Sequential oxidations of thiolates and the cobalt metallocenter in a synthetic metallopeptide: implications for the biosynthesis of nitrile hydratase
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bio-inspired↗
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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.
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Nitrile Vibration Reports Induced Electric Field and Delocalization of Electron in the Charge-Transfer State of Aryl Nitriles
An electric field is created upon photoinduced charge separation in electron donor–acceptor (D–A) molecules. The photophysics of a prototypical D–A molecule, 4-(dimethylamino)-benzonitrile (DMABN), has been under extensive investigation for decades. Here in this paper, by using the framework of the vibrational Stark effect (VSE), we show that the nitrile vibration quantifies a significant induced electric field in the intramolecular charge-transfer state of DMABN. We further demonstrate that such a phenomenon can be observed in a structurally similar aryl nitrile and that the VSE depends on solvent polarity due to dielectric screening. Finally, our current work shows how the superb sensitivity of the nitrile vibration can be used to identify the nature of electron delocalization and quantify the induced electric field in photoinduced charge transfer processes.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Investigation of Nitrile Hydration Chemistry by Two Transition Metal Hydroxide Complexes: Mn–OH and Ni–OH Nitrile Insertion Chemistry
Herein we describe the synthesis of a series of nickel complexes, including the formation of [( iPr PN H P)Ni(PMe 3 )][BPh 4 ] ( iPr PN H P = HN(CH 2 CH 2 (PiPr 2 )) 2 ). The ability of this phosphine complex to perform the 1,2-addition of H 2 O to produce the Ni–OH species [( iPr PN H P)NiOH][BPh 4 ] has been investigated. The nucleophilicity of the hydroxide moiety of both [(iPrPNHP)NiOH][BPh4] and the previously reported ( iPr PN H P)MnOH(CO) 2 was investigated through the hydration of aryl and alkyl nitriles, leading to the formation of a number of metal carboxamide (RC(O)NH–) bonds. This reactivity generated complexes with the general structures of [( iPr PN H P)Ni(NHC(O)R)][BPh 4 ] for nickel and ( iPr PN H P)Mn(NHC(O)R)(CO) 2 for manganese. Under catalytic conditions, the hydration of nitriles using nickel complexes yielded only a single turnover. However, ( iPr PN H P)MnOH(CO) 2 produced several turnovers, and the reaction conditions were probed for optimization.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Development and Scale-up of Continuous Electrocatalytic Hydrogenation of Functionalized Nitro arenes, Nitriles and Unsaturated Aldehydes
Electrolysis reactors based on the filter-press architecture of redox flow batteries have proven to be effective and scalable towards the production of commercially relevant, pharmaceutical quantities of anilines (>500 kg/year) from halogen-, hydroxyl-, and carbonyl-substituted nitroarenes. Turbulent flow through the carbon felts on which the catalysts were supported facilitated scaling towards production levels because it conferred on the reactors scale-independent, plug flow-like residence time distributions and high mass transfer coefficients. Equipping the cells with micro-reference electrodes made it possible to transfer reaction conditions first developed in batch systems to the continuous flow reactors. The catalysts prepared by incipient wetness impregnation of metal salts into lightly oxidized carbon felt supports were readily generalizable.
Egbert, Jonathan D.↗
Lithium–Sulfur Battery Cathode Enabled by Lithium–Nitrile Interaction
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catalysis (heterogeneous)↗
Nitrile O-ring Cracking: A Case of Vacuum Flange O-ring Failures
A review of recent nitrile O-ring failures in ISO-KF vacuum flange connections in glovebox applications is presented. An investigation of a single “isolated” o-ring failure leads to the discovery of cracked nitrile o-rings in a glovebox atmospheric control unit. The initial cause of the o-ring failure is attributed to ozone degradation. However, additional investigation reveals nitrile o-ring cracking on multiple gloveboxes and general purpose piping, roughly 85% of the nitrile o-rings removed for inspection show evidence of visible cracking after being in service for 18 months or less. The results of material testing and ambient air testing is presented, elevated ozone levels are not found. The contributing factors of o-ring failure, including nitrile air sensitivity, inadequate storage practices, and poor installation techniques, are discussed. A discussion of nitrile o-ring material properties, the benefits and limitations, and alternate materials are discussed. Considerations for o-ring material selection, purchasing, storage, and installation are presented in the context of lessons learned from the nitrile o-ring cracking investigation. This paper can be presented in 20 minutes and does not require special accommodations or special audio visual devices.
