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DOE OSTI2024

Cost-efficient temperature mediation of DPMS synthesis in flow using continuous flow chemistry

An efficient synthesis of diphenylmethylsilanol (DPMS) utilizing continuous flow chemistry was performed using a coil reactor and an ice bath. The inclusion of careful temperature control minimized the exothermic production of an unwanted dimer. Yields of up to 88% were obtained and dimer formation as low as 2.2% was confirmed by NMR. This material will be used in the formulation to make SX358 and its physical and chemical characteristics will be determined using DSC, DMA, TMA, compression set testing and FTIR.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Towards Elucidating Structure–Spectra Relationships in Rhamnogalacturonan II: Computational Protocols for Accurate 13C and 1H Shifts for Apiose and Its Borate Esters

Apiose is a naturally occurring, uncommon branched-chain pentose found in plant cell walls as part of the complex polysaccharide Rhamnogalacturonan II (RG-II). The structural elucidation of the three-dimensional structure of RG-II by nuclear magnetic resonance (NMR) spectroscopy is significantly complicated by the ability of apiose to cross-link via borate ester linkages to form RG-II dimers. Here, we developed a computational approach to gain insight into the structure–spectra relationships of apio–borate complexes in an effort to complement experimental assignments of NMR signals in RG-II. Our protocol involved structure optimizations using density functional theory (DFT) followed by isotropic magnetic shielding constant calculations using the gauge-invariant atomic orbital (GIAO) approach to predict chemical shifts. We evaluated the accuracy of 23 different functional–basis set (FBS) combinations with and without implicit solvation for predicting the experimental 1 H and 13 C shifts of a methyl apioside and its three borate derivatives. The computed NMR predictions were evaluated on the basis of the overall shift accuracy, relative shift ordering, and the ability to distinguish between dimers and monomers. We demonstrate that the consideration of implicit solvation during geometry optimizations in addition to the magnetic shielding constant calculations greatly increases the accuracy of NMR chemical shift predictions and can correctly reproduce the ordering of the 13 C shifts and yield predictions that are, on average, within 1.50 ppm for 13 C and 0.12 ppm for 1 H shifts for apio–borate compounds.

BASIC BIOLOGICAL SCIENCES,BIOMASS FUELS↗

DOE OSTI2023

Pseudomonas aeruginosa Dps (PA0962) Functions in H 2 O 2 Mediated Oxidative Stress Defense and Exhibits In Vitro DNA Cleaving Activity

We report the structural, biochemical, and functional characterization of the product of gene PA0962 from Pseudomonas aeruginosa PAO1. The protein, termed Pa Dps, adopts the Dps subunit fold and oligomerizes into a nearly spherical 12-mer quaternary structure at pH 6.0 or in the presence of divalent cations at neutral pH and above. The 12-Mer Pa Dps contains two di-iron centers at the interface of each subunit dimer, coordinated by conserved His, Glu, and Asp residues. In vitro, the di-iron centers catalyze the oxidation of Fe 2+ utilizing H 2 O 2 (not O 2 ) as an oxidant, suggesting Pa Dps functions to aid P. aeruginosa to survive H 2 O 2 -mediated oxidative stress. In agreement, a P. aeruginosa Δdps mutant is significantly more susceptible to H 2 O 2 than the parent strain. The Pa Dps structure harbors a novel network of Tyr residues at the interface of each subunit dimer between the two di-iron centers, which captures radicals generated during Fe 2+ oxidation at the ferroxidase centers and forms di-tyrosine linkages, thus effectively trapping the radicals within the Dps shell. Surprisingly, incubating Pa Dps and DNA revealed unprecedented DNA cleaving activity that is independent of H 2 O 2 or O 2 but requires divalent cations and 12-mer Pa Dps.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Toward closure between predicted and observed particle viscosity over a wide range of temperatures and relative humidity

