دانلود کتاب Computational Chemistry. Introduction to the Theory and Applications of Molecular and Quantum Mechanics

فهرست مطالب :

Preface to the Fourth Edition
Contents
Chapter 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
1.2.1 Application Perspective
1.2.2 Historical Perspective
1.3 Putting It All Together
1.4 The Philosophy of Computational Chemistry
1.5 Summary
Easier Questions
Harder Questions
References
Chapter 2: 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
Easier Questions
Harder Questions
References
Chapter 3: Molecular Mechanics
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 Geometries, Possibly for as Inputs for Lengthier (i.e., Ab Initio, Semiempirical, or Density Functional Kinds of Calculations)
3.3.2 To Obtain Good Geometries (and Perhaps Relative Energies) for Small- to Medium-Sized Molecules
3.3.3 To Calculate Geometries and Relative Energies of Very Large Molecules, Usually Polymeric Biomolecules (Proteins and Nucleic Acids)
3.3.4 To Calculate Heats of Formation
3.3.5 To Generate the Potential Energy Function Under Which Molecules Move, for Molecular Dynamics or Monte Carlo Calculations
3.3.6 As a (Usually Quick) Guide to the Feasibility of, or Likely Outcome of, Reactions in Organic Synthesis
3.4 Frequencies and Vibrational Spectra Calculated by MM
3.5 Strengths and Weaknesses of Molecular Mechanics
3.6 Summary
Easier Questions
Harder Questions
References
Chapter 4: Introduction to Quantum Mechanics in Computational Chemistry
4.1 Perspective
4.2 The Development of Quantum Mechanics. The Schrödinger Equation
4.2.1 The Origins of Quantum Theory: Blackbody Radiation and the Photoelectric Effect
4.2.1.1 Blackbody Radiation
4.2.1.2 The Photoelectric Effect
4.2.2 Radioactivity
4.2.3 Relativity
4.2.4 The Nuclear Atom
4.2.5 The Bohr Atom
4.2.6 The Wave Mechanical Atom and the Schrödinger Equation
4.3 The Application of the Schrödinger Equation to Chemistry by Hückel
4.3.1 Introduction
4.3.2 Hybridization
4.3.3 Matrices and Determinants
4.3.3.1 Addition and Subtraction
4.3.3.2 Multiplication by a Scalar
4.3.3.3 Matrix Multiplication
4.3.3.4 Some Important Kinds of Matrices
4.3.3.5 Matrix Diagonalization
4.3.3.6 Determinants
4.3.3.7 Some Properties of Determinants
4.3.4 The Simple Hückel Method: Theory
4.3.5 The Simple Hückel Method: Applications
4.3.5.1 The Nodal Properties of the MOs
4.3.5.2 Stability as Indicated by Energy Levels, and Aromaticity
4.3.5.3 Resonance Energies
4.3.5.4 Bond Orders
4.3.5.5 Atomic Charges
4.3.5.6 Methylenecyclopropene
4.3.6 Strengths and Weaknesses of the Simple Hückel Method
4.3.6.1 Strengths
4.3.6.2 Weaknesses
4.3.7 The Determinant Method of Calculating the Hückel c’s and Energy Levels
4.4 The Extended Hückel Method
4.4.1 Theory
4.4.1.1 Simple Hückel Method
4.4.1.2 Extended Hückel Method
4.4.1.3 Review of the EHM Procedure
4.4.1.4 Molecular Energy and Geometry Optimization in the Extended Hückel Method
4.4.2 An Illustration of the EHM: The Protonated Helium Molecule
4.4.3 The Extended Hückel Method: Applications
4.4.4 Strengths and Weaknesses of the Extended Hückel Method
4.4.4.1 Strengths
4.4.4.2 Weaknesses
4.5 Summary
Easier Questions
Harder Questions
References
Chapter 5: Ab Initio Calculations
5.1 Perspective
5.2 The Basic Principles of the Ab Initio Method
