Calculations of pKa values of carboxylic acids in aqueous solution using Möller-Plesset perturbation theory

The acidity constants of some carboxylic acids in aqueous solution have been calculated. The calculations were carried out using Möller-Plesset (MP) perturbation theory. The Polarizable Continuum Model (PCM) is used to describe the solvent. This model furnishes pK_a values that agree more closely with experimental data than those obtained at the level of Hartree-Fock (HF) and Density Functional Theory (DFT-B3LYP). The root-mean-square of errors of the calculated pK_a values are less than 1.0 for the studied acids. The molecules analyzed consist of acids with pK_a values in the range of 1.30 to 5.05, and have been partitioned into three classes. Class I includes acids with pK_a values higher than 4.00. Class II includes strong acids with pK_a values between 3.00 to 4.00. Class III includes very strong acids with pK_a values less than 3.00. The calculated pK_a values for the acids in Class I and Class II agree more closely with experimental values. The root-mean-square of errors for the Class I and Class II compounds are 0.70 and 0.78 pK_a units, respectively.     

Une nouvelle méthode numérique de détermination parspectrophotométrie de constantes d'ionisation sechevauchant

A new method of calculation has been developed to obtain two pK_a values from spectrophotometric data in cases when the values are so close together that the calculations usually applied for individual pK_a values are not appropriate. This technique, in which all the experimental data are used to solve for absorbance of monoprotonated species, pK_a1 and pK_a7 by a “complex” method of optimization, is more general than the classical least-squares method. An application is described.     

Multifunctional substances — Determination of pKa-values in overlapping ranges using an iteration procedure

Summary In multifunctional substances, pK_a-values from different functional groups may overlap. Therefore, systematically wrong results are obtained, if pK_a-values are used from titration charts without appropriate corrections. The iteration procedure presented in this article starts with the pK_a-values at the half-way neutralisation points. From these preliminary values, new positions in the charts are calculated, from which better approximations of the pK_a-values are obtained. These steps are repeated several times, until the results converge. Cefodizime (HR 221) with three acid/base functional groups was used as model substance. The disodium salt was titrated using three molar equivalents of 0.1 mol/l hydrochloric acid. Using the iteration procedure, three pK_a-values were obtained from the titration chart: 1. The amino-function: pK₁=2.85; 2. the first carboxyl-function: pK₂=3.37; 3. the second carboxyl-function: pK₃=4.18.     

A Novel QSAR Approach for Estimating Toxicity of Phenols

Abstract

Toxicity values (log IGC^?1 ₅₀) for 60 phenols tested in the 2-d static population growth inhibition assay with the ciliate Tetrahymena pyriformis were tabulated. Each chemical was selected so the series formed uniform coverage of the hydrophobicity/ionization surface. A high quality hydrophobicity-dependent (log K _ow) structure-toxicity relationship (log IGC^?1 ₅₀ = 0.741 (log K_ow) ?1.433; n = 17; r² = 0.970; s = 0.134; F = 486.55; Pr > F = 0.0001) was developed for phenols with pK_a values > 9.8. Similarly, separate hydrophobicity-dependent relationships were developed for phenols with pK_a values of 4.0, 5.1, 6.3, 7.5, and 8.7. Comparisons of intercepts and slopes, respectively, revealed phenols with pK_a values of 6.3 to be the most toxic and the least influenced by hydrophobicity. These relationships were reversed for the more acidic and basic phenols. Plots of toxicity versus pK_a for nitro-substituted phenols and phenols with log K_ow values of either 1.75 or 2.50 further demonstrated bilinearity between toxicity and ionization. In an effort to more accurately model the relationship between toxicity and ionization, the absolute value function |6.3-pK_a| was used to model ionization affects for derivatives with pK_a values between 0 and 9.8. For derivatives with pK_a value > 9.8, a value of 3.50 was used to quantitate ionization effects. The use of log K_ow in conjunction with this modified pK_a (ΔpK_a) resulted in the structure-toxicity relationship (log IGC^?1 ₅₀ = 0.567 (log K_ow)-0.226 (ΔpK_a-0.079; n = 54; r² = 0.926; s = 0.215; F = 321.06; Pr > F = 0.0001). Derivatives with a nitro group in the 4-position typically did not model well with the above equation.     

Simple methods for the estimation of ionization constants of substituted pyridine N-oxides in polar aprotic solvents and water

A direct method for the determination of the pK _a values of acids conjugated to substituted pyridine N-oxides has been proposed which is based on the pH measurement of the solution of the basic salt. It has been experimentally shown that the method is reliable when applied to N-oxides of not too low basicity (pK _a >5). Correlation has been performed between the pK _a values in aqueous and aprotic media solutions which shows the great influence of the solvation effect on the acid-base equilibria. The good correlation between the pK _a values in aqueous and non-aqueous solutions enables the pK _a values in water to be estimated with sufficient accuracy, even in the cases when the experimental limitations make the determination impossible which is shown on the basis of selected examples.     

