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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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116 records · Page 7
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Effect of cellulose reducing ends and primary hydroxyl groups modifications on cellulose-cellulase interactions and cellulose hydrolysis

Cellulose reducing ends are believed to play a vital role in the cellulose recalcitrance to enzymatic conversion. However, their role in insoluble cellulose accessibility and hydrolysis is not clear. Thus, in this study, reducing ends of insoluble cellulose derived from various sources were modified by applying reducing and/or oxidizing agents. Here, the effects of cellulose reducing ends modification on cellulose reducing ends, cellulose structure, and cellulose accessibility to cellulase were evaluated along with the impact on cellulose hydrolysis with complete as well purified cellulase components. Sodium borohydride (NaBH 4 ) reduction and sodium chlorite-acetic acid (SC/AA) oxidation were able to modify more than 90% and 60% of the reducing ends, respectively, while the bicinchoninic acid (BCA) reagent applied for various cycles oxidized cellulose reducing ends to various extents. X-ray diffractograms of the treated solids showed that these treatments did not change the cellulose crystalline structure and the change in crystallinity index was insignificant. Surprisingly, it was found that the cellulose reducing ends modification, either through selective NaBH 4 reduction or BCA oxidation, had a negligible impact on cellulose accessibility as well on cellulose hydrolysis rates or final conversions with complete cellulase at loadings as low as 0.5 mg protein/g cellulose. In fact, in contrast to what is traditionally believed, modifications of cellulose reducing ends by these two methods had no apparent impact on cellulose conversion with purified cellulase components and their synergy. However, SC/AA oxidation resulted in significant drop in cellulose conversion (10%–50%) with complete as well purified cellulase components. Nonetheless, further research revealed that the cause for drop in cellulose conversion for the SC/AA oxidation case was due to primary hydroxyl groups (PHGs) oxidation and not the oxidation of reducing ends. Furthermore, it was found that the PHGs modification affects cellulose accessibility and slows the cellulase uptake as well resulting in significant drop in cellulose conversions.

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

Criegee Intermediates Compete Well with OH as a Cleaning Agent for Atmospheric Amides

Elucidating the chemical kinetics of stabilized Criegee intermediates (sCIs) in the atmosphere is critically important for climate modeling. Here, we report a class of very rapid bimolecular reactions of two sCIs, namely, CH 2 OO and syn-CH 3 CHOO, with amides. We used electronic structure calculations and kinetics calculations to elucidate a universal mechanism by which the oxygen atom of the carbonyl group in an amide is added to the carbon atom of the COO group in the sCI with simultaneous transfer of the amide hydrogen to the terminal oxygen atom of the carbonyl oxide of the sCI. The barriers for the mechanism are submerged below reactants by ∼9 kcal/mol, which means that the tight transition state is not the rate-determining step, and the rate constants are determined by loose free energy bottlenecks between the reactants and the precursor complexes. We calculate the rate constants due to these loose and barrierless transition states by variable-reaction-coordinate variational transition-state theory. We find that bimolecular reactions of sCIs with amides are very rapid, with rate constants 1 to 5 × 10 –10 cm 3 molecule –1 s –1 , which is a factor of 2 faster than the rate constants of carboxylic acids with sCIs and 10 2 faster than the rate constants of OH reactions with amides. This has the consequence that, under a wide range of conditions, sCIs are the major sink for atmospheric amides, in contrast to the usual assumption that OH radicals are the dominant sinks.

Amides↗
DOE OSTI2026

Study of wrap mode impact on Pseudomonas aeruginosa motion in the chemotactic field of fungi

An agent-based discrete computational model biologically calibrated to Pseudomonas aeruginosa migration is used to explore the impacts of bacterial reversals and wrap mode on the efficiency of motion in different environments, both with and without chemotaxis. It is first shown that wrap mode increases the exploration of continuous multimodal chemotactic profiles such as those produced by biologically relevant fungal networks. For cells undergoing a run-reverse pattern, it is shown that the bacteria are likely to remain at the first local chemoattractant maximal production site on a hypha they find. However, with wrap mode, the bacteria can more easily escape these local sites to further explore their neighboring environment along the fungi, suggesting that wrap mode may be beneficial for migration along the fungi in liquid. In a different set of simulations of bacterial motion close to an isolated chemotactic source, wrap mode is shown to increase the ability of a bacterium to reorient toward the source while reducing the overall motion required for similar chemotactic efficiency as a run-reverse strategy, suggesting a potential metabolic benefit. In contrast, model simulations show that wrap mode can increase the rate of dispersal of P. aeruginosa in a nonchemotactic environment.

