SAMPL6: calculation of macroscopic p<Emphasis Type="Italic">K</Emphasis><Subscript>a</Subscript> values from ab initio quantum mechanical free energies

Macroscopic pK_a values were calculated for all compounds in the SAMPL6 blind prediction challenge, based on quantum chemical calculations with a continuum solvation model and a linear correction derived from a small training set. Microscopic pK_a values were derived from the gas-phase free energy difference between protonated and deprotonated forms together with the Conductor-like Polarizable Continuum Solvation Model and the experimental solvation free energy of the proton. pH-dependent microstate free energies were obtained from the microscopic pK_as with a maximum likelihood estimator and appropriately summed to yield macroscopic pK_a values or microstate populations as function of pH. We assessed the accuracy of three approaches to calculate the microscopic pK_as: direct use of the quantum mechanical free energy differences and correction of the direct values for short-comings in the QM solvation model with two different linear models that we independently derived from a small training set of 38 compounds with known pK_a. The predictions that were corrected with the linear models had much better accuracy [root-mean-square error (RMSE) 2.04 and 1.95 pK_a units] than the direct calculation (RMSE 3.74). Statistical measures indicate that some systematic errors remain, likely due to differences in the SAMPL6 data set and the small training set with respect to their interactions with water. Overall, the current approach provides a viable physics-based route to estimate macroscopic pK_a values for novel compounds with reasonable accuracy.     

<Emphasis Type="Italic">Ab initio</Emphasis> quantum-chemical study of vinylation of pyrrole and 2-phenylazopyrrole with acetylene in a KOH/DMSO system

Interaction between pyrrole and its 2-vinyl, 2-azo, and 2-phenylazo derivatives with acetylene in the gas phase and DMSO was studied using the MP2/6-311++G**//MP2/6-31G* ab initio approach and including the solvation effects within the framework of the continuum model. Possible reasons are considered for the hindered character of direct vinylation of azopyrroles with acetylene in superbasic media. The introduction of the azo group in the 2 position of the pyrrole ring leads to the increased stability of the pyrrole anion and increased acidity from pK _a = 22.1 for pyrrole and pK _a = 20.5 for vinylpyrrole to pK _a = 16.6 and 16.4 for 2-azopyrrole and 2-phenylazopyrrole, respectively. The binding energy between the pyrrole anion and the acetylene molecule decreases concurrently. The heat of formation of the pyrrole anion adducts with acetylene changes from ΔH = 4.8 kcal/mol for pyrrole to ΔH = 22.4 kcal/mol for 2-phenylazopyrrole. For all anion adducts under study, preferable isomers are Z isomers formed by the interaction of pyrrole anions with the cis-distorted acetylene molecule, but the formation of the E isomers corresponds to a lower activation barrier, which explains known Z stereoselectivity of the nucleophilic addition to monosubstituted acetylenes. When an azo group is introduced, the reaction becomes more endothermal, and the energy barriers to the formation of both Z and E isomers increase. Among other reasons for lowering of the activity of 2-arylazopyrroles during vinylation we consider possible reaction of acetylene addition at the most remote nitrogen atom of the azo group and participation of the anion center in cation chelation (K⁺ in the calculation).     

Constants of acid‒base equilibria in an aqueous amikacin aminoglycoside solution at 298 K

The acid dissociation constants of form pK₁ = 7.34 ± 0.01, pK₂ = 7.84 ± 0.01, pK₃ = 8.77 ± 0.01, pK₄ = 9.49 ± 0.01, and pK₅ = 10.70 ± 0.02 of cationic amikacin are determined by pH-metric titration at 25°C against the background of 0.1 mol/L KNO₃. K₁, K₂, K₃, and K₄ correspond to the dissociation of protons coordinated to amino groups, while K₅ characterizes the dissociation of the hydroxyl hydrogen atom, testifying to the amphoteric character of amikacin molecules. Applying density functional theory (DFT) with the B3LYP hybrid functional and the 6-311G**++ basis set, the partial charges on the atoms of an amikacin molecule are calculated. It is concluded that the dissociation of H(55)hydrogen atom occurs with a greatest partial charge of +0.53631.     

