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At least 1,387 records · Page 77
All sourcesNASA NTRSDOE OSTI
NASA NTRS1986

Multistep modeling (MSM) of biomolecular structure application to the A-G mispair in the B-DNA environment

A multistep modeling procedure has been evolved to study the structural changes introduced by lesions in DNA. We report here the change in the structure of regular B-DNA geometry due to the incorporation of Ganti-Aanti mispair in place of a regular G-C pair, preserving the helix continuity. The energetics of the structure so obtained is compared with the Ganti-Asyn configuration under similar constrained conditions. We present the methodology adopted and discuss the results.

Non-NASA Center↗
NASA NTRS1995

A correlated ab initio study of linear carbon-chain radicals CnH (n = 2-7)

Linear carbon-chain radicals CnH for n = 2-7 have been studied with correlation consistent valence and core-valence basis sets and the coupled cluster method RCCSD(T). Equilibrium structures, rotational constants, and dipole moments are reported and compared with available experimental data. The ground state of the even-n series changes from 2 sigma+ to 2 pi as the chain is extended. For C4H, the 2 sigma+ state was found to lie only 72 cm-1 below the 2 pi state in the estimated complete basis set limit for valence correlation. The C2H- and C3H- anions have also been characterized.

NASA Discipline Exobiology↗
NASA NTRS1993

Point charge representation of multicenter multipole moments in calculation of electrostatic properties

Distributed Point Charge Models (PCM) for CO, (H2O)2, and HS-SH molecules have been computed from analytical expressions using multi-center multipole moments. The point charges (set of charges including both atomic and non-atomic positions) exactly reproduce both molecular and segmental multipole moments, thus constituting an accurate representation of the local anisotropy of electrostatic properties. In contrast to other known point charge models, PCM can be used to calculate not only intermolecular, but also intramolecular interactions. Comparison of these results with more accurate calculations demonstrated that PCM can correctly represent both weak and strong (intramolecular) interactions, thus indicating the merit of extending PCM to obtain improved potentials for molecular mechanics and molecular dynamics computational methods.

Non-NASA Center↗
NASA NTRS1999

Early events in the folding of an amphipathic peptide: A multinanosecond molecular dynamics study

Folding of the capped LQQLLQQLLQL peptide is investigated at the water-hexane interface by molecular dynamics simulations for 161.5 ns. Initially placed in the aqueous phase as a beta-strand, the peptide rapidly adsorbs to the interface, where it adopts an amphipathic conformation. The marginal presence of nonamphipathic structures throughout the complete trajectory indicates that the corresponding conformations are strongly disfavored at the interface. It is further suggestive that folding in an interfacial environment proceeds through a pathway of successive amphipathic intermediates. The energetic and entropic penalties involved in the conformational changes along this pathway markedly increase the folding time scales of LQQLLQQLLQL, explaining why the alpha-helix, the hypothesized lowest free energy structure for a sequence with a hydrophobic periodicity of 3.6, has not been reached yet. The formation of a type I beta-turn at the end of the simulation confirms the importance of such motifs as initiation sites allowing the peptide to coalesce towards a secondary structure. Proteins 1999;36:383-399. Copyright 1999 Wiley-Liss, Inc.

NASA Center ARC↗
NASA NTRS1998

A model of cell wall expansion based on thermodynamics of polymer networks

A theory of cell wall extension is proposed. It is shown that macroscopic properties of cell walls can be explained through the microscopic properties of interpenetrating networks of cellulose and hemicellulose. The qualitative conclusions of the theory agree with the existing experimental data. The dependence of the cell wall yield threshold on the secretion of the wall components is discussed.

