Distributed and multicore QuBiLS-MIDAS software v2.0: Computing chiral,fuzzy, weighted and truncated geometrical molecular descriptors based on tensor algebra

Advances to the distributed, multi-core and fully cross-platform QuBiLS-MIDAS software v2.0 ( http://tomocomd.com/qubils-midas ) are reported in this article since the v1.0 release. The QuBiLS-MIDAS software is the only one that computes atom-pair and alignment-free geometrical MDs (3D-MDs) from several distance metrics other than the Euclidean distance, as well as alignment-free 3D-MDs that codify structural information regarding the relations among three and four atoms of a molecule. The most recent features added to the QuBiLS-MIDAS software v2.0 are related (a) to the calculation of atomic weightings from indices based on the vertex-degree invariant (e.g., Alikhanidi index); (b) to consider central chirality during the molecular encoding; (c) to use measures based on clustering methods and statistical functions to codify structural information among more than two atoms; (d) to the use of a novel method based on fuzzy membership functions to spherically truncate inter-atomic relations; and (e) to the use of weighted and fuzzy aggregation operators to compute global 3D-MDs according to the importance and/or interrelation of the atoms of a molecule during the molecular encoding. Moreover, a novel module to compute QuBiLS-MIDAS 3D-MDs from their headings was also developed. This module can be used either by the graphical user interface or by means of the software library. By using the library, both the predictive models built with the QuBiLS-MIDAS 3D-MDs and the QuBiLS-MIDAS 3D-MDs calculation can be embedded in other tools. A set of predefined QuBiLS-MIDAS 3D-MDs with high information content and low redundancy on a set comprised of 20,469 compounds is also provided to be employed in further cheminformatics tasks. This set of predefined 3D-MDs evidenced better performance than all the universe of Dragon (v5.5) and PaDEL 0D-to-3D MDs in variability studies, whereas a linear independence study proved that these QuBiLS-MIDAS 3D-MDs codify chemical information orthogonal to the Dragon 0D-to-3D MDs. This set of predefined 3D-MDs would be periodically updated as long as new results be achieved. In general, this report highlights our continued efforts to provide a better tool for a most suitable characterization of compounds, and in this way, to contribute to obtaining better outcomes in future applications.     

Micellar gradients in size-exclusion simulated moving bed chromatography

The selectivity of size-exclusion chromatography (SEC) can be modified by adding non-ionic micelles to the mobile phase. Surfactant-aided size-exclusion chromatography (SASEC) can therefore very well be performed in a gradient mode on an SMB, as is reported in this paper. A method has been developed for correctly positioning a micellar gradient over an SMB. The method is applied for size-exclusion chromatography with the non-ionic surfactant C12E23 as gradient forming solute, and demonstrated by applying it to a relevant chromatographic protein separation problem.     

Colloidal stability of magnetite/poly(lactic acid) core/shell nanoparticles

In this work, we describe an experimental investigation on the colloidal stability of suspensions of three kinds of particles, including magnetite, poly(lactic acid) (PLA), and composite core/shell colloids formed by a magnetite core surrounded by a PLA shell. The experiments were performed with dilute suspensions, so that recording the optical absorbance with time gives a suitable indication of the aggregation and sedimentation of the suspensions. The method allowed us to distinguish very accurately between the different surface and magnetic forces responsible for the structures acquired by particle aggregates. Thus, the pure PLA suspensions are very sensitive to ionic strength and almost unaffected by pH changes. On the contrary, the stability of magnetite systems is mainly controlled by pH. The effect of vertical magnetic fields on the stability of magnetite and magnetite/PLA suspensions is also investigated. The PLA shell reduces the magnetic responsiveness of magnetite, but it is demonstrated that the mixed particles can also form structures induced by the field, despite their lower magnetization, and they can be considered in magnetically targeted biomedical applications.     

