Outline of Topics – Biophysical Chemistry
Chemistry
and Biological Sciences 347
(ER indicates the text for this course: Physical Chemistry by Thomas Engel and Philip Reid)
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Supplement 1: Course Information (pdf)
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I. Computers in Simulations and Data Analysis
Data analysis and simulations using computers are an integral part of much of modern physical chemistry, and therefore both are an important part of this course.
There are a number of powerful software packages available for doing mathematics and data analysis on the computer.
We will use Mathematica. Tutorials are provided below for self study. In addition, some simple examples of how Mathematica can be used are found here. It is important that you learn how to use this program. Like any language, it can be frustrating at first. But with a little effort you should become adept at using it for all the homework in this course.
You can obtain Mathematica as a student at a greatly reduced rate. Licences are also available for one semester or a year.
Supplement: Mathematica for Calculations, Simulations and Data Analysis (pdf)
Mathematica Introduction: Mathematica Tutorial 1. Basics - as a Notebook (nb file) and Mathematica Tutorial 1. Basics(pdf file).
Simulating functions
Importing and exporting data
Plotting
Functions - deferred execution and iterations - Mathematica Tutorial 2. Deferred Execution and Iterative Procedures (nb file and pdf file).
Curve fitting - linear and nonlinear regression
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Homework Problem Set 1: Download pdf file. Due August 29 2008.
II. Mathematics Review
Basic math, logarithms, algebra, trigonometry
Differentiation
Integration - definite and indefinite integrals
Unit conversion
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Supplement: Mathematics Review (pdf)
III. Basic Themodynamics
Definitions (ER: Chapter 1)
State functions and equations of state
Practice Problems: in Mathematca Notebook (.nb) (Chapter 1: 1.1-1.4) - For self-study.
(on a Mac, control-click on the link, on a PC, download by right clicking on the link, save the link as a .nb file, open in Mathematica)
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Supplement 4: Description of Macroscopic Systems (pdf)
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Homework Problem Set 2: Chapter 2 (ER): P2.1, 2.2, 2.3, 2.4, 2.6, 2.8, 2.27 (Due Wednesday, Sept. 5, 2008).
(Important: Do these and all future homework problem sets using Mathematica.
Use the Practice Problem notebook supplied above for ideas on using Mathematica for unit analysis.
Please submit your work as a notebook file (.nb) via email. )
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Energy and the First Law of Thermodynamics
The basics: Heat, work, and energy (ER: Chapter 2)
Enthalpy and Heat capacity
Variation of State Functions with temperature (ER: Chapter 3)
Gas expansions - isothermal and adiabatic
Heat, deltaH, deltaE, and deltaCp as measurable
quantities - DSC and ITC
and the Kirchhoff Relationship
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Exact differentials and state functions
Molecular interpretation of enthalpy and heat capacity
changes
Effect of T and P on gases, liquids, and solids
Joule-Thomson Effect
Thermochemistry - (ER: Chapter 4)
Calorimetry - bomb, solution, ITC, DSC
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Supplement 5: Modern Calorimetry (pdf)
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Homework Problem Set 3: Chapter 3 (ER): P3.1, 3.3, 3.5, 3.9 (Use Mathematica) (Due Monday, Sept. 10, 2008)
(In addition, for P3.1, Prove dz is exact using Euler's criterion. )
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Homework Problem Set 4: Chapter 4 (ER): P4.10, 4.15, 4.21, 4.22. (Due Wednesday, Sept. 12, 2008)
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EXAM I - September 14, 2007- (A practice exam can be downloaded from here in pdf form)
Entropy and the Second Law of Thermodynamics
(ER: Chapter 5)
Entropy and the condition of spontaneity
The second law of thermodynamics
1/T is an integrating factor for dQ
General principles and examples of spontaneous processes
Combined first and second laws
The third law of thermodynamics
Calculation of entropy changes
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Homework Problem Set 5: Chapter 5 (ER): P5.10, 5.11, 5.16. (Due Wednesday, Sept. 26, 2008) .
