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.     

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.     

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.     

Crystal structure of KPb<Subscript>2</Subscript>Cl<Subscript>5</Subscript> and KPb<Subscript>2</Subscript>Br<Subscript>5</Subscript>

The KPb₂Cl₅ and KPb₂Br₅ crystals are monoclinic (P2₁/c) with a microtwinned structure. X-ray analysis of chloride resulted in the parameters a = 8.854(2) Å, b = 7.927(2) Å, c = 12.485(3) Å; β = 90.05(3)°, d_calc = 4.78(1) g/cm³ (STOE STADI4, MoK_α, 2θ_max = 80°), R₁ = 0.0702 for 4094 F ≥ 4 σ(F) reflections. For bromide, a = 9.256(2) Å, b = 8.365(2) Å, c = 13.025(3) Å; β = 90.00(3)°, d_calc = 5.62(1) g/cm³ (Bruker P4, MoK_α, 2θ_max = 70°), R₁ = 0.0692 for 3076 F ≥ 4 (F) reflections.     

High-pressure defect phase La<Subscript>x</Subscript>Cu<Subscript>3</Subscript>V<Subscript>4</Subscript>O<Subscript>12</Subscript>

Perovskite-like nonstoichiometric oxide La _x Cu₃V₄O₁₂ (space group Im \(\bar 3\), Z = 2, a = 7.313–7.354 Å) with cation-site vacancies has been prepared for the first time at high pressures (p = 6.0–8.0 GPa) and high temperatures (T = 700–1100°C). The compound has metal-type conductivity and paramagnetic properties, and undergoes a phase transition.     

A novel metal chalcogenide: HgCd<Subscript>4</Subscript>S<Subscript>5</Subscript>

A novel metal chalcogenide HgCd₄S₅ (1) was synthesized from solid-state reactions and structurally characterized. Compound 1 crystallizes in the space group C222₁ of the orthorhombic system with four formula units in a cell: a = 12.5661(5) Å, b = 7.2551(5) Å, c = 10.7520(7) Å, V = 980.2(1) ų, Cd₄HgS₅, M _r = 810.49, D _c = 5.492 g/cm³, S = 1.010, μ(MoK _α) = 25.128 mm^?1, F(000) = 1408, R = 0.0611 and wR = 0.1495. Compound 1 is characterized by a 3-D cadmium sulfide framework structure with the infinite mercury sulfide chains located in the cavities.     

X-ray diffraction study of CsZn<Subscript>2</Subscript>Br<Subscript>5</Subscript>

CsZn₂Br₅ crystals are studied by X-ray diffraction. The compound crystallizes in the monoclinic system with the unit cell parameters a = 6.8880(12) Å, b = 10.4703(19) Å, c = 6.5197(9) Å, β = 108.25°, V = 446.55 ų, ρ_calcd = 4.960 g/cm³. Refractive indices are n _p = 1.640 and n _p = 1.754.     

Synthesis and crystal structure of ternary molybdate compound K<Subscript>5</Subscript>Pb<Subscript>0.5</Subscript>Hf<Subscript>1.5</Subscript>(MoO<Subscript>4</Subscript>)<Subscript>6</Subscript>

Single crystals of triple molybdate of composition 5:1:3 K₅Pb_0.5Hf_1.5(MoO₄)₆ have been grown and their crystal structure has been solved from X-ray diffraction data (an automated diffractometer X8 APEX, MoK _α -radiation, 2173 F(hkl), R = 0.0321). Trigonal unit cell parameters are: a = b = 10.739(2) Å, c = 37.933(9) Å; V = 3789(1) ų, Z = 6, ρ_calc = 4.014 g/cm³, space group \(R\bar 3\). Three-dimensional mixed framework of the structure is formed by two types of MoO₄ tetrahedra and Pb and Hf octahedra linking via common O-vertices. Potassium atoms of three types occupy large vacancies in the framework.     

Analysis of the fine structure of XANES spectra over Ni<Emphasis Type="Italic">K</Emphasis> edge in Ni(EtOCS<Subscript>2</Subscript>)<Subscript>2</Subscript>

The NiK edge X-ray absorption near edge spectra (XANES) of the Ni(EtOCS₂)₂ complex were measured. The theoretical NiK edge XANES spectra were calculated by the total multiple scattering and finite difference methods; the potential was calculated with a muffin-tin approximation and without it. It is shown that inclusion of the non-muffin-tin effects is important for modeling the NiK XANES spectrum for the Ni(EtOCS₂)₂ complex; good agreement with experiment was achieved only in the calculations with the total potential (without the muffin-tin approximation for the shape of the potential).     

