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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 109 records · Page 6
All sourcesNASA NTRSDOE OSTI
NASA NTRS1996

Kinetic and mechanistic analysis of nonenzymatic, template-directed oligoribonucleotide ligation

The role of divalent cations in the mechanism of pyrophosphate-activated, template-directed oligoribonucleotide ligation has been investigated. The dependence of the reaction rate on Mg2+ concentration suggests a kinetic scheme in which a Mg2+ ion must bind before ligation can proceed. Mn2+, Ca2+, Sr2+, and Ba2+ can also catalyze the reaction. Although Pb2+ and Zn2+ do not catalyze the reaction in the absence of other divalent ions, they significantly modulate the reaction rate when added in the presence of Mg2+, with Pb2+ stimulating the reaction (up to 65-fold) and Zn2+ inhibiting the reaction. The logarithm of the ligation rate increases linearly, with slope of 0.95, as a function of pH, indicating that the reaction involves a single critical deprotonation step. The ligation rates observed with the different divalent metal ion catalysts (Mn2+ > Mg2+ > Ca2+ > Sr2+ = Ba2+) vary inversely with the pKa values of their bound water molecules. The pH profile and these relative ligation rates suggest a mechanism in which a metal-bound hydroxide ion located near the ligation junction promotes catalysis, most likely by deprotonation of the hydroxl nucleophile. The effects of changing either the leaving group or the attacking hydroxyl, together with the large delta S(++) value for oligonucleotide ligation (about -20 eu), are consistent with an associative transition state.

Non-NASA Center↗
NASA NTRS2017

Modeling Chemical Reactions in Classical Molecular Dynamics Simulations

An algorithm capable of incorporating multi-step reaction mechanisms into atomistic molecular dynamics (MD) simulations using traditional fixed valence force fields is proposed and implemented within the framework of LAMMPS (Large-scale Atomic Molecular Massively Parallel Simulator). This extension, referred to as fix bond/react, enables bonding topology modifications during a running MD simulation using pre- and post-reaction bonding templates to carry out a pre-specified reaction. Candidate reactants are first identified by interatomic separation, followed by the application of a generalized topology matching algorithm to confirm they match the pre-reaction template. This is followed by a topology conversion to match the post-reaction template and a dynamic relaxation to minimize high energy configurations. Two case studies, the condensation polymerization of nylon 6,6 and the formation of a highly-crosslinked epoxy, are simulated to demonstrate the robustness, stability, and speed of the algorithm. Improvements which could increase its utility are discussed.

Jacob R Gissinger↗
DOE OSTI2026

Co-templating of polyoxoniobates and silicate/germanate trimer-rings in crystals and inorganic gels

Polyoxometalate (POM) supramolecular gels are a growing family of materials, both for understanding fundamental self-assembly and fabricating flexible monolithic materials that retain the function of metal oxides. Here, we exploited the pH-dependent speciation of polyoxoniobates (PONbs), targeting the formation of PONb-containing supramolecular gels that contain other low molecular weight components (silicate, germanate, phosphate, and carbonate). The introduction of gaseous CO 2 into aqueous hexaniobate solutions resulted in the formation of both new crystalline phases and highly transparent gels. The crystalline phases, formulated Cs 24 [Nb 7 O 22 (NbO(CO 3 ) 2 ) 9 (Si 3 O 9 )]·19.6H 2 O and Cs 21 Na 3 [Nb 7 O 22 (NbO(CO 3 ) 2 ) 9 (Ge 3 O 9 )]·33.6H 2 O are templated by a rare planar [X 3 O 9 ] 6− (X = Si, Ge) ring. Crystalline phases were not obtained with phosphate; instead, the gels contain a mixture of phosphate-centred PONbs and network-forming phosphate. POM speciation within the gels, physical properties, and assembly mechanisms were benchmarked by solution and solid-state nuclear magnetic resonance (NMR) spectroscopy, vibrational spectroscopies, small-angle X-ray scattering (SAXS), and thermogravimetry-mass spectroscopy. Optical analysis and dielectric behavior of the gels confirmed that they are highly transparent ionic and electronic conductors. The alkali and hydroxide concentration controls the formation of crystalline materials or supramolecular gels while maintaining the same network building blocks, providing a rare opportunity to describe the molecular-level structure of inorganic amorphous materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1987

Oligomerization of 3'-amino-3'deoxyguanosine-5'phosphorimidazolidate on a d(CpCpCpCpC) template

3'-Amino-3'-deoxyguanosine-5'-phosphorimidazolidate (ImpGNH2) oligomerizes more rapidly and regiospecifically than related nucleotide derivatives on a d(CpCpCpCpC) template. The greater nucleophilicity of the amino group leads to efficient oligomerization even when the structure of the double-helical complex formed by the template and the substrate is not optimal for reaction. The use of amine-containing analogues should permit us to develop models of potentially prebiotic polymerization reactions that cannot be studied easily using natural nucleotides.

