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All sourcesNASA NTRSDOE OSTI
NASA NTRS2016

Discovery of X-Ray Emission from the Galactic Supernova Remnant G32.8-0.1 with Suzaku

We present the first dedicated X-ray study of the supernova remnant (SNR) G32.8-0.1 (Kes 78) with Suzaku. X-ray emission from the whole SNR shell has been detected for the first time. The X-ray morphology is well correlated with the emission from the radio shell, while anti-correlated with the molecular cloud found in the SNR field. The X-ray spectrum shows not only conventional low-temperature (kT approximately 0.6 kiloelectronvolts) thermal emission in a nonequilibrium ionization state, but also a very high-temperature (approximately 3.4 kiloelectronvolts) component with a very low ionization timescale (approximately 2.7 times 10 (sup 9) per cubic centimeter per second), or a hard nonthermal component with a photon index Gamma approximately equal to 2.3. The average density of the low-temperature plasma is rather low, of the order of 10 (sup -3) - 10 (sup -2) per cubic centimeter, implying that this SNR is expanding into a low-density cavity. We discuss the X-ray emission of the SNR, also detected in teraelectronvolts with H.E.S.S. (High Energy Stereoscopic System), together with multi-wavelength studies of the remnant and other gamma-ray emitting SNRs, such as W28 and RCW 86. Analysis of a time-variable source, 2XMM J185114.3-000004, found in the northern part of the SNR, is also reported for the first time. Rapid time variability and a heavily absorbed hard-X-ray spectrum suggest that this source could be a new supergiant fast X-ray transient.

Petre, Robert↗
DOE OSTI2022

Identification and assignment of rotational spectra using artificial neural networks

A method of identifying molecular parameters may include receiving observed transition frequencies, generating transition frequency sets and a spectral parameter sets, training one or more artificial neural networks by analyzing the transition frequency sets and the spectral parameter sets, analyzing the observed transition frequencies using the one or more trained artificial neural networks to predict estimated spectral parameters, and identifying molecular parameters by analyzing the estimated spectral parameters. A molecular parameter identification system may include a rotational spectrometer, a user interface, and a spectrum analysis application that may retrieve observed transition frequencies, identify a Hamiltonian type by a neural network analyzing the observed transition frequencies, select a second trained artificial neural network based on the identified Hamiltonian type, analyze observed transition frequencies using the second artificial neural network to identify estimated spectral parameters, and identify molecular parameters.

Prozuments, Kirills↗
NASA NTRS2020

Eta Carinae & the Homunculus: Far Infrared Sub-millimeter Spectral Lines detected with the Herschel Space Observatory

The evolved massive binary star η Carinae underwent eruptive mass loss events that formed the complex bi-polar “Homunculus” nebula harboring tens of solar masses of unusually nitrogen-rich gas and dust. Despite expectations for the presence of a significant molecular component to the gas, detections have been observationally challenged by limited access to the far-infrared and the intense thermal continuum. A spectral survey of the atomic and rotational molecular transitions was carried out with theHerschel Space Observatory, revealing a rich spectrum of broad emission lines originating in the ejecta. Velocity profiles of selected PACS lines correlate well with known substructures: Hi in the central core; NH and weak [Cii] within the Homunculus; and [Nii] emissions in fast-moving structures external to the Homunculus.We have identified transitions from [Oi], Hi, and 18 separate light C- and O-bearing molecules including CO, CH, CH+, and OH, and a wide set of N-bearing molecules,NH, NH+, N2H+, NH2, NH3, HCN, HNC, CN, and N2H+. Half of these are new detections unprecedented for any early-type massive star environment. A very low ratio[12C/13C]≤4 is estimated from five molecules and their isotopologues. We demonstrate that non-LTE effects due to the strong continuum are significant. Abundance patterns are consistent with line formation in regions of carbon and oxygen depletions with nitrogen enhancements, reflecting an evolved state of the erupting star with efficient transport of CNO-processed material to the outer layers. The results offer many opportunities for further observational and theoretical investigations of the molecular chemistry under extreme physical and chemical conditions around massive stars in their final stages of evolution.