Dissociation Constants of Silanol Groups of Silic Acids: Quantum Chemical Estimations

Dissociation constants of silanol groups on the silica surface are calculated with the DFT quantum chemical method using B3LYP and M06 functionals. Structural features of silanol fragments and the presence of hydrogen-bonded water clusters are shown to have significant effects on pK_a values of silanol groups. In particular, pK_a values are shown to vary widely depending on the features of the system of hydrogen bonds.     

p<Emphasis Type="Italic">K</Emphasis><Subscript>a</Subscript> measurements for the SAMPL6 prediction challenge for a set of kinase inhibitor-like fragments

Determining the net charge and protonation states populated by a small molecule in an environment of interest or the cost of altering those protonation states upon transfer to another environment is a prerequisite for predicting its physicochemical and pharmaceutical properties. The environment of interest can be aqueous, an organic solvent, a protein binding site, or a lipid bilayer. Predicting the protonation state of a small molecule is essential to predicting its interactions with biological macromolecules using computational models. Incorrectly modeling the dominant protonation state, shifts in dominant protonation state, or the population of significant mixtures of protonation states can lead to large modeling errors that degrade the accuracy of physical modeling. Low accuracy hinders the use of physical modeling approaches for molecular design. For small molecules, the acid dissociation constant (pK_a) is the primary quantity needed to determine the ionic states populated by a molecule in an aqueous solution at a given pH. As a part of SAMPL6 community challenge, we organized a blind pK_a prediction component to assess the accuracy with which contemporary pK_a prediction methods can predict this quantity, with the ultimate aim of assessing the expected impact on modeling errors this would induce. While a multitude of approaches for predicting pK_a values currently exist, predicting the pK_as of drug-like molecules can be difficult due to challenging properties such as multiple titratable sites, heterocycles, and tautomerization. For this challenge, we focused on set of 24 small molecules selected to resemble selective kinase inhibitors—an important class of therapeutics replete with titratable moieties. Using a Sirius T3 instrument that performs automated acid–base titrations, we used UV absorbance-based pK_a measurements to construct a high-quality experimental reference dataset of macroscopic pK_as for the evaluation of computational pK_a prediction methodologies that was utilized in the SAMPL6 pK_a challenge. For several compounds in which the microscopic protonation states associated with macroscopic pK_as were ambiguous, we performed follow-up NMR experiments to disambiguate the microstates involved in the transition. This dataset provides a useful standard benchmark dataset for the evaluation of pK_a prediction methodologies on kinase inhibitor-like compounds.     

Investigation of Solution p<Emphasis Type="Italic">K</Emphasis><Subscript>a</Subscript> and Thermodynamic Values of Lamivudine and Pefloxacin Drugs by Ab initio and DFT Methods

In this work we investigate the thermodynamic properties and pK_a value of lamivudine and pefloxacin drugs, in aqueous solutions, by ab initio and density functional theory (DFT) methods at different temperatures. Molecular structures and solute–solvent effects of the anions, cations, and neutral molecules of lamivudine and pefloxacin were studied by the polarizable continuum model (PCM). The calculation was done at the DFT-B3LYP/6-31+G(d) level of theory using Tomasi’s method to analyze the formation of intermolecular hydrogen bonds (IHB) in aqueous solution. The pK_a1 values of lamivudine and pK_a2 values of pefloxacin increase with temperature increase. In contrast, the pK_a1 values of pefloxacin decrease when the temperature increases. Further, the thermodynamic properties of the ionization processes (?H, ?S and ?G) of the drugs in aqueous solution were determined and discussed. The results of this work are in good agreement with the literature data at 298.15 K.     

