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.     

Fast evaluation of molecular auxiliary functions <Emphasis Type="Italic">A</Emphasis><Subscript>α</Subscript> and <Emphasis Type="Italic">B</Emphasis><Subscript><Emphasis Type="Italic">n</Emphasis></Subscript> by analytical relations

Analytical relations through the initial values are derived for the molecular auxiliary functions A _α (x) and B _n (x), where α =n+ɛ, 0⩽ ɛ < 1 and n=0,1,2,.... These relations are useful in the fast calculation of multicenter molecular integrals over integer and noninteger n Slater type orbitals. It is shown that the formulas obtained are numerically stable for all values of n,ɛ and x.PACS No: 31.15.+q, 31.20.EjAMS subject classification: 81-V55, 81-V45     

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.     

Potassium–conducting K<Subscript>1 − 2<Emphasis Type="Italic">x</Emphasis></Subscript>Pb<Subscript><Emphasis Type="Italic">x</Emphasis></Subscript>GaO<Subscript>2</Subscript> solid electrolytes

Solid electrolytes with potassium-cation conductivity in the K_{1 − 2x} Pb _x GaO₂ system were synthesized and studied. It was found that solid solutions based on potassium monogallate are formed in a wide range of compositions. They contain vacancies in the potassium sublattice that provide for high conductivity of electrolytes. The relationship is considered between electric characteristics of solid electrolytes and the composition and structure of solid solutions. The results are compared to the earlier obtained data for similar solid electrolytes based on potassium monoaluminate and monoferrite.     

Potassium-conducting solid electrolytes in K<Subscript>1 − 2<Emphasis Type="Italic">x</Emphasis></Subscript>Sr<Subscript><Emphasis Type="Italic">x</Emphasis></Subscript>GaO<Subscript>2</Subscript> system

New solid electrolytes with a high conductivity by K⁺ ions in the K_{1 − 2x} Sr _x GaO₂ system are synthesized and studied. It is found that the introduction of Sr²⁺ ions into potassium monogallate leads to the formation of solid solutions with KGaO₂ structure in a wide range of additive concentration. These solid solutions exhibit a high conductivity; the conductivity increases monotonically with increasing concentration of strontium within the single-phase range. The electrical characteristics are related to the electrolyte structure. The results are compared with the earlier data for the gallate solid electrolytes with the additives of four-charged cations and the systems based on potassium monoferrite and monoaluminate.     

Characteristics of the hydrogen bond and the structure of Н-complexes of <Emphasis Type="Italic">p</Emphasis>-n-propyloxybenzoic acid and <Emphasis Type="Italic">p</Emphasis>-n-propyloxy-<Emphasis Type="Italic">p</Emphasis>′-cyanobiphenyl

The conformational properties of p-n-propyloxybenzoic acid and p-n-propyloxy-p′-cyanobiphenyl molecules, which can exhibit liquid crystalline properties in the formation of Н-complexes, are studied (DFT/B3LYP)/cc-pVTZ method). It is found that a molecule of p-n-propyloxybenzoic acid has 16 conformers that can be divided into four groups with respect to relative energies (0 kcal/mol, 1.6 kcal/mol, 6.5 kcal/mol, and 8.1 kcal/mol), and a molecule of p-n-propyloxy-p′-cyanobiphenyl has six conformers with relative energies of 0 kcal/mol (two conformers, φ(С_Ph–O–C–C)=180°) and 1.6 kcal/mol (four conformers, φ(С_Ph–O–C–C)=64.4°). In all conformers of the 3-AOCB molecule, phenyl rings are turned at 35° relative to each other. A conformation with the planar arrangement of two rings has a higher energy by 1.5 kcal/mol. Barriers to the internal rotation of different groups are determined and it is established that the structural nonrigidity of the molecules is mainly due to the possible rotation of the–C₂Н₅ moiety about the C–C bond. It is shown that with increasing temperature the vibrational amplitudes of the OC₃H₇ substituent, which enhance the probabilities of transitions between the conformers, become appreciably larger. It is found that p-n-propyloxybenzoic acid and p-n-propyloxy-p′-cyanobiphenyl can form Н-complexes with the medium hydrogen bond. Two types of the structural organization of Н-complexes are considered: linear and angular. The similarity of energies of Н-complexes with different structures (NBO analysis) can be the reason for the occurrence of two liquid crystalline subphases of p-n-propyloxybenzoic acid and p-n-propyloxy-p′-cyanobiphenyl system.     

Investigation of the Role of Ionic Liquids in Tuning the p<Emphasis Type="Italic">K</Emphasis><Subscript>a</Subscript> Values of Some Anionic Indicators

The effect of imidazolium-based ionic liquids, ([C₁₂mim][Cl] and [C₈mim][Cl]), on the acid-base equilibria of two sulfonated indicators has been studied. The presence of ILs leads to decreased pK _a values because of the stronger electrostatic interaction of cationic ILs with the basic forms of the indicators with more negative charge. The longer alkyl side chain of [C₁₂mim][Cl] compared to [C₈mim][Cl] results in stronger hydrophobic interaction of this IL with the basic forms of the dyes leading to a more effective decrease in the pK _a values. Also, the transition points and transition intervals of the acid-base titration curves of the indicators were affected by the presence of ILs. It was found that the IL interaction with acid-base indicators also results in sharpening the acid-base titration curves of the indicators. From these observations, it is concluded that the presence of ILs can tune the pK _a values of indicators. All the experiments were performed spectrophotometrically and the results were obtained using curve fitting methods.     

