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DOE OSTI2020

Second Coordination Sphere Effects in an Evolved Ru Complex Based on Highly Adaptable Ligand Results in Rapid Water Oxidation Catalysis

A new Ru complex containing the deprotonated 2,2':6',2"-terpyridine-6,6"-diphosphonic acid (H 4 tPa) and pyridine (py) of general formula [Ru II (H 3 tPa-κ-N 3 O)(py) 2 ] + , 2 + , has been prepared and thoroughly characterized by means of spectroscopic and electrochemical techniques, X-ray diffraction analysis, and density functional theory (DFT) calculations. Complex 2 + presents a dynamic behavior in the solution that involves the synchronous coordination and the decoordination of the dangling phosphonic groups of the tPa 4– ligand. Yet, at oxidation state IV, complex 2 + becomes seven coordinated with the two phosphonic groups now bonded to the metal center. Further, at this oxidation state at neutral and basic pH, the Ru complex undergoes the coordination of an exogenous OH – group from the solvent that leads to an intramolecular aromatic O atom insertion into the CH bond of one of the pyridyl groups, forming the corresponding phenoxo-phosphonate Ru complex [Ru III (tPaO-κ-N 2 O P O C )(py) 2 ] 2– , 4 2– , where tPaO 5– is the 3-(hydroxo-[2,2':6',2"-terpyridine]-6,6"-diyl)bis(phosphonate) ligand. This new in situ generated Ru complex, 4 2– , has been isolated and spectroscopically and electrochemically characterized. In addition, a crystal structure has been also obtained using single-crystal X-ray diffraction techniques. Complex 4 2– turns out to be an exceptional water oxidation catalyst achieving record maximum turnover frequencies (TOF max ) on the order of 16 000 s –1 . A mechanistic analysis complemented with DFT calculations has further been carried out, showing the critical role of intramolecular second coordination sphere effects exerted by the phosphonate groups in lowering the activation energy at the rate-determining step.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Crystal structure and luminescence properties of lead-free metal halides (C 6 H 5 CH 2 NH 3 ) 3 MBr 6 (M = Bi and Sb)

Organic–inorganic hybrid metal halides have received extensive attention owing to their versatile structures and optoelectronic properties. Herein, we report two lead-free metal halides, (PMA) 3 BiBr 6 and (PMA) 3 SbBr 6 [PMA + : (C 6 H 5 CH 2 NH 3 ) + , as the abbreviation of phenylmethylammonium], which possess iso-structural zero-dimensional structures and crystallize in the monoclinic space group P2 1 /c. (PMA) 3 BiBr 6 and (PMA) 3 SbBr 6 exhibit optical band gaps of ~3.50 and 3.40 eV, respectively, and density functional theory calculations reveal their indirect bandgap behaviors. Upon 350 and 425 nm excitation, (PMA) 3 BiBr 6 and (PMA) 3 SbBr 6 exhibit broadband emission peaking at 510 nm and 625 nm with wide full-widths at half-maximum of ~153 and 175 nm, respectively. The emission mechanism of the metal halides is attributed to self-trapped exciton emission. The relationship between the crystal structure and luminescence intensity is also discussed. Lastly, both metal halides have high decomposition temperatures and are stable for long-term storage under ambient conditions, demonstrating their potential for optoelectronic applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Impact of the coordination of multiple Lewis acid functions on the electronic structure and v n configuration of a metal center

Here, the covalent bond classification (CBC) method represents a molecule as ML l X x Z z by evaluating the total number of L, X and Z functions interacting with M. The CBC method is a simplistic approach that is based on the notion that the bonding of a ligating atom (or group of atoms) can be expressed in terms of the number of electrons it contributes to a 2-electron bond. In many cases, the bonding in a molecule of interest can be described in terms of a 2-center 2-electron bonding model and the ML l X x Z z classification can be derived straightforwardly by considering each ligand independently. However, the bonding within a molecule cannot always be described satisfactorily by using a 2-center 2-electron model and, in such situations, the ML l X x Z z classification requires a more detailed consideration than one in which each ligand is treated in an independent manner. The purpose of this article is to provide examples of how the ML l X x Z z classification is obtained in the presence of multicenter bonding interactions. Specific emphasis is given to the treatment of multiple π-acceptor ligands and the impact on the v n configuration, i.e. the number of formally nonbonding electrons on an element of interest.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Libration of hydroxyl groups in layered aluminum (oxy)hydroxides and other material analogs: insights from inelastic neutron scattering and theory

