Experimental pKa Values Research Articles

Ab initio studies on acidity and tautomeric equilibrium constants of some benzoxa-, benzothia-, benzoselena-zolinone derivatives

This paper presents ab initio procedure to calculate aqueous-phase acid dissociation constants (pKa) values, accurately. In this work, dissociation and tautomeric equilibrium constants (KT) of some benzoxa-, benzothia-, benzoselena-zolinone derivatives were studied theoretically. For this purpose, Gibbs free energy values for neutral and deprotonated forms of investigated compounds were calculated at gas and aqueous phase by using Hartree–Fock (HF) and density functional theory (DFT) calculation methods. For both calculation methods it was found that 6-311G(d) basis set is the most convenient method. Solvent effects are taken into account by means of conductor-like polarizable continuum model (CPCM). It was shown that, theoretically calculated pKa values are in good agreement with the existing experimental pKa values, which are determined from capillary electrophoresis, potentiometric titration and UV–visible spectrophotometric measurements. Calculated pKa values also revealed that the DFT method (R2=0.92) gave much closed results to experimental values in comparison to Hartree–Fock method (R2=0.86). Due to the all investigated compounds have keto-enol tautomerism, KT and pKT values were calculated without need to form model compounds. Theoretically calculated KT values indicated that, keto forms are predominant for all the investigated compounds.

Electrostatic Contribution of Surface Charge Residues to the Stability of a Thermophilic Protein: Benchmarking Experimental and Predicted pKa Values

Optimization of the surface charges is a promising strategy for increasing thermostability of proteins. Electrostatic contribution of ionizable groups to the protein stability can be estimated from the differences between the pKa values in the folded and unfolded states of a protein. Using this pKa-shift approach, we experimentally measured the electrostatic contribution of all aspartate and glutamate residues to the stability of a thermophilic ribosomal protein L30e from Thermococcus celer. The pKa values in the unfolded state were found to be similar to model compound pKas. The pKa values in both the folded and unfolded states obtained at 298 and 333 K were similar, suggesting that electrostatic contribution of ionizable groups to the protein stability were insensitive to temperature changes. The experimental pKa values for the L30e protein in the folded state were used as a benchmark to test the robustness of pKa prediction by various computational methods such as H++, MCCE, MEAD, pKD, PropKa, and UHBD. Although the predicted pKa values were affected by crystal contacts that may alter the side-chain conformation of surface charged residues, most computational methods performed well, with correlation coefficients between experimental and calculated pKa values ranging from 0.49 to 0.91 (p<0.01). The changes in protein stability derived from the experimental pKa-shift approach correlate well (r = 0.81) with those obtained from stability measurements of charge-to-alanine substituted variants of the L30e protein. Our results demonstrate that the knowledge of the pKa values in the folded state provides sufficient rationale for the redesign of protein surface charges leading to improved protein stability.

Computational study of the proton affinity and basicity of structurally diverse α1‐adrenoceptor ligands

The α1‐adrenoceptor is a target for the treatment of several conditions from hypertension to benign prostatic hyperplasia. In this paper, we describe a new analysis approach to explore the conformational space of several ligands of the α1‐adrenoceptor and we also present the calculation of their proton affinity and basicity. For each compound a conformational search followed by a semi‐empirical optimisation was performed and a selection of conformations for each ligand was subjected to further optimisation using density functional theory methods. Different positions were explored to determine the favoured site of protonation, and then, the proton affinity (in the gas phase) and basicity (using the polarisable continuum model for the aqueous solution) were calculated for each of them. In addition, an alternative method using one explicit water molecule in combination with the polarisable continuum model for aqueous solvent was explored. Moreover, the acid dissociation constant (pKa) in water of these 26 compounds was calculated because this is an important parameter for a ligand when binding to its receptor. The experimental pKa values of six of these ligands and those of two compounds with a very low and a very large pKa were used to validate the theoretical methodology. Copyright © 2011 John Wiley &amp; Sons, Ltd.

