Development of models for prediction of the antioxidant activity of derivatives of natural compounds

Antioxidants are important for maintaining the appropriate balance between oxidizing and reducing species in the body and thus preventing oxidative stress. Many natural compounds are being screened for their possible antioxidant activity. It was found that a mushroom pigment Norbadione A, which is a pulvinic acid derivative, shows an antioxidant activity; the same was found for other pulvinic acid derivatives and structurally related coumarines. Based on the results of in vitro studies performed on these compounds as a part of this study quantitative structure–activity relationship (QSAR) predictive models were constructed using multiple linear regression, counter-propagation artificial neural networks and support vector regression (SVR). The models have been developed in accordance with current QSAR guidelines, including the assessment of the models applicability domains. A new approach for the graphical evaluation of the applicability domain for SVR models is suggested. The developed models show sufficient predictive abilities for the screening of virtual libraries for new potential antioxidants.     

Effect of interparticle interactions on the rate of injection of charge carriers into electroactive polymer films

A phenomenological approach is used for deriving a difference equation for the density of reduced sites in films of electroactive polymers with conspicuous interparticle interactions. The approach involves simultaneous application of the lattice methods and Broensted’s rule. This leads to generalization of equations for the surface layer that are known in theory of surface tension for nonelectrolytic solutions. Together with the Poisson equation for electric potential, the derived relationships make a complicated system of differential equations. Nevertheless, it can be solved by iterative methods. In the framework of this approach, expressions for the rates of injection of charge carriers into polymer films are obtained. Within a first approximation with regard to allowance for the forces of short-range interactions, their influence on the rates of injection of electrons and protons into a film is discussed.     

Total synthesis of pinnatoxins A and G and revision of the mode of action of pinnatoxin A

Pinnatoxins belong to an emerging class of potent marine toxins of the cyclic imine group. Detailed studies of their biological effects have been impeded by unavailability of the complex natural product from natural sources. This work describes the development of a robust, scalable synthetic sequence relying on a convergent strategy that delivered a sufficient amount of the toxin for detailed biological studies and its commercialization for use by other research groups and regulatory agencies. A central transformation in the synthesis is the highly diastereoselective Ireland-Claisen rearrangement of a complex α,α-disubstituted allylic ester based on a unique mode for stereoselective enolization through a chirality match between the substrate and the lithium amide base. With synthetic pinnatoxin A, a detailed study has been performed that provides conclusive evidence for its mode of action as a potent inhibitor of nicotinic acetylcholine receptors selective for the human neuronal α7 subtype. The comprehensive electrophysiological, biochemical, and computational studies support the view that the spiroimine subunit of pinnatoxins is critical for blocking nicotinic acetylcholine receptor subtypes, as evidenced by analyzing the effect of a synthetic analogue of pinnatoxin A containing an open form of the imine ring. Our studies have paved the way for the production of certified standards to be used for mass-spectrometric determination of these toxins in marine matrices and for the development of tests to detect these toxins in contaminated shellfish.     

Performance comparison of three types of high-speed counter-current chromatographs for the separation of components of hydrophilic and hydrophobic color additives

The performance of three types of high-speed counter-current chromatography (HSCCC) instruments was assessed for their use in separating components in hydrophilic and hydrophobic dye mixtures. The HSCCC instruments compared were: (i) a J-type coil planet centrifuge (CPC) system with a conventional multilayer-coil column, (ii) a J-type CPC system with a spiral-tube assembly-coil column, and (iii) a cross-axis CPC system with a multilayer-coil column. The hydrophilic dye mixture consisted of a sample of FD&C Blue No. 2 that contained mainly two isomeric components, 5,5'- and 5,7'-disulfonated indigo, in the ratio of ～7:1. The hydrophobic dye mixture consisted of a sample of D&C Red No. 17 (mainly Sudan III) and Sudan II in the ratio of ～4:1. The two-phase solvent systems used for these separations were 1-butanol/1.3M HCl and hexane/acetonitrile. Each of the three instruments was used in two experiments for the hydrophilic dye mixture and two for the hydrophobic dye mixture, for a total of 12 experiments. In one set of experiments, the lower phase was used as the mobile phase, and in the second set of experiments, the upper phase was used as the mobile phase. The results suggest that: (a) use of a J-type instrument with either a multilayer-coil column or a spiral-tube assembly column, applying the lower phase as the mobile phase, is preferable for separating the hydrophilic components of FD&C Blue No. 2; and (b) use of a J-type instrument with multilayer-coil column, while applying either the upper phase or the lower phase as the mobile phase, is preferable for separating the hydrophobic dye mixture of D&C Red No. 17 and Sudan II.     

