Theory of chemical bonds in metalloenzymes XIX: labile manganese oxygen bonds of the CaMn4O5 cluster in oxygen evolving complex of photosystem II

Spin polarisation effects of labile manganese–oxygen bonds in the X-ray diffraction structure of the oxygen-evolving complex (OEC) of photosystem II (PSII) at 1.9 Å resolution have been investigated by the UB3LYP computations on the basis of three different theoretical models with and without hydrogen bonds: quantum-mechanical (QM) Model I, QM(Model II)/MM and QM Model III. The spin densities on the manganese and oxygen atoms of the CaMn₄O₅ cluster revealed by these computations have elucidated internal, semi-internal and external reductions of high-valent manganese ions in the CaMn₄O₅ cluster in OEC of PSII. The internal reduction of Mn(IV) ions by the back charge transfer from oxygen dianions is remarkable in the small QM Model I, whereas it is significantly reduced in the case of more realistic QM Model III including hydrogen bonding stabilisations of oxygen dianions. However, semi-internal reduction of the CaMn₄O₅ cluster with remote amino acid residues such as Asp61 anion occurs even in QM Model III, indicating the necessity of large QM parts for redox-active systems such as OEC of PSII. The computational results have clearly demonstrated important roles of confinement effects of the CaMn₄O₅ cluster with labile Mn–O bonds with protein. These computational results have been applied to molecular design of artificial robust catalysts for water oxidation by use of sunlight.     

Theory of chemical bonds in metalloenzymes XXI. Possible mechanisms of water oxidation in oxygen evolving complex of photosystem II

ABSTRACT

Possible mechanisms for water cleavage in oxygen evolving complex (OEC) of photosystem II (PSII) have been investigated based on broken-symmetry (BS) hybrid DFT (HDFT)/def2 TZVP calculations in combination with available XRD, XFEL, EXAFS, XES and EPR results. The BS HDFT and the experimental results have provided basic concepts for understanding of chemical bonds of the CaMn₄O₅ cluster in the catalytic site of OEC of PSII for elucidation of the mechanism of photosynthetic water cleavage. Scope and applicability of the hybrid DFT (HDFT) methods have been examined in relation to relative stabilities of possible nine intermediates such as Mn-hydroxide, Mn-oxo, Mn-peroxo, Mn-superoxo, etc., in order to understand the O–O (O–OH) bond formation in the S₃ and/or S₄ states of OEC of PSII. The relative stabilities among these intermediates are variable, depending on the weight of the Hartree–Fock exchange term of HDFT. The Mn-hydroxide, Mn-oxo and Mn-superoxo intermediates are found to be preferable in the weak, intermediate and strong electron correlation regimes, respectively. Recent different serial femtosecond X-ray (SFX) results in the S₃ state are investigated based on the proposed basic concepts under the assumption of different water-insertion steps for water cleavage in the Kok cycle. The observation of water insertion in the S₃ state is compatible with previous large-scale QM/MM results and previous theoretical proposal for the chemical equilibrium mechanism in the S₃ state . On the other hand, the no detection of water insertion in the S₃ state based on other SFX results is consistent with previous proposal of the O–OH (or O–O) bond formation in the S₄ state . Radical coupling and non-adiabatic one-electron transfer (NA-OET) mechanisms for the OO-bond formation are examined using the energy diagrams by QM calculations and by QM(UB3LYP)/MM calculations . Possible reaction pathways for the O–O and O–OH bond formations are also investigated based on two water-inlet pathways for oxygen evolution in OEC of PSII. Future perspectives are discussed in relation to post HDFT calculations of the energy diagrams for elucidation of the mechanism of water oxidation in OEC of PSII.     

