EPR-ENDOR characterization of (17O, 1H, 2H) water in manganese catalase and its relevance to the oxygen-evolving complex of photosystem II

The synthesis of efficient water-oxidation catalysts demands insight into the only known, naturally occurring water-oxidation catalyst, the oxygen-evolving complex (OEC) of photosystem II (PSII). Understanding the water oxidation mechanism requires knowledge of where and when substrate water binds to the OEC. Mn catalase in its Mn(III)-Mn(IV) state is a protein model of the OEC's S(2) state. From (17)O-labeled water exchanged into the di-μ-oxo di-Mn(III,IV) coordination sphere of Mn catalase, CW Q-band ENDOR spectroscopy revealed two distinctly different (17)O signals incorporated in distinctly different time regimes. First, a signal appearing after 2 h of (17)O exchange was detected with a 13.0 MHz hyperfine coupling. From similarity in the time scale of isotope incorporation and in the (17)O μ-oxo hyperfine coupling of the di-μ-oxo di-Mn(III,IV) bipyridine model (Usov, O. M.; Grigoryants, V. M.; Tagore, R.; Brudvig, G. W.; Scholes, C. P. J. Am. Chem. Soc. 2007, 129, 11886-11887), this signal was assigned to μ-oxo oxygen. EPR line broadening was obvious from this (17)O μ-oxo species. Earlier exchange proceeded on the minute or faster time scale into a non-μ-oxo position, from which (17)O ENDOR showed a smaller 3.8 MHz hyperfine coupling and possible quadrupole splittings, indicating a terminal water of Mn(III). Exchangeable proton/deuteron hyperfine couplings, consistent with terminal water ligation to Mn(III), also appeared. Q-band CW ENDOR from the S(2) state of the OEC was obtained following multihour (17)O exchange, which showed a (17)O hyperfine signal with a 11 MHz hyperfine coupling, tentatively assigned as μ-oxo-(17)O by resemblance to the μ-oxo signals from Mn catalase and the di-μ-oxo di-Mn(III,IV) bipyridine model.     

Electronic structure of the Mn4OxCa cluster in the S0 and S2 states of the oxygen-evolving complex of photosystem II based on pulse 55Mn-ENDOR and EPR spectroscopy

The heart of the oxygen-evolving complex (OEC) of photosystem II is a Mn4OxCa cluster that cycles through five different oxidation states (S0 to S4) during the light-driven water-splitting reaction cycle. In this study we interpret the recently obtained 55Mn hyperfine coupling constants of the S0 and S2 states of the OEC [Kulik et al. J. Am. Chem. Soc. 2005, 127, 2392-2393] on the basis of Y-shaped spin-coupling schemes with up to four nonzero exchange coupling constants, J. This analysis rules out the presence of one or more Mn(II) ions in S0 in methanol (3%) containing samples and thereby establishes that the oxidation states of the manganese ions in S0 and S2 are, at 4 K, Mn4(III, III, III, IV) and Mn4(III, IV, IV, IV), respectively. By applying a "structure filter" that is based on the recently reported single-crystal EXAFS data on the Mn4OxCa cluster [Yano et al. Science 2006, 314, 821-825] we (i) show that this new structural model is fully consistent with EPR and 55Mn-ENDOR data, (ii) assign the Mn oxidation states to the individual Mn ions, and (iii) propose that the known shortening of one 2.85 A Mn-Mn distance in S0 to 2.75 A in S1 [Robblee et al. J. Am. Chem. Soc. 2002, 124, 7459-7471] corresponds to a deprotonation of a mu-hydroxo bridge between MnA and MnB, i.e., between the outer Mn and its neighboring Mn of the mu3-oxo bridged moiety of the cluster. We summarize our results in a molecular model for the S0 --> S1 and S1 --> S2 transitions.     

Mn K-edge XANES and Kbeta XES studies of two Mn-oxo binuclear complexes: investigation of three different oxidation states relevant to the oxygen-evolving complex of photosystem II.

Two structurally homologous Mn compounds in different oxidation states were studied to investigate the relative influence of oxidation state and ligand environment on Mn K-edge X-ray absorption near-edge structure (XANES) and Mn Kbeta X-ray emission spectroscopy (Kbeta XES). The two manganese compounds are the di-mu-oxo compound [L'2Mn(III)O2Mn(IV)L'2](ClO4)3, where L' is 1,10-phenanthroline (Cooper, S. R.; Calvin, M. J. Am. Chem. Soc. 1977, 99, 6623-6630) and the linear mono-mu-oxo compound [LMn(III)OMn(III)L](ClO4)2, where L- is the monoanionic N,N-bis(2-pyridylmethyl)-N'-salicylidene-1,2-diaminoethane ligand (Horner, O.; Anxolabéhère-Mallart, E.; Charlot, M. F.; Tchertanov, L.; Guilhem, J.; Mattioli, T. A.; Boussac, A.; Girerd, J.-J. Inorg. Chem. 1999, 38, 1222-1232). Preparative bulk electrolysis in acetonitrile was used to obtain higher oxidation states of the compounds: the Mn(IV)Mn(IV) species for the di-mu-oxo compound and the Mn(III)Mn(IV) and Mn(IV)Mn(IV) species for the mono-mu-oxo compound. IR, UV/vis, EPR, and EXAFS spectra were used to determine the purity and integrity of the various sample solutions. The Mn K-edge XANES spectra shift to higher energy upon oxidation when the ligand environment remains similar. However, shifts in energy are also observed when only the ligand environment is altered. This is achieved by comparing the di-mu-oxo and linear mono-mu-oxo Mn-Mn moieties in equivalent oxidation states, which represent major structural changes. The magnitude of an energy shift due to major changes in ligand environment can be as large as that of an oxidation-state change. Therefore, care must be exercised when correlating the Mn K-edge energies to manganese oxidation states without taking into account the nature of the ligand environment and the overall structure of the compound. In contrast to Mn K-edge XANES, Kbeta XES spectra show less dependence on ligand environment. The Kbeta1,3 peak energies are comparable for the di-mu-oxo and mono-mu-oxo compounds in equivalent oxidation states. The energy shifts observed due to oxidation are also similar for the two different compounds. The study of the different behavior of the XANES pre-edge and main-edge features in conjunction with Kbeta XES provides significant information about the oxidation state and character of the ligand environment of manganese atoms.     

