Rationalizing the 1.9 Å Crystal Structure of Photosystem II-A Remarkable Jahn-Teller Balancing Act Induced by a Single Proton Transfer

Orientational Jahn-Teller Isomerism in the Dark-Stable State of Nature's Water Oxidase

The tetramanganese–calcium cluster of the oxygen‐evolving complex of photosystem II adopts electronically and magnetically distinct but interconvertible valence isomeric forms in its first light‐driven oxidized catalytic state, S₂. This bistability is implicated in gating the final catalytic states preceding O−O bond formation, but it is unknown how the biological system enables its emergence and controls its effect. Here we show that the Mn₄CaO₅ cluster in the resting (dark‐stable) S₁ state adopts orientational Jahn–Teller isomeric forms arising from a directional change in electronic configuration of the “dangler” Mn^III ion. The isomers are consistent with available structural data and explain previously unresolved electron paramagnetic resonance spectroscopic observations on the S₁ state. This unique isomerism in the resting state is shown to be the electronic origin of valence isomerism in the S₂ state, establishing a functional role of orientational Jahn–Teller isomerism unprecedented in biological or artificial catalysis.

Rationalizing the Geometries of the Water Oxidising Complex in the Atomic Resolution, Nominal S3 State Crystal Structures of Photosystem II

Three atomic resolution crystal structures of Photosystem II, in the double flashed, nominal S₃ intermediate state of its Mn₄ Ca Water Oxidising Complex (WOC), have now been presented, at 2.25, 2.35 and 2.08 Å resolution. Although very similar overall, the S₃ structures differ within the WOC catalytic site. The 2.25 Å structure contains only one oxy species (O5) in the WOC cavity, weakly associated with Mn centres, similar to that in the earlier 1.95 Å S₁ structure. The 2.35 Å structure shows two such species (O5, O6), with the Mn centres and O5 positioned as in the 2.25 Å structure and O5-O6 separation of ∼1.5 Å. In the latest S₃ variant, two oxy species are also seen (O5, Ox), with the Ox group appearing only in S₃ , closely ligating one Mn, with O5-Ox separation <2.1 Å. The O5 and O6/Ox groups were proposed to be substrate water derived species. Recently, Petrie et al. (Chem. Phys. Chem., 2017) presented large scale Quantum Chemical modelling of the 2.25 Å structure, quantitatively explaining all significant features within the WOC region. This, as in our earlier studies, assumed a 'low' Mn oxidation paradigm (mean S₁ Mn oxidation level of +3.0, Petrie et al., Angew. Chem. Int. Ed., 2015), rather than a 'high' oxidation model (mean S₁ oxidation level of +3.5). In 2018 we showed (Chem. Phys. Chem., 2018) this oxidation state assumption predicted two energetically close S₃ structural forms, one with the metal centres and O5 (as OH^- ) positioned as in the 2.25 Å structure, and the other with the metals similarly placed, but with O5 (as H₂ O) located in the O6 position of the 2.35 Å structure. The 2.35 Å two flashed structure was likely a crystal superposition of two such forms. Here we show, by similar computational analysis, that the latest 2.08 Å S₃ structure is also a likely superposition of forms, but with O5 (as OH^- ) occupying either the O5 or Ox positions in the WOC cavity. This highlights a remarkable structural 'lability' of the WOC centre in the S₃ state, which is likely catalytically relevant to its water splitting function.

Explaining the Different Geometries of the Water Oxidising Complex in the Nominal S3 State Crystal Structures of Photosystem II at 2.25 Å and 2.35 Å

