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At least 19 records
All sourcesNASA NTRSDOE OSTI
NASA NTRS2019

Isotopologue Consistency of Semi-Empirically Computed InfraRed Line Lists and Further Improvement for Rare Isotopologues: CO2 and SO2 Case Studies.

The semi-empirical molecular rovibrational IR line lists, such as ExoMol, TheoReTs, and Ames, combine the experimental accuracy and theoretical power to reach better than 0.1 cm-1 accuracy for line positions and better than 80-90% agreement for line intensities. The quality of these existing semi-empirical IR lists allows further improvements of intensity and line positions for those unobserved minor isotopologues. This paper presents our new BTRHE (Best Theory + Reliable High-resolution Experiment) strategy implementation. For line intensity, the isotopologue consistency and the patterns of mass dependence in the Ames-296K SO2 and CO2 IR lists are quantitatively presented along the mass-inverse coordinates. The consistency and patterns are better than those in existing experimental data. The methodology proposed here can be used to identify inconsistencies, outliers, and mistakes in intensities, and help improve Effective Dipole Model (EDM) and molecular IR databases. We call for an experimental study on the 50006 and 60007 bands of CO2 628. For line position predictions, a simple approach combining the variational IR line lists with Effective Hamiltonian (EH) model may refine the effective rotational constants A0/B0/C0 and quartic centrifugal distortion constants of minor isotopologues. The prediction accuracy may be improved by two orders of magnitude, i.e. reaching 0-5 MHz prediction accuracy in the range of J<20-30, Ka<10-20, and 0.01-0.02 MHz accuracy for A0/B0/C0. Several important factors have been systematically investigated and discussed, e.g. convergence, uncertainties, higher order terms, fixing EH parameters, mass coordinates, etc. Amicrowave (MW) line set consisting of 644,636 strong transitions for all 30 isotopologues and corresponding refined EH(Ames) parameters are reported in the supplementary material. This approach may be easily extended to rovibrational bands, hot bands, and other molecular systems.

Xinchuan Huang↗
NASA NTRS1991

Effect of the rotational-vibrational excitation on molecular diameters

The kinetic molecular diameters of rotationally and vibrationally excited diatomic molecules and molecular ions are derived as functions of the rotational and vibrational quantum numbers of the molecules. Typical molecular diameters are studied in two cases: in low-temperature gas, where the molecular diameter is independent of the degree of rotational-vibrational excitation of the molecules, and in high-temperature gas, where the molecular diameter depends on the degree of rotational-vibrational excitation of the molecules. The rotational-vibrational excitation of molecules is shown to have a meaningful effect on the collisional properties of gases. The effect is stronger in gases of weakly-bound molecules.

Kang, S. H.↗
NASA NTRS2003

Comparison of mode estimation methods and application in molecular clock analysis

BACKGROUND: Distributions of time estimates in molecular clock studies are sometimes skewed or contain outliers. In those cases, the mode is a better estimator of the overall time of divergence than the mean or median. However, different methods are available for estimating the mode. We compared these methods in simulations to determine their strengths and weaknesses and further assessed their performance when applied to real data sets from a molecular clock study. RESULTS: We found that the half-range mode and robust parametric mode methods have a lower bias than other mode methods under a diversity of conditions. However, the half-range mode suffers from a relatively high variance and the robust parametric mode is more susceptible to bias by outliers. We determined that bootstrapping reduces the variance of both mode estimators. Application of the different methods to real data sets yielded results that were concordant with the simulations. CONCLUSION: Because the half-range mode is a simple and fast method, and produced less bias overall in our simulations, we recommend the bootstrapped version of it as a general-purpose mode estimator and suggest a bootstrap method for obtaining the standard error and 95% confidence interval of the mode.