5.2.1 Preliminaries
5.2.2 The Hartree SCF (Self-consistent Field) Method
5.2.3 The Hartree-Fock Equations
5.2.3.1 Slater Determinants
5.2.3.2 Calculating the Atomic or Molecular Energy
5.2.3.3 The Variation Theorem (Variation Principle)
5.2.3.4 Minimizing the Energy: The Hartree-Fock Equations
5.2.3.5 The Meaning of the Hartree-Fock Equations
5.2.3.6 Basis Functions and the Roothaan-Hall Equations
5.2.3.6.1 Deriving the Roothaan-Hall Equations
5.2.3.6.2 Summary of the Derivation of the Roothaan-Hall Equations
5.2.3.6.3 Using the Roothaan-Hall Equations to Do Ab Initio Calculations: The SCF Procedure
5.2.3.6.4 Using the Roothaan-Hall Equations to Do Ab Initio Calculations: The Equations in Terms of the c’s and φ’s of the LCAO Expansion
5.2.3.6.5 Using the Roothaan-Hall Equations to Do Ab Initio Calculations: Some Details
5.2.3.6.6 Using the Roothaan-Hall Equations to Do Ab Initio Calculations: An Example
5.3 Basis Sets
5.3.1 Introduction
5.3.2 Gaussian Functions, Basis Set Preliminaries, and Direct SCF
5.3.3 Types of Basis Sets and Their Uses
5.3.3.1 STO-3G
5.3.3.2 3-21G and 3-21G* Split Valence and Double-Zeta Basis Sets
5.3.3.3 6-31G*
5.3.3.4 Diffuse Functions
5.3.3.5 Large Basis Sets
5.3.3.6 Correlation-Consistent Basis Sets
5.3.3.7 Effective Core Potentials (Pseudopotentials)
5.3.3.8 Which Basis Set Should I Use?
5.4 Post-Hartree-Fock Calculations: Electron Correlation
5.4.1 Electron Correlation
5.4.2 The Møller-Plesset Approach to Electron Correlation
5.4.3 The Configuration Interaction Approach to Electron Correlation
5.4.4 The Coupled Cluster Method
5.4.5 Post-Hartree-Fock Methods: Size Consistency and Variational Behavior
5.5 Applications of the Ab Initio Method
5.5.1 Geometries
5.5.2 Energies
5.5.2.1 Energies: Preamble
5.5.2.2 Energies: Preliminaries
5.5.2.3 Energies: Calculating Quantities Relevant to Thermodynamics and to Kinetics
5.5.2.3.1 Thermodynamics, “Direct” Methods, and Isodesmic Reactions
5.5.2.3.2 Thermodynamics and High-Accuracy Calculations
5.5.2.3.3 Thermodynamics: Calculating Enthalpies of Formation
5.5.2.3.4 Kinetics: Calculating Reaction Rates
5.5.2.3.5 Energies: Concluding Remarks
5.5.3 Frequencies and Vibrational (IR) Spectra
5.5.4 Properties Arising from Electron Distribution: Dipole Moments, Charges, Bond Orders, Electrostatic Potentials, and Atoms-in-Molecules
5.5.4.1 Dipole Moments
5.5.4.2 Charges and Bond Orders
5.5.4.3 An Example of Population Analysis: H-He+
5.5.4.4 Electrostatic Potential
5.5.4.5 Atoms-in-Molecules (AIM) and Quantum Theory of Atoms in Molecules (QTAIM)
5.5.5 Miscellaneous Properties: UV and NMR Spectra, Ionization Energies, and Electron Affinities
5.5.5.1 UV Spectra
5.5.5.2 NMR Spectra
5.5.5.3 Ionization Energies and Electron Affinities
5.5.6 Visualization
5.5.6.1 Molecular Vibrations: Visualization
5.5.6.2 Electrostatic Potential: Visualization
5.5.6.3 Molecular Orbitals: Visualization
5.5.6.4 Visualization: Closing Remarks
5.6 Strengths and Weaknesses of Ab Initio Calculations
5.6.1 Strengths
5.6.2 Weaknesses
5.7 Summary
Easier Questions
Harder Questions
References
Chapter 6: 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
6.2.5.1 NDDO-Based Methods from the Dewar Group: MNDO, AM1, PM3 and SAM1, and Related Methods: Preliminaries