No-discharge atmospheric pressure chemical ionization: evaluation and application to the analysis of animal drug residues in complex matrices

Alternative ionization methods are increasingly being utilized to increase the versatility and selectivity of liquid chromatography/mass spectrometry (LC/MS). One such technique is the practice of using commercially available atmospheric pressure chemical ionization (APCI) sources with the corona discharge turned off, a process termed no-discharge APCI (ND-APCI). The relative LC/MS responses for several different classes of veterinary drugs were obtained by using ND-APCI, electrospray ionization (ESI), and APCI. While the ND-APCI-MS and -MSn spectra for these compounds were comparable with ESI, ND-APCI provided advantages in sensitivity and selectivity for some compounds. Drugs that were charged in solution as cations or sodium adducts responded particularly well with this technique. Instrumental parameters such as temperatures, gas and liquid flow rates, and source design were investigated to determine their effect on the process of ND-APCI. This paper explores advantages of using ND-APCI for the determination and confirmation of drug residues that might be found in food matrices, including malachite green residues in fish tissue and avermectin residues in milk.     

Gas-phase interaction of thiophene with the Ti(8)C(12)(+) and Ti(8)C(12) met-car clusters

The reactivity of the Ti(8)C(12)(+) met-car cation toward thiophene was investigated using density functional theory (DFT) and mass selective ion chemistry. It is shown that the experimentally observed mass spectrum can be well described by the DFT calculations. In contrast to the weak bonding interactions seen for thiophene on a TiC(001) surface, the Ti(8)C(12)(+) met-car cation is able to interact strongly with up to four thiophene molecules with the cluster staying intact. In the most stable conformation, the thiophene molecules bond to the four low-coordinated Ti(0) sites of Ti(8)C(12)(+) via a eta(5)-C,S coordination. The stability and the activity of the Ti(8)C(12)(+) met-car is observed to increase with an increasing number of attached thiophene molecules at the Ti(0) sites, which is associated with a significant transfer of electron density from thiophene to the cluster. The additional electron density on the Ti(8)C(12)(+) cation cluster, however, is not sufficient to cleave the C-S bonds of thiophene and the dissociation reaction of thiophene is predicted to be a highly activated process. By contrast, DFT calculations for the neutral Ti(8)C(12) met-car predict that the dissociation reaction leading to adsorbed S and C(4)H(4) fragments is energetically favorable for the first thiophene molecule. The binding behavior for subsequent addition of thiophene molecules to the neutral met-car is also presented and compared to that of the cation.     

Modelling migration behavior of peptide hormones in capillary electrophoresis-electrospray mass spectrometry

The applicability in capillary electrophoresis-electrospray mass spectrometry (CE-ESI-MS) of the classical semiempirical relationships between electrophoretic mobility and charge-to-mass ratio (me versus q/Malpha) has been investigated in order to describe the migration behavior of a series of bioactive peptide hormones. The influence upon the models of the separation electrolyte pH and the accuracy of the pK values of these compounds were studied first by capillary electrophoresis with ultraviolet detection (CE-UV). The classical polymer model, alpha = 1/2, resulted in slightly better correlations at any of the studied pH. Furthermore, a general linear equation can be adjusted combining all the experimental data pairs, which suggests that correlation in the whole pH range is independent of the ionic form of the studied peptide hormones. The plots of q/M1/2 against separation electrolyte pH were used to predict their electrophoretic separations, using the accurate pK values obtained in a previous work by CE-UV for charge calculations. A volatile separation electrolyte containing 50 mM of acetic acid and 50 mM of formic acid at pH 2.85 was selected for optimum CE-UV and CE-ESI-MS analysis of the peptide mixture. At this pH and taking into account the specific features of the coupling, the correlation using the classical polymer law was excellent and its parameters were similar to the ones of the general linear equation previously obtained by CE-UV. This confirmed the applicability in CE-ESI-MS of the semiempirical relationship originally established by CE-UV.     

