TY  - THES
AU  - Kopp, Philipp
TI  - Controlled single-molecule manipulation
VL  - 122
PB  - RWTH Aachen University
VL  - Dissertation
CY  - Jülich
M1  - FZJ-2026-01796
SN  - 978-3-95806-887-2
T2  - Schriften des Forschungszentrums Jülich Reihe Information / Information
SP  - viii, 136
PY  - 2026
N1  - Dissertation, RWTH Aachen University, 2025
AB  - This thesis paves the way for the assembly of supramolecular structures by autonomous robotic nanofabrication based on RL and their characterisation using the tools of nanoscience. In a proof of principle application the RL agent removed single molecules from a layer in which they were held together by strong molecule-surface and intermolecular interactions. The extension of the MoMaLab’s capabilities to include autonomous manipulation was preceded by the understanding of the contact formation with the system (PTCDA on Ag(111)), the characterisation of the tip-molecule bond and the pioneering work of HCM. Contact formation between the tip and PTCDA on Ag(111) was studied in section 4.2. Contact formation and the intermolecular interactions were systematically probed by performing 4096 vertical two-contact manipulations in a grid over an area covering two unit cells of the layer. By approaching one of the four Ocarb at the corners of PTCDA with the tip a chemical bond can be formed. It was shown that there are two types of Ocarb atoms per molecule, and four per unit cell, which differ significantly in their contact behaviour. The four different forces required for the Ocarb atoms to switch their bonding from the surface to the tip could be extracted. Analysis of the height of the bond rupture, upon tip retraction after the initial bond formation, revealed a surprising flexibility of the four corners of PTCDA. It was shown that a lateral variation in the contact position along the C-O bond towards the centre of the molecule increases the bending of the corners and thus the height of bond rupture. These ”corridors” suggest that a molecule could potentially be extracted from the layer by peeling. This peeling was indeed successfully employed by HCM and was also later rediscovered by the autonomous agent. Next is the characterisation of the tip-molecule contact and in particular its evolution during the manipulation, presented in section 4.3. It is clear that initially there is only a single bond between the tip apex and one Ocarb of PTCDA. PTCDA often remains in a vertical configuration on the tip after its separation from the surface, so called s-PTCDA. What is the tip-molecule contact of this configuration? To answer this question, molecules were attached to an artificial tip apex on the surface, in the form of an adatom, and their connection was probed by vertical two-contact manipulation. It has been shown that the unpaired Ocarb next to the adatom is attracted to the surface. Therefore, the molecule orients itself during the manipulation so that the distance between the Ocarb and the surface is minimised. It could be concluded that in the case of s-PTCDA on the tip, a single tipmolecule bond would be unstable and that the formation of a second tip-molecule bond would be expected. With the molecule attached to an adatom, the molecule can be manipulated into a junction with symmetrical contacts, leaving only the adatom as the surface contact and the apex atom as the tip contact. In chapter 5 it was shown that a quarter circle manipulation trajectory lead to a highly reproducible behaviour of the molecule during its manipulation into the symmetric junction. Further, the two separation events of the unpaired Ocarb atoms from the surface and from the tip could be observed, indicating that a diagonal configuration was indeed achieved. These events were not observed when an isolated molecule (without adatom) was lifted from the surface. Taken together with the finding that contact rupture occurred closer to the surface in the case of an isolated molecule, it could be concluded that an isolated molecule does not reach a diagonal configuration during lifting. The molecule, attached to an adatom, was repeatedly manipulated up and down along the quarter circle with hand-controlled manipulation supported by virtual reality goggles for visual feedback. An upgraded version of HCM was used for the manipulation and was presented in section 5.2. The functionality of HCM was reimplemented in a game engine called Unity™, with focus on a modular codebase for easier maintainability and extensibility. Elements were added to provide visual feedback during the manipulation - including a sphere which severed as a visual guide during the experiment described above. The accumulated experience gained from performing HCM and characterising the system, combined with the knowledge of the machine learning group at the TU Berlin, gave rise to autonomous robotic nanofabrication powered by RL and was presented in chapter 6. The robot learned by trial and error, much like a human, to find a peeling trajectory that would allow it to remove a molecule from the layer. The robot could only rely on its own experience to solve this task without any external support. Initially, the learning process was too slow to cope with the occasional change in the tip apex configuration, which could invalidate a previously learned peeling trajectory. The solution was to have the robot also learn a model of its environment as well. The removal task was performed with two types of robotic agents: randomly initialised (R) agents and pre-trained (P) agents. R-agents had no prior knowledge at the beginning of each removal task. An R-agent was selected as the base for all P-agents after it had found a successful peeling trajectory. Thus, P-agents started with the knowledge of having the task solved once for a particular tip. The higher performance of P-agents compared to R-agents demonstrated that some knowledge about the removal task was universal and could be transferred to new tip configurations. In chapter 7 the capabilities of MoMaLab were used to construct a single molecule device for SQDM. SQDM was used to characterise the potential above a PTCDA/Ag(111) monolayer as well as single and double molecular vacancies. The unit cell of the layer contained two unequal PTCDA molecules, called A and B. Molecule A (B) was aligned (misaligned) with the underlying Ag lattice. The vacancies were similarly defined. An A (B) type vacancy was created by removing molecule A (B) from the layer. Vacancies of the same type (A and AA or B and BB) were shown to behave similarly. Because the molecules in the layer received a charge transfer from the surface, it was expected that the vacancies would become positive relative to the layer. The type B vacancies fulfilled this expectation. However, it was shown that the charge transfer actually increased slightly for type A vacancies. This finding could be explained by spectroscopic analysis of the type A vacancies. The vacancy itself behaved like the backbone of a molecule, and two of the surrounding molecules showed additional charge transfer.
LB  - PUB:(DE-HGF)3 ; PUB:(DE-HGF)11
DO  - DOI:10.34734/FZJ-2026-01796
UR  - https://juser.fz-juelich.de/record/1054356
ER  -