Solubility and pKa determination of six structurally related phenothiazines

Solubilities of six structurally related phenothiazines, namely chlorpromazine hydrochloride, fluphenazine dihydrochloride, promazine hydrochloride, thioridazine hydrochloride, trifluoperazine dihydrochloride, and triflupromazine hydrochloride at constant pH were measured in the temperature range from 290K to 350K in three important drugs solvents: water, ethanol and 1-octanol using the dynamic method and UV–vis method. Dissociation constants and corresponding pKa values of drugs were obtained with Bates–Schwarzenbach method at temperature 298.15K in the buffer solutions. Our experimental pKa values for chlorpromazine hydrochloride, fluphenazine dihydrochloride, promazine hydrochloride, thioridazine hydrochloride, trifluoperazine dihydrochloride, and triflupromazine hydrochloride are 9.15, 10.01, 9.37, 8.89, 8.97, and 9.03, respectively. The basic thermal properties of pure drugs i.e. melting and solid–solid phase transition as well as glass-transition temperatures, the enthalpy of melting and phase transitions and the molar heat capacity at glass transition (at constant pressure) were measured with differential scanning microcalorimetry (DSC) technique. Molar volumes were calculated with Barton group contribution method. The experimental solubility data were correlated by means of three commonly known GE equations: the Wilson, NRTL and UNIQUAC with the assumption that the systems studied here have revealed simple eutectic mixtures. The root-mean-square deviations of temperature were used for the precision of the correlation. The activity coefficients of drugs at saturated solutions in each correlated binary mixture were calculated from the experimental data. These new data will help in all prediction-methods and their precision.

Thermodynamics of protonation of alkanolamines in aqueous solutions

The equilibrium constants, pKa, for protonation of monoethanolamine (MEA), N-methyldiethanolamine (MDEA), 2-amino-2-methyl-1-propnol (AMP), 2(2-aminoethyl)etanol)amine (AEEA) and piperazine (Pz) have been measured by potentiometric titration at temperatures from 298.15 to 363.15 K. Enthalpies of protonation, ΔHp, for these amines were measured at 298.15 K in a reaction calorimeter and compared to those calculated from the experimental pKa values. The effect of the ionic strength of the solution on the equilibrium constants and enthalpy of protonation of MDEA was studied.

Energy Levels and Redox Properties of Aqueous Mn2+/3+ from Photoemission Spectroscopy and Density Functional Molecular Dynamics Simulation

Energy-resolved photoemission spectroscopy and density functional molecular dynamics simulations are combined to construct an energy level diagram for the Mn(2+/3+) redox reaction in aqueous solution. Two peaks centered at 8.88 and 10.26 eV electron binding energies can be assigned to the Mn2+ hexa-aquo complex with a peak area ratio of 2:2.83. Using the notation of crystal field theory, the peak at lower energies can be interpreted as arising from ionization from the e(g) levels (highest occupied molecular orbital, HOMO), and the peak at higher energies are from ionization of the t(2g) levels. The difference corresponds to the average crystal field splitting, 1.38 eV. From the position of the HOMO level and the absolute redox potential, an experimental value for the reorganization free energy of the aqueous Mn3+ hexa-aquo complex is estimated to be 2.98 eV. Density functional molecular dynamics simulations can reproduce the experimental vertical ionization energy, redox free energy, and reorganization free energies fairly well, provided that the absolute potential shift in periodic boundary conditions, finite size effects, and inaccuracies of the exchange correlation functional are taken into account. Most strikingly, in the simulations, we observe spontaneous and reversible deprotonation of the aqueous Mn3+ hexa-aquo complex to form MnOH(H2O)5(2+) + H+, in line with the low experimental pKa value of this ion. The interconversion between protonation states leads to interesting redox phenomena for aqueous Mn3+, culminating in a bimodal thermal distribution of the electron affinity.