Free Energy and spontaneity (ER: Chapter 6)
Helmholtz
Gibbs
Free energy and maximal work - Derivation from Lewis and Randall (pdf)
Gibbs-Helmholtz Equation
Modified Gibbs-Helmholtz Equation
Protein stability curves - Schellman
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Supplement 6 - Equilibria and Temperature (pdf)
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Interpretation of deltaS
Entropy and protein folding
Entropy and the hydrophobic effect
Enthalpy, equilibrium constants, temperature
van't Hoff data analysis
van't Hoff analysis vs. calorimetry
Cooperativity and protein folding ( deltaH cal vs.
deltaH vh )
Phase transitions
computer simulations
What is the value in measuring deltaH and deltaCp?
Heats of ionization and buffering
Current applications of calorimetry in biochemistry
Differential scanning calorimetry (DSC)
Chemical denaturation - m values
Linear extrapolation method
Effect of pH on protein stability - linkage (Wyman)
Protein Folding - site-directed mutagenesis and thermodynamics
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Homework Problem Set 6: Download problem set from here. (Due October 17, 2008).
Additional Readings
"Forces contributing to the conformatinal stability of proteins" by Pace et al. FASEB J. 10, 75-83 (1996)
"Protein structure, stability and solubility in water and other solvents" by Pace et al. Philos. Trans. Royal Soc. London B Biol. Sci. 359, 1225-34 (2004).
IV. Intermolecular and Intramolecular Forces
Electrostatics
Dipole-dipole interactions
Bond stretching and rotation
van der Waals interactions
Hydrogen Bonds
Hydrophobic "interactions"
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EXAM II - (Practice Questions here - pdf ) - October 26, 2008
V. Binding
- A central problem in biochemistry
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Supplement 7: Binding (Updated 29 Oct 2008)
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pH - review
Binding isotherms - Computer simlulations and fitting of
data -
Binding - an all-or-nothing process?
Direct
and Indirect methods -.
Nonlinear regression and fitting of binding data
Methods
of analysis
Coordinate transformations
Why not use a Scatchard plot?
Multiple equilibria - molecular partition functions
Independent site binding
Linked functions
Allosterism - Wyman and Gill
Homework Problem
Set 8: Due November 9, 2008
Practical aspects
Methods of evaluating binding constants by non-linear
regression
Isothermal titration calorimetry (ITC)
Binding heats
EXAM
III: November 14, 2008
VI. Real Gases, (ER: Topics from CHAPTERS 7)
Equations of State
Compression Factor
Fugacity
Homework Problem Set 9: Problems P7.1 and P7.2 (E&R) Due November 16.
VII. Phases and Phase Transitions (ER: Topics from CHAPTERS 8)
Temperature dependence of chemical potential
P-T and P-V diagrams
PVT Diagrams
Clapeyron equation
Vapor pressure dependence on P
Surface tension
Supercritical fluids
Homework Problem
Set 10: Problems P8.6, P8.14, P8.30 (E&R) Due November 16.
VIII. Solution Thermodynamics (ER: Topics from CHAPTERS 9)
Defining the ideal solution
Chemical potential in vapor and solution
Binary solutions
Gibbs-Duhem equation
Colligative properties
Freezing point depression and boiling point elevation
Osmotic pressure
Activity and chemical potentials
Activity coefficients and choice of standard states
Henry's and Raoult's Laws
Experimental measurement of activity coefficients
Equilibrium constants and activities
Vapor pressure osmometry - Vapro osmometry
Homework Problem Set 11: Download from here. Due November 26.
IX. Electrolyte Solutions (ER: Chapter 10)
Coulomb's Law and Electrostatic Forces
Electrolytes and Water
Thermodynamics of Ion Solvation
Conductivity of Aqueous Solutions
Ion Mobilities
Chemical Potential of Electrolytes
Debye-Hückel Theory
Salting-in and Salting-out
The Hofmeister Series
Chaotropes and Kosmotropes - Ion Hydration - see Collins, KD (2006) Biophysical Chemistry 119, 271-281.
and Collins, KD (2004) Methods 34, 300-11.
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Homework Problem Set 12:
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X. Electrochemical Equilibria (ER: Chapter 11)
Electrochemical cells
Electromotive force and standard electrode potentials
Ionic effects and membrane equilibria - the Donnan effect
EXAM IV: November 30, 2008
FINAL: December 4, 2008 (8:00 AM)
url: http://chemistry.uah.edu/shriver.htm
The University of Alabama
in Huntsville, Huntsville, AL 35899
site updated: 20 June 2008 (jws)