Numerical simulation of DNA sample preconcentration in microdevice electrophoresis

A numerical model is presented for the accurate and efficient prediction of preconcentration and transport of DNA during sample introduction and injection in microcapillary electrophoresis. The model incorporates conservation laws for the different buffer ions, salt ions, and DNA sample, coupled through a Gaussian electric field to account for the field modifications that cause electromigration. The accuracy and efficiency required to capture the physics associated with such a complex transient problem are realized by the use of the finite element-flux corrected transport (FE-FCT) algorithm in two dimensions. The model has been employed for the prediction of DNA sample preconcentration and transport during electrophoresis in a double-T injector microdevice. To test its validity, the numerical results have been compared with the corresponding experimental data under similar conditions, and excellent agreement has been found. Finally, detailed results from a simulation of DNA sample preconcentration in electrophoretic microdevices are presented using as parameters the electric field strength and the other species concentrations. The effect of the Tris concentration on sample stacking is also investigated. These results demonstrate the great potential offered by the model for future optimization of such microchip devices with respect to significantly enhanced speed and resolution of sample separation.     

Investigation of the complexation of essential oil components with cyclodextrins

The formation of inclusion complexes of six essential oil (EO) components (β-caryophyllene, cis-ocimene, trans-ocimene, sabinene hydrate (thujanol), γ-terpinene and α-terpineol) with six cyclodextrins (CDs) (α-CD, β-CD, γ-CD, HP-β-CD, RAMEB and CRYSMEB) was investigated by using static headspace-gas chromatography and UV–visible spectroscopy. Retention studies showed that CDs could efficiently reduce the volatility of EO components except for β-caryophyllene with α-CD. In this case, no inclusion complex was detected while for other compounds the formation of 1:1 inclusion complexes was observed. Results revealed that the inclusion stability mainly depends on geometric complementarity between encapsulated molecule and CD's cavity. Molecular modelling was used to investigate the complementarities between host and guest. Thus, CDs could efficiently be regarded as promising encapsulants for EO components leading to improve their application in cosmetic, pharmaceutical and agriculture fields.     

QSAR Study on Binding Affinity of PATs (Rodenticides) to the [3H]-Mepyramine-Labelled H1 Receptor In Rat and Guinea Pig Brain

Abstract

The binding of a series of PAT analogues (rodenticides) to the [³H]-mepyramine-labelled H₁ receptor in rat and guinea pig brain was investigated topologically using negentropy (N), molecular redundancy (MRI), first-order molecular connectivity (¹X _v ), Wiener (W), and Szeged (Sz) indices. Multiple regression analyses showed that MRI provided excellent results upon introduction of indicator parameters. Predictive ability of the proposed models was discussed using cross-validation parameters.     

ToxML,a data exchange standard with content controlled vocabulary used to build better (Q)SAR models

Development of accurate quantitative structure–activity relationship (QSAR) models requires the availability of high quality validated data. International regulations such as REACH in Europe will now accept (Q)SAR-based evaluations for risk assessment. The number of toxicity datasets available for those wishing to share knowledge, or to use for data mining and modelling, is continually expanding. The challenge is the current use of a multitude of different data formats. The issues of comparing or combining disparate data apply both to public and proprietary sources. The ToxML project addresses the need for a common data exchange standard that allows the representation and communication of these data in a well-structured electronic format. It is an open standard based on Extensible Markup Language (XML). Supporting information for overall toxicity endpoint data can be included within ToxML files. This makes it possible to assess the quality and detail of the data used in a model. The data file model allows the aggregation of experimental data to the compound level in the detail needed to support (Q)SAR work. The standard is published on a website together with tools to view, edit and download it.     

Interaction of Naproxen with Crystalline and Amorphous Methylated β-Cyclodextrin in the Liquid and Solid State

Abstract

Interactions of naproxen (NAP) with amorphous, randomly methylated β-cyclodextrin at a degree of substitution per anhydroglucose unit of 1.8 (RAMEB) and with crystalline heptakis-(2,6-di-O-methyl)-β-cyclodextrin (DIMEB) were studied in aqueous solution and in the solid state using, respectively, phase-solubility analysis (at 25 °C, 37 °C and 47 °C) and differential scanning calorimetry (DSC) supported by X-ray powder diffractometry. RAMEB and DIMEB displayed similar solubilizing and complexing abilities towards NAP, suggesting analogous inclusion modes of the drug in the host cavity in aqueous solution. Differences were instead observed in interactions in the solid state, where the amorphizing capacity of RAMEB toward NAP (evaluated by DSC) was about twice that of DIMEB at each drug-to-carrier ratio. Assuming that inclusion complexation is also involved in solid-state interactions, molecular modelling accounted for the experimental results in terms of structural features of DIMEB, i.e. the particular inwards orientation of O-6-C-8 groups of three alternate glucoses on the primary hydroxyl side which hampers a deep penetration of NAP in the DIMEB cavity in the solid state. On the contrary, no obstruction of the cavity apparently occurs with RAMEB due its noncrystalline state. The aqueous dissolution rate of NAP from NAP-RAMEB and NAP-DIMEB blends containing 0.59, 0.73, 0.85, and 0.92 mass fraction of carrier linearly increased at decreasing drug-to-carrier ratios. The improvement was 5 to 20 times (from powders) and 50 to 200 times (from discs) the dissolution rate of NAP alone for both carrier. Therefore the choice of the amorphous RAMEB in pharmaceutical formulations can be recommended mainly for economic reasons, though the anhydrous and non-hygroscopic nature of crystalline DIMEB might be of particular advantage in case of moisture sensitive formulations.     

