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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 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Scalable Frontal Oligomerization: Insights from Advanced Mass Analysis

Linear oligomers of dicyclopentadiene (DCPD) are reactive precursors for thermoplastic and thermoset materials. Unlike the foul-smelling parent monomer, oligomers composed of DCPD are odorless. With appropriate modification of the end-group or backbone chemistry, telechelic DCPD oligomers have potential utility as cross-linkers and as macromonomer precursors for block and graft copolymers. Most existing methods to produce oligo-DCPD, however, require solvent, are relatively slow, and necessitate air-free techniques. Here we show that frontal ring-opening metathesis oligomerization (FROMO) of neat DCPD and other norbornene derivatives rapidly generates hundreds of grams of material in minutes with catalyst loadings of 0.5 mM. This energy-efficient catalytic process utilizes the heat generated by the reaction to self-propagate oligomerization throughout the liquid monomer. FROMO employs a terminal olefin (e.g., styrene) in which a cross-metathesis reaction (i.e., chain transfer) competes with ring-opening metathesis (i.e., propagation). Kendrick mass analysis enables rapid identification and assignment of all the chain-end types present and quantifies the degree of branching resulting from the infrequent cyclopentene ring-opening reaction. This analytical technique also detects oligomer species derived from trace impurities in the monomer or chain-transfer agent that are otherwise difficult to observe with other characterization methods. Here, the obtained oligomers possess well-defined chain-ends and molecular weight distributions.

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

Structure and Site Evolution of Framework Ni Species in MIL-127 MOFs for Propylene Oligomerization Catalysis

A mixed-valence oxotrimer metal–organic framework (MOF), Ni-MIL-127, with a fully coordinated nickel atom and two iron atoms in the inorganic node, generates a missing linker defect upon thermal treatment in helium (>473 K) to engender an open coordination site on nickel which catalyzes propylene oligomerization devoid of any cocatalysts or initiators. This catalyst is stable for ~20 h on stream at 500 kPa and 473 K, unprecedented for this chemistry. The number of missing linkers on synthesized and activated Ni-MIL-127 MOFs is quantified using temperature-programmed oxidation, 1 H nuclear magnetic resonance spectroscopy, and X-ray absorption spectroscopy to be ~0.7 missing linkers per nickel; thus, a majority of Ni species in the MOF framework catalyze propylene oligomerization. In situ NO titrations under reaction conditions enumerate ~62% of the nickel atoms as catalytically relevant to validate the defect density upon thermal treatment. Propylene oligomerization rates on Ni-MIL-127 measured at steady state have activation energies of 55–67 kJ mol –1 from 448 to 493 K and are first-order in propylene pressures from 5 to 550 kPa. Density functional theory calculations on cluster models of Ni-MIL-127 are employed to validate the plausibility of the missing linker defect and the Cossee–Arlman mechanism for propylene oligomerization through comparisons between apparent activation energies from steady-state kinetics and computation. Here this study illustrates how MOF precatalysts engender defective Ni species which exhibit reactivity and stability characteristics that are distinct and can be engineered to improve catalytic activity for olefin oligomerization.

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

Asymmetric oligomerization state and sequence patterning can tune multiphase condensate miscibility

Endogenous biomolecular condensates, composed of a multitude of proteins and RNAs, can organize into multiphasic structures with compositionally distinct phases. This multiphasic organization is generally understood to be critical for facilitating their proper biological function. However, the biophysical principles driving multiphase formation are not completely understood. Here we use in vivo condensate reconstitution experiments and coarse-grained molecular simulations to investigate how oligomerization and sequence interactions modulate multiphase organization in biomolecular condensates. We demonstrate that increasing the oligomerization state of an intrinsically disordered protein results in enhanced immiscibility and multiphase formation. Interestingly, we find that oligomerization tunes the miscibility of intrinsically disordered proteins in an asymmetric manner, with the effect being more pronounced when the intrinsically disordered protein, exhibiting stronger homotypic interactions, is oligomerized. Our findings suggest that oligomerization is a flexible biophysical mechanism that cells can exploit to tune the internal organization of biomolecular condensates and their associated biological functions.

