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运用密度泛函理论对 1.9Å 分辨率晶体结构进行评估,模拟光合作用系统 II 水氧化复合物的金属原子位置。

Modelling the metal atom positions of the Photosystem II water oxidising complex: a density functional theory appraisal of the 1.9 Å resolution crystal structure.

机构信息

Research School of Chemistry, College of Science, Australian National University, Canberra ACT 0200, Australia.

出版信息

Phys Chem Chem Phys. 2012 Aug 28;14(32):11333-43. doi: 10.1039/c2cp41020f. Epub 2012 Jul 16.

Abstract

Density functional theory (DFT) calculations are reported for a set of model compounds intended to represent the structure of the Photosystem II (PSII) water oxidising complex (WOC) as determined by the recent 1.9 Å resolution single crystal X-ray diffraction (XRD) study of Umena et al. In contrast with several other theoretical studies addressing this structure, we find that it is not necessary to invoke photoreduction of the crystalline sample below the S(1)'resting state' in order to rationalise the observed WOC geometry. Our results are consistent with crystallised PSII in the S(1) state, with S(1) corresponding to either (Mn(III))(4) or (Mn(III))(2)(Mn(IV))(2) as required by the two competing paradigms for the WOC oxidation state pattern. Of these two paradigms, the 'low-oxidation-state' paradigm provides a better match for the crystal structure, with the comparatively long Mn(2)-Mn(3) distance in particular proving difficult to reconcile with the 'high-oxidation-state' model. Best agreement with the set of metal-metal distances is obtained with a S(1) model featuring μ-O, μ-OH bridging between Mn(3) and Mn(4) and deprotonation of one water ligand on Mn(4). Theoretical modelling of the 1.9 Å structure is an important step in assessing the validity of this recent crystal structure, with implications for our understanding of the mechanism of water oxidation by PSII.

摘要

报道了一组模型化合物的密度泛函理论(DFT)计算结果,这些模型化合物旨在代表最近由 Umena 等人的 1.9 Å 分辨率单晶 X 射线衍射(XRD)研究确定的光系统 II(PSII)水氧化复合物(WOC)的结构。与其他几个针对该结构的理论研究不同,我们发现,为了合理化观察到的 WOC 几何形状,没有必要将结晶样品的光还原到 S(1)'静止状态'以下。我们的结果与处于 S(1)状态的结晶 PSII 一致,S(1)对应于 WOC 氧化态模式的两种竞争范式所要求的(Mn(III))(4)或(Mn(III))(2)(Mn(IV))(2)。在这两种范式中,“低氧化态”范式与晶体结构更为匹配,特别是 Mn(2)-Mn(3)距离较长,与“高氧化态”模型难以协调。与一组金属-金属距离的最佳匹配是具有 S(1)模型,该模型具有 Mn(3)和 Mn(4)之间的μ-O、μ-OH 桥接以及 Mn(4)上一个水配体的去质子化。对 1.9 Å 结构的理论建模是评估最近晶体结构有效性的重要步骤,对我们理解 PSII 水氧化的机制具有重要意义。

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