High-resolution Mn EXAFS of the oxygen-evolving complex in photosystem II: structural implications for the Mn4Ca cluster

The biological generation of oxygen by the oxygen-evolving complex in photosystem II (PS II) is one of nature's most important reactions. The recent X-ray crystal structures, while limited by resolutions of 3.2-3.5 A, have located the electron density associated with the Mn4Ca cluster within the multiprotein PS II complex. Detailed structures critically depend on input from spectroscopic techniques, such as EXAFS and EPR/ENDOR, as the XRD resolution does not allow for accurate determination of the position of Mn/Ca or the bridging and terminal ligand atoms. The number and distances of Mn-Mn/Ca/ligand interactions determined from EXAFS provide important constraints for the structure of the Mn4Ca cluster. Here, we present data from a high-resolution EXAFS method using a novel multicrystal monochromator that show three short Mn-Mn distances between 2.7 and 2.8 A and, hence, the presence of three di-mu-oxo-bridged units in the Mn4Ca cluster. This result imposes clear limitations on the proposed structures based on spectroscopic and diffraction data and provides input for refining such structures.     

Syntheses, structure, and properties of a manganese-calcium cluster containing a Mn4Ca2 core

We describe here a novel, simple, efficient self-assembly method for the in situ generation of [Mn4Cl4(micro-OCH2CH2OMe)4(EtOH)4] and [Mn4(micro-Cl)Cl3(micro-OCH2CH2OMe)4(HOCH2CH2OMe)3]2 cubane-type compounds which react readily with calcium species to form cluster [Mn4Ca2Cl4(micro-OCH2CH2OMe)8], the calcium atoms attached to the Mn4 unit of flatten out the cubane inducing significant conformational changes.     

The interaction of His337 with the Mn4Ca cluster of photosystem II

The most recent XRD studies of Photosystem II (PS II) reveal that the His337 residue is sufficiently close to the Mn(4)Ca core of the Water Oxidising Complex (WOC) to engage in H-bonding interactions with the μ(3)-oxo bridge connecting Mn(1), Mn(2) and Mn(3). Such interactions may account for the lengthening of the Mn-Mn distances observed in the most recent and highest resolution (1.9 ?) crystal structure of PS II compared to earlier, lower-resolution (2.9 ? or greater) XRD structures and EXAFS studies on functional PS II. Density functional theory is used to examine the influence on Mn-Mn distances of H-bonding interactions, mediated by the proximate His337 residue, which may lead to either partial or complete protonation of the μ(3)-oxo bridge on models of the WOC. Calculations were performed on a set of minimal-complexity models (in which WOC-ligating amino acid residues are represented as formate and imidazole ligands), and also on extended models in which a 13-peptide sequence (from His332 to Ala344) is treated explicitly. These calculations demonstrate that while the 2.9 ? structure is best described by models in which the μ(3)-oxo bridge is neither protonated nor involved in significant H-bonding, the 1.9 ? XRD structure is better reproduced by models in which the μ(3)-oxo bridge undergoes H-bonding interactions with the His337 residue leading to expansion of the 'close' Mn-Mn distances well known from EXAFS studies at ～ 2.7 ?. Furthermore, full μ(3)-oxo-bridge protonation remains a distinct possibility during the process of water oxidation, as evidenced by the lengthening of the Mn-Mn vectors observed in EXAFS studies of the higher oxidation states of PS II. In this context, the Mn-Mn distances calculated in the protonated μ(3)-oxo bridge structures, particularly for the peptide extended models, are in close agreement with the EXAFS data.     

Probing the local structure of liquid water by X-ray absorption spectroscopy

It was recently suggested that liquid water primarily comprises hydrogen-bonded rings and chains, as opposed to the traditionally accepted locally tetrahedral structure (Wernet et al. Science 2004, 304, 995). This controversial conclusion was primarily based on comparison between experimental and calculated X-ray absorption spectra (XAS) using computer-generated ice-like 11-molecule clusters. Here we present calculations which conclusively show that when hydrogen-bonding configurations are chosen randomly, the calculated XAS does not reproduce the experimental XAS regardless of the bonding model employed (i.e., rings and chains vs tetrahedral). Furthermore, we also present an analysis of a recently introduced asymmetric water potential (Soper, A. K. J. Phys.: Condens. Matter 2005, 17, S3273), which is representative of the rings and chains structure, and make comparisons with the standard SPC/E potential, which represents the locally tetrahedral structure. We find that the calculated XAS from both potentials is inconsistent with the experimental XAS. However, we also show the calculated electric field distribution from the rings and chains structure is strongly bimodal and highly inconsistent with the experimental Raman spectrum, thus casting serious doubt on the validity of the rings and chains model for liquid water.     

