Structural Changes in a Protein Fragment from Abalone Shell during the Precipitation of Calcium Carbonate

Mineralized tissues grow through biologically controlled processes in which specific macromolecules are involved. Some of these molecules, which are present in very low concentrations and are difficult to localize and characterize, become entrapped inside the mineralized tissue. Herein, a protein fragment, GP, which was obtained by the alkaline digestion of the green sheet of the abalone shell, is used as a probe to study the changes in molecular structure that occur during the precipitation of calcium carbonate. This important goal was achieved by exploiting a fluorescent tag in GP. The experimental results that were obtained by using spectroscopic‐, chromatographic‐, and microscopic techniques indicate that GP controls the precipitation kinetics and morphology of calcium carbonate crystals, and that it only undergoes structural reorganization when entrapped inside calcium carbonate crystals. To the best of our knowledge, this report represents one of the first studies on the conformational changes of a protein fragment that is involved in biomineralization processes on moving from the solution phase into the mineral phase.     

An ab initio and DFT study of radical addition reactions of imidoyl and thioyl radicals to methanimine

Ab initio and DFT calculations reveal that both imidoyl and thioyl radicals add to the nitrogen end of methanimine through simultaneous SOMO-π*(imine), SOMO-π(imine), SOMO-LP(N) and π*(radical)-LP(N) interactions between the radical and the imine. At the CCSD(T)/cc-pVDZ//BHandHLYP/cc-pVTZ level of theory, barriers of 13.8 and 26.1 kJ mol(-1) are calculated for the attack of the methylimidoyl radical at the carbon- and nitrogen- end of methanimine, respectively, indicating that the imidoyl radial has a preference for addition to the nitrogen end of imine. On the other hand, barriers of 25.1 and 13.4 kJ mol(-1) are calculated at the same level of theory for the addition reaction of the methanethioyl radical at the carbon- and nitrogen- end of methanimine, respectively. Natural bond orbital (NBO) analysis at the BHandHLYP/6-311G** level of theory reveals that SOMO-π*(imine), SOMO-π(imine), SOMO-LP(N) and π*(radical)-LP(N) interactions are worth 111, 89, 115 and 17 kJ mol(-1), respectively, in the transition state (4) for the reaction of methylimidoyl radical at the nitrogen end of methanimine; similar interactions are observed for the chemistry involving all the radicals studied here. These multi-component interactions are responsible for the unusual motion vectors associated with the transition states involved in these reactions.     

Clotting Activity of Polyphosphate‐Functionalized Silica Nanoparticles

We present a silica nanoparticle (SNP) functionalized with polyphosphate (polyP) that accelerates the natural clotting process of the body. SNPs initiate the contact pathway of the blood‐clotting system; short‐chain polyP accelerates the common pathway by the rapid formation of thrombin, which enhances the overall blood‐clotting system, both by accelerating fibrin generation and by facilitating the regulatory anticoagulation mechanisms essential for hemostasis. Analysis of the clotting properties of bare SNPs, bare polyP, and polyP‐functionalized SNPs in plasma demonstrated that the attachment of polyP to SNPs to form polyP‐SNPs creates a substantially enhanced synergistic effect that lowers clotting time and increases thrombin production at low concentrations. PolyP‐SNP even retains its clotting function at ambient temperature. The polyP‐SNP system has the potential to significantly improve trauma‐treatment protocols and outcomes in hospital and prehospital settings.     

Next‐Generation Sequencing as Input for Chemometrics in Differential Sensing Routines

Differential sensing (DS) methods traditionally use spatially arrayed receptors and optical signals to create score plots from multivariate data which classify individual analytes or complex mixtures. Herein, a new approach is described, in which nucleic acid sequences and sequence counts are used as the multivariate data without the necessity of a spatial array. To demonstrate this approach to DS, previously selected aptamers, identified from the literature, were used as semi‐specific receptors, Next‐Gen DNA sequencing was used to generate data, and cell line differentiation was the test‐bed application. The study of a principal component analysis loading plot revealed cross‐reactivity between the aptamers. The technique generates high‐dimensionality score plots, and should be applicable to any mixture of complex and subtly different analytes for which nucleic acid‐based receptors exist.     

