Control of 2-Dimensional Molecular Self-Organisation: Towards Designed Surfaces
Lead Research Organisation:
King's College London
Department Name: Physics
Abstract
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Publications
Abbasi-Pérez D
(2019)
Controlling the preferential motion of chiral molecular walkers on a surface.
in Chemical science
Darling GR
(2017)
Chiral segregation driven by a dynamical response of the adsorption footprint to the local adsorption environment: bitartrate on Cu(110).
in Physical chemistry chemical physics : PCCP
Floris A
(2016)
Driving Forces for Covalent Assembly of Porphyrins by Selective C-H Bond Activation and Intermolecular Coupling on a Copper Surface.
in Journal of the American Chemical Society
Guo C
(2017)
Mechanisms of Covalent Dimerization on a Bulk Insulating Surface
in The Journal of Physical Chemistry C
Haq S
(2015)
A small molecule walks along a surface between porphyrin fences that are assembled in situ.
in Angewandte Chemie (International ed. in English)
Li J
(2017)
Ethylene Dissociation on Ni 3 Al(111)
in The Journal of Physical Chemistry C
Sang H
(2019)
Externally driven molecular ratchets on a periodic potential surface: a rate equations approach.
in Physical chemistry chemical physics : PCCP
Zhao Z
(2020)
Kinetics of Growth of a Covalent Assembly of Porphyrin Molecules on a Copper Surface
in The Journal of Physical Chemistry C
| Description | Two projects have been finished and the corresponding manuscripts published in high-impact journals: (1) walking molecules (published in Angewante Chemie Int. Ed.): we studied theoretically adsorption geometries and dynamics of molecules on a copper surface. We find that the molecules stand on two legs; next we find, quite surprisingly, that the molecules diffuse on this surface in one direction only by stepping with its legs or pivoting; this depends on the initial geometry, whether it is parallel or perpendicular to the copper rows forming the surface. These results explained experimental finding of our Liverpool partners concerning the observed tracks the molecules make during their diffusion. It was possible to find similar mechanisms in nature to the way the molecule moves: inchworm or penguin. (ii) covalent self-assembly (published in JACS): we studied theoretically assembly of porphyrin based molecules on the same surface; experimentally it is known what is the STM image of a single molecule and also that after annealing the molecules form strong bonds with each other building 1D and 2D structures. Our simulations established the mechanism of such assembly: upon annealing molecules loose their H atoms at the particular positions and then diffuse towards each other fusing together and forming covalent bonds with each other. Four such positions exist for each molecule providing possibility for both 1D and 2D assemblies. Dr. Andrea Floris has been working on another project, also supported by experiments at Liverpool: covalent assembly of two other porphyrin based molecules. Dr Floris currently has a lecturer position at Lincoln and continues working on this. We have also been collaborating with a group in Wuhan (China) on two projects: (i) a mechanism of covalent assembly of 4-iodobenzoic acid (IBA) organic molecules on a calcite surface (currently under review in JACS) in which we report an unusual mechanism of dimer formation via two de-halogination reactions catalysed by the surface, and (ii) ethylene decomposition on Ni3Al(111) surface during early stages of graphene growth (currently under review in JPCC), where we propose a detailed mechanism of ethylene de-hydrogenation on this surface whereby a 2D gas of carbon dimers is formed prior to nucleation and graphene growth. We have also started working on a project related to achieving asymmetric diffusion of walking molecules on a metal surface (with Dr David Abbasi). In this work we considered a chiral molecular walker, the 1,3-bis(imidazol-1-ylmethyl)-5(1-phenylethyl)benzene, diffusing on the anisotropic Cu(110) surface along the Cu rows. As unveiled by our kinetic Monte Carlo simulations based on the rates calculated using ab initio density functional theory, that molecule moves to the nearest equivalent lattice site via the so-called inchworm mechanism in which it steps first with the rear and then with the front foot. As a result, these molecules diffuse via a two-step mechanism, and due to their inherent asymmetry, the corresponding PES is also spatially asymmetric. Taking advantage of this fact, we show how the a time-periodic external field can be tuned to separate molecules of different chirality, orientation and conformation. The consequences of these findings for molecular machines and the separation of enantiomers are also discussed. A paper has