Rationalising the Geometric Variation between the A and B Monomers in the 1.9 Å Crystal Structure of Photosystem II

Density functional theory calculations are reported on a set of models of the water‐oxidising complex (WOC) of photosystem II (PSII), exploring structural features revealed in the most recent (1.9 Å resolution) X‐ray crystallographic studies of PSII. Crucially, we find that the variation in the Mn–Mn distances seen between the A and B monomers of this crystal structure can be entirely accounted for, in the low oxidation state (LOS) paradigm, by consideration of the interplay between two hydrogen‐bonding interactions involving proximate amino acid residues with the oxo bridges of the WOC, that is, His337 with O3 (which leads to a general elongation in the Mn–Mn distances between Mn1, Mn2 and Mn3) and Arg357 with O2 (which results in a specific elongation of the Mn2?Mn3 distance).     

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.     

Resolving the Differences Between the 1.9 Å and 1.95 Å Crystal Structures of Photosystem II: A Single Proton Relocation Defines Two Tautomeric Forms of the Water‐Oxidizing Complex

Great progress has been made in characterizing the water‐oxidizing complex (WOC) in photosystem II (PSII) with the publication of a 1.9 Å resolution X‐ray diffraction (XRD) and recently a 1.95 Å X‐ray free‐electron laser (XFEL) structure. However, these achievements are under threat because of perceived conflicts with other experimental data. For the earlier 1.9 Å structure, lack of agreement with extended X‐ray absorption fine structure (EXAFS) data led to the notion that the WOC suffered from X‐ray photoreduction. In the recent 1.95 Å structure, Mn photoreduction is not an issue, but poor agreement with computational models which adopt the ‘high’ oxidation state paradigm, has again resulted in criticism of the structure on the basis of contamination with lower S states of the WOC. Here we use DFT modeling to show that the distinct WOC geometries in the 1.9 and 1.95 Å structures can be straightforwardly accounted for when the Mn oxidation states are consistent with the ‘low’ oxidation state paradigm. Remarkably, our calculations show that the two structures are tautomers, related by a single proton relocation.     

A Z‐Scheme‐Inspired Photobioelectrochemical H2O/O2 Cell with a 1 V Open‐Circuit Voltage Combining Photosystem II and PbS Quantum Dots

A biohybrid photobioanode mimicking the Z‐scheme has been developed by functional integration of photosystem II (PSII) and PbS quantum dots (QDs) within an inverse opal TiO₂ architecture giving rise to a rather negative water oxidation potential of about ?0.55 V vs. Ag/AgCl, 1 m KCl at neutral pH. The electrical linkage between both light‐sensitive entities has been established through an Os‐complex‐modified redox polymer (P_Os), which allows the formation of a multi‐step electron‐transfer chain under illumination starting with the photo‐activated water oxidation at PSII followed by an electron transfer from PSII through P_Os to the photo‐excited QDs and finally to the TiO₂ electrode. The photobioanode was coupled to a novel, transparent, inverse‐opal ATO cathode modified with an O₂‐reducing bilirubin oxidase for the construction of a H₂O/O₂ photobioelectrochemical cell reaching a high open‐circuit voltage of about 1 V under illumination.     

Water Oxidation for Simplified Models of the Oxygen‐Evolving Complex in Photosystem II

For the main parts of the mechanism for water oxidation in photosystem II there has recently been very strong experimental support for the mechanism suggested by theoretical model studies. The question addressed in the present study is to what extent this knowledge can be used for the design of artificial catalysts. A major requirement for a useful artificial catalyst is that it is small enough to be synthesized. Small catalysts also have the big advantage that they could improve the catalysis per surface area. To make the mechanism found for PSII useful in this context, it needs to be analyzed in detail. A small model system was therefore used and the ligands were replaced one by one by water‐derived ligands. Only the main chemical step of O?O bond formation was investigated in this initial study. The energetics for this small model and the larger one previously used for PSII are remarkably similar, which is the most important result of the present study. This shows that small model complexes have a potential for being very good water oxidation catalysts. It was furthermore found that there is a clear correlation between the barrier height for O?O bond formation and the type of optimal structure for the S₃ state. The analysis shows that a flexible central part of the complex is the key for efficient water oxidation.     

A New Quantum Chemical Approach to the Magnetic Properties of Oligonuclear Transition‐Metal Complexes: Application to a Model for the Tetranuclear Manganese Cluster of Photosystem II

Broken‐symmetry DFT calculations on transition‐metal clusters with more than two centers allow the hyperfine coupling constants to be extracted. Application of the proposed theoretical scheme to a tetranuclear manganese complex that models the S₂ state of the oxygen‐evolving complex of photosystem II yields hyperfine parameters that can be directly compared with experimental data. The picture shows the metal–oxo core of the model and the following parameters; exchange coupling constant J_ij, the expectation value of the site‐spin operator , and the isotropic hyperfine coupling parameters.

     

Trapped in Imidazole: How to Accumulate Multiple Photoelectrons on a Black‐Absorbing Ruthenium Complex

Ruthenium dyes incorporating a 4H‐imidazole chromophore as a ligand exhibit a spectrally broad absorption in the UV/Vis region. Furthermore, they show the ability to store two electrons within the 4H‐imidazole ligand. These features render them promising molecular systems, for example, as inter‐ or intramolecular electron relays. To optimize the structures with respect to their electron‐storage capability, it is crucial to understand the impact of structural changes accompanying photoinduced charge transfer in the electronic intermediates of multistep electron‐transfer processes. The photophysical properties of these (reactive) intermediates might impact the function of the molecular systems quite substantially. However, the spectroscopic study of short‐lived intermediates in stepwise multielectron‐transfer processes is experimentally challenging. To this end, this contribution reports on the electrochemical generation of anions identical to intermediate structures and their spectroscopic characterization by in situ resonance Raman and UV/Vis spectroelectrochemistry and computational methods. Thereby, an efficient two‐electron pathway to the 4H‐imidazole electron‐accepting ligand is identified.     

