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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 343 records · Page 19
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Hierarchical organization and assembly of the archaeal cell sheath from an amyloid-like protein

Abstract Certain archaeal cells possess external proteinaceous sheath, whose structure and organization are both unknown. By cellular cryogenic electron tomography (cryoET), here we have determined sheath organization of the prototypical archaeon, Methanospirillum hungatei . Fitting of Alphafold-predicted model of the sheath protein (SH) monomer into the 7.9 Å-resolution structure reveals that the sheath cylinder consists of axially stacked β-hoops, each of which is comprised of two to six 400 nm-diameter rings of β-strand arches (β-rings). With both similarities to and differences from amyloid cross-β fibril architecture, each β-ring contains two giant β-sheets contributed by ~ 450 SH monomers that entirely encircle the outer circumference of the cell. Tomograms of immature cells suggest models of sheath biogenesis: oligomerization of SH monomers into β-ring precursors after their membrane-proximal cytoplasmic synthesis, followed by translocation through the unplugged end of a dividing cell, and insertion of nascent β-hoops into the immature sheath cylinder at the junction of two daughter cells.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Attention-based functional-group coarse-graining: a deep learning framework for molecular prediction and design

Machine learning (ML) offers considerable promise for the design of new molecules and materials. In real-world applications, the design problem is often domain-specific, and suffers from insufficient data, particularly labeled data, for ML training. In this study, we report a data-efficient, deep-learning framework for molecular discovery that integrates a coarse-grained functional-group representation with a self-attention mechanism to capture intricate chemical interactions. Our approach exploits group-contribution concepts to create a graph-based intermediate representation of molecules, serving as a low-dimensional embedding that substantially reduces the data demands typically required for training. Using a self-attention mechanism to learn the subtle but highly relevant chemical context of functional groups, the method proposed here consistently outperforms existing approaches for predictions of multiple thermophysical properties. In a case study focused on adhesive polymer monomers, we train on a limited dataset comprising only 6,000 unlabeled and 600 labeled monomers. The resulting chemistry prediction model achieves over 92% accuracy in forecasting properties directly from SMILES strings, exceeding the performance of current state-of-the-art techniques. Furthermore, the latent molecular embedding is invertible, enabling the design pipeline to automatically generate new monomers from the learned chemical subspace. We illustrate this functionality by targeting several properties, including high and low glass transition temperatures (Tg), and demonstrate that our model can identify new candidates with values that surpass those in the training set. The ease with which the proposed framework navigates both chemical diversity and data scarcity offers a promising route to accelerate and broaden the search for functional materials.

Han, Ming [Univ. of Chicago, IL (United States)]↗
DOE OSTI2023

Expanding the substrate scope of pyrrolysyl-transfer RNA synthetase enzymes to include non-$α$-amino acids in vitro and in vivo

The absence of orthogonal aminoacyl-transfer RNA (tRNA) synthetases that accept non-L-α-amino acids is a primary bottleneck hindering the in vivo translation of sequence-defined hetero-oligomers and biomaterials. Here we report that pyrrolysyl-tRNA synthetase (PylRS) and certain PylRS variants accept α-hydroxy, α-thio and N-formyl-L-α-amino acids, as well as α-carboxy acid monomers that are precursors to polyketide natural products. These monomers are accommodated and accepted by the translation apparatus in vitro; those with reactive nucleophiles are incorporated into proteins in vivo. High-resolution structural analysis of the complex formed between one PylRS enzyme and a m-substituted 2-benzylmalonic acid derivative revealed an active site that discriminates prochiral carboxylates and accommodates the large size and distinct electrostatics of an α-carboxy substituent. This work emphasizes the potential of PylRS-derived enzymes for acylating tRNA with monomers whose α-substituent diverges substantially from the α-amine of proteinogenic amino acids. These enzymes or derivatives thereof could synergize with natural or evolved ribosomes and/or translation factors to generate diverse sequence-defined non-protein heteropolymers.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Atomistic simulations of the Escherichia coli ribosome provide selection criteria for translationally active substrates

As genetic code expansion advances beyond l-α-amino acids to backbone modifications and new polymerization chemistries, delineating what substrates the ribosome can accommodate remains a challenge. The Escherichia coli ribosome tolerates non-l-α-amino acids in vitro, but few structural insights that explain how are available, and the boundary conditions for efficient bond formation are so far unknown. Here we determine a high-resolution cryogenic electron microscopy structure of the E. coli ribosome containing α-amino acid monomers and use metadynamics simulations to define energy surface minima and understand incorporation efficiencies. Reactive monomers across diverse structural classes favour a conformational space where the aminoacyl-tRNA nucleophile is <4 Å from the peptidyl-tRNA carbonyl with a Bürgi–Dunitz angle of 76–115°. Monomers with free energy minima that fall outside this conformational space do not react efficiently. This insight should accelerate the in vivo and in vitro ribosomal synthesis of sequence-defined, non-peptide heterooligomers.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Precisely patterned nanofibres made from extendable protein multiplexes

