The mechanism of proton transport around the Schiff base in bacteriorhodopsin was investigated by ab initio molecular orbital (MO) calculations. Computations were performed for the case where there is a water molecule between the Schiff base and the Asp residue and for the case where there is no water molecule. Changes in the atomic configuration and potential energy through the proton transport process were compared between two cases. In the absence of water, the protonated Schiff base was not stable, and a proton was spontaneously detached from the Schiff base. On the other hand, a stable structure of the protonated Schiff base was obtained in the presence of water. This suggests that the presence of a water molecule is required for stability in the formation of a protonated Schiff base.

No abstract

No abstract

The mechanism of migration of Al adatoms on H-terminated Si(111) surfaces has been investigated by ab initio calculations using density functional theory. The positions of Al adatoms in the potential energy minima and the energy change along the least potential energy path for Al adatom migration have been obtained. Furthermore, we demonstrate the difference between the migration processes on H-terminated and bare Si surfaces. The activation energy required for Al adatom migration has been estimated to be 1.0 eV on bare Si surfaces, but the energy required is very small (2 meV) for Al adatom migration on H-terminated surfaces. Energetic stabilization originating from Al adsorption on H-terminated surfaces is very slight compared with that originating from Al adsorption on bare Si surfaces. Based on these theoretical results, a micro fabrication technique has been proposed for the production of Al nanostructures on H-terminated Si(111) surfaces by selective growth of Al dots only at bare Si areas.

Ab initio quantum chemical calculations using density functional theory have been performed to investigate the migration process of an Al adatom on the partly H-terminated Si(111) surfaces. The diffusion of an Al adatom from the H-terminated monohydride area to the nonterminated bare Si area has been examined with two types of computational cluster models, both of which consistently indicate similar potential energy changes. It has been revealed that the transfer of a single Al adatom from the H-terminated to the nonterminated area spontaneously proceeds without any activation energy barrier, and results in a very stable adhesion to the Si surface with an energy stabilization by 3.3 eV.