Convergence of QM/MM and Cluster Models for the Spectroscopic Properties of the Oxygen-Evolving Complex in Photosystem II

Retegan, Marius; Neese, Frank; Pantazis, Dimitrios A.

doi:10.1021/ct400477j

Cited by 59 publications

(64 citation statements)

References 106 publications

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“…The “open cubane” form of the cluster that corresponds to the multiline S = 1/2 signal of the S 2 state 70 was used as starting point. We employed our previously described QM/MM models of the S 2 state 17 for preliminary screening and set the size of the final QM-only models to sufficiently include all first-sphere hydrogen bonding interactions. The final models consist of 240–242 atoms.…”

Section: Methodsmentioning

confidence: 99%

Interaction of methanol with the oxygen-evolving complex: atomistic models, channel identification, species dependence, and mechanistic implications

Retegan

Pantazis

2016

Chem. Sci.

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Section: Methodsmentioning

confidence: 99%

Interaction of methanol with the oxygen-evolving complex: atomistic models, channel identification, species dependence, and mechanistic implications

Retegan

Pantazis

2016

Chem. Sci.

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“…The subset of the model systems shown in Figure 4 was then reoptimized on the lowest-energy BS surface, corresponding to S = 1 = 2 for core structure I and to S = 5 = 2 for core structure II. Note that we did not use QM/MM modeling for the further protein environment, as our QM models are thought to be sufficiently large [47] for the purpose of the present study.…”

Section: Methodsmentioning

confidence: 99%

On Ammonia Binding to the Oxygen‐Evolving Complex of Photosystem II: A Quantum Chemical Study

Schraut

Kaupp

2014

Chemistry A European J

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A recent EPR study (M. Perrez Navarro et al., Proc. Natl. Acad. Sci. 2013, 110, 15561) provided evidence that ammonia binding to the oxygen-evolving complex (OEC) of photosystem II in its S2 state takes place at a terminal-water binding position (W1) on the "dangler" manganese center MnA. This contradicted earlier interpretations of (14)N electron-spin-echo envelope modulation (ESEEM) and extended X-ray absorption fine-structure (EXAFS) data, which were taken to indicate replacement of a bridging oxo ligand by an NH2 unit. Here we have used systematic broken-symmetry density functional theory calculations on large (ca. 200 atom) model clusters of an extensive variety of substitution patterns and core geometries to examine these contradictory pieces of evidence. Computed relative energies clearly favor the terminal substitution pattern over bridging-ligand arrangements (by about 20-30 kcal mol(-1)) and support W1 as the preferred binding site. Computed (14)N EPR nuclear-quadrupole coupling tensors confirm previous assumptions that the appreciable asymmetry may be accounted for by strong, asymmetric hydrogen bonding to the bound terminal NH3 ligand (mainly by Asp61). Indeed, bridging NH2 substitution would lead to exaggerated asymmetries. Although our computed structures confirm that the reported elongation of an Mn-Mn distance by about 0.15 Å inferred from EXAFS experiments may only be reproduced by bridging NH2 substitution, it seems possible that the underlying EXAFS data were skewed by problems due to radiation damage. Overall, the present data clearly support the suggested terminal NH3 coordination at the W1 site. The finding is significant for the proposed mechanistic scenarios of OEC catalysis, as this is not a water substrate site, and effects of this ammonia binding on catalysis thus must be due to more indirect influences on the likely substrate binding site at the O5 bridging-oxygen position.

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“…The cost of conventional coupled-cluster implementations would be prohibitive for realistic models of the OEC, but modern approaches that exploit the locality of electron correlation, such as the domain-based local pair natural orbital (DLPNO) approximation [174,175], can be employed. Ideally, these methods would be combined with a QM/MM approach [176][177][178][179][180] to minimize the size of the OEC subsystem that has to be treated at the coupled-cluster level. It is likely that only the competent application of high-level wave function methods on carefully constructed computational models can clarify the uncertainties surrounding the computed energetics of redox isomers in the S 3 state.…”

Section: Computed Energetics Of Redox Isomersmentioning

confidence: 99%

The S3 State of the Oxygen-Evolving Complex: Overview of Spectroscopy and XFEL Crystallography with a Critical Evaluation of Early-Onset Models for O–O Bond Formation

Pantazis

2019

Inorganics

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The catalytic cycle of the oxygen-evolving complex (OEC) of photosystem II (PSII) comprises five intermediate states Si (i = 0–4), from the most reduced S0 state to the most oxidized S4, which spontaneously evolves dioxygen. The precise geometric and electronic structure of the Si states, and hence the mechanism of O–O bond formation in the OEC, remain under investigation, particularly for the final steps of the catalytic cycle. Recent advances in protein crystallography based on X-ray free-electron lasers (XFELs) have produced new structural models for the S3 state, which indicate that two of the oxygen atoms of the inorganic Mn4CaO6 core of the OEC are in very close proximity. This has been interpreted as possible evidence for “early-onset” O–O bond formation in the S3 state, as opposed to the more widely accepted view that the O–O bond is formed in the final state of the cycle, S4. Peroxo or superoxo formation in S3 has received partial support from computational studies. Here, a brief overview is provided of spectroscopic information, recent crystallographic results, and computational models for the S3 state. Emphasis is placed on computational S3 models that involve O–O formation, which are discussed with respect to their agreement with structural information, experimental evidence from various spectroscopic studies, and substrate exchange kinetics. Despite seemingly better agreement with some of the available crystallographic interpretations for the S3 state, models that implicate early-onset O–O bond formation are hard to reconcile with the complete line of experimental evidence, especially with X-ray absorption, X-ray emission, and magnetic resonance spectroscopic observations. Specifically with respect to quantum chemical studies, the inconclusive energetics for the possible isoforms of S3 is an acute problem that is probably beyond the capabilities of standard density functional theory.

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Convergence of QM/MM and Cluster Models for the Spectroscopic Properties of the Oxygen-Evolving Complex in Photosystem II

Cited by 59 publications

References 106 publications

Interaction of methanol with the oxygen-evolving complex: atomistic models, channel identification, species dependence, and mechanistic implications

Interaction of methanol with the oxygen-evolving complex: atomistic models, channel identification, species dependence, and mechanistic implications

On Ammonia Binding to the Oxygen‐Evolving Complex of Photosystem II: A Quantum Chemical Study

The S3 State of the Oxygen-Evolving Complex: Overview of Spectroscopy and XFEL Crystallography with a Critical Evaluation of Early-Onset Models for O–O Bond Formation

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