38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗
Electron localization of anions probed by nitrile vibrations
Localization and delocalization of electrons is a key concept in chemistry, and is one of the important factors determining the efficiency of electron transport through organic conjugated molecules, which have potential to act as “molecular wires”. This, in turn, substantially influences the efficiencies of organic solar cells and other molecular electronic devices. It is also necessary to understand the electronic energy landscape and the dynamics of electrons through molecular chain that govern their transport capabilities in one-dimensional conjugated chains so that we can better define the design principles of conjugated molecules for their applications. We show that nitrile ν(C≡N) vibrations respond to the degree of electron localization in nitrile-substituted organic anions by utilizing time-resolved infrared (TRIR) detection combined with pulse radiolysis. Measurements of a series of aryl nitrile anions allow us to construct a semi-empirical calibration curve between the changes in the ν(C≡N) IR shifts and the changes in the electronic charges from the neutral to the anion states in the nitriles; more electron localization in the nitrile anion results in larger IR shifts. Furthermore, the IR linewidth in anions can report a structural change accompanying changes in the electronic density distribution. Probing the shift of the nitrile ν(C≡N) IR vibrational bands enables us to determine how the electron is localized in anions of nitrile-functionalized oligofluorenes, considered as organic mixed-valence compounds. We estimate the diabatic electron transfer distance, electronic coupling strengths, and energy barriers in these organic mixed-valence compounds. The analysis reveals a dynamic picture, showing that the electron is moving back and forth within the oligomers with a small activation energy of ≤ k B T, likely controlled by the movement of dihedral angles between monomer units. Thus, implications for the electron transport capability in "molecular wires" are discussed.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Confocal Raman Microscopy Investigation of Phospholipid Monolayers Deposited on Nitrile-Modified Surfaces in Porous Silica Particles
Phospholipid bilayers deposited on a variety of surfaces offer models for investigation of the lipid membrane structure and supports for biocompatible sensors. Hybrid-supported phospholipid bilayers (HSLBs) are stable membrane models for these investigations, typically prepared by self-assembly of a lipid monolayer over an n-alkane-modified surface. HSLBs have been prepared on n-alkyl chain-modified silica and used for lipophilicity-based chromatographic separations. The structure of these hybrid bilayers differs from vesicle membranes where the lipid head group spacing is greater due to interdigitation of the lipid acyl chains with the underlying n-alkyl chains bound to the silica surface. This interdigitated structure exhibits a broader melting transition at a higher temperature due to strong interactions between the lipid acyl chains and the immobile n-alkyl chains bound to silica. In the present work, we seek to reduce the interactions between a lipid monolayer and its supporting substrate by self-assembly of 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) on porous silica functionalized with nitrile-terminated surface ligands. The frequency of Raman scattering of the surface -C≡N stretching mode at the lipid–nitrile interface is consistent with an n-alkane-like environment and insensitive to lipid head group charge, indicating that the lipid acyl chains are in contact with the surface nitrile groups. The head group area of this lipid monolayer was determined from the within-particle phospholipid concentration and silica specific surface area and found to be 54 ± 2 Å 2 , equivalent to the head group area of a DMPC vesicle bilayer. The structure of these nitrile-supported phospholipid monolayers was characterized below and above their melting transition by confocal Raman microscopy and found to be nearly identical to DMPC vesicle bilayers. Their narrow gel-to-fluid-phase melting transition is equivalent to dispersed DMPC vesicles, indicating that the acyl chain structure on the nitrile support mimics the outer leaflet structure of a vesicle membrane.
36 MATERIALS SCIENCE↗
A single diiron enzyme catalyses the oxidative rearrangement of tryptophan to indole nitrile
Abstract Nitriles are uncommon in nature and are typically constructed from oximes through the oxidative decarboxylation of amino acid substrates or from the derivatization of carboxylic acids. Here we report a third nitrile biosynthesis strategy featuring the cyanobacterial nitrile synthase AetD. During the biosynthesis of the eagle-killing neurotoxin, aetokthonotoxin, AetD transforms the 2-aminopropionate portion of 5,7-dibromo-l-tryptophan to a nitrile. Employing a combination of structural, biochemical and biophysical techniques, we characterized AetD as a non-haem diiron enzyme that belongs to the emerging haem-oxygenase-like dimetal oxidase superfamily. High-resolution crystal structures of AetD together with the identification of catalytically relevant products provide mechanistic insights into how AetD affords this unique transformation, which we propose proceeds via an aziridine intermediate. Our work presents a unique template for nitrile biogenesis and portrays a substrate binding and metallocofactor assembly mechanism that may be shared among other haem-oxygenase-like dimetal oxidase enzymes.
