Proton transfer kinetics of transition metal hydride complexes and implications for fuel-forming reactions.

Proton transfer reactions involving transition metal hydride complexes are prevalent in a number of catalytic fuel-forming reactions, where the proton transfer kinetics to or from the metal center can have significant impacts on the efficiency, selectivity, and stability associated with the catalytic cycle. This review correlates the often slow proton transfer rate constants of transition metal hydride complexes to their electronic and structural descriptors and provides perspective on how to exploit these parameters to control proton transfer kinetics to and from the metal center. A toolbox of techniques for experimental determination of proton transfer rate constants is discussed, and case studies where proton transfer rate constant determination informs fuel-forming reactions are highlighted. Opportunities for extending proton transfer kinetic measurements to additional systems are presented, and the importance of synergizing the thermodynamics and kinetics of proton transfer involving transition metal hydride complexes is emphasized.

Tuning Cobalt(II) Phosphine Complexes to be Axially Ambivalent.

We report the isolation and characterization of a series of three cobalt(II) bis(phosphine) complexes with varying numbers of coordinated solvent ligands in the axial position. X-ray quality crystals of [Co(dppv)2][BF4]2 (1), [Co(dppv)2(NCCH3)][BPh4]2 (2), and [Co(dppv)2(NCCH3)2][BF4]2 (3) (dppv = cis-1,2-bis(diphenylphosphino)ethylene) were grown under slightly different conditions, and their structures were compared. This analysis revealed multiple crystallization motifs for divalent cobalt(II) complexes with the same set of phosphine ligands. Notably, the 4-coordinate complex 1 is a rare example of a square-planar cobalt(II) complex, the first crystallographically characterized square-planar Co(II) complex containing only neutral, bidentate ligands. Characterization of the different axial geometries via EPR and UV-visible spectroscopies showed that there is a very shallow energy landscape for axial ligation. Ligand field angular overlap model calculations support this conclusion, and we provide a strategy for tuning other ligands to be axially labile on a phosphine scaffold. This methodology is proposed to be used for designing cobalt phosphine catalysts for a variety of oxidation and reduction reactions.

Photochemical H2 Evolution from Bis(diphosphine)nickel Hydrides Enables Low-Overpotential Electrocatalysis.

Molecules capable of both harvesting light and forming new chemical bonds hold promise for applications in the generation of solar fuels, but such first-row transition metal photoelectrocatalysts are lacking. Here we report nickel photoelectrocatalysts for H2 evolution, leveraging visible-light-driven photochemical H2 evolution from bis(diphosphine)nickel hydride complexes. A suite of experimental and theoretical analyses, including time-resolved spectroscopy and continuous irradiation quantum yield measurements, led to a proposed mechanism of H2 evolution involving a short-lived singlet excited state that undergoes homolysis of the Ni-H bond. Thermodynamic analyses provide a basis for understanding and predicting the observed photoelectrocatalytic H2 evolution by a 3d transition metal based catalyst. Of particular note is the dramatic change in the electrochemical overpotential: in the dark, the nickel complexes require strong acids and therefore high overpotentials for electrocatalysis; but under illumination, the use of weaker acids at the same applied potential results in a more than 500 mV improvement in electrochemical overpotential. New insight into first-row transition metal hydride photochemistry thus enables photoelectrocatalytic H2 evolution without electrochemical overpotential (at the thermodynamic potential or 0 mV overpotential). This catalyst system does not require sacrificial chemical reductants or light-harvesting semiconductor materials and produces H2 at rates similar to molecular catalysts attached to silicon.

Redox-Induced Structural Reorganization Dictates Kinetics of Cobalt(III) Hydride Formation via Proton-Coupled Electron Transfer.

