|
1 An Outline of What Computational Chemistry Is All About |
|
|
1 | (8) |
|
1.1 What You Can Do with Computational Chemistry |
|
|
1 | (1) |
|
1.2 The Tools of Computational Chemistry |
|
|
2 | (1) |
|
1.3 Putting It All Together |
|
|
3 | (1) |
|
1.4 The Philosophy of Computational Chemistry |
|
|
4 | (1) |
|
|
5 | (1) |
|
|
5 | (1) |
|
|
6 | (1) |
|
|
7 | (2) |
|
2 The Concept of the Potential Energy Surface |
|
|
9 | (36) |
|
|
9 | (4) |
|
|
13 | (8) |
|
2.3 The Born-Oppenheimer Approximation |
|
|
21 | (2) |
|
2.4 Geometry Optimization |
|
|
23 | (7) |
|
2.5 Stationary Points and Normal-Mode Vibrations - Zero Point Energy |
|
|
30 | (6) |
|
|
36 | (3) |
|
|
39 | (1) |
|
|
40 | (2) |
|
|
42 | (1) |
|
|
42 | (3) |
|
|
45 | (40) |
|
|
45 | (3) |
|
3.2 The Basic Principles of Molecular Mechanics |
|
|
48 | (12) |
|
3.2.1 Developing a Forcefield |
|
|
48 | (5) |
|
3.2.2 Parameterizing a Forcefield |
|
|
53 | (4) |
|
3.2.3 A Calculation Using Our Forcefield |
|
|
57 | (3) |
|
3.3 Examples of the Use of Molecular Mechanics |
|
|
60 | (7) |
|
3.3.1 To Obtain Reasonable Input Geometries for Lengthier (Ab Initio, Semiempirical or Density Functional) Kinds of Calculations |
|
|
61 | (3) |
|
3.3.2 To Obtain Good Geometries (and Perhaps Energies) for Small- to Medium-Sized Molecules |
|
|
64 | (1) |
|
3.3.3 To Calculate the Geometries and Energies of Very Large Molecules, Usually Polymeric Biomolecules (Proteins and Nucleic Acids) |
|
|
65 | (1) |
|
3.3.4 To Generate the Potential Energy Function Under Which Molecules Move, for Molecular Dynamics or Monte Carlo Calculations |
|
|
65 | (1) |
|
3.3.5 As a (Usually Quick) Guide to the Feasibility of, or Likely Outcome of, Reactions in Organic Synthesis |
|
|
66 | (1) |
|
3.4 Geometries Calculated by MM |
|
|
67 | (5) |
|
3.5 Frequencies and Vibrational Spectra Calculated by MM |
|
|
72 | (1) |
|
3.6 Strengths and Weaknesses of Molecular Mechanics |
|
|
73 | (5) |
|
|
73 | (1) |
|
|
74 | (4) |
|
|
78 | (1) |
|
|
79 | (3) |
|
|
82 | (1) |
|
|
82 | (3) |
|
4 Introduction to Quantum Mechanics in Computational Chemistry |
|
|
85 | (90) |
|
|
85 | (2) |
|
4.2 The Development of Quantum Mechanics. The Schrodinger Equation |
|
|
87 | (15) |
|
4.2.1 The Origins of Quantum Theory: Blackbody Radiation and the Photoelectric Effect |
|
|
87 | (4) |
|
|
91 | (1) |
|
|
91 | (1) |
|
|
92 | (2) |
|
|
94 | (2) |
|
4.2.6 The Wave Mechanical Atom and the Schrodinger Equation |
|
|
96 | (6) |
|
4.3 The Application of the Schrodinger Equation to Chemistry by Huckel |
|
|
102 | (50) |
|
|
102 | (1) |
|
|
103 | (5) |
|
4.3.3 Matrices and Determinants |
|
|
108 | (10) |
|
4.3.4 The Simple Huckel Method - Theory |
