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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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At least 559 records · Page 31
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Design, Synthesis, and Biological Activity of Novel Ornithine Decarboxylase (ODC) Inhibitors

We here describe the design, synthesis, and biological activity of novel ornithine decarboxylase (ODC) inhibitors that show significantly higher potency in vitro than α-difluoromethylornithine (DFMO), a U.S. Food and Drug Administration (FDA) approved drug. We report two X-ray structures of ODC complexed with new ODC inhibitors, computational docking, molecular dynamics, and binding free energy calculations to validate the experimental models. The X-ray structures reveal that covalent adducts with pyridoxal phosphate (PLP) are formed in the active site of the human ODC enzyme, as verified by their preparation and enzymatic testing. Finally, we verified that the cellular activity of endogenous ODC was inhibited, and polyamine levels were reduced. Given that ODC is a clinically validated target, combined with the fact that DFMO is currently the only ODC inhibitor in clinical use for several indications, the further development of more potent ODC inhibitors with superior activity and physical properties is warranted.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Development of a Systematic and Extensible Force Field for Peptoids (STEPs)

Peptoids (N-substituted glycines) are a class of biomimetic polymers that have attracted significant attention due to their accessible synthesis and enzymatic and thermal stability relative to their naturally occurring counterparts (polypeptides). While these polymers provide the promise of more robust functional materials via hierarchical approaches, they present a new challenge for computational structure prediction for material design. The reliability of calculations hinges on the accuracy of interactions represented in the force field used to model peptoids. For proteins, structure prediction based on sequence and de novo design has made dramatic progress in recent years; however, these models are not readily transferable for peptoids. Current efforts to develop and implement peptoid-specific force fields are spread out, leading to replicated efforts and a fragmented collection of parameterized sidechains. Here, we developed a peptoid-specific force field containing 70 different side chains, using GAFF2 as starting point. The new model is validated based on the generation of Ramachandran-like plots from DFT optimization compared against force field reproduced potential energy and free energy surfaces as well as the reproduction of equilibrium cis/trans values for some residues experimentally known to form helical structures. In conclusion, equilibrium cis/trans distributions (Kct) are estimated for all parameterized residues to identify which residues have an intrinsic propensity for cis or trans states in the monomeric state.

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

Transport and Energetics of Carbon Dioxide in Ionic Liquids at Aqueous Interfaces

A major hurdle in utilizing carbon dioxide (CO 2 ) lies in separating it from industrial flue gas mixtures and finding suitable storage methods that enable its application in various industries. To address this issue, we utilized a combination of molecular dynamics simulations and experiments to investigate the behavior of CO 2 in common room-temperature ionic liquids (RTIL) when in contact with aqueous interfaces. Here, our investigation of RTILs, [EMIM][TFSI] and [OMIM][TFSI], and their interaction with a pure water layer mimics the environment of a previously developed ultrathin enzymatic liquid membrane for CO 2 separation. We analyzed diffusion constants and viscosity, which reveals that CO 2 molecules exhibit faster mobility within the selected ILs compared to what would be predicted solely based on the viscosity of the liquids using the standard Einstein–Stokes relation. Moreover, we calculated the free energy of translocation for various species across the aqueous–IL interface, including CO 2 and HCO 3 – . Free energy profiles demonstrate that CO 2 exhibits a more favorable partitioning behavior in the RTILs compared to that in pure water, while a significant barrier hinders the movement of HCO 3 – from the aqueous layer. Experimental measurement of the CO 2 transport in the RTILs corroborates the model. These findings strongly suggest that hydrophobic RTILs could serve as a promising option for selectively transporting CO 2 from aqueous media and concentrating it as a preliminary step toward storage.

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

Co-Catalyst Enabled Biotransformation of Polyunsaturated Fatty Acids for Biobased Monomers

Enzymatic lipid epoxidation offers a promising approach to obtain renewable intermediates for biomaterials, but regiochemical control of these reactions has remained elusive. Here we report the discovery and application of artificial cocatalysts to direct the regioselectivity of catalytic epoxidation with the lipase CpLIP2. The methyl esters of alkyl dicarboxylic acids show the unique ability to direct regioselective epoxidation of polyunsaturated fatty acids, major components of plant and algae-based oils. We apply this transformation to the conversion of linoleic acid into sebacic acid, a dicarboxylic acid precursor valuable for biobased polyester polyurethanes, through a six-step pathway involving a regioselective Meinwald rearrangement. To highlight the route’s significance, sebacic acid was used to prepare a 100% biobased thermoplastic polyurethane, illustrating the relevance of this pathway to industrial applications. Furthermore, this regioselective chemoenzymatic oxidation and rearrangement process can be used to access multiple dicarboxylic acids that have remained previously unexplored as biobased monomers.

