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Results for “bioinorganic chemistry”

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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At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Bioinorganic Chemistry of Nitrification: Structure and Function of Ammonia Monooxygenase (Final Technical Report)

The overarching goal of this project was to elucidate biochemical mechanisms that ubiquitous microorganisms use to enable primary metabolism based on nitrification, the multi-electron oxidation of ammonia (NH 3 ) to nitrite (NO 2 – ). This chemistry enables life to substitute carbon based fuel with nitrogen. Understanding the underlying chemistry was pursued to help inform the use of ammonia as an alternative fuel source compared to petroleum, capitalizing on the widespread infrastructure for production and distribution of this substance in the US. This project specifically focused on characterizing ammonia monooxygenase, an integral membrane copper protein that initiates nitrification via the aerobic oxidation of NH 3 to hydroxylamine (NH 2 OH).

09 BIOMASS FUELS↗
DOE OSTI2024

Defining the Mechanism of Proton Pumping in Heme-Copper Oxidases

During this award, progress was made in two distinct areas of science, one was within the context of bioinorganic chemistry and another in the context of biomimetic, small molecule chemistry. The overarching goals of this work was to understand the fundamental mechanistic drivers for biological reactions specifically, proton transfer reactions. In the biochemical sphere, this goal was investigated through investigation of the bacterial proton pump, ubiquinol oxidase (UbO). Further work in the bioinorganic space was completed in collaboration with the Bandarian group on a novel natural peptide product. While in the biomimetic space, this work was explored through a computational collaborative study with the Riordan group relating to proton coupled electron transfers in iron complexes as relating to the heme active site in proton pumping enzymes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

A Comprehensive Machine Learning Model for Metal–Ligand Binding Prediction: Applications in Chemistry and Biology

A machine-learning (ML) model that predicts metal–ligand binding constants was developed using the open-source Chemprop software. The model was trained on over 30,000 experimental log K 1 values, which include both protonation and metal–ligand stability constants, comprising over 3500 ligands and 10 2 metal ions from 73 total elements, thus generalizing beyond existing limited approaches, which focus only on specific metals or ligand families. The best-performing model included a combination of SMILES-based molecular representations along with descriptors for the metal ion and experimental conditions. It had an external test R 2 value of 0.942, and MAE value of 0.834. A “SMILES-only” simpler version also produced accurate predictions and preserved the binding trends, serving as a quick and easily accessible alternative for users without computational expertise. The SMILES-only model performed comparably to density functional theory (DFT) calculations but utilized a fraction of the computational resources. The model was successfully applied across diverse domains, including bioinorganic chemistry, heavy metal remediation, and sensor development and demonstrated its effectiveness as a rapid and reliable screening tool for both academic and industrial uses.

Ligands↗
DOE OSTI2021

Spectroscopic Evidence of Hyponitrite Radical Intermediate in NO Disproportionation at a MOF-Supported Mononuclear Copper Site

Dianionic hyponitrite (N 2 O 2 2- ) is often proposed, based on model complexes, as the key intermediate in reductive coupling of nitric oxide to nitrous oxide at the bimetallic active sites of heme-copper oxidases and nitric oxide reductases. In this work, we examine the gas-solid reaction of nitric oxide with the metal–organic framework Cu I -ZrTpmC* with a suite of in situ spectroscopies and density functional theory simulations, and identify an unusual chelating N 2 O 2 .- intermediate. These results highlight the advantage provided by site-isolation in metal–organic frameworks (MOFs) for studying important reaction intermediates, and provide a mechanistic scenario compatible with the proposed one-electron couple in these enzymes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Heterologous Expression and Engineering of the Nitrogenase Cofactor Biosynthesis Scaffold NifEN

NifEN plays a crucial role in the biosynthesis of nitrogenase, catalyzing the final step of cofactor maturation prior to delivering the cofactor to NifDK, the catalytic component of nitrogenase. The difficulty in expressing NifEN, a complex, heteromultimeric metalloprotein sharing structural/functional homology with NifDK, is a major challenge in the heterologous expression of nitrogenase. Herein, we report the expression and engineering of Azotobacter vinelandii NifEN in Escherichia coli. Biochemical and spectroscopic analyses demonstrate the integrity of the heterologously expressed NifEN in composition and functionality and, additionally, the ability of an engineered NifEN variant to mimic NifDK in retaining the matured cofactor at an analogous cofactor-binding site. This is an important step toward piecing together a viable pathway for the heterologous expression of nitrogenase and identifying variants for the mechanistic investigation of this enzyme.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Redox Stability Controls the Cellular Uptake and Activity of Ruthenium-Based Inhibitors of the Mitochondrial Calcium Uniporter (MCU)

