Splitting of multiple hydrogen molecules by bioinspired diniobium metal complexes: a DFT study

Splitting of molecular hydrogen (H2) into bridging and terminal hydrides is a common step in transition metal chemistry. Herein, we propose a novel organometallic platform for cleavage of multiple H2 molecules, which combines metal centers capable of stabilizing multiple oxidation states, and ligands bearing positioned pendant basic groups. Using quantum chemical modeling, we show that low-valent, early transition metal diniobium(II) complexes with diphosphine ligands featuring pendant amines can favorably uptake up to 8 hydrogen atoms, and that the energetics are favored by the formation of intramolecular dihydrogen bonds. This result suggests new possible strategies for the development of hydrogen scavenger molecules that are able to perform reversible splitting of multiple H2 molecules

Structural Characterization of the P1+ Intermediate State of the P-Cluster of Nitrogenase

Nitrogenase is the enzyme that reduces atmospheric dinitrogen (N2) to ammonia (NH3) in biological systems. It catalyzes a series of single-electron transfers from the donor iron protein (Fe protein) to the molybdenum–iron protein (MoFe protein) that contains the iron–molybdenum cofactor (FeMo-co) sites where N2 is reduced to NH3. The P-cluster in the MoFe protein functions in nitrogenase catalysis as an intermediate electron carrier between the external electron donor, the Fe protein, and the FeMo-co sites of the MoFe protein. Previous work has revealed that the P-cluster undergoes redox-dependent structural changes and that the transition from the all-ferrous resting (PN) state to the two-electron oxidized P2+ state is accompanied by protein serine hydroxyl and backbone amide ligation to iron. In this work, the MoFe protein was poised at defined potentials with redox mediators in an electrochemical cell, and the three distinct structural states of the P-cluster (P2+, P1+, and PN) were characterized by X-ray crystallography and confirmed by computational analysis. These analyses revealed that the three oxidation states differ in coordination, implicating that the P1+ state retains the serine hydroxyl coordination but lacks the backbone amide coordination observed in the P2+ states. These results provide a complete picture of the redox-dependent ligand rearrangements of the three P-cluster redox states

Heterolytic Scission of Hydrogen Within a Crystalline Frustrated Lewis Pair

We report the heterolysis of molecular hydrogen under ambient conditions by the crystalline frustrated Lewis pair (FLP) 1-{2-[bis (pentafluorophenyOboryl] phenyl -2, 2,6,6-tetrame-thylpiperidine (KCAT). The gas-solid reaction provides an approach to prepare the solvent-free, polycrystalline ion pair KCATH2 through a single crystal to single crystal transformation. The crystal lattice of KCATH2 increases in size relative to the parent KCAT by approximately 2%. Microscopy was used to follow the transformation of the highly colored red/orange KCAT to the colorless KCATH2 over a period of 2 h at 300 K under a flow of H-2 gas. There is no evidence of crystal decrepitation during hydrogen uptake. Inelastic neutron scattering employed over a temperature range from 4-200 K did not provide evidence for the formation of polarized H-2 in a precursor complex within the crystal at low temperatures and high pressures. However, at 300 K, the INS spectrum of KCAT transformed to the INS spectrum of KCATH2. Calculations suggest that the driving force is more favorable in the solid state compared to the solution or gas phase, but the addition of H-2 into the KCAT crystal is unfavorable. Ab Initio methods were used to calculate the INS spectra of KCAT, KCATH2, and a possible precursor complex of H-2 in the pocket between the B and N of crystalline KCAT. Ex-situ NMR showed that the transformation from KCAT to KCATH2 is quantitative and our results suggest that the hydrogen heterolysis process occurs via H-2 diffusion into the FLP crystal with a rate-limiting movement of H-2 from inactive positions to reactive sites.Peer reviewe

Computational study of chemical reactions

Computers can be used to obtain detailed pictures of chemical reactions. A brief overview of a number of computational approaches which can be used to this end will be given. Computational advantages and disadvantages of selected algorithms will be discussed, as well as their applicability and their accuracy. Application of some of the methods will be presented in a study of the reaction of hydrogen peroxide and hydroxyl radical (i.e H2O2 + OH→H2O + O2H). The reaction was studied in gas as well as in condensed phase. In the gas phase two distinct reaction pathways were identified, and the rate was calculated using variational transition state theory for a temperature range of 250-500 K. The calculations explain how the unusual temperature dependence observed for temperatures above 900 K is due to the reaction occurring on the low-lying excited state surface, rather than on the ground state surface. In solution, the reaction is studied using the QM/MM methodology. The free energy barrier was found to be higher than the barrier in the gas phase, which is in accord with the experimental findings of the rate being slower in solution. This work demonstrates the power of computational studies to explain and predict characteristics of chemical reactions, as well as interpret experimental observations

