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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 127 records · Page 7
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Structural basis of sequence-specific cytosine deamination by double-stranded DNA deaminase toxin DddA

The interbacterial deaminase toxin DddA catalyzes cytosine-to-uracil conversion in double-stranded (ds) DNA and enables CRISPR-free mitochondrial base editing, but the molecular mechanisms underlying its unique substrate selectivity have remained elusive. Here, we report crystal structures of DddA bound to a dsDNA substrate containing the 5'-TC target motif. These structures show that DddA binds to the minor groove of a sharply bent dsDNA and engages the target cytosine extruded from the double helix. DddA Phe1375 intercalates in dsDNA and displaces the 5' (-1) thymine, which in turn replaces the target (0) cytosine and forms a noncanonical T–G base pair with the juxtaposed guanine. This tandem displacement mechanism allows DddA to locate a target cytosine without flipping it into the active site. Biochemical experiments demonstrate that DNA base mismatches enhance the DddA deaminase activity and relax its sequence selectivity. On the basis of the structural information, we further identified DddA mutants that exhibit attenuated activity or altered substrate preference. Our studies may help design new tools useful in genome editing or other applications.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Pincers with diverse donors and their interconversion: application to Ni(II)

Abstract A pincer ligand composed of a pyridine with ortho positions substituted by a bulky phosphine arm and a pyrazole arm (PNNH) is installed on nickel(II) to yield the diamagnetic planar complex [(PNNH)NiCl]Cl. The chloride anion can be replaced by BPh 4 − by a metathesis. The acidic pyrazole proton can be removed with LiN(SiMe 3 ) 2 to yield the square planar neutral molecule (PNN − )NiCl. The coordinated chloride can be metathetically replaced by azide to yield diamagnetic (PNN − )Ni(N 3 ). To evaluate changing the phosphine donor for a phosphine sulfide, the corresponding pincer ligand SPNNH was synthesized and installed on NiBr 2 . The reduced steric bulk from the more distant phosphorous keeps both halides coordinated in the paramagnetic molecular species (SPNNH)NiBr 2 . Several attempts to dehydrobrominate this species result in synthesis and characterization of two unexpected products. One effort revealed that the electrophilic character of P(V) leaves the phosphorus atom in (SPNNH)NiBr 2 vulnerable to nucleophilic attack, resulting in a P/C cleavage product which was characterized.

Cabelof, Alyssa C.↗
DOE OSTI2021

A Chemical Dynamics Study of the Reaction of the Methylidyne Radical (CH, X 2 Π) with Dimethylacetylene (CH 3 CCCH 3 , X 1 A 1g )

The gas-phase reaction of the methylidyne (CH; X 2 Π) radical with dimethylacetylene (CH 3 CCCH 3 ; X 1 A 1g ) was studied at a collision energy of 20.6 kJ mol -1 under single collision conditions with experimental results merged with ab initio calculations of the potential energy surface (PES) and ab initio molecule dynamics (AIMD) simulations. Here, the crossed molecular beams experiment reveals that the reaction proceeds barrierless via indirect scattering dynamics through long-lived C 5 H 7 reaction intermediate(s) ultimately dissociating to C 5 H 6 isomers along with atomic hydrogen with atomic hydrogen predominantly released from the methyl groups as verified by replacing the methylidyne with the D1-methylidyne reactant. AIMD simulations reveal that the reaction dynamics are statistical leading predominantly to p28 (1-methyl-3-methylene-cyclopropene, 13 %) and p8 (1-penten-3-yne, 81 %) plus atomic hydrogen with a significant amount of available energy being channeled into the internal excitation of the polyatomic reaction products.

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

Electronic structure and photophysics of a supermolecular iron complex having a long MLCT-state lifetime and panchromatic absorption