A high-frequency and high-field EPR study of new azide and fluoride mononuclear Mn(III) complexes

The isolation, structural characterization and electronic properties of three new six-coordinated Mn(III) complexes, [Mn(bpea)(F)(3)] (1), [Mn(bpea)(N(3))(3)] (2), and [Mn(terpy)(F)(3)] (3) are reported (bpea = N,N-bis(2-pyridylmethyl)-ethylamine; terpy = 2,2':6',2' '-terpyridine). As for [Mn(terpy)(N(3))(3)] (4) (previously described by Limburg J.; Vrettos J. S.; Crabtree R. H.; Brudvig G. W.; de Paula J. C.; Hassan A.; Barra A-L.; Duboc-Toia C.; Collomb M-N. Inorg. Chem. 2001, 40, 1698), all these complexes exhibit a Jahn-Teller distortion of the octahedron characteristic of high-spin Mn(III) (S = 2). The analysis of the crystallographic data shows an elongation along the tetragonal axis of the octahedron for complexes 1 and 3, while complex 2 presents an unexpected compression. The electronic properties were investigated using a high-field and high-frequency EPR study performed between 5 and 15 K (190-575 GHz). The spin Hamiltonian parameters determined in solid state are in agreement with the geometry of the complexes observed in the crystal structures. A negative D value found for 1 and 3 is related to the elongated tetragonal distortion, whereas the positive D value determined for 2 is in accordance with a compressed octahedron. The high E/D values, in the range of 0.103 to 0.230 for all complexes, are correlated with the highly distorted geometry present around the Mn(III) ion. HF-EPR experiments were also performed on complex 1 in solution and show that the D value is the only spin Hamiltonian parameter which is slightly modified compared to the solid state (D = -3.67 cm(-1) in solid state; D = -3.95 cm(-1) in solution).     

Linear NiII-MnIII2-NiII tetramers: an oligomeric component of the MnIII2NiII single-chain magnets

Heterometallic linear tetramers [Mn(5-R-saltmen)Ni(pao)(bpy)(2)](2)(ClO(4))(4) (5-R-saltmen(2-) = N,N'-1,1,2,2-tetramethylethylene bis(5-R-salicylideneiminate); pao(-) = pyridine-2-aldoximate; bpy = 2,2'-bipyridine, R = H, 1; Cl, 2; Br, 3; MeO, 4) have been synthesized and structurally characterized. These compounds exhibit a [Ni(II)-NO-Mn(III)-(O)(2)-Mn(III)-ON-Ni(II)] skeleton where -ON- is an oximate bridge between Mn(III) and Ni(II) ions and -(O)(2)- is a bi-phenolate bridge between Mn(III) ions. These tetramers can be seen as oligomeric units of the heterometallic Mn(III)(2)-Ni(II) chain observed in a family of single-chain magnets (Clérac, R.; Miyasaka, H.; Yamashita, M.; Coulon, C. J. Am. Chem. Soc. 2002, 124, 12837. Miyasaka, H.; Clérac, R.; Mizushima, K.; Sugiura, K.; Yamashita, M.; Wernsdorfer, W.; Coulon, C. Inorg. Chem. 2003, 42, 8203.). Magnetic measurements on these tetramers confirm the nature of the magnetic interactions reported for the Mn(III)(2)-Ni(II) chains: a strong antiferromagnetic Mn(III)/Ni(II) coupling via the oximate bridge (J(Ni-Mn) ranges from -23.7 to -26.1 K) and a weak ferromagnetic Mn(III)/Mn(III) coupling through the bi-phenolate bridge (J(Mn-Mn) ranges from +0.4 to +0.9 K). These magnetic interactions lead to tetramers with an S = 2 ground state.     

