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DOE OSTI2022

The Function of Two Radical‐SAM Enzymes, HcgA and HcgG, in the Biosynthesis of the [Fe]‐Hydrogenase Cofactor

Abstract In the biosynthesis of the iron‐guanylylpyridinol (FeGP) cofactor, 6‐carboxymethyl‐5‐methyl‐4‐hydroxy‐2‐pyridinol ( 1 ) is 3‐methylated to form 2 , then 4‐guanylylated to form 3 , and converted into the full cofactor. HcgA‐G proteins catalyze the biosynthetic reactions. Herein, we report the function of two radical S ‐adenosyl methionine enzymes, HcgA and HcgG, as uncovered by in vitro complementation experiments and the use of purified enzymes. In vitro biosynthesis using the cell extract from the Methanococcus maripaludis Δ hcgA strain was complemented with HcgA or precursors 1 , 2 or 3 . The results suggested that HcgA catalyzes the biosynthetic reaction that forms 1 . We demonstrated the formation of 1 by HcgA using the 3 kDa cell extract filtrate as the substrate. Biosynthesis in the Δ hcgG system was recovered by HcgG but not by 3 , which indicated that HcgG catalyzes the reactions after the biosynthesis of 3 . The data indicated that HcgG contributes to the formation of CO and completes biosynthesis of the FeGP cofactor.

Arriaza‐Gallardo, Francisco J.↗

DOE OSTI2024

Multivariate Machine Learning Models of Nanoscale Porosity from Ultrafast NMR Relaxometry

Abstract Nanoporous materials are of great interest in many applications, such as catalysis, separation, and energy storage. The performance of these materials is closely related to their pore sizes, which are inefficient to determine through the conventional measurement of gas adsorption isotherms. Nuclear magnetic resonance (NMR) relaxometry has emerged as a technique highly sensitive to porosity in such materials. Nonetheless, streamlined methods to estimate pore size from NMR relaxometry remain elusive. Previous attempts have been hindered by inverting a time domain signal to relaxation rate distribution, and dealing with resulting parameters that vary in number, location, and magnitude. Here we invoke well‐established machine learning techniques to directly correlate time domain signals to BET surface areas for a set of metal‐organic frameworks (MOFs) imbibed with solvent at varied concentrations. We employ this series of MOFs to establish a correlation between NMR signal and surface area via partial least squares (PLS), following screening with principal component analysis, and apply the PLS model to predict surface area of various nanoporous materials. This approach offers a high‐throughput, non‐destructive way to assess porosity in c.a. one minute. We anticipate this work will contribute to the development of new materials with optimized pore sizes for various applications.

Fricke, Sophia N.↗

DOE OSTI2022

The Function of Two Radical‐SAM Enzymes, HcgA and HcgG, in the Biosynthesis of the [Fe]‐Hydrogenase Cofactor

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Multivariate Machine Learning Models of Nanoscale Porosity from Ultrafast NMR Relaxometry

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Examining organic acid production potential and growth‐coupled strategies in Issatchenkia orientalis using constraint‐based modeling

Abstract Growth‐coupling product formation can facilitate strain stability by aligning industrial objectives with biological fitness. Organic acids make up many building block chemicals that can be produced from sugars obtainable from renewable biomass. Issatchenkia orientalis is a yeast strain tolerant to acidic conditions and is thus a promising host for industrial production of organic acids. Here, we use constraint‐based methods to assess the potential of computationally designing growth‐coupled production strains for I. orientalis that produce 22 different organic acids under aerobic or microaerobic conditions. We explore native and engineered pathways using glucose or xylose as the carbon substrates as proxy constituents of hydrolyzed biomass. We identified growth‐coupled production strategies for 37 of the substrate‐product pairs, with 15 pairs achieving production for any growth rate. We systematically assess the strain design solutions and categorize the underlying principles involved.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Morphological and Chemical Differentiation between Tunisian Populations of Pinus halepensis , Pinus brutia , and Pinus pinaster

Abstract The lipid fraction of seeds from different pine species and populations was studied regarding total lipid content, fatty acid profile and vitamin E composition. The investigated seeds contained a high percentage of lipid (13.6 to 31.5 %). Lipid fractions were found to be rich in vitamin E, which varied significantly among species and populations. P. halepensis (Ph−Hn) showed the highest content of vitamin E (256.3 mg/kg of seeds) and the uppermost content of α ‐tocopherol (44 mg/kg). However, P. halepensis (Ph−Kas) was the richest in γ ‐tocopherol (204.9 mg/kg). Lipid fractions had a low content of δ ‐tocopherol (1.2 to 3.6 mg/kg. The highest content of γ ‐tocotrienol (∼18 %) was determined for P. halepensis (Ph−Dc and Ph−Hn). Thirteen fatty acids were identified by GC‐FID with significant variation between the investigated species. The linoleic acid was the major fatty acid followed by oleic acid and palmitic acid. The chemical differentiation among species for the composition of fatty acids and vitamin E was confirmed by PCA. Significant correlations were observed between the content of vitamin E and fatty acids and ecological parameters of P. halepensis populations.