Exploiting earth-abundant iron-based metal complexes as high-performance photosensitizers demands long-lived electronically excited metal-to-ligand charge-transfer (MLCT) states, but these species suffer typically from femtosecond timescale charge-transfer (CT)-state quenching by low-lying nonreactive metal-centered (MC) states. Here, we engineer supermolecular Fe(II) chromophores based on the bis(tridentate-ligand)metal(II)-ethyne-(porphinato)zinc(II) conjugated framework, previously shown to give rise to highly delocalized low-lying 3 MLCT states for other Group VIII metal (Ru, Os) complexes. Electronic spectral, potentiometric, and ultrafast pump–probe transient dynamical data demonstrate that a combination of a strong σ-donating tridentate ligand and a (porphinato)zinc(II) moiety with low-lying π*-energy levels, sufficiently destabilize MC states and stabilize supermolecular MLCT states to realize Fe(II) complexes that express 3 MLCT state photophysics reminiscent of their heavy-metal analogs. The resulting Fe(II) chromophore archetype, FeNHCPZn, features a highly polarized CT state having a profoundly extended 3MLCT lifetime (160 ps), 3 MLCT phosphorescence, and ambient environment stability. Density functional and domain-based local pair natural orbital coupled cluster [DLPNO-CCSD(T)] theory reveal triplet-state wavefunction spatial distributions consistent with electronic spectroscopic and excited-state dynamical data, further underscoring the dramatic Fe metal-to-extended ligand CT character of electronically excited FeNHCPZn. This design further prompts intense panchromatic absorptivity via redistributing high-energy absorptive oscillator strength throughout the visible spectral domain, while maintaining a substantial excited-state oxidation potential for wide-ranging photochemistry––highlighted by the ability of FeNHCPZn to photoinject charges into a SnO 2 /FTO electrode in a dye-sensitized solar cell (DSSC) architecture. Concepts enumerated herein afford opportunities for replacing traditional rare-metal–based emitters for solar-energy conversion and photoluminescence applications.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2023

LEU Fission Plate: Experimental Prototype Design Document

The Ultracold Neutron (UCN) source at LANSCE is currently the source of the highest density of UCN in the world. We intend to use innovative new solutions to boost our UCN density in order to maintain our leadership in this competitive field. Prior studies suggest that a fission plate neutron multiplier made from low enriched uranium (LEU) installed between our spallation target and UCN source moderator can boost the density by up to a factor of ten. Here we present a prototype of this idea that uses an existing one liter volume of LEU that can boost the UCN density by roughly a factor of 2. Additional simulation studies presented here also suggest that we may find more gains by replacing some of the moderator or reflector geometries with beryllium.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2021

Photosynthetic reaction center variants made via genetic code expansion show Tyr at M210 tunes the initial electron transfer mechanism

Significance Reaction centers (RCs) are critical to photosynthetic energy conversion. RCs in all characterized photosynthetic organisms contain two symmetrically arranged branches of chromophores and enable light-induced electron transfer with high yield. We fine-tune the properties of a key bacterial RC symmetry-breaking tyrosine via its replacement with noncanonical tyrosine analogs and determine kinetic outcomes. Results are interpreted through energetic characterization made possible by resonance Stark spectroscopy. Analysis indicates this tyrosine modulates the mechanism of the initial light-induced electron transfer, affording an alternative functional pathway that maintains the RC’s robust electron transfer. Modern molecular biology, ultrafast spectroscopy, crystallography, and energetic characterization enable the mechanistic model we describe. Our results deepen understanding of RC function and may have implications for other photocatalysts and enzymes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Adsorption Processes during Electrochemical Atomic Layer Deposition of Gold

Electrochemical atomic layer deposition (e-ALD) technique offers a simple and effective "wet chemistry" approach enabling high-precision monolayer-by-monolayer deposition of metal films. The process of e-ALD of Au involves lead underpotential deposition (PbUPD) followed by its redox replacement by a Au monolayer. The time evolution of the deposit mass during "one-pot" Au e-ALD is known to exhibit a unique three-stage response that is presently not well understood. In this work, we probe this response using voltammetry, electrochemical quartz crystal microgravimetry (e-QCM), and chronoamperometry to unravel the underlying mechanistic events during Au e-ALD. Furthermore, the presence of adsorbed Au +3 -ligand complex(es) (Au-L) on the Au surface is established. In stage I of e-ALD, this Au-L adsorbed layer is reduced to Au while a Pb UPD adlayer is formed. In stage II, the Pb UPD adlayer undergoes spontaneous surface-limited redox replacement by nobler Au under open-circuit conditions. Finally, in stage III, re-adsorption of the Au-L occurs on the newly deposited Au. Quantitative analysis of the deposit mass transients obtained under a variety of conditions provides an estimate of the Au-L mass and its molecular weight.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Unification of nonequilibrium molecular dynamics and the mode-resolved phonon Boltzmann equation for thermal transport simulations

