Computer-aided prediction of QT-prolongation1

Drug-induced cardiac arrhythmia is acknowledged as a serious obstacle in successful development of new drugs. Several methods for in silico prediction of acquired long QT syndrome (LQTS) caused by the pharmacological blockade of human hERG K⁺ channels are discussed in literature. We propose to use the computer program PASS, which estimates the probabilities of about 3000 biological activities, not only for prediction of hERG blockade and QT-prolongation but also for the analysis of indirect mechanisms of these actions. After addition in the PASS training set of 163 compounds with data on QT-Prolongation and re-training, it was shown that accuracy of prediction was 87.1% and 81.8% for hERG blockade and QT-prolongation, respectively. Using computer program PharmaExpert we found that in the predicted biological activity spectra there was a certain correlation between the hERG blockade and some other molecular mechanisms of action. Possible role of 1-phosphatidylinositol-4-phospate 5-kinase, dimethylargininase and progesterone 11 alpha-monooxygenase inhibition in hERG blockade was discussed.     

Equilibrium Study on Ion-Pair Formation in Water and Distribution Between Water and m-Xylene of Tetraalkylammonium Picrates

The 1:1 ion-pair formation constants (K _IP) of tetraalkylammonium (Me₄N⁺, Et₄N⁺, Pr₄N⁺, Bu₄N⁺, and Bu₃MeN⁺) picrates in water were determined by capillary electrophoresis at 25°C. The ion-pair extraction constants (K _ex,ip) of the picrates from water to m-xylene were determined by a batch-extraction method at 25°C, and the distribution constants (K _D) of the neutral ion-pairs were calculated from the relationship K _D = K_ex,ip/K _IP. The tetraalkylammonium ion having more methylene groups generally forms a slightly more stable ion-pair with the picrate ion in water, which is attributed to the lower hydration of the cation. For Me₄N⁺, Et₄N⁺, Pr₄N⁺, and Bu₄N⁺, the distribution of the ion pair into m-xylene increases in that order, and a linear relationship was found between log K _D and the number of methylene groups in the cation. This is consistently explained by the regular solution theory. It was also revealed that the ion pairs have a strong specific interaction with water. The ion pair of Bu₃MeN⁺ has a higher distribution constant than that expected from the relationship between log K _D and the number of methylene groups for the symmetrical tetraalkylammonium ions. The cation dependence of the ion pair extractability is mostly governed by that of the distribution of the ion pair.     

On The Effect of Dielectric Constant on Formation and Stability Constants of Vanadium(v) with Leucine in Mixed Solvent of Methanol + Water at 298.15 K

Abstract

Equilibria in aqueous solutions in the system leucine + VO₂ ⁺ has been studied by a combination of potentiometric and spectrophotometric methods, in the p^H range 3–4.4 with high ligand-to-metal ratios. An equilibrium model, MY, is assumed, where M and Y represent the metal ion and fully dissociated amino acid anion, respectively. The results showed that formation and stability constants of complex system increased with decrease of dielectric constants. Linear relationships were observed when log K_P was plotted vs. 1/D, where K_P and D represent stability and dielectric constants of the system, respectively.     

Hydrogen Bonding and Solvent Effects on Complexation of Alkali Metal Cations by Lower Rim Calix[4]arene Tetra(O-[N -acetyl-D -phenylglycine methyl ester]) Derivative

Complexation of alkali metal cations with 5,11,17,23-tetra-tert-butyl-26,28,25,27-tetrakis(O-methyl-D-α-phenylglycylcarbonylmethoxy)calix[4]arene (L) was studied by means of spectrophotometric, conductometric and potentiometric titrations at 25 °C. The solvent effect on the binding ability of L was examined by using two solvents with different affinities for hydrogen bonding, viz. methanol and acetonitrile. Despite the presence of intramolecular NH···O=C hydrogen bonds in L, which need to be disrupted to allow metal ion binding, this calix[4]arene amino acid derivative was shown to be an efficient binder for smaller Li⁺ and Na⁺ cations in acetonitrile (lg K_LiL > 5, lg K_NaL = 7.66), moderately efficient for K⁺ (lg K_KL = 4.62), whereas larger Rb⁺ and Cs⁺ did not fit in its hydrophilic cavity. The complex stabilities in methanol were significantly lower (lg K_NaL = 4.45, lg K_KL = 2.48). That could be explained by different solvation of the cations and by competition between the cations and methanol molecules (via hydrogen bonds) for amide carbonyl oxygens. The influence of cation solvation on complex stability was most pronounced in the case of Li⁺ for which, contrary to the quite stable LiL⁺ complex in acetonitrile, no complexation was observed in methanol under the conditions used.     