Preparation and characterization of asymmetric alpha-alkoxy dipyrrin ligands and their metal complexes

Asymmetric alpha-substituted dipyrrins have been synthesized and characterized. The compounds were formed by a metal mediated reaction involving a single alkoxy group substituted into the alpha-position of an alpha,beta-unsubstituted dipyrrin. An alpha-methoxy dipyrrin, 5-(4-cyanophenyl)-1-methoxydipyrrin (alpha-OMe-4-cydpm), was prepared from 5-(4-cyanophenyl)-4,6-dipyrromethane. Methoxy, ethoxy, and propoxy derivatives (alpha-OMe-4-mecdpm, alpha-OEt-4-mecdpm, alpha-OPr-4-mecdpm) of 5-(4-methoxycarbonylphenyl)-4,6-dipyrromethane have also been prepared. A homoleptic, bis(1-methoxy)dipyrrinato zinc(II) complex, [Zn(alpha-OMe-4-mecdpm)(2)], has been synthesized, as has a heteroleptic cobalt(III) complex with one alpha-OMe-4-cydpm ligand and two unsubstituted 5-(4-cyanophenyl)dipyrrin (4-cydpm) ligands ([Co(alpha-OMe-4-cydpm)(4-cydpm)(2)]). The rotational barrier of the meso-aryl substituent of [Zn(alpha-OMe-4-mecdpm)(2)] was found to be 17.3 kcal mol(-1) by variable-temperature NMR spectroscopy. The compounds alpha-OMe-4-cydpm and [Zn(alpha-OMe-4-mecdpm)(2)] have also been characterized by X-ray diffraction. The formation of the new dipyrrin derivatives is shown to be general and can be performed on dipyrrins with various meso-aryl substitutents, with a variety of alcohols, and can be promoted by several metal salts.     

Selective excitation of overlapping multiplets; the application of doubly selective and chemical shift filter experiments to complex NMR spectra

Standard 1D TOCSY and NOE experiments have limitations where signals are severely overlapped. Here, two recently published selective excitation methods are evaluated, the first of which uses a chemical shift selective filter to select a single resonance based on its chemical shift, and the second of which is a doubly selective experiment comprising a 1D TOCSY preparation step and subsequent 1D NOE. We also demonstrate the improvement in spectral quality obtained by the use of the zero quantum filter, which is incorporated into both of these experiments. The application of these different methods of selectively exciting overlapped multiplets, to different types of samples is considered.     

Capillary electrophoresis off-line matrix-assisted laser desorption/ionisation mass spectrometry of intact and digested proteins using cationic-coated capillaries

Capillary electrophoresis (CE) was coupled off-line with matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOFMS) for the analysis of proteins and peptides. CE fractions were collected directly on a matrix-coated MALDI target, using a sheath-flow interface. Protein adsorption during CE separations was prevented by coating the capillaries with the physically adsorbed, cationic polymer PolyE-323. The CE/MALDI-MS system was used for the analysis of model proteins and peptides at physiological pH as well as analysis of proteins in tear fluid. Moreover, tryptic on-target digestion of the collected protein fractions, with subsequent MALDI-MS and MS/MS peptide analysis, was demonstrated.     

Asymmetric synthesis of the stereoisomers of 2-amino-5-carboxymethyl-cyclopentane-1-carboxylate

