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At least 613 records · Page 34
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

High methylation potential of mercury complexed with mixed thiolate ligands by Geobacter sulfurreducens PCA

We report some thiols, such as cysteine (CYS) at moderate concentrations (10–500 µM), can enhance methylmercury (MeHg) formation by Geobacter sulfurreducens PCA, whereas others such as dithiol 2,3-dimercaptopropanesulfonate (DMPS) and 2,3-dimercaptosuccinic acid (DMSA) abolish mercury [Hg(II)] methylation. Little is known, however, about whether Hg(II) methylation could be enhanced or inhibited by the presence of mixed thiol ligands at low concentrations observed in the environment. Surprisingly we found that mixing CYS (1 µM) with DMPS (0.025–0.5 µM) or DMSA (0.025–1 µM) substantially increased MeHg production by 1.5–3.5-fold, compared to the no-thiol control, whereas complexation with a single DMPS, or DMSA, or CYS (1 µM) strongly inhibited Hg(II) methylation. Pre-equilibration between Hg(II) and thiols before the addition of cells was necessary to observe enhanced methylation. Spectroscopic analyses indicated the formation of mixed or heteroleptic coordinated Hg(II)-S 3 /S 4 complexes, which likely facilitated exchange of Hg(II) with cells and its uptake and internal transfer to the HgcAB proteins required for methylation. These results suggest that the effects of thiols on Hg(II) methylation were more complex than previously thought (using a single thiol) and thus underscore the importance of understanding how mixed thiols and their interactions with Hg(II) may ultimately influence MeHg production in the natural environment.

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

The major trimeric antenna complexes serve as a site for qH-energy dissipation in plants

Plants and algae are faced with a conundrum: harvesting sufficient light to drive their metabolic needs while dissipating light in excess to prevent photodamage, a process known as nonphotochemical quenching. A slowly relaxing form of energy dissipation, termed qH, is critical for plants’ survival under abiotic stress; however, qH location in the photosynthetic membrane is unresolved. Here, we tested whether we could isolate subcomplexes from plants in which qH was induced that would remain in an energy-dissipative state. Interestingly, we found that chlorophyll (Chl) fluorescence lifetimes were decreased by qH in isolated major trimeric antenna complexes, indicating that they serve as a site for qH-energy dissipation and providing a natively quenched complex with physiological relevance to natural conditions. Next, we monitored the changes in thylakoid pigment, protein, and lipid contents of antenna with active or inactive qH but did not detect any evident differences. Finally, we investigated whether specific subunits of the major antenna complexes were required for qH but found that qH was insensitive to trimer composition. Because we previously observed that qH can occur in the absence of specific xanthophylls, and no evident changes in pigments, proteins, or lipids were detected, we tentatively propose that the energy-dissipative state reported here may stem from Chl–Chl excitonic interaction.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Scalable simulation of coupled adsorption and transport of methane in confined complex porous media with density preconditioning

The growing significance of shales and tight formations in the transition to less carbon-intensive and clean energy drives the research endeavor to understand the physics of gas flow within these systems. However, shales are composed of massively heterogeneous physical and chemical features. Most nano-sized pores connect to millimeter-scale fractures, leading to multiscale transport. These nano-scale pore throats demonstrate non-classical flow behavior, such as non-negligible slip velocities and adsorbed gas layers at the boundary. As a result, classical computational fluid dynamics models do not capture the physics. In this work, we develop a coupling scheme for the multiple-relaxation-time (MRT) lattice Boltzmann (LB) method that integrates the Peng-Robinson equation of state into a pseudo-potential interaction model to capture the physics of methane flow in irregular networks of channels that represent nano-scale porous media. We use atomistic simulations to calibrate and validate our model in slit nano-channels. We propose a preconditioning scheme to initialize the coupled transport and adsorption simulation of methane in complex porous media. The results of this implementation of LB agree with Direct Simulation Monte Carlo (DSMC) and Molecular Dynamics (MD) simulations. We then scale up the LB implementation through vectorization and indirect addressing. We parallelize it using Message Passing Interface (MPI) and OpenMP frameworks to simulate transport and adsorption in complex media with a million lattices. Additionally, we analyze the differences between coupled and transport-only simulations in two case studies and show that considering phase behavior, i.e., adsorption, can significantly change the flow behavior. This work constitutes an important step towards bridging the gap between molecular flow and system-scale behavior of complex disordered porous media.