Molecular systems with coincident cyclic and superhelical symmetry axes have considerable advantages for materials design as they can be readily lengthened or shortened by changing the length of the constituent monomers. Among proteins, alpha-helical coiled coils have such symmetric, extendable architectures, but are limited by the relatively fixed geometry and flexibility of the helical protomers. Here we describe a systematic approach to generating modular and rigid repeat protein oligomers with coincident C 2 to C 8 and superhelical symmetry axes that can be readily extended by repeat propagation. From these building blocks, we demonstrate that a wide range of unbounded fibres can be systematically designed by introducing hydrophilic surface patches that force staggering of the monomers; the geometry of such fibres can be precisely tuned by varying the number of repeat units in the monomer and the placement of the hydrophilic patches.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Random heteropolymers as enzyme mimics

Despite successes in replicating the primary–secondary–tertiary structure hierarchy of protein, it remains elusive to synthetically materialize protein functions that are deeply rooted in their chemical, structural and dynamic heterogeneities. We propose that for polymers with backbone chemistries different from that of proteins, programming spatial and temporal projections of sidechains at the segmental level can be effective in replicating protein behaviours; and leveraging the rotational freedom of polymer can mitigate deficiencies in monomeric sequence specificity and achieve behaviour uniformity at the ensemble level. Here, guided by the active site analysis of about 1,300 metalloproteins, we design random heteropolymers (RHPs) as enzyme mimics based on one-pot synthesis. We introduce key monomers as the equivalents of the functional residues of protein and statistically modulate the chemical characteristics of key monomer-containing segments, such as segmental hydrophobicity. The resultant RHPs form pseudo-active sites that provide key monomers with protein-like microenvironments, co-localize substrates with catalytic or cofactor-binding sidechains and catalyse reactions such as oxidation and cyclization of citronellal with isopulegol/menthoglycol selectivity. This RHP design led to enzyme-like materials that can retain catalytic activity under non-biological conditions, are compatible with scalable processing and have expanded substrate scope, including environmentally long-lasting antibiotic tetracycline.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Lignin to adipic acid in a high-yield chemical and biological redox process

Viable manufacturing pathways to produce bio-based chemicals from renewable feedstocks, such as lignin derived from plant biomass, are needed to decarbonize the chemicals manufacturing sector. Converting the recalcitrant lignin polymer to valuable bioproducts remains a longstanding challenge in biorefining, with the highest reported single-product yield from lignin currently around 20 wt%. Most existing lignin depolymerization strategies target aryl–ether bond cleavage, which can produce aromatic monomers in yields of only about 30 wt%, and still as complex mixtures with C–C-linked dimers and oligomers. The recalcitrance of these C–C linkages between aromatic moieties fundamentally limits single-product yields from lignin, prompting the development of strategies to efficiently cleave these C–C bonds. Here, in this study, we show how reductive processing of lignin from poplar accesses a hydrocarbon mixture of alkyl-aromatic monomers and oligomers that is privileged for oxidative conversion to monomeric aromatic carboxylic acids, comprising mostly benzoic acid and phthalic acid isomers in up to 73 wt% monomer yields, using a Co/Mn/Br catalyst. The soil bacterium Pseudomonas putida KT2440 was engineered to convert this mixture of aromatic carboxylic acids to muconolactone, a precursor to bio-based nylons, enabling final adipic acid yields up to 26 wt% (gram adipic acid per gram lignin) with a maximum theoretical yield of 57 wt%. This pairing of reductive and oxidative steps with lignin resembles processes in petrochemical refining and shows how lignin may be converted into a single, valuable bioproduct in high yields.

