A combinatorial algorithm for calculating ligand binding

We consider the problem of predicting the mode of binding of a small molecule to a receptor site on a protein. One plausible approach, given a rigid molecule and its geometry, is to search directly for the orientation in space that maximizes the degree of contact. The computation time required for such a naive procedure is proportional to n³m³, where n is the number of points in the site where binding can occur, and m is the number of atoms in the ligand. We give an alternative, combinatorial approach, in which only “contact–no-contact” criteria are considered. We relate this problem to the well-known combinatorial problem of finding cliques in a graph and show that we can use a solution to the clique problem not only to solve our original problem, but also the problem of avoiding energetically unfavorable matches. Our experience with this method indicates that the computation time required is proportional to nm^2.8, with a lower constant of proportionality than that of the naive procedure.     

Use of Voltammetry for Determining Antibiotics Streptomycin and Azitromycin

Conditions were selected for the voltammetric determination of streptomycin and azitromycin using electrodes of different types. The interfering effects of cations, anions, and organic substances, food proteins among them, on the analytical signals from antibiotics were estimated. Procedures for determining streptomycin and azitromycin in pharmaceuticals and for determining streptomycin in milk at nano levels were developed.__________Translated from Zhurnal Analiticheskoi Khimii, Vol. 60, No. 6, 2005, pp. 586–591.Original Russian Text Copyright © 2005 by Fedorchuk, Puchkovskaya, Anisimova, Slepchenko.Presented at the VI All-Russian Conference (with international participation) on Electrochemical Methods of Analysis (EMA-2004, Ufa, May 23–27, 2004).     

Amino derivatives of mono- and diethynyldiarylalkanes

Conclusion The synthesis of acetylenic amine derivatives of 4-ethynyldiphenylmethane, 4,4 diethynylbibenzyl, and 4,4-diethynyl-,-diethylbibenzyl has been described.Translated from Izvestiya Akademii Nauk, SSSR, Seriya Khimicheskaya, No. 2, pp. 458–459, February, 1967.     

Gamma-radiolysis of chiral molecules: R(+)-limonene, S(-)-limonene and R(-)-a-phellandrene

Three isomeric chiral terpenes, R(+)-limonene, S(-)-limonene and R(-)-a-phellandrene were γ-radiolyzed in sealed vials at room temperature with a total radiation dose of 317 kGy. The radiolyzed samples were analyzed by FT-IR, electronic absorption spectroscopy, liquid chromatography using a diode-array detector (HPLC-DAD) and by polarimetry. Despite a relatively high radiation dose used, all the chiral molecules selected have shown a low radioracemization rate. This fact and the role played by the impurities in the selective radio-degradation of one of the two enantiomers has been discussed in the context of the origin of chirality in prebiotic molecules and the chirality enhancement in a prebiotic world. The results were also discussed in the frame of the radiosterilization technique of chiral drugs, perfumes and food components. This revised version was published online in July 2006 with corrections to the Cover Date.     

Determination of Aroma Compounds in Blackberry by GC/MS Analysis

The aromatic composition of five blackberry cultivars (Bursa 2, Navaho, Nessy, Chester Thornless, and Jumbo) was studied. The Im-SPME (Immersion Solid Phase Micro Extraction) extraction technique was applied and the samples were analyzed by GC/MS. Furfural and its derivatives were found to be the major aromatic compounds and 5-hydroxymethylfurfural was the most abundant compound in all the blackberry varieties.     

Splicing I: Using mixed basis sets in ab initio calculations

The effect of mixing (or “splicing”) extended and minimal basis sets on molecular properties such as geometries, Mulliken charges, dipoles, and internal rotation barriers was studied for several test molecules. The effect is gauged by comparison with full extended basis set calculations. It is found that splicing improves most properties relative to full minimal basis set calculations, and little accuracy is lost if the splicing is done in a judicious manner.     

Development of a computer-based system for fast neutron cyclic activation analysis

We have developed a computer-controlled system for carrying out cyclic neutron activation analysis using fast neutrons. The system is basically a mechanical, pneumatic transfer system in which the sample is cycled between an irradiation position and a Ge detector. The sequence of movements between these two position is under computer control as is the timing of the various parts of the cycle. In addition, flux monitoring and correction are carried out using a computer-controlled scaler and the -ray counting is similarly controlled. The key to this control is the use of an interface containing a DCP BUS which receives signals from various valves for control of sample movement or to the scaler or ADC to initiate counting storage or calculations of the data. Finally, some preliminary data obtained with this technique are presented for the inelastic scattering reactions on barium.     

Pyridine and pyrimidine ring syntheses from 4-(4-morpholino)-3-pentenone and from ethyl 3-(4-morpholino)-2-butenoate

3-Substituted 2(1H)-pyridones are produced from reaction of 4-(4-morpholino)-3-pentenone 1 with each of the following carbon acids: cyanoacetamide, malononitrile, cyanothioacetamide, acetylacetamide, benzoyl-acetonitrile. Reaction of ethyl 3-(4-morpholino)-2-butenoate 2 with cyanoacetamide gives the corresponding hydroxypyridone. Pyrimidines are formed by reaction of 1 and of 2 with benzamidine and with S-benzylthio-urea; in the last case, the eliminated morpholine displaces the benzylthio group to give the final product.     

Free radical synthesis of 2-alkoxytetrahydrofurans

Conclusions A new method is presented for obtaining 2-alkoxy tetrahydrofurans by reacting alcohols with, - unsaturated aldehydes in the presence of a peroxide.Translated from Izvestiya Akademii Nauk SSSR, Seriya Khimicheskaya, No. 12, pp. 2829–2831, December, 1968.     

The effect of morphological changes on the coprecipitation of strontium by calcium phosphate

The coprecipitation of strontium by a calcium phosphate phase formed at an elevated pH 10.8 was investigated. The first phase obtained under these conditions in the amorphous calcium phosphate (ACP) which is transformed into crystalline hydroxyapatite (HA) after the induction period. Is has been shown that this transformation together with morphological changes of the precipitated solid phase, influences the amount of the sorbed strontium significantly. The possible consequences of this finding on practical application of coprecipitation of strontium by calcium phosphate have been discussed.