Lecture Sites

Electronic Journal Access

When on campus with a Rutgers IP address, links to electronic journals should provide full article access if Rutgers has a subscription. Away from campus, first go to the Rutgers Library page, click on the yellow "NOT LOGGED IN" button on the upper left side, and enter your Rutgers NetID when prompted. Then you should be able to read the articles through any journal links on this (or other) web pages.

The library page also has off-campus instructions.

Selected Textbooks Covering Chemical Kinetics and Reaction Mechanisms

  1. Moore, J. W. and Pearson, R. G. Kinetics and Mechanism, 1981, Wiley:New York. Excellent coverage of practical aspects of chemical kinetics with good mechanistic examples. Amazon
  2. Laidler, K. J. Chemical Kinetics, 3rd ed., 1987, Harper and Row: New York. Fairly standard, but now older, graduate chemical kinetics text; limited coverage of mechanistic issues. Amazon
  3. Steinfeld, J. I., Francisco, J. S., and Hase, W. L. Chemical Kinetics and Dynamics, 2nd ed., 1999, Prentice-Hall: Upper Saddle River, NJ. Emphasizes rate theory, unimolecular reactions, and gas-phase reactions. Amazon
  4. Anslyn, E. V. and Dougherty D. A. Modern Physical Organic Chemistry, 2006, University Science Books: Sausalito, CA. Comprehensive, up-to-date, text covering the study of organic reaction mechanisms, as well as structure and bonding. Amazon
  5. Isaacs, N. S. Physical Organic Chemistry, 2nd ed. 1996, Prentice Hall: NY. Good coverage of chemical kinetics as applied to organic reaction mechanisms, with many literature examples. Amazon
  6. Lowry, T. H. and Richardson, K. S. Mechanism and Theory in Organic Chemistry, 3rd ed., 1987, Harper and Row: New York. Older text, but has an in-depth presentation of important classes of reaction mechanisms. Amazon

Reaction Mechanism Review

  1. Basic ester hydrolysis: Bender JACS 1951. Bender and Thomas JACS 1961.
  2. Wolff rearrangement: Litovitz, Keresztes, and Carpenter JACS 2008.

Mathematics Tables and Integrators

  1. Small Table of Derivatives
  2. Large List of Derivatives
  3. Small Table of Integrals
  4. Large List of Integrals
  5. Integrator (Symbolic - Mathematica)
  6. Online Math Tools: Calculators, Integrators, Plotters, etc.

Specialized Kinetics Instrumentation

  1. TgK Scientific: Stopped-flow, Rapid quench, T-jump
  2. KinTek Corporation: Stopped-flow, Rapid Quench, Flash Photolysis
  3. Applied Photophysics: Stopped-flow, Flash Photolysis

Least-squares Fitting for Parameter Estimation

  1. "Fitting Curves to Data using Nonlinear Regression: a Practical and Nonmathematical Review", H. J. Motulsky and L. A. Ransnas, FASEB J. 1987, 365-374.
  2. Gnuplot - Free program for Windows, Mac OS, Linux, and Unix
  3. Grace - Free program for Linux and Unix
  4. SigmaPlot - Commercial package for Windows
  5. Scientist - Commercial software package for Windows
  6. Results from a sample first-order fit

Data for HW Problem 3

  1. H-compound data (col 1 = time in sec, col 2 = absorbance)
  2. D-compound data (col 1 = time in sec, col 2 = absorbance)
  3. Gnuplot commands for an exponetial fit

Short List of ODE Solvers (Numerical Integration of Rate Laws)

  1. Matlab (Windows, Mac OS X, Linux, Solaris) - solves ode's and much more ($)
  2. Octave (Windows, Mac OS X, Linux, Solaris, OS2) - very similar to Matlab, but free
  3. Scientist - Commercial software package for Windows
  4. ODE Methods (Short Wikipedia article)

Potential Energy Surfaces for Chemical Reactions/Rate Theory

  1. Generic PES
  2. Variational TS Figure
  3. Trular and Garrett, Variational Transition-state Theory
  4. Miller, Beyond Transition-State Theory: A Rigorous Quantum Theory of Chemical Reaction Rates

Texts on Kinetic Isotope Effects

  1. Melander, L. and Saunders, W. H., Jr. Reaction Rates of Isotopic Molecules, Wiley (1980), reprinted by Robert E. Krieger Publishing Co. (1987). Amazon
  2. Cook, P. F. Enzyme Mechanism from Isotope Effects CRC Press (1991). Amazon
  3. Kohen, A. and Limbach H.-H. Isotope Effects in Chemistry and Biology, CRC Press (2005). Amazon

Inhibitor Design from KIE/TS Studies

  1. Luo, M. and Schramm, V. L. J. Am. Chem. Soc. 2008, 11617-11619. "Ribosyl Geometry in the Transition State of Streptococcus pneumoniae Methylthioadenosine Nucleosidase from the 3'-D Kinetic Isotope Effect" doi

Linear Free-Energy Relationships

  1. Bronsted example: Jencks and Carriuolo (1961) doi
  2. Hammett Sigma Values

HW 3: LS Fit Results

  1. H Data, exponential fit
  2. D Data, exponential fit
  3. D Data, double exponential fit

Octave Help

  1. My tips

Nobel Prize Winners

  1. Henry Taube
  2. Rudy Marcus
  3. Manfred Eigen

Proton and Electron Transfer Reactons

  1. Simple Marcus Fit (Miller, Calcaterra, Closs 1984 Data)
  2. Rosokha, S. V. and Kochi, J. K. Acc. Chem. Res. 2008 41, 641-653. "Fresh Look at Electron-Transfer Mechanisms via the Donor/Acceptor Bindings in the Critical Encounter Complex". doi
  3. Peters, K. S. Acc. Chem. Res. 2008 "A Theory-Experiment Conundrum for Proton Transfers". doi

Proteins and Enzymes

  1. Amino Acids
  2. Peptide Bonds
  3. Protein Folding
  4. Protein Structure
  5. Alpha Helix
  6. Beta Sheet
  7. Urease Structure
  8. Glyoxylase Structure
  9. Enzyme Reaction Cartoon
  10. Chymotrypsin Active Site
  11. Carbonic Anhydrase Active Site
  12. Burst Example (Glutathione Transferase Reaction) doi
  13. Glutathione

Photochemical Kinetics

  1. Photochemical Energy Diagram
  2. Stern-Volmer Study: H2@C60 JACS 2008, 129, 14554

Nonlinear Chemical Dynamics

  1. Oregonator Time Plot
  2. Belousov-Zhabotinsky Standing Waves
  3. More BZ Standing Waves
  4. Chaos in the BZ Reaction: doi (Swinney, et al.)
  5. Lorenz Attractor: octave script (source "lorenz.m")
  6. Lorenz Attractor Time Plot
  7. Lorenz Attractor Phase Plot