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GAuche-Ethyl Alcohol: Laboratory Assignments and Interstellar Identification
Ethyl alcohol (ethanol) is known to possess a pair of closely-spaced excited torsional substates (gauche +, gauche -) at an energy of approximately 57 K above the ground (trans) torsional substrate. We report an extended analysis of some gauch- - gauch+ Q branch (delta J=0) transitions witha three-substrate fixed frame axis method (FFAM) Hamilton.
The Detection of 6.9 µm Emission Features in the Infrared Spectra of IRAS 04296+3429, IRAS 05341+0852, IRAS 22272+5435: Evidence for the Presence of Hn-PAHs in Post AGB Stars
Polycyclic aromatic hydrocarbons (PAHs) are generally believed to be ubiquitous in space and responsible for numerous telltale interstellar infrared emission bands. In Sandford et al., (2013), we suggested that polycyclic aromatic hydrocarbons with excess hydrogenation at their periphery (Hn-PAHs) may be an important subclass of these molecules in some astrophysical environments. These molecules are candidates to explain objects with anomalously large 3.4 μm features, which are presumed to be associated with the aliphatic C—H stretching vibrations of the excess hydrogen. In that work, we suggest that for Hn-PAHs to be a viable candidate as the source for this 3.4 μm feature, we must also expect to observe methylene scissoring modes at 6.9 μm. In this work, we continue to develop the Hn-PAH hypothesis with a focus on the 6.9 μm feature. We also present some new observations of three post-asymptotic giant branch (post- AGB) objects with abnormally large 3.4 μm features, IRAS 04296+3429, IRAS 05341+0852, IRAS 22272+5435, in addition to one post-AGB object with normal PAH emissions, IRAS 20000+3239. These observations were made using the FORCAST instrument in grism mode on the Stratospheric Observatory for Infrared Astronomy (SOFIA) aircraft (Adams et al. 2010) and demonstrate the presence of a 6.9 μm feature for the three objects with abnormally large 3.4 μm features and no detectable 6.9 μm feature for the normal PAH emitter. These results are consistent with the hypothesis that Hn-PAHs are a possible source of these infrared emission bands.
The Nature of Insoluble Organic Matter in Sutter’s Mill and Murchison Carbonaceous Chondrites: Testing the Effect of X-ray Computed Tomography (XCT) and Exploring Parent Body Organic Molecular Evolution
This study analyzed samples of the Murchison and Sutter’s Mill carbonaceous chondrite meteorites in support of the future analysis of samples returned from the asteroid (10155) Bennu by the OSIRIS-REx (Origins, Spectral Interpretation, Resource Identification, and Security–Regolith Explorer) mission. Focusing specifically on the insoluble organic matter (IOM), this study establishes that a total of 1.3 g of bulk sample from a single chondritic meteorite is sufficient to obtain a wide range of cosmochemical information, including light element analysis (H, C, and N), isotopic analysis (D/H, 13 C/ 12 C, and 15 N/ 14 N), and X-ray fluorescence spectroscopy for major elemental abundances. IOM isolated from the bulk meteorite samples was analyzed by light element and isotopic analysis as described above, 1 H and 13 C solid-state nuclear magnetic resonance spectroscopy, Raman spectroscopy, and complete noble gas analyses (abundances and isotopes). The samples studied included a pair from Murchison (CM2), one of which had been irradiated with high-energy X-rays in the course of computed tomographic imaging. No differences between the irradiated and non-irradiated Murchison samples were observed in the many different chemical and spectroscopic analyses, indicating that any X-ray–derived sample damage is below levels of detection. Elemental, isotopic, and molecular spectroscopic data derived from IOM isolated from the Sutter’s Mill sample reveals evidence that this meteorite falls into the class of heated CM chondrites.