NASA Discipline Plant Biology↗
NASA NTRS1995

DNA CTG triplet repeats involved in dynamic mutations of neurologically related gene sequences form stable duplexes

DNA triplet repeats, 5'-d(CTG)n and 5'-d(CAG)n, are present in genes which have been implicated in several neurodegenerative disorders. To investigate possible stable structures formed by these repeating sequences, we have examined d(CTG)n, d(CAG)n and d(CTG).d(CAG)n (n = 2 and 3) using NMR and UV optical spectroscopy. These studies reveal that single stranded (CTG)n (n > 2) forms stable, antiparallel helical duplexes, while the single stranded (CAG)n requires at least three repeating units to form a duplex. NMR and UV melting experiments show that the Tm increases in the order of [(CAG)3]2 < [(CTG)3]2 << (CAG)3.(CTG)3. The (CTG)3 duplex is stable and exhibits similar NMR spectra in solutions containing 0.1-4 M NaCl and at a pH range from 4.6 to 8.8. The (CTG)3 duplex, which contains multiple-T.T mismatches, displays many NMR spectral characteristics similar to those of B-form DNA. However, unique NOE and 1H-31P coupling patterns associated with the repetitive T.T mismatches in the CTG repeats are discerned. These results, in conjunction with recent in vitro studies suggest that longer CTG repeats may form hairpin structures, which can potentially cause interruption in replication, leading to dynamic expansion or deletion of triplet repeats.

NASA Discipline Exobiology↗
NASA NTRS1995

Finding the global minimum: a fuzzy end elimination implementation

The 'fuzzy end elimination theorem' (FEE) is a mathematically proven theorem that identifies rotameric states in proteins which are incompatible with the global minimum energy conformation. While implementing the FEE we noticed two different aspects that directly affected the final results at convergence. First, the identification of a single dead-ending rotameric state can trigger a 'domino effect' that initiates the identification of additional rotameric states which become dead-ending. A recursive check for dead-ending rotameric states is therefore necessary every time a dead-ending rotameric state is identified. It is shown that, if the recursive check is omitted, it is possible to miss the identification of some dead-ending rotameric states causing a premature termination of the elimination process. Second, we examined the effects of removing dead-ending rotameric states from further considerations at different moments of time. Two different methods of rotameric state removal were examined for an order dependence. In one case, each rotamer found to be incompatible with the global minimum energy conformation was removed immediately following its identification. In the other, dead-ending rotamers were marked for deletion but retained during the search, so that they influenced the evaluation of other rotameric states. When the search was completed, all marked rotamers were removed simultaneously. In addition, to expand further the usefulness of the FEE, a novel method is presented that allows for further reduction in the remaining set of conformations at the FEE convergence. In this method, called a tree-based search, each dead-ending pair of rotamers which does not lead to the direct removal of either rotameric state is used to reduce significantly the number of remaining conformations. In the future this method can also be expanded to triplet and quadruplet sets of rotameric states. We tested our implementation of the FEE by exhaustively searching ten protein segments and found that the FEE identified the global minimum every time. For each segment, the global minimum was exhaustively searched in two different environments: (i) the segments were extracted from the protein and exhaustively searched in the absence of the surrounding residues; (ii) the segments were exhaustively searched in the presence of the remaining residues fixed at crystal structure conformations. We also evaluated the performance of the method for accurately predicting side chain conformations. We examined the influence of factors such as type and accuracy of backbone template used, and the restrictions imposed by the choice of potential function, parameterization and rotamer database. Conclusions are drawn on these results and future prospects are given.

NASA Program Exobiology↗
NASA NTRS1994

Eddy current correction in volume-localized MR spectroscopy

The quality of volume-localized magnetic resonance spectroscopy is affected by eddy currents caused by gradient switching. Eddy currents can be reduced with improved gradient systems; however, it has been suggested that the distortion due to eddy currents can be compensated for during postprocessing with a single-frequency reference signal. The authors propose modifying current techniques for acquiring the single-frequency reference signal by using relaxation weighting to reduce interference from components that cannot be eliminated by digital filtering alone. Additional sequences with T1 or T2 weighting for reference signal acquisition are shown to have the same eddy current characteristics as the original signal without relaxation weighting. The authors also studied a new eddy current correction method that does not require a single-frequency reference signal. This method uses two free induction decays (FIDs) collected from the same volume with two sequences with opposite gradients. Phase errors caused by eddy currents are opposite in these two FIDs and can be canceled completely by combining the FIDs. These methods were tested in a phantom. Eddy current distortions were corrected, allowing quantitative measurement of structures such as the -CH = CH- component, which is otherwise undetectable.

