Estimating probabilities of correct identification from results of mass spectral library searches

This work presents a method for using mass spectral match factors reported by library search systems to obtain certain probabilistic indicators of correct identification. The overall probability that a retrieval is correct is formally separated into two independent terms. One of these is the probability that a retrieval is correct assuming that the correct match is contained in the library. This can be computed directly from test results. The other term represents the probability that the spectrum of the unknown compound is actually in the library. While the absolute value of this term cannot be computed, a relative value based solely on search results can be derived. This value may, if desired, be used to refine an initial estimate of the overall probability. Parameters used in this calculation are based on changes in test results caused by the logical removal of the test compounds from the library. These methods were parameterized from results of searching the MST/EPA/NIH Mass Spectral Database with 12,592 good quality replicate spectra and a simple mass spectral comparison function. The methodology should be equal1 applicable to other libraries and search systems.     

A spin-dependent Popov-Fedotov trick and a new loop expansion for the strong coupling negativeU Hubbard model

We calculate fluctuation effects on Bose condensation type superconductivity in the strong coupling negative U Hubbard model by means of a new loop expansion. Our method is based on a spin-dependent modification of the Popov-Fedotov trick. We replace the Popov-Fedotov chemical potential by a fictitious imaginary magnetic field. This field is absorbed in spindependent semionic Matsubara frequencies, which allows for a mixed statistics representation of the anisotropic quantum spin 1/2 Heisenberg model. We report results at one loop order for the superconducting order parameter , for the critical temperature, for the chemical potential, and for the excitation spectra both above and belowT _c. We identify mean field results in zeroth loop order and we find both dimensional and filling (v-)depending singularities in interaction fluctuations at one loop order. Renormalization of dimensional singularities is carried out in 4 dimensions. Divergencies withv (1–v)0 in the dilute limits indicate the breakdown of mean field solutions, but superconductivity persists for arbitrarily smallv(1–v) if our loop expansion is interpreted by exponential behaviour as it is suggested by the abelian nonlinear sigma model.     

Linear dichroism and fluorescence polarization of diphenyl polyenes in stretched polyethylene films

A study of the linear diehroism and fluorescence polarization of diphenylpolyenes (C₆H₅—(CH=CH)_n—C₆H₅) with n = 1,2,3,4,6,8 in stretched polyethylene films shows that the polyenes orient in the anisotropic matrix with their transition dipole (emission and absorption, π → π^*) aligned with the direction of stretch. The maximum dichroic ratio is observed for 1,6-diphenyl-1,3,5-hexatriene (DPH), with n = 3, whereas the values are substantially lower for n < 3 or n > 3. The high orientation of DPH and poor alignment of the higher polyenes may be accounted for in terms of the growing flexibility of the polyene chains with increasing chain length. The results justify the use of DPH as a convenient fluorescence probe for biological and synthetic membranes.     

Surface modification of mesoporous, macroporous, and amorphous silica with catalytically active polyoxometalate clusters

Transition-metal-substituted polyoxometalates (TMSP) of the type [MII(H2O)PW11O39]5- (M = Co, Zn) and [SiW9O37(CoII(H2O))3]10- have been chemically anchored to modified macroporous (400 nm pores), mesoporous (2.8 nm pores), and amorphous silica surfaces. The materials were characterized by solid-state 31P MAS NMR, UV-vis, FT-IR spectroscopy, and N2 adsorption experiments to verify cluster attachment and the structure of the TMSP on the support. On the basis of the spectroscopic evidence, clusters were attached datively to the surface, and the integrity of the [CoPW11] cluster was maintained for nonaqueous impregnation with TBA5[CoPW11]; partial degradation of the cluster occurred when it was impregnated from aqueous solution using the K5[CoPW11] salt. Both the amine surface groups and the cobalt centers in the clusters were found to be necessary to prevent cluster loss during washing or reaction processes. The catalytic activities of the supported TMSP clusters were tested by the epoxidation of cyclohexene to cyclohexene oxide in the presence of isobutyraldehyde. The percent conversion of the substrate and the amount of product formed per unit time were similar for [CoPW11] clusters on each of the three silica supports, but slightly lower than for purely homogeneous reactions. [SiW9Co3] clusters with three available cobalt centers exhibited higher catalytic activity with nearly identical performance on a silica support or in homogeneous solution.     

Poly-N-hydroxyethylacrylamide as a novel, adsorbed coating for protein separation by capillary electrophoresis.

