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At least 91 records · Page 5
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Mechanistic Insights into Molecular Copper Hydride Catalysis: the Kinetic Stability of CuH Monomers toward Aggregation is a Critical Parameter for Catalyst Performance

The activity of molecular copper hydride (CuH) complexes towards the selective insertion of unsaturated hydrocarbons under mild conditions has contributed significantly to versatile methodologies for upgrading these feedstocks. However, these catalysts are particularly susceptible to deleterious aggregation, leading to the depletion of active CuH species. Little is known about the mechanisms of CuH aggregation, how it influences overall catalyst performance, and how it can be controlled. We address these challenges with mechanistic studies on a model reaction of unactivated alkene hydroboration catalyzed by (IPr*CPh 3 )CuH (LCuH). Here, we report a comprehensive mechanistic investigation of this system, identifying an aggregation pathway that continuously depletes catalytically active LCuH to form inactive CuH clusters during turnover. Deactivation of LCuH is controlled primarily by the competition between the kinetics of the initial LCuH dimerization step and that of alkene insertion. We therefore propose that a more comprehensive understanding of CuH catalyst performance must account for the kinetics of the initial LCuH dimerization step, revising a previously explored thermodynamic understanding of CuH aggregation, where the concentration of active species is controlled by equilibria established between CuH dimers and monomers. With a series of (NHC)CuH congeners (NHC = N-heterocyclic carbene), we demonstrate that ostensibly minor structural modifications to the ligand peripheries can drastically affect the LCuH dimerization kinetics, while maintaining reactivity towards on–cycle alkene insertion. We employed a computational approach based on molecular dynamics simulations to provide an in-depth understanding of how specific structural ligand modifications can substantially increase the kinetic stability of monomeric CuH catalysts. Our combined experimental and computational studies suggest strategies for rational ligand design that can be broadly applied to molecular catalyst systems that are susceptible to deactivation via aggregation pathways.

Ryan, David E. [Pacific Northwest National Laborat↗
DOE OSTI2025

Tunable and Robust Optical and Structural Properties of a Cooperative Squaraine-Dye Aggregate-DNA DX-DAE Tile System

Molecular excitons, which are excitations delocalized over multiple dyes in a wavelike manner, are of interest for a wide range of applications, including quantum information science. Numerous studies have templated a variety of synthetic dyes via a DNA scaffold to induce dye aggregation to create molecular excitons upon photoexcitation. Dye aggregate optical properties are critically dependent on relative dye geometry and local environment; therefore, an understanding of dye-dye and DNA-dye interactions is critical for advancing toward more complex DNA-dye systems. The extensively studied DNA Holliday junction (HJ) and less-studied double-crossover (DX) tile motif are fundamental test beds for designing complex and ultimately modular DNA-dye architectures. Here, we report the first study of single-linked squaraine dye aggregation and exciton delocalization on a larger and more stable (compared with the HJ) DX tile motif. We first highlight a few DNA-dye constructs that support single dyes and aggregates with distinct optical properties that are both tunable—through sample design, buffer conditions, and heat treatment—and robust to environment changes, including transfer to solid phase. Next, we assess several experimental and design considerations that demonstrate directed dye-driven assembly of a novel double-tile DNA configuration. Our results demonstrate that single-linked squaraine dyes templated to DX tiles provide a viable research path to design and evaluate dye aggregate networks that support exciton delocalization. We include herein the first report of exciton delocalization in the solid phase in a DNA-dye construct. Additionally, our findings indicate that dye aggregation impacts the assembly of the DNA-dye construct, and, in some cases, thereby cooperates with the DNA to determine a final robust system configuration. Finally, we show that a controlled annealing schedule can be employed to promote the homogeneous assembly of DNA-dye constructs. The findings in this study contribute to the understanding of DNA-dye systems and the relevant factors involved in their directed assembly to achieve specific constructs with desirable properties.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Interfacing DNA nanotechnology and biomimetic photonic complexes: advances and prospects in energy and biomedicine

