1 An Outline of What Computational Chemistry Is All About 1.1 What You Can Do with Computational Chemistry, 1.2 The Tools of Computational Chemistry 1.3 Putting It All Together 1.4 The Plulosophy of Computational Chemistry 1.5 Summary References Easier Questions Harder Questions2 The Concept of the Potential Energy Surface 2.1 Perspective 2.2 Stationary Points 2.3 The Born-Oppenheimer Approximation 2.4 Geometry Optimization 2.5 Stationary Points and Normal-Mode Vibrations - Zero Point Energy 2.6 Symmetry 2.7 Summary References Easier Questions Harder Questions3 Molecular Mecbanics 3.1 Perspective 3.2 The Basic Principles of Molecular Mechanics 3.2.1 Developing a Forcefield 3.2.2 Parameterizing a Forcefield 3.2.3 A Calculation Using Our Forcefield 3.3 Examples of the Use of Molecular Mechanics 3.3.1 To Obtain Reasonable Input Geometries for Lengthier(Ab Initio, Semiempirical or Density Functional) Kinds of Calculations 3.3.2 To Obtain Good Geometries (and Perhaps Energies)for Small- to Medium-Sized Molecules 3.3.3 To Calculate the Geometries and Energies of Very Large Molecules, Usually Polymeric Biomolecules (Proteins and Nucleic Acids) 3.3.4 To Generate the Potential Energy Function Under Which Molecules Move, for Molecular Dynamics or Monte Carlo alculations 3.3.5 As a (Usually Quick) Gu ide to the Feasibility of, or Likely Outcome of, Reactions in Organic Synthesis 3.4 Geometries Calculated by MM 3.5 Frequencies and Vibrational Spectra Calculated by MM 3.6 Strengths and Weaknesses of Molecular Mechanics 3.6.1 Strengths 3.6.2 Weaknesses 3.7 Summary References Easier Questions Harder Questions 4 Introduction to Quantum Mechanics in Computational Chemistry 4.1 Perspective 4.2 The Development of Quantum Mechanics The Schrodinger Equation , 4.2.1 The Origins of Quantum Theory: Blackbody Radiation and the Photoelectric Effect 4.2.2 Radioactivity 4.2.3 Relativity 4.2.4 The Nuclear Atom 4.2.5 The Bohr Atom N 4.2.6 The Wave Mechanical Atom and the Schrodinger Equation 4.3 The Application of the Schrodinger Equation to Chemistry by Huckel 4.3.1 Introduction 4.3.2 Hybridization 4.3.3 Matrices and Determinants 4.3.4 The Simple Huckel Method - Theory 4.3.5 The Simple Huckel Method - Applications 4.3.6 Strengths and Weaknesses of the Simple Huckel Method 4.3.7 The Determinant Method of Calculating the Huckel c's and Energy Levels 4.4 The Extended Huckel Method 4.4.1 Theory 4.4.2 An Illustration of the EHM: the Ptotonated Helium Molecule 4.4.3 The Extended Huckel Method - Applications 4.4.4 Strengths and Weaknesses of the Extended Huckel Method 4.5. Summary References Easier Questions Harder Questions5 Ab initio Calculations,N 5.1 Perspective N N 5.2 The Basic Ptinciples of the Ab initio Method 5.2.1 Preliminaries 5.2.2 The Hartree SCF Method 5.2.3 The Hartree-Fock Equations 5.3 Basis Sets 5.3.1 Introduction 5.3.2 Gaussian Functions; Basis Set Preliminaries; Direct SCF 5.3.3 Types of Basis Sets and Their Uses 5.4 Post-Hartree-Fock Calculations: Electron Correlation 5.4.1 Electron Correlation 5.4.2 The MOller-Plesset Approach to Electron Correlation 5.4.3 The Configuration Interaction Approach To Electron Correlation - The Coupled Cluster Method 5.5 Applications