Guide for Atomic Force Microscopy Image Analysis To Discriminate Heteroatoms in Aromatic Molecules [A Guide for AFM Image Analysis To Discriminate Heteroatoms in Aromatic Molecules]
Abstract
Heteroatoms are essential for functional groups in organic structures and are complementary to hydrocarbon molecules in reactivities and properties. However, it is still a challenge to quickly identify heteroatoms with only non-contact atomic force microscopy (nc-AFM) to 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 (DBT), acridine (ACR), and carbazole (CBZ). We identified several features that can be used to find common heteroatoms (S and N) and discriminated them from carbon atoms (C) using nc-AFM images alone. 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, need to be considered. As a result, this work will allow for rapid identification of these common heteroatoms in petroleum with AFM.
- Authors:
-
[2]
- Brookhaven National Lab. (BNL), Upton, NY (United States)
- ExxonMobil Research and Engineering Co., Annandale, NJ (United States)
- Publication Date:
- Research Org.:
- Brookhaven National Lab. (BNL), Upton, NY (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Basic Energy Sciences (BES)
- OSTI Identifier:
- 1514492
- Report Number(s):
- BNL-211599-2019-JAAM
Journal ID: ISSN 0887-0624
- Grant/Contract Number:
- SC0012704
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Energy and Fuels
- Additional Journal Information:
- Journal Volume: 33; Journal Issue: 6; Journal ID: ISSN 0887-0624
- Publisher:
- American Chemical Society (ACS)
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 37 INORGANIC, ORGANIC, PHYSICAL AND ANALYTICAL CHEMISTRY
Citation Formats
Zahl, Percy, and Zhang, Yunlong. Guide for Atomic Force Microscopy Image Analysis To Discriminate Heteroatoms in Aromatic Molecules [A Guide for AFM Image Analysis To Discriminate Heteroatoms in Aromatic Molecules]. United States: N. p., 2019.
Web. doi:10.1021/acs.energyfuels.9b00165.
Zahl, Percy, & Zhang, Yunlong. Guide for Atomic Force Microscopy Image Analysis To Discriminate Heteroatoms in Aromatic Molecules [A Guide for AFM Image Analysis To Discriminate Heteroatoms in Aromatic Molecules]. United States. https://doi.org/10.1021/acs.energyfuels.9b00165
Zahl, Percy, and Zhang, Yunlong. Mon .
"Guide for Atomic Force Microscopy Image Analysis To Discriminate Heteroatoms in Aromatic Molecules [A Guide for AFM Image Analysis To Discriminate Heteroatoms in Aromatic Molecules]". United States. https://doi.org/10.1021/acs.energyfuels.9b00165. https://www.osti.gov/servlets/purl/1514492.
@article{osti_1514492,
title = {Guide for Atomic Force Microscopy Image Analysis To Discriminate Heteroatoms in Aromatic Molecules [A Guide for AFM Image Analysis To Discriminate Heteroatoms in Aromatic Molecules]},
author = {Zahl, Percy and Zhang, Yunlong},
abstractNote = {Heteroatoms are essential for functional groups in organic structures and are complementary to hydrocarbon molecules in reactivities and properties. However, it is still a challenge to quickly identify heteroatoms with only non-contact atomic force microscopy (nc-AFM) to 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 (DBT), acridine (ACR), and carbazole (CBZ). We identified several features that can be used to find common heteroatoms (S and N) and discriminated them from carbon atoms (C) using nc-AFM images alone. 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, need to be considered. As a result, this work will allow for rapid identification of these common heteroatoms in petroleum with AFM.},
doi = {10.1021/acs.energyfuels.9b00165},
journal = {Energy and Fuels},
number = 6,
volume = 33,
place = {United States},
year = {Mon Apr 29 00:00:00 EDT 2019},
month = {Mon Apr 29 00:00:00 EDT 2019}
}
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Cited by: 32 works
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Figures / Tables:
Figure 1: nc-AFM imaging heteroatom-containing organic compounds dibenzothiophene (DBT), carbazole (CBZ), and acridine (ACR). The chemical structures and ball-and-stick models optimized by DFT (gray C, blue N, yellow S) are shown on top of each panels. Simulated AFM images of DBT (a,b), CBZ (d,e), and ACR (g, h) obtained withmore »
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Figures / Tables found in this record:
Figures/Tables have been extracted from DOE-funded journal article accepted manuscripts.