09 BIOMASS FUELS↗
DOE OSTI2020

Electron Transfer in Microemulsion-Based Electrolytes

The use of flowing electrochemical reactors, for example, in redox flow batteries and in various electrosynthesis processes, is increasing. This technology has the potential to be of central significance in the increased deployment of renewable electricity for carbon-neutral processes. A key element of optimizing efficiency of electrochemical reactors is the combination of high solution conductivity and reagent solubility. In this work, we show a substantial rate of charge transfer for an electrochemical reaction occurring in a microemulsion containing electroactive material is loaded inside the nonpolar (toluene) subphase of the microemulsion. The measured rate constant translates to an exchange current density comparable to that in redox flow batteries. The rate could be controlled by the surfactant, which maintains partitioning of reactants and products by forming an interfacial region with ions in the aqueous phase in close proximity. The hypothesized echanism is evocative of membrane-bound enzymatic reactions. Achieving sufficient rates of electrochemical reaction is the product of an effort designed to establish a reaction condition that meets the requirements of electrochemical reactors using microemulsions to realize a separation of conducting and reactive elements of the solution, opening a door to the broad use of microemulsions to effect controlled electrochemical reactions as steps in more complex processes.

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

Electrolyte-Dependent, “Microscopically Irreversible” H-Atom Transfer Kinetics of Ce-Based Metal–Organic Framework, Ce-MOF-808

Redox reactions at the interface of metal oxides and protic electrolytes almost always involve protons and electrons in equal amounts. Given the stoichiometry, these proton-coupled electron transfer (PCET) reactions are thermochemically equivalent to net H-atom transfer (HAT) reactions. The correlation between the chemical nature of solid catalysts and HAT kinetics has been employed for decades as the design principle for energy-relevant reactions (e.g., reactions of 2H + /H 2 ). More recently, chemists have experimentally determined that a change in liquid electrolytes that alters the microenvironment at the redox-active sites has an equally profound impact on electrocatalysis involving PCET/HAT. Yet, precise correlations between the chemical nature of electrolytes and the PCET kinetics are, to date, rare in the literature. Herein, we report our findings using the Ce-based metal−organic framework, Ce-MOF-808, as a model system. Each Ce 6 (μ 3 −O) 4 (μ 3 − OH) 4 (OH) 6 (H 2 O) 6 node of this MOF undergoes a 1H + /1e − redox reaction. Using chronoamperometry and the Cottrell analysis, we have determined that the PCET hopping kinetics within the pores of Ce-MOF-808 can change by orders of magnitude by altering the buffer species and the proton activity of the electrolyte. Furthermore, in all buffers, reductive reactions were ∼3−10 times faster in kinetics than the reverse oxidative reaction with the same electrochemical driving force, suggesting that the system, at first glance, violates the principle of microscopic reversibility. Isothermal titration calorimetry (ITC) and computational simulations corroborated that the buffer-node binding thermodynamics are quite distinct, depending on the chemical nature of the buffer and the oxidation state of the node. Together, these results suggest that the substrate and the product during the oxidative vs reductive reaction of Ce-MOF-808 are chemically different species, which explains the apparent ‘microscopic irreversibility.’ Thus, the rational modulation of electrolytes can dramatically enhance PCET kinetics, even though the solid electrodes remain identical. Implications of these findings are contrasted with the electrochemical/electrocatalytic behavior of other redox-active MOFs, heterogeneous catalysts, and enzymatic systems at the solid−liquid interface.

Ce-based MOF↗
DOE OSTI2026

Photoinduced Electron Transfer Informs on Pathway Coupling in Flavin-Based Electron Bifurcation