Physi-Sorption of H2 on Pure and Boron–Doped Graphene Monolayers: A Dispersion–Corrected DFT Study

High-surface-area carbons are of interest as potential candidates to store H2 for fuel–cell power applications. Earlier work has been ambiguous and inconclusive on the effect of boron doping on H2 binding energy. Here, we describe a systematic dispersion–corrected density functional theory study to evaluate the effect of boron doping. We observe some enhancement in H2 binding, due to the presence of a defect, such as terminal hydrogen or distortion from planarity, introduced by the inclusion of boron into a graphene ring, which creates hydrogen adsorption sites with slightly increased binding energy. The increase is from −5 kJ/mol H2 for the pure carbon matrix to −7 kJ/mol H2 for the boron–doped system with the boron content of ~7%. The H2 binding sites have little direct interaction with boron. However, the largest enhancement in physi-sorption energy is seen for systems, where H2 is confined between layers at a distance of about 7 Å, where the H2 binding nearly doubles to −11 kJ/mol H2. These findings suggest that interplanar nanoconfinement might be more effective in enhancing H2 binding. Smaller coronene model is shown to be beneficial for understanding the dependence of interaction energy on the structural configurations and preferential H2 binding sites

Nickel–Sulfonate Mode of Substrate Binding for Forward and Reverse Reactions of Methyl-SCoM Reductase Suggest a Radical Mechanism Involving Long-Range Electron Transfer

Methyl-coenzyme M reductase (MCR) catalyzes both the synthesis and the anaerobic oxidation of methane (AOM). Its catalytic site contains Ni at the core of cofactor F430. The Ni ion, in its low-valent Ni(I) state, lights the fuse leading to homolysis of the C–S bond of methyl-coenzyme M (methyl-SCoM) to generate a methyl radical, which abstracts a hydrogen atom from coenzyme B (HSCoB) to generate methane and the mixed disulfide CoMSSCoB. Direct reversal of this reaction activates methane to initiate anaerobic methane oxidation. On the basis of the crystal structures, which reveal a Ni–thiol interaction between Ni(II)–MCR and inhibitor CoMSH, a Ni(I)–thioether complex with substrate methyl-SCoM has been transposed to canonical MCR mechanisms. Similarly, a Ni(I)–disulfide with CoMSSCoB is proposed for the reverse reaction. However, this Ni(I)–sulfur interaction poses a conundrum for the proposed hydrogen-atom abstraction reaction because the >6 Å distance between the thiol group of SCoB and the thiol of SCoM observed in the structures appears to be too long for such a reaction. The spectroscopic, kinetic, structural, and computational studies described here establish that both methyl-SCoM and CoMSSCoB bind to the active Ni(I) state of MCR through their sulfonate groups, forming a hexacoordinate Ni(I)–N/O complex, not Ni(I)–S. These studies rule out direct Ni(I)–sulfur interactions in both substrate-bound states. As a solution to the mechanistic conundrum, we propose that both the forward and the reverse MCR reactions emanate through long-range electron transfer from the Ni(I)–sulfonate complexes with methyl-SCoM and CoMSSCoB, respectively

Optimizing conditions for utilization of an H2 oxidation catalyst with outer coordination sphere functionalities

As a starting point for evaluating a broader range of conditions for H2 oxidation complexes, in this work we investigate an efficient and reversible Ni-based H2 oxidation and production complex with an arginine in the outer coordination sphere, [Ni(PCy2NArginine2)2]7+ (CyArg). We tested this complex under a wide range of pressures and temperatures, in two different solvents (methanol and water), to determine if simultaneous improvements in rate and overpotential could be achieved. We found that the optimal conditions combined both high temperature (72 °C) and pressure (100 atm H2) in acidic aqueous solution (pH = 1), resulting in the fastest H2 oxidation reported for any homogeneous electrocatalyst to date (TOF 1.1 × 106 s−1) operating at 240 mV overpotential. The activation free energy in water was determined to be 10 kcal mol−1 at all pressures studied. Surprisingly, in methanol under the same temperature and pressure, CyArg had a TOF for H2 oxidation of only 280 s−1 at an overpotential of 750 mV. Comparisons to the data in water, and to a control complex, [Ni(PCy2NBenzyl2)2]2+ (CyBn; Bn = benzyl), suggest that this substantial difference is likely due to a change in rate limiting step from H2 addition to deprotonation. Importantly, the optimal conditions we identified for CyArg (elevated temperature and acidic aqueous solutions), are amenable to fuel cell technologies and provide an important advancement in implementing homogeneous synthetic catalysts for renewable energy.by Arnab Dutta, Bojana Ginovska, Simone Raugei, John A. S. Roberts and Wendy J. Sha

Achieving reversible H2/H+ interconversion at room temperature with enzyme-inspired molecular complexes: a mechanistic study

