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All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Atomic understanding of structural deformations upon ablation of graphene

We investigate the atomic rearrangement in graphene under femtosecond pulse illumination with reactive molecular dynamics simulations and compare with ultra-fast laser ablation experiments. To model the impact of the laser pulse irradiation, heat is locally applied to a selected area of the graphene layer and the resulting structural deformation is simulated as a function of time, providing a detailed understanding of the bond breaking process under laser illumination and subsequent re-equilibration afterAQ3 the pulse is turned off. Analysis of the atomic dynamics indicates that the types of defects formed depend on the pulse energy and exposure duration. By varying the exposed area, we determine that the shape of the ablated area is not only a function of the pulse energy, but also of the beam spot size and pulse repetition. Furthermore, we apply a machine learning approach to extrapolate our simulated data to experimental length scales and reproduce the trends in ablated area as a function of temperature. Furthermore, our study provides a first step towards understanding the design parameters for graphene nano-patterning.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
NASA NTRS2016

Organic Analysis in the Miller Range 090657 CR2 Chondrite: Part 3 C and N Isotopic Imaging

Primitive carbonaceous chondrites contain a wide variety of organic material, ranging from soluble discrete molecules to insoluble nanoglobules of macro-molecular carbon. The relationship between the soluble organic molecules, macromolecular organic material, and host minerals are poorly understood. Large H, C and N isotopic anomalies suggest some organic components formed in low-T interstellar or outer Solar System environments. The highest isotope anomalies occur in m-scale inclusions in the most primitive materials, such as cometary dust and the least altered carbonaceous chondrites. Often, the hosts of these isotopically anomalous 'hotspots' are discrete organic nanoglobules that probably formed in the outermost reaches of the protosolar disk or cold molecular cloud. Molecular and isotopic studies of meteoritic organic matter are aimed at identifying the chemical properties and formation processes of interstellar organic materials and the subsequent chemical evolutionary pathways in various Solar System environments. The combination of soluble and insoluble analyses with in situ and bulk studies provides powerful constraints on the origin and evolution of organic matter in the Solar System. Using macroscale extraction and analysis techniques as well as microscale in situ observations we have been studying both insoluble and soluble organic material in primitive astromaterial samples. Here, we present results of bulk C and N isotopic measurements and coordinated in situ C and N isotopic imaging and mineralogical and textural studies of carbonaceous materials in a Cr2 carbonaceous chondrite. In accompanying abstracts we discuss the morphology and distribution of carbonaceous components and soluble organic species of this meteorite.

Messenger, S.↗
DOE OSTI2020

Two-Dimensional Molecular Charge Density Waves in Single-Layer-Thick Islands of a Dirac Fermion System

Charge density waves have been intensely studied in inorganic materials such as transition metal dichalcogenides however its counterpart in organic materials has yet to be explored in detail. Here we report the finding of a robust two dimensional charge density waves in molecular layers formed by α-(BEDT-TTF) 2 -I 3 on a Ag(111) surface. Low temperature scanning tunnelling microscopy images of a multi-layer thick α-(BEDT-TTF) 2 -I 3 on Ag(111) substrate reveal coexistence of 5a0 x 5a0 and √31 a0 x √31 a0 R9° charge density wave patterns commensurate with the underlying molecular lattice at 80 K. Both charge density wave patterns remain in nano-size molecular islands with just a single constituent molecular-layer thickness at 80 K and 5 K. Local tunneling spectroscopy measurements reveal the variation of the gap from 244 meV to 288 meV between the maximum and minimum charge density wave locations. Density functional theory calculations further confirm a vertical positioning of BEDT-TTF molecules in the molecular layer. While the observed charge density wave patterns are stable for the defect sites, they can be reversely switched for one molecular lattice site by means of inelastic tunnelling electron energy transfer with the electron energies exceeding 400 meV using a scanning tunneling microscope manipulation scheme.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Superresolved Motions of Single Molecular Catalysts during Polymerization Show Wide Distributions