High-frequency and field EPR investigation of (8,12-diethyl-2,3,7,13,17,18-hexamethylcorrolato)manganese(III)

High-field and frequency electron paramagnetic resonance (HFEPR) of solid (8,12-diethyl-2,3,7,13,17,18-hexamethylcorrolato)manganese(III), 1, shows that in the solid state it is well described as an S = 2 (high-spin) Mn(III) complex of a trianionic ligand, [Mn(III)C(3)(-)], just as Mn(III) porphyrins are described as [Mn(III)P(2)(-)](+). Comparison among the structural data and spin Hamiltonian parameters reported for 1, Mn(III) porphyrins, and a different Mn(III) corrole, [(tpfc)Mn(OPPh(3))], previously studied by HFEPR (Bendix, J.; Gray, H. B.; Golubkov, G.; Gross, Z. J. Chem. Soc., Chem. Commun. 2000, 1957-1958), shows that despite the molecular asymmetry of the corrole macrocycle, the electronic structure of the Mn(III) ion is roughly axial. However, in corroles, the S = 1 (intermediate-spin) state is much lower in energy than in porphyrins, regardless of axial ligand. HFEPR of 1 measured at 4.2 K in pyridine solution shows that the S = 2 [Mn(III)C(3)(-)] system is maintained, with slight changes in electronic parameters that are likely the consequence of axial pyridine ligand coordination. The present result is the first example of the detection by HFEPR of a Mn(III) complex in solution. Over a period of hours in pyridine solution at ambient temperature, however, the S = 2 Mn(III) spectrum gradually disappears leaving a signal with g = 2 and (55)Mn hyperfine splitting. Analysis of this signal, also observable by conventional EPR, leads to its assignment to a manganese species that could arise from decomposition of the original complex. The low-temperature S = 2 [Mn(III)C(3)(-)] state is in contrast to that at room temperature, which is described as a S = 1 system deriving from antiferromagnetic coupling between an S = (3/2) Mn(II) ion and a corrole-centered radical cation: [Mn(II)C(*)(2-)] (Licoccia, S.; Morgante, E.; Paolesse, R.; Polizio, F.; Senge, M. O.; Tondello, E.; Boschi, T. Inorg. Chem. 1997, 36, 1564-1570). This temperature-dependent valence state isomerization has been observed for other metallotetrapyrroles.     

Effect of Ca2+/Sr2+ substitution on the electronic structure of the oxygen-evolving complex of photosystem II: a combined multifrequency EPR, 55Mn-ENDOR, and DFT study of the S2 state

The electronic structures of the native Mn(4)O(x)Ca cluster and the biosynthetically substituted Mn(4)O(x)Sr cluster of the oxygen evolving complex (OEC) of photosystem II (PSII) core complexes isolated from Thermosynechococcus elongatus, poised in the S(2) state, were studied by X- and Q-band CW-EPR and by pulsed Q-band (55)Mn-ENDOR spectroscopy. Both wild type and tyrosine D less mutants grown photoautotrophically in either CaCl(2) or SrCl(2) containing media were measured. The obtained CW-EPR spectra of the S(2) state displayed the characteristic, clearly noticeable differences in the hyperfine pattern of the multiline EPR signal [Boussac et al. J. Biol. Chem.2004, 279, 22809-22819]. In sharp contrast, the manganese ((55)Mn) ENDOR spectra of the Ca and Sr forms of the OEC were remarkably similar. Multifrequency simulations of the X- and Q-band CW-EPR and (55)Mn-pulsed ENDOR spectra using the Spin Hamiltonian formalism were performed to investigate this surprising result. It is shown that (i) all four manganese ions contribute to the (55)Mn-ENDOR spectra; (ii) only small changes are seen in the fitted isotropic hyperfine values for the Ca(2+) and Sr(2+) containing OEC, suggesting that there is no change in the overall spin distribution (electronic coupling scheme) upon Ca(2+)/Sr(2+) substitution; (iii) the changes in the CW-EPR hyperfine pattern can be explained by a small decrease in the anisotropy of at least two hyperfine tensors. It is proposed that modifications at the Ca(2+) site may modulate the fine structure tensor of the Mn(III) ion. DFT calculations support the above conclusions. Our data analysis also provides strong support for the notion that in the S(2) state the coordination of the Mn(III) ion is square-pyramidal (5-coordinate) or octahedral (6-coordinate) with tetragonal elongation. In addition, it is shown that only one of the currently published OEC models, the Siegbahn structure [Siegbahn, P. E. M. Acc. Chem. Res.2009, 42, 1871-1880, Pantazis, D. A. et al. Phys. Chem. Chem. Phys.2009, 11, 6788-6798], is consistent with all data presented here. These results provide important information for the structure of the OEC and the water-splitting mechanism. In particular, the 5-coordinate Mn(III) is a potential site for substrate 'water' (H(2)O, OH(-)) binding. Its location within the cuboidal structural unit, as opposed to the external 'dangler' position, may have important consequences for the mechanism of O-O bond formation.     

