Browse
Submit Data
Databases
API
Help

Dataset Information

26 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Strain-induced skeletal rearrangement of a polycyclic aromatic hydrocarbon on a copper surface.

ABSTRACT: Controlling the structural deformation of organic molecules can drive unique reactions that cannot be induced only by thermal, optical or electrochemical procedures. However, in conventional organic synthesis, including mechanochemical procedures, it is difficult to control skeletal rearrangement in polycyclic aromatic hydrocarbons (PAHs). Here, we demonstrate a reaction scheme for the skeletal rearrangement of PAHs on a metal surface using high-resolution noncontact atomic force microscopy. By a combination of organic synthesis and on-surface cyclodehydrogenation, we produce a well-designed PAH-diazuleno[1,2,3-cd:1',2',3'-fg]pyrene-adsorbed flatly onto Cu(001), in which two azuleno moieties are highly strained by their mutual proximity. This local strain drives the rearrangement of one of the azuleno moieties into a fulvaleno moiety, which has never been reported so far. Our proposed thermally driven, strain-induced synthesis on surfaces will pave the way for the production of a new class of nanocarbon materials that conventional synthetic techniques cannot attain.

SUBMITTER: Shiotari A

PROVIDER: S-EPMC5524995 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Polycyclic Aromatic Hydrocarbon Degradation in the Sea-Surface Microlayer at Coastal Antarctica

Project description:As much as 400 Tg of carbon from airborne semivolatile aromatic hydrocarbons is deposited to the oceans every year, the largest identified source of anthropogenic organic carbon to the ocean. Microbial degradation is a key sink of these pollutants in surface waters, but has received little attention in polar environments. We have challenged Antarctic microbial communities from the sea-surface microlayer (SML) and the subsurface layer (SSL) with polycyclic aromatic hydrocarbons (PAHs) at environmentally relevant concentrations. PAH degradation rates and the microbial responses at both taxonomical and functional levels were assessed. Evidence for faster removal rates was observed in the SML, with rates 2.6-fold higher than in the SSL. In the SML, the highest removal rates were observed for the more hydrophobic and particle-bound PAHs. After 24 h of PAHs exposure, particle-associated bacteria in the SML showed the highest number of significant changes in their composition. These included significant enrichments of several hydrocarbonoclastic bacteria, especially the fast-growing genera Pseudoalteromonas, which increased their relative abundances by eightfold. Simultaneous metatranscriptomic analysis showed that the free-living fraction of SML was the most active fraction, especially for members of the order Alteromonadales, which includes Pseudoalteromonas. Their key role in PAHs biodegradation in polar environments should be elucidated in further studies. This study highlights the relevant role of bacterial populations inhabiting the sea-surface microlayer, especially the particle-associated habitat, as relevant bioreactors for the removal of aromatic hydrocarbons in the oceans. Graphical Abstract Particle-associated bacteria inhabiting the sea-surface microlayer showed a faster capacity to degrade PAH than subsurface bacteria.

| S-EPMC9329070 | biostudies-literature

Identification and characterization of genes encoding polycyclic aromatic hydrocarbon dioxygenase and polycyclic aromatic hydrocarbon dihydrodiol dehydrogenase in Pseudomonas putida OUS82.

Project description:Naphthalene and phenanthrene are transformed by enzymes encoded by the pah gene cluster of Pseudomonas putida OUS82. The pahA and pahB genes, which encode the first and second enzymes, dioxygenase and cis-dihydrodiol dehydrogenase, respectively, were identified and sequenced. The DNA sequences showed that pahA and pahB were clustered and that pahA consisted of four cistrons, pahAa, pahAb, pahAc, and pahAd, which encode ferredoxin reductase, ferredoxin, and two subunits of the iron-sulfur protein, respectively.

| S-EPMC205371 | biostudies-other

polycyclic aromatic hydrocarbon-degrading enrichment culture

Project description:polycyclic aromatic hydrocarbon-degrading enrichment culture Raw sequence reads

| PRJNA793526 | ENA

A Chiral Polycyclic Aromatic Hydrocarbon Monkey Saddle.

Project description:A contorted polycyclic aromatic hydrocarbon (PAH) in the shape of a monkey saddle has been synthesized in three steps from a readily available truxene precursor. The monkey saddle PAH is consisting of three five-, seven six-, and three eight-membered rings and has been unambiguously characterized by single-crystal X-ray diffraction. Owing to the three biaryl axes the monkey saddle PAH is inherently chiral. The inversion of the two enantiomeric structures into each other preferably occurs through a twisting of peripheral rings rather than by a fully planar intermediate, as has been calculated by DFT methods. Enantiomers were separated by chiral HPLC and inversion barriers determined by variable temperature circular dichroism spectroscopy, supporting the twisting mechanism.

| S-EPMC6972610 | biostudies-literature

Draft Genome Sequence of Advenella kashmirensis Strain W13003, a Polycyclic Aromatic Hydrocarbon-Degrading Bacterium.

Project description:Advenella kashmirensis strain W13003 is a polycyclic aromatic hydrocarbon (PAH)-degrading bacterium isolated from PAH-contaminated marine sediments. Here, we report the 4.8-Mb draft genome sequence of this strain, which will provide insights into the diversity of A. kashmirensis and the mechanism of PAH degradation in the marine environment.

| S-EPMC3907720 | biostudies-literature

Complete genome sequence of the polycyclic aromatic hydrocarbon-degrading bacterium Alteromonas sp. strain SN2.