On the guiding principles for understanding of geometrical structures of the CaMn4O5 cluster in oxygen-evolving complex of photosystem II. Proposal of estimation formula of structural deformations via the Jahn–Teller effects

ABSTRACT

Atmospheric oxygenation and evolution of aerobic life on our earth are a result of water oxidation by oxygenic photosynthesis in photosystem II (PSII) of plants, algae and cyanobacteria. The water oxidation in the oxygen-evolving complex (OEC) in PSII is expected to proceed through five oxidation states, known as the S _i (i = 0, 1, 2, 3 and 4) states in the Kok cycle, with the S₁ being the most stable state in the dark. The OEC in PSII involves the active catalytic site made of four Mn ions and one Ca ion, namely the CaMn₄O₅ cluster. Past decades, molecular structures of the CaMn₄O₅ cluster in OEC in PSII have been investigated by the extended X-ray absorption fine structure (EXAFS). The magneto-structural correlations were extensively investigated by electron paramagnetic resonance (EPR) spectroscopy. Recently, Kamiya and Shen groups made great breakthrough for determination of the S₁ structure of OEC of PSII by the X-ray diffraction (XRD) and X-ray free-electron laser (XFEL) experiments, providing structural foundations that are crucial for theoretical investigations of the CaMn₄O₅ cluster. Large-scale quantum mechanics/molecular mechanics calculations starting from the XRD structures elucidated geometrical, electronic and spin structures of the CaMn₄O₅ cluster, indicating an important role of the Jahn–Teller (JT) effect of Mn(III) ions. This paper presents theoretical formulas for estimation of the JT deformations of the CaMn₄O₅ cluster in OEC of PSII. Scope and applicability of the formulas are examined in relation to several different structures of the CaMn₄O₅ cluster proposed by XRD, XFEL, EXAFS and other experiments. Implications of the computational results are discussed for further refinements of geometrical parameters of the CaMn₄O₅ cluster.     

Theory of chemical bonds in metalloenzymes XXII: a concerted bond-switching mechanism for the oxygen–oxygen bond formation coupled with one electron transfer for water oxidation in the oxygen-evolving complex of photosystem II

ABSTRACT

QM(UB3LYP)/MM(AMBER) calculations were performed for the locations of the transition structure (TS) of the oxygen–oxygen (O–O) bond formation in the S₄ state of the oxygen-evolving complex (OEC) of photosystem II (PSII). The natural orbital (NO) analysis of the broken-symmetry (BS) solutions was also performed to elucidate the nature of the chemical bonds at TS on the basis of several chemical indices defined by the occupation numbers of NO. The computational results revealed a concerted bond switching (CBS) mechanism for the oxygen–oxygen bond formation coupled with the one-electron transfer (OET) for water oxidation in OEC of PSII. The orbital interaction between the σ-HOMO of the Mn(IV)₄–O₍₅₎ bond and the π*-LUMO of the Mn(V)₁=O₍₆₎ bond plays an important role for the concerted O–O bond formation for water oxidation in the CaMn₄O₆ cluster of OEC of PSII. One electron transfer (OET) from the π-HOMO of the Mn(V)₁=O₍₆₎ bond to the σ*-LUMO of the Mn(IV)₄–O₍₅₎ bond occurs for the formation of electron transfer diradical, where the generated anion radical [Mn(IV)₄–O₍₅₎]^-? part is relaxed to the ?Mn(III)₄?…?O₍₅₎^- structure and the cation radical [O₍₆₎=Mn(V)₁]⁺ ? part is relaxed to the ⁺O₍₆₎–Mn(IV)₁? structure because of the charge-spin separation for the electron-and hole-doped Mn–oxo bonds. Therefore, the local spins are responsible for the one-electron reductions of Mn(IV)₄->Mn(III)₄ and Mn(V)₁->Mn(IV)₁. On the other hand, the O₍₅₎^- and O₍₆₎⁺ sites generated undergo the O–O bond formation in the CaMn₄O₆ cluster. The Ca(II) ion in the cubane- skeleton of the CaMn₄O₆ cluster assists the above orbital interactions by the lowering of the orbital energy levels of π*-LUMO of Mn(V)₁=O₍₆₎ and σ*-LUMO of Mn(IV)₄–O₍₅₎, indicating an important role of its Lewis acidity. Present CBS mechanism for the O–O bond formation coupled with one electron reductions of the high-valent Mn ions is different from the conventional radical coupling (RC) and acid-base (AB) mechanisms for water oxidation in artificial and native photosynthesis systems. The proton-coupled electron transfer (PC-OET) mechanism for the O–O bond formation is also touched in relation to the CBS-OET mechanism.     