We analyzed the hydroxyl librational signatures of five structurally related aluminum (oxy)hydroxides, using inelastic neutron scattering (INS) and plane-wave lattice dynamics simulations. A clear trend across these aluminum-containing phases illustrates the relationship between hydrogen bonding, local atomic structure, and the spectral location and profile of the librational bands. The INS spectra have been compared to previous optical spectroscopy and computational studies, highlighting the complementary nature of the INS technique. Taking into account other structurally or chemically related material analogs, we have identified a correlation between a blueshift (to higher energy) of the upper librational band edge and the geometry of the hydrogen bond interactions, mirroring (with opposite correlation) the well-known redshift in the intramolecular O–H stretching energy with increasing hydrogen bond strength. For hydroxyl groups that do not participate in hydrogen bonding effectively, the bending librations occur at lower energies and hybridize with metal–oxygen lattice modes. Standard density functional theory approximations, including dispersion corrections, struggle to correctly predict vibrational frequencies of motions dominated by H but perform well for metal–oxygen modes, allowing us to make detailed mode assignments in several cases, including a demonstration of how layer-to-layer disorder in boehmite hydrogen bond orientations is reflected in the sharp but minor low energy peaks (at ∼70–80 meV) of the INS spectrum.

Wang, Hsiu-Wen [Oak Ridge National Laboratory (ORN↗

DOE OSTI2025

Serial-femtosecond crystallography reveals how a phytochrome variant couples chromophore and protein structural changes

The photoreaction and commensurate structural changes of a chromophore within biological photoreceptors elicit conformational transitions of the protein promoting the switch between deactivated and activated states. We investigated how this coupling is achieved in a bacterial phytochrome variant, Agp2-PAiRFP2. Contrary to classical protein crystallography, which only allows probing (cryo-trapped) stable states, we have used time-resolved serial femtosecond x-ray crystallography (tr-SFX) and pump-probe techniques with various illumination and delay times with respect to photoexcitation of the parent Pfr state. Thus, structural data for seven time frames were sorted into groups of molecular events along the reaction coordinate. They range from chromophore isomerization to the formation of Meta-F, the intermediate that precedes the functional relevant secondary structure transition of the tongue. Structural data for the early events were used to calculate the photoisomerization pathway to complement the experimental data. Late events allow identifying the molecular switch that is linked to the intramolecular proton transfer as a prerequisite for the following structural transitions.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

High-throughput genetics enables identification of nutrient utilization and accessory energy metabolism genes in a model methanogen

Archaea are widespread in the environment and play fundamental roles in diverse ecosystems; however, characterization of their unique biology requires advanced tools. This is particularly challenging when characterizing gene function. Here, we generate randomly barcoded transposon libraries in the model methanogenic archaeon Methanococcus maripaludis and use high-throughput growth methods to conduct fitness assays (RB-TnSeq) across over 100 unique growth conditions. Using our approach, we identified new genes involved in nutrient utilization and response to oxidative stress. We identified novel genes for the usage of diverse nitrogen sources in M. maripaludis including a putative regulator of alanine deamination and molybdate transporters important for nitrogen fixation. Furthermore, leveraging the fitness data, we inferred that M. maripaludis can utilize additional nitrogen sources including $\tiny{L}$-glutamine, $\tiny{D}$-glucuronamide, and adenosine. Under autotrophic growth conditions, we identified a gene encoding a domain of unknown function (DUF166) that is important for fitness and hypothesize that it has an accessory role in carbon dioxide assimilation. Finally, comparing fitness costs of oxygen versus sulfite stress, we identified a previously uncharacterized class of dissimilatory sulfite reductase-like proteins (Dsr-LP; group IIId) that is important during growth in the presence of sulfite. When overexpressed, Dsr-LP conferred sulfite resistance and enabled use of sulfite as the sole sulfur source. The high-throughput approach employed here allowed for generation of a large-scale data set that can be used as a resource to further understand gene function and metabolism in the archaeal domain.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

ARM Aerosol Measurement Science Group Charter

The Atmospheric Radiation Measurement (ARM) Aerosol Measurement Science Group (AMSG) is tasked with providing enhanced coordination of ARM Climate Research Facility observations of aerosols and atmospheric trace gases with the needs of its users. Its objective is to ensure advanced, well-characterized observational measurements and data products at the spatial and temporal scales necessary for improving climate science and climate model forecasts. The primary function of the AMSG will be to provide strategies to the ARM Technical Director and ARM Chief Operations Officer that can be used to implement a coherent measurement and data processing approach that addresses the priority aerosol science needs of ARM and Atmospheric System Research. The group fulfills the need for an integrated oversight to the planning, coordination, and leadership of aerosol instrumentation selection and deployment, measurement strategy and quality, and data product development from both science and operations perspectives.

