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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 1,153 records · Page 64
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Elongation Factor Tu Acts as a Chaperone to Activate an Antibacterial RNase Toxin

Many Gram-negative bacterial species use contact-dependent growth inhibition (CDI) systems to deliver toxic proteins into neighboring competitors. CDI + strains deploy CdiA effector proteins, which translocate their C-terminal toxin (CT) domains into target bacteria through a receptor-mediated delivery pathway. To protect against auto-intoxication, CDI + bacteria also produce CdiI immunity proteins that neutralize CT toxin activity. Here, we present the crystal structure of the CT·CdiI O32:H37 complex from Escherichia coli O32:H37. CT O32:H37 adopts the same fold as the tRNase domain of colicin D, and the nucleases share similar catalytic centers. However, unlike colicin D, which cleaves the anticodon loops of tRNA Arg isoacceptors, CT O32:H37 exhibits nonspecific RNase activity. Notably, we find that endogenous elongation factor Tu (EF-Tu) co-purifies with the over-produced CT·CdiI O32:H37 complex. Although EF-Tu does not bind stably to CT O32:H37 in the absence of CdiI O32:H37 , the translation factor is required for toxic RNase activity in vitro. AlphaFold 3 modeling and site-directed mutagenesis indicate that CT O32:H37 interacts with the N-terminal GTPase domain of EF-Tu. EF-Tu appears to stabilize residue Trp52 within the hydrophobic core of the toxin, which in turn supports the RNase active site through an unusual hydrogen-bonding interaction with the catalytic His67 residue. Furthermore, EF-Tu is hijacked as an essential co-factor to organize the toxin's catalytic center.

Nhan, Dinh Quan [University of California, Santa B↗
DOE OSTI2020

Contribution of the Hydroxyl Group on Interfacial Heat Conduction of Monohydric Alcohols: A Molecular Dynamics Study

Monohydric alcohols have been used as promising phase change materials (PCMs) for low-temperature latent heat storage. However, the heat storage/retrieval rates are limited due to the low thermal conductivity of such alcohols. In this work, nonequilibrium molecular dynamics (NEMD) simulations were performed to study the microscopic heat conduction in example monohydric alcohols, i.e., 1-dodecanol (C12H26O), 1-tetradecanol (C14H30O), and 1-hexadecanol (C16H34O). A simplified ideal crystal model was proposed to exploit the potential for improving the thermal conductivity of monohydric alcohols. The effect of ideal crystalline structures, especially the contribution of the hydroxyl group, on the microscopic heat conduction process was analyzed. The thermal conductivity of the ideal crystals of the various monohydric alcohols was predicted to be more than twice as compared to that of their respective solids. The major thermal resistance in the ideal crystals was found around the molecular interfaces, as a result of the excellent heat conduction performance along the linear molecular chains. The calculated vibrational density of states (VDOS) and interfacial heat transfer were then investigated. When the interfaces are surrounded by hydroxyl groups as walls, strong hydrogen bond (HB) interactions were observed. The interfacial heat transfer coefficient of the ideal crystalline structures of 1-tetradecanol was found to reach up to ~735.6 MW/m2 W. It was elucidated that the high interfacial heat transfer rate is clearly related to the stronger intermolecular interactions.

Engineering↗
DOE OSTI2022

Ensemble-function relationships to dissect mechanisms of enzyme catalysis

Decades of structure-function studies have established our current extensive understanding of enzymes. However, traditional structural models are snapshots of broader conformational ensembles of interchanging states. We demonstrate the need for conformational ensembles to understand function, using the enzyme ketosteroid isomerase (KSI) as an example. Comparison of prior KSI cryogenic x-ray structures suggested deleterious mutational effects from a misaligned oxyanion hole catalytic residue. However, ensemble information from room-temperature x-ray crystallography, combined with functional studies, excluded this model. Ensemble-function analyses can deconvolute effects from altering the probability of occupying a state (P-effects) and changing the reactivity of each state (k-effects); our ensemble-function analyses revealed functional effects arising from weakened oxyanion hole hydrogen bonding and substrate repositioning within the active site. Ensemble-function studies will have an integral role in understanding enzymes and in meeting the future goals of a predictive understanding of enzyme catalysis and engineering new enzymes.

