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The reduction of nitrogen oxides (NOx), which is mainly mediated by metalloenzymes and metal complexes, is a critical process in the nitrogen cycle and environmental remediation. This Frontier article highlights the importance of density functional theory (DFT) calculations to gain mechanistic insights into nitrite (NO2−) and nitric oxide (NO) reduction reactions facilitated by copper complexes by focusing on two key processes: the reduction of NO2− to NO by a monocopper complex, with special emphasis on the concerted proton–electron transfer, and the reduction of NO to N2O by a dicopper complex, which involves N–N bond formation, N2O2 isomerization, and N–O bond cleavage. These findings underscore the utility of DFT calculations in unraveling complicated reaction mechanisms and offer a foundation for future research aimed at improving the reactivity of transition metal complexes in NOx reduction reactions. [ABSTRACT FROM AUTHOR]

Distinguishing proton-coupled electron transfer (PCET) from uncoupled electron transfer (ET) in proteins can be challenging. A recent investigation [J. C. Koone, M. Simmang, D. L. Saenger, M. L. Hunsicker-Wang and B. F. Shaw, J. Am. Chem. Soc., 145, 16488–16497] reported that protein charge ladders and capillary electrophoresis can distinguish between single ET, PCET, and two-proton coupled ET (2PCET) by directly measuring the change in protein net charge upon reduction/oxidation (ΔZET). The current study used similar methods to assess PCET in zinc-free, "double copper" superoxide dismutase-1 (4Cu-SOD1), where one copper is bound at the copper site of each monomer and one copper is bound at the bridging zinc site, resulting in a quasi-type III Cu center. At pH 7.4, the net charge (Z) of the 4Cu-SOD1 dimer was unaffected by reduction of all four Cu2+ ions, i.e., ΔZ4ET = −0.09 ± 0.05 per dimer (−0.02 ± 0.01 per copper atom). These values suggest that PCET is taking place at all four Cu atoms of the homodimer. Molecular dynamics and Poisson–Boltzmann calculations suggest that a metal-coordinating histidine at the zinc site (His71) is the proton acceptor. These data show how ligands of a naturally occurring zinc site can help facilitate PCET when the right redox metal is bound. [ABSTRACT FROM AUTHOR]

Copper nitrite reductase mimetics were synthesized using three new tridentate ligands sharing the same N,N,N motif of coordination. The ligands were based on L -proline modifications, attaching a pyridine and a triazole to the pyrrolidine ring, and differ by a pendant group (R = phenyl, n-butyl and n-propan-1-ol). All complexes coordinate nitrite, as evidenced by cyclic voltammetry, UV-Vis, FTIR and electron paramagnetic resonance (EPR) spectroscopies. The coordination mode of nitrite was assigned by FTIR and EPR as κ2O chelate mode. Upon acidification, EPR experiments indicated a shift from chelate to monodentate κO mode, and 15N NMR experiments of a Zn2+ analogue, suggested that the related Cu(II) nitrous acid complex may be reasonably stable in solution, but in equilibrium with free HONO under non catalytic conditions. Reduction of nitrite to NO was performed both chemically and electrocatalytically, observing the highest catalytic activities for the complex with n-propan-1-ol as pendant group. These results support the hypothesis that a hydrogen bond moiety in the secondary coordination sphere may aid the protonation step. [ABSTRACT FROM AUTHOR]

Much of biological electron transfer occurs between proteins. These molecular processes usually involve molecular recognition and intermolecular electron transfer (inter-ET). The inter-ET reaction between copper-containing nitrite reductase (CuNiR) and partner protein pseudoazurin (PAz) is the first step in denitrification, which is affected by intermolecular association. However, the transient interaction between CuNiR and PAz and the indistinct inter-ET pathway pose challenges for people to understand the biological functions of the CuNiR–PAz complex. Thus, molecular dynamics simulation and quantum mechanical calculation were used to investigate the question in this study. The interaction of the interface residues was determined through hydrogen bonds, root-mean-square deviation, root-mean-square fluctuation, the dynamics cross-correlation matrix, and molecular mechanics Poisson–Boltzmann surface area of molecular dynamics simulations. The interactions among the residues Glu89, Gly200, Asp205, Asn91, Glu204, Thr92, and Met141 on CuNiR and the residues Lys109, Ala15, Lys10, Asn9, Ile110, Met84, and Met16 on PAz are responsible for the stabilization of the complex. The binding free energy is up to −25.33 kcal mol−1. We compared the wild-type and mutant (M84A) interfacial optimized complex models at the CAM-B3LYP level with Grimme dispersion corrections (GD3) to confirm Met84 as a relay station for promoting the inter-ET. Additionally, to test whether Met84 may combine with the adjacent Met141 to form a special two-center, three-electron (S∴S)+ structure to promote the inter-ET, QM/MM was further performed to discuss the possibility of generating an electron stepping stone. Our study will promote a deep understanding of the stable protein–protein interaction, and the identified inter-residue interaction will be theoretical guidance for enhancing the catalytic activity of CuNiR in denitrification. [ABSTRACT FROM AUTHOR]