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

Conformational and oligomeric states of SPOP from small-angle X-ray scattering and molecular dynamics simulations

Speckle-type POZ protein (SPOP) is a substrate adaptor in the ubiquitin proteasome system, and plays important roles in cell-cycle control, development, and cancer pathogenesis. SPOP forms linear higher-order oligomers following an isodesmic self-association model. Oligomerization is essential for SPOP’s multivalent interactions with substrates, which facilitate phase separation and localization to biomolecular condensates. Structural characterization of SPOP in its oligomeric state and in solution is, however, challenging due to the inherent conformational and compositional heterogeneity of the oligomeric species. Here, we develop an approach to simultaneously and self-consistently characterize the conformational ensemble and the distribution of oligomeric states of SPOP by combining small-angle X-ray scattering (SAXS) and molecular dynamics (MD) simulations. We build initial conformational ensembles of SPOP oligomers using coarse-grained molecular dynamics simulations, and use a Bayesian/maximum entropy approach to refine the ensembles, along with the distribution of oligomeric states, against a concentration series of SAXS experiments. Our results suggest that SPOP oligomers behave as rigid, helical structures in solution, and that a flexible linker region allows SPOP’s substrate-binding domains to extend away from the core of the oligomers. Additionally, our results are in good agreement with previous characterization of the isodesmic self-association of SPOP. In the future, the approach presented here can be extended to other systems to simultaneously characterize structural heterogeneity and self-assembly.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1994

Effect of leaving group on the oligomerization of 5'-AMP on montmorillonite

The oligomerization of imidazole derivative of 5'-AMP (ImpA) in the presence of montmorillonite clay yields oligomers containing up to 10 monomer units. In these reactions, the heterocyclic base, imidazole is the leaving group. In our present study, we synthesized a series of activated nucleotides of 5'AMP using other leaving groups such as pyrazole, 1,2,4-triazole, piperidine, morpholine, 4-aminopyridine, 4-methylaminopyridine, 4-dimethylaminopyridine, 2-aminobenzimidazole etc. to determine the effect of amine leaving group on the products of the oligomerization reaction. Earlier results from our laboratory showed that the presence AppA in the clay reaction of ImpA enhances the oligomerization reaction to yield higher oligomers. We also studied the effect of AppA in the clay mediated oligomerization reaction of the activated nucleotides. Oligomerization of 2-amino-benzimidazole derivative of 5'-AMP gave higher oligomers containing up to nine monomer units in the presence of AppA.

Prabahar, K. Joseph↗
DOE OSTI2023

Validation of the Cossee–Arlman mechanism for propylene oligomerization on Ni/UiO-66

Steady state rate expressions can be derived to distinguish the Cossee–Arlman and metallacycle mechanisms postulated for propylene oligomerization on nickel-based catalysts based on product selectivities, where product selectivities for the former are a function of olefin pressure because sequential coordination and insertion steps lead to independent mechanistic pathways for different hexene isomers. In contrast, the metallacycle mechanism presents pressure-independent product selectivities due to successive coordination prior to the kinetically relevant steps in each mechanism. In this work, steady state propylene oligomerization rates and selectivities were measured in the absence of an activator on nickel functionalized UiO-66 metal organic framework (MOF), Ni/UiO-66, to validate the Cossee–Arlman mechanism for light olefin oligomerization. In situ NO titrations reveal that ~5% of nickel sites were active during the reaction, and thus, not all nickel sites are relevant for catalysis. Propylene dimerization was first order in propylene pressure from 5 to 500 kPa with an apparent activation energy of ~20 kJ mol -1 from 453 to 493 K. Calculated apparent activation energies with density functional theory (DFT) calculations on cluster models of Ni/UiO-66 are in agreement with experiment to corroborate the Cossee–Arlman mechanism. Selectivities of hexene products and the ratio of hexene product selectivities on Ni/UiO-66 are in accordance with selectivity expressions derived from the Cossee–Arlman mechanism. In conclusion, analysis of product selectivities can be used more extensively to demarcate the Cossee–Arlman and metallacycle mechanisms for olefin oligomerization on metal-based catalysts.

