Determination of pKa values of active pharmaceutical ingredients

The acid dissociation constant is an important physicochemical parameter of a substance, and knowledge of it is of fundamental importance in a wide range of applications and research areas. We present a critical review of published methods and approaches for the determination of acid dissociation constants, with a special emphasis on the pK_a values of active pharmaceutical ingredients.     

Isotachophoretic determination of mobility and pKa by means of computer simulation : V. Evaluation of mo and pKa of twenty-eight dipeptides and assessment of separability

Isotachophoretic qualitative indices, R_E, for twenty-eight dipeptides were measured in the range pH 7.4–9.6. The absolute mobility, m_o, and pK_a values were evaluated by the use of the least-squares method, utilizing a simulation of the isotachophoretic steady state. The m_o values were newly evaluated and the pK_a values were in good agreement with literature values. By comparison of the evaluated m_o and pK_a values of the dipeptides with those of the constituent amino acids, simple relationships were found which may be used to estimate the m_o and pK_a values of other dipeptides. The separability of the dipeptides was also evaluated by considering the differences between their simulated effective mobilities. It is concluded that isotachophoresis is very convenient for the separation of dipeptides and their constituent amino acids.     

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.     

Ab initio calculations of pKa values of some organic acids in aqueous solution

The acidity of different classes of organic compounds in aqueous solution has been calculated. The calculations are carried out at the SCF level with inclusion of entropic and thermochemical correction to yield free energies of dissociations.

The polarized continuum model is used to describe the solvent. The model furnishes pK_a values in relatively good agreement with experimental data. Scaling different parts of solvation energies provides a significant improvement in results and signifies the importance of balance of individual contributions from electrostatic, cavity, dispersion and repulsion interactions.     

Critical validation of a new simpler approach to estimate aqueous pKa of drugs sparingly soluble in water

A simple linear approach to estimate the aqueous pK_a of compounds sparingly soluble in water, mainly drugs, from solely one pK_a value determined in any methanol/water mixture is evaluated. The parameters (slope and intercept) of the linear relationships are related to the solvent composition and can be easily calculated according to the acidic or basic functional group of the compound. The method has been tested using the available literature data for phenols, aliphatic carboxylic acids, benzoic acid derivatives, both ortho and non-ortho substituted, amines and imidazole derivatives. The study involves the whole range of solvent composition and about one hundred compounds which show a wide variety of aqueous pK_a, from 1.3 to 12.4. The differences between calculated and previously published aqueous pK_a values are less of 0.2 pK units. Consistent values are obtained whatever the composition of methanol/water mixture employed in the experimental measurements. The results support the usefulness of the tested method as a very simple approach to get reliable aqueous pK_a values for sparingly soluble drugs.     

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.     

Formation of hydrogen-bonded chains between a strong base with guanidine-like character and phenols with various pKa values - an FT-IR study

The complexes formed by phenols with 1,3,4,6,7,8-hexahydro-1-methyl-2H-pyrimido[1,2-a]pyrimidine (mTBD), an N-base with guanidine-like character, were studied as a function of the pK_a of the phenols by FT-IR spectroscopy. The following phenols were used: 4-cyanophenol (4-CNPh), pentachlorophenol (PCP) and 2,6-dichloro-4-nitrophenol (DNPh). In the case of chloroform solutions of 1:1 mixtures of the phenols with MTBD the corresponding complexes are formed completely. With increasing acidity of the phenols the hydrogen bonds become increasingly asymmetrical. The OH … N ⁻O … H⁺N hydrogen bond in the 4-CNPh-MTBD complex shows large proton polarizability. In the other cases only the polar structure is realized. With increasing phenol MTBD ratio, the formation of chains with two phenol molecules is observed. With decreasing pK_a of the phenols the fluctuation is limited to the phenol-phenolate bond and finally, the phenol-protonated MTBD bond begins to dissociate. In acetonitrile solutions, N⁺H … O⁻ hydrogen bonds are observed in the case of the 1:1 mixture of 4-CNPh with MTBD. A weak continuum indicates the presence of homoconjugated phenol-phenolate bonds with large proton polarizability. In the case of 2:1 mixtures only protonated MTBD and homoconjugated phenol-phenolate bonds are observed, independent of the pK_a of the phenols. The results are discussed with regard to the proton pathway in bacteriorhodopsin.     

(E)-2-Benzylidenebenzocyclanones, part VIII: spectrophotometric determination of pKa values of some natural and synthetic chalcones and their cyclic analogues

Abstract  

UV–Vis spectrophotometry was used to determine acid dissociation constant (pK _a) values of the natural flavonoids phloretin, phlorizin, naringenin, and naringin, as well as 4′-hydroxychalcone, 4′-(dimethylamino)chalcone, and their cyclic analogues. Comparison of the results with those previously reported for the natural flavonoids showed the applied method is a relatively straightforward and easy-to-perform technique for the determination of pK _a values of compounds with relatively low solubility. Comparative analysis of the pK _a values of the synthetic chalcones showed a strong correlation between the degree of conjugation and the acid strength of the respective compounds with different geometry. Our results provide further evidence that modification of the three-dimensional structure of open-chain bioactive compounds is the method of choice to modify not only their stereochemistry but also their physicochemical properties.     

