Computational Chemistry. A Practical Guide for Appling Techniques to Real-World Problems

Автор(ы):Young David C.
06.10.2007
Год изд.:2001
Описание: Recent years have witnessed an increase in the number of people using computational chemistry. Many of these newcomers are part-time theoreticians who work on other aspects of chemistry the rest of the time. This increase has been facilitated by the development of computer software that is increasingly easy to use. It is now so easy to do computational chemistry that calculations can be performed with no knowledge of the underlying principles. As a result, many people do not understand even the most basic concepts involved in a calculation. Their work, as a result, is largely unfocused and often third-rate. Most chemists want to avoid the paper-and-pencil type of work that theoretical chemistry in its truest form entails. However, keep in mind that it is precisely for this kind of painstaking and exacting research that many Nobel prizes have been awarded. This book will focus almost exclusively on the knowledge needed to effectively use existing computer software for molecular modeling.
Оглавление:
Computational Chemistry. A Practical Guide for Appling Techniques to Real-World Problems — обложка книги. Обложка книги.
  1. Introduction [1]
    1.1 Models, Approximations, and Reality [1]
    1.2 How Computational Chemistry Is Used [3]
      Bibliography [4]
Part I. BASIC TOPICS [5]
  2. Fundamental Principles [7]
    2.1 Energy [7]
    2.2 Electrostatics [8]
    2.3 Atomic Units [9]
    2.4 Thermodynamics [9]
    2.5 Quantum Mechanics [10]
    2.6 Statistical Mechanics [12]
      Bibliography [16]
  3. Ab initio Methods [19]
    3.1 Hartree-Fock Approximation [19]
    3.2 Correlation [21]
    3.3 Moller-Plesset Perturbation Theory [22]
    3.4 Configuration Interaction [23]
    3.5 Multi-configurational Self-consistent Field [24]
    3.6 Multi-reference Configuration Interaction [25]
    3.7 Coupled Cluster [25]
    3.8 Quantum Monte Carlo Methods [26]
    3.9 Natural Orbitals [27]
    3.10 Conclusions [27]
      Bibliography [28]
  4. Semiempirical Methods [32]
    4.1 Huckel [33]
    4.2 Extended Huckel [33]
    4.3 PPP [33]
    4.4 CNDO [34]
    4.5 MINDO [34]
    4.6 MNDO [34]
    4.7 INDO [35]
    4.8 ZINDO [35]
    4.9 SINDO1 [35]
    4.10 PRDDO [36]
    4.11 AM1 [36]
    4.12 PM3 [37]
    4.13 PM3/TM [37]
    4.14 Fenske-Hall Method [37]
    4.15 TNDO [37]
    4.16 SAM1 [38]
    4.17 Gaussian Theory [38]
    4.18 Recommendations [39]
      Bibliography [39]
  5. Density Functional Theory [42]
    5.1 Basic Theory [42]
    5.2 Linear Scaling Techniques [43]
    5.3 Practical Considerations [45]
    5.4 Recommendations [46]
      Bibliography [46]
  6. Molecular Mechanics [49]
    6.1 Basic Theory [49]
    6.2 Existing Force Fields [53]
    6.3 Practical Considerations [56]
    6.4 Recommendations [57]
      Bibliography [58]
  7. Molecular Dynamics and Monte Carlo Simulations [60]
    7.1 Molecular Dynamics [60]
    7.2 Monte Carlo Simulations [62]
    7.3 Simulation of Molecules [63]
    7.4 Simulation of Liquids [64]
    7.5 Practical Considerations [64]
      Bibliography [65]
  8. Predicting Molecular Geometry [67]
    8.1 Specifying Molecular Geometry [67]
    8.2 Building the Geometry [67]
    8.3 Coordinate Space for Optimization [68]
    8.4 Optimization Algorithm [70]
