The Paul J. Schupf Computational Chemistry Laboratory located in the Paul J. Schupf Scientific Computing Center was founded with gifts from Colby trustee Paul J. Schupf, grants from the Howard Hughes Medical Institute, and two grants from the National Science Foundation*. The main compute engine for molecular orbital calculations is an intel based 10 blade compute cluster the natural science compute cluster . The laboratory has two distributed clusters one based on seven 8 Core PowerMacintosh workstations and the other on seven Dell Precision 380 dual core 3GHz Windows/Linux systems with 4 GBytes of memory. The software available includes molecular orbital, molecular mechanics and dynamics, and chemometric analysis software. Students are introduced to molecular mechanics calculations in General Chemistry during their first year at Colby. The graphics power of the workstations in hands-on exercises helps beginning students explore the visual images in chemistry. They start with simple inorganic compounds and progress through complicated proteins, Figure 1. In sophomore Organic Chemistry students use molecular mechanics to study the shapes of molecules by finding bond lengths and angles from energy minimized structures. Hands-on exercises help students visualize the energetics of the conformations of ring systems.
In Physical Chemistry, students learn the fundamentals of computational chemistry. Weekly homework exercises teach the power of molecular mechanics, dynamics, and molecular orbital calculations, Figure 2. In PChem, students also do laboratory projects that complement the computational exercises to underscore that theory is meant to illuminate experimental observations. The true power of molecular mechanics and dynamics is found in simulation of the motion of molecules in water. These simulations involve solving Newton's equations of motion for many hundreds of atoms, Figure 3
In the Biomolecular Structure course, students use the graphics power of our workstations to understand protein structure, see Figure 1. The students download structures from the Brookhaven Protein Database. They add hydrogens, determine the minimum energy structure, and study enzyme substrate interactions.
In the senior year, students begin to draw connections between their previous coursework and their student research. In the Physical Organic course, our students do calculations that concern reactions that are the subjects of their senior research projects, Figure 4. We believe independent student research plays a very important role in undergraduate education, so we structure our courses to provide the tools and expertise for students to become proficient in research. Teaching through research is an important principle in our curriculum. For example, one of our research groups is developing a method to determine OH radicals in sea-water, Figure 5.
Molecular Mechanics and CAMD Tutorials
Feel free to download a copy of the
Colby College Molecular Mechanics Tutorial Introduction. Computational exercises
using molecular mechanics and dynamics are available:
Colby College Molecular Mechanics Exercises-MOE tutorial.
A version based on QUANTA is also available:
Colby College Molecular Mechanics Exercises-Quanta version.
(Please note that previous versions of the tutorial combined the Tutorial
and the Exercises in one file.)
The CAMD tutorial is an introduction to computer aided molecular design (pdf format). ( A Microsoft Word version is also available: The CAMD tutorial -Word version.) A Power Point presentation on the basics of CAMD is an introduction to CAMD ideas.
A Power Point presentation on Computer Aided Molecular Design and Information Technology is also available. This presentation was presented at the fall 1998 meeting of the Colby-Bowdoin-Bates (CBB) Committee on Technology Use, which is funded by the Mellon Foundation.(Many of the slides are repeats of the CAMD presentation, above)
ACS Spring 2001: Molecular Modeling in the Undergraduate Curriculum: A Power Point Presentation from the Chemical Education Molecular Modeling Symposium in San Diego is also available.
Harold Bell's Properties of Organic Compounds
We now have ISIS/Base versions of Harold Bell's Properties of Organic Compounds
Database available in
Windows and Macintosh
format versions. This database contains about 5,000 organics with
NMR chmical shifts as attached text to the 2D structures. This database
is the basis of our Web version:
Organic Compounds Database Search.
For more information on the Computational Chemistry Laboratory at Colby contact Tom Shattuck at [email protected]
Last modified: 1/30/03