S1-state Mn4Ca complex of Photosystem II exists in equilibrium between the two most-stable isomeric substates: XRD and EXAFS evidence

Photosynthetic water oxidation reaction driven by Sun and catalyzed by a unique Mn(4)Ca cluster in Photosystem II (PSII) is known to take place in an oxygen evolving complex (OEC) that cycles five serial redox states, named "Kok's S(i)-states" (i=0-4). Recently, the atomic crystal structure of PSII from Thermosynechococcus vulcanus was resolved by 1.9 ?-resolution XRD data [55]. Interestingly, it revealed an unusual oxo-bridged Mn(4)CaO(5) cluster in the dark stable S(1)-state, e.g. unusual mono-μ(2)-oxo-mono-μ(4)-oxo-mono-μ(2)-carboxylato bridges connecting Mn(a) (terminal) and Mn(b) (central) ions with unusual atomic distance of 2.9 ?. Using the UDFT/B3LYP/lacvp** geometry optimization method and a truncated cluster model of the chemically-complete OEC put in ε=4 dielectric medium, it is shown that the OEC in S(1) must be in thermal equilibrium between the most-stable isomeric substates ("S(1a) and S(1b)") owing to the quasi-reversible structure change induced by proton migration. Coincidentally, it is found that the Mn(a)-Mn(b) distances in the Mn(4)Ca clusters in S(1a) and S(1b) are given by R(ab)=3.32 ? and 2.77 ?, respectively, so that the apparent distance between Mn(a) and Mn(b) ions in isomeric equilibrium is given by 2.94 ?, in agreement with experimental R(ab)~2.9 ?. Concomitantly, the first full-k-range EXAFS spectrum from powdered PSII [45] is used to provide the second experimental evidence for the S(1)-state OEC being in thermal equilibrium between S(1a) and S(1b)-isomers. These OEC-isomers consist of all the chemically-essential 11 amino acid residues, six cofactor ions and nine essential hydrated water molecules in their chemical ionic states around physiological pH 7, thus reasonably satisfying the biochemical charge neutrality with four Mn ions staying at the oxidation states (Mn(a)(III)/Mn(b)(IV)/Mn(c)(III)/Mn(d)(IV)) with the skeleton structures of MT-5J type and T-shaped DD-4J type. These H-bonding water molecules are found to fill a cavity connecting possible substrate/products channels so as to be arranged as an indispensable part of the catalytic Mn(4)Ca cluster in the order of "current-substrates" (W1/W2 bound to Mn(a)(III)), "next-substrates" (W4/W7) and "next-after-next-substrates" (W5/W6 bound to Ca(2+)). Results show that the Jahn-Teller effect due to Mn(a)(III) ion in these isomers can reasonably explain the very-slow-exchange and very-fast-exchange processes observed in S(1) by time-resolved (18)O-exchange mass spectroscopy.     

Rotationally resolved C2 symmetric conformers of bis-(4-hydroxyphenyl)methane: prototypical examples of excitonic coupling in the S1 and S2 electronic states

Rotationally resolved microwave and ultraviolet spectra of jet-cooled bis-(4-hydroxyphenyl)methane (b4HPM) have been obtained using Fourier-transform microwave and UV laser/molecular beam spectrometers. A recent vibronic level study of b4HPM [Rodrigo, C. P.; Mu?ller, C. W.; Pillsbury, N. R.; James, W. H., III; Plusquellic, D. F.; Zwier, T. S. J. Chem. Phys. 2011, 134, 164312] has assigned two conformers distinguished by the orientation of the in-plane OH groups and has identified two excitonic origins in each conformer. In the present study, the rotationally resolved bands of all four states have been well-fit to asymmetric rotor Hamiltonians. For the lower exciton (S(1)) levels, the transition dipole moment (TDM) orientations are perpendicular to the C(2) symmetry axes and consist of 41(2):59(2) and 34(2):66(2)% a:c hybrid-type character. The S(1) levels are therefore delocalized states of B symmetry and represent the antisymmetric combinations of the zero-order locally excited states of the p-cresol-like chromophores. The TDM polarizations of bands located at ≈132 cm(-1) above the S(1) origins are exclusively b-type and identify them as the upper exciton S(2) origin levels of A symmetry. The TDM orientations and the relative band strengths from the vibronic study have been analyzed within a dipole-dipole coupling model in terms of the localized TDM orientations, μ(loc), on the two chromophores. The out-of-the-ring plane angles of μ(loc) are both near 20° and are similar to results for diphenylmethane [Stearns, J. A.; Pillsbury, N. R.; Douglass, K. O.; Mu?ller, C. W.; Zwier, T. S.; Plusquellic, D. F. J. Chem. Phys. 2008, 129, 224305]. The in-plane angles are, however, rotated by 14 and 18° relative to DPM and, in part, explain the smaller than expected exciton splittings of these two conformers.     

Ab initio molecular dynamics studies of tetrasulfur. Dynamics coupling the C2v open and D2h closed forms of S4

Ab initio molecular dynamics (AIMD) simulations were performed on the closed D(2h) and open C(2v) isomers of tetrasulfur. After a careful calibration of the electronic structure method, the calculations were done using the BPW91/aug-cc-pVTZ method. This combination of method/basis set adequately reproduces the relative benchmark CCSD(T) energy difference [Matus, M.; Dixon, D.; Peterson, K. A.; Harkless, J. A. W.; Francisco, J. S. J. Chem. Phys. 2007, 127, 174305] between these two isomers and, crucially, the fact that the D(2h) structure is a transition state linking two equivalent (mirror images) C(2v) isomers. The trajectories show that the symmetric open C(2v) isomers interconvert when passing through the D(2h) closed transition state structure and that, unlike tetraoxygen, no three-dimensional structures arise. The dynamic vibrational analysis yields peaks in good agreement with the static CCSD(T) harmonic frequencies and explains higher peaks as overtones, thus showing that unlike previous AIMD DFT-based approaches, carefully calibrated exchange-correlation functionals can produce reliable molecular dynamics results for complex PESs as the one corresponding to the lowest singlet of S(4).     

