Experimentation with different thermodynamic cycles used for pKa calculations on carboxylic acids using complete basis set and Gaussian‐n models combined with CPCM continuum solvation methods

Complete basis set and Gaussian‐n methods were combined with Barone and Cossi's implementation of the polarizable conductor model (CPCM) continuum solvation methods to calculate pK_a values for six carboxylic acids. Four different thermodynamic cycles were considered in this work. An experimental value of ?264.61 kcal/mol for the free energy of solvation of H⁺, ΔG_s(H⁺), was combined with a value for G_gas(H⁺) of ?6.28 kcal/mol, to calculate pK_a values with cycle 1. The complete basis set gas‐phase methods used to calculate gas‐phase free energies are very accurate, with mean unsigned errors of 0.3 kcal/mol and standard deviations of 0.4 kcal/mol. The CPCM solvation calculations used to calculate condensed‐phase free energies are slightly less accurate than the gas‐phase models, and the best method has a mean unsigned error and standard deviation of 0.4 and 0.5 kcal/mol, respectively. Thermodynamic cycles that include an explicit water in the cycle are not accurate when the free energy of solvation of a water molecule is used, but appear to become accurate when the experimental free energy of vaporization of water is used. This apparent improvement is an artifact of the standard state used in the calculation. Geometry relaxation in solution does not improve the results when using these later cycles. The use of cycle 1 and the complete basis set models combined with the CPCM solvation methods yielded pK_a values accurate to less than half a pK_a unit. © 2001 John Wiley & Sons, Inc. Int J Quantum Chem, 2001     

Theoretical Study of Firefly Luciferin pKa Values—Relative Absorption Intensity in Aqueous Solutions

Ground‐state vibrational analyses of firefly luciferin and its conjugate acids and bases are performed. The Gibbs free energies obtained from these analyses are used to estimate pK_a values for phenolic hydroxy and carboxy groups and the N–H⁺ bond in the N‐protonated thiazoline or benzothiazole ring of firefly luciferin. The theoretical pK_a values are corrected using the experimental values. The concentrations of these chemical species in solutions with different pH values are estimated from their corrected pK_a values, and the pH dependence of their relative absorption intensities is elucidated. With the results obtained we assign the experimental spectra unequivocally. Especially, the small peak near 400 nm at pH 1–2 in experimental absorption spectra is clarified to be due to the excitation of carboxylate anion with N‐protonated thiazoline ring of firefly luciferin. Our results show that the pK_a values of chemical species, which are contained in the aqueous solutions, are effective to assign experimental absorption spectra.     

Enantioselective Synthesis and Physicochemical Properties of Libraries of 3‐Amino‐ and 3‐Amidofluoropiperidines

The enantioselective syntheses of 3‐amino‐5‐fluoropiperidines and 3‐amino‐5,5‐difluoropiperidines were developed using the ring enlargement of prolinols to access libraries of 3‐amino‐ and 3‐amidofluoropiperidines. The study of the physicochemical properties revealed that fluorine atom(s) decrease(s) the pK_a and modulate(s) the lipophilicity of 3‐aminopiperidines. The relative stereochemistry of the fluorine atoms with the amino groups at C3 on the piperidine core has a small effect on the pK_a due to conformationnal modifications induced by fluorine atom(s). In the protonated forms, the C?F bond is in an axial position due to a dipole–dipole interaction between the N?H⁺ and C?F bonds. Predictions of the physicochemical properties using common software appeared to be limited to determine correct values of pK_a and/or differences of pK_a between cis‐ and trans‐3‐amino‐5‐fluoropiperidines.     

Intrinsic Acid–Base Properties of a Hexa‐2′‐deoxynucleoside Pentaphosphate,d(ApGpGpCpCpT): Neighboring Effects and Isomeric Equilibria

