine 477 7.3.2 Base Pairs 479 7.4 Amino Acids 489 7.5 Interview: Professor Christopher J. Cramer 492 References 496 8. Organic Reaction Dynamics 505 8.1 A Brief Introduction To Molecular Dynamics TrajectoryComputations 508 8.1.1 Integrating the Equations of Motion 508 8.1.2 Selecting the PES 510 8.1.3 Initial Conditions 511 8.2 Statistical Kinetic Theories 512 8.3 Examples of Organic Reactions With Non-Statistical Dynamics514 8.3.1 [1,3]-Sigmatropic Rearrangement of Bicyclo[3.2.0]hex-2-ene514 8.3.2 Life in the Caldera: Concerted versus Diradical Mechanisms518 8.3.2.1 Rearrangement of Vinylcyclopropane to Cyclopentene520 8.3.2.2 Bicyclo[3.1.0]hex-2-ene 20 524 8.3.2.3 Cyclopropane Stereomutation 526 8.3.3 Entrance into Intermediates from Above 530 8.3.3.1 Deazetization of 2,3-Diazabicyclo[2.2.1]hept-2-ene 31530 8.3.4 Avoiding Local Minima 533 8.3.4.1 Methyl Loss from Acetone Radical Cation 533 8.3.4.2 Cope Rearrangement of 1,2,6-Heptatriene 534 8.3.4.3 The SN2 Reaction: HO + CH3F 536 8.3.4.4 Reaction of Fluoride with Methyl Hydroperoxide 538 8.3.5 Bifurcating Surfaces: One TS, Two Products 539 8.3.5.1 C2 C6 Enyne Allene Cyclization 540 8.3.5.2 Cycloadditions Involving Ketenes 543 8.3.5.3 Diels Alder Reactions: Steps toward PredictingDynamic Effects on Bifurcating Surfaces 547 8.3.6 Stepwise Reaction on a Concerted Surface 550 8.3.6.1 Rearrangement of Protonated Pinacolyl Alcohol 550 8.3.7 Roaming Mechanism 551 8.3.8 A Roundabout SN2 reaction 553 8.3.9 Hydroboration: Dynamical or Statistical? 554 8.3.10 A Look at the Wolff Rearrangement 555 8.4 Conclusions 557 8.5 Interview: Professor Daniel Singleton 558 References 561 9. Computational Approaches to Understanding Enzymes569 9.1 Models for Enzymatic Activity 569 9.2 Strategy for Computational Enzymology 573 9.2.1 High Level QM/MM Computations of Enzymes 576 9.2.2 Chorismate Mutase 578 9.2.3 Catechol-O-Methyltransferase (COMT) 582 9.3 De Novo Design of Enzymes 586 References 592 Index 599.
- (source: Nielsen Book Data)9781118291924 20160616
(source: Nielsen Book Data)9781118291924 20160616
- Preface xv Acknowledgments xxi 1. Quantum Mechanics for Organic Chemistry 1 1.1 Approximations to the Schrodinger Equation TheHartree Fock Method 2 1.1.1 Nonrelativistic Mechanics 2 1.1.2 The Born Oppenheimer Approximation 3 1.1.3 The One-Electron Wavefunction and the Hartree FockMethod 3 1.1.4 Linear Combination of Atomic Orbitals (LCAO) Approximation4 1.1.5 Hartree Fock Roothaan Procedure 5 1.1.6 Restricted Versus Unrestricted Wavefunctions 7 1.1.7 The Variational Principle 7 1.1.8 Basis Sets 8 1.1.8.1 Basis Set Superposition Error 12 1.2 Electron Correlation Post-Hartree Fock Methods13 1.2.1 Configuration Interaction (CI) 14 1.2.2 Size Consistency 16 1.2.3 Perturbation Theory 16 1.2.4 Coupled-Cluster Theory 17 1.2.5 Multiconfiguration SCF (MCSCF) Theory and Complete ActiveSpace SCF (CASSCF) Theory 18 1.2.6 Composite Energy Methods 20 1.3 Density Functional Theory (DFT) 22 1.3.1 The Exchange-Correlation Functionals: ClimbingJacob s Ladder 24 1.3.1.1 Double Hybrid Functionals 26 1.3.2 Dispersion-Corrected DFT 26 1.3.3 Functional Selection 28 1.4 Computational Approaches to Solvation 28 1.4.1 Microsolvation 28 1.4.2 Implicit Solvent Models 29 1.4.3 Hybrid Solvation Models 34 1.5 Hybrid QM/MM Methods 35 1.5.1 Molecular Mechanics 36 1.5.2 QM/MM Theory 38 1.5.3 ONIOM 39 1.6 Potential Energy Surfaces 40 1.6.1 Geometry Optimization 42 1.7 Population Analysis 