Molecular design of N,N-disubstituted 2-aminothiazolines as selective carboxylesterase inhibitors

Selective carboxylesterase inhibitors are employed as modulators of hydrolytic metabolism of ester or amide-containing drugs. Using the Molecular Field Topology Analysis (MFTA), the models for the relationships between the structures and inhibitory activities of 5-halomethyl-2-aminothiazolines against acetylcholinesterase, butyrylcholinesterase, and carboxylesterase were built, the molecular design was performed, and a focused library of potentially active and selective carboxylesterase inhibitors was proposed.     

Hydrocarbons and fuels analyses with the supersonic gas chromatography mass spectrometry--the novel concept of isomer abundance analysis

Hydrocarbon analysis with standard GC-MS is confronted by the limited range of volatile compounds amenable for analysis and by the similarity of electron ionization mass spectra for many compounds which show weak or no molecular ions for heavy hydrocarbons. The use of GC-MS with supersonic molecular beams (Supersonic GC-MS) significantly extends the range of heavy hydrocarbons that can be analyzed, and provides trustworthy enhanced molecular ion to all hydrocarbons. In addition, unique isomer mass spectral features are obtained in the ionization of vibrationally cold hydrocarbons. The availability of molecular ions for all hydrocarbons results in the ability to obtain unique chromatographic isomer distribution patterns that can serve as a new method for fuel characterization and identification. Examples of the applicability and use of this novel isomer abundance analysis (IAA) method to diesel fuel, kerosene and oil analyses are shown. It is suggested that in similarity to the "three ions method" for identification purposes, three isomer abundance patterns can serve for fuel characterization. The applications of the Supersonic GC-MS for engine motor oil analysis and transformer oil analysis are also demonstrated and discussed, including the capability to achieve fast 1-2s sampling without separation for oil and fuel fingerprinting. The relatively fast analysis of biodiesel is described, demonstrating the provision of molecular ions to heavy triglycerides. Isomer abundance analysis with the Supersonic GC-MS could find broad range of applications including petrochemicals and fuel analysis, arson analysis, environmental oil/fuel spill analysis, fuel adulteration analysis and motor oil analysis.     

Studies of potential cerebrospinal fluid molecular markers for Alzheimer's disease

There is a need for a reliable, molecular-based ante mortem diagnostic test for Alzheimer's disease (AD). In this study, we examined the use of two-dimensional protein electrophoresis for generating molecular barcodes which may be useful for the clinical differentiation of AD patients from normals. We compared cerebrospinal fluid samples taken from AD patients with confirmed post mortem pathology to comparable specimens from normal volunteers. Using canonical correlation analysis, a panel of nine molecular markers were identified which segregated diseased cases from normal controls. Using the scaled volume image analysis variable, a principal factor analysis was also used to distinguish normal from AD spinal fluid, based on molecular markers identified using a heuristic clustering algorithm. The use of panels of molecular markers derived from proteomic analysis may offer the best prospect for developing molecular diagnostic tests for complex neurodegenerative disorders such as AD.     

Topology of molecular nanostructures in liquid alcohols

A quantitative topological analysis is conducted of the molecular nanostructures of liquid alcohols as a function of temperature. The analysis is necessary to solve the fundamental problem of the theory of solutions: finding the relationship between the macroparameters of liquids and the structure and properties of intermolecular associates. The analysis is performed using the previously proposed MDGT method, which is based on a combination of molecular dynamics calculations and graph theory. The method enables the recognition and saving of all molecular nanostructures observed in each snapshot of the molecular dynamics trajectory, averaging of data for any number of snapshots to present “averaged” concentrations of associates (dimers, trimers, etc.), and determination of the concentrations and characteristics of isomers (e.g., chains, branched chains, rings, etc.), bond lengths, angles, etc. in each group of associates.     

GRID formalism for the comparative molecular surface analysis: application to the CoMFA benchmark steroids, azo dyes, and HEPT derivatives

Shape analysis is a powerful tool in chemistry and drug design, and molecular surface defines shape in the molecular scale. In the current publication we presented a novel formalism for the comparative molecular surface analysis (s-CoMSA). The method enables both quantitative modeling of 3D-QSAR and finding possible pharmacophoric sites. The method provides very predictive models for the CBG activity of the benchmark steroid series, tinctorial properties of the heterocyclic azo dyes and anti-HIV activity of the HEPT series.     

Live single-cell molecular analysis by video-mass spectrometry.

The direct molecular analysis of a live single cell viewed under a video-microscope has been developed. The cell contents are sucked into a nano-electrospray tip, and hundreds of peaks of ionic compounds of low molecular weight are detected by nano-ESI Q-TOF mass spectrometry (MS). Cell-specific MS peaks in a single mouse-embryonic fibroblasts cell are extracted by a t-test, and one of the peaks is proceeded to MS/MS analysis for molecular identification. This method is direct and quick to identify the molecules of a cell with simultaneous observation by a video-microscope.     

