Calcium-manganese oxides as structural and functional models for active site in oxygen evolving complex in photosystem II: lessons from simple models

The oxygen evolving complex in photosystem II which induces the oxidation of water to dioxygen in plants, algae and certain bacteria contains a cluster of one calcium and four manganese ions. It serves as a model to split water by sunlight. Reports on the mechanism and structure of photosystem II provide a more detailed architecture of the oxygen evolving complex and the surrounding amino acids. One challenge in this field is the development of artificial model compounds to study oxygen evolution reaction outside the complicated environment of the enzyme. Calcium-manganese oxides as structural and functional models for the active site of photosystem II are explained and reviewed in this paper. Because of related structures of these calcium-manganese oxides and the catalytic centers of active site of the oxygen evolving complex of photosystem II, the study may help to understand more about mechanism of oxygen evolution by the oxygen evolving complex of photosystem II.     

Acetate binding at the photosystem II oxygen evolving complex: an S(2)-state multiline signal ESEEM study

Previously, using acetate deuterated in the methyl hydrogen positions, we showed that acetate binds in close proximity to the Mn cluster/Y(.)(z) tyrosine dual spin complex in acetate-inhibited photosystem II (PSII) preparations exhibiting the "split" EPR signal arising from the S(2)-Y(.)(z) interaction [Force, D. A.; Randall, D. W.; Britt, R. D. Biochemistry 1997, 36, 12062-12070]. By using paramagnetic NO to quench the paramagnetism of Y(.)(z), we are able to observe the ESEEM spectrum of deuterated acetate interacting with only the Mn cluster. A good fit of the ESEEM data indicates two (2)H dipolar hyperfine couplings of 0.097 MHz and one of 0.190 MHz. Modeling of these dipolar interactions, using our "dangler" 3 + 1 model for the S(2)-state of the Mn cluster, reveals distances consistent with direct ligation of acetate to the Mn cluster. As acetate inhibition is competitive with the essential cofactor Cl(-), this suggests that Cl(-) ligates directly to the Mn cluster. The effect of acetate binding on the structure of the Mn cluster is investigated by comparing the Mn-histidine coupling in NO/acetate-treated PSII and untreated PSII using ESEEM. We find that the addition of acetate and NO does not affect the histidine ligation to the Mn cluster. We also investigate the ability of acetate to access Y(.)(z) in Mn-depleted PSII, a PSII preparation expected to be more solvent accessible than intact PSII. We detect no coupling between Y(.)(z) and acetate. We have previously shown that small alcohols such as methanol can ligate to the Mn cluster with ease, while larger alcohols such as 2-propanol, as well as DMSO, are excluded [Force, D. A.; Randall, D. W.; Lorigan, G. A.; Clemens, K. L.; Britt, R. D. J. Am. Chem. Soc. 1998, 120, 13321-13333]. We probe the effect of acetate binding on the ability of methanol and DMSO to bind to the Mn cluster. We find that methanol is able to bind to the Mn cluster in the presence of acetate. We detect no DMSO binding in the presence of acetate. Thus, acetate binding does not increase the affinity or accessibility for DMSO binding at the Mn cluster. We also explore the possibility that the acetate binding site is also a binding site for substrate water. By comparing the ratioed three-pulse ESEEM spectra of a control, untreated PSII sample in 50% D(2)O to an NO/acetate-treated PSII sample in 50% D(2)O, we find that the binding of acetate to the oxygen evolving complex of photosystem II displaces deuterons bound very closely to the Mn cluster.     