Two-electron, one-proton reactions of a family of [CoCp(dxpe)(NCCH3)]2+ complexes (Cp = cyclopentadienyl, dxpe = 1,2-bis(di(aryl/alkyl)phosphino)ethane) form the corresponding hydride species [HCoCp(dxpe)]+ (dxpe = dppe (1,2-bis(diphenylphosphino)ethane), depe (1,2-bis(diethylphosphino)ethane), and dcpe (1,2-bis(dicyclohexylphosphino)ethane)) through a stepwise proton-coupled electron transfer process. For three [CoCp(dxpe)(NCCH3)]2+ complexes, peak shift analysis was employed to quantify apparent proton transfer rate constants from cyclic voltammograms recorded with acids ranging 22 pKa units. The apparent proton transfer rate constants correlate with the strength of the proton source for weak acids, but these apparent proton transfer rate constants curiously plateau (kpl) as the reaction becomes increasingly exergonic. The absolute apparent proton transfer rate constants across both these regions correlate with the steric bulk of the chelating diphosphine ligand, with bulkier ligands leading to slower kinetics (kplateau,depe = 3.5 × 107 M-1 s-1, kplateau,dppe = 1.7 × 107 M-1 s-1, kplateau,dcpe = 7.1 × 104 M-1 s-1). Mechanistic studies were conducted to identify the cause of the aberrant kPTapp-ΔpKa trends. When deuterated acids are employed, deuterium incorporation in the Cp ring is observed, indicating protonation of the CoCp(dxpe) species to form the corresponding hydride proceeds via initial ligand protonation. Digital simulations of cyclic voltammograms show ligand loss accompanying initial reduction gates subsequent PCET activity at higher driving forces. Together, these experiments reveal the details of the reaction mechanism: reduction of the Co(III) species is followed by dissociation of the bound acetonitrile ligand, subsequent reduction of the unligated Co(II) species to form a Co(I) species is followed by protonation, which occurs at the Cp ring, followed by tautomerization to generate the stable Co(III)-hydride product [HCoCp(dxpe)]+. Analysis as a function of chelating disphosphine ligand, solvent, and acid strength reveals that the ligand dissociation equilibrium is directly influenced by the steric bulk of the phosphine ligands and gates protonation, giving rise to the plateau of the apparent proton transfer rate constant with strong acids. The complexity of the reaction mechanism underpinning hydride formation, encompassing dynamic behavior of the entire ligand set, highlights the critical need to understand elementary reaction steps in proton-coupled electron transfer reactions.

A Cobalt Phosphine Complex in Five Oxidation States.

Here we report electrochemical, spectroscopic, and crystallographic characterization of a redox series of cobalt complexes in five sequential oxidation states. A simple bidentate phosphine ligand, cis-1,2-bis(diphenylphosphino)ethylene (dppv), allows for isolation of the 3+, 2+, 1+, 0, and 1- oxidation states of cobalt─the only known example of transition-metal complexes with redox-innocent ligands in five oxidation states. Electrochemistry of [Co(dppv)2]2+ reveals three reversible reductions and one reversible oxidation. Complexes in each oxidation state are characterized using single-crystal X-ray diffraction. The coordination number and geometry of the complex changes as a function of the oxidation state: including acetonitrile ligands, the Co3+ complex is pseudo-octahedral, the Co2+ complex is square-pyramidal, the Co+ complex is pseudo-square-planar, and the Co0 and Co- complexes approach pseudo-tetrahedral, illustrating structures predicted by crystal-field theory of inorganic transition-metal complexes.

The Nature of the Mn(III) Color Centers in Elbaite Tourmalines.

The characteristic red color of many natural tourmalines is due to the presence of Mn(III) cations substituting for aluminum and lithium. These sites originate as Mn(II) and are oxidized by natural γ-irradiation over geologic time as they sit in the Earth's crust. Presented here is a thorough analysis of the spin-allowed and spin-forbidden transitions which give rise to the color of these gemstones. Ligand field analysis, supplemented by time-dependent density functional theory, was used to correct the historical assignments of the symmetry-allowed transitions in the polarized UV-visible absorption spectrum. Heat-induced reduction of the oxidized manganese sites provided a probe of the relationship between the spin-allowed and spin-forbidden bands. Notably, the intensity of the spin-forbidden transition was highly dependent on the neighboring ions in the Y-site. Simulations and modeling showed that increased intensity was observed only when two Mn(III) ions occupied adjacent substitutions in the Y-site via a proposed exchange-coupling mechanism.

Proton-Coupled Electron Transfer Kinetics for the Photoinduced Generation of a Cobalt(III)-Hydride Complex.

Studying the formation of transition metal hydride complexes via proton-coupled electron transfer is important for developing next-generation molecular catalysts for hydrogen evolution. We report herein the study of stepwise photoinduced reduction and protonation of [CoIICp(dppe)]+ (Cp = cyclopentadienyl, dppe = 1,2-bis(diphenylphosphino)ethane) to form the corresponding hydride complex [HCoIIICp(dppe)]+. Reaction intermediates were optically tracked using transient absorption spectroscopy, and a combination of experimental fitting and kinetic simulations was used to determine apparent rate constants for electron transfer and proton transfer with a range of acid sources. A linear free energy relationship is observed between measured apparent proton transfer rate constants and acid strength, but marked differences from previously electrochemically determined protonation rate constants are found. These deviations, which stem from ground-state reactivity present in photochemical experiments, highlight the challenges in comparing mechanistic studies using different techniques.