The practice of serial X-ray crystallography (SX) depends on efficient, continuous delivery of hydrated protein crystals while minimizing background scattering. Of the two major types of sample delivery devices, fixed-target devices offer several advantages over widely adopted jet injectors, including: lower sample consumption, clog-free delivery, and the ability to control on-chip crystal density to improve hit rates. Here we present our development of versatile, inexpensive, and robust polymer microfluidic chips for routine and reliable room temperature serial measurements at both synchrotrons and X-ray free electron lasers (XFELs). Our design includes highly X-ray-transparent enclosing thin film layers tuned to minimize scatter background, adaptable sample flow layers tuned to match crystal size, and a large sample area compatible with both raster scanning and rotation based serial data collection. The optically transparent chips can be used both for in situ protein crystallization (to eliminate crystal handling) or crystal slurry loading, with prepared samples stable for weeks in a humidified environment and for several hours in ambient conditions. Serial oscillation crystallography, using a multi-crystal rotational data collection approach, at a microfocus synchrotron beamline (SSRL, beamline 12-1) was used to benchmark the performance of the chips. High-resolution structures (1.3–2.7 Å) were collected from five different proteins – hen egg white lysozyme, thaumatin, bovine liver catalase, concanavalin-A (type VI), and SARS-CoV-2 nonstructural protein NSP5. Overall, our modular fabrication approach enables precise control over the cross-section of materials in the X-ray beam path and facilitates chip adaption to different sample and beamline requirements for user-friendly, straightforward diffraction measurements at room temperature. [ABSTRACT FROM AUTHOR]

Nitrite reductases are enzymes that aid in the denitrification process by catalyzing the reduction of nitrite to nitric oxide gas. Since this reaction is the first committed step that involves gas formation, it is regarded to be a vital step for denitrification. However, the mechanism of copper-containing nitrite reductase is still under debate due to the discrepancy between the theoretical and experimental data, especially in terms of the roles of secondary shell residues Asp98 and His255 and the electron transfer mechanism between the two copper sites. Herein, we revisited the nitrite reduction mechanism of A. faecalis copper nitrite reductase using QM(B3LYP)/MM-based metadynamics. It is found that the intramolecular electron transfer from T1-Cu to T2-Cu occurs via an asynchronous proton-coupled electron transfer (PCET) mechanism, with electron transfer (ET) preceding proton transfer (PT). In particular, we found that the ET process is driven by the conformation conversion of Asp98 from the gatekeeper to the proximal one, which is much more energy-demanding than the PCET itself. These results highlight that the inclusion of an electron donor is vital to investigate electron-transfer related processes such as PCET. [ABSTRACT FROM AUTHOR]

High-valent iron-nitrido intermediates have been postulated as reactive intermediates in various enzymes, including the nitrogenases and the cytochromes P450, but so far few have been trapped and characterized. As little is known about their oxidative and spectroscopic properties, we decided to create biomimetic models of iron(IV)-imido complexes and compare their structure and reactivity with analogous iron(IV)-oxo systems. In this work we report the synthesis and spectroscopic characterization of a novel [FeIV(NTs)(Bntpen)]2+ complex (Bntpen = N1-benzyl-N1,N2,N2-tris(pyridine-2-ylmethyl)ethane-1,2-diamine) and study its reactivity patterns with respect to hydrogen atom abstraction and nitrogen atom transfer reactions. The work is compared with analogous pentadentate ligand systems as well as with iron(IV)-oxo species with the same ligand features and highlights the differences in chemical properties and reactivity patterns. It is shown that the reactivity is dependent on the metal ligand system that affects the physicochemical properties of the oxidant such as the redox potential, which is the main driving force for the reaction mechanism with substrates. [ABSTRACT FROM AUTHOR]

