ClogPalk: a method for predicting alkane/water partition coefficient

Alkane/water partition coefficients (P_alk) are less familiar to the molecular design community than their 1-octanol/water equivalents and access to both data and prediction tools is much more limited. A method for predicting alkane/water partition coefficient from molecular structure is introduced. The basis for the ClogP_alk model is the strong (R² = 0.987) relationship between alkane/water partition coefficient and molecular surface area (MSA) that was observed for saturated hydrocarbons. The model treats a molecule as a perturbation of a saturated hydrocarbon molecule with the same MSA and uses increments defined for functional groups to quantify the extent to which logP_alk is perturbed by the introduction each functional group. Interactions between functional groups, such as intramolecular hydrogen bonds are also parameterized within a perturbation framework. The functional groups and interactions between them are specified substructurally in a transparent and reproducible manner using SMARTS notation. The ClogP_alk model was parameterized using data measured for structurally prototypical compounds that dominate the literature on alkane/water partition coefficients and then validated using an external test set of 100 alkane/water logP measurements, the majority of which were for drugs.     

The Octanol/Water Partition Coefficients of Aminimides

Summary. The n-octanol/water partition coefficients of aminimides were measured. The correlation between lgP _ow and the hydration energy obtained as a result of quantum-chemical modelling of a solution is presented.Received March 25, 2003; accepted (revised) May 5, 2003 Published online September 15, 2003     

Octanol/water partitioning simulation by RP‐HPLC for structurally diverse acidic drugs: Comparison of three columns in the presence and absence of n‐octanol as the mobile phase additive

The advantageous effect of n‐octanol as a mobile phase additive for lipophilicity assessment of structurally diverse acidic drugs both in the neutral and ionized form was explored. Two RP C₁₈ columns, ABZ⁺ and Aquasil, were used for the determination of logk_w indices, and the results were compared with those previously reported on a base‐deactivated silica column. At pH 2.5, the use of n‐octanol‐saturated buffer as the mobile phase aqueous component led to high‐quality 1:1 correlation between logk_w and logP for the ABZ⁺ column, while inferior statistics were obtained for Aquasil. At physiological pH, the correlations were significantly improved if strongly ionized acidic drugs were treated separately from weakly ionized ones. In the latter case, 1:1 correlations between logD_7.4 and logk_w^oct indices were obtained in the presence of 0.25% n‐octanol. Concerning strongly ionized compounds, adequate correlations were established under the same conditions; however, slopes were significantly lower than unity, while large negative intercepts were obtained. According to the absolute difference (diff = logD_7.4–logk_w) pattern, base‐deactivated silica showed a better performance than ABZ⁺, however, the latter seems more efficient for the lipophilicity assessment of highly lipophilic acidic compounds. Aquasil may be the column of choice if logD_7.4<3 with the limitation, however, that very hydrophilic compounds cannot be measured.     

Characterization of Ascentis RP-Amide column: Lipophilicity measurement and linear solvation energy relationships

This study investigates lipophilicity determination by chromatographic measurements using the polar embedded Ascentis RP-Amide stationary phase. As a new generation of amide-functionalized silica stationary phase, the Ascentis RP-Amide column is evaluated as a possible substitution to the n  -octanol/water partitioning system for lipophilicity measurements. For this evaluation, extrapolated retention factors, log k^′_w$\text{log}{k^{\prime }}_w$, of a set of diverse compounds were determined using different methanol contents in the mobile phase. The use of n-octanol enriched mobile phase enhances the relationship between the slope (S  ) of the extrapolation lines and the extrapolated log k^′_w$\text{log}{k^{\prime }}_w$ (the intercept of the extrapolation), as well as the correlation between log P   values and the extrapolated log k^′_w$\text{log}{k^{\prime }}_w$ (1:1 correlation, r² = 0.966). In addition, the use of isocratic retention factors, at 40% methanol in the mobile phase, provides a rapid tool for lipophilicity determination. The intermolecular interactions that contribute to the retention process in the Ascentis RP-Amide phase are characterized using the solvation parameter model of Abraham. The LSER system constants for the column are very similar to the LSER constants of the n-octanol/water extraction system. Tanaka radar plots are used for quick visual comparison of the system constants of the Ascentis RP-Amide column and the n-octanol/water extraction system. The results all indicate that the Ascentis RP-Amide stationary phase can provide reliable lipophilic data.     

