Chemistry 851 Syllabus

CHEMISTRY 851

Spring Semester 2023

Table of Contents:

Course Description

Lecture Notes

Paper Project Listing

Handouts

Homeworks

Exams

Links to the Scientific Literature

Literature References

Additional Resources

Course Description:

Lecturer

Professor James E. Jackson (“Ned”)
e-mail: jackson@chemistry.msu.edu
Office: Room 381 Chemistry Building
Office Hours: W 10:00-12:00 or by appointment

Lectures: TTh 10:20-11:40, Room 183, Chemistry Building

Problem Discussion Sessions: Evenings, 5:00-7:00, Monday or Tuesday TBD, Room TBD

Primary Text ("A&D"): Modern Physical Organic Chemistry by E. V. Anslyn & D. A. Dougherty (I know it's expensive, but you should own this valuable reference)

Other Useful Texts:

Advanced Organic Chemistry, Part A, Structure and Mechanisms https://doi-org.proxy1.cl.msu.edu/10.1007/978-0-387-44899-2 (2007 Part A) https://doi-org.proxy1.cl.msu.edu/10.1007/978-0-387-71481-3 (2007 Part B)	F. A. Carey and R. J. Sundberg
Structure and Mechanism in Organic Chemistry https://ebookcentral-proquest-com.proxy1.cl.msu.edu/lib/michstate-ebooks/detail.action?docID=7103414	F. A. Carroll
Mechanism and Theory in Organic Chemistry, 3rd Edition	T. S. Lowry and K. S. Richardson
Advanced Organic Chemistry https://app-knovel-com.proxy1.cl.msu.edu/s.v?zDB3Qryz (2013, 7^th ed.)	J. March and M. B. Smith
Frontier Orbitals and Organic Chemical Reactions	I. Fleming
Determination of Organic Reaction Mechanisms	B. K. Carpenter
Reactive Molecules	C. Wentrup
Introduction to Stereochemistry https://app-knovel-com.proxy1.cl.msu.edu/s.v?hptGCWfT (2002)	K. Mislow
Organic Chemistry, 2nd Edition	J. C. Stowell
Organic Chemist's Book of Orbitals	W. Jorgensen
Basic Organic Stereochemistry	E. L. Eliel, S. H. Wilen & M. P. Doyle
Advanced Organic Chemistry https://app-knovel-com.proxy1.cl.msu.edu/s.v?sduR3A6N (2002)	R. Bruckner

Communications: Outside of our regular discussions in class, e-mail is the primary mode of communication in the class. Please keep up to date; you should have read and understood any given message within a day of receiving it.

Homework: Weekly problem sets will be assigned on Tuesday. Problems may come from A&D or other sources. Their answers will be presented and discussed by class members chosen at random at the problem discussion sessions. You should have complete answers for every assigned problem written-out using ChemDraw and ready for display using Powerpoint or Keynote. These must be e-mailed or given to me by the time we meet on Monday evenings. When you are selected to answer a problem, you will be expected to stand up and make a presentation based on your Powerpoint prepared answer. Your answer presentations will be evaluated on a 10-point scale; your semester cumulative performance will serve as the problem set component of the course grade. So be sure you (a) have written up the answers and (b) are ready to explain them to your colleagues. Alternatively, the whole class may be asked to write up answers to one or more of the problem set questions at the meeting. This is effectively an easy "pop quiz" where you've already seen the questions. We will make every effort to have keys posted on the CEM 851 website shortly after the discussion period.

Research paper + presentation: Drafts due Tuesday, 29 March (first, to which I provide feedback) and Tuesday, 12 April (final); presentations (20 minutes) are to be prepared the following week and given the next. We will also have smaller writing exercises along the way.

Exams: One midterm, Tuesday, 14 March (just after break). Final exam is officially Friday, May 5, 7:45-9:45 AM, but we will reschedule at a mutually acceptable afternoon/evening time for greater time flexibility. For the final, we have used an individual oral exam scheme which is quite effective and we will use this mode again in 2023.

Grading:	Problem Sets (weekly)	30%
	Midterm Exam	20%
	Paper + presentation	20%
	Final exam (comprehensive)	30%

Course Content: This course will attempt to cover roughly 1/2 of A&D, in what they describe as a very fast-moving semester. Topics will often use material from other sources (literature, other books, etc.)-we will develop the precise sequence as we go along. Needless to say, we'll spend more time on some parts of this very thick book than others. Readings will be put on the web or handed out in lecture, depending on length and class size. The schedule of topics will follow the book's sequence, though a given topic may get more or less time, depending on the class's response and the instructors' enthusiasm. We will also use discussion sessions for computational labs, problems, and Q&A. We will actively use the Spartan quantum chemical modeling software as a tool to illustrate various ideas, as we also gain an appreciation of the basics of computational methods.