Recently two atomic resolution crystal structures of Photosystem II, in the double flashed, nominal S3 intermediate state of its Mn4 Ca water oxidising complex (WOC), have been presented (Young et al., Nature 2016, 540, 453; Suga et al., Nature 2017, 543, 131). These structures are at 2.25 Å and 2.35 Å resolution, respectively. Although highly similar in most respects, the structures differ in a key region within the WOC catalytic site. In the 2.25 Å structure, one oxy species (O5) is observed within the WOC cavity, weakly associated with the Mn centres, similar to that seen earlier in the 1.95 Å XRD structure of the S1 intermediate (Suga et al., Nature, 2015, 517, 99). In the 2.35 Å structure, two such species are seen (O5, O6), with the Mn centres and O5 positioned as in the 2.25 Å structure and an O5-O6 separation of ∼1.5 Å, consistent with peroxo formation. This suggests O5 and O6 are substrate water derived species in this double flashed form. Recently we have presented (Petrie, et al., Chem. Phys. Chem., 2017) a large scale (220 atom) quantum chemical model of the Young et al. 2.25 Å structure, which quantitatively explains all significant features within the WOC region of that structure, particularly the positions of the metal centres and O5 group. Critical to this was our assumption of a 'low' Mn oxidation paradigm (mean S1 Mn oxidation level of +3.0, Petrie et al., Angew. Chem. Int. Ed., 2015), rather than a 'high' oxidation model (mean S1 oxidation level of +3.5), widely assumed in the literature. Here we show that our same oxidation state model predicts two classes of energetically close S3 structural forms, analogous to the S1 state, one with the metal centres and O5 positioned as in the 2.25 Å structure, and the other with the metals similarly placed, but with O5 located in the O6 position of the 2.35 Å structure. We show that the Suga et al. 2.35 Å structure is likely a superposition of two such forms, one from each class, which is consistent with reported atomic occupancies for that structure and the relative total energies we calculate for the two structural forms.

Understanding Two Different Structures in the Dark Stable State of the Oxygen-Evolving Complex of Photosystem II: Applicability of the Jahn-Teller Deformation Formula

Tanaka et al. (J. Am. Chem. Soc., 2017, 139, 1718) recently reported the three-dimensional (3D) structure of the oxygen evolving complex (OEC) of photosystem II (PSII) by X-ray diffraction (XRD) using extremely low X-ray doses of 0.03 and 0.12 MGy. They observed two different 3D structures of the CaMn4O5 cluster with different hydrogen-bonding interactions in the S1 state of OEC keeping the surrounding polypeptide frameworks of PSII the same. Our Jahn-Teller (JT) deformation formula based on large-scale quantum mechanics/molecular mechanics (QM/MM) was applied for these low-dose XRD structures, elucidating important roles of JT effects of the MnIII ion for subtle geometric distortions of the CaMn4O5 cluster in OEC of PSII. The JT deformation formula revealed the similarity between the low-dose XRD and damage-free serial femtosecond X-ray diffraction (SFX) structures of the CaMn4O5 cluster in the dark stable state. The extremely low-dose XRD structures were not damaged by X-ray irradiation. Implications of the present results are discussed in relation to recent SFX results and a blue print for the design of artificial photocatalysts for water oxidation.

Deprotonation of Water/Hydroxo Ligands in Clusters Mimicking the Water Oxidizing Complex of PSII and Its Effect on the Vibrational Frequencies of Ligated Carboxylate Groups

The IR absorptions of several first-shell carboxylate ligands of the water oxidizing complex (WOC) have been experimentally shown to be unaffected by oxidation state changes in the WOC during its catalytic cycle. Several model clusters that mimic the Mn4O5Ca core of the WOC in the S1 state, with electronic configurations that correspond to both the so-called "high" and "low" oxidation paradigms, were investigated. Deprotonation at W2, W1, or O3 sites was found to strongly reduce carboxylate ligand frequency shifts on oxidation of the metal cluster. The frequency shifts were smallest in neutrally charged clusters where the initial mean Mn oxidation state was +3, with W2 as an hydroxide and O5 a water. Deprotonation also reduced and balanced the oxidation energy of all clusters in successive oxidations.

Resolving the Differences Between the 1.9 Å and 1.95 Å Crystal Structures of Photosystem II: A Single Proton Relocation Defines Two Tautomeric Forms of the Water-Oxidizing Complex

Great progress has been made in characterizing the water-oxidizing complex (WOC) in photosystem II (PSII) with the publication of a 1.9 Å resolution X-ray diffraction (XRD) and recently a 1.95 Å X-ray free-electron laser (XFEL) structure. However, these achievements are under threat because of perceived conflicts with other experimental data. For the earlier 1.9 Å structure, lack of agreement with extended X-ray absorption fine structure (EXAFS) data led to the notion that the WOC suffered from X-ray photoreduction. In the recent 1.95 Å structure, Mn photoreduction is not an issue, but poor agreement with computational models which adopt the 'high' oxidation state paradigm, has again resulted in criticism of the structure on the basis of contamination with lower S states of the WOC. Here we use DFT modeling to show that the distinct WOC geometries in the 1.9 and 1.95 Å structures can be straightforwardly accounted for when the Mn oxidation states are consistent with the 'low' oxidation state paradigm. Remarkably, our calculations show that the two structures are tautomers, related by a single proton relocation.