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

Structural Basis of Clostridium perfringens Enterotoxin Activation and Oligomerization by Trypsin

Clostridium perfringens enterotoxin (CpE) is a β-pore forming toxin that disrupts gastrointestinal homeostasis in mammals by binding membrane protein receptors called claudins. Although structures of CpE fragments bound to claudins have been determined, the mechanisms that trigger CpE activation and oligomerization that lead to the formation of cytotoxic β-pores remain undetermined. Proteolysis of CpE in the gut by trypsin has been shown to play a role in this and subsequent cytotoxicity processes. Here, we report solution structures of full-length and trypsinized CpE using small-angle X-ray scattering (SAXS) and crystal structures of trypsinized CpE and its C-terminal claudin-binding domain (cCpE) using X-ray crystallography. Mass spectrometry and SAXS uncover that removal of the CpE N-terminus by trypsin alters the CpE structure to expose areas that are normally unexposed. Crystal structures of trypsinized CpE and cCpE reveal unique dimer interfaces that could serve as oligomerization sites. Moreover, comparisons of these structures to existing ones predict the functional implications of oligomerization in the contexts of cell receptor binding and β-pore formation. This study sheds light on trypsin’s role in altering CpE structure to activate its function via inducing oligomerization on its path toward cytotoxic β-pore formation. Its findings can incite new approaches to inhibit CpE-based cytotoxicity with oligomer-disrupting therapeutics.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1999

Oligomerization of L-gamma-carboxyglutamic acid

Unlike glutamic acid, L-gamma-carboxyglutamic acid does not oligomerize efficiently when treated with carbonyldiimidazole in aqueous solution. However, divalent ions such as Mg2+ catalyze the reaction, and lead to the formation of oligomers in good yield. In the presence of hydroxylapatite, L-gamma-carboxyglutamic acid oligomerizes efficiently in a reaction that proceeds in the absence of divalent ions but is further catalyzed when they are present. After 'feeding' 50 times with activated amino acid in the presence of the Mg2+ ion, oligomers longer than the 20-mer could be detected. The effect of hydroxylapatite on peptide elongation is very sensitive to the nature of the activated amino acid and the acceptor peptide. Glutamic acid oligomerizes more efficiently than L-gamma-carboxyglutamic acid on hydroxylapatite and adds more efficiently to decaglutamic acid in solution. One might, therefore, expect that glutamic acid would add more efficiently than L-gamma-carboxyglutamic acid to decaglutamic acid on hydroxylapatite. The contrary is true--the addition of L-gamma-carboxyglutamic acid is substantially more efficient. This suggests that oligomerization on the surface of hydroxylapatite depends on the detailed match between the structure of the surface of the mineral and the structure of the oligomer.

Non-NASA Center↗
DOE OSTI2022

Biochemical and spectroscopic characterizations of the oligomeric antenna of the coral symbiotic Symbiodiniaceae Fugacium kawagutii

Light-harvesting antennas in photosynthesis capture light energy and transfer it to the reaction centers (RCs) where photochemistry takes place. The sustainable growth of the reef-building corals relies on a constant supply of the photosynthates produced by the endosymbiotic dinoflagellate, belonging to the family of Symbiodiniaceae. The antenna system in this group consists of the water-soluble peridinin-chlorophyll $\textit{a}$-protein (PCP) and the intrinsic membrane chlorophyll $\textit{a}$-chlorophyll $c_2$-peridinin protein complex (acpPC). In this report, a nonameric acpPC is reported in a dinoflagellate, Fugasium kawagutii (formerly Symbiodinium kawagutii sp. CS-156). We found that extensive biochemical purification altered the oligomerization states of the initially isolated nonameric acpPC. The excitation energy transfer pathways in the acpPC nonamer and its variants were studied using time-resolved fluorescence and time-resolved absorption spectroscopic techniques at 77 K. Compared to the well-characterized trimeric acpPC, the nonameric acpPC contains an 11 nm red-shifted terminal energy emitter and substantially altered excited state lifetimes of Chl $\textit{a}$. The observed energetic overlap of the fluorescence terminal energy emitters with the absorption of RCs is hypothesized to enable efficient downhill excitation energy transfer. Additionally, the shortened Chl $\textit{a}$ fluorescence decay lifetime in the oligomeric acpPC indicate a protective self-relaxation strategy. We propose that the highly-oligomerized acpPC nonamer represents an intact functional unit in the Symbiodiniaceae thylakoid membrane. They perform efficient excitation energy transfer (to RCs), and are under manageable regulations in favor of photoprotection.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Design of Diverse Asymmetric Pockets in De Novo Homo-oligomeric Proteins

