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All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

H-cluster Intermediates and Catalytic Properties of Clostridium pasteurianum [FeFe]-Hydrogenase III

[FeFe]-Hydrogenases are structurally diverse enzymes that catalyze reversible H2 activation at a catalytic cofactor or H-cluster. The H-cluster is a [4Fe-4S] cubane linked by a cysteine thiolate to a diiron subsite containing unique CO, CN-, and dithiomethylamine ligands. The established H-cluster resting state of [4Fe-4S]2+-[FeII-FeI], or Hox, functions in H2 binding and oxidation, or by proton-coupled reduction initiates H2 evolution. In contrast, in Clostridium pasteurianum [FeFe]-hydrogenase III (CpIII) the resting state of the H-cluster is fully oxidized, [4Fe-4S]2+-[FeII-FeII], or Hox+1. To begin to understand if Hox+1 has a role in the mechanism of CpIII, we determined the spectroscopic and redox properties of CpIII H-cluster states under catalytic conditions. CpIII poised in Hox+1 and either equilibrated under 1 atm of H2 or reduced with sodium dithionite, resulted in a mixture of reduced states including Hox (Em8 = -407 mV), Htrans-like [4Fe-4S]+-[FeII-FeII] (Em8 = -418 mV), Hred [4Fe-4S]+-[FeII-FeI], and HredH+ [4Fe-4S]2+-[FeI-FeI] (Em8 = -455-480 mV). Under H2 the population of the Htrans-like state was >20-fold higher than Hox, implicating a role in CpIII catalysis. Unlike other enzymes, there was no spectral evidence of fully reduced states, such as HsredH+ ([4Fe-4S]+-[FeI-FeI]) or Hhyd ([4Fe-4S]+-[FeII-FeII]-H-). Thus, while the H-cluster states of CpIII encompass most of the catalytic intermediates, it is either unable to form HsredH+ and Hhyd, or these states are highly destabilized in CpIII. Thus, these results demonstrate that catalytic intermediates of reduced CpIII differ from the typical intermediates of other catalytic [FeFe]-hydrogenases and may explain the catalytic preference for H2 production.

08 HYDROGEN↗
DOE OSTI2025

A new synthetic method of [Ru(2,2′:6′,2″-terpyridine)(2,2′-bipyridine)Cl] + complexes using cis -[Ru(2,2′:6′,2″-terpyridine)(NCCH 3 ) 2 Cl] + as an intermediate and comparison to a method using [Ru(benzene)(2,2′-bipyridine)Cl] + intermediates

A new method of synthesizing [Ru(terpy)(bpy)Cl] + (terpy = 2,2′:6′,2″-terpyridine, bpy = 2,2′-bipyridine) complexes using the starting material cis-[Ru(terpy)(NCCH 3 ) 2 Cl](PF 6 ) is reported. The yields of four derivatives ([Ru(terpy)(NN)Cl](PF 6 ): NN = bpy, 1; 4,4′-(MeO) 2 bpy, 2; 4,4′-(CF 3 ) 2 bpy, 3; 2,2′-biquinoline, 4) with this method range from 58 to 94 % and are similar to or greater than a known reaction in which the starting material is [Ru(benzene)(NN)Cl](PF 6 ). However, the use of cis-[Ru(terpy)(NCCH 3 ) 2 Cl](PF 6 ) results in lower levels of homoleptic Ru byproducts in the synthesis of 1 as compared to the use of [Ru(benzene)(bpy)Cl](PF 6 ) as determined by 1 H NMR spectroscopy. In addition, a high-purity and gram-scale synthesis of cis-[Ru(terpy)(NCCH 3 ) 2 Cl](PF 6 ) that does not use column chromatography is reported, in contrast to the original synthesis disclosed in the literature.

