Chemistry and Biochemistry

Chemistry 711: Chemical Thermodynamics

Last update: for Fall 2018

Instructor: Andrew Cooksy
email: acooksy@mail.sdsu.edu
office/lab: CSL-310,307,312; tel: 594-5571

Syllabus

Lecture Meetings: Tue, Thu 5:00-6:15pm, SSW-2512
Office Hours: Mon/Wed 9:30-10:30am, Tue 4-4:30pm CSL-310.
Textbook: Andrew Cooksy, Physical Chemistry: Thermodynamics, Statistical Mechanics, and Kinetics. We will not be using the online homework available with this text, so you are welcome to look for used copies. This is a textbook for part of the undergraduate physical chemistry course, which I think will help keep the class accessible to all grad students, but it covers enough advanced topics that I expect it to extend past what students have seen in undergraduate p-chem. The lectures may occasionally extend to material beyond the scope of the textbook. We will not be using the last two chapters of the book that cover chemical kinetics or the introductory Chapter 1. We should get to most of the rest, which we will cover in class in the same order as in the book.
Solutions to End-of-Chapter problems: Worked solutions are available in the free solutions manual from Pearson (click on the "Solutions Manual (PDF)" link for our book). Please conserve paper: store this electronically and refrain from printing out the entire manual.

General Idea

This course is intended to benefit chemistry graduate students in all areas, as well as students in other departments with interests in the fundamentals of energy distribution and dynamics in molecular systems. A complete undergraduate, calculus-based p-chem course (the equivalent of our CHEM 410A and 410B) is expected. You're welcome to contact me if you want to ask about the course content or what would be suitable preparation for the course. Our emphasis will be on the principles of statistical mechanics and thermodynamics common to all applications of chemistry, so students are encouraged to bring issues from their own research or other interests to the attention of the instructor for discussion (the sooner the better).

Student learning objectives:

At the conclusion of the course, the student should be able to:

Define thermodynamic properties such as entropy, temperature, and free energy.
Describe qualitatively the distribution of energy in any molecular system, and how it changes with temperature.
Calculate basic dynamical properties of systems, such as mean free path and average collision frequency, relating these to observable properties.
Derive and use algebraic expressions for the thermodynamics of specific systems.
Predict trends in the energy distributions, thermodynamic properties, and energy level populations of molecular systems.

Course material

Chemical statistical mechanics and thermodynamics, which together provide our best theory for how energy is distributed in ordinary matter and exchanged during chemical processes.

General Plan:

Statistical Mechanics: Entropy and temperature (Chapter 2); Partition functions (Chapter 3); Extrapolation from molecular scale to the bulk (Chapter 4); Mass and energy transport (Chapters 5 and 6)
Chemical Thermodynamics: Intro to thermodynamics: heat capacities (Chapter 7); The first law of thermodynamics (Chapter 8); The second law of thermodynamics (Chapter 9); Phase transitions (Chapter 10); Solutions (Chapter 11); Reaction thermochemistry (Chapter 12); Your Application Here

Prerequisite Math

You should be comfortable with algebra and the simple derivatives and integrals (especially of the functions axⁿ, e^ax, and sin(ax) or cos(ax) ). See Chapter A in the book for a review of relevant math and physics. There is some calculus that I don't expect everyone to remember that we will review in class. If you're still not too confident or have any questions, just come and see me and we can review during office hours.

Grading criteria

Grading Scheme

homework: 10% total (at least 3 individual assignments)
three exams: 15% each (45% total)
computer project: 25%
paper presentation: 20%

The grading scale is fairly lenient:

85% ≤ A ≤ 100%
70% ≤ B < 85%
55% ≤ C < 70%

Assignment Dates for Fall 2018

exam 1: Thu Sep 27
computer project topic deadline: Tue Oct 2
exam 2: Thu Oct 25
paper topic deadline: Mon Oct 29
exam 3: Thu Nov 29
computer project write-ups: Tue Dec 11 by midnight
paper presentations: Tue Dec 18 3:30pm-5:30pm (the scheduled final exam slot)

Paper Presentation

Chem 711 students will present a 15-minute PowerPoint or whiteboard talk to the class, based primarily on one or two papers relevant to our coursework. Each presentation will be critiqued by the other students and the instructor, and constructive comments will be consolidated by the instructor and given to the presenter.

Students are graded based on both their presentation and on their participation in the evaluations of their classmates. You should email me your topic and relevant reference(s) as soon as possible, and we should have the assignments finalized no later than Monday, October 29.

Computer Project

It is fairly straightforward now to use electronic structure programs such as Gaussian to predict thermodynamic properties of chemical systems, but it helps to have some guidance. We will probably schedule two meetings of the class in the Chemistry Computer Lab (GMCS-245) to go over the use of Gaussian, specifically for calculating thermochemical properties.

By Monday, October 1, Students will select a single chemical reaction and carry out calculations to predict ΔH, ΔG, and other properties of the system. Depending on your selection, I may choose to expand or reduce the scope of the work (for example, deciding if solvation effects are appropriate to calculate, or if spectroscopic signatures of the thermodynamics would be relevant). Results will be presented in a short but professional quality report, roughly 3-4 pages, including

An introduction describing the reaction, its importance, its role in your own research.
A methods section describing the computational methods you employed.
Results and discussion (separate sections if you prefer).
A concluding paragraph: how much do you trust your results? This may be a separate section if you prefer.
A list of references.

Figures should be roughly publication-quality. All work must be completed and reports submitted to me by email no later than Tuesday, Dec 11 at midnight.

Students with Disabilities

If you are a student with a disability and believe you will need accommodations for this class, it is your responsibility to contact Student Disability Services at (619) 594-6473. To avoid any delay in the receipt of your accommodations, you should contact Student Disability Services as soon as possible. Please note that accommodations are not retroactive, and that accommodations based upon disability cannot be provided until you have presented your instructor with an accommodation letter from Student Disability Services. Your cooperation is appreciated.