Change of pH indicator's pKa value via molecular imprinting

The pKa value of the indicator is significantly changed up to several orders of magnitude by the imprinting synthesis; this fine-tuning of the reactivity for pH indicators via the imprinting synthesis may find novel applications in fabricating pH sensors with tailored pKa values.     

High accuracy quantum-chemistry-based calculation and blind prediction of macroscopic pKa values in the context of the SAMPL6 challenge

Recent advances in the development of low-cost quantum chemical methods have made the prediction of conformational preferences and physicochemical properties of medium-sized drug-like molecules routinely feasible, with significant potential to advance drug discovery. In the context of the SAMPL6 challenge, macroscopic pKa values were blindly predicted for a set of 24 of such molecules. In this paper we present two similar quantum chemical based approaches based on the high accuracy calculation of standard reaction free energies and the subsequent determination of those pKa values via a linear free energy relationship. Both approaches use extensive conformational sampling and apply hybrid and double-hybrid density functional theory with continuum solvation to calculate free energies. The blindly calculated macroscopic pKa values were in excellent agreement with the experiment.     

Constant pH Molecular Dynamics Simulations of Nucleic Acids in Explicit Solvent

The nucleosides of adenine and cytosine have pKa values of 3.50 and 4.08, respectively, and are assumed to be unprotonated under physiological conditions. However, evidence from recent NMR and X-Ray crystallography studies has revealed the prevalence of protonated adenine and cytosine in RNA macromolecules. Such nucleotides with elevated pKa values may play a role in stabilizing RNA structure and participate in the mechanism of ribozyme catalysis. With the work presented here, we establish the framework and demonstrate the first constant pH MD simulations (CPHMD) for nucleic acids in explicit solvent in which the protonation state is coupled to the dynamical evolution of the RNA system via λ-dynamics. We adopt the new functional form λ(Nexp) for λ that was recently developed for Multi-Site λ-Dynamics (MSλD) and demonstrate good sampling characteristics in which rapid and frequent transitions between the protonated and unprotonated states at pH = pKa are achieved. Our calculated pKa values of simple nucleotides are in a good agreement with experimentally measured values, with a mean absolute error of 0.24 pKa units. This work demonstrates that CPHMD can be used as a powerful tool to investigate pH-dependent biological properties of RNA macromolecules.     

Kinetics and mechanism of the pyridinolysis of s-4-nitrophenyl 4-substituted thiobenzoates in aqueous ethanol

The pyridinolysis of S-4-nitrophenyl 4-X-substituted thiobenzoates (X = H, Cl, and NO2; 1, 2, and 3, respectively) is studied kinetically in 44 wt % ethanol-water, at 25.0 degrees C and an ionic strength of 0.2 M (KCl). The reactions are measured spectrophotometrically (420-425 nm) by following the appearance of 4-nitrobenzenethiolate anion. Pseudo-first-order rate coefficients (kobsd) are obtained throughout, under excess of amine over the substrate. Plots of kobsd vs [free amine] at constant pH are linear with the slope (kN) independent of pH. The Brnsted-type plot (log kN vs pKa0 of the conjugate acids of the pyridines) for the reactions of thiolbenzoate 1 is curved with a slope at high pKa, beta1 = 0.20, and slope at low pKa0, beta2 = 0.94. The pKa value for the center of the Brnsted curvature is pKa0 = 9.7. The pyridinolysis of thiolbenzoates 2 and 3 show linear Brnsted-type plots of slopes 0.94 and 1.0, respectively. These results and other evidence indicate that these reactions occur with the formation of a zwitterionic tetrahedral intermediate (T+/-). For the pyridinolysis of thiolbenzoate 1, breakdown of T+/- to products (k2 step) is rate-limiting for weakly basic pyridines and T+/- formation (k1 step) is rate-determining for very basic pyridines. The k2 step is rate-limiting for the reactions of thiolbenzoates 2 and 3. The smallest pKa0 value for the reaction of 1 is due to the weakest electron withdrawal of H (relative to Cl and NO2) in the acyl group, which results in the smallest k-1/k2 ratio. The pKa0 values for the title reactions are smaller than those for the reactions of secondary alicyclic amines with thiolbenzoates 1-3. This is attributed to a lower leaving ability from the T+/- of pyridines than isobasic alicyclic amines. The lower p value found for the pyridinolysis of 2,4-dinitrophenyl benzoate (pKa0 = 9.5), compared with that for the pyridinolysis of 1, is explained by the greater nucleofugality from T+/- of 2,4-dinitrophenoxide than 4-nitrobenzenethiolate, which renders the k-1/k2 ratio smaller for the reactions of the benzoate relative to thiolbenzoate 1. The title reactions are also compared with the aminolysis of similar thiolbenzoates in other solvents to assess the solvent effect.     

