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At least 361 records · Page 20

Nucleation of cubic boron nitride on boron-doped diamond via plasma enhanced chemical vapor deposition

Cubic boron nitride (c-BN), with a small 1.4% lattice mismatch with diamond, presents a heterostructure with multiple opportunities for electronic device applications. However, the formation of c-BN/diamond heterostructures has been limited by the tendency to form hexagonal BN at the interface. In this study, c-BN has been deposited on free standing polycrystalline and single crystal boron-doped diamond substrates via electron cyclotron resonance plasma enhanced chemical vapor deposition (ECR-PECVD), employing fluorine chemistry. In situ x-ray photoelectron spectroscopy (XPS) is used to characterize the nucleation and growth of boron nitride (BN) films as a function of hydrogen gas flow rates during deposition. The PECVD growth rate of BN was found to increase with increased hydrogen gas flow. In the absence of hydrogen gas flow, the BN layer was reduced in thickness or etched. The XPS results show that an excess of hydrogen gas significantly increases the percent of sp2 bonding, characteristic of hexagonal BN (h-BN), particularly during initial layer growth. Reducing the hydrogen flow, such that hydrogen gas is the limiting reactant, minimizes the sp2 bonding during the nucleation of BN. TEM results indicate the partial coverage of the diamond with thin epitaxial islands of c-BN. The limited hydrogen reaction is found to be a favorable growth environment for c-BN on boron-doped diamond.

Physics↗

TCF - Sustainable Well Cement for Geothermal, Thermal Recovery, and Carbon Storage wells

Primary cementing is the most important operation performed on a subterranean well. Cement, placed in the annulus between the casing and the formations, serves as a hydraulic seal preventing fluids and gas migrations, protecting steel casing from corrosion, and supporting the well structure. Poor cementing jobs can be directly responsible for wells not reaching their full capacity, casing corrosion, compromised well integrity and, in the worst-case scenarios, well collapse. Geothermal, thermal recovery, and carbon storage wells offer environments that are especially difficult for cements to survive while the required lifespan of these wells can be years. In these wells currently used cements cannot provide durable well integrity, and new solutions are necessary. The necessity of stabilizing the electric grid, increasing its flexibility, and providing energy on demand will further expand the market of durable cement solutions for applications in high-temperature underground reservoir thermal energy storage wells (HT RTES). The design challenges of special cement systems for such wells originate from chemistry limitations of currently used well cements, aggressive environments, temperature and repeated shock conditions associated with them, and very weak formations that are not uncommon in these wells. During the last 70 years the most common systems for thermal-well construction have been Ordinary Portland Cement (OPC) (absolute majority of the wells), silica-lime system, and high aluminum cement-containing formulations. The major issues of calcium-silicate hydrates, that form during the hydration of OPC resulting in hardened material, are their poor chemical resistance to acids due to the calcium interactions with acid anions followed by its eventual dissolution, even in mild acids, such as carbonic acid from CO 2 dissolution, and inadequate bonding to the steel causing serious casing corrosion problems (Sugama & Pyatina, 2019). Performance of OPC-based cement may be significantly improved with organic additives; however, those are limited by their temperature stability. An alternative to calcium-silicate cement was developed by BNL and commercialized by Halliburton as ThermaLock TM cement. Calcium-aluminate-phosphate-based chemistry of the material allowed overcoming acid-resistance problems of OPC, especially in CO 2 -rich geothermal environments. In 2012-2015, building upon this experience, BNL developed Thermal Shock Resistant Cement (TSRC) with the support of Geothermal Technology Office (GTO) of DOE. TSRC has high-temperature stable chemistry, superior properties of cement-metal casing bond and corrosion protection (4-times better than currently used OPC-based formulation), significantly outperforms common well-cements in thermal-shock tests, has self-healing properties, and like ThermaLock TM is CO 2 resistant incorporating carbonate ions into stable hydrates (Gill et al., 2012).

15 GEOTHERMAL ENERGY↗

Constructive molecular configurations for surface-defect passivation of perovskite photovoltaics

Surface trap-mediated nonradiative charge recombination is a major limit to achieving high-efficiency metal-halide perovskite photovoltaics. The ionic character of perovskite lattice has enabled molecular defect passivation approaches through interaction between functional groups and defects. However, a lack of in-depth understanding of how the molecular configuration influences the passivation effectiveness is a challenge to rational molecule design. In this work, the chemical environment of a functional group that is activated for defect passivation was systematically investigated with theophylline, caffeine, and theobromine. When N-H and C=O were in an optimal configuration in the molecule, hydrogen-bond formation between N-H and I (iodine) assisted the primary C=O binding with the antisite Pb (lead) defect to maximize surface-defect binding. A stabilized power conversion efficiency of 22.6% of photovoltaic device was demonstrated with theophylline treatment.

