Descriptors for some compounds with pharmacological activity; calculation of properties.

Abraham model solute descriptors have been determined for nisoldipine, nizatidine, loratadine, zonisamide, oxaprozin, rebamipide, domperidone, temozolomide, 'florfenicol', florfenicol A, dapsone, chrysin, benorilate, ß-lapachone, and Ipriflavone based on published partition coefficients, molar solubilities and gas chromatographic retention indices. The calculated solute descriptors, combined with our previously published Abraham model correlations, are used to predict several important physicochemical and biological properties, such as air-water, air-blood, air-lung, air-fat, air-skin, water-lipid, water-membrane and water-skin partition coefficients, as well as permeation from water through skin.

Group Contribution and Machine Learning Approaches to Predict Abraham Solute Parameters, Solvation Free Energy, and Solvation Enthalpy.

We present a group contribution method (SoluteGC) and a machine learning model (SoluteML) to predict the Abraham solute parameters, as well as a machine learning model (DirectML) to predict solvation free energy and enthalpy at 298 K. The proposed group contribution method uses atom-centered functional groups with corrections for ring and polycyclic strain while the machine learning models adopt a directed message passing neural network. The solute parameters predicted from SoluteGC and SoluteML are used to calculate solvation energy and enthalpy via linear free energy relationships. Extensive data sets containing 8366 solute parameters, 20,253 solvation free energies, and 6322 solvation enthalpies are compiled in this work to train the models. The three models are each evaluated on the same test sets using both random and substructure-based solute splits for solvation energy and enthalpy predictions. The results show that the DirectML model is superior to the SoluteML and SoluteGC models for both predictions and can provide accuracy comparable to that of advanced quantum chemistry methods. Yet, even though the DirectML model performs better in general, all three models are useful for various purposes. Uncertain predicted values can be identified by comparing the three models, and when the 3 models are combined together, they can provide even more accurate predictions than any one of them individually. Finally, we present our compiled solute parameter, solvation energy, and solvation enthalpy databases (SoluteDB, dGsolvDBx, dHsolvDB) and provide public access to our final prediction models through a simple web-based tool, software packages, and source code.

Properties of the tert-butyl halide solvolysis transition states.

We have obtained properties (or descriptors) of the transition states in the solvolysis of tert-butyl chloride, bromide and iodide. We show that all three transition states, in both protic and in aprotic solvents, are highly dipolar and are strong hydrogen bond acids and strong hydrogen bond bases, except for the tert-butyl iodide transition state in aprotic solvents, which has a rather low hydrogen bond acidity. Thus, the transition states are stabilized by solvents that are hydrogen bond bases (nucleophiles) and are hydrogen bond acids (electrophiles). We show also that the partition of the transition states between water and solvents is aided by both nucleophilic and electrophilic solvents and conclude that the rate of solvolysis of the three halides is increased by both nucleophilic and electrophilic solvents.

Linear free energy relationship models for the retention of partially ionized acid-base compounds in reversed-phase liquid chromatography.

The LFER model of Abraham is applied to the retention of the neutral and ionic forms of 94 solutes in a C18 column and 40% v/v acetonitrile/water mobile phase. The results show that polarizability and cavity formation interactions increase retention, whereas dipole and hydrogen bonding interactions favours partition to the mobile phase and thus, they decrease retention. The coefficients of the ionic descriptors measure the effect of the electrostatic interactions and their contribution to partition of the cation or anion between the two mobile and stationary chromatographic phases. A new LFER model for application to the retention of partially dissociated acids and bases is derived averaging the descriptors of the neutral and ionic forms according to their degrees of ionization in the mobile phase. This new LFER model is satisfactorily compared to other literature modified Abraham models for a set of 498 retention data of partially dissociated acids and bases. All tested models require the calculation of the ionization degrees of the compounds at the measuring pH. Calculation of the ionization degrees in the chromatographic mobile phase (i.e. from pH and pKa in the eluent) give good correlations for all tested models. However, estimation of these ionization degrees from pH - pKa data in pure water gives biased estimations of the retention of the partially ionized solutes.

Comments on "Classification of biphasic solvent systems according to Abraham descriptors for countercurrent chromatography".

