Simple method for determining nucleobase pK(a) values by indirect labeling and demonstration of a pK(a) of neutrality in dsDNA

Phosphorothioates were substituted into double-stranded DNA to study protonated Class I A+.C basepairs by 31P NMR. The method was effective in reporting the A+.C pKa. pKa values near 7.0 were found with optimal nearest-neighbor partners. Such pKa values could expand the catalytic repertoire of nucleic acids.     

Determination of pK(a) values of N-heterocyclic bases by fluorescence spectrophotometry

Fluorimetry is a relatively fast and accurate means of determining the dissociation constants of sparingly soluble heterocyclic bases. Complications can arise, however, from the dependence of fluorescence on excited-state as well as ground-state acid-base chemistry. Several approaches to circumventing or compensating for this difficulty are discussed. To demonstrate the utility of the methods, the pK(a), values of the conjugate acids of two bases are evaluated by the methods described.     

Determination of pK(a) values of diastereomers of phosphinic pseudopeptides by CZE

A CE method was used for the determination of acidity constants (pK(a)) of a series of ten phosphinic pseudopeptides, which varied in number and type of ionogenic groups. Effective electrophoretic mobilities were measured in the 1.8-12.0 pH range in the BGEs of constant ionic strength of 25 mM. Effective electrophoretic mobilities, corrected to standard temperature of 25 degrees C, were subjected to non-linear regression analysis and the obtained apparent pK(a) values were recalculated to thermodynamic pK(a)'s by extrapolation to zero ionic strength according to the extended Debye-Hückel model. The pK(a) values of the phosphinic acid group fell typically in the 1.5-2.25 interval, C-terminal carboxylic groups in the 2.94-3.50 interval, carboxylic groups of the lateral chain of glutamate and aspartate in the 4.68-4.97 interval, imidazolyl moiety of histidine in the 6.55-8.32 interval, N-terminal amino groups in the 7.65-8.28 interval and epsilon-amino group of the lateral chain of lysine in the 10.46-10.61 interval. Further, separation of diastereomers of the phosphinic pseudopeptides was investigated in achiral BGEs. Evaluation of the resolution of the diastereomers as a function of pH of the BGE revealed that most suitable pH region for separation of the diastereomers is around the pK(a) values of the central phosphinic acid group of the pseudopeptides. Successful separation of some diastereomers was, however, achieved in the neutral and alkaline BGEs as well.     

Improved pK(a) prediction: combining empirical and semimicroscopic methods

Using three different methods we tried to compute 171 experimentally known pK(a) values of ionizable residues from 15 different proteins and compared the accuracies of computed pK(a) values in terms of the root mean square deviation (RMSD) from experiment. One method is based on a continuum electrostatic model of the protein including conformational flexibility (KBPLUS). The others are empirical approaches with PROPKA deploying physically motivated energy terms with adjustable parameters and PKAcal using an empirical function with no physical basis. PROPKA reproduced the pK(a) values with highest overall accuracy. Differentiating the data set into weakly and strongly shifted experimental pK(a) values, however, we found that PROPKA's accuracy is better if the pK(a) values are weakly shifted but on equal footing with that of KBPLUS for more strongly shifted values. On the other hand, PKAcal reproduces strongly shifted pK(a) values badly but weakly shifted values with the same accuracy as PROPKA. We tested different consensus approaches combining data from all three methods to find a general procedure for most accurate pK(a) predictions. In most of the cases we found that the consensus approach reproduced experimental data with better accuracy than any of the individual methods alone.     

Determination of intrinsic bacterial surface acidity constants using a donnan shell model and a continuous pK(a) distribution method