NASA Discipline Musculoskeletal↗
NASA NTRS1993

Modeling study on the cleavage step of the self-splicing reaction in group I introns

A three-dimensional model of the Tetrahymena thermophila group I intron is used to further explore the catalytic mechanism of the transphosphorylation reaction of the cleavage step. Based on the coordinates of the catalytic core model proposed by Michel and Westhof (Michel, F., Westhof, E. J. Mol. Biol. 216, 585-610 (1990)), we first converted their ligation step model into a model of the cleavage step by the substitution of several bases and the removal of helix P9. Next, an attempt to place a trigonal bipyramidal transition state model in the active site revealed that this modified model for the cleavage step could not accommodate the transition state due to insufficient space. A lowering of P1 helix relative to surrounding helices provided the additional space required. Simultaneously, it provided a better starting geometry to model the molecular contacts proposed by Pyle et al. (Pyle, A. M., Murphy, F. L., Cech, T. R. Nature 358, 123-128. (1992)), based on mutational studies involving the J8/7 segment. Two hydrated Mg2+ complexes were placed in the active site of the ribozyme model, using the crystal structure of the functionally similar Klenow fragment (Beese, L.S., Steitz, T.A. EMBO J. 10, 25-33 (1991)) as a guide. The presence of two metal ions in the active site of the intron differs from previous models, which incorporate one metal ion in the catalytic site to fulfill the postulated roles of Mg2+ in catalysis. The reaction profile is simulated based on a trigonal bipyramidal transition state, and the role of the hydrated Mg2+ complexes in catalysis is further explored using molecular orbital calculations.

NASA Discipline Exobiology↗
NASA NTRS2005

High-resolution spectroscopy of H2SO4, HDSO4, and D2SO4 vapor in the region 1200-10,000 cm(-1)

The high-resolution (0.05 cm(-1)) spectra of gas-phase H2SO4, HDSO4, and D2SO4 were measured over the frequency region 1200-10,000 cm(-1) using Fourier-transform infrared spectroscopy. The increased resolution of this work compared with previous studies has lead to an improved vibrational analysis of H2SO4. This study has answered unresolved questions about combination bands and overlapping features from previous gas-phase spectroscopic studies of H2SO4 and marks the first experimental measurement of the nu8 and nu15 torsional vibrations in this molecule. This work leads to a brief discussion on vibrational mode mixing in sulfuric acid.

Deuterium/chemistry↗
NASA NTRS2012

Radiation Shielding Materials Containing Hydrogen, Boron, and Nitrogen: Systematic Computational and Experimental Study