42 ENGINEERING↗
DOE OSTI2025

Energy migration and scintillation kinetics in compositionally complex (Gd 1/4 Y 1/4 Tb 1/4 Lu 1/4 ) 3 Al 5 O 12 :Ce single crystal scintillator

It is well-established that compositional tuning through binary admixture can improve scintillation performance in several materials systems, including Ce-activated garnets. Although recent work on ternary or quaternary cation admixture shows promise, the impact of this increased compositional complexity on thermal stability and carrier-defect dynamics has not been addressed. Here, we investigate a compositionally complex garnet, (Gd 1/4 Y 1/4 Tb 1/4 Lu 1/4 ) 3 Al 5 O 12 :Ce (GYTLAG), grown by the Czochralski method using temperature-dependent photoluminescence (PL), PL decay, and thermoluminescence (TL). PL and PL decay measurements support a thermally activated Tb 3+ -Ce 3+ energy transfer, where Tb 3+ emission dominates below 60 K, but Ce 3+ emission increases from 20-300 K. Thermal quenching of Ce 3+ emission occurs around T 50 = 508 K, with an activation energy of 0.6 eV. TL and wavelength-resolved TL spectra from 20–500 K show that GYTLAG contains similar trap groups to LuAG but with a broader distribution of glow peaks below room temperature, possibly caused by quaternary cation mixing. A combination of dose dependence, partial cleaning and initial rise, and glow curve fitting to a first order continuous Gaussian distribution model are used to understand the contribution of electronic point defects to scintillation decay and afterglow at room temperature. Furthermore, these results inform how increased compositional complexity influences recombination dynamics in garnet scintillators.

Compositionally complex↗
DOE OSTI2026

A simple Rice-Ashby ductile–brittle transition temperature (DBTT) model based on dislocation mobility for body-centered cubic complex concentrated alloys

A simple Rice-Ashby type model for ductile–brittle transition temperature (DBTT) of body-centered cubic (bcc) complex concentrated alloys (structures) is presented. The effect of accumulation of dislocation density on DBTT is also analyzed. The model results are compared with experimental yield stress vs. temperature data for four complex concentrated alloys: Nb 45 Ta 25 Ti 15 Hf 15 (NTTH), MoNbTaW, HfNbTaTiZr, NbTiZr and two pure bcc metals, Fe and W. It is shown that the DBTT behavior of these alloys and pure metals are in agreement with the simple ductility model presented in this manuscript. The DBTT model presented in this manuscript along with yield strength models for bcc complex concentrated alloys described in the literature should serve as a useful guide for designing such alloys with good high temperature strength and significant room temperature ductility.

Crack tip processes↗
DOE OSTI2025

Residual stress distribution in an additively manufactured complex structure by neutron diffraction measurement

Residual stress in an aerodynamically shaped Ni-based superalloy airfoil fabricated by laser powder bed fusion was measured by neutron diffraction. The experiment was conducted by considering the complex shape, implementing computer aided experiment planning, and automatic alignment at each rapid measurement. The 3-dimensional (3D) residual stress distribution in the airfoil is presented in this work, which lacks symmetry due to the complex geometry of the airfoil. In conclusion, the results provide theoretical thermal processing models a complete residual stress dataset of simulation validation on 3D shape complex structure.