High-pressure defect phase Nd<Subscript><Emphasis Type="Italic">x</Emphasis></Subscript>Cu<Subscript>3</Subscript>V<Subscript>4</Subscript>O<Subscript>12</Subscript>

A perovskite-like oxide Nd _x Cu₃V₄O₁₂ (space group Im \(\bar 3\) Z = 2, a = 7.278–7.322 Å) with cationic vacancies was prepared for the first time under triaxial compression of p = 6.0–9.0 GPa at 700–1300°C. The compound has a metal-type conductivity, paramagnetic properties, and a phase transition.     

Crystal and molecular structures of two modifications of a chelate compound of Pb[(<Emphasis Type="Italic">iso</Emphasis>-C<Subscript>4</Subscript>H<Subscript>9</Subscript>)<Subscript>2</Subscript>PS<Subscript>2</Subscript>]<Subscript>2</Subscript>

A chelate compound Pb[(iso-C₄H₉)₂PS₂]² is synthesized. Using X-ray diffraction data, the crystal structures of two modifications of this compound are determined (X8 APEX diffractometer, MoK _α radiation, 14169 F _hkl , R = 0.0480 for the low temperature α-form and 6261 F _hkl , R = 0.0387 for the β-form studied at ambient temperature). The crystals are triclinic: a = 11.047(2) Å, b = 14.486(3) Å, c = 32.048(6) Å; α = 91.30(3)°, β = 99.73(3)°, γ = 101.61(3)°, V = 4942.9(17) ų, Z = 8, ρ_calc = 1.682 g/cm³ (α-modification) and a = 11.2124(5) Å, b = 14.6989(7) Å, c = 17.1644(6) Å; α = 109.393(1)°, β = 94.989(2)°, γ = 101.649(1)°, V = 2576.83(19) ų, Z = 4, ρ_calc = 1.613 g/cm³ (β-modification), space group \(P\bar 1\) for both polymorphs. The structures are molecular, coordination cores of PbS₄ are tetragonal pyramids with Pb atoms in the vertices and S atoms in the base. In both structures intermolecular Pb...S contacts yield supramolecular ensembles comprising by four molecules, where PbS₄₊₂ cores form planar aggregates of edge-sharing octahedra. The ensembles are joined by weak intermolecular S...S interactions resulting in the development of polymeric chains along the a axis.     

A Quantum Chemical Study of C<Subscript>60</Subscript>Cl<Subscript>30</Subscript>, C<Subscript>60</Subscript>(OH)<Subscript>30</Subscript> Molecules and Fe@C<Subscript>60</Subscript>(OH)<Subscript>30</Subscript> Endocomplex

(U)PBE0/cc-pVDZ method is used to study the structure of C₆₀Cl₃₀, C₆₀(OH)₃₀ molecules and Fe@C₆₀(OH)₃₀ endocomplex. The triplet state of the endocomplex is shown to be the lowest in energy among its four states corresponding to different spin multiplicities and positions of Fe nucleus within the fullerene cavity. This state is characterized by bonding between the iron atom and one of two benzenoid cycles of the carbon cage, six internuclear Fe–C distances (208 pm), and 1s²2s²2p⁶3s²3p⁶3d^7.24s^0.14p^0.3 electron configuration of iron with spin population of 2.36.     

Molecular structure of ErCl<Subscript>3</Subscript> and YbCl<Subscript>3</Subscript> according to the data of the simultaneous electron diffraction and mass spectrometric experiment

