Molecular Structure: Understanding Steric and Electronic Effects from Molecular Mechanics

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-[3^4,10][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.