The SAMPL6 challenge on predicting aqueous p<Emphasis Type="Italic">K</Emphasis><Subscript>a</Subscript> values from EC-RISM theory

The “embedded cluster reference interaction site model” (EC-RISM) integral equation theory is applied to the problem of predicting aqueous pK_a values for drug-like molecules based on an ensemble of tautomers. EC-RISM is based on self-consistent calculations of a solute’s electronic structure and the distribution function of surrounding water. Following-up on the workflow developed after the SAMPL5 challenge on cyclohexane-water distribution coefficients we extended and improved the methodology by taking into account exact electrostatic solute–solvent interactions taken from the wave function in solution. As before, the model is calibrated against Gibbs energies of hydration from the “Minnesota Solvation Database” and a public dataset of acidity constants of organic acids and bases by adjusting in total 4 parameters, among which only 3 are relevant for predicting pK_a values. While the best-performing training model yields a root-mean-square error (RMSE) of 1 pK unit, the corresponding test set prediction on the full SAMPL6 dataset of macroscopic pK_a values using the same level of theory exhibits slightly larger error (1.7 pK units) than the best test set model submitted (1.7 pK units for corresponding training set vs. test set performance of 1.6). Post-submission analysis revealed a number of physical optimization options regarding the numerical treatment of electrostatic interactions and conformational sampling. While the experimental test set data revealed after submission was not used for reparametrizing the methodology, the best physically optimized models consequentially result in RMSEs of 1.5 if only improved electrostatic interactions are considered and of 1.1 if, in addition, conformational sampling accounts for quantum-chemically derived rankings. We conclude that these numbers are probably near the ultimate accuracy achievable with the simple 3-parameter model using a single or the two best-ranking conformations per tautomer or microstate. Finally, relations of the present macrostate approach to microstate pK_a results are discussed and some illustrative results for microstate populations are presented.     

A Quantum Chemical Study of the Acidity of Acetylene and 1,2-Dihydrobuckminsterfullerene Derivatives

DFT PBE0/cc-pVDZ method and the polarizable continuum model were used to determine pK _a values for buckminsterfullerene-acetylene hybrids C₆₀HCCH, C₆₀HCN, tert-butylacetylene, and propyne relative to tert-BuC₆₀H in a vacuum, carbon disulfide, tetrahydrofuran, and dimethyl sulfoxide. The energies of the СH-acid molecule and the carbanion (fulleride- or acetylide anion) were calculated using the same number of Gaussian orbitals. The surfaces of cavities formed by molecules and anions in a solvent are composed of spheres encompassing both atomic nuclei and lone electron pairs. An additional sphere excludes the solvent from the inner cavity of the fullerene.     

Absolute and relative p<Emphasis Type="Italic">K</Emphasis><Subscript>a</Subscript> predictions via a DFT approach applied to the SAMPL6 blind challenge

In this work, quantum mechanical methods were used to predict the microscopic and macroscopic pK_a values for a set of 24 molecules as a part of the SAMPL6 blind challenge. The SMD solvation model was employed with M06-2X and different basis sets to evaluate three pK_a calculation schemes (direct, vertical, and adiabatic). The adiabatic scheme is the most accurate approach (RMSE?=?1.40 pK_a units) and has high correlation (R²?=?0.93), with respect to experiment. This approach can be improved by applying a linear correction to yield an RMSE of 0.73 pK_a units. Additionally, we consider including explicit solvent representation and multiple lower-energy conformations to improve the predictions for outliers. Adding three water molecules explicitly can reduce the error by 2–4 pK_a units, with respect to experiment, whereas including multiple local minima conformations does not necessarily improve the pK_a prediction.     

Stability of <Emphasis Type="Italic">s</Emphasis>-, <Emphasis Type="Italic">p</Emphasis>-, and <Emphasis Type="Italic">d</Emphasis>-element diphosphates in water

The mean atomic Gibbs energies of formation of (Δ _f ? _at ⁰ ) of s-, p-, and d-element diphosphates have been calculated using ion increments of the Gibbs energy (Δ _f G ⁰). The diphosphate hydrolysis kinetics is considered, and a correlation between the Δ _f ? _at ⁰ values and the hydrolysis rate constants is presented.     

The Effect of a Cationic Gemini Surfactant,Ethonium, on the Physicochemical Properties of Quercetin in Solutions and on the Surface of Highly Dispersed Silica

The formation of supramolecular complexes with ethonium, a cationic gemini surfactant having a broad-spectrum antimicrobial activity, is shown to significantly alter the physicochemical properties (spectral, protolytic, and adsorption properties and solubility) of a natural f lavonol, quercetin. The constant of binding between quercetin and ethonium is calculated. Apparent dissociation constants pK _a1 ^a of quercetin in solutions of this cationic surfactant are for the first time determined within a broad concentration range. A shift in the pH dependence of quercetin adsorption by 0.5 units to the alkaline region upon the transition from a premicellar ethonium solution to a micellar one correlates with an increase in pK _a1 ^a under these conditions. The value of quercetin adsorption from aqueous ethonium solutions depends on the concentration of the cationic surfactant, pH of a solution, and the pK _a1 ^a value of the f lavonol bound into the supramolecular complex.     