Intrinsic acidity constants (pK(a)(int)) for Bacillus subtilis (Gram+) and Escherichia coli (Gram-) cells were calculated from potentiometric titration data at different salt concentrations. Master curves were generated by replotting charge excess data as a function of pH(S) (pH at the location of surface reactive sites) where pH(S) was determined as a function of Donnan potential, Psi(DON). This potential decreased in magnitude with increasing ionic strength, from -48.5+/-0.2 to -3.5+/-0.0 mV for B. subtilis and -47.9+/-0.3 to -3.5+/-0.0 mV for E. coli at 0.01 and 0.5 M K(+), respectively, indicating an efficient surface charge neutralization by counterions. A fully optimized continuous (FOCUS) pK(a) distribution method revealed four binding sites on B. subtilis and E. coli surfaces from the master curves with pK(a)(int) values of 3.59+/-0.38, 4.33+/-0.57, 5.94+/-0.66, and 8.64+/-0.57 for B. subtilis and 3.73+/-0.44, 4.85+/-0.71, 6.56+/-0.64, and 8.79+/-0.62 for E. coli. These were assigned to functional groups according to reported pK(a) ranges of 2.0-6.0 (carboxylic acid), 3.2-3.5 (phosphodiesters), 5.6-7.2 (phosphoric acid), and 9.0-11.0 (amine groups). Average points of zero salt effect (pH(pzse)) for B. subtilis experiments were 6.63+/-0.21 and 6.42+/-0.08 as a function of pH(bulk) and pH(S), respectively. Under the same criteria, E. coli calculations yielded 5.73+/-0.23 and 5.45+/-0.05. An understanding of metal and proton reactivity on bacterial cell surfaces can be addressed quantitatively through the use of electrostatic and chemical equilibrium modeling techniques proposed in this study. The results are consistent with those of electrical force microscopy studies used to document the intrinsic electrochemical heterogeneity of bacterial cell surfaces.     

Accurate determination of low pK values by (1)H NMR titration

The NMR titration methodology to determine acid dissociation constants in aqueous solutions is extended for pK(a) values between 0 and 2, where potentiometric titrations are no longer applicable. (1)H NMR spectra are acquired for single samples of constant acid concentration (e.g. 0.02M), controlled ionic strength (I=1M with HNO(3)/NaNO(3)) and varying pH. To avoid biased pH readings due to the acid error of the glass electrode, true, concentration-based pH values are deduced by combination of the charge balance equation with information from (1)H NMR chemical shifts of the investigated acid. The method has been tested on histidine (pK(1)=1.83+/-0.02) and yielded the dissociation constant of dichloroacetic acid (pK=1.06+/-0.01) for the first time with good accuracy and precision. Dichloroacetic acid is recommended as an NMR spectroscopical "indicator molecule" for in situ monitoring the pH in strong acidic solutions of other equilibrium systems.     

Measuring pK(a) values in protein folding transition state ensembles by NMR spectroscopy

Protein folding kinetic data have been obtained for the marginally stable N-terminal SH3 domain of the Drosophila protein drk as a function of pH in order to investigate the electrostatic properties of Asp8 in the folding transition state ensemble. The slow exchange between folded and unfolded forms of the protein gives rise to separate NMR resonances for both folded and unfolded states at equilibrium. As a result, kinetic data can be derived from magnetization transfer between these two states without the need for denaturants. Using the fact that ionization of Asp8 dominates the electrostatic behavior of the protein between pH 2 and 3, along with pKa values for titrating groups in both folded and unfolded states that have been determined in a previous study, values of 2.9 +/- 0.1 and 3.3 +/- 0.2 are obtained for the pKa of Asp8 in the transition state for the wild-type protein and for a His7Ala mutant, respectively. The data are consistent with the partial formation in the transition state ensemble of an Asp8 side chain carboxylate-a Lys21 backbone amide interaction that represents a highly conserved contact in folded SH3 domains.     

Simultaneous determination of partition coefficients and acidity constants of chlorinated phenols and gualacols by gas chromatography

The partition coefficients, P, in the n-octanol/water system and the acidity constants, K_a, of 15 chlorinated phenols and guaiacols at 20° were simultaneously determined by investigating the pH dependence of the apparent partition coefficients, P_a. For determining P_a, the relative responses of individual phenols and guaiacols in the aqueous phase after equilibration were measured by glass-capillary gas chromatography with electron-capture detection and compared with those in the octanol phase before partition. Curvefitting, linear regression, and non-linear regression were used for treating the partition data. The values of pK_a and log P were compared with the values which could be found in the literature, and are discussed in relation to their affinity to methanol/water and acetonitrile/water mixtures.     