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

Enhanced purification coupled with biophysical analyses shows cross-β structure as a core building block for Streptococcus mutans functional amyloids

Streptococcus mutans is an etiologic agent of human dental caries that forms dental plaque biofilms containing functional amyloids. Three amyloidogenic proteins, P1, WapA, and Smu_63c were previously identified. C123 and AgA are naturally occurring amyloid-forming fragments of P1 and WapA, respectively. We determined that four amyloidophilic dyes, ThT, CDy11, BD-oligo, and MK-H4, differentiate C123, AgA, and Smu_63c amyloid from monomers, but non-specific binding to bacterial cells in the absence of amyloid precludes their utility for identifying amyloid in biofilms. Congo redinduced birefringence is a more specific indicator of amyloid formation and differentiates biofilms formed by wild-type S. mutans from a triple ΔP1/WapA/Smu_63c mutant with reduced bioiflm forming capabilities. Amyloid accumulation is a late event, appearing in older S. mutans biofilms after 60hours of growth. Amyloid derived from pure preparations of all three proteins is visualized by electron microscopy as mat-like structures. Typical amyloid fibers become evident following protease digestion to eliminate non-specific aggregates and monomers. Amyloid mats, similar in appearance to those reported in S. mutans biofilm extracellular matrices, are reconstituted by co-incubation of monomers and amyloid fibers. X-ray fiber diffraction of amyloid mats and fibers from all three proteins demonstrate patterns reflective of a cross-β amyloid structure.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

A mathematical analysis of carbon fixing materials that grow, reinforce, and self-heal from atmospheric carbon dioxide

Carbon fixing materials are a new class of self-healing, self-reinforcing materials we have introduced that utilize ambient CO 2 to chemically add to an ever extending carbon backbone. This class of materials can utilize biological or non-biological photocatalysts and support a wide range of potential backbone chemistries. However, there is no analysis to date that describes their fundamental limits in terms of chemical kinetics and mass transfer. In this computational study, we employ a reaction engineering, and materials science analysis to answer basic questions about the maximum growth rate, photocatalytic requirements and limits of applicable materials. Our proposed mathematical framework envelops three main functions required for carbon fixing materials: (1) adsorption of CO 2 from air, (2) photocatalytic reduction of CO 2 into selected monomers, and (3) polymerization of CO 2 -derived monomers. First, by performing a Damköhler number analysis, we derive criteria for the cross over from kinetic control to mass transfer limited growth, setting upper limits on performance of a potential photocatalyst. Next, we analyze photocatalytic reduction of CO 2 to single carbon products, using known catalytic pathways and kinetic data. We identify formaldehyde as a C1 intermediate having unique potential for incorporation into the material backbone of carbon fixing materials. As an example, we find that a diamond-shaped reaction network graph for CO 2 reduction, passing through CO and HCOOH intermediates, accurately describes kinetic data for cobalt-promoted TiO 2 nanoparticles at room temperature and 1 atm CO 2 . Finally, as an applied case study, we consider and analyze the example of a carbon fixing poly(oxymethylene) system with embedded catalyst promoting the photocatalytic reduction of CO 2 to formaldehyde. The latter then trimerizes to a trioxane monomer which subsequently polymerizes to polyoxymethylene. This reaction engineering analysis introduces benchmarks for carbon fixing materials with respect to achievable rates of photocatalysis, adsorption, and polymerization. These results should prove valuable for the design, evaluation, and benchmarking of this emergent and new class of environmentally sustainable materials.

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

Controlled hydrogenation of a biomass-derived platform chemical formed by aldol-condensation of 5-hydroxymethyl furfural (HMF) and acetone over Ru, Pd, and Cu catalysts

Her we report that we studied the hydrogenation at temperatures from 313–393 K of a biomass-derived platform molecule, 5-hydroxymethyl furfural (HMF)-acetone-HMF (HAH) over Pd, Ru, and Cu based catalysts. HAH was selectively hydrogenated to produce partially-hydrogenated monomers (PHAH) over Cu and Ru catalysts and to fully-hydrogenated HAH monomers (FHAH) over the Ru catalyst. Pd based catalysts yielded a mixture of partially and fully hydrogenated monomers. Lumped reaction kinetics models were employed to quantify the kinetic behavior for hydrogenation over Ru, Cu, and Pd catalysts. The 5-step pathway exhibited over Pd and Ru catalysts consists of both series and parallel reaction steps, where HAH is both converted to fully hydrogenated products sequentially via series reactions of partially hydrogenated intermediates, as well as converted directly in parallel reactions to form the fully hydrogenated products. In contrast, the 3-step pathway over the Cu catalyst consists only of the consecutive reaction steps, where the final product was formed via series reactions of intermediate products. Additionally, reaction over the Cu catalyst did not hydrogenate the furan rings of the HAH molecule and yielded a different final product than those hydrogenation over Pd and Ru catalysts. Batch conditions are determined for each hydrogenated product that give the highest yields in both batch and plug flow reactors.

