We used density functional theory with a hybrid functional to investigate the structure and properties of [4H]Si (hydrogarnet) defects in α-quartz as well as the reactions of these defects with electron holes and extra hydrogen atoms and ions. The results demonstrate the depassivation mechanisms of hydrogen-passivated silicon vacancies in α-quartz, providing a detailed understanding of their stability, electronic properties, and behaviour in different charge states. While fully hydrogen passivated silicon vacancies are electrically inert, the partial removal of hydrogen atoms activates these defects as hole traps, altering the defect states and influencing the electronic properties of the material. Our calculations of the hydrogen migration mechanisms predict the low energy barriers for H+, H0, and H-, with the lowest barrier of 0.28 eV for neutral hydrogen migration between parallel c-channels and a similar barrier for H+ migration along the c-channels. The reactions of electron holes and hydrogen species with [4H]Si defects lead to the breaking of O-H bonds and the formation of non-bridging oxygen hole centres (NBOHCs) within the Si vacancies. The calculated optical absorption energies of these centres are close to those attributed to individual NBOHCs in glass samples. These findings can be useful for understanding the role of [4H]Si defects in bulk and nanocrystalline quartz as well as in SiO2-based electronic devices.
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