Cooperative order and excitation spectra in the bicomponent spin networks

A ferrimagnetic spin model composed of S = 1/2 spin-dimers and S = 5/2 spin-chains is studied by combining the bond-operator representation (for S = 1/2 spin-dimers) and Holstein-Primakoff transformation (for S = 5/2 spins). A finite interaction J _DF between the spin-dimer and the spin chain makes the spin chains ordered antiferromagnetically and the spin dimers polarized. The effective interaction between the spin chains, mediated by the spin dimers, is calculated up to the third order. The staggered magnetization in the spin dimer is shown proportional to J _DF. Due to the triplon-magnon interaction, the degeneracy of the triplons is lifted and the hybridized triplon-like excitations show different behaviors near the vanishing J _DF. A mode with longitudinal polarization is identified. The hybridized magnon-like excitations are also studied. These results are compared with the experiments on Cu₂Fe₂Ge₄O₁₃.     

Spin relaxation of Mn ions in (CdMn)Te/(CdMg)Te quantum wells under picosecond optical pumping

Spin relaxation of Mn ions in a Cd_0.97Mn_0.03Te/Cd_0.75Mg_0.25Te quantum well with photogenerated quasi-two-dimensional electron-hole plasma at liquid helium temperatures in an external magnetic field has been investigated. Heating of Mn ions by photogenerated carriers due to spin and energy exchange between the hot electron-hole plasma and Mn ions through direct sd-interaction between electron and Mn spins has been detected. This process has a short characteristic time of about 4 ns, which leads to appreciable heating of the Mn spin subsystem in about 0.5 ns. Even under uniform excitation of a dense electron-hole plasma, the Mn heating is spatially nonuniform, and leads to formation of spin domains in the quantum well magnetic subsystem. The relaxation time of spin domains after pulsed excitation is measured to be about 70 ns. Energy relaxation of excitons in the random exchange potential due to spin domains results from exciton diffusion in magnetic field B=14 T with a characteristic time of 1 to 4 ns. The relaxation time decreases with decreasing optical pump power, which indicates smaller dimensions of spin domains. In weak magnetic fields (_B=2 T) a slow down in the exciton diffusion to 15 ns has been detected. This slow down is due to exciton binding to neutral donors (formation of bound excitons) and smaller spin domain amplitudes in low magnetic fields. The optically determined spin-lattice relaxation time of Mn ions in a magnetic field of 14 T is 270±10 and 16±7 ns for Mn concentrations of 3% and 12%, respectively. Zh. éksp. Teor. Fiz. 112, 1440–1463 (October 1997)     

Calculated spin-spin coupling surfaces in the water molecule; prediction and analysis of J (O,H), J (O,D) and J (H,D) in water isotopomers

Ab initio symmetry and internal valence coordinate oxygen–proton and proton–proton spin–spin coupling surfaces for the water molecule have been computed for the first time. Calculations have been performed at the SOPPA (CCSD) level using a large basis set and a grid of forty-nine geometries on the two surfaces. Equilibrium values differ significantly from some other calculated values especially for the Fermi contact terms. The bond length dependence of J(O, H) is ‘normal’ i.e. J(O, H₁) is much more sensitive to stretching the O–H₁ bond than the O–H₂ bond. This contrasts greatly with the corresponding situation in methane.

The surfaces have been averaged over the nuclear motion using a recent highly accurate force field to give values of J (O, H) and J (O, D) for H₂ ¹⁷O, HD¹⁷O and D₂ ¹⁷O and J(H, D) for HD¹⁶O, HD¹⁷O and HD¹⁸O over a range of temperatures. For J (O, H) and J (O, D) bond stretching at first order is the dominant part of the nuclear motion correction with second order bending making an important contribution. For J (H, D) the second order bending is by far the largest contribution to the nuclear motion corrections although the other terms partially cancel this contribution. Non-additivity can be largely attributed to the bending term for J (O, H). As expected, the bending terms also contribute relatively more to the temperature dependence of the couplings for J (O, H), J (O, D) and J (H, D). Our calculated J (O, H) in H₂ ¹⁷O of -77.22Hz at 293K is in very good agreement with Wasylishen and Friedrich's observed value of -78.70 (±0.02) Hz in cyclohexane at this temperature. Our calculated J(H, D) in HD ¹⁶O at 323K of -1.233Hz is close to a recent experimental value of -1.114 (±0.003) Hz in nitromethane-d ₃ observed by Sergeyev et al. at that temperature.     