Identification of a potential general acid/base in the reversible phosphoryl transfer reactions catalyzed by tyrosine recombinases: Flp H305

Flp provides a unique opportunity to apply the tools of chemical biology to phosphoryl transfer reactions. Flp and other tyrosine recombinases catalyze site-specific DNA rearrangements via a phosphotyrosine intermediate. Unlike most related enzymes, Flp's nucleophilic tyrosine derives from a different protomer than the remainder of its active site. Because the tyrosine can be supplied exogenously, nonnatural synthetic analogs can be used. Here we examine the catalytic role of Flp's conserved H305. DNA cleavage was studied using a peptide containing either tyrosine (pKa congruent with 10) or 3-fluoro-tyrosine (pKa congruent with 8.4). Religation was studied using DNA substrates with 3'-phospho-cresol (pKa congruent with 10) or 3'-para-nitro-phenol (pKa congruent with 7.1). In both cases, the tyrosine analog with the lower pKa specifically restored the activity of an H305 mutant. These results provide experimental evidence that this conserved histidine functions as a general acid/base catalyst in tyrosine recombinases.     

In-Block Derivatization of Herbicidal Carboxylic Acids by Pentafluorobenzyl Bromide

Abstract

Herbicidal carboxylic acids were analyzed via ECD gas chromatography of their pentafluorobenzyl esters. The derivatives were formed by direct injection of a mixture of the acids and pentafluorobenzyl bromide in acetone; yields showed marked dependence on pKa of the acids. Carboxylic acids which have pKa values greater than 4.5 yielded the corresponding derivatives in poor yield unless triethylamine is included in the mixture. The procedure is fast and particularly convenient for low-level screening, identification and analysis of highly acidic chlorobenzoic, chlorophenoxyalkanoic, and arylacetic acids in the presence of less acidic carboxylic acids and phenols.     

Deprotonation of calixarenes in acetonitrile

[Structure: see text]. The pKa values for calixarenes in MeCN have been determined by selective titration with bases using a spectroscopic method. These values are as follows: calix[4]arene pKa(1) = 19.06 +/- 0.22, pKa(2) > 33; calix[6]arene pKa(1) = 15.59 +/- 0.06, pKa(2) = 23.85 +/- 0.35, pKa(3) > 33; calix[8]arene pKa(1) = 17.20 +/- 0.20, pKa(2) = 20.32 +/- 0.31, pKa(3) > 33. The trends in acidity are rationalized using structures generated by a DFT model. For mono-deprotonation, the degree and nature of hydrogen bonding in the anion is the dominant factor; for di-deprotonation, spatial separation of the anionic charges becomes important.     

Dissociation constants of phenols in methanol--water mixtures

A preferential solvation model that relates solute properties with solvent composition in binary mixtures has been applied to the dissociation pKa values of a set of 28 substituted phenols in methanol-water mixtures. The parameters of the model allow estimation of the pKa value of each phenol for any methanol-water composition. Moreover, it is demonstrated that the pKa values of the whole set of phenols at any methanol-water composition are linearly related to the pKa values of the phenols in water. Equations that relate the correlations' slope and intercept values with the solvent composition have been derived and tested with the set of phenols. The general parameters obtained for these equations allow an accurate calculation of the pKa value of any phenol, even of those not included in the original set, at any methanol-water composition solely from the pKa value of the phenol in water. These calculated pKa values can be used for quantitative structure-HPLC retention relationships. The method is tested by comparison of the calculated pKa values with the HPLC determined pKa values of 26 phenols in a polymeric column with a 50% methanol as mobile phase.     

