Molecular Structure Understanding Steric and Electronic Effects from Molecular Mechanics

by Allinger, Norman L.; Rogers, Donald W.

• ISBN13: 9780470195574
• ISBN10: 0470195576
• Edition: 1st
• Format: Hardcover
• Copyright: 2010-08-02
• Publisher: Wiley

Summary

Written by a founding father of computational chemistry, Structure and Properties of Organic Molecules provides organic, physical, computational, pharmaceutical/medicinal, and polymer chemists with a strong understanding of the structure and properties of organic molecules by bringing together the computational methods and the experimental methods commonly used for studies of molecular structure. Both a useful text and self-teaching guide, coverage includes experimental structures from electron, neutron, X-ray diffraction, microwave spectroscopy, and computational structures, ab initio, semi-emperitcal molecular orbital, and molecular mechanics calculations.

Author Biography

Norman L. Allinger received his BS from the University of California, Berkeley, in 1951 and his PhD from the University of California, Los Angeles, in 1954. He was on the faculty at Wayne State University before coming to the University of Georgia as Research Professor in 1969. He is known for his use of computational chemistry, especially molecular mechanics, to solve a variety of chemical problems. He is the senior author of the MM2, MM3, and MM4 molecular mechanics software packages.

Table of Contents

Foreword	p. xi
Preface	p. xv
Acknowledgments	p. xix
Introduction	p. 1
What, Exactly, is a Molecular Structure?	p. 3
References	p. 6
Experimental Molecular Structures	p. 7
Electron Diffraction	p. 7
Microwave Spectroscopy	p. 10
X-Ray Crystallography	p. 11
The Phase Problem	p. 12
Rigid-Body Motion	p. 14
Molecular Mechanics in Crystallography	p. 16
Neutron Diffraction	p. 17
Nuclear Magnetic Resonance Spectra	p. 19
Bond Lengths Depend on Method Used to Determine Them	p. 20
References	p. 25
Molecular Structures By Computational Methods	p. 28
A Brief History of Computers	p. 28
Computational Methods	p. 33
Semiempirical Quantum Mechanical Methods	p. 34
Self-Consistent Field Method	p. 35
Ab Initio Methods	p. 37
Density Functional Theory	p. 41
Molecular Mechanics	p. 42
References	p. 47
Molecular Mechanics of Alkanes	p. 51
Potential Energy Surface	p. 51
Force Constant Matrix	p. 57
Diagonal Part	p. 57
Vibrational Spectra	p. 58
Off-Diagonal Part	p. 63
Stretch-Bend Effect	p. 65
Urey-Bradley Force Field	p. 66
van der Waals Forces	p. 66
Dr. Miller's Nuclear Explosion	p. 73
van der Waals Interactions between Nonidentical Atoms	p. 74
Congested Molecules	p. 75
Tetracyclododecane	p. 76
Vibrational Motions of Compressed Hydrogens	p. 80
Other Very Short H&cdots;H Distances	p. 81
Alkanes Summary	p. 84
Extension of The Alkane Force Field	p. 85
Alkenes	p. 88
Functional Groups in Molecular Mechanics	p. 89
References	p. 90
Conjugated Systems	p. 92
Introduction	p. 92
Structures of Conjugated Hydrocarbons	p. 98
in-[34,10][7] Metacyclophane	p. 102
Aromatic Compounds	p. 104
Simple Benzenoid Compounds	p. 105
Corannulene	p. 108
C60-Fullerene	p. 109
Aromaticity	p. 112
Cyclooctatetraene	p. 115
[10]-[16]Annulenes	p. 116
[18]Annulene	p. 116
Triquinacene (Homoaromaticity)	p. 118
Electronic Spectra	p. 122
Structures of Conjugated Heterocycles	p. 124
Porphyrins	p. 127
References	p. 129
"Effects" in Organic Chemistry	p. 134
Electronegativity Effect	p. 137
Electronegativity Effect on Bond Lengths	p. 138
Electronegativity Effect on Bond Angles	p. 143
C-H Bond Length versus Vibrational Frequency	p. 144
Hyperconjugation	p. 147
Baker-Nathan Effect	p. 151
References	p. 160
More "Effects"-Negative Hyperconjugation	p. 162
Bohlmann Effect	p. 163
Anomeric Effect	p. 167
Dimethoxymethane	p. 169
Energetic Effects	p. 169
Structural Effects	p. 170
Angle Effects	p. 173
2-Methoxytetrahydropyran	p. 173
¿-Halo Ketone Effect	p. 177
Molecular Mechanics Model	p. 182
Energetics	p. 185
Summary	p. 186
References	p. 186
Additional Stereochemical Effects in Carbohydrates	p. 189
Glucose	p. 189
Gauche Effect	p. 193
Polyoxyethylene (POE)	p. 195
Delta-Two Effect	p. 197
Glucose Diastereomers	p. 200
Cellobiose Analog	p. 201
External Anomeric Torsional Effect	p. 204
References	p. 210
Lewis Bonds	p. 212
Hydrogen Bonds	p. 212
Quantum Mechanical Description of a Hydrogen Bond	p. 215
Hydrogen Bonding Models in Molecular Mechanics	p. 218
Hydrogen Fluoride Dimer	p. 221
Water Dimer	p. 222
Methanol Dimer	p. 223
Ethylene Glycol	p. 223
Other Lewis Bonds	p. 227
Amine-Carbonyl Interactions	p. 228
References	p. 237
Crystal Structure Calculations	p. 239
Crystalline Phase	p. 240
Anticipation of Unit Cell	p. 241
A Priori Calculations of Crystal Structures	p. 241
Molecular Mechanics Applications to Crystals	p. 242
Comparison of X-Ray Crystal Structure with Calculated Structures	p. 242
Benzene Crystal	p. 243
Biphenyl	p. 246
Ditrityl Ether	p. 247
More of the [18]Annulene Story	p. 249
References	p. 254
Heats of Formation	p. 257
Benson's Method	p. 258
Statistical Mechanics	p. 261
Heats of Formation of Alkanes from Molecular Mechanics	p. 265
Tim Clark Story	p. 269
Thermodynamic Properties of Alkanes	p. 273
Heats of Formation from Quantum Mechanics: Alkanes	p. 274
Strain Energy	p. 282
Ring Strain Energy	p. 285
Dodecahedrane	p. 287
Heats of Formation of Unsaturated Hydrocarbons	p. 291
[18]Annulene, Aromaticity	p. 294
Fullerene	p. 295
Heats of Formation of Functionalized Molecules	p. 296
References	p. 297
Concluding Remarks	p. 301
Appendix	p. 302
Introduction	p. 302
Jargon	p. 302
Basis Set Superposition Error	p. 303
Carbohydrate Conformational Nomenclature	p. 304
Conformational Search Routine	p. 305
Driver Routine	p. 308
Molecular Mechanics Programs	p. 311
Nuclear Explosion Preventer	p. 313
Quantum Chemistry Progam Exchange	p. 313
Ring Counting	p. 315
Stereographic Projections	p. 317
References	p. 319
Index	p. 321
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