Bathochromic Shifts in Rhenium Carbonyl Dyes Induced through Destabilization of Occupied Orbitals.

A series of rhenium diimine carbonyl complexes was prepared and characterized in order to examine the influence of axial ligands on electronic structure. Systematic substitution of the axial carbonyl and acetonitrile ligands of [Re(deeb)(CO)3(NCCH3)]+ (deeb = 4,4'-diethylester-2,2'-bipyridine) with trimethylphosphine and chloride, respectively, gives rise to red-shifted absorbance features. These bathochromic shifts result from destabilization of the occupied d-orbitals involved in metal-to-ligand charge-transfer transitions. Time-Dependent Density Functional Theory identified the orbitals involved in each transition and provided support for the changes in orbital energies induced by ligand substitution.

Reaction Parameters Influencing Cobalt Hydride Formation Kinetics: Implications for Benchmarking H(2)-Evolution Catalysts.

The need for benchmarking hydrogen evolution catalysts has increasingly been recognized. The influence of acid choice on activity is often reduced to the overpotential for catalysis. Through the study of a stable cobalt hydride complex, we demonstrate the influence of acid choice, beyond pKa, on the kinetics of hydride formation. A linear free energy relationship between acid pKa and second-order rate constants is observed for weaker acids. For stronger acids, however, further increases in pKa do not correlate to increases in rate constants. Further, steric bulk around the acidic proton is shown to influence rate constants dramatically. Together, these observations reveal the complex factors dictating catalyst performance.

Efficient Photochemical Dihydrogen Generation Initiated by a Bimetallic Self-Quenching Mechanism.

Artificial photosynthesis relies on coupling light absorption with chemical fuel generation. A mechanistic study of visible light-driven H2 production from [Cp*Ir(bpy)H]+ (1) has revealed a new, highly efficient pathway for integrating light absorption with bond formation. The net reaction of 1 with a proton source produces H2, but the rate of excited state quenching is surprisingly acid-independent and displays no observable deuterium kinetic isotopic effect. Time-resolved photoluminescence and labeling studies are consistent with diffusion-limited bimetallic self-quenching by electron transfer. Accordingly, the quantum yield of H2 release nearly reaches unity as the concentration of 1 increases. This unique pathway for photochemical H2 generation provides insight into transformations catalyzed by 1.

MetAnnotate: function-specific taxonomic profiling and comparison of metagenomes.

BACKGROUND: Metagenomes provide access to the taxonomic composition and functional capabilities of microbial communities. Although metagenomic analysis methods exist for estimating overall community composition or metabolic potential, identifying specific taxa that encode specific functions or pathways of interest can be more challenging. Here we present MetAnnotate, which addresses the common question: "which organisms perform my function of interest within my metagenome(s) of interest?" MetAnnotate uses profile hidden Markov models to analyze shotgun metagenomes for genes and pathways of interest, classifies retrieved sequences either through a phylogenetic placement or best hit approach, and enables comparison of these profiles between metagenomes. RESULTS: Based on a simulated metagenome dataset, the tool achieves high taxonomic classification accuracy for a broad range of genes, including both markers of community abundance and specific biological pathways. Lastly, we demonstrate MetAnnotate by analyzing for cobalamin (vitamin B12) synthesis genes across hundreds of aquatic metagenomes in a fraction of the time required by the commonly used Basic Local Alignment Search Tool top hit approach. CONCLUSIONS: MetAnnotate is multi-threaded and installable as a local web application or command-line tool on Linux systems. Metannotate is a useful framework for general and/or function-specific taxonomic profiling and comparison of metagenomes.

Protein Release by Controlled Desorption from Transiently Cationic Nanoparticles.

