GridMass: a fast two‐dimensional feature detection method for LC/MS

One of the initial and critical procedures for the analysis of metabolomics data using liquid chromatography and mass spectrometry is feature detection. Feature detection is the process to detect boundaries of the mass surface from raw data. It consists of detected abundances arranged in a two‐dimensional (2D) matrix of mass/charge and elution time. MZmine 2 is one of the leading software environments that provide a full analysis pipeline for these data. However, the feature detection algorithms provided in MZmine 2 are based mainly on the analysis of one‐dimension at a time. We propose GridMass, an efficient algorithm for 2D feature detection. The algorithm is based on landing probes across the chromatographic space that are moved to find local maxima providing accurate boundary estimations. We tested GridMass on a controlled marker experiment, on plasma samples, on plant fruits, and in a proteome sample. Compared with other algorithms, GridMass is faster and may achieve comparable or better sensitivity and specificity. As a proof of concept, GridMass has been implemented in Java under the MZmine 2 environment and is available at http://bioinformatica.mty.itesm.mx/GridMass and MASSyPup. It has also been submitted to the MZmine 2 developing community. Copyright © 2015 John Wiley & Sons, Ltd.     

Dual Drug Loaded Nanotheranostic Platforms as a Novel Synergistic Approach to Improve Pancreatic Cancer Treatment

This study focuses on the development of theranostic, dual drug-loaded nanocarriers to propose a proof-of-principle therapeutic approach in the treatment of pancreatic ductal adenocarcinoma (PDAC). The nanoconstructs consist of a core of zinc oxide nanocrystals doped with gadolinium, useful as a potential contrast agent in magnetic resonance imaging applications. After functionalizing their surface with amino-propyl groups, the physical adsorption of two hydrophobic drugs is performed: Vismodegib and Sorafenib. Their synergistic use might improve PDAC treatment and stroma depletion when co-delivered in the tumor microenvironment for future in vivo applications. To enhance the nanoconstructs’ biostability, the ensemble is coated by a lipid bilayer and a tumor targeting peptide is incorporated on the outer shell surface. As a first proof of concept, the resulting nanoconstructs are tested against two pancreatic cancer cell lines, showing a modest increase in treatment efficacy compared to the free drug counterparts and proving to spare healthy pancreatic cells. In a second testing set, the dual-drug loaded nanoconstructs are tested on both cell lines previously sensitized to a first-line chemotherapeutic drug, Gemcitabine, showing an improved treatment response. From these preliminary results, the nanotheranostic platforms might constitute a good starting point for future PDAC therapy and diagnosis studies.     

Reversible α‐Hydrogen and α‐Alkyl Elimination in PC(sp3)P Pincer Complexes of Iridium

Despite significant progress in recent years, the cleavage of unstrained C(sp³)? C(sp³) bonds remains challenging. A C? C coupling and cleavage reaction in a PC(sp³)P iridium pincer complex is mechanistically studied; the reaction proceeds via the formation of a carbene intermediate and can be described as a competition between α‐hydrogen and α‐alkyl elimination; the latter process was observed experimentally and is an unusual way of C(sp³)? C(sp³) bond scission, which has previously not been studied in detail. Mechanistic details that are based upon kinetic studies, activation parameters, and DFT calculations are also discussed. A full characterization of a C? C agostic intermediate is presented.     

Decomposition of mixtures' spectra by multivariate curve resolution of rapidly acquired TOCSY experiments

A method is presented that allows for retrieving 1D spectra of the individual components of a mixture from a sparsely acquired 2D‐TOCSY spectrum. The decomposition of the 2D‐TOCSY data into pure 1D traces is achieved using a non‐negative matrix factorization algorithm, also known as multivariate curve resolution analysis. Here, we show that the algorithm can be applied to data processed in the direct dimension only. Thus, our method can be applied to non‐linearly sampled experiments or data acquired with few indirect points. An example is shown for the spectra of a mixture of six amino acids, acquired in 15 min. Copyright © 2010 John Wiley & Sons, Ltd.     

Multidisciplinary physicochemical analysis of oligothiophenes end-capped by nitriles: electrochemistry, UV-vis-near-IR, IR, and Raman spectroscopies and quantum chemistry

In this article, we investigate a series of alpha,omega-dicyano end-capped oligothiophenes NC(C(4)H(2)S)(n)()CN ranging in length from the dimer to the hexamer (n = 2-6), in the neutral state as pure solids, by means of Fourier transform IR and Fourier transform Raman (FT-Raman) spectroscopies. The cyclic voltammetry analysis of the compounds in dichloromethane reveals that most of them show two oxidation and two reduction waves (i.e., a dual or amphoteric electrochemical behavior), associated with the injection of either positive or negative charges into the pi-conjugated system. The doped species are characterized by in situ vis-near-IR and FT-Raman spectrochemistries. Density functional theory calculations have been also performed, at the B3LYP/6-31G level, to assess information about the molecular geometries and vibrational features of the neutral and doped species and about the topologies of the molecular orbitals involved in the main electronic transitions that appear for the neutral forms in the visible spectral region and for the doped species in the near-IR region.     

Synthesis and structure of 5-methoxy-4-methylbenzopsoralen

5-Methoxy-4-methyl-2H-benzofuro[3,2-g]benzo-1-pyran-2-one was synthesized and its crystal structure was determined and compared with the optimal conformation arrived at by MM and AM1 theoretical calculations. The latter indicated that the tetracyclic skeleton is planar with total length (C2–C8) 9.23 å, and that the line joining the conters of the terminal-benzene and furan rings makes an angle of 30.5 with that joining the centers of the three rings of psoralen. The electronic properties of the reactive double bond in the pyran ring of1 are similar to those of simpler psoralens.     

Mixed vesicle formation on a ternary surfactant system: didodecyldimethylammonium bromide/dodecylethyldimethylammonium bromide/water

The formation of mixed aggregates has been investigated on a ternary system consisting of two cationic surfactants with similar polar heads and two and/or one 12 carbon atom hydrophobic tail, respectively, didodecyldimethylammonium bromide and dodecylethyldimethylammonium bromide and water. The study has been carried out by means of conductivity, zeta potential, and cryogenic transmission electronic microscopy (cryo-TEM) experiments on the very diluted region. A variety of mixed aggregates, microaggregates, vesicles, and micelles has been found, depending on system composition and total surfactant concentration. Mixed critical microaggregate concentration and mixed critical vesicle concentration have been determined from conductivity data. Furthermore, zeta potential and cryo-TEM experiments allow for the characterization of the aggregates/solution interface and of the shape and size of the aggregates. This experimental evidence has also been analyzed in terms of the theoretical packing parameter, P.     

New Materials Derived from Ybco: CrSr2RECu2O8 (RE = La, Pr, Nd, Eu, Gd, Tb, Dy, Y, Ho, Er, Lu)

Eleven new oxides, derived from yttrium barium copper oxide by replacing the square-planar copper [Cu-O4] of the basal plane of the triple perovskite-based structure with octahedral Cr(IV), have been prepared at high pressure and temperature. Their crystal structures have been determined, and their complex microstructure has been established by means of high-resolution electron microscopy and electron diffraction. The materials have a general formula of CrSr2RECu2O8 (RE = La, Pr, Nd, Eu, Gd, Tb, Dy, Y, Ho, Er, and Lu); they are tetragonal, show the symmetry of space group P4/mmm, and do not appear to be superconducting.