Representation of the molecular topology of cyclical structures by means of cycle graphs. 3. Hierarchical model of screening of chemical databases

The increase in the size and complexity of chemical databases necessitates the proposal and development of efficient methods of classification and recovery of information, which supposes proposal of a model of classification of database records and the use of a compatible model of screening for inspection of clusters and recovery of the molecules that satisfy the search criterion. The cycle graphs model based on consideration of all the cycles and chains (and equivalent cycles and chains) present in the molecular structure has been proven appropriate for classification of chemical databases, giving rise to a generation of different classification levels depending on the structural elements (cycles and chains) that are considered. In this paper we propose a screening model, compatible with the cycle graphs model, based on a hierarchy of levels of abstraction. The set of molecules that satisfies a screening model (or selection criterion) diminishes as we advance in the hierarchy of levels of the model, which allows filtering of records and, therefore, an increase in the efficiency of the screening process. In the following work of this series we describe and validate the screening tool developed.     

Unprecedented intramolecular [3 + 2] cycloadditions of azido-ketenimines and azido-carbodiimides. Synthesis of indolo[1,2-a]quinazolines and tetrazolo[5,1-b]quinazolines

N-(2-azidomethyl)phenyl ketenimines and N-(2-azidomethyl)phenyl-N'-alkyl(aryl) carbodiimides undergo, under mild thermal conditions, intramolecular [3 + 2] cycloaddition reactions between the azido group and either the C=C or the distal C=N double bonds of the ketenimine and carbodiimide functions respectively. The reaction products are indolo[1,2-a]quinazolines and/or indolo[2,1-b]quinazolines in the case of azido-ketenimines, and tetrazolo[5,1-b]quinazolines in the case of azido-carbodiimides. The formation of the two classes of indoloquinazolines implies the ulterior dinitrogen extrusion from the non-isolated, putative [3 + 2] cycloadducts between the azide and ketenimine functions, whereas in the case of azido-carbodiimides the initial cycloadducts, tetrazoloquinazolines, were cleanly isolated and further converted into 2-aminoquinazolines by thermally induced dinitrogen extrusion.     

On choosing a reference redox system for electrochemical measurements: a cautionary tale

The potential of a quasi-reference electrode can be determined by introducing an internal reference redox system (IRRS) which comprises either the oxidizable or reducible form of a reversible (and, ideally, outer-sphere) redox couple and then observing the cyclic voltammetric responses. The objective is to choose the IRRS so that the cyclic voltammetric response for the simultaneously present electroactive analyte system (ANS) can be observed independently of the IRRS response. We identify three fundamental paradigms describing the relative positioning of the IRRS and ANS on the potential scale, the operative redox components for the IRRS and ANS, and the starting potential (E _start), reversing potential (E _rev), and ending potential (E _end) for the cyclic voltammetric scan as follows: paradigm A, an optimal paradigm which can produce completely independent cyclic voltammetric responses for the IRRS or for ANS; paradigm B, a less-than-optimal paradigm which can produce an independent cyclic voltammetry (CV) response for the ANS or a mixed response for the IRRS with that response on top of the ANS response; paradigm C, a problematic paradigm that can produce an independent CV response for the IRRS or a mixed response for the ANS with that response on top of the IRRS response; and any mixed response produces a thermodynamically favored redox cross-reaction which couples the IRRS and ANS systems and which can complicate the analysis of the ANS and IRRS responses. The conclusion is that paradigm C is to be avoided.     

