Computational study on the structural and optoelectronic properties of a carbazole-benzothiadiazole based conjugated oligomer with various alkyl side-chain lengths

The effect of the alkyl side-chain length on the structural and optoelectronic properties of poly[N-9′-heptadecanyl-27-carbazole-alt-55-(4′,7′-di-2-thienyl-2′,1′,3′-benzothiadiazole)] (PCDTBT) conjugated oligomers have been studied by density functional theory (DFT) and time-dependent density functional theory (TD-DFT). The study was carried out by varying the length of alkyl side-chain attached to the nitrogen atom of the carbazole unit of the PCDTBT oligomers. The structural properties of the optimised oligomers were then studied by determining the bond-length alternation and dihedral angles (Φ) for various side-chain lengths. Total energy calculations for the determination of HOMO energy (E_HOMO), LUMO energy (E_LUMO), and fundamental energy gap (E_Gap) were performed using DFT at the B3LYP/6-31G(d), while the first singlet excitation energies (E_Opt) were calculated by TD-DFT also at the same level of theory. It was observed that there are no significant structural changes occurring as the alkyl chain lengths are varied. For the electronic properties, very small differences (i.e. ~0.01 eV) were observed for E_Gap and E_Opt while the exciton binding energies (E_B) were virtually the same. The results suggest that using shorter alkyl side-chains do not significantly affect the structural and optoelectronic properties of the carbazole-benzothiadiazole based polymer. The observations can aid future computational design studies of analogous systems by reducing large structures thus decreasing computational costs.     

Solution structures of purine base analogues 9-deazaguanine and 9-deazahypoxanthine

Deaza analogues of nucleobases are potential drugs against infectious diseases caused by parasites. A caveat is that apart from binding their target parasite enzymes, they also bind and inhibit enzymes of the host. In order to design derivatives of deaza analogues which specifically bind target enzymes, knowledge of their molecular structure, protonation state, and predominant tautomers at physiological conditions is essential. We have employed resonance Raman spectroscopy at an excitation wavelength of 260 nm, to decipher solution structure of 9-deazaguanine (9DAG) and 9-deazahypoxanthine (9DAH). These are analogues of guanine and hypoxanthine, respectively, and have been exploited to study static complexes of nucleobase binding enzymes. Such enzymes are known to perturb pK_a of their ligands, and thus, we also determined solution structures of these analogues at two, acidic and alkaline, pH. Structure of each possible protonation state and tautomer was computed using density functional theoretical calculations. Species at various pHs were identified based on isotopic shifts in experimental wavenumbers and by comparing these shifts with corresponding computed isotopic shifts. Our results show that at physiological pH, N1 of pyrimidine ring in 9DAG and 9DAH bears a proton. At lower pH, N3 is place of protonation, and at higher pH, deprotonation occurs at N1 position. The proton at N7 of purine ring remains intact even at pH 12.5. We have further compared these results with naturally occurring nucleotides. Our results identify key vibrational modes which can report on hydrogen bonding interactions, protonation and deprotonation in purine rings upon binding to the active site of enzymes.     

Functional classifications of coastal barrier island vegetation

Abstract. Due to the complexity of coastal barrier vegetation, it is useful to apply a functional-type approach to assess the response of barrier island vegetation to climate change. In this paper, a simple clustering analysis is applied to a group of 19 plant associations, based on six plant attributes and six environmental constraints. This analysis results in the suggestion that the main division of the vegetation types at Virginia Coast Reserve is between herbaceous and woody types, which differs from the existing classification which recognizes three groups: xeric-mesic herbaceous, woody and hydric-halophytic herbaceous. Considerations about grouping plant functional types are also addressed in this paper. At a global scale, inclusion of barrier plant functional types may not be so important for the climate-change response of vegetation, but it may be necessary to consider these important systems for spatially explicit modelling of landscape responses.     

Phylogenetic diversity is a better predictor of wetland community resistance to Alternanthera philoxeroides invasion than species richness

• Highly biodiversity communities have been shown to better resist plant invasions through complementarity effects. Species richness (SR) is a widely used biodiversity metric but lacks explanatory power when there are only a few species. Communities with low SR can have a wide variety of phylogenetic diversities (PD), which might allow for a better prediction of invasibility.
• We assessed the effect of diversity reduction of a wetland community assemblage typical of the Beijing area on biotic resistance to invasion of the exotic weed Alternanthera philoxeroides and compared the reduction in SR and PD in predicting community invasibility.
• The eight studied resident species performed similarly when grown alone and when grown in eight‐species communities together with the invasive A. philoxeroides. Variation partitioning showed that PD contributed more to variation in both A. philoxeroides traits and community indicators than SR. All A. philoxeroides traits and community indicators, except for evenness index, showed a linear relationship with PD. However, only stem length of A. philoxeroides differed between the one‐ and two‐species treatments, and the diversity index of the communities differed between the one‐ and two‐species treatments and between the one‐ and four‐species treatments.
• Our results showed that in natural or semi‐natural wetlands with relatively low SR, PD may be a better predictor of invasibility than SR. When designing management strategies for mitigating A. philoxeroides invasion, deliberately raising PD is expected to be more efficient than simply increasing species number.

     

Transmission from vaccinated individuals in a large SARS-CoV-2 Delta variant outbreak

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Unravelling the coordination between leaf and stem economics spectra through local and global scale approaches

The existence of a coordination between leaf and stem economic spectra in woody species has been postulated repeatedly in the literature, with contrasting results. Here, we postulated that this coordination is conditioned by climate factors, being stronger in stressful environments. To test this hypothesis we explored the coordination between leaf and stem economic spectra in a seasonally dry forest in central Argentina and at the global scale, we analysed if the outcome of their coordination varies along a climatic gradient. At the local scale, we characterized leaf and stem economic spectra in 37 woody species by measuring six leaf and stem functional traits related to resource acquisition and use, and two functional traits used as proxies of water transport and use capacities. At the global scale, a meta‐regression was performed to analyse if the outcome of the coordination among leaf and stem traits varies along gradients of the mean precipitation of the driest quarter and of the minimum temperature of the coldest month. At the local scale, we observed a high integration among the measured leaf and stem traits, and this coordination seemed to be linked to hydraulic properties. At the global scale, we found not only that the overall weighted mean effect size of the correlation between specific leaf area and wood density was significant and negative but also that the coordination between leaf and stem traits seemed to be shaped by climate and tends to become stronger under harsh climate conditions. Furthermore, although our results seem to suggest that their coordination is context‐dependent, alternative strategies could be observed under stressful conditions.     

Genomic characterization of metastatic patterns from prospective clinical sequencing of 25,000 patients

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