Abraham model correlations reported by Marlot and coworkers for the 1-octanol/water, 1-butanol/water, ethyl acetate/water, and heptane/methanol biphasic partitioning systems are compared to previously published Abraham model correlations. The previously published correlations for the fore-mentioned partitioning systems are based on more experimental data points, and exhibit much better descriptive ability as evidenced by much smaller standard deviations/standard errors and larger squared correlation coefficients.

Descriptors for terpene esters from chromatographic and partition measurements: Estimation of human odor detection thresholds.

We have used gas chromatographic retention data together with other data to obtain Abraham descriptors for 30 terpene esters. These include the air-water partition coefficient, as log Kw, for which no experimental values are available for any terpene ester. The other descriptors are the ester dipolarity, S, the hydrogen bond basicity, B, (the ester hydrogen bond acidity is zero for the esters studied), and L the logarithm of the air-hexadecane partition coefficient. Both S and B are larger than those for simple aliphatic esters, as expected from the terpene ester structures that include ring systems and ethylenic double bonds. These descriptors can then be used to obtain a large number of physicochemical and environmental properties of terpene esters. We have analyzed experimental results on human odor detection thresholds and have constructed another equation for the calculation of these thresholds, to go with a previous equation that we have reported. Then the descriptors for terpene esters can be used to estimate the important odor detection thresholds.

Characterization of hydrophilic interaction liquid chromatography retention by a linear free energy relationship. Comparison to reversed- and normal-phase retentions.

The Abraham solvation parameter model, a linear free energy relationship (LFER) approach, has been used to characterize a polymeric zwitterionic (sulfobetaine) column in HILIC mode. When acetonitrile (MeCN) is used in the preparation of mobile phases the main solute characteristics affecting the chromatographic behavior of analytes are the molecular size and the hydrogen-bonding (both acidity and basicity) interactions. The former property is more favorable in the acetonitrile-rich mobile phase, reducing thus the retention, but the latter reveals a higher affinity for the water layer adsorbed on the stationary phase, enhancing retention. However, if the aprotic acetonitrile is replaced by methanol, a hydrogen-bond acidic solvent, solute hydrogen-bond basicity does not contribute any more to retention, quite the opposite. Thus, a slightly different selectivity is observed in methanol/water than in acetonitrile/water. Normal-phase mode and HILIC-MeCN share the same main factors affecting retention. For reversed-phase and immobilized artificial membrane (IAM) chromatography, the solute molecular size increase retention because of the lower amount of energy required in the formation of a cavity in the solvated stationary phase. On the contrary, the analyte hydrogen-bond basicity favors interactions with the hydroorganic mobile phase and reduces retention. The determined parameters justify the reversed selectivity commonly observed in HILIC in reference to reversed-phase. In most instances, the least retained solutes in reversed-phase are the most retained in HILIC.

Solvation Descriptors for Zwitterionic α-Aminoacids; Estimation of Water-Solvent Partition Coefficients, Solubilities, and Hydrogen-Bond Acidity and Hydrogen-Bond Basicity.

The literature data on solubilities and water-solvent partition coefficients have been used to obtain properties or "Absolv descriptors" for zwitterionic α-aminoacids: glycine, α-alanine (α-aminopropanoic acid), α-aminobutanoic acid, norvaline (α-aminopentanoic acid), norleucine (α-aminohexanoic acid), valine (α-amino-3-methylbutanoic acid), leucine (α-amino-4-methylpentanoic acid), and α-phenylalanine. Together with equations that we have previously constructed, these descriptors can be used to estimate further solubilities and partition coefficients in a variety of organic solvents and in water-methanol and water-ethanol mixtures. It is shown that equations for neutral solutes are inadequate for the description of solubilities and partition coefficients for these α-aminoacids, and our equations developed for use with both neutral and ionic solutes must be used. The Absolv descriptors include those for hydrogen-bond acidity, A, and hydrogen-bond basicity, B. We find that both of these descriptors are far smaller in value than those for compounds that contain the corresponding ionic groups. Thus, A for α-alanine is 0.28, but A for the ethylammonium cation is 1.31; B for α-alanine is 0.83, and yet B for the acetate anion is no less than 2.93. The additional descriptors that we developed for equations that involve ions, J + and J -, are very significant for the α-aminoacids, although numerically smaller than for ionic species such as EtNH3 + and CH3CO2 -.