The regression of isothermal thermogravimetric data to evaluate degradation Ea values of polymers: A comparison with literature methods and an evaluation of lifetime prediction reliability

The thermooxidative degradation of four well known polymers, polyethylene (PE), polystyrene (PS), polycarbonate (PC) and poly(methyl methacrylate) (PMMA), was carried out in a thermogravimetric (TG) analyser, at various temperatures (in the 473–533 K range), in isothermal heating conditions. The resulting set of experimental TG data was used to determine the apparent activation energy (E_a) of degradation through two isothermal literature methods, as well as through a very simple method we set up, based on the direct regression of the experimental mass loss data, in order to verify the general applicability of our method to various polymers. The results from different methods were in good agreement. Degradation experiments in dynamic heating conditions, which were also performed, gave E_a values in good agreement with those in isothermal heating conditions for PS, PC and PMMA, while for PE a large discrepancy was observed, which was discussed and interpreted. The results suggested the general applicability of our method to all polymers, independently on their structure and degradation mechanism. A long-term (about 13 months) isothermal degradation experiment was also carried out with the same polymers at relatively low temperature (423 K). Only PE and PS evidenced appreciable mass loss in the investigated period, but the experimental data were not in agreement with those from the short-term degradations at higher temperatures, thus suggesting different degradation kinetics, and a low reliability of the lifetime predictions for polymers in service based on experiments at higher temperatures.     

Conformational dependence of charges in protein simulations

We have studied the conformational dependence of molecular mechanics atomic charges for proteins by calculating the charges fitted to the quantum mechanical (QM) electrostatic potential (ESP) for all atoms in complexes between avidin and seven biotin analogues for 20 snapshots from molecular dynamics simulations. We have studied how various other charge sets reproduce those charges. The QM charges, even if averaged over all snapshots or all residues, in general have a larger magnitude than standard Amber charges, indicating that the restraint toward zero in the restrained ESP method is too strong. This has a significant influence on the electrostatic conformational energies and the interaction energy between the biotin ligand and the protein, giving a difference between the QM and Amber charges of 43 and 8 kJ/mol for the negatively charged and neutral biotin analogues, respectively (3-4%). However, this energy difference is strongly reduced if the solvation energy (calculated by the Poisson-Boltzmann or Generalized Born methods) is added, viz., to 7 kJ/mol for charged and 3 kJ/mol for uncharged ligand. In fact, charges need to be recalculated with a QM method only for residues within 7 or 4 A of the ligand, if the error should be less than 4 kJ/mol. Unfortunately, the QM charges do not give significantly better MM/PBSA estimates of ligand-binding affinities than standard Amber charges.     

A theoretical investigation of C5

Large-scale CEPA-1 calculations have been carried out for linear C₅, a molecule of substantial interest to combustion processes and astrochemistry. The equilibrium bond lengths are predicted to be 1.289 Å (outer CC bond) and 1.283 Å (inner CC bond), with an accuracy of 0.002 Å. The calculated ν₃ band origins of 2161 cm⁻¹ (105 CGTO basis) and 2137 cm⁻¹ (150 CGTO basis) are in good agreement with the experimental value of 2169 cm⁻¹. This band has an extremely large transition moment of 0.74 D. The less intense stretching fundamental ν₄ (μ=0.18 D) is predicted to occur at 1478 ± 10 cm⁻¹. Predictions for the totally symmetric stretching and the bending vibrational frequencies (in cm⁻¹) are 2008 (1σ_g⁺), 792 (2σ_g⁺), 570 (1π_u), 209 (1π_g) and 119 (2π_u).     

Conformational dependence of the 1Lb and n → π* rotatory strengths in α-substituted phenylacetic acids

The chiroptical properties of a series of chiral phenylacetic acid derivatives are examined on a theoretical model in which electronic rotatory strengths are calculated directly from molecular wave functions derived from semiempirical molecular orbital calculations. The CNDO/S SCF-MO model is used to calculate ground state wave functions and excited states are constructed in the virtual orbital-configuration interaction approximation. Of special interest are the rotatory strengths associated with the ¹L_b transition of the phenyl chromophore and the n → π^* transition of the carboxyl chromophore. Calculations are carried out on a large number of conformational isomers of the compounds: α-methyl phenylacetie acid (and its methyl ester), α-methylmandelic acid (and its methyl ester), and mandelic acid (and its methyl ester). The dependence of rotatory strength (¹L_b and n → π^*) on conformational variables is examined and discussed, and comparisons between available experimental data and the calculated results are made. Coupling between the phenyl and carboxyl chromophoric moieties is considered and possible spectra-structure relationships are examined.     