T. R. Gull↗
DOE OSTI2020

Exploring the Light-induced Dynamics in Solvated Metallogrid Complexes with Femtosecond Pulses Across the Electromagnetic Spectrum

Oligonuclear complexes of d 4 -d 7 transition metal ion centers that undergo spin-switching have long been developed for their practical role in molecular electronics. Recently, they also have appeared as promising photochemical reactants demonstrating improved stability. However, the lack of knowledge about their photophysical properties in the solution phase compared to their mononuclear congeners is currently hampering their inclusion into advanced light-driven reactions. In the present study, the ultrafast photoinduced dynamics in a solvated [2x2] iron(II) metallogrid complex are characterized by combining transient optical, infrared absorption and X-ray emission spectroscopic measurements on the femtosecond timescale. The analysis is supported by DFT calculations. The photocycle can be described in terms of intra-site transitions, where the Fe II in the low-spin (LS) state are independently photoexcited. The Franck-Condon state decays via the formation of a vibrationally-hot high-spin (HS) state that displays coherent behavior within a few picoseconds and thermalizes within tens of picosecond to yield a metastable HS state living for several hundreds of nanoseconds. Additionally, systematic comparison with the closely related mononuclear complex [Fe(terpy) 2 ] 2+ reveals that nuclearity has a profound impact on the photoinduced dynamics. Finally, this work provides guidelines for expanding the integration of oligonuclear complexes into new photoconversion schemes that may be triggered by ultrafast spin-switching.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1982

High-resolution optical measurements of atmospheric winds from space. I - Lower atmosphere molecular absorption

A high-resolution spectroscopic technique, analogous to that used in the thermosphere to measure the vector wind fields in the upper troposphere and stratosphere, is described which uses narrow features in the spectrum of light scattered from the earth's lower atmosphere to provide Doppler information on atmospheric scattering and absorption. It is demonstrated that vector winds can be measured from a satellite throughout the lower atmosphere, using a multiple-etalon Fabry-Perot interferometer of modest aperture. It is found that molecular oxygen and water vapor absorption lines in the spectrum of sunlight scattered by the atmosphere are Doppler-shifted by the line of sight wind, so that they may be used to monitor the global wind systems in the upper troposphere and stratosphere.

Hays, P. B.↗
NASA NTRS1991

Molecular line survey of Sagittarius B2(M) from 330 to 355 GHz and comparison with Sagittarius B2(N)

A submillimeter survey of Sgr B2 is described in which sufficient spatial resolution permitted the observation of some of the source structure. The position Sgr B2(M) is examined in relation to the submillimeter emission of Sgr B2(N) and previous millimeter observational data of source (M) at a lower spatial resolution. Because the submillimeter observations are more sensitive to core emission, the molecules SO2 and CH3OH tend to dominate the spectrum. The core emission is found to be similar to that of the Orion molecular cloud, and the submillimeter and millimeter lines have high optical depths. The (N) source has a much higher column density than that of (M) except for SO and SO2, and (N) also appears to have a higher excitation which can indicate a core with a higher density.

Sutton, E. C.↗
NASA NTRS1999

Modeling the unidentified infrared emission with combinations of polycyclic aromatic hydrocarbons

The infrared emission band spectrum associated with many different interstellar objects can be modeled successfully by using combined laboratory spectra of neutral and positively charged polycyclic aromatic hydrocarbons (PAHs). These model spectra, shown here for the first time, alleviate the principal spectroscopic criticisms previously leveled at the PAH hypothesis and demonstrate that mixtures of free molecular PAHs can indeed account for the overall appearance of the widespread interstellar infrared emission spectrum. Furthermore, these models give us insight into the structures, stabilities, abundances, and ionization balance of the interstellar PAH population. These, in turn, reflect conditions in the emission zones and shed light on the microscopic processes involved in the carbon nucleation, growth, and evolution in circumstellar shells and the interstellar medium.