Neoplastic cell transformation by high-LET radiation - Molecular mechanisms
Quantitative data were collected on dose-response curves of cultured mouse-embryo cells (C3H10T1/2) irradiated with heavy ions of various charges and energies. Results suggests that two breaks formed on DNA within 80 A may cause cell transformation and that two DNA breaks formed within 20 A may be lethal. From results of experiments with restriction enzymes which produce DNA damages at specific sites, it was found that DNA double strand breaks are important primary lesions for radiogenic cell transformation and that blunt-ended double-strand breaks can form lethal as well as transformational damages due to misrepair or incomplete repair in the cell. The RBE-LET relationship for high-LET radiation is similar to that for HGPRT locus mutation, chromosomal deletion, and cell transformation, indicating that common lesions may be involved in these radiation effects.
The molecular cloud associated with NGC 7538
CO maps and preliminary H2S and H2CO data for the molecular cloud associated with NGC 7538 are used to compare the molecular distributions with those of ionized, neutral, and molecular hydrogen and dust. South of the H II regions is a ridge of high (C-13)O column density with cold, self-absorbed H I just beyond it. A dense clump within the ridge is found adjacent to the H II region in the southeast, and a lower density region of expanding gas is seen next to the H II region in the southwest. NGC 7538 is the first region which appears to show observational evidence for a molecular dissociation wave.
Candidate solar-type protostars in nearby molecular cloud cores
IRAS data have been used to examine the vicinity of nearly 100 dense clumps of molecular gas observed in lines of CO and NH3. More than one-third of these molecular cloud 'cores' contain infrared sources that appear to be newly formed, or forming, low mass stars. While about one-third of the infrared sources are associated with visible stars and have properties that resemble T Tauri stars, the remainder of the infrared sources have no optical counterparts and are probably embedded within the molecular cloud itself. These invisible sources lie close to the molecular cloud peaks and have cold, massive shells of material around them. Some of the cores without infrared sources have gas properties similar to those with embedded sources and so may be on the verge of gravitational collapse. The selection of the IRAS sample and its properties are described. The spectral energy distributions of the sources and their nature are discussed along with their physical properties, the properties of cores with and without infrared sources, and the time scale for the evolution of the sources.
Missing data, clade support and “reticulation”: the molecular systematics of Heliconius and related genera (Lepidoptera: Nymphalidae) re‐examined
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Sensitivity of Temperature Profiles Retrieved from Mars Global Surveyor Thermal Emission Spectrometer (MGS/TES) Observations to the GSFC Synthetic Mars Model Atmosphere
Part of the task of interpreting IR spectral features observed by MGS/TES due to surface minerals requires distinguishing those IR signatures from atmospheric signatures of gas and dust. Surface-atmosphere separation for MGS/TES depends on knowledge of the retrieved temperature profile. In turn, the temperature retrieval Erom the observed data depends on molecular parameters including 15 micron CO2 line shape or line intensities which contribute to defining the Mars synthetic radiative transfer model. Using a simple isothermal, homogeneous single layer model of Pinnock and Shine, we find the ratio of (the error in degrees Kelvin of the retrieved temperature profile) to (the percentage error in the absorption coefficient) (deg K/percent) to be 0.4 at 200K. This ratio at 150K and 250K is 0.2 and 0.6, respectively. A more refined model, incorporating observed MGS/TES retrieved temperature profiles, the TES instrumental resolution and the most recent molecular modelling, will yield an improved knowledge of this error sensitivity. We present results of such a sensitivity study to determine the dependence of temperature profiles inverted from MGS/TES on these and other molecular parameters. This work was supported in part by NASA's Mars Data Analysis Program.
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.