Copper(II) containing materials are widely studied for a very diverse array of applications from biology, through catalysis, to many other materials chemistry based applications. We show that, for grafted copper compounds at the surface of silica, and for the study of the selective conversion of methane to methanol using copper ion-exchanged zeolites, the application of focused X-ray beams for spectroscopic investigations is subject to significant challenges. We demonstrate how unwanted effects due to the X-rays manifest, which can prevent the study of certain types of reactive systems, and/or lead to the derivation of results that are not at all representative of the behavior of the materials in question. With reference to identical studies conducted at a beamline that does not focus its X-rays, we then delineate how the total photon throughput and the brilliance of the applied X-rays affect the apparent behavior of copper in zeolites during the stepwise, high temperature and aerobic activation approach to the selective conversion of methane to methanol. We show that the use of increasingly brilliant X-ray sources for X-ray spectroscopy can bring with it significant caveats to obtaining valid and quantitative structure–reactivity relationships (QSARS) and kinetics for this class of material. Lastly, through a systematic study of these effects, we suggest ways to ensure that valuable allocations of X-ray beam time result in measurements that reflect the real nature of the chemistry under study and not that due to other, extraneous, factors. [ABSTRACT FROM AUTHOR]

Two vanadium(III) complexes, CztBu(PyriPr)2VCl2 (1) and CztBu(PyriPr)2V(N3)2 (2), were synthesized and characterized. Chemical reduction of both 1 and 2 gives the thermally stable nitrido-bridged vanadium(IV) dimer complex, [{CztBu(PyriPr)2}V]2(μ-N)2 (3), which is a rare example of a dimeric vanadium(IV) complex bridged by two nitrido ligands. The nitride ligands of 3 are unreactive due to the well-protected environment provided by the pincer ligand and its substituents, as is supported by its X-ray crystal structure and further described by DFT calculations. [ABSTRACT FROM AUTHOR]

Vanadium porphyrin complexes are naturally occurring substances found in crude oil and have been shown to have medicinal properties as well. Little is known on their activities with substrates; therefore, we decided to perform a detailed density functional theory study on the properties and reactivities of vanadium(IV)- and vanadium(V)-oxo complexes with a TPPCl8 or 2,3,7,8,12,13,17,18-octachloro-mesotetraphenylporphyrinato ligand system. In particular, we investigated the reactivity of [VV(O)(TPPCl8)]+ and [VIV(O)(TPPCl8)] with cyclohexene in the presence of H2O2 or HCO4-. The work shows that vanadium(IV)- oxo and vanadium(V)-oxo are sluggish oxidants by themselves and react with olefins slowly. However, in the presence of hydrogen peroxide, these metal-oxo species can be transformed into a side-on vanadium-peroxo complex, which reacts with substrates more efficiently. Particularly with anionic axial ligands, the side-on vanadium-peroxo and vanadium-oxo complexes produced epoxides from cyclohexene via small barrier heights. In addition to olefin epoxidation, we investigated aliphatic hydroxylation mechanisms by the same oxidants and some oxidants show efficient and viable cyclohexene hydroxylation mechanisms. The work implies that vanadium-oxo and vanadium-peroxo complexes can react with double bonds through epoxidation, and under certain conditions also undergo hydroxylation, but the overall reactivity is highly dependent on the equatorial ligand, the local environment and the presence or absence of anionic axial ligands. [ABSTRACT FROM AUTHOR]

Through the use of time-resolved pH-jump spectroscopy, we demonstrate how proton transfer is coupled to inter-copper electron transfer in a copper nitrite reductase (CuNiR). Combined use of electron paramagnetic resonance spectroscopy with solvent viscosity- and pressure-dependence pH-jump stopped-flow spectroscopy is used to show that solvent-slaved protein motions are linked to this proton coupled electron transfer step in CuNiR. [ABSTRACT FROM AUTHOR]

Two cobalt(iii) complexes containing inexpensive Schiff-base ligands have been found to be active for proton reduction at low overpotentials. The dinitro and tetranitro derivatized Schiff-base complexes show catalytic activity at −0.96 V and −1.1 V vs. Fc+/Fc, respectively, resulting in overpotentials of 120 mV and 280 mV. Foot-of-the-wave analysis is used to examine the kinetic properties of these complexes, yielding a theoretical TOFmax of up to 4100 s−1. Experimental TOFs of 7 s−1and 3 s−1 are observed. Catalytic Tafel plots are also presented in order to benchmark the relationship between turnover frequency and overpotential. [ABSTRACT FROM AUTHOR]

