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.     

Atomic Absorption Assay of Noble Metals in Ores with the Use of Sample Decomposition by Ultrasound

An atomic absorption assay of gold, silver, and palladium in various types of ores is performed with the use of ultrasound at the fire assay stage. It is shown that ultrasound can reduce the temperature and duration of fusion and increase the recovery of noble metals into the lead button.     

Efficacy testing of disinfectants

The U.S. Environmental Protection Agency's (EPA) Office of Pesticide Programs (OPP) has the responsibility for regulating antimicrobial products, including sporicides, used to treat and decontaminate inanimate surfaces. In response to the anthrax (Bacillus anthracis) attacks of 2001 and the associated need for verifying the performance of chemicals for building decontamination, the EPA initiated research in late 2003 to evaluate and improve efficacy test methods for sporicides. The OPP Microbiology Laboratory located at the Environmental Science Center, Ft. Meade, MD is the lead laboratory. Through funding provided by EPA's Office of Research and Development (Safe Buildings Program), a collaborative research plan has been established to address several key issues. Research is currently being conducted on 2 fronts: (1) the evaluation of quantitative methodology for assessing the efficacy of sporicides, and (2) the development and comparative testing of selected modifications to improve the AOAC Sporicidal Activity Test (AOAC Method 966.04). Future studies will include the evaluation of candidate surrogates of B. anthracis using a quantitative method, and a multilaboratory validation study of a quantitative method-surrogate combination. The General Referee is serving as the Principal Investigator for all research described in this report, and has the overall responsibility for the technical conduct of the projects. In cases where the General Referee has oversight of projects that involve official collaborative studies and validation support from AOAC INTERNATIONAL, AOAC officials and the Committee Chair will determine the appropriate mechanism for formal study review. The 2003 General Referee report provides the background on the development and direction of the research projects. The preliminary data, general conclusions, next steps, and recommendations are provided in this report.     

Recherches sur la formation et la transformation des esters LXXVII [1]. Etude à l'aide de H2[18O] de la scission de quelques monoesters phosphoreux et de l'acide propargyl-benzènephosphonique

(1) Monopotassium phosphite KH₂PO₃ heated at 300°C with CO[¹⁸O] exchanges one atom of oxygen after 3 hours, one to two atoms after 6 hours, and its three O atoms after 12 hours; the probable mecanism of this exchange is discussed. When the same treatment is carried out in the presence of o-phenylene diamine hydrochloride, the exchange is total (three O) after 3 hours at 300°C. Treated by this last procedure, benzenephosphonic acid C₆H₅PO(OH)₂ undergoes equally a total exchange of its O atoms in 3 hours.     

A comparative analysis of the total syntheses of the amphidinolide T natural products

In this article we compare and contrast the strategies and tactics used in the syntheses of the amphidinolide T family of natural products that have been reported by Fürstner, Ghosh and ourselves. Similar approaches to the trisubstituted THF ring present in the targets are utilized in all of the syntheses, but each strategy showcases a different means of macrocyclization.     

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.     

Observation of vibration-electronic exchange in gas-surface collisions

Intensity increase of exoelectronic emission in the interaction of vibrationally excited hydrogen beam (v1) with emitter surface (CaSO₄) has been found. The effect proves to be due to the transfer of vibrational energy from molecules to trapped electrons, i.e. to the v-e transition in gas-surface collisions.

---

- (v1) (CaSO₄). , .. v-e- -.

     

Preparation of a new carboranyl lactoside for the treatment of cancer by boron neutron capture therapy: synthesis and toxicity of fluoro carboranyl glycosides for in vivo 19F-NMR spectroscopy

The synthesis of new ortho-carboranyl lactosides 8, 17, 19 and glucosides 22 and 23 for the use in boron neutron capture therapy is reported. Carboranyl lactosides 17 and 19 as well as the glucosides 22 and 23 contain a fluorine atom to allow a noninvasive determination of these compounds in tumor cells by 19F-NMR spectroscopy. In cloning efficiency tests on human bronchial carcinoma cells the carboranyl lactosides 17 and 19 displayed almost no cytotoxicity. Thus, the considerably cytotoxic carboranyl alcohol 11 is detoxified when linked to a sugar moiety such as in carboranyl glucoside 22.     

Determination of iodide in drinking water by isotope dilution analysis

The most suitable way of determination iodine-deficiency is to measure iodine concentrations in water and urine. For this reason, a method that can determine iodide concentrations in drinking water and suitable for routine analysis, is developed. Water samples have been collected from four Aegean localities: Izmir, Salihli, Ödemis and Tire situated in the western Turkey. The method is based on substochiometric isotope dilution analysis. Iodile concentrations vary within 9.86–85.14 μg/l ranges in the analyzed samples. Mean value is 44.92±22.07 μg/l.