Benchmarking and validating algorithms that estimate p<Emphasis Type="Italic">K</Emphasis><Subscript>a</Subscript> values of drugs based on their molecular structures

The REGDIA regression diagnostics algorithm in S-Plus is introduced in order to examine the accuracy of pK _a predictions made with four updated programs: PALLAS, MARVIN, ACD/pKa and SPARC. This report reviews the current status of computational tools for predicting the pK _a values of organic drug-like compounds. Outlier predicted pK _a values correspond to molecules that are poorly characterized by the pK _a prediction program concerned. The statistical detection of outliers can fail because of masking and swamping effects. The Williams graph was selected to give the most reliable detection of outliers. Six statistical characteristics (F _exp, R ², , MEP, AIC, and s(e) in pK _a units) of the results obtained when four selected pK _a prediction algorithms were applied to three datasets were examined. The highest values of F _exp, R ², , the lowest values of MEP and s(e), and the most negative AIC were found using the ACD/pK _a algorithm for pK _a prediction, so this algorithm achieves the best predictive power and the most accurate results. The proposed accuracy test performed by the REGDIA program can also be applied to test the accuracy of other predicted values, such as log P, log D, aqueous solubility or certain physicochemical properties of drug molecules.     

Determination of thermodynamic pKa values of pharmaceuticals from five different groups using capillary electrophoresis

A determination of the thermodynamic acid dissociation constants (pK_a) of 22 frequently used pharmaceuticals using capillary electrophoresis in aqueous media is presented in this work. The investigated pharmaceuticals belong to different pharmacological groups: macrolides, fluoroquinolones, sulfonamides, β‐lactams, tetracyclines, and other miscellaneous pharmaceuticals. The electrophoretic mobilities of the investigated analytes were monitored in a pH range from 2.00 to 10.82. The data were fitted with an appropriate mathematical model using a nonlinear regression analysis to obtain pK_a values. Experimentally obtained data were well described by the mathematical model chosen for each analyte that was confirmed by r² values higher than 0.99 for most of the investigated analytes. Extrapolations to zero ionic strength were used to determine the thermodynamic pK_a values. Experimentally obtained acid dissociation constants were interpreted using structural formulae of investigated analytes and the moieties corresponding to specific pK_a were identified.     

Determination of pKa values of tenoxicam from H NMR chemical shifts and of oxicams from electrophoretic mobilities (CZE) with the aid of programs SQUAD and HYPNMR

In this work it is explained, by the first time, the application of programs SQUAD and HYPNMR to refine equilibrium constant values through the fit of electrophoretic mobilities determined by capillary zone electrophoresis experiments, due to the mathematical isomorphism of UV-vis absorptivity coefficients, NMR chemical shifts and electrophoretic mobilities as a function of pH. Then, the pK_a values of tenoxicam in H₂O/DMSO 1:4 (v/v) have been obtained from ¹H NMR chemical shifts, as well as of oxicams in aqueous solution from electrophoretic mobilities determined by CZE, at 25 °C. These values are in very good agreement with those reported by spectrophotometric and potentiometric measurements.     

Thermodynamic cycle for the calculation of ab initio pKa values for hydroxamic acids

A thermodynamic cycle to calculate pK_a values (Minus log of acid dissociation constants) of hydroxamic acids is presented. Hydroxamic acids exist mainly as amide isomers in the aqueous medium. The amide form of hydroxamic acids has two deprotonation sites and may yield either an N-ion or an O-ion upon deprotonation. The thermodynamic cycle proposed includes the gas-phase N–H deprotonation of the hydroxamic acid, the solvent phase transformation of the N-ion to the O-ion and the solvation of the hydroxamic acid molecule and the O-ion in water. The CBS-QB3 method was employed to obtain gas-phase free energy differences between 12 hydroxamic acids and their respective anions. The aqueous solvation Gibbs free energy changes were calculated at the HF/6-31G(d)/CPCM and HF/6-31+G(d)/CPCM levels of theory using HF/6-31+G(d)/CPCM geometries. For the proton, literature values of the gas-phase free energy of formation and the solvation free energy change were used. The free energy change for the transformation of the N-ion to O-ion in the aqueous medium was calculated by employing CBS-QB3/CPCM in the aqueous medium. For this, the hydroxamic acids were divided in two classes according to the substituent at the carbonyl carbon. A common transformation free energy difference for aliphatic substituted hydroxamic acids and a separate common transformation free energy difference for aromatic substituted hydroxamic acids were obtained. The pK_a calculation yielded a root mean square error of 0.32 pK_a units.     