The protonation states of oxo-bridged Mn(IV) dimers resolved by experimental and computational Mn K pre-edge X-ray absorption spectroscopy

In nature, the protonation of oxo bridges is a commonly encountered mechanism for fine-tuning chemical properties and reaction pathways. Often, however, the protonation states are difficult to establish experimentally. This is of particular importance in the oxygen evolving complex of photosystem II, where identification of the bridging oxo protonation states is one of the essential requirements toward unraveling the mechanism. In order to establish a combined experimental and theoretical protocol for the determination of protonation states, we have systematically investigated a series of Mn model complexes by Mn K pre-edge X-ray absorption spectroscopy. An ideal test case for selective bis-μ-oxo-bridge protonation in a Mn dimer is represented by the system [Mn(IV)2(salpn)2(μ-OHn)2](n+). Although the three species [Mn(IV)2(salpn)2(μ-O)2], [Mn(IV)2(salpn)2(μ-O)(μ-OH)](+) and [Mn(IV)2(salpn)2(μ-OH)2](2+) differ only in the protonation of the oxo bridges, they exhibit distinct differences in the pre-edge region while maintaining the same edge energy. The experimental spectra are correlated in detail to theoretically calculated spectra. A time-dependent density functional theory approach for calculating the pre-edge spectra of molecules with multiple metal centers is presented, using both high spin (HS) and broken symmetry (BS) electronic structure solutions. The most intense pre-edge transitions correspond to an excitation of the Mn 1s core electrons into the unoccupied orbitals of local e(g) character (d(z)(2) and d(xy) based in the chosen coordinate system). The lowest energy experimental feature is dominated by excitations of 1s-α electrons, and the second observed feature is primarily attributed to 1s-β electron excitations. The observed energetic separation is due to spin polarization effects in spin-unrestricted density functional theory and models final state multiplet effects. The effects of spin polarization on the calculated Mn K pre-edge spectra, in both the HS and BS solutions, are discussed in terms of the strength of the antiferromagnetic coupling and associated changes in the covalency of Mn-O bonds. The information presented in this paper is complemented with the X-ray emission spectra of the same compounds published in an accompanying paper. Taken together, the two studies provide the foundation for a better understanding of the X-ray spectroscopic data of the oxygen evolving complex (OEC) in photosystem II.

Experimental and computational X-ray emission spectroscopy as a direct probe of protonation states in oxo-bridged Mn(IV) dimers relevant to redox-active metalloproteins

The protonation state of oxo bridges in nature is of profound importance for a variety of enzymes, including the Mn4CaO5 cluster of photosystem II and the Mn2O2 cluster in Mn catalase. A set of dinuclear bis-μ-oxo-bridged Mn(IV) complexes in different protonation states was studied by Kβ emission spectroscopy to form the foundation for unraveling the protonation states in the native complex. The valence-to-core regions (valence-to-core XES) of the spectra show significant changes in intensity and peak position upon protonation. DFT calculations were performed to simulate the valence-to-core XES spectra and to assign the spectral features to specific transitions. The Kβ(2,5) peaks arise primarily from the ligand 2p to Mn 1s transitions, with a characteristic low energy shoulder appearing upon oxo-bridge protonation. The satellite Kβ" peak provides a more direct signature of the protonation state change, since the transitions originating from the 2s orbitals of protonated and unprotonated μ-oxo bridges dominate this spectral region. The energies of the Kβ" features differ by ~3 eV and thus are well resolved in the experimental spectra. Additionally, our work explores the chemical resolution limits of the method, namely, whether a mixed (μ-O)(μ-OH2) motif can be distinguished from a symmetric (μ-OH)2 one. The results reported here highlight the sensitivity of Kβ valence-to-core XES to single protonation state changes of bridging ligands, and form the basis for further studies of oxo-bridged polymetallic complexes and metalloenzyme active sites. In a complementary paper, the results from X-ray absorption spectroscopy of the same Mn(IV) dimer series are discussed.