Synthesis and vibrational spectroscopy of Fe-57-labeled models of [NiFe] hydrogenase: first direct observation of a nickel-iron interaction

A new route to iron carbonyls has enabled synthesis of 57Fe-​labeled [NiFe] hydrogenase mimic (OC)​357Fe(pdt)​Ni(dppe) (pdt = 1,​3-​propanedithiolate)​. Its study by nuclear resonance vibrational spectroscopy revealed Ni-​57Fe vibrations, as confirmed by calcns. The modes are absent for [(OC)​357Fe(pdt)​Ni(dppe)​]​+, which lacks Ni-​57Fe bonding, underscoring the utility of the analyses in identifying metal-​metal interactions

Nuclear Resonance Vibrational Spectroscopy: A Modern Tool to Pinpoint Site-Specific Cooperative Processes

Nuclear resonant vibrational spectroscopy (NRVS) is a synchrotron radiation (SR)-based nuclear inelastic scattering spectroscopy that measures the phonons (i.e., vibrational modes) associated with the nuclear transition. It has distinct advantages over traditional vibration spectroscopy and has wide applications in physics, chemistry, bioinorganic chemistry, materials sciences, and geology, as well as many other research areas. In this article, we present a scientific and figurative description of this yet modern tool for the potential users in various research fields in the future. In addition to short discussions on its development history, principles, and other theoretical issues, the focus of this article is on the experimental aspects, such as the instruments, the practical measurement issues, the data process, and a few examples of its applications. The article concludes with introduction to non-57Fe NRVS and an outlook on the impact from the future upgrade of SR rings

Characterization of the [3Fe-4S](0/1+) cluster from the D14C variant of Pyrococcus furiosus ferredoxin via combined NRVS and DFT analyses.

The D14C variant of Pyrococcus furiosus ferredoxin provides an extraordinary framework to investigate a [3Fe-4S] cluster at two oxidation levels and compare the results to its physiologic [4Fe-4S] counterpart in the very same protein. Our spectroscopic and computational study reveals vibrational property changes related to the electronic and structural aspects of both Fe-S clusters

Nuclear resonance vibrational spectroscopy reveals the FeS cluster composition and active site vibrational properties of an O-2-tolerant NAD(+)-reducing [NiFe] hydrogenase

Hydrogenases are complex metalloenzymes that catalyze the reversible splitting of molecular hydrogen into protons and electrons essentially without overpotential. The NAD(+)-reducing soluble hydrogenase (SH) from Ralstonia eutropha is capable of H-2 conversion even in the presence of usually toxic dioxygen. The molecular details of the underlying reactions are largely unknown, mainly because of limited knowledge of the structure and function of the various metal cofactors present in the enzyme. Here, all iron-containing cofactors of the SH were investigated by Fe-57 specific nuclear resonance vibrational spectroscopy (NRVS). Our data provide experimental evidence for one [2Fe2S] center and four [4Fe4S] clusters, which is consistent with the amino acid sequence composition. Only the [2Fe2S] cluster and one of the four [4Fe4S] clusters were reduced upon incubation of the SH with NADH. This finding explains the discrepancy between the large number of FeS clusters and the small amount of FeS cluster-related signals as detected by electron paramagnetic resonance spectroscopic analysis of several NAD(+)-reducing hydrogenases. For the first time, Fe-CO and Fe-CN modes derived from the [NiFe] active site could be distinguished by NRVS through selective C-13 labeling of the CO ligand. This strategy also revealed the molecular coordinates that dominate the individual Fe-CO modes. The present approach explores the complex vibrational signature of the Fe-S clusters and the hydrogenase active site, thereby showing that NRVS represents a powerful tool for the elucidation of complex biocatalysts containing multiple cofactors.DFG, EXC 314, Unifying Concepts in Catalysi

Docking and Migration of Carbon Monoxide in Nitrogenase: The Case for Gated Pockets from Infrared Spectroscopy and Molecular Dynamics

Evidence of a CO docking site near the FeMo cofactor in nitrogenase has been obtained by Fourier transform infrared spectroscopy-monitored low-temperature photolysis. We investigated the possible migration paths for CO from this docking site using molecular dynamics calculations. The simulations support the notion of a gas channel with multiple internal pockets from the active site to the protein exterior. Travel between pockets is gated by the motion of protein residues. Implications for the mechanism of nitrogenase reactions with CO and N₂ are discussed

Vibrational characterization of a diiron bridging hydride complex – a model for hydrogen catalysis

A diiron complex containing a bridging hydride and a protonated terminal thiolate of the form [(μ,κ2-bdtH)(μ-PPh2)(μ-H)Fe2(CO)5]+ has been investigated through 57Fe nuclear resonance vibrational spectroscopy (NRVS) and interpreted using density functional theory (DFT) calculations. We report the Fe–μH–Fe wagging mode, and indications for Fe–μD stretching vibrations in the D-isotopologue, observed by 57Fe-NRVS. Our combined approach demonstrates an asymmetric sharing of the hydride between the two iron sites that yields two nondegenerate Fe–μH/D stretching vibrations. The studied complex provides an important model relevant to biological hydrogen catalysis intermediates. The complex mimics proposals for the binuclear metal sites in [FeFe] and [NiFe] hydrogenases. It is also an appealing prototype for the ‘Janus intermediate’ of nitrogenase, which has been proposed to contain two bridging Fe–H–Fe hydrides and two protonated sulfurs at the FeMo-cofactor. The significance of observing indirect effects of the bridging hydride, as well as obstacles in its direct observation, is discussed in the context of biological hydrogen intermediates.DFG, 390540038, EXC 2008: Unifying Systems in Catalysis "UniSysCat

Copper electroplating process for sub-half-micron ULSI structures

We have utilized electroplating technology in a damascene process to produce low resistance copper interconnects in sub-half-micron ULSI patterns having aspect ratios of 2.4:1. The use of a pulsed-voltage plating technique allows trench filling capability without voids. Samples of 150 mm diameter were patterned and sputtered with a barrier layer, followed by a copper seed layer. Pulsed-voltage electroplating, deposited about 2 microns of copper uniformly (1 sigma < 5%) over the surface. The electroplated copper has low levels of impurities, excellent adhesion, excellent step coverage, and rates comparable to other deposition methods. We present details of the electroplating equipment, and data on the filling characteristics of the copper metallization which prevent void formation and reduce contact resistance

Hydride bridge in [NiFe]-hydrogenase observed by nuclear resonance vibrational spectroscopy

The metabolism of many anaerobes relies on [NiFe]-hydrogenases, whose characterization when bound to substrates has proven non-trivial. Presented here is direct evidence for a hydride bridge in the active site of the 57Fe-labelled fully reduced Ni-R form of Desulfovibrio vulgaris Miyazaki F [NiFe]-hydrogenase. A unique ‘wagging’ mode involving H- motion perpendicular to the Ni(m-H)57Fe plane was studied using 57Fe-specific nuclear resonance vibrational spectroscopy and density functional theory (DFT) calculations. On Ni(m-D)57Fe deuteride substitution, this wagging causes a characteristic perturbation of Fe–CO/CN bands. Spectra have been interpreted by comparison with Ni(m-H/D)57Fe enzyme mimics [(dppe)Ni(m-pdt)(m-H/D)57Fe(CO)3] þ and DFT calculations, which collectively indicate a low-spin Ni(II)(m-H)Fe(II) core for Ni-R, with H- binding Ni more tightly than Fe. The present methodology is also relevant to characterizing Fe–H moieties in other important natural and synthetic catalysts