Optimal characterization of structure for prediction of properties

Different topological and physicochemical parameters have been used to predict hydrophobicity (logP, octanol-water) of chemicals. We calculated a hydrogen bonding parameter (HB₁) and a large number of molecular connectivity and complexity indices for a diverse set of 382 molecules. It is known from earlier studies that topological indices (TIs) predict properties of congeneric sets reasonably well. Since HB₁ is an approximate quantifier of hydrogen bonding and has integral values, we used HB₁ to classify the diverse set into strongly and weakly hydrogen bonding subsets. In an attempt to examine the utility of Us in predicting properties of relatively similar groups of molecules, we carried out a correlation of logP with TIs for a subset (n = 139) of the original diverse set (n = 382) with a weak hydrogen bonding ability (HB₁ = 0). Results show that TIs give a better predictive model for the more homogeneous subset as compared to the diverse set of molecules.     

Identification of chemicals and their metabolites from PHY906, a Chinese medicine formulation,in the plasma of a patient treated with irinotecan and PHY906 using liquid chromatography/tandem mass spectrometry (LC/MS/MS)

Traditional Chinese Medicine (TCM) is increasingly being used in combination with Western medicine. In general, TCM is comprised of multiple components in sharp contrast to Western medicine, where a single active chemical is used. Presently, there are no well-established standards for most of the chemical compounds of TCM and their respective metabolites. Moreover, there are no formal analytical methods for the identification of these chemicals, especially in trace amounts. The ability to measure the pharmacokinetic behaviors of chemicals and their metabolites from these herbal formulations are critical in understanding of the action of TCM. This paper describes the use of LC/MS/MS along with enzyme treatments and n-octanol/water partition coefficient, to investigate the chemical components of PHY906 and their metabolites in the plasma of a patient with metastatic colorectal cancer (mCRC) treated with irinotecan and PHY906. The chemicals from an aqueous extract of PHY906 and the plasma from a patient was prepared and separated on an Agilent ZORBAX-SB C₁₈ column, and eluted with acetonitrile/0.05% (v/v) formic acid. From the PHY906 aqueous extract, a total of 57 compounds and 27 metabolites were identified and tentatively assigned structures based on their identified mass spectrometry, enzyme digestion and n-octanol/water partition coefficient. In contrast, analysis of patient plasma identified only 33 chemicals and new metabolites. These findings demonstrated that LC/MS/MS was and effective and reliable method for studying the parent chemicals of the Chinese herbal medicine PHY906 and their metabolites in a patient with metastatic colorectal cancer.     

An electrochemical method for determination of the standard Gibbs energy of anion transfer between water and n-octanol

The transfer of the ions Cl⁻, Br⁻, I⁻, ClO₄⁻, SCN⁻, NO₃⁻, BF₄⁻, and (C₆H₅)₄B⁻ across the water|n-octanol (W|OC) liquid interface was studied and the standard Gibbs energies of ion transfer were determined. The ion transfer was achieved by oxidation of decamethylferrocene dissolved in a droplet of n-octanol that was attached to a graphite electrode immersed in the aqueous solutions of the respective alkali salts of the anions. The electrode reaction can be described by the equation: dmfc_(OC)+X_(W)⁻⇄dmfc⁺_(OC)+X⁻_(OC)+e⁻, where X⁻ is the transferred anion. Square-wave voltammetry at this three-phase arrangement was utilised to determine the formal potential of the decamethylferrocene/decamethylferrocenium (dmfc/dmfc⁺) couple under the condition of ion transfer across the water|n-octanol interface. For calibration the standard Gibbs energies of ion transfer have been extrapolated to octanol from the series of known data for methanol, ethanol, n-propanol, and n-butanol. All these data are consistent and the experimental dependence of the formal potentials on the standard Gibbs energies is as predicted by theory. The validity of data is further supported by calculations of Gibbs energies of ion transfer using the Born theory. Until now it was not possible to perform electrochemical measurements at the water|n-octanol interface because in the conventional four-electrode cells this interface cannot be polarised. With the new method it is now for the first time possible to determine the Gibbs energies of transfer of ions across the water|n-octanol interface. These values are of very wide use for assessing the lipophilicity of compounds in chemistry, medicine, and pharmacology.     

Comparison of Reliability of log P Values Calculated from a Group Contribution Approach and from the Autocorrelation Method

Abstract

The values of log P (n-octanol/water partition coefficient) for 1449 chemicals were calculated from the fragmental/regression model of Klopman and co-workers (J. Chem. Inf. Comput. Sci. 1994, 34, 752-781) and from the autocorrelation/backpropagation neural network model implemented in AUTOLOGP_TM (Version 4.0). Both models provided good simulation results but the superiority of the latter was demonstrated.     

