Innovative Software Gives Columbia Chemists Cutting Edge

by Eric Pflanzer

Do the words organic chemistry and orgo lab elicit the same excitement as MCAT Review? Is the path of your future medical career, starting with the Peace Corps in Zaire en route to 72nd and Park Ave, being impeded by a mere carbon atom? Well, your friends in Havemeyer understand the difficulty of chemistry and have initiated original programs to aid you, the struggling student. The Chemistry Department is currently developing several software packages that will greatly facilitate students' comprehension and enjoyment of this central science. With both computer-aided lectures and innovative chemical software, Columbia undergraduates will be among the first in the world to benefit from this new technology developed right here on campus!

IR Tutor is one of the first packages created for the aid of organic chemistry students. The brainchild of Dr. Charles Abrams, first a graduate student and later a staff associate, IR Tutor was developed in collaboration with the Perkin Elmer Corporation -- the Black & Decker of any laboratory, supplying the lion's share of analytical and diagnostic instrumentation needed by chemists. Both public and private institutions expressed interest in the software for its versatility and usefulness in training any novice of the organic world.

Your professors saw the need for enhancing a textbook only class and decided to remedy the problem themselves by initiating the development of software packages as educational tools. Students have always had difficulties grasping the concepts of intra- and intermolecular interactions diagramed in books and simple blackboard sketches. Imagine a professor's challenge in teaching students the theory behind the carbon-hydrogen stretch vibration of methyl groups produced by incident infrared light. "What's that?" you would ask. Well, check out IR Tutor and learn in a few minutes of interactive play as three-dimensional computer-generated visualizations guide you through a world of molecules.

Armed with your remote control, you've already exploited infrared's power to scan TV-land in search of ESPN and CNN. Now, learn to use IR to explore the world of CnHn. IR Tutor first provides the student with a short cartoon history of the discovery of infrared radiation. The student can actually perform a virtual experiment and study her/his own results. We learn that the infrared makes up only a tiny portion of the electromagnetic spectrum, just beyond the visible region that humans can visually perceive and before the microwaves. When you sense heat on you skin - that's the infrared portion of electromagnetic radiation reaching you.
The software then leads you through an intelligent reasoning of the quantum harmonic oscillator theory on which infrared spectroscopy is based. IR Tutor greatly facilitates your learning of quantum mechanics by providing vivid three dimensional interactive images with sound. No book permits you to manipulate experimental conditions on demand, but IR Tutor enables you to tailor examples to suit your needs.

For example, with the click of a mouse, you stretch and compress atomic spheres bound by a spring, which shows you how two atoms at equilibrium bond length can change their potential energy. This potential energy manifests itself as a vibrational frequency, and IR Tutor teaches you how to look at two bound atoms' potential energy as proportional to the square of the displacement of the two atoms from their position equilibrium. So, as you sit back, IR Tutor's 3-D models demonstrate how the vibrational frequency of a bond is proportional to both the bond's strength and the mass of the bound atoms.

Next, the software demonstrates how this vibrational frequency characterizes a bond by its ability to absorb or emit energy. When incident infrared's electric field matches a dipole bond's vibrational frequency, the bond absorbs this radiation, producing a peak on your spectrum graph. So once you grasp these ideas, your Tutor then elaborates this simple plan. Remember that most molecules possess several dozens, or even hundreds of bonds! But since each bond wiggle can be characterized by certain distinct movements, each wiggle will absorb IR at a different range! Just like you have the tango or the macarena, molecules can have several dances, a.k.a. normal modes, such as the in-plane bend or the anti-symmetric stretch .

Picture a molecule. Ethanol, nicotine, or caffeine will do just fine. Each molecule possesses similar functional groups such as methyl-CH3 and methylene-CH2, but each also has its own special, unique functional groups -- like ethanol's hydroxyl -OH or caffeine's amide -CON. So, each functional group will have an inherent IR absorption pattern that arises from its constituent bonds. The IR spectrum identifies the compound like a big fingerprint, since the functional groups reveal themselves through an IR scan.

Many organic chemistry students have already learned IR spectroscopy with the invaluable help of IR Tutor. Students of Prof. Nicholas Turro's Intensive Organic Chemistry for First-Years started interpreting spectra just minutes after sitting at the IR Tutor. Paul Wehn (CC'00) described his high school organic lectures in AP Chemistry as "boring and uninspiring." He added that "we didn't have any computer technology geared toward teaching organic chemistry. All we did was memorize wood ball and stick models. " Both Wehn and his fellow student Ben Schwarz recommends IR Tutor "to all students of chemistry." He believes the software "shows you how to think of molecules and energy interactions."
Logon to IR Tutor and get ready to learn how to conceive molecules in an unprecedented way. This powerful software also teaches you how to mentally visualize a chemical bond. After you leave IR Tutor, you'll gain better mental skills to actually improve your own conception of matter. The student and commercial success of the IR Tutor has greatly motivated the Chemistry Department to pursue further work in the field of computer visualization as a valuable educational tool. So Prof. Turro currently uses computer-generated reaction mechanisms to enhance the usual chalk and arrows of the common organic class. He also has established a newsgroup on his website for his students. Currently, the chemists in the Department are developing more educational software packages for technical research and laboratory methodology. Possibly forthcoming are teaching aids for DRIFT IR (a new method of spectroscopy), Liquid Cell, and KBr Pellet methodology in IR spectroscopy.

Columbia students should consider themselves fortunate for being able to access some of the latest educational scientific computer software. You can check these coming software programs in the 308 Havemeyer undergraduate computer lab and, of course, in your forthcoming chemistry classes.