Hydrogen bond interactions at the TiO2 surface: Their contribution to the pH dependent photo-catalytic degradation of p-nitrophenol

We have obtained pK_a values of p-nitrophenol–TiO₂ by measuring the adsorption equilibrium constants of p-nitrophenol (PNP) on the TiO₂ surface at different pH values. These values have been obtained from Langmuir isotherms and from a plot of 1/rate vs. 1/[PNP]_o obtained during TiO₂ catalyzed solar light photo-degradation of PNP. Two limit equilibrium constants are readily obtained depending on the solution pH: at pH 5 at which the TiO₂ surface is mainly positively charged and at pH 8 when it is negatively charged. With these and other adsorption equilibrium constants and the PNP pK_a value in solution, thermodynamic cycles are established in order to obtain the PNP pK_a when it is adsorbed on positively charged, neutral and negatively charged TiO₂ surfaces. From these pK_a values useful information on the PNP–TiO₂ interaction is readily obtained. For instance, the PNP nitro group interacts with the TiO₂ surface via a hydrogen bond, arising from the complex of water molecules with the Ti⁴⁺ ions on its surface. The weaker the hydrogen bond donor, the stronger the oxygen nitro group basicity. Therefore, pK_a changes on the phenolic hydroxyl group result from these interactions. Linear free energy correlations, maximum PNP adsorption capacity values (Q_L) and FTIR ATR, spectrum support this proposal. A k_obs vs. pH degradation profile of p-nitrophenol is also provided.     

Acid dissociation constants of uridine-5′-diphosphate compounds determined by phosphorus nuclear magnetic resonance spectroscopy and internal pH referencing

The acid dissociation constant (pK_a) of small, biological molecules is an important physical property used for investigating enzyme mechanisms and inhibitor design. For phosphorus-containing molecules, the ³¹P nuclear magnetic resonance (NMR) chemical shift is sensitive to the local chemical environment, particularly to changes in the electronic state of the molecule. Taking advantage of this property, we present a ³¹P NMR approach that uses inorganic phosphate buffer as an internal pH reference to determine the pK_a values of the imide and second diphosphate of uridine-5′-diphosphate compounds, including the first reported values for UDP-GlcNAc and UDP-S-GlcNAc. New methods for using inorganic phosphate buffer as an internal pH reference, involving mathematical correction factors and careful control of the chemical shift reference sample, are illustrated. A comparison of the newly determined imide and diphosphate pK_a values of UDP, UDP-GlcNAc, and UDP-S-GlcNAc with other nucleotide phosphate and thio-analogs reveals the significance of the monosaccharide and sulfur position on the pK_a values.     

Acidity of several polyprotic acids, amiodarone and quetiapine hemifumarate in pure methanol

Methanol is the organic solvent closest to water and able to dissolve a huge amount of organic compounds. Therefore, it is a good candidate for pK_a determination of drugs sparingly soluble in water or a basic drug presented as a salt which pK_a is close to that of its counter-acid. In this work, the acidic dissociation constants in pure methanol of the most common acids used in pharmaceutical preparations (lactic, tartaric, fumaric, maleic and citric) were determined. In addition, the pK_a values of the antipsychotic quetiapine presented as hemifumarate (Seroquel) and the very insoluble antiarrhythmic amiodarone were also determined by potentiometry. From these values, the aqueous pK_a of these drugs were estimated by means of previously established equations. Estimated values are consistent with those from literature and show the interest of methanol for drug discovery pK_a measurements.     

Application of variable anti-connectivity index to active sites. Modelling pK a values of aliphatic monocarboxylic acids

A partial distance-weighted variable anti-connectivity topological index was introduced for modelling pK _a values of 31 aliphatic carboxylic acids and haloalkyl-carboxylic acids. The partial distance-weighted variable anti-connectivity index showed superior modelling capabilities compared with the index calculated from the complete graph, because it is capable of accounting correctly for the intramolecular interactions of unconnected vertices to specific bond strengths (active site), thereby improving the RMS_CV error by about 30% (0.221 pK _a units).     

