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At least 1,153 records · Page 64

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DOE OSTI2021

A Chemical Dynamics Study of the Reaction of the Methylidyne Radical (CH, X 2 Π) with Dimethylacetylene (CH 3 CCCH 3 , X 1 A 1g )

The gas-phase reaction of the methylidyne (CH; X 2 Π) radical with dimethylacetylene (CH 3 CCCH 3 ; X 1 A 1g ) was studied at a collision energy of 20.6 kJ mol -1 under single collision conditions with experimental results merged with ab initio calculations of the potential energy surface (PES) and ab initio molecule dynamics (AIMD) simulations. Here, the crossed molecular beams experiment reveals that the reaction proceeds barrierless via indirect scattering dynamics through long-lived C 5 H 7 reaction intermediate(s) ultimately dissociating to C 5 H 6 isomers along with atomic hydrogen with atomic hydrogen predominantly released from the methyl groups as verified by replacing the methylidyne with the D1-methylidyne reactant. AIMD simulations reveal that the reaction dynamics are statistical leading predominantly to p28 (1-methyl-3-methylene-cyclopropene, 13 %) and p8 (1-penten-3-yne, 81 %) plus atomic hydrogen with a significant amount of available energy being channeled into the internal excitation of the polyatomic reaction products.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Porting fragmentation methods to GPUs using an OpenMP API: Offloading the resolution-of-the-identity second-order Møller–Plesset perturbation method

Here, using an OpenMP Application Programming Interface, the resolution-of-the-identity second-order Møller–Plesset perturbation (RI-MP2) method has been off-loaded onto graphical processing units (GPUs), both as a standalone method in the GAMESS electronic structure program and as an electron correlation energy component in the effective fragment molecular orbital (EFMO) framework. First, a new scheme has been proposed to maximize data digestion on GPUs that subsequently linearizes data transfer from central processing units (CPUs) to GPUs. Second, the GAMESS Fortran code has been interfaced with GPU numerical libraries (e.g., NVIDIA cuBLAS and cuSOLVER) for efficient matrix operations (e.g., matrix multiplication, matrix decomposition, and matrix inversion). The standalone GPU RI-MP2 code shows an increasing speedup of up to 7.5× using one NVIDIA V100 GPU with one IBM 42-core P9 CPU for calculations on fullerenes of increasing size from 40 to 260 carbon atoms using the 6-31G(d)/cc-pVDZ-RI basis sets. A single Summit node with six V100s can compute the RI-MP2 correlation energy of a cluster of 175 water molecules using the correlation consistent basis sets cc-pVDZ/cc-pVDZ-RI containing 4375 atomic orbitals and 14 700 auxiliary basis functions in ~0.85 h. In the EFMO framework, the GPU RI-MP2 component shows near linear scaling for a large number of V100s when computing the energy of an 1800-atom mesoporous silica nanoparticle in a bath of 4000 water molecules. The parallel efficiencies of the GPU RI-MP2 component with 2304 and 4608 V100s are 98.0% and 96.1%, respectively.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Probing C–I bond fission in the UV photochemistry of 2-iodothiophene with core-to-valence transient absorption spectroscopy

