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.     

Capillary zone electrophoresis of basic drugs in non-aqueous acetonitrile with buffers based on a conventional pH scale

Summary The pK _a ^* values of 10 nitrogen-containing basic drugs in non-aqueous acetonitrile were determined from the pH^* dependence of their electrophoretic mobilities. The pH^* scale in the organic solvent was established using background electrolytes with known conventional pK _a ^* values, making further calibration with reference pH electrodes unnecessary. In acetonitrile the pK _a ^* values of analytes (or their conjugated cation acids, BH⁺, respectively) were 5.2±8.9 pK units>those in water. The observed change in pK _a ^* values of cationic analytes was, however, much less than the known respective change for neutral acids type HA. From the pK _a ^* values and the actual mobilities, it is possible to predict pH^* conditions to enable separation of analytes, and this was demonstrated for two pairs of common drugs.     

Spectrophotometric Determination of the Ionization Constants of Aqueous Nitrophenols at Temperatures up to 225 °C

The UV-visible spectra of aqueous o-, m-, and p-nitrophenol were measured as a function of pH at temperatures from 50 to 225 °C at a pressure of 7 MPa. These were used to determine equilibrium constants for the acid ionization reaction of each isomer. The new results were combined with literature data on the ionization of nitrophenols and used for parameter optimization in the thermodynamic model of Marshall and Franck (J. Phys. Chem. Ref. Data 10:295–304, [1981]), to describe the dependence of ionization properties on temperature and pressure. The model yields predictions of the ionization constants for o-, m-, and p-nitrophenol, log ₁₀ K _a, to at least 250 °C and 20 MPa with an estimated uncertainty in log ₁₀ K _a of less than ±0.06.     

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.     

Outliers detection in the statistical accuracy test of a p<Emphasis Type="Italic">K</Emphasis><Subscript>a</Subscript> prediction

The regression diagnostics algorithm REGDIA in S-Plus is introduced to examine the accuracy of pK _a predicted with four programs: PALLAS, MARVIN, PERRIN and SYBYL. On basis of a statistical analysis of residuals, outlier diagnostics are proposed. Residual analysis of the ADSTAT program is based on examining goodness-of-fit via graphical diagnostics of 15 exploratory data analysis plots, such as bar plots, box-and-whisker plots, dot plots, midsum plots, symmetry plots, kurtosis plots, differential quantile plots, quantile-box plots, frequency polygons, histograms, quantile plots, quantile-quantile plots, rankit plots, scatter plots, and autocorrelation plots. Outliers in pK _a relate to molecules which are poorly characterized by the considered pK _a program. Of the seven most efficient diagnostic plots (the Williams graph, Graph of predicted residuals, Pregibon graph, Gray L–R graph, Index graph of Atkinson measure, Index graph of diagonal elements of the hat matrix and Rankit Q–Q graph of jackknife residuals) the Williams graph was selected to give the most reliable detection of outliers. The six statistical characteristics, F_exp,R²,R_P²,MEP,AIC{F_{\rm exp},R^{2},R_{\rm P}^{2},{\it MEP},{\it AIC}}, and s in pK _a units, successfully examine the specimen of 25 acids and bases of a Perrin’s data set classifying four pK _a prediction algorithms. The highest values F_exp,R²,R_P²{F_{\rm exp},R^{2},R_{\rm P}^{2}} and the lowest value of MEP and s and the most negative AIC have been found for PERRIN algorithm of pK _a prediction so this algorithm achieves the best predictive power and the most accurate results. The proposed accuracy test of the REGDIA program can also be extended to test other predicted values, as log P, log D, aqueous solubility or some physicochemical properties.     

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.     

The metastable Ni7±xS6, and mixed Ni6±x(S1−ySey)5, phases

The closely related, narrowly non-stoichiometric, metastable as well as thermodynamically stable “phases” in the metal-rich part of the Ni–S phase diagram near the nominal composition Ni_7±xS₆ have been carefully re-investigated via electron diffraction and transmission electron microscope imaging. Two quite distinct polymorphs have been identified, a minority incommensurate interface-modulated polymorph and a (heavily twinned) majority I1a1, a=2a_p, b=2b_p, c=−a_p+c_p superstructure (of an underlying Bmmb, a_p3.3, b_p16.4, c_p11.3 Å parent structure) polymorph. The incommensurate polymorph is shown to be very closely related to the only known polymorph of Ni_6±xSe₅ and is rapidly stabilized to room temperature upon doping of the sulfide compounds with selenium.     

