Confinement of polyaniline chains in capillary layers: an ordering effect of the uniaxially aligned surfaces

An ordering effect of uniaxially aligned poly(tetrafluoroethylene) (PTFE) substrates prepared by rubbing on polyaniline (PANI) molecules at the interfaces of PTFE/PANI film and PTFE/PANI solution has been investigated using electronic absorption spectroscopy. It was observed slight dichroism in electronic spectra from only very thin (thickness approximately 20 nm and less) PANI films as well as from PANI solutions of capillary thickness (10 to 30 microm) confined by oriented PTFE surfaces. The ordering effect is discussed in terms of a hydrodynamic flow arising upon sample formation and steric factors at the PTFE surface, which cause uniaxial deformation of the polymer coil on the rubbed PTFE surface.     

Synthesis and Stereochemistry of (1S,3S,4S,7R11R)-3-(4-Nitrophenyl)-11-aza-2,6-dioxatricyclo[5,3,1,04,11]undecane

The reaction of (1S,2S)-2-amino-1-(4-nitrophenyl)-1,3-propanediol with glutaraldehyde has been studied. It has been established on the basis of AM1 and PM3 calculations and ¹H NMR spectra recorded in the presence of the shift reagent Eu(fod)₃ that (1S,3S,4S,7R,11R)-3-(4-nitrophenyl)-11-aza-2,6-dioxatricyclo[5,3,1,0^4,11]undecane is formed as the result of the reaction.     

Quantum delocalization of benzene in the ring puckering coordinates

The effect of quantum mechanical delocalization of atomic nuclei on the conformation of the six‐membered ring structure in two hydrocarbons, cyclohexane and benzene, is investigated using ab initio path integral approach. A striking feature of benzene species is revealed using ring puckering coordinate representation, which demonstrates that the zero point motion of the heavy atom skeleton dominates over the out‐of‐plane thermal motions of the ring. Even more unexpected is the fact, that this is true not only at low temperature of 150 K, at which such behavior would not be surprising, but also at room temperature, where the nuclear quantum effects are usually of lesser importance, especially in the case of such heavy nuclei as carbon. In view of this finding the planar conformation of benzene, whose equilibrium (T = 0 K) geometry results from the well‐known properties of the electronic structure, can be elucidated also at nonzero temperature. According to our simulations, it appears as a consequence of quantum delocalization of the carbon nuclei rather than a trivial time average over the classical configurations of the puckered ring. This interesting behavior is contrasted with the clearly nonplanar structure of cyclohexane, whose ring puckering states can be unequivocally assigned even if the nuclear delocalization is taken into account. © 2014 Wiley Periodicals, Inc.     

"Reported, but still unknown." A closer look into 3,4-bis- and 3,4,5-tris(trifluoromethyl)pyrazoles

Straightforward practical synthetic approaches to 3,4-bis- and 3,4,5-tris(trifluoromethyl)pyrazoles have been developed. The key step of the both syntheses is a transformation of the carboxylic group in a pyrazole core into the trifluoromethyl group by sulfur tetrafluoride. The elaborated synthetic protocols allow gram-scale preparation of the target products. The obtained compounds are comprehensively characterized by means of crystallographic analysis, determination of pK(a) values and fluorescence measurements.     

Regioselectivity of the interaction of (1<Emphasis Type="Italic">S</Emphasis>,2<Emphasis Type="Italic">S</Emphasis>)-2-amino-1-(4-nitrophenyl)-1,3-propanediol with some symmetrical ketones

The interaction of (1S,2S)-2-amino-1-(4-nitrophenyl)-1,3-propanediol with a series of symmetrical ketones has been studied. As a result isomeric oxazolidines are formed in a ratio of 85:15. These oxazolidines were shown to decompose readily under the action of hydrazine.Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 10, pp. 1518–1523, October, 2004.     

Site-specific N-glycosylation analysis: matrix-assisted laser desorption/ionization quadrupole-quadrupole time-of-flight tandem mass spectral signatures for recognition and identification of glycopeptides