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

Ultrafast charge transfer coupled to quantum proton motion at molecule/metal oxide interface

Understanding how the nuclear quantum effects (NQEs) in the hydrogen bond (H-bond) network influence the photoexcited charge transfer at semiconductor/molecule interface is a challenging problem. By combining two kinds of emerging molecular dynamics methods at the ab initio level, the path integral–based molecular dynamics and time-dependent nonadiabatic molecular dynamics, and choosing CH 3 OH/TiO 2 as a prototypical system to study, we find that the quantum proton motion in the H-bond network is strongly coupled with the ultrafast photoexcited charge dynamics at the interface. The hole trapping ability of the adsorbed methanol molecule is notably enhanced by the NQEs, and thus, it behaves as a hole scavenger on titanium dioxide. The critical role of the H-bond network is confirmed by in situ scanning tunneling microscope measurements with ultraviolet light illumination. It is concluded the quantum proton motion in the H-bond network plays a critical role in influencing the energy conversion efficiency based on photoexcitation.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2022

Lytic polysaccharide monooxygenase increases cellobiohydrolases activity by promoting decrystallization of cellulose surface

Efficient depolymerization of crystalline cellulose requires cooperation between multiple cellulolytic enzymes. Through biochemical approaches, molecular dynamics (MD) simulation, and single-molecule observations using high-speed atomic force microscopy (HS-AFM), we quantify and track synergistic activity for cellobiohydrolases (CBHs) with a lytic polysaccharide monooxygenase (LPMO) from Phanerochaete chrysosporium. Increasing concentrations of LPMO (AA9D) increased the activity of a glycoside hydrolase family 6 CBH, Cel6A, whereas the activity of a family 7 CBH (Cel7D) was enhanced only at lower concentrations of AA9D. MD simulation suggests that the result of AA9D action to produce chain breaks in crystalline cellulose can oxidatively disturb the crystalline surface by disrupting hydrogen bonds. HS-AFM observations showed that AA9D increased the number of Cel7D molecules moving on the substrate surface and increased the processivity of Cel7D, thereby increasing the depolymerization performance, suggesting that AA9D not only generates chain ends but also amorphizes the crystalline surface, thereby increasing the activity of CBHs.

09 BIOMASS FUELS↗
DOE OSTI2024

Facet-dependent dispersion and aggregation of aqueous hematite nanoparticles

Nanoparticle aggregates in solution controls surface reactivity and function. Complete dispersion often requires additive sorbents to impart a net repulsive interaction between particles. Facet engineering of nanocrystals offers an alternative approach to produce monodisperse suspensions simply based on facet-specific interaction with solvent molecules. Here, we measure the dispersion/aggregation of three morphologies of hematite (α-Fe 2 O 3 ) nanoparticles in varied aqueous solutions using ex situ electron microscopy and in situ small-angle x-ray scattering. We demonstrate a unique tendency of (104) hematite nanoparticles to maintain a monodisperse state across a wide range of solution conditions not observed with (001)- and (116)-dominated particles. Density functional theory calculations reveal an inert, densely hydrogen-bonded first water layer on the (104) facet that favors interparticle dispersion. Results validate the notion that nanoparticle dispersions can be controlled through morphology for specific solvents, which may help in the development of various nanoparticle applications that rely on their interfacial area to be highly accessible in stable suspensions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Constructive molecular configurations for surface-defect passivation of perovskite photovoltaics

Surface trap-mediated nonradiative charge recombination is a major limit to achieving high-efficiency metal-halide perovskite photovoltaics. The ionic character of perovskite lattice has enabled molecular defect passivation approaches through interaction between functional groups and defects. However, a lack of in-depth understanding of how the molecular configuration influences the passivation effectiveness is a challenge to rational molecule design. In this work, the chemical environment of a functional group that is activated for defect passivation was systematically investigated with theophylline, caffeine, and theobromine. When N-H and C=O were in an optimal configuration in the molecule, hydrogen-bond formation between N-H and I (iodine) assisted the primary C=O binding with the antisite Pb (lead) defect to maximize surface-defect binding. A stabilized power conversion efficiency of 22.6% of photovoltaic device was demonstrated with theophylline treatment.