The importance of valencep functions in the bonding of Na2, K2, and Cu2 and their positive and negative ions

Summary The relative importance of the valencep functions for describing the bonding in the valence isoelectronic Na₂, K₂, and Cu₂ molecules and their positive and negative ions is investigated. In absolute magnitude the contribution of thep functions to the dissociation energy follows the trend Cu>Na>K while by percentage of the dissociation energy the importance of thep functions follows the polarizabilities, i.e. K>Na>Cu. The bonding in K₂, K ₂ ⁺ , and K ₂ ^– is analyzed to explain the observed trends.Dedicated to Prof. Klaus Ruedenberg     

Crystal growth, structure determination, and optical properties of new potassium-rare-earth silicates K3RESi2O7 (RE=Gd, Tb, Dy, Ho, Er, Tm, Yb, Lu)

Single crystals of K₃RESi₂O₇ (RE=Gd, Tb, Dy, Ho, Er, Tm, Yb, Lu) were grown from a potassium fluoride flux. Two different structure types were found for this series. Silicates containing the larger rare earths, RE=Gd, Tb, Dy, Ho, Er, Tm, Yb crystallize in a structure K₃RESi₂O₇ that contains the rare-earth cation in both a slightly distorted octahedral and an ideal trigonal prismatic coordination environment, while in K₃LuSi₂O₇, containing the smallest of the rare earths, lutetium is found solely in an octahedral coordination environment. The structure of K₃LuSi₂O₇ crystallizes in space group P6₃/mmc with a=5.71160(10) Å and c=13.8883(6) Å. The structures containing the remaining rare earths crystallize in the space group P6₃/mcm with the lattice parameters of a=9.9359(2) Å, c=14.4295(4) Å, (K₃GdSi₂O₇); a=9.88730(10) Å, c=14.3856(3) Å, (K₃TbSi₂O₇); a=9.8673(2) Å, c=14.3572(4) Å, (K₃DySi₂O₇); a=9.8408(3) Å, c=14.3206(6) Å, (K₃HoSi₂O₇); a=9.82120(10) Å, c=14.2986(2) Å, (K₃ErSi₂O₇); a=9.80200(10) Å, c=14.2863(4) Å, (K₃TmSi₂O₇); a=9.78190(10) Å, c=14.2401(3) Å, (K₃YbSi₂O₇). The optical properties of the silicates were investigated and K₃TbSi₂O₇ was found to fluoresce in the visible.     

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.     

Acidity,lipophilicity, solubility,absorption, and polar surface area of some ACE inhibitors

Computational chemical methods have been used to correlate the molecular properties of the 10 ACE inhibitors (captopril, enalapril, perindopril, lisinopril, ramipril, trandolapril, quinapril, fosinopril, benazepril, and cilazapril) and some of their active metabolites (enalaprilat, perindoprilat, ramiprilat, trandolaprilat, quinaprilat, fosinoprilat, benazeprilat, and cilazaprilat). The computed pK _a values correlate well with the available experimental values. In the dicarboxylic ACE inhibitors, the carboxyalkyl carboxylate group of the ACE inhibitors studied is more acidic than the C-terminal carboxylate. However, at physiological pH = 7.4 both carboxyl groups of ACE inhibitors are completely ionized and the dicarboxyl-containing ACE inhibitors behave as strong acids. The available experimental partition coefficients of these ACE inhibitors investigated are well reproduced by the neural network-based ALOGPs and the fragment-based KoWWiN methods. All parent drugs (and prodrugs), with the exception of fosinopril, are compounds with low lipophilicity. Calculated pK _a, lipophilicity, solubility, absorption, and polar surface area of the most effective ACE inhibitors for the prevention of myocardial infarction, perindopril and ramipril, were found similar. Therefore, it is probable that the experimentally observed differences in the survival benefits in the first year after acute myocardial infarction in patients 65 years of age or older correlate closely to the physicochemical and pharmacokinetic characteristics of the specific ACE inhibitor that is used.     

Crystalline inclusion compounds of tetrabenzo-18-crown-6 with uncharged organic molecules. Solid-state structure of the nitroethane complex

Diethylaminoethyl (DEAE) groups were introduced into -cyclodextrin (-CD) and -CD. The products, DEAE-CDs with various numbers of substituents, trappedp-nitrophenoxide and 3,4-dinitrophenoxide preferentially over their respective conjugate acids. This caused a decreased pK _a of the guest nitrophenol. Some signals of the proton-NMR of both guest nitrophenol and host DEAE-CD changed upon host-guest interaction. The relation between the number of DEAE groups and the extent of the pK _a decrease, as well as association constants, is discussed.     

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.     

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.