Spectrophotometry, Infrared↗
NASA NTRS1988

The 2.5-12 micrometers spectrum of comet Halley from the IKS-VEGA experiment

The infrared instrument IKS flown on board the VEGA space probes was designed for the detection of emission bands of parent molecules, and for a measurement of the size and temperature of the thermal emitting nuclear region. The instrument had three channels with cooled detectors: an "imaging channel" designed to modulate the signal of the nucleus and two spectroscopic channels operating at 2.5-5 and 6-12 micrometers, respectively, equipped with circular variable filters of resolving power approximately 50. This paper presents and discusses the results from the spectral channels. On VEGA 1, usable spectra were obtained at distances D from the comet nucleus ranging from 250,000 to 40,000 km corresponding to fields of view 4000 and 700 km in diameter, respectively. The important internal background signal caused by the instrument itself, which could not be cooled, had to be eliminated. Since no sky chopping was performed, we obtain difference spectra between the current spectrum and a reference spectrum with little or no cometary signal taken at the beginning of the observing sequence (D approximately 200,000 km). Final discrimination between cometary signal and instrumental background is achieved using their different time evolution, since the instrumental background is proportional to the slow temperature drift of the instrument, and the cometary signal due to parent molecules or dust grains is expected to vary in first order as D-1. The 2.5-5 micrometers IKS spectra definitely show strong narrow signals at 2.7 and 4.25 micrometers, attributed to the nu 3 vibrational bands of H2O and CO2, respectively, and a broader signal in the region 3.2-3.5 micrometers, which may be attributed to CH-bearing molecules. All these signals present the expected D-1 intensity variation. Weaker emission features at 3.6 and 4.7 micrometers could correspond to the nu 1 and nu 5 bands of H2CO and the (1 - 0) band of CO, respectively. Molecular production rates are derived from the observed emissions, assuming that they are due to resonance fluorescence excited by the Sun's infrared radiation. For the strong bands of H2O and CO2, the rovibrational lines are optically thick, and radiative transfer is taken into account. We derive production rates, at the moment of the VEGA 1 flyby, of approximately 10(30) sec-1 for H2O, approximately 2.7 x 10(28) sec-1 for CO2, approximately 5 x 10(28) sec-1 for CO, and 4 x 10(28) sec-1 for H2CO, if attributions to CO and H2CO are correct. The production rate of carbon atoms in CH-bearing molecules is approximately 9 x 10(29) sec-1 assuming fluorescence of molecules in the gas phase, but could be much less if the 3.2-3.5 micrometers emission is attributed to C-H stretch in polycyclic aromatic hydrocarbons or small organic grains. In addition, marginal features are present at 4.85 and 4.45 micrometers, tentatively attributed to OCS and molecules with the CN group, respectively. Broad absorption at 2.8-3.0 micrometers, as well as a narrow emission at 3.15 micrometers, which follow well the D-1 intensity variation, might be due to water ice. Emission at 2.8 micrometers is also possibly present, and might be due to OH created in vibrationally excited states after water photodissociation. The 6-12 micrometers spectrum does not show any molecular emission, nor emission in the 7.5-micrometers region. The spectrum is dominated by silicate emission showing a double structure with maxima at 9.0 and 11.2 micrometers, which suggests the presence of olivine.

NASA Discipline Number 52-10↗
NASA NTRS1987

Structure, vibrational spectrum, and energetics of the CH5(+) ion - A theoretical investigation

Analytic derivative techniques are utilized to determine molecular geometries, vibration spectra, molecular force field, proton affinity, and energetics of clustering of protonated methane. It is observed that the geometries are gradient optimized, while the harmonic force fields and IR intensities are also determined analytically at the SCF level. It is determined that the frequency of the torsional model for rotation of the H2 about the pseudothreefold axis of the CH3(+) group is extremely low, and the proton affinity of CH4 is calculated as 129.0 kcal/mol.

