2013-14: text book: T. W. Shattuck, Physical Chemistry, Colby College, Waterville, ME, 2013.

Syllabus CH341: Thermodynamics and Kinetics- Semester 1
Syllabus CH342: Quantum Mechanics, Spectroscopy, and Statistical Mechanics- Semester 2

Thermodynamics and Kinetics- Semester 1   ( Thermodynamics and Kinetics- Semester 1 2006)
Quantum Mechanics, Spectroscopy, and Statistical Mechanics- Semester 2

Thermodynamics and Kinetics- Semester 1
Quantum Mechanics, Spectroscopy, and Statistical Mechanics- Semester 2

CH341 Laboratory Manual
CH342 Laboratory Manual

Sample Exams

Solve the Secular Equation HΨ = ESΨ

The Secular Equations applet solves the generalized eigen value problem, which is used for Extended Huckel Molecular Orbital calculations. Instructions for the Secular Equations Solver cover two examples, LiH and CH4.

CNDO Molecular Orbital Program

Complete Neglect of Differential Overlap:
CNDO Molecular Orbital Applet with forms based input.
CNDO Molecular Orbital Applet with text file based input.

Mopac Molecular Orbital Program

You can download the executable file for the OS-X version of Mopac 7 from WebMo.net (or the old Power PC version of Mopac 6.)
Here is a test data file for BF3 to check out MOPAC. Cut and paste this data into a Word document and then save the document in "text only" format (with "LF only" for OS-X). Here are some instructions on how to use MOPAC to do calculations on diatomic molecules. Here is a data file for linear ozone.

You can download the executable file for the Windows version of Mopac 6 or MOPAC 7 (from www.webmo.net) or MOPAC 7 (from CCL)

Here is an application to help you write the input file for MOPAC calculations. You can run it from our web site or please feel free to copy the source to your own computer. If you copy the application to your own system, you can run it by opening the "zmatrix.html" file from the browser menu.

MM3-Molecular Mechanics

Build the 3D-structure of a molecule, predict the enthalpy of formation, and the normal modes of vibration. Run an MM3 molecular mechanics calculation: web-MM3 (The old Marvin-only version is MarvinMM3d )

Units Conversions

Here is an energy conversion application that you will find helpful, especially for converting Hartrees and eV to kJ/mol.

Spectroscopy Tools

The NMR Course Homepage has many useful resources in spectroscopy.

NMR and IR:
JCamp NMR and IR Spectrum Viewer (Spectra files with a ".dx" or ".jdx" extension)(Requires IE-11 or a recent version of Safari)

Mass Spectrometry: The Fragment Finder finds the possible formulas that match a given molar mass. Then the M+1 and M+2 ratios and the exact masses of each of the possible fragments is calculated.
Formula Finder finds the possible formulas that match a given molar mass and several fragments. Then the M+1 and M+2 ratios and the exact masses of each of the possible fragments is calculated.
Isotope Cluster calculates the isotope pattern for a given molecular formula. It includes 3rd and 4th period representative and transition metal elements.

Dynamic NMR: Exchange: Chemical Exchange Lineshape Simulation for 2 site exchange (uses Java for plotting). If you don't want to use the Java dependent version use Exchange(Netscape) or Exchange(IE) for Internet Explorer.

Group Theory: ABC is an applet that calculates the point group for a molecule.

Statistical Mechanics:

ABC is an applet that calculates the point group, Principal Moments of Inertia, Rotational Constants, and Entropy of Rotation of a polyatomic molecule.

Equilibrium Constants from Molecular Structure is an applet that uses statistical mechanics to calculate the equilibrium constant for a simple bimolecular chemical reaction involving diatomic molecules and atoms. Equilibrium Constants for Polyatomics is for reactions involving polyatomic molecules.


The Kinetics Mechanism Simulation (for Windows and Mac IE) application integrates the rate laws for a mechanism with up to four reversible steps. A short tutorial-style introduction will help you get started. Some examples are also available.

The Classical Trajectory Reaction Dynamics applets calculate trajectories for the endothermic-late barrier H + HF and the exothermic-early barrier H + HBr reactions.

Excel Spreadsheets

Here are some Excel examples for A General Approach for Calculating Speciation and Poising Capacity of Redox Systems with Multiple Oxidation States. These programs calculate the redox speciation, titration curves, and pe-pH diagrams for most redox systems.

General Resources

Uncertainty Calculator does propagation of errors calculations for any equation.

Nonlinear Least Squares Curve Fitting does curve fits for a variety of useful equations and gives the uncertainty in the fit parameters. A 4-parameter version is also available.

Matrix Diagonalization The eigen JavaScript application diagonalizes real, symmetric matrices. This application is useful for Huckel molecular orbital calculations. Huckel Molecular Orbital Instructions are available.

HTML Editor is a JavaScript based HTML editor that you can use to design your own web pages.
LetrSet is a JavaScript based HTML type setter that you can use to add fancy headings to your own web pages. A page of examples is available in the LetrSet Gallery.

WWW Links

Colby - Webmo Computational Chemistry on the WWW
The National Institutes of Standards and Technology Chemical Web Book includes thermochemical and gas phase IR and mass spectral data.
The National Library of Medicine ChemIDplus includes physical property and toxicology data.
The RasMol Home page is a source for RasMol/RasMac applications and information.
CORINA Obtain quality 3D coordinates for your own chemical structures from the CORINA progam, from Prof. Gasteiger's research team in the Computer-Chemie-Centrum at the Institute for Organic Chemistry, University of Erlangen-Nürnberg, Germany.
ChemInfo at the Univ. of Indiana will help you find and learn how to use chemistry information resources on the Internet and elsewhere.
Science in the Headlines at the National Reseach Council gives a summary of issues in the news with links to press releases and summaries of related reports.
Chem Center is a resource center provided by the ACS.
Computational Chemistry List (CCL) provides information and free software for computational chemistry.

CH341 Links

Integral Tables
National Cancer Institute Database is searchable by substructure, similarity, and by traditional QSAR descriptors.
The Klotho Biochemical Compounds Declarative Database includes 3D-Chime structures of over 400 biochemical compounds.
3D Pharmaceutical Structure Data Base has 3D-structures for important pharmaceuticals including dynamics trajectories and electrostatic maps by Akira Dobashi's group at Tokyo University of Pharmacy and Life Science, Department of Structural Organic Chemistry (Japan).
3D-Drug Structures at University of Oxford.
The Protein Data Bank at Brookhaven National Labs is a repository of X-ray and NMR 3D-structures of proteins and nucleic acids.
Molecular Biology related 3D-structures at California Lutheran College in a Chime format.
The molecule of the month pages contain alot of interesting information on useful compounds. The University of Bristol MOTM page has a good article on water under extreme conditions.
Techniques for Searching Databases of Three-Dimensional (3D) Structures with Receptor-Based Queries by Douglas R. Henry and Osman F. Guner is a good introduction to information technology in drug design. A local copy with figures that work with Chime is also available.
Pharmacophores and 3D Searches and Search for Novel Protein Kinase C Agonists by Daniel W. Zaharevitz provides a short introduction to the concept of a pharmacophore.

CH342 Links

Integral Tables
The Gaussian Basis Set Order Form at Pacific Northwest Laboratory provides a wide variety of atomic basis sets.

For more information or corrections contact Tom Shattuck at twshattu@Colby.edu.

CCG has kindly supplied a teaching license for the classroom use of MOE

Colby Chemistry Home Page

Last modified: 2/14/2014