The intrinsic acid‐base properties of the hexa‐2′‐deoxynucleoside pentaphosphate, d(ApGpGpCpCpT) [=(A1?G2?G3?C4?C5?T6)=(HNPP)^5?] have been determined by ¹H NMR shift experiments. The pK_a values of the individual sites of the adenosine (A), guanosine (G), cytidine (C), and thymidine (T) residues were measured in water under single‐strand conditions (i.e., 10 % D₂O, 47 °C, I=0.1 M , NaClO₄). These results quantify the release of H⁺ from the two (N7)H⁺ (G?G), the two (N3)H⁺ (C?C), and the (N1)H⁺ (A) units, as well as from the two (N1)H (G?G) and the (N3)H (T) sites. Based on measurements with 2′‐deoxynucleosides at 25 °C and 47 °C, they were transferred to pK_a values valid in water at 25 °C and I=0.1 M . Intramolecular stacks between the nucleobases A1 and G2 as well as most likely also between G2 and G3 are formed. For HNPP three pK_a clusters occur, that is those encompassing the pK_a values of 2.44, 2.97, and 3.71 of G2(N7)H⁺, G3(N7)H⁺, and A1(N1)H⁺, respectively, with overlapping buffer regions. The tautomer populations were estimated, giving for the release of a single proton from five‐fold protonated H₅(HNPP)^±, the tautomers (G2)N7, (G3)N7, and (A1)N1 with formation degrees of about 74, 22, and 4 %, respectively. Tautomer distributions reveal pathways for proton‐donating as well as for proton‐accepting reactions both being expected to be fast and to occur practically at no “cost”. The eight pK_a values for H₅(HNPP)^± are compared with data for nucleosides and nucleotides, revealing that the nucleoside residues are in part affected very differently by their neighbors. In addition, the intrinsic acidity constants for the RNA derivative r(A1?G2?G3? C4?C5?U6), where U=uridine, were calculated. Finally, the effect of metal ions on the pK_a values of nucleobase sites is briefly discussed because in this way deprotonation reactions can easily be shifted to the physiological pH range.     

Physicochemical Properties of a New Multicomponent Cosolvent System for the pKa Determination of Poorly Soluble Pharmaceutical Compounds

A mixture of cosolvents is described that significantly improves the solubility of most pharmaceutical compounds. The mixture consists of equal volumes of MeOH, 1,4‐dioxane, and MeCN, thereby containing polar and nonpolar solvents, and is referred to as MDM (from MeOH, dioxane, and MeCN). MDM is mixed with H₂O until the required composition is reached. The utility of this system is that it enables analytical measurements to be performed on a wide range of compounds where measurements would be impaired in aqueous solution. We present the physicochemical characteristics of MDM/H₂O mixtures (density, dielectric constant, p_sK_w) and the principles of pK_a measurement in this solvent/H₂O mixture. We also present pK_a values in H₂O of several drug compounds determined from values measured in MDM/H₂O mixtures.     

High-molecular-weight hydrolyzed polyacrylamides. II. Potentiometric titrations

Potentiometric titrations in water of high-molecular-weight partly hydrolyzed polyacrylamides were analyzed by the Lifson—Katchalsky rodlike model. A fair concordance was found between theory and experimental curves with pK₀ of acid functions of about 4.75 when 0 < τ < 0.49. Two methods were derived to calculate the parameter n of the extended Henderson-Hasselbach equation by using a series expansion of pK_a vs. α, not yet reported in the literature. A new equation for n was established and comparison between two sets of values of n, obtained by using the theoretical ΔpK curves and series expansion is discussed.     

Experimental and computational study of the pKa of coumaric acid derivatives

The dissociation constant (pK_a) of a drug is a key parameter in drug discovery and pharmaceutical formulation. The hydroxy substituent has a significant effect on the acidity of hydroxycinnamic acid. In this work, the acidic constants of coumaric acids are obtained experimentally by spectrophotometry using the chemometric method and calculated theoretically using ab initio quantum mechanical method at the HF/6‐31G* level of theory in combination with the SMD continuum solvation method. Rank annihilation factor analysis (RAFA) is an efficient chemometric technique based on the elimination of the contribution of one of the chemical components from the data matrix. RAFA cannot be performed because the pure spectrum of HA^? is not available. So, two‐rank annihilation factor analysis (TRAFA) is proposed for the determination of the pK_a OF H₂A. A comparison between the pK_a values obtained previously by TRAFA for the molecules o‐coumaric acid (4.13, 9.58), m‐coumaric acid (4.48, 10.35), and p‐coumaric acid (4.65, 9.92) makes it clear that there is good agreement between the results obtained by TRAFA and ab initio quantum mechanical method.     

Potentiometric and Voltammetric Study of 6‐Benzylaminopurine and Its Derivatives

The protonation‐deprotonation equilibrium of 6‐benzylaminopurine (6‐BAP) and its derivatives was studied by potentiometry and voltammetry. The effect of Cl‐ or OCH₃‐group in position 2′, 3′ and 4′ of the benzene ring of 6‐BAP on both pK_a values was investigated. To determine the enthalpy and entropy, the temperature dependence of pK_a was employed. It was found that with increasing temperature the pK_a decreased. In comparison with 6‐BAP the chloro‐ or methoxy‐ group resulted in pK_a increase. The first pK_a values were also determined by linear sweep (LSV) and elimination voltammetry with linear scan (EVLS). New approaches were shown not only for the determination of pK_a from voltammetric titration curves but also for the evaluation of the reduction processes of benzylaminopurines.     