Bipyridine↗
DOE OSTI2024

Observational evidence for Criegee intermediate oligomerization reactions relevant to aerosol formation in the troposphere

Criegee intermediates are reactive intermediates that are implicated in transforming the composition of Earth’s troposphere and in the formation of secondary organic aerosol, impacting Earth’s radiation balance, air quality and human health. Yet, direct identification of their signatures in the field remains elusive. Here, from particulate and gas-phase mass-spectrometric measurements in the Amazon rainforest, we identify sequences of masses consistent with the expected signatures of oligomerization of the CH 2 OO Criegee intermediate, a process implicated in ozonolysis-driven aerosol formation. In this study, we assess the potential contributions of oligomerization through laboratory ozonolysis experiments, direct kinetic studies of Criegee intermediate reactions, and high-level theoretical calculations. Global atmospheric models built on these kinetics results indicate that Criegee intermediate chemistry may play a larger role in altering the composition of Earth’s troposphere than is captured in current atmospheric models, especially in areas of high humidity. However, the models still capture only a relatively small fraction of the observed signatures, suggesting considerable underestimates of Criegee intermediate concentrations and reactivity and/or the dominance of other, presently uncharacterized, oxidation mechanisms. Resolving the remaining uncertainties in emission inventories and the effects of atmospheric water vapour on key chemical reactions will be required to definitively assess the role of Criegee intermediate oligomerization reactions.

58 GEOSCIENCES↗
NASA NTRS1986

Gyrating and intermediate ion distributions upstream from the earth's bow shock

Study of ISEE 2 fast plasma data reveals that many suprathermal ion events that in previous studies would have been identified as intermediate ion events are actually gyrating ion events. Of 190 apparently intermediate ion events selected on the basis of their signature in energy-time spectrograms, half are actually found to be gyrating ion events. Using a model bow shock, the shock geometries and spacecraft locations for the observed gyrating and intermediate ion events are compared and found to be quite similar. Both gyrating and intermediate ion events are found to be associated with upstream MHD-like wave activity. Most gyrating ion events are associated with large-amplitude, monochromatic, weakly compressive waves, whereas many intermediate ion events are associated with smaller-amplitude, nonmonochromatic, weakly compressive waves. Some intermediate ion events are found to have no associated waves. Detailed study of the gyrating ion distributions reveals that the distributions are typically gyrotropic within about 4 earth radii of the bow shock, whereas at larger distances (up to about 10 earth radii) upstream from the shock the distributions are frequently 'gyrophase bunched'. In light of these observational characteristics, it is concluded that gyrating ion distributions are most likely generated both through coherent wave disruption of field-aligned beams and through reflection of solar wind ions off the shock.

Fuselier, S. A.↗
NASA NTRS1989

MHD intermediate shock discontinuities. I - Rankine-Hugoniot conditions

Recent numerical investigations have focused attention once more on the role of intermediate shocks in MHD. Four types of intermediate shock are identified using a graphical representation of the MHD Rankine-Hugoniot conditions. This same representation can be used to exhibit the close relationship of intermediate shocks to switch-on shocks and rotational discontinuities. The conditions under which intermediate discontinuities can be found are elucidated. The variations in velocity, pressure, entropy and magnetic-field jumps with upstream parameters in intermediate shocks are exhibited graphically. The evolutionary arguments traditionally advanced against intermediate shocks may fail because the equations of classical MHD are not strictly hyperbolic.

Kennel, C. F.↗
NASA NTRS2013

Evidence of a Weakly Absorbing Intermediate Mode of Aerosols in AERONET Data from Saharan and Sahelian Sites

Accurate retrievals of aerosol size distribution are necessary to estimate aerosols' impact on climate and human health. The inversions of the Aerosol Robotic Network (AERONET) usually retrieve bimodal distributions. However, when the inversion is applied to Saharan and Sahelian dust, an additional mode of intermediate size between the coarse and fine modes is sometimes seen. This mode explains peculiarities in the behavior of the Angstrom exponent, along with the fine mode fraction retrieved using the spectral deconvolution algorithm, observed in a March 2006 dust storm. For this study, 15 AERONET sites in northern Africa and on the Atlantic are examined to determine the frequency and properties of the intermediate mode. The mode is observed most frequently at Ilorin in Nigeria. It is also observed at Capo Verde and multiple sites located within the Sahel but much less frequently at sites in the northern Sahara and the Canary Islands. The presence of the intermediate mode coincides with increases in Angstrom exponent, fine mode fraction, single-scattering albedo, and to a lesser extent percent sphericity. The Angstrom exponent decreases with increasing optical depth at most sites when the intermediate mode is present, but the fine mode fraction does not. Single-scattering albedo does not steadily decrease with fine mode fraction when the intermediate mode is present, as it does in typical mixtures of dust and biomass-burning aerosols. Continued investigation is needed to further define the intermediate mode's properties, determine why it differs from most Saharan dust, and identify its climate and health effects.

