Aromaticity determines the relative stability of kinked vs. straight topologies in polycyclic aromatic hydrocarbons

It is well-known that kinked phenacenes are more stable than their isomeric linear acenes, the archetypal example being phenanthrene that is more stable than anthracene by about 4-8 kcal/mol. In previous studies, the origin of the higher stability of kinked polycyclic aromatic hydrocarbons (PAHs) was found to be better π-bonding interactions, i.e., larger aromaticity, in kinked as compared to linear PAHs. Some years ago, however, Dominikowska and Palusiak (2011) found that dicationic linear anthracene is more stable than the dicationic kinked phenanthrene. Therefore, these authors showed that, in some cases, the linear topology in PAHs can be preferred over the kinked one. Our results using energy decomposition analyses in combination with the turn-upside-down approach show that the origin of the higher stability of dicationic anthracene is the same as in the neutral species, i.e., better π-bonding interactions. A similar result is found for the kinked and straight pyrano-chromenes. We conclude that the aromaticity is the driving force that determines the relative stability of kinked vs. straight topologies in PAHs

Projecte Articles Mirall. Les regles de l’aromaticitat

El 1931, Erich Hückel va publicar un article transcendental, la llavor de la que ara és la famosa fórmula 4n + 2, la regla de l’aromaticitat en annulens que porta el seu nom. Des d’aleshores, el recompte d’electrons s’ha estès a altres classes de compostos, fet que ha generat una multitud de regles que intenten descriure el concepte d’aromaticitat i el seu impacte en la química

Fmoc–RGDS based fibrils: atomistic details of their hierarchical assembly

We describe the 3D supramolecular structure of Fmoc–RGDS fibrils, where Fmoc and RGDS refer to the hydrophobic N-(fluorenyl-9-methoxycarbonyl) group and the hydrophilic Arg-Gly-Asp-Ser peptide sequence, respectively. For this purpose, we performed atomistic all-atom molecular dynamics simulations of a wide variety of packing modes derived from both parallel and antiparallel ß-sheet configurations. The proposed model, which closely resembles the cross-ß core structure of amyloids, is stabilized by p–p stacking interactions between hydrophobic Fmoc groups. More specifically, in this organization, the Fmoc-groups of ß-strands belonging to the same ß-sheet form columns of p-stacked aromatic rings arranged in a parallel fashion. Eight of such columns pack laterally forming a compact and dense hydrophobic core, in which two central columns are surrounded by three adjacent columns on each side. In addition to such Fmoc¿Fmoc interactions, the hierarchical assembly of the constituent ß-strands involves a rich variety of intra- and inter-strand interactions. Accordingly, hydrogen bonding, salt bridges and p–p stacking interactions coexist in the highly ordered packing network proposed for the Fmoc–RGDS amphiphile. Quantum mechanical calculations, which have been performed to quantify the above referred interactions, confirm the decisive role played by the p–p stacking interactions between the rings of the Fmoc groups, even though both inter-strand and intra-strand hydrogen bonds and salt bridges also play a non-negligible role. Overall, these results provide a solid reference to complement the available experimental data, which are not precise enough to determine the fibril structure, and reconcile previous independent observations.Peer ReviewedPostprint (published version

Clock genes and photoperiodism in the aphid Acyrthosiphon pisum

Aphids have a strong seasonal response, namely the development of a sexual morphs triggered by the shortening of photoperiod in autumn that produce an overwintering egg in which an embryonic diapause takes place. From this egg, an asexual parthenogenetic female emerges giving way to the asexual phase of the aphid life cycle in which several asexual generations occur. Based on the response to short photoperiods, two strains of aphids can be found: the holocyclic develop the seasonal response under short photoperiods, while the anholocyclic do not. The sequencing of the genome of the pea aphid Acyrthosiphon pisum places this species as an excellent model to investigate the the involvement of the circadian clock in the seasonal response. In the present thesis, the characterisation of the circadian clock genes revealed an extensive alternative splicing, although it could not be associated to any of the strains or photoperiods. Moreover, the expression of circadian clock genes analysed at different moments of the day showed a robust cycling of period and timeless. Furthermore, the rhythm in expression of period and timeless was rapidly dampened under DD (continuous darkness conditions), thus supporting the model of a seasonal response based on a heavily dampened circadian oscillator. Additionally, changes in expression of some of the circadian clock genes were associated to the induction of the seasonal response. The localisation of transcripts of period and timeless in the aphid brain revealed two groups cells: the Dorsal Neurons (DN) and the Lateral Neurons (LN) in the protocerebrum. The location of DN coincided with a region previously described as essential for the sesasonal response. The involvement of several elements that may participate as output of the circadian clock were also studied. We failed to detect the aphid Pdf gene in the genome and PDH with antibodies, suggesting that PDF may be genuinely absent in aphids. We show the localisation of melatonin in the aphid nervous ganglia, which is the second report of in situ localisation of melatonin in insects and the first in Hemimetabola. Moreover, we observed an increase of melatonin content associated to the induction of the seasonal response. The analysis of the aphid AANAT genes, candidates to regulate the synthesis of melatonin, revealed concomitant levels of expression with those of melatonin in some cases. Furthermore, despite the localisation of some of the AANAT transcripts in the nervous ganglia, none of them colocalised with melatonin. Finally, the aphid Ptth gene was identified and characterised showing typical insect PTTH features. Additionally, Ptth transcripts were localised in two pairs of neurons in the aphid brain allowing to identify them as the NSC group II and consequently discarding them as essential for the seasonal response. The results presented in this thesis provide support to the involvement of at least some of the circadian clock elements in the seasonal response