Dissociation behavior of doubly-charged tryptic peptides: correlation of gas-phase cleavage abundance with ramachandran plots

Analysis of fragmentation patterns from 5654 unique doubly charged tryptic peptides is obtained. Great variability of average relative abundance of bond cleavage is found between different amino acid combinations. There exist similarities as well as differences between b and y ions. Strong enhancement or suppression of cleavage gives insight into possible chemical interactions at reactive conformations formed by preferred phi-psi angles.     

Time evolution studies of the H2O/quartz interface using sum frequency generation, atomic force microscopy, and molecular dynamics

Many interfacial studies on solid surfaces, for example, quartz/water, assume that a standard cleaning procedure regenerates the surface reproducibly. In the reported work, the results of two surface specific techniques, sum frequency generation (SFG) spectroscopy and atomic force microscopy, show that the effects of prolonged exposure to Nanopure water and to pH 10 NaOH are distinctly different. In conjunction with the experimental data, molecular mechanics is used to correlate the SFG spectral frequencies to the hydrogen stretching vibrations of the surface-bound water molecules. It is found that after 17 days of soaking in water, water molecules penetrate into the SiO2 matrix to produce a swollen and amorphous layer; it is likely that broken Si-O bonds from the polishing process serve as nucleation sites for hydration and swelling. Disorder introduced in the interfacial water layer is detected by the rising intensity of the weakly hydrogen-bonded SFG peak at 3450 cm(-1). Dominance of the 3450 cm(-1) is absent in a pH 10, NaOH-soaked quartz disk, indicating that the strong hydrogen-bonded network in water remains intact.     

Determination of perfluorooctanoic acid (PFOA) extractable from the surface of commercial cookware under simulated cooking conditions by LC/MS/MS

Salts of pentadecafluorooctanoic acid (PFOA) are polymerization aids used in the manufacture of fluoropolymers; one of the applications of fluoropolymers is the coating of metal cookware products. A method was developed to determine if PFOA might be present in and extracted from the surface of commercial frying pans coated with a DuPont fluoropolymer under simulated cooking conditions. Commercial grade cookware was obtained, then extracted with water and ethanol/water mixtures at 100 and 125 degrees C, and the resulting extracts were analyzed by liquid chromatography tandem mass spectrometry (LC/MS/MS). Detection and quantification limits as low as 100 pg cm(-2) were demonstrated. None of the fluoropolymer treated cookware samples analyzed showed detectable levels of PFOA when extracted under simulated cooking conditions.     

Extending the use of certified reference sediments for assessment of accuracy in determinations of trace metals

Straightforward analysis for components in a single certified reference sediment is of limited use for assessing the accuracy of environmental determinations. A systematic approach requires mixing of certified sediments, one with another and with environmental samples, and the preparation of secondary reference material by the laboratory. Use of Youden pairs, reference material embedded in samples and linear models should enable valid accuracy statements to be made based on well known statistical concepts. For assessing accuracy, reference sediments which are matched in particle size, and are end-members for components or sediment types are most useful.     

A new photochemically removable protecting group for amines

A new arylmethylsulfonyl chloride reacts with secondary or primary amines to give sulfonamides which can be photochemically cleaved, making it suitable for use as a photoremovable protecting group.     

General deoxyribozyme-catalyzed synthesis of native 3'-5' RNA linkages

An elusive goal for nucleic acid enzymology has been deoxyribozymes that ligate RNA rapidly, sequence-generally, with formation of native 3'-5' linkages, and in preparatively useful yield. Using in vitro selection, we have identified Mg2+- and Zn2+-dependent deoxyribozymes that simultaneously fulfill all four of these criteria. The new deoxyribozymes operate under practical incubation conditions and have modest RNA substrate sequence requirements, specifically D downward arrowRA for 9DB1 and A downward arrowR for 7DE5 (D = A, G, or U; R = A or G). These requirements are comparable to those of deoxyribozymes such as 10-23 and 8-17, which are already widely used as biochemical tools for RNA cleavage. We anticipate that the 9DB1 and 7DE5 deoxyribozymes will find immediate practical application for RNA ligation.     

