A new approach to predict the biological activity of molecules based on similarity of their interaction fields and the logP and logD values: application to auxins

The activity of a biological compound is dependent both on specific binding to a target receptor and its ADME (Absorption, Distribution, Metabolism, Excretion) properties. A challenge to predict biological activity is to consider both contributions simultaneously in deriving quantitative models. We present a novel approach to derive QSAR models combining similarity analysis of molecular interaction fields (MIFs) with prediction of logP and/or logD. This new classification method is applied to a set of about 100 compounds related to the auxin plant hormone. The classification based on similarity of their interaction fields is more successful for the indole than the phenoxy compounds. The classification of the phenoxy compounds is however improved by taking into account the influence of the logP and/or the logD values on biological activity. With the new combined method, the majority (8 out of 10) of the previously misclassified derivatives of phenoxy acetic acid are classified in accord with their bioassays. The recently determined crystal structure of the auxin-binding protein 1 (ABP1) enabled validation of our approach. The results of docking a few auxin related compounds with different biological activity to ABP1 correlate well with the classification based on similarity of MIFs only. Biological activity is, however, better predicted by a combined similarity of MIFs + logP/logD approach.     

Note on the application of the reduced graph model in conjunction with search trees to the enumeration ofKekulé structures

The reduced graph model, when used in conjunction with the search trees method, provides a novel combinatorial procedure for the enumeration and generation ofKekulé structures. The procedure is suited for large benzenoid hydrocarbons consisting of cata- and thin peri-condensed parts.

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Zur Anwendung des Reduced Graph Model im Zusammenhang mit Search Trees zur Ermittlung der Anzahl möglicherKekulé-Strukturen

Zusammenfassung Das Modell erlaubt mit der im Titel genannten Kombination eine neuartige Methode zur Ermittlung und Generierung vonKekulé-Strukturen. Das Verfahren ist für große benzoide Kohlenwasserstoffe geeignet, die aus cata- und (dünnen) peri-kondensierten Teilstrukturen bestehen.

     

Ammonium nitrate changes during thermal analysis

A study was made of the difference occurring in ammonium nitrate during investigation by DTA and by DSC. The results show that the DTA of ammonium nitrate (p.a.) is accompanied by the crystal transformation IV III II I and melting. During DSC investigation of the same ammonium nitrate samples, the salt undergoes the transformations IV III and IV II in parallel; then follow the crystal transformations III II I and melting. The investigation conditions and the history of the samples do not essentially influence the crystal transformations during thermal analysis.

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Zusammenfassung Bei DTA und DSC von Ammoniumnitrat zu beobachtende Unterschiede wurden untersucht. Bei der DTA von p.a. Ammoniumnitrat verlaufen die Kristallumwandlungen IV III II I sowie der Schmelzvorgang. Während der DSC der gleichen Ammoniumnitratproben verlaufen die Übergänge IV III und IV II parallel, worauf die Kristallumwandlungen III II I und der Schmelzvorgang folgen. Die experimentellen Bedingungen und die Vorgeschichte der Proben hat keinen wesentlichen Einfluß auf die während der thermischen Analyse verlaufenden Kristallumwandlungen.

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. ( ..) IV III II I . , IV III IV II - , III II ar I . .

     

Gas-phase structure of protonated histidine and histidine methyl ester: combined experimental mass spectrometry and theoretical ab initio study

Gas-phase H/D exchange experiments with CD3OD and D2O and quantum chemical ab initio G3(MP2) calculations were carried out on protonated histidine and protonated histidine methyl ester in order to elucidate their bonding and structure. The H/D exchange experiments show that both ions have three equivalent fast hydrogens and one appreciably slower exchangeable hydrogen assigned to the protonated amino group participating in a strong intramolecular hydrogen bond (IHB) with the nearest N(sp2) nitrogen of the imidazole fragment and to the distal ring NH-group, respectively. It is taken for granted that the proton exchange in the IHB is much faster than the H/D exchange. Unlike in other protonated amino acids (glycine, proline, phenylalanine, tyrosine, and tryptophan) studied earlier, the exchange rate of the carboxyl group in protonated histidine is slower than that of the amino group. The most stable conformers and the enthalpies of neutral and protonated histidine and its methyl ester are calculated at the G3(MP2) level of theory. It is shown that strong intramolecular hydrogen bonding between the amino group and the imidazole ring nitrogen sites is responsible for the stability and specific properties of the protonated histidine. It is found that the proton fluctuates between the amino and imidazole groups in the protonated form across an almost vanishing barrier. Proton affinity (PA) of histidine calculated by the G3(MP2) method is 233.2 and 232.4 kcal mol(-1) for protonation at the imidazole ring and at the amino group nitrogens, respectively, which is about 3-5 kcal mol(-1) lower than the reported experimental value.     

