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The synthesis and investigation of [Rh(DHMPE) 2 ][BF 4 ] ( 1 ) are reported. 1 features proton-responsive 1,2-bis[(dihydroxymethyl)phosphino]ethane (DHMPE) ligands, which readily capture CO 2 from atmospheric sources upon deprotonation. The protonation state of the DHMPE ligand was observed to have a significant impact on the catalytic reactivity of 1 with CO 2 . Deprotonation and CO 2 binding to 1 result in a ∼10-fold rate enhancement in catalytic degenerate CO 2 reduction with formate, monitored by 12 C/ 13 C isotope exchange between H 12 CO 2 - and 13 CO 2 . Studies performed using a similar complex lacking the hydroxyl ligand functionality ([Rh(DEPE) 2 ][BF 4 ] where DEPE = 1,2-bis(diethylphosphino)ethane) do not show the same rate enhancements when base is added. Based upon the cation-dependent activity of the catalyst, Eyring analysis, and cation sequestration experiments, CO 2 binding to 1 is proposed to facilitate preorganization of formate/CO 2 in the transition state via ligand-based encapsulation of Na + or K + cations to lower the activation energy and increase the observed catalytic rate. Incorporation of proton-responsive DHMPE ligands provides a unique approach to accelerate the kinetics of catalytic CO 2 reduction to formate.

X-ray scattering has become a major tool in the structural characterization of nanoscale materials. Thanks to the widely available experimental and computational atomic models, coordinate-based X-ray scattering simulation has played a crucial role in data interpretation in the past two decades. However, simulation of real-space pair distance distribution functions (PDDFs) from small- and wide-angle X-ray scattering, SAXS/WAXS, has been relatively less exploited. This study presents a comparison of PDDF simulation methods, which are applied to molecular structures that range in size from β-cyclo-dextrin [1 kDa molecular weight (MW), 66 non-hydrogen atoms] to the satellite tobacco mosaic virus capsid (1.1 MDa MW, 81 960 non-hydrogen atoms). The results demonstrate the power of interpretation of experimental SAXS/WAXS from the real-space view, particularly by providing a more intuitive method for understanding of partial structure contributions. Furthermore, the computational efficiency of PDDF simulation algorithms makes them attractive as approaches for the analysis of large nanoscale materials and biological assemblies. The simulation methods demonstrated in this article have been implemented in stand-alone software, SolX 3.0 , which is available to download from https://12idb.xray.aps.anl.gov/solx.html., (© Zuo and Tiede 2024.)

Appreciating that the role of the solute-solvent and other outer-sphere interactions is essential for understanding chemistry and chemical dynamics in solution, experimental approaches are needed to address the structural consequences of these interactions, complementing condensed-matter simulations and coarse-grained theories. High-energy X-ray scattering (HEXS) combined with pair distribution function analysis presents the opportunity to probe these structures directly and to develop quantitative, atomistic models of molecular systems in situ in the solution phase. However, at concentrations relevant to solution-phase chemistry, the total scattering signal is dominated by the bulk solvent, prompting researchers to adopt a differential approach to eliminate this unwanted background. Though similar approaches are well established in quantitative structural studies of macromolecules in solution by small- and wide-angle X-ray scattering (SAXS/WAXS), analogous studies in the HEXS regime-where sub-ångström spatial resolution is achieved-remain underdeveloped, in part due to the lack of a rigorous theoretical description of the experiment. To address this, herein we develop a framework for differential solution scattering experiments conducted at high energies, which includes concepts of the solvent-excluded volume introduced to describe SAXS/WAXS data, as well as concepts from the time-resolved X-ray scattering community. Our theory is supported by numerical simulations and experiment and paves the way for establishing quantitative methods to determine the atomic structures of small molecules in solution with resolution approaching that of crystallography., (open access.)

Emulating angstrom-scale dynamics of the highly selective biological ion channels is a challenging task. Recent work on angstrom-scale artificial channels has expanded our understanding of ion transport and uptake mechanisms under confinement. However, the role of chemical environment in such channels is still not well understood. Here, we report the anomalously enhanced transport and uptake of ions under confined MoS 2 -based channels that are ~five angstroms in size. The ion uptake preference in the MoS 2 -based channels can be changed by the selection of surface functional groups and ion uptake sequence due to the interplay between kinetic and thermodynamic factors that depend on whether the ions are mixed or not prior to uptake. Our work offers a holistic picture of ion transport in 2D confinement and highlights ion interplay in this regime., Competing Interests: Competing interests statement:The authors declare no competing interest.

The application of grazing-incidence total X-ray scattering (GITXS) for pair distribution function (PDF) analysis using >50 keV X-rays from synchrotron light sources has created new opportunities for structural characterization of supported thin films with high resolution. Compared with grazing-incidence wide-angle X-ray scattering, which is only useful for highly ordered materials, GITXS/PDFs expand such analysis to largely disordered or nanostructured materials by examining the atomic pair correlations dependent on the direction relative to the surface of the supporting substrate. A characterization of nanocrystalline In 2 O 3 -derived thin films is presented here with in-plane-isotropic and out-of-plane-anisotropic orientational ordering of the atomic structure, each synthesized using different techniques. The atomic orientations of such films are known to vary based on the synthetic conditions. Here, an azimuthal orientational analysis of these films using GITXS with a single incident angle is shown to resolve the markedly different orientations of the atomic structures with respect to the planar support and the different degrees of long-range order, and hence, the terminal surface chemistries. It is anticipated that orientational analysis of GITXS/PDF data will offer opportunities to extend structural analyses of thin films by providing a means to qualitatively determine the major atomic orientation within nanocrystalline and, eventually, non-crystalline films., (open access.)

Photosynthetic conversion of light energy into chemical energy occurs in sheet-like membrane-bound compartments called thylakoids and is mediated by large integral membrane protein-pigment complexes called reaction centers (RCs). Oxygenic photosynthesis of higher plants, cyanobacteria and algae requires the symbiotic linking of two RCs, photosystem II (PSII) and photosystem I (PSI), to split water and assimilate carbon dioxide. Worldwide there is a large research investment in developing RC-based hybrids that utilize the highly evolved solar energy conversion capabilities of RCs to power catalytic reactions for solar fuel generation. Of particular interest is the solar-powered production of H 2 , a clean and renewable energy source that can replace carbon-based fossil fuels and help provide for ever-increasing global energy demands. Recently, we developed thylakoid membrane hybrids with abiotic catalysts and demonstrated that photosynthetic Z-scheme electron flow from the light-driven water oxidation at PSII can drive H 2 production from PSI. One of these hybrid systems was created by self-assembling Pt-nanoparticles (PtNPs) with the stromal subunits of PSI that extend beyond the membrane plane in both spinach and cyanobacterial thylakoids. Using PtNPs as site-specific probe molecules, we report the electron microscopic (EM) imaging of oligomeric structure, location and organization of PSI in thylakoid membranes and provide the first direct visualization of photosynthetic Z-scheme solar water-splitting biohybrids for clean H 2 production., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 Elsevier B.V. All rights reserved.)