Evolution, Molecular↗
NASA NTRS1993

Molecular dynamics of interface rupture

Several situations have been studied in which a fluid-vapor or fluid-fluid interface ruptures, using molecular dynamics simulations of 3000 to 20,000 Lennard-Jones molecules in three dimensions. The cases studied are the Rayleigh instability of a liquid thread, the burst of a liquid drop immersed in a second liquid undergoing shear, and the rupture of a liquid sheet in an extensional flow. The late stages of the rupture process involve the gradual withdrawal of molecules from a thinning neck, or the appearance and growth of holes in a sheet. In all cases, it is found that despite the small size of the systems studied, tens of angstroms, the dynamics is in at least qualitative accord with the behavior expected from continuum calculations, and in some cases the agreement is to within tens of percent. Remarkably, this agreement occurs even though the Eulerian velocity and stress fields are essentially unmeasurable - dominated by thermal noise. The limitations and prospects for such molecular simulation techniques are assessed.

Koplik, Joel↗
NASA NTRS1983

Resin characterization in cured graphite fiber reinforced composites using diffuse reflectance-FTIR

The feasibility of using diffuse reflectance in combination with Fourier transform infrared spectroscopy to obtain information on cured graphite fiber reinforced polymeric matrix resin composites was investigated. Several graphite/epoxy, polysulfone, and polyimide composites exposed to thermal or radiation environments were examined. An experimental polyimide-sulfone adhesive tape was also studied during processing. In each case, significant changes in resin molecular structure was observed due to environmental exposure. These changes in molecular structure were correlated with previously observed changes in material properties providing new insights into material behavior.

Young, P. R.↗
NASA NTRS2004

DNA in a Tunnel: A Comfy Spot for Recognition - or -The Structure of BsoBI Complexed with DNA. What can we Learn about Function via Structure Determination and how can this be Applied to Bone or Muscle Biology?

The structure and function of a biologically active molecule are related. To understand its function, it is necessary (but not always sufficient) to know the structure of the molecule. There are many ways of relating the molecular function with the structure. Mutation analysis can identify pertinent amino acids of an enzyme, or alternatively structure comparison of the of two similar molecules with different function may lead to understanding which parts are responsible for a functional aspect, or a series of "structural cartoons" - enzyme structure, enzyme plus substrate, enzyme with transition state analog, and enzyme with product - may give insight in the function of a molecule. As an example we will discuss the structure and function of the restriction enzyme BsoBI from Bacillus stearothemzophilus in complex with its cognate DNA. The enzyme forms a unique complex with DNA in that it completely encircles the DNA. The structure reveals the enzyme-DNA contacts, how the DNA is distorted compared with the canonical forms, and elegantly shows how two distinct DNA sequences can be recognized with the same efficiency. Based on the structure we may also propose a hypothesis how the enzymatic mechanism works. The knowledge gained thru studies such as this one can be used to alter the function by changing the molecular structure. Usually this is done by design of inhibitors specifically active against and fitting into an active site of the enzyme of choice. In the case of BsoBI one of the objectives of the study was to alter the enzyme specificity. In bone biology there are many candidates available for molecular study in order to explain, alter, or (temporarily) suspend activity. For example, the understanding of a pathway that negatively regulates bone formation may be a good target for drug design to stimulate bone formation and have good potential as the basis for new countermeasures against bone loss. In principle the same approach may aid muscle atrophy, radiation damage, immune response changes and other risks identified for long-duration Space travel.

vanderWoerd, Mark↗
NASA NTRS1973

Competition between charge exchange and chemical reaction - The D2/+/ + H system

Study of the special features of molecular charge exchange and its competition with chemical reaction in the case of the D2(+) + H system. The trajectory surface hopping (TSH) model proposed by Tully and Preston (1971) is used to study this competition for a number of reactions involving the above system. The diatomics-in-molecules zero-overlap approximation is used to calculate the three adiabatic surfaces - one triplet and two singlet - which are needed to describe this system. One of the significant results of this study is that the chemical reaction and charge exchange are strongly coupled. It is also found that the number of trajectories passing into the chemical regions of the three surfaces depends very strongly on the surface crossings.-

