Control of 2-Dimensional Molecular Self-Organisation: Towards Designed Surfaces

Lead Research Organisation: King's College London
Department Name: Physics


Organic molecular monolayers at surfaces often constitute the central working component in nanotechnologies such as sensors, molecular electronics, smart coatings, organic solar cells, catalysts, medical devices, etc. A central challenge in the field is to achieve controlled creation of desired 2D molecular architectures at surfaces. Within this context, the past decade has witnessed a real and significant step-change in the 'bottom-up' self-organisation of 2D molecular assemblies at surfaces. The enormous variety and abundance of molecular structures formed via self-oeganisation has now critically tipped the argument strongly in favour of a 'bottom-up' construction strategy, which harnesses two powerful attributes of nanometer-precision (inaccessible to top-down methods) and highly parallel fabrication (impossible with atomic/molecular manipulation). Thus, bottom-up molecular assembly at surfaces holds the real possibility of becoming a dominating synthesis protocol in 21st century nanotechnologies

Uniquely, the scope and versatility of these molecular architectures at 2D surfaces have been directly captured at the nanoscale via imaging with scanning probe microscopies and advanced surface spectroscopies. At present, however, the field is largely restricted to a 'make and see' approach and there is scarce understanding of any of the parameters that ultimately control molecular surface assembly. For example: (1) molecular assemblies at surfaces show highly polymorphic behaviour, and a priori control of assembly is practically non-existent; (2) little is understood of the influence and balance of the many interactions that drive molecular recognition and assembly (molecule-molecule interactions including dispersion, directional H-bonding and strong electrostatic and covalent interactions); (3) the role of surface-molecule interactions is largely uncharted even though they play a significant role in the diffusion of molecules and their subsequent assembly; (4), there is ample evidence that the kinetics of self-assembly is the major factor in determining the final structure, often driving polymorphic behaviour and leading to widely varied outcomes, depending on the conditions of formation; (5) a gamut of additional surface phenomena also also influence assembly e.g. chemical reactions between molecules, thermally activated internal degrees of freedom of molecules, surface reconstructions and co-assembly via coordinating surface atoms.

The main objective of this project is to advance from experimental phenomena-reporting to knowledge-based design, and its central goal is to identify the role played by thermodynamic, entropic, kinetic and chemical factors in dictating molecular organisation at surfaces under given experimental conditions. To address this challenge requires a two-pronged approach in which ambitious and comprehensive theory development is undertaken alongside powerful imaging and spectroscopic tools applied to the same systems. This synergy of experiment and theory is absolutely essential to develop a fundamental understanding, which would enable a roadmap for controlled and engineered self-assembly at surfaces to be proposed that would, ultimately, allow one to 'dial up' a required structure at will. Four important and qualitatively different classes of assembly at surfaces will be studied: Molecular Self-Assembly; Hierarchical Self-Assembly; Metal-Organic Self Assembly; and, on-surface Covalent Assembly.


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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.
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