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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 451 records · Page 25
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Structure of the E. coli agmatinase, SPEB

Agmatine amidinohydrolase, or agmatinase, catalyzes the conversion of agmatine to putrescine and urea. This enzyme is found broadly across kingdoms of life and plays a critical role in polyamine biosynthesis and the regulation of agmatine concentrations. Here we describe the high-resolution X-ray crystal structure of the E . coli agmatinase, SPEB. The data showed a relatively high degree of pseudomerohedral twinning, was ultimately indexed in the P 3 1 space group and led to a final model with eighteen chains, corresponding to three full hexamers in the asymmetric unit. There was a solvent content of 38.5% and refined R/R free values of 0.166/0.216. The protein has the conserved fold characteristic of the agmatine ureohydrolase family and displayed a high degree of structural similarity among individual protomers. Two distinct peaks of electron density were observed in the active site of most of the eighteen chains of SPEB. As the activity of this protein is known to be dependent upon manganese and the fold is similar to other dinuclear metallohydrolases, these peaks were modeled as manganese ions. The orientation of the conserved active site residues, in particular those amino acids that participate in binding the metal ions and a pair of acidic residues (D153 and E274 in SPEB) that play a role in catalysis, are similar to other agmatinase and arginase enzymes and is consistent with a hydrolytic mechanism that proceeds via a metal-activated hydroxide ion.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2000

NASA Lessons Learned from Space Lubricated Mechanisms

This document reviews the lessons learned from short-life and long life lubricated space mechanisms. A short-life lubricated mechanisms complete their life test qualification requirements after a few cycles. The mechanisms include the hinges, motors and bearings for deployment, release mechanisms, latches, release springs and support shops. Performance testing can be difficult and expensive but must be accomplished. A long-life lubricated mechanisms requires up to 5 years of life testing, or 10 to 100 years of successful flight. The long-life mechanisms include reaction wheels, momentum wheels, antenna gimbals, solar array drives, gyros and despin mechanisms. Several instances of how a mechanisms failed either in test, or in space use, and the lessons learned from these failures are reviewed. The effect of the movement away from CFC-113 cleaning solvent to ODC (Ozone-Depleting Chemical) -free is reviewed, and some of the alternatives are discussed.

Predmore, Roamer E.↗
NASA NTRS2007

DNA Recombinase Proteins, their Function and Structure in the Active Form, a Computational Study

Homologous recombination is a crucial sequence of reactions in all cells for the repair of double strand DNA (dsDNA) breaks. While it was traditionally considered as a means for generating genetic diversity, it is now known to be essential for restart of collapsed replication forks that have met a lesion on the DNA template (Cox et al., 2000). The central stage of this process requires the presence of the DNA recombinase protein, RecA in bacteria, RadA in archaea, or Rad51 in eukaryotes, which leads to an ATP-mediated DNA strand-exchange process. Despite many years of intense study, some aspects of the biochemical mechanism, and structure of the active form of recombinase proteins are not well understood. Our theoretical study is an attempt to shed light on the main structural and mechanistic issues encountered on the RecA of the e-coli, the RecA of the extremely radio resistant Deinococcus Radiodurans (promoting an inverse DNA strand-exchange repair), and the homolog human Rad51. The conformational changes are analyzed for the naked enzymes, and when they are linked to ATP and ADP. The average structures are determined over 2ns time scale of Langevian dynamics using a collision frequency of 1.0 ps(sup -1). The systems are inserted in an octahedron periodic box with a 10 Angstrom buffer of water molecules explicitly described by the TIP3P model. The corresponding binding free energies are calculated in an implicit solvent using the Poisson-Boltzmann solvent accessible surface area, MM-PBSA model. The role of the ATP is not only in stabilizing the interaction RecA-DNA, but its hydrolysis is required to allow the DNA strand-exchange to proceed. Furthermore, we extended our study, using the hybrid QM/MM method, on the mechanism of this chemical process. All the calculations were performed using the commercial code Amber 9.