The mechanism of reequilibration of solids in the presence of a fluid phase

The preservation of morphology (pseudomorphism) and crystal structure during the transformation of one solid phase to another is regularly used as a criterion for a solid-state mechanism, even when there is a fluid phase present. However, a coupled dissolution-reprecipitation mechanism also preserves the morphology and transfers crystallographic information from parent to product by epitaxial nucleation. The generation of porosity in the product phase is a necessary condition for such a mechanism as it allows fluid to maintain contact with a reaction interface which moves through the parent phase from the original surface. We propose that interface-coupled dissolution-reprecipitation is a general mechanism for reequilibration of solids in the presence of a fluid phase.     

Determination of the reference value of nitrogen mass fraction in the reference material of Polish soil

Ensuring a traceability and meaningful of a measurements is one of the most important stages of each analysis, each measurement. It is especially important for measurement of the environmental samples, like soil, which is a very complex matrix. A certified reference materials (CRMs) should be routinely used for this purpose. The paper discusses the procedure for preparation of the soil samples for certification as CRM. As for agricultural reasons there is a growing demand for CRMs regarding a nitrogen mass fraction in the Polish soil, we prepared such a material and established the reference value with associated measurement uncertainty. Homogeneity and stability of the material were shown to be appropriate for the intended purpose. The presented approach can also be used in a process of manufacture of a laboratory reference material, which can be used for a routine quality control.     

Effects of lysophospholipids on membrane order of phosphatidylcholine

Lysophospholipids are known to play a role in a wide range of cellular processes involving membrane–protein or membrane–membrane interactions; however lysolipids–lamellar lipids interactions remain unclear. The effects of lysolipids on membrane order and dynamics were examined using optical birefringence and fluorescence techniques. We found that lysophosphatidic acid (LPA) induces a considerable disorder in chain orientation for synthetic lipid of dimyristoyl-phosphatidylcholines (DMPC), whereas a slight order for natural lipid of egg yolk phosphatidylcholine (Egg-PC), e.g. the chain order decreases by 10% at 0.1 mole ratio for DMPC in comparison with the membranes without LPA and increases by 3.4% at 0.09 mole ratio for Egg-PC. Also, membrane fluidity corresponds with the change in the chain disorder, namely, the fluidity increases for DMPC membranes, while decreases for Egg-PC membranes by addition of LPA. The difference in the effects of LPA is interpreted by a difference in the chain packing between the synthetic and the natural lipid bilayers. LPA can be incorporated into natural lipid membranes without disturbance, and readjusts itself to a more favorable hydrophobic match with the bilayers. Lysophophatidylcholine (LPC) also induces a disorder in DMPC membranes, but the decrease in chain order is only half compared with that for LPA.     

Regularities of formation of emboli of liquid polymer solutions in aqueous medium

Work on creating the basis for embolic compositions for the treatment of a wide range of pathologies of various organs was conducted. This basis is a solution of a biocompatible water-insoluble polymer in a biocompatible water-soluble solvent. Formation of the embolus in such an aqueous medium takes place in the transition of the solvent into the aqueous phase and the formation of a solid polymer clot occluding a blood vessel. Criteria for selection of the polymer and the solvent for the basis were formulated, and a number of polymers and solvents that meet these criteria were selected for further research. Research on the solubility of the selected polymers in solvents was carried out, and the rheoviscometric characteristics of polymer solutions, as well as parameters of solid emboli formation of polymer solutions in aqueous media, were found. The solution of cellulose acetate plasticized with OPADRY CA 500F190000 polyethylene glycol in dimethylsulfoxide with concentration of no less than 60 g/L was recognized as optimal for further studies.     

Computation of Electromagnetic Properties of Molecular Ensembles

We outline a methodology for efficiently computing the electromagnetic response of molecular ensembles. The methodology is based on the link that we establish between quantum-chemical simulations and the transfer matrix (T-matrix) approach, a common tool in physics and engineering. We exemplify and analyze the accuracy of the methodology by using the time-dependent Hartree-Fock theory simulation data of a single chiral molecule to compute the T-matrix of a cross-like arrangement of four copies of the molecule, and then computing the circular dichroism of the cross. The results are in very good agreement with full quantum-mechanical calculations on the cross. Importantly, the choice of computing circular dichroism is arbitrary: Any kind of electromagnetic response of an object can be computed from its T-matrix. We also show, by means of another example, how the methodology can be used to predict experimental measurements on a molecular material of macroscopic dimensions. This is possible because, once the T-matrices of the individual components of an ensemble are known, the electromagnetic response of the ensemble can be efficiently computed. This holds for arbitrary arrangements of a large number of molecules, as well as for periodic or aperiodic molecular arrays. We identify areas of research for further improving the accuracy of the method, as well as new fundamental and technological research avenues based on the use of the T-matrices of molecules and molecular ensembles for quantifying their degrees of symmetry breaking. We provide T-matrix-based formulas for computing traditional chiro-optical properties like (oriented) circular dichroism, and also for quantifying electromagnetic duality and electromagnetic chirality. The formulas are valid for light-matter interactions of arbitrarily-high multipolar orders.     