Electrophoresis of Spherical Particles with a Random Distribution of Zeta Potential or Surface Charge

Electrophoresis is often used to measure the "average" zeta (zeta) potential on particles. However, it has been found by previous researchers that in making predictions of colloidal forces and stability, the distribution of zeta potential on the particles is important. This paper provides a straightforward method for measuring charge nonuniformity on colloidal spheres. It is shown that if the charge or zeta potential is random on a group of spheres, each covered with N equal-area patches, then the average magnitude of the dipole moment on the spheres is 0.92sigma(zeta)/N, and the average magnitude of the quadrupole moment is 1.302sigma(zeta)/N, where sigma(zeta) is the standard deviation of zeta potential over the surface of individual spheres. This is true for any random distribution of zeta potential, and the results emphasize that "random" implies nonuniform. It is demonstrated that since typical translational mobility measurements are much less sensitive to random charge nonuniformity than rotational mobility measurements, the latter measurement is better suited for measuring the second moment (sigma(zeta)) of zeta potential. Monte Carlo simulations were done to confirm and extend the analytical results. Copyright 2000 Academic Press.     

Open-tubular capillary electrochromatography/electrospray ionization-mass spectrometry using polymeric surfactant as a stationary phase coating

We describe the use of the polymeric surfactant poly(sodium undecylenic sulfate) (poly-SUS) as a stationary phase coating in open-tubular capillary electrochromatography (OT-CEC) coupled with electrospray ionization-mass spectrometry (ESI-MS) for the analysis of beta-blocker and benzodiazepine analytes. The production of a polymeric surfactant coating on the capillary inner wall involves (i) adsorption of the cationic polymer poly(diallyldimethylammonium chloride) (PDADMAC) to the inner surface of capillary, and (ii) adsorption of the negatively charged poly-SUS onto the cationic polymer layer via strong physical interaction of the two polymer layers. As compared with micellar electrokinetic chromatography (MEKC) coupled with ESI-MS, the main advantage of this proposed method is minimization of introduction of the monomeric or polymeric surfactant into the mass spectrometer, thus avoiding the interference of the nonvolatile micelle in ESI-MS. The effects of buffer pH and applied voltage on the separation of the analytes are also discussed. Under optimum conditions, four of the five beta-blockers and four benzodiazepines are separated.     

Interpolation of diabatic potential energy surfaces

A method is presented for constructing diabatic potential energy matrices from ab initio quantum chemistry data. The method is similar to that reported previously for single adiabatic potential energy surfaces, but correctly accounts for the nuclear permutation symmetry of diabatic potential energy matrices and other complications that arise from the derivative coupling of electronic states. The method is tested by comparison with an analytic model for the two lowest energy states of H(3).     

Presentations of the amalgamated free product of two infinite cycles

LetH=〈a,b;a ^k =b ^l 〉, wherek,l≧2 andk+l>4. McCool and Pietrowski have proved that any pair of generators forH is Nielsen equivalent to a pairx=a ^r andy=b ^s where $$(a){\text{ }}gcd(r, s) = gcd(r, k) = gcd(s, l) = 1,$$ $$(b){\text{ }}0< 2r \leqq ks{\text{ }}and{\text{ }}0< 2s \leqq lr.$$ In terms ofx andy,H can be presented as $$G = \left\langle {x,{\text{ }}y;{\text{ }}x^{ks} = y^{lr} ,\left[ {x,{\text{ }}y^l } \right] = \left[ {x^k ,{\text{ }}y} \right] = 1} \right\rangle$$ and Zieschang has shown that ifr=1 ors=1, thenH can be defined by a single relation inx andy. We establish the exact converse of Zieschang's result, namely thatH is not defined by a single relation inx andy unlessr=1 ors=1. The proof is based on an observation of Magnus which associates polynomials with relators and some elementary facts about cyclotomic polynomials.