One-pot synthesis of meridianins and meridianin analogues via indolization of nitrosoarenes

Meridianins, marine alkaloids known as kinase inhibitors with an indole skeleton, and meridianin analogues were produced regioselectively and in moderate to good yields by thermal annulation of nitrosoarenes with 2-amino-4-ethynylpyrimidine and 2-chloro-4-ethynylpyrimidine, respectively, through a novel and atom-economical indolization process.     

A Survey of Orbitrap All Ion Fragmentation Analysis Assessed by an R MetaboList Package to Study Small-Molecule Metabolites

Leukemia cell and melanoma tumor tissue extracts were studied for small (mostly m/z?<?250) polar metabolites by LC-ESI-HRMSⁿ analysis powered by a hybrid Quadrupole-Orbitrap. MS data were simultaneously acquired in fast polarity switching mode operating in MS¹ and MS/MS (All Ion Fragmentation, AIF) full-scan analyses at high mass resolution. Positive metabolite assignments were achieved by AIF analysis considering at least two characteristic transitions. Targeted metabolite profiling was achieved by the relative quantification of 18 metabolites through spiking of their respective deuterated counterparts. Manual data processing of MS¹ and AIF scans were compared for the accurate determination of natural metabolites and their deuterated analogs by chromatographic alignment and peak area integration. Evaluation of manual and automated (MetaboList R package) AIF data processing yielded comparable results. The versatility of AIF analysis also enabled the untargeted metabolite profiling of leukemia and melanoma samples in which 22 and 53 compounds were, respectively, identified outside those studied by labeling. The main limitation of this method was that low abundance metabolites with scan rates below 8 scans/peak could not be accurately quantified by AIF analysis. The combination of AIF analysis with MetaboList R package represents an opportunity to move towards automated, faster, and more global metabolomics approaches supported by an entirely flexible open source data processing platform freely available from Comprehensive R Archive Network (CRAN, https://CRAN.R-project.org/package=MetaboList).     

Flowrate correction for the determination of isotherms and Darken thermodynamic factors from Zero Length Column (ZLC) experiments

The ZLC method is a simple and rapid approach to measure adsorption equilibrium isotherms. When extending this technique to the measurement of large concentration steps, the primary problem is how to estimate the outlet flowrate from the measured concentration signal. In this paper, two different corrections to calculate the outlet flowrate are introduced. Based on simulations of the ZLC system that are in good agreement with reported experimental results, a series of desorption cases were simulated. Isotherms were calculated using the two approximations of the outlet flowrate. The comparisons are used to identify the range in which the approximations are applicable. Darken’s thermodynamic correction factors were also calculated to verify the validity of the flow corrections.     

Supramolecular ligand-ligand and ligand-substrate interactions for highly selective transition metal catalysis

The use of non covalent supramolecular ligand-ligand and ligand-substrate interactions in transition metal-catalysed transformations is a new, rapidly emerging area of research. Non-covalent interactions between monodentate ligands such as hydrogen bonding, coordinative bonding, ion pairing, π-π interactions and the formation of inclusion compounds, have been shown to impart higher activity and chemo-, regio-, and stereoselectivity to the corresponding transition metal complexes in a number of catalytic applications. Analogously, supramolecular ligand-substrate interactions, and particularly hydrogen bonding, have been used to direct the regio- and stereochemistry of several metal-catalysed reactions. The catalytic systems relying on supramolecular interactions are generally capable of self-assembling from simpler components in the environment where catalysis is to take place, and are therefore very well-suited for combinatorial catalyst discovery strategies and high-throughput screening.     

Planar mixed flow and chaos: Lyapunov exponents and the conjugate-pairing rule

In this work we characterize the chaotic properties of atomic fluids subjected to planar mixed flow, which is a linear combination of planar shear and elongational flows, in a constant temperature thermodynamic ensemble. With the use of a recently developed nonequilibrium molecular dynamics algorithm, compatible and reproducible periodic boundary conditions are realized so that Lyapunov spectra analysis can be carried out for the first time. Previous studies on planar shear and elongational flows have shown that Lyapunov spectra organize in different ways, depending on the character of the defining equations of the system. Interestingly, planar mixed flow gives rise to chaotic spectra that, on one hand, contain elements common to those of shear and elongational flows but also show peculiar, unique traits. In particular, the influence of the constituent flows in regards to the conjugate-pairing rule (CPR) is analyzed. CPR is observed in homogeneously thermostated systems whose adiabatic (or unthermostated) equations of motion are symplectic. We show that the component associated with the shear tends to selectively excite some of those degrees, and is responsible for violations in the rule.     

Penning ionization of N2O molecules by He*(2(3,1)S) and Ne*(3P2,0) metastable atoms: a crossed beam study

The energetics of [Rg... N2O]* autoionizing collision complexes (where Rg=He or Ne) and their dynamical evolution have been studied in a crossed beam apparatus, respectively, by Penning ionization electron spectroscopy (PIES) and by mass spectrometry (MS) techniques in the thermal energy range. The PIES spectra, detected by an electron energy analyzer, were recorded for both complexes at four different collision energies. Such spectra allowed the determination of the energy shifts for Penning electron energy distributions, and the branching ratios for the population of different electronic states and for the vibrational population in the molecular nascent ions. For the [Ne...N2O]* collision complex it was found, by MS, that the autoionization leads to the formation of N2O+, NO+, O+, and NeN2O+ product ions whose total and partial cross sections were measured in the collision energy range between 0.03 and 0.2 eV. The results are analyzed exploiting current models for the Penning ionization process: the observed collision energy dependence in the PIES spectra as well as in the cross sections are correlated with the nature of the N2O molecule orbitals involved in the ionization and are discussed in term of the Rg-N2O interaction potentials, which are estimated by using a semiempirical method developed in our laboratory.     

Molecular modeling of DNA cross-linking analogues based on the azinomycin scaffold

In this work, we present molecular modeling studies carried out using six DNA sequences and six azinomycin analogues, including the naturally occurring compound azinomycin B, selected on the basis of known cell cytotoxicity and structural analogies (epoxide and aziridine alkylating moieties). Among several computational methods the Stochastic Dynamics with Energy Minimization (SDEM) approach yielded results superior to the others with the natural compound (r(2) > 0.9) and was adopted for studying other DNA adducts, obtaining good correlation between the average theoretical cross-linking properties and the antitumor activity scale. As a result, some interesting SAR considerations have been highlighted and a cross-linking conformation different from that of the azinomycin was identified in a less potent, simplified analogue.