Abstract. Atmospheric aerosols can exist in amorphous semi-solid or glassy phase states whose viscosity varies with atmospheric temperature and relative humidity. The temperature and humidity dependence of viscosity has been hypothesized to be predictable from the combination of a water–organic binary mixing rule of the glass transition temperature, a glass-transition-temperature-scaled viscosity fragility parameterization, and a water uptake parameterization. This work presents a closure study between predicted and observed viscosity for sucrose and citric acid. Viscosity and glass transition temperature as a function of water content are compiled from literature data and used to constrain the fragility parameterization. New measurements characterizing viscosity of sub-100 nm particles using the dimer relaxation method are presented. These measurements extend the available data of temperature- and humidity-dependent viscosity to −28 ∘C. Predicted relationships agree well with observations at room temperature and with measured isopleths of constant viscosity at ∼107 Pa s at temperatures warmer than −28 ∘C. Discrepancies at colder temperatures are observed for sucrose particles. Simulations with the kinetic multi-layer model of gas–particle interactions suggest that the observed deviations at colder temperature for sucrose can be attributed to kinetic limitations associated with water uptake at the timescales of the dimer relaxation experiments. Using the available information, updated equilibrium phase-state diagrams (-80∘C

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2022

Characterization of a modified printed optical particle spectrometer for high-frequency and high-precision laboratory and field measurements

Abstract. The printed optical particle spectrometer (POPS) is a lightweight, low-cost instrument for measurements of aerosol number concentrations and size distributions. This work reports on modifications of the Handix Scientific commercial version of the POPS to facilitate its use in multi-instrument aerosol sampling systems. The flow system is modified by replacing the internal pump with a needle valve and a vacuum pump. The instrument is integrated into closed-flow systems by routing the sheath flow from filtered inlet air. A high-precision multichannel analyzer (MCA) card is added to sample the analog pulse signal. The MCA card is polled at 10 Hz frequency using an external data acquisition system and improves upon the count-rate limitation associated with the POPS internal data acquisition system. The times required to change the concentration between 90 % and 10 % and vice versa for a step change in concentration were measured to be 0.17 and 0.41 s at a flow rate of 5 cm3 s−1. This yields a sampling frequency of ∼ 1–2 Hz, below which the amplitude of measured fluctuations is captured with > 70 % efficiency. The modified POPS was integrated into the dual tandem differential mobility analyzer system to explore the coalescence of dimer particles. Results show that the pulse-height response increases upon dimer coalescence. The magnitude of the increase is broadly consistent with the change in light-scattering amplitude predicted by the T-matrix method. It is anticipated that this modified version of the POPS will extend the utilization of the technique for a range of field and laboratory applications.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2026

Dielectric Resonator Design for Low Power and Low Temperature Microwave Plasma

Waveguide-based microwave plasmas generally operate at high temperatures (2000 - 6000K)[1], making it difficult to directly interface solid materials with the plasma without significant thermal damage. Dielectric microwave resonators (DMRs), long studied for wave-based manipulation of electromagnetic radiation for telecom and optics, can focus radiation to extremely small mode volumes, creating intense localized fields with low-power input.[2] This phenomenon can be used for applications ranging from efficient plasma electronics to near-ambient plasma-materials interactions. Such DMR-based plasmas have been demonstrated a handful of times in the literature, but the majority of research towards this utilize the lowest frequency resonance mode.[3], [4], [5] By carefully controlling the geometry of cylindrical resonators, a variety of electromagnetic modes can be excited. In this work, COMSOL Multiphysics simulations are used to study the electric field enhancement and absorption properties of CaTiO3 DMRs as a function of geometry and excitation frequency. Whereas previous studies have utilized the HEM111 resonance frequency to drive low power plasma excitation, we find that higher order resonance frequencies are more effective at field enhancement and result in less power loss within the dielectric material, hence less wasted heating. The effectiveness of these modes is also geometry dependent and can be computationally optimized for plasma generation. Complementing these computational efforts, we demonstrate a new closed-system reactor design built in a WR-650 waveguide and experimentally demonstrate the formation of atmospheric argon microwave plasma using < 30 W input power on DMR dimers. We observe a shifting resonance frequency as the DMRs heat in response to microwave excitation and develop a Python-based lock-in mechanism to effectively track the DMR resonance over time, leading to stable plasma operation. We use infrared thermal imaging to monitor the temperature of the DMR dimers and surrounding quartz chamber, demonstrating thermal temperatures < 60 degreesC. Finally, we utilize optical emission spectroscopy (OES) to probe the plasma properties as a function of the resonance mode.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2024

Conformational heterogeneity of the BTK PHTH domain drives multiple regulatory states

