Molecular Structure: Understanding Steric and Electronic Effects from Molecular Mechanics
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.
What, Exactly, is a Molecular Structure?
2 EXPERIMENTAL MOLECULAR STRUCTURES.
The Phase Problem.
Molecular Mechanics in Crystallography.
Nuclear Magnetic Resonance Spectra 19.
Bond Lengths Depend on Method Used to Determine Them.
3 MOLECULAR STRUCTURES BY COMPUTATIONAL METHODS.
A Brief History of Computers.
Semiempirical Quantum Mechanical Methods.
Self-Consistent Field Method.
Ab Initio Methods.
Density Functional Theory.
4 MOLECULAR MECHANICS OF ALKANES.
Potential Energy Surface.
Force Constant Matrix.
Urey–Bradley Force Field.
van der Waals Forces.
Dr. Miller’s Nuclear Explosion.
van der Waals Interactions between Nonidentical Atoms.
Vibrational Motions of Compressed Hydrogens.
Other Very Short H···H Distances.
Extension of The Alkane Force Field.
Functional Groups in Molecular Mechanics.
5 CONJUGATED SYSTEMS.
Structures of Conjugated Hydrocarbons.
Simple Benzenoid Compounds.
Structures of Conjugated Heterocycles.
6 "EFFECTS" IN ORGANIC CHEMISTRY.
Electronegativity Effect on Bond Lengths.
Electronegativity Effect on Bond Angles.
C–H Bond Length versus Vibrational Frequency.
7 MORE "EFFECTS"—NEGATIVE HYPERCONJUGATION.
α-Halo Ketone Effect.
Molecular Mechanics Model.
8 ADDITIONAL STEREOCHEMICAL EFFECTS IN CARBOHYDRATES.
External Anomeric Torsional Effect.
9 LEWIS BONDS.
Quantum Mechanical Description of a Hydrogen Bond.
Hydrogen Bonding Models in Molecular Mechanics.
Hydrogen Fluoride Dimer.
Other Lewis Bonds.
10 CRYSTAL STRUCTURE CALCULATIONS.
Anticipation of Unit Cell.
A Priori Calculations of Crystal Structures.
Molecular Mechanics Applications to Crystals.
Comparison of X-Ray Crystal Structure with Calculated Structures.
More of the Annulene Story.
11 HEATS OF FORMATION.
Heats of Formation of Alkanes from Molecular Mechanics.
Tim Clark Story.
Thermodynamic Properties of Alkanes.
Heats of Formation from Quantum Mechanics: Alkanes.
Ring Strain Energy.
Heats of Formation of Unsaturated Hydrocarbons.
Heats of Formation of Functionalized Molecules.
Basis Set Superposition Error.
Carbohydrate Conformational Nomenclature.
Conformational Search Routine.
Molecular Mechanics Programs.
Nuclear Explosion Preventer.
Quantum Chemistry Progam Exchange.
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