Non-NASA Center↗
DOE OSTI2022

Discovery and molecular basis of subtype-selective cyclophilin inhibitors

Abstract Although cyclophilins are attractive targets for probing biology and therapeutic intervention, no subtype-selective cyclophilin inhibitors have been described. We discovered novel cyclophilin inhibitors from the in vitro selection of a DNA-templated library of 256,000 drug-like macrocycles for cyclophilin D (CypD) affinity. Iterated macrocycle engineering guided by ten X-ray co-crystal structures yielded potent and selective inhibitors (half maximal inhibitory concentration (IC 50 ) = 10 nM) that bind the active site of CypD and also make novel interactions with non-conserved residues in the S2 pocket, an adjacent exo-site. The resulting macrocycles inhibit CypD activity with 21- to >10,000-fold selectivity over other cyclophilins and inhibit mitochondrial permeability transition pore opening in isolated mitochondria. We further exploited S2 pocket interactions to develop the first cyclophilin E (CypE)-selective inhibitor, which forms a reversible covalent bond with a CypE S2 pocket lysine, and exhibits 30- to >4,000-fold selectivity over other cyclophilins. These findings reveal a strategy to generate isoform-selective small-molecule cyclophilin modulators, advancing their suitability as targets for biological investigation and therapeutic development.

Biochemistry & Molecular Biology↗
NASA NTRS1996

Template-Directed Ligation of Peptides to Oligonucleotides

Synthetic oligonucleotides and peptides have enjoyed a wide range of applications in both biology and chemistry. As a consequence, oligonucleotide-peptide conjugates have received considerable attention, most notably in the development of antisense constructs with improved pharmacological properties. In addition, oligonucleotide-peptide conjugates have been used as molecular tags, in the assembly of supramolecular arrays and in the construction of encoded combinatorial libraries. To make these chimeric molecules more accessible for a broad range of investigations, we sought to develop a facile method for joining fully deprotected oligonucleotides and peptides through a stable amide bond linkage. Furthermore, we wished to make this ligation reaction addressable, enabling one to direct the ligation of specific oligonucleotide and peptide components.To confer specificity and accelerate the rate of the reaction, the ligation process was designed to be dependent on the presence of a complementary oligonucleotide template.

Bruick, Richard K.↗
DOE OSTI2022

Superhydrophilicity of $α$-alumina surfaces results from tight binding of interfacial waters to specific aluminols

Understanding the microscopic driving force of water wetting is challenging and important for design of materials. The relations between structure, dynamics and hydrogen bonds of interfacial water can be investigated using molecular dynamics simulations. Here, contact angles at the alumina (0001) and ($11\bar{2}0$) surfaces are studied using both classical molecular dynamics simulations and experiments. To test the superhydrophilicity, the free energy cost of removing waters near the interfaces are calculated using the density fluctuations method. The strength of hydrogen bonds is determined by their lifetime and geometry. Both surfaces are superhydrophilic and the (0001) surface is more hydrophilic. Interactions between surfaces and interfacial waters promote a templating effect whereby the latter are aligned in a pattern that follows the underlying lattice of the surfaces. Translational and rotational dynamics of interfacial water molecules are slower than in bulk water. Hydrogen bonds between water and both surfaces are asymmetric, water-to-aluminol ones are stronger than aluminol-to-water ones. Molecular dynamics simulations eliminate the impacts of surface contamination when measuring contact angles and the results reveal the microscopic origin of the macroscopic superhydrophilicity of alumina surfaces: strong water-to-aluminol hydrogen bonds.

