yaInChI: modified InChI string scheme for line notation of chemical structures

A modified InChI (International Chemical Identifier) string scheme, yaInChI (yet another InChI), is suggested as a method for including the structural information of a given molecule, making it straightforward and more easily readable. The yaInChI theme is applicable for checking the structural identity with higher sensitivity and generating three-dimensional (3-D) structures from the one-dimensional (1-D) string with less ambiguity than the general InChI method. The modifications to yaInChI provide non-rotatable single bonds, stereochemistry of organometallic compounds, allene and cumulene, and parity of atoms with a lone pair. Additionally, yaInChI better preserves the original information of the given input file (SDF) using the protonation information, hydrogen count +1, and original bond type, which are not considered or restrictively considered in InChI and SMILES. When yaInChI is used to perform a duplication check on a 3D chemical structure database, Ligand.Info, it shows more discriminating power than InChI. The structural information provided by yaInChI is in a compact format, making it a promising solution for handling large chemical structure databases.     

Compressibility of a zinc single crystal under confining pressure

Abstract

In the present study, the two compressibility moduli of a zinc single crystal were measured at room temperature up to 18 GPa. The results are compared with those obtained by Bridgman from a different experimental method. This study required a gaseous hydrostatic confining pressure, and then it has been necessary to develop an original diamond anvil cell with a large optical aperture allowing the use of sophisticated video imaging and image analysis techniques. A model is proposed for the zinc volume-pressure relation.     

Single-column ion chromatography of passive monitors for atmospheric pollution

Nitrite, nitrate and sulfate anions deposited on passive monitors were determined by using single-column ion chromatography. These monitors were exposed outdoors for various periods of time in an atmosphere with a very low degree of pollution, and they were used to evaluate the rate of deposition of some corrosive species on metallic materials. Two types of passive monitors were studied, namely sulfation and nitration plates. Comparison of the results obtained by using the classical turbidimetric method and single-column ion chromatography shows that turbidimetry is inappropriate for low sulfate concentrations (<2.5 mg/plate) deposited on sulfation plates. Thus, ion chromatography should be used to obtain a representative value of sulfate deposition because it allows the determination of sulfate in amounts as low as 200 μg/plate without further preconcentration. For nitration plates, ion chromatography permits simultaneous determination of nitrite, nitrate and sulfate from the same plate, whereas only nitrite can be determined by the classical colorimetric method. Both gluconate/borate and phthalate eluents were investigated and the results show that phthalate eluent is more appropriate for these plates. It was found that the pH of the sample has an important effect on the area of the sulfate peak. For both eluents, the area increases when the sample pH is lower than 6. This demonstrates the importance of an adequate sample treatment before injection in order to obtain reproducible and accurate values.     

马氏环境中的马氏链与马氏双链

本文研究了马氏环境中的马氏链,利用马氏双链的性质,得到了马氏环境中的马氏链回返于小柱集上的概率的若干估计式.     

Effect of FeCl3 and acetone on the structure of Na–montmorillonite studied by Mössbauer and XRD measurements

⁵⁷Fe Mössbauer spectroscopy, X-ray diffraction, X-ray fluorescence spectroscopy and infrared spectroscopy were used to study the effect of FeCl₃ and acetone on the structure of a Na–bentonite. XRD indicated the incorporation of Fe³⁺ ions into the interlayer space since the basal lattice spacing of montmorillonite increased to 1.6 from 1.24 nm after treatment with FeCl₃ dissolved in acetone. Interlayer Na⁺ ions could be exchanged to Fe³⁺. Magnetically split Mössbauer subspectra with internal magnetic fields 41 and 46 T at 74 K, were associated with two main Fe³⁺ microenvironments within the interlayer regions. The resultant Fe–montmorillonite was successfully applied as a catalyst in the preparation of 1,1-diacetates from aromatic aldehydes and acetic acid anhydride.     

Determination of piezoelectric coefficients of ferroelectric thin films using GaAs:Cr adaptive interferometer

We report on simple interferometric technique for the measurement of piezoelectric coefficients of thin films using GaAs:Cr adaptive photodetectors in the geometry of modified Mach–Zehnder interferometer. The technique needs no special vibroinsulation and automatically adjusts and keeps the operation point of the interferometer. Strong hysteresis effects with a slightly asymmetric form of the hysteresis loop were observed at the dependence of d₃₃ coefficients of the Pb(Zr,Ti)O₃ (PZT) thin film versus DC electric field. The obtained values of d₃₃ coefficients are in agreement with known data.     