Source record↗

DOE OSTI2021

Production-Ready CsPbBr3 Module Fabrication

The purpose of this SBIR was to work on evaluation, development, and testing of CsPbBr3 semiconductors for use in commercial gamma-ray detection. The overarching goal was to demonstrate the capability to fabricate functional detectors through resources available to H3D, Inc in pursuit of an alternative to CdZnTe for room-temperature semiconductor detectors. Throughout the project, CdZnTe crystals from Redlen were used as a control group to demonstrate whether the fabrication processes could produce reasonable results. The CdZnTe crystals were diced into roughly 6 mm x 6 mm x 4.5 mm pieces and electrodes were evaporated onto planar faces. In one case, pixels were patterned through a laser ablation method; in the other, a rudimentary pixel shadow-mask was fabricated, and the pixels were generated in the evaporation process. A 16 mm x 16 mm x 14 mm CsPbBr3 crystal was diced into four smaller crystals. These CsPbBr3 had electrodes applied in a similar way to the CdZnTe samples with a rudimentary mask used for pixels on the cathode. Tested CdZnTe pieces were found to generally function with reasonable, low-energy performance. CsPbBr3 crystals were found to be non-functional under forward bias with a large dark-current. A separate attempt, using reverse bias in a non-H3D, Inc test system, observed a dark current similar to previous observations, and some active pixels but no waveforms were observed.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2023

A randomized multiplex CRISPRi-Seq approach for the identification of critical combinations of genes

Identifying virulence-critical genes from pathogens is often limited by functional redundancy. To rapidly interrogate the contributions of combinations of genes to a biological outcome, we have developed a mu ltiplex, r andomized C RISPR i nterference s equencing (MuRCiS) approach. At its center is a new method for the randomized self-assembly of CRISPR arrays from synthetic oligonucleotide pairs. When paired with PacBio long-read sequencing, MuRCiS allowed for near-comprehensive interrogation of all pairwise combinations of a group of 44 Legionella pneumophila virulence genes encoding highly conserved transmembrane proteins for their role in pathogenesis. Both amoeba and human macrophages were challenged with L. pneumophila bearing the pooled CRISPR array libraries, leading to the identification of several new virulence-critical combinations of genes. lpg2888 and lpg3000 were particularly fascinating for their apparent redundant functions during L. pneumophila human macrophage infection, while lpg3000 alone was essential for L. pneumophila virulence in the amoeban host Acanthamoeba castellanii . Thus, MuRCiS provides a method for rapid genetic examination of even large groups of redundant genes, setting the stage for application of this technology to a variety of biological contexts and organisms.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

A randomized multiplex CRISPRi-Seq approach for the identification of critical combinations of genes

Ellis, Nicole A. (ORCID:0000000195928415)↗

DOE OSTI2021

Mechanisms and functions of membrane lipid remodeling in plants

Lipid remodeling, defined herein as post-synthetic structural modifications of membrane lipids, play crucial roles in regulating the physicochemical properties of cellular membranes and hence their many functions. Processes affected by lipid remodeling include lipid metabolism, membrane repair, cellular homeostasis, fatty acid trafficking, cellular signaling and stress tolerance. Glycerolipids are the major structural components of cellular membranes and their composition can be adjusted by modifying their head groups, their acyl chain lengths and the number and position of double bonds. This focused review summarizes recent advances in our understanding of mechanisms of membrane lipid remodeling with emphasis on the lipases and acyltransferases involved in the modification of phosphatidylcholine and monogalactosyldiacylglycerol, the major membrane lipids of extraplastidic and photosynthetic membranes, respectively. We also discuss the role of triacylglycerol metabolism in membrane acyl chain remodeling. Finally, we discuss emerging data concerning the functional roles of glycerolipid remodeling in plant stress responses. Illustrating the molecular basis of lipid remodeling may lead to novel strategies for crop improvement and other biotechnological applications such as bioenergy production.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Density Measurement of NaCl-MgCl 2 -PuCl 3 and NaCl-UCl 3 -PuCl 3 Molten Salt Systems by Neutron Radiographic Dilatometry