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

Recycling the Energy of Indoor Light: Highly Efficient Organic Photovoltaics via a Ternary Strategy

A ternary approach in organic photovoltaics (OPV) is simple and reliable to effectively tune the optical, electrical and morphological properties of the photoactive layer for high efficiency as well as long-term stability under 1 sun. However, there have been few papers reporting spectra and weak illumination compared to outdoor light. In this study, by using two compatible 16 structures, we demonstrate a simultaneous modulation of light absorption and molecular donor polymers (PM7 and PM7 D1) with slightly-different band gaps and similar chemical packing under ambient conditions, which resulted in efficient indoor OPVs exhibiting power conversion efficiency (PCE) over 20% under 1000 lux of warm white light-emitting diode (2900 K). From morphological analysis, we infer that PM7 serves to seed nucleation of PM7 D1 in the ternary blend, templating its crystallization and alignment along the PM7 backbone. Such templating effect leads to increased domain spacing and relative degree of crystallinity (rDoC) compared to those of each binary system. We further show that higher rDoC helps suppress both bimolecular and trap-assisted recombination of photogenerated charges in the ternary devices. As a result, the complementary absorption and synergistic molecular assembly of the two donor polymers enhance the short-circuit current density as to increase the average PCEs from 9.6 to 10.3% under 1 sun and from 18.7 to 20.0% under 1000 lux. We envision that our strategy of incorporating both a planar and a flexible donor polymer with similar chemical structures can be generally applicable to attain a high performance ternary OPV under both 1 sun and indoor light.

14 SOLAR ENERGY↗
NASA NTRS1999

Nonenzymatic oligomerization reactions on templates containing inosinic acid or diaminopurine nucleotide residues

The template-directed oligomerization of nucleoside-5'-phosphoro-2-methyl imidazolides on standard oligonucleotide templates has been studied extensively. Here, we describe experiments with templates in which inosinic acid (I) is substituted for guanylic acid, or 2,6-diaminopurine nucleotide (D) for adenylic acid. We find that the substitution of I for G in a template is strongly inhibitory and prevents any incorporation of C into internal positions in the oligomeric products of the reaction. The substitution of D for A, on the contrary, leads to increased incorporation of U into the products. We found no evidence for the template-directed facilitation of oligomerization of A or I through A-I base pairing. The significance of these results for prebiotic chemistry is discussed.

NASA Discipline Exobiology↗
NASA NTRSDate not supplied

REACTER 2.0: Quantum-Informed Reaction Constraints and Automated Interaction Typing

REACTER is a heuristic method for modeling chemical reactions in classical molecular dynamics simulations, implemented in LAMMPS as fix bond/react. The authors recently extended LAMMPS to support alphanumeric labels for atom types, bond types etc., which enables the pre- and post-reaction templates required by the REACTER protocol to be portable between different simulations and greatly simplifies the task of creating simulation-ready reaction templates. To further increase the generality of reaction templates, support for wildcard characters within atom types has been added, along with the automatic assignment of interaction types for new bonds, angles, etc. based on the involved atom types. In some cases, this feature can express a class of reactions with one pair of reaction templates, where previously dozens may have been required. Advanced reaction constraints have also been added, including an Arrhenius constraint to enforce an effective activation energy, a root-mean-square-deviation option for complex geometrical constraints, as well as a custom constraint that leverages LAMMPS’ powerful built-in variable framework. Other new features include variable support for various inputs (e.g., to allow reaction rates or cutoffs to be dependent on overall conversion), on-the-fly update of molecule IDs, and the ability to create new atoms positioned with respect to the reaction site. The new features are applied to modeling polymeric, thermosetting and composite materials, and advanced applications of the new reaction constraints are demonstrated. For example, REACTER is shown to accurately reproduce mechanically-induced bond breaking, as characterized by third-order DFT-based tight-binding (DFTB3) simulations, via a constraint on the total potential energy of the involved atoms.

polymer simulations↗
DOE OSTI2024

Structural Characterization and Dynamics of AdhE Ultrastructures from Clostridium thermocellum Show a Containment Strategy for Toxic Intermediates

Clostridium thermocellum, a cellulolytic thermophilic anaerobe, is considered by many to be a prime candidate for the realization of consolidated bioprocessing (CBP) and is known as an industry standard for biofuel production. C. thermocellum is among the best biomass degraders identified to date in nature and produces ethanol as one of its main products. Many studies have helped increase ethanol titers in this microbe; however, ethanol production using C. thermocellum is still not economically viable. Therefore, a better understanding of its ethanol synthesis pathway is required. The main pathway for ethanol production in C. thermocellum involves the bifunctional aldehyde-alcohol dehydrogenase (AdhE). To better understand the function of the C. thermocellum AdhE, we used cryo-electron microscopy (cryo-EM) to obtain a 3.28 A structure of the AdhE complex. This high-resolution structure, in combination with molecular dynamics simulations, provides insight into the substrate channeling of the toxic intermediate acetaldehyde, indicates the potential role of C. thermocellum AdhE to regulate activity and cofactor pools, and establishes a basis for future engineering studies. The containment strategy found in this enzyme offers a template that could be replicated in other systems where toxic intermediates need to be sequestered to increase the production of valuable biochemicals.

