Ni cation sites exchanged onto microporous materials catalyze ethene oligomerization to butenes and heavier oligomers but also undergo rapid deactivation. The use of mesoporous supports has been reported previously to alleviate deactivation in regimes of high ethene pressures and low temperatures that cause capillary condensation of ethene within mesoporous voids. Here, we reproduce these prior findings on mesoporous Ni‐MCM‐41 and report that, in sharp contrast, reaction conditions that nominally correspond to ethene capillary condensation in microporous Ni‐Beta or Ni‐FAU zeolites do not mitigate deactivation, likely because confinement within microporous voids restricts the formation of condensed phases of ethene that are effective at solvating and desorbing heavier intermediates that are precursors to deactivation. Deactivation rates are found to transition from a first‐order to a second‐order dependence on Ni site density in Ni‐FAU zeolites with increasing ethene pressure, suggesting a transition in the dominant deactivation mechanism involving a single Ni site to one involving two Ni sites, reminiscent of the effects of increasing H2pressure on changing the kinetic order of deactivation in our prior work on Ni‐Beta zeolites.
This content will become publicly available on July 7, 2024
- NSF-PAR ID:
- 10463046
- Date Published:
- Journal Name:
- The Journal of Chemical Physics
- Volume:
- 159
- Issue:
- 1
- ISSN:
- 0021-9606
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
-
more » « less
Abstract -
more » « less
Abstract Many phenolic compounds found as contaminants in natural waters are susceptible to oxidation by manganese oxides. However, there is often variability between oxidation rates reported in pristine matrices and studies using more environmentally relevant conditions. For example, the presence of cations generally results in slower phenolic oxidation rates. However, the underlying mechanism of cation interference is not well understood. In this study, cation co‐solutes inhibit the transformation of four target phenols (bisphenol A, estrone,
p ‐cresol, and triclosan) by acid birnessite. Oxidation rates for these compounds by acid birnessite follow the same trend (Na+ > K+ > Mg2+ > Ca2+) when cations are present as co‐solutes. We further demonstrate that the same trend applies to these cations when they are absent from solution but pre‐exchanged with the mineral. We analyze valence state, surface area, crystallinity, and zeta potential to characterize changes in oxide structure. The findings of this study show that pre‐exchanged cations have a large effect on birnessite reactivity even in the absence of cation co‐solutes, indicating that the inhibition of phenolic compound oxidation is not due to competition for surface sites, as previously suggested. Instead, the reaction inhibition is attributed to changes in aggregation and the mineral microstructure. -
Abstract Background The pond snail, Lymnaea stagnalis ( L. stagnalis ), has served as a valuable model organism for neurobiology studies due to its simple and easily accessible central nervous system (CNS). L. stagnalis has been widely used to study neuronal networks and recently gained popularity for study of aging and neurodegenerative diseases. However, previous transcriptome studies of L. stagnalis CNS have been exclusively carried out on adult L. stagnalis only. As part of our ongoing effort studying L. stagnalis neuronal growth and connectivity at various developmental stages, we provide the first age-specific transcriptome analysis and gene annotation of young (3 months), adult (6 months), and old (18 months) L. stagnalis CNS. Results Using the above three age cohorts, our study generated 55–69 millions of 150 bp paired-end RNA sequencing reads using the Illumina NovaSeq 6000 platform. Of these reads, ~ 74% were successfully mapped to the reference genome of L. stagnalis . Our reference-based transcriptome assembly predicted 42,478 gene loci, of which 37,661 genes encode coding sequences (CDS) of at least 100 codons. In addition, we provide gene annotations using Blast2GO and functional annotations using Pfam for ~ 95% of these sequences, contributing to the largest number of annotated genes in L. stagnalis CNS so far. Moreover, among 242 previously cloned L. stagnalis genes, we were able to match ~ 87% of them in our transcriptome assembly, indicating a high percentage of gene coverage. The expressional differences for innexins, FMRFamide, and molluscan insulin peptide genes were validated by real-time qPCR. Lastly, our transcriptomic analyses revealed distinct, age-specific gene clusters, differentially expressed genes, and enriched pathways in young, adult, and old CNS. More specifically, our data show significant changes in expression of critical genes involved in transcription factors, metabolisms (e.g. cytochrome P450), extracellular matrix constituent, and signaling receptor and transduction (e.g. receptors for acetylcholine, N-Methyl-D-aspartic acid, and serotonin), as well as stress- and disease-related genes in young compared to either adult or old snails. Conclusions Together, these datasets are the largest and most updated L. stagnalis CNS transcriptomes, which will serve as a resource for future molecular studies and functional annotation of transcripts and genes in L. stagnalis .more » « less