Inspired by the contribution of the protein scaffold to the efficiency with which enzymes function, we used outer coordination sphere features to develop a novel molecular electrocatalyst for the reversible production/oxidation of H2 at 25 °C: [Ni(PCy2NPhe2)2]2+ (CyPhe; PR2NR’2 = 1,5-diaza-3,7-diphosphacyclooctane, Cy = cyclohexyl, Phe = phenylalanine). Electrocatalytic reversibility is observed in aqueous, acidic methanol. The aromatic rings in the peripheral phenylalanine groups appear to be essential to achieving reversibility based on the observation that reversibility for arginine (CyArg) or glycine (CyGly) complexes is only achieved with elevated temperature (>50 °C) in 100% water. A complex with a hydroxyl group in the para-position of the aromatic ring, R’ = tyrosine (CyTyr), shows similar reversible behavior. NMR spectroscopy and molecular dynamics studies suggest that interactions between the aromatic groups as well as between the carboxylic acid groups limit conformational flexibility, contributing to reversibility. NMR spectroscopy studies also show extremely fast proton exchange along a pathway from the Ni-H through the pendant amine to the carboxyl group. Further, a complex containing a side chain similar to tyrosine but without the carboxyl group (CyTym; Tym = Tyramine) does not display reversible catalysis and has limited proton exchange from the pendant amine, demonstrating an essential role for the carboxylic acid and the proton pathway in achieving catalytic reversibility. This minimal pathway mimics proton pathways found in hydrogenases. The influence of multiple factors on lowering barriers and optimizing relative energies to achieve reversibility for this synthetic catalyst is a clear indication of the intricate interplay between the first, second, and outer coordination spheres that begins to mimic the complexity observed in metalloenzymes.by Nilusha Priyadarshani, Arnab Dutta, Bojana Ginovska, Garry W. Buchko, Molly O'Hagan, Simone Raugei and Wendy J. Sha

Analysis of the Activation and Heterolytic Dissociation of H₂ by Frustrated Lewis Pairs: NH₃/BX₃ (X = H, F, and Cl)

We performed a computational study of H₂ activation and heterolytic dissociation promoted by prototype Lewis acid/base pairs NH₃/BX₃ (X = H, F, and Cl) to understand the mechanism in frustrated Lewis pairs (FLPs). Although the NH₃/BX₃ pairs form strong dative bonds, electronic structure theories make it possible to explore the potential energy surface away from the dative complex, in regions relevant to H₂ activation in FLPs. A weakly bound precursor complex, H₃N·H₂·BX₃, was found in which the H₂ molecule interacts side-on with B and end-on with N. The BX₃ group is pyramidal in the case of X = H, similar to the geometry of BH₅, but planar in the complexes with X = F and Cl. The latter complexes convert to ion pairs, [NH₄⁺]­[BHX₃^–] with enthalpy changes of 7.3 and −9.4 kcal/mol, respectively. The minimum energy paths between the FLP and the product ion pair of the chloro and fluoro complexes were calculated and analyzed in great detail. At the transition state (TS), the H₂ bond is weakened and the BX₃ moiety has undergone significant pyramidal distortion. As such, the FLP is prepared to accept the incipient proton and hydride ion on the product-side. The interaction energy of the H₂ with the acid/base pair and the different contributions for the precursor and TS complex from an energy decomposition analysis expose the dominant factors affecting the reactivity. We find that structural reorganization of the precursor complex plays a significant role in the activation and that charge-transfer interactions are the dominant stabilizing force in the activated complex. The electric field clearly has a role in polarizing H₂, but its contribution to the overall interaction energy is small compared to that from the overlap of the <i>p</i>_N, σ_H–H, σ*_H–H, and <i>p</i>_B orbitals at the TS. Our detailed analysis of the interaction of H₂ with the FLP provides insight into the important components that should be taken into account when designing related systems to activate H₂

Visualizing biomolecular electrostatics in virtual reality with UnityMol‐APBS

International audienceVirtual reality is a powerful tool with the ability to immerse a user within a completely external environment. This immersion is particularly useful when visualizing and analyzing interactions between small organic molecules, molecular inorganic complexes, and biomolecular systems such as redox proteins and enzymes. A common tool used in the biomedical community to analyze such interactions is the APBS software, which was developed to solve the equations of continuum electrostatics for large biomolecular assemblages. Numerous applications exist for using APBS in the biomedical community including analysis of protein ligand interactions and APBS has enjoyed widespread adoption throughout the biomedical community. Currently, typical use of the full APBS toolset is completed via the command line followed by visualization using a variety of two-dimensional external molecular visualization software. This process has inherent limitations: visualization of three-dimensional objects using a two-dimensional interface masks important information within the depth component. Herein, we have developed a single application, UnityMol-APBS, that provides a dual experience where users can utilize the full range of the APBS toolset, without the use of a command line interface, by use of a simple \ac{GUI} for either a standard desktop or immersive virtual reality experience