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At least 595 records · Page 33
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Structural Insights into the Dynamics of Water in SOD1 Catalysis and Drug Interactions

Superoxide dismutase 1 (SOD1) is a crucial enzyme that protects cells from oxidative damage by converting superoxide radicals into H 2 O 2 and O 2 . This detoxification process, essential for cellular homeostasis, relies on a precisely orchestrated catalytic mechanism involving the copper cation, while the zinc cation contributes to the structural integrity of the enzyme. This study presents the 2.3 Å crystal structure of human SOD1 (PDB ID: 9IYK), revealing an assembly of six homodimers and twelve distinct active sites. The water molecules form a complex hydrogen-bonding network that drives proton transfer and sustains active site dynamics. Our structure also uncovers subtle conformational changes that highlight the intrinsic flexibility of SOD1, which is essential for its function. Additionally, we observe how these dynamic structural features may be linked to pathological mutations associated with amyotrophic lateral sclerosis (ALS). By advancing our understanding of hSOD1’s mechanistic intricacies and the influence of water coordination, this study offers valuable insights for developing therapeutic strategies targeting ALS. Our structure’s unique conformations and active site interactions illuminate new facets of hSOD1 function, underscoring the critical role of structural dynamics in enzyme catalysis. Moreover, we conducted a molecular docking analysis using SOD1 for potential radical scavengers and Abelson non-receptor tyrosine kinase (c-Abl, Abl1) inhibitors targeting misfolded SOD1 aggregation along with oxidative stress and apoptosis, respectively. The results showed that CHEMBL1075867, a free radical scavenger derivative, showed the most promising docking results and interactions at the binding site of hSOD1, highlighting its promising role for further studies against SOD1-mediated ALS.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Reactions of NO 3 with aromatic aldehydes: gas-phase kinetics and insights into the mechanism of the reaction

Rate coefficients for the reaction of NO3 radicals with a series of aromatic aldehydes were measured in a 7300 L simulation chamber at ambient temperature and pressure by relative and absolute methods. The rate coefficients for benzaldehyde (BA), ortho-tolualdehyde (O-TA), meta-tolualdehyde (M-TA), para-tolualdehyde (P-TA), 2,4-dimethyl benzaldehyde (2,4-DMBA), 2,5-dimethyl benzaldehyde (2,5-DMBA) and 3,5-dimethyl benzaldehyde (3,5-DMBA) were k 1 = 2.6 ± 0.3, k 2 = 8.7 ± 0.8, k 3 = 4.9 ± 0.5, k 4 = 4.9 ± 0.4, k 5 = 15.1 ± 1.3, k 6 = 12.8 ± 1.2 and k 7 = 6.2 ± 0.6, respectively, in the units of 10 -15 cm 3 molec. -1 s -1 at 298 ± 2 K. The rate coefficient k 13 for the reaction of the NO 3 radical with deuterated benzaldehyde (benzaldehyde-d1) was found to be half that of k 1 . The end product of the reaction in an excess of NO 2 was measured to be C 6 H 5 C(O)O 2 NO 2 . Furthermore, theoretical calculations of aldehydic bond energies and reaction pathways indicate that the NO 3 radical reacts primarily with aromatic aldehydes through the abstraction of an aldehydic hydrogen atom. The atmospheric implications of the measured rate coefficients are briefly discussed.

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

Photoenzymatic Hydrogenation of Heteroaromatic Olefins Using ‘Ene’‐Reductases with Photoredox Catalysts

Abstract Flavin‐dependent ‘ene’‐reductases (EREDs) are highly selective catalysts for the asymmetric reduction of activated alkenes. This function is, however, limited to enones, enoates, and nitroalkenes using the native hydride transfer mechanism. Here we demonstrate that EREDs can reduce vinyl pyridines when irradiated with visible light in the presence of a photoredox catalyst. Experimental evidence suggests the reaction proceeds via a radical mechanism where the vinyl pyridine is reduced to the corresponding neutral benzylic radical in solution. DFT calculations reveal this radical to be “dynamically stable”, suggesting it is sufficiently long‐lived to diffuse into the enzyme active site for stereoselective hydrogen atom transfer. This reduction mechanism is distinct from the native one, highlighting the opportunity to expand the synthetic capabilities of existing enzyme platforms by exploiting new mechanistic models.