14 SOLAR ENERGY↗

Examining the role of glycoside hydrolases in local rheology of Pseudomonas aeruginosa biofilms

Current research strategies in the treatment of biofilm infections have focused on dispersal, in which bacteria are made to vacate the extracellular polymeric substance (EPS) surrounding them and return to a planktonic state where antimicrobial treatments are more effective. Glycoside hydrolases (GHs), which cleave bonds in EPS polysaccharides, have been shown to promote dispersal in Pseudomonas aeruginosa biofilms. The dispersal mechanism is possibly due to GHs’ ability to directly release bacteria from the EPS, disrupt EPS’ ability to regulate the environment, or reduce overall mechanical stability. In this work, passive microrheology is used to examine the relevance of the last mechanism by exploring the effects of three GHs (α-amylase, cellulase, and xylanase) known to disperse P. aeruginosa on local biofilm viscoelasticity. Compared to control studies in wild-type strains, it is found that treatment with all three GHs results in statistically relatively less elastic and stiffer biofilms, indicating that changes to mechanical stability may be a factor in effective dispersal. Both cellulase and xylanase were observed to have the greatest impact in creating a less stiff and elastic biofilm; these GHs have been observed to be effective at dispersal in the published results. Each GH was further tested on biofilms grown with strains that produced EPS missing specific polysaccharide components. Cellulase specifically targeted Psl, which forms the major structural and mechanical backbone of the EPS, explaining its efficacy in dispersal. However, xylanase did not appear to exhibit any affinity to any polysaccharide within the EPS based on the microrheology results. Overall, these results suggest that the local microrheology of the biofilms is impacted by GHs and that may be one of the factors that is causing the ability of these therapeutics to enhance dispersal.

59 BASIC BIOLOGICAL SCIENCES↗

On electron beam-induced degradation of vinyl ester thermosets

We have demonstrated that electron beam radiolysis induces scissions of the C-O-C bonds along the backbone of the chains of unsaturated polyester thermosets of different compositions based on dicyclopentadiene, isophthalic acid, epoxy vinyl ester, and terephthalic acid. The radiolysis is imminent irrespective of the degree of crosslinking in the thermosets both in neat resins and in the presence of solvents. Electron Paramagnetic Resonance (EPR) results show the formation of the alkoxyl radicals and C-centered radicals as the primary intermediate products of the C-O-C scissions. While the alkoxyl radicals of these resins exhibit very good stability even six months after the irradiation, the C-centered radicals decay very rapidly via their reactions with oxygen that is available either as adsorbed in the resins, dissolved in solvents or from the environment. The radiolytically produced •OH radicals in the unsaturated-ester aqueous solutions play a major role in inducing scissions on the backbone of the polymer chains. The solvated electrons (e s ) from organic solvents, such as dimethyl sulfoxide and isopropyl alcohol, also induce direct scission of the C-O-C bonds, giving rise to the formation of alkoxyl radicals and C-centered radicals. However, a considerable fraction of es is scavenged by the dissolved O 2 to produce O 2 - . Despite the radiation-induced scissions, irradiation of the resins at a dose level of 1000 kGy results in an increase of the glass transition temperature, Tg. This is due to the simultaneous radiation-induced polymerization of the vinyl monomers, toluene, and styrene that are present in the resins. The increase in Tg is observed in all the resins except for the terephthalic polyester resin in aqueous solution, in which the absence of these monomers results in Tg decreasing sharply with irradiation. This work demonstrates that ionizing radiation triggers continuous free radical-chain reactions that lead to the formation of recyclable oligomers.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗

Characterization of biological materials with soft X-ray scattering

The complex structure of biological assemblies is crucial for function yet challenging to discern given the chemical similarities between constituent components. Hard X-ray techniques, for example, rely on small density differences between domains that lead to modest scattering intensities. Resonant soft X-ray scattering (RSoXS) uses X-rays below 2 keV to access absorption edges of low-Z elements. In this way, RSoXS can enhance scattering contrast between domains of different chemical compositions or bonding motifs, thus providing structural information about specific chemical motifs. RSoXS is emerging as a technique applicable for biological systems, having been used to characterize protein structure in solution and polysaccharide organization in plant cell walls. Sample environment instrumentation, however, is challenging in the current state of the art, particularly with liquid samples. Here, this chapter contains a brief introduction to RSoXS and current beamline capabilities, and provides methods to prepare, store, and mount biological samples for RSoXS characterization. Furthermore, key details during RSoXS and X-ray absorption data acquisition are highlighted and some future opportunities in RSoXS instrumentation for biological systems are discussed.