Determination of pKa values of organic bases in aqueous acetonitrile solutions using capillary electrophoresis

Capillary electrophoresis (CE) was used for the determination of ionisation constants (pKa) of a variety of organic bases in aqueous acetonitrile solutions over the range 0-60% (v/v) acetonitrile. These bases are used as test compounds in HPLC column evaluation, thus knowledge of their pKa in hydro-organic solutions is useful. The base pKa decreased with acetonitrile concentration and significant shifts from the aqueous pKa (up to -0.8) were found using 60% acetonitrile. The CE application was confirmed to be very suitable for fast and accurate pKa measurement in aqueous organic solutions.     

Kinetics and mechanism of the pyridinolysis of 4-nitrophenyl and 2,4-dinitrophenyl S-methyl thiocarbonates

The reactions of 4-nitrophenyl and 2,4-dinitrophenyl S-methyl thiocarbonates (1 and 2, respectively) with a series of 3- and/or 4-substituted pyridines in aqueous solution, at 25.0 degrees C and an ionic strength of 0.2 M (KCl), are subjected to a kinetic investigation. The reactions are studied by following spectrophotometrically the release of 4-nitrophenoxide (400 nm) or 2,4-dinitrophenoxide (360 nm) anions. Under amine excess, pseudo-first-order rate coefficients (kobsd) are found. Plots of kobsd vs [pyridine] are linear and pH-independent, with slope kN. The Br?nsted-type plot (log kN vs pKa of pyridinium ions) for the reactions of 1 is linear, with slope beta = 1.1, in contrast to the plot for the reactions of 2, which is biphasic, with slopes beta1 = 0.25 (high pKa) and beta2 = 0.90 (low pKa) and the curvature center at pKa = p = 7.3. The latter Br?nsted plot is consistent with a stepwise mechanism, through a zwitterionic tetrahedral intermediate (T+/-) on the reaction path, and a change of the rate-determining step, from breakdown to formation of T+/-, as pyridine basicity increases. For the reactions of 1 the beta value indicates that the mechanism is also stepwise with expulsion of the nucleofuge from T+/- as the rate-determining step. By comparison of the reactions under investigation among each other and with similar aminolyses, the following conclusions can be drawn. (i) Thiocarbonate 2 is more reactive than 1 toward pyridines. (ii) The pka0 value for the pyridinolysis of 2,4-dinitrophenyl methyl carbonate (4) is larger than that for thiocarbonate 2. (iii) The k1 values (pyridine attack to form T+/-) are smaller for thiocarbonates 1 and 2 than the corresponding oxy carbonates 3 and 4, respectively. This is not in accordance with the electronic effects of MeS and MeO and could be attributed to steric hindrance of the MeS group toward pyridine attack. (iv) The kN values for the pyridinolysis of carbonates 3 and 4 are larger than those for thiocarbonates 1 and 2, respectively, when the k2 step is rate-limiting.     

Rapid screening of pKa values of pharmaceuticals by pressure-assisted capillary electrophoresis combined with short-end injection

A method applying pressure-assisted capillary electrophoresis combined with short-end injection has been developed for the rapid screening of the pKa values of pharmaceuticals. The electrophoretic separation is performed on a short capillary length with short-end injection under an applied pressure, and the effective mobility is measured in a series of 10 different buffers with constant ionic strength (I = 0.05). The application of pressure not only reduces migration times, particularly in lower pH buffers, but also improves the repeatability of effective mobility measurements. The influence of pressure on the effective mobility was investigated at various pH values. It was observed for the first time that an increase in pressure resulted in a slight decrease in the effective mobility when the pH was above the pKa for acidic analytes, whereas an increased effective mobility with increasing pressures was observed when the pH was below the pKa. However, the observed effective mobility shift by the applied pressure did not significantly affect the determined pKa values. The determined pKa values were in good agreement with published data. Furthermore, a stacking condition was applied to increase the sensitivity, and a concentration down to 2 microM could readily be detected with UV detection using a 50 microm I.D. capillary. This technique is particularly suitable for measurement of pKa values for compounds with poor aqueous solubility. The method also omits the commonly used preconditioning steps with sodium hydroxide and water. The exclusion of excessive preconditioning steps and the use of pressure reduces the total cycling analysis time, and makes it possible to determine the pKa in less than 40 min per compound without loss of accuracy.     