Full-length Bruton’s tyrosine kinase (BTK) has been refractory to structural analysis. The nearest full-length structure of BTK to date consists of the autoinhibited SH3–SH2–kinase core. Precisely how the BTK N-terminal domains (the Pleckstrin homology/Tec homology [PHTH] domain and proline-rich regions [PRR] contain linker) contribute to BTK regulation remains unclear. We have produced crystals of full-length BTK for the first time but despite efforts to stabilize the autoinhibited state, the diffraction data still reveal only the SH3–SH2–kinase core with no electron density visible for the PHTH–PRR segment. Cryo-electron microscopy (cryoEM) data of full-length BTK, on the other hand, provide the first view of the PHTH domain within full-length BTK. CryoEM reconstructions support conformational heterogeneity in the PHTH–PRR region wherein the globular PHTH domain adopts a range of states arrayed around the autoinhibited SH3–SH2–kinase core. On the way to activation, disassembly of the SH3–SH2–kinase core opens a new autoinhibitory site on the kinase domain for PHTH domain binding that is ultimately released upon interaction of PHTH with phosphatidylinositol (3,4,5)-trisphosphate. Membrane-induced dimerization activates BTK and we present here a crystal structure of an activation loop swapped BTK kinase domain dimer that likely represents the conformational state leading to trans-autophosphorylation. Together, these data provide the first structural elucidation of full-length BTK and allow a deeper understanding of allosteric control over the BTK kinase domain during distinct stages of activation.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Dual engagement of the nucleosomal acidic patches is essential for deposition of histone H2A.Z by SWR1C

The yeast SWR1C chromatin remodeling enzyme catalyzes the ATP-dependent exchange of nucleosomal histone H2A for the histone variant H2A.Z, a key variant involved in a multitude of nuclear functions. How the 14-subunit SWR1C engages the nucleosomal substrate remains largely unknown. Studies on the ISWI, CHD1, and SWI/SNF families of chromatin remodeling enzymes have demonstrated key roles for the nucleosomal acidic patch for remodeling activity, however a role for this nucleosomal epitope in nucleosome editing by SWR1C has not been tested. Here, we employ a variety of biochemical assays to demonstrate an essential role for the acidic patch in the H2A.Z exchange reaction. Utilizing asymmetrically assembled nucleosomes, we demonstrate that the acidic patches on each face of the nucleosome are required for SWR1C-mediated dimer exchange, suggesting SWR1C engages the nucleosome in a ‘pincer-like’ conformation, engaging both patches simultaneously. Loss of a single acidic patch results in loss of high affinity nucleosome binding and nucleosomal stimulation of ATPase activity. We identify a conserved arginine-rich motif within the Swc5 subunit that binds the acidic patch and is key for dimer exchange activity. In addition, our cryoEM structure of a Swc5–nucleosome complex suggests that promoter proximal, histone H2B ubiquitylation may regulate H2A.Z deposition. Together these findings provide new insights into how SWR1C engages its nucleosomal substrate to promote efficient H2A.Z deposition.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1977

A production parylene coating process for hybrid microcircuits

The real impetus for developing a production parylene coating process for internal hybrid passivation came as a result of the possibility of loose conductive particles in hybrid microelectronic circuits, causing intermittent and sometimes permanent failures. Because of the excellent mechanical properties of parylene, it is capable of securing the loose particles in place and prevent such failures. The process of coating described consists of (1) vaporizing the initial charge, which is in the form of a dimer; (2) conversion of the dimer into a reactive monomer; and (3) deposition and subsequent polymerization of the monomer in the deposition chamber which forms a uniform parylene film over all the cold surfaces in contact. Experimental results are discussed in terms of wire bond reliability, resistor drift, high-temperature storage characteristics of parylene, and coating acceptance standards. It is concluded that internal cavities of microelectronic circuits can be successfully coated with parylene provided appropriate tooling is used to protect external leads from the parylene monomer.

Kale, V. S.↗

NASA NTRS1977

Nitrogen-induced absorption of oxygen in the Herzberg continuum

Total absorption of O2 induced by collisions with N2 has been measured at room temperature in the Hersberg continuum using a one meter normal incidence grating monochromator. The enhanced absorption is ascribed to the formation of O2-O2 and O2-N2 dimers. The interaction constants for these dimers are determined and utilized to investigate their effect on the absorption of solar radiation in the stratosphere.

