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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 73 records · Page 4
All sourcesNASA NTRSDOE OSTI
NASA NTRS1993

Multipole correction of atomic monopole models of molecular charge distribution. I. Peptides

The defects in atomic monopole models of molecular charge distribution have been analyzed for several model-blocked peptides and compared with accurate quantum chemical values. The results indicate that the angular characteristics of the molecular electrostatic potential around functional groups capable of forming hydrogen bonds can be considerably distorted within various models relying upon isotropic atomic charges only. It is shown that these defects can be corrected by augmenting the atomic point charge models by cumulative atomic multipole moments (CAMMs). Alternatively, sets of off-center atomic point charges could be automatically derived from respective multipoles, providing approximately equivalent corrections. For the first time, correlated atomic multipoles have been calculated for N-acetyl, N'-methylamide-blocked derivatives of glycine, alanine, cysteine, threonine, leucine, lysine, and serine using the MP2 method. The role of the correlation effects in the peptide molecular charge distribution are discussed.

NASA Discipline Exobiology↗
NASA NTRS1995

Stable loop in the crystal structure of the intercalated four-stranded cytosine-rich metazoan telomere

In most metazoans, the telomeric cytosine-rich strand repeating sequence is d(TAACCC). The crystal structure of this sequence was solved to 1.9-A resolution. Four strands associate via the cytosine-containing parts to form a four-stranded intercalated structure held together by C.C+ hydrogen bonds. The base-paired strands are parallel to each other, and the two duplexes are intercalated into each other in opposite orientations. One TAA end forms a highly stabilized loop with the 5' thymine Hoogsteen-base-paired to the third adenine. The 5' end of this loop is in close proximity to the 3' end of one of the other intercalated cytosine strands. Instead of being entirely in a DNA duplex, this structure suggests the possibility of an alternative conformation for the cytosine-rich telomere strands.

NASA Discipline Exobiology↗
NASA NTRS1975

Spectra and structure of organophosphorus compounds. XII - Infrared and Raman spectra of /CH3/2PH and /CD3/2PH

The vibrational spectra of (CH3)2PH and (CD3)2PH have been studied and assignments made. In the infrared, the region between 4000 and 33 wavelength/cm was recorded for the gaseous and solid states, while Raman spectra from 3500 to 10 wavelength/cm in the gaseous, liquid and solid states were observed. There is some evidence of weak hydrogen bonding, based on the behavior of the phosphorus-hydrogen stretching and bending modes. There also appears to be considerable interaction between the methyl rocking and phosphorus-carbon stretching modes. The a double prime and a prime torsional modes appear to be accidentally degenerate at 182 and 142 wavelength/cm for the 'light' and 'heavy' compounds, respectively. This gives barriers of 2.14 and 2.30 kcal/mole, respectively.

Durig, J. R.↗
NASA NTRS1992

Concerted hydrogen atom exchange between three HF molecules

We have investigated the termolecular reaction involving concerted hydrogen exchange between three HF molecules, with particular emphasis on the effects of correlation at the various stationary points along the reaction. Using an extended basis, we have located the geometries of the stable hydrogen-bonded trimer, which is of C(sub 3h) symmetry, and the transition state for hydrogen exchange, which is of D(sub 3h) symmetry. The energies of the exchange reation were then evaluated at the correlated level, using a large atomic natural orbital basis and correlating all valence electrons. Several correlation treatments were used, namely, configration interaction with single and double excitations, coupled-pair functional, and coupled-cluster methods. We are thus able to measure the effect of accounting for size-extensivity. Zero-point corrections to the correlated level energetics were determined using analytic second derivative techniques at the SCF level. Our best calculations, which include the effects of connected triple excitations in the coupled-cluster procedure, indicate that the trimer is bound by 9 +/- 1 kcal/mol relative to three separate monomers, in excellent agreement with previous estimates. The barrier to concerted hydrogen exchange is 15 kcal/mol above the trimer, or only 4.7 kcal/mol above three separated monomers. Thus the barrier to hydrogen exchange between HF molecules via this termolecular process is very low.