General synthesis of di-mu-oxo dimanganese complexes as functional models for the oxygen evolving complex of photosystem II

A series of complexes with the formula [Mn(III/IV)2(mu-O)2(L)2(X)2]3+ have been prepared in situ from Mn(II)LCl2 precursors by a general preparative method (L = terpy, Cl-terpy, Br-terpy, Ph-terpy, tolyl-terpy, mesityl-terpy, t Bu3-terpy, EtO-terpy, py-phen, dpya, Me2N-terpy, or HO-terpy, and X = a labile ligand such as water, chloride, or sulfate). The parent complex, where L = terpy and X = water, is a functional model for the oxygen-evolving complex of photosystem II (Limburg, et al. J. Am. Chem. Soc. 2001, 123, 423-430). Crystals of Mn(II)(dpya)Cl2, Mn(II)(Ph-terpy)Cl2, Mn(II)(mesityl-terpy)Cl2, and an organic-soluble di-mu-oxo di-aqua dimanganese complex, [Mn(III/)(IV)2(mu-O)2(mesityl-terpy)2(OH2)2](NO3)3, were obtained and characterized by X-ray crystallography. Solutions of the in situ-formed di-mu-oxo dimanganese complexes were characterized by electrospray mass spectrometry, EPR spectroscopy, and UV-visible spectroscopy, and the rates of catalytic oxygen-evolving activity were assayed. The use of Mn(II)LCl2 precursors leads to higher product purity of the Mn dimers while achieving the 1:1 ligand to Mn stoichiometry appropriate for catalytic activity assay. These methods can be used to screen the catalytic activity of other di-mu-oxo dimanganese complexes generated by using a ligand library.     

Theoretical models for the conformations and the protonation of triacetonamine

Summary In this paper we propose theoretical models for the conformations of triacetonamine and protonated triacetonamine (Vincubine, an anticancer chemotherapeutic agent) developed by quantum and molecular mechanics techniques. We discuss the theoretical factors which are involved in the stabilization of the conformations calculated by the MNDO, MM2 and COPEANE methods and show the relative percent abundance of each molecular shape. Graphic representations of the conformers are depicted.     

Theoretical and experimental investigations of the electronic Rydberg states of diazomethane: assignments and state interactions

The electronic states of diazomethane in the region 3.00-8.00 eV have been characterized by ab initio calculations, and electronic transitions in the region 6.32-7.30 eV have been examined experimentally using a combination of 2 + 1 REMPI spectroscopy and photoelectron imaging in a molecular beam. In the examined region, three Rydberg states of 3p character contribute to the transitions, 2(1)A2(3p(y) <-- pi), 2(1)B1(3p(z) <-- pi), and 3(1)A1(3p(x) <-- pi). The former two states are of mostly pure Rydberg character and exhibit a resolved K structure, whereas the 3(1)A1(3p(x) <-- pi) state is mixed with the valence 2(1)A1(pi* <-- pi) state, which is unbound and is strongly predissociative. Analyses of photoelectron kinetic energy distributions indicate that the ground vibrational level of the 2(1)B1(3p(z)) state is mixed with the 2(1)A2(3p(y)) nu(9) level, which is of B1 vibronic symmetry. The other 2(1)A2(3p(y)) vibronic states exhibit pure Rydberg character, generating ions in single vibrational levels. The photoelectron spectra of the 3(1)A1(3p(x) <-- pi) state, on the other hand, give rise to many states of the ion as a result of strong mixing with the valence state, as evidenced also in the ab initio calculations. The equilibrium geometries of the electronic states of neutral diazomethane were calculated by CCSD(T), using the cc-pVTZ basis, and by B3LYP, using the 6-311G(2df,p) basis. Geometry and frequencies of the ground state of the cation were calculated by CCSD(T)/cc-pVTZ, using the unrestricted (UHF) reference. Vertical excitation energies were calculated using EOM-CCSD/6-311(3+,+)G* at the B3LYP optimized geometry. The theoretical results show that the 2(1)A2(3p(y) <-- pi) and 2(1)B1(3p(z) <-- pi) states have geometries similar to the ion, which has C(2v) symmetry, with slight differences due to the interactions of the electron in the 3p orbital with the nuclei charge distributions. The geometry of the 3(1)A1(3p(x) <-- pi) state is quite different and has Cs symmetry. The experimental and theoretical results agree very well, both in regard to excitation energies and to vibrational modes of the ion.     

