A Computational Study of the S2 State in the Oxygen-Evolving Complex of Photosystem II by Electron Paramagnetic Resonance Spectroscopy

The S₂ state produces two basic electron paramagnetic resonance signal types due to the manganese cluster in oxygen-evolving complex, which are influenced by the solvents, and cryoprotectant added to the photosystem II samples. It is presumed that a single manganese center oxidation occurs on S₁ → S₂ state transition. The S₂ state has readily visible multiline and g4.1 electron paramagnetic resonance signals and hence it has been the most studied of all the Kok cycle intermediates due to the ease of experimental preparation and stability. The S₂ state was studied using electron paramagnetic resonance spectroscopy at X-band frequencies. The aim of this study was to determine the spin states of the g4.1 signal. The multiline signal was observed to arise from a ground state spin ½ centre while the g4.1 signal generated at ≈140 K NIR illumination was proposed to arise from a spin 52 center with rhombic distortion. The ‘ground’ state g4.1 signal was generated solely or by conversion from the multiline. The data analysis methods used involved numerical simulations of the experimental spectra on relevant models of the oxygen-evolving complex cluster. A strong focus in this paper was on the ‘ground’ state g4.1 signal, whether it is a rhombic 52 spin state signal or an axial 32 spin state signal. The data supported an X-band CW-EPR-generated g4.1 signal as originating from a near rhombic spin 5/2 of the S₂ state of the PSII manganese cluster.     

On Ammonia Binding to the Oxygen‐Evolving Complex of Photosystem II: A Quantum Chemical Study

A recent EPR study (M. Perrez Navarro et al., Proc. Natl. Acad. Sci.­ 2013 , 110, 15561) provided evidence that ammonia binding to the oxygen‐evolving complex (OEC) of photosystem II in its S₂ state takes place at a terminal‐water binding position (W1) on the “dangler” manganese center Mn_A. This contradicted earlier interpretations of ¹⁴N electron‐spin‐echo envelope modulation (ESEEM) and extended X‐ray absorption fine‐structure (EXAFS) data, which were taken to indicate replacement of a bridging oxo ligand by an NH₂ unit. Here we have used systematic broken‐symmetry density functional theory calculations on large (ca. 200 atom) model clusters of an extensive variety of substitution patterns and core geometries to examine these contradictory pieces of evidence. Computed relative energies clearly favor the terminal substitution pattern over bridging‐ligand arrangements (by about 20–30 kcal mol^?1) and support W1 as the preferred binding site. Computed ¹⁴N EPR nuclear‐quadrupole coupling tensors confirm previous assumptions that the appreciable asymmetry may be accounted for by strong, asymmetric hydrogen bonding to the bound terminal NH₃ ligand (mainly by Asp61). Indeed, bridging NH₂ substitution would lead to exaggerated asymmetries. Although our computed structures confirm that the reported elongation of an Mn–Mn distance by about 0.15 Å inferred from EXAFS experiments may only be reproduced by bridging NH₂ substitution, it seems possible that the underlying EXAFS data were skewed by problems due to radiation damage. Overall, the present data clearly support the suggested terminal NH₃ coordination at the W1 site. The finding is significant for the proposed mechanistic scenarios of OEC catalysis, as this is not a water substrate site, and effects of this ammonia binding on catalysis thus must be due to more indirect influences on the likely substrate binding site at the O5 bridging‐oxygen position.     

Face-Centered-Cubic Ag Nanoclusters: Origins and Consequences of the High Structural Regularity Elucidated by Density Functional Theory Calculations

Face-centered-cubic (FCC) silver nanoclusters (NCs) adopting either cubic or half-cubic growth modes have been recently reported, but the origin of these atomic assembly patterns and how they are achieved, which would inform our understanding of larger FCC silver nanomaterials, are both unknown. In this study, the cubic and half-cubic growth modes have been unified based on common structural characteristics, and differentiated depending on the starting blocks (cubic vs. half cubic). In both categories, the silver atoms adopt octahedral Ag₆, linear AgS₂ (in projection drawing), or tetrahedral AgS₃P binding modes, and the sulfur atoms adopt T-shaped SAg₃ and orthogonal SAg₄ modes. An additional T-shaped AgS₃ mode is oriented on the surface edge in cubic NCs to complete the cubic framework. Density functional theory calculations indicated that the high structural regularity originates from the strong diffusing capacity of the Ag(5d) and S(3p) orbitals, and the angular momentum distribution of the formed superatomic orbitals. The equatorial orientation of μ⁴-S or μ⁴-Ag determines whether growth stops or continues. In particular, a density-of-states analysis indicated that the octahedral silver atoms are chemically more reactive than the silver atoms in the AgS₃P motif, regardless of whether the parent NC functions as an electron donor or acceptor.     

