Freshman Organic Chemistry (Yale CHEM 125) | Full 37-Lecture Course:

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This is Yales’ Freshman Organic Chemistry course, the first semester in a two-semester introductory course, formally called Chemistry 125 (CHEM 125). It focuses on current theories of structure and mechanism in organic chemistry, their historical development, and their basis in experimental observation.

37 lectures in all, the course prepares students in chemistry and physics, and is an introduction for original science and intellectual skills necessary for creative research.

The course is taught by Professor J. Michael McBride, who is the Richard M. Colgate Professor of Chemistry at Yale University.

Course materials for Yale Chemistry 125 (CHEM 125)

1. How Do You Know? (#1)

- Freshman Organic Chemistry (CHEM 125) Professor McBride outlines the course with its goals and requirements, including the required laboratory course. To the course's prime question "How do you know" he proposes two unacceptable answers (divine and human authority), and two acceptable answers (experiment and logic). He illustrates the fruitfulness of experiment and logic using the rise of science in the seventeenth century. London's Royal Society and the "crucial" experiment on light by Isaac N...

2. Force Laws, Lewis Structures and Resonance (#2)

- Freshman Organic Chemistry (CHEM 125) Professor McBride begins by following Newton's admonition to search for the force law that describes chemical bonding. Neither direct (Hooke's Law) nor inverse (Coulomb, Gravity) dependence on distance will do - a composite like the Morse potential is needed. G. N. Lewis devised a "cubic-octet" theory based on the newly discovered electron, and developed it into a shared pair model to explain bonding. After discussing Lewis-dot notation and formal charge, P...

3. Double Minima, Earnshaw's Theorem and Plum-Puddings (#3)

- Freshman Organic Chemistry (CHEM 125) Continuing the discussion of Lewis structures and chemical forces from the previous lecture, Professor McBride introduces the double-well potential of the ozone molecule and its structural equilibrium. The inability for inverse-square force laws to account for stable arrangements of charged particles is prescribed by Earnshaw's Theorem, which may be visualized by means of lines of force. J.J. Thomson circumvented Earnshaw's prohibition on structure by postu...

4. Coping with Smallness and Scanning Probe Microscopy (#4)

- Freshman Organic Chemistry (CHEM 125) This lecture asks whether it is possible to confirm the reality of bonds by seeing or feeling them. It first describes the work of "clairvoyant" charlatans from the beginning of the twentieth century, who claimed to "see" details of atomic and molecular structure, in order to discuss proper bases for scientific belief. It then shows that the molecular scale is not inconceivably small, and that Newton and Franklin performed simple experiments that measure su...

5. X-Ray Diffraction (#5)

$5. X-Ray Diffraction$
- Freshman Organic Chemistry (CHEM 125) Professor McBride introduces the theory behind light diffraction by charged particles and its application to the study of the electron distribution in molecules by x-ray diffraction. The roles of molecular pattern and crystal lattice repetition are illustrated by shining laser light through diffraction masks to generate patterns reminiscent of those encountered in X-ray studies of ordered solids. 00:00 - Chapter 1. Introduction: Focusing Lux 07:11 - Chapte...

6. Seeing Bonds by Electron Difference Density (#6)

- Freshman Organic Chemistry (CHEM 125) Professor McBride uses a hexagonal "benzene" pattern and Franklin's X-ray pattern of DNA, to continue his discussion of X-ray crystallography by explaining how a diffraction pattern in "reciprocal space" relates to the distribution of electrons in molecules and to the repetition of molecules in a crystal lattice. He then uses electron difference density mapping to reveal bonds, and unshared electron pairs, and their shape, and to show that they are only one...

7. Quantum Mechanical Kinetic Energy (#7)

- Freshman Organic Chemistry (CHEM 125) After pointing out several discrepancies between electron difference density results and Lewis bonding theory, the course proceeds to quantum mechanics in search of a fundamental understanding of chemical bonding. The wave function ψ, which beginning students find confusing, was equally confusing to the physicists who created quantum mechanics. The Schrödinger equation reckons kinetic energy through the shape of ψ. When ψ curves toward zero, kinetic ene...

8. One-Dimensional Wave Functions (#8)

- Freshman Organic Chemistry (CHEM 125) Professor McBride expands on the recently introduced concept of the wave function by illustrating the relationship of the magnitude of the curvature of the wave function to the kinetic energy of the system, as well as the relationship of the square of the wave function to the electron probability density. The requirement that the wave function not diverge in areas of negative kinetic energy leads to only certain energies being allowed, a property which is e...

9. Chladni Figures and One-Electron Atoms (#9)

- Freshman Organic Chemistry (CHEM 125) After showing how a double-minimum potential generates one-dimensional bonding, Professor McBride moves on to multi-dimensional wave functions. Solving Schrödinger's three-dimensional differential equation might have been daunting, but it was not, because the necessary formulas had been worked out more than a century earlier in connection with acoustics. Acoustical "Chladni" figures show how nodal patterns relate to frequencies. The analogy is pursued by s...

10. Reality and the Orbital Approximation (#10)

- Freshman Organic Chemistry (CHEM 125) In discussions of the Schrödinger equation thus far, the systems described were either one-dimensional or involved a single electron. After discussing how increased nuclear charge affects the energies of one-electron atoms and then discussing hybridization, this lecture finally addresses the simple fact that multi-electron systems cannot be properly described in terms of one-electron orbitals. 00:00 - Chapter 1. Atom-in-a-Box Plots: Assessing Probability ...

11. Orbital Correction and Plum-Pudding Molecules (#11)

- Freshman Organic Chemistry (CHEM 125) 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 orbitals of CH4 and NH3 ...

