Structure-Activity Relationships in the Control of Chemical Risks

Abstract

Cluster significance analysis is a tool that allows the identification of ‘embedded clusters’ in QSAR datasets. It is successfully applied to an eye irritation data set to show that these data are indeed asymmetric. The method identifies five parameters that form an embedded cluster of eye irritants amongst non irritants, although full separation is not achieved. This method has considerable potential to identify potential non-linearity in toxicology data sets and for parameter reduction. It is shown also that this can be obtained relatively quickly with an analysis performed on 100,000 subsets containing the same information as an analysis on 1,000,000 subsets.     

Investigation of dynamic streaming potential by dimensional analysis

The theory of streaming potential at sinusoidal flow of liquid in a porous medium is a convenient and fruitful tool for determination of the interface properties of materials and also for construction of apparatus for zeta potential measurements and electrokinetic transducers. An investigation of the dynamic streaming potential by the method of dimensional analysis is presented. This method provides a wider approach to the problem under consideration. As a result, relationships between streaming potential in a porous medium and mechanical quantities are established. These quantities include pressure gradient in a liquid inside pores and capillaries, acceleration of capillaries, and the solid part of a porous medium, and the viscous friction force the liquid exerts on the solid part. The corresponding formulas for streaming potential are presented. The relationship between the streaming potential and viscous friction force does not depend on the frequency of oscillation and pore size. All these formulas in particular cases are transformed to known formulas for the streaming potential.     

Molecular conformations in a phospholipid bilayer extracted from dipolar couplings: a computer simulation study

This paper describes an analysis of NMR dipolar couplings in a bilayer formed by dimyristoylphosphatidylcholine (DMPC). The couplings are calculated from a trajectory generated in a molecular dynamics (MD) simulation based on a realistic atom-atom interaction potential. The analysis is carried out employing a recently developed approach that focuses on the construction of the conformational distribution function. This approach is a combination of two models, the additive potential (AP) model and the maximum entropy (ME) method, and is therefore called APME. In contrast to the AP model, the APME procedure does not require an intuition-based choice of the functional form of the torsional potential and is, unlike the ME method, applicable to weakly ordered systems. The conformational distribution function for the glycerol moiety of the DMPC molecule derived from the APME analysis of the dipolar couplings is in reasonable agreement with the "true" distributions calculated from the trajectory. Analyses of dipolar couplings derived from MD trajectories can, in general, serve as guidelines for experimental investigations of bilayers and other complex biological systems.     

Implementation of an adaptive umbrella sampling method for the calculation of multidimensional potential of mean force of chemical reactions in solution

We describe the implementation of an adaptive umbrella sampling method, making use of the weighted histogram analysis method, for computing multidimensional potential of mean force for chemical reaction in solution. The approach is illustrated by investigating the effect of aqueous solution on the free energy surface for the proton transfer reaction of [H(3)N-H-NH(3)](+) using a combined quantum mechanical and molecular mechanical AM1/TIP3P potential.     

CZE-ESI-MS联用测定小肽混合物的研究

研究肽的分离行为、测定方法及测定条件对蛋白质组学研究具有重要意义 .毛细管电泳 ( CE)作为一种高效、快速的分离方法 ,样品用量少 ,已被广泛应用于生物领域中 ,尤其是小肽和蛋白质的分离分析 .质谱 ( MS)能够进行微量鉴定 ,并提供精确的分子量和结构信息 ,使其成为小肽和蛋白质检测和序列测定的强有力的支撑技术之一 [1～ 3] .其中 ,电喷雾 ( ESI)质谱作为一种软电离技术 ,易与常规的高分辨率分离方法如高效液相色谱、毛细管电泳等实现在线联用 ,具有分离效率高、检测灵敏度高和样品定性方便等特点 ,因而在小肽和蛋白质的测定中得到广…     

示波极谱-四苯硼钠法的应用

示波极谱－四苯硼钠法是以示波极谱图形的突变来确定终点，其终点直观，不受溶液的颜色，沉淀，赋形剂的影响，可将重量分析，非水滴定，萃取－光度分析变为示波滴定分析，具有准，快，简，省的特点，有广泛的应用前景.     

Development of High Pressure Liquid Chromatography (HPLC) for Fractionation and Fingerprinting of Petroporphyrin Mixtures

Abstract

A method is described which permits the analysis of fossil porphyrin mixtures by HPLC. This method involves the fractionation of the demetallated petroporphyrin mixtures on silica columns followed by rechromatography of the trapped fractions on ODS columns. This coupling of the two modes of HPLC provides a fast and effective method for the separation of isomeric porphyrins and for the petroporphyrin fingerprinting of geological (oil/shale) samples. Representative examples of analysis are discussed in terms of the potential applicability of the technique in the areas of structure elucidation and geochemical correlations.     