Extraction of certain actinide and lanthanide elements from different acidic media by polyurethane foams loaded with di-(2-ethylhexyl)phosphoric acid (HDEHP)

The extraction of cerium(III) from weakly acidic chloride solutions by HDEHP-nitrobenzene-loaded polyurethane foams could be analyzed quantitatively in terms of the equation: log(9.056 D_c)=log K_c+2.14 log (C_d?6C_c)+3 pH+log f_c where D_c is the distribution ratio of cerium(III) between the foam and aqueous phases, C_d and C_c are the total HDEHP and Ce(III) concentrations on the foam, respectively, log f_c=[Ce³⁺]_(sq)/[ΣCe(III)]_(aq), and K_c is the equilibrium constant of the equation: Ce _(aq) ³⁺ +2.14(HX)_2.8(o) ? ? CeX₆·H_3(o)+3H _(aq) ⁺ . Values of K_c under the different extraction conditions tested are given.     

Complexation Properties of a Carbon-Bridged Cryptand with Metal Ions in Aqueous Solution at 25°C

Abstract

Thermodynamic quantities (log K, ΔH, and ΔS) for the interactions of a carbon-bridged cryptand with Li⁺, Na⁺, K⁺, Ca²⁺, Sr²⁺, Ba²⁺, and Pb²⁺ were determined at 25° C by calorimetric titration in aqueous solution. The cryptand forms complexes with Na⁺, Sr²⁺, Ba²⁺, and Pb²⁺ with log K ≤ 2. Complexation was not detected for Li⁺, K⁺, and Ca²⁺. Weak interactions with Li⁺ and K⁺ and a log K value of 2.4 for Na⁺ suggest that the cavity size of the cryptand is close to that of Na⁺ but too small for K⁺ and too large for Li⁺. The carbon-bridged cryptand selectively binds Sr²⁺ (log K = 3.2) over Ca²⁺ and Ba²⁺ by more than one order of magnitude.     

Features of Formation of Mixed-Ligand Complexes of Aluminum Tetraphenylporphine

Formation of extra complexes of aluminum tetraphenylporphine was studied by spectrophotometric titration. The effect of the nature of acido ligands on the stability of mixed-ligand complexes of aluminum tetraphenylporphine was determined. The stability constant (log K _st) of sterically unstrained complexes (Cl)Al(L)TPP and (OH)Al(L)TPP increases linearly with increasing basicity of the extra ligand (log KBH⁺); in the case of sterically distorted complexes (OAc)Al(L)TPP and (Acac)Al(L)TPP changes in log K _st and log KBH⁺ vary in the same direction. The geometries and energy characteristics of six-coordinate complexes of aluminum porphyrins were calculated quantum-chemically. The calculated enthalpies and Gibbs energies of formation of the complexes are consistent with the experiment. The possibility of the bidentate coordination of acetate and acetylacetonate in the porphyrin extra complexes was proved.     

Experimental Evidence for a Calix[4]arene-Proton Complex

From extraction experiments and γ-activity measurements, the extraction constant corresponding to the equilibrium H⁺(aq) + 1 ·Na⁺(nb) ⇆ 1 ·H⁺(nb) + Na⁺(aq) taking place in the two-phase water-nitrobenzene system (1 = p-tert-butylcalix[4]arene-tetrakis(N, N-diethylacetamide); aq = aqueous phase, nb = nitrobenzene phase) was evaluated as log K _ex(H⁺, 1 ·Na⁺) = −1.4 ± 0.1. Further, the stability constant of the p-tert-butylcalix[4]arene-tetrakis(N,N-diethylacetamide)-H⁺ complex in water saturated nitrobenzene was calculated for a temperature of 25°C as log β_nb(1 · H⁺) = 8.1 ± 0.1.     