-
more » « less
The radical
S -adenosylmethionine (rSAM) enzyme SuiB catalyzes the formation of an unusual carbon–carbon bond between the sidechains of lysine (Lys) and tryptophan (Trp) in the biosynthesis of a ribosomal peptide natural product. Prior work on SuiB has suggested that the Lys–Trp cross-link is formed via radical electrophilic aromatic substitution (rEAS), in which an auxiliary [4Fe-4S] cluster (AuxI), bound in the SPASM domain of SuiB, carries out an essential oxidation reaction during turnover. Despite the prevalence of auxiliary clusters in over 165,000 rSAM enzymes, direct evidence for their catalytic role has not been reported. Here, we have used electron paramagnetic resonance (EPR) spectroscopy to dissect the SuiB mechanism. Our studies reveal substrate-dependent redox potential tuning of the AuxI cluster, constraining it to the oxidized [4Fe-4S]2+state, which is active in catalysis. We further report the trapping and characterization of an unprecedented cross-linked Lys–Trp radical (Lys–Trp•) in addition to the organometallic Ω intermediate, providing compelling support for the proposed rEAS mechanism. Finally, we observe oxidation of the Lys–Trp• intermediate by the redox-tuned [4Fe-4S]2+AuxI cluster by EPR spectroscopy. Our findings provide direct evidence for a role of a SPASM domain auxiliary cluster and consolidate rEAS as a mechanistic paradigm for rSAM enzyme-catalyzed carbon–carbon bond-forming reactions. -
ABSTRACT Microbes face a trade-off between being metabolically independent and relying on neighboring organisms for the supply of some essential metabolites. This balance of conflicting strategies affects microbial community structure and dynamics, with important implications for microbiome research and synthetic ecology. A “gedanken” (thought) experiment to investigate this trade-off would involve monitoring the rise of mutual dependence as the number of metabolic reactions allowed in an organism is increasingly constrained. The expectation is that below a certain number of reactions, no individual organism would be able to grow in isolation and cross-feeding partnerships and division of labor would emerge. We implemented this idealized experiment using in silico genome-scale models. In particular, we used mixed-integer linear programming to identify trade-off solutions in communities of Escherichia coli strains. The strategies that we found revealed a large space of opportunities in nuanced and nonintuitive metabolic division of labor, including, for example, splitting the tricarboxylic acid (TCA) cycle into two separate halves. The systematic computation of possible solutions in division of labor for 1-, 2-, and 3-strain consortia resulted in a rich and complex landscape. This landscape displayed a nonlinear boundary, indicating that the loss of an intracellular reaction was not necessarily compensated for by a single imported metabolite. Different regions in this landscape were associated with specific solutions and patterns of exchanged metabolites. Our approach also predicts the existence of regions in this landscape where independent bacteria are viable but are outcompeted by cross-feeding pairs, providing a possible incentive for the rise of division of labor. IMPORTANCE Understanding how microbes assemble into communities is a fundamental open issue in biology, relevant to human health, metabolic engineering, and environmental sustainability. A possible mechanism for interactions of microbes is through cross-feeding, i.e., the exchange of small molecules. These metabolic exchanges may allow different microbes to specialize in distinct tasks and evolve division of labor. To systematically explore the space of possible strategies for division of labor, we applied advanced optimization algorithms to computational models of cellular metabolism. Specifically, we searched for communities able to survive under constraints (such as a limited number of reactions) that would not be sustainable by individual species. We found that predicted consortia partition metabolic pathways in ways that would be difficult to identify manually, possibly providing a competitive advantage over individual organisms. In addition to helping understand diversity in natural microbial communities, our approach could assist in the design of synthetic consortia.more » « less