The mitochondrial calcium uniporter (MCU) is the ion channel that mediates Ca 2+ uptake in mitochondria. Inhibitors of the MCU are valuable as potential therapeutic agents and tools to study mitochondrial Ca 2+ . The best-known inhibitor of the MCU is the ruthenium compound Ru360. Although this compound is effective in permeabilized cells, it does not work in intact biological systems. We have recently reported the synthesis and characterization of Ru265, a complex that selectively inhibits the MCU in intact cells. In this work, the physical and biological properties of Ru265 and Ru360 are described in detail. Using atomic absorption spectroscopy and X-ray fluorescence imaging, we show that Ru265 is transported by organic cation transporter 3 (OCT3) and taken up more effectively than Ru360. As an explanation for the poor cell uptake of Ru360, we show that Ru360 is deactivated by biological reductants. These data highlight how structural modifications in metal complexes can have profound effects on their biological activities.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Synthesis and Characterization of a Masked Terminal Nickel-Oxide Complex

In exploring terminal nickel-oxo complexes, postulated to be the active oxidant in natural and non-natural oxidation reactions, we report the synthesis of the pseudo-trigonal bipyramidal Ni II complexes (K)[Ni II (L Ph )(DMF)] (1[DMF]) and (NMe 4 ) 2 [Ni II (L Ph )(OAc)] (1[OAc]) (L Ph =2,2’,2’’-nitrilo-tris-(N-phenylacetamide); DMF=N,N-dimethylformamide; - OAc=acetate). Both complexes were characterized using NMR, FTIR, ESI-MS, and X-ray crystallography, showing the L Ph ligand to bind in a tetradentate fashion, together with an ancillary donor. The reaction of 1[OAc] with peroxyphenyl acetic acid (PPAA) resulted in the formation of [(L Ph )Ni III -O-H∙∙∙OAc] 2- , 2, that displays many of the characteristics of a terminal Ni=O species. 2 was characterized by UV-Vis, EPR, and XAS spectroscopies and ESI-MS. 2 decayed to yield a Ni II -phenolate complex 3 (through aromatic electrophilic substitution) that was characterized by NMR, FTIR, ESI-MS, and X-ray crystallography. 2 was capable of hydroxylation of hydrocarbons and epoxidation of olefins, as well as oxygen atom transfer oxidation of phosphines at exceptional rates. While the oxo-wall remains standing, this complex represents an excellent example of a masked metal-oxide that displays all of the properties expected of the ever elusive terminal M=O beyond the oxo-wall.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Amino Acid Sequence Controls Enhanced Electron Transport in Heme-Binding Peptide Monolayers

Metal-binding proteins have the exceptional ability to facilitate long-range electron transport in nature. Despite recent progress, the sequence-structure–function relationships governing electron transport in heme-binding peptides and protein assemblies are not yet fully understood. In this work, the electronic properties of a series of heme-binding peptides inspired by cytochrome bc1 are studied using a combination of molecular electronics experiments, molecular modeling, and simulation. Self-assembled monolayers (SAMs) are prepared using sequence-defined heme-binding peptides capable of forming helical secondary structures. Following monolayer formation, the structural properties and chemical composition of assembled peptides are determined using atomic force microscopy and X-ray photoelectron spectroscopy, and the electronic properties (current density–voltage response) are characterized using a soft contact liquid metal electrode method based on eutectic gallium–indium alloys (EGaIn). Our results show a substantial 1000-fold increase in current density across SAM junctions upon addition of heme compared to identical peptide sequences in the absence of heme, while maintaining a constant junction thickness. These findings show that amino acid composition and sequence directly control enhancements in electron transport in heme-binding peptides. Overall, this study demonstrates the potential of using sequence-defined synthetic peptides inspired by nature as functional bioelectronic materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Stabilization of a Heme-HNO Model Complex Using a Bulky Bis-Picket Fence Porphyrin and Reactivity Studies with NO