    8.5 Level of Theory [70]
    8.6 Recommendations [71]
      Bibliography [71]
  9. Constructing a Z-Matrix [73]
    9.1 Z-Matrix for a Diatomic Molecule [73]
    9.2 Z-Matrix for a Polyatomic Molecule [73]
    9.3 Linear Molecules [74]
    9.4 Ring Systems [75]
      Bibliography [77]
  10. Using Existing Basis Sets [78]
    10.1 Contraction Schemes [78]
    10.2 Notation [81]
    10.3 Treating Core Electrons [84]
    10.4 Common Basis Sets [85]
    10.5 Studies Comparing Results [89]
      Bibliography [90]
  11. Molecular Vibrations [92]
    11.1 Harmonic Oscillator Approximation [92]
    11.2 Anharmonic Frequencies [94]
    11.3 Peak Intensities [95]
    11.4 Zero-point Energies and Thermodynamic Corrections [96]
    11.5 Recommendations 96 Bibliography [96]
  12. Population Analysis [99]
    12.1 Mulliken Population Analysis [99]
    12.2 Lowdin Population Analysis [100]
    12.3 Natural Bond-Order Analysis [100]
    12.4 Atoms in Molecules [101]
    12.5 Electrostatic Charges [102]
    12.6 Charges from Structure Only [102]
    12.7 Recommendations [103]
      Bibliography [105]
  13. Other Chemical Properties [107]
    13.1 Methods for Computing Properties [107]
    13.2 Multipole Moments [110]
    13.3 Fermi Contact Density [110]
    13.4 Electronic Spatial Extent and Molecular Volume [111]
    13.5 Electron Affinity and lonization Potential [111]
    13.6 Hyperfine Coupling [112]
    13.7 Dielectric Constant [112]
    13.8 Optical Activity [113]
    13.9 Biological Activity [113]
    13.10 Boiling Point and Melting Point [114]
    13.11 Surface Tension [114]
    13.12 Vapor Pressure [115]
    13.13 Solubility [115]
    13.14 Diffusivity [115]
    13.15 Visualization [115]
    13.16 Conclusions [121]
      Bibliography [121]
  14. The Importance of Symmetry [125]
    14.1 Wave Function Symmetry [127]
    14.2 Transition Structures [127]
      Bibliography [127]
  15. Efficient Use of Computer Resources [128]
    15.1 Time Complexity [128]
    15.2 Labor Cost [132]
    15.3 Parallel Computers [132]
      Bibliography [133]
  16. How to Conduct a Computational Research Project [135]
    16.1 What Do You Want to Know? How Accurately? Why? [135]
    16.2 How Accurate Do You Predict the Answer Will Be? [135]
    16.3 How Long Do You Predict the Research Will Take? [136]
    16.4 What Approximations Are Being Made? Which Are Significant? [136]
      Bibliography [142]
Part II. ADVANCED TOPICS [145]
  17. Finding Transition Structures [147]
    17.1 Introduction [147]
    17.2 Molecular Mechanics Prediction [148]
    17.3 Level of Theory [149]
    17.4 Use of Symmetry [151]
    17.5 Optimization Algorithms [151]
    17.6 From Starting and Ending Structures [152]
    17.7 Reaction Coordinate Techniques [154]
    17.8 Relaxation Methods [155]
    17.9 Potential Surface Scans [155]
    17.10 Solvent Effects [155]
    17.11 Verifying That the Correct Geometry Was Obtained [155]
    17.12 Checklist of Methods for Finding Transition Structures [156]
      Bibliography [157]
  18. Reaction Coordinates [159]
    18.1 Minimum Energy Path [159]
    18.2 Level of Theory [160]
    18.3 Least Motion Path [161]
    18.4 Relaxation Methods [161]
    18.5 Reaction Dynamics [162]
    18.6 Which Algorithm to Use [162]
      Bibliography [162]
  19. Reaction Rates [164]
    19.1 Arrhenius Equation [164]