A novel neutron radiographic technique was developed and implemented to measure the change in volume as a function of temperature of select plutonium-containing liquid chloride mixtures from melt to 1250 K. These measurements were performed at Los Alamos National Laboratory by members of the molten salt research group under support from Gateway for Accelerated Innovation in Nuclear (GAIN) voucher NE-21-25117: “Density Measurements of Plutonium Bearing Salts via Neutron Beam Dilatometry”. This technical report contains a description of the experimental method and a summary of the results. Initial characterization of the {NaCl, MgCl 2 , UCl 3 , PuCl 3 } salts used in this experiment includes a combination of x-ray diffraction, differential scanning calorimetry, gamma ray spectroscopy, and inductively coupled plasma mass spectrometry. Four samples of NaCl + MgCl 2 + x mol% PuCl 3 and four samples of NaCl + UCl 3 + x mol% PuCl 3 were prepared at the Plutonium Facility, shipped to the Los Alamos Neutron Science Center (LANSCE), and radiographed with the density via neutron radiography (DvNR) apparatus. Density data in the form of meniscus heights were recorded as a function of temperature. The results show a linear dependence of density with temperature and a third order polynomial dependence of density with composition as a function of PuCl 3 addition in the corresponding halide salt mixture. Additions of PuCl 3 result in a significant increase in density of the salt mixture and a slight reduction in the coefficient of volumetric expansion. These results represent a first measurement of the density of plutonium chloride salt mixtures and, in combination with additional measurements, may lead to a generalized description of the density of such salt systems for arbitrary compositions and temperature.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2022

Synthesis and Characterization of Homoleptic Rare Earth Nitrato Complexes with the Quaternary Ammonium Cations Et 4 N + and n Pr 4 N +

Two periodic series of homoleptic rare earth nitrato com plexes, [R 4 N] x [M(NO 3 ) y ](M = La-Nd, Sm-Lu, Y); R = Et, $n$ Pr; x = 2-3; y = 5-6) have been synthesized, and charac terized by single crystal X-ray diffraction, IR and Raman spectroscopy, comparing the solid state speciation of the nitrate ions as a function of lanthanide ion and quarternary ammonium cation. The series of the form [Et 4 N] 3 [Ln(NO 3 ) 6 ] crystallizes in the rhombohedral space group $R$$\bar{3}$, as a twelve-coordinate hexanitrato complex [Et 4 N] 3 [Ln(NO 3 ) 6 ] with cocrystallized HNO 3 for La, Pr, and Nd. For Ce, a distinct orthorhombic phase retaining the same formula, [Et 4 N] 3 [Ce(NO 3 ) 6 ] is isolated in the absence of HNO 3 to prevent oxidation of the Ce(III) to Ce(IV) in nitric acid. A ten-coordinate pentanitrato complex, [Et 4 N] 2 [Ln(NO 3 ) 5 ], in monoclinic symmetry forms for the remainder of the series, and for Y(III). The entire series crystallized in the presence of [ $n$ Pr 4 N] + counterions forms a pentanitrato complex [ $n$ Pr 4 N] 2 [M(NO 3 ) 5 ] in the orthorhombic space group, $Pccn$. In conclusion, analysis of trends in the structural and spectroscopic characteristics of these series reveal insight into the structure directing influences of both the lanthanide contraction and the quarternary ammonium cations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Generalising G 2 geometry: involutivity, moment maps and moduli

We analyse the geometry of generic Minkowski N = 1, D = 4 flux compactifications in string theory, the default backgrounds for string model building. In M-theory they are the natural string theoretic extensions of G2 holonomy manifolds. In type II theories, they extend the notion of Calabi-Yau geometry and include the class of flux backgrounds based on generalised complex structures first considered by Graña et al. (GMPT). Using E 7(7) × $\mathbb{R}$ + generalised geometry we show that these compactifications are characterised by an SU(7) ⊂ E 7(7) structure defining an involutive subbundle of the generalised tangent space, and with a vanishing moment map, corresponding to the action of the diffeomorphism and gauge symmetries of the theory. The Kähler potential on the space of structures defines a natural extension of Hitchin’s G 2 functional. Using this framework we are able to count, for the first time, the massless scalar moduli of GMPT solutions in terms of generalised geometry cohomology groups. It also provides an intriguing new perspective on the existence of G 2 manifolds, suggesting possible connections to Geometrical Invariant Theory and stability.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2024