45 1.7.1 Orbital-Based Population Methods 46 1.7.2 Topological Electron Density Analysis 47 1.8 Interview: Stefan Grimme 48 References 51 2. Computed Spectral Properties and Structure Identification61 2.1 Computed Bond Lengths and Angles 61 2.2 IR Spectroscopy 62 2.3 Nuclear Magnetic Resonance 66 2.3.1 General Considerations 68 2.3.2 Scaling Chemical Shift Values 69 2.3.3 Customized Density Functionals and Basis Sets 71 2.3.4 Methods for Structure Prediction 73 2.3.5 Statistical Approaches to Computed Chemical Shifts 74 2.3.6 Computed Coupling Constants 76 2.3.7 Case Studies 77 2.3.7.1 Hexacyclinol 77 2.3.7.2 Maitotoxin 79 2.3.7.3 Vannusal B 80 2.3.7.4 Conicasterol F 81 2.3.7.5 1-Adamantyl Cation 81 2.4 Optical Rotation, Optical Rotatory Dispersion, ElectronicCircular Dichroism, and Vibrational Circular Dichroism 82 2.4.1 Case Studies 85 2.4.1.1 Solvent Effect 85 2.4.1.2 Chiral Solvent Imprinting 86 2.4.1.3 Plumericin and Prismatomerin 87 2.4.1.4 2,3-Hexadiene 88 2.4.1.5 Multilayered Paracyclophane 89 2.4.1.6 Optical Activity of an Octaphyrin 90 2.5 Interview: Jonathan Goodman 90 References 93 3. Fundamentals of Organic Chemistry 99 3.1 Bond Dissociation Enthalpy 99 3.1.1 Case Study of BDE: Trends in the R X BDE 102 3.2 Acidity 104 3.2.1 Case Studies of Acidity 107 3.2.1.1 Carbon Acidity of Strained Hydrocarbons 107 3.2.1.2 Origin of the Acidity of Carboxylic Acids 113 3.2.1.3 Acidity of the Amino Acids 116 3.3 Isomerism and Problems With DFT 119 3.3.1 Conformational Isomerism 119 3.3.2 Conformations of Amino Acids 121 3.3.3 Alkane Isomerism and DFT Errors 123 3.3.3.1 Chemical Consequences of Dispersion 131 3.4 Ring Strain Energy 132 3.4.1 RSE of Cyclopropane (28) and Cylcobutane (29) 138 3.5 Aromaticity 144 3.5.1 Aromatic Stabilization Energy (ASE) 145 3.5.2 Nucleus-Independent Chemical Shift (NICS) 150 3.5.3 Case Studies of Aromatic Compounds 155 3.5.3.1 [n]Annulenes 155 3.5.3.2 The Mills Nixon Effect 166 3.5.3.3 Aromaticity Versus Strain 171 3.5.4 Stacking 173 3.6 Interview: Professor Paul Von RagueSchleyer 177 References 180 4. Pericyclic Reactions 197 4.1 The Diels Alder Reaction 198 4.1.1 The Concerted Reaction of 1,3-Butadiene with Ethylene199 4.1.2 The Nonconcerted Reaction of 1,3-Butadiene with Ethylene207 4.1.3 Kinetic Isotope Effects and the Nature of theDiels Alder Transition State 209 4.1.4 Transition State Distortion Energy 214 4.2 The Cope Rearrangement 215 4.2.1 Theoretical Considerations 217 4.2.2 Computational Results 219 4.2.3 Chameleons and Centaurs 227 4.3 The Bergman Cyclization 233 4.3.1 Theoretical Considerations 237 4.3.2 Activation and Reaction Energies of the Parent BergmanCyclization 239 4.3.3 The cd Criteria and Cyclic Enediynes 244 4.3.4 Myers Saito and Schmittel Cyclization 249 4.4 Bispericyclic Reactions 256 4.5 Pseudopericyclic Reactions 260 4.6 Torquoselectivity 267 4.7 Interview: Professor Weston Thatcher Borden 278 References 282 5. Diradicals and Carbenes 297 5.1 Methylene 298 5.1.1 Theoretical Considerations of Methylene 298 5.1.2 The H C H Angle in Triplet Methylene 299 5.1.3 The Methylene and Dichloromethylene Singlet TripletEnergy Gap 300 5.2 Phenylnitrene and Phenylcarbene 304 5.2.1 The Low Lying States of Phenylnitrene and Phenylcarbene305 5.2.2 Ring Expansion of Phenylnitrene and Phenylcarbene 312 5.2.3 Substituent Effects on the Rearrangement of Phenylnitrene317 5.3 Tetramethyleneethane 324 5.3.1 Theoretical Considerations of Tetramethyleneethane 326 5.3.2 Is TME a Ground-State Singlet or Triplet? 