Neural network studies : Part 3. Prediction of partition coefficients

In a previous paper (N. Bodor, A. Harget and M.-J. Huang, J. Am. Chem. Soc., 113 (1991) 9480) we demonstrated the utility of a neural network approach in the estimation of the aqueous solubility of organic compounds. This approach has now been extended to the prediction of partition coefficients. A training set of AM1 calculated properties and experimental values for 302 compounds was used and, after training, the neural network was tested for its ability to predict the partition coefficients of 21 compounds not included in the training set. We also tested six more compounds with molecular properties out of the training set property range. A comparison was made with the results obtained from a previous study which had used a regression analysis approach (N. Bodor and M.-J. Huang, J. Pharm. Sci., 81 (1992) 272). The neural network results compared favorably with those given by the regression analysis approach, both for the training set and for the new compounds.     

Determination of liquid-liquid partition coefficients by separation methods

By essence, all kinds of chromatographic methods use the partitioning of solutes between a stationary and a mobile phase to separate them. Not surprisingly, separation methods are useful to determine accurately the liquid-liquid distribution constants, commonly called partition coefficient. After briefly recalling the thermodynamics of the partitioning of solutes between two liquid phases, the review lists the different methods of measurement in which chromatography is involved. The shake-flask method is described. The ease of the HPLC method is pointed out with its drawback: the correlation is very sensitive to congeneric effect. Microemulsion electrokinetic capillary electrophoresis has become a fast and reliable method commonly used in industry. Counter-current chromatography (CCC) is a liquid chromatography method that uses a liquid stationary phase. Since the CCC solute retention volumes are only depending on their partition coefficients, it is the method of choice for partition coefficient determination with any liquid system. It is shown that Ko/w, the octanol-water partition coefficients, are obtained by CCC within the -1 < log Ko/w < 4 range, without any correlation or standardization using octanol as the stationary phase. Examples of applications of the knowledge of liquid-liquid partition coefficient in the vast world of solvent extraction and hydrophobicity estimation are presented.     

Analytical methods vs. numerical results for reacting layered systems

We consider here reactions in layered systems. We model a situation in which the mixing of the reactants precedes the chemical reaction and show that the overall decay kinetics is determined by the initial striation thickness distribution. Thus the kinetics is controlled by the diffusive motion of the spatial inhomogeneities (clusters). Different numerical approaches to the problem are discussed and the results of the numerical modeling are compared with the analytical considerations.     

Prediction of partition coefficients by multiscale hybrid atomic-level/coarse-grain simulations

Coarse-grain models are becoming an increasingly important tool in computer simulations of a wide variety of molecular processes. In many instances it is, however, desirable to describe key portions of a molecular system at the atomic level. There is therefore a strong interest in the development of simulation methodologies that allow representations of matter with mixed granularities in a multiscale fashion. We report here a strategy to conduct mixed atomic-level and coarse-grain simulations of molecular systems with a recently developed coarse-grain model. The methodology is validated by computing partition coefficients of small molecules described in atomic detail and solvated by water or octane, both of which are represented by coarse-grain models. Because the present coarse-grain force field retains electrostatic interactions, the simplified solvent particles can interact realistically with the all-atom solutes. The partition coefficients computed by this approach rival the accuracy of fully atomistic simulations and are obtained at a fraction of their computational cost. The present methodology is simple, robust and applicable to a wide variety of molecular systems.     

Sorbent-based sampling methods for volatile and semi-volatile organic compounds in air. Part 2. Sorbent selection and other aspects of optimizing air monitoring methods

Sorbent tubes/traps are widely used in combination with gas chromatographic (GC) analytical methods to monitor the vapour-phase fraction of organic compounds in air. Applications range from atmospheric research and ambient air monitoring (indoor and outdoor) to occupational hygiene (personal exposure assessment) and measuring chemical emission levels. Part 1 of this paper reviewed the main sorbent-based air sampling strategies including active (pumped) tube monitoring, diffusive (passive) sampling onto sorbent tubes/cartridges plus sorbent trapping/focusing of whole air samples that are either collected in containers (such as canisters or bags) or monitored online. Options for subsequent extraction and transfer to GC(MS) analysis were also summarised and the trend to thermal desorption (TD)-based methods and away from solvent extraction was explained. As a result of this trend, demand for TD-compatible sorbents (alternatives to traditional charcoal) is growing. Part 2 of this paper therefore continues with a summary of TD-compatible sorbents, their respective advantages and limitations and considerations for sorbent selection. Other analytical considerations for optimizing sorbent-based air monitoring methods are also discussed together with recent technical developments and sampling accessories which have extended the application range of sorbent trapping technology generally.     

