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At least 19 records

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

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

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

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

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

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

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

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

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

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

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

Phenomenology of Intermediate Molecular Dynamics at Metal-Oxide Interfaces

Reaction intermediates buried within a solid-liquid interface are difficult targets for physiochemical measurements. They are inherently molecular and locally dynamic, while their surroundings are extended by a periodic lattice on one side and the solvent dielectric on the other. Challenges compound on a metal-oxide surface of varied sites and especially so at its aqueous interface of many prominent reactions. Recently, phenomenological theory coupled with optical spectroscopy has become a more prominent tool for isolating the intermediates and their molecular dynamics. The following article reviews three examples of the SrTiO3-aqueous interface subject to the oxygen evolution from water: reaction-dependent component analyses of time-resolved intermediates, a Fano resonance of a mode at the metal-oxide–water interface, and reaction isotherms of metastable intermediates. The phenomenology uses parameters to encase what is unknown at a microscopic level to then circumscribe the clear and macroscopically tuned trends seen in the spectroscopic data.

Chemistry

Meeting liquid biofuel and bioproduct goals: biotechnological design of the intermediate oilseeds pennycress and camelina, and beyond

The European Union and the United States have set ambitious goals to produce biofuels as part of broader decarbonization and energy security initiatives. One of the more feasible routes to liquid biofuels production is the conversion of seed oils [triacylglycerols (TAGs)] to renewable diesel, biodiesel, and sustainable aviation fuel (SAF) using the hydrotreated ester and fatty acids (HEFA) process. Camelina and pennycress are attractive oilseed feedstocks in that they can be grown in the offseason as intermediate crops on tens of millions of hectares of farmland annually, providing ecosystem benefits and not competing with established food crops. Considerably more TAG could be produced by engineering vegetative portions of crops such as sorghum and miscanthus to accumulate economically-viable amounts. Here, this review highlights recent advances in developing pennycress and camelina as intermediate oilseed crops not only for biofuels production but for making higher value oils such as those enriched in astaxanthin, vitamin E, and medium-chain fatty acids. Given the magnitude of renewable liquid fuel demands, we also describe how advances in oil production from vegetative parts of biomass crops can complement intermediate oilseed cropping systems to meet biofuel and bioproduct targets.

biomass crops

The role of transition metal formyl intermediates in the reduction of CO and CO 2

Transition-metal formyl (metalloformyl) complexes occupy a central position in the activation of small molecules, particularly in the reduction of carbon monoxide (CO) and carbon dioxide (CO 2 ). This review examines five decades of progress in the synthesis of metalloformyl complexes and investigations into their structure and reactivity. The bonding in the M–CHO unit is best described as a resonance hybrid between a classical σ-bound formyl ligand and an oxycarbene-like electronic structure, which governs their distinctive spectroscopic signatures and versatile reactivity. Established synthetic routes are summarized, including pathways involving hydride addition and CO insertion, alongside a discussion of the thermodynamic and kinetic factors that control formyl stability. Decomposition pathways and Lewis-acid stabilization strategies are analyzed as key design principles for extending metalloformyl lifetimes under catalytic conditions. Particular attention is given to hydride transfer processes and the role of metalloformyl intermediates as both reactive substrates and hydride sources in reduction chemistry. Lastly, emerging catalytic strategies that exploit metalloformyl intermediates in CO 2 and CO reduction are evaluated, highlighting how control of hydricity, redox potential, and secondary-sphere interactions enables selective C—H bond formation under comparatively mild conditions. Collectively, these studies establish metalloformyl complexes as mechanistically informative and functionally relevant intermediates that bridge fundamental organometallic chemistry with modern approaches to small-molecule activation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH

Cleavage at the nsp5–nsp6 site of SARS-CoV-2 main protease intermediate precursor is faster from a monomer than a dimer form