Hydration preferences for Mn4Ca cluster models of photosystem II: location of potential substrate-water binding sites

Density functional theory calculations are reported on a set of three model structures of the Mn₄Ca cluster in the water‐oxidizing complex of Photosystem II (PSII), which share the structural formula [CaMn₄C₉H₁₀N₂O₁₆]^q+ ? (H₂O)_n (q=?1, 0, 1, 2, 3; n=0–7). In these calculations we have explored the preferred hydration sites of the Mn₄Ca cluster across five overall oxidation states (S₀ to S₄) and all feasible magnetic‐coupling arrangements to identify the most likely substrate–water binding sites. We have also explored charge‐compensated structures in which the overall charge on the cluster is maintained at q=0 or +1, which is consistent with the experimental data on sequential proton loss in the real system. The three model structures have skeletal arrangements that are strongly reminiscent, in their relative metal‐atom positions, of the 2.9‐, 3.7‐, and 3.5 Å‐resolution crystal structures, respectively, whereas the charge states encompassed in our study correspond to an assignment of (Mn^III)₃Mn^II for S₀ and up to (Mn^IV)₃Mn^III for S₄. The three models differ principally in terms of the spatial relationship between one Mn (Mn(4)) and a generally robust Mn₃Ca tetrahedron that contains Mn(1), Mn(2), and Mn(3). Oxidation‐state distributions across the four manganese atoms, in most of the explored charge states, are dependent on details of the cluster geometry, on the extent of assumed hydration of the clusters, and in some instances on the imposed magnetic‐coupling between adjacent Mn atoms. The strongest water‐binding sites are generally those on Mn(4) and Ca. However, one structure type displays a high‐affinity binding site between Ca and Mn(3), the S‐state‐dependent binding‐energy pattern of which is most consistent with the substrate water‐exchange kinetics observed in functional PSII. This structure type also permits another water molecule to access the cluster in a manner consistent with the substrate–water interaction with the Mn cluster, seen in electron spin‐echo envelope modulation (ESEEM) studies of the functional enzyme in the S₀ and S₂ states. It also rationalizes the significant differences in hydrogen‐bonding interactions of the substrate water observed in the FTIR measurements of the S₁ and S₂ states. We suggest that these two water‐binding sites, which are molecularly close, model the actual substrate‐binding sites in the enzyme.     

Structural coupling of an arginine side chain with the oxygen-evolving Mn4Ca cluster in photosystem II as revealed by isotope-edited Fourier transform infrared spectroscopy

Photosynthetic oxygen evolution by plants, algae, and cyanobacteria is performed at the Mn(4)Ca cluster in photosystem II (PSII) by light-driven water oxidation. It has been proposed that CP43-Arg357, which is located in the vicinity of the Mn(4)Ca cluster, plays a key role in the O(2) evolution mechanism; however, direct evidence for its involvement in the reaction has not yet been obtained. In this study, we have for the first time detected the structural coupling of CP43-Arg357 with the Mn(4)Ca cluster by means of isotope-edited Fourier transform infrared (FTIR) spectroscopy. Light-induced FTIR difference spectra upon the S(1)→S(2) transition (S(2)/S(1) difference spectra) of the Mn(4)Ca cluster were measured using isolated PSII core complexes from Synechocystis sp. PCC 6803 cells, where the Arg side chains were labeled with either [η(1,2)-(15)N(2)]Arg or [ζ-(13)C]Arg. Bands due to Arg side chain vibrations, which were extracted by taking a double difference between the S(2)/S(1) spectra of isotope-labeled and unlabeled samples, were found at 1700-1600 and 1700-1550 cm(-1) for [η(1,2)-(15)N(2)]Arg- and [ζ-(13)C]Arg-labeled PSII, respectively. These frequency regions are in good agreement with those of the CN/NH(2) vibrations of a guanidinium group in difference spectra between isotope-labeled and unlabeled Arg in aqueous solutions. The detected Arg bands in the S(2)/S(1) difference spectra were attributed to CP43-Arg357, which is the only Arg residue located near the Mn(4)Ca cluster. The presence of relatively high frequency bands arising from unlabeled Arg suggested that the guanidinium N(η)H(2) is engaged in strong hydrogen bonding. These results indicate that CP43-Arg357 interacts with the Mn(4)Ca cluster probably through direct hydrogen bonding to a first coordination shell ligand of a redox-active Mn ion. This structural coupling of CP43-Arg357 may play a crucial role in the water oxidation reactions.     