|
|
118 | (15) |
|
4.3.5 The Simple Huckel Method - Applications |
|
|
133 | (11) |
|
4.3.6 Strengths and Weaknesses of the Simple Huckel Method |
|
|
144 | (2) |
|
4.3.7 The Determinant Method of Calculating the Huckel c's and Energy Levels |
|
|
146 | (6) |
|
4.4 The Extended Huckel Method |
|
|
152 | (13) |
|
|
152 | (8) |
|
4.4.2 An Illustration of the EHM: the Protonated Helium Molecule |
|
|
160 | (3) |
|
4.4.3 The Extended Huckel Method - Applications |
|
|
163 | (1) |
|
4.4.4 Strengths and Weaknesses of the Extended Huckel Method |
|
|
164 | (1) |
|
|
165 | (3) |
|
|
168 | (4) |
|
|
172 | (1) |
|
|
172 | (3) |
|
|
175 | (216) |
|
|
175 | (1) |
|
5.2 The Basic Principles of the Ab initio Method |
|
|
176 | (56) |
|
|
176 | (1) |
|
5.2.2 The Hartree SCF Method |
|
|
177 | (4) |
|
5.2.3 The Hartree-Fock Equations |
|
|
181 | (51) |
|
|
232 | (23) |
|
|
232 | (1) |
|
5.3.2 Gaussian Functions; Basis Set Preliminaries; Direct SCF |
|
|
233 | (5) |
|
5.3.3 Types of Basis Sets and Their Uses |
|
|
238 | (17) |
|
5.4 Post-Hartree-Fock Calculations: Electron Correlation |
|
|
255 | (26) |
|
5.4.1 Electron Correlation |
|
|
255 | (6) |
|
5.4.2 The Møller-Plesset Approach to Electron Correlation |
|
|
261 | (8) |
|
5.4.3 The Configuration Interaction Approach to Electron Correlation - The Coupled Cluster Method |
|
|
269 | (12) |
|
5.5 Applications of the Ab initio Method |
|
|
281 | (91) |
|
|
281 | (10) |
|
|
291 | (41) |
|
5.5.3 Frequencies and Vibrational Spectra |
|
|
332 | (5) |
|
5.5.4 Properties Arising from Electron Distribution: Dipole Moments, Charges, Bond Orders, Electrostatic Potentials, Atoms-in-Molecules (AIM) |
|
|
337 | (22) |
|
5.5.5 Miscellaneous Properties - UV and NMR Spectra, Ionization Energies, and Electron Affinities |
|
|
359 | (5) |
|
|
364 | (8) |
|
5.6 Strengths and Weaknesses of Ab initio Calculations |
|
|
372 | (1) |
|
|
372 | (1) |
|
|
372 | (1) |
|
|
373 | (1) |
|
|
373 | (15) |
|
|
388 | (1) |
|
|
389 | (2) |
|
6 Semiempirical Calculations |
|
|
391 | (54) |
|
|
391 | (2) |
|
6.2 The Basic Principles of SCF Semiempirical Methods |
|
|
393 | (19) |
|
|
393 | (3) |
|
6.2.2 The Pariser-Parr-Pople (PPP) Method |
|
|
396 | (2) |
|
6.2.3 The Complete Neglect of Differential Overlap (CNDO) Method |
|
|
398 | (1) |
|
6.2.4 The Intermediate Neglect of Differential Overlap (INDO) Method |
|
|
399 | (1) |
|
6.2.5 The Neglect of Diatomic Differential Overlap (NDDO) Methods |
|
|
400 | (12) |
|
6.3 Applications of Semiempirical Methods |
|
|
412 | (24) |
|
|
412 | (7) |
|
|
419 | (4) |
|
6.3.3 Frequencies and Vibrational Spectra |
|
|
423 | (3) |
|