Linear-scaling molecular orbital calculations for the pKa values of ionizable residues in proteins

In this report, we present a computational methodology for the pKa prediction of proteins, based on linear-scaling molecular orbital calculations for their solution-conformations obtained from NMR measurements. The method is used to predict the pKa values of five carboxylic acids (Asp7, Glu10, Glu19, Asp27, and Glu43) in turkey ovomucoid third domain (OMTKY3), and six aspartates residues (Asp 22, Asp 44, Asp 54, Asp 75, Asp 83, and Asp 93) in barnase. For OMTKY3, all the predicted pKa values are within 1 pH units from the available experimental ones, except for the case of Glu 43. For barnase, the root-mean-square deviation from experiment is 1.46 pH units. As a result, the proposed pKa calculation method correctly reproduces the relative order of the pKa values among the carboxylic acids located in different sites of the proteins. The calculated pKa values are decomposed into the contributions of short- and long-range structural difference effects. The results indicate that in both proteins the pKa value of the given carboxylic acid is partially influenced by long-range interactions with distant charged residues, which significantly contribute to determining the relative order of the pKa values. The current methodology based on LSMO provides us useful information about the titration behavior in a protein.     

Computational determination of aqueous pKa values of protonated benzimidazoles (part 1)

Benzimidazoles are the organic compounds investigated in this work. The experimental determination of the pKa values of protonated benzimidazoles in water is a challenge because of their low solubility. In addition, some derivatives are involved in tautomeric equilibria which increase the complexity of the theoretical pKa determinations. In the present study, different approaches are considered to develop a methodology for the accurate prediction of aqueous pKa values of protonated benzimidazoles at 298.15 K. We have considered different reaction schemes for approximating the acid dissociation equilibrium; two distinct equations are used for the calculation of pKa values, and a number of levels of theory and empirical corrections are applied in the process of working toward this aim. The best correlations between the experimental and calculated data are obtained at the B3LYP/6-31+G(d,p)-PCM(opt) level of theory. The predictive capabilities of the methodologies attempted are tested with two compounds that were not included in the set of benzimidazoles initially investigated. The direct calculations differ significantly from the expected values, but the pKa values calculated using the correlation equations are very similar and in reasonable agreement with the expected pKa values.     

pKa calculations of aliphatic amines, diamines, and aminoamides via density functional theory with a Poisson-Boltzmann continuum solvent model

In order to make reliable predictions of the acid-base properties of macroligands with a large number of ionizable sites such as dendrimers, one needs to develop and validate computational methods that accurately estimate the acidity constants (pKa) of their chemical building blocks. In this article, we couple density functional theory (B3LYP) with a Poisson-Boltzmann continuum solvent model to calculate the aqueous pKa of aliphatic amines, diamines, and aminoamides, which are building blocks for several classes of dendrimers. No empirical correction terms were employed in the calculations except for the free energy of solvation of the proton (H+) adjusted to give the best match with experimental data. The use of solution-phase optimized geometries gives calculated pKa values in excellent agreement with experimental measurements. The mean absolute error is <0.5 pKa unit in all cases. Conversely, calculations for diamines and aminoamides based on gas-phase geometries lead to a mean absolute error >0.5 pKa unit compared to experimental measurements. We find that geometry optimization in solution is essential for making accurate pKa predictions for systems possessing intramolecular hydrogen bonds.     

Ab initio procedure for aqueous-phase pKa calculation: the acidity of nitrous acid

We present an ab initio procedure for accurately calculating aqueous-phase pKa values and apply it to study the acidity of nitrous acid (HNO2, or HONO). The aqueous-phase pK(a) of nitrous acid was obtained from calculated gas-phase acidities and solvation free energies via a thermodynamic cycle and the solvation model chemistry of Barone et al. (J. Chem. Phys. 1997, 107, 3210). Solvation free energies were calculated at the HF/6-31G(d) level using the dielectric-polarizable continuum and the integral equation formalism-polarizable continuum solvent models (D-PCM and IEF-PCM, respectively), with the D-PCM model yielding the most accurate pKa values. For HF free energies of solvation, significant improvements in accuracy could be made by moving to the larger 6-311++G(3df,3pd) and aug-cc-pVQZ basis sets. Solvation free energies were also calculated using the density functional theory (DFT) methods B3LYP, TPSS, PBE0, B1B95, VSXC, B98 and O3LYP, with the most accurate methods being TPSS and VSXC, which provided average errors of less than 0.11 pKa units. Solvation free energies calculated with the different DFT methods were relatively insensitive to the basis set used. Our theoretical calculations are compared with experimental results obtained using stopped flow spectrophotometry. The pKa of nitrous acid was measured as 3.16 at 25 degrees C, and the enthalpy and entropy of nitrous acid dissociation were calculated from measurements as 6.7 kJ mol(-1) and -38.4 J mol(-1) K(-1), respectively, between 25 and 45 degrees C. The UV/visible absorption spectra of the nitrite ion and nitrous acid were also examined, and molar extinction coefficients were obtained for each.     

