Liquid Crystal ordering of DNA Dickerson Dodecamer duplexes with different 5’- Phosphate terminations

Abstract

The onset of liquid crystal (LC) phases in concentrated aqueous solutions of DNA oligomers crucially depends on the end-to-end interaction between the DNA duplexes, which can be provided by the aromatic stacking of the terminal base-pairs or by the pairing of complementary dangling-ends. Here we investigated the LC behavior of three blunt-end 12-base-long DNA duplexes synthesized with hydroxyl, phosphate and triphosphate 5’-termini. We experimentally characterized the concentration-temperature phase diagrams and we quantitatively estimated the end-to-end stacking free energy, by comparing the empirical data with the predictions of coarse-grained linear aggregation models.

The preservation of LC ordering, even in presence of the bulky and highly charged triphosphate group, indicates that attractive stacking interactions are still present and capable of induce linear aggregation of the DNA duplexes. This finding strengthens the potential role of chromonic like self-assembly for the prebiotic formation of linear polymeric nucleic acids.     

Porous nanographene formation on γ-alumina nanoparticles via transition-metal-free methane activation

γ-Al₂O₃ nanoparticles promote pyrolytic carbon deposition of CH₄ at temperatures higher than 800 °C to give single-walled nanoporous graphene (NPG) materials without the need for transition metals as reaction centers. To accelerate the development of efficient reactions for NPG synthesis, we have investigated early-stage CH₄ activation for NPG formation on γ-Al₂O₃ nanoparticles via reaction kinetics and surface analysis. The formation of NPG was promoted at oxygen vacancies on (100) surfaces of γ-Al₂O₃ nanoparticles following surface activation by CH₄. The kinetic analysis was well corroborated by a computational study using density functional theory. Surface defects generated as a result of surface activation by CH₄ make it kinetically feasible to obtain single-layered NPG, demonstrating the importance of precise control of oxygen vacancies for carbon growth.

Oxygen vacancies on the (100) surface of γ-Al₂O₃ nanoparticles catalyse CH₄-CVD for single-layered nanoporous graphenes with no transition metal reaction centre. The rate-limiting step is the proton transfer (PT) in the activation of CH₄ on them.     

Electrophilic Vinylation of Thiols under Mild and Transition Metal-Free Conditions

The iodine(III) reagents vinylbenziodoxolones (VBX) were employed to vinylate a series of aliphatic and aromatic thiols, providing E-alkenyl sulfides with complete chemo- and regioselectivity, as well as excellent stereoselectivity. The methodology displays high functional group tolerance and proceeds under mild and transition metal-free conditions without the need for excess substrate or reagents. Mercaptothiazoles could be vinylated under modified conditions, resulting in opposite stereoselectivity compared to previous reactions with vinyliodonium salts. Novel VBX reagents with substituted benziodoxolone cores were prepared, and improved reactivity was discovered with a dimethyl-substituted core.     

HS-SPME-GC-MS approach for the analysis of volatile salivary metabolites and application in a case study for the indirect assessment of gut microbiota

In this work, a straightforward analytical approach based on headspace solid-phase microextraction coupled with gas chromatography-mass spectrometry was developed for the analysis of salivary volatile organic compounds without any prior derivatization step. With a sample volume of 500 μL, optimal conditions were achieved by allowing the sample to equilibrate for 10 min at 50 °C and then extracting the samples for 10 min at the same temperature, using a carboxen/polydimethylsiloxane fibre. The method allowed the simultaneous identification and quantification of 20 compounds in sample headspace, including short-chain fatty acids and their derivatives which are commonly analysed after analyte derivatization. The proof of applicability of the methodology was performed with a case study regarding the analysis of the dynamics of volatile metabolites in saliva of a single subject undergoing 5-day treatment with rifaximin antibiotic. Non-stimulated saliva samples were collected over 3 weeks from a nominally healthy volunteer before, during, and after antibiotic treatment. The variations of some metabolites, known to be produced by the microbiota and by bacteria that are susceptible to antibiotics, suggest that the study of the dynamics of salivary metabolites can be an excellent indirect method for analysing the gut microbiota. This approach is novel from an analytical standpoint, and it encourages further studies combining saliva metabolite profiles and gut microbiota dynamics.

Graphical abstract

     

Addressing Charge-Transfer and Locally-Excited States in a Twisted Biphenyl Push-Pull Chromophore

We present the synthesis and spectroscopic characterization of a twisted push–pull biphenyl molecule undergoing photoinduced electron transfer. Steady-state and transient absorption spectra suggest, in this rigid molecular structure, a subtle interplay between locally-excited and charge-transfer states, whose equilibrium and dynamics is only driven by solvation. A theoretical model is presented for the solvation dynamics and, with the support of quantum chemical calculations, we demonstrate the existence of two sets of states, having either local or charge-transfer character, that only “communicate” thanks to solvation, which is the sole driving force for the charge-separation process.     

Computational study of alkynes insertion into metal-hydride bonds catalyzed by bimetallic complexes

Density Functional Theory investigations on the insertion mechanism of phenylacetylene into metal-hydride bonds in bimetallic (Pt,Os) catalysts have been carried out. The results obtained have been also compared with the non-reactive monometallic (Os-based) system, to elucidate the cooperative effects and to explain the observed absence of reactivity. The identified reaction path involves phenylacetylene coordination followed by the insertion into the metal-hydride bond, leading to the formation of the experimentally observed products. Both steps do not require large energies compatible with the experimental conditions. The comparison with the reaction path for the monometallic species gives some hints on the cooperative effects due to the presence of the second metal which is related to its role in the CO release for creating a coordination site for phenylacetylene and not in the insertion energetics. The calculations provide a detailed analysis of the reaction complexity and provide a rationale for the efficiency of the process.     

Non-polytropic effect on shock-induced phase transitions in a hard-sphere system

By adopting a simplified model of a non-polytropic hard-sphere system where heat capacity depends on the temperature, we demonstrate the importance of non-polytropic effect on the shock-induced phase transitions. We show explicitly that with the increase of the shock strength the perturbed temperature (the temperature after a shock) increases and the vibrational modes are gradually excited, and as a result, shock-induced phase transitions are qualitatively and quantitatively different from the phase transitions observed in a simple polytropic model. The effect on the admissibility (stability) of a shock wave is also analyzed.     

On the comparison principle for unbounded solutions of elliptic equations with first order terms

We prove a comparison principle for unbounded weak sub/super solutions of the equation

$\lambda u?\text{div}(A(x)Du)=H(x,Du)\text{ in }\mathrm{\Omega }$

where $A(x)$ is a bounded coercive matrix with measurable ingredients, $\lambda \ge 0$ and $\xi ?H(x,\xi )$ has a super linear growth and is convex at infinity. We improve earlier results where the convexity of $H(x,?)$ was required to hold globally.