An investigation of the active site cofactors of the molybdenum and vanadium nitrogenases (FeMoco and FeVco) was performed using high-resolution X-ray spectroscopy. Synthetic heterometallic iron–sulfur cluster models and density functional theory calculations complement the study of the MoFe and VFe holoproteins using both non-resonant and resonant X-ray emission spectroscopy. Spectroscopic data show the presence of direct iron–heterometal bonds, which are found to be weaker in FeVco. Furthermore, the interstitial carbide is found to perturb the electronic structures of the cofactors through highly covalent Fe–C bonding. The implications of these conclusions are discussed in light of the differential reactivity of the molybdenum and vanadium nitrogenases towards various substrates. Possible functional roles for both the heterometal and the interstitial carbide are detailed. [ABSTRACT FROM AUTHOR]

Immobilization of metal complexes to electrode surfaces has emerged as an attractive strategy to combine homogeneous and heterogeneous catalysis. We recently reported the immobilization of cobalt dithiolene catalytic units via incorporation into extended one and two dimensional (1D and 2D) frameworks. We extend here this methodology to the formation of 1D nickel, iron, and zinc dithiolene coordination polymers based on benzene-1,2,4,5-tetrathiolate (BTT) frameworks and investigate their catalytic H2-evolving activities under fully aqueous conditions. The nickel dithiolene coordination polymer is an active electrocatalyst for the hydrogen evolution reaction (HER). An overpotential of 470 mV was required to reach a current density of 10 mA cm−2 at pH 1.3, making this system one of the best performing heterogenized molecular catalysts for HER. This overpotential is 90 mV lower than that of the cobalt analogue, suggesting that the nickel coordination polymer is a more efficient H2-evolving catalyst. Additionally, no decrease in activity is observed for the nickel polymer during the first hour of electrolysis, indicating that it is stable under prolonged electrolysis. [ABSTRACT FROM AUTHOR]

The active sites of hydrogenases have inspired the design of molecular catalysts for hydrogen evolution and oxidation. In this feature article, we showcase key elements of bio-inspiration before embarking on a tour of a representative series of molecular hydrogen evolving catalysts (HECs) and describing the toolbox available for benchmarking their performances. We then show how such catalysts can be immobilized on conducting substrates to prepare electrode materials active for hydrogen evolution and oxidation with a special emphasis on cobalt diimine–dioxime complexes and DuBois' nickel diphosphine compounds. We finally discuss the optimization required for implementing molecular-engineered materials into operational devices and illustrate how such molecular approaches can be expanded to other fuel-forming processes such as the electrochemical valorisation of carbon dioxide and the oxygen reduction or water oxidation reactions. [ABSTRACT FROM AUTHOR]

Penta-coordinate iron carbonyl complexes that are built around the rigid Fe(PNP) motif (PNP = (C6H5)2PN(R)P(C6H5)2) are synthesized and structurally and spectroscopically characterized. These complexes allow for facile customization of the secondary ligand sphere with various types of linkers and functional groups. The new [Fe(S2C6H4)(PNP)(CO)] complexes show dihydrogen production electrocatalysis at overpotentials of 0.09–0.21 V vs. Pt under mildly acidic conditions (and activities from 0.28 to 3.51 s−1). The most active compound exhibits a turnover frequency (TOF) of 3.51 s−1 at an overpotential of only 0.15 V vs. Pt. Trends in activity are further analyzed. It is found that (a) a decrease in overpotential correlates strongly with the electron withdrawing strength of the PNP amine substituent, and (b) aliphatic substituents give comparatively higher TOFs than aromatic ones. An EC-type mechanism is shown to proceed by initial reduction of the FeII metal center and proposed formation of an FeIII hydride intermediate. Analogous cobalt compounds were synthesized and characterized, but were found to have low stability in acidic media under turnover conditions, and hence, are unsuitable as catalysts for proton reduction. [ABSTRACT FROM AUTHOR]

We demonstrate the covalent attachment and catalytic function of a nickel-phosphine H2 evolution catalyst to a p-Si(111) photoelectrode. The covalently assembled semiconductor☋molecular construct achieves a synergistic improvement (ΔVonset = +200 mV) as compared to a solution of [(PNP)2Ni]2+ in contact with a p-Si(111)–CH3 photoelectrode. [ABSTRACT FROM AUTHOR]

Members of the cytochrome c oxidase family exhibit nitrite reductase activity. In this work, we have characterized a ferrous heme a3-nitro species in ba3-oxidase by resonance Raman spectroscopy. This provides the first evidence for the structure of a nitrite-bound species in the binuclear heme/copper center of cytochrome c oxidases. [ABSTRACT FROM AUTHOR]