Structure–Reactivity Relationship in the Frustrated Lewis Pair (FLP)‐Catalyzed Hydrogenation of Imines

The autoinduced, frustrated Lewis pair (FLP)‐catalyzed hydrogenation of 16‐benzene‐ring substituted N‐benzylidene‐tert‐butylamines with B(2,6‐F₂C₆H₃)₃ and molecular hydrogen was investigated by kinetic analysis. The pK_a values for imines and for the corresponding amines were determined by quantum‐mechanical methods and provided a direct proportional relationship. The correlation of the two rate constants k₁ (simple catalytic cycle) and k₂ (autoinduced catalytic cycle) with pK_a difference between imine and amine pairs (ΔpK_a) or Hammett's σ parameter served as useful parameters to establish a structure–reactivity relationship for the FLP‐catalyzed hydrogenation of imines.     

Capillary electrokinetic fractionation mass spectrometry (CEkF/MS): Technology setup and application to metabolite fractionation from complex samples coupled at‐line with ultrahigh‐resolution mass spectrometry

Capillary electrokinetic fractionation (CEkF) is investigated as a new, simple, and robust approach for semipreparative and analytical sample analysis based on pK_a‐dependant pH‐driven electrophoretic mobility. CEkF was optimized with contactless conductivity detection and conducted with 10 kV reverse voltage for 10 min, then coupled on/at‐line to ESI/MS. We propose a semi‐empirical model with 14 representative compounds based on the correlation between sample/medium pH regulating the partial charge, the electrokinetic loading of the capillary and intensity (I) of analytes. According to the model, an empirical function (I = f (pH)) could be derived to calculate the acid dissociation constant (pK_a) of various model compounds based on their pH‐dependant MS intensity profiles with the RSD < 4.05. Using the ultrahigh‐resolution of ion cyclotron resonance Fourier transform MS, the pK_a model was further illustrated in real samples into the structure prediction of important compounds in wine over two vintages. The established CEkF was successfully used to selectively fractionate sulfur compounds from the complex wine samples at pH 1.66. The proposed CEkF approach should allow in the future the simultaneous pK_a evaluation of multiple constituents without complicated separation out of a complex mixture in metabolomics or environmental chemistry.     

Relative pKa of some anilinium derivatives in methanol,acetonitrile, and tetrahydrofurane solvents

In this study, the relative pK_a values of nine anilinium derivatives in methanol (MeOH), acetonitrile (AN), and tetrahydrofurane (THF) solutions were successfully calculated with mean absolute deviations of 0.63, 0.68, and 0.75 pK_a units, respectively. To this aim, their gas‐phase basicities were computed using the CBS‐QB3 composite method. Also, conductor‐like polarizable continuum model (CPCM) with UAHF, UAKS and UA0 cavities and SM8 solvation models at HF/6‐31+G(d) level of theory were applied for the calculation of the solvation Gibbs free energies. The obtained results indicate that there is reliable correlation between the experimental and computed pK_a values in the studied solutions. Therefore, to extend the pK_a database for anilines, correlation equations were used to predict the pK_a values in the investigated solvents.     

pKa prediction for acidic phosphorus‐containing compounds using multiple linear regression with computational descriptors

Ninety‐six acidic phosphorus‐containing molecules with pK_a 1.88 to 6.26 were collected and divided into training and test sets by random sampling. Structural parameters were obtained by density functional theory calculation of the molecules. The relationship between the experimental pK_a values and structural parameters was obtained by multiple linear regression fitting for the training set, and tested with the test set; the R² values were 0.974 and 0.966 for the training and test sets, respectively. This regression equation, which quantitatively describes the influence of structural parameters on pK_a, and can be used to predict pK_a values of similar structures, is significant for the design of new acidic phosphorus‐containing extractants. © 2016 Wiley Periodicals, Inc.     