Chemistry↗
Peptidomimetic nitrile warheads as SARS-CoV-2 3CL protease inhibitors
Tragically, the death toll from the COVID-19 pandemic continues to rise, and with variants being observed around the globe new therapeutics, particularly direct-acting antivirals that are easily administered, are desperately needed. Studies targeting the SARS-CoV-2 3CL protease, which is critical for viral replication, with different peptidomimetics and warheads is an active area of research for development of potential drugs. To date, however, only a few publications have evaluated the nitrile warhead as a viral 3CL protease inhibitor, with only modest activity reported. This article describes our investigation of P3 4-methoxyindole peptidomimetic analogs with select P1 and P2 groups with a nitrile warhead that are potent inhibitors of SARS-CoV-2 3CL protease and demonstrate in vitro SARS-CoV-2 antiviral activity. A selectivity for SARS-CoV-2 3CL protease over human cathepsins B, S and L was also observed with the nitrile warhead, which was superior to that with the aldehyde warhead. A co-crystal structure with SARS-CoV-2 3CL protease and a reversibility study indicate that a reversible, thioimidate adduct is formed when the catalytic sulfur forms a covalent bond with the carbon of the nitrile. Furthermore, this effort also identified efflux as a property limiting antiviral activity of these compounds, and together with the positive attributes described these results provide insight for further drug development of novel nitrile peptidomimetics targeting SARS-CoV-2 3CL protease.
60 APPLIED LIFE SCIENCES↗
The Lifetimes of Nitriles (-C*N) and Acids (-COOH) during Ultraviolet Photolysis and Their Survival in Space
Nitriles are one of the most common classes of molecules observed in the gas phase in space, with over a dozen having been positively identified in interstellar and circumstellar environments through the detection of their rotational transitions. Acids, in contrast, are much less common. In this paper we present laboratory data comparing the stability of two structurally related acid-nitrile pairs to ultraviolet (UV) photolytic destruction: acetic acid vs. acetonitrile (CH3-COOH vs. CH3-CN) and glycine vs. aminoacetonitrile (H2N-CH2-COOH vs. H2N-CH2-CN). We find that the nitriles are destroyed ten and five times more slowly (respectively) by UV photolysis than are the corresponding acids. This suggests that whatever their relative formation rates, acids may be less abundant than nitriles in interstellar environments in part because they are more rapidly destroyed by photolysis. The results of this infrared (IR) spectral matrix isolation study indicate that during the lifetime of a typical interstellar cloud, even in its darkest regions, a population of acids in the gas phase will likely be diminished by at least half. Since aminoacetonitrile is a precursor to the amino acid glycine, and far more stable, presolar aminoacetonitrile may be a contributor to the deuterium enriched glycine detected in meteorites. It would clearly be informative to search for aminoacetonitrile (the nitrile corresponding to glycine) in the regions where the amino acid glycine has been reported.
Bernstein, Max P.↗
Quantum chemical study of relative reactivities of a series of amines and nitriles - Relevance to prebiotic chemistry
Using the Iterative Extended Huckel Theory (IEHT) calculations of the electron distribution and orbital energies of a series of thirteen amines, nitriles and amino-nitriles relevant to prebiotic and cosmo-chemistry have been carried out. Ground state properties such as the energy and nature of the highest occupied (HOMO) and lowest empty (LEMO) molecular orbitals, net atomic charges and number of nonbonding electrons have been identified as criteria for correlating the relative nucleophilicity of amine and nitrile nitrogens and the electrophilicity of nitrile and other unsaturated carbon atoms. The results of such correlations can be partially verified by known chemical behavior of these compounds and are used to predict and understand their role in prebiotic organic synthesis.