The motion of single molecular ruthenium catalysts during and after single turnover events of ring-opening metathesis polymerization is imaged through single-molecule superresolution tracking with a positional accuracy of ±32 nm. This tracking is achieved through the real-time incorporation of spectrally tagged monomer units into active polymer chain ends during living polymerization; thus, by design, only active-catalyst motion is detected and imaged, without convolution by inactive catalysts. The catalysts show diverse individualistic diffusive behaviors with respect to time that persist for up to 20 s. Catalysts occupy three mobility populations: quasi-stationary (23%), intermediate (53%, 65 nm), and large (24%, 145 nm) step sizes. Differences in catalyst mobility populations also exist between individual aggregates (p < 0.001). Such differential motion indicates widely different local catalyst microenvironments during the catalytic turnover. These mobility differences are uniquely observable through single-catalyst microscopy and are not measurable through traditional ensemble analytical techniques for characterizing the behavior of molecular catalysts, such as nuclear magnetic resonance spectroscopy. The measured distributions of active molecular catalyst motions would not be readily predictable through modeling or first-principles, and the range likely impacts individual catalyst turnover rate and selectivity. This range plausibly contributes to property distributions observable in bulk polymers, such as molecular weight polydispersity (e.g., 1.9 in this system), leading to a revised understanding of the mechanistic, microscale origins of macroscale polymer properties.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1994

Structure and chemistry in the northwestern condensation of the Serpens molecular cloud core

We present single-dish and interferometric observations of gas and dust in the core of the Serpens molecular cloud, focusing on the northwestern condensation. Single-dish molecular line observations are used to probe the structure and chemistry of the condensation while high-resolution images of CS and CH30H are combined with continuum observations from lambda = 1.3 mm to lambda = 3.5 cm to study the subcondensations and overall distribution of dust. For the northwestern condensation, we derive a characteristic density of 3 x 10(exp 5)/ cu cm and an estimated total mass of approximately 70 solar mass. We find compact molecular emission associated with the far-infrared source S68 FIRS 1, and with a newly detected subcondensation named S68 N. Comparison of the large-and small-scale emission reveals that most of the material in the northwest condensation is not directly associated with these compact sources, suggesting a youthful age for this region. CO J = 1 approaches 0 observations indicate widespread outflow activity. However, no unique association of embedded objects with outflows is possible with our observations. The SiO emission is found to be extended with the overall emission centered about S68 FIRS 1; the offset of the peak emission from all of the known continuum sources and the coincidence between the blueshifted SiO emission and blueshifted high-velocity gas traced by CO and CS is consistent with formation of SiO in shocks. Derived abundances of CO and HCO(+) are consistent with quiescent and other star-forming regions while CS, HCN, and H2CO abundances indicate mild depletions within the condensation. Spectral energy distribution fits to S68 FIRS 1 indicate a modest luminosity (50-60 solar luminosity), implying that it is a low-mass (0.5-3 solar mass) young stellar object. Radio continuum observations of the triple source toward S68 FIRS 1 indicate that the lobe emission is varying on timescales less than or equal to 1 yr while the central component is relatively constant over approximately 14 yr. The nature of a newly detected compact emission region, S68 N, is less certain due to the absence of firm continuum detections; based on its low luminosity (less than 5 solar luminosity) and strong molecular emission, S68 N may be prestellar subcondensation of gas and dust.

Mcmullin, Joseph P.↗
NASA NTRS2017

Effect of Tube-Based X-Ray Microtomography Imaging on the Amino Acid and Amine Content of the Murchison CM2 Chondrite

X-ray and synchrotron X-ray micro-computed tomography (micro-CT) are increasingly being used for three dimensional reconnaissance imaging of chondrites and returned extraterrestrial material prior to detailed chemical and mineralogical analyses. Although micro-CT imaging is generally considered to be a non-destructive technique since silicate and metallic minerals in chondrites are not affected by X-ray exposures at the intensities and wavelengths typically used, there are concerns that the use of micro-CT could be detrimental to the organics in carbonaceous chondrites. We recently conducted a synchrotron micro-CT experiment on a powdered sample of the Murchison CM2 carbonaceous chondrite exposed to a monochromatic high energy (approximately 48 kiloelectronvolts) total X-ray radiation dose of approximately 1 kilogray (kGy) using the Advanced Photon Source beamline 13-BMD (13-Bending Magnet-D Beamline) at Argonne National Laboratory and found that there were no detectable changes in the amino acid abundances or enantiomeric compositions in the chondrite after exposure relative to a Murchison control sample that was not exposed. However, lower energy bremsstrahlung X-rays could interact more with amino acids and other lower molecular weight amines in meteorites. To test for this possibility, three separate micro-CT imaging experiments of the Murchison meteorite using the GE Phoenix v/tome/x s 240 kilovolt microfocus high resolution tungsten target X-ray tube instrument at the American Museum of Natural History (AMNH) were conducted and the amino acid abundances and enantiomeric compositions were determined. We also investigated the abundances of the C1-C5 amines in Murchison which were not analyzed in the first study.