47 OTHER INSTRUMENTATION↗

First-principles insights into chromium-induced oxide phases in NiO

The high-temperature oxidation of Ni–Cr alloys leads to complex oxide scales comprising Ni(Cr)O solid solutions, NiCr 2 O 4 spinel, and Cr 2 O 3 corundum within the NiO matrix. Understanding the atomic-scale mechanisms of Cr segregation and precipitate formation is crucial for enhancing oxidation resistance. Here, we employ density functional theory calculations to investigate Cr behavior on NiO(100), (110), and (111) surfaces and in the bulk. Our results reveal that isolated Cr atoms preferentially segregate to the surfaces, stabilizing Ni(Cr)O solid solutions via strong Cr–O bonding, whereas Cr pairs and clusters favor subsurface migration and bulk aggregation, promoting nucleation of NiCr 2 O 4 and Cr 2 O 3 phases. These findings elucidate a size-dependent segregation mechanism linking Cr coordination environments to oxide phase evolution. This atomic-scale insight informs strategies to tailor oxide microstructures and enhance the high-temperature oxidation resistance of Ni–Cr alloys.

Chromium Segregation↗

A Miniaturized, High-Bandwidth Optical Fiber Fabry–Perot Cavity Vibration Sensor Demonstrated up to 800 °C

A typical structural health monitoring technique involves measuring the vibrational characteristics of components or systems to detect signs of degradation or damage. Many industrial applications require engineered systems to safely operate under extreme, high-temperature environments that pose challenges not only to materials but also to sensors that would be used for structural health monitoring. Here, in this study, miniaturized optical Fabry-Perot cavities (FPCs) were developed and tested as a means of measuring the resonant frequencies of metal components that are most relevant to extreme-environment applications. Two of the three candidate FPC designs tested up to 800 ° C provided accurate measurements (validated by theoretical models and laser Doppler vibrometry) of the fundamental vibrational mode of the specimen to which each was bonded, although both sensors failed during thermal cycling. An analysis of the reflected optical spectrum from the FPC and X-ray computed tomography revealed two opportunities to improve the sensor reliability. First, the Cu optical fiber coating that was used could either be replaced with a more oxidation-resistant material or protected with commercially available films. Second, the adhesives used to bond the fibers to metal capillaries and establish the FPC could be replaced with a more robust solution, although the Resbond 907TS adhesive appeared to outperform Resbond 907.

Birri, Anthony [Oak Ridge National Laboratory (ORN↗

A nitrogenase-like enzyme system catalyzes methionine, ethylene, and methane biogenesis

Bacterial production of hydrocarbon gases like ethylene and methane affects soil ecosystems and the climate. This study reveals that methane and ethylene from land and freshwater bacteria are directly produced by a previously unknown methionine biosynthesis pathway. This pathway employs a nitrogenase-like reductase that is distinct from known nitrogenases and nitrogenase-like reductases. The nitrogenase-like methylthio-alkane reductase specifically functions in carbon-sulfur bond breakage to reduce ubiquitous and significant volatile organic sulfur compounds such as dimethyl sulfide and (2-methylthio)ethanol. The liberated methanethiol serves as the immediate precursor to methionine. Whereas ethylene or methane is released into the environment. This pathway provides a biological route to the synthesis of ethylene in the absence of oxygen. Finally, anaerobic ethylene production by this pathway apparently explains the long-standing observation of ethylene accumulation in oxygen-depleted soils Methane production reveals an additional bacterial pathway that is distinct from archaeal methanogenesis.

10 SYNTHETIC FUELS↗

Autonomous Infrared and Small (Wide) Angle X-Ray Scattering (IR-S(W)AXS) Capability