We present the polymer poly-N-hydroxyethylacrylamide (PHEA) (polyDuramide) as a novel, hydrophilic, adsorbed capillary coating for electrophoretic protein analysis. Preparation of the PHEA coating requires a simple and fast (30 min) protocol that can be easily automated in capillary electrophoresis instruments. Over the pH range of 3-8.4, the PHEA coating is shown to reduce electroosmotic flow (EOF) by about 2 orders of magnitude compared to the bare silica capillary. In a systematic comparative study, the adsorbed PHEA coating exhibited minimal interactions with both acidic and basic proteins, providing efficient protein separations with excellent reproducibility on par with a covalent polyacrylamide coating. Hydrophobic interactions between proteins and a relatively hydrophobic poly-N,N-dimethylacrylamide (PDMA) adsorbed coating, on the other hand, adversely affected separation reproducibility and efficiency. Under both acidic and basic buffer conditions, the adsorbed PHEA coating produced an EOF suppression performance comparable to that of covalent polyacrylamide coating and superior to that of adsorbed PDMA coating. The protein separation performance in PHEA-coated capillaries was retained for 275 consecutive protein separation runs at pH 8.4, and for more than 800 runs at pH 4.4. The unique and novel combination of hydrophilicity and adsorptive coating ability of PHEA makes it a suitable wall coating for automated microscale analysis of proteins by capillary array systems.     

Photophysical properties of a tetraphenoxy-substituted perylene bisimide derivative characterized by single-molecule spectroscopy.

We present a detailed study of the photophysical properties of a tetraphenoxy-substituted perylene bisimide derivative. The probe molecules were immobilized in a Shpol'skii matrix of hexadecane and investigated by single-molecule spectroscopy at cryogenic temperatures. By using single-molecule spectroscopic techniques we reveal the triplet substate kinetics and the fluorescence quantum yield, and we provide an estimate for the S1-S0 transition dipole moment.     

Coordination of 9-ethylguanine to the mixed-ligand compound alpha-[Ru(azpy)(bpy)Cl2] (azpy = 2-phenylazopyridine and bpy = 2,2'-bipyridine). An unprecedented ligand positional shift, correlated to the cytotoxicity of this type of [RuL2Cl2] (with L = azpy or bpy) complex

The striking difference in cytotoxic activity between the inactive cis-[Ru(bpy)(2)Cl(2)] and the recently reported highly cytotoxic alpha-[Ru(azpy)(2)Cl(2)] (alpha indicating the isomer in which the coordinating Cl atoms, pyridine nitrogens, and azo nitrogens are in mutual cis, trans, cis orientation) encouraged the synthesis of the mixed-ligand compound cis-[Ru(azpy)(bpy)Cl(2)]. The synthesis and characterization of the only occurring isomer, i.e., alpha-[Ru(azpy)(bpy)Cl(2)], 1 (alpha denoting the isomer in which the Cl ligands are cis related to each other and the pyridine ring of azpy is trans to the pyridine ring of bpy), are described. The solid-state structure of 1 has been determined by X-ray structure analysis. The IC(50) values obtained for several human tumor cell lines have indicated that compound 1 shows mostly a low to moderate cytotoxicity. The binding of the DNA model base 9-ethylguanine (9-EtGua) to the hydrolyzed species of 1 has been studied and compared to DNA model base binding studies of cis-[Ru(bpy)(2)Cl(2)] and alpha-[Ru(azpy)(2)Cl(2)]. The completely hydrolyzed species of 1, i.e., alpha-[Ru(azpy)(bpy)(H(2)O)(2)](2+), has been reacted with 9-EtGua in water at room temperature for 24 h. This resulted in the monofunctional binding of only one 9-EtGua, coordinated via the N7 atom. The product has been isolated as alpha-[Ru(azpy)(bpy)(9-EtGua)(H(2)O)](PF(6))(2), 2, and characterized by 2D NOESY NMR spectroscopy. The NOE data show that the 9-EtGua coordinates (under these conditions) at the position trans to the azo nitrogen atom. Surprisingly, time-dependent (1)H NMR data of the 9-EtGua adduct 2 in acetone-d(6) show an unprecedented positional shift of the 9-EtGua from the position trans to the azo nitrogen to the position trans to the bpy nitrogen atom, resulting in the adduct alpha'-[Ru(azpy)(bpy)(9-EtGua)(H(2)O)](PF(6))(2) (alpha' indicating 9-EtGua is trans to the bpy nitrogen). This positional isomerization of 9-EtGua is correlated to the cytotoxicity of 1 in comparison to both the cytotoxicity and 9-EtGua coordination of cis-[Ru(bpy)(2)Cl(2)], alpha-[Ru(azpy)(2)Cl(2)], and beta-[Ru(azpy)(2)Cl(2)]. This positional isomerization process is unprecedented in model base metal chemistry and could be of considerable biological significance.