Khouja, Mariem↗

DOE OSTI2020

Structure and activity of supported bimetallic NiPd nanoparticles: influence of preparation method on CO 2 reduction

Here, bimetallic Ni-Pd and monometallic reference catalysts were prepared by decomposing organometallic precursors, Ni(cod) 2 and Pd 2 (dba) 3 , leading to nanoparticles with sizes ranging from 3 to 6 nm. Two different synthesis procedures were followed: i) solution synthesis using capping ligand (hexadecylamine) followed by impregnation of pre-formed nanoparticles on SiO 2 , called Sol-immobilization (SI); and 2) direct precursor decomposition onto SiO 2 , without stabilizer, called Direct Decomposition (DD). Samples prepared by SI procedure are alloyed bimetallic nanoparticles, whereas samples obtained by DD one show phase segregation. Interestingly, DD samples show better activity for CO 2 hydrogenation into CO (reverse water-gas shift reaction - RWGS) than SI ones. The best compromise between activity for CO 2 activation (at lower temperature) and CO selectivity was achieved with Ni DD and NiPd DD catalysts. Moreover, the addition of palladium increased the concentration of surface undercoordinated sites, which chemisorb CO weakly, thus improving activity and selectivity, in opposition to other samples that chemisorb CO strongly, in multiband configuration. In the presence of Pd, different decomposition rates drive the formation of smaller and more active Ni clusters. The knowledge acquired here on the influence of synthesis conditions on the catalytic properties of Ni-Pd catalysts should guide us to better catalysts for CO 2 transformations into valuable products.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Tracking the Light-Induced Excited-State Dynamics and Structural Configurations of an Extraordinarily Long-Lived Metastable State at Room Temperature

Time-resolved X-ray (Tr-XAS) and optical transient absorption (OTA) spectroscopy in the pico-microsecond time scale coupled with Density Functional theory calculations are applied to study the light-induced spin crossover processes of a Fe-based macrocyclic complex in solution. Tr-XAS analysis after light illumination shows the formation of a seven-coordinated high spin quintet metastable state which relaxes to a six-coordinated high spin configuration before decaying to ground state. Kinetic analysis of the macrocyclic complex reveals an unprecedented long-lived decay lifetime of ~42.6 µs. Comparative studies with a non-macrocyclic counterpart illustrate a significantly shortened ~568-old decay lifetime of ~75 ns, and highlight the importance of the ligand arrangement in stabilizing the reactivity of the excited state. Lastly, OTA analysis shows the seven-coordinated high spin state to be formed within ~6.2 ps. Finally, these findings provide a complete understanding of the spin crossover reaction and relaxation pathways of the macrocyclic complex, and reveal the importance of a flexible coordination environment for their rational design.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Tailoring Chemical Absorption-Precipitation to Lower the Regeneration Energy of a CO 2 Capture Solvent

Solvent-based CO 2 capture consumes significant amounts of energy for solvent regeneration. To improve energy efficiency, this study investigates CO 2 fixation in a solid form through solvation, followed by ionic self-assembly-aided precipitation. Based on the hypothesis that CO 3 2- ions may bind with monovalent metal ions, we introduced Na + into an aqueous hexane-1,6-diamine solution where CO 2 forms carbamate and bicarbonate. Then, Na + ions in the solvent act as a seed for ionic self-assembly with diamine carbamate to form an intermediate ionic complex. The recurring chemical reactions lead to the formation of an ionic solid from a mixture of organic carbamate/carbonate and inorganic sodium bicarbonate (NaHCO 3 ), which can be easily removed from the aqueous solvent through sedimentation or centrifugation and heated to release the captured CO 2 . Mild-temperature heating of the solids at 80–150 °C causes decomposition of the solid CO 2 -diamine-Na molecular aggregates and discharge of CO 2 . This sorbent regeneration process requires 6.5–8.6 GJ/t CO 2 . It was also found that the organic carbamate/carbonate solid, without NaHCO 3 , contains a significant amount of CO 2 , up to 6.2 mmol CO 2 /g-sorbent, requiring as low as 2.9–5.8 GJ/t CO 2 . In conclusion, molecular dynamic simulations support the hypothesis of using Na + to form relatively less stable, yet sufficiently solid, complexes for the least energy-intensive recovery of diamine solvents compared to bivalent carbonate–forming ions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Soil water percolation and nutrient fluxes as a function of topographical, seasonal and soil texture variation in Central Amazonia, Brazil