6.2.5.2 Enthalpies of Formation (Heats of Formation) from Semiempirical Electronic Energies
6.2.5.3 MINDO
6.2.5.4 MNDO
6.2.5.5 AM1
6.2.5.6 PM3 and Extensions (PM3(tm), PM5, PM6, and PM7)
6.2.5.7 Polarized Molecular Orbital Model, PMO; Dispersion Effects
6.2.5.8 OMx, Orthogonalization Method x (x = 1, 2, 3)
6.2.5.8.1 General Comments on NDDO Methods
6.3 Applications of Semiempirical Methods
6.3.1 Geometries
6.3.2 Energies
6.3.2.1 Energies: Preliminaries
6.3.2.2 Energies: Calculating Quantities Relevant to Thermodynamics and Kinetics
6.3.3 Frequencies and Vibrational Spectra
6.3.4 Properties Arising from Electron Distribution: Dipole Moments, Charges, Bond Orders
6.3.4.1 Dipole Moments
6.3.4.2 Charges and Bond Orders
6.3.5 Miscellaneous Properties: UV Spectra, Ionization Energies, and Electron Affinities
6.3.5.1 UV Spectra
6.3.5.2 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
Easier Questions
Harder Questions
References
Chapter 7: 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
7.2.3.1 Functionals: The Hohenberg-Kohn Theorems
7.2.3.2 The Kohn-Sham Energy and the Kohn-Sham (KS) Equations
7.2.3.3 Solving the KS Equations
7.2.3.4 The Exchange-Correlation Energy Functional: Various Levels of Kohn-Sham DFT
7.2.3.4.1 The Local Density Approximation (LDA) Rung 1
7.2.3.4.2 The Local Spin Density Approximation (LSDA) Rung 2
7.2.3.4.3 Gradient-Corrected Functionals; the Generalized Gradient Approximation (GGA) Rung 3
7.2.3.4.4 Meta-generalized Gradient Approximation Functionals (Meta-GGA, MGGA) Rung 4
7.2.3.4.5 Hybrid GGA (HGGA) Functionals; the Adiabatic Correction Method (ACM) Rung 5
7.2.3.4.6 Hybrid Meta-GGA (HMGGA) Functionals Rung 6
7.2.3.4.7 Fully Nonlocal Theory Rung 7
7.2.3.4.8 Dispersion
7.2.3.4.9 Is DFT a Semiempirical Method?
7.3 Applications of Density Functional Theory
7.3.1 Geometries
7.3.2 Energies
7.3.2.1 Energies: Preliminaries
7.3.2.2 Energies: Calculating Quantities Relevant to Thermodynamics and Kinetics
7.3.2.2.1 Thermodynamics
7.3.2.2.2 Kinetics
7.3.3 Frequencies and Vibrational Spectra
7.3.4 Properties Arising from Electron Distribution: Dipole Moments, Charges, Bond Orders, and 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 Some Newer Developments in DFT
7.5 Strengths and Weaknesses of DFT
7.6 Summary
Easier Questions
Harder Questions
References
Chapter 8: Some “Special” Topics: (8.1) Solvation, (8.2) Singlet Diradicals, and (8.3) a Note on Heavy Atoms and Transition Metals
8.1 Solvation
8.1.1 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 Singlet Diradicals, Beyond Model Chemistries
8.2.3.1 A CASSCF Calculation on 1,4-Butanediyl
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
Solvation
Easier Questions
Harder Questions
Singlet Diradicals
Easier Questions
Harder Questions
Heavy Atoms and Transition Metals
Easier Questions
Harder Questions
References
Chapter 9: Selected Literature Highlights, Books, Websites, Software, and Hardware
9.1 From the Literature
9.1.1 Molecules
9.1.1.1 Oxirene. To Be or Not to Be
9.1.1.2 Nitrogen Pentafluoride: Warranted Optimism?
9.1.1.3 Pyramidane: A Realistic Goal
9.1.1.4 Polynitrogens: More Than a Computational Playground?
9.1.2 Mechanisms
9.1.2.1 A Call for Caution in Applying Computational Chemistry to Reaction Mechanisms: The Morita-Baylis-Hillman Reaction
