Course: Freshman Organic Chemistry with J. Michael McBride Dnatube
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Lec 1 - How Do You Know?
"Lec 1 - How Do You Know?" 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...
Lec 2 - Force Laws, Lewis Structures and ...
"Lec 2 - Force Laws, Lewis Structures and Resonance" 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...
Lec 3 - Double Minima, Earnshaw's Theore ...
"Lec 3 - Double Minima, Earnshaw's Theorem and Plum-Puddings" 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...
Lec 4 - Coping with Smallness and Scanni ...
"Lec 4 - Coping with Smallness and Scanning Probe Microscopy" 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...
Lec 5 - X-Ray Diffraction
"Lec 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...
Lec 6 - Seeing Bonds by Electron Differe ...
"Lec 6 - Seeing Bonds by Electron Difference Density" 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...
Lec 7 - Quantum Mechanical Kinetic Energy
"Lec 7 - Quantum Mechanical Kinetic Energy" 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...
Lec 8 - One-Dimensional Wave Functions
"Lec 8 - One-Dimensional Wave Functions" 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...
Lec 9 - Chladni Figures and One-Electron ...
"Lec 9 - Chladni Figures and One-Electron Atoms" 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...
Lec 10 - Reality and the Orbital Approxi ...
"Lec 10 - Reality and the Orbital Approximation" 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...
Lec 11 - Orbital Correction and Plum-Pud ...
"Lec 11 - Orbital Correction and Plum-Pudding Molecules" 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....
Lec 12 - Overlap and Atom-Pair Bonds
"Lec 12 - Overlap and Atom-Pair Bonds" 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...
Lec 13 - Overlap and Energy-Match
"Lec 13 - Overlap and Energy-Match" 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...
Lec 14 - Checking Hybridization Theory w ...
"Lec 14 - Checking Hybridization Theory with XH_3" 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...
Lec 15 - Chemical Reactivity: SOMO, HOMO ...
"Lec 15 - Chemical Reactivity: SOMO, HOMO, and LUMO" 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...
Lec 16 - Recognizing Functional Groups
"Lec 16 - Recognizing Functional Groups 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...
Lec 17 - Reaction Analogies and Carbonyl ...
"Lec 17 - Reaction Analogies and Carbonyl Reactivity" 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...
Lec 18 - Amide, Carboxylic Acid and Alky ...
"Lec 18 - Amide, Carboxylic Acid and Alkyl Lithium" 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...
Lec 19 - Oxygen and the Chemical Revolut ...
"Lec 19 - Oxygen and the Chemical Revolution (Beginning to 1789)" 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...
Lec 20 - Rise of the Atomic Theory (1790 ...
"Lec 20 - Rise of the Atomic Theory (1790-1805)" 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...
Lec 21 - Berzelius to Liebig and Wöhler ...
"Lec 21 - Berzelius to Liebig and Wöhler (1805-1832)" 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...
Lec 22 - Radical and Type Theories (1832 ...
"Lec 22 - Radical and Type Theories (1832-1850)" 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...
Lec 23 - Valence Theory and Constitution ...
"Lec 23 - Valence Theory and Constitutional Structure (1858)" 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...
Lec 24 - Determining Chemical Structure ...
"Lec 24 - Determining Chemical Structure by Isomer Counting (1869)" 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...
Lec 25 - Models in 3D Space (1869-1877); ...
"Lec 25 - Models in 3D Space (1869-1877); Optical Isomers" 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...
Lec 26 - Van't Hoff's Tetrahedral Carbon ...
"Lec 26 - Van't Hoff's Tetrahedral Carbon and Chirality" 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...
Lec 27 - Communicating Molecular Structu ...
"Lec 27 - Communicating Molecular Structure in Diagrams and Words" 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...
Lec 28 - Stereochemical Nomenclature; Ra ...
"Lec 28 - Stereochemical Nomenclature; Racemization and Resolution" 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...
Lec 29 - Preparing Single Enantiomers an ...
"Lec 29 - Preparing Single Enantiomers and the Mechanism of Optical Rotation" 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....
Lec 30 - Esomeprazole as an Example of D ...
"Lec 30 - Esomeprazole as an Example of Drug Testing and Usage" 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...
Lec 31 - Preparing Single Enantiomers an ...
"Lec 31 - Preparing Single Enantiomers and Conformational Energy" 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,...
Lec 32 - Stereotopicity and Baeyer Strai ...
"Lec 32 - Stereotopicity and Baeyer Strain Theory" 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...
Lec 33 - Conformational Energy and Molec ...
"Lec 33 - Conformational Energy and Molecular Mechanics" 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...
Lec 34 - Sharpless Oxidation Catalysts a ...
"Lec 34 - Sharpless Oxidation Catalysts and the Conformation of Cycloalkanes" 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...
Lec 35 - Understanding Molecular Structu ...
"Lec 35 - Understanding Molecular Structure and Energy through Standard Bonds" 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...
Lec 36 - Bond Energies, the Boltzmann Fa ...
"Lec 36 - Bond Energies, the Boltzmann Factor and Entropy" 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...
Lec Last - Potential Energy Surfaces, Tr ...
"Lec Last - Potential Energy Surfaces, Transition State Theory and Reaction Mechanism" 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...
Freshman Organic Chemistry with J. Michael McBride
Source of these courses is Yale
This is the first semester in a two-semester introductory course focused on current theories of structure and mechanism in organic chemistry, their historical development, and their basis in experimental observation. The course is open to freshmen with excellent preparation in chemistry and physics, and it aims to develop both taste for original science and intellectual skills necessary for creative research.
Yale Website: http://www.dnatube.com/school/yale
COURSE NAME: Freshman Organic Chemistry with J. Michael McBride