Essentials of Computational Chemistry: Theories and Models | Book Club |
About Course
This book is provided under the UKABCS Educational Capacity-Building Initiative at a discounted price of 620 EGP instead of 1200 EGP, supporting students and researchers.
Description
This book provides a comprehensive introduction to the theories and models used in computational chemistry. It covers essential topics such as quantum mechanics, molecular mechanics, and molecular dynamics, offering practical insights into how computational methods are applied in chemical research. The book is a valuable resource for students, researchers, and professionals seeking to understand the fundamentals of computational chemistry.
Implementation Plan for the Book Club Over Two Months
1. Book Selection
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Book: Essentials of Computational Chemistry: Theories and Models.
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Level: Intermediate to Advanced.
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Total Chapters: 12 (approximate).
2. Chapter Division
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The book will be divided into 8 parts (one part per week).
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Each week, members will read 1-2 chapters depending on the length and complexity.
3. Weekly Schedule
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Week 1: Chapter 1 (Introduction to Computational Chemistry) + Chapter 2 (Quantum Mechanics Basics).
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Week 2: Chapter 3 (Molecular Mechanics) + Chapter 4 (Force Fields).
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Week 3: Chapter 5 (Molecular Dynamics) + Chapter 6 (Monte Carlo Simulations).
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Week 4: Chapter 7 (Electronic Structure Methods) + Chapter 8 (Density Functional Theory).
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Week 5: Chapter 9 (Molecular Orbital Theory) + Chapter 10 (Spectroscopic Properties).
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Week 6: Chapter 11 (Case Studies in Computational Chemistry) + Chapter 12 (Conclusion and Future Directions).
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Week 7: Review and Recap of Key Concepts.
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Week 8: Final Discussion and Evaluation.
4. Weekly Meetings
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Duration: 1-2 hours per meeting.
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Agenda:
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Discuss the assigned chapters.
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Explain complex concepts with the help of an instructor.
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Answer members’ questions.
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Open discussion on ideas presented in the chapters.
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Use interactive tools like presentations or videos to enhance understanding.
5. Interactive Activities
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Workshops: Organize practical workshops on using computational chemistry tools (e.g., molecular dynamics software).
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Side Discussions: Create a Facebook or WhatsApp group for discussions outside meetings.
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Weekly Challenges: For example, writing a summary of the week’s chapters or analyzing a small dataset.
6. Final Evaluation
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At the end of the two months, conduct a final evaluation:
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Survey to assess the reading and meeting experience.
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General discussion session about the book as a whole.
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Members share their personal evaluation of the book and what they learned.
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What Will You Learn?
- Understand the fundamental theories and models in computational chemistry.
- Learn techniques for quantum mechanics, molecular mechanics, and molecular dynamics.
- Gain practical skills in using computational chemistry tools and software.
- Explore electronic structure methods and density functional theory.
- Apply computational methods to solve chemical research problems.
Course Content
Before You Start: Book Club Orientation
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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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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
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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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