Therapeutic release from hydrogels is traditionally controlled by encapsulation within nanoparticles; however, this strategy is limited for the release of proteins due to poor efficiency and denaturation. To overcome this problem, we designed an encapsulation-free release platform where negatively charged proteins are adsorbed to the exterior of transiently cationic nanoparticles, thus allowing the nanoparticles to be formulated separately from the proteins. Release is then governed by the change in nanoparticle surface charge from positive to neutral. To achieve this, we synthesized eight zwitterionic poly(lactide-block-carboxybetaine) copolymer derivatives and formulated them into nanoparticles with differing surface chemistry. The nanoparticles were colloidally stable and lost positive charge at rates dependent on the hydrolytic stability of their surface ester groups. The nanoparticles (NPs) were dispersed in a physically cross-linked hyaluronan-based hydrogel with one of three negatively charged proteins (transferrin, panitumumab, or granulocyte-macrophage colony-stimulating factor) to assess their ability to control release. For all three proteins, dispersing NPs within the gels resulted in significant attenuation of release, with the extent modulated by the hydrolytic stability of the surface groups. Release was rapid from fast-hydrolyzing ester groups, reduced with slow-hydrolyzing bulky ester groups, and very slow with nonhydrolyzing amide groups. When positively charged lysozyme was loaded into the nanocomposite gel, there was no significant attenuation of release compared to gel alone. These data demonstrate that electrostatic interactions between the protein and NP are the primary driver of protein release from the hydrogel. All released proteins retained bioactivity as determined with in vitro cell assays. This release strategy shows tremendous versatility and provides a promising new platform for controlled release of anionic protein therapeutics.

Halide Mixing Inhibits Exciton Transport in Two-dimensional Perovskites Despite Phase Purity.

Halide mixing is one of the most powerful techniques to tune the optical bandgap of metal-halide perovskites. However, halide mixing has commonly been observed to result in phase segregation, which reduces excited-state transport and limits device performance. While the current emphasis lies on the development of strategies to prevent phase segregation, it remains unclear how halide mixing may affect excited-state transport even if phase purity is maintained. Here, we study exciton transport in phase pure mixed-halide 2D perovskites of (PEA)2Pb(I1-x Br x )4. Using transient photoluminescence microscopy, we show that, despite phase purity, halide mixing inhibits exciton transport. We find a significant reduction even for relatively low alloying concentrations. By performing Brownian dynamics simulations, we are able to reproduce our experimental results and attribute the decrease in diffusivity to the energetically disordered potential landscape that arises due to the intrinsic random distribution of alloying sites.

Mechanistic basis for tuning iridium hydride photochemistry from H2 evolution to hydride transfer hydrodechlorination.

The photochemistry of metal hydride complexes is dominated by H2 evolution, limiting access to reductive transformations based on photochemical hydride transfer. In this article, the innate H2 evolution photochemistry of the iridium hydride complexes [Cp*Ir(bpy-OMe)H]+ (1, bpy-OMe = 4,4'-dimethoxy-2,2'-bipyridine) and [Cp*Ir(bpy)H]+ (2, bpy = 2,2'-bipyridine) is diverted towards photochemical hydrodechlorination. Net hydride transfer from 1 and 2 to dichloromethane produces chloromethane with high selectivity and exceptional photochemical quantum yield (Φ ≤ 1.3). Thermodynamic and kinetic mechanistic studies are consistent with a non-radical-chain reaction sequence initiated by "self-quenching" electron transfer between excited state and ground state hydride complexes, followed by proton-coupled electron transfer (PCET) hydrodechlorination that outcompetes H-H coupling. This unique photochemical mechanism provides a new hope for the development of light-driven hydride transfer reactions.

Inter-ligand intramolecular through-space anisotropic shielding in a series of manganese carbonyl phosphorous compounds.

Eight novel manganese carbonyl complexes of the type [Mn(bpy-tBu)(CO)3PR3]+ (bpy-tBu = 4,4'-di-tert-butyl-2,2'-bipyridine; R = Cy, nBu, Me, p-tol, Ph, p-F-Ph, OEt, and OMe), have been synthesized and characterized by 1H NMR, FTIR, UV/Vis, HRMS and CV. X-ray crystallographic structures of [Mn(bpy-tBu)(CO)3(PCy3)]+ and [Mn(bpy-tBu)(CO)3(PPh3)]+ were obtained. The short Mn-P bond length allows for close proximity of the bipyridine ligand and the phosphine R groups, resulting in strong anisotropic shielding of certain bipyridine protons by aryl R groups (reordering the bipyridine 1H NMR pattern in the most extreme case). Electrochemical analysis of the compound series reveals that while each is a competent precatalyst for electrochemical carbon dioxide reduction (to carbon monoxide), the lability of the PR3 ligand results in similar catalytic performance amongst the series.

Remote homology and the functions of metagenomic dark matter.