inversions↗
DOE OSTI2025

Key Intermediate Nanostructures in the Self-Assembly of Amphiphilic Polypeptoids Revealed by Cryo-TEM

Amphiphilic copolypeptoids are known to form a variety of nanostructures (fibers, tubes, sheets, etc.), but the assembly mechanisms and key intermediates remain underexplored. This study investigates the intermediate structures formed during the early stages of self-assembly in diblock copolypeptoids using cryo-transmission electron microscopy (cryo-TEM). Here we focused on two diblock copolypeptoids, one with a free N-terminus and the other with a capped N-terminus, which ultimately form less-ordered nanofibers and well-ordered nanosheets, respectively. Through cryo-TEM imaging of vitrified solutions at various time points during the self-assembly process, the study identified micelles and vesicles as key intermediate structures. Notably, the formation of vesicles as intermediates is unusual in crystallization-driven self-assembly and suggests a unique pathway in polypeptoid self-assembly. The study provides direct imaging evidence of key intermediates in polypeptoid self-assembly, advancing the understanding of their self-assembly mechanisms.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Nature of the Reactive Biferric Peroxy Intermediate P′ in the Arylamine Oxygenases and Related Binuclear Fe Enzymes

Binuclear nonheme iron enzymes activate O 2 to perform a wide range of chemical transformations. The process of O 2 activation typically involves a biferric peroxy-level intermediate P. It has been previously found that this intermediate undergoes further activation, either protonation or rearrangement to form P′ or further oxidation to form high-valent intermediates Q or X. Here, this study defines the structure of the P′ intermediate in the N-oxygenases CmlI (and AurF based on previous data) using nuclear resonance vibrational spectroscopy (NRVS) in conjugation with density functional theory (DFT) calculations. These results, combined with variable temperature variable field (VTVH) magnetic circular dichroism (MCD) spectroscopy on the 1-electron cryoreduced P′, define the structure of the P′ intermediate as a μ-1,2-hydroxoperoxo biferric site with a second hydroxide bridge. Reaction coordinate calculations demonstrate that single electron transfer (SET) is facilitated by protonation of the peroxo, activating its reductive cleavage, and that the additional hydroxide bridge does not impact this reaction. VTVH MCD studies further reveal that the hydroxide bridge is absent in the biferrous site, suggesting that during the O 2 reaction with the biferrous site, a water molecule forms the hydroxide bridge in providing the proton that activates the peroxide in P′ for reactivity.

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

Single-molecule reaction mapping uncovers diverse behaviours of electrocatalytic surface Pd–H intermediates

Many vital electrocatalytic transformations hinge on reactive surface metal–hydrogen intermediates (M–H*), yet the low concentration and transient nature of such intermediates present formidable challenges to in-depth investigation. Here we use single-molecule super-resolution reaction imaging to directly probe surface palladium–hydrogen (Pd–H*) intermediates on individual palladium nanocubes during electrocatalytic hydrogen evolution. Our approach visualizes hydrogen spillover from palladium to the surrounding substrate surface over hundreds of nanometres away and dissects substantial inter- and intraparticle heterogeneity. Through Gaussian-broadening kinetic analysis, we reveal that ensemble-averaged measurements systematically overestimate the stability of Pd–H*. Moreover, we resolve three subpopulations of palladium nanocubes with distinct reactivity features, uncovering critical correlations between intermediate stability, hydrogenation reactivity and transition-state properties. Finally, our findings highlight the necessity of single-particle resolution for capturing the intrinsic complexity of electrocatalysts; our approach is also broadly applicable to interrogate surface-reactive intermediates across a wide array of electrocatalytic pathways.