Determination of chloride by stripping chronopotentiometry with silver-film electrode

The experimental parameters of cathodic stripping chronopotentiometry of chloride at a silver-film electrode are investigated and optimized. The chloride preconcentration is achieved in the form of silver chloride by a controlled potential oxidation of the working electrode under vigorous stirring. Cathodic stripping of the deposit is obtained by the constant current, under the condition of diffusive mass transfer. Deaeration of the solution is not necessary. A detection limit of 35 μ dm⁻³ (10⁻⁶ mol dm⁻³) is obtained at a deposition time of 180 s, with a reproducibility of 6.7 % (expressed as relative standard deviation, RSD).     

Use of x-ray fluorescence spectrometry in ion-exchange studies of leach liquors

Equilibrium and kinetic studies of ion exchange of a complex leach liquor from coal ash, with strongly basic resins and a liquid ion exchanger are reported. The multi-component system was studied by determining the composition of the effluents and by non-destructive analysis of the loaded ion exchangers by XRF spectrometry. In the case of column operation, the elution processes were investigated by the same method, which was very appropriate for non-destructive monitoring of resin regeneration steps done repeatedly with the same resin sample.     

On lower bounds of number of perfect matchings in fullerene graphs

Couting perfect matchings in graphs is a very difficult problem. Some recently developed decomposition techniques allowed us to estimate the lower bound of the number of perfect matchings in certain classes of graphs. By applying these techniques, it will be shown that every fullerene graph with p vertices contains at least p/2+1 perfect matchings. It is a significant improvement over a previously published estimate, which claimed at least three perfect matchings in every fullerene graph. As an interesting chemical consequence, it is noted that every bisubstituted derivative of a fullerene still permits a Kekulé structure.     

Delphinidin–Aluminum(III) Complexes in Aqueous and Non-Aqueous Media: Spectroscopic Characterization and Theoretical Study

Summary. The study of delphinidin complexation with trivalent aluminum in acidic aqueous buffered (pH 3.0 and 3.8) and methanolic solutions was performed utilizing electronic absorption spectroscopy and quantum chemical calculations. In its structure delphinidin possesses several chelating sites in competition towards aluminum(III). Molar ratio plots denoted the formation of only one aluminum(III):delphinidin complex of stoichiometry of 1:1 in both investigated media. Semiempirical calculations, performed at the restricted HF AM1 level, enabled the determination of the structural features of free delphinidin and structural modifications caused by chelation of aluminum(III). Considering the pigment molecular structure and the results of the theoretical calculations it is possible to equally implicate C3′–C4′ and C4′–C5′ hydroxyl groups as those with the predominant chelating power.     

Fluorescence-dip infrared spectroscopy and predissociation dynamics of OH A 2Sigma+ (v = 4) radicals

Fluorescence-dip infrared spectroscopy, an UV-IR double-resonance technique, is employed to characterize the line positions, linewidths, and corresponding lifetimes of highly predissociative rovibrational levels of the excited A (2)Sigma(+) electronic state of the OH radical. Various lines of the 4 <--2 overtone transition in the excited A (2)Sigma(+) state are observed, from which the rotational, centrifugal distortion, and spin-rotation constants for the A (2)Sigma(+) (v = 4) state are determined, along with the vibrational frequency for the overtone transition. Homogeneous linewidths of 0.23-0.31 cm(-1) full width at half maximum are extracted from the line profiles, demonstrating that the N = 0 to 7 rotational levels of the OH A (2)Sigma(+) (v = 4) state undergo rapid predissociation with lifetimes of < or =23 ps. The experimental linewidths are in near quantitative agreement with first-principles theoretical predictions.     

Concentrations of some elements in the coastal sea sediments: Bays with marinas

Summary Surface sediments and sediment cores from two bays in the Adriatic sea (Punat Bay and Soline Bay, Croatia) have been analyzed for a number of elements, in particular: Ti, V, Mn, Fe, Cu, Zn, As and Pb, by using XRF. Maps of elemental distribution in surface sediments show increased concentrations for some elements present in antifouling paints (Cu, Zn, Pb) near the service areas in the villages or marinas. Core profiles for these elements were used to evaluate the environmental impact of newly constructed marinas. Source partition indicates the influence of other sources located in near by villages. The critical factor in these considerations was shown to be water exchange with the open sea.