Separation of the Isotopes of Uranium by the Separation Nozzle Process

The separation nozzle process is based on the partial spatial separation of components of different mass in an expanding supersonic jet stream. The process is of especial interest for the separation of uranium isotopes. Details of a systematic experimental determination of the most favorable operating conditions for such a separation are given and the construction and testing of a closed circulation system, the basic unit of a ten membered pilot cascade separator for uranium isotope separation, is described. The optimum values of the specific cost factors obtained experimentally for the separation nozzle process are compared with the corresponding values estimated for the gaseous diffusion process.     

Application of a Cholesterol-Based Stationary Phase for the Analysis of Brevetoxins

A high-performance liquid chromatography protocol for the analysis of brevetoxins has been developed using a silica hydride-based cholesterol column. Brevetoxins are neurotoxins produced by harmful algae that have additional potential as drugs for a number of illnesses/diseases. To develop the optimum conditions, a number of different experimental approaches were tested. These include isocratic and gradient elution, different organic mobile phase components, and temperature variations. A separate protocol was developed for the compounds brevenal and brevenol, also produced by the same algae that make brevetoxins. Brevenal is a natural product under investigation as a therapy for chronic respiratory diseases, such as cystic fibrosis or asthma. The goal of this study was to provide a protocol for the analysis of these compounds that could be further developed into a validated method depending on a particular laboratory's capabilities and to highlight some of the unique features of the cholesterol stationary phase.     

Benefits of the implementation of a metrological structure for water analyses

Traceability of measurements still often remains a non-operational notion for end-user chemists. A practical project, sponsored by the French Ministry of Research, has been conducted to evaluate and to demonstrate possible benefits of the implementation of a metrological structure for improvement of the quality of water analyses. LNE (Laboratoire National d'Essais) was in charge of the build up of the traceability chain in a concrete case of determination of some heavy metals (cadmium and lead) in a groundwater. Pure solutions for calibration and a matrix RM have been certified by LNE and then used by 46 labs (mainly French) in a inter-laboratory study. Results have shown a measurable bias in lead analysis in the groundwater for all methods in routine use by laboratories. This project has demonstrated the interest of a metrological approach for method calibration, method validation and estimation of measurement uncertainty.     

Problems of validation of computerised instruments for accredited chemical laboratories

 Some problems of validation of computerised instruments are reviewed briefly, taking essential standards and guides into account. The significant role of certified standard reference materials is underlined. An attitude of suppliers towards the validation of instruments is presented, and producers' responsibilities and obligations are discussed. The "black-box" concept is recommended as a preliminary step for the validation of computerised instruments. Two examples for gel permeation chromatography are given that illustrate a bad manufacturer's practice (BMP) and good manufacturer's practice (GMP). In the case of BMP, a need is expressed for a guide and for regulations that should be implemented into the quality assurance system. It has been proposed that the EURACHEM/VAM draft of guidance for qualification/validation of instruments should be amended by incorporating the "black-box" approach as a preliminary procedure for validation of computerised instruments, a retrospective validation procedure if the need for current validation was not foreseen or not specified, and a procedure (or selection rules) for qualification of the supplier. Moreover, the mechanisms of inspection to control the observance of the standardised rules and commonly recognised recommendations should also be considered by international quality organisations. Received: 19 November 1996 · Accepted: 20 March 1997     

Calculation of the Liquid and Gas Permeability of Hydrophobic Low-Porosity Membranes of an Arbitrary Thickness

A method for calculating the liquid and gas permeability of hydrophobic low-porosity membranes of an arbitrary thickness is described. The calculation is based on the solution of a problem on percolation—the procedure of finding the distribution of liquid and gas over the membrane thickness. The dependence of the permeability for liquid on the share of pores that are potentially accessible to being filled with liquid is obtained for both thin and thick membranes. This dependence is of a universal nature and can easily be recalculated into a dependence of permeability on the pressure drop for membranes with any distribution of pores by size. Numerical estimates of principal characteristics for a membrane that possesses pores of three types are performed. The characteristics in question include permeabilities for liquid and gas; fluxes of the liquid; critical pressures, at which the permeability for liquid turns other than zero; and the working range of pressures, in which the membrane is capable of working normally. All these data permit the optimization of the operation of similar membranes, in particular, gas-delivering membranes that are used in hydrogen–oxygen fuel cells with a solid polymer electrolyte.     

A general framework for the measurement of band broadening properties of GC capillary columns

In the approach to the developement of a practical procedure for the evaluation of band broadening properties of gas capillary columns, the expression for the variance of a solute band is cast in a dimensionless form. This expression supplies the basis for a valid bench mark for column evaluation. Experimental results demonstrate the applicability of the method.     