Spodium Bonds: Noncovalent Interactions Involving Group 12 Elements

The term spodium (Sp) bond is proposed to refer to a net attractive interaction between any element of Group 12 and electron‐rich atoms (Lewis bases or anions). These noncovalent interactions are markedly different from coordination bonds (antibonding Sp–ligand orbital involved). Evidence is provided for the existence of this interaction by calculations at the RI‐MP2/aug‐cc‐pVTZ level of theory, atoms‐in‐molecules, and natural bond orbital analyses and by examining solid‐state structures in the Cambridge Structure Database.     

Quantitative Monitoring and Visualization of Hydrogen Sulfide In Vivo Using a Luminescent Probe Based on a Ruthenium(II) Complex

Development of novel bioanalytical methods for monitoring of H₂S is key toward understanding the physiological and pathological functions of this gasotransmitter in live organisms. A ruthenium(II)‐complex‐based luminescence probe, Ru‐MDB (MDB: 4’‐methyl‐[2,2’‐bipyridine]‐4‐yl)methyl 2‐((2,4‐dinitrophenyl)thio)benzoate), was developed by introducing a new H₂S responsive masking moiety to a red‐emitting Ru^II luminophore. Cleavage of this masking group by a H₂S‐triggered reaction leads to a luminescence “off–on” response. The long‐lived emissions of Ru‐MDB and its reaction product with H₂S allowed quantitative detection of H₂S in autofluorescence‐rich human sera and adult zebrafish organs using the time‐gated luminescence mode. Ru‐MDB exhibits red emission, a large Stokes shift, high specificity and sensitivity for H₂S detection, and low cytotoxicity, which enables imaging and flow cytometry analysis of lysosomal H₂S generation in live inflamed cells under drug stimulation. Monitoring of H₂S in live Daphnia magna, zebrafish embryos, adult zebrafish, and mice, was conducted by in vivo imaging using Ru‐MDB as a probe.     

Assessing the Influence of Mutation on GTPase Transition States by Using X‐ray Crystallography, 19F NMR,and DFT Approaches

We report X‐ray crystallographic and ¹⁹F NMR studies of the G‐protein RhoA complexed with MgF₃⁻, GDP, and RhoGAP, which has the mutation Arg85′Ala. When combined with DFT calculations, these data permit the identification of changes in transition state (TS) properties. The X‐ray data show how Tyr34 maintains solvent exclusion and the core H‐bond network in the active site by relocating to replace the missing Arg85′ sidechain. The ¹⁹F NMR data show deshielding effects that indicate the main function of Arg85′ is electronic polarization of the transferring phosphoryl group, primarily mediated by H‐bonding to O^3G and thence to P^G. DFT calculations identify electron‐density redistribution and pinpoint why the TS for guanosine 5′‐triphosphate (GTP) hydrolysis is higher in energy when RhoA is complexed with RhoGAP_Arg85′Ala relative to wild‐type (WT) RhoGAP. This study demonstrates that ¹⁹F NMR measurements, in combination with X‐ray crystallography and DFT calculations, can reliably dissect the response of small GTPases to site‐specific modifications.     

Protonation‐Dependent Base Flipping at Neutral pH in the Catalytic Triad of a Self‐Splicing Bacterial Group II Intron

NMR spectroscopy has revealed pH‐dependent structural changes in the highly conserved catalytic domain 5 of a bacterial group II intron. Two adenines with pK_a values close to neutral pH were identified in the catalytic triad and the bulge. Protonation of the adenine opposite to the catalytic triad is stabilized within a G(syn)–AH⁺(anti) base pair. The pH‐dependent anti‐to‐syn flipping of this G in the catalytic triad modulates the known interaction with the linker region between domains 2 and 3 (J23) and simultaneously the binding of the catalytic Mg²⁺ ion to its backbone. Hence, this here identified shifted pK_a value controls the conformational change between the two steps of splicing.     

One‐Pot Protection‐Glycosylation Reactions for Synthesis of Lipid II Analogues

(2,6‐Dichloro‐4‐methoxyphenyl)(2,4‐dichlorophenyl)methyl trichloroacetimidate ( 3 ) and its polymer‐supported reagent 4 can be successfully applied to a one‐pot protection‐glycosylation reaction to form the disaccharide derivative 7 d for the synthesis of lipid II analogues. The temporary protecting group or linker at the C‐6 position and N‐Troc protecting group of 7 d can be cleaved simultaneously through a reductive condition. Overall yields of syntheses of lipid II ( 1 ) and neryl‐lipid II N^ε‐dansylthiourea are significantly improved by using the described methods.     

NMR of Natural Products as Potential Drugs

This review outlines methods to investigate the structure of natural products with emphasis on intramolecular hydrogen bonding, tautomerism and ionic structures using NMR techniques. The focus is on 1H chemical shifts, isotope effects on chemical shifts and diffusion ordered spectroscopy. In addition, density functional theory calculations are performed to support NMR results. The review demonstrates how hydrogen bonding may lead to specific structures and how chemical equilibria, as well as tautomeric equilibria and ionic structures, can be detected. All these features are important for biological activity and a prerequisite for correct docking experiments and future use as drugs.