Facilitating photoinduced electron transfer (PET) while minimizing rapid charge-recombination processes to produce a long-lived charge-separated (CS) state represents a primary challenge associated with achieving efficient solar fuel production. Natural photosynthetic systems employ intermolecular interactions to arrange the electron-transfer relay in reaction centers and promote a directional flow of electrons. This work explores a similar tactic through the synthesis and ground- and excited-state characterization of two Cu(I)bis(phenanthroline) chromophores with homoleptic and heteroleptic coordination geometries and which are functionalized with negatively charged sulfonate groups. The addition of sulfonate groups enables solubility in pure water, and it also induces assembly with the dicationic electron acceptor methyl viologen (MV 2+ ) via bimolecular, dynamic electrostatic interactions. The effect of the sulfonate groups on the ground- and excited-state properties was evaluated by comparison with the unsulfonated analogues in 1:1 acetonitrile/water. The excited-state lifetimes for all sulfonated complexes are similar to what we expect from previous literature, with the exception of the sulfonated heteroleptic complex whose metal-to-ligand charge-transfer (MLCT) lifetime in water has two components that are fit to 10 and 77 ns. For the sulfonated complexes, we detected reduced MV +• in both solvent environments following MLCT excitation, but control measurements in 1:1 acetonitrile/water with the unsulfonated analogues showed no PET to MV 2+ , indicating that electrostatically driven supramolecular assemblies of the sulfonated complexes with MV 2+ facilitate the observed PET. Additionally, the strength of the intermolecular interactions driving the formation of these assemblies changes drastically with the solvent environment. In 1:1 acetonitrile/water, PET occurred from both sulfonated complexes with quantum yields (Φ ET ) of 2-3% but increased to a remarkable 98% for the sulfonated heteroleptic complex with a 3 μs CS-state lifetime in water.

Controlling the ion transport through graphene oxide (GO) membrane is challenging, particularly in the aqueous environment due to its strong swelling tendency. Fine-tuning the interlayer spacing and chemistry is critical to create highly selective membranes. We investigate the effect of single-site divalent cations in tuning GO membrane properties. Competitive ionic permeation test indicates that Cu 2+ cations dominate the transport through the 2D channels of GO membrane over other cations (Mg 2+ /Ca 2+ /Co 2+ ). Without/With the single-site M 2+ modifications, pristine GO, Mg-GO, Ca-GO, and Cu-GO membranes show interlayer spacings of ∼13.6, 15.6, 14.5, and 12.3 Å in wet state, respectively. The Cu-GO membrane shows a two-fold decrease of NaCl (1 M) permeation rate comparing to pristine GO, Mg-GO, and Ca-GO membranes. In reverse osmosis tests using 1000 ppm NaCl and Na 2 SO 4 as feeds, Cu-GO membrane shows rejection of ∼78% and ∼94%, respectively, which are 5%-10% higher than its counterpart membranes., Competing Interests: The authors declare no competing financial interests., (© 2022 The Authors.)

High-energy X-ray scattering and pair distribution function analysis (HEXS/PDF) is a powerful method to reveal the structure of materials lacking long-range order, but is underutilized for molecular complexes in solution. We demonstrate the application of HEXS/PDF with 0.26 Å resolution to uncover the solution structure of five bimetallic Cu I /Ru II /Os II complexes. HEXS/PDF of each complex in acetonitrile solution confirms the pairwise distances in the local coordination sphere of each metal center as well as the metal⋅⋅⋅metal distances separated by over 12 Å. The metal⋅⋅⋅metal distance detected in solution is compared with that from the crystal structure and molecular models to confirm that distortions to the metal bridging ligand are unique to the solid state. This work presents the first example of observing sub-Ångström conformational differences by direct comparison of solution phase and solid-state structures and shows the potential for HEXS/PDF in the determination of solution structure of single molecules., (© 2021 Wiley-VCH GmbH.)

The development and investigation of materials that leverage unique interfacial effects on electronic structure and redox chemistry are likely to play an outstanding role in advanced technologies for wastewater treatment. Here, the use of surface functionalization of metal oxides with a Ru II poly(pyridyl) complex was reported as a way to create hybrid assemblies with optimized electrochemical performance for water remediation, superior to those that could be achieved with the molecular catalyst or metal-oxide electrodes used individually. Mechanistic analysis demonstrated that the molecularly functionalized electrodes could suppress the formation of hydroxyl radicals (i. e., the dominant remediation pathway for bare metal-oxide electrodes), allowing the water remediation to proceed through the highly oxidizing Ru 3+ ions in the surface-bound complexes. Furthermore, the underlying metal-oxide substrates played a crucial role in altering the electronic structure and electrochemical properties of the surface-bound catalyst, such that the competing side reaction (i. e., water splitting) was largely inhibited., (© 2021 Wiley-VCH GmbH.)

The structure, chemistry, and charge of interfaces between materials and aqueous fluids play a central role in determining properties and performance of numerous water systems. Sensors, membranes, sorbents, and heterogeneous catalysts almost uniformly rely on specific interactions between their surfaces and components dissolved or suspended in the water-and often the water molecules themselves-to detect and mitigate contaminants. Deleterious processes in these systems such as fouling, scaling (inorganic deposits), and corrosion are also governed by interfacial phenomena. Despite the importance of these interfaces, much remains to be learned about their multiscale interactions. Developing a deeper understanding of the molecular- and mesoscale phenomena at water/solid interfaces will be essential to driving innovation to address grand challenges in supplying sufficient fit-for-purpose water in the future. In this Review, we examine the current state of knowledge surrounding adsorption, reactivity, and transport in several key classes of water/solid interfaces, drawing on a synergistic combination of theory, simulation, and experiments, and provide an outlook for prioritizing strategic research directions.

Sequential infiltration synthesis (SIS) is a route to the precision deposition of inorganic solids in analogy to atomic layer deposition but occurs within (vs upon) a soft material template. SIS has enabled exquisite nanoscale morphological complexity in various oxides through selective nucleation in block copolymers templates. However, the earliest stages of SIS growth remain unresolved, including the atomic structure of nuclei and the evolution of local coordination environments, before and after polymer template removal. We employed In K-edge extended X-ray absorption fine structure and atomic pair distribution function analysis of high-energy X-ray scattering to unravel (1) the structural evolution of InO x H y clusters inside a poly(methyl methacrylate) (PMMA) host matrix and (2) the formation of porous In 2 O 3 solids (obtained after annealing) as a function of SIS cycle number. Early SIS cycles result in InO x H y cluster growth with high aspect ratio, followed by the formation of a three-dimensional network with additional SIS cycles. That the atomic structures of the InO x H y clusters can be modeled as multinuclear clusters with bonding patterns related to those in In 2 O 3 and In(OH) 3 crystal structures suggests that SIS may be an efficient route to 3D arrays of discrete-atom-number clusters. Annealing the mixed inorganic/polymer films in air removes the PMMA template and consolidates the as-grown clusters into cubic In 2 O 3 nanocrystals with structural details that also depend on SIS cycle number.