Elemental composition from moment analyses of the low-resolution isotope pattern

The basic principles of an approach to mass spectral elemental analysis based on the moments of the low-resolution isotopic pattern are presented. The moment analyses are faster and more general than conventional methods of isotopic pattern analysis. The procedure is applied to the analysis of compounds which exhibit ‘pure’ molecular ions and the analysis of compounds which produce significant fragment ions at masses overlapping the molecular ion. It appears as though reasonable selectivity can be achieved for low relative molecular mass compounds (relative molecular mass < 400 a) using standard instrumentation and data acquisition softy are. Preliminary studies of instrumental factors affecting the measurement of moments are discussed.     

Molecular weight determination of hyaluronic acid by gel filtration chromatography coupled to matrix-assisted laser desorption ionization mass spectrometry.

An analytical approach has been described for the molecular weight characterization of enzymatically degraded hyaluronic acid (HA). The approach involved the combined use of aqueous gel filtration chromatography (GFC) with matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS). Microfractions were collected across an eluting peak from the chromatography system, followed by mass spectrometric analysis of these narrow fractions. The molecular mass determined by MALDI-MS and the signal obtained from the chromatography established a calibration curve for other hyaluronic acid samples analyzed by this GFC system. Results of one HA sample were obtained from both the calibration curve and direct fraction-by-fraction MALDI-MS analysis, and comparison of these results showed reasonable agreement. In contrast, molecular weights resulted from external calibration using dextran and pullullan standards showed drastically different numbers. Therefore, the GFC-MALDI-MS approach is a reliable method for the molecular weight characterization of polydisperse polysaccharides for which suitable calibration standards are unavailable for conventional GFC analysis.     

Discrimination of herbal medicines by molecular spectroscopy and chemical pattern recognition

The molecular spectroscopy (including near infrared diffuse reflection spectroscopy, Raman spectroscopy and infrared spectroscopy) with OPUS/Ident software was applied to clustering ginsengs according to species and processing methods. The results demonstrate that molecular spectroscopic analysis could provide a rapid, nondestructive and reliable method for identification of Chinese traditional medicine. It's found that the result of Raman spectroscopic analysis was the best one among these three methods. Comparing with traditional methods, which are laborious and time consuming, the molecular spectroscopic analysis is more effective.     

Novel properties from experimental charge densities: an application to the zwitterionic neurotransmitter taurine

The charge distribution of taurine (2-aminoethane-sulfonic acid) is revisited by using an orbital-based method that describes the density in a fixed molecular orbital basis with variable orbital occupation numbers. A new neutron data set is also employed to explore whether this improves the deconvolution of thermal motion and charge density. A range of molecular properties that are novel for experimentally determined charge densities are computed, including Weinhold population analysis, Mayer bond orders, and local kinetic energy densities, in addition to charge topological analysis and quantum theory of atoms-in-molecules (QTAIM) integrated properties. The ease with which a distributed multipole analysis can be performed on the fitted density matrix makes it straightforward to compute molecular moments, the lattice energy, and the electrostatic interaction energies of molecules removed from the crystal. Results are compared with high-level (QCISD) gas-phase calculations and band structure calculations employing density functional theory. Finally, the avenues available for extending the range of molecular properties that can be calculated from experimental charge densities still further using this approach are discussed.     

Short metal capillary columns packed with polymer-coated fibrous materials in high-temperature gas chromatography

The high-temperature gas chromatographic (GC) separation of several semivolatile compounds is studied with a short metal capillary column packed with fibrous material, having a polydimethylsiloxane coating thereon. Taking advantage of the excellent heat-resistance of the fiber and also the combination of the surface-deactivated metal capillary, a temperature-programmed separation up to 450 degrees C is successfully demonstrated for the separation of polymer standard samples. The average molecular weight of the commercially-available polymer standard samples for size exclusion chromatography (SEC) is estimated by high-temperature GC analysis and compared with the nominal value determined by a conventional SEC method. Although a slight deviation for the number-average molecular weight is observed between the GC and SEC analysis, the data for the weight-average molecular weight shows a good agreement in these methods. The results also suggest the future possibility of the fiber-packed metal capillary as a miniaturized GC column with an increased sample loading capacity.     

Competitive adsorption of neutral comb polymers and sodium dodecyl sulfate at the air/water interface

The interfacial behavior of aqueous solutions of four different neutral polymers in the presence of sodium dodecyl sulfate (SDS) has been investigated by surface tension measurements and ellipsometry. The polymers comprised linear poly(ethylene oxide) with low and high molecular masses (10(3) and 10(6) Dalton (Da), respectively), and two high molecular mass methacrylate-based comb polymers containing poly(ethylene oxide) side chains. The adsorption isotherms of SDS, determined by Gibbs analysis of surface tension data, are nearly the same in the presence of the high molecular mass linear polymer and the comb polymers. Analysis of the ellipsometric data reveals that while a single surface layer model is appropriate for films of polymer alone, a more sophisticated interfacial layer model is necessary for films of SDS alone. For the polymer/surfactant mixtures, a novel semiempirical approach is proposed to determine the surface excess of polymer, and hence quantify the interfacial composition, through analysis of data from the two techniques. The replacement of the polymer due to surfactant adsorption is much less pronounced for the high molecular mass linear polymer and for the comb polymers than for the low molecular mass linear polymer. This finding is rationalized by the significantly higher adsorption driving force of the larger polymer molecules as well as by their more amphiphilic structure in the case of the comb polymers.     