Multiwavelength Spectrophotometric Determination of Acid Dissociation Constants. Deconvolution of Binary Mixtures of Ionizable Compounds

ABSTRACT

A spectral deconvolution method based on target factor analysis has been developed to determine pK_a values of binary mixtures of monoprotic and/or diprotic ionizable compounds. The technique makes use of the approach of Frans and Harris, which has been implemented previously for mixtures of monoprotic compounds (Anal. Chem. 1985, 57, 1718-1721), to extract the unknown pK_a values. The method has been illustrated by using the multiwavelength spectrophotometrictitation data of binary mixtures of: I. benzoic acid and phenol, 2. benzoic acid and nicotinic acid, 3. p-aminosalicylic acid and phthalic acid. It was demonstrated that the pK_a values as determined in this study are in good agreement with the literature.     

The relationship among pKa, pH, and binding constants in the interactions between boronic acids and diols—it is not as simple as it appears

In our continuing efforts into designing boronic acid-based sensors that recognize cell-surface carbohydrates, it has been necessary to examine various factors that affect the binding affinity between a boronic acid moiety and a diol. The current prevailing view is that the strongest boronic acid/diol complexes are generated by a combination of high solution pH and a low boronic acid pK_a. However, there has never been a systematic examination of the relationship among the binding constants, boronic acid pK_a, and the pH of the solution. Herein we report our findings with a series of 25 arylboronic acids with various substituents and their binding affinities with diols. We have found that (1) the relationship between the pK_a of monosubstituted phenylboronic acid and its substituents can be described using a Hammet plot; (2) the optimal pH for binding is not always above the pK_a of the boronic acid, and is affected by the pK_a values of the boronic acid and the diol, and other unknown factors; and (3) the general belief that boronic acids with lower pK_a values show greater binding affinities for diols is not always true.     

Determination de pKa d'acides conjugues de carbanions dans le DMSO anhydre. Reexamen des correlations entre cés pKa et les potentiels d'oxydation Eox determines dans le mĕme solvant

The pK_a values of several pseudo-acids of general formula

in anhydrous DMSO have been determined.The pK_a values have been correlated with the oxidation potential E_ox of their conjugated carbanions (enolate anions). The variation of E_ox of these enolate anions (and even those of cyclopentadienyl, indenyl, fluorenyl and triphenylmethyl carbanions) as a function of the pK_a of their acidic form is consistent with a correlation line whose slope is ?0.067 V/unity pK_a.In DMSO, all the β-carbonylated nitriles are in their enolic form, except the 2-cyano-esters which are entirely in the carbonyl form. In spite of this, their acidity is intermediate between that of the methylketones (Z = CH₃) and the aldehydes (Z = H). Thus, in DMSO medium, for β-carbonylated nitriles it appears that the acidity is not dependent on the enolization tendency.     

Evaluation of the acidic properties of hydroxycoumarins and choice of solvents for performing potentiometric analysis

The relative acidity constants (pK_a) for 17 hydroxycoumarins in water, methanol, acetone (Ac), dimethylformide (DMFA), and dimethyl sulfoxide (DMSO) have been determined by Henderson's method. The existence of a linear relationship between pK_a in water and pK_a in acetone, dimethylformamide, and dimethyl sulfoxide has been established. From the pK_a values the sequence of neutralization of the hydroxy groups has been determined: their acidic properties decrease in the sequence 4-OH > 7-OH > 6-OH > 8-OH. A quantitative evaluation of the conditions of titration in five solvents on the basis of the titration constants (pK_t) and of the values of the potential jumps and the shape of the potentiometric titration curves has permitted acetone to be proposed as the optimum solvent for the performance of potentiometric analysis.All-Union Scientific-Research Institute of Drug Chemistry and Technology, Khar'kov. Translated from Khimiya Prirodnykh Soedinenii, No. 6, pp. 770–773, November–December, 1985.     

Calculation of amino acid pKaS in a protein from a continuum electrostatic model: Method and sensitivity analysis

We used continuum electrostatic theory to calculate pK_as of amino acids in protein. A Green's function formalism, based on a finite-difference solution to the Poisson–Boltzmann equation for a unit point charge, yields electrostatic potentials that allow calculation of amino acid pK_as to an estimated accuracy of tenths of a pK_a unit. Improvements over previous methods include the ability to focus the finite difference grid to arbitrarily small grid spacing, an analytical representation of the molecular surface, and a novel procedure to calculate the reaction field potential. Using this method, we performed a sensitivity analysis of calculated pK_as in the photosynthetic reaction center. Calculated pK_as are most sensitive for residues that are not well-exposed to solvent. Variations in the parameters of the continuum electrostatic model cause pK_a shifts that are larger than the accuracy of the numerical method, but probably not large enough to account for some of the discrepancies between calculated and experimentally measured pK_as that have been reported for the reaction center. © 1996 by John Wiley & Sons, Inc.     