Conformational dependence of intramolecular vibrational redistribution in methanol

Previous state-selected spectra of methanol in the 5nu(1) OH stretch overtone region [O. V. Boyarkin, T. R. Rizzo, and D. S. Perry, J. Chem. Phys. 110, 11346 (1999)] revealed a structure indicating an intramolecular vibrational redistribution on three time scales. Whereas in that work, methanol in the 5nu(1) bright state was prepared close to the staggered conformation, methanol in the "partially eclipsed" conformation is prepared here by double resonance excitation through a torsionally excited intermediate state. The excited molecules are detected by infrared laser assisted photofragment spectroscopy. In partially eclipsed methanol, the strong coupling of the nu(1) OH stretch to the nu(2) CH stretch becomes weaker, but the coupling responsible for the widths of the narrowest features becomes stronger.     

Conformational analysis of N-benzyl-N-o-tolyl-p-methylbenzene-sulfonamides from dynamic H NMR experiments and theoretical calculations

Theoretical studies of molecular conformations of four N-benzyl-N-o-tolyl-p-methylbenzenesulfonamides, by means of semiempirical PM3, ab initio (RHF and MP2) methods, and DFT approach, are presented and discussed in comparison with the experimental data. The free energy (ΔG^#) of rotation obtained by the dynamic shape analysis of the ¹H NMR spectra is ca. 16 kcal/mol for those systems for which the barrier has been probed experimentally. Failure to determine the barrier in the experimental spectra in the case of one system is attributed to the chiral conformation of the global minimum. The rotational profile was established at the PM3 level and verified at the DFT level of theory. The solvent effect, the 0th-order vibrational corrections, and the temperature dependence of the Boltzman distribution of conformers and kinetic equilibrium are discussed.     

Conformational changes accompanying electronic excitation of CD3 NO

Analysis of the 675 nm absorption of CD₃NO shows that the conformation changes from eclipsed in the ground state to staggered in the à ¹A″(ne*) excited state. The internal-rotation barrier V₃ increases from 383 to 475± 50 cm^?1.     

Conformational dependence of the second hyperpolarizability of quadrupolar molecules

Hatree–Fock calculations at ab initio and semiempirical levels were carried out for the averaged polarizability α and second hyperpolarizability γ of two pairs of quadrupolar isomers with different donor and acceptor groups. These properties were correlated with the antibonding/bonding π occupation number (π*/π ratio). It was found that isomers with extended π systems had low π*/π ratios and high α and γ values, while low α and γ values were obtained for isomers with large π*/π ratios and no extended π system. The PM3 and PM6 α values were found to be in excellent agreement with the HF/6-31+G(d,p) ones. The PM3 values for γ were significantly larger than those calculated by HF/6-31+G(d,p), with an average PM3/HF ratio of 1.43. The PM6 results were noticeably better with a ratio of 0.85. The calculation of α and γ at MP2/6-31+G(d,p) level for representative isomers showed that the contribution of the electron correlation to their values was small and that the HF/6-31+G(d,p) method provides reliable values at much lower computational cost.     

Structure of small TiCn clusters: A theoretical study

A theoretical study of the TiC_n (n = 1–8) clusters has been carried out at the B3LYP/6-311+G(d) level. Molecular properties for three different isomers, namely linear, cyclic, and fan species, have been determined. The fan isomers, where the titanium atom is essentially side-bonded to the entire C_n unit, are predicted to be more stable than both linear and cyclic isomers. Only for the largest studied species, TiC₈, the cyclic isomer is located lower in energy. An even–odd parity effect in the incremental binding energies is observed for the three isomers, n-even species being in general more stable for linear and fan isomers, whereas for the cyclic species n-odd clusters are favoured. A topological analysis of the electronic charge density shows that all cyclic isomers correspond to true monocyclic rings, whereas for the fan species a variety of different connectivities has been observed.     

The temperature dependence of the HO2 + HO2 reaction

The temperature dependence of the rate constant for the reaction HO₂ + HO₂ → H₂O₂ + O₂ (2k₁) has been determined using flash photolysis techniques, over the temperature range 298–510 K, in a nitrogen diluent at a total pressure of 700 Torr. The overall second order state constant is given by k₁ = (4.14 ± 1.15) × 10^?13 exp[(630 ± 115)/T] cm³ molecule^?1 s^?1, where the quoted errors refer to one standard deviation. This result is compared with previous findings and the negative activation energy is shown to be consistent with the observation that the rate constant is pressure dependent at 700 Torr.