Domain-based local pair natural orbital CCSD(T) calculations of strongly correlated electron systems: Examination of dynamic equilibrium models based on multiple intermediates in S1 state of photosystem II

ABSTRACT

Domain-based local pair natural orbital (DLPNO) coupled cluster single and double (CCSD) methods with perturbative triples (T) correction with NormalPNO were used to compute energies for twelve different S₁ structures of the CaMn₄O₅ cluster in the oxygen evolving complex (OEC) of photosystem II (PSII). The DLPNO-CCSD(T₀) calculations with TightPNO for the important six structures among them revealed that the right (R)-opened S_1XYZW structures were more stable than the corresponding left (L)-opened structures (X?=?O₍₅₎, Y?=?W2, Z?=?W1, and W?=?O₍₄₎) of CaMn₄O₅. The three different S₁ structures belonging to the R-opened type (S_1acca, S_1bbca, and S_1abcb, where O^2-?=?a, OH^-?=?b and H₂O?=?c) were found nearly degenerated in energy, indicating the possibility of the coexistence of different structures in the S₁ state. The DLPNO-CCSD(T₀) calculations with TightPNO supported the proposal of a dynamic equilibrium model based on the multi-intermediate structures for the S₁ state, which is also in agreement with EPR and other experimental and hybrid DFT computational results. Implications of the computational results are discussed in relation to scope and applicability of NormalPNO and TightPNO for the CCSD(T₀) calculations of strongly correlated electron systems such as 3d transition-metal complexes.     

Characteristics of ESEEM and HYSCORE spectra of S>1/2 centers in orientationally disordered systems

One- and two-dimensional electron-spin echo envelope modulation (ESEEM) spectra of Kramers’ multiplets in orientationally disordered systems are simulated using a simple mathematical model. A fairly general high-field spin Hamiltonian is considered with a general g-tensor and arbitrary relative orientations between all tensors involving the electron-spin S, the nuclear spin I, and their interaction. The zero field splitting (ZFS) and the nuclear quadrupole interactions are, however, approximated by their respective secular part in a way that retains all orientation dependencies and it is assumed that the nuclear quadrupole interaction is smaller than the hyperfine interaction. These approximations yield an effective sublevel nuclear Hamiltonian for each EPR transition and are sufficient to account for the most important characteristics of the ESEEM spectra of high electronic multiplets in orientationally disordered systems. Moreover, they allow to obtain some analytical expressions that for I=1/2 illuminate important aspects of 2D hyperfine sublevel correlation (HYSCORE) experiments in S=3/2, 5/2 systems. The pulses are considered as ideal and selective with respect to the different EPR transitions. The contributions of the latter to the echo intensity are weighed according to their different nutation angles and equilibrium Boltzmann populations. For simple axial cases with I=1/2, analytical expressions, analogous to the S=1/2 case, were derived for: (i) the modulation depth, (ii) the lineshapes of the HYSCORE cross-correlation ridges, and (iii) ENDOR powder pattern. Experimental results obtained from Mn(D₂O)₆²⁺ and VO(D₂O)₅²⁺ in frozen solutions are presented, compared, and analyzed in light of the theoretical part.     

Intensity of the EPR spectrum in quenched samples of Yba2Cu3Ox compounds

The temperature dependence of the intensity of the EPR signal is measured in the high-temperature superconductor YBa₂Cu₃O_6.85 and in the nonsuperconducting compound YBa₂Cu₃O_6.25. The copper-oxygen cluster model with spin S=2 best describes the results obtained in a sample with an oxygen index of 6.25. The interpretation of the experimental results for a sample with an oxygen index of 6.85, on the other hand, requires the additional assumption that the cluster S=2 also has a 200-fold degenerate level at a distance ∼110 K. Fiz. Tverd. Tela (St. Petersburg) 39, 432–436 (March 1997)     