Flavin-based electron bifurcation (FBEB) is an enzymatic mechanism that generates extremely high-energy electrons to drive unfavorable chemical reactions. It is utilized by the NADHdependent ferredoxin:NADP + -oxidoreductase (Nfn) enzyme in hyperthermophile Pyrococcus furiosus to bifurcate electrons from NADPH into the coupled low-potential (endergonic) and highpotential (exergonic) pathways. This process enables P. furiosus to live in harsh and uninviting environments. Despite its biological importance, the mechanisms used by Nfn to facilitate exceptional directional control over short-lived, high-energy electrons and to prevent undesired transfer, particularly along the low-potential pathway, are still not well understood. To elucidate how the protein environment contributes to electronic control in the lowpotential pathway, new techniques must be utilized to probe these unstable intermediates. In this study, we have adapted lowtemperature photoexcitation combined with electron paramagnetic resonance (EPR) to accumulate the short-lived intermediate and place it in the context of the other cofactors involved in the low-potential pathway of Nfn. We observed coincident growth of both the radical intermediate and its nearby [4Fe-4S] cluster over 4.5 h of illumination with NADPH at cryogenic temperatures. The photogenerated paramagnetic species were stable in LN 2 storage indefinitely and recombined when warmed to higher temperatures. The results provide insights into the electron transfer steps and cofactor interactions along the low potential pathway, facilitating a more robust mechanistic understanding of the high-energy events of electron bifurcation. Furthermore, through comparison of cryogenic and room temperature experiments, a potential gating step involving the movement of key residues important for the reversibility of electron flow along this pathway is suggested.

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

Nitrogenase Bioelectrocatalysis: ATP-Independent Ammonia Production Using a Redox Polymer/MoFe Protein System

Nitrogenase is the only biological catalyst that is understood to be able to convert nitrogen gas to ammonia. In microorganisms, the MoFe catalytic protein of nitrogenase is reduced by a transient Fe protein binding and separate hydrolysis of ATP. Yet, the requirement of 16 ATP molecules by the Fe protein for the 8 electron transfer is an energy-intense caveat to the enzymatic synthesis of NH 3 and is challenging from an electrochemical perspective. Thus, we report the redox polymer-based ATP-free mediated electron-transfer system of MoFe nitrogenase using cobaltocene-functionalized poly(allylamine) (Cc-PAA), which is able to reduce the MoFe nitrogenase directly with a low redox potential of -0.58 V vs SHE. An efficient immobilization of MoFe nitrogenase via Cc-PAA allowed for the bioelectrocatalytic reduction of N 3 – , NO 2 – , and N 2 to NH 3 . Bulk bioelectrosynthetic experiments produced 7 ± 2 and 30 ± 5 nmol of NH 3 from NO 2 – and N 3 – reduction for 30 min, respectively. In addition, biosynthetic N 2 reduction to NH 3 was confirmed by 15 N 2 labeling experiments with NMR analysis. This mediated electron-transfer approach of the immobilized nitrogenase using the Cc-PAA redox polymer provides a valuable technological basis for scale-up and industrial uses in the future of bioelectrosynthesis.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2020

Supported Metal Pair-Site Catalysts

Complexes with neighboring metal centers in isolated pairs and their analogues on surfaces are drawing increasing attention as catalysts. These include molecular homogeneous catalysts incorporating various ligands, enzymes, and solids that include pairs of metal atoms mounted on supports. Catalysts in this broad class are active for numerous reactions and offer unexplored opportunities to address challenging reactions, such as oxidation of methane and oxidation of water in artificial photosynthesis. The subject of supported metal pair-site catalysts is in its infancy, facing challenges in (a) precise synthesis, (b) structure determination at the atomic scale, and (c) stabilization in reactive atmospheres. In this Perspective, we summarize key characteristics of molecular and enzymatic catalysts that incorporate neighboring metal centers and build on this foundation to assess the emerging literature of metal pair-site catalysts on various supports. The supported catalysts include those synthesized by anchoring molecular dinuclear precursors to support surfaces and those synthesized by selective formation of dinuclear surface species from mononuclear surface species. Examples of metals in this class are rhodium and iridium, and examples of supports are MgO and Fe 2 O 3 . We summarize characterization of these materials by electron microscopy and spectroscopy, emphasizing atomic-resolution aberration-corrected scanning transmission electron microscopy and spectroscopies that provide atomic-scale structural information and allow characterization of functioning catalysts, especially X-ray absorption spectroscopy. Finally, we list some opportunities for research, including suggestions that might lead to structurally well-defined supported metal pair-sites with new catalytic properties.

