Course Content
Before You Start: Book Club Orientation
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Essentials of Computational Chemistry: Theories and Models | Book Club
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Essentials of Computational Chemistry: Theories and Models | Book Club
Chapter 1 : What are Theory ,Computation ,and Modeling?
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1 What are Theory, Computation
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1. 2 Quantum Mechanics
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1.3 Computable Quantities
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1 .3 .3 Chemical Properties
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1 .4 .3 Algorithms
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Chapter 2 : Molecular Mechanics
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2 1 History and Fundamental Assumptions
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2. 2 .2 Valence Angle Bending
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2 .2 .4 van der Waals Interactions
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2. 2. 6 Cross Terms and Additional Non bonded Terms
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2 .3 Force field Energies and Thermodynamics
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2. 4 Geometry Optimization
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2. 4. 2 Optimization Aspects Specific to Force Fields
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2. 5 Menagerie of Modern Force Fields
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2. 5. 2 Validation
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2. 7 Case Study 2R∗,4S ∗ 1 Hydroxy 2,4 dimethylhex 5 ene
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Chapter3
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3. 1 Relationship Between MM Optima and Real Systems
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3 .3 .1 Harmonic Oscillator Trajectories
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3. 3. 3 Practical Issues in Propagation
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3. 4 Monte Carlo
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3. 6 Key Details in Formalism
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3. 6. 5 The Multiple Minima Problem
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Chapter4
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4. 1 Quantum Mechanics and the Wave Function
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4 .2 .2 The Variational Principle
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4 .3. 2 The Secular Equation
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4 .5 Many electron Wave Functions
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4. 5. 4 Slater Determinants
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Chapter5
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5. 2 Extended H¨uckel Theory
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5 .4 INDO Formalism
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5 .5 Basic NDDO Formalism 5
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5 .6 General Performance Overview of Basic NDDO Models
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5. 7 Ongoing Developments in Semiempirical MO Theory
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5 .8 Case Study Asymmetric Alkylation of Benzaldehyde
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5 .1 Semiempirical Philosophy
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chapter 6
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6. 1 Ab Initio Implementations of Hartree–Fock Molecular
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6 .2 Basis Sets
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6. 2. 1 Functional Forms
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6. 2. 2 Contracted Gaussian Functions
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6. 2. 3 Single ζ, Multiple ζ, and Split Valence
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6. 2 .4 Polarization Functions
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6 .2. 5 Diffuse Functions
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6 .2. 6 The HF Limit
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6. 2 .7 Effective Core Potentials
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6. 2. 8 Sources
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6. 3 Key Technical and Practical Points of Hartree–
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6. 3 .2 Symmetry
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6. 3. 3 Open shell Systems
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6. 3. 4 Efficiency of Implementation and Use
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6 .4 General Performance Overview of Ab Initio HF Theory 6 .4 .1 Energetics
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6. 4. 2 Geometries
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6. 4 .3 Charge Distributions
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6. 5 Case Study Polymerization of 4 Substituted Aromatic Enynes
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Chapter 7
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7 1 Dynamical vs Non dynamical Electron Correlation
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7 2 3 Full Configuration Interaction
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7 3 2 Multireference
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7 4 3 Multireference
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7 6 1 Basis Set Convergence
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Chapter 8
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8 3 Kohn Sham self consistent Field Methodology
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8 5 Advantages and Disadvantages of DFT Compared to MO Theory
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8 6 General Performance Overview of DFT
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8 7 Case Study Transition Metal Catalyzed Carbonylation of Methanol
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Chapter 9
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9 .1 Properties Related to Charge
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9. 1. 1 Electric Multipole Moments
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9. 1. 2 Molecular Electrostatic Potential
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9 .1 .3 Partial Atomic Charges
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9. 1 .4 Total Spin
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9. 1. 5 Polarizability and Hyperpolarizability
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9 .1. 6 ESR Hyperfine Coupling Constants
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9. 2 Ionization Potentials and Electron Affinities
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9 3 Spectroscopy of Nuclear Motion