The UV photochemistry of small heteroaromatic molecules serves as a testbed for understanding fundamental photo-induced chemical transformations in moderately complex compounds, including isomerization, ring-opening, and molecular dissociation. Here, a combined experimental-theoretical study of 268 nm UV light-induced dynamics in 2-iodothiophene (C 4 H 3 IS) is performed. The dynamics are experimentally monitored with a femtosecond extreme ultraviolet (XUV) probe that measures iodine N-edge 4d core-to-valence transitions. Experiments are complemented by density functional theory calculations of both the pump-pulse induced valence excitations and the XUV probe-induced core-to-valence transitions. Possible intramolecular relaxation dynamics are investigated by ab initio molecular dynamics simulations. Furthermore, gradual absorption changes up to ~0.5 to 1 ps after excitation are observed for both the parent molecular species and emerging iodine fragments, with the latter appearing with a characteristic rise time of 160 ± 30 fs. Comparison of spectral intensities and energies with the calculations identifies an iodine dissociation pathway initiated by a predominant π → π* excitation. In contrast, initial excitation to a nearby n ⟂ → σ* state appears unlikely based on a significantly smaller oscillator strength and the absence of any corresponding XUV absorption signatures. Excitation to the π → π* state is followed by contraction of the C–I bond, enabling a nonadiabatic transition to a dissociative π→σ C-I * state. For the subsequent fragmentation, a relatively narrow bond-length region along the C–I stretch coordinate between 230 and 280 pm is identified, where the transition between the parent molecule and the thienyl radical + iodine atom products becomes prominent in the XUV spectrum due to rapid localization of two singly occupied molecular orbitals on the two fragments.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Cooperative actin filament nucleation by the Arp2/3 complex and formins maintains the homeostatic cortical array in Arabidopsis epidermal cells

Abstract Precise control over how and where actin filaments are created leads to the construction of unique cytoskeletal arrays within a common cytoplasm. Actin filament nucleators are key players in this activity and include the conserved actin-related protein 2/3 (Arp2/3) complex as well as a large family of formins. In some eukaryotic cells, these nucleators compete for a common pool of actin monomers and loss of one favors the activity of the other. To test whether this mechanism is conserved, we combined the ability to image single filament dynamics in the homeostatic cortical actin array of living Arabidopsis (Arabidopsis thaliana) epidermal cells with genetic and/or small molecule inhibitor approaches to stably or acutely disrupt nucleator activity. We found that Arp2/3 mutants or acute CK-666 treatment markedly reduced the frequency of side-branched nucleation events as well as overall actin filament abundance. We also confirmed that plant formins contribute to side-branched filament nucleation in vivo. Surprisingly, simultaneous inhibition of both classes of nucleator increased overall actin filament abundance and enhanced the frequency of de novo nucleation events by an unknown mechanism. Collectively, our findings suggest that multiple actin nucleation mechanisms cooperate to generate and maintain the homeostatic cortical array of plant epidermal cells.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Materials Data on CoH3(CN)6 by Materials Project

Co(H(CN)2)3 crystallizes in the trigonal P-31m space group. The structure is zero-dimensional and consists of one cobalt molecule and three H(CN)2 clusters. In each H(CN)2 cluster, C+2.33+ is bonded in a single-bond geometry to one N3- atom. The C–N bond length is 1.17 Å. N3- is bonded in a linear geometry to one C+2.33+ and one H1+ atom. The N–H bond length is 1.27 Å. H1+ is bonded in a linear geometry to two equivalent N3- atoms.

36 MATERIALS SCIENCE↗

DOE OSTI2020

Materials Data on Eu2Si3Ni8 by Materials Project

Eu2(Ni2Si)3(Ni)2 crystallizes in the tetragonal P4_2/nmc space group. The structure is three-dimensional and consists of eight nickel molecules and one Eu2(Ni2Si)3 framework. In the Eu2(Ni2Si)3 framework, Eu2+ is bonded in a distorted single-bond geometry to two equivalent Ni1+ and one Si4- atom. Both Eu–Ni bond lengths are 2.79 Å. The Eu–Si bond length is 2.83 Å. There are two inequivalent Ni1+ sites. In the first Ni1+ site, Ni1+ is bonded in a 2-coordinate geometry to one Eu2+ and two equivalent Si4- atoms. There are one shorter (2.32 Å) and one longer (2.33 Å) Ni–Si bond lengths. In the second Ni1+ site, Ni1+ is bonded in a 4-coordinate geometry to four Si4- atoms. There are a spread of Ni–Si bond distances ranging from 2.18–2.55 Å. There are two inequivalent Si4- sites. In the first Si4- site, Si4- is bonded in a 10-coordinate geometry to six Ni1+ atoms. In the second Si4- site, Si4- is bonded in a 4-coordinate geometry to two equivalent Eu2+ and four equivalent Ni1+ atoms.