On amplitudes and field redefinitions

We derive an off-shell recursion relation for correlators that holds at all loop orders. This allows us to prove how generalized amplitudes transform under generic field redefinitions, starting from an assumed behavior of the one-particle-irreducible effective action. The form of the recursion relation resembles the operation of raising the rank of a tensor by acting with a covariant derivative. This inspires a geometric interpretation, whose features and flaws we investigate.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2021

Anisotropic flow of identified hadrons in $\mathrm{X}$e-$\mathrm{X}$e collisions at $\sqrt{s_{NN}}$ = 5.44 $\mathrm{T}$e$\mathrm{V}$

Measurements of elliptic (v 2 ) and triangular (v 3 ) flow coefficients of π ± , K ± , $p+\bar{p}$, $K$$^{0}_{S}$, and $Λ+\bar{Λ}$ obtained with the scalar product method in Xe-Xe collisions at $\sqrt{s_{NN}}$ = 5.44 TeV are presented. The results are obtained in the rapidity range |y| < 0.5 and reported as a function of transverse momentum, p T , for several collision centrality classes. The flow coefficients exhibit a particle mass dependence for p T < 3 GeV/c, while a grouping according to particle type (i.e., meson and baryon) is found at intermediate transverse momenta (3 < p T < 8 GeV/c). The magnitude of the baryon v 2 is larger than that of mesons up to p T = 6 GeV/c. The centrality dependence of the shape evolution of the p T -differential v 2 is studied for the various hadron species. The v 2 coefficients of π ± , K ± , and $p+\bar{p}$ are reproduced by MUSIC hydrodynamic calculations coupled to a hadronic cascade model (UrQMD) for p T < 1 GeV/c. A comparison with v n measurements in the corresponding centrality intervals in Pb-Pb collisions at $\sqrt{s_{NN}}$ = 5.02 TeV yields an enhanced v 2 in central collisions and diminished value in semicentral collisions.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2025

Using mid-infrared spectroscopy to estimate soil microbial properties at the continental scale

Understanding microbial community properties is critical to improving the predictions of biogeochemical processes for enhancing soil carbon sequestration. Here, in this observational study, mid-infrared (MIR) spectroscopy and partial least squares regression was used to predict soil microbial and chemical properties from diverse ecosystems across the continental USA. Random calibration and validation demonstrated the prediction potential for soil properties using MIR spectra, with the strongest predictions for microbial respiration, followed by microbial biomass carbon and nitrogen, ß-glucosidase activity, as well as soil chemical properties including organic carbon and total nitrogen. Microbial properties were mainly positively correlated to spectral regions associated with aliphatic C-H groups and C=O stretches of polysaccharides and negatively correlated to quartz and silicate-associated regions. We conclude that MIR spectroscopy can characterize soil microbial functions and be useful for the improvement of continental-scale soil carbon modeling and prediction programs.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Designing sequence-defined peptoids for fibrillar self-assembly and silicification

In the biological environment, mineral crystals exquisitely controlled by biomacromolecules often show intricate hierarchical structures and superior mechanical properties. Among these biominerals, spicules, hybrid silica/protein superstructures serving as skeletal elements in demosponges, represent an excellent example for motivating the synthesis of silica materials. Herein, by designing sequence-defined peptoids containing side chains with a strong binding to silica, we demonstrated that self-assembly of these peptoids into fiber structures enables the mimicking of both biocatalytic and templating functions of silicatein filaments for the formation of silica fibers at near-neutral pH and ambient temperature. We further showed that the presence of amino groups is significant for the nucleation of silica on self-assembled peptoid nanofibers. Molecular dynamics simulation further confirmed that having silica-binding of amino side chains is critical for self-assembled peptoid fibers in triggering silica formation. Here, we demonstrated that tuning inter-peptoid interactions by varying carboxyl and amino side chains significantly influences the assembly kinetics and final morphologies of peptoid assemblies as scaffolds for directing silica mineralization to form silica spheres, fibers, and sheets. The formation of silica shell on peptoid fibers increased the mechanical property of peptoid hydrogel materials by nearly 1000-fold, highlighting the great potential of using silicification to enhance the mechanical property of hydrogel materials for applications including tissue engineering. Since peptoids are highly robust and programmable, we expect that self-assembly of peptoids containing solid-binding side chains into hierarchical materials opens new opportunities in the design and synthesis of highly tunable scaffolds that direct the formation of composite nanomaterials.

59 BASIC BIOLOGICAL SCIENCES↗