Abstract Understanding soil water dynamics and transport of nutrients is challenging in tropical rainforests due to the uniqueness of several properties related to soils, vegetation and seasonality that make relating patterns found in temperate environments to tropical sites difficult. We address the need for better edaphic characterization in tropical environments by investigating soil water percolation rates and chemistry across topographic, soil texture and seasonal gradients in a mature tropical rainforest in Central Amazonia, Brazil. We utilized a passive wick flux meter (e.g., drainage lysimeter) to directly measure real‐time percolation fluxes at 60‐cm depth, and to sample a suite of chemical species across plateau, slope and valley topographic positions. We found percolation flux volume and chemical exports generally increase with decreasing elevation and clay content, which was lowest in the valley. Daily percolation flux was observed to be 2.39 ± 0.44 in plateau, 3.01 ± 0.50 in slope and 6.16 ± 0.83 mm in valley. Most solutes were present in small amounts of <1 mg L −1 , such as PO₄ 3− , Fe 2+ /Fe 3+ and Mn 2+ ; however, NO 3 − concentrations were >20 mg L −1 , even exceeding 100 mg L −1 in the valley. Based on additional isotopic analysis, we speculate high NO 3 − concentrations are partially an artefact of root decomposition following installation of the flux meters. The empirical relationships we show among percolation volume and nutrient exports under varying topographies and soil textures can improve Earth System Model performance by better constraining ecohydrological relationships to nutrient fluxes, which can in‐turn better illuminate the important factors that govern their behaviour.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2023

A new climatology of South American extratropical cyclogenesis with an intercomparison among ERA5 , JRA55 and the Brazilian Navy

Abstract In South America, the most destructive extratropical cyclones occur over the southeastern quadrant of the continent, a region that includes some of the world's largest population centres. However, there are few studies of cyclogenesis in this region, and little is known about how the varying origins of these storms impact subsequent behaviour. By supplementing an observational record with current reanalysis data, this study reveals the general characteristics of cyclones that develop in the lee regions of the Andes and those that develop nearer the Atlantic coast. The comparative climatologies demonstrate that cyclone development in these separate contexts is driven by topography, local atmospheric circulations and basin‐scale climate oscillations. The analysis further reveals a low‐frequency seesaw of lee and coastal cyclogenesis, with cross‐basin ocean temperature differences playing a teleconnectional role.

Meteorology & Atmospheric Sciences↗

DOE OSTI2022

Bio‐Based Piezo‐ and Thermoresistive Photocurable Sensing Materials from Acrylated Epoxidized Soybean Oil

Abstract Bio‐based photocurable polymers are increasingly in demand as environmentally friendly materials for advanced applications. Together with functional fillers, these represent a next step for the generation of functional and active smart materials, compatible with additive manufacturing technologies. Herein, acrylated epoxidized soybean oil (AESO) mixed with different amounts of reduced graphene oxide (rGO) up to 6 wt% in order to obtain UV‐curable piezoresistive and thermoresistive materials, is reported. It is shown that the addition of rGO to AESO hinders the curing process, but always maintains double bond conversions higher than 50%. Composites are characterized by a good dispersion of micrometric filler clusters. Further, the thermal stabilities are close to 300 °C and crosslinking degrees are above 1.75 mmol cm –3 . The Young modulus of the composites decreases with the addition of the rGO fillers, in particular for the higher filler contents, and electrical conductivities up to 0.13 S m –1 are obtained for the composites with the highest rGO content. UV‐curable composites with piezoresistive and thermoresistive responses suitable for applications are thus obtained, characterized by gauge factors around 26 for deformations up to 2% and maximum thermoresistive sensitivity of S = 0.43, values similar to the values obtained for petroleum‐based materials.

