Chem 552, Spring 2007
Section 552-1 BU 476, 8:05-9:25 TR
Prof. John Bartmess, BU 609
Office Hours: Open

Be aware that I'm also teaching Chem 360 MWF 9:05-9:55 AM, so I won't be around then. I also am not available for the 30 minutes before that class, due to reviewing notes, so pretty much don't come looking for me before 10 AM MWF.

Text:
Anslyn & Dougherty, "Modern Physical Organic Chemistry." (Same as Chem 550).
There will also be occasional PowerPoint presentations, that will be posted on this web site, as well as used in class. I will make you aware of these ahead of time, so that you can print these out as needed, or bring your laptops to class. However, printouts can be annotated more easily. Grading: there will be two exams and a final (essentially a third exam, non-cumulative), each counting 1/3 of the points for the course. My tenative days for the exams are Feb 13 and Mar 27. I will not move these earlier, but they may be moved a lecture later if the timing of the coverage works better.

Topics and Schedule
Note that there's no exact timings given; this is the first time through this text, so we'll see where we are, when.

Chapter 7: Energy Surfaces and Kinetic Analyses
7.2 Transition State Theory (TST), and Related Topics
7.4 Kinetic Experiments
7.5 Complex Reactions - Deciphering Mechanisms
7.6 Methods for Following Kinetics
7.7 Calculating Rate Constants
7.8 Considering Multiple Reaction Coordinates

Chapter 8: Experiments Related to Thermodynamics and Kinetics
8.1 Isotope Effects
8.3 Hammett Plots,
8.4 Other Linear Free Energy Relationships
8.5 Acid/Base Related Effects / Bronsted Relationships
8.7 Summary of Linear Free Energy Relationships
8.8 Miscellaneous Experiments for Studying Mechanisms

Chapter 9: Catalysis
9.1 General Principles of Catalysis
9.2 Forms of Catalysis
9.3 Bronsted Acid/Base Catalysis
9.4 Enzymatic Catalysis

Chapter 10:
10.11 Carbene Additions and Insertion

Chapter 11:
11.5.16 SN1 Reactions Involving Non-Classical Carbocations
11.6 Radical reactions
11.11 Rearrangements Involving Radicals

Chapter 14. Advanced Concepts in Electronic Structure Theory
14.1 Introductory Quantum Mechanics
14.2 Calculational Methods - Solving the Schrodinger Equation for Complex Systems
14.3 A Brief Overview of the Implementation and Results of HMOT
14.4 Perturbation Theory - Orbital Mixing Rules
14.5 Some Topics in Organic Chemistry for Which Molecular Orbital Theory Lends Insights

Chapter 15: Thermal Pericyclic Reactions

Chapter 16: Photochemistry

The goals of this course are two-fold:

First, to examine certain reactions in much greater detail than you have probably encountered before, including looking at the original literature. This is to understand how the researchers reached the conclusions they did from the available data, what constitutes "proof" of a mechanism, and how such knowledge can be used to further extend known reactivities. There is a connection between microscopic and macroscopic/observed events. Science assumes that this is specific and proved, but the exact way we deduce what the microscopic is, from the macroscopic observables, needs examination for you to learn this.

Perhaps most important is the role of the little glitch in science: "Eureka" is the popular image of scientific discoveries; "that wasn't supposed to happen" is by far more common.

Second, to teach you the use of a variety of "tools": skills, methods, logical inference, instrumental techniques, and so forth.

These tools are both modern and venerable. The role of history in chemistry is greater than for other sciences, in that we refer to the literature much more than other hard science disciplines. (This frequently results in an attitude on the part of librarians, about chemists always causing trouble.)

Be aware that many of the tools, especially spectroscopic methods, are relative recent in widespread use:
      GC: 1952 (aka VPLC, VPC, GLC)
      IR: 1945
      nmr: 1960+
      Mass Spec: 1945/1960
      Xray crystallography: 1945
      uv: 1950
      theory: 1960/(routine chemical accuracy {±2 kcal/mol} 1995 G2)

Thus one should not waste time looking for nmr spectra in the literature before about 1960!

Not incidentally, these skills are definitely among those needed to deal with the cumulative exams successfully.

The final exam is not cumulative, being more of a third hour exam. However, the various "tools" learned all semester will be applied to new chemical systems as time goes on, and thus knowledge of and an ability to use them is expected.

This is the nature of your professional training in graduate school: it's not the grade in the course that counts in the long run, but rather your retention of the material, and the ability to use the skills learned over time, in your career. You are reaching a point in your training where you will soon no longer be given highly organized information, but will need to acquire it on your own. Use this course and its material to build a strong foundation, on which to learn those skills.

The Organic Mechanic's Toolbox

"Why, every quantum mechanic in the galaxy would give the rest of his life to work on that thing..."
       - "Forbidden Planet", 1956

If you are going to work on mechanisms, you need to be a mechanic. A mechanic needs good tools to do good work ... but one should never blame one's failures on the tools. Here are some of the "tools" (skills, techniques, methods) that chemists have developed to probe mechanisms.

Structure - Reactivity (Hammer on it for a while and see what breaks)
     Structures of Reactants/Products/Byproducts
     Intermediates: trap, synthesize
     Substituents
     Polar/Resonance/Steric Effects
     Linear Free Energy Relationships
     Regiochemistry
     Stereochemistry
     Isotopic Labeling
     Kinetic, Equilibrium, Solvent Isotope Effects (KIE, EIE, SIE)
     Solvent Effects on rates and equilibria

Kinetics (How quickly did it break?)
     Rate equation/Order/Molecularity
     Activation Parameters (Eact, A, ΔH‡, ΔS‡)
     Rate vs. Product Determining Steps
     Isotopic Exchange
     Reaction Coordinate / Hammond Postulate
     Synthesis of intermediates

Spectroscopy (What do the pieces look like?)
     Structure and Existence
       Intermediates
       Reactants
       Products
       Byproducts
     Relationship to Kinetics

Thermochemistry (How hard did you have to bash it to get it to break?)
     Acid/Base, pKas
     Redox (IEs, EAs, Oxidation/reduction Potentials)
     Bond Strengths
     Heat/Entropy of formation
     Solvation Energetics

Molecular Orbital Theory (When all else fails, read the manual!)
     Orbital symmetry
     Calculations of structures, energetics
     Justification of structure-reactivity (HOMO-LUMO, etc.)

Logic (Now that you broke it, put it back together)

Prediction (How easy is the next one to break?)