Potentiometric and spectrophotometric pKa determination of water-insoluble compounds: validation study in a new cosolvent system

In this paper the validation of pK_a determination in MDM-water mixtures is presented. The MDM-water mixture is a new multicomponent cosolvent mixture (consisting of equal volumes of methanol, dioxane and acetonitrile, as organic solvents) that dissolves a wide range of poorly water-soluble compounds. The cosolvent dissociation constants (p_sK_a) of 50 chemically diverse compounds (acids, bases and ampholytes) were measured in 15-56 wt% MDM-water mixtures by potentiometric or spectrophotometric titration and the aqueous pK_a values obtained by extrapolation. Three different extrapolation procedures were compared in order to choose the best extrapolation in MDM-water mixture using a sub-set of 30 water-soluble compounds. The extrapolated results are in good agreement with pK_a values measured in aqueous medium. No significant difference was found among these extrapolation procedures thus the widely used Yasuda-Shedlovsky plot was proposed for MDM cosolvent also. Further we also present that the single point estimation based on measurement in 20%/v MDM-mixture using a general calibration equation may be suitable for rapid pK_a determination in the early phase of drug research.     

Calculations of pKa values of carboxylic acids in aqueous solution using density functional theory

With the specific aim of calculating the acidity equilibrium constant (K_a) of carboxylic acids in aqueous solution we investigated the solute-solvent interactions of these acids and their corresponding anions. The pK_a (−lg K_a) values have been calculated using density functional theory (DFT). The polarized continuum model (PCM) is used to describe the solvent. Using these methods, we successfully predicted the pK_as of 66 carboxylic acids in aqueous with the average error of 0.5 in pK_a units. Two different thermodynamic cycles have been studied. The theoretical values are in better agreement with the experimental results for those acids with moderate strength of acidity with the pK_a value higher than 3.     

The Use of Proton Nuclear Magnetic Resonance Spectroscopy for the Determin- ation of pK a Values in Aqueous/Organic Solutions for Basic Analytes Employed in Column Characterisation Protocols

Proton nuclear magnetic spectroscopy has been used to measure pK _a values of two basic analytes in a range of aqueous/organic eluents. The results support the hypothesis that the poor correlation in terms of ion exchange capacity with values greater than pH 7 may be attributed to the difference in the ionisation of the silica surface and not differences in ionisation of the basic analytes under the differing chromatographic conditions (i.e. temperature, type and amount of modifier) employed in two commonly used HPLC stationary phase characterisation procedures (Tanaka and Snyder).     

Determination of acidity constants,ionic mobilities,and hydrodynamic radii of carborane-based inhibitors of carbonic anhydrases by capillary electrophoresis

Capillary electrophoresis (CE) has been applied for determination of the thermodynamic acidity constants (pK_a) of the sulfamidoalkyl and sulfonamidoalkyl groups, the actual and limiting ionic mobilities and hydrodynamic radii of important compounds, eight carborane-based inhibitors of carbonic anhydrases, which are potential new anticancer drugs. Two types of carboranes were investigated, (i) icosahedral cobalt bis(dicarbollide)(1-) ion with sulfamidoalkyl moieties, and (ii) 7,8-nido-dicarbaundecaborate with sulfonamidoalkyl side chains. First, the mixed acidity constants, pK_a^mix, of the sulfamidoalkyl and sulfonamidoalkyl groups of the above carboranes and their actual ionic mobilities were determined by nonlinear regression analysis of the pH dependences of their effective electrophoretic mobility measured by capillary electrophoresis in the pH range 8.00−12.25, at constant ionic strength (25 mM), and constant temperature (25°C). Second, the pK_a^mix were recalculated to the thermodynamic pK_as using the Debye–Hückel theory. The sulfamidoalkyl and sulfonamidoalkyl groups were found to be very weakly acidic with the pK_as in the range 10.78−11.45 depending on the type of carborane cluster and on the position and length of the alkyl chain on the carborane scaffold. These pK_as were in a good agreement with the pK_as (10.67−11.27) obtained by new program AnglerFish (freeware at https://echmet.natur.cuni.cz ), which provides thermodynamic pK_as and limiting ionic mobilities directly from the raw CE data. The absolute values of the limiting ionic mobilities of univalent and divalent carborane anions were in the range 18.3−27.8 TU (Tiselius unit, 1 × 10⁻⁹ m²/Vs), and 36.4−45.9 TU, respectively. The Stokes hydrodynamic radii of univalent and divalent carborane anions varied in the range 0.34−0.52 and 0.42−0.52 nm, respectively.     