The identification of glycosylation sites in proteins is often possible through a combination of proteolytic digestion, separation, mass spectrometry (MS) and tandem MS (MS/MS). Liquid chromatography (LC) in combination with MS/MS has been a reliable method for detecting glycopeptides in digestion mixtures, and for assigning glycosylation sites and glycopeptide sequences. Direct interfacing of LC with MS relies on electrospray ionization, which produces ions with two, three or four charges for most proteolytic peptides and glycopeptides. MS/MS spectra of such glycopeptide ions often lead to ambiguous interpretation if deconvolution to the singly charged level is not used. In contrast, the matrix-assisted laser desorption/ionization (MALDI) technique usually produces singly charged peptide and glycopeptide ions. These ions require an extended m/z range, as provided by the quadrupole-quadrupole time-of-flight (QqTOF) instrument used in these experiments, but the main advantages of studying singly charged ions are the simplicity and consistency of the MS/MS spectra. A first aim of the present study is to develop methods to recognize and use glycopeptide [M+H]+ ions as precursors for MS/MS, and thus for glycopeptide/glycoprotein identification as part of wider proteomics studies. Secondly, this article aims at demonstrating the usefulness of MALDI-MS/MS spectra of N-glycopeptides. Mixtures of diverse types of proteins, obtained commercially, were prepared and subjected to reduction, alkylation and tryptic digestion. Micro-column reversed-phase separation allowed deposition of several fractions on MALDI plates, followed by MS and MS/MS analysis of all peptides. Glycopeptide fractions were identified after MS by their specific m/z spacing patterns (162, 203, 291 u) between glycoforms, and then analyzed by MS/MS. In most cases, MS/MS spectra of [M+H]+ ions of glycopeptides featured peaks useful for determining sugar composition, peptide sequence, and thus probable glycosylation site. Peptide-related product ions could be used in database search procedures and allowed the identification of the glycoproteins.     

Prediction of cyclohexane-water distribution coefficient for SAMPL5 drug-like compounds with the QMPFF3 and ARROW polarizable force fields

We present the performance of blind predictions of water—cyclohexane distribution coefficients for 53 drug-like compounds in the SAMPL5 challenge by three methods currently in use within our group. Two of them utilize QMPFF3 and ARROW, polarizable force-fields of varying complexity, and the third uses the General Amber Force-Field (GAFF). The polarizable FF’s are implemented in an in-house MD package, Arbalest. We find that when we had time to parametrize the functional groups with care (batch 0), the polarizable force-fields outperformed the non-polarizable one. Conversely, on the full set of 53 compounds, GAFF performed better than both QMPFF3 and ARROW. We also describe the torsion-restrain method we used to improve sampling of molecular conformational space and thus the overall accuracy of prediction. The SAMPL5 challenge highlighted several drawbacks of our force-fields, such as our significant systematic over-estimation of hydrophobic interactions, specifically for alkanes and aromatic rings.     

Principles of demineralization: modern strategies for the isolation of organic frameworks. Part I. Common definitions and history

In contrast to biomineralization phenomena, that are among the most widely studied topics in modern material and earth science and biomedicine, much less is systematized on modern view of demineralization. Biomineralized structures and tissues are composites, containing a biologically produced organic matrix and nano- or microscale amorphous or crystalline minerals. Demineralization is the process of removing the inorganic part, or the biominerals, that takes place in nature via either physiological or pathological pathways in organisms. In vitro demineralization processes, used to obtain mechanistic information, consist in the isolation of the mineral phase of the composite biomaterials from the organic matrix. Physiological and pathological demineralization include, for example, bone resorption mediated by osteoclasts. Bioerosion, a more general term for the process of deterioration of the composite biomaterials represents chemical deterioration of the organic and mineral phase followed by biological attack of the composite by microorganisms and enzymes. Bioerosional organisms are represented by endolithic cyanobacteria, fungi, algae, plants, sponges, phoronids and polychaetes, mollusks, fish and echinoids.In the history of demineralization studies, the driving force was based on problems of human health, mostly dental caries. In this paper we summarize and integrate a number of events, discoveries, milestone papers and books on different aspect of demineralization during the last 400 years. Overall, demineralization is a rapidly growing and challenging aspect of various scientific disciplines such as astrobiology, paleoclimatology, geomedicine, archaeology, geobiology, dentistry, histology, biotechnology, and others to mention just a few.     

Regioselectivity in the reaction of paraformaldehyde with (1S,2S)-2-aryl(hetaryl)methylamino-1-(4-nitrophenyl)-1,3-propanediols

The reaction of paraformaldehyde with (1S,2S)-2-aryl(hetaryl)methylamino-1-(4-nitrophenyl)-1,3-propanediols produces a mixture of isomeric 3-aryl(hetaryl)methyl-4-hydroxymethyl-5-(4-nitrophenyl)- and 3-aryl(hetary)methyl-4-hydroxy(4-nitrophenyl)methyloxazolidines and is reversible. Université d'Auvergne, Faculté de Farmacie, 28, Place Henri Dunant, Clermont-Ferrand, France. Samara State University, Samara 443011, Russia. Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 4, pp. 536–541, April, 1999.     

Best Approximation and Cyclic Variation Diminishing Kernels

We study best uniform approximation of periodic functions from

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where the kernelK(x, y) is strictly cyclic variation diminishing, and related problems including periodic generalized perfect splines. For various approximation problems of this type, we show the uniqueness of the best approximation and characterize the best approximation by extremal properties of the error function. The results are proved by using a characterization of best approximants from quasi-Chebyshev spaces and certain perturbation results.