Adsorption geometry and reaction mechanism of bio/organic molecules on Ge(100)

Abstract

My main research interest for my graduated studies was to develop new ways to control the attachment of organic molecules on the semiconductor surfaces and to understand their interfacial architecture at the atomic level. For my Ph. D thesis work, I have interested the adsorption structure and mechanism of simple gas phase molecules: $H_2$, liquid phase molecules: pyrimidine $(C_4H_4N_2)$, water $(H_2O)$, thiophene $(C_4H_4S)$ and the complex solid phase molecules: purine $(C_5H_4N_4)$, histidine $(C_6H_9N_3O_2)$. The thesis consists of five chapters. Summaries of each chapters are as follows. Study of the adsorption and decomposition of $H_2O$ on Ge(100) The adsorption and decomposition of water on Ge(100) have been investigated using real-time scanning tunneling microscopy (STM) and density-functional theory (DFT) calculations. The STM results revealed two distinct adsorption features of $H_2O$ on Ge(100) corresponding to molecular adsorption and H-OH dissociative adsorption. In the molecular adsorption geometry, $H_2O$ molecules are bound to the surface via Ge-O dative bonds between the O atom of $H_2O$ and the electrophillic down atom of the Ge dimer. In the dissociative adsorption geometry, the $H_2O$ molecule dissociates into H and OH, which bind covalently to a Ge-Ge dimer on Ge(100) in a H-Ge-Ge-OH configuration. The DFT calculations showed that the dissociative adsorption geometry is more stable than the molecular adsorption geometry. This finding is consistent with the STM results, which showed that the dissociative product becomes dominant as the $H_2O$ coverage is increased. The simulated STM images agreed very well with the experimental images. In the real-time STM experiments, we also observed a structural transformation of the $H_2O$ molecule from the molecular adsorption to the dissociative adsorption geometry. Cyclo-addition reaction of Lewis acidic molecule: $AlCl_3$ The adsorption and decomposition of $AlCl_3$ on Ge(100) was studied u...