Thin water films are 2-D, nanoconfined layers that form on solid surfaces exposed to humid atmospheres—environments ubiquitous across catalysis, corrosion science, soil science, and subsurface geochemistry. At relative humidity (RH) values below saturation, these films are Å–nm thick and exhibit properties that differ sharply from bulk water, including disrupted H-bonding and impeded mass transport. Owing to their high surface-to-volume ratio, dissolution of the solid can rapidly drive strong supersaturation with respect to secondary phases. Reactivity in thin water films is highly sensitive to film thickness, and critically, thickness evolves during reaction because the hygroscopicity of the interfacial system changes as ions accumulate or diminish in the film and as reaction products transform. To accurately probe and control these dynamics, a capability is needed that can measure and automatically maintain a constant water-film thickness while simultaneously monitoring solid dissolution, nucleation, and growth. This project developed an autonomous Infrared/Small Angle X-ray Scattering-Wide Angle X-ray Scattering (IR/(W)SAXS) for investigating reactivity in thin water films on solid surfaces exposed to humidified gases. The capability consists of an IR spectrometer, a (W)SAXS instrument, and a mass flow controller system for generating variably humidified gas flows to a custom reaction cell. Progress on each of the major components of the capability are detailed below.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Unusual zwitterionic catalytic site of SARS–CoV-2 main protease revealed by neutron crystallography

The main protease (3CL M pro ) from SARS–CoV-2, the etiological agent of COVID-19, is an essential enzyme for viral replication. 3CL M pro possesses an unusual catalytic dyad composed of Cys 145 and His 41 residues. A critical question in the field has been what the protonation states of the ionizable residues in the substrate-binding active-site cavity are; resolving this point would help understand the catalytic details of the enzyme and inform rational drug development against this pernicious virus. Here, we present the room-temperature neutron structure of 3CL M pro , which allowed direct determination of hydrogen atom positions and, hence, protonation states in the protease. We observe that the catalytic site natively adopts a zwitterionic reactive form in which Cys 145 is in the negatively charged thiolate state and His 41 is doubly protonated and positively charged, instead of the neutral unreactive state usually envisaged. The neutron structure also identified the protonation states, and thus electrical charges, of all other amino acid residues and revealed intricate hydrogen-bonding networks in the active-site cavity and at the dimer interface. The fine atomic details present in this structure were made possible by the unique scattering properties of the neutron, which is an ideal probe for locating hydrogen positions and experimentally determining protonation states at near-physiological temperature. Our observations provide critical information for structure-assisted and computational drug design, allowing precise tailoring of inhibitors to the enzyme's electrostatic environment.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Discovery of Stacking Heterogeneity, Layer Buckling, and Residual Water in COF-999-NH 2 and Implications on CO 2 Capture

Covalent organic frameworks (COFs), with their modular architectures and tunable functionalities, provide a versatile platform to design sorbents for the direct capture of CO 2 from air. Here, for this work, we combined density functional theory, molecular dynamics, and grand canonical Monte Carlo simulations with experiment to understand structural factors for furthering COF-999-NH 2 ’s performance as the precursor to COF-999 for direct air CO 2 capture. Small energy differences among laterally shifted stackings suggest intrinsic stacking heterogeneity. The simulations show pronounced layer buckling coupled to extensive amine–nitrile hydrogen bonding and persistent pore water, which initiates undesired polymerization and undermines uptake. The predicted presence of water is confirmed by subsequent experiments. These insights point to a single, actionable design rule: exclude retained water by introducing hydrophobic pore environments to maximize the CO 2 capture efficiency.

adsorption↗

Influence of point defects on the electronic and topological properties of monolayer WTe 2

In some topological insulators such as monolayers of WTe 2 or graphene with spin-orbit coupling, band inversion originates from chemical bonding and space group symmetry, in contrast to materials such as Bi 2 Se 3 , where the band inversion derives from relativistic effects in the atoms. In the former, band inversion is susceptible to changes of the chemical environment, e.g., by defects, while the latter are less affected by defects due to the larger energy scale associated with atomic relativistic effects. Motivated by recent experiments, we study the effect of Te vacancies and Te adatoms on the electronic properties of WTe 2 . We find that the Te vacancies have a formation energy of 2.21 eV, while the formation energy of the Te adatoms is much lower with 0.72 eV. Here, the vacancies strongly influence the band structure and we present evidence that band inversion is already reversed at the nominal composition of WTe 1.97 . In contrast, we show that the adatoms do not change the electronic structure in the vicinity of the Fermi level and thus the topological properties.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

In Situ Structural Determination of a Homogeneous Ruthenium Racemization Catalyst and Its Activated Intermediates Using X-Ray Absorption Spectroscopy

The activation process of a known Ru-catalyst, dicarbonyl(pentaphenylcyclopentadienyl)ruthenium chloride, has been studied in detail using time resolved in situ X-ray absorption spectroscopy. The data provide bond lengths of the species involved in the process as well as information about bond formation and bond breaking. On addition of potassium tert-butoxide, the catalyst is activated and an alkoxide complex is formed. The catalyst activation proceeds via a key acyl intermediate, which gives rise to a complete structural change in the coordination environment around the Ru atom. The rate of activation for the different catalysts was found to be highly dependent on the electronic properties of the cyclopentadienyl ligand. During catalytic racemization of 1-phenylethanol a fast-dynamic equilibrium was observed.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Three pairs of fungal Trametes strains isolated from distinct geographic origins show conserved genomic features and adaptive response to plant biomass