Hansen, Austin [University of California, Riversid↗
DOE OSTI2020

Spectroscopic Studies of Charge-Transfer Character and Photoresponses of F 4 TCNQ-Based Donor–Acceptor Complexes

F 4 TCNQ (2,3,5,6-tetrafluoro-7,7,8,8-tetracyanoquinodimethane) is used widely as a hole-doping agent in photoresponsive organic semiconducting materials, yet relatively little is known about the photoresponses of the F 4 TCNQ· - anion generated via doping. Furthermore, there is still relatively little systematic exploration of how the properties of the local material or chemical environment impacts the driving force for generating these charge-transfer complexes. Here we present spectroscopic and photophysical studies of F 4 TCNQ in charge-transfer complexes (CTCs) with the electron donor N,N’-Diphenyl-N-N’-di-p-tolylbenzene-1,4-diamine (MPDA) both in dichloroethane solution and polystyrene matrices. Integer charge transfer (ICT) between donor and acceptor occurs readily in dichloroethane solvent to form F 4 TCNQ· - :MPDA + CTCs, due to a ~150 mV difference in MPDA + /MPDA and F 4 TCNQ/F 4 TCNQ· - reduction potentials. Ultrafast spectroscopic studies of the CTC as well as electrochemically generated F 4 TCNQ· - and MDPA + reveal that the photoresponses of these CTCs are dominated by that of the dopant anion, including rapid deactivation (800 fs) after excitation to the anion D 1 excited state, followed by slower (~10 ps) vibrational cooling in the anion D 0 state. Excitation to the higher-lying D 2 state results in a rapid relaxation to the D 1 state, in contrast to direct D 2 -D 0 relaxation previously observed for F 4 TCNQ· - in gas phase. CTCs embedded in polystyrene (PS) matrices are observed to lose their integer charge-transfer character upon evaporation of solvent, as evidenced by changes to electronic and vibrational absorption features associated with F 4 TCNQ· - . This change is attributed to the loss of solvent stabilization of the ion pair formed through the charge-transfer reaction. Ultrafast spectral measurements reveal that the photoresponses of the partial charge-transfer (PCT) species embedded in PS are still highly similar to those of the ICT species and unlike that of neutral F 4 TCNQ, implying the electronic properties of the PCT state are likewise dominated by properties of the reduced acceptor molecule. We conclude that excitation of ICT or PCT states introduces optical losses for photoresponses of doped organic semiconductor materials due to the large anion absorption cross section and its rapid, dissipative deactivation dynamics.