Spin state and exchange in the quasi-one-dimensional antiferromagnet KFeS2

We report the optical spectra and single crystal magnetic susceptibility of the one-dimensional antiferromagnet KFeS₂. Measurements have been carried out to ascertain the spin state of Fe³⁺ and the nature of the magnetic interactions in this compound. The optical spectra and magnetic susceptibility could be consistently interpreted using aS=1/2 spin ground state for the Fe³⁺ ion. The features in the optical spectra have been assigned to transitions within thed-electron manifold of the Fe³⁺ ion, and analysed in the strong field limit of the ligand field theory. The high temperature isotropic magnetic susceptibility is typical of a low-dimensional system and exhibits a broad maximum at ∼565K. The susceptibility shows a well defined transition to a three dimensionally ordered antiferromagnetic state atT _N=250 K. The intra and interchain exchange constants,J andJ′, have been evaluated from the experimental susceptibilities using the relationship between these quantities, andχ _max,T _max, andT _N for a spin 1/2 one-dimensional chain. The values areJ=−440.71 K, andJ′=53.94 K. Using these values ofJ andJ′, the susceptibility of a spin 1/2 Heisenberg chain was calculated. A non-interacting spin wave model was used belowT _N. The susceptibility in the paramagnetic region was calculated from the theoretical curves for an infiniteS=1/2 chain. The calculated susceptibility compares well with the experimental data of KFeS₂. Further support for a one-dimensional spin 1/2 model comes from the fact that the calculated perpendicular susceptibility at 0K (2.75×10⁻⁴ emu/mol) evaluated considering the zero point reduction in magnetization from spin wave theory is close to the projected value (2.7×10⁻⁴ emu/mol) obtained from the experimental data.     

UNO DMRG CASCI calculations of effective exchange integrals for m-phenylene-bis-methylene spin clusters

ABSTRACT

Theoretical examinations of the ferromagnetic coupling in the m-phenylene-bis-methylene molecule and its oligomer were carried out. These systems are good candidates for exchange-coupled systems to investigate strong electronic correlations. We studied effective exchange integrals (J), which indicated magnetic coupling between interacting spins in these species. First, theoretical calculations based on a broken-symmetry single-reference procedure, i.e. the UHF, UMP2, UMP4, UCCSD(T) and UB3LYP methods, were carried out with a GAUSSIAN program code under an SR wave function. From these results, the J value by the UHF method was largely positive because of the strong ferromagnetic spin polarisation effect. The J value by the UCCSD(T) and UB3LYP methods improved an overestimation problem by correcting the dynamical electronic correlation. Next, magnetic coupling among these spins was studied using the CAS-based method of the symmetry-adapted multireference methods procedure. Thus, the UNO DMRG CASCI (UNO, unrestricted natural orbital; DMRG, density matrix renormalised group; CASCI, complete active space configuration interaction) method was mainly employed with a combination of ORCA and BLOCK program codes. DMRG CASCI calculations in valence electron counting, which included all orbitals to full valence CI, provided the most reliable result, and support the UB3LYP method for extended systems.     

Spin solitons and waves in chiral molecular ferrimagnets

Resonance modes corresponding to a spin-soliton resonance have been found in the electron spin resonance spectra of [Cr(CN)₆][Mn(S)-pnH-(H₂O)]H₂O two-dimensional (2D) chiral single crystals and [Mn{(R/S)-pn}]₂[Mn{(R/S)-pn}₂(H₂O)][Cr(CN)₆]₂ chiral single crystals with a 3D magnetic order. It is also established that the chiral crystals of both types exhibit a spin-wave resonance analogous to the excitation of standing spin waves in thin magnetic films. At the same time, racemic crystals of the first type do not exhibit spin-soliton resonance. The entire body of experimental data indicates that the chirality of crystals influences the spin excitations (standing spin waves and solitons) in these media.     

High spin state of Mn in an ideal monolayer on Ag(001)

We studied the magnetic properties of ultra-thin Mn films deposited on Ag (001) held at 80 K with soft X-ray absorption and magnetic circular dichroism. The observed shape and branching ratio of the Mn 2p absorption edge as a function of Mn coverage demonstrate that, up to , the Mn adopts a stable high spin state similar to the Mn atom Hund's rule ⁶ S _5/2 ground state. Above this coverage a rapid transition from localized high spin to itinerant low spin behavior of the Mn 3d electrons is evidenced. Magnetic circular dichroism shows no sign of long range ferromagnetic order in these films at 80 K. The data, first confirm the large atomic-like local magnetic moment, and second are in line with the in-plane antiferromagnetic order, reported recently (Phys. Rev. B 57, 1141 (1998)), for Mn in the nearly ideal on-top Mn monolayer formed by 0.9 ML deposited at 80 K. Received: 4 May 1998     

