Development of an Accurate Mass Retention Time Database for Untargeted Metabolomic Analysis and Its Application to Plasma and Urine Pediatric Samples

Liquid-chromatography coupled to high resolution mass spectrometry (LC-HRMS) is currently the method of choice for untargeted metabolomic analysis. The availability of established protocols to achieve a high confidence identification of metabolites is crucial. The aim of this work is to describe the workflow that we have applied to build an Accurate Mass Retention Time (AMRT) database using a commercial metabolite library of standards. LC-HRMS analysis was carried out using a Vanquish Horizon UHPLC system coupled to a Q-Exactive Plus Hybrid Quadrupole-Orbitrap Mass Spectrometer (Thermo Fisher Scientific, Milan, Italy). The fragmentation spectra, obtained with 12 collision energies, were acquired for each metabolite, in both polarities, through flow injection analysis. Several chromatographic conditions were tested to obtain a protocol that yielded stable retention times. The adopted chromatographic protocol included a gradient separation using a reversed phase (Waters Acquity BEH C18) and a HILIC (Waters Acquity BEH Amide) column. An AMRT database of 518 compounds was obtained and tested on real plasma and urine samples analyzed in data-dependent acquisition mode. Our AMRT library allowed a level 1 identification, according to the Metabolomics Standards Initiative, of 132 and 124 metabolites in human pediatric plasma and urine samples, respectively. This library represents a starting point for future metabolomic studies in pediatric settings.     

Expanding the Chemical Space of Non-Proteinogenic N4-Substituted Asparagine: Racemic,Enantioenriched, and Deuterated Derivatives

A site-selective carbamoylation strategy to access non-proteinogenic N⁴-modified asparagines has been described. The protocol is characterized by mild reaction conditions, high functional group compatibility, and a wide diversity of functionalized carbamoyl radicals making possible the access to peptides, pharmaceuticals, and natural N⁴-asparagine conjugates, as well as enantioenriched unnatural N⁴-asparagines. Besides that, deuterated analogues were achieved with the insertion of D₂O and enantioenriched derivatives could be obtained in 15 min in continuous-flow conditions.     

A Dual Photoredox- and Cp2TiCl2-Catalyzed Approach for the Direct Access to α-Vinyl-β-hydroxy Esters

For the first time, a dual photoredox- and titanocene-catalyzed methodology for the regioselective access to α-vinyl-β-hydroxy esters towards aldehyde allylation with 4-bromobut-2-enoate is reported. The protocol is based on the Barbier-type properties of the inexpensive and available Cp₂TiCl₂ in catalytic amount (5 mol%). The developed mild reaction conditions gave access to a library of differently functionalized α-vinyl-β-hydroxy esters in moderate diastereoselectivity, employing the commercially available ethyl 4-bromobut-2-enoate and both aromatic and aliphatic aldehydes. The reaction was realized under visible light irradiation, in the presence of an organophotocatalyst (3DPAFIPN, 2 mol%) combined with Hantzsch's ester as the sacrificial reductant. In contrast to other Barbier-type reactions employing ethyl 4-bromobut-2-enoate, the photoredox system ensures a better regioselectivity. Moreover, the use of preformed organometallic nucleophilic species (e. g., dienolborinates), and the need of metal reductants or stoichiometric amount of transition metals in low oxidation state for Barbier-type reactions, is avoided. To support the experimental evidence, a detailed photophysical study shed light on the mechanism of the reaction.     

Simulation on the Effect of Brownian Motion on Nanoparticle Trajectories in a Pulsed Microplasma Cluster Source

We describe a simulation of the nanoparticle trajectories in a pulsed cluster beam source. Clusters, formed by condensation of atomic vapor in a helium bath, and considered here as rigid spheres having a diameter of 1.5nm, were tracked during their travel inside the source cavity, an aerodynamic lens, and a cylindrical nozzle. Steady state supersonic laminar flow of helium is considered in an axi-symmetric geometry aiming to simulate, within some limitations, the conditions under which cluster formation takes place in a pulsed microplasma cluster source. In spite of the unsteady nature of the pulsed source, the time scale characterizing particle motion in the flow field is significantly smaller than the characteristic time constant for the evolution of gas pressure in the source. For this reason, a steady simulation can shed some light on the understanding of processes governing nanoparticle motion in a pulsed vaporization source. The extent to which the Brownian diffusion can affect the particle extraction from the source is investigated. Simulations have shown that the Brownian motion perturbs the clusters from the trajectories dictated by the carrier gas and increases the rate of cluster deposition on the source internal walls. However, it does not hinder the aerodynamic focalization produced by the lens even in nano-size cluster regime. This result is qualitatively confirmed by experiment.     