Efficient nanomaterials for artificial photosynthesis require fast and robust unidirectional electron transfer (ET) from photosensitizers through charge-separation and accumulation units to redox-active catalytic sites. We explored the ultrafast time-scale limits of photo-induced charge transfer between a Ru(II)tris(bipyridine) derivative photosensitizer and PpcA, a 3-heme c-type cytochrome serving as a nanoscale biological wire. Four covalent attachment sites (K28C, K29C, K52C, and G53C) were engineered in PpcA enabling site-specific covalent labeling with expected donor-acceptor (DA) distances of 4-8 Å. X-ray scattering results demonstrated that mutations and chemical labeling did not disrupt the structure of the proteins. Time-resolved spectroscopy revealed three orders of magnitude difference in charge transfer rates for the systems with otherwise similar DA distances and the same number of covalent bonds separating donors and acceptors. All-atom molecular dynamics simulations provided additional insight into the structure-function requirements for ultrafast charge transfer and the requirement of van der Waals contact between aromatic atoms of photosensitizers and hemes in order to observe sub-nanosecond ET. This work demonstrates opportunities to utilize multi-heme c-cytochromes as frameworks for designing ultrafast light-driven ET into charge-accumulating biohybrid model systems, and ultimately for mimicking the photosynthetic paradigm of efficiently coupling ultrafast, light-driven electron transfer chemistry to multi-step catalysis within small, experimentally versatile photosynthetic biohybrid assemblies.

Heteroleptic copper(i) bis(phenanthroline) complexes with surface anchoring carboxylate groups have been synthesized and immobilized on nanoporous metal oxide substrates. The species investigated are responsive to the external environment and this work provides a new strategy to control charge transfer processes for efficient solar energy conversion.

Amorphous thin film materials and heterogenized molecular catalysts supported on electrode and other functional interfaces are widely investigated as promising catalyst formats for applications in solar and electrochemical fuels catalysis. However the amorphous character of these catalysts and the complexity of the interfacial architectures that merge charge transport properties of electrode and semiconductor supports with discrete sites for multi-step catalysis poses challenges for probing mechanisms that activate and tune sites for catalysis. This minireview discusses advances in soft X-ray spectroscopy and high-energy X-ray scattering that provide opportunities to resolve interfacial electronic and atomic structures, respectively, that are linked to catalysis. This review discusses how these techniques can be partnered with advances in nanostructured interface synthesis for combined soft X-ray spectroscopy and high-energy X-ray scattering analyses of thin film and heterogenized molecular catalysts. These combined approaches enable opportunities for the characterization of both electronic and atomic structures underlying fundamental catalytic function, and that can be applied under conditions relevant to device applications.

Worldwide there is a large research investment in developing solar fuel systems as clean and sustainable sources of energy. The fundamental mechanisms of natural photosynthesis can provide a source of inspiration for these studies. Photosynthetic reaction center (RC) proteins capture and convert light energy into chemical energy that is ultimately used to drive oxygenic water-splitting and carbon fixation. For the light energy to be used, the RC communicates with other donor/acceptor components via a sophisticated electron transfer scheme that includes electron transfer reactions between soluble and membrane bound proteins. Herein, we reengineer an inherent interprotein electron transfer pathway in a natural photosynthetic system to make it photocatalytic for aqueous H 2 production. The native electron shuttle protein ferredoxin (Fd) is used as a scaffold for binding of a ruthenium photosensitizer and H 2 catalytic function is imparted to its partner protein, ferredoxin-NADP + -reductase (FNR), by attachment of cobaloxime molecules. We find that this 2-protein biohybrid system produces H 2 in aqueous solutions via light-induced interprotein electron transfer reactions (TON > 2500 H 2 /FNR), providing insight about using native protein-protein interactions as a method for fuel generation.

To understand design principles for assembling photosynthetic biohybrids that incorporate precisely-controlled sites for electron injection into redox enzyme cofactor arrays, we investigated the influence of chirality in assembly of the photosensitizer ruthenium(II)bis(2,2'-bipyridine)(4-bromomethyl-4'-methyl-2,2'-bipyridine), Ru(bpy) 2 (Br-bpy), when covalently conjugated to cysteine residues introduced by site-directed mutagenesis in the triheme periplasmic cytochrome A (PpcA) as a model biohybrid system. For two investigated conjugates that show ultrafast electron transfer, A23C-Ru and K29C-Ru, analysis by circular dichroism spectroscopy, CD, demonstrated site-specific chiral discrimination as a factor emerging from the close association between [Ru(bpy) 3 ] 2+ and heme cofactors. CD analysis showed the A23C-Ru and K29C-Ru conjugates to have distinct, but opposite, stereoselectivity for the Λ and Δ-Ru(bpy) 2 (Br-bpy) enantiomers, with enantiomeric excesses of 33.1% and 65.6%, respectively. In contrast, Ru(bpy) 2 (Br-bpy) conjugation to a protein site with high flexibility, represented by the E39C-Ru construct, exhibited a nearly negligible chiral selectivity, measured by an enantiomeric excess of 4.2% for the Λ enantiomer. Molecular dynamics simulations showed that site-specific stereoselectivity reflects steric constraints at the conjugating sites and that a high degree of chiral selectivity correlates to reduced structural disorder for [Ru(bpy) 3 ] 2+ in the linked assembly. This work identifies chiral discrimination as means to achieve site-specific, precise geometric positioning of introduced photosensitizers relative to the heme cofactors in manner that mimics the tuning of cofactors in photosynthesis.

Porous, high-surface-area electrode architectures are described that allow structural characterization of interfacial amorphous thin films with high spatial resolution under device-relevant functional electrochemical conditions using high-energy X-ray (>50 keV) scattering and pair distribution function (PDF) analysis. Porous electrodes were fabricated from glass-capillary array membranes coated with conformal transparent conductive oxide layers, consisting of either a 40 nm-50 nm crystalline indium tin oxide or a 100 nm-150 nm-thick amorphous indium zinc oxide deposited by atomic layer deposition. These porous electrodes solve the problem of insufficient interaction volumes for catalyst thin films in two-dimensional working electrode designs and provide sufficiently low scattering backgrounds to enable high-resolution signal collection from interfacial thin-film catalysts. For example, PDF measurements were readily obtained with 0.2 Å spatial resolution for amorphous cobalt oxide films with thicknesses down to 60 nm when deposited on a porous electrode with 40 µm-diameter pores. This level of resolution resolves the cobaltate domain size and structure, the presence of defect sites assigned to the domain edges, and the changes in fine structure upon redox state change that are relevant to quantitative structure-function modeling. The results suggest the opportunity to leverage the porous, electrode architectures for PDF analysis of nanometre-scale surface-supported molecular catalysts. In addition, a compact 3D-printed electrochemical cell in a three-electrode configuration is described which is designed to allow for simultaneous X-ray transmission and electrolyte flow through the porous working electrode., (open access.)

