Molecular Mechanisms of Proton-coupled Electron Transfer and Water Oxidation in Photosystem II by Shin Nakamura

Author:Shin Nakamura
Language: eng
Format: epub
ISBN: 9789811515842
Publisher: Springer Singapore

(2)The adopted QM regions used for geometry optimization studies were different. In the current study, all main chain amides and the amino acid residues interacting with water network (i.e., W1 through to W9) were included in the QM region, whereas the main chain of D1-Phe182, which interacted with W6 was not included Yang’s study. The absence of an amide directly interacting with a water molecule could influence hydrogen bond interactions within the water network.

(3)The region for the normal mode calculation were different. Yang et al. [26] abstracted a narrow part of QM region to perform normal mode analysis, thereby excluding the Cl− ion and most of the amino acids that directly interacted with the water network. In contrast, the current study included the Cl− ion and all the amino acids and the main chain amides that interacted with water in the QM region. Indeed, when we performed the normal mode analysis using an abstracted narrow part of our QM region in an effort to replicate Yang’s work, the calculated OH frequencies obtained had changed significantly when compared to the original series (Table 4.1). However, these calculated frequencies did not reproduce Yang’s; hence, it can be concluded that even though a sufficiently large QM region was crucial for normal mode analysis to obtain accurate vibrational modes and frequencies, the exact reasons for the disagreement between the two studies remain unknown.

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