Styrene oxide DNA adducts: quantitative determination using <Superscript>31</Superscript>P monitoring

The reaction of styrene oxide, a potential carcinogen in humans, with DNA constituents has been used to develop an improved method for quantification of DNA adducts. To enable monitoring of DNA adducts caused by xenobiotics at physiological relevant levels, a robust, reliable and powerful method based on monitoring of phosphorus in nucleotides is described. An efficient enzymatic digestion step and a sample-preconcentration procedure are essential, and enable separation of alkylated nucleotides from the large excess of native nucleotides. The adducts are detected by means of the phosphorus signal measured at mass m/z=31 with an inductively-coupled-plasma mass spectrometer. Bis(4-nitrophenyl)phosphate (BNPP) serves as internal standard for quantification of the adducts. The absolute limit of detection, 45 fmol, corresponds to detection of three modified nucleotides among 10⁷ native nucleotides (the calculation is based on use of 50 g calf thymus DNA). An adduct formation ratio at the DNA of 3.6 adducts per 1000 nucleotides was measured, which is 75% lower than for reaction with monomeric 2-deoxy-nucleotides. In addition, a substantial amount of phosphate adducts were detected, but in DNA the rate of phosphate formation was lower than with monomeric nucleotides. Most probably these adducts escaped unnoticed when ³¹P-post-labelling was employed.     

Ion Association and Hydration in Aqueous Solutions of Nickel(II) and Cobalt(II) Sulfate

Aqueous solutions of nickel(II) and cobalt(II) sulfate have been investigated at 25 ^∘C by dielectric relaxation spectroscopy (DRS) over a wide range of frequencies (0.2 ≤ ν (GHz) ≤ 89) and salt concentrations (0.025 ≤ c(mol-L⁻¹) ≤ 1.4). The spectra indicate, as for MgSO₄(aq) studied previously, the simultaneous presence of double solvent-separated, solvent-shared and contact ion pairs in both NiSO₄(aq) and CoSO₄(aq). The stepwise formation constants for each ion-pair type and the overall association constant, obtained from the data are in good agreement with ultrasonic relaxation and other estimates. The DR spectra at higher concentrations (c ≥ 0.5 mol-L⁻¹) suggest the existence of a nonlinear triple ion M₂SO₄²⁺(aq). Consistent with the very strong hydration of the salts, which have ‘effective’ hydration numbers approaching 27 at infinite dilution, there are no significant differences in any of the relaxation or thermodynamic parameters for NiSO₄(aq) and CoSO₄(aq), except that the triple ion appears to be somewhat more stable for the latter.     

Dissociation equilibrium between uncharged and charged local anesthetic lidocaine in a surface-adsorbed film

The dissociation equilibrium between uncharged local anesthetic lidocaine (LC) and charged local anesthetic LC (LCH⁺) in a surface-adsorbed film was investigated by measuring the surface tension and pH of aqueous solutions of a mixture of hydrochloric acid and LC. The surface tension values decreased slightly with increasing total molality m_t at 0X₂0.5, where X₂ is the mole fraction of LC in the mixture, while they decreased rapidly with increasing m_t at 0.5<X₂1. It was shown from the pH measurements that almost all LC molecules were changed into LCH⁺ ions by protonation at 0X₂0.5 and both forms coexisted only at 0.5<X₂1. The quantities of the respective LC and LCH⁺ transferred from the aqueous solution to the adsorbed film, i.e., their surface densities, were calculated by applying the thermodynamic equations derived to the surface tension and pH data. A greater quantity of LC than LCH⁺ existed in the adsorbed film at the coexisting composition. The partitioning behavior of LC and LCH⁺ in the adsorbed film was characterized by three composition regions: (1) slight partitioning of low surface-active LCH⁺ in the region at 0X₂0.5, (2) preferential partitioning of LC at 0.5<X₂<around 0.7, and (3) negative partitioning of LCH⁺ at around 0.7X₂1. The present results clearly indicate that uncharged local anesthetics transfer into hydrophobic environments such as cell membranes more than charged ones.     

Quantitative analysis of docetaxel in human plasma using liquid chromatography coupled with tandem mass spectrometry

An assay for the quantitative determination of docetaxel in human plasma is described. Docetaxel was extracted from the matrix using liquid-liquid extraction with ter-butylmethylether, followed by high-performance liquid chromatographic analysis using an alkaline eluent. Paclitaxel was used as internal standard. Positive ionization electrospray tandem mass spectrometry was performed for selective and sensitive detection. The method was validated according to the FDA guidelines on bioanalytical method validation. The validated range for docetaxel was from 0.25--1000 ng/mL using 200 microL plasma aliquots. The method requires only a limited volume (200 microL) of human plasma and the method can be applied in studies requiring a low lower limit of quantitation of 0.25 ng/mL. The assay was applied successfully in several clinical and pharmacological studies with docetaxel.     