Vibrational spectral studies of ion-ion and ion-solvent interactions. II. Zinc nitrate in water/dioxane mixtures

Raman and infrared spectral data have been collected forp-dioxane and solvated and bound nitrate ions for Zn(NO₃)₂/p-dioxane/water systems. It is concluded that Zn²⁺ is preferentially solvated by water and that this aquation is also responsible for a lower concentration of ion pairs than is found for methanol/Zn(NO₃)₂ solutions for which the dielectric constant of the bulk solvent is similar. Values of K₁ (M^–1), the association constant for Zn(NO₃)⁺, are 0.22±0.02 (2/1 solvent,D=12.6) and 0.071±0.01 (4/1 solvent,D=33.0). The log K₁ against 1/D plot is not linear.     

Experimental Evidence for a Calix[4]arene-Proton Complex

Summary. From extraction experiments and γ-activity measurements, the extraction constant corresponding to the equilibrium H⁺(aq) + 1 ·Na⁺(nb) ⇆ 1 ·H⁺(nb) + Na⁺(aq) taking place in the two-phase water-nitrobenzene system (1 = p-tert-butylcalix[4]arene-tetrakis(N, N-diethylacetamide); aq = aqueous phase, nb = nitrobenzene phase) was evaluated as log K _ex(H⁺, 1 ·Na⁺) = −1.4 ± 0.1. Further, the stability constant of the p-tert-butylcalix[4]arene-tetrakis(N,N-diethylacetamide)-H⁺ complex in water saturated nitrobenzene was calculated for a temperature of 25°C as log β_nb(1 · H⁺) = 8.1 ± 0.1.     

Limonoids from the Twigs and Leaves of Chukrasia tabularis

Seven new limonoids, tabularisins J–P ( 1 – 7 , resp.), together with eight known compounds, were isolated from the twigs and leaves of Chukrasia tabularis. Their structures were determined primarily by spectroscopic methods. The potassium channel blocking activities of some of these isolates were evaluated, and a few of them exerted significant activities on the delayed rectifier (I_K) K⁺ current.     

The Association Constants of H<Superscript><Emphasis Type="Italic">+</Emphasis></Superscript> and Ca<Superscript><Emphasis Type="Italic">2 +</Emphasis></Superscript> with 2-Keto-D-Gluconate in Aqueous Solutions

2-Keto-D-gluconate (kG) is naturally produced in soils, sediments and rock faces through the microbial oxidation of glucose. Studies have qualitatively shown kG to enhance the dissolution of soil minerals. However, quantitative information, such as the log K values for the formation of metal–kG complexes, are not available. This paper presents the results of potentiometric titration studies that employ H⁺ and Ca²⁺ ion selective electrodes (ISEs) to determine the conditional ion association constants (log Q values) for the protonation and deprotonation of kG and the formation of Ca–kG complexes. The experimentally-determined log Q values were then converted to the corresponding ion association constants (the zero ionic strength condition; log K values) by employing a modified Davies equation for charged species and the Setchenów equation for neutral species. The log K values were determined by potentiometric titrations at constant kG concentration, varied ionic strengths, 25 or 22 ^∘C, and in the absence of CO₂. The computer model GEOCHEM-PC was used to determine the aqueous speciation of ions other than kG and the computer model FITEQL was used to estimate conditional log Q values for reactions in the various chemical models. Based on our evaluations, equilibrium constants for the following reactions were determined: H⁺+ kG^– ⇌ HkG⁰, log K_a1 = (3.00 ± 0.06), kG^–⇌ H_–1kG^2–+ H⁺, log K_a–1 = –(11.97 ± 0.41), and Ca²⁺+ kG^–⇌ CakG⁺, log K₁₀₁ = (1.74 ± 0.04).     

Localization of Hydrogen and Content of Oxonium Cations in Alunite via Neutron Diffraction

Polycrystalline alunite‐d₆ KAl₃(OD)₆(SO₄)₂, prepared by hydrothermal reaction of Al₂(SO₄)₃, K₂SO₄ and D₂SO₄, was studied by neutron powder diffraction performed on the diffractometer E2 (HMI‐BENSC, Berlin). Rietveld refinement of the data set for T = 2 K yielded the crystallographic data: space group R3m, Z = 3, trigonal setting, a = 694.3(1) pm, c = 1722.7(2) pm, N(I/σ(I) > 1) = 172, N(Var.) = 19, R_p = 0.036, wR_p = 0.046, R_B(I/σ(I) > 1) = 0.020. The deuterium nuclei could be located precisely. Three equivalent O–D bonds with nuclear distances r(O(4)–D) = 96.6(3) pm directed to each of the terminal oxygen atoms of the SO₄ groups are found. Partial substitution of K⁺ by D₃O⁺ was also considered in the refinement procedure. In good agreement with results of other methods a site occupation fraction n(D₃O⁺) = 0.0104 was obtained.     