Internal electric field in cytochrome C explored by visible electronic circular dichroism spectroscopy

Electronic circular dichroism (ECD) is a valuable tool to explore the secondary and tertiary structure of proteins. With respect to heme proteins, the corresponding visible ECD spectra, which probe the chirality of the heme environment, have been used to explore functionally relevant structural changes in the heme vicinity. While the physical basis of the obtained ECD signal has been analyzed by Woody and co-workers in terms of multiple electronic coupling mechanism between the electronic transitions of the heme chromophore and of the protein (Hsu, M.C.; Woody, R.W. J. Am. Chem. Soc. 1971, 93, 3515), a theory for a detailed quantitative analysis of ECD profiles has only recently been developed (Schweitzer-Stenner, R.; Gorden, J. P.; Hagarman, A. J. Chem. Phys. 2007, 127, 135103). In the present study this theory is applied to analyze the visible ECD-spectra of both oxidation states of three cytochromes c from horse, cow and yeast. The results reveal that both B- and Q-bands are subject to band splitting, which is caused by a combination of electronic and vibronic perturbations. The B-band splittings are substantially larger than the corresponding Q-band splittings in both oxidation states. For the B-bands, the electronic contribution to the band splitting can be assigned to the internal electric field in the heme pocket, whereas the corresponding Q-band splitting is likely to reflect its gradient (Manas, E. S.; Vanderkooi, J. M.; Sharp, K. A. J. Phys. Chem. B 1999, 103, 6344). We found that the electronic and vibronic splitting is substantially larger in the oxidized than in the reduced state. Moreover, these states exhibit different signs of electronic splitting. These findings suggest that the oxidation process increases the internal electric field and changes its orientation with respect to the molecular coordinate system associated with the N-Fe-N lines of the heme group. For the reduced state, we used our data to calculate electric field strengths between 27 and 31 MV/cm for the investigated cytochrome c species. The field of the oxidized state is more difficult to estimate, owing to the lack of information about its orientation in the heme plane. Based on band splitting and the wavenumber of the band position we estimated a field-strength of ca. 40 MV/cm for oxidized horse heart cytochrome c. The thus derived difference between the field strengths of the oxidized and reduced state would contribute at least -55 kJ/mol to the enthalpic stabilization of the oxidized state. Our data indicate that the corresponding stabilization energy of yeast cytochrome c is smaller.     

Metal oxidation states in biological water splitting

A central question in biological water splitting concerns the oxidation states of the manganese ions that comprise the oxygen-evolving complex of photosystem II. Understanding the nature and order of oxidation events that occur during the catalytic cycle of five S_i states (i = 0–4) is of fundamental importance both for the natural system and for artificial water oxidation catalysts. Despite the widespread adoption of the so-called “high-valent scheme”—where, for example, the Mn oxidation states in the S₂ state are assigned as III, IV, IV, IV—the competing “low-valent scheme” that differs by a total of two metal unpaired electrons (i.e. III, III, III, IV in the S₂ state) is favored by several recent studies for the biological catalyst. The question of the correct oxidation state assignment is addressed here by a detailed computational comparison of the two schemes using a common structural platform and theoretical approach. Models based on crystallographic constraints were constructed for all conceivable oxidation state assignments in the four (semi)stable S states of the oxygen evolving complex, sampling various protonation levels and patterns to ensure comprehensive coverage. The models are evaluated with respect to their geometric, energetic, electronic, and spectroscopic properties against available experimental EXAFS, XFEL-XRD, EPR, ENDOR and Mn K pre-edge XANES data. New 2.5 K ⁵⁵Mn ENDOR data of the S₂ state are also reported. Our results conclusively show that the entire S state phenomenology can only be accommodated within the high-valent scheme by adopting a single motif and protonation pattern that progresses smoothly from S₀ (III, III, III, IV) to S₃ (IV, IV, IV, IV), satisfying all experimental constraints and reproducing all observables. By contrast, it was impossible to construct a consistent cycle based on the low-valent scheme for all S states. Instead, the low-valent models developed here may provide new insight into the over-reduced S states and the states involved in the assembly of the catalytically active water oxidizing cluster.     