Nano-size confinement induces many intriguing non-Fourier heat conduction phenomena, such as nonlinear temperature gradients, temperature jumps near the contacts, and size-dependent thermal conductivity. Over the past decades, these effects have been studied and interpreted by nonequilibrium molecular dynamics (NEMD) and phonon Boltzmann transport equation (BTE) simulations separately, but no theory that unifies these two methods has ever been established. In this work, we unify these methods using a quantitative mode-level comparison and demonstrate that they are equivalent for various thermostats. We show that different thermostats result in different non-Fourier thermal transport characteristics due to the different mode-level phonon excitations inside the thermostats, which explains the different size-dependent thermal conductivities calculated using different reservoirs, even though they give the same bulk thermal conductivity. Specifically, the Langevin thermostat behaves like a thermalizing boundary in phonon BTE and provides mode-level thermal-equilibrium phonon outlets, while the Nose-Hoover chain thermostat and velocity rescaling method behave like biased reservoirs, which provide a spatially uniform heat generation and mode-level nonequilibrium phonon outlets. These findings explain why different experimental measurement methods can yield different size-dependent thermal conductivity. They also indicate that the thermal conductivity of materials can be tuned for various applications by specifically designing thermostats. Finally, the unification of NEMD and phonon BTE will largely facilitate the study of thermal transport in complex systems in the future by, e.g., replacing computationally unaffordable first-principles NEMD simulations with computationally less expensive spectral BTE simulations.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2020

Overcoming Fundamental Limitations in Adsorbent Design: Alkene Adsorption by Non‐porous Copper(I) Complexes

Abstract Purifying alkenes from alkanes requires cryogenic distillation. This consumes energy equivalent to countries of ca. 5 million people. Replacing distillation with adsorption processes would significantly increase energy efficiency. Trade‐offs between kinetics, selectivity, capacity, and heat of adsorption have prevented production of an optimal adsorbent. We report adsorbents that overcome these trade‐offs. [Cu‐Br] 3 and [Cu‐H] 3 are air‐stable trinuclear complexes that undergo reversible solid‐state inter‐molecular rearrangements to produce dinuclear [Cu‐Br⋅(alkene)] 2 and [Cu‐H⋅(alkene)] 2 . The reversible solid‐state rearrangement, confirmed in situ using powder X‐ray diffraction, allows adsorbent design trade‐offs to be overcome, coupling low heat of adsorption (−10 to −17 kJ mol −1 alkene ), high alkene:alkane selectivity (47; 29), and uptake capacity (>2.5 mol alkene mol −1 Cu3 ). Most remarkably, [Cu‐H] 3 displays fast uptake and regenerates capacity within 10 minutes.

Parasar, Devaborniny↗
DOE OSTI2023

Fractionated and purified hybrid poplar lignins as a polyol replacement in rigid polyurethane/polyisocyanurate foams

This study introduces fractionated lignin as an innovative component in the formulation of rigid polyurethane/polyisocyanurate (PUR/PIR) foams. Low-density PUR/PIR rigid foams were prepared by replacing 80% of the petrochemical-based polyol with a hybrid poplar (HP) lignin, recovered via alkaline pretreatment, and also with a fraction of this lignin, isolated via the Aqueous Lignin Purification with Hot Agents (ALPHA) process. The as-recovered HP and ALPHA-fractionated HP lignins were characterized to determine hydroxyl content, molecular weight (Mw) distribution, and pH. Both lignin-based foams met minimum standard requirements in terms of closed cell content, compression strength, and thermal conductivity. Notably, the foams made with ALPHA-based lignin outperformed the as-recovered lignin-based foams in all measured foam properties. Moreover, the ALPHA-based foam had comparable performance to the control foam (without lignin) except for density and even surpassed the control foam in closed cell content and compressive strength. This investigation of the molecular properties of lignin suggests that significant reductions in lignin average molecular weight and polydispersity (PDI) can positively impact the properties of lignin-based rigid foams.

09 BIOMASS FUELS↗
DOE OSTI2026

Benchmarking the performance of uncertainty quantification methods for neural network-based interatomic potentials

Machine-learned interatomic potentials (ML-IAPs) continue to gain popularity as accurate, computationally efficient replacements for traditional, physics-based interatomic potentials and expensive ab initio methods. Uncertainty quantification (UQ) of ML-IAPs is a growing area of research as UQ is critical in many applications of IAPs, such as developing curated datasets, active learning-based data augmentation, self-improving models, and estimating the uncertainty of molecular dynamics simulations. In this paper, we construct and benchmark a series of different neural network potentials (NNPs) with varying network architectures to determine the performance of these models with respect to both the mean and uncertainty calibration error. Each NNP method is specifically designed to predict either epistemic or aleatoric uncertainty with particular focus on the differences in behavior between the epistemic and aleatoric uncertainty estimates. We benchmark these methods using multiple datasets common in the ML-IAP literature. The results show that the aleatoric uncertainty from single-shot model architectures is a competitive alternative to ensemble-based epistemic uncertainty predictions in regions of sufficient data-density. However, in regions where the representative data is sparse, aleatoric uncertainty models tend to overpredict and epistemic methods tend to underpredict the actual model error. We conclude that the type of UQ is crucial when discussing performance of probabilistic model results as different methods have different performance characteristics depending on the regime in which they are evaluated. Therefore, the type of UQ method should be carefully evaluated against both the data characteristics and requirements for the intended application.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