Thermodynamic Estimate of pKa Values of the Carboxylic Acids in Aqueous Solution with the Density Functional Theory

AbstractThe 96 pKa values of 85 carboxylic acids in aqueous solution were calculated with the density functional theory method at the level of B3LYP/6‐31+G(d,p) and the polarizable continuum model (PCM) was used to describe the solvent. In the calculations of pKa values, the dissociation Gibbs free energies were directly calculated using carboxylic acid dissociation reactions in aqueous solution, i. e., no thermodynamic cycle was employed, which is different from the previous literatures. A highly significant correlation of R2=0.95 with a standard deviation (SD) of 0.36 between the experimental pKa values and the calculated dissociation Gibbs free energies [ΔG(calc.)] was found. The slope of pKa vs. (G(calc.)/(20303RT) is only 47.6% of the theoretically expected value, which implies that the ΔG(calc.) value from the theoretical calculation is larger than the actual one for all 85 carboxylic acids studied. Thus, by adding the 0.476 scaling‐factor into the slope, we can derive a reliably procedure that can reproduce the experimental pKa values of carboxylic acids. The pKa values furnished by this procedure are in good agreement with the experimental results for carboxylic acids in aqueous solution.

Modelling dissociation constants of organic acids by local molecular parameters

The dissociation constant pKa defines the ionization degree of organic compounds. It is an important parameter that affects their toxicity and environmental behavior and fate. Among the present approaches to predict pKa values of organic chemicals, increment methods show a good performance but are limited by missing values of special groups. The purpose of this study is to develop models for predicting the pKa of organic acids directly from their molecular structures. A quantum chemical method was introduced by employing local molecular parameters. Experimental pKa values of more than 1000 organic acids, including phenols, aromatic carboxylic acids, aliphatic carboxylic acids and alcohols were selected, and all molecules were optimized using the semi-empirical AM1 Hamiltonian. Simple models with several descriptors for different subsets were calibrated by multilinear regression (MLR). Substituent positions on aromatic rings were also taken into account. The obtained models yield good predictive squared correlation coefficients q2 and superior performance compared with other quantum chemical models. The prediction capability is further evaluated using cross validation. The models unravel that the potential of oxygen atom conjoint to ionizable hydrogen atom to accept extra electronic charge is the single most important contribution to the dissociation of hydrogen atom. Non-linear statistical analysis methods were also applied because of the non-linear character of the employed descriptors. The study was supported by the China Scholarship Council and by the EU project OSIRIS (IP, contact No. 037017), which is gratefully acknowledged.

Theoretical Study on the Redox Cycle of Bovine Glutathione Peroxidase GPx1: pKa Calculations, Docking, and Molecular Dynamics Simulations.

Three approaches of computational chemistry [quantum mechanics (QM) calculations, docking, and molecular dynamics (MD) simulations] were used to investigate the redox cycle of bovine erythrocyte glutathione peroxidase from class 1 (GPx1, EC 1.11.1.9). The pKa calculations for two redox states of the active-site selenocysteine of GPx1 (selenol, Sec45-SeH, and selenenic acid, Sec45-SeOH) were estimated using a bulk solvent model (B3LYP-IEFPCM and B3LYP-CPCM-COSMO-RS). The calculated pKa values of Sec45-SeH and Sec45-SeOH were corrected via a simple linear fit to a training set of organoselenium compounds, which consisted of aliphatic selenols and aromatic selenenic acids with available experimental pKa values. Based on docking calculations, binding sites for both molecules of the cofactor glutathione (GSH) are described. MD simulations on the dimer of GPx1 have been performed for all chemical states of the redox cycle: without GSH and with one or two molecules of GSH bound at the active site. Conformational analyses of MD trajectories indicate high mobility of the Arg177 and His79 residues. These residues can approach the vicinity of Sec45 and take part in the catalytic mechanism. On the basis of the calculated data, new atomistic details for a generally accepted mechanism of GPx1 are proposed.