Evaluation of the acidic properties of hydroxycoumarins and choice of solvents for performing potentiometric analysis

The relative acidity constants (pK_a) for 17 hydroxycoumarins in water, methanol, acetone (Ac), dimethylformide (DMFA), and dimethyl sulfoxide (DMSO) have been determined by Henderson's method. The existence of a linear relationship between pK_a in water and pK_a in acetone, dimethylformamide, and dimethyl sulfoxide has been established. From the pK_a values the sequence of neutralization of the hydroxy groups has been determined: their acidic properties decrease in the sequence 4-OH > 7-OH > 6-OH > 8-OH. A quantitative evaluation of the conditions of titration in five solvents on the basis of the titration constants (pK_t) and of the values of the potential jumps and the shape of the potentiometric titration curves has permitted acetone to be proposed as the optimum solvent for the performance of potentiometric analysis.     

Tautomeric equilibrium of 1-β-D-ribofuranosyl-2-keto-4-(n-methoxyamino)pyrimidine

The 1-β-D-ribofuranosides of 2-keto-4-(N-methoxyamino)pyrimidine, 2-keto-4-(N-methyl-N-methoxyamino)pyrimidine, and 2-keto-3-methyl-4-(N-methoxyamino)pyrimidine were synthesized, and their pK_a values were determined by spectrophotometry. The pK_a values of the compounds are evidence that the tautomeric equilibrium between the oxime and hydroxyamine forms of 1-β-D-ribofuranosyl-2-keto-4-(N-methoxyamino)pyrimidine in aqueous solutions is shifted to favor the oxime form (K_T?25).     

The Protonation and Deprotonation Equilibria of Hypericin Revisited

 The protonation and deprotonation behaviour and the assignment of pK _a values of hypericin are reviewed and discussed. Three experiments (electrospray MS, ¹H NMR, acid–base indicator equilibria) provided additional evidences for the assignment of pK _a values of −5 and −6 to mono- and diprotonation at the carbonyl groups of hypericin, of pK _a = 2 to monodeprotonation at the bay-region, and of pK _a = 11 to dideprotonation at the bay- and peri-regions.     

Benchmarking pKaprediction

Background  

pK_avalues are a measure of the protonation of ionizable groups in proteins. Ionizable groups are involved in intra-protein, protein-solvent and protein-ligand interactions as well as solubility, protein folding and catalytic activity. The pK_ashift of a group from its intrinsic value is determined by the perturbation of the residue by the environment and can be calculated from three-dimensional structural data.     

Effects of Aerosol-OT reversed micelles in carbon tetrachloride on acid-base indicator equilibria

ApparentpK _a values of thymol blue solubilized in Aerosol-OT reversed micelles in carbon tetrachloride at 25 °C were determined spectrophotometrically. The effects of the Aerosol-OT concentration and the (water)/(surfactant)R ratio were investigated. The apparentpK _a values increase as a function of increasing (R). All the measuredpK _a values are less than that in water. The decrease ranges from 1.23 units (detergent=0.4 M,R=1.39) to 0.42 units (Aerosol-OT=0.6 M,R=9,25). These results are rationalized in terms of decreased hydronium ion activity in the micellar core due to its binding to the detergent SO₃ ^? groups.     

Low solubility of unconjugated bilirubin in dimethylsulfoxide – water systems: implications for pK<Subscript><Emphasis Type="Italic">a</Emphasis></Subscript> determinations

Background

Aqueous pK _a values of unconjugated bilirubin are important determinants of its solubility and transport. Published pK _a data on an analog, mesobilirubin-XIIIα, studied by ¹³C-NMR in buffered solutions containing 27 and 64 vol% (C²H₃)₂SO because of low aqueous solubility of mesobilirubin, were extrapolated to obtain pK _a values in water of 4.2 and 4.9. Previous chloroform-water partition data on bilirubin diacid led to higher estimates of its pK _a , 8.12 and 8.44, and its aqueous solubility. A thermodynamic analysis, using this solubility and a published solubility in DMSO, suggested that the systems used to measure ¹³C-NMR shifts were highly supersaturated. This expectation was assessed by measuring the residual concentrations of bilirubin in the supernatants of comparable DMSO-buffer systems, after mild centrifugation to remove microprecipitates.