09 BIOMASS FUELS↗
DOE OSTI2024

Designing Ta C Virtual Substrates for Vertical Al x Ga 1 − x N Power Electronics Devices

Power electronics are critical for a sustainable energy future, playing a key role in electrification and integration of renewable energy sources into the grid. Advances in ultrawide band gap materials are needed to handle higher powers in smaller form factors while reducing electrical and thermal losses. High Al content Al x Ga 1 − x N is theoretically capable of meeting these demands, but its impact in power electronics has been severely restricted by a lack of substrates that can satisfy conductivity, lattice matching, and/or thermal expansion requirements. We demonstrate that electrically conductive Ta C can be used as a virtual substrate for Al x Ga 1 − x N heteroepitaxy. Scaleably sputtered Ta C grown on Al 2 O 3 , followed by high-temperature face-to-face annealing, produces a thin film Ta C template with an effective hexagonal lattice constant matched to Al 0.70 Ga 0.30 N . Annealing of the Ta C promotes recrystallization, significantly improving crystallinity and reducing crystalline defects from as-deposited columnar grains to a step-and-terrace surface morphology, enabling the subsequent growth of high-quality Al 0.70 Ga 0.30 N by molecular beam epitaxy. X-ray diffraction and scanning transmission electron microscopy confirm that the Al x Ga 1 − x N layer is heteroepitaxially aligned, strain-free, and lattice-matched, transitioning abruptly from Ta C to Al x Ga 1 − x N without intermediate phases. These results demonstrate Ta C virtual substrates as electrically conductive, lattice-matched, and thermally compatible templates for vertical Al x Ga 1 − x N devices that can meet the growing power needs of a sustainable energy future. Published by the American Physical Society 2024

36 MATERIALS SCIENCE↗
DOE OSTI2020

Anisotropic Dynamics and Mechanics of Macromolecular Crystals Containing Lattice-Patterned Polymer Networks

The mechanical and functional properties of many crystalline materials depend on cooperative changes in lattice arrangements in response to external perturbations. However, the flexibility and adaptiveness of crystalline materials are limited. Additionally, the bottom-up, molecular-level design of crystals with desired dynamic and mechanical properties at the macroscopic level remains a considerable challenge. To address these challenges, we had previously integrated mesoporous, cubic ferritin crystals with hydrogel networks, resulting in hybrid materials (polymer integrated crystals or PIX) which could undergo dramatic structural changes while maintaining crystalline periodicity and display efficient self-healing. Here, the dynamics and mechanics of these ferritin-PIX were devoid of directionality, which is an important attribute of many molecular and macroscopic materials/devices. In this study, we report that such directionality can be achieved through the use of ferritin crystals with anisotropic symmetries (rhombohedral or trigonal), which enable the templated formation of patterned hydrogel networks in crystallo. The resulting PIX expand and contract anisotropically without losing crystallinity, undergo prompt bending motions in response to stimuli, and self-heal efficiently, capturing some of the essential features of sophisticated biological devices like skeletal muscles.

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

Trapping of spermine, Kukoamine A, and polyamine toxin blockers in GluK2 kainate receptor channels

Abstract Kainate receptors (KARs) are a subtype of ionotropic glutamate receptor (iGluR) channels, a superfamily of ligand-gated ion channels which mediate the majority of excitatory neurotransmission in the central nervous system. KARs modulate neuronal circuits and plasticity during development and are implicated in neurological disorders, including epilepsy, depression, schizophrenia, anxiety, and autism. Calcium-permeable KARs undergo ion channel block, but the therapeutic potential of channel blockers remains underdeveloped, mainly due to limited structural knowledge. Here, we present closed-state structures of GluK2 KAR homotetramers in complex with ion channel blockers NpTx-8, PhTx-74, Kukoamine A, and spermine. We find that blockers reside inside the GluK2 ion channel pore, intracellular to the closed M3 helix bundle-crossing gate, with their hydrophobic heads filling the central cavity and positively charged polyamine tails spanning the selectivity filter. Molecular dynamics (MD) simulations of our structures illuminate interactions responsible for different affinity and binding poses of the blockers. Our structures elucidate the trapping mechanism of KAR channel block and provide a template for designing new blockers that can selectively target calcium-permeable KARs in neuropathologies.

