Interdisciplinary research – Direct Imaging of Single Molecule

Interdisciplinary research has immense potential. I have talked about one of the major discoveries of modern science based on interdisciplinary research in my previous blog, posted on 29th July 2013 ( interdisciplinary-research-nobel-prize-chemistry-won-biologists/). Today, let us take another example, where one chemist and one physicist came together and presented us with the direct image of internal covalent bond structure of a single molecule using one of the advanced imaging tools, non-contact Atomic force microscope (nc-AFM). Image1Dr. Felix R.Fischer (, a young Assistant Professor of Chemistry at University of California (UC), Berkeley along with his collaborator Dr. Michael Crommie (, also a UC Berkeley Professor of Physics captured the images of internal bond structure of oligo (phenylene-1, 2 ethynylenes) [Reactant1] when it undergoes cyclization to give different cyclic compounds (one of which is shown in the inset picture Chemists generally determine structure of molecules using different spectroscopic techniques (NMR, IR, Uv-vis, etc.) in an indirect manner. The molecular structures, we generally see in the textbooks result from the indirect way of structure determination, either theoretical or experimental or both. It is more like putting together various parts to solve a puzzle. But now, with this ground breaking work of two scientists from UC Berkeley, one can directly see for the very first time in the history of science, how a single molecule undergoes transformation in a chemical reaction, how the atoms reorganized themselves at a certain condition to produce another molecule. No more solving puzzle for next generation of chemists to determine the molecular structure.

HOW interdisciplinary research made it possible:

Well, it was not easy task for the scientists to come up with these spectacular molecular images. Imaging techniques such as scanning tunneling microscopy (STM), tunneling electron microscopy (TEM), have their limitations, and are often destructive to the organic molecular structure. Advanced technique like nc-AFM where a single carbon monoxide molecule sits on the tip (probe) helps in enhancing the spatial resolution of the microscope, and this method is also non-destructive. The thermal cyclization of the Reactant 1 was probed on an atomically cleaned silver surface, Ag(001) under ultra-high vacuum at single molecular level by STM and nc-AFM. Before probing, the reaction surface and the molecules were chilled at liquid helium temperature, 40K (-2700C). Then the researchers first located the surface molecules by STM and then performed further finetuning with nc-AFM, and the result is what we see in the inset picture. For cyclization, the Reactant 1 was heated at 900C, the products were chilled and probed.  Chilling after heating did not alter the structure of the products. The mechanism of thermal cyclization was also clearly understood, and the mechanistic pathway was in agreement with the theoretical calculations. From the blurred images of STM, Dr. Fischer and Dr. Crommie along with their coworkers presented us crystal clear molecular images with visible internal bond structure. This ground breaking work shows the potential of nc-AFM and unveils secrets of surface bound chemical reactions which will definitely have a huge impact on oil and chemical industries where heterogeneous catalysis is widely used. This technique will also help in creating customized nanostructure for use in electronic devices.

Again this path breaking work was possible due to the collaborative research between chemists and physicists. Hence, the interdisciplinary researches have endless potential.


1.    de Oteyza DG, Gorman P, Chen Y-C, Wickenburg S, Riss A, Mowbray DJ, Etkin G, Pedramrazi Z, Tsai H-Z, Rubio A, Crommie MF, Fischer FR. Direct Imaging of Covalent bond structure in Single-molecule chemical reactions. Science (2013); 340: 1434-1437


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