9.1.2.2 The Diels-Alder Reaction. A One- or Two-Step Dance?
9.1.2.3 Abstraction of H from Amino Acids by the OH. Radical. Unavoidable Complexity?
9.1.3 Concepts
9.1.3.1 Resonance Versus Inductive Effects
9.1.3.2 Homoaromaticity
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
References
Answers
Chapter 1: Harder Questions, Suggested Answers
Q1
Chapter 1: Harder Questions, Answers
Q2
Chapter 1: Harder Questions, Answers
Q3
Chapter 1: Harder Questions, Answers
Q4
Chapter 1: Harder Questions, Answers
Q5
Chapter 1: Harder Questions, Answers
Q6
Chapter 1: Harder Questions, Answers
Q7
Chapter 1: Harder Questions, Answers
Q8
Chapter 1: Harder Questions, Answers
Q9
Chapter 1: Harder Questions, Answers
Q10
Chapter 2: Harder Questions, Suggested Answers
Q1
Chapter 2: Harder Questions, Answers
Q2
Chapter 2: Harder Questions, Answers
Q3
Chapter 2: Harder Questions, Answers
Q4
Chapter 2: Harder Questions, Answers
Q5
Chapter 2: Harder Questions, Answers
Q6
Chapter 2: Harder Questions, Answers
Q7
Chapter 2: Harder Questions, Answers
Q8
Chapter 2: Harder Questions, Answers
Q9
Chapter 2: Harder Questions, Answers
Q10
Chapter 3: Harder Questions, Suggested Answers
Q1
Chapter 3: Harder Questions, Answers
Q2
Chapter 3: Harder Questions, Answers
Q3
Chapter 3: Harder Questions, Answers
Q4
Chapter 3: Harder Questions, Answers
Q5
Chapter 3: Harder Questions, Answers
Q6
Chapter 3: Harder Questions, Answers
Q7
Chapter 3: Harder Questions, Answers
Q8
Chapter 3: Harder Questions, Answers
Q9
Chapter 3: Harder Questions, Answers
Q10
Chapter 4: Harder Questions, Suggested Answers
Q1
Chapter 4: Harder Questions, Answers
Q2
Chapter 4: Harder Questions, Answers
Q3
Chapter 4: Harder Questions, Answers
Q4
Chapter 4: Harder Questions, Answers
Q5
Chapter 4: Harder Questions, Answers
Q6
Chapter 4: Harder Questions, Answers
Q7
Chapter 4: Harder Questions, Answers
Q8
Chapter 4: Harder Questions, Answers
Q9
Chapter 4: Harder Questions, Answers
Q10
Chapter 5: Harder Questions and Suggested Answers
Q1
Chapter 5: Harder Questions and Answers
Q2
Chapter 5: Harder Questions and Answers
Q3
Chapter 5: Harder Questions and Answers
Q4
Chapter 5: Harder Questions and Answers
Q5
Chapter 5: Harder Questions and Answers
Q6
Chapter 5: Harder Questions and Answers
Q7
Chapter 5: Harder Questions and Answers
Q8
Chapter 5: Harder Questions and Answers
Q9
Chapter 5: Harder Questions and Answers
Q10
Chapter 6: Harder Questions, Suggested Answers
Q1
Chapter 6: Harder Questions, Answers
Q2
Chapter 6: Harder Questions, Answers
Q3
Chapter 6: Harder Questions, Answers
Q4
Chapter 6: Harder Questions, Answers
Q5
Chapter 6: Harder Questions, Answers
Q6
Chapter 6: Harder Questions, Answers
Q7
Chapter 6: Harder Questions, Answers
Q8
Chapter 6: Harder Questions, Answers
Q9
Chapter 6: Harder Questions, Answers
Q10
Chapter 7: Harder Questions, Suggested Answers
Q1
Chapter 7: Harder Questions, Answers
Q2
Chapter 7: Harder Questions, Answers
Q3
Chapter 7: Harder Questions, Answers
Q4
Chapter 7: Harder Questions, Answers
Q5
Chapter 7: Harder Questions, Answers
Q6
Chapter 7: Harder Questions, Answers
Q7
Chapter 7: Harder Questions, Answers
Q8
Chapter 7: Harder Questions, Answers
Q9
Chapter 7; Harder Questions, Answers
Q10
Chapter 8: Harder Questions, Suggested Answers
Solvation
Chapter 8: Harder Questions, Suggested Answers
Singlet Diradicals
Chapter 8: Harder Questions, Suggested Answers
Heavy Atoms and Transition Metals
Index