Theoretical interpretation of scanning probe images of molecules on surfaces
Scanning tunnelling microscopy (STM) and atomic force microscopy (AFM) can produce images of molecules with extremely high resolution. However, Claims that dynamic force microscopy has the capability to resolve intermolecular bonds in real space continue to be vigorously debated. Several studies hav...
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| Format: | Thesis (University of Nottingham only) |
| Language: | English |
| Published: |
2017
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| Online Access: | https://eprints.nottingham.ac.uk/41928/ |
| _version_ | 1848796384836190208 |
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| author | Abdur Rashid, Mohammad |
| author_facet | Abdur Rashid, Mohammad |
| author_sort | Abdur Rashid, Mohammad |
| building | Nottingham Research Data Repository |
| collection | Online Access |
| description | Scanning tunnelling microscopy (STM) and atomic force microscopy (AFM) can produce images of molecules with extremely high resolution. However, Claims that dynamic force microscopy has the capability to resolve intermolecular bonds in real space continue to be vigorously debated. Several studies have now shown that tip flexibility, especially at very close tip-sample separations, is responsible for the striking intra- and intermolecular resolution observed with various scanning probe microscopy techniques. The apparent intermolecular features can be observed with dynamic force microscopy even when no bonding interaction is present, suggesting that such features are in fact an artefact and cannot be interpreted as a real-space image of an intermolecular bond.
We have studied the interaction between fullerene (C60) molecules using a sum of pairwise Lennard-Jones (12-6) potentials, and investigated how flexibility in the tip can produce a bond like feature between the molecules in a C60 island where there is no chemical bond present except the weak van der Waals force. We also investigate how the potential between the molecules is dependent on their relative orientations. For a given configuration of the tip and the sample molecules, our results allow us to predict the form of the intermolecular potential that would be observed using non contact atomic force microscopy (NC-AFM).
Our study on the Si(111)-(7x7) reconstructed surface using the same model provides a better understating on the origin of ‘sub-atomic’ contrast observed in experiment suggesting that the contrast can arise from a flexible tip exploring an asymmetric potential created due to the positioning of the surrounding surface atoms. We have also simulated NC-AFM images of 2D bi-isonicotinic acid lattice using the same model. The geometry of the lattice have been optimized using DFT before simulating AFM images. Simulation results are in a good agreement with the experiment.
The theoretical work is accompanied by a variety of experimental results obtained by the group of Prof Philip Moriarty at the University of Nottingham. |
| first_indexed | 2025-11-14T19:47:08Z |
| format | Thesis (University of Nottingham only) |
| id | nottingham-41928 |
| institution | University of Nottingham Malaysia Campus |
| institution_category | Local University |
| language | English |
| last_indexed | 2025-11-14T19:47:08Z |
| publishDate | 2017 |
| recordtype | eprints |
| repository_type | Digital Repository |
| spelling | nottingham-419282025-02-28T13:44:34Z https://eprints.nottingham.ac.uk/41928/ Theoretical interpretation of scanning probe images of molecules on surfaces Abdur Rashid, Mohammad Scanning tunnelling microscopy (STM) and atomic force microscopy (AFM) can produce images of molecules with extremely high resolution. However, Claims that dynamic force microscopy has the capability to resolve intermolecular bonds in real space continue to be vigorously debated. Several studies have now shown that tip flexibility, especially at very close tip-sample separations, is responsible for the striking intra- and intermolecular resolution observed with various scanning probe microscopy techniques. The apparent intermolecular features can be observed with dynamic force microscopy even when no bonding interaction is present, suggesting that such features are in fact an artefact and cannot be interpreted as a real-space image of an intermolecular bond. We have studied the interaction between fullerene (C60) molecules using a sum of pairwise Lennard-Jones (12-6) potentials, and investigated how flexibility in the tip can produce a bond like feature between the molecules in a C60 island where there is no chemical bond present except the weak van der Waals force. We also investigate how the potential between the molecules is dependent on their relative orientations. For a given configuration of the tip and the sample molecules, our results allow us to predict the form of the intermolecular potential that would be observed using non contact atomic force microscopy (NC-AFM). Our study on the Si(111)-(7x7) reconstructed surface using the same model provides a better understating on the origin of ‘sub-atomic’ contrast observed in experiment suggesting that the contrast can arise from a flexible tip exploring an asymmetric potential created due to the positioning of the surrounding surface atoms. We have also simulated NC-AFM images of 2D bi-isonicotinic acid lattice using the same model. The geometry of the lattice have been optimized using DFT before simulating AFM images. Simulation results are in a good agreement with the experiment. The theoretical work is accompanied by a variety of experimental results obtained by the group of Prof Philip Moriarty at the University of Nottingham. 2017-07-12 Thesis (University of Nottingham only) NonPeerReviewed application/pdf en arr https://eprints.nottingham.ac.uk/41928/1/Thesis_Mohammad_2017.04.11_final.pdf Abdur Rashid, Mohammad (2017) Theoretical interpretation of scanning probe images of molecules on surfaces. PhD thesis, University of Nottingham. |
| spellingShingle | Abdur Rashid, Mohammad Theoretical interpretation of scanning probe images of molecules on surfaces |
| title | Theoretical interpretation of scanning probe images of molecules on surfaces |
| title_full | Theoretical interpretation of scanning probe images of molecules on surfaces |
| title_fullStr | Theoretical interpretation of scanning probe images of molecules on surfaces |
| title_full_unstemmed | Theoretical interpretation of scanning probe images of molecules on surfaces |
| title_short | Theoretical interpretation of scanning probe images of molecules on surfaces |
| title_sort | theoretical interpretation of scanning probe images of molecules on surfaces |
| url | https://eprints.nottingham.ac.uk/41928/ |