Validation studies of the site-directed docking program LibDock

The performance of the site-features docking algorithm LibDock has been evaluated across eight GlaxoSmithKline targets as a follow-up to a broad validation study of docking and scoring software (Warren, G. L.; Andrews, W. C.; Capelli, A.; Clarke, B.; Lalonde, J.; Lambert, M. H.; Lindvall, M.; Nevins, N.; Semus, S. F.; Senger, S.; Tedesco, G.; Walls, I. D.; Woolven, J. M.; Peishoff, C. E.; Head, M. S. J. Med. Chem. 2006, 49, 5912-5931). Docking experiments were performed to assess both the accuracy in reproducing the binding mode of the ligand and the retrieval of active compounds in a virtual screening protocol using both the DJD (Diller, D. J.; Merz, K. M., Jr. Proteins 2001, 43, 113-124) and LigScore2 (Krammer, A. K.; Kirchoff, P. D.; Jiang, X.; Venkatachalam, C. M.; Waldman, M. J. Mol. Graphics Modell. 2005, 23, 395-407) scoring functions. This study was conducted using DJD scoring, and poses were rescored using all available scoring functions in the Accelrys LigandFit module, including LigScore2. For six out of eight targets at least 30% of the ligands were docked within a root-mean-square difference (RMSD) of 2.0 A for the crystallographic poses when the LigScore2 scoring function was used. LibDock retrieved at least 20% of active compounds in the top 10% of screened ligands for four of the eight targets in the virtual screening protocol. In both studies the LigScore2 scoring function enhanced the retrieval of crystallographic poses or active compounds in comparison with the results obtained using the DJD scoring function. The results for LibDock accuracy and ligand retrieval in virtual screening are compared to 10 other docking and scoring programs. These studies demonstrate the utility of the LigScore2 scoring function and that LibDock as a feature directed docking method performs as well as docking programs that use genetic/growing and Monte Carlo driven algorithms.     

Oxidation state dependence of the geometry, electronic structure, and magnetic coupling in mixed oxo- and carboxylato-bridged manganese dimers

Approximate density functional theory has been used to investigate changes in the geometry and electronic structure of the mixed oxo- and carboxylato-bridged dimers [Mn(2)(mu-O)(2)(O(2)CH)(NH(3))(6)](n+)and [Mn(2)(mu-O)(O(2)CH)(2)(NH(3))(6)](n+)in the Mn(IV)Mn(IV), Mn(III)Mn(IV), and Mn(III)Mn(III) oxidation states. The magnetic coupling in the dimer is profoundly affected by changes in both the bridging ligands and Mn oxidation state. In particular, change in the bridging structure has a dramatic effect on the nature of the Jahn-Teller distortion observed for the Mn(III) centers in the III/III and III/IV dimers. The principal magnetic interactions in [Mn(2)(mu-O)(2)(O(2)CH)(NH(3))(6)](n+)() involve the J(xz/xz)and J(yz/yz) pathways but due to the tilt of the Mn(2)O(2) core, they are less efficient than in the planar di-mu-oxo structure and, consequently, the calculated exchange coupling constants are generally smaller. In both the III/III and III/IV dimers, the Mn(III) centers are high-spin, and the Jahn-Teller effect gives rise to axially elongated Mn(III) geometries with the distortion axis along the Mn-O(c) bonds. In the III/IV dimer, the tilt of the Mn(2)O(2) core enhances the crossed exchange J(x)()()2(-)(y)()()2(/)(z)()()2 pathway relative to the planar di-mu-oxo counterpart, leading to significant delocalization of the odd electron. Since this delocalization pathway partially converts the Mn(IV) ion into low-spin Mn(III), the magnetic exchange in the ground state can be considered to arise from two interacting spin ladders, one is the result of coupling between Mn(IV) (S = 3/2) and high-spin Mn(III) (S = 2), the other is the result of coupling between Mn(IV) (S = 3/2) and low-spin Mn(III) (S = 1). In [Mn(2)(mu-O)(O(2)CH)(2)(NH(3))(6)](n+)(), both the III/III dimer and the lowest energy structure for the III/IV dimer involve high-spin Mn(III), but the Jahn-Teller axis is now orientated along the Mn-oxo bond, giving rise to axially compressed Mn(III) geometries with long Mn-O(c) equatorial bonds. In the IV/IV dimer, the ferromagnetic crossed exchange J(yz)()(/)(z)()()2 pathway partially cancels J(yz/yz) and, as a consequence, the antiferromagnetic J(xz/xz) pathway dominates the magnetic coupling. In the III/III dimer, the J(yz/yz) pathway is minimized due to the smaller Mn-O-Mn angle, and since the ferromagnetic J(yz)()(/)(z)()()2 pathway largely negates J(xz/xz), relatively weak overall antiferromagnetic coupling results. In the III/IV dimer, the structures involving high-spin and low-spin Mn(III) are almost degenerate. In the high-spin case, the odd electron is localized on the Mn(III) center, and the resulting antiferromagnetic coupling is similar to that found for the IV/IV dimer. In the alternative low-spin structure, the odd electron is significantly delocalized due to the crossed J(yz)()(/)(z)()()2 pathway, and cancellation between ferromagnetic and antiferromagnetic pathways leads to overall weak magnetic coupling. The delocalization partially converts the Mn(IV) ion into high-spin Mn(III), and consequently, the spin ladders arising from coupling of Mn(IV) (S = 3/2) with high-spin (S = 2) and low-spin (S = 1) Mn(III) are configurationally mixed. Thus, in principle, the ground-state magnetic coupling in the mixed-valence dimer will involve contributions from three spin-ladders, two associated with the delocalized low-spin structure and the third arising from the localized high-spin structure.     