Identification of differential metabolic characteristics between tumor and normal tissue from colorectal cancer patients by gas chromatography–mass spectrometry

Colorectal cancer (CRC) is one of the most common human malignancies and encompasses cancers of the colon and rectum. Although the gold‐standard colonoscopy screening method is effective in detecting CRC, this method is invasive and can result in severe complications for patients. The purpose of this study was to determine differences in metabolites between CRC and matched adjacent nontumor tissues from CRC patients, to identify potential biomarkers that may be informative and developed screening methods. Metabolomic analysis was performed on clinically localized CRC tissue and matched adjacent nontumor tissue from 20 CRC patients. Unsupervised analysis, supervised analysis, univariate analysis and pathway analysis were used to identify potential metabolic biomarkers of CRC. The levels of 25 metabolites in CRC tissues were significantly altered compared with the matched adjacent nontumor tissues. Four metabolites (lactic acid, alanine, phosphate and aspartic acid) demonstrated good area under the curve of receiver‐operator characteristic with acceptable sensitivities and specificities, indicating their potential as important biomarkers for CRC. Alterations of amino acid metabolism and enhanced glycolysis may be major factors in the development and progression of CRC. Lactic acid, alanine, phosphate, and aspartic acid could be effective diagnostic indicators for CRC.     

Quantitative structure-activity relationships for calmodulin inhibitors

Using the discriminant analysis method, we completely distinguished 24 calmodulin inhibitors in three groups, as classified by Zimmer et al. The resultant discriminant functions distinguished the three groups in terms of positive potential surface area on the side chain, as well as the total and neutral surface areas on the ring in the inhibitor molecules. Group assignment of additional calmodulin inhibitors from other sources was then estimated according to the discriminant functions. The relationship between structure and inhibitory potency on calmodulin-activated phosphodiesterase for group I inhibitors, together with those estimated, was studied using the adaptive least squares method with several parameters dependent on molecular conformations. A "best conformer" was selected for each inhibitor on the basis of quantitative structure-activity relationship (QSAR). The results of QSAR analysis of group I inhibitors showed that hydrophobicity was important for the ring moiety but not for the side chain. The negative potential surface area of the side chain is necessary for activity. It is desirable for the nitrogen atom in the side chain, which is considered the center of the negative potential area, to be located far from the ring moiety. Thus, the ring moiety and side chain may possibly play different roles in interactions with the receptor system.     

Low-temperature synthesis and characteristics of fractal graphene layers

Large scale fractal graphene layers are obtained by complex method of liquid phase exfoliation and self-organization. Atomic force microscopy (AFM) is used to study the surface properties of formed layers and to assess their thickness. Surface potential of graphene and potential transition between the graphene and substrate is measured by Kelvin probe method. The influence of the effect of dielectric confinement on the optical properties of graphene is discussed in this work. Raman scattering spectra were used for structural analysis and assessment of the level of defects. Current-voltage characteristics of graphene ribbons were measured and discussed for different number of layers.     

Potentiometric stripping analysis (PSA) for monitoring of antimony in samples of vegetation from a mining area

A potentiometric stripping analysis (PSA) method has been developed and checked for the fast and reliable determination of antimony in vegetation samples of Cistus ladanifer from a mining area in Badajoz, Southwest Spain. The method, modified from previous PSA methods for Sb in environmental samples, is based on dry ashing of the homogenized leaves, dissolution in hydrochloric acid, and PSA analysis on a mercury film plated on to a glassy carbon disk electrode. The influence of experimental variables such as the deposition potential, the deposition time, the signal stability and the calibration parameters, has been investigated. The method has been compared with an independent technique (instrumental neutron activation analysis) by analysis of standards and reference materials and comparison of the results. As a result of automation of the PSA equipment, the proposed method enables unattended analysis of 20 digested samples in a total time of 2 h, thus providing a useful tool for Sb monitoring of a large number of samples.     

The direct current method for measuring charged membrane conductance

This paper deals with a method for measuring electrical resistance in charged membranes. The method is based on the application of a step change in direct current and on the analysis of the potential transient subsequent to the application of the current step. p]Membrane electrical resistance was determined by an extrapolation to zero time of potential differences measured after the current step. p]Experimental results obtained with commercial ion-exchange membranes were in good agreement with those computed from the Fick equation. The method developed gives more accurate values with a standard deviation lower than traditional techniques and allows the resistance of an asymmetrical membrane to be determined in both current directions.     