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

Templated synthesis enhances the cobalt adsorption capacity of a porous organic polymer

Divalent transition metals such as Co(II) are important targets for removal from water sources, due to their potential toxicity as well as their high value. In this study, we found that a series of porous organic polymers based on amide-linked tetraphenylmethane units are effective Co(II) ion adsorbents in aqueous solution. To increase the density of Co(II) binding sites, we then developed a templated synthesis in which the branched, rigid monomers are pre-assembled around Co(II) ions prior to polymerization. Furthermore, after polymer formation, the Co(II) template ions are removed to yield a material rich in Co(II) binding sites. Ion adsorption isotherms show that the Co(II)-templated material has an ion adsorption capacity significantly greater than those of the non-templated materials, highlighting the utility of a templated synthetic route. SEM and TEM images show the morphology of the templated polymer to be dramatically different from the non-templated polymers and to be similar in size and shape to the Co(II)–monomer precursors, emphasizing the role of the template ions in directing the formation of the resulting polymer. This guest-templated approach requires no functionalization of the generic monomer and represents a promising synthetic route to high-capacity ion adsorbents for water purification and aqueous separations.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Initiator-dependent kinetics of lyotropic liquid crystal-templated thermal polymerization

In this study, we examine the polymerization kinetics with different thermal initiators in lamellar and hexagonal lyotropic liquid crystal (LLC) structures directed by Pluronic L64. Ammonium persulfate is used to initiate the polymerization from the water phase, whereas azobisisobutyronitrile and benzoyl peroxide are employed to commence the reaction through the monomer phase. While the mesophase structure remains intact for all the initiation systems, the kinetics of polymerization and conversion vary significantly. The obtained differential scanning calorimetry (DSC) results reveal that, under same conditions, initiation from water (IFW) system results in enhanced reaction rates as well as higher monomer conversions compared to initiation from oil (IFO) one. Higher termination rate in LLC nanoconfinements induces lower reaction rates in IFO system. Moreover, our work on different LLC structures show that the effect of nanoconfinement on polymerization rate can be minimized through IFW. Chemorheology not only confirms the results obtained from DSC, but also shows that, in similar monomer conversions, the polymers obtained from IFW system exhibit an improved mechanical properties over the samples produced though IFO process.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Decorrelated singlet and triplet exciton delocalization in acetylene-bridged Zn-porphyrin dimers

The controlled delocalization of molecular excitons remains an important goal towards the application of organic chromophores in processes ranging from light-initiated chemical transformations to classical and quantum information processing. In this study, we present a methodology to couple optical and magnetic spectroscopic techniques and assess the delocalization of singlet and triplet excitons in model molecular chromophores. By comparing the steady-state and time-resolved optical spectra of Zn-porphyrin monomers and weakly coupled dimers, we show that we can use the identity of substituents bound at specific positions of the macromolecules' rings to control the inter-ring delocalization of singlet excitons stemming from their B states through acetylene bridges. While broadened steady-state absorption spectra suggest the presence of delocalized B state excitons in mesityl-substituted Zn-tetraphenyl porphyrin dimers (Zn 2 U-D), we confirm this conclusion by measuring an enhanced ultrafast non-radiative relaxation from these inter-ring excitonic states to lower lying electronic states relative to their monomer. In contrast to the delocalized nature of singlet excitons, we use time-resolved EPR and ENDOR spectroscopies to show that the triplet states of the Zn-porphyrin dimers remain localized on one of the two macrocyclic sub-units. We use the analysis of EPR and ENDOR measurements on unmetallated model porphyrin monomers and dimers to support this conclusion. The results of DFT calculations also support the interpretation of localized triplet states. These results demonstrate researchers cannot conclude triplet excitons delocalize in macromolecular based on the presence of spatially extended singlet excitons, which can help in the design of chromophores for application in spin conversion and information processing technologies.

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

Generating forces in confinement via polymerization

Understanding how to produce forces using biomolecular building blocks is essential for the development of adaptive synthetic cells and living materials. Here we ask whether a dynamic polymer system can generate deformation forces in soft shells by pure self-assembly, motivated by the fact that biological polymer networks like the cytoskeleton can exert forces, move objects, and deform membranes by simply growing, even in the absence of molecular motors. We address this question by investigating polymer force generation by varying the release rate, the structure, and the interactions of self-assembling monomers. First, we develop a toy computational model of polymerization in a soft elastic shell that reveals the emergence of spontaneous bundling which enhances shell deformation. We then extend our model to account more explicitly for monomer binding dynamics. We find that the rate at which monomers are released into the interior of the shell is a crucial parameter for achieving deformation through polymer growth. Lastly, we demonstrate that the introduction of multivalent particles that can join polymers can either improve or impede polymer performance, depending on the amount and on the structure of the multivalent particles. Our results provide guidance for the experimental realization of polymer systems that can perform work at the nanoscale, for example through rationally designed self-assembling proteins or nucleic acids.