    19.2 Relative Rates [165]
    19.3 Hard-sphere Collision Theory [165]
    19.4 Transition State Theory [166]
    19.5 Variational Transition State Theory [166]
    19.6 Trajectory Calculations [167]
    19.7 Statistical Calculations [168]
    19.8 Electronic-state Crossings [169]
    19.9 Recommendations 169 Bibliography [170]
  20. Potential Energy Surfaces [173]
    20.1 Properties of Potential Energy Surfaces [173]
    20.2 Computing Potential Energy Surfaces [175]
    20.3 Fitting PES Results to Analytic Equations [176]
    20.4 Fitting PES Results to Semiempirical Models [177]
      Bibliography [177]
  21. Conformation Searching [179]
    21.1 Grid Searches [180]
    21.2 Monte Carlo Searches [182]
    21.3 Simulated Annealing [183]
    21.4 Genetic Algorithms [184]
    21.5 Distance-geometry Algorithms [185]
    21.6 The Fragment Approach [186]
    21.7 Chain-Growth [186]
    21.8 Rule-based Systems [186]
    21.9 Using Homology Modeling [187]
    21.10 Handling Ring Systems [189]
    21.11 Level of Theory [190]
    21.12 Recommended Search Algorithms [190]
      Bibliography [190]
  22. Fixing Self-Consistent Field Convergence Problems [193]
    22.1 Possible Results of an SCF Procedure [193]
    22.2 How to Safely Change the SCF Procedure [194]
    22.3 What to Try First [195]
      Bibliography [196]
  23. QM/MM [198]
    23.1 Nonautomated Procedures [198]
    23.2 Partitioning of Energy [198]
    23.3 Energy Subtraction [200]
    23.4 Self Consistent Method [201]
    23.5 Truncation of the QM Region [202]
    23.6 Region Partitioning [203]
    23.7 Optimization [203]
    23.8 Incorporating QM Terms in Force Fields [203]
    23.9 Recommendations [204]
      Bibliography [204]
  24. Solvation [206]
    24.1 Physical Basis for Solvation Effects [206]
    24.2 Explicit Solvent Simulations [207]
    24.3 Analytic Equations [207]
    24.4 Group Additivity Methods [208]
    24.5 Continuum Methods [208]
    24.6 Recommendations [212]
      Bibliography [213]
  25. Electronic Excited States [216]
    25.1 Spin States [216]
    25.2 CIS [216]
    25.3 Initial Guess [217]
    25.4 Block Diagonal Hamiltonians [218]
    25.5 Higher Roots of a CI [218]
    25.6 Neglecting a Basis Function [218]
    25.7 Imposing Orthogonality: DFT Techniques [218]
    25.8 Imposing Orthogonality: QMC Techniques [219]
    25.9 Path Integral Methods [219]
    25.10 Time-dependent Methods [219]
    25.11 Semiempirical Methods [220]
    25.12 State Averaging [220]
    25.13 Electronic Spectral Intensities [220]
    25.14 Recommendations [220]
      Bibliography [221]
  26. Size Consistency [223]
    26.1 Correction Methods [224]
    26.2 Recommendations [225]
      Bibliography [226]
  27. Spin Contamination [227]
    27.1 How Does Spin Contamination Affect Results? [227]
    27.2 Restricted Open-shell Calculations [228]
    27.3 Spin Projection Methods [229]
    27.4 Half-electron Approximation [229]
    27.5 Recommendations [230]
      Bibliography [230]
  28. Basis Set Customization [231]
    28.1 What Basis Functions Do [231]
    28.2 Creating Basis Sets from Scratch [231]
    28.3 Combining Existing Basis Sets [232]
    28.4 Customizing a Basis Set [233]
    28.5 Basis Set Superposition Error [237]
      Bibliography [238]
  29. Force Field Customization [239]
    29.1 Potential Pitfalls [239]
    29.2 Original Parameterization [240]