Komornicki, Andrew↗
NASA NTRS1980

Modelling of DNA-protein recognition

Computer model-building procedures using stereochemical principles together with theoretical energy calculations appear to be, at this stage, the most promising route toward the elucidation of DNA-protein binding schemes and recognition principles. A review of models and bonding principles is conducted and approaches to modeling are considered, taking into account possible di-hydrogen-bonding schemes between a peptide and a base (or a base pair) of a double-stranded nucleic acid in the major groove, aspects of computer graphic modeling, and a search for isogeometric helices. The energetics of recognition complexes is discussed and several models for peptide DNA recognition are presented.

Rein, R.↗
NASA NTRS1992

Concerted hydrogen atom exchange between three HF molecules

The termolecular reaction involving concerted hydrogen-atom exchange between three HF molecules was investigated with particular attention given to the effects of correlation at the various stationary points along the reaction. Using large segmented Gaussian basis sets to locate the (HF)3 stationary points at the SCF level, the geometries of the stable hydrogen-bonded trimer, which is of C(3h) symmetry, were located, together with the transition state for hydrogen exchange, which is of D(3h) symmetry. Then, using a large atomic natural orbital basis and correlating all valence electrons, the energetics of the exchange reaction were evaluated at the correlated level.

Komornicki, Andrew↗
NASA NTRS1995

Proton affinity determinations and proton-bound dimer structure indications in C2 to C15, (alpha),(omega)-alkyldiamines

The 'kinetic method' was used to determine the proton affinity (PA) of a,coalkyldiamines from collision induced dissociation (CID) studies of protonated heterodimers. These PA values were consistently lower than those reported in the proton affinity scale. The apparent discrepancy was rationalized in terms of differences in the conformation of the protonated diamine monomers. The minimum energy species, formed by equilibrium proton transfer processes, have a cyclic conformation and the ion charge is shared by both amino-groups which are bridged by the proton. On the other hand, the species formed through dissociation of protonated dimers have a linear structure and the charge is localized on one of the amino-groups. Thus, the difference in the PA values obtained by both methods is a measure of the additional stability acquired by the protonated diamines through cyclization and charge delocalization. The major collision dissociation pathway of the protonated diamine monomers involved elimination of an ammonia moiety. Other reactions observed included loss of the second amino-group and several other bond cleavages. CID of the protonated dimers involved primarily formation of a protonated monomer through cleavage of the weaker hydrogen bond and subsequently loss of ammonia at higher collision energies. As observed from the CID studies, doubly charged ions were also formed from the diamines under conditions of the electrospray ionization.

Karpas, Z.↗
NASA NTRS2006

A Quasi-Laue Neutron Crystallographic Study of D-Xylose Isomerase

Hydrogen atom location and hydrogen bonding interaction determination are often critical to explain enzymatic mechanism. Whilst it is difficult to determine the position of hydrogen atoms using X-ray crystallography even with subatomic (less than 1.0 Angstrom) resolution data available, neutron crystallography provides an experimental tool to directly localise hydrogeddeuteriwn atoms in biological macromolecules at resolution of 1.5-2.0 Angstroms. Linearisation and isomerisation of xylose at the active site of D-xylose isomerase rely upon a complex hydrogen transfer. Neutron quasi-Laue data were collected on Streptomyces rubiginosus D-xylose isomerase crystal using the LADI instrument at ILL with the objective to provide insight into the enzymatic mechanism (Myles et al. 1998). The neutron structure unambiguously reveals the protonation state of His 53 in the active site, identifying the model for the enzymatic pathway.