Microtomography Imaging↗
DOE OSTI2023

Molecular detection of per- and polyfluoroalkyl substances in water using time-of-flight secondary ion mass spectrometry

Detection of per- and polyfluoroalkyl substances (PFASs) is crucial in environmental mitigation and remediation of these persistent pollutants. We demonstrate that time-of-flight secondary ion mass spectrometry (ToF-SIMS) is a viable technique to analyze and identify these substances at parts per trillion (ppt) level in real field samples without complicated sample preparation due to its superior surface sensitivity. Several representative PFAS compounds, such as perfluorooctanesulfonic acid (PFOS), perfluorobutanoic acid (PFBA), perfluoropentanoic acid (PFPeA), perfluoheptanoic acid (PFHpA), and perfluorononanoic acid (PFNA), and real-world groundwater samples collected from monitoring wells installed around at a municipal wastewater treatment plant located in Southern California were analyzed in this work. ToF-SIMS spectral comparison depicts sensitive identification of pseudo-molecular ions, characteristic of reference PFASs. Additionally, principal component analysis (PCA) shows clear discrimination among real samples and reference compounds. Our results show that characteristic molecular ion and fragments peaks can be used to identify PFASs. Furthermore, SIMS two-dimensional (2D) images directly exhibit the distribution of perfluorocarboxylic acid (PFCA) and PFOS in simulated mixtures and real wastewater samples. Such findings indicate that ToF-SIMS is useable to determine PFAS compounds in complex environmental water samples. In conclusion, ToF-SIMS provides simple sample preparation and high sensitivity in mass spectral imaging, offering an alternative solution for environmental forensic analysis of PFASs in wastewater in the future.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

3D track reconstruction of low-energy electrons in the MIGDAL low pressure optical time projection chamber

Here, we demonstrate three-dimensional track reconstruction of electrons in a low pressure (50 Torr) optical TPC consisting of two glass GEMs with an ITO strip readout in CF 4 and CF 4 /Ar mixtures. The reconstructed tracks show a variety of event topologies, including short tracks from photoelectrons induced by 55 Fe 5.9 keV X-rays and long tracks from gamma ray interactions and beta decays. Algorithms for event identification and track ridge detection are discussed as well as multiple methods for integrating information from the camera image and ITO waveforms with the goal of full 3D reconstruction of the track.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
NASA NTRS1988

The large-scale distribution of molecular gas in the first Galactic quadrant

The emission parameters for the molecular component of the interstellar medium are determined throughout the first Galactic quadrant. Face-on maps of the peak midplane molecular density, scale height, and offset from b = 0 deg with roughly 300 pc resolution are presented. These maps are compared with the distribution of cataloged H II regions to test whether both species trace the same Galactic locations. The properties of the spiral (or ringlike) arms are deduced from the derived images and pitch-angle upper limits are estimated. The H II regions are strongly correlated with the dense molecular rings.

Clemens, Dan P.↗
DOE OSTI2026

A Step-by-Step Protocol from METASPACE to Biological Interpretation

Mass spectrometry imaging (MSI) represents an exceptional tool for exploring complex biological systems spatially at the molecular level. However, due to its multidimensional nature and large-scale data output, it presents considerable challenges when it comes to extracting meaningful biological insights. Recent advancements, such as the METASPACE platform, have enabled researchers to efficiently process, annotate, and interpret MSI datasets by leveraging machine learning and cloud-based infrastructure. In this tutorial, we present a detailed and user-friendly R-pipeline designed to help METASPACE users navigate untargeted metabolomic annotations and transform them into practical insights about their biological systems. By combining METASPACE annotations with rapid R-based screening, this workflow not only streamlined the analytical process but also enhanced the understanding of spatial molecular distribution, especially for complex systems. Here, this easy-to-follow approach has the potential for applications in diagnostics, drug discovery, environmental and ecological processes, and more. We envision this pipeline to be particularly useful for newcomers to the field of MSI and

Moreno Pedraza, Abigail↗
DOE OSTI2022

Stabilization of Dinuclear Rhodium and Iridium Clusters on Layered Titanate and Niobate Supports