The genomes of white-rot fungi hold extended repertoires of enzymes active on virtually all the chemical bonds that intertwine lignocellulose polymers, and several Trametes species have been identified as powerful tools for biorefinery or bioremediation. However, only few studies have addressed the intra-species polymorphism one would expect from fungal strains collected in contrasted environments. We compared the genome sequence of pairs of strains collected in different geographic areas, for each of three fungal species. Using an updated list of the predicted functions for fungal ligno- and cellulolytic enzymes (CAZymes), we observed a high conservation of the gene repertoires among the six strains. We compared the adaptative response of the fungi grown on crystalline cellulose, wheat straw, aspen or pine sawdust by transcriptomics and secretomics. The gene regulation profiles were determined by the species and the substrates, rather than the strain. The secretomes did not show marked differences in the sets of secreted CAZymes after 3 day-growth on the substrates. We identified five transcription factor genes and two sesquiterpenoid synthesis genes induced during growth on lignocellulose. Wider studies using larger sets of strains will be necessary to evaluate the genericity of our findings, and to assess the phenotype diversity one could expect from geographic diversity as compared to taxonomic diversity in Trametes fungi.

Drula, E. [French National Research Institute for ↗

QMMM 2023: A program for combined quantum mechanical and molecular mechanical modeling and simulations

Combined quantum mechanical and molecular mechanical (QM/MM) methods play an important role in multiscale modeling and simulations. QMMM 2023 is a general-purpose program for single-point calculations, geometry optimizations, transition-state optimizations, and molecular dynamics (MD) at the QM/MM level. It calls a QM package and an MM package to perform the required single-level calculations and combines them into a QM/MM energy by a variety of schemes. QMMM 2023 supports GAMESS-US, Gaussian, and ORCA as QM packages and Tinker as the MM package. Four types of treatments are available for embedding the QM subsystem in the MM environment: mechanical embedding with gas-phase calculations of the QM region, electronic embedding that allows polarization of the QM region by the MM environment, polarizable embedding for mutual polarization of the QM and MM regions, and flexible embedding for both mutual polarization and partial charge transfer between the QM and MM regions. Boundaries between QM and MM regions that pass through covalent bonds can be treated by several methods, including the redistributed charge (RC) scheme, redistributed charge and dipole (RCD) scheme, balanced-RC scheme, balanced-RCD scheme, screened charge scheme that takes account of charge penetration effects, and smeared charge scheme that delocalizes the MM charges near the QM–MM boundary. Geometry optimization can be done using the optimizer implemented in QMMM 2023 or the Berny optimizer in Gaussian through external calls to Gaussian. Molecular dynamics simulations can be performed at the pure-MM level, pure-QM level, fixed-partitioning QM/MM level, and adaptive-partitioning QM/MM level. As a result, the adaptive-partitioning treatments permit on-the-fly relocation of the QM–MM boundary by dynamically reclassifying atoms or groups into the QM or MM subsystems.

97 MATHEMATICS AND COMPUTING↗

Study of beyond nearest-neighbor environment and intermediate-range order in a sodium aluminosilicate geopolymer using Reverse Monte Carlo modeling

A large scale three-dimensional structural model of a geopolymer with an approximate composition of NaAlSi 2 O 6 .5.5H 2 O obtained by Reverse Monte Carlo (RMC) modeling based on experimental high-energy x-ray diffraction is presented for the first time in order to obtain information regarding beyond nearest-neighbor environment and intermediate-range order (IRO). RMC model exhibits a three-dimensional network consisting of randomly cross-linked AlO 4 and SiO 4 tetrahedral units with uniformly distributed Na atoms and H 2 O molecules. The bond angle distributions, i.e. T-O-T, O-T-O and Na-O-Na angles, are somewhat distorted with lower values compared to analogous crystal systems. The origin of the first peak in the structure factor indicating IRO is investigated using the partial structure factors; Na-Na, Si-Na, Al-Si, O-H, and H-H atom pairs are found to be the main contributors. Ring size distribution analysis demonstrates that the structure mainly involves 6-, 7- and 8-membered rings. Finally, the coherence length of these IRO characteristics is ~10.3 Å.

36 MATERIALS SCIENCE↗