36 MATERIALS SCIENCE↗

DOE OSTI2020

Materials Data on Zr6BH42C12I13O12 by Materials Project

Zr6BC6H18(OI2)6(CH3OH)6I crystallizes in the trigonal R-3 space group. The structure is zero-dimensional and consists of three hydriodic acid molecules, eighteen methanol molecules, and three Zr6BC6H18(OI2)6 clusters. In each Zr6BC6H18(OI2)6 cluster, Zr is bonded in a distorted single-bond geometry to one B, one O, and four I atoms. The Zr–B bond length is 2.69 Å. The Zr–O bond length is 1.93 Å. There are two shorter (2.91 Å) and two longer (2.95 Å) Zr–I bond lengths. B is bonded in an octahedral geometry to six equivalent Zr atoms. C is bonded in a tetrahedral geometry to three H and one O atom. All C–H bond lengths are 1.10 Å. The C–O bond length is 1.41 Å. There are three inequivalent H sites. In the first H site, H is bonded in a single-bond geometry to one C atom. In the second H site, H is bonded in a single-bond geometry to one C atom. In the third H site, H is bonded in a single-bond geometry to one C atom. O is bonded in a bent 150 degrees geometry to one Zr and one C atom. There are two inequivalent I sites. In the first I site, I is bonded in an L-shaped geometry to two equivalent Zr atoms. In the second I site, I is bonded in an L-shaped geometry to two equivalent Zr atoms.

36 MATERIALS SCIENCE↗

DOE OSTI2020

Materials Data on HW2C9NO10 by Materials Project

W2HW2H(NO)2(CO)18 crystallizes in the monoclinic C2 space group. The structure is zero-dimensional and consists of thirty-six formaldehyde molecules, two W2H clusters, and two W2H(NO)2 clusters. In each W2H cluster, W5+ is bonded in a single-bond geometry to one H1+ atom. The W–H bond length is 1.92 Å. H1+ is bonded in a bent 120 degrees geometry to two equivalent W5+ atoms. In each W2H(NO)2 cluster, W5+ is bonded in a linear geometry to one N3- and one H1+ atom. The W–N bond length is 1.90 Å. The W–H bond length is 1.95 Å. N3- is bonded in a linear geometry to one W5+ and one O2- atom. The N–O bond length is 1.17 Å. H1+ is bonded in a bent 120 degrees geometry to two equivalent W5+ atoms. O2- is bonded in a single-bond geometry to one N3- atom.

36 MATERIALS SCIENCE↗

NASA NTRS1973

Spin contamination in unrestricted Hartree-Fock calculations.

Several pi-electron doublets are treated by both the unrestricted Hartree-Fock method and the restricted approximation of Longuet-Higgins and Pople. For two of the molecules, which contain oxygen heteroatoms, serious spin contamination occurs in the UHF wavefunctions, and this negates the usefulness of the single annihilation procedure that is often used for spin-density calculations. The restricted approximation provides a convenient alternative, especially because configuration interaction is easily taken into account.

Schug, J. C.↗

NASA NTRS1985

Electron emission and acoustic emission from the fracture of graphite/epoxy composites

In past studies it has been shown that the fracture of materials leads to the emission of a variety of species, including electrons, ions, neutral molecules, and photons, all encompassed by the term 'fractoemission' (FE). In this paper, electron emission (EE) from the fracture of single graphite fibers and neat epoxy resin is examined. Measurements of EE are also combined with the detection of acoustic emission (AE) during the testing of graphite-epoxy composite specimens with various fiber orientation. The characteristics of these signals are related to known failure mechanisms in fiber-reinforced plastics. This study suggests that by comparing data from AE and FE measurements, one can detect and distinguish the onset of internal and external failure in composites. EE measurements are also shown to be sensitive to the locus of fracture in a composite material.