Parametrization of the magnetic behavior of the triangular spin ladder chains organically templated: (C2N2H10)[M(HPO3)F3] (M(III) = Fe, Cr, and V). Crystal structure and thermal and spectroscopic properties of the iron(III) phase

A new iron(III) phosphite templated by ethylenediamine has been synthesized using solvothermal conditions under autogenous pressure. The (C2N2H10)[Fe(HPO3)F3] compound has been characterized by single-crystal X-ray diffraction data and spectroscopic and magnetic techniques. The crystal structure is formed by chains extended along the c axis and surrounded by ethylenediammonium cations. A study by diffuse-reflectance spectroscopy has been performed, and the calculated Dq, B, and C parameters for the Fe(III) cations are 1030, 720, and 3080 cm(-1), respectively. The M?ssbauer spectrum at room temperature is characteristic of Fe(III) ions. The electron spin resonance (ESR) spectra carried out at different temperatures show isotropic signals with a g value of 2.00(1). The thermal evolution of the intensity of the ESR signals indicates the existence of antiferromagnetic interactions for the Fe(III) phase. The magnetic susceptibility data of the Cr(III) and V(III) compounds show antiferromagnetic couplings. The J-exchange parameters of the Fe(III) and Cr(III) compounds have been calculated by using a model for a triangular spin ladder chain. The values are J1 = -1.63(1) K and J2 = -0.87(2) K with g = 2.02 for the Fe(III) phase and J(1) = -0.56(2) K and J2 = -0.40(2) K with g = 1.99 for the Cr(III) compound. In the case of the V(III) phase, the fit has been performed considering a linear chain with the magnetic parameters D = 2.5 cm(-1) and J = -1.15(1) K.     

Synthesis of conformationally constrained lysine analogues

The synthesis of two conformationally constrained lysine analogues is reported. The synthesis of the novel analogue 1 based on the 3-aza-bicyclo[3.1.0]hexane system is accomplished from the known tricycle 3 in eight steps. The synthesis of the analogue 2 is accomplished in eight steps from 4-hydroxy proline. Both analogues are synthesized appropriately protected for Fmoc/Boc solid-phase peptide synthesis.     

Study of the factors that control the ratio of the products between 5-fluorouracil, uracil, and tetrahydrobenzoxazepine O,O-acetals bearing electron-withdrawing groups on the nitrogen atom

(RS)-1-(2-Nitrobenzenesulfonyl)- and (RS)-1-(4-nitrobenzenesulfonyl)-3-methoxy-1,2,3,5-tetrahydro-4,1-benzoxazepines are better substrates than 1-acyl-3-methoxy-1,2,3,5-tetrahydro-4,1-benzoxazepine derivatives for the Lewis acid mediated condensation reaction with pyrimidine bases to give O,N-acetals. Acetonitrile, stannic chloride, 50 degrees C, and a reaction time higher than 48 h are the optimum conditions for such condensation reactions. Under these conditions, 5-fluorouracil preferably links to the aminalic carbon through its N-1" position, while the attachment of the uracil fragment is through N-3" or N-1" of the cyclic or acyclic products, respectively. The causes that influence the course of the reactions are analyzed and discussed. Examination of the (1)H NMR spectra revealed the presence of a single form for the secondary amine 11 and of two conformers for the tertiary sulfonamides 7a,b, 9a,b, and 10b and for the amides 7d and 13, with the following distribution: 7a, 59/41; 7b, 53/47; 9a, 52/48; 9b, 59/41; 10b, 56/44; 7d, 50/50; 13, 80/20. On increasing the temperature, the (1)H NMR spectrum (DMSO-d(6)) of 7b showed coalescence at 110 degrees C. The torsional barrier determined [DeltaG(c)++ value of 19.0 +/- 0.2 kcal.mol(-1) (79.1 +/- 1.0 kJ.mol(-1))] proved to be the highest ever observed for sulfonamide moieties.