Mechanosensitive channels in bacteria as membrane tension reporters
The purpose of this short review is to discuss recent data on the molecular structure and mechanism of gating of MscL, a mechanosensitive channel of large conductance from Escherichia coli. MscL is the first isolated molecule shown to convert mechanical stress of the membrane into a simple response, the opening of a large aqueous pore. The functional complex appears to be a stable homo-pentamer of 15-kDa subunits, the gating transitions in which are driven by stretch forces conveyed through the lipid bilayer. We have measured the open probability of MscL and the kinetics of transitions as a function of membrane tension. The parameters extracted from the single-channel current recordings and dose-response curves such as the energy difference between the closed, open, and intermediate conducting states, and the transition-related changes in protein dimensions suggest a large conformational rearrangement of the channel complex. The estimations show that in native conditions MscL openings could be driven primarily by forces of osmotic nature. The thermodynamic and spatial parameters reasonably correlate with the available data on the structure of a single MscL subunit and multimeric organization of the complex. Combined with the functional analysis of mutations, these data give grounds to hypotheses on the nature of the channel mechanosensitivity.
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.
A preferential vibration dissociation coupling model for nonequilibrium flowfields
A preferential vibration-dissociation coupling model is incorporated into a radiatively coupled viscous shock laver code that also includes chemical, radiative, and thermal nonequilibrium. Stagnation point flow profiles are obtained for various Fire 2 flight conditions and for a typical 14 km/sec AOTV case, and comparisons are made with Fire 2 experimental data. Adjustments in molecular absorption coefficients are also made for several diatomic species. Based on comparisons with experimental data, very little preferential dissociation behavior is present in the Fire 2 flight conditions.
Investigation on the Origins of Comets as Revealed through IR High Resolution Spectroscopy: I. Molecular Abundances
We report and analyze molecular abundances updatedin twenty comets by employingmodern data reduction procedures and molecular models. Using boxplots and scatterplots, we examine how the different molecular species are distributed among the comet population, while by means of pie charts we investigate the relative proportions of these molecular species in each comet. We compare these results with the orbital parametersof the selected targets in order to identify trends related to the dynamical history of each comet. In this way, we identify at least three chemical classes based mainly on relative abundances of CO, CH3OH, CH4, C2H6, HCN and NH3. The combination of relative abundances and orbital parameters is then compared with chemical models of planetary system formation and may offer an alternative approach to investigate the origin and evolution of the material in cometary nuclei.Our study also confirms the need to add more objects to our sample in order to improve the statistics, especially for hyper-volatiles (i.e. CH4and CO) in Jupiter Family comets.
Ab Initio Calculations Applied to Problems in Metal Ion Chemistry
Electronic structure calculations can provide accurate spectroscopic data (such as molecular structures) vibrational frequencies, binding energies, etc.) that have been very useful in explaining trends in experimental data and in identifying incorrect experimental measurements. In addition, ab initio calculations. have given considerable insight into the many interactions that make the chemistry of transition metal systems so diverse. In this review we focus on cases where calculations and experiment have been used to solve interesting chemical problems involving metal ions. The examples include cases where theory was used to differentiate between disparate experimental values and cases where theory was used to explain unexpected experimental results.
Surface accommodation of molecular contaminants
Theoretical consideration and supporting data are presented regarding the nature of the transport mechanisms which cause the adsorption of gases on spacecraft surfaces. Particular attention is given to the concept of a sticking coefficient which is the ratio of the thermally accommodated mass to the total incident mass. Existing molecular accommodation data are examined in terms of spacecraft applications and recent contamination-control data are introduced. Two distinct yet linked concepts emerge which are the accommodation and sticking coefficients, and surface roughness contributes significantly to both coefficients. A general equation regarding the coefficients is developed, and the data are found to fit the equation basically. It is concluded that a more precise characterization of the coefficients can be obtained through experimentation under simulated spacecraft conditions.
Warm neutral halos around molecular clouds. III - Interpretation of H I and CO J = 1-0 data
The physical characteristics of the transition region separating the molecular and the atomic medium in interstellar clouds are studied using H I 21-cm and CO J = 1-0 data. Strong evidence is found for general heating of the surface layers of molecular clouds and for the existence of large heated neutral atomic halos around the molecular clouds. The heating of the molecular cloud surface is manifested through the general existence of limb brightening in the CO emission, with a characteristic depth of 1.7 pc, dependent on the Galactic latitude. The heated H I halos have a characteristic depth of 4.7 pc and a maximal extent of about 10 pc.