Sequential spectrofluorimetric determination of free and total glycerol in biodiesel in a multicommuted flow system

A new procedure for spectrofluorimetric determination of free and total glycerol in biodiesel samples is presented. It is based on the oxidation of glycerol by periodate, forming formaldehyde, which reacts with acetylacetone, producing the luminescent 3,5-diacetyl-1,4-dihydrolutidine. A flow system with solenoid micro-pumps is proposed for solution handling. Free glycerol was extracted off-line from biodiesel samples with water, and total glycerol was converted to free glycerol by saponification with sodium ethylate under sonication. For free glycerol, a linear response was observed from 5 to 70 mg L⁻¹ with a detection limit of 0.5 mg L⁻¹, which corresponds to 2 mg kg⁻¹ in biodiesel. The coefficient of variation was 0.9% (20 mg L⁻¹, n = 10). For total glycerol, samples were diluted on-line, and the linear response range was 25 to 300 mg L⁻¹. The detection limit was 1.4 mg L⁻¹ (2.8 mg kg⁻¹ in biodiesel) with a coefficient of variation of 1.4% (200 mg L⁻¹, n = 10). The sampling rate was ca. 35 samples h⁻¹ and the procedure was applied to determination of free and total glycerol in biodiesel samples from soybean, cottonseed, and castor beans.     

Study of the capillary electrophoresis profile of intact α-1-acid glycoprotein isoforms as a biomarker of atherothrombosis

α-1-Acid glycoprotein (AGP) is a serum glycoprotein that presents several isoforms. Changes in the isoforms of AGP have been related to different pathological states including cardiovascular diseases (CVDs) such as acute myocardial infarction. However, to our knowledge, the role of variations of AGP isoforms as a potential biomarker of atherothrombosis has not been addressed. In this work, a preliminary study about differences in the capillary zone electrophoresis (CZE) profile of intact (non-hydrolyzed) AGP isoforms between healthy individuals and patients with atherothrombosis, specifically abdominal aortic aneurysm (AAA) and carotid atherosclerosis (CTA), has been performed. Biological samples (plasmas and sera) were analyzed by CZE after immunoaffinity chromatography purification. Up to 13 peaks corresponding to groups of isoforms of intact AGP from plasma samples were detected by CZE-UV. Electrophoretic profiles were aligned, peaks assigned, and linear discriminant analysis (LDA) of percentage of the corrected areas of AGP peaks was employed to discriminate and classify the CZE profiles of AGP samples. LDA enabled to accomplish 92.9% of correct classification of the AGP samples when the three groups of samples were considered. Besides, the LDA model showed high predictive power in the groups healthy vs. sick, healthy vs. AAA, and healthy vs. CTA. The described method was a successful approach to study the potential of AGP isoforms profile as a biomarker of atherothrombosis. To the best of our knowledge this has been the first time that a possible role of the CZE profile of intact AGP isoforms as a biomarker of vascular diseases has been demonstrated.     

Determination of propazine by differential pulse polarography in micellar and emulsified media

An electroanalytical study of the herbicide propazine's reduction process in micellar solutions and oil-in-water emulsions is reported. The anionic surfactant sodium pentanesulphonate was chosen as the most suitable. The differential pulse polarograms of micellar solutions had two reduction peaks below pH 2.0, whereas only one peak was obtained above pH 2.O. Ethyl acetate was chosen as the organic solvent to form propazine emulsions. Unlike in micellar solutions, the DPP polarograms of propazine emulsions showed only one peak even at pH < 2.0, suggesting that propazine hydrolysis was hindered in the emulsified medium. The limiting current is diffusion-controlled and the electrode process is irreversible. Propazine can be determined by differential pulse polarography over the 1.0 × 10^–1 – 1.0 × 10^–1moll^–1 and 1.0 × 10^–15 – 4.0 × 10^–1 moll^–1 concentration ranges and the limit of detection was 2.8 × 10^–1 moll^–1. Of the potential interferents simazine, methoprotryne and terbutryn (alls-triazines), thiram (a dithiocarbamate), dinoseb (nitrophenolic), and heptachlor (chlorinated cyclo-diene herbicide), only the first two were significant (10% error for equimolar concentrations). The method was applied to the determination of propazine in spiked drinking water. At a concentration level of 2.0 × 10^–1 moll^–1 a recovery of 94 ± 6% was obtained, after tenfold concentration on Sep-Pak.     