The saturated vapors of ErCl₃ and YbCl₃ were studied in a simultaneous electron diffraction and mass spectrometric experiment at 1165 K and 1170 K, respectively. In the vapors of these compounds, we found up to 3 mol.% dimers along with the monomers. The parameters of the r _g effective configuration of the monomer molecules were determined. For ErCl₃ and YbCl₃, the internuclear distances r _g(Ln-Cl) were 2.436(5) Å and 2.416(5) Å, and the bond angles ∠_g(Cl-Ln-Cl) were 117.0(10)° and 117.2(10)°, respectively. The equilibrium configurations and vibration frequencies of the monomer and dimer molecules were calculated by the HF, B3LYP, and MP2 methods using the combination of the ECP_D energy-consistent quasirelativistic core potential, including 4f electrons [Kr4d ¹⁰4f ⁿ ], and the contracted [5s4p3d] valence basis set for Er and Yb atoms and the MIDIX [4s3p1d] basis set for Cl atoms. The parameters of the effective r _g configuration of the monomer molecules corresponding to the temperature of the experiment were calculated. The difference between the calculated equilibrium r _e(Ln-Cl) and temperature-averaged r _g(Ln-Cl) distances was found to be 0.001–0.002 Å and did not exceed the error of the r _g(Ln-Cl) parameter determined in the electron diffraction experiment. The experimental parameters of the r _g structure were shown to be consistent with the idea about the planar equilibrium geometrical configuration of ErCl₃ and YbCl₃ molecules.     

The thermodynamic properties of the [(Me<Subscript>3</Subscript>Si)<Subscript>7</Subscript>C<Subscript>60</Subscript>]<Subscript>2</Subscript> fullerene complex

The temperature dependence of the heat capacity C _p ^o of the [(Me₃Si)₇C₆₀]₂ fullerene complex was measured for the first time using precision adiabatic vacuum calorimetry over the temperature range 6.7–340 K and high-accuracy differential scanning calorimetry at 320–635 K. For the most part, the error in the C _p ^o values was about ±0.5%. An irreversible endothermic effect caused by the splitting of the dimeric bond between fullerene fragments and the thermal decomposition of the complex was observed at 448–570 K. The thermodynamic characteristics of this transformation were calculated and analyzed. Multifractal analysis of the low-temperature (T < 50 K) heat capacity was performed, and conclusions were drawn concerning the character of the heterodynamicity of the structure. The experimental data obtained were used to calculate the standard thermodynamic functions C _p ^o (T), H ^o (T) ? H ^o (0), S ^o (T) ? S ^o (0), and G ^o (T) ? H ^o (0) over the temperature range from T → 0 to 445 K and estimate the standard entropy of formation of the compound from simple substances at 298.15 K. The standard thermodynamic properties of [(Me₃Si)₇C₆₀]₂ are compared with those of the (C₆₀)₂ dimer, the [(η⁶-Ph₂)₂Cr]⁺[C₆₀]^?? fulleride, and the initial C₆₀ fullerene.     

High-pressure nonstoichiometric phase Sm<Subscript><Emphasis Type="Italic">x</Emphasis></Subscript>Cu<Subscript>3</Subscript>V<Subscript>4</Subscript>O<Subscript>12</Subscript>

Perovskite-like nonstoichiometric oxide Sm _x Cu₃V₄O₁₂ (space group Im \(\bar 3\), Z = 2, a = 7.276?7.314 Å) with cationic vacancies and a homogeneity region was prepared barothermally (p = 6.0?9.0 GPa, T = 700?1100°C) for the first time. Structural and isotropic thermal parameters, as well as bond lengths and bond angles, were determined. The compound has metal-type conductivity and paramagnetic properties.     

High-pressure defect phase Tm<Subscript><Emphasis Type="Italic">x</Emphasis></Subscript>Cu<Subscript>3</Subscript>V<Subscript>4</Subscript>O<Subscript>12</Subscript>

Perovskite-related oxide Tm _x Cu₃V₄O₁₂ (space group Im \(\bar 3\), Z = 2, a = 7.262?7.273 Å) with vacancies in the cationic sublattice has been prepared for the first time under barothermal conditions (p = 7.0?9.0 GPa, T = 900?1100°C). Electric resistivity (10–300 K) and magnetic susceptibility (0–300 K) were studied as a function of temperature. Tm _x Cu₃V₄O₁₂ is shown to have a metallic conductivity and paramagnetism.     

Structure of aluminum(III) dipivaloylmethanate AlO<Subscript>6</Subscript>C<Subscript>33</Subscript>H<Subscript>57</Subscript>

The structure of aluminum(III) tris-dipivaloylmethanate (Bruker Nonius X8 Apex diffractometer with a 4K CCD detector, λMoK _α, graphite monochromator, T = 150(2) K) is determined, and the synthetic procedure for its preparation is suggested. Crystal data are: C2/c space group, a = 28.1587(12) Å, b = 18.5170(7) Å, c = 21.5332(8) Å, β = 97.573(1)°, V = 11129.8(8) ų, Z = 12, d _x = 1.033 g/cm³, R = 6.93. The complex has a molecular structure; the aluminum atom is octahedrally surrounded by six oxygen atoms of three chelating ligands; Al-O distances are 1.860(2)–1.873(2)0A; O-Al-O angles fall within 88.08(9)–91.96(10)° and 177.93(9)–179.83(14)°. The known crystal packings of metal tris-dipivaloylmethanates are analyzed. Three types of the arrangement of the molecules in the crystals denoted as α, β, and γ are identified.     

