Making Molecules Vibrate

Due to this prominent role in chemistry, IR spectroscopy is a key element of undergraduate teaching. Students typically learn about it in two different classes: In the quantum chemistry class, they derive the equations to describe the spectrum to expect the vibration of certain bonds. These calculations, however, are typically only feasible (by hand) for small molecules of two or three atoms. In their organic chemistry (lab) courses, they learn how to use lookup tables to match the IR fingerprint to the IR spectra tabulated in reference books.

At present, the quantum mechanical and organic chemistry views are completely disconnected: For example, if a student is interested in understanding how changes in a particular molecule cause changes in the IR-spectrum, the quantum mechanics is too complex, and the lookup tables most likely do not have tabulated the exact change. Hence, it is impossible for students to develop a deep, intuitive understanding of how the structure is connected to the spectrum.

Advances in computational techniques, coupled with web technologies, allow creating a virtual lab that allows for this exploration of the link between structure and vibrational spectrum.

The web app, ir.cheminfo.org, described in a recent article in The Journal of Chemical Education, has been developed in collaboration between the Laboratory of Molecular Simulation and the cheminformatics group, allows students to draw (almost) any organic molecule, then performs a quantum-chemical calculation on a web service, and then interactively display the result—linking animations of the vibrations directly to the peaks in the spectrum; the student can now see which part of the molecule is causing which part of the IR-fingerprint. There is no barrier to changing a functional group on the molecule and seeing how it changes the IR spectrum.

The most surprising feedback on the beta version of this app indicated another feature of this “virtual laboratory approach” was from universities in developing countries where they have limited access to a real IR spectrometer. That our program allowed them to still teach an IR spectroscopy course, illustrates the importance of our approach. One only needs a simple web browser to access this app is the important technological innovation underlying the design of our app. Motivated by the idea that our virtual lab can make a difference in places they need this the most, the team is currently working on extending this approach to other spectroscopy techniques.