After discussing the statistical basis of the law of mass action, the lecture turns to developing a framework for understanding reaction rates. A potential energy surface that associates energy with polyatomic geometry can be realized physically for a linear, triatomic system, but it is more practical to use collective energies for starting material, transition state, and product, together with Eyring theory, to predict rates. Free-radical chain halogenation provides examples of predicting reaction equilibria and rates from bond dissociation energies. The lecture concludes with a summary of the semester's topics from the perspective of physical-organic chemistry.

37 - Potential Energy Surfaces, Transition State Theory and Reaction Mechanism

After discussing the classic determination of the heat of atomization of graphite by Chupka and Inghram, the values of bond dissociation energies, and the utility of average bond energies, the lecture focuses on understanding equilibrium and rate processes through statistical mechanics. The Boltzmann factor favors minimal energy in order to provide the largest number of different arrangements of "bits" of energy. The slippery concept of disorder is illustrated using Couette flow. Entropy favors "disordered arrangements" because there are more of them than there are of recognizable ordered arrangements.

36 - Bond Energies, the Boltzmann Factor and Entropy

Professor Barry Sharpless of Scripps describes the Nobel-prizewinning development of titanium-based catalysts for stereoselective oxidation, the mechanism of their reactions, and their use in preparing esomeprazole. Conformational energy of cyclic alkanes illustrates the use of molecular mechanics.

34 - Sharpless Oxidation Catalysts and the Conformation of  Cycloalkanes

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 are useful for understanding heats of formation, especially when corrected for strain. Heat of atomization is the natural target for bond energy schemes, but experimental measurement requires spectroscopic determination of the heat of atomization of elements in their standard states.

35 - Understanding Molecular Structure and Energy through Standard Bonds

Understanding conformational relationships makes it easy to draw idealized chair structures for cyclohexane and to visualize axial-equatorial interconversion. After quantitative consideration of the conformational energies of ethane, propane, and butane, cyclohexane is used to illustrate the utility of molecular mechanics as an alternative to quantum mechanics for estimating such energies. To give useful accuracy this empirical scheme requires thousands of arbitrary parameters. Unlike quantum mechanics, it assigns strain to specific sources such as bond stretching, bending, and twisting, and van der Waals repulsion or attraction.

33 - Conformational Energy and Molecular Mechanics

Why ethane has a rotational barrier is still debatable. Analyzing conformational and configurational stereotopicity relationships among constitutionally equivalent groups reveals a subtle discrimination in enzyme reactions. When Baeyer suggested strain-induced reactivity due to distorting bond angles away from those in an ideal tetrahedron, he assumed that the cyclohexane ring is flat. He was soon corrected by clever Sachse, but Sachse's weakness in rhetoric led to a quarter-century of confusion.

32 - Stereotopicity and Baeyer Strain Theory

After mentioning some legal implications of chirality, the discussion of configuration concludes using esomeprazole as an example of three general methods for producing single enantiomers. Conformational isomerism is more subtle because isomers differ only by rotation about single bonds, which requires careful physico-chemical consideration of energies and their relation to equilibrium and rate constants. Conformations have their own notation and nomenclature. Curiously, the barrier to rotation about the C-C bond of ethane was established by measuring its heat capacity.

31 - Preparing Single Enantiomers and Conformational Energy

The chemical mode of action of omeprazole is expected to be insensitive to its stereochemistry, making clinical trials of the proposed virtues of a chiral switch crucial. Design of the clinical trials is discussed in the context of marketing. Otolaryngologist Dr. Dianne Duffey provides a clinician's perspective on the testing and marketing of pharmaceuticals, on the FDA approval process, on clinical trial system, on off-label uses, and on individual and institutional responsibility for evaluating pharmaceuticals.

30 - Esomeprazole as an Example of Drug Testing and Usage

Within a lecture on biological resolution, the synthesis of single enantiomers, and the naming and 3D visualization of omeprazole, Professor Laurence Barron of the University of Glasgow delivers a guest lecture on the subject of how chiral molecules rotate polarized light. Mixing wave functions by coordinated application of light's perpendicular electric and magnetic fields shifts electrons along a helix that can be right- or left-handed, but so many mixings are involved, and their magnitudes are so subtle, that predicting net optical rotation in practical cases is rarely simple.

29 - Preparing Single Enantiomers and the Mechanism of Optical Rotation

Determination of the actual atomic arrangement in tartaric acid in 1949 motivated a change in stereochemical nomenclature from Fischer's 1891genealogical convention (D, L) to the CIP scheme (R, S) based on conventional group priorities. Configurational isomers can be interconverted by racemization and epimerization. Pure enantiomers can be separated from racemic mixtures by resolution schemes based on selective crystallization of conglomerates or temporary formation of diastereomers.