Abstract Self-assembled photonic systems with well-organized spatial arrangement and engineered optical properties can be used as efficient energy materials and as effective biomedical agents. The lessons learned from natural light-harvesting antennas have inspired the design and synthesis of a series of biomimetic photonic complexes, including those containing strongly coupled dye aggregates with dense molecular packing and unique spectroscopic features. These photoactive components provide excellent features that could be coupled to multiple applications including light-harvesting, energy transfer, biosensing, bioimaging, and cancer therapy. Meanwhile, nanoscale DNA assemblies have been employed as programmable and addressable templates to guide the formation of DNA-directed multi-pigment complexes, which can be used to enhance the complexity and precision of artificial photonic systems and show the potential for energy and biomedical applications. This review focuses on the interface of DNA nanotechnology and biomimetic photonic systems. We summarized the recent progress in the design, synthesis, and applications of bioinspired photonic systems, highlighted the advantages of the utilization of DNA nanostructures, and discussed the challenges and opportunities they provide. Graphical Abstract

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

An Optimized Fibril Network Morphology Enables High‐Efficiency and Ambient‐Stable Polymer Solar Cells

Abstract Morphological stability is crucially important for the long‐term stability of polymer solar cells (PSCs). Many high‐efficiency PSCs suffer from metastable morphology, resulting in severe device degradation. Here, a series of copolymers is developed by manipulating the content of chlorinated benzodithiophene‐4,8‐dione (T1‐Cl) via a random copolymerization approach. It is found that all the copolymers can self‐assemble into a fibril nanostructure in films. By altering the T1‐Cl content, the polymer crystallinity and fibril width can be effectively controlled. When blended with several nonfullerene acceptors, such as TTPTT‐4F, O‐INIC3, EH‐INIC3, and Y6, the optimized fibril interpenetrating morphology can not only favor charge transport, but also inhibit the unfavorable molecular diffusion and aggregation in active layers, leading to excellent morphological stability. The work demonstrates the importance of optimization of fibril network morphology in realizing high‐efficiency and ambient‐stable PSCs, and also provides new insights into the effect of chemical structure on the fibril network morphology and photovoltaic performance of PSCs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Machine learning approaches for influenza A virus risk assessment identifies predictive correlates using ferret model in vivo data

In vivo assessments of influenza A virus (IAV) pathogenicity and transmissibility in ferrets represent a crucial component of many pandemic risk assessment rubrics, but few systematic efforts to identify which data from in vivo experimentation are most useful for predicting pathogenesis and transmission outcomes have been conducted. To this aim, we aggregated viral and molecular data from 125 contemporary IAV (H1, H2, H3, H5, H7, and H9 subtypes) evaluated in ferrets under a consistent protocol. Three overarching predictive classification outcomes (lethality, morbidity, transmissibility) were constructed using machine learning (ML) techniques, employing datasets emphasizing virological and clinical parameters from inoculated ferrets, limited to viral sequence-based information, or combining both data types. Among 11 different ML algorithms tested and assessed, gradient boosting machines and random forest algorithms yielded the highest performance, with models for lethality and transmission consistently better performing than models predicting morbidity. Comparisons of feature selection among models was performed, and highest performing models were validated with results from external risk assessment studies. Our findings show that ML algorithms can be used to summarize complex in vivo experimental work into succinct summaries that inform and enhance risk assessment criteria for pandemic preparedness that take in vivo data into account.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Characterization and molecular simulation of lignin in Cyrene pretreatment of switchgrass

Biomass-derived solvents have been proposed as a novel pathway in biorefining for the realization of biofuels and bioproducts derived from lignocellulosic biomass. Cyrene derived from cellulose has recently been shown to have a high potential as a green organic solvent for pretreating poplar biomass. However, due to its high dynamic viscosity nature, high Cyrene concentration could cause negative effects on the sugar release of the pretreated biomass as well as driving up the operational cost of the lignin recovery. In this study, we combine experimental and computational approaches to examine the impact of Cyrene pretreatment with reduced Cyrene concentration under mild conditions on switchgrass lignin. Our experimental studies indicated correlation between pretreatment condition and recovery and structure modification of lignin. Switchgrass lignin extracted by Cyrene pretreatment possessed high preservation of β-O-4 ether inter-unit linkage, which could provide versatility in the integration of downstream lignin valorization into the modern biorefinery industries. Molecular modeling examining the solvation of switchgrass lignin polymer and the disaggregation of low-molecular weight lignin aggregates under pretreatment conditions indicated that a preferential interaction exists between Cyrene and lignin, which likely drives lignin release, and that the disruption of inter-lignin contacts can be modulated as a non-monotonic function of Cyrene : water ratio. Further, while Cyrene–lignin interactions permit the solubilization of lignin, simulations with proxy reactive-species reveal that changes to the diffusion of these reactive proxies and their localization near linkage sites under Cyrene conditions may inhibit chemical processes. In conclusion, the results indicated that loss of pretreatment efficacy caused by low Cyrene concentration could be compensated by prolonged pretreatment time and high catalyst dosage.