Linear free energy relationship analysis of permeability across polydimethylsiloxane (PDMS) membranes and comparison with human skin permeation in vitro.

The aim of the present work is to evaluate the similarity between PDMS membranes and human skin in vitro in permeation study by linear free energy relationship (LFER) analyses. The values of the permeability coefficient log Kp (cm/s) under reliable experimental conditions were collected from the literature for a set of 94 compounds including both neutral and ionic species, which cover a broad range of structural diversity. The values of log Kp (cm/s) have been correlated with Abraham descriptors to yield an equation with R2 = 0.952 and SD = 0.38 log units. The established LFER model for log Kp (cm/s) across PDMS membranes showed no close analogy with that through human skin in vitro. A further critical analysis of the coefficients of the LFER models confirmed that the PDMS permeation system is a very poor model for human skin permeation.

Partition of Neutral Molecules and Ions from Water to o-Nitrophenyl Octyl Ether and of Neutral Molecules from the Gas Phase to o-Nitrophenyl Octyl Ether.

We have set out an equation for partition of 87 neutral molecules from water to o-nitrophenyl octyl ether, NPOE, an equation for partition of the 87 neutral molecules and 21 ionic species from water to NPOE, and an equation for partition of 87 neutral molecules from the gas phase to NPOE. Comparison with equations for partition into other solvents shows that, as regards partition of neutral (nonelectrolyte) compounds, NPOE would be a good model for 1,2-dichloroethane and for nitrobenzene. In terms of partition of ions and ionic species, NPOE is quite similar to 1,2-dichloroethane and not far away from other aprotic solvents such as nitrobenzene.

Descriptors for Cyclooctasulfur: Estimation of Water-Solvent Partition Coefficients, Solubilities in Solvents, and Physicochemical Properties.

We have used literature data on the solubility of cyclooctasulfur in a number of solvents to drive Abraham descriptors for cyclooctasulfur. These can then be used in linear free-energy relationships that we have already constructed to predict partition coefficients and solubilities in a very large number of additional solvents. Cyclooctasulfur is very hydrophobic, has zero hydrogen bond acidity and zero hydrogen bond basicity, and dissolves best in nonpolar or only moderately polar solvents. We have also obtained enthalpies of solvation of cyclooctasulfur in solvents; again our linear free-energy relationships can be used to predict enthalpies of solvation in further solvents.

Structural properties governing drug-plasma protein binding determined by high-performance liquid chromatography method.

The high-performance liquid chromatography (HPLC) method employing stationary phases immobilized with plasma proteins was used for this study to investigate the structural properties governing drug-plasma protein binding. A set of 65 compounds with a broad range of structural diversity (in terms of volume, hydrogen-bonding, polarity and electrostatic force) were selected for this purpose. The Abraham linear free energy relationship (LFER) analyses of the retention factors on the immobilized HSA (human serum albumin) and AGP (α1-acid glycoprotein) stationary phases showed that McGowan's characteristic molecular volume (V), dipolarity/polarizability (S) and hydrogen bond basicity (B) are the three significant molecular descriptors of solutes determining the interaction with immobilized plasma proteins, whereas excess molar refraction (E) is less important and hydrogen bond acidity (A) is not of statistical significance in both systems, for electrically neutral compounds. It was shown that ionised acids, as carboxylate anions, bind very strongly to the immobilized HSA stationary phase and that ionised bases, as cations bind strongly to the AGP stationary phase. This is the first time that the effect of ionised species on plasma protein binding has been determined quantitatively; the increased binding of acids to HSA is due almost entirely to acids in their ionised form.

Descriptors for Pentane-2,4-dione and Its Derivatives.

We have used equations for partition coefficients of compounds from water and the gas phase to various solvents to obtain descriptors for pentane-2,4-dione and 21 of its derivatives. These descriptors can then be used to estimate further partition coefficients into a wide variety of solvents. The descriptors also yield information about the properties of pentane-2,4-dione and its derivatives. Pentane-2,4-dione and its alkyl derivatives are quite polar, with substantial hydrogen bond basicity but with no hydrogen bond acidity. In contrast 1,1,1-trifluoropentane-2,4-dione and hexafluoropentan-2,4-dione have significant hydrogen bond acidities.

Modeling Aquatic Toxicity through Chromatographic Systems.