Conformation dependence of pKa’s of the chromophores from the purple asFP595 and yellow zFP538 fluorescent proteins

Two members of the green fluorescent protein family, the purple asFP595 and yellow zFP538 proteins, are perspective fluorescent markers for use in multicolor imaging and resonance energy-transfer applications. We report the results of quantum based calculations of the solution pK_a values for selected protonation sites of the denatured asFP595 and zFP538 chromophores in the trans- and cis-conformations in order to add in the interpretation of photo-physical properties of these proteins. The pK_a values were determined from the theromodynamic cycle based on B3LYP/6-311++G(2df, 2p) calculations of the gas phase free energies of the molecules and the B3LYP/6-311++G(d, p) calculations of solvation energies. The results show that the pK_a’s of the protonation sites of the chromophore from asFP595 noticeably depend on the isomer conformation (cis- or trans-), while those of zFP538 are much less sensitive to isomerization.     

Estimation of the pK a of the amine groups of benzhydrylamine resin and its lysyl derivative by measurement of swelling

Summary For better evaluation of the potential of benzhydrylamine resin (BHAR), used as a solid support for peptide synthesis, as a novel anion-exchange resin, the pK _a of its amine group was estimated by microscopic measurement of the sizes of the dry and swollen beads. Using the volume of the bead occupied by the solvent (as a percentage) as the swelling parameter, a plot of the degree of swelling of BHAR loaded with 2.4 mmol g^–1 amine groups against the pH of the medium produced a decreasing sigmoidal-type curve with increasing pH. By considering the point of inflection of the curve, a pK _a value of approximately 7.5 was estimated for the amine group of the BHAR. The same approach was also applied to the lysyl derivative of the BHAR (Lys-BHAR) and pK _a values around 6.5 and 10.0 were obtained for the and amine groups, respectively.     

Determination of weak (2.0–2.5) dissociation constants of non-UV absorbing solutes by capillary electrophoresis

Summary Capillary electrophoresis (CE) has proved to be a fast and convenient method for the determination of the dissociation constants of non-UV absorbing solutes in the acidic pK _A range (2.0–2.5). The electroosmotic flow was reversed by washing the capillary with 0.2% polybren aqueous solution. A series of background electrolytes was prepared with phenylphosphonic acid (pK _A=1.29) and β-alanine (pK _A=3.55) with the same ionic strength and a high buffer capacity in order to improve the repeatability (0.1–0.2 %) of the electrophoretic mobility and to determine the values of pK _A accurately. This procedure was applied to the determination of the dissociation constants of several alkyl-alkylphosphonic acids whose pK _A values have not yet been published in the literature. In this work, their dissociation constants have been found to vary between 1.91 and 2.34 for alkyl-methylphosphonic acids and between 2.10 and 2.38 for alkyl-ethylphosphonic acids.     

Investigation of the Role of Ionic Liquids in Tuning the p<Emphasis Type="Italic">K</Emphasis><Subscript>a</Subscript> Values of Some Anionic Indicators

The effect of imidazolium-based ionic liquids, ([C₁₂mim][Cl] and [C₈mim][Cl]), on the acid-base equilibria of two sulfonated indicators has been studied. The presence of ILs leads to decreased pK _a values because of the stronger electrostatic interaction of cationic ILs with the basic forms of the indicators with more negative charge. The longer alkyl side chain of [C₁₂mim][Cl] compared to [C₈mim][Cl] results in stronger hydrophobic interaction of this IL with the basic forms of the dyes leading to a more effective decrease in the pK _a values. Also, the transition points and transition intervals of the acid-base titration curves of the indicators were affected by the presence of ILs. It was found that the IL interaction with acid-base indicators also results in sharpening the acid-base titration curves of the indicators. From these observations, it is concluded that the presence of ILs can tune the pK _a values of indicators. All the experiments were performed spectrophotometrically and the results were obtained using curve fitting methods.     

