Molecular Modeling Basics

✍ Scribed by Jan H. Jensen

• Publisher: CRC Press
• Year: 2010
• Tongue: English
• Leaves: 181
• Edition: 1
• Category: Library

✦ Synopsis

Molecular modeling is becoming an increasingly important part of chemical research and education as computers become faster and programs become easier to use. The results, however, have not become easier to understand. Addressing the need for a "workshop-oriented" book, Molecular Modeling Basics provides the fundamental theory needed to understand not only what molecular modeling programs do, but also the gist of research papers that describe molecular modeling results. Written in a succinct manner using informal language, the book presents concise coverage of key concepts suitable for novices to the field. It begins by examining the potential energy surface (PES), which provides the connection between experimental data and molecular modeling. It explores ways to calculate energy by molecular and quantum mechanics. It describes molecular properties and the condensed phase, and shows how to extract and interpret information from a program output. The author uses hands-on exercises to illustrate concepts and he supplements the text with a blog containing animated tutorials and interactive figures. Drawn from the author’s own lecture notes from a class he taught for many years at the University of Iowa, this volume introduces topics in such a way that beginners can clearly comprehend molecular modeling results. A perfect supplement to a molecular modeling textbook, the book offers students the "hands-on" practice they need to grasp sophisticated concepts. In addition to his blog, the author maintains a website describing his research and one detailing his seminars.

✦ Table of Contents

Molecular Modeling Basics
......Page 4
Dedication......Page 6
Contents......Page 8
Prefaces......Page 10
About the Author......Page 14
1.2 Reactants, products, and transition states: Stationary points......Page 16
1.3 Real and imaginary frequencies: Characterizing stationary points in many dimensions......Page 18
1.4 The frequencies of planar ammonia......Page 21
1.5 Energy minimization: Finding and connecting stationary points......Page 23
1.6 Eight practical comments regarding geometry optimizations......Page 27
1.7 The local minima problem, conformational search, and molecular dynamics......Page 29
1.8 The multiple minima problem: Energy and free energy......Page 33
1.9 Vibrational frequencies......Page 36
2.1 Molecular mechanics force fields......Page 40
2.2 And now for something completely different: Quantum mechanics......Page 44
2.3 The hydrogen atom and the Born–Oppenheimer approximation......Page 45
2.4 The H2+ molecule......Page 47
2.5 The orbital approximation and the variational principle......Page 49
2.6 Electron spin and the Schrödinger equation: RHF, ROHF, and UHF......Page 52
2.7 Basis set......Page 58
2.8 The self-consistent field procedure......Page 65
2.9 Guessing at the orbitals......Page 69
2.10 Four practical comments regarding RHF calculations......Page 70
2.11 Semiempirical methods......Page 71
2.12 The correlation energy......Page 75
2.13 Density functional theory (DFT)......Page 78
2.14 Energy vs. free energy......Page 83
3.1 The electron density......Page 92
3.2 The electrostatic potential......Page 93
3.3 Charges, dipoles, and higher multipoles......Page 95
3.4 Molecules in solution: Explicit solvent models......Page 100
3.5 Molecules in solution: Implicit solvent models......Page 107
3.6 Excited states......Page 110
3.7 Other spectroscopy......Page 113
4.2 Atoms......Page 118
4.3 Bonding......Page 122
4.4 Molecular geometry......Page 125
4.5 Intermolecular interactions......Page 129
4.6 Molecular geometry and motion......Page 133
4.7 Molecular motion and energy......Page 139
4.8 Chemical kinetics......Page 145
5.1 Introductory remarks......Page 154
5.2 Atoms......Page 155
5.3 Bonding......Page 159
5.4 Molecular geometry......Page 162
5.5 Intermolecular interactions......Page 164
5.6 Molecular geometry and motion......Page 168
5.7 Molecular motion and energy......Page 175
5.8 Chemical kinetics......Page 176

✦ Subjects

Химия и химическая промышленность;Матметоды и моделирование в химии;