Non-noble-metal, thin-film oxides are widely investigated as promising catalysts for oxygen evolution reactions (OER). Amorphous cobalt oxide films electrochemically formed in the presence of borate (CoBi) and phosphate (CoPi) share a common cobaltate domain building block, but differ significantly in OER performance that derives from different electron-proton charge transport properties. Here, we use a combination of L edge synchrotron X-ray absorption (XAS), resonant X-ray emission (RXES), resonant inelastic X-ray scattering (RIXS), resonant Raman (RR) scattering, and high-energy X-ray pair distribution function (PDF) analyses that identify electronic and structural factors correlated to the charge transport differences for CoPi and CoBi. The analyses show that CoBi is composed primarily of cobalt in octahedral coordination, whereas CoPi contains approximately 17% tetrahedral Co(II), with the remainder in octahedral coordination. Oxygen-mediated 4 p-3 d hybridization through Co-O-Co bonding was detected by RXES and the intersite dd excitation was observed by RIXS in CoBi, but not in CoPi. RR shows that CoBi resembles a disordered layered LiCoO 2 -like structure, whereas CoPi is amorphous. Distinct domain models in the nanometer range for CoBi and CoPi have been proposed on the basis of the PDF analysis coupled to XAS data. The observed differences provide information on electronic and structural factors that enhance oxygen evolving catalysis performance.

Periplasmic cytochrome A (PpcA) is a representative of a broad class of multiheme cytochromes functioning as protein "nanowires" for storage and extracellular transfer of multiple electrons in the δ-proteobacterium Geobacter sulfurreducens. PpcA contains three bis-His coordinated hemes held in a spatial arrangement that is highly conserved among the multiheme cytochromes c 3 and c 7 families, carries low potential hemes, and is notable for having one of the lowest number of amino acids utilized to maintain a characteristic protein fold and site-specific heme function. Low temperature X-band electron paramagnetic resonance (EPR) spectroscopy has been used to characterize the electronic configuration of the Fe(III) and the ligation mode for each heme. The three sets of EPR signals are assigned to individual hemes in the three-dimensional crystal structure. The relative energy levels of the Fe(III) 3d orbitals for individual hemes were estimated from the principal g-values. The observed g-tensor anisotropy was used as a probe of electronic structure of each heme, and differences were determined by specifics of axial ligation. To ensure unambiguous assignment of highly anisotropic low-spin (HALS) signal to individual hemes, EPR analyses of iron atom electronic configurations have been supplemented with investigation of porphyrin macrocycles by one-dimensional 1 H NMR chemical shift patterns for the methyl substituents. Within optimized geometry of hemes in PpcA, the magnetic interactions between hemes were found to be minimal, similar to the c 3 family of tetraheme cytochromes.

Bacterial microcompartments (BMCs) are proteinaceous organelles that encapsulate enzymes involved in CO 2 fixation (carboxysomes) or carbon catabolism (metabolosomes). Metabolosomes share a common core of enzymes and a distinct signature enzyme for substrate degradation that defines the function of the BMC (e.g., propanediol or ethanolamine utilization BMCs, or glycyl-radical enzyme microcompartments). Loci encoding metabolosomes also typically contain genes for proteins that support organelle function, such as regulation, transport of substrate, and cofactor (e.g., vitamin B 12 ) synthesis and recycling. Flavoproteins are frequently among these ancillary gene products, suggesting that these redox active proteins play an undetermined function in many metabolosomes. Here, we report the first characterization of a BMC-associated flavodoxin (Fld1C), a small flavoprotein, derived from the noncanonical 1,2-propanediol utilization BMC locus (PDU1C) of Lactobacillus reuteri. The 2.0 Å X-ray structure of Fld1C displays the α/β flavodoxin fold, which noncovalently binds a single flavin mononucleotide molecule. Fld1C is a short-chain flavodoxin with redox potentials of -240 ± 3 mV oxidized/semiquinone and -344 ± 1 mV semiquinone/hydroquinone versus the standard hydrogen electrode at pH 7.5. It can participate in an electron transfer reaction with a photoreductant to form a stable semiquinone species. Collectively, our structural and functional results suggest that PDU1C BMCs encapsulate Fld1C to store and transfer electrons for the reactivation and/or recycling of the B 12 cofactor utilized by the signature enzyme.

The insertion of cobaloxime catalysts in the heme-binding pocket of heme oxygenase (HO) yields artificial hydrogenases active for H 2 evolution in neutral aqueous solutions. These novel biohybrids have been purified and characterized by using UV/visible and EPR spectroscopy. These analyses revealed the presence of two distinct binding conformations, thereby providing the cobaloxime with hydrophobic and hydrophilic environments, respectively. Quantum chemical/molecular mechanical docking calculations found open and closed conformations of the binding pocket owing to mobile amino acid residues. HO-based biohybrids incorporating a {Co(dmgH) 2 } (dmgH 2 =dimethylglyoxime) catalytic center displayed up to threefold increased turnover numbers with respect to the cobaloxime alone or to analogous sperm whale myoglobin adducts. This study thus provides a strong basis for further improvement of such biohybrids, using well-designed modifications of the second and outer coordination spheres, through site-directed mutagenesis of the host protein., (© 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.)

Pyrazolate-bridged dinuclear Pt(II) complexes represent a series of molecules with tunable absorption and emission properties that can be directly modulated by structural factors, such as the Pt-Pt distance. However, direct experimental information regarding the structure of the emissive triplet excited state has remained scarce. Using time-resolved wide-angle X-ray scattering (WAXS), the excited triplet state molecular structure of [Pt(ppy)(μ-t-Bu2pz)]2 (ppy = 2-phenylpyridine; t-Bu2pz = 3,5-di-tert-butylpyrazolate), complex 1, was obtained in a dilute (0.5 mM) toluene solution utilizing the monochromatic X-ray pulses at Beamline 11IDD of the Advanced Photon Source. The excited-state structural analysis of 1 was performed based on the results from both transient WAXS measurements and density functional theory calculations to shed light on the primary structural changes in its triplet metal-metal-to-ligand charge-transfer (MMLCT) state, in particular, the Pt-Pt distance and ligand rotation. We found a pronounced Pt-Pt distance contraction accompanied by rotational motions of ppy ligands toward one another in the MMLCT state of 1. Our results suggest that the contraction is larger than what has previously been reported, but they are in good agreement with recent theoretical efforts and suggest the ppy moieties as targets for rational synthesis aimed at tuning the excited-state structure and properties.