Carra, Claudio↗
DOE OSTI2012

Combining H/D exchange mass spectroscopy and computational docking reveals extended DNA-binding surface on uracil-DNA glycosylase

X-ray crystallography provides excellent structural data on protein–DNA interfaces, but crystallographic complexes typically contain only small fragments of large DNA molecules. We present a new approach that can use longer DNA substrates and reveal new protein–DNA interactions even in extensively studied systems. Our approach combines rigid-body computational docking with hydrogen/ deuterium exchange mass spectrometry (DXMS). DXMS identifies solvent-exposed protein surfaces; docking is used to create a 3-dimensional model of the protein–DNA interaction. We investigated the enzyme uracil-DNA glycosylase (UNG), which detects and cleaves uracil from DNA. UNG was incubated with a 30 bp DNA fragment containing a single uracil, giving the complex with the abasic DNA product. Compared with free UNG, the UNG– DNA complex showed increased solvent protection at the UNG active site and at two regions outside the active site: residues 210–220 and 251–264. Computational docking also identified these two DNA-binding surfaces, but neither shows DNA contact in UNG–DNA crystallographic structures. Our results can be explained by separation of the two DNA strands on one side of the active site. These non-sequence-specific DNA-binding surfaces may aid local uracil search, contribute to binding the abasic DNA product and help present the DNA product to APE-1, the next enzyme on the DNA-repair pathway.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

Exceptional ion rejection ability of directional solvent for non-membrane desalination

The recently demonstrated directional solvent extraction (DSE) is promising for very low temperature, membrane-free water desalination. In this paper, we combine atomistic simulations and experimental validation to demonstrate that the currently used directional solvent, decanoic acid, can reject all major salt ions in seawater, with very high rejection rates. The salinities of the DSE recovered water show that ion rejection rates are ∼98%–99%—similar to those of the best reverse osmosis membranes. Our test also shows that the DSE process can desalt seawater to produce fresh water that meets drinking water standards.

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

Molecular Level Understanding of the Free Energy Landscape in Early Stages of Metal-Organic Framework Nucleation

The assembly mechanism of hierarchical materials controlled by the choice of solvent and presence of spectator ions. In this paper, we use enhanced sampling molecular dynamics methods to investigate these effects on the configurational landscape of metal-linker interactions in the early stages of synthesis, using MIL-101(Cr) as a prototypical example. Microsecond-long well-tempered metadynamics (WTmetaD) uncover a complex free energy structural landscape, with distinct crystal (C) and non-crystal (NC) like configurations and their equilibrium population. In presence of ions (Na+, F-), we observe a complex effect on the crystallinity of secondary building units (SBUs), by encouraging/suppressing salt bridges between C configurations and consequently controlling the percentage of defects. Solvent effects are assessed by introducing N, N-dimethylformamide (DMF) instead of water, where SBU adducts are appreciably more stable and compact. These results shed light on how solvent nature and ionic strength impact the free energy of nucleation phenomena that ultimately control materials synthesis and defect formation. The work described in this publication was supported by the US Department of Energy (DOE), Office of Science, Office of Basic Energy Sciences and performed at Pacific Northwest National Laboratory (PNNL). The authors acknowledge the use of the UCL Legion High Performance Computing Facility (Legion @ UCL) and associated support services in the completion of this work. This research used resources of the National Energy Research Scientific Computing Centre, a DOE Office of Science User Facility. Battelle operates PNNL for DOE under Contract DE-AC05-76RL01830.

Kollias, Loukas↗
DOE OSTI2022

Surfactant-free syntheses and pair distribution function analysis of osmium nanoparticles

A surfactant-free synthesis of precious metal nanoparticles (NPs) performed in alkaline low-boiling-point solvents has been recently reported. Monoalcohols are here investigated as solvents and reducing agents to obtain colloidal Os nanoparticles by using low-temperature (<100 °C) surfactant-free syntheses. The effect of the precursor (OsCl 3 or H 2 OsCl 6 ), precursor concentration (up to 100 mM), solvent (methanol or ethanol), presence or absence of a base (NaOH), and addition of water (0 to 100 vol %) on the resulting nanomaterials is discussed. It is found that no base is required to obtain Os nanoparticles as opposed to the case of Pt or Ir NPs. The robustness of the synthesis for a precursor concentration up to 100 mM allows for the performance of X-ray total scattering with pair distribution function (PDF) analysis, which shows that 1–2 nm hexagonal close packed (hcp) NPs are formed from chain-like [OsO x Cl y ] complexes.