A challenge for design of protein–small-molecule recognition is that incorporation of cavities with size, shape, and composition suitable for specific recognition can considerably destabilize protein monomers. This challenge can be overcome through binding pockets formed at homo-oligomeric interfaces between folded monomers. Interfaces surrounding the central homo-oligomer symmetry axes necessarily have the same symmetry and so may not be well suited to binding asymmetric molecules. To enable general recognition of arbitrary asymmetric substrates and small molecules, we developed an approach to designing asymmetric interfaces at off-axis sites on homo-oligomers, analogous to those found in native homo-oligomeric proteins such as glutamine synthetase. We symmetrically dock curved helical repeat proteins such that they form pockets at the asymmetric interface of the oligomer with sizes ranging from several angstroms, appropriate for binding a single ion, to up to more than 20 Å across. Of the 133 proteins tested, 84 had soluble expression in E. coli, 47 had correct oligomeric states in solution, 35 had small-angle X-ray scattering (SAXS) data largely consistent with design models, and 8 had negative-stain electron microscopy (nsEM) 2D class averages showing the structures coming together as designed. Both an X-ray crystal structure and a cryogenic electron microscopy (cryoEM) structure are close to the computational design models. The nature of these proteins as homo-oligomers allows them to be readily built into higher-order structures such as nanocages, and the asymmetric pockets of these structures open rich possibilities for small-molecule binder design free from the constraints associated with monomer destabilization.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Supported Organochromium Ethylene Oligomerization Enabled by Surface Lithiation

Here, in this work, supported organochromium ethylene polymerization catalysts have been tuned to mediate ethylene oligomerization via surface lithiation, which provides a generalizable protocol to control stereoelectronics and redox states of surface organometallic active sites. The homoleptic chromium(IV) alkyl complex Cr(CH 2 SiMe 3 ) 4 was grafted on high-surface-area anatase titania (TiO 2 ) nanoparticles as well as on silica to produce Cr/TiO 2 and Cr/SiO 2 , respectively. Treatment of these materials with excess n-butyllithium led to the reduced chromium complexes Cr/Li x TiO 2 and Cr/Li/SiO 2 , each of which still retains one hydrocarbyl ligand on chromium. A set of heterogeneous complexes were studied by electron paramagnetic resonance and X-ray absorption spectroscopy, which indicate a reduction in the oxidation state of the major chromium species to Cr II upon lithiation. Cr/Li x TiO 2 converts ethylene to hexenes with a high selectivity (>80%), which was persistent over 10 days at 80 °C, achieving >950 turnovers. The exclusive formation of C 4 and C 6 olefins, preferring the trimerization product, without a statistical (Flory–Schulz) distribution is characteristic of the oxidative cyclization oligomerization mechanism rather than the traditional Cossee–Arlman mechanism, whereas Cr/Li/SiO 2 produced a mixture of trimerization and polymerization products, suggesting site heterogeneity in the silica-based material. On the other hand, the unreduced chromium(IV) materials as well as low lithium-containing Cr/Li x TiO 2 (x < 0.16) exclusively produced ultrahigh molecular weight polyethylene, determined by differential scanning calorimetry and gel permeation chromatography analysis, likely formed via a linear-insertion mechanism, with a crossover from the polymerization to oligomerization regime observed at ~16% Li intercalation.