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

Novel, active, and uncultured hydrocarbon-degrading microbes in the ocean

ABSTRACT Given the vast quantity of oil and gas input to the marine environment annually, hydrocarbon degradation by marine microorganisms is an essential ecosystem service. Linkages between taxonomy and hydrocarbon degradation capabilities are largely based on cultivation studies, leaving a knowledge gap regarding the intrinsic ability of uncultured marine microbes to degrade hydrocarbons. To address this knowledge gap, metagenomic sequence data from the Deepwater Horizon (DWH) oil spill deep-sea plume was assembled to which metagenomic and metatranscriptomic reads were mapped. Assembly and binning produced new DWH metagenome-assembled genomes that were evaluated along with their close relatives, all of which are from the marine environment (38 total). These analyses revealed globally distributed hydrocarbon-degrading microbes with clade-specific substrate degradation potentials that have not been reported previously. For example, methane oxidation capabilities were identified in all Cycloclasticus . Furthermore, all Bermanella encoded and expressed genes for non-gaseous n -alkane degradation; however, DWH Bermanella encoded alkane hydroxylase, not alkane 1-monooxygenase. All but one previously unrecognized DWH plume member in the SAR324 and UBA11654 have the capacity for aromatic hydrocarbon degradation. In contrast, Colwellia were diverse in the hydrocarbon substrates they could degrade. All clades encoded nutrient acquisition strategies and response to cold temperatures, while sensory and acquisition capabilities were clade specific. These novel insights regarding hydrocarbon degradation by uncultured planktonic microbes provides missing data, allowing for better prediction of the fate of oil and gas when hydrocarbons are input to the ocean, leading to a greater understanding of the ecological consequences to the marine environment. IMPORTANCE Microbial degradation of hydrocarbons is a critically important process promoting ecosystem health, yet much of what is known about this process is based on physiological experiments with a few hydrocarbon substrates and cultured microbes. Thus, the ability to degrade the diversity of hydrocarbons that comprise oil and gas by microbes in the environment, particularly in the ocean, is not well characterized. Therefore, this study aimed to utilize non-cultivation-based ‘omics data to explore novel genomes of uncultured marine microbes involved in degradation of oil and gas. Analyses of newly assembled metagenomic data and previously existing genomes from other marine data sets, with metagenomic and metatranscriptomic read recruitment, revealed globally distributed hydrocarbon-degrading marine microbes with clade-specific substrate degradation potentials that have not been previously reported. This new understanding of oil and gas degradation by uncultured marine microbes suggested that the global ocean harbors a diversity of hydrocarbon-degrading bacteria, which can act as primary agents regulating ecosystem health.

Howe, Kathryn L.↗
DOE OSTI2021

Hydrolysis of methylphosphonic anhydride solid to methylphosphonic acid probed by Raman and infrared reflectance spectroscopies

Much is still unknown about the mechanisms and rates of environmental degradation of organophosphorous pesticides and agents. In this study we focus on the degradation of one organophosphorous compound, namely solid methyl phosphonic acid anhydride [CH3P(O)OHOP(O)OHCH3, MPAN] and its rate of conversion to methyl phosphonic acid (MPA) via heterogeneous hydrolysis. Pure MPAN was synthesized and loaded in open sample cups placed inside exposure chambers containing saturated salt solutions to control the relative humidity (RH). The reaction was monitored in the sample cup at various times using both infrared hemispherical reflectance (HRF) spectroscopy and Raman spectroscopy. Calibrated HRF and Raman spectra of both pure reagents as well as gravimetrically prepared mixtures were used to quantify the concentrations of MPAN and MPA throughout the reaction. Results show that both HRF and Raman spectroscopies are convenient non-invasive methods for detection of solid chemicals. The MPAN degradation rate displayed a very strong dependence on relative humidity: At room temperature the reaction showed 50% conversion of the MPAN in 761 ± 54 hours at 33% RH, 33 ± 4 hours at 43% RH, 17 ± 2 hours at 54% RH and just 7 ± 1 hours at 75% RH. Although MPAN hydrolysis is a second-order reaction, the 33 and 43% RH data, at early reaction times, could be fit with a zeroth order reaction, indicating water vapor and MPAN concentrations were not initially rate controlling. The 54 and 75% RH experiments showed significant deliquescence and decay data could only be fit assuming multiple reactions, implying chemical and/or physical processes partially controlled the hydrolysis rate, in contrast to a single process at low relative humidity.

