Kinetics and mechanism of the pyridinolysis of s-4-nitrophenyl 4-substituted thiobenzoates in aqueous ethanol

The pyridinolysis of S-4-nitrophenyl 4-X-substituted thiobenzoates (X = H, Cl, and NO2; 1, 2, and 3, respectively) is studied kinetically in 44 wt % ethanol-water, at 25.0 degrees C and an ionic strength of 0.2 M (KCl). The reactions are measured spectrophotometrically (420-425 nm) by following the appearance of 4-nitrobenzenethiolate anion. Pseudo-first-order rate coefficients (kobsd) are obtained throughout, under excess of amine over the substrate. Plots of kobsd vs [free amine] at constant pH are linear with the slope (kN) independent of pH. The Brnsted-type plot (log kN vs pKa0 of the conjugate acids of the pyridines) for the reactions of thiolbenzoate 1 is curved with a slope at high pKa, beta1 = 0.20, and slope at low pKa0, beta2 = 0.94. The pKa value for the center of the Brnsted curvature is pKa0 = 9.7. The pyridinolysis of thiolbenzoates 2 and 3 show linear Brnsted-type plots of slopes 0.94 and 1.0, respectively. These results and other evidence indicate that these reactions occur with the formation of a zwitterionic tetrahedral intermediate (T+/-). For the pyridinolysis of thiolbenzoate 1, breakdown of T+/- to products (k2 step) is rate-limiting for weakly basic pyridines and T+/- formation (k1 step) is rate-determining for very basic pyridines. The k2 step is rate-limiting for the reactions of thiolbenzoates 2 and 3. The smallest pKa0 value for the reaction of 1 is due to the weakest electron withdrawal of H (relative to Cl and NO2) in the acyl group, which results in the smallest k-1/k2 ratio. The pKa0 values for the title reactions are smaller than those for the reactions of secondary alicyclic amines with thiolbenzoates 1-3. This is attributed to a lower leaving ability from the T+/- of pyridines than isobasic alicyclic amines. The lower p value found for the pyridinolysis of 2,4-dinitrophenyl benzoate (pKa0 = 9.5), compared with that for the pyridinolysis of 1, is explained by the greater nucleofugality from T+/- of 2,4-dinitrophenoxide than 4-nitrobenzenethiolate, which renders the k-1/k2 ratio smaller for the reactions of the benzoate relative to thiolbenzoate 1. The title reactions are also compared with the aminolysis of similar thiolbenzoates in other solvents to assess the solvent effect.     

Characterization and comparison of Cm(III) and Eu(III) complexed with 2,6-di(5,6-dipropyl-1,2,4-triazin-3-yl)pyridine using EXAFS, TRFLS, and quantum-chemical methods

The complexation of Cm(III) and Eu(III) with 2,6-di(5,6-dipropyl-1,2,4-triazin-3-yl)pyridine (n-C3H7-BTP) in nonaqueous organic solution is studied with extended X-ray absorption spectroscopy. Bond lengths are the same in both complexes. Quantum-chemical calculations performed at different levels support this finding. On the other hand, the Cm.(n-C3H7-BTP)3 complex is formed at much lower ligand-to-metal concentration ratio than the Eu.(n-C3H7-BTP)3 complex, as shown by time-resolved laser-induced fluorescence spectroscopy. This is in good agreement with n-C3H7-BTP's high selectivity for trivalent actinides over lanthanides in liquid-liquid extraction.     

Detection of tyrosine phosphorylated peptides via skimmer collision-induced dissociation/ion trap mass spectrometry

Phosphorylation of proteins is an important post-translational protein modification in cellular response to environmental change and occurs in both prokaryotes and eukaryotes. Identification of the amino acid on individual proteins that become phosphorylated in response to extracellular stimulus is essential for understanding the mechanisms involved in the intracellular signals that these modifications facilitate. Most protein kinases catalyze the phosphorylation of proteins on serine, threonine or tyrosine. Although tyrosine phosphorylation is often the least abundant of the three major phosphorylation sites, it is important owing to its role in signal pathways. Currently available methods for the identification of phosphorylation sites can often miss low levels of tyrosine phosphorylations. This paper describes a method for the identification of phosphotyrosine-containing peptides using electrospray ionization on an ion trap mass spectrometer. Skimmer-activated collision-induced dissociation (CID) was used to generate the phosphotyrosine immonium ion at m/z 216. This method is gentle enough that the protonated molecule of the intact peptide is still observed. In-trap CID was employed for the verification of the phosphotyrosine immonium ion. Using this technique, low levels of phosphotyrosine-containing peptides can be identified from peptide mixtures separated by nanoflow micro liquid chromatography/mass spectrometry.     

Synthesis of AX7593, a quinazoline-derived photoaffinity probe for EGFR

[structure: see text] The synthesis of a photoaffinity probe for EGFR is described. O-Alkylation of 4-(meta-azidoanilino)-6-methoxy-7-hydroxy-quinazoline with a protected tetraethyleneglycol linker followed by the attachment of tetramethylrhodamine yielded the fluorescent probe AX7593. Photoaffinity labeling of EGFR by AX7593 (K(b) = 280 nM) was shown to have an efficiency of 34% and to be competitive with the EGFR inhibitors PP2 and AG1478.     