The key objectives of this study are to investigate, both computationally and experimentally, which forms, compositions, and layerings of hydrogen, boron, and nitrogen containing materials will offer the greatest shielding in the most structurally robust combination against galactic cosmic radiation (GCR), secondary neutrons, and solar energetic particles (SEP). The objectives and expected significance of this research are to develop a space radiation shielding materials system that has high efficacy for shielding radiation and that also has high strength for load bearing primary structures. Such a materials system does not yet exist. The boron nitride nanotube (BNNT) can theoretically be processed into structural BNNT and used for load bearing structures. Furthermore, the BNNT can be incorporated into high hydrogen polymers and the combination used as matrix reinforcement for structural composites. BNNT's molecular structure is attractive for hydrogen storage and hydrogenation. There are two methods or techniques for introducing hydrogen into BNNT: (1) hydrogen storage in BNNT, and (2) hydrogenation of BNNT (hydrogenated BNNT). In the hydrogen storage method, nanotubes are favored to store hydrogen over particles and sheets because they have much larger surface areas and higher hydrogen binding energy. The carbon nanotube (CNT) and BNNT have been studied as potentially outstanding hydrogen storage materials since 1997. Our study of hydrogen storage in BNNT - as a function of temperature, pressure, and hydrogen gas concentration - will be performed with a hydrogen storage chamber equipped with a hydrogen generator. The second method of introducing hydrogen into BNNT is hydrogenation of BNNT, where hydrogen is covalently bonded onto boron, nitrogen, or both. Hydrogenation of BN and BNNT has been studied theoretically. Hyper-hydrogenated BNNT has been theoretically predicted with hydrogen coverage up to 100% of the individual atoms. This is a higher hydrogen content than possible with hydrogen storage; however, a systematic experimental hydrogenation study has not been reported. A combination of the two approaches may be explored to provide yet higher hydrogen content. The hydrogen containing BNNT produced in our study will be characterized for hydrogen content and thermal stability in simulated space service environments. These new materials systems will be tested for their radiation shielding effectiveness against high energy protons and high energy heavy ions at the HIMAC facility in Japan, or a comparable facility. These high energy particles simulate exposure to SEP and GCR environments. They will also be tested in the LaRC Neutron Exposure Laboratory for their neutron shielding effectiveness, an attribute that determines their capability to shield against the secondary neutrons found inside structures and on lunar and planetary surfaces. The potential significance is to produce a radiation protection enabling technology for future exploration missions. Crew on deep space human exploration missions greater than approximately 90 days cannot remain below current crew Permissible Exposure Limits without shielding and/or biological countermeasures. The intent of this research is to bring the Agency closer to extending space missions beyond the 90-day limit, with 1 year as a long-term goal. We are advocating a systems solution with a structural materials component. Our intent is to develop the best materials system for that materials component. In this Phase I study, we have shown, computationally, that hydrogen containing BNNT is effective for shielding against GCR, SEP, and neutrons over a wide range of energies. This is why we are focusing on hydrogen containing BNNT as an innovative advanced concept. In our future work, we plan to demonstrate, experimentally, that hydrogen, boron, and nitrogen based materials can provide mechanically strong, thermally stable, structural materials with effective radiation shielding against GCR, SEP, and neutrons.

Radiation↗
NASA NTRSDate not supplied

TECHNO-ECONOMIC ANALYSIS OF A CRYOGENIC FLUX CAPACITOR FOR GRID STORAGE

The Cryogenic Flux Capacitor (CFC) is a cold, dense fluid storage core with integrated design features that afford the designer flexibility and provide new possibilities for the storage and discharge of energy. The stored energy, in this case, is represented by hydrogen physically bonded within the nanoscale pores within the aerogel composite blanket material, and the process of bonding or debonding is governed by principles of physical adsorption (physisorption) and thermodynamics. The large surface area afforded by the nanoporous aerogel (~1,000 m2/g) allows for storage densities close to, or in some cases exceeding, that of normal boiling point liquids. Its performance easily exceeds what can be achieved via ambient temperature, high-pressure gas storage for an equivalent volume. CFC storage is predicted to be easily scalable, is constructed from readily available commercial materials, lends itself to a range of pressure applications, and is geometry insensitive.