Meilleur, Flora↗
NASA NTRS2007

Nanoparticles modified with multiple organic acids

Surface-modified nanoparticles of boehmite, and methods for preparing the same. Aluminum oxyhydroxide nanoparticles are surface modified by reaction with selected amounts of organic acids. In particular, the nanoparticle surface is modified by reactions with two or more different carboxylic acids, at least one of which is an organic carboxylic acid. The product is a surface modified boehmite nanoparticle that has an inorganic aluminum oxyhydroxide core, or part aluminum oxyhydroxide core and a surface-bonded organic shell. Organic carboxylic acids of this invention contain at least one carboxylic acid group and one carbon-hydrogen bond. One embodiment of this invention provides boehmite nanoparticles that have been surface modified with two or more acids one of which additional carries at least one reactive functional group. Another embodiment of this invention provides boehmite nanoparticles that have been surface modified with multiple acids one of which has molecular weight or average molecular weight greater than or equal to 500 Daltons. Yet, another embodiment of this invention provides boehmite nanoparticles that are surface modified with two or more acids one of which is hydrophobic in nature and has solubility in water of less than 15 by weight. The products of the methods of this invention have specific useful properties when used in mixture with liquids, as filler in solids, or as stand-alone entities.

Cook, Ronald Lee↗
NASA NTRS1994

Structure and stability of hydrous minerals at high pressure

The presence of even small amounts of hydrogen in the Earth's deep interior may have profound effects on mantle melting, rheology, and electrical conductivity. The recent discovery of a large class of high-pressure H-bearing silicates further underscores the potentially important role for hydrous minerals in the Earth's mantle. Hydrogen may also be a significant component of the Earth's core, as has been recently documented by studies of iron hydride at high pressure. In this study, we explore the role of H in crystal structures at high pressure through detailed Raman spectroscopic and x ray diffraction studies of hydrous minerals compressed in diamond anvil cells. Brucite, Mg(OH)2, has a simple structure and serves as an analogue for the more complex hydrous silicates. Over the past five years, this material has been studied at high pressure using shock-compression, powder x ray diffraction, infrared spectroscopy, Raman spectroscopy, and neutron diffraction. In addition, we have recently carried out single-crystal synchrotron x-ray diffraction on Mg(OH)2 and Raman spectroscopy on Mg(OD)2 at elevated pressure. From all these studies, an interesting picture of the crystal chemical behavior of this material at high pressure is beginning to emerge. Some of the primary conclusions are as follows: First, hydrogen bonding is enhanced by the application of pressure. Second, layered minerals which are elastically anisotropic at low pressure may not be so at high pressure. Furthermore, the brucite data place constraints on the effect of hydrogen on seismic velocities and density at very high pressure. Third, the stability of hydrous minerals may be enhanced at high P by subtle structural rearrangements that are difficult to detect using traditional probes and require detailed spectroscopic analyses. Finally, brucite appears to be unique in that it undergoes pressure-induced disordering that is confined solely to the H-containing layers of the structure.

Duffy, T. S.↗
NASA NTRS1990

Microwave spectra of van der Waals complexes of importance in planetary atmospheres

The Fourier-transform Fabry-Perot pulsed-molecular-beam microwave spectrometer at NIST was used to study the microwave spectra of a number of molecular dimers and trimers that may be present in planetary atmospheres. The weak van der Waals bonds associated with these species usually give rise to rotational-tunneling splittings in the microwave spectra. The microwave spectrum of the water dimer species was used to illustrate the complications that can arise in the study of the rotational spectra of these loosely bound species. In addition to the water dimer species, the microwave spectra of the following hydrogen-bonded and van der Waals complexes were studied: (CO2)2-H2O, CO2-(H2O)2, CO2-H2S, N2-H2O, CO-H2O, SO2-H2O, and O3-H2O.