Environmental risk assessment requires information about the toxicity of the growing number of chemical products coming from different origins that can contaminate water and become toxicants to aquatic species or other living beings via the trophic chain. Direct toxicity measurements using sensitive aquatic species can be carried out but they may become expensive and ethically questionable. Literature refers to the use of chromatographic measurements that correlate to the toxic effect of a compound over a specific aquatic species as an alternative to get toxicity information. In this work, we have studied the similarity in the response of the toxicity to different species and we have selected eight representative aquatic species (including tadpoles, fish, water fleas, protozoan, and bacteria) with known nonspecific toxicity to chemical substances. Next, we have selected four chromatographic systems offering good perspectives for surrogation of the eight selected aquatic systems, and thus prediction of toxicity from the chromatographic measurement. Then toxicity has been correlated to the chromatographic retention factor. Satisfactory correlation results have been obtained to emulate toxicity in five of the selected aquatic species through some of the chromatographic systems. Other aquatic species with similar characteristics to these five representative ones could also be emulated by using the same chromatographic systems. The final aim of this study is to model chemical products toxicity to aquatic species by means of chromatographic systems to reduce in vivo testing.

Revisiting blood-brain barrier: A chromatographic approach.

Drugs designed to reach a pharmacological CNS target must be effectively transported across the blood-brain barrier (BBB), a thin monolayer of endothelial cells tightly attached together between the blood and the brain parenchyma. Because of the lipidic nature of the BBB, several physicochemical partition models have been studied as surrogates for the passive permeation of potential drug candidates across the BBB (octanol-water, alkane-water, PAMPA...). In the last years, biopartition chromatography is gaining importance as a noncellular system for the estimation of biological properties in early stages of drug development. Microemulsions (ME) are suitable mobile phases, because of their ease of formulation, stability and adjustability to a large number of compositions mimicking biological structures. In the present work, several microemulsion liquid chromatographic (MELC) systems have been characterized by means of the Abraham's solvation parameter model, in order to assess their suitability as BBB distribution or permeability surrogates. In terms of similarity between BBB and MELC systems (dispersion forces arising from solute non-bonded electrons, dipolarity/polarizability, hydrogen-bond acidity and basicity, and molecular volume), the passive permeability surface area product (log PS) for neutral (including zwitterions), fully and partially ionized drugs was found to be well correlated with the ME made of 3.3% SDS (w/v; surfactant) 0.8% heptane (w/v; oil phase) and 6.6% 1-butanol (w/v; co-surfactant) in 50mM aqueous phosphate buffer, pH 7.4.

An equation for the prediction of human skin permeability of neutral molecules, ions and ionic species.

Experimental values of permeability coefficients, as log Kp, of chemical compounds across human skin were collected by carefully screening the literature, and adjusted to 37°C for the effect of temperature. The values of log Kp for partially ionized acids and bases were separated into those for their neutral and ionic species, forming a total data set of 247 compounds and species (including 35 ionic species). The obtained log Kp values have been regressed against Abraham solute descriptors to yield a correlation equation with R2=0.866 and SD=0.432 log units. The equation can provide valid predictions for log Kp of neutral molecules, ions and ionic species, with predictive R2=0.858 and predictive SD=0.445 log units calculated by the leave-one-out statistics. The predicted log Kp values for Na+ and Et4N+ are in good agreement with the observed values. We calculated the values of log Kp of ketoprofen as a function of the pH of the donor solution, and found that log Kp markedly varies only when ketoprofen is largely ionized. This explains why models that neglect ionization of permeants still yield reasonable statistical results. The effect of skin thickness on log Kp was investigated by inclusion of two indicator variables, one for intermediate thickness skin and one for full thickness skin, into the above equation. The newly obtained equations were found to be statistically very close to the above equation. Therefore, the thickness of human skin used makes little difference to the experimental values of log Kp.

Equations for water-triolein partition coefficients for neutral species; comparison with other water-solvent partitions, and environmental and toxicological processes.