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

Electrolyte Organization Leads to Potential-Dependence in Thermochemical Catalysis of Nonpolar Reactions

Electrochemical polarization is now known to play a key role in thermochemical catalysis at solid–liquid interfaces. However, existing frameworks cannot account for why even nonpolar, nonfaradaic reactions are sensitive to interfacial polarization. In order to uncover the molecular basis of this phenomenon, we herein study the potential-dependent reaction kinetics of ethylene and trans-2-butene hydrogenation at Pt–liquid interfaces. Measurements were performed in aqueous and ortho-difluorobenzene (o-DFB) solutions, spontaneously polarizing the Pt–liquid interfaces by, respectively, varying the pH or dissolving distinct metallocene redox buffers into solution. Here, we find that at comparable mechanistic regimes, the rates of both ethylene and trans-2-butene hydrogenation are maximized near the same electrochemical potential, E. Moreover, the potential-dependence, defined as $\frac{∂ln 𝑟}{∂𝐸}$, of trans-2-butene hydrogenation is approximately 2.2× greater than that of ethylene hydrogenation across the full potential range studied. These observations are all consistent with a model in which polarization of the Pt surface away from the local potential of zero free charge (E PZFC ) induces electrostatic organization of the polar solvent and charged ions near the interface, which impedes olefin adsorption and surface reaction because these surface reactions induce electrolyte displacement. Accordingly, interfacial polarization alters the free energy landscape and thus the rate of nonpolar heterogeneous catalysis by controlling the degree of electrostatic organization of polar and charged spectators at the interface, which do not in general need to be specifically chemisorbed onto the surface but could simply be close enough to the surface to be perturbed by the olefin adsorption. These results point toward electrochemical design handles, namely, the electrolyte, catalyst potential, and local E PZFC of the catalyst, with which to tune interfacial catalysis of thermochemical organic transformations.

adsorption↗
NASA NTRS1995

A simulated RTM process for fabricating polyimide (AMB-21) carbon fiber composites

An experimental polyimide matrix, AMB-21 - supplied by NASA/LeRC, was especially formulated to be non-carcinogenic. It was also expected to be amenable to a Resin Transfer Molding Process (RTM). AMB-21 is a solid at room temperature and must be heated to a very high temperature to obtain a fluid state. However, even after heating it to a realistic high temperature, it was found to be too viscous for use in a RTM process. As a result, a promising approach was experimented leading to the introduction of the resin into a solvent solution in order to obtain a viscosity suitable for RTM. A mixture of methanol and tetrahydroferone was found to be a suitable solvent mixture. The matrix solution was introduced into carbon-fiber preform using two techniques: (1) injection of matrix into a Resin Transfer Mold after positioning the preform into the 'mold cavity', and (2) infiltration of matrix into the preform using the 'autoclave through-the-thickness transfer process'. After completing the resin transfer (infiltration) process, the 'filled' preform was heated to 300 F for one hour to reduce the solvent content. The temperature was then increased to 400 F under a vacuum to complete the solvent evaporation and to remove volatile products of the polyimide imidization. The impregnated preform was removed from the mold and press-cured at 200 psi and 600 FF for two hours. The resulting panel was found to be of reasonably good quality. This observation was based on the results obtained from short beam shear strength (700-8000 psi) tests and microscopic examination of the cross-section indicating a very low level of porosity. Further, the flash around the molded panels from the compression molding was free of porosity indicating the removal of volatiles, solvents, and other imidization products. Based on these studies, a new RTM mold containing a diaphragm capable of applying 200 psi at 600 F has been designed and constructed with the expectation that it will allow the incorporation of all of the above processing steps, including the consolidation with the preform in the mold cavity. Moreover, the new diaphragm design will enable to process larger preform panels. Processing studies with the diaphragm mold are being initiated.