Atomically dispersed organometallic clusters can provide well-defined nuclearity of active sites for both fundamental studies as well as new regimes of activity and selectivity in chemical transformations. More recently, dinuclear clusters adsorbed onto solid surfaces have shown novel catalytic properties resulting from the synergistic effect of two metal centers to anchor different reactant species. Difficulty in synthesizing, stabilizing, and characterizing isolated atoms and clusters without agglomeration challenges allocating catalytic performance to atomic structure. Here, we explore the stability of dinuclear rhodium and iridium clusters adsorbed onto layered titanate and niobate supports using molecular precursors. Both systems maintain their nuclearity when Statistical analysis of HAADF-STEM images revealed that rhodium and iridium dimers had mean cluster-to-cluster distances very similar to what is expected from a random distribution of atoms over a large area, indicating that they are dispersed without aggregation. The stability of dinuclear rhodium clusters supported on titanate nanosheets was also investigated by X-ray absorption fine structure (EXAFS), DRIFTS, and first-principles calculations. Both X-ray absorption spectroscopy and HAADF-STEM simulations, guided by density functional theory (DFT)-optimized structure models, suggested that rhodium dimers adsorb onto the nanosheets in an end-on binding mode that is stable up to 100 degrees C under reducing conditions. Finally, this study highlights that crystalline nanosheets derived from layered metal oxides can be used as model supports to selectively stabilize dinuclear clusters, which could have implications for heterogeneous catalysis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Multidisciplinary studies with mutated HIV-1 capsid proteins reveal structural mechanisms of lattice stabilization

Abstract HIV-1 capsid (CA) stability is important for viral replication. E45A and P38A mutations enhance and reduce core stability, thus impairing infectivity. Second-site mutations R132T and T216I rescue infectivity. Capsid lattice stability was studied by solving seven crystal structures (in native background), including P38A, P38A/T216I, E45A, E45A/R132T CA, using molecular dynamics simulations of lattices, cryo-electron microscopy of assemblies, time-resolved imaging of uncoating, biophysical and biochemical characterization of assembly and stability. We report pronounced and subtle, short- and long-range rearrangements: (1) A38 destabilized hexamers by loosening interactions between flanking CA protomers in P38A but not P38A/T216I structures. (2) Two E45A structures showed unexpected stabilizing CA NTD -CA NTD inter-hexamer interactions, variable R18-ring pore sizes, and flipped N-terminal β-hairpin. (3) Altered conformations of E45A a α9-helices compared to WT, E45A/R132T, WT PF74 , WT Nup153 , and WT CPSF6 decreased PF74, CPSF6, and Nup153 binding, and was reversed in E45A/R132T. (4) An environmentally sensitive electrostatic repulsion between E45 and D51 affected lattice stability, flexibility, ion and water permeabilities, electrostatics, and recognition of host factors.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Pressure-induced polyamorphic transition in CaA l 2 O 4 glass

In situ high-pressure ultrasonic velocity measurements of CaAl 2 O 4 glass reveal abrupt irreversible discontinuities in the elastic wave velocities at ~8–10 GPa. Total structure factor and pair distribution functions measured by synchrotron x-ray diffraction show a rapid change in the intermediate range structure attributed to a rearrangement of calcium ions over this narrow pressure region. Atomistic models obtained from molecular dynamics simulations reveal that this intermediate range structure is explained by a transition of Ca–O void radius distribution from a bimodal distribution with peaks at ~2.1 and ~2.4 Å to a single distribution centered at ~2.1 Å. Further, these abrupt structural changes involving the rapid increase in elastic wave velocity are markedly different to the continuous transformations observed in conventional network-forming glasses, such as SiO 2 .

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
NASA NTRS1990

Global and radial variations in the efficiency of massive star formation among galaxies

In order to determine the regions within galaxies which give rise to the most efficient star formation and to test the hypothesis that galaxies with high infrared luminosities per unit molecular mass are efficiently producing high mass stars, researchers have undertaken an H alpha imaging survey in galaxies whose CO distributions have been measured as part of the Five College Radio Astronomy Observatory (FCRAO) Extragalactic CO Survey. From these images researchers have derived global H alpha fluxes and distributions for comparison with far infrared radiation (FIR) fluxes and CO fluxes and distributions. Here, researchers present results on the global massive star formation efficiency (SFE = L sub H sub alpha/M(H2)) as a function of morphological type and environment, and on the radial distribution of the SFE within both peculiar and isolated galaxies. On the basis of comparison of the global L sub H sub alpha/M(H2) and L sub FIR/M(H2) for 111 galaxies, researchers conclude that environment rather than morphological type has the strongest effect on the global efficiency of massive star formation. Based on their study of a small sample, they find that the largest radial gradients are observed in the interacting/peculiar galaxies, indicating that environment affects the star formation efficiency within galaxies as well.