Theoretical models for the oxygen radical mechanism of water oxidation and of the water oxidizing complex of photosystem II

Hybrid density functional theory is used to study reasonably realistic models of the oxygen-evolving manganese complex in photosystem II. Since there is not yet any X-ray structure of the complex, other types of experimental and theoretical information are used to construct the model complexes. In these complexes, three manganese centers are predicted to be closely coupled by mu-oxo bonds in a triangular orientation. Using these models, the previously suggested oxygen radical mechanism for O2 formation is reinvestigated. It is found that the oxygen radical in the S3 state now appears in a bridging position between two manganese atoms. It is still suggested that only one manganese atom is redox-active. Instead, a number of surprisingly large trans-effects are found, which motivate the existence and define the function of the other manganese atoms in the Mn4 cluster. Calcium has a strong chelating effect which helps in the creation of the necessary oxygen radical. In the present model the chemistry preceding the actual O-O bond formation occurs in an incomplete cube with a missing corner and with two manganese and one calcium in three of the corners. The external water providing the second oxygen of O2 enters in the missing corner of the cube. The present findings are in most cases in good agreement with experimental results as given in particular by EXAFS.     

55Mn pulse ENDOR at 34 GHz of the S0 and S2 states of the oxygen-evolving complex in photosystem II

55Mn pulse ENDOR experiments at 34 GHz (Q-band) are reported for the S0 and S2 states of the oxygen-evolving complex of photosystem II. Their numerical analysis (i) shows that in both states all four Mn ions are magnetically coupled, (ii) allows a refinement of the hyperfine interaction (HFI) parameters obtained earlier for the S2 state at X-band (Peloquin, J. M.; Campbell, K. A.; Randall, D. W.; Evanchik, M. A.; Pecoraro, V. L.; Armstrong, W. H.; Britt, R. D. J. Am. Chem. Soc. 2000, 122, 10926-10942), (iii) provides the first reliable 55Mn HFI tensors for the S0 state, and (iv) leads to the suggestion that the Mn oxidation states in S0 and S2 are Mn4(III, III, III, IV) and Mn4(III, IV, IV, IV), respectively. In addition, a Q-band EPR spectrum is reported for the S0 state, and inversion-recovery experiments at 4.5 K directly show that the electron spin-lattice relaxation for the S0 state is about 2 orders of magnitude faster than that for the S2 state.     

Studies of a dinuclear manganese complex with phenoxo and bis-acetato bridging in the Mn2(II,II) and Mn2(II,III) states: Coordination structural shifts and oxidation state control in bridged dinuclear complexes

The dinucleating ligand, 2,6-bis{[(2-(2-pyridyl)ethyl)(2-pyridylmethyl)-amino]-methyl}-4-methylphenol) (L1OH) reacts with Mn(ClO4)2.6H2O to form the dinuclear complex [Mn2(II,II)(L1O)(mu-OOCCH3)2]ClO4 (1). The electrolytic oxidation of 1 at 0.7 V (vs Ag/AgCl) produces the mixed valent complex [Mn2(II,III)(L1O)(mu-OOCCH3)2](ClO4)2 (1ox) quantitatively, while electrolysis at 0.20 V converts 1ox back to 1. X-ray crystallographic structures show that both 1 and 1ox are dinuclear complexes in which the two manganese ions are each in distorted octahedral coordination environments bridged by the phenoxo oxygen and two acetate ions. The structural changes that occur upon the oxidation 1 to 1ox suggest an extended pi-bonding system involving the phenoxo ring C-O(phenoxo)-Mn(II)-N(pyridyl) chain. In addition, as 1 is oxidized to 1ox, the rearrangements in the coordination sphere resulting from the oxidation of one Mn(II) ion to Mn(III) are transmitted via the bridging Mn-O(phenoxo) bonds and cause structural changes that render the site of the second manganese ion unfit for the +3 state and hence unstable to reduction. Thus the electrolytic oxidation of 1ox in acetonitrile at 1.20 V takes up slightly greater than 1 F of charge/mol of 1ox, but the starting complex, 1ox, is recovered, showing the instability of the Mn2(III,III) state that is formed with respect to reduction to 1ox. Variable-temperature magnetic susceptibility measurements of 1 and 1ox over the temperature range from 1.8 to 300 K can be modeled with magnetic coupling constants J = -4.3 and -4.1 cm(-1), respectively showing the weak antiferromagnetic coupling between the two manganese ions in each dinuclear complex, which is commonly observed among similar phenoxo- and bis-1,3-carboxylato-bridged dinuclear Mn2(II,II) and Mn2(II,III) complexes.     