Dickinson, J. T.↗

NASA NTRS1985

Two-frequency laser-induced fluorescence technique for rapid velocity-field measurements in gas flows

A technique is presented for measurements of two-dimensional velocity fields in gas flows. The single-mode frequency of an argon-ion laser is fixed in the wing of an absorption line of iodine molecules that are seeded at low level in the flow of interest. The emitted fluorescence is detected with an image-intensified 100 x 100 photodiode-array camera. two pairs of counterpropagating laser sheets sequentially probe the flow to determine two velocity components. The frequency in one pair is shifted with respect to the other by an acousto-optic modulator. This two-frequency scheme eliminates the need to determine the slope of the line externally and offers the potential for combined pressure and velocity-field measurements.

Hiller, B.↗

NASA NTRS1990

Electronic and molecular structure of carbon grains

Clusters of carbon atoms have been studied with large-scale ab initio calculations. Planar, single-sheet graphite fragments with 6 to 54 atoms were investigated, as well as the spherical C(sub 60) Buckminsterfullerene molecule. Polycyclic aromatic hydrocarbons (PAHs) have also been considered. Thermodynamic differences between diamond- and graphite-like grains have been studied in particular. Saturation of the peripheral bonds with hydrogen is found to provide a smooth and uniform convergence of the properties with increasing cluster size. For the graphite-like clusters the convergence to bulk values is much slower than for the three-dimensional complexes.

Almloef, Jan↗

NASA NTRS2008

Gas Sensors Based on Coated and Doped Carbon Nanotubes

Efforts are underway to develop inexpensive, low-power electronic sensors, based on single-walled carbon nanotubes (SWCNTs), for measuring part-per-million and part-per-billion of selected gases (small molecules) at room temperature. Chemically unmodified SWCNTs are mostly unresponsive to typical gases that one might wish to detect. However, the electrical resistances of SWCNTs can be made to vary with concentrations of gases of interest by coating or doping the SWCNTs with suitable materials. Accordingly, the basic idea of the present development efforts is to incorporate thus-treated SWCNTs into electronic devices that measure their electrical resistances.

Li, Jing↗

NASA NTRS2010

Multiple Velocity Profile Measurements in Hypersonic Flows using Sequentially-Imaged Fluorescence Tagging

Nitric-oxide planar laser-induced fluorescence (NO PLIF) was used to perform velocity measurements in hypersonic flows by generating multiple tagged lines which fluoresce as they convect downstream. For each laser pulse, a single interline, progressive scan intensified CCD camera was used to obtain separate images of the initial undelayed and delayed NO molecules that had been tagged by the laser. The CCD configuration allowed for sub-microsecond acquisition of both images, resulting in sub-microsecond temporal resolution as well as sub-mm spatial resolution (0.5-mm x 0.7-mm). Determination of axial velocity was made by application of a cross-correlation analysis of the horizontal shift of individual tagged lines. Quantification of systematic errors, the contribution of gating/exposure duration errors, and influence of collision rate on fluorescence to temporal uncertainty were made. Quantification of the spatial uncertainty depended upon the analysis technique and signal-to-noise of the acquired profiles. This investigation focused on two hypersonic flow experiments: (1) a reaction control system (RCS) jet on an Orion Crew Exploration Vehicle (CEV) wind tunnel model and (2) a 10-degree half-angle wedge containing a 2-mm tall, 4-mm wide cylindrical boundary layer trip. The experiments were performed at the NASA Langley Research Center's 31-inch Mach 10 wind tunnel.