The solution structures of highly active Ir water-oxidation catalysts are elucidated by combining density functional theory, high-energy X-ray scattering (HEXS), and extended X-ray absorption fine structure (EXAFS) spectroscopy. We find that the catalysts are Ir dimers with mono-μ-O cores and terminal anionic ligands, generated in situ through partial oxidation of a common catalyst precursor. The proposed structures are supported by (1)H and (17)O NMR, EPR, resonance Raman and UV-vis spectra, electrophoresis, etc. Our findings are particularly valuable to understand the mechanism of water oxidation by highly reactive Ir catalysts. Importantly, our DFT-EXAFS-HEXS methodology provides a new in situ technique for characterization of active species in catalytic systems.

Amorphous thin film oxygen evolving catalysts, OECs, of first-row transition metals show promise to serve as self-assembling photoanode materials in solar-driven, photoelectrochemical `artificial leaf' devices. This report demonstrates the ability to use high-energy X-ray scattering and atomic pair distribution function analysis, PDF, to resolve structure in amorphous metal oxide catalyst films. The analysis is applied here to resolve domain structure differences induced by oxyanion substitution during the electrochemical assembly of amorphous cobalt oxide catalyst films, Co-OEC. PDF patterns for Co-OEC films formed using phosphate, Pi, methylphosphate, MPi, and borate, Bi, electrolyte buffers show that the resulting domains vary in size following the sequence Pi < MPi < Bi. The increases in domain size for CoMPi and CoBi were found to be correlated with increases in the contributions from bilayer and trilayer stacked domains having structures intermediate between those of the LiCoOO and CoO(OH) mineral forms. The lattice structures and offset stacking of adjacent layers in the partially stacked CoMPi and CoBi domains were best matched to those in the LiCoOO layered structure. The results demonstrate the ability of PDF analysis to elucidate features of domain size, structure, defect content and mesoscale organization for amorphous metal oxide catalysts that are not readily accessed by other X-ray techniques. PDF structure analysis is shown to provide a way to characterize domain structures in different forms of amorphous oxide catalysts, and hence provide an opportunity to investigate correlations between domain structure and catalytic activity.

Herein we report the creation of a novel solar fuel biohybrid for light-driven H2 production utilizing the native electron transfer protein ferredoxin (Fd) as a scaffold for binding of a ruthenium photosensitizer (PS) and a molecular cobaloxime catalyst (Co). EPR and transient optical experiments provide direct evidence of a long-lived (>1.5 ms) Ru(III)-Fd-Co(I) charge separated state formed via an electron relay through the Fd [2Fe-2S] cluster, initiating the catalytic cycle for 2H(+) + 2e(-) → H2.

PpcA, a tri-heme cytochrome c7 from Geobacter sulfurreducens, was investigated as a model for photosensitizer-initiated electron transfer within a multi-heme "molecular wire" protein architecture. Escherichia coli expression of PpcA was found to be tolerant of cysteine site-directed mutagenesis, demonstrated by the successful expression of natively folded proteins bearing cysteine mutations at a series of sites selected to vary characteristically with respect to the three -CXXCH- heme binding domains. The introduced cysteines readily reacted with Ru(II)-(2,2'-bpy)2(4-bromomethyl-4'-methyl-2,2'-bipyridine) to form covalently linked constructs that support both photo-oxidative and photo-reductive quenching of the photosensitizer excited state, depending upon the initial heme redox state. Excited-state electron-transfer times were found to vary from 6 × 10(-12) to 4 × 10(-8) s, correlated with the distance and pathways for electron transfer. The fastest rate is more than 10(3)-fold faster than previously reported for photosensitizer-redox protein constructs using amino acid residue linking. Clear evidence for inter-heme electron transfer within the multi-heme protein is not detected within the lifetimes of the charge-separated states. These results demonstrate an opportunity to develop multi-heme c-cytochromes for investigation of electron transfer in protein "molecular wires" and to serve as frameworks for metalloprotein designs that support multiple-electron-transfer redox chemistry.

Solar energy conversion of water into environmentally clean fuels, such as hydrogen, offers one of the best long-term solutions for meeting future global energy needs. In photosynthesis, high quantum yield charge separation is achieved by a series of rapid, photoinitiated electron transfer steps that take place in proteins called reaction centers (RCs). Of current interest are new strategies that couple RC photochemistry to the direct synthesis of energy-rich molecules, offering opportunities to more directly tune the products of photosynthesis and potentially to increase solar energy conversion capacity. Innovative designs link RC photochemistry with synthetic molecular catalysts to create earth abundant biohybrid complexes that use light to rapidly produce hydrogen from water., (Copyright © 2014 Elsevier Ltd. All rights reserved.)

Surface binding and interactions of anionic porphyins bound to cationic proteins have been studied for nearly three decades and are relevant as models for protein surface molecular recognition and photoinitiated electron transfer. However, interpretation of data in nearly all reports explicitly or implicitly assumed interaction of porphyrin with monodisperse proteins in solutions. In this report, using small-angle X-ray scattering with solution phase samples, we demonstrate that horse heart cytochrome (cyt) c, triheme cytochrome c7 PpcA from Geobacter sulfurreducens, and hen egg lysozyme multimerize in the presence of zinc tetrakis(4-sulfonatophenyl)porphyrin (ZnTPPS). Multimerization of cyt c showed a pH dependence with a stronger apparent binding affinity under alkaline conditions and was weakened in the presence of a high salt concentration. Ferric-cyt c formed complexes larger than those formed by ferro-cyt c. Free base TPPS and FeTPPS facilitated formation of complexes larger than those of ZnTPPS. No increase in protein aggregation state for cationic proteins was observed in the presence of cationic porphyrins. All-atom molecular dynamics simulations of cyt c and PpcA with free base TPPS corroborated X-ray scattering results and revealed a mechanism by which the tetrasubstituted charged porphyrins serve as bridging ligands nucleating multimerization of the complementarily charged protein. The final aggregation products suggest that multimerization involves a combination of electrostatic and hydrophobic interactions. The results demonstrate an overlooked complexity in the design of multifunctional ligands for protein surface recognition.