Evaluation of the stability of dye heteroassociates formed in aqueous solutions

The additive tetraphenylarsonium-tetraphenylborate model of interactions was found to be applicable to the problem of “preexperimental” evaluation of the stability of associates formed by dye cations (Ct⁺) and anions (An^?) in aqueous solutions. The possibility of predicting equilibrium association constants K _as from preliminarily calculated ΔG(Ct⁺) and ΔG(An^?) and of solving the inverse problem was analyzed. The invariability of the ΔG(Ct⁺) and ΔG(An^?) values and the problem of bringing calculation results in consistency with the experimental K _as values are discussed.     

The SAMPL5 challenge for embedded-cluster integral equation theory: solvation free energies,aqueous p<Emphasis Type="Italic">K</Emphasis><Subscript>a</Subscript>, and cyclohexane–water log <Emphasis Type="Italic">D</Emphasis>

We predict cyclohexane–water distribution coefficients (log D _7.4) for drug-like molecules taken from the SAMPL5 blind prediction challenge by the “embedded cluster reference interaction site model” (EC-RISM) integral equation theory. This task involves the coupled problem of predicting both partition coefficients (log P) of neutral species between the solvents and aqueous acidity constants (pK _a) in order to account for a change of protonation states. The first issue is addressed by calibrating an EC-RISM-based model for solvation free energies derived from the “Minnesota Solvation Database” (MNSOL) for both water and cyclohexane utilizing a correction based on the partial molar volume, yielding a root mean square error (RMSE) of 2.4 kcal mol^?1 for water and 0.8–0.9 kcal mol^?1 for cyclohexane depending on the parametrization. The second one is treated by employing on one hand an empirical pK _a model (MoKa) and, on the other hand, an EC-RISM-derived regression of published acidity constants (RMSE of 1.5 for a single model covering acids and bases). In total, at most 8 adjustable parameters are necessary (2–3 for each solvent and two for the pK _a) for training solvation and acidity models. Applying the final models to the log D _7.4 dataset corresponds to evaluating an independent test set comprising other, composite observables, yielding, for different cyclohexane parametrizations, 2.0–2.1 for the RMSE with the first and 2.2–2.8 with the combined first and second SAMPL5 data set batches. Notably, a pure log P model (assuming neutral species only) performs statistically similarly for these particular compounds. The nature of the approximations and possible perspectives for future developments are discussed.     

Elastic properties of a nematic in a tetrapalladium organyl-pentadecane system

The temperature dependences of birefringence Δn, anisotropy of permittivity ?_a, and elastic constants K ₁₁ and K ₃₃ in the nematic phase of a tetrapalladium organyl-pentadecane system with a pentadecane content of 55 wt % have been investigated experimentally. It has been shown that, as temperature is elevated, ?_a, K ₁₁, and K ₃₃ values decrease and Δn remains unchanged. Elastic constants K ₁₁ and K ₃₃ have been established to vary from 3.4 × 10^?7 to 5.6 × 10^?6 dyn and from 1.3 × 10^?6 to 27.4 × 10^?5 dyn, respectively. The value of ?_a has been revealed to vary over the range 0.2–0.5. It has been found that, at temperatures above the N₂ → Cr phase transition by 6°C, an imposed electric field induces the growth of tetrapalladium organyl crystals.     