Project description:Alteromonas sp. strain SN2, able to metabolize polycyclic aromatic hydrocarbons, was isolated from a crude oil-contaminated sea-tidal flat. Here we report the complete 4.97-Mb genome sequence and annotation of strain SN2. These will advance the understanding of strain SN2's adaptation to the sea-tidal flat ecosystem and its pollutant metabolic versatility.

| S-EPMC3147666 | biostudies-literature

Genome Sequence of the Polycyclic Aromatic Hydrocarbon-Degrading Bacterium Strain Marinobacter nanhaiticus D15-8WT.

Project description:Marinobacter nanhaiticus strain D15-8W(T) was isolated from a phenanthrene-degrading consortium, enriched from sediment of the South China Sea. Here, we present the draft genome of strain D15-8W(T), which contains 5,358,309 bp with a G+C content of 58.53% and contains 4,829 protein-coding genes and 47 tRNA genes.

| S-EPMC3668009 | biostudies-literature

Phylogenetic comparison of two polycyclic aromatic hydrocarbon-degrading mycobacteria.

Project description:Two mycobacterial strains previously isolated from fossil-fuel-contaminated environments and shown to degrade four- and/or five-ring polycyclic aromatic hydrocarbons were further characterized. The two strains, PYR-I and RJGII-135, had similar growth characteristics, colony morphologies, and scotochromogenic pigmentations. DNA amplification fingerprints obtained with total genomic DNA indicated some strain similarities but with several distinctly different bands. Moreover, phylogenetic analysis based upon essentially full-length 16S rRNA gene sequences separates the two strains as distinct species within the fast-growing group of mycobacteria. Although both strains are thermosensitive, strain PYR-I has the bulged U between positions 184 and 193 characteristic of thermotolerant mycobacteria. Both strains are of potential use for reintroduction into and bioremediation of polycyclic aromatic hydrocarbon-contaminated soils.

| S-EPMC167601 | biostudies-other

Characterization of a polycyclic aromatic hydrocarbon degradation gene cluster in a phenanthrene-degrading Acidovorax strain.

Project description:Acidovorax sp. strain NA3 was isolated from polycyclic aromatic hydrocarbon (PAH)-contaminated soil that had been treated in a bioreactor and enriched with phenanthrene. The 16S rRNA gene of the isolate possessed 99.8 to 99.9% similarity to the dominant sequences recovered during a previous stable-isotope probing experiment with [U-(13)C]phenanthrene on the same soil (D. R. Singleton, S. N. Powell, R. Sangaiah, A. Gold, L. M. Ball, and M. D. Aitken, Appl. Environ. Microbiol. 71:1202-1209, 2005). The strain grew on phenanthrene as a sole carbon and energy source and could mineralize (14)C from a number of partially labeled PAHs, including naphthalene, phenanthrene, chrysene, benz[a]anthracene, and benzo[a]pyrene, but not pyrene or fluoranthene. Southern hybridizations of a genomic fosmid library with a fragment of the large subunit of the ring-hydroxylating dioxygenase gene from a naphthalene-degrading Pseudomonas strain detected the presence of PAH degradation genes subsequently determined to be highly similar in both nucleotide sequence and gene organization to an uncharacterized Alcaligenes faecalis gene cluster. The genes were localized to the chromosome of strain NA3. To test for gene induction by selected compounds, RNA was extracted from amended cultures and reverse transcribed, and cDNA associated with the enzymes involved in the first three steps of phenanthrene degradation was quantified by quantitative real-time PCR. Expression of each of the genes was induced most strongly by phenanthene and to a lesser extent by naphthalene, but other tested PAHs and PAH metabolites had negligible effects on gene transcript levels.

| S-EPMC2681696 | biostudies-literature

Novel rhamnolipid biosurfactants produced by a polycyclic aromatic hydrocarbon-degrading bacterium Pseudomonas aeruginosa strain NY3.

Project description:A novel rhamnolipid biosurfactant-producing and Polycyclic Aromatic Hydrocarbon (PAH)-degrading bacterium Pseudomonas aeruginosa strain NY3 was isolated from petroleum-contaminated soil samples. Strain NY3 was characterized by its extraordinary capacity to produce structurally diverse rhamnolipids. A total of 25 rhamnolipid components and 37 different parent molecular ions, representing various metal ion adducts (Na(+), 2Na(+) and K(+)), were detected by matrix-assisted laser desorption ionization time-of-flight mass spectrometry. Among these compounds are ten new rhamnolipids. In addition to its biosurfactant production, strain NY3 was shown to be capable of efficient degradation of PAHs as well as synergistic improvement in the degradation of high molecular weight PAHs by its biosurfactant. These findings have added novel members to the rhamnolipid group and expanded current knowledge regarding the diversity and productive capability of rhamnolipid biosurfactants from a single specific strain with variation of only one carbon source. Additionally, this paper lays the foundation for improvement in the yield of NY3BS and study of the degradation pathway(s) of PAHs in P. aeruginosa strain NY3.

| S-EPMC4158028 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data