Essentials of Computational Chemistry: Theories and Models

Essentials of Computational Chemistry, Theories and Models, Second Edition provides an accessible introduction to this fast developing subject. Extensively revised and updated, the Second Edition has been carefully developed to encourage student understanding and to establish seamless
connections with the primary literature for the advanced reader. The book opens with a presentation of classical models, before gradually moving on to increasingly more complex quantum mechanical and dynamical theories. Coverage and examples are drawn from inorganic, organic and biological chemistry.
evolving topics like density functional theory, continuum solvation models, and computational thermochemistry brought firmly up–to–datecarefully guides the reader through key equations, providing background information and placing each in context.numerous examples and applications with selected case studies designed as a basis for classroom discussion.supplementary website with exercises problems and updates: www.pollux.chem.umn.edu/8021/
Invaluable to all students taking a first course in computational chemistry, molecular modelling, computational quantum chemistry or electronic structure theory. This book will also be of interest to postgraduates, researchers and professionals needing an up–to–date, accessible introduction to this subject.
Reviews of the First Edition
"This is an excellent text for graduates or advanced undergraduates in any field of chemistry……the text provides an excellent introduction to the field for students and researchers in any area of chemistry" Theoretical Chemistry Accounts, 2003
"…..this book has a lot to recommend to undergraduate students as a way of getting them involved in computational chemistry…Professor Cramer has done a superb job and deserves congratulating" The Alchemist, 2003
" ‘Essentials’ is a useful tool not only for teaching and learning but also as a quick reference, and thus will most probably become one of the standard text books for computational chemistry"
Journal of Chemical Information and Computer Science, 2003

Spis treści:
Preface to the First Edition.
Preface to the Second Edition.
Acknowledgments.
1. What are Theory, Computation, and Modeling?
1.1 Definition of Terms.
1.2 Quantum Mechanics.
1.3 Computable Quantities.
1.3.1 Structure.
1.3.2 Potential Energy Surfaces.
1.3.3 Chemical Properties.
1.4 Cost and Efficiency.
1.4.1 Intrinsic Value.
1.4.2 Hardware and Software.
1.4.3 Algorithms.
1.5 Note on Units.
Bibliography and Suggested Additional Reading.
References.
2..
   Molecular Mechanics.
2.1 History and Fundamental Assumptions.
2.2 Potential Energy Functional Forms.
2.2.1 Bond Stretching.
2.2.2 Valence Angle Bending.
2.2.3 Torsions.
2.2.4 van der Waals Interactions.
2.2.5 Electrostatic Interactions.
2.2.6 Cross Terms and Additional Non–bonded Terms.
2.2.7 Parameterization Strategies.
2.3 Force–field Energies and Thermodynamics.
2.4 Geometry Optimization.
2.4.1 Optimization Algorithms.
2.4.2 Optimization Aspects Specific to Force Fields.
2.5 Menagerie of Modern Force Fields.
2.5.1 Available Force Fields.
2.5.2 Validation.
2.6 Force Fields and Docking.
2.7 Case Study: (2R∗,4S∗)–1–Hydroxy–2,4–dimethylhex–5–ene.
Bibliography and Suggested Additional Reading.
References.
3. Simulations of Molecular Ensembles.
3.1 Relationship Between MM Optima and Real Systems.
3.2 Phase Space and Trajectories.
3.2.1 Properties as Ensemble Averages.
3.2.2 Properties as Time Averages of Trajectories.
3.3 Molecular Dynamics.
3.3.1 Harmonic Oscillator Trajectories.
3.3.2 Non–analytical Systems.
3.3.3 Practical Issues in Propagation.
3.3.4 Stochastic Dynamics.
3.4 Monte Carlo.
3.4.1 Manipulation of Phase–space Integrals.
3.4.2 Metropolis Sampling.
3.5 Ensemble and Dynamical Property Examples.
3.6 Key Details in Formalism.
3.6.1 Cutoffs and Boundary Conditions.
3.6.2 Polarization.
3.6.3 Control of System Variables.
3.6.4 Simulation Convergence.
3.6.5 The Multiple Minima Problem.
3.7 Force Field Performance in Simulations.
3.8 Case Study: Silica Sodalite.
Bibliography and Suggested Additional Reading.
