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Molecular Structure: Understanding Steric and Electronic Effects from Molecular Mechanics

ISBN: 978-0-470-60884-5
350 pages
July 2010
Molecular Structure: Understanding Steric and Electronic Effects from Molecular Mechanics (0470608846) cover image
A guide to analyzing the structures and properties of organic molecules

Until recently, the study of organic molecules has traveled down two disparate intellectual paths—the experimental, or physical, method and the computational, or theoretical, method. Working somewhat independently of each other, these disciplines have guided research for decades, but they are now being combined efficiently into one unified strategy.

Molecular Structure delivers the essential fundamentals on both the experimental and computational methods, then goes further to show how these approaches can join forces to produce more effective analysis of the structure and properties of organic compounds by:

  • Looking at experimental structures: electron, neutron, X-ray diffraction, and microwave spectroscopy as well as computational structures: ab initio, semi-empirical molecular orbital, and molecular mechanics calculations

  • Discussing various electronic effects, particularly stereoelectronic effects, including hyperconjugation, negative hyperconjugation, the Bohlmann and anomeric effects, and how and why these cause changes in structures and properties of molecules

  • Illustrating complex carbohydrate effects such as the gauche effect, the delta-two effect, and the external anomeric torsional effect

  • Covering hydrogen bonding, the CH bond, and how energies, especially heats of formation, can be affected

  • Using molecular mechanics to tie all of these things together in the familiar language of the organic chemist, valence bond pictures

Authored by a founding father of computational chemistry, Molecular Structure broadens the scope of the subject by serving as a pioneering guide for workers in the fields of organic, biological, and computational chemistry, as they explore new possibilities to advance their discoveries. This work will also be of interest to many of those in tangential or dependent fields, including medicinal and pharmaceutical chemistry and pharmacology.

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Foreword.

Preface.

Acknowledgments.

1 INTRODUCTION.

What, Exactly, is a Molecular Structure?

References.

2 EXPERIMENTAL MOLECULAR STRUCTURES.

Electron Diffraction.

Microwave Spectroscopy.

X-Ray Crystallography.

The Phase Problem.

Rigid-Body Motion.

Molecular Mechanics in Crystallography.

Neutron Diffraction.

Nuclear Magnetic Resonance Spectra 19.

Bond Lengths Depend on Method Used to Determine Them.

References.

3 MOLECULAR STRUCTURES BY COMPUTATIONAL METHODS.

A Brief History of Computers.

Computational Methods.

Semiempirical Quantum Mechanical Methods.

Self-Consistent Field Method.

Ab Initio Methods.

Density Functional Theory.

Molecular Mechanics.

References.

4 MOLECULAR MECHANICS OF ALKANES.

Potential Energy Surface.

Force Constant Matrix.

Diagonal Part.

Vibrational Spectra.

Off-Diagonal Part.

Stretch–Bend Effect.

Urey–Bradley Force Field.

van der Waals Forces.

Dr. Miller’s Nuclear Explosion.

van der Waals Interactions between Nonidentical Atoms.

Congested Molecules.

Tetracyclododecane.

Vibrational Motions of Compressed Hydrogens.

Other Very Short H···H Distances.

Alkanes Summary.

Extension of The Alkane Force Field.

Alkenes.

Functional Groups in Molecular Mechanics.

References.

5 CONJUGATED SYSTEMS.

Introduction.

Structures of Conjugated Hydrocarbons.

in-[34,10][7]Metacyclophane.

Aromatic Compounds.

Simple Benzenoid Compounds.

Corannulene.

C60-Fullerene.

Aromaticity.

Cyclooctatetraene.

[10]–[16]Annulenes.

[18]Annulene.

Triquinacene (Homoaromaticity).

Electronic Spectra.

Structures of Conjugated Heterocycles.

Porphyrins.

References.

6 "EFFECTS" IN ORGANIC CHEMISTRY.

Electronegativity Effect.

Electronegativity Effect on Bond Lengths.

Electronegativity Effect on Bond Angles.

C–H Bond Length versus Vibrational Frequency.

Hyperconjugation.

Baker–Nathan Effect.

References.

7 MORE "EFFECTS"—NEGATIVE HYPERCONJUGATION.

Bohlmann Effect.

Anomeric Effect.

Dimethoxymethane.

Energetic Effects.

Structural Effects.

Angle Effects.

2-Methoxytetrahydropyran.

α-Halo Ketone Effect.

Molecular Mechanics Model.

Energetics.

Summary.

References.

8 ADDITIONAL STEREOCHEMICAL EFFECTS IN CARBOHYDRATES.

Glucose.

Gauche Effect.

Polyoxyethylene (POE).

Delta-Two Effect.

Glucose Diastereomers.

Cellobiose Analog.

External Anomeric Torsional Effect.

References.

9 LEWIS BONDS.

Hydrogen Bonds.

Quantum Mechanical Description of a Hydrogen Bond.

Hydrogen Bonding Models in Molecular Mechanics.

Hydrogen Fluoride Dimer.

Water Dimer.

Methanol Dimer.

Ethylene Glycol.

Other Lewis Bonds.

Amine–Carbonyl Interactions.

References.

10 CRYSTAL STRUCTURE CALCULATIONS.

Crystalline Phase.

Anticipation of Unit Cell.

A Priori Calculations of Crystal Structures.

Molecular Mechanics Applications to Crystals.

Comparison of X-Ray Crystal Structure with Calculated Structures.

Benzene Crystal.

Biphenyl.

Ditrityl Ether.

More of the [18]Annulene Story.

References.

11 HEATS OF FORMATION.

Benson’s Method.

Statistical Mechanics.

Heats of Formation of Alkanes from Molecular Mechanics.

Tim Clark Story.

Thermodynamic Properties of Alkanes.

Heats of Formation from Quantum Mechanics: Alkanes.

Strain Energy.

Ring Strain Energy.

Dodecahedrane.

Heats of Formation of Unsaturated Hydrocarbons.

[18]Annulene, Aromaticity.

Fullerene.

Heats of Formation of Functionalized Molecules.

References.

Concluding Remarks.

Appendix.

Introduction.

Jargon.

Basis Set Superposition Error.

Carbohydrate Conformational Nomenclature.

Conformational Search Routine.

Driver Routine.

Molecular Mechanics Programs.

Nuclear Explosion Preventer.

Quantum Chemistry Progam Exchange.

Ring Counting.

Stereographic Projections.

References.

Index.

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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.
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"The book is written in an informal style, designed to appeal to the non-specialist, and should be accessible to anybody with a background in chemistry." (Chemistry World, 1 August 2011)
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