Investigation of the Doughnut Effect in Cy3-Labeled Protein Microarrays using Scanning Near-Field Optical Microscope

We demonstrate the fluorescence mapping of protein microarrays by the technique of scanning near-field optical microscopy (SNOM) and confocal microscopy. Micron sized spots (300 μm) of human Immunoglobulin G (hIgG) protein with and without a Cy3 dye labeling have been fabricated on glass substrates by an immobilization method which makes use of calixcrown derivatives termed Prolinker. We have also tried to probe into the well-known “doughnut effect” observed in fluorescence images of proteins using the SNOM technique. The topographic and fluorescence SNOM images revealed that the number of proteins at the boundary of the spot were more than at the center in the case of the microarray spot which showed brighter luminescence at the edge than at the center in the confocal image.     

Novel regiochemistry in the aqueous singlet oxygen ene reactions of carboxylic acid salts: a comparison of substrate structure

The singlet oxygen (¹Δ_g) photooxidations of angelic acid salt (1), tiglic acid salt (2), 2,3-dimethyl-2-butenoic acid salt (3), 3-ethoxycarbonyl-5,6-dihydro-2-methyl-4H-pyrane acid salt (4), cis-3-hexenoic acid salt (5), and trans-3-hexenoic acid salt (6) were conducted in deuterated water. The major and minor ene allylic hydroperoxide products were quantified and indicate that the allylic hydrogen geminal to the carboxylate group is preferentially abstracted in 1-4, whereas the allylic hydrogen α to the carboxylate is slightly favored for 5 and 6. We have attributed the observed regiochemistry in 1-4 to stabilizing hydrogen bonding interactions between the solvent and the perepoxide, which leads to the major ene product.     

The Mechanism of Thionyl Chloride Reaction with Dialkyl Alkylphosphonothionate Using 31 P NMR

Based on 31 P NMR studies of thionyl chloride reaction with dialkyl alkylphosphonothionates, a method for preparation of alkylphosphonic dichloride has been investigated. A mechanism via intermediacy of ester chloride is suggested.     

Electronic structure and properties of isoelectronic magic clusters: Al13X (X=H,Au,Li,Na,K,Rb,Cs)

The equilibrium structure, stability, and electronic properties of the Al(13)X (X=H,Au,Li,Na,K,Rb,Cs) clusters have been studied using a combination of photoelectron spectroscopy experiment and density functional theory. All these clusters constitute 40 electron systems with 39 electrons contributed by the 13 Al atoms and 1 electron contributed by each of the X (X=H,Au,Li,Na,K,Rb,Cs) atom. A systematic study allows us to investigate whether all electrons contributed by the X atoms are alike and whether the structure, stability, and properties of all the magic clusters are similar. Furthermore, quantitative agreement between the calculated and the measured electron affinities and vertical detachment energies enable us to identify the ground state geometries of these clusters both in neutral and anionic configurations.     

A small molecule discrimination map of the antibiotic resistance kinome

Kinase-mediated resistance to antibiotics is a significant clinical challenge. These enzymes share a common protein fold characteristic of Ser/Thr/Tyr protein kinases. We screened 14 antibiotic resistance kinases against 80 chemically diverse protein kinase inhibitors to map resistance kinase chemical space. The screens identified molecules with both broad and narrow inhibition profiles, proving that protein kinase inhibitors offer privileged chemical matter with the potential to block antibiotic resistance. One example is the flavonol quercetin, which inhibited a number of resistance kinases in vitro and in vivo. This activity was rationalized by determination of the crystal structure of the aminoglycoside kinase APH(2″)-IVa in complex with quercetin and its antibiotic substrate kanamycin. Our data demonstrate that protein kinase inhibitors offer chemical scaffolds that can block antibiotic resistance, providing leads for co-drug design.     

Modeling the geometric, electronic, and redox properties of iron(III)-containing amphiphiles with asymmetric [NN'O] headgroups

Two iron(III)-containing amphiphiles 1 and 2 have been synthesized with the [NN'O] ligands HL(tBu-ODA) (2-((octadecyl(pyridin-2-ylmethyl)amino)methyl)-4,6-di-tert-butylphenol) and HL(I-ODA) (2-((octadecyl(pyridin-2-ylmethyl)amino)methyl)-4,6-diiodophenol), respectively. Compound 1 is monometallic, whereas EXAFS data suggest that 2 is a mixture of mono- and bimetallic species. The archetypical [Fe(III)(L(NN'O))(2)](+) complexes 3-9 have been isolated and characterized in order to understand the geometric, electronic, and redox properties of the amphiphiles. Preference for a monometallic or bimetallic nuclearity is dependent on (i) the nature of the solvent used for synthesis and (ii) the type of the substituent in the phenol moiety. In methanol, the tert-butyl-, methoxy-, and chloro-substituted 3, 4, and 5 are monometallic species, whereas the bromo- and iodo-substituted 6 and 7 form bimetallic complexes taking advantage of stabilizing methoxo bridges generated by solvent deprotonation. In dichloromethane, the bromo- and iodo-substituted 8 and 9 are monometallic species; however, these species favor meridional coordination in opposition to the facial coordination observed for the tert-butyl- and methoxy-substituted compounds. Molecular structures for species 5, 7, 8, and 9 have been solved by X-ray diffraction. Furthermore, the electronic spectrum of the amphiphile 1 was expected to be similar to those of facial/cis archetypes with similar substituents, but close resemblance was observed with the profile for those meridional/cis species, suggesting a similar coordination mode. This trend is discussed based on DFT calculations, where preference for the meridional/cis coordination mode appears related to the presence of tertiary amine nitrogen on the ligand, as when a long alkyl chain is attached to the [NN'O] headgroup.     