Avva, V. Sarma↗
DOE OSTI2023

Assessing Implicit and Explicit Polarizable Solvation Models for Nuclear–Electronic Orbital Systems: Quantum Proton Polarization and Solvation Energetics

Accurate simulations of many chemical processes require the inclusion of both nuclear quantum effects and a solvent environment. The nuclear–electronic orbital (NEO) approach, which treats electrons and select nuclei quantum mechanically on the same level, combined with a polarizable continuum model (PCM) for the solvent environment, addresses this challenge in a computationally practical manner. In this work, the NEO-PCM approach is extended beyond the IEF-PCM (integral equation formalism PCM) and C-PCM (conductor PCM) approaches to the SS(V)PE (surface and simulation of volume polarization for electrostatics) and ddCOSMO (domain decomposed conductor-like screening model) approaches. IEF-PCM, SS(V)PE, C-PCM, and ddCOSMO all exhibit similar solvation energies as well as comparable nuclear polarization within the NEO framework. The calculations show that the nuclear density does not leak out of the molecular cavity because it is much more localized than the electronic density. Finally, the polarization of quantized protons is analyzed in both continuum solvent and explicit solvent environments described by the polarizable MB-pol model, illustrating the impact of specific hydrogen-bonding interactions captured only by explicit solvation. Furthermore, these calculations highlight the relationship among solvation formalism, nuclear polarization, and energetics.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2019

Microscopic Dynamics in an Ionic Liquid Augmented with Organic Solvents

We introduce the complex microscopic dynamics of 1-butyl-3-methyl-imidazolium bis(trifluromethylsulfonyl)imide, [Bmim + ][TFSI – ], ionic liquid mixed with organic solvents to improve its properties for energy storage applications. To probe the microscopic dynamics on different length and time scales, we have used different neutron scattering spectrometers for quasielastic neutron scattering measurements to compare the effects of solvation in several organic solvents with nearly the same dipole moment but broadly varying bulk diffusivity. The ionic liquid–solvent mixtures show a nanoscopic phase separation into an ionic liquid-rich and a solvent-rich phase, as revealed by the model-free dynamic susceptibility data and further corroborated by the cluster histogram analysis of molecular dynamics (MD) simulation. In both phases, we observe a long-range translational mobility of the [Bmim + ] cation, which scales with the bulk diffusivities of the organic solvents; this correlation becomes stronger in the solvent-rich phase. Furthermore, various localized motion modes of the [Bmim + ] cation are observed. A combination of neutron scattering and MD simulations reveals the parameters governing solvent-controlled diffusivity in an ionic liquid, which helps formulate new electrolytes optimized for effective energy storage devices.

25 ENERGY STORAGE↗
DOE OSTI2023

Solvent Induced Proton Polarization within the Nuclear–Electronic Orbital Framework

To explicitly account for nuclear quantum effects and solvent environments in simulations of chemical processes, the nuclear-electronic orbital approach is coupled with a polarizable continuum model (PCM). This NEO–PCM approach is used to explore the influence of solvation on nuclear polarization through applications to a water dimer and a set of protonated water tetramers. Nuclear polarization in these species is analyzed in terms of changes in proton density and oxygen–hydrogen bond length. Solvation is shown to enhance nuclear polarization with increasing dielectric constant. For the water dimer, the internal, hydrogen-bonded proton is shown to polarize more than the external, free proton. Moreover, proton quantization leads to greater solvent polarization through their mutual polarization. Furthermore, these calculations highlight the complex interplay among electronic, nuclear, and solvent polarization in chemical systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Theoretical analysis of co-solvent effect on the proton transfer reaction of glycine in a water–acetonitrile mixture