Quantum-chemical study on the relation between thermodynamic parameters in the iodination of benzene with N-I and O-I reagents and pK a values of the corresponding NH and oh acids

Thermodynamic parameters of direct iodination of benzene with several iodinating agents were calculated using semiempirical (PM3), ab initio (3-21G**), and DFT (B3LYP/LanL2DZ) methods, as well as in terms of the polarization continuum model (PCM or Tomasi model). A close to linear correlation was found between the calculated thermodynamic parameters (ΔH ≠ , ΔG ≠ ) and pKT and experimental pKa values of acids whose anions are incorporated into iodine-containing intermediates.

Comparison of Nine Programs Predicting pKa Values of Pharmaceutical Substances

Knowledge of the possible ionization states of a pharmaceutical substance, embodied in the pK(a) values (logarithm of the acid dissociation constant), is vital for understanding many properties essential to drug development. We compare nine commercially available or free programs for predicting ionization constants. Eight of these programs are based on empirical methods: ACD/pK(a) DB 12.0, ADME Boxes 4.9, ADMET Predictor 3.0, Epik 1.6, Marvin 5.1.4, Pallas pKalc Net 2.0, Pipeline Pilot 5.0, and SPARC 4.2; one program is based on a quantum chemical method: Jaguar 7.5. We compared their performances by applying them to 197 pharmaceutical substances with 261 carefully determined and highly reliable experimental pK(a) values from a literature source. The programs ADME Boxes 4.9, ACD/pK(a) DB 12.0, and SPARC 4.2 ranked as the top three with mean absolute deviations of 0.389, 0.478, and 0.651 and r(2) values of 0.944, 0.908, and 0.894, respectively. ACD/pK(a) DB 12.0 predicted all sites, whereas ADME Boxes 4.9 and SPARC 4.2 failed to predict 5 and 18 sites, respectively. The performance of the quantum chemical-based program Jaguar 7.5 was not as expected, with a mean absolute deviation of 1.283 and an r(2) value of 0.579, indicating the potential for further development of this type of approach to pK(a) prediction.

Titration_DB: Storage and analysis of NMR‐monitored protein pH titration curves

NMR-monitored pH titration experiments are routinely used to measure site-specific protein pKa values. Accurate experimental pKa values are essential in dissecting enzyme catalysis, in studying the pH-dependence of protein stability and ligand binding, in benchmarking pKa prediction algorithms, and ultimately in understanding electrostatic effects in proteins. However, due to the complex ways in which pH-dependent electrostatic and structural changes manifest themselves in NMR spectra, reported apparent pKa values are often dependent on the way that NMR pH-titration curves are analyzed. It is therefore important to retain the raw NMR spectroscopic data to allow for documentation and possible re-interpretation. We have constructed a database of primary NMR pH-titration data, which is accessible via a web interface. Here, we report statistics of the database contents and analyze the data with a global perspective to provide guidelines on best practice for fitting NMR titration curves. Titration_DB is available at http://enzyme.ucd.ie/Titration_DB. Proteins 2010. (c) 2009 Wiley-Liss, Inc.

IEF-PCM Calculations of Absolute pKa for Substituted Phenols in Dimethyl Sulfoxide and Acetonitrile Solutions

Absolute (nonrelative) pKa calculations for substituted phenols were carried out in nonaqueous media, demonstrating the predictive power of the integral equation formalism PCM method with a mean unsigned error of 0.6 pKa units for DMSO and 0.7 pKa units for MeCN at the B3LYP/6-31+G** level of theory combined with the scaled B3LYP/6-311+G** gas-phase data. At the same time, the correlation between the calculated and experimental pKa values yielded the value of the linear regression slope very close to unity for both DMSO and MeCN. Computation of pKa of neutral acids in nonaqueous solutions with a reasonable precision obviously depends on carefully tuned cavities, optimized for nonaqueous solutions. The ability of continuum solvation model to compensate charge escape from the cavity, which is prominent in the case of anions, is also required. And finally, good quality gas-phase data is essential to achieve required pKa precision.