electrocatalysis↗
NASA NTRS1972

Mechanisms of deterioration of intermediate moisture food systems

A study of shelf stability in intermediate moisture foods was made. Major efforts were made to control lipid oxidation and nonenzymatic browning. In order to determine means of preventing these reactions, model systems were developed having the same water activity content relationship of intermediate moisture foods. Models were based on a cellulose-lipid and protein-lipid system with glycerol added as the humectant. Experiments with both systems indicate that lipid oxidation is promoted significantly in the intermediate moisture range. The effect appeared to be related to increased mobility of either reactants or catalysts, since when the amount of water in the system reached a level where capillary condensation occurred and thus free water was present, the rates of oxidation increased. With added glycerol, which is water soluble and thus increases the amount of mobile phase, the increase in oxidation rate occurs at a lower relative humidity. The rates of oxidation were maximized at 61% RH and decreased again at 75% RH probably due to dilution. No significant non-enzymatic browning occurred in the protein-lipid systems. Prevention of oxidation by the use of metal chelating agents was enhanced in the cellulose system, whereas, with protein present, the lipid soluble chain terminating antioxidants (such as BHA) worked equally as well. Preliminary studies of foods adjusted to the intermediate moisture range bear out the results of oxidation in model systems. It can be concluded that for most fat containing intermediate moisture foods, rancidity will be the reaction most limiting stability.

Labuza, T. P.↗
NASA NTRS1990

Formation, structure, and stability of MHD intermediate shocks

It was recently shown by Wu (1987) that intermediate shocks are admissible and can be formed through nonlinear wave steepening from continuous waves. In this paper, the formation, structure, and stability of intermediate shocks in dissipative MHD are considered in detail. The differences between the conventional theory and the present one are pointed out and clarified. It is shown that all four types of intermediate shocks can be formed from smooth waves. It is also shown that there are free parameters in the structure of the intermediate shocks, and that these parameters are related to the shock stability. In addition, the paper shows that a rotational discontinuity can not exist with finite width, indicates how this is related to the existence of time-dependent intermediate shocks, and shows why the conventional theory is not a good approximation to dissipative MHD solutions whenever there is rotation in magnetic field.

Wu, C. C.↗
NASA NTRS1992

The back photoreaction of the M intermediate in the photocycle of bacteriorhodopsin: mechanism and evidence for two M species

The back photoreaction of the M intermediate in the photocycle of bacteriorhodopsin is investigated both for the native pigment and its D96N mutant. The experimental setup is based on creating the M intermediate by a first pulse, followed by a (blue) laser pulse which drives the back photoreaction of M. Experiments are carried out varying the delay between the two pulses, as well as the temperature over the -25 degrees C-20 degrees C range. It is found that the kinetic patterns of the M back photoreaction change with time after the generation of this intermediate. The data provide independent evidence for the suggestion of a photocycle mechanism based on two distinct M intermediates. They are thus in keeping with the consecutive model of Varo and Lanyi (Biochemistry 30, 5016-5022; 1991), although they cannot exclude other models such as those based on branched or parallel cycles. More generally, we offer a "photochemical" approach to discriminating between intermediate stages in the photocycle which does not depend on spectroscopic and/or kinetic data. While markedly affecting the rate of the M --> N transition in the photocycle, the rate of the thermal step in back photoreaction of M, at both room and low temperatures, is not significantly affected by the D96N mutation. It is proposed that while Asp 96 is the Schiff-base protonating moiety in the M --> N transition, another residue (most probably Asp 85) reprotonates the Schiff base following light absorption by M.

NASA Discipline Exobiology↗
DOE OSTI2024

Life Cycle Greenhouse Gas Emissions of Growing Intermediate Winter Oilseed Feedstocks for Sustainable Aviation Fuel Production

