A scanning tunneling microscopy and density-functional theory investigation of electrocyclic reactions on the silicon(100)-2x1 surface

Scanning Tunneling Microscopy (STM) and Density-Functional Theory (DFT) were used to study cycloaddition reactions of small organics on the Si(100)-2x1 surface, in particular the reaction of 1,3-cyclohexadiene (1,3-CHD). Several different reaction products of 1,3-CHD were observed on the surface by STM, including two theoretically predicted conformers of the [2+2] intradimer product and two previously unreported interdimer [4+2] products. Full DFT geometry optimized calculations were performed for all observed products. This provided relative energies and structural information and allowed an in depth analysis of the mechanism and product distribution. The kinetic product was identified from the STM product distribution, while the thermodynamic product was identified by DFT calculation. Based on a comparison of these two products, a plausible two-step, kinetically controlled, radical reaction mechanism was proposed. Further DFT calculations of the tip—molecule—surface system were used to simulate STM images of 1,3-CHD on the surface. These studies showed the emergence of conduction channels within the STM tunneling energy window due to a mixing of tip and molecule states, and which in turn is responsible for the contrast in STM images. Additional STM investigation of the reaction of 2,3-dimethyl-1,3-butadiene and 2,3-dimethoxy-1,3-butadiene with Si(100), showed a number of reaction products on the surface and the striking differences in cycloaddition reactions involving cyclic and chainlike reactants.