6.3.4 Properties Arising from Electron Distribution: Dipole Moments, Charges, Bond Orders |
|
|
426 | (5) |
|
6.3.5 Miscellaneous Properties - UV Spectra, Ionization Energies, and Electron Affinities |
|
|
431 | (3) |
|
|
434 | (1) |
|
6.3.7 Some General Remarks |
|
|
435 | (1) |
|
6.4 Strengths and Weaknesses of Semiempirical Methods |
|
|
436 | (1) |
|
|
436 | (1) |
|
|
436 | (1) |
|
|
437 | (1) |
|
|
438 | (5) |
|
|
443 | (1) |
|
|
443 | (2) |
|
7 Density Functional Calculations |
|
|
445 | (76) |
|
|
445 | (2) |
|
7.2 The Basic Principles of Density Functional Theory |
|
|
447 | (20) |
|
|
447 | (1) |
|
7.2.2 Forerunners to Current DFT Methods |
|
|
448 | (1) |
|
7.2.3 Current DFT Methods: The Kohn-Sham Approach |
|
|
449 | (18) |
|
7.3 Applications of Density Functional Theory |
|
|
467 | (42) |
|
|
468 | (9) |
|
|
477 | (7) |
|
7.3.3 Frequencies and Vibrational Spectra |
|
|
484 | (3) |
|
7.3.4 Properties Arising from Electron Distribution - Dipole Moments, Charges, Bond Orders, Atoms-in-Molecules |
|
|
487 | (4) |
|
7.3.5 Miscellaneous Properties - UV and NMR Spectra, Ionization Energies and Electron Affinities, Electronegativity, Hardness, Softness and the Fukui Function |
|
|
491 | (18) |
|
|
509 | (1) |
|
7.4 Strengths and Weaknesses of DFT |
|
|
509 | (1) |
|
|
509 | (1) |
|
|
510 | (1) |
|
|
510 | (2) |
|
|
512 | (6) |
|
|
518 | (1) |
|
|
518 | (3) |
|
8 Some "Special" Topics: Solvation, Singlet Diradicals, A Note on Heavy Atoms and Transition Metals |
|
|
521 | (40) |
|
|
521 | (14) |
|
|
522 | (1) |
|
8.1.2 Ways of Treating Solvation |
|
|
522 | (13) |
|
|
535 | (12) |
|
|
535 | (1) |
|
8.2.2 Problems with Singlet Diradicals and Model Chemistries |
|
|
535 | (2) |
|
8.2.3 (1) Singlet Diradicals: Beyond Model Chemistries. (2) Complete Active Space Calculations (CAS) |
|
|
537 | (10) |
|
8.3 A Note on Heavy Atoms and Transition Metals |
|
|
547 | (5) |
|
|
547 | (1) |
|
8.3.2 Heavy Atoms and Relativistic Corrections |
|
|
548 | (1) |
|
8.3.3 Some Heavy Atom Calculations |
|
|
549 | (1) |
|
|
550 | (2) |
|
|
552 | (1) |
|
|
553 | (5) |
|
|
558 | (1) |
|
|
558 | (1) |
|
|
558 | (1) |
|
|
558 | (1) |
|
|
558 | (1) |
|
|
559 | (1) |
|
Heavy Atoms and Transition Metals |
|
|
559 | (2) |
|
|
559 | (1) |
|
|
560 | (1) |
|
9 Selected Literature Highlights, Books, Websites, Software and Hardware |
|
|
561 | (24) |
|
|
561 | (11) |
|
|
561 | (5) |
|
|
566 | (2) |
|
|
568 | (4) |
|
|
572 | (5) |
|
|
572 | (4) |
|
9.2.2 Websites for Computational Chemistry in General |
|
|
576 | (1) |
|
9.3 Software and Hardware |
|
|
577 | (5) |
|
|
577 | (4) |
|
|
581 | (1) |
|
|
582 | (1) |
|
|
582 | (3) |
Answers |
|
585 | (70) |
Index |
|
655 | |