The salt–cocrystal spectrum in salicylic acid–adenine: the influence of crystal structure on proton‐transfer balance

At one extreme of the proton‐transfer spectrum in cocrystals, proton transfer is absent, whilst at the opposite extreme, in salts, the proton‐transfer process is complete. However, for acid–base pairs with a small ΔpK_a (pK_a of base ? pK_a of acid), prediction of the extent of proton transfer is not possible as there is a continuum between the salt and cocrystal ends. In this context, we attempt to illustrate that in these systems, in addition to ΔpK_a, the crystalline environment could change the extent of proton transfer. To this end, two compounds of salicylic acid (SaH) and adenine (Ad) have been prepared. Despite the same small ΔpK_a value (≈1.2), different ionization states are found. Both crystals, namely adeninium salicylate monohydrate, C₅H₆N₅⁺·C₇H₅O₃^?·H₂O, I , and adeninium salicylate–adenine–salicylic acid–water (1/2/1/2), C₅H₆N₅⁺·C₇H₅O₃^?·2C₅H₅N₅·C₇H₆O₃·2H₂O, II , have been characterized by single‐crystal X‐ray diffraction, IR spectroscopy and elemental analysis (C, H and N) techniques. In addition, the intermolecular hydrogen‐bonding interactions of compounds I and II have been investigated and quantified in detail on the basis of Hirshfeld surface analysis and fingerprint plots. Throughout the study, we use crystal engineering, which is based on modifications of the intermolecular interactions, thus offering a more comprehensive screening of the salt–cocrystal continuum in comparison with pure pK_a analysis.     

Theoretical calculation of the pKa values of some drugs in aqueous solution

In this work, calculations of pK_a values have been performed on benzoic acid and its para‐substituted derivatives and some drugs by using Gaussian 98 software package. Gas‐phase energies were calculated with HF/6‐31 G** and B3LYP/6‐31 G** levels of theory. Free energies of solvation have been computed using the polarizable continuum model (PCM), conductor‐like PCM (CPCM), and the integral equation formalism‐PCM at the same levels which have been used for geometry determination in the gas‐phase. The results that show the calculated pK_a values using the B3LYP are better than those using the corresponding HF. In comparison to the other models, the results obtained indicate that the PCM model is a suitable solvation model for calculating pK_a values. For the investigated compounds, a good agreement between the experimental and the calculated pK_a values was also observed. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

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

Determination of acid‐dissociation constants, pK_a, 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 pK_a 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 pK_a values. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

Accurate pKa Calculation of the Conjugate Acids of Alkanolamines,Alkaloids and Nucleotide Bases by Quantum Chemical Methods

The pK_a of the conjugate acids of alkanolamines, neurotransmitters, alkaloid drugs and nucleotide bases are calculated with density functional methods (B3LYP, M08‐HX and M11‐L) and ab initio methods (SCS‐MP2, G3). Implicit solvent effects are included with a conductor‐like polarizable continuum model (CPCM) and universal solvation models (SMD, SM8). G3, SCS‐MP2 and M11‐L methods coupled with SMD and SM8 solvation models perform well for alkanolamines with mean unsigned errors below 0.20 pK_a units, in all cases. Extending this method to the pK_a calculation of 35 nitrogen‐containing compounds spanning 12 pK_a units showed an excellent correlation between experimental and computational pK_a values of these 35 amines with the computationally low‐cost SM8/M11‐L density functional approach.     

Effect of Preferential Solvation on the Thermodynamic Properties of Antidepressant Drug Trazodone in Aqueous Ethanol: Linear Free‐Energy Relationships

Dissociation constants (pK_a) of trazodone hydrochloride (TZD⋅HCl) in EtOH/H₂O media containing 0, 10, 20, 30, 40, 50, 60, 70, and 80% (v/v) EtOH at 288.15, 298.15, 308.15, and 318.15 K were determined by potentiometric techniques. At any temperature, pK_a decreased as the solvent was enriched with EtOH. The dissociation and transfer thermodynamic parameters were calculated, and the results showed that a non‐spontaneous free‐energy change (Δ_dissG^o>0) and unfavorable enthalpy (Δ_dissH^o>0) and entropy (Δ_dissS^o<0) changes occurred on dissociation of trazodone hydrochloride. The free‐energy change or pK_a varied nonlinearly with the reciprocal dielectric constant, indicating the inadequacy of the electrostatic approach. The dissociation equilibria are discussed on the basis of the standard thermodynamics of transfer, solvent basicity, and solute‐solvent interactions. The values of Δ_transG^o and Δ_transH^o increased negatively with increasing EtOH content, revealing a favorable transfer of trazodone hydrochloride from H₂O to EtOH/H₂O mixtures and preferential solvation of H⁺ and trazodone (TZD). Also, Δ_transS^o values were negative and reached a minimum, in the H₂O‐rich zone that has frequently been related to the initial promotion and subsequent collapse of the lattice structure of water. The pK_a or Δ_dissG^o values correlated well with the Dimroth‐Reichardt polarity parameter E_T(30), indicating that the physicochemical properties of the solute in binary H₂O/organic solvent mixtures are better correlated with a microscopic parameter than the macroscopic one. Also, it is suggested that preferential solvation plays a significant role in influencing the solvent dependence of dissociation of trazodone hydrochloride. The solute‐solvent interactions were clarified on the basis of the linear free‐energy relationships of Kamlet and Taft. The best multiparametric fit to the Kamlet‐Taft equation was evaluated for each thermodynamic parameter. Therefore, these parameters in any EtOH/H₂O mixture up to 80% were accurately derived by means of the obtained equations.     

