Hydrogen activation by [NiFe]-hydrogenases

Hydrogenase-1 (Hyd-1) from Escherichia coli is a membrane-bound enzyme that catalyses the reversible oxidation of molecular H2 The active site contains one Fe and one Ni atom and several conserved amino acids including an arginine (Arg(509)), which interacts with two conserved aspartate residues (Asp(118) and Asp(574)) forming an outer shell canopy over the metals. There is also a highly conserved glutamate (Glu(28)) positioned on the opposite side of the active site to the canopy. The mechanism of hydrogen activation has been dissected by site-directed mutagenesis to identify the catalytic base responsible for splitting molecular hydrogen and possible proton transfer pathways to/from the active site. Previous reported attempts to mutate residues in the canopy were unsuccessful, leading to an assumption of a purely structural role. Recent discoveries, however, suggest a catalytic requirement, for example replacing the arginine with lysine (R509K) leaves the structure virtually unchanged, but catalytic activity falls by more than 100-fold. Variants containing amino acid substitutions at either or both, aspartates retain significant activity. We now propose a new mechanism: heterolytic H2 cleavage is via a mechanism akin to that of a frustrated Lewis pair (FLP), where H2 is polarized by simultaneous binding to the metal(s) (the acid) and a nitrogen from Arg(509) (the base)

The role of solvent and the outer coordination sphere on H2 Oxidation Using [Ni(PCy2NPyz2)2]2+

Hydrogenase enzymes are reversible catalysts for H2 production/oxidation, operating with fast rates and minimal overpotentials in water. Many synthetic catalyst mimics of hydrogenase operate in organic solvents. However, recent work has demonstrated the importance of water in the performance of some model complexes. In this work, the H2 oxidation activity of [Ni(PCy2N(3–pyridazyl)methyl2)2]2+ (CyPyz) was compared as a function of acetonitrile, methanol, and water. The reactivity was compared under neutral and acidic conditions in all three solvents and improvement in catalytic activity, from 2 to 40 s–1, was observed with increasing hydrogen bonding ability of the solvent. In addition, the overpotential for catalysis drops significantly in the presence of acid in all solvents, from as high as 600 mV to as low as 70 mV, primarily due to the shift in the equilibrium potential under these conditions. Finally, H2 production was also observed in the same solution, demonstrating bidirectional (irreversible) homogeneous H2 production/oxidation. A structurally and electronically similar complex with a benzyl instead of a pyridazyl group was not stable under these conditions, limiting the evaluation of the contributions of the outer coordination sphere. Collectively, we show that by tuning conditions we can promote fast, efficient H2 oxidation and bidirectional catalysis.by Arnab Dutta, Sheri Lense, John A. S. Roberts, Monte L. Helm 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

In silico identification software (ISIS): a machine learning approach to tandem mass spectral identification of lipids

Liquid chromatography-mass spectrometry-based metabolomics has gained importance in the life sciences, yet it is not supported by software tools for high throughput identification of metabolites based on their fragmentation spectra. An algorithm (ISIS: in silico identification software) and its implementation are presented and show great promise in generating in silico spectra of lipids for the purpose of structural identification. Instead of using chemical reaction rate equations or rules-based fragmentation libraries, the algorithm uses machine learning to find accurate bond cleavage rates in a mass spectrometer employing collision-induced dissociation tandem mass spectrometry. A preliminary test of the algorithm with 45 lipids from a subset of lipid classes shows both high sensitivity and specificity

Active Hydrogenation Catalyst with a Structured, Peptide-Based Outer-Coordination Sphere

The synthesis, catalytic activity, and structural features of a rhodium-based hydrogenation catalyst containing a phosphine ligand coupled to a 14-residue peptide are reported. Both CD and NMR spectroscopy show that the peptide adopts a helical structure in 1:1:1 TFE/MeCN/H₂O that is maintained when the peptide is attached to the ligand and when the ligand is attached to the metal complex. The metal complex hydrogenates aqueous solutions of 3-butenol to 1-butanol at 360 ± 50 turnovers/Rh/h at 294 K. This peptide-based catalyst represents a starting point for developing and characterizing a peptide-based outer-coordination sphere that can be used to introduce enzyme-like features into molecular catalysts