Nakano, Yuji↗
DOE OSTI2020

Why Boron Nitride is such a Selective Catalyst for the Oxidative Dehydrogenation of Propane

Abstract Boron‐containing materials, and in particular boron nitride, have recently been identified as highly selective catalysts for the oxidative dehydrogenation of alkanes such as propane. To date, no mechanism exists that can explain both the unprecedented selectivity, the observed surface oxyfunctionalization, and the peculiar kinetic features of this reaction. We combine catalytic activity measurements with quantum chemical calculations to put forward a bold new hypothesis. We argue that the remarkable product distribution can be rationalized by a combination of surface‐mediated formation of radicals over metastable sites, and their sequential propagation in the gas phase. Based on known radical propagation steps, we quantitatively describe the oxygen pressure‐dependent relative formation of the main product propylene and by‐product ethylene. Free radical intermediates most likely differentiate this catalytic system from less selective vanadium‐based catalysts.

Venegas, Juan M.↗
DOE OSTI2021

Electrochemically Triggered Chain Reactions for the Conversion of Furan Derivatives

Abstract We report an electrochemical method for coupling biomass‐derived C5/C6 compounds to value‐added fuel precursors. Using only 2 % of equivalent charges, 2‐methylfuran (2‐MF) was oxidized to yield a cation radical, which readily reacted with 3‐hexene‐2,5‐dione, a derivate of 2,5‐dimethylfuran, to produce 3‐(5‐methylfuran‐2‐yl)hexane‐2,5‐dione. The product was converted to 4‐ethylnonane (a component of biodiesel/jet fuel) in a single step in excellent yield. Importantly, the reaction was not sensitive to oxygen, and a trace amount of water was found to promote the reaction. Detailed mechanistic studies confirmed the proposed reaction pathways. Key to the mechanism is the radical generation that is enabled by electrochemistry. The radical is regenerated at the end of a reaction cycle to ensure chain propagation for an average of ca. 47 times, resulting in an apparent Faradaic efficiency of 4700 %.

Chen, Rong↗
DOE OSTI2020

Synthesis, Electronic Properties and Reactivity of [B 12 X 11 (NO 2 )] 2– (X=F–I) Dianions

Nitro-functionalized undecahalogenated closo-dodecaborates [B 12 X 11 (NO 2 )] 2– were synthesized in high purities and characterized by NMR, IR, and Raman spectroscopy, single crystal X-diffraction, mass spectrometry, and gas-phase ion vibrational spectroscopy. The NO 2 substituent leads to an enhanced electronic and electrochemical stability compared to the parent perhalogenated [B 12 X 12 ] 2– (X=F–I) dianions evidenced by photoelectron spectroscopy, cyclic voltammetry, and quantum-chemical calculations. The stabilizing effect decreases from X=F to X=I. Thermogravimetric measurements of the salts indicate the loss of the nitric oxide radical (NO . ). The homolytic NO . elimination from the dianion under very soft collisional excitation in gas-phase ion experiments results in the formation of the radical [B 12 X 11 O] 2–. . Theoretical investigations suggest that the loss of NO . proceeds via the rearrangement product [B 12 X 11 (ONO)] 2– . The O-bonded nitrosooxy structure is thermodynamically more stable than the N-bonded nitro structure and its formation by radical recombination of [B 12 X 11 O] 2–. and NO . is demonstrated.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Theoretical and Experimental Investigation of Functionalized Cyanopyridines Yield an Anolyte with an Extremely Low Reduction Potential for Nonaqueous Redox Flow Batteries

Abstract Cyanopyridines and cyanophenylpyridines were investigated as anolytes for nonaqueous redox flow batteries (RFBs). The three isomers of cyanopyridine are reduced at potentials of −2.2 V or lower vs. ferrocene +/0 (Fc +/0 ), but the 3‐CNPy⋅ − radical anion forms a sigma‐dimer that is re‐oxidized at E ≈−1.1 V, which would lead to poor voltaic efficiency in a RFB. Bulk electrochemical charge‐discharge cycling of the cyanopyridines in acetonitrile and 0.50 M [NBu 4 ][PF 6 ] shows that 2‐CNPy and 4‐CNPy lose capacity quickly under these conditions, due to irreversible chemical reaction/decomposition of the radical anions. Density‐functional theory (DFT) calculations indicated that adding a phenyl group to the cyanopyridines would, for some isomers, limit dimerization and improve the stability of the radical anions, while shifting their E 1/2 only about +0.10 V relative to the parent cyanopyridines. Among the cyanophenylpyridines, 3‐CN‐6‐PhPy and 3‐CN‐4‐PhPy are the most promising as anolytes. They exhibit reversible reductions at E 1/2 =−2.19 and −2.22 V vs. ferrocene +/0 , respectively, and retain about half of their capacity after 30 bulk charge‐discharge cycles. An improved version of 3‐CN‐6‐PhPy with three methyl groups (3‐cyano‐4‐methyl‐6‐(3,5‐dimethylphenyl)pyridine) has an extremely low reduction potential of −2.50 V vs. Fc +/0 (the lowest reported for a nonaqueous RFB anolyte) and loses only 0.21 % of capacity per cycle during charge‐discharge cycling in acetonitrile.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Gas–Phase Preparation of the 14π Hückel Polycyclic Aromatic Anthracene and Phenanthrene Isomers (C 14 H 10 ) via the Propargyl Addition–BenzAnnulation (PABA) Mechanism

