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Results for “Hydrogen Bonding”

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 181 records · Page 10
All sourcesNASA NTRSDOE OSTI
NASA NTRS1975

Hydrogen interactions with metals

Review of the literature on the nature and extent of hydrogen interactions with metals and the role of hydrogen in metal failure. The classification of hydrogen-containing systems is discussed, including such categories as covalent hydrides, volatile hydrides, polymeric hydrides, and transition metal hydride complexes. The use of electronegativity as a correlating parameter in determining hydride type is evaluated. A detailed study is made of the thermodynamics of metal-hydrogen systems, touching upon such aspects as hydrogen solubility, the positions occupied by hydrogen atoms within the solvent metal lattice, the derivation of thermodynamic functions of solid solutions from solubility data, and the construction of statistical models for hydrogen-metal solutions. A number of theories of hydrogen-metal bonding are reviewed, including the rigid-band model, the screened-proton model, and an approach employing the augmented plane wave method to solve the one-electron energy band problem. Finally, the mechanism of hydrogen embrittlement is investigated on the basis of literature data concerning stress effects and the kinetics of hydrogen transport to critical sites.

Mclellan, R. B.↗
NASA NTRS1961

The Electrochemical Fluorination of Organosilicon Compounds

The electrochemical fluorination of tetramethylsilane, hexamethyl-disiloxane, diethyldichlorosilane, amyltrichlorosilane, and phenyltri-chlorosilane was conducted in an Inconel cell equipped with nickel electrodes. A potential of approximately 5.0 volts and a current of approximately 1.0 ampere were used for the electrolysis reaction. In all cases the fluorinations resulted in considerable scission of the carbon-silicon bonds yielding hydrogen and the various fluorinated decomposition products; no fluoroorganosilicon compounds were identified. The main decomposition products were silicon tetrafluoride, the corresponding fluorinated carbon compounds, and the various organofluorosilanes. It is suggested that this is due to the nucleophilic attack of the fluoride ion (or complex fluoride ion) on the carbon-silicon bond.

Seaver, Robert E.↗
NASA NTRS2000

Photochemistry Saturn's Atmosphere: Effects of an Influx of External Oxygen - 2

We use a one-dimensional diurnally averaged model of photochemistry and diffusion in Saturn's stratosphere to investigate the influence of extraplanetary debris on atmospheric chemistry. In particular, we consider the effects of an influx of oxygen from micrometeoroid ablation or from ring-particle diffusion; the contribution from cometary impacts, satellite debris, or ring vapor is deemed to be less important. The photochemical model results are compared directly with Infrared Space Observatory (ISO) observations to constrain the influx of extraplanetary oxygen to Saturn. From the ISO observations, we determine that the column densities of CO2 and H2O above 10 mbar in Saturn's atmosphere are (6.3 +/- 1) x 10(exp 14) and (1.4 +/- 0.4) x 10(exp 15)/ square cm, respectively; our models indicate that a globally averaged oxygen influx of (4+/-2) x 10(exp 6) O atoms /sq cm/s is required to explain these observations. Models with a locally enhanced influx of H20 operating over a small fraction of the projected area do not provide as good a fit to the ISO H2O observations. If volatile oxygen compounds comprise one-third to one-half of the exogenic source by mass, then Saturn is currently being bombarded with (3 +/- 2) x 10(exp -16) g/square cm/s of extraplanetary material. To reproduce the observed CO2/H2O ratio in Saturn's stratosphere, some of the exogenic oxygen must arrive in the form of a carbon-oxygen bonded species such as CO or CO2. An influx consistent with the composition of cometary ices fails to reproduce the high observed CO2/H2O ratio, suggesting that (i) the material has ices that are slightly more carbon-rich than is typical for comets, (ii) a contribution from an organic-rich component is required, or (iii) some of the hydrogen-oxygen bonded material is converted to carbon-oxygen bonded material without photochemistry (e.g., during the ablation process). We have also reanalyzed the 5-micron CO observations of Noll and Larson and determine that the CO lines are most sensitive to the 100- to 400-mbar column density for which we derive a range of (0.7-1.5) x 10(exp 17)/square cm; the CO observations do not allow us to distinguish between an external or internal source of CO on Saturn. If we assume that all the extraplanetary oxygen derives from a micrometeoroid source, then the unfocused dust flux at 9.5 AU must be (i) (1 +/- 0.7) x 10(exp -16) g/square cm/s if interstellar grains are the source of the external oxygen on Saturn, (ii) (4 +/- 3) x 10 (exp -17) g/ sq. cm./s if IDPs on randomly inclined, highly eccentric orbits (e.g., Halley-type comet grains) are the source of the external oxygen, or (iii) (2+/- 1.4) x 10(exp -18)/g/sq cm/s if IDPs on low inclination, low eccentricity orbits (e.g., Kuiper-belt grains) are the source of the external oxygen. These estimates can be used in combination with future Cassini dust detection data to determine the ultimate source of the dust at Saturn's distance from the Sun.

