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IBM and University of Aberdeen collaborate to identify molecules from the deep sea

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For the first time, atomic force microscopy helps scientists reveal the exact chemical structure of a natural compound; opens new possibilities in drug discovery.

In a pioneering research project scientists at IBM and the University of Aberdeen have collaborated to "see", for the first time, the structure of a marine compound from the deepest place on the Earth using an atomic force microscope. 

The results, which are being published in the journal Nature Chemistry, open up new possibilities in biological research which could lead to the faster development of new medicines in the future.

Watch the video here.

Cures from the Deep Sea

For several years scientists at the Marine Biodiscovery Centre at the University of Aberdeen have been focused on harnessing the potential of marine organisms as a source for the discovery of chemical compounds, which could be used to develop new treatments for cancer, inflammation, infection, and parasitic diseases.

Professor Marcel Jaspars, Director of the Marine Biodiscovery Centre at the University of Aberdeen comments, "The Earth’s natural environment is rich with a diverse range of unique organisms from which a vast array of chemical compounds can be sourced, many of which are entirely unknown to science. These compounds have the potential to be used in the development of pharmaceuticals and other novel biomedical products. But in order to harness this potential we must first understand these compounds in terms of their molecular structure in order to determine whether they are viable for use in medicine."

Last year, Professor. Jaspars began work on a species of bacterium from a mud sample taken from the Mariana Trench - 10,916 meters (35,818 feet) below sea level.

Using high-resolution mass spectrometry, the university quickly identified the chemical composition of the compound, but determining its exact molecular structure was more challenging. Even the use of state-of-the-art nuclear magnetic resonance techniques would not allow them to determine the exact structure.

Four options

The scientists were left with four potential structures, none of which could be ruled out. They considered taking a chemical synthesis of the proposed structures, but this is a very complex task that can take several months.

ooking for an alternative method, Professor Jaspars, contacted IBM scientists in Zurich, who last year, for the first time, imaged the "anatomy" or chemical structure of an organic molecule using an atomic force microscope, with the hope that they could do the same for the compound extracted from the deep-sea bacterium.

To their pleasent surprise, after only one week IBM scientists were able to image individual molecules with atomic resolution using a technique called noncontact atomic force microscopy. These images together with first principles calculations confirmed the identification as cephalandole A, which is actually known and originally isolated from a Taiwanese orchid.

"The technique demonstrates that scanning probe microscopes can add powerful functionality in identifying the structure of molecules which are challenging to resolve with conventional techniques," said Leo Gross, scientist, IBM Research - Zurich.

The experiment was the first successful use of AFM in the determination of, what was at the time, an unknown molecular structure.