Ensuring an adequate supply of feedstock is a key challenge to achieving a significant production volume of sustainable aviation fuels (SAFs). One promising feedstock for SAFs is intermediate winter oilseeds added to existing crop production as alternatives to the winter fallow period. In this work, three intermediate winter oilseed crops─camelina ( Camelina sativa L. Crantz .), carinata ( Brassica carinata ), and pennycress ( Thlaspi arvense L .)─are evaluated for their life cycle greenhouse gas (GHG) emissions when harvested and processed into hydroprocessed renewable jet (HRJ). We evaluate solvent extraction (SE) and mechanical pressing as alternative oil extraction methods and examine the impacts of various allocation methods used in the oil extraction process. The GHG emissions reduction potential of camelina-, carinata-, and pennycress-derived HRJs are 50.4%, 65.2%, and 65.7%, respectively, compared to petroleum jet fuel, with SE as an oil extraction method and under mass-based allocation. Combined with the estimated production potential of camelina, carinata, and pennycress as intermediate winter oilseed, 2.5 billion gallons of HRJ can be produced annually, and the total GHG savings could amount to 19.3 million tons when these HRJs replace petroleum jet fuels. In addition, we collect literature information to assess the impacts of these intermediate winter oilseeds on indirect land use change emissions and soil organic carbon sequestration potentials.

camelina↗
DOE OSTI2026

Unimolecular Dynamics of Partially Deuterated Hydroperoxyalkyl Intermediates (•QOOD) in Cyclohexane and Cyclopentane Oxidation

The hydroperoxyalkyl radicals (•QOOH) formed in cyclohexane and cyclopentane oxidation with carbon radical center at the β site relative to the hydroperoxy group have recently been observed through their infrared fingerprint and time- and energy-resolved unimolecular dissociation dynamics to hydroxyl (OH) radical and cyclic ether products. Partial deuteration shifts the IR transitions associated with OH/OD motion to lower frequencies, providing a new window on the IR spectroscopy and unimolecular dynamics of these transient intermediates. Specifically, the overtone OD stretch (2ν OD ) has been identified at 5215.0 cm –1 and 5216.0 cm –1 for the β-QOOD intermediates in cyclohexane and cyclopentane oxidation, respectively. Unimolecular decay rates of the •QOOD intermediates at these energies have been obtained from the time-resolved appearance of OD products. The experimental rates are compared with statistical microcanonical rates evaluated using RRKM theory, including heavy-atom tunneling associated with simultaneous O–O bond elongation and C–O–O angle contraction along the reaction pathway. The experimental rates provide a further test of the previously determined transition state (TS) barriers, which were computed utilizing a benchmarking approach that builds on higher-level reference calculations for the smaller ethane oxidation system. Here, the experimental rate measurements for both •QOOD intermediates agree well with the computed rates after accounting for small changes in zero-point energy and a minor empirical adjustment of the TS barriers in both systems.

Ethers↗
DOE OSTI2026

Beyond Thermal Limits: Manipulating Reactive Intermediate Coverages and Turnover Rates via Visible Photon-Mediated Catalysis on Rh-Doped Perovskite Oxides

Catalyst behavior depends on surface adsorbate energetics that are constrained by scaling relationships on metal surfaces. External stimuli (e.g., photons), however, can disrupt these limitations by modulating key intermediate coverages via non-thermal reaction pathways. Here, low-energy visible photon fluxes are utilized to selectively control coverages of strongly bound intermediates on isolated Rh active sites doped within a semiconductor perovskite oxide host (SrTiO 3 ). Red light (632 nm) facilitates selective photolytic CO desorption from rhodium gem-dicarbonyl (Rh(CO) 2 ) species that are ubiquitous reaction intermediates, including for the probe reaction studied herein CO oxidation to CO 2 . Thermochemical CO 2 formation rates (408 K) on Rh-doped SrTiO 3 are limited by adsorbed CO, exhibiting a negative apparent CO rate order (−0.6) and a positive O 2 rate order (+0.4). Arrhenius analyses, anaerobic CO oxidation measurements, and in situ spectroscopies assert that, thermochemically, lattice oxygens from the doped perovskite contribute to CO 2 formation rates. Notably, under red light illumination (0.76–2.02 W cm –2 ), the apparent CO rate order shifts to positive (+1). This, combined with decreasing apparent activation energies and CO coverages (wavelength-agnostic) with increasing photon flux, indicates that photons act selectively toward driving Rh(CO) 2 photolysis, even within complex reaction networks, thereby enhancing Rh accessibility, O 2 dissociation, and consequent rates. Finally, low-energy red light enables more stoichiometric feeds, leading to 650% higher CO 2 rates than those achieved thermally. Overall, this work elucidates how low-energy light can be leveraged, not just to improve reaction rates, but to selectively affect rates of individual elementary steps and key intermediate coverages, thereby breaking conventional scaling relationships that limit thermal catalyst performance.