Polycyclic aromatic hydrocarbons (PAHs) imply the missing link between resonantly stabilized free radicals and carbonaceous nanoparticles, commonly referred to as soot particles in combustion systems and interstellar grains in deep space. Whereas gas phase formation pathways to the simplest PAH – naphthalene (C 10 H 8 ) – are beginning to emerge, reaction pathways leading to the synthesis of the 14π Hückel aromatic PAHs anthracene and phenanthrene (C 14 H 10 ) are still incomplete. Here, by utilizing a chemical microreactor in conjunction with vacuum ultraviolet (VUV) photoionization (PI) of the products followed by detection of the ions in a reflectron time-of-flight mass spectrometer (ReTOF-MS), the reaction between the 1'- and 2'-methylnaphthyl radicals (C 11 H 9 •) with the propargyl radical (C 3 H 3 •) accesses anthracene (C 14 H 10 ) and phenanthrene (C 14 H 10 ) via the Propargyl Addition–BenzAnnulation (PABA) mechanism in conjunction with a hydrogen assisted isomerization. Furthermore, the preferential formation of the thermodynamically less stable anthracene isomer compared to phenanthrene suggests a kinetic, rather than a thermodynamics control of the reaction.

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

One Electron Multiple Proton Transfer in Model Organic Donor–Acceptor Systems: Implications for High-Frequency EPR

EPR spectroscopy is an important spectroscopic method for identification and characterization of radical species involved in many biological reactions. The tyrosyl radical is one of the most studied amino acid radical intermediates in biology. Often in conjunction with histidine residues, it is involved in many fundamental biological electron and proton transfer processes, such as in the water oxidation in photosystem II. As biological processes are typically extremely complicated and hard to control, molecular bio-mimetic model complexes are often used to clarify the mechanisms of the biological reactions. In this work, we present theoretical calculations to investigate the sensitivity of magnetic resonance parameters to proton-coupled electron transfer events, as well as conformational substates of the molecular constructs which mimic the tyrosine-histidine (Tyr-His) pairs found in a large variety of proteins. Upon oxidation of the phenol, the Tyr analog, these complexes can perform not only one-electron one-proton transfer (EPT), but also one-electron two-proton transfers (E2PT). It is shown that in aprotic environment the g X -components of the electronicg-tensor are extremely sensitive to the first proton transfer from the phenoxyl oxygen to the imidazole nitrogen (EPT product), leading to a significant increase of the g X -value of up to 0.003, but are not sensitive to the second proton transfer (E2PT). In the latter case, the change of the g X -value is much smaller (ca. 0.0001), which is too small to be distinguished even by high-frequency EPR. The 14 N hyperfine values are also too similar to allow differentiation between the different protonation states in EPT and E2PT. The magnetic resonance parameters were also calculated as a function of the rotation angles around single bonds. It was demonstrated that rotation of the phenoxyl group results in large positive changes (> 0.001) in the g X -values. Analysis of the data reveals that the main source of these changes is related to the strength of the H-bond between phenoxyl oxygen and the proton(s) on N 1 and N 2 positions of the imidazole.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Nitrogen-doped char as a catalyst for wet oxidation of phenol-contaminated water