Preston, R. K.↗
NASA NTRS1971

Long-term aging of elastomers: Chemical stress relaxation of fluorosilicone rubber and other studies

Aerospace applications of elastomers are considered, including: propellant binders, bladder materials for liquid propellant expulsion systems, and fuel tank sealants for high-speed aircraft. A comprehensive molecular theory for mechanical properties of these materials has been developed but has only been tested experimentally in cases where chemical degradation processes are excluded. Hence, a study is being conducted to ascertain the nature, extent, and rate of chemical changes that take place in some elastomers of interest. Chemical changes that may take place in the fluorosilicone elastomer, LS 420, which is regarded as a fuel and high-temperature-resistant rubber are investigated. The kinetic analysis of the chemical stress relaxation and gel permeation chromatography studies comprise the major portion of the report.

Kalfayan, S. H.↗
NASA NTRS1991

A simulation of the collapse and fragmentation of cooling molecular clouds

The application of the Smoothed Particle Hydrodynamics method to the fragmentation of rotating cloud and disk systems is described, allowing for molecular cooling due to H2 and CO. A novel approach to solving Poisson's equation for disklike structures which exploits the multigrid algorithm is also described. Numerical studies are presented which investigate the evolution of both rotating clouds and Maclaurin disks, in each case with both an isothermal equation of state and with molecular cooling. The results establish the influence of molecular cooling on the fragmentation of molecular clouds. The isothermal sequences, if they fragment at all, do so into far fewer lumps than the cooling sequences. This is not due to a cooling instability as such, but rather to the reduced thermal support. One of the sequences shows a remarkable similarity to the W49A star-forming region.

Monaghan, Joe J.↗
NASA NTRS1988

Molecular dynamics study of ion capture from water by a model ionophore, tetraprotonated cryptand SC24

The molecular dynamics of chloride capture from water by the tetraprotonated cryptand SC24 has been studied for the cases of 19 distances between the criptand and the chloride. The chloride capture is found to be characterized by a rapid cooperative change in the conformation of the cryptand when the Cl(-) begins to enter the ligand and just as it encounters the energy barrier. The conformational transition is associated with a shift of three N-H bonds from the pure endo orientation, such that they point toward the chloride.

Owenson, Brian↗
NASA NTRS2000

Molecular Spectroscopy in Astrophysics: The Case of Polycyclic Aromatic Hydrocarbons

The role of molecular spectroscopy in astrophysics and astrochemistry is discussed in the context of the study of large, complex, carbon-bearing molecules, namely, Polycyclic Aromatic Hydrocarbons or PAHs. These molecular species are now thought to be widespread in the interstellar medium in their neutral and ionized forms. Identifying the carriers responsible for unidentified interstellar spectral bands will allow to derive important information on cosmic elemental abundances as well as information on the physical conditions (density, temperature) reigning in specific interstellar environments. These, in turn, are key elements for a correct understanding of the energetic mechanisms that govern the origin and the evolution of the interstellar medium. A multidisciplinary approach - combining astronomical observations with laboratory simulations and theoretical modeling - is required to address these complex issues. Laboratory spectra of several PAHs, isolated at low temperature in inert gas matrices or seeded in a supersonic jet expansion, are discussed here and compared to the astronomical spectra of reddened, early type, stars. The electronic spectroscopy of PAHs in the ultraviolet, visible, and near-infrared domains is reviewed and an assessment of the potential contribution of PAHs to the interstellar extinction in the ultraviolet and in the visible is discussed.