Ions Can Move a Proton‐Coupled Electron‐Transfer Reaction into Tunneling Regime

The effects of charged species on proton‐coupled electron‐transfer (PCET) reaction should be of significance for understanding/application of important chemical and biological PCET systems. Such species can be found in proximity of activated complex in a PCET reaction, although they are not involved in the charge transfer process. Reported here is the first study of the above‐mentioned effects. Here, the effects of Na⁺, K⁺, Li⁺, Ca²⁺, Mg²⁺, and Me₄N⁺ observed in PCET reaction of ascorbate monoanions with hexacyanoferrate(III) ions in H₂O reveal that, in presence of ions, this over‐the‐barrier reaction entered into tunneling regime. The observations are: a) dependence of the rate constant on the cation concentration, where the rate constant is 71 (at I = 0.0023), and 821 (at 0.5M K⁺), 847 (at 1.0M Na⁺), and 438 M ^?1 s^?1 (at 0.011M Ca²⁺); b) changes of kinetic isotope effect (KIE) in the presence of ions, where k_H/k_D=4.6 (at I = 0.0023), and 3.4 (in the presence of 0.5M K⁺), 3.3 (at 1.0M Na⁺), 3.9 (at 0.001M Ca²⁺), and 3.9 (at 0.001M Mg²⁺), respectively; c) the isotope effects on Arrhenius pre‐factor where A_H/A_D=0.97 (0.15) in absence of ions, and 2.29 (0.60) (at 0.5M Na⁺), 1.77 (0.29) (at 1.0M Na⁺), 1.61 (0.25) (at 0.5M K⁺), 0.42 (0.16) (at 0.001M Ca²⁺) and 0.16 (0.19) (at 0.001M Mg²⁺); d) isotope differences in the enthalpies of activation in H₂O and in D₂O, where ΔΔH^?(D,H)=3.9 (0.4) kJ mol^?1 in the absence of cations, 1.3 (0.6) at 0.5M Na⁺, 1.8 (0.4) at 0.5M K⁺, 1.5 (0.4) at 1.0M Na⁺, 5.5 (0.9) (at 0.001M Ca²⁺), and 7.9 (2.8) (at 0.001M Mg²⁺) kJ mol^?1; e) nonlinear proton inventory in reaction. In the H₂O/dioxane 1 : 1, the observed KIE is 7.8 and 4.4 in the absence and in the presence of 0.1M K⁺, respectively, and A_H/A_D=0.14 (0.03). The changes when cations are present in the reaction are explained in terms of termolecular encounter complex consisting of redox partners, and the cation where the cation can be found in a near proximity of the reaction‐activated complex thus influencing the proton/electron double tunneling event in the PCET process. A molecule of H₂O is involved in the transition state. The resulting ‘configuration’ is more ‘rigid’ and more appropriate for efficient tunneling with Na⁺ or K⁺ (extensive tunneling observed), i.e., there is more precise organized H transfer coordinate than in the case of Ca²⁺ and Mg²⁺ (moderate tunneling observed) in the reaction.     

Influence of the dielectric constant on ion-pair and ion-ligand complex formation

The effect of dielectric constant on ion association of triethylammonium picrate and methylimidazolium picrate and on ion-ligand complex formation between the cations Et₃NH⁺ and MeImH⁺ and 1-methylimidazole was investigated from conductance data carried out in nitrobenzene-benzene mixtures (34.8K _A satisfy in first approximation the relation logK _A 1/D. The center-to-center distance å has been calculated and compared to the value obtained for nonhydrogenbonded ion pairs. The ion-ligand association constantK ₁ ⁺ increases as the dielectric constant of the medium decreases. Plots of logK ₁ ⁺ against 1/D give straight lines, the slopes of which are consistent with the predictions of a theory that interprets the effect of the dielectric constant in terms of changes in the polarization energy of the solvent around the complexed and the uncomplexed ions. For these interactions, the complexed ions can be approximated as charged spheres, the volume of which is equal to that of the bare ion plus the volume of the ligand.     