Komornicki, Andrew↗
NASA NTRS2004

The Far-Infrared Spectrum of Arp 220

ISO/LWS grating observations of the ultraluminous infrared galaxy Arp 220 shows absorption in molecular lines of OH, H 2 0 , CH, NH, and "3, well as in the [0 I] 63 pm line and emission in the [C 111 158 pm line. We have modeled the continuum and the emission/absorption of all observed features by means of a non-local radiative transfer code. The continuum from 25 to 1300 pm is modeled AS A WARM (106 K) NUCLEAR REGION THAT IS OPTICALLY THICK IN THE FAR-INFRARED, attenuated by an extended region (size 2") that is heated mainly through absorption of nuclear infrared radiation. The molecular absorption in the nuclear region is characterized by high excitation due to the high infrared radiation density. The OH column densities are high toward the nucleus and the extended region (about 2 x 10 sup 17 cm sup-2). The H2O column density is also high toward the nucleus (2 - 10 x 1017 cm-2) and lower in the extended region. The column densities in a halo that accounts for the absorption by the lowest lying levels are similar to what are found in the diffuse clouds toward the star forming regions in the Sgr B2 molecular cloud complex near the Galactic Center. Most notable are the high column densities found for NH and NH3 toward the nucleus, with values of about 1.5 x 10supl6 cmsup-2 and about 3 x 10supl6 cmsup-2, respectively, whereas the NH2 column density is lower than about 2 x 10sup15 cmsup-2. A combination of PDRs in the extended region and hot cores with enhanced H20 photodissociation and a possible shock contribution in the nuclei may explain the relative column densities of OH and H20, whereas the nitrogen chemistry may be strongly affected by cosmic ray ionization. The [C II] 158 pm line is well reproduced by our models and its "deficit" relative to the CII/FIR ratio in normal and starburst galaxies is suggested to be mainly a consequence of the dominant non-PDR component of far- infrared radiation, ALTHOUGH OUR MODELS ALONE CANNOT RULE OUT EXTINCTION EFFECTS IN THE NUCLEI.

Gonzalez-Alfonso, Eduardo↗
NASA NTRS2005

The Far-Infrared Spectrum of Arp 220

ISO/LWS grating observations of the ultraluminous infrared galaxy Arp 220 shows absorption in molecular lines of OH, H(sub 2)O, CH, NH, and NH(sub 3), as well as in the [O I] 63 micron line and emission in the [C II] 158 micron line. We have modeled the continuum and the emission/absorption of all observed features by means of a non-local radiative transfer code. The continuum from 25 to 1300 microns is modeled as a warm (106 K) nuclear region that is optically thick in the far-infrared, attenuated by an extended region (size 2") that is heated mainly through absorption of nuclear infrared radiation. The molecular absorption in the nuclear region is characterized by high excitation due to the high infrared radiation density. The OH column densities are high toward the nucleus (2 - 6 x 10(exp 17) cm(exp -2)) and the extended region (approximately 2 x 10(exp 17) cm(exp -2)). The H(sub 2)O column density is also high toward the nucleus (2 - 10 x 10(exp 17) cm(exp -2)) and lower in the extended region. The column densities in a halo that accounts for the absorption by the lowest lying levels are similar to what are found in the diffuse clouds toward the star forming regions in the Sgr B2 molecular cloud complex near the Galactic Center. Most notable are the high column densities found for NH and NH(sub 3) toward the nucleus, with values of approximately 1.5 x 10(exp 16) cm(exp -2) and approximately 3 x 10(exp 16) cm(exp -2), respectively, whereas the NH(sub 2) column density is lower than approximately 2 x 10(exp 15) cm(exp -2). A combination of PDRs in the extended region and hot cores with enhanced H(sub 2)O photodissociation and a possible shock contribution in the nuclei may explain the relative column densities of OH and H(sub 2)O, whereas the nitrogen chemistry may be strongly affected by cosmic ray ionization. The [C II] 158 micron line is well reproduced by our models and its deficit relative to the CII/FIR ratio in normal and starburst galaxies is suggested to be mainly a consequence of the dominant non-PDR component of far-infrared radiation, although our models alone cannot rule out extinction effects in the nuclei.