Residual stress↗
DOE OSTI2024

Advanced manufacturing of 3D custom boron-carbide collimators designed for complex environments for neutron scattering

Scattered-beam collimation is a very useful method to reduce unwanted backgrounds and to boost the desired sample signal instead. This approach is of particular interest for samples contained within a complex environment that gives rise to much unwanted parasitic scatter. As neutron scattering instrument and techniques advances, small samples are becoming of more and more interest, which necessitates optimized collimation. Here, in this work, we describe a concept for the design and fabrication of advanced scattered-beam collimation 3D printed from B 4 C specifically tailored for samples contained within a complex environment. This concept is demonstrated through the use of a diamond anvil cell for high pressure experimentation, a technique that very typically requires small samples. The collimators here are designed through a modeling procedure via Monte Carlo neutron ray tracing that encompasses the entire system: the instrument, the complex environment and the collimator. Since the first approach of simply scaling up of the print-size was not successful, a novel concept of a multi-part alternate-blade collimator was developed. This approach addresses printing constraints but gives greater flexibility in design. Its performance is computationally compared against an unprintable progressively tighter blade collimator to assess the effect of alternating blades. No strong difference was observed. Its performance was validated through experimentation at the Spallation Neutron Source. The results emphasize the critical importance of ultra-high precision alignment while showing good overall agreement between simulation and experiment and underscore the feasibility of the method and its real-world application.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2020

Complex Langevin and other approaches to the sign problem in quantum many-body physics

In this work, we review the theory and applications of complex stochastic quantization to the quantum many-body problem. Along the way, we present a brief overview of a number of ideas that either ameliorate or in some cases altogether solve the sign problem, including the classic reweighting method, alternative Hubbard–Stratonovich transformations, dual variables (for bosons and fermions), Majorana fermions, density-of-states methods, imaginary asymmetry approaches, and Lefschetz thimbles. We discuss some aspects of the mathematical underpinnings of conventional stochastic quantization, provide a few pedagogical examples, and summarize open challenges and practical solutions for the complex case. Finally, we review the recent applications of complex Langevin to quantum field theory in relativistic and nonrelativistic quantum matter, with an emphasis on the nonrelativistic case.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2022

Crystalline phase transitions and water-soluble complexes of copper(Ⅰ) 2-hydroxyethanethiolate

We report the coordination polymer copper(I) 2-hydroxyethanethiolate, (CuSCH 2 CH 2 OH) n , though insoluble in all common solvents, dissolved readily in basic aqueous solutions of the thiolate anion (HOCH 2 CH 2 S – ) of 2-mercaptoethanol to form a single species: the tetranuclear cluster [Cu 4 (μ-SCH 2 CH 2 OH) 6 ] 2– . From this solution were grown X-ray quality single crystals of copper(I) 2-hydroxyethanethiolate. This compound underwent a hitherto unknown crystal phase transition at ca. 6 °C, from point group P2 1 2 1 2 1 to Pna2 1 , with noticeable changes in the geometry of the Cu-S layer and in the orientation of the alkylthiolate side chains. When the bulky base tetrabutylammonium hydroxide was employed in the aqueous thiolate solution used to dissolve (CuSCH 2 CH 2 OH) n , the water-soluble polynuclear copper(I) complex bis(tetrabutylammonium) hexakis(μ-2-hydroxyethanethiolato) tetracuprate(I), [(C 4 H 9 ) 4 N] 2 [Cu 4 (μ-SCH 2 CH 2 OH) 6 ], could be isolated as X-ray quality crystals. Structural characterization of this complex revealed a tetrahedral arrangement of copper(I) centers with thiolates bridging the edges of the tetrahedra. On standing, this complex degraded to a larger polynuclear Cu(I) sulfide cluster.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

First principles investigation of dopants and defect complexes in CdSe$_x$Te$_{1-x}$