Joshua Schmitt↗
DOE OSTI2023

Mechanistic insights to drive catalytic hydrogenation of formamide intermediates to methanol via deaminative hydrogenation

Amine-promoted hydrogenation of CO 2 to methanol typically proceeds via a formamide intermediate when amines are used as additives or if the hydrogenation is performed in carbon capture solvents. The catalysts used for the hydrogenation of the formamide intermediate dictate the selectivity of the products formed: 1) Deoxygenative hydrogenation (C–O bond cleavage) resulting in N-methylation of amine and deactivation of the solvent, 2) Deaminative hydrogenation (C–N bond cleavage) resulting in formation of methanol and regeneration of the solvent. To date, catalytic reductions of CO 2 with amine promoters suffer from poor selectively for methanol which we attribute to the limiting formamide intermediate, though to date, the conditions that favor C–N cleavage have yet to be fully understood. To better understand the reactivity of the formamide intermediates, a range of heterogenous catalysts were used to study the hydrogenation of formamide. Well-known gas phase CO 2 hydrogenation catalysts catalyze the hydrogenation of formamide to N-methyl product via C–O bond cleavage. However, the selectivity can be readily shifted to selective C–N bond cleavage by addition of an additive with sufficient basicity for both homogenous and heterogeneous catalytic systems. The base additive shifts the selectivity by deprotonating a hemiaminal intermediate formed in situ during the formamide hydrogenation. This prevents dehydration process leading to N-methylated product, which is a key capture solvent deactivation pathway that hinders amine use in carbon capture, utilization, and storage (CCUS). The findings from this study provide a roadmap on how to improve the selectivity of known heterogenous catalysts, enabling catalytic reduction of captured CO 2 to methanol.

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

Weakening the N–H Bonds of NH 3 Ligands: Triple Hydrogen-Atom Abstraction to Form a Chromium(V) Nitride

Weakening and cleaving N-H bonds is crucial for improving molecular ammonia oxidation catalysts. In this work, we report the synthesis and hydrogen atom abstraction chemistry of bis(ammonia) Cr porphyrin complexes Cr(TPP)(NH 3 ) 2 and Cr(TMP)(NH 3 ) 2 (TPP = 5,10,15,20-tetraphenyl-meso-porphyrin and TMP = 5,10,15,20-tetramesityl-meso-porphyrin) using bulky aryloxyl radicals. The triple hydrogen atom abstraction reaction results in the formation of Cr V (por)(≡N), with the nitride deriving from ammonia, as indicated by UV-Vis and FT-IR spectroscopy, and a single crystal structural determination of Cr(TPP)(≡N). Subsequent oxidation of this chromium(V)-nitrido complex results in the formation of Cr III (por), with scission of the Cr≡N bond. A computational analysis illustrates the progression from Cr II to Cr V and evaluates the energetics of abstracting hydrogen atoms from Cr II -NH 3 to generate Cr V ≡N. The formation and isolation of Cr V (por)(≡N) illustrates the stability of these species and the need to chemically activate the nitride moiety for atom transfer or N-N coupling reactivity.

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

Experimental and computational kinetics study of the liquid-phase hydrogenation of C=C and C=O bonds

Solvent effects on adsorption equilibrium and reaction kinetics are evaluated for hydrogenation reactions catalyzed by Pd/alumina in a series of different solvents. Three reactants – cyclohexene, benzene and benzaldehyde – and three solvents – n-heptane (HEP), methylcyclohexane (MCHA), decalin (DL) – have been investigated. Kinetic analysis of hydrogenation of cyclohexene reveals that hydrogen adsorbs on different sites from those where cyclohexene and the solvents adsorb; however, the presence of hydrogen on these separate sites affects the heats of adsorption of the hydrocarbons. When the solvent is a weakly interacting linear alkane (HEP), the rate determining step of the reaction is the first hydrogenation of adsorbed cyclohexene. Furthermore, this conclusion is supported by DFT calculations that show a higher enthalpy barrier for the first hydrogenation than for the second, while statistical thermodynamics analysis validates the physical significance of the entropy of adsorption parameters derived from the kinetic fitting of experimental data. By contrast, with solvents such as MCHA and DL, which interact more strongly with the metal surface and compete for active sites with the reactant and the surface intermediate, the rate limiting step seems to shift to the second hydrogenation step.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1960

Bonded and Sealed External Insulations for Liquid-Hydrogen-Fueled Rocket Tanks During Atmospheric Flight

Several currently available nonmetallic insulation materials that may be bonded onto liquid-hydrogen tanks and sealed against air penetration into the insulation have been investigated for application to rockets and spacecraft. Experimental data were obtained on the thermal conductivities of various materials in the cryogenic temperature range, as well as on the structural integrity and ablation characteristics of these materials at high temperatures occasioned by aerodynamic heating during atmospheric escape. Of the materials tested, commercial corkboard has the best overall properties for the specific requirements imposed during atmospheric flight of a high-acceleration rocket vehicle.

