Hehre W.J. A Guide to Molecular Mechanics and Quantum Chemical Calculations

Wavefunction, Inc. 2003. - 796 p.
Over the span of two decades, molecular modeling has emerged as aviable and powerful approach to chemistry. Molecular mechanics calculations coupled with computer graphics are now widely used in lieu of tactile models to visualize molecular shape and quantify steric demands. Quantum chemical calculations, once a mere novelty, continue to play an ever increasing role in chemical research and teaching. They offer the real promise of being able to complement experiment as a means to uncover and explore new chemistry.
In short, no one method of calculation is likely to be ideal for all applications, and the ultimate choice of specific methods rests on a balance between accuracy and cost. This guide attempts to help chemists find that proper balance. It focuses on the underpinnings of molecular mechanics and quantum chemical methods, their relationship with chemical observables, their performance in reproducing known quantities and on the application of practical models to the investigation of molecular structure and stability and chemical reactivity and selectivity.

Contents

Potential Energy Surfaces

Introduction
Potential Energy Surfaces and Geometry
Potential Energy Surfaces and Thermodynamics
Potential Energy Surfaces and Kinetics
Thermodynamic vs Kinetic Control of Chemical Reactions
Potential Energy Surfaces and Mechanism

Section I Theoretical Models

Quantum Chemical Models

Theoretical Models and Theoretical Model Chemistry
Schr?dinger Equation
Bo-Oppenheimer Approximation
Hartree-Fock Approximation
LCAO Approximation
Roothaan-Hall Equations
Correlated Models
Kohn-Sham Equations and Density Functional Models
Configuration Interaction Models
M?ller-Plesset Models
Models for Open-Shell Molecules
Models for Electronic Excited States
Gaussian Basis Sets
STO-G Minimal Basis Set
-G, -G and -G Split-Valence Basis Sets
-G*, -G**, -G* and -G** Polarization Basis Sets
-G(*) Basis Set
cc-pVDZ, cc-pVTZ and cc-pVQZ Basis Sets
Basis Sets Incorporating Diffuse Functions
Pseudopotentials
Semi-Empirical Models
Molecules in Solution
Cramer/Truhlar Models for Aqueous Solvation
Nomenclature
References

Molecular Mechanics Models

Introduction
SYBYL and MMFF Force Fields
Limitations of Molecular Mechanics Models
References

Graphical Models

Introduction
Molecular Orbitals
Electron Density
Spin Density
Electrostatic Potential
Polarization Potential
Local Ionization Potential
Property Maps
Electrostatic Potential Map
LUMO Map
Local Ionization Potential Map
Spin Density Map
Animations
Choice of Quantum Chemical Model
References

Section II Choosing a Model

Equilibrium Geometries

Introduction
Main-Group Hydrides
Hydrocarbons
Molecules with Heteroatoms
Larger Molecules
Hypervalent Molecules
Molecules with Heavy Main-Group Elements
Molecules with Transition Metals
Transition-Metal Inorganic Compounds
Transition-Metal Coordination Compounds
Transition-Metal Organometallics
Bimetallic Carbonyls
Organometallics with Second and Third-Row Transition Metals
Bond Angles Involving Transition-Metal Centers
Reactive Intermediates
Carbocations
Anions
Carbenes and Related Compounds
Radicals
Hydrogen-Bonded Complexes
Geometries of Excited States
Structures of Molecules in Solution
Pitfalls
References

Reaction Energies

Introduction
Homolytic Bond Dissociation Reactions
Singlet-Triplet Separation in Methylene
Heterolytic Bond Dissociation Reactions
Absolute Basicities
Absolute Acidities
Absolute Lithium Cation Affinities
Hydrogenation Reactions
Reactions Relating Multiple and Single Bonds
Structural Isomerization
Isodesmic Reactions
Bond Separation Reactions
Relative Bond Dissociation Energies
Relative Hydrogenation Energies
Relative Acidities and Basicities
Reaction Energies in Solution
Pitfalls
References

Vibrational Frequencies and Thermodynamic Quantities

Introduction
Diatomic Molecules
Main-Group Hydrides
CHX Molecules
Characteristic Frequencies
Infrared and Raman Intensities
Thermodynamic Quantities
Entropy
Correction for Non-Zero Temperature
Correction for Zero-Point Vibrational Energy
Pitfalls
References

Equilibrium Conformations

Introduction
Conformational Energy Differences in Acyclic Molecules
Conformational Energy Differences in Cyclic Molecules
Barriers to Rotation and Inversion
Ring Inversion in Cyclohexane
Pitfalls
References

Transition-State Geometries and Activation Energies

Introduction
Transition-State Geometries
Absolute Activation Energies
Relative Activation Energies
Solvent Effects on Activation Energies
Pitfalls
References

Dipole Moments

Introduction
Diatomic and Small Polyatomic Molecules
Hydrocarbons
Molecules with Heteroatoms
Hypervalent Molecules
Dipole Moments for Flexible Molecules
References

Overview of Performance and Cost

Introduction
Computation Times
Summary
Recommendations

Section III Doing Calculations

Obtaining and Using Equilibrium Geometries

Introduction
Obtaining Equilibrium Geometries
Verifying Calculated Equilibrium Geometries
Using Approximate Equilibrium Geometries to Calculate Thermochemistry
Using Localized MP Models to Calculate Thermochemistry
Using Approximate Equilibrium Geometries to Calculate Molecular Properties
References

Using Energies for Thermochemical and Kinetic Comparisons

Introduction
Calculating Heats of Formation from Bond Separation Reactions
References

Dealing with Flexible Molecules

Introduction
Identifying the Important Conformer
Locating the Lowest-Energy Conformer
Using Approximate Equilibrium Geometries to Calculate Conformational Energy Differences
Using Localized MP Models to Calculate Conformational Energy Differences
Fitting Energy Functions for Bond Rotation
References

Obtaining and Using Transition-State Geometries

Introduction
What Do Transition States Look Like?
Finding Transition States
Verifying Calculated Transition-State Geometries
Using Approximate Transition-State Geometries to Calculate Activation Energies
Using Localized MP Models to Calculate Activation Energies
Reactions Without Transition States

Obtaining and Interpreting Atomic Charges

Introduction
Why Can’t Atomic Charges be Determined Experimentally or Calculated Uniquely?
Methods for Calculating Atomic Charges
Population Analyses
Fitting Schemes
Which Charges are Best?
Hartree-Fock vs Correlated Charges
Using Atomic Charges to Construct Empirical Energy Functions for Molecular Mechanics/Molecular Dynamics Calculations
References

Section IV Case Studies

Stabilizing Unstable Molecules

Introduction
Favoring Dewar Benzene
Making Stable Carbonyl Hydrates
Stabilizing a Carbene: Sterics vs Aromaticity
Favoring a Singlet or a Triplet Carbene
References

Kinetically-Controlled Reactions

Introduction
Thermodynamic vs Kinetic Control
Rationalizing Product Distributions
Anticipating Product Distributions
Altering Product Distributions
Improving Product Selectivity
References

Applications of Graphical Models

Introduction
Structure of Benzene in the Solid State
Acidities of Carboxylic Acids
Stereochemistry of Base-Induced Eliminations
Stereochemistry of Carbonyl Additions
References

Appendix A Supplementary Data
Appendix B Common Terms and Acronyms
Index
Index of Tables
Index of Figures