326 5.4 Oxyallyl Diradical 330 5.5 Benzynes 333 5.5.1 Theoretical Considerations of Benzyne 333 5.5.2 Relative Energies of the Benzynes 336 5.5.3 Structure of m-Benzyne 341 5.5.4 The Singlet Triplet Gap and Reactivity of theBenzynes 345 5.6 Tunneling of Carbenes 349 5.6.1 Tunneling control 353 5.7 Interview: Professor Henry Fritz Schaefer355 5.8 Interview: Professor Peter R. Schreiner 357 References 360 6. Organic Reactions of Anions 373 6.1 Substitution Reactions 373 6.1.1 The Gas Phase SN2 Reaction 374 6.1.2 Effects of Solvent on SN2 Reactions 385 6.2 Asymmetric Induction Via 1,2-Addition to Carbonyl Compounds391 6.3 Asymmetric Organocatalysis of Aldol Reactions 404 6.3.1 Mechanism of Amine-Catalyzed Intermolecular AldolReactions 409 6.3.2 Mechanism of Proline-Catalyzed Intramolecular AldolReactions 417 6.3.3 Comparison with the Mannich Reaction 421 6.3.4 Catalysis of the Aldol Reaction in Water 426 6.3.5 Another Organocatalysis Example The ClaisenRearrangement 429 6.4 Interview: Professor Kendall N. Houk 432 References 435 7. Solution-Phase Organic Chemistry 445 7.1 Aqueous Diels Alder Reactions 446 7.2 Glucose 452 7.2.1 Models Compounds: Ethylene Glycol and Glycerol 453 7.2.1.1 Ethylene Glycol 453 7.2.1.2 Glycerol 458 7.2.2 Solvation Studies of Glucose 460 7.3 Nucleic Acids 468 7.3.1 Nucleic Acid Bases 469 7.3.1.1 Cytosine 469 7.3.1.2 Guanine 473 7.3.1.3 Adenine 475 7.3.1.4 Uracil and Thymine 477 7.3.2 Base Pairs 479 7.4 Amino Acids 489 7.5 Interview: Professor Christopher J. Cramer 492 References 496 8. Organic Reaction Dynamics 505 8.1 A Brief Introduction To Molecular Dynamics TrajectoryComputations 508 8.1.1 Integrating the Equations of Motion 508 8.1.2 Selecting the PES 510 8.1.3 Initial Conditions 511 8.2 Statistical Kinetic Theories 512 8.3 Examples of Organic Reactions With Non-Statistical Dynamics514 8.3.1 [1,3]-Sigmatropic Rearrangement of Bicyclo[3.2.0]hex-2-ene514 8.3.2 Life in the Caldera: Concerted versus Diradical Mechanisms518 8.3.2.1 Rearrangement of Vinylcyclopropane to Cyclopentene520 8.3.2.2 Bicyclo[3.1.0]hex-2-ene 20 524 8.3.2.3 Cyclopropane Stereomutation 526 8.3.3 Entrance into Intermediates from Above 530 8.3.3.1 Deazetization of 2,3-Diazabicyclo[2.2.1]hept-2-ene 31530 8.3.4 Avoiding Local Minima 533 8.3.4.1 Methyl Loss from Acetone Radical Cation 533 8.3.4.2 Cope Rearrangement of 1,2,6-Heptatriene 534 8.3.4.3 The SN2 Reaction: HO + CH3F 536 8.3.4.4 Reaction of Fluoride with Methyl Hydroperoxide 538 8.3.5 Bifurcating Surfaces: One TS, Two Products 539 8.3.5.1 C2 C6 Enyne Allene Cyclization 540 8.3.5.2 Cycloadditions Involving Ketenes 543 8.3.5.3 Diels Alder Reactions: Steps toward PredictingDynamic Effects on Bifurcating Surfaces 547 8.3.6 Stepwise Reaction on a Concerted Surface 550 8.3.6.1 Rearrangement of Protonated Pinacolyl Alcohol 550 8.3.7 Roaming Mechanism 551 8.3.8 A Roundabout SN2 reaction 553 8.3.9 Hydroboration: Dynamical or Statistical? 554 8.3.10 A Look at the Wolff Rearrangement 555 8.4 Conclusions 557 8.5 Interview: Professor Daniel Singleton 558 References 561 9. Computational Approaches to Understanding Enzymes569 9.1 Models for Enzymatic Activity 569 9.2 Strategy for Computational Enzymology 573 9.2.1 High Level QM/MM Computations of Enzymes 576 9.2.2 Chorismate Mutase 578 9.2.3 Catechol-O-Methyltransferase (COMT) 582 9.3 De Novo Design of Enzymes 586 References 592 Index 599.