水在C12-EOx-C12•2Br/正己醇/正庚烷W/O微乳中的状态

以FT-IR方法研究了水/C₁₂-EO_x-C₁₂•2Br/正己醇/正庚烷形成的W/O微乳中水的状态. 结果表明, 其中的水存在4种状态, 分别为阳离子头基结合水、反离子结合水、类似本体的水以及束缚在微乳栅栏层中的水. 由解卷积技术分解FT-IR谱图, 进而获得每个表面活性剂分子对应于这4种状态水分子的数目n_N＋, n_Br-, n_b和n_f. 随着水含量(W₀)增加, n_b急剧增大, n_N＋少许上升, 而n_f和n_Br-维持不变, 这说明微乳水核逐渐长大, 且在所考察W₀范围内, 表面活性剂头基解离度保持不变.     

Green synthesis of imidazo[1,2-a]pyridines using calix[6]arene-SO3H surfactant in water

In this research, green synthesis of imidazo[1,2-a]pyridines in the presence of calix[n]arenes-SO₃H as a Brønsted acid catalyst and surfactant is described. Using of calix[n]arenes in water provided a hydrophobic cavity that successfully carried out the synthesis reactions at short times with high yields. This catalyst system is recoverable with a simple extraction using an organic solvent and reusable for at least for 5 cycles without any losses of its activity.     

Synthesis of amphiphilic sulfonamide halogenated porphyrins: MALDI-TOFMS characterization and evaluation of 1-octanol/water partition coefficients

Porphyrins are key precursors for development of photosensitizers for photodynamic therapy. A new series of ortho-halogenated tetraarylporphyrins with sulfonamide substituents have been synthesized via chlorosulfonation reaction and characterized by MALDI-TOFMS. To predict their partition properties, log K_OW of a selected range of the synthesized halogenated amphiphilic porphyrins is described. A significant effect of the number and type of halogen group as well as on the number of sulfonamide side chain was observed. The determined 1-octanol/water partition coefficients showed that it is possible to obtain compounds with a wide range of lipophilicities, from log K_OW=−2.71 till log K_OW>4, which are suitable to optimize the biological efficacy of this class of sensitizers.     

SAMPL7 blind challenge: quantum–mechanical prediction of partition coefficients and acid dissociation constants for small drug-like molecules

The physicochemical properties of a drug molecule determine the therapeutic effectiveness of the drug. Thus, the development of fast and accurate theoretical approaches for the prediction of such properties is inevitable. The participation to the SAMPL7 challenge is based on the estimation of logP coefficients and pK_a values of small drug-like sulfonamide derivatives. Thereby, quantum mechanical calculations were carried out in order to calculate the free energy of solvation and the transfer energy of 22 drug-like compounds in different environments (water and n-octanol) by employing the SMD solvation model. For logP calculations, we studied eleven different methodologies to calculate the transfer free energies, the lowest RMSE value was obtained for the M06L/def2-TZVP//M06L/def2-SVP level of theory. On the other hand, we employed an isodesmic reaction scheme within the macro pK_a framework; this was based on selecting reference molecules similar to the SAMPL7 challenge molecules. Consequently, highly well correlated pK_a values were obtained with the M062X/6–311+G(2df,2p)//M052X/6–31+G(d,p) level of theory.

     

Thermodynamic aspects of solubility,solvation and partitioning processes of some sulfonamides

The thermodynamic aspects of sublimation processes of three sulfonamides with the general structures C₆H₅–SO₂NH–C₆H₄–R (R = 4-NO₂) and 4-NH₂–C₆H₄–SO₂NH–C₆H₄–R (R = 4-NO₂; 4-CN) were studied by investigating the temperature dependence of vapor pressure using the transpiration method. These data together with those obtained earlier for C₆H₅–SO₂NH–C₆H₄–R (R = 4-Cl) and 4-NH₂–C₆H₄–SO₂NH–C₆H₄–R (R = 4-Cl; 4-OMe; 4-C₂H₅) were analyzed and compared. A correlation was derived between sublimation Gibbs free energies and the sum of H-bond acceptor factors of the molecules. Solubility processes of the compounds in water, phosphate buffer with pH 7.4 and n-octanol (as phases modeling various drug delivery pathways) were investigated and corresponding thermodynamic functions were calculated as well. Thermodynamic characteristics of the sulfonamides solvation were evaluated. Also in this case a correlation between solubility/solvation Gibbs free energy values and the sum of H-bond acceptor factors was observed. For the sulfonamides with various substituents at para-position the processes of transfer from one solvent (water or buffer) to n-octanol were studied by a diagram method combined with analysis of enthalpic and entropic terms. Distinguishing between enthalpy and entropy, as is possible through the present approach, leads to the insight that the contribution of these terms is different for different molecules (entropy- or enthalpy-determined). Thus, in contrast to the interpretation of only the Gibbs free energy of transfer (extensively used for pharmaceuticals in the form of the partition coefficient, log P), the analysis of thermodynamic functions of the transfer process provides additional mechanistic information. This may be important for further evaluation of the physiological distribution of drug molecules and may provide a better understanding of biopharmaceutical properties of drugs.     