Calculation of affinities of peptides for proteins

Several methodologies were employed to calculate the Gibbs standard free energy of binding for a collection of protein-ligand complexes, where the ligand is a peptide and the protein is representative for various protein families. Almost 40 protein-ligand complexes were employed for a continuum approach, which considers the protein and the peptide at the atomic level, but includes solvent as a polarizable continuum. Five protein-ligand complexes were employed for an all-atom approach that relies on a combination of the double decoupling method with thermodynamic integration and molecular dynamics. These affinities were also computed by means of the linear interaction energy method. Although it generally proved rather difficult to predict the absolute free energies correctly, for some protein families the experimental ranking order was correctly reproduced by the continuum and all-atom approach. Considerable attention has also been given to correctly analyze the affinities of charged peptides, where it is required to judge the effect of one or more ions that are being decoupled in an all-atom approach to preserve electroneutrality. The various methods are further judged upon their merits.     

A Simple Method of the Determination of the Structural Heterogeneity of Microporous Solids

A new procedure for determining the structural heterogeneity of microporous solids is presented. Applying the concept of a general adsorption isotherm equation, a method for solving this equation for adsorption in micropores is developed, and the applicability of a new simple algorithm for determining the parameters of microporous structure of two commercial carbons is shown. Copyright 2001 Academic Press.     

Comparison of near-infrared and Raman spectroscopy for the determination of the density of polyethylene pellets

In this study, we compare near-infrared (NIR) and Raman spectroscopy for the determination of the density of linear low density polyethylene (PE) (in a pellet form). As generally known, Raman spectral features are more selective than those of NIR for most chemical samples. NIR spectroscopy has been more extensively used for the quantitative analysis of polymers, but Raman spectroscopy is the better choice as long as the problem of reproducibility of Raman measurements (especially for solid samples), mostly resulting from insufficient sample representation due to probing only localized chemical information and the sensitivity of sample placement with regard to the focal plane, can be overcome. To improve sample representation and reproducibility of Raman measurements, we have employed the wide area illumination (WAI) Raman scheme, capable of illuminating a laser onto a large sample area (28.3 mm²) for Raman spectral collection (a 6-mm laser spot with a focal length of 248 mm). Diffuse reflectance NIR spectra of PE pellets were collected using a sample moving system which allowed for the scanning of large areas. The prediction error was 0.0008 g cm⁻³ for Raman spectroscopy and 0.0011 g cm⁻³ for NIR spectroscopy. The harmonization of inherently selective Raman features and a reproducible spectral collection with correct sample representations using the WAI scheme led to an accurate determination of the density of the PE pellets.     

On the structure of the inverse kinematics map of a fragment of protein backbone

Loop closure in proteins requires computing the values of the inverse kinematics (IK) map for a backbone fragment with 2n > or = 6 torsional degrees of freedom (dofs). It occurs in a variety of contexts, e.g., structure determination from electron-density maps, loop insertion in homology-based structure prediction, backbone tweaking for protein energy minimization, and the study of protein mobility in folded states. The first part of this paper analyzes the global structure of the IK map for a fragment of protein backbone with 6 torsional dofs for a slightly idealized kinematic model, called the canonical model. This model, which assumes that every two consecutive torsional bonds C(alpha)--C and N--C(alpha) are exactly parallel, makes it possible to separately compute the inverse orientation map and the inverse position map. The singularities of both maps and their images, the critical sets, respectively, decompose SO(3) x R(3) into open regions where the number of IK solutions is constant. This decomposition leads to a constructive proof of the existence of a region in R(3) x SO(3) where the IK of the 6-dof fragment attains its theoretical maximum of 16 solutions. The second part of this paper extends this analysis to study fragments with more than 6 torsional dofs. It describes an efficient recursive algorithm to sample IK solutions for such fragments, by identifying the feasible range of each successive torsional dof. A numerical homotopy algorithm is then used to deform the IK solutions for a canonical fragment into solutions for a noncanonical fragment. Computational results for fragments ranging from 8 to 30 dofs are presented.     

Acid hydrolysis of carboxymethylcellulose of low degree of substitution

Cotton cellulose was swollen in a sodium hydroxide solution and carboxymethylated by a two-bath method for different periods of time for each process. The kinetics of acid hydrolysis and the crystallinity of the swollen and carboxymethylated samples were measured. The proportion of broken bonds, rate constants for hydrolysis, and permeability of cellulose to hydrolyzing agents were calculated. The susceptibility of glycosidic linkages to acid hydrolysis was improved by carboxymethylation more than by swelling in alkali. The increased accessibility of carboxymethylcellulose to acid was regarded as a consequence of increased intra-and intercrystalline swelling and of the glycosidic bonds' weakness caused by the electron-attracting carboxymethyl group on the C-6 position.