Structure and stability of Ne+He(n): experiment and diffusion quantum Monte Carlo theory with "on the fly" electronic structure

New data are reported for the mass-spectrometry fragmentation patterns of helium clusters, either pure or containing a Ne or an Ar atom. The patterns for He(n)+ and Ar+He(n) show clear evidence of structure, while those of Ne+He(n) do not. To better understand the surprising result for the Ne+He(n) fragments, diffusion quantum Monte Carlo (DMC) calculations of the energies and structural properties of these ions were performed using a diatomics-in-molecule (DIM) parametrization of the potential energy. Using DIM for electronic energy evaluation allows us to sample 10(9) configurations even for a cluster as large as Ne+He14. The results of the DMC calculation are very surprising. For n > 7, the DMC random walkers rarely venture within 100 cm(-1) of the minimum potential energy. Analysis of the resulting particle density distributions shows that the zero-point energy does more than spread the wave function around the potential-energy minima, resulting in very diffuse wave functions. For some of the clusters the quantum effects nearly exclude the region of the potential minimum from the overall wave function. An important result of this effect is that the incremental bonding energy of the nth helium atom varies quite smoothly with n, for n > 5. This eliminates the expected shell structure and explains the lack of magic-number-type features in the data.     

SVM-BALSA: remote homology detection based on Bayesian sequence alignment

Biopolymer sequence comparison to identify evolutionarily related proteins, or homologs, is one of the most common tasks in bioinformatics. Support vector machines (SVMs) represent a new approach to the problem in which statistical learning theory is employed to classify proteins into families, thus identifying homologous relationships. Current SVM approaches have been shown to outperform iterative profile methods, such as PSI-BLAST, for protein homology classification. In this study, we demonstrate that the utilization of a Bayesian alignment score, which accounts for the uncertainty of all possible alignments, in the SVM construction improves sensitivity compared to the traditional dynamic programming implementation over a benchmark dataset consisting of 54 unique protein families. The SVM-BALSA algorithms returns a higher area under the receiver operating characteristic (ROC) curves for 37 of the 54 families and achieves an improved overall performance curve at a significance level of 0.07.     

Evaluation of a fluorescein-labeled estradiol derivative for use in affinity capillary electrophoresis

A fluorescein-labeled estradiol derivative was assessed for use in affinity capillary electrophoresis (ACE) in a competitive immunoassay format, in which the fluorescently labeled estradiol competed with unlabeled estradiol for a mouse anti-estradiol antibody. The preparation of the labeled estradiol produced a mixture of fluorescein-containing compounds that led to multiple peaks in the electropherogram and to which the antibody responded differently. Two of the components of the mixture, towards which the mouse antibody showed most affinity, were isolated using fraction collection via capillary electrophoresis (CE). The two fractions of the labeled estradiol products isolated by CE were characterized using mass spectrometric methods. The two active fluorescein-conjugated products differed in the carboxylate on the fluorescein moiety, one having a methyl group instead of the acidic hydrogen for the other. The estradiol antibody showed a stronger binding for the conjugate containing the methyl group, as determined from the estimated binding constants using Scatchard analysis. The isolated fractions of labeled estradiol were shown to be applicable to the ACE immunoassay method.     

Catalytic,three-component assembly reaction for the synthesis of pyrrolidines

[reaction: see text] Copper(I) salts catalyze the three-component assembly reaction between an alpha-diazo ester, an imine, and various alkenes and alkynes to form substituted pyrrolidines with excellent to good diastereoselectivities in high yields. The transition metal-catalyzed decomposition of the alpha-diazo compound in the presence of the imine likely generates a transient azomethine ylid that undergoes addition with various dipolarophiles in a highly convergent manner.     

A comparison of the AMBER*, OPLSAA and HF potential energy surfaces for a series of diastereomeric cyclic urea HIV-1 inhibitors

The LM:MC conformational search method was used to identify the low energy structures on the OPLS-AA/GBSA(water) and AMBER*/GBSA(water) surfaces for a diastereomeric series of cyclic urea molecules that have been shown to be potent inhibitors of the HIV-1 protease enzyme. The lowest energy structures from each search were then subjected to geometry optimization and frequency analysis using the HF/6-311G** method in conjunction with the self-consistent reaction field (SCRF) treatment for water. A comparison of the diastereomeric energies and structures indicates that the OPLSAA/GBSA(water) surface is in good agreement with the HF/6-311G**/SCRF(water) surface.     

Preparation and reactivity of O2-sulfonated diazeniumdiolates

We report the facile preparation of O2-sulfonated diazeniumdiolates and mechanistic investigation of their reactions with representative nucleophiles. This new class of compounds extends the range of O2-substituted diazeniumdiolates available for potential applications in research and medicine.