been submitted. Another paper is under preparation in which an analytical model has been developed to study this kind of molecular ratchet. New results (added on 06.03.2021): the covalent self-assembly story (see above) has been continued: I devised a 4th year project for a 4th year student at KCL (Mr Zelong Zhao) to perform kinetic Monte Carlo simulations of the covalent assembly of porphyrins on the copper surface based on the mechanism we developed during this EPSRC award (the one that was published in JACS). The method enables one to perform simulations that would reproduce in real time the processes under study - the growth of a molecular based assembly in our case. This work was extremely successful and was recently published in J. Phys. Chem. C. Basically, it has confirmed that our mechanism does indeed lead - via the kinetic steps proposed in JACS - to the growth of an assembly. In addition to this, a new collaboration with Profs R. Raval and D. Amabilino has been initiated as a continuation of our joint work on molecular walkers that started during this award . This time our experimental partners have been looking at the same molecule BIPEB that we investigated (with Dr David Abbasi) during our asymmetric walk work described above, but using a simplified fences structure formed by adsorbed oxygens. The molecule can form a number of configurations on the surface and fences get the molecules trapped and hence available for a more detailed investigation with scanning tunneling microscopy (STM). In my group simulations of the STM images of the molecule in different configurations on the copper surface have so far been done. The collaborative work is in progress. The main idea is to understand the movement of this molecule on the surface, specifically, how it can change its configurations in time. These transitions have been explored in our ratchet paper, and the experimentalists became really interested in exploring this further at the experimental level. |
| Exploitation Route | Our findings could be utilised by the academic community working in nanotechnology and surface assembly. We also hope that our new results on asymmetric walkers - still to be finalised and published - could be useful for building new structures in nanotechnology. |
| Sectors | Chemicals,Electronics,Energy,Environment,Pharmaceuticals and Medical Biotechnology |
| Description | We cannot directly utilise our findings so far, however, eventually they may find applications in various areas related to nanotechnology and new materials. Our work on "walking molecules" enables understanding of how biological molecules walk; this knowledge can be utilised in building biological machines. Our work on covalent self-assembly provides a fundamental understanding of processes involved in creating this robust assemblies on metal surfaces and of difficulties involved in growing them. |
| First Year Of Impact | 2016 |
| Sector | Education,Electronics,Energy,Environment |
| Description | Liverpool |
| Organisation | University of Liverpool |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | we have developed a theory for the experiments performed by our partners. |
| Collaborator Contribution | Experimental results were provided to us, we have used them to understand the physics and chemistry by means of theoretical simulations. |
| Impact | Two papers are ready for submission. It is multidisciplinary: we use physics methods, our partners use physics, nanotechnology and surface chemistry methods. |
| Start Year | 2013 |
| Description | Nottingham |
| Organisation | University of Nottingham |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | our theory provides an input to experiments performed by this partner |
| Collaborator Contribution | experimental results from the partner serve as the basis for our theory |
| Impact | Two papers are ready for submission. The partner uses chemistry synthesis methods, we use physics methods. |
| Start Year | 2014 |
| Description | Wuhan University, Prof Yu Wang |
| Organisation | Wuhan University |
| Department | Department of Physics |
| Country | China |
| Sector | Academic/University |
| PI Contribution | we trained two master students to work in computational material science |
| Collaborator Contribution | Two master students worked on two projects relevant for our research |
| Impact | two papers have been submitted in these projects: one in JACS and another in JPCC |
| Start Year | 2015 |
| Description | Andrea CP2K |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other academic audiences (collaborators, peers etc.) |
| Results and Impact | Questions were asked after the talk. |
| Year(s) Of Engagement Activity | 2014 |
| URL | https://www.epcc.ed.ac.uk/content/cp2k-uk-workshop-2014 |