    29.3 Adding New Parameters [240]
      Bibliography [241]
  30. Structure-Property Relationships [243]
    30.1 QSPR [243]
    30.2 QSAR [247]
    30.3 3D QSAR [247]
    30.4 Comparative QSAR [249]
    30.5 Recommendations [249]
      Bibliography [249]
  31. Computing NMR Chemical Shifts [252]
    31.1 Ab initio Methods [252]
    31.2 Semiempirical Methods [253]
    31.3 Empirical Methods [253]
    31.4 Recommendations [254]
      Bibliography [254]
  32. Nonlinear Optical Properties [256]
    32.1 Nonlinear Optical Properties [256]
    32.2 Computational Algorithms [257]
    32.3 Level of Theory [259]
    32.4 Recommendations [259]
      Bibliography [260]
  33. Relativistic Effects [261]
    33.1 Relativistic Terms in Quantum Mechanics [261]
    33.2 Extension of Nonrelativistic Computational Techniques [262]
    33.3 Core Potentials [262]
    33.4 Explicit Relativistic Calculations [263]
    33.5 Effects on Chemistry [263]
    33.6 Recommendations [264]
      Bibliography [264]
  34. Band Structures [266]
    34.1 Mathematical Description of Energy Bands [266]
    34.2 Computing Band Gaps [266]
    34.3 Computing Band Structures [268]
    34.4 Describing the Electronic Structure of Crystals [269]
    34.5 Computing Crystal Properties [270]
    34.6 Defect Calculations [271]
      Bibliography [271]
  35. Mesoscale Methods [273]
    35.1 Brownian Dynamics [273]
    35.2 Dissipative Particle Dynamics [274]
    35.3 Dynamic Mean-field Density Functional Method [274]
    35.4 Nondynamic Methods [275]
    35.5 Validation of Results [275]
    35.6 Recommendations [275]
      Bibliography [276]
  36. Synthesis Route Prediction [277]
    36.1 Synthesis Design Systems [277]
    36.2 Applications of Traditional Modeling Techniques [279]
    36.3 Recommendations [280]
      Bibliography [280]
Part III. APPLICATIONS [281]
  37. The Computational Chemist's View of the Periodic Table [283]
    37.1 Organic Molecules [283]
    37.2 Main Group Inorganics, Noble Gases, and Alkali Metals [285]
    37.3 Transition Metals [286]
    37.4 Lanthanides and Actinides [289]
      Bibliography [290]
  38. Biomolecules [296]
    38.1 Methods for Modeling Biomolecules [296]
    38.2 Site-specific Interactions [297]
    38.3 General Interactions [298]
    38.4 Recommendations [298]
      Bibliography [298]
  39. Simulating Liquids [302]
    39.1 Level of Theory [302]
    39.2 Periodic Boundary Condition Simulations [303]
    39.3 Recommendations [305]
      Bibliography [305]
  40. Polymers [307]
    40.1 Level of Theory [307]
    40.2 Simulation Construction [309]
    40.3 Properties [310]
    40.4 Recommendations [315]
      Bibliography [315]
  41. Solids and Surfaces [318]
    41.1 Continuum Models [318]
    41.2 Clusters [318]
    41.3 Band Structures [319]
    41.4 Defect Calculations [319]
    41.5 Molecular Dynamics and Monte Carlo Methods [319]
    41.6 Amorphous Materials [319]
    41.7 Recommendations [319]
      Bibliography [320]
Appendix. Software Packages [322]
  A.1 Integrated Packages [322]
  A.2 Ab initio and DFT Software [332]
  A.3 Semiempirical Software [340]
  A.4 Molecular Mechanics/Molecular Dynamics/Monte Carlo Software [344]
  A.5 Graphics Packages [349]
  A.6 Special-purpose Programs [352]
Bibliography [358]
GLOSSARY [360]
Bibliography [370]
INDEX [371]
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