Catalytic wet oxidation (CWO) of aqueous effluents rich in organic compounds is a very promising technology for the treatment of liquid wastes from biomass conversion processes. CWO reactions occur through the formation of free radical species, produced in the presence of an oxidant, which act on organic contaminates in the effluent. Although the reaction is well known, there exists a lack of affordable catalysts to conduct this process at the lower temperatures and pressures in novel bioenergy processes. Here, this study assessed the catalytic effect of nitrogen-doped chars as such an option. Phenol in aqueous solution was used as a model waste effluent. Treatment was conducted at moderate temperatures (190 to 260 °C), oxygen partial pressure of 1 MPa, and reaction times of 15, 30, and 45 min in stainless steel and glass-lined tube reactors. High pressure liquid chromatography (HPLC) analyses of the products quantified phenol and by-product concentrations used in the calculation of reaction activation energy. The char catalyst was studied by X-ray photoelectron spectroscopy (XPS), transmission electron microscopy (TEM), and scanning electron microscopy (SEM) in order to gain insight into its structure and surface composition. The results indicate that nitrogen-doped char catalysts accelerate the oxidation of phenol by decreasing its reaction activation energy from 82.2 kJ/mol (non-catalyzed) to 40.4 kJ/mol (catalyzed). An analysis from first principles using density functional theory (DFT) was conducted to ascertain which N functional group has the most significant impact on free radical formation in the presence of oxygen. Among all the N functional groups studied, the dipyridinic functional groups showed the most promising characteristics to facilitate the formation of hydroxyl free radicals.

Advanced Oxidation Processes for Organic Pollutant↗
DOE OSTI2024

Large-scale atomistic model construction of subbituminous and bituminous coals for solvent extraction simulations with reactive molecular dynamics

Large-scale atomistic models for complex polycyclic aromatic hydrocarbon systems help understand the chemical properties and behaviors of complex feedstocks such as coal or petroleum. However, the development and utilization of large-scale models remain limited due to the difficulty in achieving the varied structural characteristics necessary to capture stochastic nature of these feedstocks. Here we demonstrate a systematic workflow to construct stochastic molecular systems from a broad analytical suite: high-resolution transmission electron microscopy (HRTEM), carbon-13 nuclear magnetic resonance spectroscopy ( 13 C NMR), laser desorption ionization mass spectroscopy (LDI-MS), and elemental analysis. We present a model construction and analysis utility of a new Python-based module. We selected one subbituminous and three high-volatile bituminous coals to construct large-scale models (~40,000 atoms). The constructed models were utilized to examine the affinity for solvent extraction (naphthalene or tetralin) and the effect of structural properties (e.g., aromatic cluster size, functional groups, and cross-linking) in reactive molecular dynamics simulations. Complex chemical reactions were monitored with bond order transitions, intermediates formation, and mass distributions. Reactive molecular dynamics simulations suggest a plausible chemical extraction process and products for the complex fossil feedstocks. The results indicated that radical formations with bond breaking of bridging oxygens and carbons were required at high temperatures to facilitate hydrogeneration and extraction of gas molecules from radical-free molecules. We observed that aliphatic chains of tetralin were easily decomposed and combined with radicals to form small size of molecules with aryl bonding, mainly increasing molecules in the 500–1000 Da, while naphthalene had little impact on chemical extraction process.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Discovery and engineering of enzymes for new-to-nature photobiocatalysis

Photobiocatalysis integrates enzymatic catalysis with photochemistry, enabling challenging radical transformations with high selectivity under mild conditions. Early developments in this field were largely driven by the discovery that enzyme-bound cofactors can form photoactive charge–transfer complexes with substrates, thereby initiating radical chemistry upon light irradiation. Recent advances, however, have substantially expanded the mechanistic landscape of photobiocatalysis through diverse mechanisms. This review summarizes major developments in photobiocatalysis reported since 2024. Rather than cataloging individual reactions, we focus on the fundamental mechanisms of radical generation and interception within enzyme active sites, and discuss how these mechanistic principles guide the discovery, engineering, and design of enzymes for new-to-nature photobiocatalysis.

Bai, Zibo [University of Illinois Urbana-Champaign↗
DOE OSTI2023

Probing O 2 -dependence of tetrahydrofuranyl reactions via isomer-resolved speciation

Low-temperature oxidation of tetrahydrofuran involves competing reactions that depend on temperature, pressure, and oxygen concentration, including ring-opening and subsequent oxidation of initial radicals ($\dot{R}$), HOO-elimination yielding dihydrofuran isomers, and the formation of peroxy radicals ($RO\dot{O}$). Here, the latter species, upon isomerization, lead to hydroperoxy-substituted radicals ($\dot{Q}OOH$) that undergo reaction either via unimolecular decomposition or second-O 2 -addition. Quantitative measurements of partially oxidized intermediates formed from each type of reaction provide critical constraints that are required for accurate modeling of combustion. To examine the influence of temperature and oxygen concentration on intermediates from tetrahydrofuran, isomer-resolved speciation measurements were conducted at 810 Torr in a jet-stirred reactor (JSR) from 500 – 1000 K. Resulting from negative-temperature coefficient behavior, species concentrations peaked at two temperatures, 600 K and 800 K, which were then selected for separate experiments to quantify O 2 -dependence using concentrations of 0.37 • 10 18 – 7.40 • 10 18 molecules cm –3 .