DFT/electrostatic calculations of pK(a) values in cytochrome c oxidase

Using classical electrostatic calculations, earlier we examined the dependence of the protonation state of bovine cytochrome c oxidase (CcO) on its redox state. Based on these calculations, we have proposed a model of CcO proton pumping that involves His291, one of the Cu(B) histidine ligands, which was found to respond to redox changes of the enzyme Fe(a)(3)-Cu(B) catalytic center. In this work, we employ combined density functional and continuum electrostatic calculations to evaluate the pK(a)() values of His291 and Glu242, two key residues of the model. The pK(a) values are calculated for different redox states of the enzyme, and the influence of different factors on the pK(a)'s is analyzed in detail. The calculated pK(a)() values of Glu242 are between 9.4 and 12.0, depending on the redox state of the protein, which is in excellent agreement with recent experimental measurements. Assuming the reduced state of heme a(3), His291 of the oxidized Cu(B) center possesses a pK(a)() between 2.1 and 4.0, while His291 of the reduced Cu(B) center has a pK(a) above 17. The obtained results support the proposal that the His291 ligand of the Cu(B) center in CcO is a proton pump element.     

The relationship between proton-proton NMR coupling constants and substituent electronegativities—I : An empirical generalization of the karplus equation

A new coupling constant-torsion angle relation for the three-bond ¹H-¹H spin-spin coupling constant is formulated. The relation includes a correction for the electronegativity of substituents. The correction term is written as a function of the electronegativity, the H-C-C-H torsion angle, and the orientation of each substituent relative to the coupled protons. A dataset consisting of 315 experimental coupling constants was used to derive six empirical parameters by means of an iterative least-squares minimization procedure. The precision of the proposed equation, expressed as the root-mean-square deviation (0.48 Hz), is superior to any hitherto reported. It is shown that separate treatment of CH₂CH₂, CH₂CH and CHCH fragments even improves this precision. An application in the field of monosubstituted cyclohexanes is given.     

The pK(a) values of N,N,N',N'-tetrakis-(2-hydroxypropyl)ethylenediamine

Aqueous solutions of the industrially important chelating agent N,N,N',N'-tetrakis(2-hydroxypropyl)ethylenediamine exhibit basic properties. The proton dissociation constants were determined to be 8.99 +/- 0.04 (pK(1)) and 4.30 +/- 0.04 (pK(2)) by potentiometric titration at 25 degrees in 0.15M sodium chloride.     

Determination of the overlapping pK(a) values of chrysin using UV-vis spectroscopy and ab initio methods

The overlapping pK(a) values of 5,7-dihydroxyflavone (chrysin) in EtOH-water solutions were determined by means of a UV-vis spectroscopic method that uses absorbance diagrams, at constant ionic strength (0.050 M) and temperature (25.0+/-0.1 degrees C). It was observed that the pK(a) values increase when the polarity-polarizability and solvation abilities of the reaction medium decrease. In order to calculate the pK(a1) and pK(a2) of chrysin in pure water, various relationships between the determined pK(a) and properties of solvents (relative permittivity, alpha-parameter of Taft and parameter Acity), are proposed. Moreover, with the aim of explaining the first pK(a1) value obtained, the molecular conformations and solute-solvent interactions of the 7(O(-))chrysinate monoanion were also investigated, using ab initio methods. Several ionization reactions and equilibria in water, which possesses a high hydrogen-bond-donor ability, are proposed. These reactions and equilibria constituted the necessary theoretical basis to calculate the first acidity constant of chrysin. The HF/6-31G(d) and HF/6-31+G(d) methods were used for calculations. Tomasi's method was used to analyze the formation of intermolecular hydrogen bonds between the 7(O(-))chrysinate monoanion and water molecules. It was proposed that in alkaline aqueous solutions the monoanion of chrysin is solvated with one water molecule. The agreement between the experimental and theoretical pK(a1) values provides good support for the acid-base reactions proposed in this paper.     