Osmanović, Dino [University of California at Los A↗
DOE OSTI2026

Towards a theoretical understanding of excitonic properties of phthalocyanine thin films. I. Low-temperature exciton absorption spectra

Phthalocyanine (Pc)-based molecular thin films have emerged in recent years as a promising class of organic semiconductor materials for optoelectronic applications owing to their long exciton coherence length and fast exciton diffusion. However, the dependence of their exciton properties on the dimensionality and thermodynamic conditions, presence of metal ions, and effects of chemical modifications to the PC systems is not yet fully understood. As a first step towards a more comprehensive theoretical understanding of the excitonic properties of Pc thin films, we model their low-temperature exciton absorption spectra by employing the Frenkel Hamiltonian. The latter is derived from quantum-chemical estimates of site energies and exciton–exciton couplings. The predicted exciton absorption spectra of octabutoxy phthalocyanine (H 2 OBPc) is found to be strongly dependent on the dimensionality of the model as well as the distance cutoff for including the monomer–monomer exciton coupling. We also caution that the widely used dipole–dipole approximation could substantially overestimate the excitonic coupling between different monomers compared to a more accurate evaluation using the respective transition densities.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Delocalized Excitation Transfer in Open Quantum Systems with Long-Range Interactions

The interplay between coherence and system-environment interactions is at the basis of a wide range of phenomena, from quantum information processing to charge and energy transfer in molecular systems, biomolecules, and photochemical materials. In this work, we use a Frenkel exciton model with long-range interacting qubits coupled to a damped collective bosonic mode to investigate vibrationally assisted transfer processes in donor-acceptor systems featuring internal substructures analogous to light-harvesting complexes. We find that certain delocalized excitonic states maximize the transfer rate and that the entanglement is preserved during the dissipative transfer over a wide range of parameters. We investigate the reduction in transfer caused by static disorder, white noise, and finite temperature and study how transfer efficiency scales as a function of the number of dimerized monomers and the component number of each monomer, finding which excitonic states lead to optimal transfer. Finally, we provide a realistic experimental setting to realize this model in analog trapped-ion quantum simulators. Analog quantum simulation of systems comprising many and increasingly complex monomers could offer valuable insights into the design of light-harvesting materials, particularly in the nonperturbative intermediate parameter regime examined in this study, where classical simulation methods are resource intensive.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2023

Monomeric crystal structure of the vaccine carrier protein CRM 197 and implications for vaccine development

CRM 197 is a genetically detoxified mutant of diphtheria toxin (DT) that is widely used as a carrier protein in conjugate vaccines. Protective immune responses to several bacterial diseases are obtained by coupling CRM 197 to glycans from these pathogens. Wild-type DT has been described in two oligomeric forms: a monomer and a domain-swapped dimer. Their proportions depend on the chemical conditions and especially the pH, with a large kinetic barrier to interconversion. A similar situation occurs in CRM 197 , where the monomer is preferred for vaccine synthesis. Despite 30 years of research and the increasing application of CRM 197 in conjugate vaccines, until now all of its available crystal structures have been dimeric. Here, CRM 197 was expressed as a soluble, intracellular protein in an Escherichia coli strain engineered to have an oxidative cytoplasm. The purified product, called EcoCRM, remained monomeric throughout crystallization. The structure of monomeric EcoCRM is reported at 2.0 Å resolution with the domain-swapping hinge loop (residues 379–387) in an extended, exposed conformation, similar to monomeric wild-type DT. The structure enables comparisons across expression systems and across oligomeric states, with implications for monomer–dimer interconversion and for the optimization of conjugation.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Chemically recyclable thermoplastics from reversible-deactivation polymerization of cyclic acetals

Identifying plastics capable of chemical recycling to monomer (CRM) is the foremost challenge in creating a sustainable circular plastic economy. Polyacetals are promising candidates for CRM but lack useful tensile strengths owing to the low molecular weights produced using current uncontrolled cationic ring-opening polymerization (CROP) methods. Here, we present reversible-deactivation CROP of cyclic acetals using a commercial halomethyl ether initiator and an indium(III) bromide catalyst. Using this method, we synthesize poly(1,3-dioxolane) (PDXL), which demonstrates tensile strength comparable to some commodity polyolefins. Depolymerization of PDXL using strong acid catalysts returns monomer in near-quantitative yield and even proceeds from a commodity plastic waste mixture. Our efficient polymerization method affords a tough thermoplastic that can undergo selective depolymerization to monomer.

Abel, Brooks A.↗