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

Pressure effects on reactivity and extinction of n -dodecane diffusion cool flame

Low-temperature combustion at high pressure has gained increasing interest owing to the growing demand for clean and efficient propulsion and energy systems. In particular, cool flame structure, extinction limits, and fuel reactivities at high pressure are critical in affecting the engine performance at near-limit conditions. Here, this paper investigates the effects of pressure on the cool flame extinction limit, structure, radical index, reactivity, and oxygen concentration dependence by experiments, analysis, and modeling. A large n-alkane, namely n-dodecane (n C 12 H 26 ), is selected to study its diffusion cool flame dynamics and reactivity in a high-pressure counterflow burner up to 10 atm. The experimental results show that higher pressure increases the cool flame extinction strain rates, and that the pressure-weighted extinction strain rate (aP) is proportional to the square of pressure, P 2 . A scaling analysis explains the relationship between the dependence of flame structure, heat release rate, and pressure-weighted cool flame strain rate on pressure. Furthermore, radical indexes at different pressures are measured by isolating the thermal and transport effects from the chemical contribution to diffusion cool flame extinction. The radical index clearly shows that the low-temperature reactivity increases with pressure. In addition, due to the critical role of multiple oxygen addition reactions in low-temperature chemistry, the relationship between the cool flame extinction limit and the oxygen concentration is explored. It is found that the cool flame extinction limits are proportional to the n th power of the oxygen concentration, [O 2 ] n , and increasing pressure leads to stronger extinction limit dependence (larger n) on the oxygen concentration. The present experiment and detailed kinetic analysis show clearly that increasing pressure promotes the low-temperature chemistry including the oxygen addition reactions, while the scaling analysis explains well the experimental results.

33 ADVANCED PROPULSION SYSTEMS↗
DOE OSTI2025

Experimental and modeling study of the autoignition behavior of a saturated heterocycle: Pyrrolidine

Experiments are conducted in both rapid compression machine (RCM) and shock tube (ST) to better quantify autoignition behavior (e.g., ignition delay, heat release) and understand heteroatomic effects in heterocyclic compounds, which are important reference components for the combustion of biomass-derived liquid fuels. These tests focus on the nitrogen-containing, five-membered saturated ring, pyrrolidine, at diluted conditions covering pressures of 20 and 50 bar, temperatures of 720–1450 K and a range of stoichiometries (ϕ = 0.5–2). A chemical kinetic model is developed and coupled to an existing combustion kinetics framework describing key nitrogen containing intermediates (e.g. pyrrole, ammonia and NOx). H-abstraction reactions by OH, H, CH 3 and HO 2 , are determined using ab-initio transition state theory methods, while analogies to cyclopentane are adopted for many other reactions, such as ring-opening. Here, the autoignition measurements reveal the lack of negative temperature coefficient (NTC) behavior and low-temperature chemistry for pyrrolidine, as opposed to its saturated hydrocarbon analogue, cyclopentane. Interestingly, at the lowest temperatures (T < 750 K), the reactivity of cyclopentane is greater than pyrrolidine, while at higher temperatures, pyrrolidine becomes more reactive. Agreement between the experimental measurements and the model is good, and it is found that H-abstraction reactions by HO 2 and ensuing chemistry play key roles in controlling the reactivity of this cyclic amine. Most of the fluxes, i.e., >70 %, are predicted to move through 1- or 2-pyrroline (C 4 H 7 N) and then the cyclic C 4 H 6 N radical, at both lower and higher temperatures, to form either CH 2 CHCHCHNH via ring-opening or pyrrole via β-scission. It appears that the ring opens more easily at lower temperature whereas the C–H β-scission dominates at higher temperature and lower pressure, such that the reaction of the fuel radical intermediate carrying an unpaired electron on the nitrogen atom with HO 2 is the next most notable in promoting oxidation. When comparing pyrrolidine and cyclopentane, which exhibits distinct pathways in different temperature regimes, the pyrrolidine pathways and sensitivity analysis align more closely to the high temperature case of cyclopentane where the important role of HO 2 radicals is seen to provide chain branching through HO 2 reaction with the fuel, accompanied by H 2 O 2 formation and decomposition to OH. The formation of 5-membered diene rings and ring opening reactions are also found to be highly relevant. Of particular note, it is found that there is little influence of small molecule nitrogen-chemistry, e.g., NH 2 , HCN, NO/NO 2 on the reactivity of the pyrrolidine mixtures investigated here where no recirculated combustion gases are included.

Autoignition↗