Moses, Julianne I.↗
NASA NTRS1994

Theoretical investigation of gas-surface interactions

The goal of this project was to develop computational tools for the calculation of the electronic structure of molecules containing heavy atoms, and to use these tools in the study of catalytic processes, with the overall objective of gaining an understanding of the catalytic process which could be used to design more efficient catalysts. The main catalytic system of interest was the combustion of hydrogen on platinum surfaces. Under this project, a flexible Dirac-Hartree-Fock (DHF) program has been developed, a code to calculate DHF correlation energies at the second-order Moeller-Plesset perturbation (PP2) level is almost complete, and code to include correlation at the MCSCF and MCSCF/MP2 level is planned. The tools so far developed have been validated and used to calibrate some more approximate methods, and applied to investigate the importance of relativistic effects in the bonding of hydrogen to platinum.

Dyall, Kenneth G.↗
NASA NTRS1994

Crystal structure of intercalated four-stranded d(C3T) at 1.4 angstroms resolution

The crystal structure of d(C3T), solved at 1.4 angstroms resolution, reveals that the molecule forms a four-stranded intercalated complex. It consists of two parallel-stranded duplexes, each of which is held together by cytosine-protonated cytosine base pairs. The two duplexes are intercalated with each other and have opposite strand orientation. The molecule has a flat, lath-like appearance, and the covalently bonded cytosines have a slow right-handed twist of 17.1 degrees. However, there is considerable asymmetry. On one of the flat sides, the phosphate groups are rotated away from the center of the molecule. They are held in this orientation by bridging water molecules that bind the NH of cytosine and a phosphate group of an opposite chain. There is also considerable microheterogeneity in the structure. The cytosine hemiprotonation occurs even at pH 7 where stable crystals form.

Non-NASA Center↗
NASA NTRS1989

Molecular modeling of calmodulin: a comparison with crystallographic data

Two methods of side-chain placement on a modeled protein have been examined. Two molecular models of calmodulin were constructed that differ in the treatment of side chains prior to optimization of the molecule. A virtual bond analysis program developed by Purisima and Scheraga was used to determine the backbone conformation based on 2.2 angstroms resolution C alpha coordinates for the molecules. In the first model, side chains were initially constructed in an extended conformation. In the second model, a conformational grid search technique was employed. Calcium ions were treated explicitly during energy optimization using CHARMM. The models are compared to a recently published refined crystal structure of calmodulin. The results indicate that the initial choices for side-chains, but also significant effects on the main-chain conformation and supersecondary structure. The conformational differences are discussed. Analysis of these and other methods makes possible the formulation of a methodology for more appropriate side-chain placement in modeled proteins.

NASA Discipline Exobiology↗
NASA NTRS1976

H2 molecules and the intercloud medium

The paper discusses expected column densities of H2 in the intercloud medium and the possible use of molecules as indicators of intercloud physical conditions. Molecule formation by the H(-) process and on graphite grains is treated, and it is shown that the Barlow-Silk hypothesis of a 1-eV semichemical hydrogen-graphite bond leads to a large enhancement of the intercloud molecule-formation rate. Rotational-excitation calculations are presented for both cloud and intercloud conditions which show, in agreement with Jura (1975), that the presently observed optically thin H2 absorption components are more likely to originate in cold clouds than in the intercloud medium.

Hill, J. K.↗
NASA NTRS1990

Electronic and molecular structure of carbon grains

Clusters of carbon atoms have been studied with large-scale ab initio calculations. Planar, single-sheet graphite fragments with 6 to 54 atoms were investigated, as well as the spherical C(sub 60) Buckminsterfullerene molecule. Polycyclic aromatic hydrocarbons (PAHs) have also been considered. Thermodynamic differences between diamond- and graphite-like grains have been studied in particular. Saturation of the peripheral bonds with hydrogen is found to provide a smooth and uniform convergence of the properties with increasing cluster size. For the graphite-like clusters the convergence to bulk values is much slower than for the three-dimensional complexes.

Almloef, Jan↗
NASA NTRS1998

Transient cavities in liquids and the nature of the hydrophobic effect

The size distributions of transient cavities in water and organic liquids, obtained from computer simulations, have provided a new means to analyze the nature of the hydrophobic effect and to evaluate the adequacy of different analytical models of this effect. The poor solubility of non-polar solutes in water is attributed to a low probability of finding in water cavities of atomic and molecular size. It has been shown that water applies more force per unit area of cavity surface than do hydrocarbon liquids. Models that successfully capture the main characteristics of the hydrophobic effect must at least include information about the density and the radial distribution of oxygen atoms in liquid water. One such model, quantitatively accurate for molecular solutes of arbitrary shape, is presented.

NASA Center ARC↗
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↗