Basicity of some aliphatic amines in mixed H2O?CH3CN solvents

The values of pK_a^ms (K_a^ms represents ionization constant of conjugate acid of amine base in mixed water–acetonitrile solvent) for all amines, except for charged amine bases, show a mild decrease (ca. 0.1–0.4 pK units) with the increase in CH₃CN content from 2 to ∼60% v/v. However, the pK_a^ms values at 70% v/v CH₃CN become nearly equal or slightly larger (by ≤0.7 pK units) than the corresponding pK_a^ms at 2% v/v CH₃CN for all neutral and charged amines. The values of pK_a^ms for phenol increase from 10.17 to 13.38 with the increase in the content of CH₃CN from 2 to 70% v/v in mixed aqueous solvent. Taft reaction constants, ρ*, obtained from the plots of pK_a^ms against ∑σ* for primary and secondary amines decrease by ca. 0.8 ρ* units with the increase in the CH₃CN content from 2 to 70% v/v. The values of pK_a^ms show an empirical linear relationship with the corresponding values of pK_a^w (where pK_a^w represents the pK_a obtained in aqueous solvent containing 2% v/v CH₃CN), which allows the estimation of a pK_a in mixed H₂O CH₃CN solvents from that in water. © 2000 John Wiley & Sons, Inc. Int J Chem Kinet 32: 146–152, 2000     

SAMPL7 blind challenge: quantum–mechanical prediction of partition coefficients and acid dissociation constants for small drug-like molecules

The physicochemical properties of a drug molecule determine the therapeutic effectiveness of the drug. Thus, the development of fast and accurate theoretical approaches for the prediction of such properties is inevitable. The participation to the SAMPL7 challenge is based on the estimation of logP coefficients and pK_a values of small drug-like sulfonamide derivatives. Thereby, quantum mechanical calculations were carried out in order to calculate the free energy of solvation and the transfer energy of 22 drug-like compounds in different environments (water and n-octanol) by employing the SMD solvation model. For logP calculations, we studied eleven different methodologies to calculate the transfer free energies, the lowest RMSE value was obtained for the M06L/def2-TZVP//M06L/def2-SVP level of theory. On the other hand, we employed an isodesmic reaction scheme within the macro pK_a framework; this was based on selecting reference molecules similar to the SAMPL7 challenge molecules. Consequently, highly well correlated pK_a values were obtained with the M062X/6–311+G(2df,2p)//M052X/6–31+G(d,p) level of theory.

     

Role of bridging diamine linkers on the rate of ligand substitution in a series of dinuclear PtII complexes

A series of dinuclear platinum^II complexes of the type [{trans‐Pt(H₂O)(NH₃)₂}₂‐NH₂(CH₂)_nH₂N]⁴⁺ (where n = 2, 3, 4, and 6) were synthesized to investigate the influence of the bridging diamine linker on the reactivity of the platinum centers. The pK_a values were determined, and the rates of substitution of the aqua moieties by a series of neutral nucleophiles viz. thiourea, 1,3‐dimethyl‐2‐thiourea, and 1,1,3,3‐tetramethyl‐2‐thiourea were studied as a function of concentration and temperature. All reactions studied gave excellent fits to a single exponential and obeyed the simple rate law, k_obs=k₂[Nu]. Negative activation entropies support an associative mode of substitution. The results obtained suggest that the rate of substitution is definitely influenced by the length of the diamine chain, with the rate of substitution decreasing as the length of the diamine chain increases. © 2006 Wiley Periodicals, Inc. Int J Chem Kinet 38: 202–210, 2006