A <Emphasis Type="Italic">k</Emphasis>-nearest neighbor classification of hERG K<Superscript>+</Superscript> channel blockers

A series of 172 molecular structures that block the hERG K⁺ channel were used to develop a classification model where, initially, eight types of PaDEL fingerprints were used for k-nearest neighbor model development. A consensus model constructed using Extended-CDK, PubChem and Substructure count fingerprint-based models was found to be a robust predictor of hERG activity. This consensus model demonstrated sensitivity and specificity values of 0.78 and 0.61 for the internal dataset compounds and 0.63 and 0.54 for the external (PubChem) dataset compounds, respectively. This model has identified the highest number of true positives (i.e. 140) from the PubChem dataset so far, as compared to other published models, and can potentially serve as a basis for the prediction of hERG active compounds. Validating this model against FDA-withdrawn substances indicated that it may even be useful for differentiating between mechanisms underlying QT prolongation.     

Tetraalkylammonium Picrates in the Dichloromethane–Water System: Ion-Pair Formation and Liquid–Liquid Distribution of Free Ions and Ion Pairs

Equilibria concerning picrates of tetraalkylammonium ions (Me₄N⁺, Et₄N⁺, Pr₄N⁺, Bu₄N⁺, Bu₃MeN⁺) in a dichloromethane−water system have been investigated at 25 ^∘C. The 1:1 ion-pair formation constants (K _IP,o ^o) in dichloromethane at infinite dilution were conductometrically determined. The distribution constants (K _D ^o) of the ion pairs and the free cations between the solvents were determined by a batch-extraction method. The K _IP,o ^o value varies in the cation sequence, Bu₄N⁺ ≈ Pr₄N⁺ ≈ Et₄N⁺ < Bu₃MeN⁺ < < Me₄N⁺; this trend is explained by the electrostatic cation−anion interaction taking into account the structures of the ion pairs determined by density functional theory calculations. For the ion pairs of the symmetric R₄N⁺ cations, there is a linear positive relationship between log₁₀ K _D ^o and the number of methylene groups in the cation (N _{CH 2}). The ion pair of asymmetric Bu₃MeN⁺ has a higher distribution constant than that expected from the above log₁₀ K _D ^o versus N _{CH 2} relationship. These cation dependencies of log₁₀ K _D ^o for the ion pairs are explained theoretically by using the Hildebrand-Scatchard equation. For all the cations, the log₁₀ K _D ^o value of the free cation increases linearly with N _{CH 2}; the variation of log₁₀ K _D ^o is discussed by decomposing the distribution constant into the Born-type electrostatic contribution and the non-Born one, and attributed to the latter that is governed by the differences in the molar volumes of the cations. The cation dependencies of the ion-pair extractability and ion pairing in water are also discussed. An erratum to this article can be found at     

Structural and dynamical aspects of PEG/LiClO4 in solvent mixtures via NMR spectroscopy

Motivated by the potential usefulness of polyethylene glycol (PEG)/Li⁺ salt mixtures in several industrial applications, we investigated the structure and dynamics of PEG/LiClO₄ mixtures in D₂O and its mixtures with CD₃CN and DMSO-d₆, in a series of PEG-based polymers with a wide variation in their molecular weights. ¹H NMR chemical shifts, T₁/T₂ relaxation rates, pulsed-field gradient NMR diffusion experiments, and 2D HOESY NMR studies have been performed to understand the structural and dynamical aspects of these mixtures. Increasing the temperature of the medium results in a significant perturbation in the H-bonded structure of PEG in its PEG/LiClO₄/D₂O mixtures as observed from the increase in chemical shifts. On the other hand, the addition of molecular cosolvents has a negligible effect. The hydrodynamic structure of PEG shows a pronounced variation at low temperature with increasing molecular weight, which, however, disappears at higher temperatures. Increasing the temperature leads to a decrease in the hydrodynamic structure of PEG, which can be explained on the basis of solvation–desolvation phenomena. The 2D HOESY NMR spectra reveal a new finding of Li⁺-water binding in the PEG/LiClO₄/D₂O mixtures with the addition of molecular solvents, suggesting that the Li⁺ cation diffuses freely in the D₂O mixtures of polymers as compared with the polymer mixtures with DMSO or CD₃CN.