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Freshman Organic Chemistry

Yale Course , Fall 2008 , Prof. J. Michael McBride       Subscribe to feed

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Lecture 6: Seeing Bonds by Electron Difference Density

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Lecture Details :

Professor McBride uses an 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-twentieth as dense as would be expected for Lewis shared pairs. Anomalous difference density in the carbon-fluorine bond raises the course's second great question, "Compared to what?"

Course Description :

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.

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  1. How Do You Know?
  2. Force Laws, Lewis Structures and Resonance
  3. Double Minima, Earnshaws Theorem and Plum-Puddings
  4. Coping with Smallness and Scanning Probe Microscopy
  5. X-Ray Diffraction
  6. Seeing Bonds by Electron Difference Density
  7. Quantum Mechanical Kinetic Energy
  8. One-Dimensional Wave Functions
  9. Chladni Figures and One-Electron Atoms
  10. Reality and the Orbital Approximation
  11. Orbital Correction and Plum-Pudding Molecules
  12. Overlap and Atom-Pair Bonds
  13. Overlap and Energy-Match
  14. Checking Hybridization Theory with XH_3
  15. Chemical Reactivity: SOMO, HOMO, and LUMO
  16. Recognizing Functional Groups
  17. Reaction Analogies and Carbonyl Reactivity
  18. Amide, Carboxylic Acid and Alkyl Lithium
  19. Oxygen and the Chemical Revolution
  20. Rise of the Atomic Theory
  21. Berzelius to Liebig and Wöhler
  22. Radical and Type Theories (1832-1850)
  23. Valence Theory and Constitutional Structure (1858)
  24. Determining Chemical Structure by Isomer Counting (1869)
  25. Models in 3D Space (1869-1877); Optical Isomers
  26. Vant Hoffs Tetrahedral Carbon and Chirality
  27. Communicating Molecular Structure in Diagrams and Words
  28. Stereochemical Nomenclature; Racemization and Resolution
  29. Preparing Single Enantiomers and the Mechanism of Optical Rotation
  30. Esomeprazole as an Example of Drug Testing and Usage
  31. Preparing Single Enantiomers and Conformational Energy
  32. Stereotopicity and Baeyer Strain Theory
  33. Conformational Energy and Molecular Mechanics
  34. Sharpless Oxidation Catalysts and the Conformation of Cycloalkanes
  35. Understanding Molecular Structure and Energy through Standard Bonds
  36. Bond Energies, the Boltzmann Factor and Entropy
  37. Potential Energy Surfaces, Transition State Theory and Reaction Mechanism