Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “oligomerization”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 19 records

Cellulose synthesis complexes are homo-oligomeric and hetero-oligomeric in Physcomitrium patens

The common ancestor of seed plants and mosses contained homo-oligomeric cellulose synthesis complexes (CSCs) composed of identical subunits encoded by a single CELLULOSE SYNTHASE (CESA) gene. Seed plants use different CESA isoforms for primary and secondary cell wall deposition. Both primary and secondary CESAs form hetero-oligomeric CSCs that assemble and function in planta only when all the required isoforms are present. The moss Physcomitrium (Physcomitrella) patens has seven CESA genes that can be grouped into two functionally and phylogenetically distinct classes. Previously, we showed that PpCESA3 and/or PpCESA8 (class A) together with PpCESA6 and/or PpCESA7 (class B) form obligate hetero-oligomeric complexes required for normal secondary cell wall deposition. Here, we show that gametophore morphogenesis requires a member of class A, PpCESA5, and is sustained in the absence of other PpCESA isoforms. Further, PpCESA5 also differs from the other class A PpCESAs as it is able to self-interact and does not co-immunoprecipitate with other PpCESA isoforms. These results are consistent with the hypothesis that homo-oligomeric CSCs containing only PpCESA5 subunits synthesize cellulose required for gametophore morphogenesis. Analysis of mutant phenotypes also revealed that, like secondary cell wall deposition, normal protonemal tip growth requires class B isoforms (PpCESA4 or PpCESA10), along with a class A partner (PpCESA3, PpCESA5, or PpCESA8). Thus, P. patens contains both homo-oligomeric and hetero-oligomeric CSCs.

59 BASIC BIOLOGICAL SCIENCES↗

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↗

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↗

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↗

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↗

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↗

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↗

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↗

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↗

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↗

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↗

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↗

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↗

The Role of Lewis Acid Sites in γ-Al 2 O 3 Oligomerization

Olefin oligomerization by γ-Al 2 O 3 has recently been reported, and it was suggested that Lewis acid sites are catalytic. The goal of this study is to determine the number of active sites per gram of alumina to confirm that Lewis acid sites are indeed catalytic. Addition of an inorganic Sr oxide base resulted in a linear decrease in the propylene oligomerization conversion at loadings up to 0.3 wt %; while, there is a >95 % loss in conversion above 1 wt % Sr. Additionally, there was a linear decrease in the intensity of the Lewis acid peaks of absorbed pyridine in the IR spectra with an increase in Sr loading, which correlates with the loss in propylene conversion, suggesting that Lewis acid sites are catalytic. Characterization of the Sr structure by XAS and STEM indicates that single Sr 2+ ions are bound to the γ-Al 2 O 3 surface and poison one catalytic site per Sr ion. The maximum loading needed to poison all catalytic sites, assuming uniform surface coverage, was ~0.4 wt % Sr, giving an acid site density of ~0.2 sites per nm2 of γ-Al 2 O 3 , or approximately 3 % of the alumina surface.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Structure-function studies reveal ComEA contains an oligomerization domain essential for transformation in gram-positive bacteria

An essential step in bacterial transformation is the uptake of DNA into the periplasm, across the thick peptidoglycan cell wall of Gram-positive bacteria, or the outer membrane and thin peptidoglycan layer of Gram-negative bacteria. ComEA, a DNA-binding protein widely conserved in transformable bacteria, is required for this uptake step. Here we determine X-ray crystal structures of ComEA from two Gram-positive species, Bacillus subtilis and Geobacillus stearothermophilus, identifying a domain that is absent in Gram-negative bacteria. X-ray crystallographic, genetic, and analytical ultracentrifugation (AUC) analyses reveal that this domain drives ComEA oligomerization, which we show is required for transformation. We use multi-wavelength AUC (MW-AUC) to characterize the interaction between DNA and the ComEA DNA-binding domain. Finally, we present a model for the interaction of the ComEA DNA-binding domain with DNA, suggesting that ComEA oligomerization may provide a pulling force that drives DNA uptake across the thick cell walls of Gram-positive bacteria.

59 BASIC BIOLOGICAL SCIENCES↗

Production of drop-in biodiesel blendstocks via competitive acid-catalyzed dehydration reactions using ethanol oligomerization products

Ethanol can be converted into diesel fuel ethers using a three-step catalytic approach that involves ethanol oligomerization to larger alcohols, hydrogenolysis of the esters followed by dehydration of the C4 to C8 alcohols into ethers. In this paper we report results for the dehydration of a mixture of C4 – C8 alcohols using a zeolite Y catalyst in a continuous flow reactor. Mono-molecular dehydration of the alcohols produces olefins while bi-molecular dehydration of the alcohol produces ethers. Increasing the pressure increases the ether selectivity while decreasing the pressure produces more olefins. Linear alcohol feeds produce more C8+ ethers, while branched and secondary alcohols lead to more olefins. Olefin and coke selectivities increase with increasing carbon chain length of alcohols. Secondary alcohols lead to higher coke selectivities. Furthermore, ethanol/Butanol oligomerization experiments showed that the incoming dehydration feedstock can be grown to larger C6+ alcohol fractions, leading to higher yields of C10+ diesel-range ethers.

09 BIOMASS FUELS↗

Effects of oligomerization and decomposition on the nanoparticle growth: a model study

Abstract. The rate at which freshly formed secondary aerosol particles grow is an important factor in determining their climate impacts. The growth rate of atmospheric nanoparticles may be affected by particle-phase oligomerization and decomposition of condensing organic molecules. We used the Model for Oligomerization and Decomposition in Nanoparticle Growth (MODNAG) to investigate the potential atmospheric significance of these effects. This was done by conducting multiple simulations with varying reaction-related parameters (volatilities of the involved compounds and reaction rates) using both artificial and ambient measured gas-phase concentrations of organic vapors to define the condensing vapors. While our study does not aim at providing information on any specific reaction, our results indicate that particle-phase reactions have significant potential to affect the nanoparticle growth. In simulations in which one-third of a volatility basis set bin was allowed to go through particle-phase reactions, the maximum increase in growth rates was 71 % and the decrease 26 % compared to the base case in which no particle-phase reactions were assumed to take place. These results highlight the importance of investigating and increasing our understanding of particle-phase reactions.

54 ENVIRONMENTAL SCIENCES↗

A Hybrid Structural Method for Investigating Low Molecular Weight Oligomeric Structures of Amyloid Beta

Spurred in part by the failure of recent therapeutics targeting amyloid β plaques in Alzheimer's Disease (AD), attention is increasingly turning to the oligomeric forms of this peptide that form early in the aggregation process. However, while numerous amyloid β fibril structures have been characterized, primarily by NMR spectroscopy and cryo-EM, obtaining structural information on the low molecular weight forms of amyloid β that presumably precede and/or seed fibril formation has proved challenging. Furthermore, these transient forms are heterogeneous, and depend heavily on experimental conditions such as buffer, temperature, concentration, and degree of quiescence during measurement. Here, we present the concept for a new approach to delineating structural features of early-stage low molecular weight amyloid β oligomers, using a solvent accessibility assay in conjunction with simultaneous fluorescence measurements.

60 APPLIED LIFE SCIENCES↗