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

Machine Learning-Guided Identification of PET Hydrolases from Natural Diversity

The enzymatic depolymerization of poly(ethylene terephthalate) (PET) is emerging as a leading chemical recycling technology for waste polyester. As part of this endeavor, new candidate enzymes identified from natural diversity can serve as useful starting points for enzyme evolution and engineering. In this study, we improved upon HMM searches by applying an iterative machine learning strategy to identify 400 putative PET-degrading enzymes (PET hydrolases) from naturally occurring homologs. Using high-throughput (HTP) experimental techniques, we successfully expressed and purified >200 enzyme candidates and assayed them for PET hydrolysis activity as a function of pH, temperature, and substrate crystallinity. From this library, we discovered 91 previously unknown PET hydrolases, 35 of which retain activity at pH 4.5 on crystalline material, which are conditions relevant to developing more efficient commercial processes. Notably, four enzymes showed equal to or higher activity than LCC-ICCG, a benchmark PET hydrolase, at this challenging condition in our screening assay, and 11 of which have pH optima <7. Using these data, we identified regions of PETases statistically correlated to activity at lower pH. We additionally investigated the effect of condition-specific activity data on trained machine learning predictors and found a precision (putative hit rate) improvement of up to 30% compared to a Hidden Markov Model alone. Our findings show that by pointing enzyme discovery toward conditions of interest with multiple rounds of experimental and machine learning, we can discover large sets of active enzymes and explore factors associated with activity at those conditions.

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

Determinants of Stereoselectivity in Monoterpene Synthases

Monoterpene synthases (MTSs) catalyze the conversion of an achiral prenyl diphosphate precursor, most commonly geranyl diphosphate (GPP), into structurally and stereochemically diverse products. However, remains poorly understood. Here, we combine enzymatic assays with six MTSs and selected variants, along with extensive molecular dynamics simulations to the mechanistic basis of stereoselectivity. We demonstrate that the preferred helical binding conformation of GPP, determined from free-energy calculations and selected crystal structures of MTSs, correlates well with the experimentally determined stereoselectivity of MTSs, whereas only a poor correlation is observed between the binding of enantiomers of linalyl diphosphate (LPP), a chiral intermediate of MTS catalysis, and the stereochemical reaction outcomes. Free energy maps indicate that enzyme-bound GPP conformers preferentially occupy regions that enable a direct and stereochemically faithful transition from GPP to subsequent carbocations. In contrast, LPP frequently populates regions of the energy surface where conformational scrambling can occur, thus leading to a lack of correlation between LPP enantiomer binding and product stereochemistry. Overall, these findings establish that the configuration of GPP is the primary determining factor for stereochemical outcomes in MTSs, offering a new framework for designing stereoselective terpene synthases.

Srividya, Narayanan (ORCID:0000000179347987)↗
DOE OSTI2021

Discovery of SARS-CoV-2 Papain-like Protease Inhibitors through a Combination of High-Throughput Screening and a FlipGFP-Based Reporter Assay

The papain-like protease (PL pro ) of SARS-CoV-2 is a validated antiviral drug target. Through a fluorescence resonance energy transfer-based high-throughput screening and subsequent lead optimization, we identified several PL pro inhibitors including Jun9-72-2 and Jun9-75-4 with improved enzymatic inhibition and antiviral activity compared to GRL0617, which was reported as a SARS-CoV PL pro inhibitor. Significantly, we developed a cell-based FlipGFP assay that can be applied to predict the cellular antiviral activity of PL pro inhibitors in the BSL-2 setting. X-ray crystal structure of PL pro in complex with GRL0617 showed that binding of GRL0617 to SARS-CoV-2 induced a conformational change in the BL2 loop to a more closed conformation. Molecular dynamics simulations showed that Jun9-72-2 and Jun9-75-4 engaged in more extensive interactions than GRL0617. Overall, the PL pro inhibitors identified in this study represent promising candidates for further development as SARS-CoV-2 antivirals, and the FlipGFP-PL pro assay is a suitable surrogate for screening PL pro inhibitors in the BSL-2 setting.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Tyrosinase-Mediated Synthesis of Nanobody–Cell Conjugates

A convenient enzymatic strategy is reported for the modification of cell surfaces. Using a tyrosinase enzyme isolated from Agaricus bisporus, unique tyrosine residues introduced at the C-termini of nanobodies can be site-selectively oxidized to reactive o-quinones. These reactive intermediates undergo rapid modification with nucleophilic thiol, amine, and imidazole residues present on cell surfaces, producing novel nanobody–cell conjugates that display targeted antigen binding. We extend this approach toward the synthesis of nanobody–NK cell conjugates for targeted immunotherapy applications. The resulting NK cell conjugates exhibit targeted cell binding and elicit targeted cell death.