基于纳米金粒子可视化分析检测的研究进展

基于纳米金粒子表面等离子共振性质发展起来的可视化分析,由于具有灵敏度高、可设计性强、分析过程快速等优点已被广泛地应用于各类目标分析物的检测,成为一种极具潜力的分析手段。本文综述了基于纳米金粒子表面等离子共振可视化分析检测的研究进展,并对其发展趋势进行了展望。     

A novel method for fast determination of vitamin B6 by fast continuous cyclic voltammetry

In this work a novel method for the determination of Vitamin B6 in flow-injection systems has been developed. The fast Fourier transform continuous cyclic voltammetry (FFTCV) at gold microelectrode in flowing solution system was used for determination of Vitamin B6. This method is rapid, simple and highly sensitive procedures allowing the determination of Vitamin B6 in pharmaceutical analysis. The effects of various parameters on the sensitivity of the method were investigated. The best performance was obtained with the pH value of 2, scan rate value of 30 V/s, accumulation potential of 200 mV and accumulation time of 0.3 s. The proposed method has some advantages over other reported methods such as, no need for the removal of oxygen from the test solution, a sub-nanomolar detection limit, and finally the method is fast enough for the determination of any such compound, in a wide variety of chromatographic methods. To obtain a sensitive determination, the integration range of currents was set for all the potential scan ranges, including oxidation and reduction of the Au surface electrode, while performing the measurements. The potential waveform, consisting of the potential steps for cleaning, accumulation and potential ramp of analyte, was applied on an Au disk microelectrode (12.5 μm in radius) in a continuous way. The detection limit of the method for Vitamin B6 was 2.8 pg/ml. The relative standard deviation of the method at 2.1% was 8 runs. Published in Russian in Elektrokhimiya, 2008, Vol. 44, No. 2, pp. 173–181. The text was submitted by the authors in English.     

Analysis of the statistical error in umbrella sampling simulations by umbrella integration

Umbrella sampling simulations, or biased molecular dynamics, can be used to calculate the free-energy change of a chemical reaction. We investigate the sources of different sampling errors and derive approximate expressions for the statistical errors when using harmonic restraints and umbrella integration analysis. This leads to generally applicable rules for the choice of the bias potential and the sampling parameters. Numerical results for simulations on an analytical model potential are presented for validation. While the derivations are based on umbrella integration analysis, the final error estimate is evaluated from the raw simulation data, and it may therefore be generally applicable as indicated by tests using the weighted histogram analysis method.     

Generation of OPLS-like charges from molecular electrostatic potential using restraints

A new method for generating atom-centered charges for use in condensed phase computer simulations is presented, which is based on a restrained electrostatic potential (RESP) procedure. Charges are calculated from a least-squares fit to the quantum mechanical electrostatic potential with a restraint applied to reduce their magnitude. The restraint developed here offers advantages over that used in RESP. The magnitude of the restraint is optimized to yield charges as close to the equivalent OPLS values as possible while still reproducing the molecule's electrostatic potential. A cross-validation analysis is used to show that the restraint is insensitive to the selection of OPLS molecules from which it is derived. Thus, with this method, OPLS-like charges may be produced from the electrostatic potential for atom types not in the OPLS force field. In addition, the restraint is shown to reduce the conformational dependence of the charges. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 483–498, 1999     

Fast calculation of the electrostatic potential in ionic crystals by direct summation method

An efficient real space method is derived for the evaluation of the Madelung's potential of ionic crystals. The proposed method is an extension of Evjen's method. It takes advantage of a general analysis of the potential convergence in real space. Indeed, we show that the series convergence is exponential as a function of the number of canceled multipolar moments in the unit cell. The method proposed in this work reaches such an exponential convergence rate. Its efficiency is comparable to Ewald's method. However, unlike the latter, it uses only simple algebraic functions.     

Application of abrasive stripping voltammetry in corrosion science. I. determination of the corrosion potentials of metals

The application of abrasive stripping voltammetry for the determination of the corrosion potential of metal powders is described. Micro amounts of a metal are fixed on a paraffin-impregnated graphite electrode immersed in suitable electrolyte solutions and polarization curves are recorded. The value of the corrosion potential is determined by Tafel analysis. The precision of the method is ±0.5% (mean rel. dev.) of the final potential value. Received: 24 March 1998 / Accepted: 27 August 1998     

Gas chromatographic analysis of phenylurea herbicides following catalytic hydrolysis on silica gel

Summary A method is described for the rapid catalytic hydrolysis of phenylurea herbicides on silica gel at elevated temperatures. After derivatisation of the anilines produced with heptafluorobutyric acid anhydride final analysis is done on a gas chromatograph equipped with an electroncapture detector. Detection limits are in the 1–5 picogram range. The method has successfully been applied to residue analysis of water samples at the 1 ppb level. The determination of free anilines present in water samples and the potential of various techniques to be used to discriminate between free anilines and parent herbicides are also discussed.     

涂膏热解法制备钛基Sn、Sb氧化物电极

研究了涂膏热解法制备Ti/Sn、Sb氧化物电极的新工艺，考察了SnCl4、SbCl3加入量和烧结温度对电极寿命和析氧电位的影响，并对电极进行了SEM、EDS、XRD测试.结果表明，在涂层厚度相近时，涂膏法制备的电极与热解法相比，具有表面氧化物分布均匀和TiO2不易裸露的优点，从而提高了析氧电位，延长了电极寿命，使电极具有很高的电催化活性和电化学稳定性.