Shardanand, MR.↗

NASA NTRS1981

Synthesis of oligoguanylates on oligocytidylate templates

The influence of template length in the self-condensation of guanosine 5'-phosphorimidazole in the presence of oligocytidylate templates is investigated. Reactions were carried out with cyclic cytidine 2',3'-phosphate, oligo- or polyC, and radioactively labeled guanosine 5'-phosphorimidazolide in the presence of Zn(+2) or Pb(+2) catalyst; product yields were determined by paper chromatography, thin-layer chromatography, and high-performance liquid chromatography. In the absence of a catalytic metal or in the presence of Pb(+2), a significant template effect is observed starting with the cytidine dimer and increasing in yield up to the hexamer template. Oligomers longer than the template are observed, and are predominantly 2'-5' linked in the presence of Pb(+2) and of mixed linkages in the uncatalyzed reaction. With the zinc ion as the catalyst, the template effect is first observed with the pentamer and is maximal with the heptamer. Products are predominantly 3'-5', and only a small proportion of them are longer than the template. The importance of the demonstrated formation of molecules with up to 10 guanosine units from oligocytidines as short as the dimer on the primitive earth is noted.

Fakhrai, H.↗

NASA NTRS1989

The rotational spectrum and structure of chlorine peroxide

The dimerization products of the ClO + ClO reaction were investigated in a flowing chemical reactor using submillimeter wave spectroscopy. The major products were identified as the chlorine peroxide (Cl2O2) and chlorine dioxide (OClO). The rotational constants as well as a complete set of quartic centrifugal distortion constants were determined. The identification of the chlorine peroxide supports the earlier proposed ClO-dimer mechanisms, which partly explain the ozone hole formation during the Antarctic springtime.

Birk, Manfred↗

NASA NTRS1990

Reactivity of pi-complexes of Ti, V, and Nb towards dithioacetic acid: Synthesis and structure of novel metal sulfur-containing complexes

In order to use sulfur-containing resources economically and with minimal environmental damage, it is important to understand the desulfurization processes. Hydrodesulfurization, for example, is carried out on the surface of a heterogeneous metal sulfide catalyst. Studies of simple, soluble inorganic systems provide information regarding the structure and reactivity of sulfur-containing compounds with metal complexes. Further, consistent with recent trends in materials chemistry, many model compounds warrant further study as catalyst precursors. The reactivity of low-valent organometallic sandwich pi-complexes toward dithiocarboxylic acids is described. For example, treatment of bisbenzene vanadium with CH3CSSH affords a divanadium tetrakis(dithioacetate) complex. The crystallographically determined V-V bond distance, 2.800(2), is nearly the same as the V-V bond distance in a V(mu-nu squared-S2)2V' unit in the mineral patonite (VS4)n. The stability of the V2S4 core in the dimer is demonstrated by evidence of V2S4(+) in the mass spectrum (70 eV, solid probe) of the vanadium dimer. Several other systems relevant to HDS catalysis are also discussed.

Duraj, Stan A.↗

NASA NTRS1992

Determination of monomer concentrations in crystallizing lysozyme solutions

We have developed a non-optical technique for the study of aggregation in lysozyme and other protein solutions. By monitoring the rate at which lysozyme traverses a semipermeable membrane it was possible to quantitate the degree of aggregation in supersaturated solutions. Using this technique, we have measured the concentration of monomers and larger aggregates in under- and oversaturated lysozyme solutions, and in the presence of crystals, at pH 4.0 and 3 percent NaCl (0.1M NaAc). Comparison of these concentration profiles with (110) face growth rate data supports the theory that tetragonal lysozyme crystals grow by addition of preformed aggregates and not by monomer addition. The data suggest that a considerable population of aggregates larger than dimers are present at lysozyme concentrations above 22 mg/ml. Determination of dimer concentrations, and equilibrium constants for subsequent aggregation levels, are currently underway.

Wilson, L. J.↗

NASA NTRS1992

Direct observation of ClO from chlorine nitrate photolysis

Chlorine nitrate photolysis has been investigated with the use of a molecular beam technique. Excitation at both 248 and 193 nanometers led to photodissociation by two pathways, ClONO2 yields ClO + NO2 and ClONO2 yields Cl + NO3, with comparable yields. This experiment provides a direct measurement of the ClO product channel and consequently raises the possibility of an analogous channel in ClO dimer photolysis. Photodissociation of the ClO dimer is a critical step in the catalytic cycle that is presumed to dominate polar stratospheric ozone destruction. A substantial yield of ClO would reduce the efficiency of this cycle.