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

Identification of and Structural Insights into Hit Compounds Targeting N -Myristoyltransferase for Cryptosporidium Drug Development

Each year, approximately 50,000 children under 5 die as a result of diarrhea caused by Cryptosporidium parvum, a protozoan parasite. There are currently no effective drugs or vaccines available to cure or prevent Cryptosporidium infection, and there are limited tools for identifying and validating targets for drug or vaccine development. We previously reported a high throughput screening (HTS) of a large compound library against Plasmodium N-myristoyltransferase (NMT), a validated drug target in multiple protozoan parasite species. To identify molecules that could be effective against Cryptosporidium, we counter-screened hits from the Plasmodium NMT HTS against Cryptosporidium NMT. We identified two potential hit compounds and validated them against CpNMT to determine if NMT might be an attractive drug target also for Cryptosporidium. We tested the compounds against Cryptosporidium using both cell-based and NMT enzymatic assays. We then determined the crystal structure of CpNMT bound to Myristoyl-Coenzyme A (MyrCoA) and structures of ternary complexes with MyrCoA and the hit compounds to identify the ligand binding modes. The binding site architectures display different conformational states in the presence of the two inhibitors and provide a basis for rational design of selective inhibitors.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

C10-Benzoate Esters of Anhydrotetracycline Inhibit Tetracycline Destructases and Recover Tetracycline Antibacterial Activity

Tetracyclines (TCs) are an important class of antibiotics threatened by enzymatic inactivation. These tetracycline-inactivating enzymes, also known as tetracycline destructases (TDases), are a subfamily of class A flavin monooxygenases (FMOs) that catalyze hydroxyl group transfer and oxygen insertion (Baeyer–Villiger type) reactions on TC substrate scaffolds. Semisynthetic modification of TCs (e.g., tigecycline, omadacycline, eravacycline, and sarecycline) has proven effective in evading certain resistance mechanisms, such as ribosomal protection and efflux, but does not protect against TDase-mediated resistance. Here, we report the design, synthesis, and evaluation of a new series of 22 semisynthetic TDase inhibitors that explore D-ring substitution of anhydrotetracycline (aTC) including 14 C10-benzoate ester and eight C9-benzamides. Overall, the C10-benzoate esters displayed enhanced bioactivity and water solubility compared to the corresponding C9-benzamides featuring the same heterocyclic aryl side chains. The C10-benzoate ester derivatives of aTC were prepared in a high-yield one-step synthesis without the need for protecting groups. The C10-esters are water-soluble, stable toward hydrolysis, and display dose-dependent rescue of tetracycline antibiotic activity in E. coli expressing two types of tetracycline destructases, represented by TetX7 (Type 1) and Tet50 (Type 2). The best inhibitors recovered tetracycline antibiotic activity at concentrations as low as 2 μM, producing synergistic scores <0.5 in the fractional inhibitory concentration index (FICI) against TDase-expressing strains of E. coli and clinical P. aeruginosa. The C10-benzoate ester derivatives of aTC reported here are promising new leads for the development of tetracycline drug combination therapies to overcome TDase-mediated antibiotic resistance.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

Local Environment Affects the Activity of Enzymes on a 3D Molecular Scaffold

The ability to coordinate and confine enzymes presents an opportunity to affect their performance and to create chemically active materials. Recent studies show that polymers and biopolymers can be used to scaffold enzymes, and that can lead to the modulated biocatalytic efficiency. In this work, we investigated the role of microenvironments on enzyme activity using a well-defined molecular scaffold. An enzyme, glucose oxidase (GO x ), was positioned at different locations of a three-dimensional (3D) octahedral DNA scaffold (OS), allowing the enzyme’s polyanionic environments to be altered. Using electrical sensing, based on a bipolar junction transistor, we measured directly and in real-time the enzyme’s proton generation at these different microenvironments. We found a 200% enhancement of immobilized enzyme over free GOx and about a 30% increase in catalytic rates when the enzyme was moved on the same molecular scaffold to a microenvironment with a higher local concentration of polyanions, which suggests a role of local pH on the enzymatic activity.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2025

Chaotrope-Based Approach for Rapid In Vitro Assembly and Loading of Bacterial Microcompartment Shells

Bacterial microcompartments (BMCs) are proteinaceous organelles that self-assemble into selectively permeable shells that encapsulate enzymatic cargo. BMCs enhance catalytic pathways by reducing crosstalk among metabolites, preventing harmful intermediates from leaking into the cytosol and increasing reaction efficiency via enzyme colocalization. The intrinsic properties of BMCs make them attractive for biotechnological engineering. However, in vivo expression methods for shell synthesis have significant drawbacks that limit the potential design space for these nanocompartments. Here, we describe the development of an efficient and rapid method for the in vitro assembly of BMC shells from their protein building blocks. Our method enables large-scale construction of BMC shells by utilizing urea as a chaotropic agent to control self-assembly and provides an approach for encapsulation of both biotic and abiotic cargo under a broad range of reaction conditions. We demonstrate an enhanced level of control over the assembly of BMC shells in vitro and expand the design parameter space for engineering BMC systems with specialized and enhanced catalytic properties.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