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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05:48
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11:35
Essentials of Computational Chemistry: Theories and Models | Book Club
Chapter 1 : What are Theory ,Computation ,and Modeling?
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06:00
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06:26
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00:00
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00:00
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07:29
Chapter 2 : Molecular Mechanics
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2 1 History and Fundamental Assumptions
00:00 -
2. 2 .2 Valence Angle Bending
06:45 -
2 .2 .4 van der Waals Interactions
06:39 -
2. 2. 6 Cross Terms and Additional Non bonded Terms
07:19 -
2 .3 Force field Energies and Thermodynamics
06:38 -
2. 4 Geometry Optimization
06:57 -
2. 4. 2 Optimization Aspects Specific to Force Fields
00:00 -
2. 5 Menagerie of Modern Force Fields
00:00 -
2. 5. 2 Validation
00:00 -
2. 7 Case Study 2R∗,4S ∗ 1 Hydroxy 2,4 dimethylhex 5 ene
09:10
Chapter3
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3. 1 Relationship Between MM Optima and Real Systems
08:12 -
3 .3 .1 Harmonic Oscillator Trajectories
06:47 -
3. 3. 3 Practical Issues in Propagation
07:24 -
3. 4 Monte Carlo
06:39 -
3. 6 Key Details in Formalism
07:42 -
3. 6. 5 The Multiple Minima Problem
08:11
Chapter4
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4. 1 Quantum Mechanics and the Wave Function
07:42 -
4 .2 .2 The Variational Principle
07:45 -
4 .3. 2 The Secular Equation
07:11 -
4 .5 Many electron Wave Functions
07:32 -
4. 5. 4 Slater Determinants
07:43
Chapter5
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5. 2 Extended H¨uckel Theory
08:49 -
5 .4 INDO Formalism
08:39 -
5 .5 Basic NDDO Formalism 5
07:12 -
5 .6 General Performance Overview of Basic NDDO Models
07:13 -
5. 7 Ongoing Developments in Semiempirical MO Theory
06:59 -
5 .8 Case Study Asymmetric Alkylation of Benzaldehyde
07:38 -
5 .1 Semiempirical Philosophy
06:53
chapter 6
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6. 1 Ab Initio Implementations of Hartree–Fock Molecular
07:38 -
6 .2 Basis Sets
04:26 -
6. 2. 1 Functional Forms
06:45 -
6. 2. 2 Contracted Gaussian Functions
06:53 -
6. 2. 3 Single ζ, Multiple ζ, and Split Valence
06:31 -
6. 2 .4 Polarization Functions
07:10 -
6 .2. 5 Diffuse Functions
05:08 -
6 .2. 6 The HF Limit
05:10 -
6. 2 .7 Effective Core Potentials
06:44 -
6. 2. 8 Sources
07:32 -
6. 3 Key Technical and Practical Points of Hartree–
07:31 -
6. 3 .2 Symmetry
06:49 -
6. 3. 3 Open shell Systems
09:06 -
6. 3. 4 Efficiency of Implementation and Use
07:06 -
6 .4 General Performance Overview of Ab Initio HF Theory 6 .4 .1 Energetics
08:44 -
6. 4. 2 Geometries
06:12 -
6. 4 .3 Charge Distributions
07:40 -
6. 5 Case Study Polymerization of 4 Substituted Aromatic Enynes
03:59
Chapter 7
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7 1 Dynamical vs Non dynamical Electron Correlation
07:32 -
7 2 3 Full Configuration Interaction
09:18 -
7 3 2 Multireference
08:07 -
7 4 3 Multireference
06:37 -
7 6 1 Basis Set Convergence
06:34
Chapter 8
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8 3 Kohn Sham self consistent Field Methodology
08:16 -
8 5 Advantages and Disadvantages of DFT Compared to MO Theory
07:13 -
8 6 General Performance Overview of DFT
07:22 -
8 7 Case Study Transition Metal Catalyzed Carbonylation of Methanol
07:10
Chapter 9
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9 .1 Properties Related to Charge
04:28 -
9. 1. 1 Electric Multipole Moments
07:21 -
9. 1. 2 Molecular Electrostatic Potential
07:07 -
9 .1 .3 Partial Atomic Charges
09:31 -
9. 1 .4 Total Spin
08:14 -
9. 1. 5 Polarizability and Hyperpolarizability
06:46 -
9 .1. 6 ESR Hyperfine Coupling Constants
06:40 -
9. 2 Ionization Potentials and Electron Affinities
08:17 -
9 3 Spectroscopy of Nuclear Motion
07:22 -
9 .3 .2 Vibrational
08:05 -
9 .4 NMR Spectral Properties
06:36 -
9. 4. 2 Chemical Shifts and Spin–spin Coupling Constants
07:30 -
9. 5 Case Study Matrix Isolation
05:13
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
07:14 -
10. 6 Case Study
03:12
Chapter 11
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11 .1 Condensed phase Effects on Structure and
04:40 -
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
07:30 -
11 .2 Electrostatic Interactions with a Continuum
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11. 2 .1 The Poisson Equation
09:43 -
11. 2 .2 Generalized Born
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11 .2 .3 Conductor like Screening Model
07:22 -
1.1. 3 Continuum Models for Non electrostatic Interactions
07:19 -
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
06:30 -
11 .4 .5 Molecular Dynamics with Implicit Solvent
07:19 -
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
03:24
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
06:42 -
12 2 5 Potentials of Mean Force
08:52 -
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
07:44 -
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
06:08
Chapter 13
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Hybrid QuantalClassical Models 13 1 Motivation
05:18 -
13 2 Boundaries Through Space
06:36 -
13 2 2 PolarizedQMUnpolarizedMM
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13 2 3 Fully Polarized Interactions
04:42 -
13 3 Boundaries Through Bonds
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13 3 2 Link Atoms
07:49 -
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
06:00 -
13 5 Case Study Catalytic Mechanism of Yeast Enolase
04:28
Chapter 14
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14 1 Determinantal Configurational Representation of Excit
08:47 -
14 2 Singly Excited States
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14 2 2 CI Singles
06:02 -
14 2 3 Rydberg States
04:51 -
14 3 General Excited State Methods
07:43 -
14 3 2 Propagator Methods and Time dependent DFT
07:11 -
14 4 Sum and Projection Methods
07:10 -
14 5 Transition Probabilities
06:12 -
14 6 Solvatochromism
06:43 -
14 7 Case Study Organic Light Emitting Diode Alq3
04:09
Chapter 15
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15 Adiabatic Reaction Dynamics
06:51 -
15 1 1 Unimolecular Reactions
07:28 -
15 2 Reaction Paths and Transition States
08:42 -
15 3 Transition state Theory
07:11 -
15 3 1 2 Kinetic isotope effects
06:12 -
15 3 2 Variational Transition state Theory
06:21 -
15 3 3 Quantum Effects on the Rate Constant
06:50 -
15 4 Condensed phase Dynamics
06:57 -
15 5 Non adiabatic Dynamics
06:24 -
15 5 2 Marcus Theory
07:28 -
Case Study Isomerization of Propylene Oxide
04:20
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