TiO<Subscript>2</Subscript>/TiO<Subscript>2−<Emphasis Type="Italic">x</Emphasis></Subscript>N<Subscript><Emphasis Type="Italic">y</Emphasis></Subscript> nanocomposite and its acetaldehyde photodecomposition ability

Nitrogen-doped titania was coupled with the commercial titania nanoparticles by mechanical milling in liquid medium. The as-prepared nanocomposites (TiO₂/TiO_2−x N _y ) were characterized by X-ray diffraction (XRD), Brunauer–Emmett–Teller (BET) specific surface area, UV–Vis spectroscopy, chemiluminescence, and acetaldehyde decomposition activity techniques. When a small amount of nitrogen-doped titania was added into the commercial titania, higher intensity and longer lifetime of ¹O₂ was observed, and the photocatalytic activity was efficiently improved. The TiO_2−x N _y acts as the acceptor of photoinduced holes. The recombination of the electron-hole was effectively depressed by the heterogeneous electron transfer. This could be an effective way to obtain highly active photocatalysts.     

Planar Four-Coordinate Carbon in Star-Like Perlithioannulenes C<Subscript><Emphasis Type="Italic">n</Emphasis></Subscript>Li<Subscript><Emphasis Type="Italic">n</Emphasis></Subscript> (<Emphasis Type="Italic">n</Emphasis> = 3–6)

The structure and stability of perlithioannulenes C _n Li _n (n = 3–6) were examined ab initio [MP2(full)/6-311+G**] and in terms of the density functional theory (B3LYP/6-311+G**). The systems with n = 3, 5, and 6 may be stabilized as planar star-like structures with bridging lithium atoms and hypercoordinate carbon atoms. Star-like structures are the most stable isomers of odd-numbered annulenes (n = 3, 5), while the most stable isomers of even-numbered annulenes (n = 4, 6) have less symmetric nonplanar structures.     

<Emphasis Type="Italic">N</Emphasis>′-tetrazolylmethoxyl derivatives of <Emphasis Type="Italic">N</Emphasis>-methyldiazene <Emphasis Type="Italic">N</Emphasis>-oxides

A preparation method was developed for previously unknown tetrazole derivatives containing in the 1, 2, and/or 5 positions of the tetrazole ring N-methyldiazene-N-oxide-N′-oxymethyl groups.     

Crystallization and Simulation Studies in <Emphasis Type="Italic">m</Emphasis>-Dinitrobenzene–<Emphasis Type="Italic">p</Emphasis>-Chloroaniline Eutectic System

Thaw-melt method showed that the phase diagram of m-dinitrobenzene (m-DNB)–p-chloroaniline (p-CA) system belongs to simple eutectic type. The kinetics of solidification followed Hillig and Turnbull’s equation. Excess thermodynamic functions and FT-IR spectral studies indicated some weak interaction between the component molecules in the eutectic. The mechanical strength of the eutectic was found to be higher than those of its components. Molecular stability was predicted on the basis of frontier molecular orbital analysis. The value was found to be 0.06073 a.u. for eutectic, indicating. the possibility of charge transfer interaction during the eutectic formation. Results showed that the eutectic is stabilized by hydrogen-bond formation. Calculated interaction energy of reactants and eutectic was found to be–17.4 kJ mol^–1.     

Oxidation of reaction products of <Emphasis Type="Italic">p</Emphasis>-aryl-<Emphasis Type="Italic">С</Emphasis>,<Emphasis Type="Italic">С</Emphasis>-disubstituted nitrones and dimethyl 3-methylenecyclopropane-1,2-dicarboxylate

Oxidation with 2,3-dichloro-4,5-dicyanobenzoquinone of 2,4-dihydro-1Н-azeto[1,2-a]quinoline-3,4 -dicarboxylates obtained in the reaction of N-aryl-С,С-disubstituted nitrones with Feist’s acid ester resulted in the formation of 2-vinylquinoline-3,4-dicarboxylates in good yields.     

Directed Aminomethylation of Pyrrole,Indole, and Carbazole with <Emphasis Type="Italic">N</Emphasis>,<Emphasis Type="Italic">N</Emphasis>,<Emphasis Type="Italic">N′</Emphasis>,<Emphasis Type="Italic">N′</Emphasis>-Tetramethylmethanediamine

Catalytic aminomethylation of pyrrole and indole with N,N,N′,N′-tetramethylmethanediamine in the presence of 5 mol % of ZrOCl₂·8H₂O proceeds selectively at the positions 2, 5 of pyrrole and 1, 3 of indole. Carbazole under the same conditions affords 3-formyl-9-aminomethyl derivative. The reaction in the presence of 5 mol % of K₂CO₃ occurs as monoaminomethylation: for pyrrole at the position 2, for indole at the position 3, and for carbazole at the nitrogen atom of the substrate. Water-soluble 1,1′-(1H-pyrrole-2,5-diyl)bis(N,N-dimethylmethanamine) exhibits a fungistatic activity with respect to phytopathogenic fungi Rhizoctonia solani.     