Hybrid silicas/waterborne polyurethane composite properties: In situ formation vs. grafting methods

Journal of Sol-Gel Science and Technology - A series of composites of commercial waterborne polyurethane and hybrid silica were prepared by the sol–gel process through in situ synthesis....     

Photooxidation of n-octanal in air: experimental and theoretical study

Dilute mixtures of n-octanal in synthetic air (up to 100 ppm) were photolyzed with fluorescent UV lamps (275-380 nm) at 298 K. The main photooxidation products were 1-hexene, CO, vinyl alcohol, and acetaldehyde. The photolysis rates and the absolute quantum yields were found to be slightly dependent on the total pressure. At 100 Torr, Φ(100) = 0.41 ± 0.06, whereas at 700 Torr the total quantum yield was Φ(700) = 0.32 ± 0.02. Two decomposition channels were identified: the radical channel C(7)H(15)CHO → C(7)H(15) + HCO and the molecular channel C(7)H(15)CHO → C(6)H(12) + CH(2)═CHOH, having absolute quantum yields of 0.022 and 0.108 at 700 Torr. The product CH(2)═CHOH tautomerizes to acetaldehyde. Carbon balance data lower than unities suggest the existence of unidentified decomposition channel(s) which substantially contributes to the photolysis. On the basis of experimental and theoretical evidence, n-octanal photolysis predominantly proceeds to form Norrish type II products as the major ones.     

Empirical methods for computing molecular partition coefficients: II. Inclusion of conformational flexibility within fragment–based approaches

A novel algorithm for computing the water/1-octanol partition coefficient, log P , of conformationally flexible molecules, has been investigated using calculations upon a number of uncharged, linear dipeptides. In this method (which appears to be the first to consider explicitly the effects of the population of accessible conformational minima in both phases), the partition coefficient for each dipeptide was calculated from the overall energy change associated with moving the relevant gas-phase conformational distribution into water and into 1-octanol. These energies were computed using solvation contributions based upon the solvent accessible molecular surface area and two sets of empirical parameters. In these initial studies, gas-phase conformational minima were generated using systematic search methods. While the standard error in the computed log P values was disappointing, reasonable agreement was observed between calculated and experimental log P values for the set of model dipeptides, especially when specific hydration interactions involving polar fragments were correctly included in the empirical solvation term. These results indicate that the physical basis of many correction factors employed in the ClogP algorithm for computing log P probably arise from neglect of the redistribution of conformer populations as flexible molecules partition between water and 1-octanol.     

Prediction of partition and distribution coefficients in various solvent pairs with COSMO-RS

Performance of COSMO-RS method as a tool for partition and distribution modeling in 20 solvent pairs—composed of neutral or acidic aqueous solution and organic solvents of different polarity, ranging from alcohols to toluene and hexane—was evaluated. Experimental partition/distribution data of lignin-related and drug-like compounds (neutral, acidic, moderately basic) were used as reference. Several aspects of partition modeling were addressed: accounting for mutual saturation of aqueous and organic phases, variability of systematic prediction errors across solvent pairs, taking solute ionization into account. COSMO-RS was found to predict extraction outcome for both ligneous and drug-like compounds in various solvent pairs fairly well without any additional empirical input. The solvent-specific systematic errors were found to be moderate, despite being statistically significant, and related to the solvent hydrophobicity. Accounting for mutual solubilities of the two liquids was proven crucial in cases where water was considerably soluble in the organic solvent. The root mean square error of a priori logP prediction varied, depending mainly on the solvent pair, from 0.2 to 0.7, overall value being 0.6 log units. The accuracy was higher in case of hydrophilic than hydrophobic solvents. The logD predictions were less accurate, due to pK_a prediction being an additional source of error, and also because of the complexity of modeling the behaviour of ionic species in the two-phase system. A simple correction for partitioning of free ions was found to notably improve logD prediction accuracy in case of the most hydrophilic organic phase (butanol/water).     