Molecular-Level Overhaul of y-Aminopropyl Aminosilicone/Triethylene Glycol Post-Combustion CO2-Capture Solvents

Capturing carbon dioxide (CO2) from post-combustion gas streams is an energy-intensive process that is required prior to either converting or sequestering CO2. There are a few commercial offerings of 1st and 2nd generation aqueous amine technologies, however the cost of capturing CO2 with these technologies remains high. To decrease costs of capture, researchers are designing efficient solvent systems with the goal of being drop-in replacements for 1st and 2nd generation infrastructure. One approach has seen the development of water-lean solvents that aim to increase efficiency by reducing the water content in solution. Water-lean solvents such as GE’s GAP/TEG are promising technologies, with potential to halve the parasitic load to a coal-fired power plant, only if the intrinsically high solution viscosities and hydrolysis of the siloxane moieties could be mitigated. We present here, an integrated multidisciplinary approach to overhaul the GAP/TEG solvent system at the molecular level to mitigate hydrolysis while also reducing viscosity. We present molecular-level insights into chemical speciation of CO2-containing ions, showing that co-solvents and diluents have a negligible effect on reducing viscosity and are not needed. This finding allowed for the design of singlecomponent siloxane-free diamine derivatives with site-specific incorporation of selective chemical moieties for direct placement and orientation of hydrogen bonding to reduce viscosity. Ultimately, we present new single-component diamine formulations less susceptible to hydrolysis that exhibit up to a 98% reduction in viscosity compared to the initial GAP/TEG formulation.

Cantu Cantu, David↗
DOE OSTI2023

Characterizing the Self-Assembly Properties of Monoolein Lipid Isosteres

Living cells feature lipid compartments which exhibit a variety of shapes and structures that assist essential cellular processes. Many natural cell compartments frequently adopt convoluted nonlamellar lipid architectures that facilitate specific biological reactions. Improved methods for controlling the structural organization of artificial model membranes would facilitate investigations into how membrane morphology affects biological functions. Monoolein (MO) is a single-chain amphiphile which forms nonlamellar lipid phases in aqueous solution and has wide applications in nanomaterial development, the food industry, drug delivery, and protein crystallization. However, even if MO has been extensively studied, simple isosteres of MO, while readily accessible, have seen limited characterization. An improved understanding of how relatively minor changes in lipid chemical structure affect self assembly and membrane topology could instruct the construction of artificial cells and organelles for modeling biological structures and facilitate nanomaterial-based applications. Here, we investigate the differences in self-assembly and large-scale organization between MO and two MO lipid isosteres. We show that replacing the ester linkage between the hydrophilic headgroup and hydrophobic hydrocarbon chain with a thioesther or amide functional group results in the assembly of lipid structures with different phases not resembling those formed by MO. Using light and cryo-electron microscopy, small-angle X-ray scattering, and infrared spectroscopy, we demonstrate differences in the molecular ordering and large-scale architectures of the self-assembled structures made from MO and its isosteric analogues. These results improve our understanding of the molecular underpinnings of lipid mesophase assembly and may facilitate the development of MO-based materials for biomedicine and as model lipid compartments.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Rigorous Oxidation State Assignments for Supported Ga-Containing Catalysts Using Theory-Informed X-ray Absorption Spectroscopy Signatures from Well-Defined Ga(I) and Ga(III) Compounds

