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Before You Start: Book Club Orientation

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Book Club System: How It Works & How You Win

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

1. 2 Quantum Mechanics

1.3 Computable Quantities

1 .3 .3 Chemical Properties

1 .4 .3 Algorithms

Chapter 2 : Molecular Mechanics

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2 1 History and Fundamental Assumptions

2. 2 .2 Valence Angle Bending

2 .2 .4 van der Waals Interactions

2. 2. 6 Cross Terms and Additional Non bonded Terms

2 .3 Force field Energies and Thermodynamics

2. 4 Geometry Optimization

2. 4. 2 Optimization Aspects Specific to Force Fields

2. 5 Menagerie of Modern Force Fields

2. 5. 2 Validation

2. 7 Case Study 2R∗,4S ∗ 1 Hydroxy 2,4 dimethylhex 5 ene

Chapter3

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3. 1 Relationship Between MM Optima and Real Systems

3 .3 .1 Harmonic Oscillator Trajectories

3. 3. 3 Practical Issues in Propagation

3. 4 Monte Carlo

3. 6 Key Details in Formalism

3. 6. 5 The Multiple Minima Problem

Chapter4

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4. 1 Quantum Mechanics and the Wave Function

4 .2 .2 The Variational Principle

4 .3. 2 The Secular Equation

4 .5 Many electron Wave Functions

4. 5. 4 Slater Determinants

Chapter5

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5. 2 Extended H¨uckel Theory

5 .4 INDO Formalism

5 .5 Basic NDDO Formalism 5

5 .6 General Performance Overview of Basic NDDO Models

5. 7 Ongoing Developments in Semiempirical MO Theory

5 .8 Case Study Asymmetric Alkylation of Benzaldehyde

5 .1 Semiempirical Philosophy

chapter 6

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6. 1 Ab Initio Implementations of Hartree–Fock Molecular

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–

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

Chapter 7

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7 1 Dynamical vs Non dynamical Electron Correlation

7 2 3 Full Configuration Interaction

7 3 2 Multireference

7 4 3 Multireference

7 6 1 Basis Set Convergence

Chapter 8

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8 3 Kohn Sham self consistent Field Methodology

8 5 Advantages and Disadvantages of DFT Compared to MO Theory

8 6 General Performance Overview of DFT

8 7 Case Study Transition Metal Catalyzed Carbonylation of Methanol

Chapter 9

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9 .1 Properties Related to Charge

9. 1. 1 Electric Multipole Moments

9. 1. 2 Molecular Electrostatic Potential

9 .1 .3 Partial Atomic Charges

9. 1 .4 Total Spin

9. 1. 5 Polarizability and Hyperpolarizability

9 .1. 6 ESR Hyperfine Coupling Constants

9. 2 Ionization Potentials and Electron Affinities

9 3 Spectroscopy of Nuclear Motion

9 .3 .2 Vibrational

9 .4 NMR Spectral Properties

9. 4. 2 Chemical Shifts and Spin–spin Coupling Constants

9. 5 Case Study Matrix Isolation

Chapter 10

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10 .1 Microscopic–macroscopic Connection

10.2 Zero-point Vibrational Energy

10 .3 Ensemble Properties and Basic Statistical Mechanics

10. 3 .1 Ideal Gas Assumption

10. 4 Standard state Heats and Free Energies of Formation

10. 5 Technical Caveats

10. 6 Case Study

Chapter 11

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11 .1 Condensed phase Effects on Structure and

11. 1. 1 Free Energy of Transfer and Its Physical Components

11 .1. 2 Solvation as It Affects Potential Energy Surfaces

11 .2 Electrostatic Interactions with a Continuum

11. 2 .1 The Poisson Equation

11. 2 .2 Generalized Born

11 .2 .3 Conductor like Screening Model

1.1. 3 Continuum Models for Non electrostatic Interactions

11. 4 Strengths and Weaknesses of Continuum Solvation Models

11. 4. 2 Partitioning

11 .4. 3 Non isotropic Media

11. 4. 4 Potentials of Mean Force and Solvent Structure

11 .4 .5 Molecular Dynamics with Implicit Solvent

11 .4 .6 Equilibrium vs

11 .4 .6 Equilibrium vs

11. 5 Case Study Aqueous Reductive Dechlorination

Chapter 12

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12 Explicit Models for Condensed Phases 12 1 Motivation

12 2 Computing Free energy Differences

12 2 2 Free energy

12 2 3 Slow Growth and Thermodynamic Integration

12 2 4 Free energy Cycles

12 2 5 Potentials of Mean Force

12 2 6 Technical Issues and Error Analysis

12 3 Other Thermodynamic Properties

12 4 Solvent Models

12 4 2 Quantal Models

12 5 Relative Merits of Explicit and Implicit Solvent Models

12 5 2 SpeedEfficiency

12 5 3 Non equilibrium Solvation

12 5 4 Mixed ExplicitImplicit Models

12 6 Case Study Binding of Biotin Analogs to Avidin

Chapter 13

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Hybrid QuantalClassical Models 13 1 Motivation

13 2 Boundaries Through Space

13 2 2 PolarizedQMUnpolarizedMM

13 2 3 Fully Polarized Interactions

13 3 Boundaries Through Bonds

13 3 2 Link Atoms

13 3 3 Frozen Orbitals

13 4 EmpiricalValenceBondMethods

13 4 2 Following Reaction Paths

13 4 3 Generalization to QMMM

13 5 Case Study Catalytic Mechanism of Yeast Enolase

Chapter 14

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14 1 Determinantal Configurational Representation of Excit

14 2 Singly Excited States

14 2 2 CI Singles

14 2 3 Rydberg States

14 3 General Excited State Methods

14 3 2 Propagator Methods and Time dependent DFT

14 4 Sum and Projection Methods

14 5 Transition Probabilities

14 6 Solvatochromism

14 7 Case Study Organic Light Emitting Diode Alq3

Chapter 15

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15 Adiabatic Reaction Dynamics

15 1 1 Unimolecular Reactions

15 2 Reaction Paths and Transition States

15 3 Transition state Theory

15 3 1 2 Kinetic isotope effects

15 3 2 Variational Transition state Theory

15 3 3 Quantum Effects on the Rate Constant

15 4 Condensed phase Dynamics

15 5 Non adiabatic Dynamics

15 5 2 Marcus Theory

Case Study Isomerization of Propylene Oxide

Essentials of Computational Chemistry: Theories and Models | Book Club |

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