Diverse polyanions based on MnBi4 and MnSb4 tetrahedra: polymorphism, structure, and bonding in Ca21Mn4Bi18 and Ca21Mn4Sb18

New transition-metal-containing Zintl phases, Ca21Mn4Bi18 and Ca21Mn4Sb18, have been synthesized by high-temperature reactions, and their structures have been determined by single-crystal X-ray diffraction. Ca21Mn4Bi18 crystallizes in the monoclinic space group C2/c (No. 15, Z = 4) with a = 17.470(2) A, b = 17.392(2) A, c = 17.208(2) A, beta = 93.253(2) degrees (R1 = 0.0405, wR2 = 0.0840) and is isostructural with the recently reported Ca21Mn4Sb18. The compound with the same formula, which is also reported herein, is in turn a new polymorph of Ca21Mn4Sb18 and crystallizes in the monoclinic space group C2/m (No. 12, Z = 4) with a = 17.415(6) A, b = 16.567(6) A, c = 17.047(6) A, beta = 92.068(4) degrees (R1 = 0.0432, wR2 = 0.0788). This new polymorph of Ca21Mn4Sb18 is isostructural with another related compound, Sr21Mn4Sb18. Despite the similarity in their chemical formulas, the structures of Ca21Mn4Bi18 and Ca21Mn4Sb18 are very different: Ca21Mn4Bi18 contains unique [Mn4Bi10] cluster anions made up of four MnBi4 tetrahedra connected through edge-sharing. The structure of Ca21Mn4Sb18 features edge- and corner-shared MnSb4 tetrahedra, which make [Mn4Sb11] tetramers. The latter are linked to each other through external Sb-Sb bonds to form larger isolated [Mn8Sb22] polyanions. Electronic band structure calculations performed using the TB-LMTO-ASA method show a small band gap at the Fermi level, suggesting narrow-gap semiconducting behavior for both compounds.     

Characterization of calcium carbonate polymorphs with Ca K edge X-ray absorption fine structure spectroscopy

Ca K edge X-ray absorption fine structure (XAFS) spectroscopy was utilized for the characterization and quantification of calcium carbonate polymorphs and their mixtures. The advantage of the XAFS is the small sample quantity required for measurements, and a flexible sample environment. The near-edge XAFS spectra of calcite, aragonite and vaterite were measured with the conversion electron yield (CEY) method, and the obtained spectra showed characteristic features that can be utilized as fingerprints. The quantification of mixed polymorphs was examined by using a linear combination fitting of reference XAFS spectra. Though the quality of the fits was satisfactory, discrepancies in the evaluated values were observed between those with X-ray diffraction (XRD) and XAFS. The nonuniformity of samples may be enhanced by the surface sensitivity of the CEY method.     

Electronic structure of transition metal-cysteine complexes from X-ray absorption spectroscopy

The electronic structures of HgII, NiII, CrIII, and MoV complexes with cysteine were investigated by sulfur K-edge X-ray absorption near-edge structure (XANES) spectroscopy and density functional theory. The covalency in the metal-sulfur bond was determined by analyzing the intensities of the electric-dipole allowed pre-edge features appearing in the XANES spectra below the ionization threshold. Because of the well-defined structures of the selected cysteine complexes, the current work provides a reference set for further sulfur K-edge XAS studies of bioinorganic active sites with transition metal-sulfur bonds from cysteine residues as well as more complex coordination compounds with thiolate ligands.     