Mendes‐Felipe, Cristian↗

DOE OSTI2024

Ionic Thermoelectric Generators in Vertical and Planar Topologies Based on Fluorinated Polymer Hybrid Materials with Ionic Liquids

Abstract Ionic thermoelectrics (TEs), in which voltage generation is based on ion migration, are suitable for applications based on their low cost, high flexibility, high ionic conductivity, and wide range of Seebeck coefficients. This work reports on the development of ionic TE materials based on the poly(vinylidene fluoride‐trifluoroethylene), Poly(VDF‐co‐TrFE), as host polymer blended with different contents of the ionic liquid, IL, 1‐ethyl‐3‐methylimidazolium bis(trifluoromethylsulfonyl)imide, [EMIM][TFSI]. The morphology, physico‐chemical, thermal, mechanical, and electrical properties of the samples are evaluated together with the TE response. It is demonstrated that the IL acts as a nucleating agent for polymer crystallization. The mechanical properties and ionic conductivity values are dependent on the IL content. A high room temperature ionic conductivity of 0.008 S cm −1 is obtained for the sample with 60 wt% of [EMIM][TFSI] IL. The TE properties depend on both IL content and device topology‐vertical or planar‐the largest generated voltage range being obtained for the planar topology and the sample with 10 wt% of IL content, characterized by a Seebeck coefficient of 1.2 mV K −1 . Based on the obtained maximum power density of 4.9 µW m −2 , these materials are suitable for a new generation of TE devices.

Pereira, Nelson↗

DOE OSTI2023

A phase-field model for hydraulic fracture nucleation and propagation in porous media

Many geo-engineering applications, for example, enhanced geothermal systems, rely on hydraulic fracturing to enhance the permeability of natural formations and allow for sufficient fluid circulation. Over the past few decades, the phase-field method has grown in popularity as a valid approach to modeling hydraulic fracturing because of the ease of handling complex fracture propagation geometries. However, existing phase-field methods cannot appropriately capture nucleation of hydraulic fractures because their formulations are solely energy-based and do not explicitly take into account the strength of the material. Thus, in this work, we propose a novel phase-field formulation for hydraulic fracturing with the main goal of modeling fracture nucleation in porous media, for example, rocks. Built on the variational formulation of previous phase-field methods, the proposed model incorporates the material strength envelope for hydraulic fracture nucleation through two important steps: (i) an external driving force term, included in the damage evolution equation, that accounts for the material strength; (ii) a properly designed damage function that defines the fluid pressure contribution on the crack driving force. In conclusion, the comparison of numerical results for two-dimensional test cases with existing analytical solutions demonstrates that the proposed phase-field model can accurately model both nucleation and propagation of hydraulic fractures. Additionally, we present the simulation of hydraulic fracturing in a three-dimensional domain with various stress conditions to demonstrate the applicability of the method to realistic scenarios.

15 GEOTHERMAL ENERGY↗

DOE OSTI2026

Molecular basis and biological relevance of bacterial and plant pinoresinol/lariciresinol reductase specificities

A bacterial pinoresinol/lariciresinol reductase (PLR) homolog named NrPinZ was obtained from a Novosphingobium rhizosphaerae sp. LY bacterial strain, with NrPinZ being part of its 5-step biochemical system catabolizing pinoresinol into coniferyl aldehyde and vanillin. Recombinant NrPinZ reduces racemic 8–8′ furanofuran lignans [(±)-pinoresinols, medioresinols, and syringaresinols] with similar overall catalytic efficiencies. In those reductions, only one of the two furan ring systems is reduced. Two other bacterial PLR homologs, NaPinZ and SlPinZ, from N. aromaticivorans F199 and Sphingobium lignivorans SYK-6, respectively, had comparable substrate versatilities and catalytic efficacies. Plant PLR homologs, by comparison, are either enantiospecific, enantioselective, or variants thereof, being able to reduce either one or both furan rings. For example, a recombinant enantioselective PLR (PLR_Tp2) from western red cedar (Thuja plicata) preferentially reduces both (+)-pinoresinol furan rings to afford (−)-secoisolariciresinol. BoltZ-2 modeling of NrPinZ and PLR_Tp2, together with substrate docking of (+)- and (−)-pinoresinols, medioresinols, and syringaresinols, was very instructive. The NrPinZ active site P1/P2 sub-pockets allow for both racemic forms to be catabolized. Conversely, the smaller P1 pocket in PLR_Tp2 preferentially positions (+)-pinoresinol for downstream metabolism into (−)-secoisolariciresinol, thereby providing a biochemical explanation for the different stereochemical outcomes. NrPinZ, NaPinZ, and SlPinZ, catalyzing substrate versatile catabolism of both racemic forms, may have important ramifications for gymnosperm and angiosperm lignin and lignan biodegradation, including its evolutionary significance and potential in enzyme engineering.