Halomethanes in tri-n-octylamine and squalane mixtures at infinite dilution

The retention behavior of eight halomethanes and four saturated hydrocarbons was measured in gas chromatographic stationary phases consisting in tri-n-octylamine (TOA), squalane (SQ) and six TOA+SQ mixtures, at 55.0, 58.5, 62.5 and 65.0°C. Equlibrium constants for complex formation were extracted from experimental data by using a lattice model developed by Martire. The results may be interpreted in terms of the formation of weak hydrogen-bonded complexes, with sociation constants of about 0.13 L-mol^–1 for haloforms and 0.07 L-mol^–1 for dihalomethanes at 60°C.     

Low-temperature single crystal X-ray diffraction and high-pressure Raman studies on [(CH3)2NH2]2[SbCl5]

The structure of bis(dimethylammonium) pentachloroantimonate(III), [(CH₃)₂NH₂]₂[SbCl₅], BDP, was studied at 15 K and ambient pressure by single-crystal X-ray diffraction as well as at ambient temperature and high pressures up to 4.87(5) GPa by Raman spectroscopy. BDP crystallizes in the orthorhombic Pnma space group with a=8.4069(4), b=11.7973(7), c=14.8496(7) Å, and Z=4; R₁=0.0381, wR₂=0.0764. The structure consists of distorted [SbCl₆]³⁻ octahedra forming zig-zag [{SbCl₅}_n]²ⁿ⁻ chains that are cross-linked by dimethylammonium [(CH₃)₂NH₂]⁺ cations. The organic and inorganic substructures are bound together by the N-H…Cl hydrogen bonds. The distortions of [SbCl₆]³⁻ units increase, partly due to the influence of the hydrogen bonds which became stronger, with decreasing temperature. The preliminary room temperature, high-pressure X-ray diffraction experiments suggest that BDP undergoes a first-order phase transition below ca. 0.44(5) GPa that destroys single-crystal samples. The transition is accompanied by changes in the intensities and positions of the Raman lines below 400 cm⁻¹.     

Enzymatic oxidation of tert-butylcatechol in the presence of sulfhydryl compounds: Application to the amperometric detection of penicillamine

The high sensitivity that can be attained using an enzymatic system and mediated by 4-tert-butylcatechol (4-TBC) has been verified by on-line interfacing of a rotating biosensor and continuous flow/stopped-flow/continuous-flow processing. Horseradish peroxidase, HRP, [EC 1.11.1.7], immobilized on a rotating disk, in presence of hydrogen peroxide catalyzed the oxidation of 4-TBC, whose back electrochemical reduction was detected on glassy carbon electrode surface at −150 mV. Thus, when penicillamine (PA) was added to the solution, these thiol-containing compounds participate in Michael type addition reactions with 4-TBC to form the corresponding thioquinone derivatives, decreasing the peak current obtained proportionally to the increase of its concentration. The highest response for PA was obtained around pH 7. This method could be used to determine PA concentration in the range 0.02-80 μM (r = 0.998). The determination of PA was possible with a limit of detection of 7 nM, in the processing of as many as 50 samples per hour. The HRP-rotating biosensor was successfully applied to the determination of PA in pharmaceutical formulations.     

Dynamic Covalent Identification of an Efficient Heparin Ligand

Despite heparin being the most widely used macromolecular drug, the design of small‐molecule ligands to modulate its effects has been hampered by the structural properties of this polyanionic polysaccharide. Now a dynamic covalent selection approach is used to identify a new ligand for heparin, assembled from extremely simple building blocks. The amplified molecule strongly binds to heparin (K_D in the low μm range, ITC) by a combination of electrostatic, hydrogen bonding, and CH–π interactions as shown by NMR and molecular modeling. Moreover, this ligand reverts the inhibitory effect of heparin within an enzymatic cascade reaction related to blood coagulation. This study demonstrates the power of dynamic covalent chemistry for the discovery of new modulators of biologically relevant glycosaminoglycans.