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).     

Investigation of the calcium-binding site of the oxygen evolving complex of photosystem II using 87Sr ESEEM spectroscopy

The proximity of the calcium/strontium binding site of the oxygen evolving complex (OEC) of photosystem II (PSII) to the paramagnetic Mn cluster is explored with (87)Sr three-pulse electron spin-echo envelope modulation (ESEEM) spectroscopy. CW-EPR spectra of Sr(2+)-substituted Ca(2+)-depleted PSII membranes show the modified g = 2 multiline EPR signal as previously reported. We performed three-pulse ESEEM on this modified multiline signal of the Mn cluster using natural abundance Sr and (87)Sr, respectively. Three-pulse ESEEM of the natural abundance Sr sample exhibits no detectable modulation by the 7% abundance (87)Sr. On the other hand, that of the (87)Sr enriched (93%) sample clearly reveals modulation arising from the I = (9)/(2) (87)Sr nucleus weakly magnetically coupled to the Mn cluster. Using a simple point dipole approximation for the electron spin, analysis of the (87)Sr ESEEM modulation depth via an analytic expression suggests a Mn-Ca (Sr) distance of 4.5 A. Simulation of three-pulse ESEEM with a numerical matrix diagonalization procedure gave good agreement with this analytical result. A more appropriate tetranuclear magnetic/structural model for the Mn cluster converts the 4.5 A point dipole distance to a 3.8-5.0 A range of distances. DFT calculations of (43)Ca and (87)Sr quadrupolar interactions on Ca (and Sr substituted) binding sites in various proteins suggest that the lack of the nuclear quadrupole induced splitting in the ESEEM spectrum of (87)Sr enriched PSII samples is related to a very high degree of symmetry of the ligands surrounding the Sr(2+) ion in the substituted Ca site. Numerical simulations show that moderate (87)Sr quadrupolar couplings decrease the envelope modulation relative to the zero quadrupole case, and therefore we consider that the 3.8-5.0 A range obtained without quadrupolar coupling included in the simulation represents an upper limit to the actual manganese-calcium distance. This (87)Sr pulsed EPR spectroscopy provides independent direct evidence that the calcium/strontium binding site is close to the Mn cluster in the OEC of PSII.     

Anomalous magnetic properties of tetraphenylporphinato Co(II) complex in the solid state

The α,β,γ,δ-tetraphenylporphinatocobalt(II) complex is found to exist in two distinct, but interconvertible, polycrystalline forms. The one with a tetragonal crystal symmetry (species B) gives the EPR spectrum which has been attributed to the low-spin electronic configuration of Co(II) ion in an axial crystal field. The other form (species A) having a triclinic crystal symmetry shows no easily detectable EPR signal even at liquid helium temperature.Magnetic susceptibility and magnetization meaurements demonstrated that the complex is paramagnetic in both forms, but the species (A) is characterized by ferromagnetic exchange coupling, while the species (B) behaves as a normal paramagnet.The experimental susceptibility versus 1/T curve can be reproduced quite well by using the Ising method. The g values thus obtained (g_| = 5.2,g_⊥ = 0) can not be explained by a low-spin electronic configuration, but are consistent with a high-spin ground state. Assigning a high-spin state to the species (A), the first such case in Co(II) porphine complexes, can not only explain the absence of EPR signal, but is also supported by the results of X-ray structural analyses.     