methyl phosphonic acid, methyl phosphonic anhydrid↗
DOE OSTI2022

Defining Lipidomic Responses to Coronavirus Infection

Highly pathogenic human coronavirus infection can cause a severe atypical, rapid onset pneumonia with a mortality rate of up to 10% for severe acute respiratory syndrome coronavirus 1 (SARS-CoV 1), 35% for Middle East respiratory syndrome coronavirus (MERS-CoV), or 1% for severe acute respiratory syndrome coronavirus 2 (SARS-CoV 2 causative agent of COVID 19). While medical countermeasures successfully controlled the worldwide SARS-CoV epidemic, the MERS-CoV epidemic is still ongoing and continues to be a concern for travelers in the Middle East and the multi-year SARS-CoV 2 pandemic underscore the importance of defining biomarkers that are diagnostic and/or predictive of severe disease outcomes for respiratory viruses. Systems biology approaches provide global snapshots of infection induced changes in host cells/tissues and provide extremely rich datasets for understanding host pathogen interactions. Metabolites, especially lipids, are critical for viral replication but less is understood about infection induced changes to lipids due to limits in lipid species detection and identification. To characterize how individual lipid species and proteins with lipid associated functions contribute to highly pathogenic human coronavirus replication and disease severity, existing datasets were probed to determine cell type specific lipid responses to MERS-CoV infection and verification studies were performed to determine if modification of the host lipid signature (by inhibiting enzymatic functions that produce specific lipid species) can perturb CoV replication in human lung cells. MERS-CoV infects human lung epithelial, endothelial and fibroblast cells. All three cell types were infected with MERS-CoV and samples collected to analyze lipids, proteins, metabolites, and transcripts from 12 to 48 hours post infection. Time matched mock-infected cells were collected in parallel for each cell type. Following sample and statistical analysis, functional enrichment and bioinformatic analysis was performed to identify differentially expressed lipids and proteins. Two lipid species were found to be significantly upregulated following MERS-CoV infection, ceramides, and triacylglycerol both of which are indicative of cells undergoing apoptotic cell death. In contrast, sphingomyelins (lipid molecules that can serve as a precursor for one pathway for ceramide synthesis) had significantly decreased expression in MERS-CoV infected cells. An inhibitor of acid sphingomyelinase (that converts sphingomyelin to ceramides and phosphorylcholine) reduced MERS-CoV replication suggesting that production of ceramides is key for successful viral replication and transmission. Acyl-CoA-synthetase 3 (ACSL3), the only protein whose function is lipid associated and had increased differential expression in our dataset, regulates the synthesis of triacylglycerol (increased expression). Inhibitors that directly block ACSL3 (Triacsin C) but not steps later in the triacylglycerol synthesis pathway (Etomoxir) inhibit MERS-CoV replication suggesting that triacylglycerol production and/or ACSL3 activity is also key for viral replication. ACSL3 expression is also upregulated in lung cancer cells and is predicted to promote continued cell viability which would also enhance viral replication. The differentially expressed lipid and lipid-associated protein species identified in our studies suggest that MERS-CoV infection is activating cellular death pathways to limit the number of cells that become infected but also stimulating the production of lipid-associated enzymes that can prolong host cell viability and the amount of time progeny virions can be produced and released. As the inhibitors that worked against MERS-CoV infection were also efficacious against SARS-CoV 2 infection, countermeasures that target these host pathways may provide novel ways to block highly pathogenic human coronavirus infection and/or prevent severe disease outcomes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Nicotine-Inspired, De Novo-Designed SARS-CoV-2 Main Protease Inhibitors Reveal Unique Chemistry for Covalently Conjugating Both Cysteine and Histidine Residues in the Catalytic Dyad

Anecdotal reports about smokers with low SARS-CoV-2 infection rates prompted a search for nicotine and its pyrolysis products as SARS-CoV-2 main protease (M Pro ) inhibitors. From this search, 3-vinylpyridine was discovered as a weak binder for the M Pro S1 subsite and was used subsequently as a de novo starting point for covalent inhibitor design that quickly yielded a highly potent inhibitor, SR-A-174, with an IC 50 value of 60 nM. Representing a novel class of M Pro inhibitors, SR-A-174 features an N,N -diaryl-α,α-dichloroacetamide scaffold that facilitated rapid exploration of alternative covalent warheads and various N-substituents, leading to the identification of multiple inhibitors with potent antiviral activity. Eight such M Pro inhibitor structures were determined, all demonstrating covalent binding to catalytic Cys145 of M Pro . In six determined structures, binding is dominated by the covalent bond plus van der Waals contacts, which contrasts with the extensive hydrogen bond networks formed with peptidomimetic inhibitors such as nirmatrelvir. Strikingly, two N,N -diaryl-α,α-dichloroacetamide inhibitors exhibit an unprecedented dual covalent modification mode of the catalytic dyad, forming bonds to both Cys145 and His41 with a concomitant loss of both chlorides and displacing the inhibitors from the S1 subsite. This dyad-targeting reactivity suggests a novel route for bioconjugation of both cysteine and histidine.

SARS-CoV-2↗