Theoretical predictions of enforced structural changes in molecules

Abstract

A very simple quantum chemical model is proposed to simulate the effect of external forces acting on a single molecule. It involves optimising the geometry of a molecule with an external force applied to selected nuclei. This approach is used to investigate conformational transitions of the pyranose ring, which have been the subject of several atomic force microscopy (AFM) experiments, and to generate a number of previously unknown isomers of azobenzene.

Keywords:

• external forces
• geometry optimisation
• AFM modelling

Notes

Note

The model proposed here is very simple and clearly does not fully reflect the physics involved in a real experiment, i.e. the actual interaction between a probe tip and a tethered molecule, which must involve the electron density. We have recently developed a more physical, revised model which maintains the relative simplicity of this model but also affects the electrons. Results with our revised model reproduce those presented here but at significantly lower applied external forces which agree far better with forces found in actual AFM experiments. Our revised model will be presented in a later paper.