Cluster size convergence for the energetics of the oxygen evolving complex in PSII

Density functional theory calculations have been made to investigate the stability of the energetics for the oxygen evolving complex of photosystem II. Results published elsewhere have given excellent agreement with experiments for both energetics and structures, where many of the experimental results were obtained several years after the calculations were done. The computational results were obtained after a careful extension from small models to a size of about 200 atoms, where stability of the results was demonstrated. However, recently results were published by Isobe et al., suggesting that very different results could be obtained if the model was extended from 200 to 340 atoms. The present study aims at understanding where this difference comes from. © 2017 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.     

Oxygen-evolving Mn cluster in photosystem II: the protonation pattern and oxidation state in the high-resolution crystal structure

Extensive quantum chemical DFT calculations were performed on the high-resolution (1.9 ?) crystal structure of photosystem II in order to determine the protonation pattern and the oxidation states of the oxygen-evolving Mn cluster. First, our data suggest that the experimental structure is not in the S(1)-state. Second, a rather complete set of possible protonation patterns is studied, resulting in very few alternative protonation patterns whose relevance is discussed. Finally, we show that the experimental structure is a mixture of states containing highly reduced forms, with the largest contribution (almost 60%) from the S(-3)-state, Mn(II,II,III,III).     

Second virial coefficients of oxygen—oxygen and carbon—oxygen interactions in different electronic states

Second virial coefficients of oxygen—oxygen and carbon—oxygen interactions in different electronic states have been calculated up to 20000 K. The results show that the virial coefficients of excited states are greater than the corresponding ground state values. The influence of the excited states on the total virial coefficients, calculated by assuming a Botlzmann distribution along the different states, has been found strong (up to 40%) in the carbon—oxygen system, while a minor effect (up to 3%) has been observed for the oxygen—oxygen system.     

Light-harvesting and structural organization of Photosystem II: from individual complexes to thylakoid membrane

Photosystem II (PSII) is responsible for the water oxidation in photosynthesis and it consists of many proteins and pigment-protein complexes in a variable composition, depending on environmental conditions. Sunlight-induced charge separation lies at the basis of the photochemical reactions and it occurs in the reaction center (RC). The RC is located in the PSII core which also contains light-harvesting complexes CP43 and CP47. The PSII core of plants is surrounded by external light-harvesting complexes (lhcs) forming supercomplexes, which together with additional external lhcs, are located in the thylakoid membrane where they perform their functions. In this paper we provide an overview of the available information on the structure and organization of pigment-protein complexes in PSII and relate this to experimental and theoretical results on excitation energy transfer (EET) and charge separation (CS). This is done for different subcomplexes, supercomplexes, PSII membranes and thylakoid membranes. Differences in experimental and theoretical results are discussed and the question is addressed how results and models for individual complexes relate to the results on larger systems. It is shown that it is still very difficult to combine all available results into one comprehensive picture.     

One polynuclear copper(II) complex based on salicylaldehyde phenoxyacylhydrazone: structural and magnetic studies

One new copper(II) complex with a multidentate Schiff-base ligand salicylaldehyde phenoxyacylhydrazone (H₂L), {[Cu₄(L)₄(DMF)]·DMF}_n (1) has been synthesized and structurally characterized. Complex 1 exhibits a coordination polymer with a 1-D infinite chain-like structure, resulting from the Cu(II) centers linked by N–N single bonds. Magnetic behavior of 1 shows that it is antiferromagnetic.     