Se alloying is a common approach to improve the performance of CdTe solar cells by tuning the bandgap, defect levels, and carrier density. A fundamental understanding of these improvements, specifically the effect of Se alloying on the behavior of defects and dopants in CdTe, remains unclear. Here, in this work, we present a density functional theory (DFT) study of point defect energetics in CdTe and CdSe x Te 1-x with x = 0.25, leading to a comparison of how native defects, dopants (As and Cu), impurities (Cl and O), and related defect complexes behave in CdTe vs CdSe x Te 1-x . Our calculations, performed by combining semi-local and nonlocal hybrid functionals, show a general lowering of the formation energies of native defects as well as substitutional defects formed by As and Cl upon Se addition. For successful p-type doping with As, destabilizing Cl-based defects in the CdSeTe lattice would be essential. We find evidence for some low-energy defect complexes of As, Cl, and O in CdSe 0.25 Te 0.75 . The computed defect formation energies further enable estimates of temperature-dependent defect concentrations and self-consistent Fermi levels. A comparison of defect energetics with the energies of impurity phases reveals that As, Cu, Cl, and O overwhelmingly prefer being segregated to unwanted As 2 O 5 , AsCl 3 , Cd 2 AsCl 2 , and CuO x phases rather than remain at defect sites, but such segregation is less likely to happen in CdSe 0.25 Te 0.75 than in CdTe. Overall, our work presents a list of likely defects and complexes in CdTe and Se-incorporated CdTe, paving the way to explain and mitigate limited dopant activation in experimental observations.

CdTe↗
DOE OSTI2021

Catalytic Dehydrogenation of Alkanes by PCP–Pincer Iridium Complexes Using Proton and Electron Acceptors

Dehydrogenation to give olefins offers the most broadly applicable route to the chemical transformation of alkanes. Furthermore, transition-metal-based catalysts can selectively dehydrogenate alkanes using either olefinic sacrificial acceptors or a purge mechanism to remove H 2 ; both of these approaches have significant practical limitations. Here, we report the use of pincer-ligated iridium complexes to achieve alkane dehydrogenation by proton-coupled electron transfer, using pairs of oxidants and bases as proton and electron acceptors. Up to 97% yield was achieved with respect to oxidant and base, and up to 15 catalytic turnovers with respect to iridium, using t-butoxide as base coupled with various oxidants, including oxidants with very low reduction potentials. Mechanistic studies indicate that (pincer)IrH 2 complexes react with oxidants and base to give the corresponding cationic (pincer)IrH + complex, which is subsequently deprotonated by a second equivalent of base; this affords (pincer)Ir which is known to dehydrogenate alkanes and thereby regenerates (pincer)IrH 2 .

02 PETROLEUM↗
DOE OSTI2022

Microcavity-Modified Emission from Rare-Earth Ion-Based Molecular Complexes

Despite the remarkable optical properties of rare-earth ion materials, their applications as light sources and in quantum technologies are often hindered by their long lifetimes and weak emission. Leveraging the natural compatibility of rare-earth ion molecular complexes with photonic structures, here we modify their photoluminescence properties by coupling them to a flexible open Fabry-Perot cavity. The full in situ tunability of the Fabry-Perot cavity allows fine control over its cavity modes and the achievement of resonant coupling between the rare-earth ion emission and the cavity modes. This configuration allows us to achieve a maximum photoluminescence enhancement factor of 30 and accelerate the decay rate up to two orders of magnitude. Our pump-power-dependent spectroscopic studies of the emitter-cavity system suggest that the cavity-modified emission is primarily caused by amplified spontaneous emission. These results suggest that integrating rare-earth ion molecular complexes with photonic structures could be a viable approach for the effective tuning of their optical properties. This natural compatibility, together with their versatile molecular structures and the resultant electronic states, renders rare-earth ion molecular complexes a potential alternative material platform for lighting and quantum applications.