Determination of the acid dissociation constant of bromocresol green and cresol red in water/AOT/isooctane reverse micelles by multiple linear regression and extended principal component analysis

The pKa of 3',3",5',5"tetrabromo-m-cresolsulfonephtalein (Bromocresol Green) and o-cresolsulphonephtalein (Cresol Red) was spectrophotometrically measured in a water/AOT/isooctane microemulsion in the presence of a series of buffers carrying different charges at different water/surfactant ratios. Extended Principal Component Analysis was used for a precise determination of the apparent pKa and of the spectra of the acid and base forms of the dye. The apparent pKa of dyes in water-in-oil microemulsions depends on the charge of the acid and base forms of the buffers present in the water pool. Combination with multiple linear regression increases the precision. Results are discussed taking into account the profile of the electrostatic potential in the water pool and the possible partition of the indicator between the aqueous core and the surfactant. The pKa corrected for these effects are independent of w0 and are close to the value of the pKa in bulk water. On the basis of a tentative hypothesis it is possible to calculate the true pKa of the buffer in the pool.     

Accurate pKa determination for a heterogeneous group of organic molecules.

Single-molecule studies that allow to compute pKa values, proton affinities (gas-phase acidity/basicity) and the electrostatic energy of solvation have been performed for a heterogeneous set of 26 organic compounds. Quantum mechanical density functional theory (DFT) using the Becke-half&half and B3LYP functionals on optimized molecular geometries have been carried out to investigate the energetics of gas-phase protonation. The electrostatic contribution to the solvation energies of protonated and deprotonated compounds were calculated by solving the Poisson equation using atomic charges generated by fitting the electrostatic potential derived from the molecular wave functions in vacuum. The combination of gas-phase and electrostatic solvation energies by means of the thermodynamic cycle enabled us to compute pKa values for the 26 compounds, which cover six distinct chemical groups (carboxylic acids, benzoic acids, phenols, imides, pyridines and imidazoles). The computational procedure for determining pKa values is accurate and transferable with a root-mean-square deviation of 0.53 and 0.57 pKa units and a maximum error of 1.0 pKa and 1.3 pKa units for Becke-half&half and B3LYP DFT functionals, respectively.     

Direct measurement of a pK(a) near neutrality for the catalytic cytosine in the genomic HDV ribozyme using Raman crystallography

The hepatitis delta virus (HDV) ribozyme uses a cytosine to facilitate general acid-base catalysis. Biochemical studies suggest that C75 has a pKa perturbed to near neutrality. To measure this pKa directly, Raman spectra were recorded on single ribozyme crystals using a Raman microscope. A spectral feature arising from a single neutral cytosine was identified at 1528 cm(-1). At low pH, this mode was replaced with a new spectral feature. Monitoring these features as a function of pH revealed pKa values for the cytosine that couple anticooperatively with Mg2+ binding, with values of 6.15 and 6.40 in the presence of 20 and 2 mM Mg2+, respectively. These pKa values agree well with those obtained from ribozyme activity experiments in solution. To correlate the observed pKa with a specific nucleotide, crystals of C75U, which is catalytically inactive, were examined. The Raman difference spectra show that this mutation does not affect the conformation of the ribozyme. However, crystals of C75U did not produce a signal from a protonatable cytosine, providing strong evidence that protonation of C75 is being monitored in the wild-type ribozyme. These studies provide the first direct physical measurement of a pKa near neutrality for a catalytic residue in a ribozyme and show that ribozymes, like their protein enzyme counterparts, can optimize the pKa of their side chains for proton transfer.