14 SOLAR ENERGY↗
DOE OSTI2020

A molecular mediator for reductive concerted proton-electron transfers via electrocatalysis

Electrocatalytic approaches to the activation of unsaturated substrates via reductive concerted proton-electron transfer (CPET) must overcome competing, often kinetically dominant hydrogen evolution. We introduce the design of a molecular mediator for electrochemically triggered reductive CPET through the synthetic integration of a Brønsted acid and a redox mediator. Cathodic reduction at the cobaltocenium redox mediator substantially weakens the homolytic nitrogen-hydrogen bond strength of a Brønsted acidic anilinium tethered to one of the cyclopentadienyl rings. The electrochemically generated molecular mediator is demonstrated to transform a model substrate, acetophenone, to its corresponding neutral α-radical via a rate-determining CPET.

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

Autonomous self-repair in piezoelectric molecular crystals

Living tissue uses stress-accumulated electrical charge to close wounds. Self-repairing synthetic materials, which are typically soft and amorphous, usually require external stimuli, prolonged physical contact, and long healing times. We overcome many of these limitations in piezoelectric bipyrazole organic crystals, which recombine following mechanical fracture without any external direction, autonomously self-healing in milliseconds with crystallographic precision. Kelvin probe force microscopy, birefringence experiments, and atomic-resolution structural studies reveal that these noncentrosymmetric crystals, with a combination of hydrogen bonds and dispersive interactions, develop large stress-induced opposite electrical charges on fracture surfaces, prompting an electrostatically driven precise recombination of the pieces via diffusionless self-healing.

Bhunia, Surojit↗
DOE OSTI2021

First-principles design of a single-atom–alloy propane dehydrogenation catalyst

The complexity of heterogeneous catalysts means that a priori design of new catalytic materials is difficult, but the well-defined nature of single-atom–alloy catalysts has made it feasible to perform unambiguous theoretical modeling and precise surface science experiments. Herein we report the theory-led discovery of a rhodium-copper (RhCu) single-atom–alloy catalyst for propane dehydrogenation to propene. Although Rh is not generally considered for alkane dehydrogenation, first-principles calculations revealed that Rh atoms disperse in Cu and exhibit low carbon-hydrogen bond activation barriers. Surface science experiments confirmed these predictions, and together these results informed the design of a highly active, selective, and coke-resistant RhCu nanoparticle catalyst that enables low-temperature nonoxidative propane dehydrogenation.

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

A scalable metal-organic framework as a durable physisorbent for carbon dioxide capture

A hydrophobic CO 2 physisorbent Most materials for carbon dioxide (CO 2 ) capture of fossil fuel combustion, such as amines, rely on strong chemisorption interactions that are highly selective but can incur a large energy penalty to release CO 2 . Lin et al . show that a zinc-based metal organic framework material can physisorb CO 2 and incurs a lower regeneration penalty. Its binding site at the center of the pores precludes the formation of hydrogen-bonding networks between water molecules. This durable material can preferentially adsorb CO2 at 40% relative humidity and maintains its performance under flue gas conditions of 150°C. —PDS

Science & Technology - Other Topics↗
DOE OSTI2023

Structure of a ribonucleotide reductase R2 protein radical

Aerobic ribonucleotide reductases (RNRs) initiate synthesis of DNA building blocks by generating a free radical within the R2 subunit; the radical is subsequently shuttled to the catalytic R1 subunit through proton-coupled electron transfer (PCET). Here we present a high-resolution room temperature structure of the class Ie R2 protein radical captured by x-ray free electron laser serial femtosecond crystallography. The structure reveals conformational reorganization to shield the radical and connect it to the translocation path, with structural changes propagating to the surface where the protein interacts with the catalytic R1 subunit. Restructuring of the hydrogen bond network, including a notably short O–O interaction of 2.41 angstroms, likely tunes and gates the radical during PCET. These structural results help explain radical handling and mobilization in RNR and have general implications for radical transfer in proteins.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Linking the Salmonella enterica 1,2-Propanediol Utilization Bacterial Microcompartment Shell to the Enzymatic Core via the Shell Protein PduB