Predicted open reading frames (ORFs) that lack detectable homology to known proteins are termed ORFans. Despite their prevalence in metagenomes, the extent to which ORFans encode real proteins, the degree to which they can be annotated, and their functional contributions, remain unclear. To gain insights into these questions, we applied sensitive remote-homology detection methods to functionally analyze ORFans from soil, marine, and human gut metagenome collections. ORFans were identified, clustered into sequence families, and annotated through profile-profile comparison to proteins of known structure. We found that a considerable number of metagenomic ORFans (73,896 of 484,121, 15.3%) exhibit significant remote homology to structurally characterized proteins, providing a means for ORFan functional profiling. The extent of detected remote homology far exceeds that obtained for artificial protein families (1.4%). As expected for real genes, the predicted functions of ORFans are significantly similar to the functions of their gene neighbors (p < 0.001). Compared to the functional profiles predicted through standard homology searches, ORFans show biologically intriguing differences. Many ORFan-enriched functions are virus-related and tend to reflect biological processes associated with extreme sequence diversity. Each environment also possesses a large number of unique ORFan families and functions, including some known to play important community roles such as gut microbial polysaccharide digestion. Lastly, ORFans are a valuable resource for finding novel enzymes of interest, as we demonstrate through the identification of hundreds of novel ORFan metalloproteases that all possess a signature catalytic motif despite a general lack of similarity to known proteins. Our ORFan functional predictions are a valuable resource for discovering novel protein families and exploring the boundaries of protein sequence space. All remote homology predictions are available at http://doxey.uwaterloo.ca/ORFans.

Aquatic metagenomes implicate Thaumarchaeota in global cobalamin production.

Cobalamin (vitamin B12) is a complex metabolite and essential cofactor required by many branches of life, including most eukaryotic phytoplankton. Algae and other cobalamin auxotrophs rely on environmental cobalamin supplied from a relatively small set of cobalamin-producing prokaryotic taxa. Although several Bacteria have been implicated in cobalamin biosynthesis and associated with algal symbiosis, the involvement of Archaea in cobalamin production is poorly understood, especially with respect to the Thaumarchaeota. Based on the detection of cobalamin synthesis genes in available thaumarchaeotal genomes, we hypothesized that Thaumarchaeota, which are ubiquitous and abundant in aquatic environments, have an important role in cobalamin biosynthesis within global aquatic ecosystems. To test this hypothesis, we examined cobalamin synthesis genes across sequenced thaumarchaeotal genomes and 430 metagenomes from a diverse range of marine, freshwater and hypersaline environments. Our analysis demonstrates that all available thaumarchaeotal genomes possess cobalamin synthesis genes, predominantly from the anaerobic pathway, suggesting widespread genetic capacity for cobalamin synthesis. Furthermore, although bacterial cobalamin genes dominated most surface marine metagenomes, thaumarchaeotal cobalamin genes dominated metagenomes from polar marine environments, increased with depth in marine water columns, and displayed seasonality, with increased winter abundance observed in time-series datasets (e.g., L4 surface water in the English Channel). Our results also suggest niche partitioning between thaumarchaeotal and cyanobacterial ribosomal and cobalamin synthesis genes across all metagenomic datasets analyzed. These results provide strong evidence for specific biogeographical distributions of thaumarchaeotal cobalamin genes, expanding our understanding of the global biogeochemical roles played by Thaumarchaeota in aquatic environments.

Electrocatalytic CO2 Reduction with a Homogeneous Catalyst in Ionic Liquid: High Catalytic Activity at Low Overpotential.

We describe a new strategy for enhancing the efficiency of electrocatalytic CO2 reduction with a homogeneous catalyst, using a room-temperature ionic liquid as both the solvent and electrolyte. The electrochemical behavior of fac-ReCl(2,2'-bipyridine)(CO)3 in neat 1-ethyl-3-methylimidazolium tetracyanoborate ([emim][TCB]) was compared with that in acetonitrile containing 0.1 M [Bu4N][PF6]. Two separate one-electron reductions occur in acetonitrile (-1.74 and -2.11 V vs Fc(+/0)), with a modest catalytic current appearing at the second reduction wave under CO2. However, in [emim][TCB], a two-electron reduction wave appears at -1.66 V, resulting in a ∼0.45 V lower overpotential for catalytic reduction of CO2 to CO. Furthermore, the apparent CO2 reduction rate constant, kapp, in [emim][TCB] exceeds that in acetonitrile by over one order of magnitude (kapp = 4000 vs 100 M(-1) s(-1)) at 25 ± 3 °C. Supported by time-resolved infrared measurements, a mechanism is proposed in which an interaction between [emim](+) and the two-electron reduced catalyst results in rapid dissociation of chloride and a decrease in the activation energy for CO2 reduction.