Dataset Information

On-Surface Thermal Stability of a Graphenic Structure Incorporating a Tropone Moiety.

ABSTRACT: On-surface synthesis, complementary to wet chemistry, has been demonstrated to be a valid approach for the synthesis of tailored graphenic nanostructures with atomic precision. Among the different existing strategies used to tune the optoelectronic and magnetic properties of these nanostructures, the introduction of non-hexagonal rings inducing out-of-plane distortions is a promising pathway that has been scarcely explored on surfaces. Here, we demonstrate that non-hexagonal rings, in the form of tropone (cycloheptatrienone) moieties, are thermally transformed into phenyl or cyclopentadienone moieties upon an unprecedented surface-mediated retro-Buchner-type reaction involving a decarbonylation or an intramolecular rearrangement of the CO unit, respectively.

SUBMITTER: Marquez IR

PROVIDER: S-EPMC8837919 | biostudies-literature | 2022 Jan

REPOSITORIES: biostudies-literature

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On-Surface Thermal Stability of a Graphenic Structure Incorporating a Tropone Moiety.

Márquez Irene R IR Ruíz Del Árbol Nerea N Urgel José I JI Villalobos Federico F Fasel Roman R López María F MF Cuerva Juan M JM Martín-Gago José A JA Campaña Araceli G AG Sánchez-Sánchez Carlos C

Nanomaterials (Basel, Switzerland) 20220129 3

On-surface synthesis, complementary to wet chemistry, has been demonstrated to be a valid approach for the synthesis of tailored graphenic nanostructures with atomic precision. Among the different existing strategies used to tune the optoelectronic and magnetic properties of these nanostructures, the introduction of non-hexagonal rings inducing out-of-plane distortions is a promising pathway that has been scarcely explored on surfaces. Here, we demonstrate that non-hexagonal rings, in the form o ...[more]

PMID: 35159831

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Project description:BackgroundThe search for distant homologs has become an import issue in genome annotation. A particular difficulty is posed by divergent homologs that have lost recognizable sequence similarity. This same problem also arises in the recognition of novel members of large classes of RNAs such as snoRNAs or microRNAs that consist of families unrelated by common descent. Current homology search tools for structured RNAs are either based entirely on sequence similarity (such as blast or hmmer) or combine sequence and secondary structure. The most prominent example of the latter class of tools is Infernal. Alternatives are descriptor-based methods. In most practical applications published to-date, however, the information contained in covariance models or manually prescribed search patterns is dominated by sequence information. Here we ask two related questions: (1) Is secondary structure alone informative for homology search and the detection of novel members of RNA classes? (2) To what extent is the thermodynamic propensity of the target sequence to fold into the correct secondary structure helpful for this task?ResultsSequence-structure alignment can be used as an alternative search strategy. In this scenario, the query consists of a base pairing probability matrix, which can be derived either from a single sequence or from a multiple alignment representing a set of known representatives. Sequence information can be optionally added to the query. The target sequence is pre-processed to obtain local base pairing probabilities. As a search engine we devised a semi-global scanning variant of LocARNA's algorithm for sequence-structure alignment. The LocARNAscan tool is optimized for speed and low memory consumption. In benchmarking experiments on artificial data we observe that the inclusion of thermodynamic stability is helpful, albeit only in a regime of extremely low sequence information in the query. We observe, furthermore, that the sensitivity is bounded in particular by the limited accuracy of the predicted local structures of the target sequence.ConclusionsAlthough we demonstrate that a purely structure-based homology search is feasible in principle, it is unlikely to outperform tools such as Infernal in most application scenarios, where a substantial amount of sequence information is typically available. The LocARNAscan approach will profit, however, from high throughput methods to determine RNA secondary structure. In transcriptome-wide applications, such methods will provide accurate structure annotations on the target side.AvailabilitySource code of the free software LocARNAscan 1.0 and supplementary data are available at http://www.bioinf.uni-leipzig.de/Software/LocARNAscan.

Dataset Information

On-Surface Thermal Stability of a Graphenic Structure Incorporating a Tropone Moiety.

Publications

On-Surface Thermal Stability of a Graphenic Structure Incorporating a Tropone Moiety.

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