Cobaloximes are popular H2 evolution molecular catalysts but have so far mainly been studied in nonaqueous conditions. We show here that they are also valuable for the design of artificial hydrogenases for application in neutral aqueous solutions and report on the preparation of two well-defined biohybrid species via the binding of two cobaloxime moieties, {Co(dmgH)2} and {Co(dmgBF2)2} (dmgH2 = dimethylglyoxime), to apo Sperm-whale myoglobin (SwMb). All spectroscopic data confirm that the cobaloxime moieties are inserted within the binding pocket of the SwMb protein and are coordinated to a histidine residue in the axial position of the cobalt complex, resulting in thermodynamically stable complexes. Quantum chemical/molecular mechanical docking calculations indicated a coordination preference for His93 over the other histidine residue (His64) present in the vicinity. Interestingly, the redox activity of the cobalt centers is retained in both biohybrids, which provides them with the catalytic activity for H2 evolution in near-neutral aqueous conditions.

The domain structure of an amorphous, "blue layer" iridium-oxide water-oxidation catalyst film (BL) electrodeposited from the soluble precursor complex, [Cp*Ir(H2O)3]SO4, was characterized by X-ray pair distribution function (PDF) analysis. The results show that the experimental PDF can be fit remarkably well using a single Ir5O22 cluster extracted from the rutile lattice. The model includes distortions that indicate the presence of Ir(μ-O)3Ir or distorted Ir(μ-O)2Ir substructures, and hence deviations from a rutile structure. The five Ir atom cluster is suggested to represent the population-averaged distribution of metal-oxo clusters in the film. BL is found to be distinguished from other amorphous film water-oxidation catalysts because of the remarkably small domain size and homogeneity. As such, the blue layer catalyst provides a model for investigating ligand-determined metal-oxide cluster assembly and catalyst mechanism.

We have designed two new supramolecular assemblies based on Co(ii)-templated coordination of Ru(bpy)3(2+) (bpy = 2,2'-bipyridyl) analogues as photosensitizers and electron donors to a cobaloxime macrocycle, which are of interest as proton reduction catalysts. The self-assembled photocatalyst precursors were structurally characterized by Co K-edge X-ray absorption spectroscopy and solution-phase X-ray scattering. Visible light excitation of one of the assemblies has yielded instantaneous electron transfer and charge separation to form a transient Co(i) state which persists for 26 ps. The development of a linked photosensitizer-cobaloxime architecture supporting efficient Co(i) charge transfer is significant since it is mechanistically critical as the first photo-induced electron transfer step for hydrogen production, and has not been detected in previous photosensitizer-cobaloxime linked dyad assemblies. X-band EPR spectroscopy has revealed that the Co(ii) centres of both assemblies are high spin, in contrast to most previously described cobaloximes, and likely plays an important role in facilitating photoinduced charge separation. Based on the results obtained from ultrafast and nanosecond transient absorption optical spectroscopies, we propose that charge recombination occurs through multiple ligand states present within the photosensitizer modules. The studies presented here will enhance our understanding of supramolecular photocatalyst assembly and direct new designs for artificial photosynthesis.

The direct conversion of sunlight into fuel is a promising means for the production of storable renewable energy. Herein, we use Nature's specialized photosynthetic machinery found in the Photosystem I (PSI) protein to drive solar fuel production from a nickel diphosphine molecular catalyst. Upon exposure to visible light, a self-assembled PSI-[Ni(P2(Ph)N2(Ph))2](BF4)2 hybrid generates H2 at a rate 2 orders of magnitude greater than rates reported for photosensitizer/[Ni(P2(Ph)N2(Ph))2](BF4)2 systems. The protein environment enables photocatalysis at pH 6.3 in completely aqueous conditions. In addition, we have developed a strategy for incorporating the Ni molecular catalyst with the native acceptor protein of PSI, flavodoxin. Photocatalysis experiments with this modified flavodoxin demonstrate a new mechanism for biohybrid creation that involves protein-directed delivery of a molecular catalyst to the reducing side of Photosystem I for light-driven catalysis. This work further establishes strategies for constructing functional, inexpensive, earth-abundant solar fuel-producing PSI hybrids that use light to rapidly produce hydrogen directly from water.

This tutorial review illustrates opportunities for the resolution of structure-function relationships to aid in the development of new materials for solar energy conversion using a combination of spectroscopy and catalysis measurements with X-ray scattering analyses to provide in situ structural characterization of solar fuels catalysts. As an example, the use of molecular cobaloxime catalysts in bimolecular and supramolecular photocatalysis schemes for proton reduction is briefly reviewed. These highlight the need to develop new modular, hierarchical, self-healing supramolecular architectures for solar fuels catalysis. Examples of the X-ray scattering structural analysis of amorphous materials in the context of photocatalytic function are discussed in detail.

Upon electrochemical oxidation of the precursor complexes [Cp*Ir(H(2)O)(3)]SO(4) (1) or [(Cp*Ir)(2)(OH)(3)]OH (2) (Cp* = pentamethylcyclopentadienyl), a blue layer of amorphous iridium oxide containing a carbon admixture (BL) is deposited onto the anode. The solid-state, amorphous iridium oxide material that is formed from the molecular precursors is significantly more active for water-oxidation catalysis than crystalline IrO(2) and functions as a remarkably robust catalyst, capable of catalyzing water oxidation without deactivation or significant corrosion for at least 70 h. Elemental analysis reveals that BL contains carbon that is derived from the Cp* ligand (∼ 3% by mass after prolonged electrolysis). Because the electrodeposition of precursors 1 or 2 gives a highly active catalyst material, and electrochemical oxidation of other iridium complexes seems not to result in immediate conversion to iridium oxide materials, we investigate here the nature of the deposited material. The steps leading to the formation of BL and its structure have been investigated by a combination of spectroscopic and theoretical methods. IR spectroscopy shows that the carbon content of BL, while containing some C-H bonds intact at short times, is composed primarily of components with C═O fragments at longer times. X-ray absorption and X-ray absorption fine structure show that, on average, the six ligands to iridium in BL are likely oxygen atoms, consistent with formation of iridium oxide under the oxidizing conditions. High-energy X-ray scattering (HEXS) and pair distribution function (PDF) analysis (obtained ex situ on powder samples) show that BL is largely free of the molecular precursors and is composed of small, <7 Å, iridium oxide domains. Density functional theory (DFT) modeling of the X-ray data suggests a limited set of final components in BL; ketomalonate has been chosen as a model fragment because it gives a good fit to the HEXS-PDF data and is a potential decomposition product of Cp*.