- (source: Nielsen Book Data)9781118291924 20160616
(source: Nielsen Book Data)9781118291924 20160616
eReserve
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Instructor's copy | |
(no call number) | Unknown |
CHEM-261-01
- Course
- CHEM-261-01 -- Computational Chemistry
- Instructor(s)
- Markland, Thomas Edward
- Book
- xx, 596 p. : ill. ; 25 cm.
Essentials of Computational Chemistry provides a balanced introduction to this dynamic subject. Suitable for both experimentalists and theorists, a wide range of samples and applications are included drawn from all key areas. The book carefully leads the reader thorough the necessary equations providing information explanations and reasoning where necessary and firmly placing each equation in context.
(source: Nielsen Book Data)9780470091814 20160527
(source: Nielsen Book Data)9780470091814 20160527
Essentials of Computational Chemistry provides a balanced introduction to this dynamic subject. Suitable for both experimentalists and theorists, a wide range of samples and applications are included drawn from all key areas. The book carefully leads the reader thorough the necessary equations providing information explanations and reasoning where necessary and firmly placing each equation in context.
(source: Nielsen Book Data)9780470091814 20160527
(source: Nielsen Book Data)9780470091814 20160527
Science Library (Li and Ma)
Science Library (Li and Ma) | Status |
---|---|
Stacks | |
QD455.3 .E4 C73 2004 | Unknown On reserve at Li and Ma Science Library 2-hour loan |
CHEM-261-01
- Course
- CHEM-261-01 -- Computational Chemistry
- Instructor(s)
- Markland, Thomas Edward
- Book
- xxii, 638 p. : ill. ; 24 cm.
"Understanding Molecular Simulation: From Algorithms to Applications" explains the physics behind the 'recipes' of molecular simulation for materials science. Computer simulators are continuously confronted with questions concerning the choice of a particular technique for a given application. A wide variety of tools exist, so the choice of technique requires a good understanding of the basic principles. More importantly, such understanding may greatly improve the efficiency of a simulation program. The implementation of simulation methods is illustrated in pseudocodes and their practical use in the case studies used in the text. Since the first edition only five years ago, the simulation world has changed significantly - current techniques have matured and new ones have appeared. This new edition deals with these new developments; in particular, there are sections on: transition path sampling and diffusive barrier crossing to simulaterare events; dissipative particle dynamic as a course-grained simulation technique; novel schemes to compute the long-ranged forces; Hamiltonian and non-Hamiltonian dynamics in the context constant-temperature and constant-pressure molecular dynamics simulations; multiple-time step algorithms as an alternative for constraints; defects in solids; the pruned-enriched Rosenbluth sampling, recoil-growth, and concerted rotations for complex molecules; and, parallel tempering for glassy Hamiltonians. Examples are included that highlight current applications and the codes of case studies are available on the World Wide Web. Several new examples have been added since the first edition to illustrate recent applications. Questions are included in this new edition. No prior knowledge of computer simulation is assumed.
(source: Nielsen Book Data)9780122673511 20160528
(source: Nielsen Book Data)9780122673511 20160528
"Understanding Molecular Simulation: From Algorithms to Applications" explains the physics behind the 'recipes' of molecular simulation for materials science. Computer simulators are continuously confronted with questions concerning the choice of a particular technique for a given application. A wide variety of tools exist, so the choice of technique requires a good understanding of the basic principles. More importantly, such understanding may greatly improve the efficiency of a simulation program. The implementation of simulation methods is illustrated in pseudocodes and their practical use in the case studies used in the text. Since the first edition only five years ago, the simulation world has changed significantly - current techniques have matured and new ones have appeared. This new edition deals with these new developments; in particular, there are sections on: transition path sampling and diffusive barrier crossing to simulaterare events; dissipative particle dynamic as a course-grained simulation technique; novel schemes to compute the long-ranged forces; Hamiltonian and non-Hamiltonian dynamics in the context constant-temperature and constant-pressure molecular dynamics simulations; multiple-time step algorithms as an alternative for constraints; defects in solids; the pruned-enriched Rosenbluth sampling, recoil-growth, and concerted rotations for complex molecules; and, parallel tempering for glassy Hamiltonians. Examples are included that highlight current applications and the codes of case studies are available on the World Wide Web. Several new examples have been added since the first edition to illustrate recent applications. Questions are included in this new edition. No prior knowledge of computer simulation is assumed.