Results

Extensive sedimentation was observed from numerous systems, many of which appeared optically clear. The very low supernatant concentrations at the lowest pH values (4.1-5.9) were compatible with the above thermodynamic analysis. Extensive sedimentation and low supernatant concentrations occurred also at pH as high as 7.2.

Conclusions

The present study strongly supports the validity of the aqueous solubility of bilirubin diacid derived from partition data, and, therefore, the corresponding high pK _a values. Many of the mesobilirubin systems in the ¹³C-NMR studies were probably supersaturated, contained microsuspensions, and were not true solutions. This, and previously documented errors in pH determinations that caused serious errors in pK _a values of the many soluble reference acids and mesobilirubin, raise doubts regarding the low pK _a estimates for mesobilirubin from the ¹³C-NMR studies.

     

The Protonation and Deprotonation Equilibria of Hypericin Revisited

Summary.  The protonation and deprotonation behaviour and the assignment of pK _a values of hypericin are reviewed and discussed. Three experiments (electrospray MS, ¹H NMR, acid–base indicator equilibria) provided additional evidences for the assignment of pK _a values of −5 and −6 to mono- and diprotonation at the carbonyl groups of hypericin, of pK _a = 2 to monodeprotonation at the bay-region, and of pK _a = 11 to dideprotonation at the bay- and peri-regions. Received September 26, 2001. Accepted October 1, 2001     

The 3-Thioxo-1,2-Dithiol-4-yl Group: A Versatile One Endowed Also With a –R Electronic Effect

The pK_a values in an aqueous solution of some 4-aminodithiolethiones, 4-aminodithiolones, 5-phenyl-4-hydroxydithiolethione, and 5-phenyl-4-hydroxydithiolone were determined by UV-VIS spectrophotometry at 298 K. These compounds exhibited unexpectedly very low pK_a values in the range of 0–2 for amino derivatives and in the range of 7 for hydroxy derivatives. Electronic structure calculations by ab initio and DFT methods together with an X-ray measurement indicated that these results may be attributed to a markedly negative π charge on the carbon 5 together with a positive π charge on the basic substituent of the carbon 4. As a result, the dithiole nucleus exerts in this case a strong ─R effect. Although they were very low, pK _a values of 4-aminodithiolethiones remained still higher than those found with 5-aminodithiolethiones, which were also determined in this work for comparison. The latter were not unexpectedly in the range -3 < pH < ?2.     

Basicities and structures of 4,4,6-trimethyl-2-arylamino-5,6-dihydro-4H-1,3-thiazines and 4,4,6-trimethyl-2-arylamino-5,6-dihydro-4H-1,3-oxazines

The relative basicities of 4,4,6-trimethyl-2-arylamino-5,6-dihydro-4H-1,3-thiazines and 4,4,6-trimethyl-2-arylamino-5, 6-dihydro-4H-1,3-oxazines, which are capable of amine-imine tautomerism, and of model compounds with fixed amine and imine structures were determined by potentiometric titration in methanol. Good correlation of the pK _a values with the Hammett constants in the investigated reaction series was found. The inapplicability of the use of the pK _a values of model compounds for the determination of the tautomeric equilibrium constants in the case of some N-heterocyclic amines of nonaromatic character with an aryl substituent attached to the exocyclic nitrogen atom of the amidine fragment of the molecule is demonstrated.Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 12, pp. 1621–1624, December, 1976.     

Towards the comprehensive, rapid, and accurate prediction of the favorable tautomeric states of drug-like molecules in aqueous solution

Generating the appropriate protonation states of drug-like molecules in solution is important for success in both ligand- and structure-based virtual screening. Screening collections of millions of compounds requires a method for determining tautomers and their energies that is sufficiently rapid, accurate, and comprehensive. To maximise enrichment, the lowest energy tautomers must be determined from heterogeneous input, without over-enumerating unfavourable states. While computationally expensive, the density functional theory (DFT) method M06-2X/aug-cc-pVTZ(-f) [PB-SCRF] provides accurate energies for enumerated model tautomeric systems. The empirical Hammett–Taft methodology can very rapidly extrapolate substituent effects from model systems to drug-like molecules via the relationship between pK_T and pK_a. Combining the two complementary approaches transforms the tautomer problem from a scientific challenge to one of engineering scale-up, and avoids issues that arise due to the very limited number of measured pK_T values, especially for the complicated heterocycles often favoured by medicinal chemists for their novelty and versatility. Several hundreds of pre-calculated tautomer energies and substituent pK_a effects are tabulated in databases for use in structural adjustment by the program Epik, which treats tautomers as a subset of the larger problem of the protonation states in aqueous ensembles and their energy penalties. Accuracy and coverage is continually improved and expanded by parameterizing new systems of interest using DFT and experimental data. Recommendations are made for how to best incorporate tautomers in molecular design and virtual screening workflows.