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

Observational evidence for Criegee intermediate oligomerization reactions relevant to aerosol formation in the troposphere

Criegee intermediates are reactive intermediates that are implicated in transforming the composition of Earth’s troposphere and in the formation of secondary organic aerosol, impacting Earth’s radiation balance, air quality and human health. Yet, direct identification of their signatures in the field remains elusive. Here, from particulate and gas-phase mass-spectrometric measurements in the Amazon rainforest, we identify sequences of masses consistent with the expected signatures of oligomerization of the CH 2 OO Criegee intermediate, a process implicated in ozonolysis-driven aerosol formation. In this study, we assess the potential contributions of oligomerization through laboratory ozonolysis experiments, direct kinetic studies of Criegee intermediate reactions, and high-level theoretical calculations. Global atmospheric models built on these kinetics results indicate that Criegee intermediate chemistry may play a larger role in altering the composition of Earth’s troposphere than is captured in current atmospheric models, especially in areas of high humidity. However, the models still capture only a relatively small fraction of the observed signatures, suggesting considerable underestimates of Criegee intermediate concentrations and reactivity and/or the dominance of other, presently uncharacterized, oxidation mechanisms. Resolving the remaining uncertainties in emission inventories and the effects of atmospheric water vapour on key chemical reactions will be required to definitively assess the role of Criegee intermediate oligomerization reactions.

58 GEOSCIENCES↗
DOE OSTI2024

Molecular basis of TMED9 oligomerization and entrapment of misfolded protein cargo in the early secretory pathway

Intracellular accumulation of misfolded proteins causes serious human proteinopathies. The transmembrane emp24 domain 9 (TMED9) cargo receptor promotes a general mechanism of cytotoxicity by entrapping misfolded protein cargos in the early secretory pathway. However, the molecular basis for this TMED9-mediated cargo retention remains elusive. Here, we report cryo–electron microscopy structures of TMED9, which reveal its unexpected self-oligomerization into octamers, dodecamers, and, by extension, even higher-order oligomers. The TMED9 oligomerization is driven by an intrinsic symmetry mismatch between the trimeric coiled coil domain and the tetrameric transmembrane domain. Using frameshifted Mucin 1 as an example of aggregated disease-related protein cargo, we implicate a mode of direct interaction with the TMED9 luminal Golgi-dynamics domain. The structures suggest and we confirm that TMED9 oligomerization favors the recruitment of coat protein I (COPI), but not COPII coatomers, facilitating retrograde transport and explaining the observed cargo entrapment. Our work thus reveals a molecular basis for TMED9-mediated misfolded protein retention in the early secretory pathway.

Science & Technology - Other Topics↗
NASA NTRS1990

Oligomerizations of deoxyadenosine bis-phosphates and of their 3-prime-5-prime, 3-prime-3-prime, and 5-prime-5-prime dimers - Effects of a pyrophosphate-linked, poly(T) analog

The effect of a 3-prime-5-prime pyrophosphate-linked oligomer of pTp on oligomerizations of pdAp and of its 3-prime-5-prime, 3-prime-3-prime, and 5-prime-5-prime dimers was investigated, using HPLC to separate the reaction mixtures; peak detection was by absorbance monitoring at 254 nm. It was expected that the dimers would form stable complexes with the template, with the degree of stability depending upon the internal linkage of each dimer. It was found that, although the isomers differ substantially in their oligomerization behavior in the absence of template, the analog-template catalyzes the oligomerization to about the same extent in all three cases.

Visscher, J.↗
NASA NTRS1999

Nonenzymatic oligomerization reactions on templates containing inosinic acid or diaminopurine nucleotide residues

The template-directed oligomerization of nucleoside-5'-phosphoro-2-methyl imidazolides on standard oligonucleotide templates has been studied extensively. Here, we describe experiments with templates in which inosinic acid (I) is substituted for guanylic acid, or 2,6-diaminopurine nucleotide (D) for adenylic acid. We find that the substitution of I for G in a template is strongly inhibitory and prevents any incorporation of C into internal positions in the oligomeric products of the reaction. The substitution of D for A, on the contrary, leads to increased incorporation of U into the products. We found no evidence for the template-directed facilitation of oligomerization of A or I through A-I base pairing. The significance of these results for prebiotic chemistry is discussed.