The co-solvent effect on the proton transfer reaction of glycine in a water–acetonitrile mixture was examined using the reference interaction-site model self-consistent field theory. The free energy profiles of the proton transfer reaction of glycine between the carboxyl oxygen and amino nitrogen were computed in a water–acetonitrile mixture solvent at various molar fractions. Two types of reactions, the intramolecular proton transfer and water-mediated proton transfer, were considered. In both types of the reactions, a similar tendency was observed. In the pure water solvent, the zwitterionic form, where the carboxyl oxygen is deprotonated while the amino nitrogen is protonated, is more stable than the neutral form. The reaction free energy is −10.6 kcal mol{sup −1}. On the other hand, in the pure acetonitrile solvent, glycine takes only the neutral form. The reaction free energy from the neutral to zwitterionic form gradually increases with increasing acetonitrile concentration, and in an equally mixed solvent, the zwitterionic and neutral forms are almost isoenergetic, with a difference of only 0.3 kcal mol{sup −1}. The free energy component analysis based on the thermodynamic cycle of the reaction also revealed that the free energy change of the neutral form is insensitive to the change of solvent environment but the zwitterionic form shows drastic changes. In particular, the excess chemical potential, one of the components of the solvation free energy, is dominant and contributes to the stabilization of the zwitterionic form.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Computation of Hydration Free Energies Using the Multiple Environment Single System Quantum Mechanical/Molecular Mechanical Method

A recently-developed MESS-E-QM/MM method (multiple-environment single-system quantum mechanical molecular/mechanical calculations with a Roothaan-step extrapolation) is applied to the computation of hydration free energies for the blind SAMPL4 test set and for twelve small molecules. First, free energy simulations are performed with classical molecular mechanics force field using fixed-geometry solute molecules and explicit TIP3P solvent, then the non-Boltzmann-Bennett method is employed to compute the QM/MM correction (QM/MM-NBB) to the molecular mechanical hydration free energies. For the SAMPL4 set, MESS-E-QM/MM-NBB corrections to the hydration free energy can be obtained 2 or 3 orders of magnitude faster than fully converged QM/MM-NBB corrections, and, on average, the hydration free energies predicted with MESS-E-QM/MM-NBB fall within 0.10–0.20 kcal/mol of full-converged QM/MM-NBB results. Here, out of five density functionals (BLYP, B3LYP, PBE0, M06-2X, and ωB97X-D), the BLYP functional is found to be most compatible with the TIP3P solvent model and yields the most accurate hydration free energies against experimental values for solute molecules included in this study.

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

Theoretical Investigation of Solvent Effects on the Hydrodeoxygenation of Propionic Acid over a Ni(111) Catalyst Model

The effect of two solvents, liquid water and 1,4-dioxane, has been studied from first principles on the hydrodeoxygenation of propionic acid over a Ni (111) catalyst surface model. A mean-field microkinetic model was developed to investigate these effects at a temperature of 473 K. Under all reaction conditions, a decarbonylation mechanism is favored significantly over a decarboxylation pathway. Although no significant solvent effects were observed on the decarbonylation rate, a substantial solvent stabilization of two key surface intermediates in the decarboxylation mechanism, CH 3 CCOO and CH 3 CHCOO, lead to a notable increase of the decarboxylation rate by two orders of magnitude in liquid water and by one order of magnitude in liquid 1,4-dioxane. Furthermore, a significant solvent stabilization of the transition state of C-H bond cleavage of the α-carbon of CH 3 CHCO, relative to the stabilization of the C-C bond cleavage of the α-carbon of CH 3 CHCO, leads to a change in dominant pathway in the liquid phase environments. Finally, a sensitivity analysis shows that the C-OH bond cleavage of propionic acid and C-C bond cleavage of the α-carbon of CH 3 CHCO are the most rate controlling states in the gas phase. In contrast, in solvents the dehydrogenation of CH 3 CHCO becomes the most influential step. This shift in rate controlling state is attributed to the solvent effect on the dehydrogenation of CH 3 CHCO, which is facilitated in aqueous phase. Altogether, it is likely that the investigated (111) facet of Ni is not active for the hydrodeoxygenation of propionic acid in neither the gas nor liquid phase and other Ni facets or phases must be responsible for the experimentally observed kinetics.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2017