GeneMCL in microarray analysis

Accurately and reliably identifying the actual number of clusters present with a dataset of gene expression profiles, when no additional information on cluster structure is available, is a problem addressed by few algorithms. GeneMCL transforms microarray analysis data into a graph consisting of nodes connected by edges, where the nodes represent genes, and the edges represent the similarity in expression of those genes, as given by a proximity measurement. This measurement is taken to be the Pearson correlation coefficient combined with a local non-linear rescaling step. The resulting graph is input to the Markov Cluster (MCL) algorithm, which is an elegant, deterministic, non-specific and scalable method, which models stochastic flow through the graph. The algorithm is inherently affected by any cluster structure present, and rapidly decomposes a graph into cohesive clusters. The potential of the GeneMCL algorithm is demonstrated with a 5,730 gene subset (IGS) of the Van't Veer breast cancer database, for which the clusterings are shown to reflect underlying biological mechanisms.     

Computer-Assisted Solution of Chemical Problems—The Historical Development and the Present State of the Art of a New Discipline of Chemistry

The topic of this article is the development and the present state of the art of computer chemistry, the computer-assisted solution of chemical problems. Initially the problems in computer chemistry were confined to structure elucidation on the basis of spectroscopic data, then programs for synthesis design based on libraries of reaction data for relatively narrow classes of target compounds were developed, and now computer programs for the solution of a great variety of chemical problems are available or are under development. Previously it was an achievement when any solution of a chemical problem could be generated by computer assistance. Today, the main task is the efficient, transparent, and non-arbitrary selection of meaningful results from the immense set of potential solutions—that also may contain innovative proposals. Chemistry has two aspects, constitutional chemistry and stereochemistry, which are interrelated, but still require different approaches. As a result, about twenty years ago, an algebraic model of the logical structure of chemistry was presented that consisted of two parts: the constitution-oriented algebra of be- and r-matrices, and the theory of the stereochemistry of the chemical identity group. New chemical definitions, concepts, and perspectives are characteristic of this logic-oriented model, as well as the direct mathematical representation of chemical processes. This model enables the implementation of formal reaction generators that can produce conceivable solutions to chemical problems—including unprecedented solutions—without detailed empirical chemical information. New formal selection procedures for computer-generated chemical information are also possible through the above model. It is expedient to combine these with interactive methods of selection. In this review, the Munich project is presented and discussed in detail. It encompasses the further development and implementation of the mathematical model of the logical structure of chemistry as well as the experimental verification of the computer-generated results. The article concludes with a review of new reactions, reagents, and reaction mechanisms that have been found with the PC-programs IGOR and RAIN.     

Organoelement Compounds with Al?Al,Ga?Ga,and In?In Bonds

In the attempt to synthesize compounds with aluminum in a low oxidation state and an Al Al bond, by the reduction of alkylaluminum halides with alkali metals, analogous to a Wurtz coupling, in general the deposition of elemental aluminum and the formation of the corresponding trialkylaluminum compounds is observed. Thus, tetrasubstituted dialuminum compounds R₂Al AlR₂, apart from a few poorly characterized examples, were for a long time considered part of an unverified class of substances. Only with the sterically very highly shielded tetrakis[bis(trimethylsilyl)methyl]dialuminum did we achieve the synthesis of the first completely characterized organoelement compound with unlimited stability, which shows aluminum in the oxidation state + II and has an Al Al bond. In the meantime, corresponding compounds for the elements gallium and indium have been obtained. With the simple access to tetrasubstituted dimetal compounds, a fascinating new research area has opened for preparative chemistry, in which the particular interest will naturally lie in the reactive properties of the metal-metal bond.     

IR- und Raman-Spektren einiger Kaliumpentafluorometallate-monohydrate

The IR- and Raman Spectra of several compounds of the stoichiometryM ₂ ^I M ^IIIF₅H₂O and their deuterated analogs have been interpreted on the basis of their crystal structures. The compounds studied were divided into two classes regarding the bonding of water molecules. The main spectroscopic difference between the two classes was found in the region of H₂O vibrations in good agreement with theoretical predictions. The metal—fluorine and metal—oxygene vibrations gave no direct information concerning the two types of water.     

pH sensitivity of Si--C linked organic monolayers on crystalline silicon surfaces.

The electrochemical behavior of Si--C linked organic monolayers is studied in electrolyte-insulator-Si devices, under conditions normally encountered in potentiometric biosensors, to gain fundamental knowledge on the behavior of such Si electrodes under practical conditions. This is done via titration experiments, Mott-Schottky data analysis, and data fitting using a site-binding model. The results are compared with those of native SiO(2) layers and native SiO(2) layers modified with hexamethyldisilazane. All samples display pH sensitivity. The number of Si--OH groups on the alkylated samples is calculated to be less than 0.7 % of that of a pure SiO(2) insulator, which still causes a pH sensitivity of approximately 25 mV per pH unit in the pH range: 4-7. The alkylated samples hardly suffer from response changes during up- and down-going titrations, which indicates that very little oxide is additionally formed during the measurements. The pK(a) values of all samples with monolayers (4.0-4.4) are lower than that of native SiO(2) (6.0). The long-term drift (of approximately 1 mV h(-1)) is moderate. The results indicate that biosensors composed of alkylated Si substrates are feasible if a cross-sensitivity towards pH in the sensor signal is taken into account.