NASA Discipline Exobiology↗
NASA NTRS1991

Attempted nonenzymatic template-directed oligomerizations on a polyadenylic acid template: implications for the nature of the first genetic material

Previous attempts to produce nonenzymatic template-directed oligomerizations of activated pyrimidines on polypurine templates have been unsuccessful. The only efficient reactions are those where the template is composed primarily of pyrimidines, especially cytosine. Because molecular evolution requires that a synthesized daughter polynucleotide be capable of acting as a template for the synthesis of the original polynucleotide, the one-way replication achieved thus far is inadequate to initiate an evolving system. Several uracil analogs were used in this investigation in order to search for possible replacements for uracil. The monomers used in this investigation were the imidazolides of UMP, xanthosine 5'-monophosphate, the bis-monophosphates of the acyclic nucleosides of uracil, and 2,4-quinazolinedione. The concentrations of various salts, buffers, pH, and temperature were among the different variables investigated in attempts to find conditions that would permit template-directed oligomerizations. Although the different monomers in this study demonstrated varying abilities to form very short oligomers, we were unable to detect any enhancement of this oligomerization that could be attributed to the poly(A) template. Although special conditions might be found that would allow purine-rich templates to work, these reactions cannot be considered robust. The results of our experiments suggest that pyrimidines were not part of the original replicating system on the primitive Earth. It has already been shown that ribose is an unlikely component of the first replicating systems, and we now suggest that phosphate was absent as well. This is due to the low solubility of phosphate in the present ocean (3 x 10(-6) M), as well as the difficulty of prebiotic activation of phosphates.

Non-NASA Center↗
NASA NTRS1997

Effect of dinucleoside pyrophosphates on the oligomerization of activated mononucleotides on Na(+)-montmorillonite: reaction of 5'-phosphoro-4-(dimethylamino)pyridinium [4-(CH3)2NpypA] with A5'ppA

The oligomerization of adenosine 5'-phosphoro-4-(dimethylamino)pyridinium (4-(CH3)2-NpypA) and diadenosine 5',5'-pyrophosphate (A5'ppA) (9:1) on Na(+)-montmorillonite was studied. The oligomers were isolated and analyzed by selective enzymatic hydrolyses and the oligomeric composition and the percent of 3',5'-phosphodiester linkages present in each fraction was determined. The longest oligomers formed (11-mers) are slightly shorter than those produced in the absence of A5'ppA (12-mers). Smaller amounts of A5'ppA are incorporated into the oligomers than in the ImpA/A5'ppA reaction. The regioselectivity of 3',5'-phosphodiester bond formation is comparable to that of the oligomerization of 4-(CH3)2NpypA alone. An explanation of these data is proposed and the possible effect of dinucleoside pyrophosphate on prebiotic RNA formation is discussed.

Non-NASA Center↗
DOE OSTI2023

Characterizing the Impact of Oligomerization on Redox Flow Cell Performance

Abstract Redox flow batteries (RFBs) are hindered by complex failure modes, particularly crossover through the membrane, resulting in capacity fade and reduced cycling efficiencies. Redox‐active oligomers (RAOs) have recently been proposed for mitigating this phenomenon while maintaining sufficient transport properties; however, to date, few studies have quantified how the chemical and electrochemical properties of RAOs influence their performance in redox flow cells. Here, we demonstrate that oligomeric derivatives of 2,2,6,6‐tetramethylpiperidine 1‐oxyl (TEMPO) exhibit lower diffusivities than the monomeric species but retain facile charge transfer characteristics. The size‐dependent variations in mass transport rates directly translate to differences in flow cell polarization and symmetric cycling performance. Post‐mortem analyses reveal that oligomerization does not meaningfully alter decay processes as evinced by similar capacity fade across all species. Broadly, these findings corroborate and extend upon previously developed relationships between molecular size, electrochemical properties, and flow cell performance.

36 MATERIALS SCIENCE↗