Discovery of a small-molecule inhibitor of Dvl–CXXC5 interaction by computational approaches

The Wnt/β-catenin signaling pathway plays a significant role in the control of osteoblastogenesis and bone formation. CXXC finger protein 5 (CXXC5) has been recently identified as a negative feedback regulator of osteoblast differentiation through a specific interaction with Dishevelled (Dvl) protein. It was reported that targeting the Dvl–CXXC5 interaction could be a novel anabolic therapeutic target for osteoporosis. In this study, complex structure of Dvl PDZ domain and CXXC5 peptide was simulated with molecular dynamics (MD). Based on the structural analysis of binding modes of MD-simulated Dvl PDZ domain with CXXC5 peptide and crystal Dvl PDZ domain with synthetic peptide–ligands, we generated two different pharmacophore models and applied pharmacophore-based virtual screening to discover potent inhibitors of the Dvl–CXXC5 interaction for the anabolic therapy of osteoporosis. Analysis of 16 compounds selected by means of a virtual screening protocol yielded four compounds that effectively disrupted the Dvl–CXXC5 interaction in the fluorescence polarization assay. Potential compounds were validated by fluorescence spectroscopy and nuclear magnetic resonance. We successfully identified a highly potent inhibitor, BMD4722, which directly binds to the Dvl PDZ domain and disrupts the Dvl–CXXC5 interaction. Overall, CXXC5–Dvl PDZ domain complex based pharmacophore combined with various traditional and simple computational methods is a promising approach for the development of modulators targeting the Dvl–CXXC5 interaction, and the potent inhibitor BMD4722 could serve as a starting point to discover or design more potent and specific the Dvl–CXXC5 interaction disruptors.     

Facile pyrazolylborate ligand degradation at lanthanide centers: X-ray crystal structures of pyrazolylborinate-bridged bimetallics

Adventitious hydrolysis of a number of different complexes with the molecular formula Ln(Tp(Me2))(2)X [Tp(Me2) = (HB(dmpz)(3)), where X is a basic anionic ligand] in various solvents, yielded crystals of highly insoluble dimers of the general formula [Ln(Tp(Me2))(mu-BOp(Me2))](2) (1) [Ln = La, Ce, Sm; BOp(Me2) = (HBO(dmpz)(2))(2)(-); dmpzH = 3,5-dimethylpyrazole]. The results of several single-crystal X-ray determinations are reported. One metal nitrogen distance, that lying across from the two negatively charged bridging oxygen atoms, is 0.06 A longer than the others, suggesting an unusual trans influence at a lanthanide center. The formation of 1 is proposed to involve the intermediacy of Ln(Tp(Me2))(2)OH formed by protonolysis with adventitious water.     

Compartmental modeling of reversible intermolecular two-state excited-state processes coupled with rotational diffusion or with added quencher

Analysis of related time-resolved fluorescence measurements can possibly lead to the determination of the kinetic parameters of excited-state processes. A deterministic identifiability analysis on an error-free fluorescence decay data surface has to be executed to verify whether the parameters of a particular model can be determined and may point to the minimal experimental conditions under which this will become possible. In this work, similarity transformation is chosen as an identifiability analysis approach because it also gives the explicit relationships between the true and alternative model parameters. Results are presented for two kinetic models of a reversible intermolecular two-state excited-state process in isotropic environments: (a) with coupled species-dependent rotational diffusion described by Brownian reorientation and (b) with added quencher. For model a, both spherically and cylindrically symmetric rotors, with no change in the principal axes of rotation in the latter, are considered. The fluorescence delta-response functions I(parallel)(t) and I(perpendicular)(t), for fluorescence polarized respectively parallel and perpendicular to the electric vector of linearly polarized excitation, are used to define the sum S(t) = I( parallel)(t) + 2 I( perpendicular)(t) and the difference D(t) = I(parallel)(t) - I(perpendicular)(t) function. The identifiability analysis is carried out using the S(t) and D(t) functions. The analysis involving S(t) shows that two physically acceptable possible solutions for the overall rate constants of the excited-state process exist. Inclusion of information from polarized fluorescence measurements on the rotational kinetic behavior contained in D(t) results in the unique set of rate constants and rotational diffusion coefficients when the rotational diffusion coefficients are different. For model b, it is shown that addition of quencher plays formally the same role as rotational diffusion as far as the identification is concerned. When the quenching rate constants are different, the rate constants of a reversible intermolecular two-state excited-state process with added quencher can be uniquely determined.