12. Overlap and Atom-Pair Bonds (#12)

- Freshman Organic Chemistry (CHEM 125) 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 the key to bonding. ...

13. Overlap and Energy-Match (#13)

- Freshman Organic Chemistry (CHEM 125) Professor McBride uses this lecture to show that covalent bonding depends primarily on two factors: orbital overlap and energy-match. First he discusses how overlap depends on hybridization; then how bond strength depends on the number of shared electrons. In this way quantum mechanics shows that Coulomb's law answers Newton's query about what "makes the Particles of Bodies stick together by very strong Attractions." Energy mismatch between the constituent ...

14. Checking Hybridization Theory with XH_3 (#14)

- Freshman Organic Chemistry (CHEM 125) This lecture brings experiment to bear on the previous theoretical discussion of bonding by focusing on hybridization of the central atom in three XH_3 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 atoms works to crea...

15. Chemical Reactivity: SOMO, HOMO, and LUMO (#15)

- Freshman Organic Chemistry (CHEM 125) Professor McBride begins by using previous examples of "pathological" bonding and the BH_3 molecule to illustrate how a chemist's use of localized bonds, vacant atomic orbitals, and unshared pairs to understand molecules compares with views based on the molecule's own total electron density or on computational molecular orbitals. This lecture then focuses on understanding reactivity in terms of the overlap of singly-occupied molecular orbitals (SOMOs) and, ...

16. Recognizing Functional Groups (#16)

- Freshman Organic Chemistry (CHEM 125) This lecture continues the discussion of the HOMO/LUMO view of chemical reactivity by focusing on ways of recognizing whether a particular HOMO should be unusually high in energy (basic), or a particular LUMO should be unusually low (acidic). The approach is illustrated with BH_3, which is both acidic and basic and thus dimerizes by forming unusual "Y" bonds. The low LUMOs that make both HF and CH_3F acidic are analyzed and compared underlining the distinct...

17. Reaction Analogies and Carbonyl Reactivity (#17)

- Freshman Organic Chemistry (CHEM 125) Continuing the examination of molecular orbital theory as a predictor of chemical reactivity, this lecture focuses on the close analogy among seemingly disparate organic chemistry reactions: acid-base, SN2 substitution, and E2 elimination. All these reactions involve breaking existing bonds where LUMOs have antibonding nodes while new bonds are being formed. The three-stage oxidation of ammonia by elemental chlorine is analyzed in the same terms. The analys...

18. Amide, Carboxylic Acid and Alkyl Lithium (#18)

- Freshman Organic Chemistry (CHEM 125) 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 tha...

19. Oxygen and the Chemical Revolution (Beginning to 1789) (#19)

- Freshman Organic Chemistry (CHEM 125) 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 Swedi...

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

- Freshman Organic Chemistry (CHEM 125) 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 es...

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

- Freshman Organic Chemistry (CHEM 125) 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 ...

22. Radical and Type Theories (1832-1850) (#22)

- Freshman Organic Chemistry (CHEM 125) 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-sighted...

23. Valence Theory and Constitutional Structure (1858) (#23)

- Freshman Organic Chemistry (CHEM 125) 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. 00:00 - Chapter 1. Archibald Couper: "Look to the Elements" 10:25 - Chapter 2. Tetra...

24. Determining Chemical Structure by Isomer Counting (1869) (#24)

- Freshman Organic Chemistry (CHEM 125) 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 wi...

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

- Freshman Organic Chemistry (CHEM 125) 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 ra...

26. Van't Hoff's Tetrahedral Carbon and Chirality (#26)

- Freshman Organic Chemistry (CHEM 125) 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 would not be observed for another sixty-one 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 stere...

27. Communicating Molecular Structure in Diagrams and Words (#27)

- Freshman Organic Chemistry (CHEM 125) 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 dispu...

28. Stereochemical Nomenclature; Racemization and Resolution (#28)

- Freshman Organic Chemistry (CHEM 125) Determination of the actual atomic arrangement in tartaric acid in 1949 motivated a change in stereochemical nomenclature from Fischer's 1891 genealogical 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...

29. Preparing Single Enantiomers and the Mechanism of Optical Rotation (#29)

- Freshman Organic Chemistry (CHEM 125) 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 mixing...

30. Esomeprazole as an Example of Drug Testing and Usage (#30)

- Freshman Organic Chemistry (CHEM 125) 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 ins...

31. Preparing Single Enantiomers and Conformational Energy (#31)

- Freshman Organic Chemistry (CHEM 125) 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 nomenclatu...

32. Stereotopicity and Baeyer Strain Theory (#32)

- Freshman Organic Chemistry (CHEM 125) 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 rhetori...

33. Conformational Energy and Molecular Mechanics (#33)

- Freshman Organic Chemistry (CHEM 125) 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 ...

34. Sharpless Oxidation Catalysts and the Conformation of Cycloalkanes (#34)

- Freshman Organic Chemistry (CHEM 125) Professor Barry Sharpless of Scripps describes the Nobel prize-winning 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. 00:00 - Chapter 1. Introduction for Professor Barry Sharpless 02:52 - Chapter 2. The Reactivity of Allyic Alcohols and Vanadium-Catalyzed Epoxidations 11:44 - ...

35. Understanding Molecular Structure and Energy through Standard Bonds (#35)

- Freshman Organic Chemistry (CHEM 125) 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 unde...

36. Bond Energies, the Boltzmann Factor and Entropy (#36)

- Freshman Organic Chemistry (CHEM 125) 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 illustra...

37. Potential Energy Surfaces, Transition State Theory and Reaction Mechanism (#37)

- Freshman Organic Chemistry (CHEM 125) 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 halogenatio...

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Full 37-Lecture Course: Freshman Organic Chemistry

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