Chemistry 156

Physical Chemistry in Molecular Biology

CHEMISTRY 156, PROBLEM SETS AND GRADED EXERCISES

1. Unit I. Principles of Thermodynamics
   • Problem Set I, differentials and the First Law
   • Problem Set II , applications of the First and Second Laws

2. Units II and III. Chemical Equilibrium
   • Problem Set III, additional problems relating to chemical equilibrium, spring, 2004 version
   • Problem Set IV, additional problem involving chemical potential and phase equilibria, spring, 2006
   • Graded Exercise I, spring, 2002 version
   • Graded Exercise I, spring, 2004 version
   • Graded Exercise I, spring, 2006 version
     Material relating to the graded exercise such as a description of Maple can be found on the Handouts page.

3. Units IV and V. Chemical Kinetics
   • Problem Set III, additional problems relating to kinetics and diffusion, spring, 2002 version
   • Problem Set III, additional problems relating to kinetics and diffusion, spring, 2004 version
   • Graded Exercise II, Spring, 2006 Version (dealing with rate laws and mechanisms)
     Material relating to the graded exercise such as the executable for the program KINMECH can be found on the Handouts page.

4. Determination of Chemical Structure (no longer included in Chemistry 156)
   • Graded Exercise 2, Spring 2002 Version (dealing with molecular modeling)
   • Graded Exercise 2, Spring 2004 Version (dealing with molecular modeling)

     The graded exercise deals with the application of molecular modeling to the state of ionization of amino acids. The Brown group has produced an excellent gas-phase structure of glycine. Use Web of Science or SciFinder Scholar to find the references.
     For the 2002 version of the exercise, the following X-ray structures have been extracted from the Cambridge Crystallographic database and are available in the pdb format:
     

     • TGLYSU04. Three forms of glycine-- ⁺H₃NCH₂COO^-, H₂NCH₂COO^-, and H₃NCH₂COOH --are present in the unit cell.
     • GLYHCL01. Glycine hydrochloride; glycine is present as ⁺H₃NCH₂COOH.
     • YODTOA. Alanine is present as ⁺H₃NCHRCOOH.
     • RIWKUD, Serine is present as ⁺H₃NCHRCOOH.

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last revised, 1 March 2006