John Silzel
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Ghemical in the Undergraduate Setting

April 9, 2015



I've been involved of late with expanding the physical chemistry curriculum at Biola University to include both a "Life Sciences" track and a "Chemistry" track. This pedagogy is common and was being used when I attended the University of California myself, back in the stone age. Textbooks for physical chemistry reflect this two-track system, which I suspect arose because the calculus and linear algebra required to properly introduce future chemistry professionals to the subject are, regrettably, not usually required of "life science majors" (in this case, the term mostly means pre-medical students, since many biological science majors do not take physical chemistry at all). And so most universities offer "Physical Chemistry for the Life Sciences" which is often chosen even by very capable future MDs because of the perception of lower "GPA risk".

A problem in both tracks, actually, is how to effectively introduce students to the quantum mechanical treatment of many-electron systems. A deep mathematical treatment of the subject must usually wait until graduate school. However, to treat only diatomic molecules, and do so in a very qualitative way neglects the development of students' understanding of the orbital approximation, and leaves them with very little fundamental understanding of molecular spectroscopy. The usual compromise is to apply the "particle in a box" to conjugated systems (which is, I think, dishonest since it fails in nearly every case outside the undergraduate lab), and of course generalize the quantum harmonic oscillator and rigid rotor to polyatomic systems. Even so, this sometimes involves a lot of unsatisfying handwaving and what always seems to me to be too-rushed linear algebra. Our "Chemistry Track" has some familiarity with MATLAB, and so our students can at least diagonalize a 1-D force constants matrix for CO2 or acetylene. It's a start, and it's how I was taught back when dinosaurs roamed the earth.

I have chosen Engel and Reid's texts for both tracks, partly because the authors (and chapter author Warren Hehre, who was on faculty at Irvine while I was there) seem to be on the forefront of the trend to introduce quantum chemistry software in undergraduate homework problems. I routinely use open source code in my own research, and so in both tracks I enable students' use of the free Ghemical software, which implements RHF in C++ code within a fine and reasonably approachable OpenGL-based GUI. (It even runs on the Raspberry Pi 2.) Rather than deal with the diversity of operating systems run by students' personal computers, or the (predominantly Windows) public computers at Biola, I distribute to students a bootable live media containing Linux Mint and the Ghemical package. Ghemical is easy to use and perfectly adequate to expose "Chemistry Track" students to HF basis set selection, correlation energy, and the limitations of SCF methods. "Life Science Track" students can use the software to learn LCAO concepts, get a conceptual understanding of MO hybridization, and a better three-dimensional understanding of molecular structure. (I also introduce the Ballview MD software for study of very large biomolecules, but that's another story.)

A problem with the otherwise excellent Ghemical software is the lack of documentation. I have found that a short "guide" to the use of this teaching tool is all that is really needed to allow my students to tackle the homework problems I adapt from the Engle and Reid texts. (The problems are specifically written for the Spartan software, but easily adapted to Ghemical.)

For fellow faculty interested in the use of Ghemical I am linking my "Ghemical Guide" here. Please let me know if you find it useful or have questions. This document does not do the software justice, but does seem to be adequate to get the more curious students exploring the features of this promising code.

Articles:
>Technical Computing
>Physical Chemistry


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