Simulation and Experiment
Molecular systems present interesting examples of physical processes at the nano-scale. To study these processes, we requires both experimental and theoretical/simulation methods to fully grasp what is going on. In my PhD I have had the opportunity to use an STM/AFM microcscope to directly image a variety of atoms and molecules. I have then utilized a number of theoretical methods, including Monte Carlo simulations and Huckel theory simulations, to simulate the systems I imaged.
C60 - A Molecular Football
Since it's discovery in 1985, C60 has been the subject of much scientific interest. When deposited on a surface and imaged using STM, it is possible to thoroughly investigate it's electronic and physical properties. It is also possible to determine it's orientation on the surface by observing the shape of the molecule. This can be then compared to simulated STM scans to determine what orientation the molecule is in.
Top. Wire frame molecule showing molecular orientation.
Middle. Simulated STM scan via Huckel theory.
Bottom. STM scan of a molecule in that orientation for comparison.
Scanning Probe Microscopy
Scanning Probe Microscopy (SPM) is a technique used to image surface in ultra high resolution. It employs an atomically sharp tip to raster over a surface, by interacting with the surface it can detect changes in topography and electronic structure. An example image of a cluster of C60 molecules is shown. The red circle indicates a single molecule within the island, it is approximately 1nm across.
The image was taken via a Scanning Tunneling Microscop (STM), a class of SPM, and it can investigate the electronic structure of surface elements such as individual molecules.
Monte Carlo and Huckel Theory Simulation
Using Monte Carlo methods to study an assembly of molecules allows us to observe how molecular islands form and order. Here an island of C60 molecules are simulated and visualised as they would be seen in an STM image. The molecules start out orientationally disordered, but then interact with one another and so rotate to an ordered configuration as the simulation progresses. This simulation was written in MATLAB.
Images reproduced from
Jeremy Leaf, Andrew Stannard, Samuel P. Jarvis, Philip Moriarty, and Janette L. Dunn. J. Phys. Chem. C, 2016, 120 (15), pp 8139–8147