Crystal structure of a cobalt oxide LuBaCo<Subscript>4</Subscript>O<Subscript>7</Subscript>

Crystals of LuBaCo₄O_7+δ (114Lu) have been obtained by spontaneous crystallization of slowly cooled nonstoichiometric melt of the system Lu-Ba-Co-O. The crystals have been characterized by EDX microprobe and synchrotron radiation powder diffraction. Structure refinement has been carried out (automated diffractometer Bruker X8 APEX with a CCD detector, MoK _α, graphite monochromator, ?_max = 32.54°). Parameters of the hexagonal unit cell: space group P6₃ mc, a = 6.2601(1) Å c = 10.2017(3) Å V = 346.23(1) Å₃, Z = 2, d _calc = 6.331 g/cm₃. Framework structure of the wurtzite type has been refined anisotropically to R-factor 0.0174. Charge balance in the compound and geometrical matching of structural fragments are discussed.     

Preparation,crystal structure and mechanism of thermal decomposition of complex [Dy(<Emphasis Type="Italic">p</Emphasis>-MOBA)<Subscript>3</Subscript>Phen]<Subscript>2</Subscript>

1,10-Phenanthrolinetris(4-methoxybenzoate)dysprosium, Dy(p-MOBA)₃Phen (where p-MOBA = p-methoxybenzoate and Phen = 1,10-phenanthroline), (I) has been synthesized. The complex was characterized by various techniques including elemental analysis, UV, IR, XRD, molar conductance, and TG-DTG. The crystals consist of binuclear molecules and monoclinic, space group P2 ₁/n: a = 14.143(6) Å, b = 17.550(7) Å, c = 14.493(6) Å, β = 117.357(4)°, Z = 2, ρ _c = 1.655 g cm^?3, F(000) = 1588; R ₁ = 0.0176, wR ₂ = 0.0455. In the complex, each Dy³⁺ ion is nine-coordinate to one 1,10-phenanthroline molecule, one bidentate chelating carboxylate group, and four bridging carboxylate groups in which the carboxylate groups are bonded to the Dy³⁺ ions in three modes: bridging bidentate, bridging tridentate, and chelating bidentate. The thermal decomposition mechanism of I has been determined on the basis of thermal analysis. In addition, the lifetime equation at a weight-loss of 10% was deduced as lnτ = ?28.8361 + 19478.37/T by isothermal thermogravimetric analysis.     

Synthesis,structure, and physicochemical properties of the Cr(<Emphasis Type="Italic">iso</Emphasis>-Bu<Subscript>2</Subscript>PS<Subscript>2</Subscript>)<Subscript>3</Subscript> chelate compound

A paramagnetic (μ_ef = 3.86 BM) complex Cr(i-Bu₂PS₂)₃ (I) has been synthesized. Single crystals I were grown, and the crystal structure of the compound was determined from X-ray diffraction data (X8 APEX diffractometer, MoK _α radiation, 4516 F _hkl , R = 0.0604). Monoclinic crystals, space group P2₁/n, unit cell parameters a = 14.2665(5) Å, b = 11.4400(4) Å, c = 23.1299(8) Å, β = 90.245(1)°, V = 3775.0(2) ų, Z = 4, d _calc = 1.196 g/cm³. The structure is based on discrete mononuclear molecules. The coordination polyhedron of the Cr atom is a distorted S₆ octahedron formed from the S atoms of three cyclic bidentate ligands — i-Bu₂PS ₂ ⁻ ions. Electron spectroscopy data correspond to the octahedral structure of the CrS₆ chromophore. Original Russian Text Copyright ? 2007 by E. A. Sankova, L. A. Glinskaya, T. E. Kokina, R. F. Klevstova, and S. V. Larionov __________ Translated from Zhurnal Strukturnoi Khimii, Vol. 48, No. 2, pp. 374–378, March–April, 2007.