28 - Stereochemical Nomenclature; Racemization and Resolution

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Organic Chemistry - Audio

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-dollar patent disputes involving popular drugs. International agreements provide descriptive, unambiguous, unique, systematic "IUPAC" names that are reasonably convenient for most organic molecules of modest molecular weight.

27 - Communicating Molecular Structure in Diagrams and Words

With his tetrahedral carbon models van't Hoff explained the mysteries of known optical isomers possessing stereogenic centers and predicted the existence of chiral allenes, a class of molecules that that would not be observed for another 61 years. Symmetry operations that involve inverting an odd number of coordinate axes interconvert mirror-images. Like printed words, only a small fraction of molecules are achiral. Verbal and pictorial notation for stereochemistry are discussed.

26 - Van't Hoff's Tetrahedral Carbon and Chirality

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 separation of racemic acid into tartaric acid and its mirror-image.

25 - Models in 3-D Space (1869-1877); Optical Isomers

Half a century before direct experimental observation became possible, most structures of organic molecules were assigned by inspired guessing based on plausibility. But Wilhelm Körner developed a strictly logical system for proving the structure of benzene and its derivatives based on isomer counting and chemical transformation. His proof that the six hydrogen positions in benzene are equivalent is the outstanding example of this chemical logic but was widely ignored because, in Palermo, he was far from the seats of chemical authority.

24 - Determining Chemical Structure by Isomer Counting (1869)

Work by Wöhler and Liebig on benzaldehyde inspired a general theory of organic chemistry focusing on so-called radicals, collections of atoms which appeared to behave as elements and persist unchanged through organic reactions. Liebig's French rival, Dumas, temporarily advocated radicals, but converted to the competing theory of types which could accommodate substitution reactions. These decades teach more about the psychology, sociology, and short-sightedness of leading chemists than about fundamental chemistry, but both theories survive in competing schemes of modern organic nomenclature. The HOMO-LUMO mechanism of addition to alkenes and the SOMO mechanism of free-radical chain reactions are introduced.

22 - Radical and Type Theories (1830-1850)

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.

23 - Valence Theory and Constitutional Structure (1858)

The most prominent chemist in the generation following Lavoisier was Berzelius in Sweden. Together with Gay-Lussac in Paris and Davy in London, he discovered new elements, and improved atomic weights and combustion analysis for organic compounds. Invention of electrolysis led not only to new elements but also to the theory of dualism, with elements being held together by electrostatic attraction. Wöhler's report on the synthesis of urea revealed isomerism but also persistent naiveté about treating quantitative data. In their collaborative investigation of oil of bitter almonds Wöhler and Liebig extended dualism to organic chemistry via the radical theory.

21 - Berzelius to Liebig and Wöhler (1805-1832)

This lecture traces the development of elemental analysis as a technique for the determination of the composition of organic compounds beginning with Lavoisier's early combustion and fermentation experiments, which showed a new, if naïve, attitude toward handling experimental data. Dalton's atomic theory was consistent with the empirical laws of definite, equivalent, and multiple proportions. The basis of our current notation and of precise analysis was established by Berzelius, but confusion about atomic weight multiples, which could have been clarified early by the law of Avogadro and Gay-Lussac, would persist for more than half a century.

20 - Rise of the Atomic Theory (1790-1805)

This lecture begins a series describing the development of organic chemistry in chronological order, beginning with the father of modern chemistry, Lavoisier. The focus is to understand the logic of the development of modern theory, technique and nomenclature so as to use them more effectively. Chemistry begins before Lavoisier's "Chemical Revolution," with the practice of ancient technology and alchemy, and with discoveries like those of Scheele, the Swedish apothecary who discovered oxygen and prepared the first pure samples of organic acids. Lavoisier's Traité Élémentaire de Chimie launched modern chemistry with its focus on facts, ideas, and words. Lavoisier weighed gases and measured heat with a calorimeter, as well as clarifying language and chemical thinking. His key concepts were conservation of mass for the elements and oxidation, a process in which reaction with oxygen could make a "radical" or "base" into an acid.

19 - Oxygen and the Chemical Revolution (Beginning to 1789)

This lecture completes the first half of the semester by analyzing three functional groups in terms of the interaction of localized atomic or pairwise orbitals. Many key properties of biological polypeptides derive from the mixing of such localized orbitals that we associate with "resonance" of the amide group. The acidity of carboxylic acids and the aggregation of methyl lithium into solvated tetramers can be understood in analogous terms. More amazing than the panoply of modern experimental and theoretical tools is that their results would not have surprised traditional organic chemists who already had developed an understanding of organic structure with much cruder tools. The next quarter of the semester is aimed at understanding how our scientific predecessors developed the structural model and nomenclature of organic chemistry that we still use.

18 - Amide, Carboxylic Acid and Alkyl Lithium

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