Linear free energy relationships, LFERs, have been constructed for water-triolein partition coefficients for neutral species. It is shown that separate equations are required for wet and dry triolein. From a comparison of the equation coefficients for water-wet triolein with those for 52 other water-solvent systems it is shown that there is little correspondence between triolein and any of the 52 other solvents - only the water-isopropyl myristate system is close to the water-wet triolen system. A comparison of equation coefficients for the water-wet triolein system with LFER coefficients of 16 environmentally important processes shows that wet triolein is not a suitable model for any of the processes, although a number of other water-solvent systems are possible models for some of the environmental processes. A comparison of LFER coefficients with those of 17 aqueous toxicological processes reveals that most of the water-solvent systems, including water-wet triolein, will be poor models for any of the toxicological systems, but the water-lower alcohol systems show promise as models for a number of the toxicological systems. Our method of comparison of coefficients for LFERs that have exactly the same independent variables can be extended to various other types of system.

An assessment of air quality reflecting the chemosensory irritation impact of mixtures of volatile organic compounds.

We present a method to assess the air quality of an environment based on the chemosensory irritation impact of mixtures of volatile organic compounds (VOCs) present in such environment. We begin by approximating the sigmoid function that characterizes psychometric plots of probability of irritation detection (Q) versus VOC vapor concentration to a linear function. First, we apply an established equation that correlates and predicts human sensory irritation thresholds (SIT) (i.e., nasal and eye irritation) based on the transfer of the VOC from the gas phase to biophases, e.g., nasal mucus and tear film. Second, we expand the equation to include other biological data (e.g., odor detection thresholds) and to include further VOCs that act mainly by "specific" effects rather than by transfer (i.e., "physical") effects as defined in the article. Then we show that, for 72 VOCs in common, Q values based on our calculated SITs are consistent with the Threshold Limit Values (TLVs) listed for those same VOCs on the basis of sensory irritation by the American Conference of Governmental Industrial Hygienists (ACGIH). Third, we set two equations to calculate the probability (Qmix) that a given air sample containing a number of VOCs could elicit chemosensory irritation: one equation based on response addition (Qmix scale: 0.00 to 1.00) and the other based on dose addition (1000*Qmix scale: 0 to 2000). We further validate the applicability of our air quality assessment method by showing that both Qmix scales provide values consistent with the expected sensory irritation burden from VOC mixtures present in a wide variety of indoor and outdoor environments as reported on field studies in the literature. These scales take into account both the concentration of VOCs at a particular site and the propensity of the VOCs to evoke sensory irritation.

Descriptors for ions and ion-pairs for use in linear free energy relationships.

The determination of Abraham descriptors for single ions is reviewed, and equations are given for the partition of single ions from water to a number of solvents. These ions include permanent anions and cations and ionic species such as carboxylic acid anions, phenoxide anions and protonated base cations. Descriptors for a large number of ions and ionic species are listed, and equations for the prediction of Abraham descriptors for ionic species are given. The application of descriptors for ions and ionic species to physicochemical processes is given; these are to water-solvent partitions, HPLC retention data, immobilised artificial membranes, the Finkelstein reaction and diffusion in water. Applications to biological processes include brain permeation, microsomal degradation of drugs, skin permeation and human intestinal absorption. The review concludes with a section on the determination of descriptors for ion-pairs.

Dose-Response Functions for the Olfactory, Nasal Trigeminal, and Ocular Trigeminal Detectability of Airborne Chemicals by Humans.

We gathered from the literature 47 odor and 37 trigeminal (nasal and ocular) chemesthetic psychometric (i.e., detectability or dose-response) functions from a group of 41 chemicals. Vapors delivered were quantified by analytical methods. All functions were very well fitted by the sigmoid (logistic) equation: y = 1 / (1 + e({-(x-C)/D})), where parameter C quantifies the detection threshold concentration and parameter D the steepness of the function. Odor and chemesthetic functions showed no concentration overlap: olfactory functions grew along the parts per billion (ppb by volume) range or lower, whereas trigeminal functions grew along the part per million (ppm by volume) range. Although, on average, odor detectability rose from chance detection to perfect detection within 2 orders of magnitude in concentration, chemesthetic detectability did it within one. For 16 compounds having at least 1 odor and 1 chemesthetic function, the average gap between the 2 functions was 4.6 orders of magnitude in concentration. A quantitative structure-activity relationship (QSAR) using 5 chemical descriptors that had previously described stand-alone odor and chemesthetic threshold values, also holds promise to describe, and eventually predict, olfactory and chemesthetic detectability functions, albeit functions from additional compounds are needed to strengthen the QSAR.