Estimation of Molecular Acidity via Electrostatic Potential at the Nucleus and Valence Natural Atomic Orbitals

An effective approach of estimating molecular pK(a) values from simple density functional calculations is proposed in this work. Both the molecular electrostatic potential (MEP) at the nucleus of the acidic atom and the sum of valence natural atomic orbitals are employed for three categories of compounds, amines and anilines, carbonyl acids and alcohols, and sulfonic acids and thiols. A strong correlation between experimental pK(a) values and each of these two quantities for each of the three categories has been discovered. Moreover, if the MEP is subtracted by the isolated atomic MEP for each category of compounds, we observe a single unique linear relationship between the resultant MEP difference and experimental pK(a) data of amines, anilines, carbonyl acids, alcohols, sulfonic acids, thiols, and their substituents. These results can generally be utilized to simultaneously estimate pK(a) values at multiple sites with a single calculation for either relatively small molecules in drug design or amino acids in proteins and macromolecules.

Basicity of organic bases and superbases in acetonitrile by the polarized continuum model and DFT calculations

The basicities of a large number of organic bases and superbases, including nitrogen basic centers in various chemical environments occurring in phosphazenes, amidines, amines, anilines and pyridines, have been studied in acetonitrile by the isodensity polarized continuum model employing two DFT computational schemes differing in the basis sets for final single-point calculations. It turned out that the B3LYP/6-311+G(d,p)//B3LYP/6-31G(d) method serves the purpose giving good agreement for basicities with experiment for both gas phase and acetonitrile solutions treating widely different bonding situations of basic nitrogen atoms on an equal footing. An attempt is made to correlate the experimental pKa(MeCN) values with the proton affinities (PA) in MeCN. The results are less accurate than those achieved by using basicities in acetonitrile. In particular, the PA(MeCN)s frequently failed in reproducing the pKa(MeCN) values in systems possessing multiple intramolecular hydrogen (IMH) bonds formed via corona effects. In such cases the use of basicities is mandatory instead. A useful corollary of these calculations on systems with multiple IMH bonds is that comparison of the theoretical and experimental pKa values can provide an insight into the structure of the most stable conformations in solutions.

Estimation of the pKa values of water ligands in transition metal complexes using density functional theory with polarized continuum model solvent corrections

The deprotonation energies of the water ligands in a set of 40 d-block metal complexes have been calculated using density functional theory with polarized continuum model solvent corrections. The complexes include 13 aqua ions [M(OH(2))(n)](2+/3+) and a variety of aqua complexes with organic co-ligands, whose experimental pK(a) values have been reported in the literature. For comparison, the deprotonation energies of a set of 60 organic and inorganic molecules with experimental pK(a) values ranging from -25 (HSbF(6)) to +52 (C(2)H(6)) have also been calculated. Three different classes of acids are identified as giving different slopes in plots of pK(a) versus deprotonation energies; namely non-hydroxy acids, hydroxy acids, and the metal complexes. The correlation coefficients for the straight lines obtained for these three classes are 0.96, 0.97 and 0.92 respectively. Better correlations are found for sub-sets of the complexes, such as the 31 first row complexes (correlation coefficient 0.95).For several of the complexes, comparison of the calculated and observed pK(a) values, together with changes in the geometry upon optimization, offer new insights into the possible solution structures. It is concluded that DFT calculations incorporating solvent corrections can be used to give reasonable estimates of pK(a) values for the aqua ligands in a range of complex types.