Investigation of the chromatographic behaviour of some selenium species—Comparison with their octanol-water partitioning

The retention behaviour of selenites (Se(IV)), selenates (Se(VI)), seleno-dl-methionine (Se-Met), selenocystine (Se-Cyst), selenocystamine (Se-CM) and selenourea (Se-U) was investigated using a Discovery end-capped reversed-phase column as stationary phase and different mobile phase conditions. Extrapolated to 100% aqueous mobile phase retention factors (log k_w) of the investigated Se species, determined using different methanol fractions (φ) as organic modifier, were compared with the corresponding actual values. The proper operation of this column even at 100% aqueous phase proved to be valuable for the accurate determination of log k_w values of Se-CM and Se-Cyst, presenting a convex curvature log k = f(φ) at low MeOH fractions, often neglected in the extrapolation procedure. The effect of the presence of n-decylamine as well as saturation of the mobile phase with n-octanol was also studied. For ampholytic Se-Met and Se-Cyst the effect of n-decylamine in retention reflected the predominance of zwitterionic nature in the case of Se-Met in contrary to the non-zwitterionic species found in the case of Se-Cyst, in accordance with our previous findings concerning partitioning experiments in the n-octanol/water system. Finally, an attempt was made to correlate log k_w values with the logarithm of n-octanol/water distribution coefficient, log D, of the investigated Se species and an indicative log D value of Se-U was derived.     

Determination of the n‐octanol/water partition coefficients of weakly ionizable basic compounds by reversed‐phase high‐performance liquid chromatography with neutral model compounds

A strategy to utilize neutral model compounds for lipophilicity measurement of ionizable basic compounds by reversed‐phase high‐performance liquid chromatography is proposed in this paper. The applicability of the novel protocol was justified by theoretical derivation. Meanwhile, the linear relationships between logarithm of apparent n‐octanol/water partition coefficients (logK_ow′′) and logarithm of retention factors corresponding to the 100% aqueous fraction of mobile phase (logk_w) were established for a basic training set, a neutral training set and a mixed training set of these two. As proved in theory, the good linearity and external validation results indicated that the logK_ow′′–logk_w relationships obtained from a neutral model training set were always reliable regardless of mobile phase pH. Afterwards, the above relationships were adopted to determine the logK_ow of harmaline, a weakly dissociable alkaloid. As far as we know, this is the first report on experimental logK_ow data for harmaline (logK_ow = 2.28 ± 0.08). Introducing neutral compounds into a basic model training set or using neutral model compounds alone is recommended to measure the lipophilicity of weakly ionizable basic compounds especially those with high hydrophobicity for the advantages of more suitable model compound choices and convenient mobile phase pH control.     

Substituted benzotriazoles as inhibitors of copper corrosion in borate buffer solutions

The adsorption of substituted 1,2,3-benzotriazoles (R-BTAs) onto copper is measured via ellipsometry in a pure borate buffer (pH 7.4) and satisfactorily described by Temkin’s isotherm. The adsorption free energy (?ΔG _a ⁰ ) values of these azoles are determined. The (?ΔG _a ⁰ ) values are found to rise as their hydrophobicity, characterized by the logarithm of the partition coefficient of a substituted BTA in a model octanol–water system (logP), grows. The minimum concentration sufficient for the spontaneous passivation of copper (C _min) and a shift in the potential of local copper depassivation with chlorides (E _pt) after an azole is added to the solution (i.e., ΔE = E _pt ⁱⁿ ? E _pt ^backgr characterizing the ability of its adsorption to stabilize passivation) are determined in the same solution containing a corrosion additive (0.01М NaCl) for each azole under study. Both criteria of the passivating properties of azoles (logC _min and ΔE) are shown to correlate linearly with logP, testifying to the role played by surface activity of this family of organic inhibitors in protecting copper in an aqueous solution.     

Equations for the Partition of Neutral Molecules, Ions and Ionic Species from Water to Water–Ethanol Mixtures

Equations set up for the transfer of neutral solutes from water to water?Cethanol mixtures can also be used to correlate the transfer of ions and ionic species, as log₁₀ P, where P is the partition coefficient. Only two additional terms are required in the equations, one for anions and one for cations. The extended equations can fit log₁₀ P values for anions and cations with a standard deviation of about 0.2 to 0.3 log units for transfer of 41 anions and cations from water to various water?Cethanol mixtures from 10?% ethanol to 100?% ethanol by volume. The log₁₀ P values for carboxylate anions and protonated amine cations as obtained from the variation of pK _a with solvent are quite compatible with log₁₀ P values for simple anions and cations.