Rotamer decomposition and protein dynamics: Efficiently analyzing dihedral populations from molecular dynamics

Molecular mechanics methods have matured into powerful methods to understand the dynamics and flexibility of macromolecules and especially proteins. As multinanosecond to microsecond length molecular dynamics (MD) simulations become commonplace, advanced analysis tools are required to generate scientifically useful information from large amounts of data. Some of the key degrees of freedom to understand protein flexibility and dynamics are the amino acid residue side chain dihedral angles. In this work, we present an easily automated way to summarize and understand the relevant dihedral populations. A tremendous reduction in complexity is achieved by describing dihedral timeseries in terms of histograms decomposed into Gaussians. Using the familiar and widely studied protein lysozyme, it is demonstrated that our approach captures essential properties of protein structure and dynamics. A simple classification scheme is proposed that indicates the rotational state population for each dihedral angle of interest and allows a decision if a given side chain or peptide backbone fragment remains rigid during the course of an MD simulation, adopts a converged distribution between conformational substates or has not reached convergence yet. © 2012 Wiley Periodicals, Inc.     

Viscosity Mixing Rules for Binary Systems Containing One Ionic Liquid

In this work the applicability of four of the most commonly used viscosity mixing rules to [ionic liquid (IL)+molecular solvent (MS)] systems is assessed. More than one hundred (IL+MS) binary mixtures were selected from the literature to test the viscosity mixing rules proposed by 1) Hind (Hi), 2) Grunberg and Nissan (G–N), 3) Herric (He) and 4) Katti and Chaudhri (K–C). The analyses were performed by estimating the average (absolute or relative) deviations, AADs and ARDs, between the available experimental data and the predicted ideal mixture viscosity values obtained by means of each rule. The interaction terms corresponding to the adjustable parameters inherent to each rule were also calculated and their trends discussed.     

Artificial Neural Networks in water analysis: Theory and applications

Artificial Neural Networks (ANNs) have seen an explosion of interest over the last two decades and have been successfully applied in all fields of chemistry and particularly in analytical chemistry. Inspired from biological systems and originated from the perceptron, i.e. a program unit that learns concepts, ANNs are capable of gradual learning over time and modelling extremely complex functions. In addition to the traditional multivariate chemometric techniques, ANNs are often applied for prediction, clustering, classification, modelling of a property, process control, procedural optimisation and/or regression of the obtained data. This paper aims at presenting the most common network architectures such as Multi-layer Perceptrons (MLPs), Radial Basis Function (RBF) and Kohonen's self-organisations maps (SOM). Moreover, back-propagation (BP), the most widespread algorithm used today and its modifications, such as quick-propagation (QP) and Delta-bar-Delta, are also discussed. All architectures correlate input variables to output variables through non-linear, weighted, parameterised functions, called neurons. In addition, various training algorithms have been developed in order to minimise the prediction error made by the network. The applications of ANNs in water analysis and water quality assessment are also reviewed. Most of the ANNs works are focused on modelling and parameters prediction. In the case of water quality assessment, extended predictive models are constructed and optimised, while variables correlation and significance is usually estimated in the framework of the predictive or classifier models. On the contrary, ANNs models are not frequently used for clustering/classification purposes, although they seem to be an effective tool. ANNs proved to be a powerful, yet often complementary, tool for water quality assessment, prediction and classification.     

Molecular Dynamic Study for Chiral Discrimination of α-Phenylethylamine by Modified Cyclodextrin in Gas Chromatography

IntroductionAfter the introduction of modified cyclodextrins (CDs) as a new type ofchiral stationaryphases, great progress has been made in enantioselective gas chromatography, which hasraised many questions about the mechanism of chiral recognition and intermolecularinteractionsl. Theoretical computational methods in conjunction with modellingprocedures have been extensively used to investigate the nature of binding processesresponsible for inclusion complex formation2'3. It is of interest t…     

Molecular dynamics simulation study of drugs adsorption in UiO-66

Metal-organic frameworks (MOFs) are novel porous materials that have been extensively used in sensors, catalysis, gas storage and separation, and drug deliver owing to their adjustable pore size, large surface area and high porosity. Among diverse MOFs, UiO-66 can be a promising carrier for drug delivery due to high porosity and chemical stability. However, the adsorption mechanism of drugs in UiO-66 has not been identified and need a further investigation. Hence, we utilized molecular dynamic (MD) simulation to investigate the adsorption mechanism of UiO-66 as drug carriers. The MD simulation of UiO-66 exhibits the busulfan loading of 80 %, ibuprofen of 20 % and 5-fluorouracil of 30 %, respectively. We also demonstrated that the host-guest interaction between UiO-66 and drugs is dominated by the Van der Waals force. UiO-66 shows the highest affinity for busulfan compared with ibuprofen and 5-fluorouracil. In addition, it is certified the linear relation between the adsorption atoms and the interaction energy, which could help us to predict the interaction energy between drugs and UiO-66 by the contact atoms.