A Guide to Molecular Mechanics and Quantum Chemical Calculations
Warren J Hehre, "A Guide to Molecular Mechanics and Quantum Chemical Calculations"
Wavefunction | 2003 | ISBN: 189066118X | 796 pages | PDF | 10,1 MB
Chapter 1 introduces Potential Energy Surfaces as the connection between structure and energetics, and shows how molecular equilibrium and transition-state geometry as well as thermodynamic and kinetic information follow from interpretation of potential energy surfaces. Following this, the guide is divided into four sections:
Section I. Theoretical Models (Chapters 2 to 4)
Chapters 2 and 3 introduce Quantum Chemical Models and Molecular Mechanics Models as a means of evaluating energy as a function of geometry. Specific models are defined. The discussion is to some extent “superficial”, insofar as it lacks both mathematical rigor and algorithmic details, although it does provide the essential framework on which practical models are constructed.
Graphical Models are introduced and illustrated in Chapter 4. Among other quantities, these include models for presentation and interpretation of electron distributions and electrostatic potentials as well as for the molecular orbitals themselves. Property maps, which typically combine the electron density (representing overall molecular
size and shape) with the electrostatic potential, the local ionization potential, the spin density, or with the value of a particular molecular orbital (representing a property or a reactivity index where it can be accessed) are introduced and illustrated.
Section II. Choosing a Model (Chapters 5 to 11)
This is the longest section of the guide. Individual chapters focus on the performance of theoretical models to account for observable quantities:
Equilibrium Geometries (Chapter 5),
Reaction Energies (Chapter 6),
Vibrational Frequencies and Thermodynamic Quantities (Chapter 7),
Equilibrium Conformations (Chapter 8),
Transition State Geometries and Activation Energies (Chapter 9)
Dipole Moments (Chapter 10).
Specific examples illustrate each topic, performance statistics and graphical summaries provided and, based
on all these, recommendations given. The number of examples provided in the individual chapters is actually fairly small (so as not to completely overwhelm the reader), but additional data are provided as Appendix A to this guide.
Concluding this section,
Overview of Performance and Cost (Chapter 11), is material which estimates computation times for a number of
“practical models” applied to “real molecules”, and provides broad recommendations for model selection.
Section III. Doing Calculations (Chapters 12 to 16)
Because each model has its individual strengths and weaknesses, as well as its limitations, the best “strategies” for approaching “real problems” may involve not a single molecular mechanics or quantum chemical model, but rather a combination of models. For example, simpler (less costly) models may be able to provide equilibrium conformations and geometries for later energy and property calculations using higher-level (more costly) models, without
seriously affecting the overall quality of results. Practical aspects or “strategies” are described in this section: Obtaining and Using
Equilibrium Geometries (Chapter 12),
Using Energies for Thermochemical and Kinetic Comparisons (Chapter 13),
Dealing with Flexible Molecules (Chapter 14),
Obtaining and Using Transition-State Geometries (Chapter 15)
Obtaining and Interpreting Atomic Charges (Chapter 16).
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Warren J Hehre, "A Guide to Molecular Mechanics and Quantum Chemical Calculations"
Wavefunction | 2003 | ISBN: 189066118X | 796 pages | PDF | 10,1 MB
Chapter 1 introduces Potential Energy Surfaces as the connection between structure and energetics, and shows how molecular equilibrium and transition-state geometry as well as thermodynamic and kinetic information follow from interpretation of potential energy surfaces. Following this, the guide is divided into four sections:
Section I. Theoretical Models (Chapters 2 to 4)
Chapters 2 and 3 introduce Quantum Chemical Models and Molecular Mechanics Models as a means of evaluating energy as a function of geometry. Specific models are defined. The discussion is to some extent “superficial”, insofar as it lacks both mathematical rigor and algorithmic details, although it does provide the essential framework on which practical models are constructed.
Graphical Models are introduced and illustrated in Chapter 4. Among other quantities, these include models for presentation and interpretation of electron distributions and electrostatic potentials as well as for the molecular orbitals themselves. Property maps, which typically combine the electron density (representing overall molecular
size and shape) with the electrostatic potential, the local ionization potential, the spin density, or with the value of a particular molecular orbital (representing a property or a reactivity index where it can be accessed) are introduced and illustrated.
Section II. Choosing a Model (Chapters 5 to 11)
This is the longest section of the guide. Individual chapters focus on the performance of theoretical models to account for observable quantities:
Equilibrium Geometries (Chapter 5),
Reaction Energies (Chapter 6),
Vibrational Frequencies and Thermodynamic Quantities (Chapter 7),
Equilibrium Conformations (Chapter 8),
Transition State Geometries and Activation Energies (Chapter 9)
Dipole Moments (Chapter 10).
Specific examples illustrate each topic, performance statistics and graphical summaries provided and, based
on all these, recommendations given. The number of examples provided in the individual chapters is actually fairly small (so as not to completely overwhelm the reader), but additional data are provided as Appendix A to this guide.
Concluding this section,
Overview of Performance and Cost (Chapter 11), is material which estimates computation times for a number of
“practical models” applied to “real molecules”, and provides broad recommendations for model selection.
Section III. Doing Calculations (Chapters 12 to 16)
Because each model has its individual strengths and weaknesses, as well as its limitations, the best “strategies” for approaching “real problems” may involve not a single molecular mechanics or quantum chemical model, but rather a combination of models. For example, simpler (less costly) models may be able to provide equilibrium conformations and geometries for later energy and property calculations using higher-level (more costly) models, without
seriously affecting the overall quality of results. Practical aspects or “strategies” are described in this section: Obtaining and Using
Equilibrium Geometries (Chapter 12),
Using Energies for Thermochemical and Kinetic Comparisons (Chapter 13),
Dealing with Flexible Molecules (Chapter 14),
Obtaining and Using Transition-State Geometries (Chapter 15)
Obtaining and Interpreting Atomic Charges (Chapter 16).
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