Chemical and steric effects in simulating noncontact atomic force microscopy images of organic molecules on a Cu (111) substrate
Abstract
Noncontact mode of atomic force microscopy (nc-AFM) employing a CO-functionalized tip is a very powerful tool for studying molecular structures. However, interpreting nc-AFM images for nonplanar molecules can sometimes be problematic. To illustrate and resolve the nature of such problematic systems, we employ real-space pseudopotentials constructed within density functional theory to simulate nc-AFM images. In this work, we focus on several representative nonplanar organic molecules (pentacene, naphthanthrone, olympicene, and 6-phenylhexa-1,3,5-triynybenzene (PHTB)) on a typical substrate: the Cu (111) surface. This substrate results in significant distortions in the molecular geometries of pentacene and naphthanthrone. Including these distortions in simulated nc-AFM imaging notably improves the agreement between the simulated and measured images. In naphthanthrone, the relatively large interaction between the O atom and the Cu substrate offers a straightforward explanation for the absence of the C = O bond in the measured image. Nonplanar features such as tilting or twisting are also apparent in olympicene and PHTB. A “triangular” bright feature associated with the –CH2 group in olympicene appears in simulated and measured nc-AFM images. This feature is directly related to the tilting angle of the molecule with respect to the Cu substrate. The “defective” benzene ring feature and the faint ellipsoidalmore »
- Publication Date:
- Research Org.:
- Univ. of Texas, Austin, TX (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC); Welch Foundation
- OSTI Identifier:
- 1800353
- Grant/Contract Number:
- FG02-06ER46286; F-1837
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Physical Review Materials
- Additional Journal Information:
- Journal Volume: 4; Journal Issue: 5; Journal ID: ISSN 2475-9953
- Publisher:
- American Physical Society (APS)
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND SUPERFLUIDITY; Materials Science
Citation Formats
Fan, Dingxin, Sakai, Yuki, and Chelikowsky, James R. Chemical and steric effects in simulating noncontact atomic force microscopy images of organic molecules on a Cu (111) substrate. United States: N. p., 2020.
Web. doi:10.1103/physrevmaterials.4.053802.
Fan, Dingxin, Sakai, Yuki, & Chelikowsky, James R. Chemical and steric effects in simulating noncontact atomic force microscopy images of organic molecules on a Cu (111) substrate. United States. https://doi.org/10.1103/physrevmaterials.4.053802
Fan, Dingxin, Sakai, Yuki, and Chelikowsky, James R. Wed .
"Chemical and steric effects in simulating noncontact atomic force microscopy images of organic molecules on a Cu (111) substrate". United States. https://doi.org/10.1103/physrevmaterials.4.053802. https://www.osti.gov/servlets/purl/1800353.
@article{osti_1800353,
title = {Chemical and steric effects in simulating noncontact atomic force microscopy images of organic molecules on a Cu (111) substrate},
author = {Fan, Dingxin and Sakai, Yuki and Chelikowsky, James R.},
abstractNote = {Noncontact mode of atomic force microscopy (nc-AFM) employing a CO-functionalized tip is a very powerful tool for studying molecular structures. However, interpreting nc-AFM images for nonplanar molecules can sometimes be problematic. To illustrate and resolve the nature of such problematic systems, we employ real-space pseudopotentials constructed within density functional theory to simulate nc-AFM images. In this work, we focus on several representative nonplanar organic molecules (pentacene, naphthanthrone, olympicene, and 6-phenylhexa-1,3,5-triynybenzene (PHTB)) on a typical substrate: the Cu (111) surface. This substrate results in significant distortions in the molecular geometries of pentacene and naphthanthrone. Including these distortions in simulated nc-AFM imaging notably improves the agreement between the simulated and measured images. In naphthanthrone, the relatively large interaction between the O atom and the Cu substrate offers a straightforward explanation for the absence of the C = O bond in the measured image. Nonplanar features such as tilting or twisting are also apparent in olympicene and PHTB. A “triangular” bright feature associated with the –CH2 group in olympicene appears in simulated and measured nc-AFM images. This feature is directly related to the tilting angle of the molecule with respect to the Cu substrate. The “defective” benzene ring feature and the faint ellipsoidal C ≡ C feature in PHTB can be ascribed to its twisted nature. The ability to simulate such subatomic images in nc-AFM reflects the accuracy and efficiency of calculating quantum forces in real space.},
doi = {10.1103/physrevmaterials.4.053802},
journal = {Physical Review Materials},
number = 5,
volume = 4,
place = {United States},
year = {Wed May 27 00:00:00 EDT 2020},
month = {Wed May 27 00:00:00 EDT 2020}
}
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