Suenram, R. D.↗
NASA NTRS2002

Morphology and the Strength of Intermolecular Contact in Protein Crystals

The strengths of intermolecular contacts (macrobonds) in four lysozyme crystals were estimated based on the strengths of individual intermolecular interatomic interaction pairs. The periodic bond chain of these macrobonds accounts for the morphology of protein crystals as shown previously. Further in this paper, the surface area of contact, polar coordinate representation of contact site, Coulombic contribution on the macrobond strength, and the surface energy of the crystal have been evaluated. Comparing location of intermolecular contacts in different polymorphic crystal modifications, we show that these contacts can form a wide variety of patches on the molecular surface. The patches are located practically everywhere on this surface except for the concave active site. The contacts frequently include water molecules, with specific intermolecular hydrogen-bonds on the background of non-specific attractive interactions. The strengths of macrobonds are also compared to those of other protein complex systems. Making use of the contact strengths and taking into account bond hydration we also estimated crystal-water interfacial energies for different crystal faces.

Matsuura, Yoshiki↗
NASA NTRS2016

Titan as the Abode of Life

Titan is the only world we know other than Earth that has a liquid on its surface. It has a thick atmosphere composed of nitrogen and methane with a thick organic haze. There are lakes, rain, and clouds of methane and ethane. Here, we address the question of carbon-based life living in Titan liquids. Photochemically produced organics, particularly acetylene, in Titan's atmosphere could be a source of biological energy when reacted with atmospheric hydrogen. Light levels on the surface of Titan are more than adequate for photosynthesis but the biochemical limitations due to the few elements available in the environment may lead only to simple ecosystems that only consume atmospheric nutrients. Life on Titan may make use of the trace metals and other inorganic elements produced by meteorites as they ablate in the atmosphere. It is conceivable that H2O molecules on Titan could be used in a biochemistry that is rooted in hydrogen bonds in a way that metals are used in enzymes by life on Earth. Previous theoretical work has shown possible membrane structures in Titan liquids, azotosomes, composed of small organic nitrogen compounds, such as acrylonitrile. The search for a plausible information molecule for life in Titan liquids remains an open research topic - polyethers have been considered and shown to be insoluble at Titan temperatures. Possible search strategies for life on Titan include looking for unusual concentrations of certain molecules reflecting biological selection. Homochirality is a special and powerful example of such biology selection. Environmentally, a depletion of hydrogen in the lower atmosphere may be a sign of metabolism. A discovery of life in liquid methane and ethane would be our first compelling indication that the Universe is full of diverse and wondrous life forms.

H2O molecules on Titan↗
NASA NTRS1999

Tetragonal Lysozyme Interactions Studied by Site Directed Mutagenesis

A number of recent experimental and theoretical studies have indicated that tetragonal lysozyme crystal growth proceeds by the addition of aggregates, formed by reversible self association of the solute molecules in the bulk solution. Periodic bond chain and atomic force microscopy studies have indicated that the probable growth unit is at minimum a 43 tetramer, and most likely an octamer composed of two complete turns about the 43 axis. If these results are correct, then there are intermolecular interactions which are only formed in the solution and others only formed at the joining of the growth unit to the crystal surface. We have set out to study these interactions, and the correctness of this hypothesis, using site directed mutagenesis of specific amino acid residues involved in the different bonds. We had initially expressed wild type lysozyme in S. cervasiae with yields of approximately 5 mg/L, which were eventually raised to approximately 40 mg/L. We are now moving the expression to the Pichia system, with anticipated yields of 300 to (3)500 mg/L, comparable to what can be obtained from egg whites. An additional advantage of using recombinant protein is the greater genetic homogeneity of the material obtained and the absence of any other contaminating egg proteins. The first mutation experiments are TYR 23 (Registered) PHE or ALA and ASN 113 (Registered) ALA or ASP. Both TYR 23 and ASN 113 form part of the postulated dimerization intermolecular binding site which lead to the formation of the 43 helix. Tyrosine also participates in an intermolecular hydrogen bond with ARG 114. The results of these and subsequent experiments will be discussed.