of the Ab initio Method 5.5.1 Geometries 5.5.2 Energies 5.5.3 Frequencies and Vibrational Spectra 5.5.4 Properties Arising from Electron Distribution: Dipole Moments, Charges, Bond Orders, Electrostatic Potentials, Atoms-in-Molecules (AIM) 5.5.5 Miscellaneous Properties - UV and NMR Spectra, Ionization Energies, and Electron Affinities 5.5.6 Visualhation 5.6 Strengths and Weaknesses of Ab initio Calculations 5.6.1 Strengths 5.6.2 Weaknesses 5.7 Summary References N Easier Questions Harder Questions6 Semiempirical Calculations 6.1 Perspective 6.2 The Basic Principles of SCF Semiempirical Methods 6.2.1 Preliminaries 6.2.2 The Pariser-Parr-Pople (PPP) Method 6.2.3 The Complete Neglect of Differential Overlap (CNDO) Method 6.2.4 The Intermediate Neglect of Differential Overlap (INDO) Method 6.2.5 The Neglect of Diatomic Differential Overlap (NDDO) Methods 6.3 Applications of Semiempirical Methods 6.3.1 Geometries 6.3.2 Energies 6.3.3 Frequencies and Vibrational Spectra 6.3.4 Properties Arising from Electron Distribution: Dipole Moments, Charges, Bond Orders 6.3.5 Miscellaneous Properties-UV Spectra, Ionization Energies and Electron Affinities 6.3.6 Visualization 6.3.7 Some General Remarks 6.4 Strengths and Weaknesses of Semiempirical Methods 6.4.1 Strengths 6.4.2 Weaknesses 6.5 Summary References Easier Questions Harder Questions7 Density Functional Calculations 7.1 Perspective 7.2 The Basic Principles of Density Functional Theory 7.2.1 Preliminaries 7.2.2 Forerunners to Current DFT Methods 7.2.3 Current DFT Methods: The Kohn-Sham Approach 7.3 Applications of Density Functional Theory 7.3.1 Geometries 7.3.2 Energies 7.3.3 Frequencies and Vibrational Spectra 7.3.4 Properties Arising from Electron Distribution - Dipole Moments, Charges, Bond Orders, Atoms-in-Molecules 7.3.5 Miscellaneous Properties-UV and NMR Spectra, Ionization Energies and Electron Affinities, Electronegativity, Hardness, Softness and the Fukui Function 7.3.6 Visualization 7.4 Strengths and Weaknesses of DFT 7.4.1 Strengths 7.4.2 Weaknesses 7.5 Summary References Easier Questions Harder Questions8 Some "Special" Topics: Solvation, Singlet Diradicals, A Note on Heavy Atoms and Transition Metals 8.1 Solvation 8.1.I Perspective 8.1.2 Ways of Treating Solvation 8.2 Singlet Diradicals 8.2.1 Perspective 8.2.2 Problems with Singlet Diradicals and Model Chemistries 8.2.3 (1) Singlet Diradicals: Beyond Model Chemistries. (2) Complete Active Space Calculations (CAS) 8.3 A Note on Heavy Atoms and Transition Metals 8.3.1 Perspective 8.3.2 Heavy Atoms and Relativistic Corrections 8.3.3 Some Heavy Atom Calculations 8.3.4 Transition Metals 8.4 Summary References Solvation Easier Questions Harder Questions Singlet Diradicals Easier Questions Harder Questions Heavy Atoms and Transition Metals Easier Questions Harder Questions9 Selected Literature Highlights, Books, Websites, Software and Hardware 9.1 From the Literature 9.1.1 Molecules 9.1.2 Mechanisms 9.1.3 Concepts 9.2 To the Literature 9.2.1 Books 9.2.2 Websites for Computational Chemistry in General 9.3 Software and Hardware 9.3.1 Software 9.3.2 Hardware 9.3.3 Postscript ReferencesAnswersIndex
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