Sol-Gel Synthesis and Properties of Y<Subscript>1–<Emphasis Type="Italic">x</Emphasis></Subscript>Ba<Subscript><Emphasis Type="Italic">x</Emphasis></Subscript>FeO<Subscript>3</Subscript> Nanocrystals

The sol-gel method was used to prepare Y_1–xBa_xFeO₃ (x = 0, 0.05, 0.1, 0.15, 0.2) nanocrystals. The influence of the dopant content on the particle size and magnetic properties of yttrium ferrite was examined.     

New “s<Emphasis Type="Italic">p</Emphasis><Superscript><Emphasis Type="Italic">2</Emphasis></Superscript>-bonded” carbanucleosides

By reaction of 2,3-dichloro-, 2,3,5-trichloro-, 2,5-dichloro-3-phenylsulfonyl-, 2-chloro-3-phenylsulfonyl-4,4-ethylenedioxycyclopent-2-en-1-ones with uracyl 3- and 2-uracyl derivatives were obtained of the corresponding chlorocyclopentenone.     

1,3-Diamino-2-Hydroxypropane-<Emphasis Type="Italic">N</Emphasis>,<Emphasis Type="Italic">N</Emphasis>,<Emphasis Type="Italic">N</Emphasis>′,<Emphasis Type="Italic">N</Emphasis>′-Tetraacetic Acid: Crystal and Molecular Structures

The synthesis, IR spectroscopic study, and X-ray diffraction analysis (CIF file CCDC no. 1574078) are carried out for 1,3-diamino-2-hydroxypropane-N,N,N′,N′-tetraacetic acid (I). The structural units of a crystal of compound I are (H_4.5HPdta)^0.5– anions, (H_5.5HPdta)^0.5+ cations, and molecules of water of crystallization joined by a branched network of hydrogen bonds: strong intermolecular O–H…O and intramolecular N–H…O bonds.     

Magnetic properties of CuCr<Subscript>2–<Emphasis Type="Italic">х</Emphasis></Subscript>Sb<Subscript><Emphasis Type="Italic">x</Emphasis></Subscript>Se<Subscript>4</Subscript> (<Emphasis Type="Italic">х</Emphasis> = 0–0.5) solid solutions

Magnetic properties of spinel solid solutions CuCr_2–х Sb _x Se₄ (х = 0–0.5) were measured in the temperature range 5–300 K in a constant (50 Oe and 10 kOe) magnetic field. The results are interpreted in terms of the ionic model suggested earlier for CuCr₂Х₄ compounds.     

Synthesis and electrochemical evaluation of La<Subscript>1−<Emphasis Type="Italic">x</Emphasis></Subscript>Sr<Subscript><Emphasis Type="Italic">x</Emphasis></Subscript>MnO<Subscript>3</Subscript> catalysts for zinc-air batteries

La_1-x Sr _x MnO₃ (x?=?0.1～0.4) catalysts for primary and rechargeable zinc-air batteries have been successfully synthesized by the citrate method and their electrochemical properties measured. The materials can catalyze both ORR and OER, and the one with ideal composition of La_0.8Sr_0.2MnO₃ catalyst exhibits the highest catalytic activity and durability in alkaline medium. The resulting primary zinc-air cell shows a peak power density of 146 mW cm^?2 at 235 mA cm^?2. The secondary cell exhibits a charge-discharge voltage gap of 1.0 V at 10 mA cm^?2, which is highly stable over many charge-discharge cycles.     

Transport and thermal characteristics of Cs<Subscript>1 − <Emphasis Type="Italic">x</Emphasis></Subscript>Rb<Subscript><Emphasis Type="Italic">x</Emphasis></Subscript>H<Subscript>2</Subscript>PO<Subscript>4</Subscript>

The transport and thermal properties of Cs_{1 − x} Rb _x H₂PO₄ in a wide range of compositions were studied. The binary salts Cs_{1 − x} Rb _x H₂PO₄ (x = 0–0.9) contain solid solutions with a structure of CsH₂PO₄. The binary salts were synthesized by mechanically mixing the starting components and growing crystals by isothermal evaporation from aqueous solutions. The properties of Cs_{1 − x} Rb _x H₂PO₄ salts obtained by different procedures were found to differ considerably. At higher rubidium contents in compounds obtained by mechanical mixing, the superionic transition temperature rose insignificantly, the high-temperature phase conductivity decreased twofold, the low-temperature conductivity increased within the limits of the order of magnitude, and the system of hydrogen bonds was slightly weakened. In Cs_{1 − x} Rb _x H₂PO₄ crystals grown from solutions, the temperature of the superionic transition decreased along with its slowing down, and the low-temperature conductivity increased by more than three orders of magnitude because of the higher contents of residual acid aqueous centers in the structure of the salt. These systems are characterized by increased thermal stability.