Crawford, Lisa↗
NASA NTRS1998

Tetragonal Lysozyme Interactions Studied by Site Directed Mutagenesis

A number of recent experimental and theoretical studies have indicated that tetragonal lysozyme crystal growth proceeds by the addition of aggregates, formed by reversible self association of the solute molecules in the bulk'solution. Periodic bond chain and atomic force microscopy studies have indicated that the probable growth unit is at minimum a 43 tetramer, and most likely an octamer composed of two complete turns about the 4(sub 3) axis. If these results are correct, then there are intermolecular interactions which are only formed in the solution and others only formed at the joining of the growth unit to the crystal surface. We have set out to study these interactions, and the correctness of this hypothesis, using site directed mutagenesis of specific amino acid residues involved in the different bonds. We had initially expressed wild type lysozyme in S. cervasiae with yields of approximately 5 mg/L, which were eventually raised to approximately 40 mg/L. We are now moving the expression to the Pichia system, with anticipated yields of 300 to greater than 500 mg/L, comparable to what can be obtained from egg whites. An additional advantage of using recombinant protein is the greater genetic homogeneity of the material obtained and the absence of any other contaminating egg proteins. The first mutation experiments are TYR 23 yields PHE or ALA and ASN 113 yields ALA or ASP. Both TYR 23 and ASN 113 form part of the postulated dimerization intermolecular binding site which lead to the formation of the 4(sub 3) helix. Tyrosine also participates in an intermolecular hydrogen bond with ARG 114. The results of these and subsequent experiments will be discussed.

Crawford, Lisa↗
NASA NTRS2010

Water in the Oceanic Lithosphere: Salt Lake Crater Xenoliths, Oahu, Hawaii

Water can be present in nominally anhydrous minerals of peridotites in the form of hydrogen bonded to structural oxygen. Such water in the oceanic upper mantle could have a significant effect on its physical and chemical properties. However, the water content of the MORB source has been inferred indirectly from the compositions of basalts. Direct determinations on abyssal peridotites are scarce because they have been heavily hydrothermally altered. Here we present the first water analyses of minerals from spinel peridotite xenoliths of Salt Lake Crater, Oahu, Hawaii, which are exceptionally fresh. These peridotites are thought to represent fragments of the Pacific oceanic lithosphere that was refertilized by alkalic Hawaiian melts. A few have unradiogenic Os and radiogenic Hf isotopes and may be fragments of an ancient (~2 Ga) depleted and recycled lithosphere. Water contents in olivine (Ol), orthopyroxene (Opx), and clinopyroxene (Cpx) were determined by FTIR spectrometry. Preliminary H_{2}O contents show ranges of 8-10 ppm for Ol, 151-277 ppm for Opx, and 337-603 ppm for Cpx. Reconstructed bulk rock H_{2}O contents range from 88-131 ppm overlapping estimates for the MORB source. Water contents between Ol minerals of the same xenolith are heterogeneous and individual OH infrared bands vary within a mineral with lower 3230 cm^{-1} and higher 3650-3400 cm^{-1} band heights from core to edge. This observation suggests disturbance of the hydrogen in Ol likely occurring during xenolith entrainment to the surface. Pyroxene water contents are higher than most water contents in pyroxenes from continental peridotite xenoliths and higher than those of abyssal peridotites. Cpx water contents decrease with increasing degree of depletion (e.g. increasing Fo in Ol and Cr# in spinel) consistent with an incompatible behavior of water. However Cpx water contents also show a positive correlation with LREE/HREE ratios and LREE concentrations consistent with refertilization. Opx water contents increase with increasing degree of depletion and decrease with LREE/HREE ratios which is inconsistent with the incompatible behavior of H. Calculated water contents of melts in equilibrium with Cpx or Opx range from 1.4 to 3.8 wt % which is higher than that of all Hawaiian lavas. Calculated melts in equilibrium with Cpx and Opx have variable but mostly high H_{2}O/Ce ratios (194 to 1146) consistent with those of rejuvenated stage lavas from Niihau and the South Arch volcanic field, but unlike the drier shield building stage tholeiites. Whether the high water contents recorded in Salt Lake Crater xenoliths were acquired before and/or during interaction of the oceanic lithosphere with the Hawaiian plume will be discussed.

Peslier, Anne H.↗