Science & Technology - Other Topics↗
DOE OSTI2024

Buffer-layer-controlled nickeline vs zinc-blende/wurtzite-type MnTe growths on c -plane Al 2 O 3 substrates

In the recent past, MnTe has proven to be a crucial component of the intrinsic magnetic topological insulator (IMTI) family [MnTe] m [Bi2Te 3 ] n , which hosts a wide range of magneto-topological properties depending on the choice of m and n. However, bulk crystal growth allows only a few combinations of m and n for these IMTIs due to the strict limitations of the thermodynamic growth conditions. One way to overcome this challenge is to utilize atomic layer-by-layer molecular beam epitaxy (MBE) technique, which allows arbitrary sequences of [MnTe]m and [Bi 2 Te 3 ] n to be formed beyond the thermodynamic limit. For such MBE growth, finding optimal growth templates and conditions for the parent building block, MnTe, is a key requirement. Here, we report that two different hexagonal phases of MnTe - nickeline (NC) and zinc-blende/wurtzite (ZB-WZ) structures, with distinct in-plane lattice constants of 4.20 ± 0.04 Å and 4.39 ± 0.04 Å, respectively - can be selectively grown on c-plane Al 2 O 3 substrates using different buffer layers and growth temperatures. Moreover, we provide the first comparative studies of different MnTe phases using atomic-resolution scanning transmission electron microscopy and show that ZB and WZ-like stacking sequences can easily alternate between the two. Surprisingly, In 2 Se 3 buffer layer, despite its lattice constant (4.02 Å) being closer to that of the NC phase, fosters the ZB-WZ instead, whereas Bi 2 Te 3 , sharing the same lattice constant (4.39 Å) with the ZB-WZ phase, fosters the NC phase. Furthermore, these discoveries suggest that lattice matching is not always the most critical factor determining the preferred phase during epitaxial growth. Overall, this will deepen our understanding of epitaxial growth modes for chalcogenide materials and accelerate progress toward new IMTI phases as well as other magneto-topological applications.

36 MATERIALS SCIENCE↗
DOE OSTI2024

ezAlign: A Tool for Converting Coarse-Grained Molecular Dynamics Structures to Atomistic Resolution for Multiscale Modeling

Soft condensed matter is challenging to study due to the vast time and length scales that are necessary to accurately represent complex systems and capture their underlying physics. Multiscale simulations are necessary to study processes that have disparate time and/or length scales, which abound throughout biology and other complex systems. Herein we present ezAlign, an open-source software for converting coarse-grained molecular dynamics structures to atomistic representation, allowing multiscale modeling of biomolecular systems. The ezAlign v1.1 software package is publicly available for download at github.com/LLNL/ezAlign. Its underlying methodology is based on a simple alignment of an atomistic template molecule, followed by position-restraint energy minimization, which forces the atomistic molecule to adopt a conformation consistent with the coarse-grained molecule. The molecules are then combined, solvated, minimized, and equilibrated with position restraints. Validation of the process was conducted on a pure POPC membrane and compared with other popular methods to construct atomistic membranes. Additional examples, including surfactant self-assembly, membrane proteins, and more complex bacterial and human plasma membrane models, are also presented. By providing these examples, parameter files, code, and an easy-to-follow recipe to add new molecules, this work will aid future multiscale modeling efforts.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2026

Lattice-scale variations in viscosity are correlated with solution structure at mineral-water interfaces

At solid-liquid interfaces, the viscosity increases markedly from the bulk due to the collective interactions of ions and water molecules, influencing phenomena relevant to nanofluidics, colloidal dynamics, and electrochemistry. Here, in this study, we investigated dissipative forces at the boehmite-water interface using 3D atomic force microscopy. We observed an increase in interfacial solution viscosity, η, by 10-100-fold as the nanoprobe approached the surface in normal direction, with up to four oscillatory features showing average peaks of η/η bulk = 44-71. Moreover, the viscosity showed sub-nanometer variations within 0.5 nm from the interface, templated by the underlying crystal lattice and correlated with the interfacial solution structure. Beyond a near-wall region of approximately 1.2 nm, the dissipative response was comparable to that in bulk solution. Molecular dynamics simulations, along with statistical mechanical analyses, provided details on hydrodynamic structures near the interface. Specifically, the lattice-dependent dissipative responses are correlated with extensive hydrogen bonding by interfacial water molecules, which increased friction, particularly along the [001] direction. These results demonstrate how solution viscosity at mineral-water interfaces is anisotropic and correlated with the local solution structure, providing insights into the dynamics of nanocrystal attachment.

Viscosity↗