CHEM 640: Biological Physical Chemistry (3 credits)

Fall 2006




The course gives an introduction to the basic principles of physical chemistry with applications to biological systems. Topics include the laws of thermodynamics, phase equilibria, chemical equilibria, chemical reaction kinetics and quantum chemistry.



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Line number: 12844
Instructor: Krzysztof Kuczera, 5090 Malott, phone: 864-5060
  kkuczera@ku.edu
Time & Place: 9:00-9:50 MWF, DHDC 2092
Textbook: P. Atkins and J. de Paula, Physical Chemistry
  for the Life Sciences, W.H. Freeman, 2006.
Discussion meetings: Wednesdays 3:00-3:50, 2007 Malott
  Thursdays 3:00-3:50, 4047 Wescoe
Office hours: T,W 10:00-11:00 am or by appointment



The overall course grade will be determined by the sum of four components: pre-class quizzes, problem portfolio, the average of two partial exam scores (hour-exam) and the final exam score (final-exam):




\begin{displaymath}grade ~=~ 0.15 \cdot (quiz) ~+~ 0.10\cdot(portfolio) ~+~ 0.25... ...mework) ~+~ 0.25 \cdot (final-exam) ~+~ 0.25 \cdot (hour-exam) \end{displaymath}



Exam dates:

Exam 1 September 29
Exam 2 November 3
FINAL Thursday, December 14, 7:30-10:00 am



Quizzes. We will have on-line quizzes on BlackBoard 1-2 times a week. The quizzes will cover material needed for the next lecture and will have a deadline 1 hour before start of class. The goal is to keep everybody engaged in reading text and notes, so that more class time may be dedicated to discussion and interactive problem solving.



Homework. Problem sets will be assigned weekly.



Reading:I recommended reading the relevant chapters of textbook and Web Lecture Notes both before and after the material is covered in class. In order to better understand the material it is useful to look at alternative presentations of material, such as


1. Tinoco, Sauer & Wang, Physical Chemistry, Principles and Applications in Biological Sciences, 3$^{rd}$ Ed. QH345.T56 2002

2. Eisenberg & Crothers, Physical Chemistry with Applications to the Life Sciences. QD453.2E37 1979

3. Alberty & Silbey, Physical Chemistry. QD453.2.A45 2001

Problem solving:Learning of the complex concepts of physical chemistry cannot be achieved without the experience and insight gained by problem solving. Solutions to sample problems are given in textbook, will be discussed in class, presented on Web site, assigned as homework and covered in discussion sections. Familiarity with the problems covered is ABSOLUTELY NECESSARY for success in the exams. Problem portfolios will be used to help with this.



Problem portfolios: To organize the mass of problems we will be tackling in class, each student will prepare a problem portfolio in a signed 1-3 inch three-ring binder. Enter all examples solved in class, given in lecture notes, as well as solutions to homework and trial exam problems in the portfolio in the following way:


  1. Start each problem on a new sheet


  2. At top (front or back) of sheet give problem text - cut and paste from xerox or printout, copy by hand or at least give brief summary of text.


  3. Provide one-sentence summary of problem area, e.g "Problem deals with gas expansion"


  4. Solution should contain brief explanation of equations, e.g. don't just write "pV = nRT", but rather "For ideal gas pV = nRT".


  5. Use the correct number of significant digits.


  6. Use SI units for all quantities


  7. Try to provide a comment to the final answer, e.g. if the answer is "w = 10 kJ" you could say "the work done is positive, energy enters the system".
I will examine the portfolios at the end of September to give you feedback and collect folders for grading at the final exam.



Syllabus


Dates Topic Chapter
     
08/18-08/21 Introduction, Gases F
08/23-09/08 The First Law & Thermochemistry 1
09/11-09/22 The Second Law & Entropy 2
09/25-09/27 Free energy 2
09/29 Exam #1  
10/02-10/06 Phase equilibria of pure substances 3
10/09-10/16 Mixtures 3
10/18-11/01 Chemical Equilibrium 4
11/03 Exam #2  
11/06-11/10 Chemical Reaction Kinetics 6
11/13-11/17 Reaction Mechanisms 7-8
11/20-12/06 Introduction to Quantum Mechanics 9



Class website:
Lecture notes, sample problems and sample exams will be on the site
      http://oolung.chem.ku.edu/~kuczera/640/640.html
Announcements, quizzes and homeworks will be given both on the site and on BlackBoard.

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