Bacterial microcompartments (MCPs) are protein-based organelles that house the enzymatic machinery for metabolism of niche carbon sources, allowing enteric pathogens to outcompete native microbiota during host colonization. While much progress has been made toward understanding MCP biogenesis, questions still remain regarding the mechanism by which core MCP enzymes are enveloped within the MCP protein shell. Here, we explore the hypothesis that the shell protein PduB is responsible for linking the shell of the 1,2-propanediol utilization (Pdu) MCP from Salmonella enterica serovar Typhimurium LT2 to its enzymatic core. Using fluorescent reporters, we demonstrate that all members of the Pdu enzymatic core are encapsulated in Pdu MCPs. We also demonstrate that PduB is critical for linking the entire Pdu enzyme core to the MCP shell. Using MCP purifications, transmission electron microscopy, and fluorescence microscopy, we find that shell assembly can be decoupled from the enzymatic core, as apparently empty MCPs are formed in Salmonella strains lacking PduB. Mutagenesis studies reveal that PduB is incorporated into the Pdu MCP shell via a conserved, lysine-mediated hydrogen bonding mechanism. Finally, growth assays and system-level pathway modeling reveal that unencapsulated pathway performance is strongly impacted by enzyme concentration, highlighting the importance of minimizing polar effects when conducting these functional assays. Together, these results provide insight into the mechanism of enzyme encapsulation within Pdu MCPs and demonstrate that the process of enzyme encapsulation and shell assembly are separate processes in this system, a finding that will aid future efforts to understand MCP biogenesis.

1, 2-propanediol utilization↗
DOE OSTI2026

Tulane virus protease as a structural surrogate for inhibitor screening of human norovirus proteases

Human norovirus (HuNoV) is a significant cause of gastroenteritis worldwide, affecting people of all age groups. There are currently no vaccines or drugs available, leaving susceptible populations vulnerable to severe or protracted illness. A HuNoV cultivation system is pivotal for screening norovirus antivirals. While the human intestinal enteroid cultivation system allows robust replication of multiple HuNoV strains, it presents technical and cost barriers. Tulane virus (TV), a surrogate for HuNoV, replicates well in monkey kidney cell lines and is closely related to norovirus in cellular biology. Here, we determined the structures of TV protease (TV-Pro) alone and in complex with rupintrivir, a picornavirus inhibitor that also inhibits HuNoV proteases (HuNoV-Pro). Our data validate TV as an efficient surrogate system for rapid screening of HuNoV protease inhibitors. The TV protease structure exhibits significant backbone similarity to the GI.1 HuNoV protease in the substrate-binding domain, with the BII-CII loop in an open conformation stabilized by hydrogen bonds as present in the GI.1 protease. Structural differences in the S2 pocket and two amino acid changes in the S4 pocket result in slightly altered P2 and P4 substrate and inhibitor conformations. Despite these differences, we confirm previous findings that the TV protease can cleave the GI.1 and GII HuNoV polyprotein substrates with high and moderate efficiency, respectively. We found that rupintrivir efficiently inhibits TV protease in vitro and inhibits TV replication in cell culture with similar efficacy in combination with P-glycoprotein efflux pump inhibitors. We conclude that TV is a valuable surrogate for HuNoV protease inhibitor screening and outline strategies to improve its compatibility as such.

crystal structures↗
DOE OSTI2022

C6 Hydroxymethyl-Substituted Carbapenem MA-1-206 Inhibits the Major Acinetobacter baumannii Carbapenemase OXA-23 by Impeding Deacylation

Acinetobacter baumannii has become a major nosocomial pathogen, as it is often multidrug-resistant, which results in infections characterized by high mortality rates. The bacterium achieves high levels of resistance to β-lactam antibiotics by producing β-lactamases, enzymes which destroy these valuable agents. Historically, the carbapenem family of b-lactam antibiotics have been the drugs of choice for treating A. baumannii infections. However, their effectiveness has been significantly diminished due to the pathogen’s production of carbapenem-hydrolyzing class D β-lactamases (CHDLs); thus, new antibiotics and inhibitors of these enzymes are urgently needed. Here, we describe a new carbapenem antibiotic, MA-1-206, in which the canonical C6 hydroxyethyl group has been replaced with hydroxymethyl. The antimicrobial susceptibility studies presented here demonstrated that this compound is more potent than meropenem and imipenem against A. baumannii producing OXA-23, the most prevalent CHDL of this pathogen, and also against strains producing the CHDL OXA-24/40 and the class B metallo-β-lactamase VIM-2. Our kinetic and mass spectrometry studies revealed that this drug is a reversible inhibitor of OXA-23, where inhibition takes place through a branched pathway. X-ray crystallographic studies, molecular docking, and molecular dynamics simulations of the OXA-23-MA-1-206 complex show that the C6 hydroxymethyl group forms a hydrogen bond with the carboxylated catalytic lysine of OXA-23, effectively preventing deacylation. These results provide a promising strategy for designing a new generation of CHDL-resistant carbapenems to restore their efficacy against deadly A. baumannii infections. Carbapenem antibiotics are the drugs of choice for treatment of deadly infections caused by Gram-negative bacteria. However, their efficacy is severely compromised by the wide spread of carbapenem-hydrolyzing class D β-lactamases (CHDLs). The importance of this research is the discovery that substitution of the canonical hydroxyethyl group of carbapenems by a hydroxymethyl significantly enhances stability against inactivation by the major CHDL of Acinetobacter baumannii, OXA-23. These results provide a novel strategy for designing next-generation, carbapenemase-stable carbapenems to fight multidrug-resistant infections caused by Gram-negative pathogens