Our previous studies of severe acute respiratory syndrome coronavirus 2 main protease (MPro) precursor monomer indicate that the initial N-terminal nonstructural protein (nsp)4/nsp5 cleavage occurs intramolecularly, with a small fraction of the active site loop equilibrium being in the active state. To understand the influence of dimer formation of MPro upon N-terminal cleavage on the subsequent C-terminal nsp5/nsp6 intermolecular cleavage kinetics, the stepwise processing of a monomeric, inactive precursor containing the native terminal cleavage sites of MPro (MBP- (−6) MPro C145A(+3) -GB1-6H, 86.2 kDa) by mature WT MPro (MPro WT ) was investigated. Differential scanning fluorimetry and analytical ultracentrifugation measurements of various MPro constructs suggest that the C145A mutation decreases the dimer dissociation constant (K dimer ) by ∼26-fold, relative to WT C145 and H41A. The monomeric precursor’s nsp4–nsp5 site appears to saturate MProWT’s active sites and cleave faster, followed by a slower first-order cleavage at the C-terminal site. No detectable product resulting from the C-terminal cleavage is observed until most of the N-terminal cleavage is complete. The initial intermediate product (termed MPro C145A-IP ) is a homodimer with an estimated K dimer of <0.05 μM. In contrast, the first-order kinetics observed for the cleavage of the monomeric form of the intermediate product is at least 300 times faster than that of the dimer form. Room-temperature X-ray structure of the MPro C145A-IP –ensitrelvir complex is like that of the MPro WT –ensitrelvir complex and reveals a dynamic C-terminal region including MPro residues 302 to 306. These results are interpreted from the point of view of a mechanism in which nsp5–nsp6 cleavage may occur from a monomeric intermediate, and dimer formation restricts this cleavage.

60 APPLIED LIFE SCIENCES

Surface intermediates identified using IR spectroscopy during the catalytic oxidation of C 2 H 6 on IrO 2 (1 1 0) at near-ambient pressures

Characterizing surface intermediates during catalysis is essential for developing mechanistic models of catalytic reactions and for identifying rate-controlling steps. Here, in this work, we used polarization-dependent reflection absorption infrared spectroscopy (PD-RAIRS) to investigate surface intermediates that form on IrO 2 (1 1 0) during the catalytic oxidation of C 2 H 6 at pressures near 0.5 Torr. Our results show that adsorbed CO and HCO 2 are the only intermediates detectable with PD-RAIRS across a wide range of temperatures and reactant compositions during complete C 2 H 6 oxidation, giving rise to dominant peaks at about 2093 and 1310 cm −1 , respectively. These assignments were corroborated by RAIRS measurements following CO and HCOOH adsorption in ultrahigh vacuum, RAIRS with C 2 H 6 – 18 O 2 mixtures during catalysis and vibrational frequencies and IR intensities computed using density functional theory. We find that increasing the C 2 H 6 mole fraction in the reaction mixture raises the CO surface coverage relative to HCO 2 , correlating with increasing catalytic oxidation rates. The formation of CO and HCO 2 surface species at temperatures well below catalytic ignition indicates that the overall rate of C 2 H 6 oxidation on IrO 2 (1 1 0) is governed by steps late in the reaction sequence, such as H 2 O formation, CO oxidation and HCO 2 dehydrogenation. These findings provide key insight into the mechanism of alkane oxidation on IrO 2 (1 1 0) and valuable input for first-principles microkinetic modeling.

Pope, Connor [Univ. of Florida, Gainesville, FL (U

Tailoring the Intermediate Phase to Control Formation of γ‑CsPbI3 Films

Controlling the crystallization pathway of inorganic CsPbI3 perovskite is essential for achieving high efficiency and stability in optoelectronic devices. Here, we report a solvent-engineering strategy that combines an antisolvent process with vacuum treatment (AVT) to modulate evaporation dynamics of the precursor, guiding the formation of highly oriented (CH3)2NH2PbI3 (DMAPbI3) and Cs4PbI6 intermediate phases. Synchrotron and in situ analyses revealed correlations between intermediate orientation and γ-CsPbI3 crystallinity. This directional crystallization pathway promotes vertical alignment and grain enlargement in γ-CsPbI3 films, resulting in fewer voids, lower defect densities, and reduced tensile strain. Photovoltaic devices based on AVT-processed films achieved a power conversion efficiency of 18.47% with a fill factor of 83.14% and retained 101.9% of their initial efficiency after 526 h without encapsulation. This study first reports that the quality of DMAPbI3 and Cs4PbI6 intermediates, controlled by combination of antisolvent and vacuum treatment, plays a crucial role in achieving high-quality γ-CsPbI3 films.

Yoon, Geon Woo