Boltz-2 molecular modeling↗

DOE OSTI2022

De novo design and Rosetta-based assessment of high-affinity antibody variable regions (Fv) against the SARS-CoV -2 spike receptor binding domain ( RBD )

The continued emergence of new SARS-CoV-2 variants has accentuated the growing need for fast and reliable methods for the design of potentially neutralizing antibodies (Abs) to counter immune evasion by the virus. Here, we report on the de novo computational design of high-affinity Ab variable regions (Fv) through the recombination of VDJ genes targeting the most solvent-exposed hACE2-binding residues of the SARS-CoV-2 spike receptor binding domain (RBD) protein using the software tool OptMAVEn-2.0. Subsequently, we carried out computational affinity maturation of the designed variable regions through amino acid substitutions for improved binding with the target epitope. Immunogenicity of designs was restricted by preferring designs that match sequences from a 9-mer library of “human Abs” based on a human string content score. We generated 106 different antibody designs and reported in detail on the top five that trade-off the greatest computational binding affinity for the RBD with human string content scores. We further describe computational evaluation of the top five designs produced by OptMAVEn-2.0 using a Rosetta-based approach. We used Rosetta SnugDock for local docking of the designs to evaluate their potential to bind the spike RBD and performed “forward folding” with DeepAb to assess their potential to fold into the designed structures. Ultimately, our results identified one designed Ab variable region, P1.D1, as a particularly promising candidate for experimental testing. This effort puts forth a computational workflow for the de novo design and evaluation of Abs that can quickly be adapted to target spike epitopes of emerging SARS-CoV-2 variants or other antigenic targets.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

V‐Groove Si Nanopatterning for the Direct Epitaxy of Orientation‐Patterned III–V Nonlinear Optical Crystals

Orientation‐patterned (OP) III–V semiconductors—used as quasi‐phase‐matched crystals for nonlinear optics applications—are typically epitaxially grown on expensive III–V substrates using a complex process requiring three separate epitaxy steps. In this work, a method is demonstrated for growing orientation‐patterned III–V crystals on Si substrates through V‐groove nanopatterning and a single epitaxial growth. V‐groove Si allows for suppression of random antiphase domain formation that is typical of III–V growth on (001)‐oriented Si through the use of (111)‐faceted trenches patterned on (001)‐oriented Si substrates. By alternating the directions of the V‐groove trenches between [110] and [10], antiphase boundaries can be selectively induced at the boundaries between the two directions of trenches due to the difference in symmetry between the III–V material and Si. This approach allows for a greatly simplified process for growing OP‐III‐Vs and more broadly is a new, robust approach for precisely patterning antiphase boundaries of arbitrary shape and length scales down to 50 nm.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2020

Calibration, measurement, and characterization of soil moisture dynamics in a central Amazonian tropical forest

Soil moisture plays a key role in hydrological, biogeochemical, and energy budgets of terrestrial ecosystems. Accurate soil moisture measurements in remote ecosystems such as the Amazon are difficult and limited because of logistical constraints. Time domain reflectometry (TDR) sensors are widely used to monitor soil moisture and require calibration to convert the TDR's dielectric permittivity measurement (K a ) to volumetric water content (θ v ). In this study, our objectives were to develop a field-based calibration of TDR sensors in an old-growth upland forest in the central Amazon, to evaluate the performance of the calibration, and then to apply the calibration to determine the dynamics of soil moisture content within a 14.2 -m-deep vertical soil profile. Depth-specific TDR calibration using local soils in a controlled laboratory setting yielded a novel K a –θ v third-degree polynomial calibration. The sensors were later installed to their specific calibration depth in a 14.2-m pit. The widely used K a –θ v relationship (Topp model) underestimated the site-specific θ v by 22–42%, indicating significant error in the model when applied to these well-structured, clay-rich tropical forest soils. The calibrated wet- and dry-season θ v data showed a variety of depth and temporal variations highlighting the importance of soil textural differentiation, root uptake depths, as well as event to seasonal precipitation effects. Data such as these are greatly needed for improving our understanding of ecohydrological processes within tropical forests and for improving models of these systems in the face of changing environmental conditions.

54 ENVIRONMENTAL SCIENCES↗