Tetradentate vs pentadentate coordination in copper(II) complexes of pyridylbis(aminophenol) ligands depends on nucleophilicity of phenol donors

The ligand binding preferences of a series of potentially pentadentate pyridylbis(aminophenol) ligands were explored. In addition to the previously reported ligands 2,2'-(2-methyl-2-(pyridin-2-yl)propane-1,3-diyl)bis(azanediyl)bis(methylene)diphenol (H(2)L(1)) and 6,6'-(2-methyl-2-(pyridin-2-yl)propane-1,3-diyl)bis(azanediyl)bis(methylene)bis(2,4-di-tert-butylphenol) (H(2)L(1-tBu)), four new ligands were synthesized: 6,6'-(2-methyl-2(pyridine-2-yl)propane-1,3-diyl)bis(azanediyl)bis(methylene)bis(2,4-dibromophenol) (H(2)L(1-Br)), 6,6'-(2-methyl-2(pyridine-2-yl)propane-1,3diyl)bis(azanediyl)bis(methylene)bis(2-methoxyphenol) (H(2)L(1-MeO)), 2,2'-(2-methyl-2(pyridine-2-yl)propane-1,3diyl)bis(azanediyl)bis(methylene)bis(4-nitrophenol) (H(2)L(1-NO2)), and 2,2'-(2-phenylpropane-1,3-diyl)bis(azanediyl)bis(methylene)diphenol (H(2)L(2)). These ligands, when combined with copper(II) salts and base, form either tricopper(II) species or monocopper(II) species depending on the nucleophilicity of the phenol groups in the ligands. All copper complexes were characterized by X-ray crystallography, cyclic voltammetry, and spectroscopic methods in solution. The ligands in trimeric complexes [{CuL(1)(CH(3)CN)}(2)Cu](ClO(4))(2) (1), [{CuL(1)Cl}(2)Cu] (1a), and [{CuL(2)(CH(3)CN)}(2)Cu](ClO(4))(2) (1b) and monomeric complex [CuL(1-tBu)(CH(3)OH)] (2) coordinate in a tetradentate mode via the amine N atoms and the phenolato O atoms. The pyridyl groups in 1, 1a, and 2 do not coordinate, but instead are involved in hydrogen bonding. Monomeric complexes [CuL(1-Br)] (3a), [CuL(1-NO2)] (3b), and [CuL(1-MeO)Na(CH(3)OH)(2)]ClO(4) (3c) have their ligands coordinated in a pentadentate mode via the amine N atoms, the phenolato O atoms, and the pyridyl N atom. The differences in tetradentate vs pentadentate coordination preferences of the ligands correlate to the nucleophilicity of the phenolate donor groups, and coincide with the electrochemical trends for these complexes.     

Efficient and selective enzymatic acylation reaction: separation of furanosyl and pyranosyl nucleosides

Candida antarctica lipase-B (CAL-B) immobilized on lewatite selectively acylated the primary hydroxyl group of the furanosyl nucleoside in a mixture of 1-(alpha-D-arabinofuranosyl)thymine and 1-(alpha-D-arabinopyranosyl)thymine. This selective biocatalytic acylation of furanosyl nucleoside has enabled us an easy separation of arabinofuranosyl thymine from an inseparable mixture with arabinopyranosyl thymine. The primary hydroxyl selective acylation methodology of arabinonucleoside has also been successfully used for the separation of 1-(beta-D-xylofuranosyl)thymine and 1-(beta-D-xylopyranosyl)thymine from a mixture of the two, which demonstrate the generality of the enzymatic methodology for separation of furanosyl and pyranosyl nucleosides.     

A novel methodology for online detection of bearing health status for naturally progressing defect

A methodology is proposed for the online detection of health status of rolling element bearing into various damage stages for naturally progressing defect. Various damage identification parameters are derived from processing vibration data in time domain, frequency domain and time–frequency domain. The parameters are fused into a single parameter, Mahalanobis distance, by application of Gram–Schmidt Orthogonalization process. Chebyshev?s inequality is applied to the Mahalanobis distance for online monitoring and damage stage detection. A simulation study is first carried out to show working of the proposed methodology in presence of varying trends of damage identification parameters. The proposed methodology is then validated on experimental data. The first validation is on the vibration data acquired from a bearing having seeded defect. Later, two accelerated life tests are conducted on a specially designed test rig at different load and speed combinations on the bearings for ensuring naturally induced and progressed defects. The methodology is successfully verified on the vibration data acquired from the naturally induced and progressed defect experiments.