Solid-state NMR spectroscopy reveals that water is nonessential to the core structure of alpha-synuclein fibrils

Protein aggregation is implicated in the etiology of numerous neurodegenerative diseases. An understanding of aggregation mechanisms is enhanced by atomic-resolution structural information, of which relatively little is currently available. Lewy bodies, the pathological hallmark of Parkinson's disease, contain large quantities of fibrillar alpha-synuclein (AS). Here we present solid-state NMR spectroscopy studies of dried AS fibrils. The spectra have high resolution and sensitivity, and the site-resolved chemical shifts agree very well with those previously observed for hydrated fibrils. The conserved chemical shifts indicate that bulk water is nonessential to the fibril core structure. Moreover, the sample preparation procedure yields major improvements in spectral sensitivity, without compromising spectral resolution. This advance will greatly assist the atomic-resolution structural analysis of AS fibrils.     

Geometric and electrostatic study of the [4Fe-4S] cluster of adenosine-5'-phosphosulfate reductase from broken symmetry density functional calculations and extended X-ray absorption fine structure spectroscopy

Adenosine-5'-phosphosulfate reductase (APSR) is an iron-sulfur protein that catalyzes the reduction of adenosine-5'-phosphosulfate (APS) to sulfite. APSR coordinates to a [4Fe-4S] cluster via a conserved CC-X(~80)-CXXC motif, and the cluster is essential for catalysis. Despite extensive functional, structural, and spectroscopic studies, the exact role of the iron-sulfur cluster in APS reduction remains unknown. To gain an understanding into the role of the cluster, density functional theory (DFT) analysis and extended X-ray fine structure spectroscopy (EXAFS) have been performed to reveal insights into the coordination, geometry, and electrostatics of the [4Fe-4S] cluster. X-ray absorption near-edge structure (XANES) data confirms that the cluster is in the [4Fe-4S](2+) state in both native and substrate-bound APSR while EXAFS data recorded at ~0.1 ? resolution indicates that there is no significant change in the structure of the [4Fe-4S] cluster between the native and substrate-bound forms of the protein. On the other hand, DFT calculations provide an insight into the subtle differences between the geometry of the cluster in the native and APS-bound forms of APSR. A comparison between models with and without the tandem cysteine pair coordination of the cluster suggests a role for the unique coordination in facilitating a compact geometric structure and "fine-tuning" the electronic structure to prevent reduction of the cluster. Further, calculations using models in which residue Lys144 is mutated to Ala confirm the finding that Lys144 serves as a crucial link in the interactions involving the [4Fe-4S] cluster and APS.     

The structure of 4-methylphenol and its water cluster revealed by rotationally resolved UV spectroscopy using a genetic algorithm approach

The structure of 4-methylphenol (p-cresol) and its binary water cluster have been elucidated by rotationally resolved laser-induced fluorescence spectroscopy. The electronic origins of the monomer and the cluster are split into four sub-bands by the internal rotation of the methyl group and of the hydroxy group in case of the monomer, and the water moiety in case of the cluster. From the rotational constants of the monomer the structure in the S1 state could be determined to be distorted quinoidally. The structure of the p-cresol-water cluster is determined to be trans linear, with a O-O hydrogen bond length of 290 pm in the electronic ground state and of 285 pm in the electronically excited state. The S1-state lifetime of p-cresol, p-cresol-d1, and the binary water cluster have been determined to be 1.6, 9.7, and 3.8 ns, respectively.     

Towards models of the oxygen-evolving complex (OEC) of photosystem II: a Mn4Ca cluster of relevance to low oxidation states of the OEC

Synthetic access has been achieved into high oxidation state Mn/Ca chemistry with the 4?:?1 Mn?:?Ca stoichiometry of the oxygen-evolving complex (OEC) of plants and cyanobacteria; the anion of (Et(3)NH)(2)[Mn(III)(4)Ca(O(2)CPh)(4)(shi)(4)] has a square pyramidal metal topology and an S = 0 ground state.     