09 BIOMASS FUELS↗
DOE OSTI2024

Learning Molecular Mixture Property Using Chemistry-Aware Graph Neural Network

Recent advances in machine learning (ML) are expediting materials discovery and design. One significant challenge facing ML for materials is the expansive combinatorial space of potential materials formed by diverse constituents and their flexible configurations. This complexity is particularly evident in molecular mixtures, a frequently explored space for materials, such as battery electrolytes. Owing to the complex structures of molecules and the sequence-independent nature of mixtures, conventional ML methods have difficulties in modeling such systems. Here, we present MolSets, a specialized ML model for molecular mixtures, to overcome the difficulties. Representing individual molecules as graphs and their mixture as a set, MolSets leverages a graph neural network and the deep sets architecture to extract information at the molecular level and aggregate it at the mixture level, thus addressing local complexity while retaining global flexibility. We demonstrate the efficacy of MolSets in predicting the conductivity of lithium battery electrolytes and highlight its benefits in the virtual screening of the combinatorial chemical space. Published by the American Physical Society 2024

Zhang, Hengrui (ORCID:0000000231831654)↗
NASA NTRS1994

Alpha-A crystallin: quantitation of C-terminal modification during lens aging

Previous studies have demonstrated that the C-terminal region of alpha-A crystallin is susceptible to age-dependent, posttranslational modification. To quantitate the amount of modification, alpha-A crystallin was purified from total proteins of the aging bovine lens, then digested with lys-C endoproteinase. Reverse phase, high pressure liquid chromatography was used to resolve and quantitate the resulting peptides, to determine the amount of C-terminal peptide relative to peptides from other regions of the protein that have not been reported to undergo modification. The results indicate that relative to alpha-A crystallin from newborn lens, posttranslational modification has occurred in approximately 45-55% of the C-terminal region from mature lens. These results demonstrate extensive modification of the C-terminal region of alpha-A crystallin from the mature lens, indicating that during the aging process, posttranslational modifications in this region may make significant contributions to the aggregated state and/or molecular chaperone properties of the molecule.

NASA Discipline Cell Biology↗
NASA NTRS2026

Molecular Inventory and Comparative Organic Profiling of A Homogenized Aggregate Sample From Asteroid (101955) Bennu

Evaluating the distribution and diversity of solvent-soluble organic molecules in extraterrestrial materials provide information about the physicochemical environments where prebiotic chemistry occurred and is essential for assessing the inventory of prebiotic compounds available to the early Earth. In this work, we conducted a comprehensive molecular characterization of solvent-soluble organic compounds in a homogenized aggregate sample (ID: OREX-800107-128) of unsorted regolith from asteroid (101955) Bennu returned by NASA’s OSIRIS-REx mission. Using two-dimensional gas chromatography coupled with high-resolution time-of-flight mass spectrometry (GC×GC-HRMS), we identified 87 organic compounds across several molecular classes, including alkanes, polycyclic aromatic hydrocarbons, and nitrogen-, oxygen-, and sulfur-bearing species. Comparison with the organic inventory of CI (Orgueil), C2-ungrouped (Tagish Lake and Tarda), and CM2 (Murchison) carbonaceous chondrites revealed that Bennu sample OREX-800107-128 is most similar to Tagish Lake and Tarda yet compositionally distinct from all of these meteorites. This Bennu sample exhibits a relatively high abundance of low-molecular-weight aromatics (e.g., toluene), pyridine derivatives, and sulfur species such as dimethyl sulfite, consistent with episodic low-temperature aqueous alteration. The presence of these organic compounds suggests that this material experienced chemically diverse processes in the parent body conducive to complex organic synthesis, including aldol condensation reactions responsible for N- and O-bearing compounds. We also compared the molecular distributions of this Bennu sample and previously analyzed samples from (162173) Ryugu to assess potential common origins between these two carbonaceous asteroids. Bennu shows more chemically diverse and nitrogen-rich organic materials than Ryugu. While both asteroids share broadly similar primitive compositions, the observed chemical differences indicate distinct evolutionary histories within a likely common formation environment though whether Bennu and Ryugu derive from a single compositionally heterogeneous parent body or from multiple closely related progenitors remains unresolved. Further detailed comparative analyses of material from Bennu, Ryugu, and specific carbonaceous meteorites (e.g., Tagish Lake and Tarda) will provide new insights into how the N-rich molecular profile observed in Bennu samples was formed and evolved in the outer Solar System.