Full atomistic reaction mechanism with kinetics for CO reduction on Cu(100) from ab initio molecular dynamics free-energy calculations at 298 K

Significance Converting CO 2 to fuels is of great interest nowadays. Copper (Cu) is the only metal that produces hydrocarbon products, making it of interest for learning the reaction mechanisms underlying the selectivity and activity of Cu catalysts. In this report, we examine the reaction mechanism of CO reduction on Cu(100) at pH 7 including explicitly the aqueous solvent with ab initio molecular metadynamics simulations (AIMμD) free-energy calculations, which we find to explain all experimental observations. We expect that this understanding will suggest how to modify the Cu catalyst or replace it with a new material to enhance production of just a single such product while reducing the energy requirements (overpotential).

36 MATERIALS SCIENCE↗
DOE OSTI2018

Towards High-Resolution Tissue Imaging Using Nanospray Desorption Electrospray Ionization Mass Spectrometry Coupled to Shear Force Microscopy

Constant mode ambient mass spectrometry imaging (MSI) of tissue sections with high lateral resolution of better than 10 μm was performed by combining shear force microscopy with nanospray desorption electrospray ionization (nano-DESI). Shear force microscopy enabled precise control of the distance between the sample and nano-DESI probe during MSI experiments and provided information on sample topography. Proof-of-concept experiments were performed using lung and brain tissue sections representing spongy and dense tissues, respectively. Topography images obtained using shear force microscopy were comparable to the results obtained using contact profilometry over the same region of the tissue section. Variations in tissue height were found to be dependent on the tissue type and were in the range of 0–5 μm for lung tissue and 0–3 μm for brain tissue sections. Ion images of phospholipids obtained in this study are in good agreement with literature data. Normalization of nano-DESI MSI images to the signal of the internal standard added to the extraction solvent allowed us to construct high-resolution ion images free of matrix effects. .

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2021

Solvent and Temperature Effects on Photoinduced Proton-Coupled Electron Transfer in the Marcus Inverted Region

Concerted proton-coupled electron transfer (PCET) in the Marcus inverted region was recently demonstrated. Understanding the requirements for such reactivity is fundamentally important and holds promise as a design principle for solar energy conversion systems. Herein, we investigate the solvent polarity and temperature dependence of photoinduced proton-coupled charge separation (CS) and charge recombination (CR) in anthracene–phenol–pyridine triads: 1 (10-(4-hydroxy-3-(4-methylpyridin-2-yl)benzyl)anthracene-9-carbonitrile) and 2 (10-(4-hydroxy-3-(4-methoxypyridin-2-yl)benzyl)anthracene-9-carbonitrile). Both the CS and CR rate constants increased with increasing polarity in acetonitrile:n-butyronitrile mixtures. The kinetics were semi-quantitatively analyzed where changes in dielectric and refractive index, and thus consequently changes in driving force (–ΔG°) and reorganization energy (λ), were accounted for. The results were further validated by fitting the temperature dependence, from 180 to 298 K, in n-butyronitrile. The analyses support previous computational work where transitions to proton vibrational excited states dominate the CR reaction with a distinct activation free energy (ΔG* CR ~ 140 meV). However, the solvent continuum model fails to accurately describe the changes in ΔG° and λ with temperature via changes in dielectric constant and refractive index. Satisfactory modeling was obtained using the results of a molecular solvent model, which predicts that λ decreases with temperature, opposite to that of the continuum model. To further assess the solvent polarity control in the inverted region, the reactions were studied in toluene. Nonpolar solvents decrease both ΔG° CR and λ, slowing CR into the nanosecond time regime for 2 in toluene at 298 K. This demonstrates how PCET in the inverted region may be controlled to potentially use proton-coupled CS states for efficient solar fuel production and photoredox catalysis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