We report the synthesis and characterization of novel mixed-metal binuclear ruthenium(II)-cobalt(II) photocatalysts for hydrogen evolution in acidic acetonitrile. First, 2-(2'-pyridyl)benzothiazole (pbt), 1, was reacted with RuCl(3)·xH(2)O to produce [Ru(pbt)(2)Cl(2)]·0.25CH(3)COCH(3), 2, which was then reacted with 1,10-phenanthroline-5,6-dione (phendione), 3, in order to produce [Ru(pbt)(2)(phendione)](PF(6))(2)·4H(2)O, 4. Compound 4 was then reacted with 4-pyridinecarboxaldehyde in order to produce [Ru(pbt)(2)(L-pyr)](PF(6))(2)·9.5H(2)O, 5 (where L-pyr = (4-pyridine)oxazolo[4,5-f]phenanthroline). Compound 5 was then reacted with [Co(dmgBF(2))(2)(H(2)O)(2)] (where dmgBF(2) = difluoroboryldimethylglyoximato) in order to produce the mixed-metal binuclear complex, [Ru(pbt)(2)(L-pyr)Co(dmgBF(2))(2)(H(2)O)](PF(6))(2)·11H(2)O·1.5CH(3)COCH(3), 6. [Ru(Me(2)bpy)(2)(L-pyr)Co(dmgBF(2))(2)(OH(2))](PF(6))(2), 7 (where Me(2)bpy = 1,10-phenanthroline, 4,4'-dimethyl-2,2'-bipyridine) and [Ru(phen)(2)(L-pyr)Co(dmgBF(2))(2)(OH(2))](PF(6))(2), 8 were also synthesised. All complexes were characterized by elemental analysis, ESI MS, HRMS, UV-visible absorption, (11)B, (19)F, and (59)Co NMR, ESR spectroscopy, and cyclic voltammetry, where appropriate. Photocatalytic studies carried out in acidified acetonitrile demonstrated constant hydrogen generation longer than a 42 hour period as detected by gas chromatography. Time resolved spectroscopic measurements were performed on compound 6, which proved an intramolecular electron transfer from an excited Ru(II) metal centre to the Co(II) metal centre via the bridging L-pyr ligand. This resulted in the formation of a cobalt(I)-containing species that is essential for the production of H(2) gas in the presence of H(+) ions. A proposed mechanism for the generation of hydrogen is presented.

Pair distribution function (PDF) analysis was applied for structural characterization of the cobalt oxide water-splitting catalyst films using high energy X-ray scattering. The catalyst was found to be composed of domains consistent with a cobalt dioxide lattice sheet structure, possibly containing a Co(4)O(4) cubane-type "defect". The analysis identifies the film to consist of domains composed of 13-14 cobalt atoms with distorted coordination geometries that can be modeled by alteration in terminal oxygen atom positions at the domain edge. Phosphate is seen as a disordered component in the films. This work establishes an approach that can be applied to study the structure of in situ cobalt oxide water-splitting film under functional catalytic conditions.

High-resolution mapping of cofactor-specific photochemistry in photosynthetic reaction centers (RCs) from Rhodobacter sphaeroides was achieved by polarization selective ultrafast spectroscopy in single crystals at cryogenic temperature. By exploiting the fixed orientation of cofactors within crystals, we isolated a single transition within the multicofactor manifold, and elucidated the site-specific photochemical functions of the cofactors associated with the symmetry-related active A and inactive B branches. Transient spectra associated with the initial excited states were found to involve a set of cofactors that differ depending upon whether the monomeric bacteriochlorophylls, BChl(A), BChl(B), or the special pair bacteriochlorophyll dimer, P, was chosen for excitation. Proceeding from these initial excited states, characteristic photochemical functions were resolved. Specifically, our measurements provide direct evidence for an alternative charge separation pathway initiated by excitation of BChl(A) that does not involve P*. Conversely, the initial excited state produced by excitation of BChl(B) was found to decay by energy transfer to P. A clear sequential kinetic resolution of BChl(A) and the A-side bacteriopheophytin, BPh(A), in the electron transfer proceeding from P* was achieved. These experiments demonstrate the opportunity to resolve photochemical function of individual cofactors within the multicofactor RC complexes using single crystal spectroscopy.

Solar fuels research aims to mimic photosynthesis and devise integrated systems that can capture, convert, and store solar energy in the form of high-energy molecular bonds. Molecular hydrogen is generally considered an ideal solar fuel because its combustion is essentially pollution-free. Cobaloximes rank among the most promising earth-abundant catalysts for the reduction of protons to molecular hydrogen. We have used multifrequency EPR spectroscopy at X-band, Q-band, and D-band combined with DFT calculations to reveal electronic structure and establish correlations among the structure, surroundings, and catalytic activity of these complexes. To assess the strength and nature of ligand cobalt interactions, the BF(2)-capped cobaloxime, Co(dmgBF(2))(2), was studied in a variety of different solvents with a range of polarities and stoichiometric amounts of potential ligands to the cobalt ion. This allows the differentiation of labile and strongly coordinating axial ligands for the Co(II) complex. Labile, or weakly coordinating, ligands such as methanol result in larger g-tensor anisotropy than strongly coordinating ligands such as pyridine. In addition, a coordination number effect is seen for the strongly coordinating ligands with both singly ligated LCo(dmgBF(2))(2) and doubly ligated L(2)Co(dmgBF(2))(2) . The presence of two strongly coordinating axial ligands leads to the smallest g-tensor anisotropy. The relevance of the strength of the axial ligand(s) to the catalytic efficiency of Co(dmgBF(2))(2) is discussed. Finally, the influence of molecular oxygen and formation of Co(III) superoxide radicals LCo(dmgBF(2))(2)O(2)(•) is studied. The experimental results are compared with a comprehensive set of DFT calculations on Co(dmgBF(2))(2) model systems with various axial ligands. Comparison with experimental values for the "key" magnetic parameters such as g-tensor and (59)Co hyperfine coupling tensor allows the determination of the conformation of the axially ligated Co(dmgBF(2))(2) complexes. The data presented here are vital for understanding the influence of solvent and ligand coordination on the catalytic efficiency of cobaloximes.

Solar energy conversion of water into the environmentally clean fuel hydrogen offers one of the best long-term solutions for meeting future energy demands. Nature provides highly evolved, finely tuned molecular machinery for solar energy conversion that exquisitely manages photon capture and conversion processes to drive oxygenic water-splitting and carbon fixation. Herein, we use one of Nature's specialized energy-converters, the Photosystem I (PSI) protein, to drive hydrogen production from a synthetic molecular catalyst comprised of inexpensive, earth-abundant materials. PSI and a cobaloxime catalyst self-assemble, and the resultant complex rapidly produces hydrogen in aqueous solution upon exposure to visible light. This work establishes a strategy for enhancing photosynthetic efficiency for solar fuel production by augmenting natural photosynthetic systems with synthetically tunable abiotic catalysts.

Silver metal nanoparticle (NP) enhanced fluorescence is investigated in thin films of cyanobacterial Photosystem I trimer complexes (PSI) by correlating confocal laser scanning microscopy, dark-field imaging, and fluorescence lifetime measurements. PSI represents an interesting light-harvesting complex with a 20 nm diameter that is not uniformly contained within the surface-localized plasmon field of the NPs. With weak far-field illumination, 5- to 20-fold fluorescence enhancement is observed for PSI complexes adjacent to NPs, arising from efficient nanoparticle light collection and subsequent localized, surface plasmon excitation of PSI. Enhanced PSI fluorescence is detected most prominently near "rafts" of aggregated NPs that more completely fill the confocal field of view. These results demonstrate opportunities to probe energy transfer within photosynthetic complexes using plasmonic excitation and to design nanostructures for optimizing artificial light-harvesting systems.

