molecular biology
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Despite cautions from their conservative elders, young chemists like Paternó and van't Hoff began interpreting molecular graphs in terms of the arrangement of a molecule's atoms in 3-dimensional space. Benzene was one such case, but still more significant was the prediction, based on puzzling isomerism involving "optical activity," that molecules could be "chiral," that is, right- or left-handed. Louis Pasteur effected the first artificial...more
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Oxidation and reduction in cellular respiration. Reconciling the biology and chemistry definitions of oxidation and reduction.
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The lecture opens with tricks ("Z-effective" and "Self Consistent Field") that allow one to correct approximately for the error in using orbitals that is due to electron repulsion. This error is hidden by naming it "correlation energy." Professor McBride introduces molecules by modifying J.J. Thomson's Plum-Pudding model of the atom to rationalize the form of molecular orbitals. There is a close analogy in form between the molecular orbita...more
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This lecture begins by applying the united-atom "plum-pudding" view of molecular orbitals, introduced in the previous lecture, to more complex molecules. It then introduces the more utilitarian concept of localized pairwise bonding between atoms. Formulating an atom-pair molecular orbital as the sum of atomic orbitals creates an electron difference density through the cross product that enters upon squaring a sum. This "overlap" term is th...more
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Although molecular mechanics is imperfect, it is useful for discussing molecular structure and energy in terms of standard covalent bonds. Analysis of the Cambridge Structural Database shows that predicting bond distances to within 1% required detailed categorization of bond types. Early attempts to predict heats of combustion in terms of composition proved adequate for physiology, but not for chemistry. Group- or bond-additivity schemes a...more
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Youthful chemists Couper and Kekulé replaced radical and type theories with a new approach involving atomic valence and molecular structure, and based on the tetravalence and self-linking of carbon. Valence structures offered the first explanation for isomerism, and led to the invention of nomenclature, notation, and molecular models closely related to those in use today.
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This lecture brings experiment to bear on the previous theoretical discussion of bonding by focusing on hybridization of the central atom in three XH3 molecules. Because independent electron pairs must not overlap, hybridization can be related to molecular structure by a simple equation. The "Umbrella Vibration" and the associated rehybridization of the central atom is used to illustrate how a competition between strong bonds and stable at...more
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It is important that chemists agree on notation and nomenclature in order to communicate molecular constitution and configuration. It is best when a diagram is as faithful as possible to the 3-dimensional shape of a molecule, but the conventional Fischer projection, which has been indispensable in understanding sugar configurations for over a century, involves highly distorted bonds. Ambiguity in diagrams or words has led to multibillion-d...more
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