Gonzalez-Alfonso, Eduardo↗
DOE OSTI2022

Ancestral archaea expanded the genetic code with pyrrolysine

The pyrrolysyl-tRNA synthetase (PylRS) facilitates the cotranslational installation of the 22nd amino acid pyrrolysine. Owing to its tolerance for diverse amino acid substrates, and its orthogonality in multiple organisms, PylRS has emerged as a major route to install noncanonical amino acids into proteins in living cells. Recently, a novel class of PylRS enzymes was identified in a subset of methanogenic archaea. Enzymes within this class (ΔPylSn) lack the N-terminal tRNA-binding domain that is widely conserved amongst PylRS enzymes, yet remain active and orthogonal in bacteria and eukaryotes. In this study, we use biochemical and in vivo UAG-readthrough assays to characterize the aminoacylation efficiency and substrate spectrum of a ΔPylSn class PylRS from the archaeon Candidatus Methanomethylophilus alvus. We show that, compared with the full-length enzyme from Methanosarcina mazei, the Ca. M. alvus PylRS displays reduced aminoacylation efficiency but an expanded amino acid substrate spectrum. To gain insight into the evolution of ΔPylSn enzymes, we performed molecular phylogeny using 156 PylRS and 105 pyrrolysine tRNA (tRNA Pyl ) sequences from diverse archaea and bacteria. This analysis suggests that the PylRS•tRNA Pyl pair diverged before the evolution of the three domains of life, placing an early limit on the evolution of the Pyl-decoding trait. Furthermore, our results document the coevolutionary history of PylRS and tRNA Pyl and reveal the emergence of tRNA Pyl sequences with unique A73 and U73 discriminator bases. The orthogonality of these tRNA Pyl species with the more common G73-containing tRNA Pyl will enable future efforts to engineer PylRS systems for further genetic code expansion.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Twins in rotational spectroscopy: Does a rotational spectrum uniquely identify a molecule?

Rotational spectroscopy is the most accurate method for determining structures of molecules in the gas phase. It is often assumed that a rotational spectrum is a unique “fingerprint” of a molecule. The availability of large molecular databases and the development of artificial intelligence methods for spectroscopy make the testing of this assumption timely. In this paper, we pose the determination of molecular structures from rotational spectra as an inverse problem. Within this framework, we adopt a funnel-based approach to search for molecular twins, which are two or more molecules, which have similar rotational spectra but distinctly different molecular structures. Here we demonstrate that there are twins within standard levels of computational accuracy by generating rotational constants for many molecules from several large molecular databases, indicating that the inverse problem is ill-posed. However, some twins can be distinguished by increasing the accuracy of the theoretical methods or by performing additional experiments.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2022

Genetic and Structural Analysis of SARS-CoV-2 Spike Protein for Universal Epitope Selection

Evaluation of immunogenic epitopes for universal vaccine development in the face of ongoing SARS-CoV-2 evolution remains a challenge. Herein, we investigate the genetic and structural conservation of an immunogenically relevant epitope (C662–C671) of spike (S) protein across SARS-CoV-2 variants to determine its potential utility as a broad-spectrum vaccine candidate against coronavirus diseases. Comparative sequence analysis, structural assessment, and molecular dynamics simulations of C662–C671 epitope were performed. Mathematical tools were employed to determine its mutational cost. We found that the amino acid sequence of C662–C671 epitope is entirely conserved across the observed major variants of SARS-CoV-2 in addition to SARS-CoV. Its conformation and accessibility are predicted to be conserved, even in the highly mutated Omicron variant. Costly mutational rate in the context of energy expenditure in genome replication and translation can explain this strict conservation. These observations may herald an approach to developing vaccine candidates for universal protection against emergent variants of coronavirus.

59 BASIC BIOLOGICAL SCIENCES↗