Substituted benzotriazoles as inhibitors of copper corrosion in borate buffer solutions

The adsorption of substituted 1,2,3-benzotriazoles (R-BTAs) onto copper is measured via ellipsometry in a pure borate buffer (pH 7.4) and satisfactorily described by Temkin’s isotherm. The adsorption free energy (?ΔG _a ⁰ ) values of these azoles are determined. The (?ΔG _a ⁰ ) values are found to rise as their hydrophobicity, characterized by the logarithm of the partition coefficient of a substituted BTA in a model octanol–water system (logP), grows. The minimum concentration sufficient for the spontaneous passivation of copper (C _min) and a shift in the potential of local copper depassivation with chlorides (E _pt) after an azole is added to the solution (i.e., ΔE = E _pt ⁱⁿ ? E _pt ^backgr characterizing the ability of its adsorption to stabilize passivation) are determined in the same solution containing a corrosion additive (0.01М NaCl) for each azole under study. Both criteria of the passivating properties of azoles (logC _min and ΔE) are shown to correlate linearly with logP, testifying to the role played by surface activity of this family of organic inhibitors in protecting copper in an aqueous solution.     

Volumetric,Viscometric and Speed of Sound Studies of Binary Mixtures of <Emphasis Type="Italic">Tert</Emphasis>-butyl Acetate with Fluorobenzene,Chlorobenzene and Bromobenzene at (298.15 and 308.15) K and at Atmospheric Pressure 0.087 MPa

Volumetric, viscometric and speed of sound studies of binary mixtures of tert-butyl acetate with fluorobenzene, chlorobenzene and bromobenzene have been made over the entire range of composition, at (298.15 and 308.15) K and at atmospheric pressure (p?=?0.089 MPa). From the experimental values of density, viscosity, and speed of sound, the excess molar volumes V^E, deviations in viscosity ?η and deviation in isentropic compressibility ΔK _S have been calculated. The V^E and ΔK _S values are negative while the ?η the values are positive over the entire composition range for the binary mixtures. The derived parameters have been fitted with the Redlich–Kister polynomial equation. The interaction parameters of McAllister model are used to correlate the experimental values of density, viscosity and speed of sound.     

Theoretical Study of Substituent Effect in Aryl Group Migration in (<Emphasis Type="Italic">para</Emphasis>-C<Subscript>6</Subscript>H<Subscript>4</Subscript>X)Mn(CO)5 Complexes

In this study, we report substituent effect on aryl group migration in (para-C₆H₄X)Mn(CO)₅ complexes using mpw1pw91 quantum chemical calculations. These calculations reveal good linear relationships between barrier energy (ΔE), activation energy (ΔH^?), activation free energy (ΔG^?) values and rate constants with Hammett constants of X-substituents. The occupancy values of Mn–CO_cis and Mn–C(O)-(para-C₆H₄X) bonds in reactant, transition state and product were calculated by Natural bond orbital (NBO) method.     

Thermodynamic characteristics of protolytic equilibria in aqueous solutions of glycyl peptides

Protolytic equilibria in aqueous solutions of glycyl-DL-serine, glycyl-DL-threonine, and glycyl-DL-valine are investigated by means of potentiometry and calorimetry. Dissociation constants and heat effects of the above dipeptides are determined. Standard thermodynamic characteristics (pK°, Δ_disG°, Δ_disH°, Δ_disS°) of the investigated equilibria are calculated. The obtained results are compared to corresponding data on relative compounds.     

Basicity of isomeric ditetrazolylbenzenes and their <Emphasis Type="Italic">N-tert</Emphasis>-butyl derivatives

The basicity constants \((pK_{BH^ + } ,pK_{BH^{2 + } } )\) of 1,2-, 1,3-, and 1,4-bis(tetrazol-5-yl)benzenes and their N-tert-butyl derivatives in aqueous sulfuric acid and the dissociation constants (pK _HB) of the corresponding H-complexes with p-fluorophenol in carbon tetrachloride were determined by UV and IR spectroscopy. Mono-and diprotonation of isomeric ditetrazolylbenzenes is observed in the acidity range (H ₀) from ?1 to ?5 (\(pK_{BH^ + } \) ?2.5 to ?3.0; \(pK_{BH^{2 + } } \) ?3.8 to ?4.9). Introduction of a tert-butyl group into the 2-position of the heteroring almost does not affect the basicity of ditetrazolyl benzenes. Among the examined compounds, 1,2-bis(2-tert-butyltetrazol-5-yl)benzene is the strongest proton acceptor with respect to p-fluorophenol as standard proton donor, presumably due to formation of a complex with bifurcated (three-center) hydrogen bond.