A simple molecular model for N-SmAd-NdRe-N1Re-SmA1 phase sequence in highly polar compounds

Our earlier model of re-entrant liquid crystalline phases exhibited by highly polar compounds, in which the mutual orientation of near-neighbour molecules can change from an antiparallel to a parallel configuration, has been extended to include both nematic and smectic interactions. We show that, as the McMillan parameter alpha is decreased, the SmA_d-SmA₁ line goes over to the SmA_d-N_1Re line, finally becoming the N_dRe-N_1Re transition line, the latter ending in a critical point. This sequence is in agreement with the predictions of Prost's Landau model as well as with an experimental result. The phase sequence N-SmA_d-N_dRe-N_1Re-SmA₁ is obtained on cooling for a range of alpha_A values.     

A simple molecular model for N-SmAd-NdRe-N1Re-SmA1 phase sequence in highly polar compounds

Our earlier model of re-entrant liquid crystalline phases exhibited by highly polar compounds, in which the mutual orientation of near-neighbour molecules can change from an antiparallel to a parallel configuration, has been extended to include both nematic and smectic interactions. We show that, as the McMillan parameter alpha is decreased, the SmA_d-SmA₁ line goes over to the SmA_d-N_1Re line, finally becoming the N_dRe-N_1Re transition line, the latter ending in a critical point. This sequence is in agreement with the predictions of Prost's Landau model as well as with an experimental result. The phase sequence N-SmA_d-N_dRe-N_1Re-SmA₁ is obtained on cooling for a range of alpha_A values.     

Fruit tree model for uptake of organic compounds from soil

Apples and other fruits are frequently cultivated in gardens and are part of our daily diet. Uptake of pollutants into apples may therefore contribute to the human daily intake of toxic substances. In current risk assessment of polluted soils, regressions or models are in use, which were not intended to be used for tree fruits. A simple model for uptake of neutral organic contaminants into fruits is developed. It considers xylem and phloem transport to fruits through the stem. The mass balance is solved for the steady-state, and an example calculation is given. The Fruit Tree Model is compared to the empirical equation of Travis and Arms (T&A), and to results from fruits, collected in contaminated areas. For polar compounds, both T&A and the Fruit Tree Model predict bioconcentration factors fruit to soil (BCF, wet weight based) of > 1. No empirical data are available to support this prediction. For very lipophilic compounds (1ogK(ow) > 5), T&A overestimates the uptake. The conclusion from the Fruit Tree Model is that the transfer of lipophilic compounds into fruits is not relevant. This was also found by an empirical study with PCDD/F. According to the Fruit Tree Model, polar chemicals are transferred efficiently into fruits, but empirical data to verify these predictions are lacking.     

Fruit tree model for uptake of organic compounds from soil

Apples and other fruits are frequently cultivated in gardens and are part of our daily diet. Uptake of pollutants into apples may therefore contribute to the human daily intake of toxic substances. In current risk assessment of polluted soils, regressions or models are in use, which were not intended to be used for tree fruits. A simple model for uptake of neutral organic contaminants into fruits is developed. It considers xylem and phloem transport to fruits through the stem. The mass balance is solved for the steady-state, and an example calculation is given. The Fruit Tree Model is compared to the empirical equation of Travis and Arms (T&A), and to results from fruits, collected in contaminated areas. For polar compounds, both T&A and the Fruit Tree Model predict bioconcentration factors fruit to soil (BCF, wet weight based) of >1. No empirical data are available to support this prediction. For very lipophilic compounds (log K OW >5), T&A overestimates the uptake. The conclusion from the Fruit Tree Model is that the transfer of lipophilic compounds into fruits is not relevant. This was also found by an empirical study with PCDD/F. According to the Fruit Tree Model, polar chemicals are transferred efficiently into fruits, but empirical data to verify these predictions are lacking.     

A simple molecular theory of double reentrance exhibited by highly polar compounds

We show by simple model calculations that dipole-induced dipole and interchain interactions lead to a parallel alignment of molecules with strong longitudinal dipoles for intermolecular separations below a certain value. On the other hand an antiparallel alignment is favoured for larger separations because of dipole-dipole interactions. We incorporate this change in the intermolecular configuration, which naturally leads to two 'lengths' in the problem, in developing a simple McMillan type molecular theory of the double reentrance phenomenon in which the following phase sequence is observed on cooling the sample: isotropic-nematic-smectic A_d-reentrant nematic-smectic A₁. The calculated properties including the phase diagram are in broad agreement with experimental trends.     

Non-bonded organo-mineral interactions and sorption of organic compounds on soil surfaces: a model approach

Molecular mechanics and molecular dynamics calculations have been performed on organo-mineral composites that model the sorption of high-molecular-weight humic polymers on mineral surfaces and the sorption of low-molecular-weight organic contaminants on both mineral and organic surfaces in soil. Muscovite mica was chosen as a mineral model; an oxidized topological lignin-carbohydrate complex was chosen as a humic model; benzene, sodium benzoate, atrazine, and DDT represent different classes of contaminants. Sorption energies were estimated based on molecular mechanics calculations. Flexible linear polymers undergo drastic conformational changes when approaching the mineral surface, to ensure a gain in the interaction energy that outweighs a loss in the conformational energy proper. Therefore, the gas-phase conformation composi tion of environmental organic polymers is not directly related to their spatial organization in soil composites. Molecular dynamics simulation suggests high stability of the organic polymer coatings of mineral surfaces in the environment. Low-molecular-weight organic molecules demonstrate much less affinity for the mineral surface, which implies unhindered exchanges between the surface and its near environment. Ionizable compounds, e.g. salts of organic acids, are different, because they can form strong associations with a mineral surface through cation bridges. Sorption energies are compound-specific and depend on the sorbate-sorbent orientation. The calculations suggest some preference for the edges of a model muscovite sheet in comparison with the basal oxygen surface as a sorption site. Coating of mineral surfaces with organic polymers does not hinder the sorption of organic molecules except in the special case of organic ions.     