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

Electrocatalytic properties of a novel ruthenium( ii ) terpyridine-based complex towards CO 2 reduction

The electrocatalytic properties of Ru complexes are of great technological interest given their potential application in reactions such water splitting and CO 2 reduction. In this work, a novel terpyridine-based Ru(II) complex, [RuCl(trpy)(acpy)], trpy = 2,2':6',2"-terpyridine, acpy - = 2-pyridylacetate was synthesized and its spectroscopic, electrochemical and catalytic properties were explored in detail. In dry acetonitrile, the complex exhibits two reduction peaks at -1.95 V and -2.20 V vs. Fc/Fc + , attributed to consecutive 1 e - reduction. Under CO 2 atmosphere, a catalytic wave is observed (E onset = 2.1 V vs. Fc/Fc + ), with CO as the main reduction product. Bulk electrolysis reveals a turnover number (TON) of 12 (k obs = 1.5 s -1 ). In the presence of 1% water, an improvement in the catalytic activity is observed (TON CO = 21 and k obs = 2.0 s -1 ) and, additionally, formate was also detected (TON HCOO = 7). Spectroelectrochemical experiments allowed the identification of a metallocarboxylate (Ru–COO - ) intermediate under anhydrous conditions, while in water, the partial labilization of the acpy- ligand was observed in the course of the catalytic cycle. The experimental data was combined with DFT calculations, allowing the proposal of a catalytic cycle. Here the results establish important relationships between selectivity, ligand structure and reaction conditions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Modeling dark- and light-induced crystal structures and single-crystal optical absorption spectra of ruthenium-based complexes that undergo SO 2 -linkage photoisomerization

A family of coordination complexes of the type [Ru(SO 2 )(NH 3 ) 4 X] m+ Y n – (m, n = 1 or 2) exhibit optical switching capabilities in their single-crystal states. This striking effect is caused by the light-induced formation of SO 2 -linkage photoisomers, which are metastable if kept at suitably cool temperatures. We modeled the dark- and light-induced states of these large crystalline complexes via plane-wave (PW)- and molecular-orbital (MO)-based density functional theory (DFT) and time-dependent DFT in order to calculate their structural and optical properties; the calculated results are compared with experimental data. We show that the PW-DFT-based periodic models replicate the structural properties of these complexes more effectively than the MO-DFT-based molecular-fragment models, observing only small deviations in key bond lengths relative to the experimentally derived crystal structures. The periodic models were also found to more effectively simulate trends seen in experimental optical absorption spectra, with optical absorbance and coverage of the visible region increasing with the formation of the photoinduced geometries. The contribution of the metastable photoisomeric species more heavily focuses on the lower-energy end of the spectra. Spectra generated from the molecular-fragment models are limited by the geometry of the fragment used and the number of excited-state roots considered in those calculations. In general, periodic models outperform the molecular-fragment models owing to their ability to better appreciate the periodic phenomena that are present in these crystalline materials as opposed to MO approaches, which are finite methods. We thus demonstrate that PW-DFT-based periodic models should be considered as a more than viable method for simulating the optical and electronic properties of these single-crystal optical switches.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Subdomain cryo-EM structure of nodaviral replication protein A crown complex provides mechanistic insights into RNA genome replication

For positive-strand RNA [(+)RNA] viruses, the major target for antiviral therapies is genomic RNA replication, which occurs at poorly understood membrane-bound viral RNA replication complexes. Recent cryoelectron microscopy (cryo-EM) of nodavirus RNA replication complexes revealed that the viral double-stranded RNA replication template is coiled inside a 30- to 90-nm invagination of the outer mitochondrial membrane, whose necked aperture to the cytoplasm is gated by a 12-fold symmetric, 35-nm diameter “crown” complex that contains multifunctional viral RNA replication protein A. Here we report optimizing cryo-EM tomography and image processing to improve crown resolution from 33 to 8.5 Å. This resolves the crown into 12 distinct vertical segments, each with 3 major subdomains: A membrane-connected basal lobe and an apical lobe that together comprise the ~19-nm-diameter central turret, and a leg emerging from the basal lobe that connects to the membrane at ~35-nm diameter. Despite widely varying replication vesicle diameters, the resulting two rings of membrane interaction sites constrain the vesicle neck to a highly uniform shape. Labeling protein A with a His-tag that binds 5-nm Ni-nanogold allowed cryo-EM tomography mapping of the C terminus of protein A to the apical lobe, which correlates well with the predicted structure of the C-proximal polymerase domain of protein A. These and other results indicate that the crown contains 12 copies of protein A arranged basally to apically in an N-to-C orientation. Moreover, the apical polymerase localization has significant mechanistic implications for template RNA recruitment and (-) and (+)RNA synthesis.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Solvent Phase Optimizations Improve Correlations with Experimental Stability Constants for Aqueous Lanthanide Complexes