Loew, G. H.↗
The infrared spectra of nitriles and related compounds frozen in Ar and H2O
We present the 2320-2050 cm-1 (4.31-4.88 micrometers) infrared spectra of 16 solid-state nitriles, isonitriles, and related compounds in order to facilitate the assignment of absorption features in a spectral region now becoming accessible to astronomers for the first time through the Infrared Space Observatory (ISO). This frequency range spans the positions of the strong C triple bond N stretching vibration of these compounds and is inaccessible from the ground due to absorption by CO2 in the terrestrial atmosphere. Band positions, profiles, and intrinsic strengths (A values) were measured for compounds frozen in Ar and H2O matrices at 12 K. The molecular species examined included acetonitrile, benzonitrile (phenylcyanide), 9-anthracenecarbonitrile, dimethylcyanamide, isopropylnitrile (isobutyronitrile), methylacrylonitrile, crotononitrile, acrylonitrile (vinyl cyanide), 3-aminocrotononitrile, pyruvonitrile, dicyandiamide, cyanamide, n-butylisocyanide, methylisocyanoacetate, diisopropylcarbodiimide, and hydrogen cyanide. The C triple bond N stretching bands of the majority of nitriles fall in the 2300-2200 cm-1 (4.35-4.55 micrometers) range and have similar positions in both Ar and H2O matrices, although the bands are generally considerably broader in the H2O matrices. In contrast, the isonitriles and a few exceptional nitriles and related species produce bands at lower frequencies spanning the 2200-2080 cm-1 (4.55-4.81 micrometers) range. These features also have similar positions in both Ar and H2O matrices, and the bands are broader in the H2O matrices. Three of the compounds (pyruvonitrile, dicyandiamide, and cyanamide) show unusually large shifts of their C triple bond N stretching frequencies when changing from Ar to H2O matrices. We attribute these shifts to the formation of H2O:nitrile complexes with these compounds. The implications of these results for the identification of the 2165 cm-1 (4.62 micrometers) "XCN" interstellar feature and the 4550 cm-1 (2.2 micrometers) feature of various objects in the solar system are discussed.
NASA Center ARC↗
Gas Phase Computational Studies on the Competition Between Nitrile and Water Ligands in Uranyl Complexes
The formation of uranyl dicationic complexes containing water and nitrile (acetonitrile, propionitrile, and benzonitrile) ligands, [UO2(H2O)n(RCN)m]2+, has been studied using density functional theory (DFT) with a relativistic effective core potential (RECP) to account for scalar relativistic effects on uranium. It is shown that nitrile addition is favored over the addition of water ligands. Decomposition of these complexes to [UO2OH(H2O)n(RCN)m]+ by the loss of either H3O+ or (RCN+H)+ is also examined. It is found that this reaction occurs when the coordination sphere of uranyl is unsaturated. Additionally, this reaction is influenced by the size of the nitrile ligand with reactions involving acetonitrile being the most prevalent.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Functionalization of Carbon Monoxide and tert ‐Butyl Nitrile by Intramolecular Proton Transfer in a Bis(Phosphido) Thorium Complex
Abstract We report intramolecular proton transfer reactions to functionalize carbon monoxide and tert ‐butyl nitrile from a bis(phosphido) thorium complex. The reaction of (C 5 Me 5 ) 2 Th[PH(Mes)] 2 , Mes=2,4,6‐Me 3 C 6 H 2 , with 1 atm of CO yields (C 5 Me 5 ) 2 Th( κ 2 ‐(O,O)‐OCH 2 PMes‐C(O)PMes), in which one CO molecule is inserted into each thorium–phosphorus bond. Concomitant transfer of two protons, formerly coordinated to phosphorus, are now bound to one of the carbon atoms from one of the inserted CO molecules. DFT calculations were employed to determine the lowest energy pathway. With tert ‐butyl nitrile, t BuCN, only one nitrile inserts into a thorium–phosphorus bond, but the proton is transferred to nitrogen with one phosphido remaining unperturbed affording (C 5 Me 5 ) 2 Th[PH(Mes)][ κ 2 ‐(P,N)‐N(H)C(CMe 3 )P(Mes)]. Surprisingly, reaction of this compound with KN(SiMe 3 ) 2 removes the proton bound to nitrogen, not phosphorus.
Vilanova, Sean P.↗
Monitoring Local Electric Fields using Stark Shifts on Napthyl Nitrile-Functionalized Silicon Photoelectrodes
in this paper, we report spectroscopic measurements of the local electric field using vibrational Stark shifts of napthyl nitrile-functionalized silicon under electrochemical working conditions. The C$\equiv$N bond is particularly sensitive to applied electric fields and serves as a good probe for the local electric fields at the silicon–aqueous interface. Here, surface-enhanced Raman spectra (SERS) are collected at a silicon surface using a water immersion lens as a function of the reference potential in a three-terminal potentiostat. In deionized (DI) water and KCl solutions, the nitrile (i.e., C$\equiv$N) stretch downshifts by 4.7 and 8.6 cm –1 , respectively, under an applied potential of –1 V vs Ag/AgCl. Density functional theory (DFT) calculations of the napthyl nitrile complex carried out under various electric fields establish the Stark tuning rate to be 0.5622 cm–1/(MV cm –1 ). Based on this relation, electric fields of –8.4 and –15.2 MV/cm were obtained under negative applied potentials. These measurements report the electric field strength within the double (i.e., Helmholtz) layer, which is responsible for pulling positively charged ions (e.g., H + ) toward the surface in reduction reaction processes.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