Allen, Lori E.↗
NASA NTRS2014

Magnetite as Possible Template for the Synthesis of Chiral Organics in Carbonaceous Chondrites

The main goal of the Japanese Aerospace Ex-ploration Agency (JAXA) Hayabusa-2 mission is to visit and return to Earth samples of a C-type asteroid (162173) 1999 JU3 in order to understand the origin and nature of organic materials in the Solar System. Life on Earth shows preference towards the set of organics with particular spatial arrangements, this 'selectivity' is a crucial criterion for life. With only rare exceptions, life 'determines' to use the left- (L-) form over the right- (D-) form of amino acids, resulting in a L-enantiomeric excess (ee). Recent studies have shown that L-ee is found within the alpha-methyl amino acids in meteorites [1, 2], which are amino acids with rare terrestrial occurrence, and thus point towards a plausible abiotic origin for ee. One of the proposed origins of chiral asymmetry of amino acids in meteorites is their formation with the presence of asymmetric catalysts [3]. The catalytic mineral grains acted as a surface at which nebular gases (CO, H2 and NH3) were allowed to condense and react through Fisher Tropsch type (FTT) syntheses to form the organics observed in meteorites [4]. Magnetite is shown to be an effective catalyst of the synthesis of amino acids that are commonly found in meteorites [5]. It has also taken the form as spiral magnetites (a.k.a. 'plaquettes'), which were found in various carbonaceous chondrites (CCs), including C2s Tagish Lake and Esseibi, CI Orgueil, and CR chondrites [e.g., 6, 7, 8]. In addition, L-ee for amino acids are common in the aqueously altered CCs, as opposed to the unaltered CCs [1]. It seems possible that the synthesis of amino acids with chiral preferences is correlated to the alteration process experienced by the asteroid parent body, and related to the configuration of spiral magnetite catalysts. Since C-type asteroids are considered to be enriched in organic matter, and the spectral data of 1999 JU3 indicates a certain de-gree of aqueous alteration [9], the Hayabusa-2 mission serves as a perfect chance to attest this argument. In order to understand the distribution of spiral magnetites among different meteorite classes, as well as to investigate their spiral configurations and correlation to molecular asymmetry, we observed polished thin sections of CCs using scanning electron microscope (SEM) imaging. Individual magnetite grains were picked, embedded in epoxy, thin-sectioned using an ultra-microtome, and studied with electron backscatter diffraction (EBSD) in order to reconstruct the crystal orientation along the stack of magnetite disks.

Chan, Q. H. S.↗
NASA NTRS1997

Monolithic InGaAs JFET Active Pixel Tunable Image Sensor (MAPTIS)

A new Monolithic InGaAs Active Pixel Multispectral Image Sensor is described. This Infrared sensor will utilize high quality InGaAs grown by Molecular Beam Epitaxy on InP substrate for the fabrication of a high speed Junction Field Effect Transistor array.

hyper↗
DOE OSTI2021

Hydrogen bonded trimesic acid networks on Cu(111) reveal how basic chemical properties are imprinted in HR-AFM images

High resolution non-contact atomic force microscopy measurements characterize assemblies of trimesic acid molecules on Cu(111) and the link group interactions, providing the first fingerprints utilizing CO-based probes for this widely studied paradigm for hydrogen bond driven molecular self assembly. The enhanced submolecular resolution offered by this technique uniquely reveals key aspects of the competing interactions. Accurate comparison between full-density-based modeled images and experiment allows to identify key structural elements in the assembly in terms of the electron-withdrawing character of the carboxylic groups, interactions of those groups with Cu atoms in the surface, and the valence electron density in the intermolecular region of the hydrogen bonds. This study of trimesic acid assemblies on Cu(111) combining high resolution atomic force microscopy measurements with theory and simulation forges clear connections between fundamental chemical properties of molecules and key features imprinted in force images with submolecular resolution.

77 NANOSCIENCE AND NANOTECHNOLOGY↗