Bathel, Brett F.↗

NASA NTRS2006

Stable Carbon Isotopic Signatures of Abiotic Organics from Hydrothermal Synthesis Experiments

Stable carbon isotopes can be powerful biogeochemical markers in the study of life's origins. Biogenic carbon fixation produces organics that are depleted in C-13 by about -20 to -30%0. Less attention has been paid to the isotopic signatures of abiotic processes. The possibility of abiotic processes producing organics with morphologies and isotopic signatures in the biogenic range has been at the center of recent debate over the Earth's earliest microfossils. The abiotic synthesis of organic compounds in hydrothermal environments is one possible source of endogenous organic matter to the prebiotic earth. Simulated hydrothermal settings have been shown to synthesize, among other things, single chain amphiphiles and simple lipids from a mix of CO, CO2, and H2. A key characteristic of these amphiphilic molecules is the ability to self-assemble in aqueous phases into more organized structures called vesicles, which form a selectively permeable boundary and serve the function of containing and concentrating other organic molecules. The ability to form cell like structures also makes these compounds more likely to be mistaken for biogenic. Hydrothermal simulation experiments were conducted from oxalic or formic acid in water at 175 C for 72 hr. The molecular and isotopic composition of the products of these reactions were determined and compared to biogenic fractionations . Preliminary results indicate isotopic fractionation during abiotic hydrocarbon synthesis in hydrothermal environments is on par with biological carbon fixation.

Stern, Jennifer C.↗

DOE OSTI2021

Amino‐Functionalised Hybrid Ultramicroporous Materials that Enable Single‐Step Ethylene Purification from a Ternary Mixture

Abstract Pyrazine‐linked hybrid ultramicroporous (pore size <7 Å) materials (HUMs) offer benchmark performance for trace carbon capture thanks to strong selectivity for CO 2 over small gas molecules, including light hydrocarbons. That the prototypal pyrazine‐linked HUMs are amenable to crystal engineering has enabled second generation HUMs to supersede the performance of the parent HUM, SIFSIX‐3‐Zn , mainly through substitution of the metal and/or the inorganic pillar. Herein, we report that two isostructural aminopyrazine‐linked HUMs, MFSIX‐17‐Ni (17=aminopyrazine; M=Si, Ti), which we had anticipated would offer even stronger affinity for CO 2 than their pyrazine analogs, unexpectedly exhibit reduced CO 2 affinity but enhanced C 2 H 2 affinity. MFSIX‐17‐Ni are consequently the first physisorbents that enable single‐step production of polymer‐grade ethylene (>99.95 % for SIFSIX‐17‐Ni ) from a ternary equimolar mixture of ethylene, acetylene and CO 2 thanks to coadsorption of the latter two gases. We attribute this performance to the very different binding sites in MFSIX‐17‐Ni versus SIFSIX‐3‐Zn .

Mukherjee, Soumya↗

DOE OSTI2021

Amino‐Functionalised Hybrid Ultramicroporous Materials that Enable Single‐Step Ethylene Purification from a Ternary Mixture

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2026

Viral Nuclease Inhibitors: Small molecule disruptors of the UL12 alkaline nuclease display broad anti-herpes virus activity

Herpes simplex virus 1 (HSV-1) UL12 encodes a highly conserved 5′ → 3′ alkaline exonuclease that is essential for the production of infectious virus. Together with the viral single-stranded DNA-binding/annealing protein ICP8, UL12 functions as a two-component recombinase that mediates recombination-dependent viral DNA replication. Here, we present the crystal structure of the catalytic domain of the HSV alkaline nuclease (UL12), which provides the first view of an α-herpesvirus alkaline nuclease. Using this structure, we optimized a series of small-molecule viral nuclease inhibitors (VNIs) that target the UL12 active site and potently inhibit UL12 exonuclease activity in vitro. We have thus established a robust platform for structure-based docking, SAR analysis and rational inhibitor design. Because UL12 orthologs are conserved across all human herpesviruses, we examined the activity of these compounds against the β- and γ-herpesvirus alkaline nucleases UL98 and SOX and found that they inhibit all three enzymes. The VNIs also exhibit antiviral activity against HSV-1 and HCMV in cell culture. EC 50 and IC 50 values were in the nanomolar to low micromolar range. Together, these findings establish herpesvirus alkaline nucleases as conserved, druggable antiviral targets and provide a foundation for the development of broad-spectrum anti-herpesvirus therapeutics, either as standalone agents or in combination with existing nucleoside analogs.

Sharma, Nidhi↗