Isolation of the first ferromagnetically coupled Mn(III/IV) complex

Binuclear manganese complexes Mn2(III/IV)(dtsalpn)2DCBI, 1, Mn2(III/III)(dtsalpn)2HDCBI, 2, containing the ligand dicarboxyimidazole (DCBI) have been prepared in order to address the issue of imidazole bridged and ferromagnetically coupled Mn sites in high oxidation states of the OEC in Photosystem II (PS II). Temperature dependent magnetic susceptibility studies of 1 indicates that the interaction between the two Mn(III)/Mn(IV) ions is ferromagnetic (J = +1.4 cm(-1)). Variable temperature EPR spectra of 1 shows that a g = 2 multiline is as an excited state signal corresponding to S = 1/2.     

Orbital Configuration of the Valence Electrons, Ligand Field Symmetry, and Manganese Oxidation States of the Photosynthetic Water Oxidizing Complex: Analysis of the S(2) State Multiline EPR Signals

A theoretical framework is presented for analysis of all three "multiline" EPR spectra (MLS) arising from the tetramanganese (Mn(4)) cluster in the S(2) oxidation state of the photosynthetic water oxidizing complex (WOC). Accurate simulations are presented which include anisotropy of the g and (four) (55)Mn hyperfine tensors, chosen according to a database of (55)Mn(III) and (55)Mn(IV) hyperfine tensors obtained previously using unbiased least-squares spectral fitting routines. In view of the large (30%) anisotropy common to Mn(III) hyperfine tensors in all complexes, previous MLS simulations which have assumed isotropic hyperfine constants have required physically unrealistic parameters. A simple model is found which offers good simulations of both the native "19-21-line" MLS and the "26-line" NH(3)-bound form of the MLS. Both a dimer-of-dimers and distorted-trigonal magnetic models are examined to describe the symmetry of the Heisenberg exchange interactions within the Mn(4) cluster and thus define the initial electronic basis states of the cluster. The effect of rhombic symmetry distortions is explicitly considered. Both magnetic models correspond to one of several possible structural models for the Mn(4) cluster proposed independently from Mn EXAFS studies. Simulated MLS were constructed for each of the eight (or seven) doublet states of the Mn(4) cluster in the WOC for the two viable oxidation models (3Mn(III)-1Mn(IV) or 3Mn(IV)-1Mn(III)), and using a wide range of axial Mn hyperfine tensors, with either coaxial or orthogonal tensor alignments. We find accurate simulations using the 3Mn(III)-1Mn(IV) oxidation model. In the dimer-of-dimers coupling model, the spin state conversion between two doublet states |S(12),S(34),S(T)|(7)/(2),4,(1)/(2)> and |(7)/(2),3,(1)/(2)> is found to explain the large (25%) contraction in the hyperfine splitting observed upon conversion from the native MLS to the NH(3)-bound MLS. Stabilization of this excited state as the new ground state is caused by change in the intermanganese exchange coupling, without appreciable change in the intrinsic hyperfine tensors. The lack of good simulations of the Ca(2+)-depleted MLS suggests that Ca(2+)-depletion changes both Mn ligation and intermanganese exchange coupling. The 3Mn(IV)-1Mn(III) oxidation model is disfavored because only approximate simulations could be found for the native MLS and no agreement with the NH(3)-bound MLS was obtained. The scalar part of the hyperfine tensors for both Mn(III) and Mn(IV) ions were found to approximate (+/-5%) the values for the dimanganese(III,IV) catalase enzyme, suggesting similar overall ligand types. However, the large (30%) anisotropic part of the Mn(III) hyperfine interaction is opposite in sign to that found in all tetragonally extended six-coordinate Mn(III) ions (i.e., the usual Jahn-Teller splitting). The distribution of spin density from the high-spin d(4) electron configuration of each Mn(III) ion corresponds to a flattened (oblate) ellipsoid. This electronic distribution is favored in five-coordinate ligand fields having trigonally compressed bipyramidal geometry, but it could also arise, in principle, in strained six-coordinate ligand fields having tetragonally compressed geometry, i.e. [Mn(2)(&mgr;-O)](4+) (reverse Jahn-Teller distortion). The resulting valence electronic configurations are described as e'(2)e"(2) and (d(pi))(3)(d(x)()()2(-)(y)()()2)(1), respectively, in contrast to the (d(pi))(3)(d(z)()()2)(1) configuration common to unstrained six-coordinate tetragonally-extended Mn(III) ions, such as found in the [Mn(2)(&mgr;-O)(2)](3+) core in several synthetic dimers and catalase. Both of the former geometries predict strongly oxidizing Mn(III) ions, thereby suggesting a structural basis for the oxidative reactivity of the Mn(4) cluster in the WOC. The magnetic model needed to explain the MLS is not readily reconciled with the simplest structural and electronic models deduced from EXAFS studies of the WOC.     

Cooperative pull and push effects on the O-O bond cleavage in acylperoxo complexes of [(Salen)MnIIIL]: ensuring formation of manganese(V) oxo species

The acidity (pull) and the axial ligand (push) effects on the O-O bond cleavage in the [(Salen)Mn(III)(RCO(3))L] acylperoxo complexes, with model L = none, NH(3), and HCO(2)(-) (1), have been studied with B3LYP density functional calculations. The acidic conditions have been mimicked by explicit protonation of 1 to afford a variety of [(Salen)Mn(III)(RCO(3)H)L] (2) and [(SalenH)Mn(III)(RCO(3))L] (3) complexes in ground quintet states. The protonation assists the O-O bond heterolysis, thus primarily forming highly reactive Mn(V)(O) species, and consequently suppresses formation of the less reactive Mn(IV)(O) species through homolytic channel described earlier in 1 [Khavrutskii, I. V.; Rahim, R. R.; Musaev, D. G.; Morokuma, K. J. Phys. Chem. B 2004, 108, 3845-3854]. In addition to the qualitative change of the O-O bond cleavage mode, the protonation affects the rate of the O-O bond cleavage. Therefore, varying the acidity of the reaction media helps control the O-O bond cleavage mode and rate.     