Prediction of soil organic carbon partition coefficients by soil column liquid chromatography

To avoid the limitation of the widely used prediction methods of soil organic carbon partition coefficients (KOC) from hydrophobic parameters, e.g., the n-octanol/water partition coefficients (KOW) and the reversed phase high performance liquid chromatographic (RP-HPLC) retention factors, the soil column liquid chromatographic (SCLC) method was developed for KOC prediction. The real soils were used as the packing materials of RP-HPLC columns, and the correlations between the retention factors of organic compounds on soil columns (ksoil) and KOC measured by batch equilibrium method were studied. Good correlations were achieved between ksoil and KOC for three types of soils with different properties. All the square of the correlation coefficients (R2) of the linear regression between log ksoil and log KOC were higher than 0.89 with standard deviations of less than 0.21. In addition, the prediction of KOC from KOW and the RP-HPLC retention factors on cyanopropyl (CN) stationary phase (kCN) was comparatively evaluated for the three types of soils. The results show that the prediction of KOC from kCN and KOW is only applicable to some specific types of soils. The results obtained in the present study proved that the SCLC method is appropriate for the KOC prediction for different types of soils, however the applicability of using hydrophobic parameters to predict KOC largely depends on the properties of soil concerned.     

Determination of partition behavior of organic surrogates between paperboard packaging materials and air

The suitability of recycled paperboard packaging materials for direct food contact applications is a major area of investigation. Chemical contaminants (surrogates) partitioning between recycled paper packaging and foods may affect the safety and health of the consumer. The partition behavior of all possible organic compounds between cardboards and individual foodstuffs is difficult and too time consuming for being fully investigated. Therefore it may be more efficient to determine these partition coefficients indirectly through experimental determination of the partitioning behavior between cardboard samples and air. In this work, the behavior of organic pollutants present in a set of two paper and board samples intended to be in contact with foods was studied. Adsorption isotherms have been plotted and partition coefficients between paper and air have been calculated as a basis for the estimation of their migration potential into food. Values of partition coefficients (Kpaper/air) from 47 to 1207 were obtained at different temperatures. For the less volatile surrogates such as dibutyl phthalate and methyl stearate higher Kpaper/air values were obtained. The adsorption curves showed that the more volatile substances are partitioning mainly in air phase and increasing the temperature from 70 to 100 degrees C their concentrations in air (Cair) have almost doubled. The analysis of surrogates was performed with a method based on solvent extraction and gas chromatographic-flame ionization detection (GC-FID) quantification.     

Determination of volatile organic compounds in ambient air. Comparison of methods

Two analytical methods for the determination of benzene vapour in ambient air are compared in this paper. The methods differ from each other in the sampling technique, type of sorbent, method of extraction and method of detection. The investigation of the methods using various techniques for sample analysing showed a significant influence of the way in which the analysis is carried out, on the final result of the analysis. Calculation of the standard deviations, relative standard deviations and confidence intervals allowed for assessment of the precision and repeatability of the methods. Of the two examined methods, that using an automated system of contaminant sampling and thermodesorption was more precise. This method has been applied to measurements of concentrations of benzene, toluene and xylenes in ambient air.     

Automated QSPR modeling and data curation of physicochemical properties using KNIME platform: Prediction of partition coefficients

In the last two decades, the volumes of chemical and biological data are constantly increasing. The problem of converting data sets into knowledge is both expensive and time-consuming, as a result a workflow technology with platforms such as KNIME, was built up to facilitate searching through multiple heterogeneous data sources and filtering for specific criteria then extracting hidden information from these large data. Before any QSAR modeling, a manual data curation is extremely recommended. However, this can be done, for small datasets, but for the extensive data accumulated recently in public databases a manual process of big data will be hardly feasible. In this work, we suggest using KNIME as an automated solution for workflow in data curation, development, and validation of predictive QSAR models from a huge dataset.In this study, we used 250250 structures from NCI database, only 3520 compounds could successfully pass through our workflow safely with their corresponding experimental log P, this property was investigated as a case study, to improve some existing log P calculation algorithms.     

The air/water partitioning of radioiodine: An experimental assessment

An understanding of radioiodine volatility is important in relation to nuclear reactor safety. In this paper, findings of an ongoing experimental assessment of radioiodine partitioning are described. Radiochemical methods of determining liquid and gas phase speciation are presented along with experimental results demonstrating the validity of these methods. These results also indicate that the majority of the gaseous organic iodides detected at TMI-2 following the accident were in a low molecular weight form such as methyl iodide. It is concluded that, for 10^–4 M CsI solutions, the partition coefficient increases by an order of magnitude with increasing pH and, the aqueous and gaseous concentrations of both molecular iodine and organic iodide decrease with increasing pH over the pH range of 4 to 12.Presently employed at Ontario Hydro, Toronto, M5G 1X5.