Rice and ORNL vibrational spectroscopy captures 3D organic molecular structures

Houston, TX and Oak Ridge, TN--By measuring the vibrations between atoms using femtosecond-long laser pulses, researchers at Rice University and Oak Ridge National Laboratory (ORNL) can determine the three-dimensional positions of atoms within molecules without the restrictions imposed by other techniques such as x-ray diffraction (XRD) and nuclear magnetic resonance (NMR) imaging.¹

The new technique, called multiple-dimensional vibrational spectroscopy, can capture the structure of molecules at room temperature (as well as very low or high temperatures) and in many kinds of samples, including crystals, powders, gels, liquids, and gases. It will be useful in the study of catalysis, energy storage, organic solar cells, and biomembranes, among other areas, says Rice University chemist Junrong Zheng.

Zheng and his co-authors at Rice and ORNL analyzed variations of a model molecule, 4′-methyl-2′nitroacetanilide (MNA), and compared the results with computer-generated and XRD models. The images matched nicely, says Zheng. “The atoms in every molecule are always vibrating, and each bond between atoms vibrates at a certain frequency, and in a certain direction,” he notes. “We found that if we can measure the direction of one vibration and then another, then we can know the angle between these two vibrations—and therefore the angle between the bonds.”

Ultrafast mid-IR and terahertz pulses

The one-of-a-kind spectrometer developed by Zheng uses polarized ultrafast (100 fs) mid-IR laser pulses, along with ultrafast terahertz pulses, to read the vibrational energies inherent to every atom. Those energies determine how atoms bond to form a molecule; a determination of the length and angles of those bonds can be extracted from the measurements. The spectrometer reads only intramolecular interactions among vibrations and ignores interactions between molecules.

“The important part of this paper is to demonstrate that our method can determine three-dimensional molecular structures no matter whether they’re in liquids or solids,” says Zheng. “Typically, when organic chemists synthesize a molecule, they know its makeup but have no idea what the structure is. Their first option is to make a single crystal of the molecule and use XRD to determine the precise structure. But in many cases it’s very tedious, if not impossible, to grow a single crystal. People also use NMR to learn the structure, but the trouble with many molecules is the solubility is really bad. Insoluble molecules can’t be read well by either method.”

The researchers began with the chemical formula and already knew, through Fourier-transform IR (FT-IR) spectroscopy, how many vibrational frequencies were contained in a given molecule. Then they measured each vibrational mode, one by one. Once they got the cross-angles, they translated the information to a model.

Could ultimately be used on viruses

For now, as a proof of concept, Zheng and his team analyze molecules for which the structure is already known. Over time, the technique should be able to handle much larger molecules, like viruses that contain thousands or tens of thousands of atoms. “This is just the first demonstration that this method works,” says Zheng. “These are simple molecules, 23 or 24 atoms. I think it will take some time to get to proteins. My expectation is that it will take 10 to 20 years to develop. Remember, for NMR, it took 50 years to be able to read the structure of proteins.”

REFERENCE:

1. Hailong Chen et al., J. Phys. Chem. A, publication date (Web): August 12, 2013; doi: 10.1021/jp406304c

Source: http://news.rice.edu/2013/08/15/rice-technique-expands-options-for-molecular-imaging/