Stability constants provide insight into ion complexation in water. While computational studies have been shown to model the energy of the complexation successfully using a thermodynamic cycle approach, it does not extend to calculating the stability constants for 1:1 lanthanide to ligand complexes in solution. Using B3LYP and 6-31+G* Pople basis with small core effective core potential (ECP) on the lanthanum ion, and a solvent model based on the full solute electron density (SMD) solvation model we computed and compared with previously published stability constants of the ligands: acetate, acetohydroximate, acetylacetonate, methanoate, tropolonate, hydroxide, catecholate, malonate, oxalate, phthalate, and sulfate. The best R 2 values for the thermodynamic cycle can only be determined by separating the mono and divalent ions to achieve an R 2 value of 0.86 and 0.74 for mono and divalent ions, respectively. We show that by optimizing the lanthanide-ligand structures in implicit solvent, we achieve an improved correlation between experimental and computed stability constants of R 2 value of 0.89 for the combined mono and divalent ions.

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

Complexity Phase Diagram for Interacting and Long-Range Bosonic Hamiltonians

Here, we classify phases of a bosonic lattice model based on the computational complexity of classically simulating the system. We show that the system transitions from being classically simulable to classically hard to simulate as it evolves in time, extending previous results to include on-site number-conserving interactions and long-range hopping. Specifically, we construct a complexity phase diagram with easy and hard “phases” and derive analytic bounds on the location of the phase boundary with respect to the evolution time and the degree of locality. We find that the location of the phase transition is intimately related to upper bounds on the spread of quantum correlations and protocols to transfer quantum information. Remarkably, although the location of the transition point is unchanged by on-site interactions, the nature of the transition point does change. Specifically, we find that there are two kinds of transitions, sharp and coarse, broadly corresponding to interacting and noninteracting bosons, respectively. Our Letter motivates future studies of complexity in many-body systems and its interplay with the associated physical phenomena.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Michaelis-like complex of SARS-CoV-2 main protease visualized by room-temperature X-ray crystallography

SARS-CoV-2 emerged at the end of 2019 to cause an unprecedented pandemic of the deadly respiratory disease COVID-19 that continues to date. The viral main protease (M pro ) is essential for SARS-CoV-2 replication and is therefore an important drug target. Understanding the catalytic mechanism of M pro , a cysteine protease with a catalytic site comprising the noncanonical Cys145–His41 dyad, can help in guiding drug design. Here, a 2.0 Å resolution room-temperature X-ray crystal structure is reported of a Michaelis-like complex of M pro harboring a single inactivating mutation C145A bound to the octapeptide Ac-SAVLQSGF-CONH 2 corresponding to the nsp4/nsp5 autocleavage site. The peptide substrate is unambiguously defined in subsites S5 to S3′ by strong electron density. Superposition of the Michaelis-like complex with the neutron structure of substrate-free M pro demonstrates that the catalytic site is inherently pre-organized for catalysis prior to substrate binding. Induced fit to the substrate is driven by P1 Gln binding in the predetermined subsite S1 and rearrangement of subsite S2 to accommodate P2 Leu. The Michaelis-like complex structure is ideal for in silico modeling of the SARS-CoV-2 M pro catalytic mechanism.

3CL protease↗