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Structural basis for varying drug resistance of SARS-CoV-2 M pro E166 variants

ABSTRACT Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) main protease (M pro ) has an essential role in the virus lifecycle and, accordingly, it is a target for antiviral drugs. Multiple studies have identified an M pro mutation (E166V) that confers strong resistance to clinically relevant inhibitors, including nirmatrelvir, but the underlying mechanism is not fully understood. Here, we report on crystal structures of SARS-CoV-2 M pro E166V in complex with nirmatrelvir, ensitrelvir, and bofutrelvir. The structures suggest that resistance is caused in part by the loss of a direct hydrogen bond and also, especially for nirmatrelvir, by a steric clash with the substituted valine residue. In comparison, the binding of bofutrelvir shows greater flexibility, which may help alleviate this steric effect and allow bofutrelvir to fit the mutant active site despite the loss of a direct polar contact. Thermal stability analyses also corroborate E166V most severely affecting the binding of nirmatrelvir and, to lesser and different extents, ensitrelvir and bofutrelvir. We further show that E166I causes even more severe nirmatrelvir resistance, whereas E166A and E166L have much milder effects. These studies shed light on the molecular mechanisms of a key M pro drug resistance mutation and may help inform the design of next-generation inhibitors. IMPORTANCE Using a combination of high-resolution X-ray crystallographic and biochemical analyses, we reveal the molecular mechanisms by which a mutation in the severe acute respiratory syndrome coronavirus 2 main protease (M pro ) confers strong resistance against clinically relevant antiviral drugs that inhibit M pro activity. The results presented here may help inform the design of next-generation inhibitors to combat the problem of therapy resistance.

Microbiology↗
DOE OSTI2021

Demystifying the Diffuse Vibrational Spectrum of Aqueous Protons Through Cold Cluster Spectroscopy

The ease with which the pH is routinely determined for aqueous solutions masks the fact that the cationic product of Arrhenius acid dissolution, the hydrated proton, or H + (aq), is a remarkably complex species. Here, we review how results obtained over the past 30 years in the study of H + ·(H 2 O) n cluster ions isolated in the gas phase shed light on the chemical nature of H + (aq). This effort has also revealed molecular-level aspects of the Grotthuss relay mechanism for positive-charge translocation in water. Recently developed methods involving cryogenic cooling in radiofrequency ion traps and the application of two-color, infrared–infrared (IR–IR) double-resonance spectroscopy have established a clear picture of how local hydrogen-bond topology drives the diverse spectral signatures of the excess proton. This information now enables a new generation of cluster studies designed to unravel the microscopic mechanics underlying the ultrafast relaxation dynamics displayed by H + (aq).

Chemistry↗
DOE OSTI2020

Well-designed Crosslinked Polymer Electrolyte Enables High Ionic Conductivity and Enhanced Salt Solvation

A new facile single-step method to fabricate crosslinked polymer electrolyte membranes consisting of branched poly(ethyleneimine), (PEI) and poly(ethylene oxide), (PEO) is demonstrated. The membranes exhibit excellent ionic conductivity (1.2 × 10 –3 S cm –1 at 80 °C) with minimal addition of plasticizer (20 wt%). The amine functional group in the PEI-PEO crosslinked matrix provides Lewis basic and hydrogen bonding characteristics that facilitate the dissolution of lithium salt and enables a higher cation transport number than a PEO crosslinked matrix. The glass transition temperature, degree of crystallinity, and room temperature storage modulus increases with decreasing crosslink density and increasing ratio of free amines. The resultant ionic conductivity and mechanical strength can be flexibly tailored by varying the molar ratio of free amine moieties in the crosslinked PEI-PEO matrix. This study provides an improved synthesis method, in-depth characterization, and fundamental insights on the effect of free amine moieties on the transport properties of a highly conductive gel polymer electrolyte.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