(source: Nielsen Book Data)9780122673511 20160528
(source: Nielsen Book Data)9780122673511 20160528
www.sciencedirect.com ScienceDirect
- www.sciencedirect.com ScienceDirect
- www.myilibrary.com MyiLibrary
- Google Books (Full view)
Science Library (Li and Ma)
Science Library (Li and Ma) | Status |
---|---|
Stacks | |
QD461 .F86 2002 | Unknown On reserve at Li and Ma Science Library 2-hour loan |
CHEM-261-01
- Course
- CHEM-261-01 -- Computational Chemistry
- Instructor(s)
- Markland, Thomas Edward
- Book
- xiii, 300 p. : ill. ; 25 cm.
- Foreword.Preface.Preface to the Second Edition.PART A: THE DEFINITION OF THE MODEL. Elementary Quantum Chemistry. Electron Density and Hole Functions. The Electron Density as Basic Variable: Early Attempts. The Hohenberg-Kohn Theorems. The Kohn-Sham Approach. The Quest for Approximate Exchange-Correlation Functionals. The Basic Machinery of Density Functional Programs. PART B: THE PERFORMANCE OF THE MODEL. Molecular Structures and Vibrational Frequencies. Relative Energies and Thermochemistry. Electric Properties. Magnetic Properties. Hydrogen Bonds and Weakly Bound Systems. Chemical Reactivity: Exploration of Potential Energy Surfaces.Bibliography.Index.
- (source: Nielsen Book Data)9783527303724 20160528
(source: Nielsen Book Data)9783527303724 20160528
- Foreword.Preface.Preface to the Second Edition.PART A: THE DEFINITION OF THE MODEL. Elementary Quantum Chemistry. Electron Density and Hole Functions. The Electron Density as Basic Variable: Early Attempts. The Hohenberg-Kohn Theorems. The Kohn-Sham Approach. The Quest for Approximate Exchange-Correlation Functionals. The Basic Machinery of Density Functional Programs. PART B: THE PERFORMANCE OF THE MODEL. Molecular Structures and Vibrational Frequencies. Relative Energies and Thermochemistry. Electric Properties. Magnetic Properties. Hydrogen Bonds and Weakly Bound Systems. Chemical Reactivity: Exploration of Potential Energy Surfaces.Bibliography.Index.
- (source: Nielsen Book Data)9783527303724 20160528
(source: Nielsen Book Data)9783527303724 20160528
eReserve
eReserve | Status |
---|---|
Instructor's copy | |
(no call number) | Unknown |
CHEM-261-01
- Course
- CHEM-261-01 -- Computational Chemistry
- Instructor(s)
- Markland, Thomas Edward
- Book
- ix, 333 p. : ill. ; 24 cm.
- Elementary wave mechanics-- density matrices-- density-functional theory-- the chemical potential-- chemical potential derivatives-- Thomas-Fermi and related models-- the Kohn-Sham method - basic principles and elaboration-- extensions-- aspects of atoms and molecules-- functionals-- convex functions and functionals-- second quantization for fermions-- the uniform electron gas-- tables of values of electronegativities and hardness-- the review literature of density-functional theory.
- (source: Nielsen Book Data)9780195042795 20160528
(source: Nielsen Book Data)9780195042795 20160528
- Elementary wave mechanics-- density matrices-- density-functional theory-- the chemical potential-- chemical potential derivatives-- Thomas-Fermi and related models-- the Kohn-Sham method - basic principles and elaboration-- extensions-- aspects of atoms and molecules-- functionals-- convex functions and functionals-- second quantization for fermions-- the uniform electron gas-- tables of values of electronegativities and hardness-- the review literature of density-functional theory.
- (source: Nielsen Book Data)9780195042795 20160528
(source: Nielsen Book Data)9780195042795 20160528
site.ebrary.com ebrary
Science Library (Li and Ma)
Science Library (Li and Ma) | Status |
---|---|
Stacks | |
QC176.8 .E4 P37 1989 | Unknown On reserve at Li and Ma Science Library 1-year loan |
CHEM-261-01
- Course
- CHEM-261-01 -- Computational Chemistry
- Instructor(s)
- Markland, Thomas Edward