Unusual oxidation state distributions observed for two mixed-valence heptanuclear manganese disc-like clusters

The synthesis, structures and magnetic properties of two new mixed-valence heptanuclear manganese clusters are described. Both complexes utilize triethanolamine (teaH(3)) as a bridging ligand, displaying near planar, disc-like metal topologies and are of formulae [Mn(II)(4)Mn(IV)(3)(tea)(teaH(2))(3)(peolH)(4)](BF(4))(2)·solv (1) and [Mn(II)(4)Mn(III)(3)F(3)(tea)(teaH)(teaH(2))(2)(piv)(4)(Hpiv)(chp)(3)]·0.5MeCN (2). Compound 1 is a rare mixed-valence compound containing Mn(II) and Mn(IV) ions only and is the first example of a heptanuclear disc with a {Mn(II)(4)Mn(IV)(3)} oxidation state distribution. Compound 2 is a {Mn(II)(4)Mn(III)(3)} complex and displays a unique arrangement of oxidation states within the disc, when compared to other known {Mn(II)(4)Mn(III)(3)} examples. Variable temperature DC and AC magnetic susceptibility studies were carried out for 1 and 2 in the 2-300 K temperature range. Compound 1 displayed an increase in the χ(M)T susceptibility values as the temperature is decreased indicating dominant ferromagnetic interactions are present within the cluster. Fits of the χ(M)T vs. T data reveals an S = 23/2 ground state, with several close lying excited states within 1 cm(-1). Compound 2 displays an overall decrease in the χ(M)T value as the temperature is decreased down to 2 K indicating dominant antiferromagnetic interactions present with a probable S = 4 ground state as determined from the DC and AC susceptibility data.     

An electron paramagnetic resonance study of Mn2(H2O)(OAc)4(tmeda)2 (tmeda = N,N,N',N'-tetramethylethylenediamine): a model for dinuclear manganese enzyme active sites

The complex Mn2(H2O)(OAc)4(tmeda)2 (tmeda = N,N,N',N'-tetramethylethylenediamine) is a model for the active site of hydrolase enzymes containing acetate-bridged dimanganese cores. The two high-spin Mn(II) ions are antiferromagnetically coupled, as determined by previous magnetic susceptibility studies (Yu, S.-B; Lippard, S. J.; Shweky, I; Bino, A. Inorg. Chem. 1992, 31, 3502-3504) to yield a spin "ladder" with total spin S = 0, 1, 2, ..., 5 in increasing energy. In this study, the complex was characterized by Q-band and X-band EPR spectroscopy in frozen solution. Analysis of the temperature dependence of these EPR spectra indicates that the primary spectral contribution is from the S = 2 manifold. The EPR spectra were simulated using a full spin Hamiltonian for this manifold of a coupled spin system, which provided the fit parameters J = -2.9 cm-1, g = 2.00, and D2 = -0.060 +/- 0.003 cm-1. An additional multiline EPR signal is observed which is proposed to arise from the total spin S = 5/2 ground state of a Mn(II) trimer of the type Mn3(OAc)6(tmeda)2.     

The reaction OH + C2H4: an example of rotational channel switching

The low-temperature data for the reaction between OH and C(2)H(4) is treated canonically as either a two-well or one-well problem using the "Multiwell" suite of codes, in which a "well" refers to a minimum in the potential energy surface. The former is analogous to the two transition state model of Greenwald et al. [Greenwald, E. E.; North, S. W.; Georgievskii, Y.; Klippenstein, S. J. J. Phys. Chem. A2005, 109, 6031], while the latter reflects the dominance of the so-called "inner transition state". External rotations are treated adiabatically, causing changes in the magnitude of effective barriers as a function of temperature. Extant data are well-described with either model using only the average energy transferred in a downward direction, upon collision, ΔE(d)(T), as a fitting parameter. The best value for the parameters describing the rate coefficient as a function of temperature (200 < T/K < 400) (Data at lower temperature is too sparse to yield a recommendation.) and pressure in the form used in the NASA/JPL format [Sander, S. P.; Abbatt, J.; Barker, J. R.; Burkholder, J. B.; Friedl, R. R.; Golden, D. M.; Huie, R. E.; Kolb, C. E.; Kurylo, M. J.; Moortgat, G. K et al., Chemical Kinetics and Photochemical Data for Use in Atmospheric Studies, Evaluation Number 17, Jet Propulsion Laboratory, 2011] are k(0) = 1.0 × 10(-28)(T/300)(-3.5) cm(6) molecule(-2) s(-1) and k(∞) to 8.0 × 10(-12)(T/300)(-2.3) cm(3) molecule(-1) s(-1).