References.
4. Foundations of Molecular Orbital Theory.
4.1 Quantum Mechanics and the Wave Function.
4.2 The Hamiltonian Operator.
4.2.1 General Features.
4.2.2 The Variational Principle.
4.2.3 The Born–Oppenheimer Approximation.
4.3 Construction of Trial Wave Functions.
4.3.1 The LCAO Basis Set Approach.
4.3.2 The Secular Equation.
4.4 H¨uckel Theory.
4.4.1 Fundamental Principles.
4.4.2 Application to the Allyl System.
4.5 Many–electron Wave Functions.
4.5.1 Hartree–product Wave Functions.
4.5.2 The Hartree Hamiltonian.
4.5.3 Electron Spin and Antisymmetry.
4.5.4 Slater Determinants.
4.5.5 The Hartree–Fock Self–consistent Field Method.
Bibliography and Suggested Additional Reading.
References.
5. Semiempirical Implementations of Molecular Orbital Theory..
5.1 Semiempirical Philosophy.
5.1.1 Chemically Virtuous Approximations.
5.1.2 Analytic Derivatives.
5.2 Extended Hückel Theory.
5.3 CNDO Formalism.
5.4 INDO Formalism.
5.4.1 INDO and INDO/S.
5.4.2 MINDO/3 and SINDO1.
5.5 Basic NDDO Formalism.
5.5.1 MNDO.
5.5.2 AM1.
5.5.3 PM3.
5.6 General Performance Overview of Basic NDDO Models.
5.6.1 Energetics.
5.6.2 Geometries.
5.6.3 Charge Distributions.
5.7 Ongoing Developments in Semiempirical MO Theory.
5.7.1 Use of Semiempirical Propert ies in SAR.
5.7.2 d Orbitals in NDDO Models.
5.7.3 SRP Models.
5.7.4 Linear Scaling.
5.7.5 Other Changes Functional Form.
5.8 Case Study: Asymmetric Alkylation of Benzaldehyde.
Bibliography and Suggested Additional Reading.
References.
6. Ab Initio Implementations of Hartree–Fock Molecular Orbital.
Theory.
6.1 Ab Initio Philosophy.
6.2 Basis Sets.
6.2.1 Functional Forms.
6.2.2 Contracted Gaussian Functions.
6.2.3 Single–ζ, Multiple–ζ, and Split–Valence.
6.2.4 Polarization Functions.
6.2.5 Diffuse Functions.
6.2.6 The HF Limit.
6.2.7 Effective Core Potentials.
6.2.8 Sources.
6.3 Key Technical and Practical Points of Hartree–Fock Theory.
6.3.1 SCF Convergence.
6.3.2 Symmetry.
6.3.3 Open–shell Systems.
6.3.4 Efficiency of Implementation and Use.
6.4 General Performance Overview of Ab Initio HF Theory.
6.4.1 Energetics.
6.4.2 Geometries.
6.4.3 Charge Distributions.
6.5 Case Study: Polymerization of 4–Substituted Aromatic Enynes.
Bibliography and Suggested Additional Reading.
References.
7. Including Electron Correlation in Molecular Orbital Theory.
7.1 Dynamical vs. Non–dynamical Electron Correlation.
7.2 Multiconfiguration Self–Consistent Field Theory.
7.2.1 Conceptual Basis.
7.2.2 Active Space Specification.
7.2.3 Full Configuration Interaction.
7.3 Configuration Interaction.
7.3.1 Single–determinant Reference.
7.3.2 Multireference.
7.4 Perturbation Theory.
7.4.1 General Principles.
7.4.2 Single–reference.
7.4.3 Multireference.
7.4.4 First–order Perturbation Theory for Some Relativistic Effects.
7.5 Coupled–cluster Theory.
7.6 Practical Issues in Application.
7.6.1 Basis Set Convergence.
7.6.2 Sensitivity to Reference Wave Function.
7.6.3 Price/Performance Summary.
7.7 P