Gray, V. H.↗
DOE OSTI2024

Hydrogenation of calcite and change in chemical bonding at high pressure: Diamond formation above 100GPa

Synchrotron X-ray diffraction (XRD) and Raman spectroscopy in laser heated diamond anvil cells and first principles molecular dynamics (FPMD) calculations have been used to investigate the reactivity of calcite and molecular hydrogen (H 2 ) at high pressures up to 120 GPa. We find that hydrogen reacts with calcite starting below 0.5 GPa at room temperature forming chemical bonds with carbon and oxygen. This results in the unit cell volume expansion; the hydrogenation level is much higher for powdered samples. Single-crystal XRD measurements at 8–24 GPa reveal the presence of previously reported III, IIIb, and VI calcite phases; some crystallites show up to 4% expansion, which is consistent with the incorporation of ≤ 1 hydrogen atom per formula unit. At 40–102 GPa XRD patterns of hydrogenated calcite demonstrate broadened features consistent with the calcite VI structure with incorporated hydrogen atoms. Above 80 GPa, the C–O stretching mode of calcite splits suggesting a change in the coordination of C–O bonds. Laser heating at 110 GPa results in the formation of C–C bonds manifested in the crystallization of diamond recorded by in situ XRD at 300 K and 110 GPa and by Raman spectroscopy on recovered samples commenced with C 13 calcite. We explored several theoretical models, which show that incorporation of atomic hydrogen results in local distortions of CO 3 groups, formation of corner-shared C–O polyhedra, and chemical bonding of H to C and O, which leads to the lattice expansion and vibrational features consistent with the experiments. In conclusion, the experimental and theoretical results support recent reports on tetrahedral C coordination in high-pressure carbonate glasses and suggest a possible source of the origin of ultradeep diamonds.

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

Analysis of defects in In 2 O 3 :H synthesized in presence of water vapor and hydrogen gas mixture

Using hybrid functional-based density functional theory calculations, we analyze the structure and kinetics of defects formed in two competing synthesis routes to prepare hydrogen-doped In 2 O 3 films, using a hydrogen and oxygen gas mixture vs synthesis in the presence of water vapor. For both of these synthesis routes, we find that H + is the dominant defect species: when the Fermi level is close to the conduction band, H + has a lower formation energy than other intrinsic or extrinsic defects. Our results also suggest that water molecules spontaneously split into H + (which occupies octahedral voids) and OH – interstitials (which occupies vacant oxygen lattice sites or oxygen vacancies). From the analysis of the binding energies between these different defects, we conclude that these defects do not cluster and are most likely to stay spatially distributed throughout the films. In addition, the sum of formation energies of an oxygen (i.e., O$^{2–}_i$) and a H + interstitial is close to the formation energy of a OH – interstitial, meaning that water molecules are completely split into 2H + and O$^{2–}_i$ at the synthesis conditions. Further, in the presence of H 2 + O 2 gas mixture, oxygen interstitials occupy oxygen vacancies while hydrogen interstitials occupy vacant oxygen lattice sites and form bonds with lattice oxygens. Our analysis of the defect equilibria suggests that the hydrogen content in films synthesized in the presence of water vapor is higher than films synthesized in the presence of a hydrogen gas mixture. At high dopant concentrations, a hydrogen bond network is formed in the system and this leads to large distortions in the lattice.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