Gallium-based heterogeneous catalysts originally developed for commercial use in propane dehydroaromatization have been explored extensively as potential replacements for Pt- and Cr-based catalysts used in propane dehydrogenation for on-demand propylene production. In a large number of experimental and theoretical studies, active sites with a variety of Ga nuclearities, coordination environments, and oxidation states have been proposed. Isolated Ga(I) ions are often invoked, despite the scarcity of well-defined molecular species and their well-documented instability. In this study, we investigate the appearance of a high-intensity, low-energy white line at the Ga K-edge upon reduction of Ga/HZSM-5 by H 2 at a temperature of ca. 500 °C, accompanied by a dramatic reduction in the extended X-ray absorption fine structure (EXAFS) intensity. In contrast, Ga/γ-Al 2 O 3 does not show such behavior. In order to lay a rigorous foundation for characterizing these types of systems and to establish experimental signatures for the elusive Ga(I) oxidation state, we recorded Ga K-edge X-ray absorption spectra [including high-energy-resolution fluorescence detection-X-ray absorption near-edge spectroscopy (HERFD-XANES)] for several well-defined molecular and crystalline Ga(I) compounds. XANES is essential to establishing the presence of Ga(I), despite the overlap in edge energies with organoGa(III) compounds, because Ga(I)-containing oxide materials show very weak EXAFS scattering. Compared to the XANES of trigonal Ga(III)-containing materials, Ga(I) spectra display a significantly more intense white line feature. Theoretical simulations agree well with this experimental observation and reveal that the strong XANES intensity originates from the superposition of transitions to several empty, nearly degenerate p-like states. Finally, these signatures provide compelling evidence for assigning the intense white line and dramatic loss of EXAFS intensity in Ga/HZSM-5 to the near-quantitative reduction of Ga(III) to Ga(I), while the weaker white line and conventional EXAFS signal of Ga/γ-Al 2 O 3 point to, at most, a minor fraction of Ga(I) sites.

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

Reducing sputter induced stress and damage for efficient perovskite/silicon tandem solar cells

Reducing damages caused by sputtering of transparent conductive oxide (TCO) electrodes is critical in achieving highly efficient and stable perovskite/silicon tandem solar cells. Here we study the sputter caused damage to bathocuproine (BCP), which is widely used in highly efficient p-i-n structure single junction perovskite solar cells. While BCP buffer layer protects the underneath layers from damage, itself can be damaged by sputtering of TCOs at a wide range of target-substrate distances, supported by molecular dynamic simulation. More intriguingly, it is observed that TCO easily peeled off after sputtering when the sputtering target is close to substrate. This is ascribed to formation of stress during cooling down process after sputtering due to different thermal expansion coefficients of the layers. Our studies explain why tin oxide (SnO2) made by atomic layer deposition can replace BCP for a much better tandem device performance. SnO2 has high affinity with sputtered TCO electrode to suppress peeling-off issue and has higher bond energy to resist sputter induced damage, thus it allows a wider window of target-substrate distances than BCP during TCO sputtering. Ultimately, we demonstrate an efficient perovskite/silicon monolithic tandem solar cell with efficiency of 26.0% to illustrate the beneficial effects of reduced stress and damage.

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

Screening a knowledge‐based library of low molecular weight compounds against the proline biosynthetic enzyme 1‐pyrroline‐5‐carboxylate 1 ( PYCR1)

Abstract Δ 1 ‐pyrroline‐5‐carboxylate reductase isoform 1 (PYCR1) is the last enzyme of proline biosynthesis and catalyzes the NAD(P)H‐dependent reduction of Δ 1 ‐pyrroline‐5‐carboxylate toL‐proline. High PYCR1 gene expression is observed in many cancers and linked to poor patient outcomes and tumor aggressiveness. The knockdown of thePYCR1gene or the inhibition of PYCR1 enzyme has been shown to inhibit tumorigenesis in cancer cells and animal models of cancer, motivating inhibitor discovery. We screened a library of 71 low molecular weight compounds (average MW of 131 Da) against PYCR1 using an enzyme activity assay. Hit compounds were validated with X‐ray crystallography and kinetic assays to determine affinity parameters. The library was counter‐screened against human Δ 1 ‐pyrroline‐5‐carboxylate reductase isoform 3 and proline dehydrogenase (PRODH) to assess specificity/promiscuity. Twelve PYCR1 and one PRODH inhibitor crystal structures were determined. Three compounds inhibit PYCR1 with competitive inhibition parameter of 100 μM or lower. Among these, (S)‐tetrahydro‐2H‐pyran‐2‐carboxylic acid (70 μM) has higher affinity than the current best tool compoundN‐formyl‐l‐proline, is 30 times more specific for PYCR1 over human Δ 1 ‐pyrroline‐5‐carboxylate reductase isoform 3, and negligibly inhibits PRODH. Structure‐affinity relationships suggest that hydrogen bonding of the heteroatom of this compound is important for binding to PYCR1. The structures of PYCR1 and PRODH complexed with 1‐hydroxyethane‐1‐sulfonate demonstrate that the sulfonate group is a suitable replacement for the carboxylate anchor. This result suggests that the exploration of carboxylic acid isosteres may be a promising strategy for discovering new classes of PYCR1 and PRODH inhibitors. The structure of PYCR1 complexed withl‐pipecolate and NADH supports the hypothesis that PYCR1 has an alternative function in lysine metabolism.

Biochemistry & Molecular Biology↗