X-ray photoelectron spectroscopy and near-edge X-ray absorption fine structure study of water adsorption on pyridine-terminated thiolate self-assembled monolayers

Adsorption of water on self-assembled monolayers (SAMs) of 4-(4-mercaptophenyl)pyridine on gold at low temperatures under ultrahigh vacuum conditions is studied by synchrotron radiation X-ray photoelectron and absorption spectroscopy. Water adsorption induces a strong modification of the chemical state of the pyridine N atoms at the SAM/ice interface, indicative for strong H bonding and partial proton transfer between water molecules and pyridine moieties. Additionally, the initial molecular orientation within the SAM is changed upon formation of an adsorbed water multilayer.     

The crystal structure and magnetic properties of a new ferrimagnetic semiconductor: Ca21Mn4Sb18

Single crystals of the new transition metal Zintl phase, Ca(21)Mn(4)Sb(18), were prepared by high temperature melt synthesis. The crystal structure was determined by single crystal X-ray diffraction to be monoclinic in the space group C2/c. Crystal information was obtained at 90 K, and unit cell parameters were determined (a = 17.100(2) A, b = 17.073(2) A, c = 16.857(2) A, beta = 92.999(2) degrees, Z = 2, R1 = 0.0540, wR2 = 0.1437). The structure can be described as containing 4 discreet units per formula unit: 1 linear [Mn(4)Sb(10)](22-) anion, 2 dumbbell-shaped [Sb(2)](4-) anions, 4 individual Sb(3-) anions, and 21 Ca(2+) cations. The [Mn(4)Sb(10)](22-) anion contains four edge-shared MnSb(4) tetrahedra with distances between Mn ions of 3.388(4) A, 2.782(4) A, and 2.760(4) A. Electron counting suggests that the Mn are 2+. Temperature dependent magnetization shows a ferromagnetic-like transition temperature at approximately 52 K which is suppressed with increasing magnetic field. The paramagnetic regime is best fit to a ferrimagnetic model, providing a total effective moment of 4.04(2) mu(B), significantly less than that expected for 4 Mn(2+) ions (11.8 mu(B)). Temperature dependent resistivity shows that this compound is a semiconductor with an activation energy of 0.159(2) eV (100-300 K).     

X-ray emission and X-ray photoelectron studies of the electronic structure of the polymeric cubane cluster compounds Mo4S4Cl4, GaMo4S8, and GaMo4S4Te4

X-ray emission and X-ray photoelectron spectroscopy was used to study the electronic structures of the polymeric cubane cluster compounds Mo₄S₄Cl₄, GaMo₄S₈, and GaMo₄S₄Te₄. It is revealed that the ligand orbitals make significant contributions to the highest occupied molecular orbitals (M−M bonds). Substitution in the series Cl−S−Te increases the covalence of the metal—bridging ligand bonds. The experimental spectra allowed the construction of a qualitative scheme of the electronic structure of Mo₄S₄Cl₄. Institute of Inorganic Chemistry, Siberian Branch, Russian Academy of Sciences. Translated fromZhurnal Strukturnoi Khimii, Vol. 36, No. 6, pp. 1038–1045, November–December, 1995. Translated by I. Izvekova     

What spectroscopy reveals concerning the Mn oxidation levels in the oxygen evolving complex of photosystem II: X-ray to near infra-red

Photosystem II (PS II), found in oxygenic photosynthetic organisms, catalyses the most energetically demanding reaction in nature, the oxidation of water to molecular oxygen and protons. The water oxidase in PS II contains a Mn(4)Ca cluster (oxygen evolving complex, OEC), whose catalytic mechanism has been extensively investigated but is still unresolved. In particular the precise Mn oxidation levels through which the cluster cycles during functional turnover are still contentious. In this, the first of several planned parts, we examine a broad range of published data relating to this question, while considering the recent atomic resolution PS II crystal structure of Umena et al. (Nature, 2011, 473, 55). Results from X-ray, UV-Vis and NIR spectroscopies are considered, using an approach that is mainly empirical, by comparison with published data from known model systems, but with some reliance on computational or other theoretical considerations. The intention is to survey the extent to which these data yield a consistent picture of the Mn oxidation states in functional PS II - in particular, to test their consistency with two current proposals for the mean redox levels of the OEC during turnover; the so called 'high' and 'low' oxidation state paradigms. These systematically differ by two oxidation equivalents throughout the redox accumulating catalytic S state cycle (states S(0)S(3)). In summary, we find that the data, in total, substantially favor the low oxidation proposal, particularly as a result of the new analyses we present. The low oxidation state scheme is able to resolve a number of previously 'anomalous' results in the observed UV-Visible S state turnover spectral differences and in the resonant inelastic X-ray spectroscopy (RIXS) of the Mn pre-edge region of the S(1) and S(2) states. Further, the low oxidation paradigm is able to provide a 'natural' explanation for the known sensitivity of the OEC Mn cluster to cryogenic near infra-red (NIR) induced turnover to alternative spin/redox states in S(2) and S(3).     