Analytical techniques for polymers with complex architectures

Complex polymers are distributed in more than one direction of molecular heterogeneity. In addition to the molar mass distribution, they are frequently distributed with respect to chemical composition, functionality, and molecular architecture. For the characterization of the different types of molecular heterogeneity it is necessary to use a wide range of analytical techniques. Preferably, these techniques should be selective towards a specific type of heterogeneity. The combination of two selective analytical techniques is assumed to yield a two-dimensional information on the molecular heterogeneity. For the analysis of complex polymers different liquid chromatographic techniques have been developed, including size exclusion chromatography (SEC) separating with respect to hydrodynamic volume, and liquid adsorption chromatography (LAC) which is used to separate according to chemical composition. Liquid chromatography at the critical point of adsorption (LC-CC) has been shown to be a versatile method for the determination of the functionality type distribution of macromonomers, the molecular architecture of homopolymers and the chemical heterogeneity of block and graft copolymers. The present paper presents the principle ideas of combining different analytical techniques in multidimensional analysis schemes for the analysis of polymers with complex architectures. Branched block and graft copolymers can efficiently be analyzed with respect to chemical composition and molar mass by LC-CC and two-dimensional chromatography. The chemical heterogeneity as a function of molar mass can be determined by combining interaction chromatography and FTIR spectroscopy. For the analysis of star-like polymers LC-CC is shown to be a powerful technique when the molar mass of different segments (blocks, grafts) must be determined.     

Off-line comprehensive 2-dimensional hydrophilic interaction × reversed phase liquid chromatography analysis of procyanidins

The development of an off-line comprehensive 2-dimensional liquid chromatography (2-D-LC) method for the analysis of procyanidins is reported. In the first dimension, oligomeric procyanidins were separated according to molecular weight by hydrophilic interaction chromatography (HILIC), while reversed phase LC was employed in the second dimension to separate oligomers based on hydrophobicity. Fluorescence, UV and electrospray ionisation mass spectrometry (ESI-MS) were employed for identification purposes. The combination of these orthogonal separation methods is shown to represent a significant improvement compared to 1-dimensional methods for the analysis of complex high molecular weight procyanidin fractions, by simultaneously providing isomeric and molecular weight information. The low correlation (r² < 0.2100) between the two LC modes afforded a practical peak capacity in excess of 2300 for the optimal off-line method. The applicability of the method is demonstrated for the analysis of phenolic extracts of apple and cocoa.     

DATA类逆转录酶抑制剂的三维定量构效关系

采用对接方法得到HIV-1抑制剂DATA(二芳基三嗪类)分子的活性构象, 进一步用比较分子场分析(CoMFA)和比较分子相似性分析(CoMSIA)法对DATA类逆转录酶抑制剂(RTIs)的三维定量构效关系(3D-QSAR)进行了研究, 建立3D-QSAR模型, 以指导进一步结构修饰. 用此模型预测了5个DATA类似物, 预测偏差较小, 表明了所建立的模型具有较强的预测能力.     

Peptidomics: the comprehensive analysis of peptides in complex biological mixtures

Progress in the sequencing of genomes has resulted in an increasing demand for a functional analysis of gene products in order to understand the underlying physiology. Proteomics has established itself as a highly valuable technology for producing functionally related data in an unparalleled fashion, but is methodologically restricted to the analysis of proteins with higher molecular masses (>10 kDa). The development of a technology which covers peptides with low molecular weight and small proteins (0.5 to 15 kDa) was necessary, since peptides, amongst them families of hormones, cytokines and growth factors, play a central role in many biological processes. To summarise the technologies used for this approach the term "peptidomics" is introduced. In this article, we present the rationale and first results of a novel, universal peptide display approach for the analysis and visualisation of peptides and small proteins from biological samples. Special attention is given to samples derived from extracellular fluids such as blood plasma and cerebrospinal fluid. Additionally, a high throughput identification procedure for the analysis of peptides in their native and processed molecular form is outlined.     

Graphical analysis and visualization of three-dimensional properties of molecules and solids

A simple approach is presented for visualizing three-dimensional properties of molecular and crystalline systems by using PC-based molecular drawing software. This allows a scientist with lower-cost PC-graphics capability to carry out analysis of data, such as wave functions and electron density, which would otherwise require a dedicated graphics workstation and expensive specialized software. In this approach, a data set [x,y,z,f1(x,y,z)] is transformed to a new set of data [x,y,z] for values of f1 meeting specified requirements. The function f1, which varies throughout a chemical system is difficult to visualize. However, a more manageable data set is obtained if the set of Cartesian coordinates corresponding to locations in the system where f1 has a specified value are used. This set of points can then be visualized and plotted with standard graphics software or PC-based molecular modeling programs. In addition, the use of PC-based molecular graphics permits one to superimpose the data describing molecular properties on drawings of the molecular geometry. The entire object can then be rotated to facilitate a clear analysis of the property of the molecule.