Structural, magnetic coupling and oxidation state trends in models of the CaMn4 cluster in photosystem II

Density functional theory calculations are reported on a set of isomeric structures I, II and III that share the structural formula [CaMn4C9H10N2O16]q+.(H2O)3 (q= -1, 0, 1, 2, 3). Species I has a skeletal structure, which has been previously identified as a close match to the ligated CaMn4 cluster in Photosystem II, as characterized in the most recent 3.0 angstroms crystal structure. Structures II and III are rearrangements of I, which largely retain that model's bridging ligand framework, but feature metal atom positions broadly consistent with, respectively, the earlier 3.5 and 3.2 angstroms crystal structures for the Photosystem II water-oxidising complex (WOC). Our study explores the influence of the cluster charge state (and hence S state) on several important properties of the model structures; including the relative energies of the three models, their interconversion, trends in the individual Mn oxidation states, preferred hydration sites and favoured modes of magnetic coupling between the manganese atoms. We find that, for several of the explored cluster charge states, modest differences in the bridging-ligand geometry exert a powerful influence over the individual manganese oxidation states, but throughout these states the robustness of the tetrahedron formed by the Ca and three of the Mn atoms remains a significant feature and contrasts with the positional flexibility of the fourth Mn atom. Although structure I is lowest in energy for most S states, the energy differences between structures for a given S state are not large. Overall, structure II provides a better match for the EXAFS derived metal-metal distance parameters for the earlier S states (S0 to S2), but not for S3 in which a significant structural change is observed experimentally. In this S state structure III provides a closer fit. The implications of these results, for the possible action of the WOC, are discussed.     

Self-organization in the flow of complex fluids (colloid and polymer systems). Part 2: Theoretical models

Flow induced transitions in complex fluids are usually accompanied by changes in the internal media structure and the flow symmetry. In this review paper, we discuss the theoretical models and approaches that have been used for the analysis of different types of flow instabilities and flow patterns. The main attention is focused on the basic fluid models which reveal vortex and banding flow structures at high shear rates. The Oldroyd-B fluid is one of such models. The Reynolds and the Weissenberg (or Deborah) numbers are the parameters governing its flow behavior. For this model, the secondary flow patterns arising in viscometric flows of different geometries at the bifurcation point are described. Complex fluids which are able to exist in multiple states can form coexisting bands of different structures with different rheological properties and flowing with different shear rates at the same shear stress. Shear banding is typical for fluids demonstrating non-monotonous flow curves described by such models as the diffusive Johnson-Segalman fluid model, for example. Recent progress in exploring this phenomenon is discussed.     

Inhibitor binding influences the protonation states of histidines in SARS-CoV-2 main protease

The main protease (M^pro) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an attractive target for antiviral therapeutics. Recently, many high-resolution apo and inhibitor-bound structures of M^pro, a cysteine protease, have been determined, facilitating structure-based drug design. M^pro plays a central role in the viral life cycle by catalyzing the cleavage of SARS-CoV-2 polyproteins. In addition to the catalytic dyad His41–Cys145, M^pro contains multiple histidines including His163, His164, and His172. The protonation states of these histidines and the catalytic nucleophile Cys145 have been debated in previous studies of SARS-CoV M^pro, but have yet to be investigated for SARS-CoV-2. In this work we have used molecular dynamics simulations to determine the structural stability of SARS-CoV-2 M^pro as a function of the protonation assignments for these residues. We simulated both the apo and inhibitor-bound enzyme and found that the conformational stability of the binding site, bound inhibitors, and the hydrogen bond networks of M^pro are highly sensitive to these assignments. Additionally, the two inhibitors studied, the peptidomimetic N3 and an α-ketoamide, display distinct His41/His164 protonation-state-dependent stabilities. While the apo and the N3-bound systems favored N_δ (HD) and N_ϵ (HE) protonation of His41 and His164, respectively, the α-ketoamide was not stably bound in this state. Our results illustrate the importance of using appropriate histidine protonation states to accurately model the structure and dynamics of SARS-CoV-2 M^pro in both the apo and inhibitor-bound states, a necessary prerequisite for drug-design efforts.

The main protease (M^pro) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an attractive target for antiviral therapeutics.