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9 .3 .2 Vibrational
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9 .4 NMR Spectral Properties
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9. 4. 2 Chemical Shifts and Spin–spin Coupling Constants
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9. 5 Case Study Matrix Isolation
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Chapter 10
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10 .1 Microscopic–macroscopic Connection
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10.2 Zero-point Vibrational Energy
10 .3 Ensemble Properties and Basic Statistical Mechanics
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10. 3 .1 Ideal Gas Assumption
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10. 4 Standard state Heats and Free Energies of Formation
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10. 5 Technical Caveats
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10. 6 Case Study
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Chapter 11
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11 .1 Condensed phase Effects on Structure and
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11. 1. 1 Free Energy of Transfer and Its Physical Components
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11 .1. 2 Solvation as It Affects Potential Energy Surfaces
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11 .2 Electrostatic Interactions with a Continuum
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11. 2 .1 The Poisson Equation
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11. 2 .2 Generalized Born
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11 .2 .3 Conductor like Screening Model
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1.1. 3 Continuum Models for Non electrostatic Interactions
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11. 4 Strengths and Weaknesses of Continuum Solvation Models
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11. 4. 2 Partitioning
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11 .4. 3 Non isotropic Media
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11. 4. 4 Potentials of Mean Force and Solvent Structure
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11 .4 .5 Molecular Dynamics with Implicit Solvent
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11 .4 .6 Equilibrium vs
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11 .4 .6 Equilibrium vs
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11. 5 Case Study Aqueous Reductive Dechlorination
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Chapter 12
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12 Explicit Models for Condensed Phases 12 1 Motivation
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12 2 Computing Free energy Differences
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12 2 2 Free energy
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12 2 3 Slow Growth and Thermodynamic Integration
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12 2 4 Free energy Cycles
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12 2 5 Potentials of Mean Force
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12 2 6 Technical Issues and Error Analysis
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12 3 Other Thermodynamic Properties
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12 4 Solvent Models
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12 4 2 Quantal Models
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12 5 Relative Merits of Explicit and Implicit Solvent Models
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12 5 2 SpeedEfficiency
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12 5 3 Non equilibrium Solvation
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12 5 4 Mixed ExplicitImplicit Models
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12 6 Case Study Binding of Biotin Analogs to Avidin
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Chapter 13
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Hybrid QuantalClassical Models 13 1 Motivation
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13 2 Boundaries Through Space
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13 2 2 PolarizedQMUnpolarizedMM
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13 2 3 Fully Polarized Interactions
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13 3 Boundaries Through Bonds
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13 3 2 Link Atoms
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13 3 3 Frozen Orbitals
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13 4 EmpiricalValenceBondMethods
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13 4 2 Following Reaction Paths
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13 4 3 Generalization to QMMM
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13 5 Case Study Catalytic Mechanism of Yeast Enolase
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Chapter 14
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14 1 Determinantal Configurational Representation of Excit
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14 2 Singly Excited States
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14 2 2 CI Singles
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14 2 3 Rydberg States
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14 3 General Excited State Methods
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14 3 2 Propagator Methods and Time dependent DFT
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14 4 Sum and Projection Methods
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14 5 Transition Probabilities
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14 6 Solvatochromism
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14 7 Case Study Organic Light Emitting Diode Alq3
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Chapter 15
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15 Adiabatic Reaction Dynamics
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15 1 1 Unimolecular Reactions
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15 2 Reaction Paths and Transition States
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15 3 Transition state Theory
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15 3 1 2 Kinetic isotope effects
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15 3 2 Variational Transition state Theory
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15 3 3 Quantum Effects on the Rate Constant
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15 4 Condensed phase Dynamics
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15 5 Non adiabatic Dynamics
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15 5 2 Marcus Theory
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Case Study Isomerization of Propylene Oxide
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