On the bromination of hypericin: The gymnochrome chromophores

Summary Stepwise electrophilic bromination of hypericin in pyridine as the solvent yields regioselectively 2,5-dibromohypericin, 2,5,9-tribromohypericin, and 2,5,9,12-tetrabromohypericin. The compounds were characterized by means of NMR-, UV-Vis-, and fluorescence-spectra, andpK _a andpK* _a measurements. These properties were compared with those of hypericin on the one hand and of the recently isolated gymnochromes on the other hand.

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Zur Bromierung des Hypericins: Die Gymnochrom-Chromophore

Zusammenfassung Schrittweise elektrophile Bromierung von Hypericin in Pyridin als Lösungsmittel liefert regioselektiv 2,5-Dibromhypericin, 2,5,9-Tribromhypericin und 2,5,9,12-Tetrabromhypericin. Diese Verbindungen wurden durch NMR-, UV-Vis- und Fluoreszenz-Spektrometrie sowie durchpK _a - undpk* _a -Messungen charakterisiert. Diese Eigenschaften wurden mit jenen des Hypericins und der kürzlich isolierten Gymnochrome verglichen.

     

Cyclopropenimine as a hydrogen bond acceptor—towards the strongest non-phosphorus superbases

Utilizing dialkylamino cyclopropenimines as hydrogen bond acceptors in tri-substituted guanidines and cyclopropenimines, we computationally designed the most basic superbases possessing intramolecular hydrogen bonds (IHB-superbases) so far. The values of proton affinity in the gas phase range between 296.6 and 306 kcal mol⁻¹, with estimated pK_a values in acetonitrile between 35.5 and 39.7. The obtained PAs of five new IHB-superbases surpass the basicity of the paradigmatic P4-tBu Schwesinger phosphazene, whereas pK_a values come close to that of P4-tBu. None of the designed superbases contain phosphorus, which puts them among few most basic non-phosphorus superbases desiged so far.     

Base Equilibria of Substituted Pyridines in Nitromethane

In the framework of our studies on acid=nbase equilibria in systems comprisingsubstituted pyridines and nonaqueous solvents, acid dissociation constants havebeen determined potentiometrically for a variety of cationic acids conjugatedwith pyridine and its derivatives in the polar protophobic aprotic solvent nitromethane. The potentiometric method enabled a check as to whether and to whatextent cationic homoconjugation equilibria of the BH⁺/B type, as well as cationicheteroconjugation equilibria in BH⁺/B₁ systems without proton transfer, are setup in nitromethane. The equilibrium constants were compared with thosedetermined in water and two other polar protophobic aprotic solvents, propylenecarbonate and acetonitrile. The pK _a values of acids conjugate to the N-bases innitromethane fall in the pK _a range of 5.84 to 17.67, i.e., 6 to 7 pK _a units, onaverage, higher than in water, 1 to 2 units higher than in propylene carbonate,and less than 1 unit lower than in acetonitrile. This means that the basicity ofthe pyridine derivatives increases on going from propylene carbonate throughnitromethane to acetonitrile. Further, it was found that the sequence of the pK _achanges of the protonated amines was consistent in all three media, thus providingthe basis for establishing linear correlations among these values. In the majorityof the BH⁺/B systems in nitromethane, cationic homoconjugation equilibria havebeen established. The cationic homoconjugation constants, log K _BHB+, arerelatively low, falling in the range 1.60–2.89. A comparison of the homoconjugationconstants in nitromethane with those in propylene carbonate and acetonitrile showsthat nitromethane is a more favorable solvent for the cationic homoconjugationequilibria than the other two solvents. Moreover, results of the potentiometricmeasurements revealed that cationic heteroconjugation equilibria were not presentin the majority of the BH⁺/B₁ systems in nitromethane. The heteroconjugationconstant could be determined in one system only, with logdiK _BHB1 + = 2.56.