Nitroxyl, HNO/NO – , the one-electron reduced form of NO, is suggested to take part in distinct signaling pathways in mammals and is also a key intermediate in various heme-catalyzed NO x interconversions in the nitrogen cycle. Cytochrome P450nor (Cyt P450nor) is a heme-containing enzyme that performs NO reduction to N 2 O in fungal denitrification. The reactive intermediate in this enzyme, termed “Intermediate I”, is proposed to be an Fe-NHO/Fe-NHOH type species, but it is difficult to study its electronic structure and exact protonation state due to its instability. Here, we utilize a bulky bis-picket fence porphyrin to obtain the first stable heme-HNO model complex, [Fe(3,5-Me-BAFP)(MI)(NHO)], as a model for Intermediate I, and more generally HNO adducts of heme proteins. Due to the steric hindrance of the bis-picket fence porphyrin, [Fe(3,5-Me-BAFP)(MI)(NHO)] is stable (τ 1/2 = 56 min at -30 °C), can be isolated as a solid, and is available for thorough spectroscopic characterization. In particular, we were able to solve a conundrum in the literature and provide the first full vibrational characterization of a heme-HNO complex using IR and nuclear resonance vibrational spectroscopy (NRVS). Reactivity studies of [Fe(3,5-Me-BAFP)(MI)(NHO)] with NO gas show a 91 ± 10% yield for N 2 O formation, demonstrating that heme-HNO complexes are catalytically competent intermediates for NO reduction to N 2 O in Cyt P450nor. In conclusion, the implications of these results for the mechanism of Cyt P450nor are further discussed.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Rapid Electron Transfer Self-Exchange in Conformationally Dynamic Copper Coordination Complexes

Here we report the electron transfer (ET) self-exchange rate constants (k 11 ) for a pair of Cu II/I complexes utilizing dpa R (dpa = dipicolylaniline, R = OMe, SMe) ligands assessed by NMR line-broadening experiments. These ligands afford copper complexes that are conformationally dynamic in one oxidation state. With R = OMe, the Cu I complex is dynamic, while with R= SMe, the Cu II complex is dynamic. Both complexes exhibit unexpectedly large k 11 of 2.48(6) x 10 5 and 2.21(9) × 10 6 M –1 s –1 for [CuCl(dpa OMe )] +/0 and [CuCl(dpa SMe )] +/0 , respectively. Among the fastest reported for molecular copper coordination complexes to date, that of [CuCl(dpa SMe )] +/0 exceeds all others by an order of magnitude and compares only to those observed in type 1 blue copper proteins. The dynamicity of these complexes establish pre-steady-state con-formational equilibria that minimize the inner sphere reorganization energies to 0.71 and 0.62 eV for R = OMe and SMe, respectively. In contrast to the emphasis on rigidity in the formulation of entatic states applied to blue copper proteins, the success of these two systems highlight the relevance of conformational dynamicity in mediating rapid ET.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Enzymatic Nitrogen Incorporation Using Hydroxylamine

Hydroxylamine-derived reagents have enabled versatile nitrene transfer reactions for introducing nitrogen-containing functionalities in small-molecule catalysis as well as biocatalysis. These reagents, however, result in poor atom economy and stoichiometric organic waste. Activating hydroxylamine (NH 2 OH) for nitrene transfer offers a low-cost and sustainable route to amine synthesis, since water is the sole byproduct. Despite its presence in nature, however, hydroxylamine is not known to be used for enzymatic nitrogen incorporation in biosynthesis. Here, we report an engineered heme enzyme that can utilize hydroxylammonium chloride, an inexpensive commodity chemical, for nitrene transfer. Directed evolution of Pyrobaculum arsenaticum protoglobin generated efficient enzymes for benzylic C–H primary amination and styrene aminohydroxylation. Mechanistic studies supported a stepwise radical pathway involving rate-limiting hydrogen atom transfer. Furthermore, this unprecedented activity is a useful addition to the ‘nitrene transferase’ repertoire and hints at possible future discovery of natural enzymes that use hydroxylamine for amination chemistry.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Developing scandium and yttrium coordination chemistry to advance theranostic radiopharmaceuticals

The octadentate siderophore analog 3,4,3-LI(1,2-HOPO), denoted 343-HOPO hereafter, is known to have high affinity for both trivalent and tetravalent lanthanide and actinide cations. Here we extend its coordination chemistry to the rare-earth cations Sc$^{3+}$ and Y$^{3+}$ and characterize fundamental metal–chelator binding interactions in solution via UV-Vis spectrophotometry, nuclear magnetic resonance spectroscopy, and spectrofluorimetric metal-competition titrations, as well as in the solid-state via single crystal X-ray diffraction. Sc$^{3+}$ and Y$^{3+}$ binding with 343-HOPO is found to be robust, with both high thermodynamic stability and fast room temperature radiolabeling, indicating that 343-HOPO is likely a promising chelator for in vivo applications with both metals. As a proof of concept, we prepared a $^{86}$Y-343-HOPO complex for in vivo PET imaging, and the results presented herein highlight the potential of 343-HOPO chelated trivalent metal cations for therapeutic and theranostic applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