Salama, Farid↗
NASA NTRS1997

Formation of Carbon Nanotube Based Gears: Quantum Chemistry and Molecular Mechanics Study of the Electrophilic Addition of o-Benzyne to Fullerenes, Graphene, and Nanotubes

Considerable progress has been made in recent years in chemical functionalization of fullerene molecules. In some cases, the predominant reaction products are different from those obtained (using the same reactants) from polycyclic aromatic hydrocarbons (PAHs). One such example is the cycloaddition of o-benzyne to C60. It is well established that benzyne adds across one of the rings in naphthalene, anthracene and other PAHs forming the [2+4] cycloaddition product (benzobicyclo[2.2.2.]-octatriene with naphthalene and triptycene with anthracene). However, Hoke et al demonstrated that the only reaction path for o-benzyne with C60 leads to the [2+2] cycloaddition product in which benzyne adds across one of the interpentagonal bonds (forming a cyclobutene ring in the process). Either reaction product results in a loss of aromaticity and distortion of the PAH or fullerene substrate, and in a loss of strain in the benzyne. It is not clear, however, why different products are preferred in these cases. In the current paper, we consider the stability of benzyne-nanotube adducts and the ability of Brenner's potential energy model to describe the structure and stability of these adducts. The Brenner potential has been widely used for describing diamondoid and graphitic carbon. Recently it has also been used for molecular mechanics and molecular dynamics simulations of fullerenes and nanotubes. However, it has not been tested for the case of functionalized fullerenes (especially with highly strained geometries). We use the Brenner potential for our companion nanogear simulations and believe that it should be calibrated to insure that those simulations are physically reasonable. In the present work, Density Functional theory (DFT) calculations are used to determine the preferred geometric structures and energetics for this calibration. The DFT method is a kind of ab initio quantum chemistry method for determining the electronic structure of molecules. For a given basis set expansion, it is comparable in accuracy to the MP2 method (better than Hartree Fock, but less accurate than more extensive electron correlation methods such as MP4 or CCSD). However, for systems with large numbers of basis functions it more efficient than any other methods that include electron correlation effects. In this presentation we show the results of DFT calculations for the reaction of benzyne with naphthalene, C60, and nanotube models. We compare energies for [2+2] and [2+4] cycloaddition products. The preferred products for the naphthalene and C60 reactions have been determined by experiment and, thus, these cases serve as a validation of our quantum chemical approach. We also compare the DFT and Brenner potential results. Finally we can predict the likelihood of reaction between benzyne and nanotubes.

Jaffe, Richard↗
NASA NTRS1999

A New Probe of the Molecular Gas Content in Galaxies: Application to M101

Recent studies of nearby spiral galaxies suggest that photodissoiation regions (PDRS) are capable of producing much of the observed HI in galaxy disks. In that case, measurements of the observed HI column density and the far-ultraviolet (FUV) photon flux responsible for the photodissociation process provide a new probe of the volume density of the local underlying molecular hydrogen. We develop the method and apply it to the giant Scd spiral M101. The HI column density and amount of FUV emission have been measured for a sample of 35 candidate PDRs located throughout the disk of M101 using the Very Large Array and the Ultraviolet Imaging Telescope. We find that, after correction for the known gradient of metallicity in the Interstellar Medium (ISM) of M101 and for the extinction of the ultraviolet emission, molecular gas with a narrow range of density from 30-1000/ cubic cm is found near star-forming regions at all radii in the disk of M101 out to a distance of 12 seconds approximately equals 26 kpc, close to the photometric limit of R(sub 25) approximately equals 13.5 seconds. In this picture, the ISM is virtually all molecular in the inner parts of M101. The strong decrease of the HI column density in the inner disk of the galaxy at R(sub G) < 10 kpc is a consequence of a strong increase in the dust-to-gas ratio there, resulting in an increase of the H(sub 2) formation rate on grains and a corresponding disappearance of hydrogen in its atomic form.