Comparing photosynthetic and photovoltaic efficiencies is not a simple issue. Although both processes harvest the energy in sunlight, they operate in distinctly different ways and produce different types of products: biomass or chemical fuels in the case of natural photosynthesis and nonstored electrical current in the case of photovoltaics. In order to find common ground for evaluating energy-conversion efficiency, we compare natural photosynthesis with present technologies for photovoltaic-driven electrolysis of water to produce hydrogen. Photovoltaic-driven electrolysis is the more efficient process when measured on an annual basis, yet short-term yields for photosynthetic conversion under optimal conditions come within a factor of 2 or 3 of the photovoltaic benchmark. We consider opportunities in which the frontiers of synthetic biology might be used to enhance natural photosynthesis for improved solar energy conversion efficiency.

In this report, we have investigated the correlations between structure and light-induced electron transfer of one known and three new axially coordinated cobaloxime-based supramolecular photocatalysts for the reduction of protons to hydrogen. Solution-phase X-ray scattering and ultrafast transient optical spectroscopy analyses were used in tandem to correlate the self-assembled photocatalysts' structural integrity in solution with electron transfer and charge separation between the photosensitizer and catalyst fragments. Biphasic excited state decay kinetics were observed for several of the assemblies, suggesting that configurational dispersion plays a role in limiting photoinduced electron transfer. Notably, an assembly featuring a "push-pull" donor-photosensitizer-acceptor triad motif exhibits considerable ultrafast excited state quenching and, of the assemblies examined, presents the strongest opportunity for efficient solar energy conversion. These results will assist in the design and development of next-generation supramolecular photocatalyst architectures.

Electron paramagnetic resonance (EPR) was used to study light-induced electron transfer in Photosystem I-flavodoxin complexes. Deuteration of flavodoxin enables the signals of the reduced flavin acceptor and oxidized primary donor, P(700)(+), to be well-resolved at X- and D-band EPR. In dark-adapted samples, photoinitiated interprotein electron transfer does not occur at 5 K. However, for samples prepared in dim light, significant interprotein electron transfer occurs at 5 K and a concomitant loss of the spin-correlated radical pair P(+)A(1A)(-) signal is observed. These results indicate a light-induced reorientation of flavodoxin in the PSI docking site that allows a high quantum yield efficiency for the interprotein electron transfer reaction.

The 3(') untranslated region (3(') UTR) of turnip crinkle virus (TCV) genomic RNA contains a cap-independent translation element (CITE), which includes a ribosome-binding structural element (RBSE) that participates in recruitment of the large ribosomal subunit. In addition, a large symmetric loop in the RBSE plays a key role in coordinating the incompatible processes of viral translation and replication, which require enzyme progression in opposite directions on the viral template. To understand the structural basis for the large ribosomal subunit recruitment and the intricate interplay among different parts of the molecule, we determined the global structure of the 102-nt RBSE RNA using solution NMR and small-angle x-ray scattering. This RNA has many structural features that resemble those of a tRNA in solution. The hairpins H1 and H2, linked by a 7-nucleotide linker, form the upper part of RBSE and hairpin H3 is relatively independent from the rest of the structure and is accessible to interactions. This global structure provides insights into the three-dimensional layout for ribosome binding, which may serve as a structural basis for its involvement in recruitment of the large ribosomal subunit and the switch between viral translation and replication. The experimentally determined three-dimensional structure of a functional element in the 3(') UTR of an RNA from any organism has not been previously reported. The RBSE structure represents a prototype structure of a new class of RNA structural elements involved in viral translation/replication processes.

Advances in X-ray light sources and detectors have created opportunities for advancing our understanding of structure and structural dynamics for supramolecular assemblies in solution by combining X-ray scattering measurement with coordinate-based modeling methods. In this review the foundations for X-ray scattering are discussed and illustrated with selected examples demonstrating the ability to correlate solution X-ray scattering measurements to molecular structure, conformation, and dynamics. These approaches are anticipated to have a broad range of applications in natural and artificial photosynthesis by offering possibilities for structure resolution for dynamic supramolecular assemblies in solution that can not be fully addressed with crystallographic techniques, and for resolving fundamental mechanisms for solar energy conversion by mapping out structure in light-excited reaction states., (© Springer Science+Business Media B.V. 2009)

We report a "top-down" method that uses mainly duplexes' global orientations and overall molecular dimension and shape restraints, which were extracted from experimental NMR and small-angle X-ray scattering data, respectively, to determine global architectures of RNA molecules consisting of mostly A-form-like duplexes. The method is implemented in the G2G (from global measurement to global structure) toolkit of programs. We demonstrate the efficiency and accuracy of the method by determining the global structure of a 71-nt RNA using experimental data. The backbone root-mean-square deviation of the ensemble of the calculated global structures relative to the X-ray crystal structure is 3.0+/-0.3 A using the experimental data and is only 2.5+/-0.2 A for the three duplexes that were orientation restrained during the calculation. The global structure simplifies interpretation of multidimensional nuclear Overhauser spectra for high-resolution structure determination. The potential general application of the method for RNA structure determination is discussed.

The structure and properties of hairpin-forming bis(oligonucleotide) conjugates possessing perylenediimide (PDI) chromophores as hairpin linkers have been investigated using a combination of spectroscopic and computational methods. These conjugates exist predominantly as monomer hairpins at room temperature in the absence of added salt and as head-to-head hairpin dimers in the presence of >50 mM NaCl. The hairpin dimer structure is consistent with the results of small-angle X-ray scattering in aqueous solution and molecular dynamics simulation. The structure of the nonconjugated PDI dimer in water is investigated using potential of mean force calculations. The salt dependence is attributed to increased cation condensation in the hairpin dimer vs monomer. Upon heating at low salt concentrations, the hairpin dimer undergoes sequential dissociation to form the monomer hairpin followed by conversion to a random coil structure; whereas at high salt concentrations both dissociation processes occur over the same temperature range. The monomer and dimer hairpins have distinct spectroscopic properties both in the ground state and excited singlet state. The UV and CD spectra provide evidence for electronic interaction between PDI and the adjacent base pair. Low fluorescence quantum yields are observed for both the monomer and dimer. The transient absorption spectrum of the dimer undergoes time-dependent spectral changes attributed to a change in the PDI-PDI torsional angle from ca. 20 degrees in the Franck-Condon singlet state to ca. 0 degrees in the relaxed singlet state, a process which occurs within ca. 40 ps.