sample return↗
NASA NTRS1993

Localization of the chaperone binding site

The hypothesis derived from models of the multi-oligomeric chaperone complex suggests that partially denatured proteins bind in a central cavity in the aggregate. To test this hypothesis, the molecular chaperone, alpha crystallin, was bound to partially denatured forms of gamma crystallin, and the binding site was visualized by immunogold localization. In an alternative approach, gold particles were directly complexed with gamma crystallin, followed by binding to the alpha crystallin aggregate. In both cases, binding was localized to the central region of the aggregate, confirming for the first time that partially denatured proteins do indeed bind to a central region of the molecular chaperone aggregate.

Non-NASA Center↗
DOE OSTI2022

Revealing aggregation of non-fullerene acceptors in intermixed phase by ultraviolet-visible absorption spectroscopy

Non-fullerene acceptor (NFA) aggregation is crucial in determining bulk-heterojunction (BHJ) organic photovoltaic (OPV) performance. However, it is still a big challenge to characterize the nanostructure of NFAs in the disordered donor-acceptor intermixed phase. Here, we demonstrate a method to characterize NFA aggregation and composition in the intermixed phase by measuring NFA concentration-dependent ultraviolet-visible (UV-vis) absorption spectroscopy of BHJ films. In various polymer:NFA films, an absorption shift as a function of increasing molecular concentration (ASIMC) phenomenon is observed, and different NFA aggregation behaviors can be distinguished. The ASIMC method was then applied to study the influence of processing conditions on the NFA concentration in the intermixed phase of devices to establish a correlation with device efficiency. The current work provides a feasible tool to study the nanostructure of NFAs in the complex polymer matrix and to understand the variations in the NFA concentration in the intermixed phase under non-equilibrium conditions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1998

Modeling the Growth Rates of Tetragonal Lysozyme Crystal Faces

The measured macroscopic growth rates of the (110) and (101) faces of tetragonal lysozyme show an unexpectedly complex dependence on the supersaturation. The growth rates decay asymptotically to zero when the supersaturation is lowered to zero and increase rapidly when the supersaturation is increased. When supersaturations are increased still further the growth rates attain a maximum before starting to decrease. However, growth of these crystals is known to proceed by the classical dislocation and 2D nucleation growth mechanisms. This anomaly can be explained if growth is assumed to occur not by monomer units but by lysozyme aggregates. Analysis of the molecular packing of these crystals revealed that they were constructed of strongly bonded 4(sub 3) helices, while weaker bonds were responsible for binding the helices to each other. It follows that during crystal growth the stronger bonds are formed before the weaker ones. Thus, the growth of these crystals could be viewed as a two step process: aggregate growth units corresponding to the 4(sub 3) helix are first formed in the bulk solution by stronger intermolecular bonds and then attached to the crystal face by weaker bonds on dislocation hillocks or 2D islands. This will lead to a distribution of aggregates in the solution with monomers and lower order aggregates being predominant at low supersaturations and higher order aggregates being predominant at high supersaturations. If the crystal grows mostly by higher order aggregates, such as tetramers and octamers, it would explain the anomalous dependence of the growth rates on the supersaturation. Besides the analysis of molecular packing, a comprehensive analysis of the measured (110) and (101) growth rates was also undertaken in this study. The distribution of aggregates in lysozyme nutrient solutions at various solution conditions were determined from reversible aggregation reactions at equilibrium. The supersaturation was defined for each aggregate species with respect to its concentration at saturation in order to apply growth rate models to this process. The measured growth rates were then compared with the predicted ones from several dislocation and 2D nucleation growth models, employing tetramer and octamer growth units in polydisperse solutions and monomer units in monodisperse solutions. For the (110) face, the calculations consistently showed that the measured growth rates followed the expected model relations with octamer growth units. For the (101) face, it is not possible to obtain a clear agreement between the predicted and measured growth rates for a single growth unit as done for the (110) face. However, the calculations do indicate that the average size of the growth unit is between a tetramer and an octamer. This suggests that tetramers, octamers and other intermediate size growth units all participate in the growth process for this face. These calculations show that it is possible to model the macroscopic protein crystal growth rates if the molecular level processes can be account for, particularly protein aggregation processes in the bulk solution. Our recent investigations of tetragonal lysozyme crystals employing high resolution atomic force microscopy scans have further confirmed the growth of these crystals by aggregate growth units corresponding to 4(sub 3) helices.

