SYLLABUS, CHEMISTRY 156, SPRING, 2006

 

Chemistry 156, "Physical Chemistry in Molecular Biology", is a one-semester course in physical chemistry for students concentrating in Molecular Biology, Chemistry-Geology, Environmental Analysis, and PPA-Chemistry.  It also provides an introduction to physical chemistry for students who have only taken two semesters of calculus and the spring, 2006 version will substitute for Chemistry 158b.  Chemistry 156 will not be offered in the future but will be merged with Chemistry 158b.  As a step in the transition, this year's form of Chemistry 156 will focus on chemical thermodynamics and chemical kinetics.  The following text has been adopted for the course:

 

I. Tinoco, Jr., K. Sauer, J. C. Wang, and J. D. Puglisi, Physical Chemistry, 4th. ed., Prentice-Hall, Englewood Cliffs, NJ, 2002.

 

References will also be made to material available on the World Wide Web.  An annotated list of useful sources of chemical data on the WWW is MolData.  MolData and the Web page for the course can be accessed via the URL http://pages.pomona.edu/~wsteinmetz.  You might want to refer to the sources on reserve if you find that the treatment in the course text is incomplete.

 

Your course grade will be based on your performance on the two midterm examinations and the two graded exercises.  However, the instructor reserves the right of adjusting the letter grade upward or downward based on subjective criteria such as improvement in the course.  The graded work will be weighted as follows:

 

1) first closed-book examination on the principles of chemical thermodynamics, Monday, 13 February (30%),

 

2) second closed-book examination on phase equilibria, Monday, 6 March (20%),

 

3) first graded exercise on equilibrium calculations, due in class on Monday, 3 April (20%),

 

4) second graded exercised on rates laws and mechanisms, due in class on Wednesday, 19 April (15%),

 

5) third closed-book examination covering the theoretical treatment of elementary kinetics, Wednesday, 3 May (15%).

 

Homework will be assigned but will not be graded.  One learns science by doing science and you are strongly encouraged to work on the homework problems.  If you have difficulties with a problem, refer to your resources: the text, your notes, your peers, or the instructor, and make another stab at the problem.  Hand in your work so it may be checked for accuracy.

 

The following monographs and texts will be on reserve in the Pomona Science Library:

 

1) A. G. Marshall, Biophysical Chemistry, Wiley, New York, 1978.

2) K. E. van Holde, Physical Biochemistry, Prentice-Hall, Englewood Cliffs, NJ, 1971.

 

ORDER OF TOPICS

 

Unit I: Principles of Chemical Thermodynamics

18 Jan.  Introduction, partial derivatives and differentials

20 Jan.  The First Law, heat, and work

23Jan.  Calorimetry and enthalpy

25 Jan.  Enthalpy changes of reactions

27 Jan.  Statistical thermodynamics: microstates and configurations

30 Jan.  Statistical thermodynamics: entropy, and the Boltzmann equation

  1 Feb.  The Second Law and thermodynamic efficiency

  3 Feb.  The calorimetric determination of entropy

  6 Feb.  Conditions for change and Gibbs free energy

  8 Feb.  The use of differentials in thermodynamics

10 Feb.  The thermodynamics of protein denaturation

13 Feb.  In-class, closed-book examination over Unit I

 

Unit II: Thermodynamic Treatment of Phase Equilibria

15 Feb.  Chemical potential, part I

17 Feb.  Chemical potential, part II

20 Feb.  Ideal solutions

22 Feb.  Standard states

24 Feb.  Osmosis and dialysis

27 Feb.  The Donnan effect

 1 Mar.  The thermodynamics of phase equilibria, part I

 3 Mar.  The thermodynamics of phase equilibria, part II

 6 Mar.   In-class, closed-book examination over Unit II

 

Unit III. Thermodynamics of Chemical Reactions

  8 Mar.  Relation of the equilibrium constant to DG°

10 Mar.  The mass balance in equilibrium calculations, binding

            11 Mar.-19 Mar., SPRING BREAK

20 Mar.  Cooperativity

22 Mar.  Ionic activity coefficients and the model of Debye and Hückel

24 Mar.  The charge balance in equilibrium calculations, ionic equilibria

27 Mar.  Thermodynamics of electrochemical cells

29 Mar.  The electrochemical measurement of pH

31 Mar.  Cesar Chavez Day, classes cancelled

27-30 Mar.  Robbins Lectures in Chemistry.  Your attendance is expected. 

Professor George Whitesides from Harvard will speak on nanotechnology.

  3 Apr.   Graded Exercise I covering Unit III due in class

 

Unit IV: Experimental Chemical Kinetics

  3 Apr.  Introduction to chemical kinetics (Graded Exercise I due in class)

  5 Apr.  Experimental determination of kinetic rate laws

  7 Apr.  The steady-state approximation

10 Apr.  Enzyme kinetics

12 Apr.  The determination of reaction mechanisms

14 Apr.  Oscillatory chemical reactions and bifurcations

19 Apr.  Graded Exercise II covering Unit IV due in class

 

Unit V: Theoretical Understanding of Elementary Reactions 

17 Apr.  Kinetic gas theory and the collisional model

19 Apr.  Diffusion and the random walk model (Graded Exercise II due in class)

21 Apr.  Diffusion controlled reactions

24 Apr.  Potential energy surfaces and ACT theory

26 Apr.  Applications of ACT theory

28 Apr.  Photochemistry

 1 May   Chemical dynamics examined through NMR

  3  May  In-class, closed-book examination over Unit V

 

syl156.htm, 14 Dec. 2005