An electron paramagnetic resonance study of a manganese(IV) ion in a trigonal environment

An electron paramagnetic resonance (E.P.R.) study on ammonium 9-molybdomanganate (NH₄)₆MnMo₉O₃₂.8H₂O, has been carried out. The system has a Mn(IV) central ion and can be considered as a d ³ ion in a D ₃ environment. The results are fitted to a spin hamiltonian with S = 3/2 and I = 5/2 which is due to ⁵⁵Mn. The values of the spin hamiltonian parameters determined were

A ligand field theory approach has been taken in an attempt to interpret the observed zero-field splitting parameter.     

Investigation of the magnetic properties of chains with alternating ferro-and antiferromagnetic exchange interactions in the Heisenberg model with spin S=1/2

The quantum Monte Carlo method is used to calculate the susceptibility and pairwise spin-spin correlation functions of chains with alternating ferro (K)-and antiferromagnetic (J)-exchange interactions within the Heisenberg model with spin S=1/2. From the susceptibility, the energy gap between the ground state and excited triplet states is determined or arbitrary ratios K/J. The value of the gap coincides with the Haldane gap for spin S=1 when K/J>1.25. Fiz. Tverd. Tela (St. Petersburg) 41, 1650–1651 (September 1999)     

Molecular magnetism of a linear Fe(III)-Mn(II)-Fe(III) complex. Influence of long-range exchange interaction

The magnetic properties of [L-Fe(III)-dmg₃Mn(II)-Fe(III)-L] (ClO₄)₂ have been characterized by magnetic susceptibility, EPR, and Mössbauer studies. L represents 1,4,7-trimethyl-, 1,4,7-triazacyclononane and dmg represents dimethylglyoxime. X-ray diffraction measurements yield that the arrangement of the three metal centers is strictly linear with atomic distancesd _Fe-Mn=0.35 nm andd _Fe-Fe=0.7 nm. Magnetic susceptibility measurements (3–295 K) were analyzed in the framework of the spin-Hamiltonian formalism considering Heisenberg exchange and Zeeman interaction:=J _Fe-Mn(S _Fe1+S _Fe2)S _Mn +J _Fe-Fe(S _Fe1 S _Fe2) +g_B S _total B. The spinsS _Fe1=S _Fe2 =S _Mn=5/2 of the complex are antiferromagnetically coupled, yielding a total spin ofS _total=5/2 with exchange coupling constantsF _Fe-Mn=13.4 cm^–1 andJ _Fe-Fe= 4.5 cm^–1. Magnetically split Mössbauer spectra were recorded at 1.5 K under various applied fields (20 mT, 170 mT, 4T). The spin-Hamiltonian analysis of these spectra yields isotropic magnetic hyperfine coupling withA _total/(g _{N N})=–18.5 T. The corresponding local componentA _Fe is related toA _total via spin-projection:A _total=(6/7)A_Fe. The resultingA _Fe/(g _NN)=–21.6 T is in agreement with standard values of ferric high-spin complexes. Spin-Hamiltonian parameters as obtained from Mössbauer studies and exchange coupling constants as derived from susceptibility measurements are corroborated by temperature-dependent EPR studies.     

Structural Assignment of Stilbenethiols and Chalconethiols and Differentiation of Their Isomeric Derivatives by Means of 1H‐ and 13C‐NMR Spectroscopy

Abstract

The ¹H‐ and ¹³C‐NMR spectra of some substituted stilbenes and chalcones were assigned unambiguously on the basis of a combination of homo‐ (COSY) and heteronuclear (HETCOR) two‐dimensional methods, the chemical shifts, as well as spin‐coupling constants. The A_ik empirical parameters of the –O–C(S)–N(CH₃)₂, –S–C(O)–N(CH₃)₂, and –SH group were calculated to help predict the chemical shifts of substituted stilbenes, 4′‐nitrostilbenes, and chalcones. The ¹H‐ and ¹³C‐NMR spectra have been shown to be able to differentiate between the isomers of O‐stilbenyl (4, 5) and S‐stilbenyl N,N‐dimethylthiocarbamates (7, 8) as well as O‐chalconyl (6) and S‐chalconyl N,N‐dimethylthiocarbamates (9).