Looking at Atoms in Molecules to Make Cleaner Fuels from Petroleum

New method quickly identifies atoms that are neither carbon nor hydrogen in small molecules and resolves their chemical structures in complex mixtures.

Looking at Atoms in Molecules to Make Cleaner Fuels from Petroleum
Image courtesy of the Center for Functional Nanomaterials at Brookhaven National Laboratory
(Top) Non-contact atomic force microscopy images can identify pollutant-causing atoms in aromatic hydrocarbon compounds found in crude oil. (Bottom) nc-AFM images of dibenzothiophene, carbazole, and acridine, with corresponding chemical structure.

The Science

CFN staff and users from ExxonMobil have developed a new approach to identifying atoms that are neither carbon nor hydrogen within a specific type of molecule in crude oil. Atoms like nitrogen and sulfur are commonly found in these molecules and are important to how they react with other chemicals. The team used non-contact atomic force microscopy (nc–AFM), a process in which a scientist uses a very sharp probe to scan a surface without touching it. The tool then creates an image based on the interactions between probe and surface. Scientists used these measurements to determine the chemical structure of molecules that can be found in complex mixtures of crude oil.

The Impact

NOx and SOx are two major pollutants that result from burning fossil fuels. Unfortunately, traditional methods of figuring out a molecule’s chemical composition don’t produce clear results for complex molecule mixtures.  Crude oil is one of the most complex molecule mixtures on the planet. Being able to identify hydrocarbon molecules (molecules made of mostly carbon and hydrogen) that have nitrogen and sulfur can improve methods to refine cleaner fuels from crude oil.


Heteroatoms are essential to the functional groups in organic hydrocarbons molecules that provide chemical reactivity and other properties. It is challenging to quickly identify heteroatoms in small molecules and resolve chemical structures in complex unknown mixtures. This study aimed to understand the effect of elemental types on the contrast of atomic force microscopy (AFM) images using a few selected model heterocycles, including dibenzothiophene, acridine, and carbazole. We identified several features that can be used to find sulfur and nitrogen heteroatoms and discriminate them from carbon atoms using only non-contact AFM. The mechanism of the atom and bond contrast was studied with image simulations and was found to be mostly correlated to van der Waals radii, but other factors such as bonding geometry, electron density, and substrate interaction, are considered. This work will allow for rapid AFM identification of these heteroatoms commonly found in petroleum. While nc-AFM and molecule imaging is not that new, it still is a very demanding experiment and requires not only a dedicated microscope, but also experimental expertise. The Center for Functional Nanomaterials, a Department of Energy Office of Science user facility at Brookhaven National Lab, is offering this nc-AFM service to users from around the world.


Percy Zahl
Center for Functional Nanomaterials, Brookhaven National Laboratory
pzahl@bnl.gov; 631-344-2968


This research used resources of the Center for Functional Nanomaterials, which is a U.S. DOE Office of Science Facility, at Brookhaven National Laboratory under Contract No. DE-SC0012704.


P. Zahl and Y. Zhang, “Guide for Atomic Force Microscopy Image Analysis To Discriminate Heteroatoms in Aromatic Molecules.” Energy Fuels 33, 6, 4775 (2019).  [DOI: 10.1021/acs.energyfuels.9b00165].

Related Links

Brookhaven National Laboratory press release: “Imaging the Chemical Structure of Individual Molecules, Atom by Atom.” [https://www.bnl.gov/newsroom/news.php?a=216673].

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