X-ray emission spectroscopy and the electronic structure of heterocyclic compounds

The electronic structure of the pyridine molecule has been investigated by x-ray emission spectroscopy. The NK _y and CK _y emission spectra have been measured. Ab initio and MNDO calculations have been carried out and individual bands in the spectra have been identified subsequently. The calculations produce spectral contours which approximate those of the experimental spectra.For Communication 3 see [1].Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 11, pp. 1484–1487, November, 1993.     

Conversion of core oxos to water molecules by 4e-/4H+ reductive dehydration of the Mn4O2(6+) core in the manganese-oxo cubane complex Mn4O4(Ph2PO2)6: a partial model for photosynthetic water binding and activation

Reaction of the Mn4O4(6+) "cubane" core complex, Mn4O4L6 (1) (L = diphenylphosphinate, Ph2PO2-), with a hydrogen atom donor, phenothiazine (pzH), forms the dehydrated cluster Mn4O2L6 (2), which has lost two mu-oxo bridges by reduction to water (H2O). The formation of 2 was established by electrospray mass spectrometry, whereas FTIR spectroscopy confirmed the release of water molecules into solution during the reduction of 1. UV-vis and EPR spectroscopies established the stoichiometry and chemical form of the pzH product by showing the production of 4 equiv of the neutral pz radical. By contrast, the irreversible decomposition of 1 to individual Mn(II) ions occurs if the reduction is performed using electrons provided by various proton-lacking reductants, such as cobaltocene or electrochemical reduction. Thus, cubane 1 undergoes coupled four-electron/four-proton reduction with the release of two water molecules, a reaction formally analogous to the reverse sequence of the steps that occur during photosynthetic water oxidation leading to O2 evolution. 1H NMR of solutions of 2 reveal that all six of the phosphinate ligands exhibit paramagnetic broadening, due to coordination to Mn ions, and are magnetically equivalent. A symmetrical core structure is thus indicated. We hypothesize that this structure is produced by the dynamic averaging of phosphinato ligand coordination or exchange of mu-oxos between vacant mu-oxo sites. The paramagnetic 1H NMR of water molecules in solution shows that they are able to freely exchange with water molecules that are bound to the Mn ion(s) in 2, and this exchange can be inhibited by the addition of coordinating anions, such as chloride. Thus, 2 possesses open or labile coordination sites for water and anions, in contrast to solutions of 1, which reveal no evidence for water coordination. Complex 2 exhibits greater paramagnetism than that of 1, as seen by 1H NMR, and it possesses a broad (440 G wide) EPR absorption, centered at g = 2, that follows a Curie-Weiss temperature dependence (10-40 K) and is visible only at low temperatures, compared to EPR-silent 1. Its comparison to a spin-integration standard reveals that 2 contains 2 equiv of Mn(II), which is in agreement with the formal oxidation state of 2Mn(II)2Mn(III) that was derived from the titration. The EPR and NMR data for 2 are consistent with a loss of two of the intermanganese spin-exchange coupling pathways, versus 1, which results in two "wingtip" Mn(II) S = 5/2 spins that are essentially magnetically uncoupled from the diamagnetic Mn2O2 base. Bond-enthalpy data, which show that O2 evolution via the reaction 1-->2 + O2, is strongly favored thermodynamically but is not observed in the ground state due to an activation barrier, are included. This activation barrier is hypothesized to arise, in part, from the constraining effect of the facially bridging phosphinate ligands.