Li, Meirong↗
DOE OSTI2023

Molecular Dynamic Studies of Dye–Dye and Dye–DNA Interactions Governing Excitonic Coupling in Squaraine Aggregates Templated by DNA Holliday Junctions

Dye molecules, arranged in an aggregate, can display excitonic delocalization. The use of DNA scaffolding to control aggregate configurations and delocalization is of research interest. Here, we applied Molecular Dynamics (MD) to gain an insight on how dye–DNA interactions affect excitonic coupling between two squaraine (SQ) dyes covalently attached to a DNA Holliday junction (HJ). We studied two types of dimer configurations, i.e., adjacent and transverse, which differed in points of dye covalent attachments to DNA. Three structurally different SQ dyes with similar hydrophobicity were chosen to investigate the sensitivity of excitonic coupling to dye placement. Each dimer configuration was initialized in parallel and antiparallel arrangements in the DNA HJ. The MD results, validated by experimental measurements, suggested that the adjacent dimer promotes stronger excitonic coupling and less dye–DNA interaction than the transverse dimer. Additionally, we found that SQ dyes with specific functional groups (i.e., substituents) facilitate a closer degree of aggregate packing via hydrophobic effects, leading to a stronger excitonic coupling. This work advances a fundamental understanding of the impacts of dye–DNA interactions on aggregate orientation and excitonic coupling.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2022

Anion chemical composition of poly(ethylene oxide)-based sulfonylimide and sulfonate lithium ionomers controls ion aggregation and conduction

Maximizing ion conduction in single-ion-conducting ionomers is essential for their application in energy-related technologies such as Li-ion batteries. Understanding the anion chemical composition impacts on ion conduction offers new perspectives to maximize ion transport, since the current approach of lowering T g has apparently reached a limit (lowest T g ~ 190 K, highest conductivity ~10 -5 –10 -4 S cm -1 ). Here, a series of random ionomers are synthesized by copolymerizing poly(ethylene glycol)methacrylate with either sulfonylimide lithium methacrylate (MTLi) or sulfonate lithium methacrylate (MSLi) using reversible addition–fragmentation chain transfer (RAFT) polymerization. Li-Ion conduction and self-diffusion coefficients (DLi+) of the ionomers are characterized with dielectric relaxation spectroscopy (DRS) and pulsed-field-gradient (PFG) NMR diffusometry, respectively. Increasing ion content decreases the Li-ion conductivity and D Li+ , as expected from the increased T g . Moreover, a considerably lower ionic conductivity and D Li+ are observed for MSLi compared to MTLi at constant ion content and T g /T. As revealed from X-ray scattering, strong ion aggregation in MSLi results in much lower conductivity and DLi+ compared with less aggregated MTLi based on the more delocalized sulfonylimide anion. These results emphasize the detrimental and molecularly specific role of ion aggregation in Li-ion conductivity, and highlight the necessity for minimizing ion aggregation via the rational choice of anion chemical composition.

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

PhenoProfiling: Mapping phenotypic outcomes to molecular determinants of biochemical activity

The aggregate genomes of the trillions of microorganisms within soil, animal hosts, and aquatic systems encode for an extensive functional capacity for myriad biochemical activities. C, N, P, and S metabolism, synthesis of signaling molecules and vitamins, mineralization, and other activities are essential to microbe, community, and plant physiology, and more broadly to climate, water, animal, flora, and human health. The current understanding of the molecular basis for the function of microbial communities stems primarily from comparative metagenomic and metatranscriptomic studies. These same tools are employed to ascertain the impacts to the community resulting from perturbations, such as climate change, emerging pollutants, fires, and seawater infiltration for environmental communities, and dietary changes, xenobiotic exposure, and various disease states for the human gut microbiome. Such studies can identify the potential for a specific function, but they cannot determine that a particular cell is functionally active, nor can they determine the molecular architecture required for function. In short, genes and transcripts alone fail to reveal the complex subcellular arrangement of proteins and molecules that elicit a given phenotype in a microbial cell.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