The stereoisomers of 2-amino-5-carboxymethyl-cyclopentane-1-carboxylate may be prepared stereoselectively from diester derivatives of (E,E)-octa-2,6-diendioc acid, with the key step utilising the conjugate addition of homochiral lithium N-benzyl-N- alpha-methylbenzylamide. The trans-C(1)-C(2)-stereoisomers are readily prepared via a diastereoselective tandem conjugate addition cyclisation protocol with lithium (R)-N-benzyl-N- alpha-methylbenzylamide, with subsequent hydrogenolysis and ester hydrolysis giving the (1R,2R,5R)- and (1R,2R,5S)- beta-amino diacids in good yields. The preparation of the cis-C(1)-C(2)-stereoisomers utilises a protocol involving N-oxidation and Cope elimination of the major diastereoisomeric product arising from conjugate addition and cyclisation, giving homochiral (R)-5-carboxymethyl-cyclopentene-1-carboxylate. Conjugate addition of either lithium (R)- or (S)-N-benzyl-N- alpha-methylbenzylamide to (R)-5-carboxymethyl-cyclopentene-1-carboxylate, and diastereoselective protonation with 2,6-di-tert-butyl phenol gives, after hydrogenolysis and ester hydrolysis, the (1S,2R,5R)- and (1R,2S,5R)- beta-amino diacids in good yield. The use of (S)-N-benzyl-N- alpha-methylbenzylamide in the initial conjugate addition and cyclisation reaction, and subsequent repetition of the elimination and conjugate addition strategy allows stereoselective access to all stereoisomers of 2-amino-5-carboxymethyl-cyclopentane-1-carboxylate.     

Determination of perfluorooctanoic acid and perfluorooctanesulfonate in human tissues by liquid chromatography/single quadrupole mass spectrometry

A method is described that permits the measurement of the levels of perfluorooctanoic acid (PFOA) and perfluorooctane sulfonate (PFOS) in human liver, kidney, adipose tissue, brain, basal ganglia, hypophysis, thyroid, gonads, pancreas, lung, skeletal muscle and blood, even in subjects not occupationally exposed to these compounds. The purification of samples involved the use of trifunctional (tC18) and strong anion-exchange (SAX) solid-phase extraction cartridges, and the analysis utilized a high-performance liquid chromatograph coupled to a single quadrupole mass spectrometer (LC/MS). The analyses were conducted on a mixed-bed reversed-phase column by gradient runs using 3 mM ammonium acetate/methanol mixtures at different proportions as the mobile phase. The detector was used in electrospray negative ion mode by recording simultaneously the ions m/z 413.0 (PFOA) and 499.0 (PFOS). Perfluorononanoic acid (PFNA), added to the samples before the purification, was used as the internal standard (ion monitored = m/z 463.6). The recovery rates of the extraction procedure ranged from 79.6 to 95.6% (CV% 1.7-7.4%) for PFOA, from 79.7 to 100.8% (CV% = 1.2-7.1) for PFOS, and from 89.1 to 102.3% (CV% = 0.9-5.2 %) for PFNA. The calibration curves were linear up to at least 400 ng of analytes per gram of tissue. The detection limits (signal-to-noise ratio = 3) were 0.1 ng/g for both PFOA and PFOS measured in all tissues except adipose tissue, where the limits were about 0.2 ng/g. The content of analytes in tissues varied from 0.3 to 3.8 ng/g (respectively: basal ganglia and lung) for PFOA, and from 1.0 to 13.6 ng/g (respectively: skeletal muscle and liver) for the linear isomer of PFOS. The method is suitable to evaluate the content of PFOA and PFOS in different tissues taken from the general population exposed to very low concentrations of these pollutants.     

Improved asymmetric S(N)Ar reaction of beta-dicarbonyl compounds catalyzed by quaternary ammonium salts derived from cinchona alkaloids

The scope and limitation of the asymmetric nucleophilic aromatic substitution reaction of alpha-substituted 1,3-dicarbonyl compounds and activated aromatic systems catalyzed by N-benzyl-O-benzoylcinchoninium or cinchonidinium salts are presented. Several novel O-benzoylcinchona alkaloid derived salts have been prepared and evaluated as catalysts in this reaction, which can proceed with enantioselectivites up to 96% ee. Various 1,3-dicarbonyl compounds and activated aromatic systems are evaluated for the aromatic nucleophilic substitution reaction, and it has been found that the yield and enantioselectivity are very dependent on the substrate and reagent. The scope of the functionalization of the products to, e.g., spiro-oxoindole, a ring-opening reaction of 1,3 alpha,alpha-disubstituted dicarbonyl compounds with several nucleophiles, and the diastereoselective reduction of the keto functionality in the optically active S(N)Ar product are reported.