Chromatographic models for the sorption of neutral organic compounds by soil from water and air.

The solvation parameter model is used to construct models for the estimation of the soil-water and soil-air distribution constants and to characterize the contribution of fundamental intermolecular interactions to the underlying sorption processes. Wet soil is shown to be quite cohesive and polar but relatively non-selective for dipole-type, lone-pair electron and hydrogen-bond interactions. Using a comparison of system constant ratios chromatographic systems employing reversed-phase liquid chromatography on polar bonded phases are shown to provide suitable models for estimating soil-water distribution constants. No suitable gas chromatographic models were found for the soil-air distribution constant but the requirements for such a system are indicated. Models are also provided for adsorption at the air-water interface. Estimation methods based on either the solvation parameter model or chromatographic model reproduce experimental distribution constants for a wide variety of compounds with a similar error (0.2-0.3 log units) to that expected in the experimental data.     

Fruit Tree model for uptake of organic compounds from soil and air

The current European risk assessment for chemicals considers only tap water, while in reality other beverages play an important role. A good part of beverages are made from fruits, for example apple juice and vine. A mathematical model was developed to predict uptake of neutral organic chemicals from soil and air into fruits. The new fruit tree model considers eight compartments, i.e. two soil compartments, fine roots, thick roots, stem, leaves, fruits, and air. Chemical equilibrium, advective transport in xylem and phloem, diffusive exchange to soil and air and growth dilution are the main processes. The parameterization is for a square-meter of an apple orchard. The model predicts that polar, non-volatile compounds will effectively be transported from soil to fruits, while lipophilic compounds will preferably accumulate from air into fruits. Results from various experiments show no disagreement with the model predictions.     

Transient molecular dynamics simulations of liquid viscosity for nonpolar and polar fluids

A transient molecular dynamics (TMD) method for obtaining fluid viscosity is extended to multisite, force-field models of both nonpolar and polar liquids. The method overlays a sinusoidal velocity profile over the peculiar particle velocities and then records the transient decay of the velocity profile. The viscosity is obtained by regression of the solution of the momentum equation with an appropriate constitutive equation and initial and boundary conditions corresponding to those used in the simulation. The transient velocity decays observed appeared to include both relaxation and retardation effects. The Jeffreys viscoelastic model was found to model accurately the transient responses obtained for multisite models for n-butane, isobutane, n-hexane, water, methanol, and 1-hexanol. TMD viscosities obtained for saturated liquids over a wide range of densities agreed well for the polar fluids, both with nonequilibrium molecular dynamics (NEMD) results using the same force-field models and with correlations based on experimental data. Viscosities obtained for the nonpolar fluids agreed well with the experimental and NEMD results at low to moderate densities, but underpredicted experimental values at higher densities where shear-thinning effects and viscous heating may impact the TMD simulations.     

一个新的拓扑指数用于有机化合物的QSPR/QSAR研究

在分子图的邻接矩阵和距离矩阵的基础上提出了一个新的拓扑指数Xu,该拓扑指数易于计算,对C~2-C~1~6饱和烷烃有较高的结构区分能力,通过适当的处理可方便地推广到含多重键杂原子体系。该指数与饱和烷烃的正常沸点等理化性质,不饱和链烃类化合物的热容以及某些脂肪醇的毒性和疏水性参数均具有较好的性质相关性。绝大多数理化性质与Xu指数均能建立简单线性模型,且相关系数均大于0.99,表明该指数有望在QSPR/QSAR研究中作为一个新的参数而获得推广应用。     

QSPR modelling of the soil sorption coefficient from training sets of different sizes

Quantitative structure–property relationship (QSPR) modelling has been used in many scientific fields. This approach has been extensively applied in environmental research to predict physicochemical properties of compounds with potential environmental impact. The soil sorption coefficient is an important parameter for the evaluation of environmental risks, and it helps to determine the final fate of substances in the environment. In the last few years, different QSPR models have been developed for the determination of the sorption coefficient. In this study, several QSPR models were generated and evaluated for the prediction of log K_oc from the relationship with log P. These models were obtained from an extensive and diverse training set (n = 639) and from subsets of this initial set (i.e. halves, fourths and eighths). The aim of this study was to investigate whether the size of the training set affects the statistical quality of the obtained models. Furthermore, statistical equivalence was verified between the models obtained from smaller sets and the model obtained from the total training set. The results confirmed the equivalence between the models, thus indicating the possibility of using smaller training sets without compromising the statistical quality and predictive capability, as long as most chemical classes in the test set are represented in the training set.