Preliminary Outline:

* Electrons, Orbitals, Bonds, & Shapes of molecules

* Molecular Modeling: Intro to Spartan

* Stereochemistry

* Conformational, Strain, Steric, & Stereoelectronic Effects

* Basic Tools of Physical Organic Chemistry
        Thermochemistry, Kinetics, and Correlations (Linear Free Energy Relations)
        Structural Probes: Stereochemical and Isotopic labeling
        Kinetic Probes: Solvent and Isotope Effects
        Acid/base catalysis

* Nucleophilic Substitution

* Addition and Elimination Reactions

* Hydrocarbon Acidity, Carbanions & other C Nucleophiles

* Carbenes

* Carbonyl Compounds

* Aromaticity and Aromatic Substitution Reactions

* Radical Chemistry

* Pericyclic Reactions & Orbital Symmetry Rules

* Photochemistry

Note to the Class:

First of all, PLAN AHEAD! It seems obvious, but this subject matter takes time and repeated review to sink in to the point where it becomes useful. To be honest, I develop a new appreciation of this stuff each time I go through it. Read the assignments early and take time to digest and review the ideas. Similarly, start problem sets early, and give yourself time to think about them. Building the ability to solve problems is the goal of the course! Problems are powerful teaching tools that cement your understanding by forcing you to use your knowledge in new ways. They are also a good part of your grade; if you view each problem set as a take-home test, for which there's no reason not to get 100%, then the concepts and tools taught here will become your friends.

Secondly, COMMUNICATE! If you're having trouble with a difficult or poorly explained concept, it's likely your neighbor is too. In class, you should tactfully stop me and ask that critical clarifying question right away--I don't want to waste anyone's time talking to lost faces. If a particular point gets out of hand, of course, I reserve the right to postpone that discussion until after the lecture. Outside class, find me, preferably during my scheduled office hours. Or, talk it over with a classmate or more advanced student in your lab. Not only is it OK to study together, I encourage it. Putting new concepts into your own words as you discuss them with colleagues always helps to hammer out an understanding. Obviously, problem sets and take-home tests must be your own work, but even there, talking the problems over can help you to understand the chemistry.

Third, VISUALIZE! There is no substitute for the ability to mentally see the three-dimensional nature of molecules and the processes they undergo. Much of what we know about the subtleties of organic reactions comes from tracking stereochemistry, a fundamentally three-dimensional property of molecules. Yet we learn mostly from flat, two-dimensional representations-images from books, blackboards, slides, etc. Such pictures, even more than "methyl, ethyl, propyl, butyl..," are the language of organic chemistry, and it is essential early on to develop a "mind's eye" that can see the three-dimensional molecule that a two-dimensional drawing represents. As we mentally translate meaning (thoughts) into sounds (spoken words) without even noticing that we are doing so, so we need to train our hands to draw flat pictures even as we are thinking of three-dimensional objects. So build a model, look at it from all angles, note symmetry, connectivity, stereochemical centers, etc. Then, without the model, picture the structure, the geometric relationships of its various parts, and practice (practice, practice) drawing it.

Fourth, LEARN TO COUNT! This may sound like an insult; it is not. It is simply essential that you know how many electrons there are around an atom in a given setting, and that you keep track of hydrogens and how many bonds are formed to a given center. This sounds trivial, yet simply obeying the rules of valence and conservation of charge and mass (i.e. atoms and electrons appearing/disappearing) would raise the average organic exam score by a substantial margin. Part of the difficulty arises from the convention of leaving out hydrogens in drawing organic structures, unless they are needed to indicate stereochemistry or participate in a reaction step. H atoms are then often forgotten completely and extra bonds sprout from a given carbon atom.... Don't laugh--we've all drawn these erroneous structures. The key is learning to check drawings reflexively to protect against such obscene blunders.Finally, WELCOME TO CEM 851! I look forward to getting to know you all this spring.

Lecture Notes: TBA

Paper Project Listing: TBA

Handouts:

Wenthold et al. "Transition State Spectroscopy of Cyclooctatetraene"

Hoffmann and Hopf "Learning from Molecules in Distress"

Factors affecting orbital interactions

Remarks on symmetry and the Dn point groups

BDEs and Heats of formation chart

Measures of Aromaticity

Pericyclic Reaction Glossary

    Pictures of MOs (HF/6-31G* level, computed with GAMESS and drawn with MacMolPlt
         H₂O (linear)
         H₂O (bent)
         ¹CH₂(bent)
         CH₄
         CH₄(square planar)
         CH₄(square pyramidal)
         C₂
         N₂
         O₂
         CO
         CO₂
         H₂CO
         HCCH
         H₂CCH₂
         H₃CCH₃