catalysts↗
DOE OSTI2024

The transformation of lepidocrocite (γ-FeOOH) with Fe($\tiny{II}$) (aq) in slightly acidic media: intermediate pathways and biomimetic behavior

Lepidocrocite (LP) is commonly found in natural or anthropogenic environments and oxidized alloy steel waste storage containers. Despite its importance, the end products formed and its mineral transformation pathways, including intermediate steps and underlying mechanisms under Fe(II) (aq) catalysis still need to be clarified due to decades of dispersed research. Here, in this work, we investigated LP's catalytic transformation with 10 mM and 0.2 mM Fe(II) (aq) at their natural solution pH's via bulk (X-ray Diffraction/XRD, Raman and Attenuated Total Reflectance Fourier Transform Infrared/ATR-FTIR) and micro/nano-scale (semi in situ Transmission Electron Microscopy/TEM) analysis. In general, we observed that goethite (GT) and LP were the main end products. However, a series of two major distinct intermediate events that were initiated by a dissolution type of reaction along with an “induction period” (lack of dissolution) on LP occurred. Fascinatingly, two of the intermediate steps along its mineral transformation presented novel types of non-classical mechanisms of crystallization via some type of guided oriented particle attachment. Furthermore, one of these intermediate steps is biomimetic in appearance, similar to what is observed during bacterial particle attachment. However, it uses inorganic nano-wire antennas that have a sensory-like function as observed with bacterial fimbriae and/or flagellum through an electron transparent film (similar to a bio-film matrix). Finally, this work leads us to comprehend the evolution of some well documented crystal morphologies for GT commonly observed in natural and anthropogenic settings.

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

Thermal and photoinduced chemistry of the aromatic Criegee intermediate, benzaldehyde oxide: Implications for indoor air quality

Essential oils contain a complex mixture of volatile organic compounds, ranging from terpenes to aromatics. When released into the indoor air environment or into the atmosphere, they may undergo oxidation to generate complex reactive intermediates that affect indoor air quality. Cinnamaldehyde is one such aromatic molecule that is abundant in essential oils. When released into the indoor air environment, it may undergo oxidation to form a carbonyl oxide (Criegee intermediate) with an aromatic substituent: benzaldehyde oxide. In this manuscript, we present a high-level quantum chemical study that shows that, unlike smaller atmospherically relevant Criegee intermediates, benzaldehyde oxide is expected to undergo solar photolysis on timescales that are competitive with its ground state unimolecular and bimolecular chemistry. We show that aromatic substitution leads to a drastic bathochromic shift in the spectroscopically relevant excited states, revealing that photolysis in the indoor or outdoor environment should not be neglected when modeling the climate and air quality implications of Criegee intermediates with extended conjugation. Here, we predict a range of products that may be important for forming lower volatility compounds via tropospherically relevant photochemistry. To motivate future experimental validation of our results, we propose a viable synthetic procedure of the relevant precursor for generating and stabilizing benzaldehyde oxide.

atmospheric photochemistry↗
NASA NTRS1990

MHD intermediate shocks in coronal mass ejections

A simplified model of coronal mass ejections is considered in which at least a portion of the interaction with the background corona involves a shock wave, and the allowable shock solutions and their compressive signatures are examined. The MHD shock-jump equations have a maximum of three possible types of solutions with an entropy rise for fixed values of the physical variables (slow, intermediate, and fast shocks). However, one of the three solution classes (the intermediate shock) is widely believed to not occur in nature and is regarded as nonevolutionary or extraneous. Without the intermediate shock, there is no multiplicity of solutions in that only one shock (or none) can occur for given physical values. All three potential shock types are considered, and it is shown solely on the basis of the shock-jump equations, that intermediate shocks must exist along some segment of the shock front for certain parametric regimes and for conditions that probably occur in some coronal mass ejections.

Steinolfson, R. S.↗