Smith, Denise A.↗
NASA NTRS1997

Infrared Line Emission from Molecular Gas Heated by X-Rays and Energetic Electrons

"I propose to carry out a detailed study using infrared observations (and in some cases, optical and ultraviolet observations) of dense interstellar gas exposed to intense fluxes of X-rays and/or energetic electrons. This is undoubtedly the dominant source of line emission for clouds exposed to X-rays from active galactic nuclei, supernova shocks, or embedded X-ray sources (e.g., X-ray binaries), or to high-temperature or relativistic electrons in galaxy clusters, near powerful radio sources, or supernova remnants. Detailed physical and chemical models of such clouds will be used to analyze infrared observations of the Great Annihilator X-ray source in the Galactic Center, cD galaxies in massive cooling flows, and the nuclei of Seyfert galaxies which will be obtained with the Infrared Space Observatory (ISO), UV and optical observations of the Crab Nebula obtained with the Hubble Space Telescope, and ground-based near-infrared observations of Seyfert nuclei. Results from this work will also be of great relevance to observations obtained with the Submillimeter Wave Astronomical Satellite (SWAS). In the first year of funding of this proposal, my chief collaborators (D.J. Hollenbach and A.G.G.M. Tielens, both of NASA Ames Research Center) and I concentrated on completing our models of the physical conditions in, and the resulting line emission from, dense gas irradiated by X-rays. As noted in the original proposal, some important physical processes were not yet thoroughly incorporated into our models at the time of submission. We completed our modeling of the physical conditions and line emission for essentially the entire range of parameter space (five orders of magnitude in X-ray flux to gas density ratio) occupied by typical dense interstellar clouds in which the gas is mostly neutral and X-rays are important for the ionization, chemistry, and thermal balance.

Maloney, Philip R.↗
NASA NTRSDate not supplied

Effects of Simulated Microgravity and LINC-Complex on Chromosome 8 of Human Mammary Cells

Previously, human breast epithelial cells were studied under simulated microgravity to determine the role of the LINC-complex in maintaining nuclear morphology and gene expression. Data from that study was used in this project to understand how the LINC-complex influences gene expression at chromosome 8 under simulated microgravity. Differentially expressed genes found in clusters typically indicate a molecular relationship amongst them. Visual and data analyses (GO, pathways) identified 51 genes within clusters on chromosome 8 across various simulated microgravity conditions that did not share any molecular relationship. Additional results also determined that cells with a disrupted LINC-complex experienced more differential gene expression than the control, and that extended periods of simulated microgravity exacerbated differential gene expression in chromosome 8 of LINC-disrupted cells. These results suggest that the stressful simulated microgravity environment coupled with disrupted biological processes, such as in the case of the LINC-complex, can increase differential gene expression in chromosomes. Future studies where additional analyses are performed to further analyze gene expression of clusters under simulated microgravity could potentially elucidate the molecular relationship amongst affected genes.

Simulated microgravity↗
NASA NTRS1978

Study of diatomic molecules. 2: Intensities

The theory of perturbations, giving the diatomic effective Hamiltonian, is used for calculating actual molecular wave functions and intensity factors involved in transitions between states arising from Hund's coupling cases a,b, intermediate a-b, and c tendency. The Herman and Wallis corrections are derived, without any knowledge of the analytical expressions of the wave functions, and generalized to transitions between electronic states with whatever symmetry and multiplicity. A general method for studying perturbed intensities is presented using primarily modern spectroscopic numerical approaches. The method is used in the study of the ScO optical emission spectrum.

Femenias, J. L.↗
NASA NTRS1988

Studies of molecular-beam epitaxy growth of GaAs on porous Si substrates

GaAs has been grown on porous Si directly and on Si buffer layer-porous Si substrates by molecular-beam epitaxy. In the case of GaAs growth on porous Si, transmission electron microscopy (TEM) reveals that the dominant defects in GaAs layers grown on porous Si are microtwins and stacking faults, which originate from the GaAs/porous Si interface. GaAs is found to penetrate into the porous Si layers. By using a thin Si buffer layer (50 nm), GaAs penetration diminishes and the density of microtwins and stacking faults is largely reduced and localized at the GaAs/Si buffer interface. However, there is a high density of threading dislocations remaining. Both Si (100) aligned and four degree tilted substrates have been examined in this study. TEM results show no observable effect of the tilted substrates on the quality of the GaAs epitaxial layer.

Mii, Y. J.↗