Density Functional Theory Calculations of 95Mo NMR Parameters in Solid‐State Compounds

The application of periodic density functional theory‐based methods to the calculation of ⁹⁵Mo electric field gradient (EFG) and chemical shift (CS) tensors in solid‐state molybdenum compounds is presented. Calculations of EFG tensors are performed using the projector augmented‐wave (PAW) method. Comparison of the results with those obtained using the augmented plane wave + local orbitals (APW+lo) method and with available experimental values shows the reliability of the approach for ⁹⁵Mo EFG tensor calculation. CS tensors are calculated using the recently developed gauge‐including projector augmented‐wave (GIPAW) method. This work is the first application of the GIPAW method to a 4d transition‐metal nucleus. The effects of ultra‐soft pseudo‐potential parameters, exchange‐correlation functionals and structural parameters are precisely examined. Comparison with experimental results allows the validation of this computational formalism.     

Structural and Magnetic Properties of CoGen− (n=2–11) Clusters: Photoelectron Spectroscopy and Density Functional Calculations

A series of cobalt‐doped germanium clusters, CoGe_n^?/0 (n=2–11), are investigated by using anion photoelectron spectroscopy combined with density functional theory calculations. For both anionic and neutral CoGe_n (n=2–11) clusters, the critical size of the transition from exo‐ to endohedral structures is n=9. Natural population analysis shows that there is electron transfer from the Ge_n framework to the Co atom at n=7–11 for both anionic and neutral CoGe_n clusters. The magnetic moments of the anionic and neutral CoGe_n clusters decrease to the lowest values at n=10 and 11. The transfer of electrons from the Ge_n framework to the Co atom and the minimization of the magnetic moments are related to the evolution of CoGe_n structures from exo‐ to endohedral.     

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

Three atomic resolution crystal structures of Photosystem II, in the double flashed, nominal S₃ intermediate state of its Mn₄Ca Water Oxidising Complex (WOC), have now been presented, at 2.25, 2.35 and 2.08 Å resolution. Although very similar overall, the S₃ structures differ within the WOC catalytic site. The 2.25 Å structure contains only one oxy species (O5) in the WOC cavity, weakly associated with Mn centres, similar to that in the earlier 1.95 Å S₁ structure. The 2.35 Å structure shows two such species (O5, O6), with the Mn centres and O5 positioned as in the 2.25 Å structure and O5−O6 separation of ∼1.5 Å. In the latest S₃ variant, two oxy species are also seen (O5, Ox), with the Ox group appearing only in S₃, closely ligating one Mn, with O5−Ox separation <2.1 Å. The O5 and O6/Ox groups were proposed to be substrate water derived species. Recently, Petrie et al. (Chem. Phys. Chem., 2017 ) presented large scale Quantum Chemical modelling of the 2.25 Å structure, quantitatively explaining all significant features within the WOC region. This, as in our earlier studies, assumed a ‘low’ Mn oxidation paradigm (mean S₁ Mn oxidation level of +3.0, Petrie et al., Angew. Chem. Int. Ed., 2015 ), rather than a ‘high’ oxidation model (mean S₁ oxidation level of +3.5). In 2018 we showed (Chem. Phys. Chem., 2018 ) this oxidation state assumption predicted two energetically close S₃ structural forms, one with the metal centres and O5 (as OH⁻) positioned as in the 2.25 Å structure, and the other with the metals similarly placed, but with O5 (as H₂O) located in the O6 position of the 2.35 Å structure. The 2.35 Å two flashed structure was likely a crystal superposition of two such forms. Here we show, by similar computational analysis, that the latest 2.08 Å S₃ structure is also a likely superposition of forms, but with O5 (as OH⁻) occupying either the O5 or Ox positions in the WOC cavity. This highlights a remarkable structural ‘lability’ of the WOC centre in the S₃ state, which is likely catalytically relevant to its water splitting function.     

Synthesis and Reactivity of Functionalized Binary and Ternary Thiometallate Complexes [(RT)4S6], [(RSn)3S4]2−, [(RT)2(CuPPh3)6S6], and [(RSn)6(OMe)6Cu2S6]4− (R=C2H4COOH,CMe2CH2COMe; T=Ge,Sn)

Caged chalcogens : A series of novel, functionalized T_nS_m cages (T=Ge, Sn; n/m=4:6, 3:4) with terminal COO(H) or COMe groups were synthesized and show further reactivity toward Cu^I complexes (an example of which is shown here) and to hydrazines. This led to the generation of functionalized Cu/T/S clusters or the formation of Schiff bases at the C?O groups, respectively, with or without further fragmentation of the T/S core.

     

Cover Picture: Synthesis and Reactivity of Functionalized Binary and Ternary Thiometallate Complexes [(RT)4S6], [(RSn)3S4]2−, [(RT)2(CuPPh3)6S6], and [(RSn)6(OMe)6Cu2S6]4− (R=C2H4COOH,CMe2CH2COMe; T=Ge,Sn) (Chem. Eur. J. 27/2009)

Proof‐of‐principle is reported for a directed functionalization and derivatization of chalcogenidometallate cages with respect to the formation of hybrid compounds containing (M)/T/E semi‐conductor nodes (M=Cu; T=Ge, Sn; E=S). In their Full Paper on page 6595 ff. , S. Dehnen et al. show how it is possible to generate functionalized ternary CuSnS or CuGeS clusters and to transfer COMe ligands into CR(N–NH₂) or CR(N–NHPh) terminal groups by reaction of a series of novel, functionalized thiometallate cages [(RT)_nS_m] (n/m=4/6, 3/4), the R ligands of which are terminated by COO(H) or COMe.