Acidity of meta- and para-substituted aromatic acids: a conceptual DFT study

Quantum chemical computations with full geometry optimization at the B3LYP/6-31G(d) level in aqueous phase at 298 K are performed to calculate a set of molecular properties for 45 aromatic organic acids such as benzoic acid, phenol, cinnamic acid, benzohydroxamic acid, anilinium ion and their meta- and para-substituted derivatives. In a separate set of calculations the 6-31+G(d) basis set is employed for substituted benzoic and cinnamic acids as representative test cases, to test the effect of diffuse functions. Molecular descriptors such as ionization potential, electron affinity, hardness, chemical potential, global electrophilicity and free energy of deprotonation of these acids are computed. The local descriptors such as Fukui functions and group philicity (ω+g) are calculated with Mulliken Population Analysis (MPA) and Hirschfeld Population Analysis (HPA) schemes. These aromatic acids are reacted with a strong base, OH−. The computed Gibbs free energy of deprotonation, the fractional number of electrons transferred, ΔN and electrophilicity based charge transfer index (ECT) in acid–base reaction with a strong base, OH−, ω+g and group charges are correlated with the experimental pKa values of these acids. It is found that this approach is particularly effective in discussing trends of changes in acidity of intimately related molecules. The effect of substituents on these descriptors is also studied. These parameters are correlated with experimental Hammett substituent constants (σ). The ECT, fractional number of electron transfer (ΔN) and group charge correlate strongly with pKa and σ in separate groups of aromatic acids. Minimum energy, maximum hardness and minimum electrophilicity principles are tested for the acid–base reactions.

Determination of aqueous acid‐dissociation constants of aspartic acid using PCM/DFT method

AbstractDetermination of acid‐dissociation constants, pKa, of aspartic acid in aqueous solution, using density functional theory calculations combined with the conductor‐like polarizable continuum model (CPCM) and with integral‐equation‐formalism polarizable continuum model (IEFPCM) based on the UAKS and UAHF radii, was carried out. The computed pKa values derived from the CPCM and IEFPCM with UAKS cavity model of bare structures of the B3LYP/6‐31+G(d,p)‐optimized tetrahydrated structures of aspartic acid species are mostly close to the experimental pKa values. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008

Computation of pKa Values of Substituted Aniline Radical Cations in Dimethylsulfoxide Solution

A newly developed computation strategy was used to calculate the absolute pKa values of 18 substituted aniline radical cations in dimethylsulfoxide (DMSO) solution with the error origin elucidated and deviation minimized. The B3LYP/6-311++G(2df,2p) method was applied and was found to be capable of reproducing the gas-phase proton-transfer free energies of substituted anilines with a precision of 0.83 kcal/mol. The IEF-PCM solvation model with gas-phase optimized structures was adopted in calculating the pKa values of the substituted neutral anilines in DMSO, regenerating the experimental results within a standard deviation of 0.4 pKa unit. When the IEF-PCM solvation model was applied to calculate the standard redox potentials of anilide anions, it showed that the computed values agreed well with experiment, but the redox potentials of substituted anilines were systematically overestimated by 0.304 eV. The cause of this deviation was found to be related to the inaccuracy of the calculated solvation free energies of aniline radical cations. By adjusting the size of the cavity in the IEF-PCM method, we derived a reliable procedure that can reproduce the experimental pKa values of aniline radical cations within 1.2 pKa units to those from experiment.

First-principles calculation of pKa for cocaine, nicotine, neurotransmitters, and anilines in aqueous solution.

The absolute pKa values of 24 representative amine compounds, including cocaine, nicotine, 10 neurotransmitters, and 12 anilines, in aqueous solution were calculated by performing first-principles electronic structure calculations that account for the solvent effects using four different solvation models, i.e., the surface and volume polarization for electrostatic interaction (SVPE) model, the standard polarizable continuum model (PCM), the integral equation formalism for the polarizable continuum model (IEFPCM), and the conductor-like screening solvation model (COSMO). Within the examined computational methods, the calculations using the SVPE model lead to the absolute pKa values with the smallest root-mean-square-deviation (rmsd) value (1.18). When the SVPE model was replaced by the PCM, IEFPCM, and COSMO, the rmsd value of the calculated absolute pKa values became 3.21, 2.72, and 3.08, respectively. All types of calculated pKa values linearly correlate with the experimental pKa values very well. With the empirical corrections using the linear correlation relationships, the theoretical pKa values are much closer to the corresponding experimental data and the rmsd values become 0.51-0.83. The smallest rmsd value (0.51) is also associated with the SVPE model. All of the results suggest that the first-principles electronic structure calculations using the SVPE model are a reliable approach to the pKa prediction for the amine compounds.