Liquid-liquid phase separation of a surfactant-solubilized membrane protein

Solubilization of membrane proteins requires surfactants, whose structural properties play a crucial role in determining the protein phase behavior. We show that ionization of a pH-sensitive surfactant, lauryldymethylamino-N-oxide, bound to the bacterial photosynthetic Reaction Center, induces protein phase segregation in micrometric "droplets." Liquid-liquid phase separation takes place in a narrow pH range, is promoted by increasing temperature, and vanishes by adding salt. After a fast initial droplet growth, the nearly arrested kinetics at a later stage leaves the system in a finely divided, long-lasting emulsified state.     

Rare fluctuations of native proteins sampled by equilibrium hydrogen exchange

We present a method for determining the ensembles of native protein structures that result from the large fluctuations of low probability revealed by hydrogen-exchange experiments. The measured protection factors are used to bias Monte Carlo simulations to sample the structures of the exchange competent species. The approach is illustrated by its application to the case of alpha-lactalbumin.     

Ultrastructural architecture of colonies of different morphologies produced by phenotypic switching of a clinical strain of Candida tropicalis and biofilm formation by variant phenotypes

Candida tropicalis has been identified as one of the most prevalent pathogenic yeast species of the Candida-non-albicans (CNA) group. Study of switching in C. tropicalis has not been the subject of extensive research. Therefore, we investigated switching event and characterized the ultrastructural architecture of different phenotypes and biofilm produced in a C. tropicalis clinical strain. Cells switched heritably, reversibly, and at a high frequency between four phenotypes readily distinguishable by the shape of colonies formed on agar at 25°C. SEM analysis was used to verify the architecture of whole Candida colonies at ultrastructural level. The smooth phenotype (parental phenotype) colony showed a hemispherical shape character, while the semi-smooth was characterized by the presence of shallow marginal depressions. The ring and rough phenotypes exhibited more complex architecture and were characterized by the presence of deep central and peripheral depressions areas. The biofilm-forming ability varied among the switch phenotypes. After 12h incubation, the smooth phenotype formed less biofilm compared to the other phenotypes (P<0.05). The electron microscopy analysis revealed that filamentation (pseudohyphae) was associated with ring and rough colonies. The ultrastructural analysis allowed the observation of the arrangement of individual cells within the colonies. At the deep central and peripheral depressions areas of the ring and rough colonies extracellular material was seen in different arrangements. The data presented here open new avenues to study a possible role for extracellular material in the formation and maintenance of the architecture of switch phenotypes in C. tropicalis. It is therefore essential that more strains be investigated to determine the biological significance of extracellular material in C. tropicalis phenotypic switching phenomenon.     

Dipyridylketone as a versatile ligand precursor for new cationic heteroleptic cyclometalated iridium complexes

Three new bis-cyclometalated iridium(III) complexes, of general formula [Ir(2-phenylpyridine)(2)(L)](+), are reported. The compounds contain a dipyridine-type ligand (L) derived from di-2-pyridylketone (dipyridin-2-ylmethanol, 2,2'-(hydrazonomethylene)dipyridine and 3-hydroxy-3,3-di(pyridine-2-yl)propanenitrile) and were synthesized through two different reaction pathways. The alternative synthetic pathway herein proposed, namely the direct reactions on the complex [Ir(2-phenylpyridine)(2)(2,2'-dipyridylketone)](+), overcame the inconveniences encountered with the standard reaction between the dimeric precursor [Ir(2-phenylpyridine)(2)(μ-Cl)](2) and the ancillary ligands (L). The photophysical characterization of the iridium complexes reveals that modifications on the ancillary ligand introduce large changes in the photophysical behaviour of the complexes. High emission quantum yield is associated with the presence of a saturated carbon between the two pyridyl moieties: [Ir(2-phenylpyridine)(2)(2,2'-dipyridylketone)](+) and [Ir(2-phenylpyridine)(2)(2,2'-(hydrazonomethylene)dipyridine)](+) are extremely low emissive, while [Ir(2-phenylpyridine)(2)(dipyridin-2-ylmethanol)](+) and [Ir(2-phenylpyridine)(2)(3-hydroxy-3,3-di(pyridine-2-yl)propanenitrile)](+) are good photoemitters. DFT and TD-DFT calculations confirmed the mixed LC/MLCT character of the excited states involved in the absorption and emission processes and highlighted the role of the π-conjugation between the two subunits of the ancillary ligand in determining the nature of the LUMO.