Evaluation of a reversed-phase column (supelcosil LC-ABZ) under isocratic and gradient elution conditions for estimating octanol-water partition coefficients

The solvation parameter model is used to identify suitable chromatographic models for estimating the octanol-water partition coefficient for neutral compounds of varied structure by reversed-phase liquid chromatography. The stationary phase Supelcosil LC-ABZ with methanol-water mobile phases affords a series of suitable correlation models for estimating the octanol-water partition coefficient (log KOW) under isocratic and gradient elution conditions. Isocratic separations with mobile phase compositions containing from about 25 to 40% (v/v) methanol provide the most accurate results for log KOW values in the range -0.1 to 4.0. Gradient separations programmed from 5 to 100% (v/v) methanol are suitable for faster separations of compounds with large log KOW values. The standard error in the estimate for the regression models of the predicted log KOW values against literature values are 0.135 log units for the 30% (v/v) methanol-water isocratic system and 0.263 log units for the methanol-water gradient system. Isocratic retention factors predicted from two gradient separations with gradient times of 15 and 45 min afford a poorer fit for the correlation models between log KOW and the estimated retention factors than that of either the above isocratic and gradient models. Plots of the retention factor (log k) as a function of mobile phase composition are generally non-linear. Values of log kw obtained by non-linear extrapolation to a volume fraction of 0% (v/v) methanol do not afford a useful model for estimating log KOW.     

pK(a) values and geometries of secondary and tertiary amines complexed to boronic acids-implications for sensor design

[structure in text] The pK(a) values and the geometries of secondary and tertiary amines adjacent to boronic acids were determined using potentiometric and (11)B NMR titrations. The studies showed that the secondary ammonium ion has a pK(a) similar to that of the tertiary ammonium species, which leads to the formation of tetrahedral boron centers at pH values above approximately 5.5. Therefore, secondary amines as well as tertiary amines, when placed proximal to boron centers, can be used to create tetrahedral boronic acids at neutral pH for diol complexation.     

Measurement of side-chain carboxyl pK(a) values of glutamate and aspartate residues in an unfolded protein by multinuclear NMR spectroscopy

A triple-resonance NMR pulse scheme is presented for measuring aspartic and glutamic acid side-chain pK(a) values in unfolded protein states where chemical shift overlap is limiting. The experiment correlates side-chain carboxyl carbon chemical shifts of these residues with the backbone amide proton chemical shift of the following residue. The methodology is applied to an (15)N, (13)C labeled sample of the N-terminal SH3 domain of the Drosophila protein drk, which exists in equilibrium between folded (F(exch)) and unfolded (U(exch)) states under nondenaturing conditions. Residue-specific pK(a) values of side-chain carboxyl groups are presented for the first time for an unfolded protein (drk U(exch) state), determined from a pH titration. Results indicate that deviations from pK(a) values measured for model compounds are likely due to local effects, while long-range electrostatic interactions appear to be of minor importance for this protein.     

Analysis of anticancer platinum(II)-complexes by microemulsion electrokinetic chromatography: separation of diastereomers and estimation of octanol-water partition coefficients

Microemulsion electrokinetic chromatography (MEEKC) was applied for the separation and lipophilicity estimation of oxaliplatin and eight novel anticancer oxaliplatin derivatives. Solubility and permeability have to be balanced in modern drug development, and the octanol-water partition coefficient (log P) still represents one of the most useful quantifiable parameters providing a reasonable estimation of a drug's lipophilicity. Therefore, the capacity factors from MEEKC were correlated to log P values derived by the traditional shake flask method. The MEEKC method was accomplished using a microemulsion of heptane/sodium dodecyl sulfate (SDS)/butanol in phosphate buffer at pH 7.4 and 37 degrees C with all analytes being in a neutral state during the run. This experimental setup allowed a baseline separation of all platinum complexes within 11 min. Remarkably, beside the very good resolution and precision of the measurements, separation of diastereomers of the complexes and quantification of the diastereomeric ratios could be achieved. Correlating the capacity factors with the corresponding log P values resulted in a linear dependency with a correlation factor of r = 0.9935. Consequently, the applied MEEKC method was found to be a highly valuable technique not only for the separation of platinum complexes but as well for the estimation of the octanol-water partition coefficient with many advantages in comparison to other methods.