Minton, Timothy K.↗

NASA NTRS1992

Metal-organic chemical vapour deposition of polycrystalline tetragonal indium sulphide (InS) thin films

The dimeric indium thiolate /(t Bu)2In(mu-S sup t Bu)/2 has been used as a single-source precursor for the MOCVD of InS thin films. The dimeric In2S2 core is proposed to account for the formation of the nonequilibrium high-pressure tetragonal phase in the deposited films. Analysis of the deposited films has been obtained by TEM, with associated energy-dispersive X-ray analysis and X-ray photoelectron spectroscopy.

Macinnes, Andrew N.↗

NASA NTRS1993

Evaluation of ovostatin and ovostatin assay

Ovostatin is a 780,000 MW protein, originally isolated from chicken egg white, which is active as a protease inhibitor. Structural studies indicate that the protein is a tetramer of identical subunits of 165,000 MW which can be separated upon reduction with beta- mercaptoethanol. Chicken ovostatin is an inhibitor of metalloproteases such as collagenase and thermolysin, and of acid proteases such as pepsin and rennin. Ovostatin isolated from duck eggs and from crocodile eggs appears to be similar to chicken egg ovostatin, but with significant differences in structure and function. Duck ovostatin contains a reactive thiol ester which is not found in the chicken protein, and duck and crocodile ovostatin inhibit serine protease such as trypsin and chymotrypsin, while chicken ovostatin does not. Electron microscopy of ovostatin indicates that two subunits associated near the middle of each polypeptide to form a dimer with four arms. Two of these dimers then associate to produce a tetramer with eight arms, with the protease binding site near the center of the molecule. Upon binding of the protease, a conformational change causes all eight arms to curl toward the center of the molecule, effectively trapping the protease and sterically hindering access of the substrates to its active site. The structural organization and mechanism of action proposed for ovostatin are nearly identical to that proposed for alpha(sub 2)- macroglobulin, a serum protease inhibitor which may play an important role in regulation of proteases in animal tissues. Although the general arrangement of subunits appears to be the same for all ovostatins studied, some differences have been observed, with chicken ovostatin more closely resembling reptilian ovostatin than the duck protein. This is a surprising result, given the evolutionary relatedness of chickens and ducks. It is possible that the differences in structures may be due to deformed subunit arrangements which occur during the processing and fixing necessary for electron microscopy. Examination of the native structure of these proteins using X-ray crystallography would help clarify these discrepancies.

Moriarity, Debra M.↗

NASA NTRS1994

Archean geochemistry of formaldehyde and cyanide and the oligomerization of cyanohydrin

The sources and speciation of reduced carbon and nitrogen inferred for the early Archean are reviewed in terms of current observations and models, and known chemical reactions. Within this framework hydrogen cyanide and cyanide ion in significant concentration would have been eliminated by reaction with excess formaldehyde to form cyanohydrin (glycolonitrile), and with ferrous ion to formferrocyanide. Natural reactions of these molecules would under such conditions deserve special consideration in modeling of primordial organochemical processes. As a step in this direction, transformation reactions have been investigated involving glycolonitrile in the presence of water. We find that glycolonitrile, formed from formaldehyde and hydrogen cyanide or cyanide ion, spontaneously cyclodimerizes to 4-amino-2-hydroxymethyloxazole. The crystalline dimer is the major product at low temperatue (approximately 0 C); the yield diminishes with increasing temperature at the expense of polymerization and hydrolysis products. Hydrolysis of glycolamide and of oxazole yields a number of simpler organic molecules, including ammonia and glycolamide. The spontaneous polymerization of glycolonitrile and its dimer gives rise to soluble, cationic oligomers of as yet unknown structure, and, unless arrested, to a viscous liquid, insoluble in water. A loss of cyanide by reaction with formaldehyde, inferred for the early terrestrial hydrosphere and cryosphere would present a dilemma for hypotheses invoking cyanide and related compounds as concentrated reactants capable of forming biomolecular precursor species. Attempts to escape from its horns may take advantage of the efficient concentration and separation of cyanide as solid ferriferrocyanide, and most directly of reactions of glycolonitrile and its derivatives.

Arrhenius, T.↗