Using a two-step hydride transfer to achieve 1,4-reduction in the catalytic hydrogenation of an acyl pyridinium cation

The stoichiometric reduction of N-carbophenoxypyridinium tetraphenylborate (6) by CpRu(P-P)H (Cp = eta(5)-cyclopentadienyl; P-P = dppe, 1,2-bis(diphenylphosphino)ethane, or dppf, 1,1'-bis(diphenylphosphino)ferrocene), and Cp*Ru(P-P)H (Cp* = eta(5)-pentamethylcyclopentadienyl; P-P = dppe) gives mixtures of 1,2- and 1,4-dihydropyridines. The stoichiometric reduction of 6 by Cp*Ru(dppf)H (5) gives only the 1,4-dihydropyridine, and 5 catalyzes the exclusive formation of the 1,4-dihydropyridine from 6, H(2), and 2,2,6,6-tetramethylpiperidine. In the stoichiometric reductions, the ratio of 1,4 to 1,2 product increases as the Ru hydrides become better one-electron reductants, suggesting that the 1,4 product arises from a two-step (e(-)/H(*)) hydride transfer. Calculations at the UB3LYP/6-311++G(3df,3pd)//UB3LYP/6-31G* level support this hypothesis, indicating that the spin density in the N-carbophenoxypyridinium radical (13) resides primarily at C4, while the positive charge in 6 resides primarily at C2 and C6. The isomeric dihydropyridines thus result from the operation of different mechanisms: the 1,2 product from a single-step H(-) transfer and the 1,4 product from a two-step (e(-)/H(*)) transfer.     

Folding kinetics of a naturally occurring helical peptide: implication of the folding speed limit of helical proteins

The folding mechanism and dynamics of a helical protein may strongly depend on how quickly its constituent alpha-helices can fold independently. Thus, our understanding of the protein folding problem may be greatly enhanced by a systematic survey of the folding rates of individual alpha-helical segments derived from their parent proteins. As a first step, we have studied the relaxation kinetics of the central helix (L9:41-74) of the ribosomal protein L9 from the bacterium Bacillus stearothermophilus , in response to a temperature-jump ( T-jump) using infrared spectroscopy. L9:41-74 has been shown to exhibit unusually high helicity in aqueous solution due to a series of side chain-side chain interactions, most of which are electrostatic in nature, while still remaining monomeric over a wide concentration range. Thus, this peptide represents an excellent model system not only for examining how the folding rate of naturally occurring helices differs from that of the widely studied alanine-based peptides, but also for estimating the folding speed limit of (small) helical proteins. Our results show that the T-jump induced relaxation rate of L9:41-74 is significantly slower than that of alanine-based peptides. For example, at 11 degrees C its relaxation time constant is about 2 micros, roughly seven times slower than that of SPE(5), an alanine-rich peptide of similar chain length. In addition, our results show that the folding rate of a truncated version of L9:41-74 is even slower. Taken together, these results suggest that individual alpha-helical segments in proteins may fold on a time scale that is significantly slower than the folding time of alanine-based peptides. Furthermore, we argue that the relaxation rate of L9:41-74 measured between 8 and 45 degrees C provides a realistic estimate of the ultimate folding rate of (small) helical proteins over this temperature range.     

Module assembly for protein-surface recognition: geranylgeranyltransferase I bivalent inhibitors for simultaneous targeting of interior and exterior protein surfaces

Synthetic chemical probes designed to simultaneously targeting multiple sites of protein surfaces are of interest owing to their potential application as site specific modulators of protein-protein interactions. A new approach toward bivalent inhibitors of mammalian type I geranylgeranyltransferase (GGTase I) based on module assembly for simultaneous recognition of both interior and exterior protein surfaces is reported. The inhibitors synthesized in this study consist of two modules linked by an alkyl spacer; one is the tetrapeptide CVIL module for binding to the interior protein surface (active pocket) and the other is a 3,4,5-alkoxy substituted benzoyl motif that contains three aminoalkyl groups designed to bind to the negatively charged protein exterior surface near the active site. The compounds were screened by two distinct enzyme inhibition assays based on fluorescence spectroscopy and incorporation of a [(3)H]-labeled prenyl group onto a protein substrate. The bivalent inhibitors block GGTase I enzymatic activity with K(i) values in the submicromolar range and are approximately one order of magnitude and more than 150 times more effective than the tetrapeptide CVIL and the methyl benzoate derivatives, respectively. The bivalent compounds 6 and 8 were shown to be competitive inhibitors, suggesting that the CVIL module anchors the whole molecule to the GGTase I active site and delivers the other module to the targeting protein surface. Thus, our module-assembly approach resulted in simultaneous multiple-site recognition, and as a consequence, synergetic inhibition of GGTase I activity, thereby providing a new approach in designing protein-surface-directed inhibitors for targeting protein-protein interactions.     

Uncertainties in the oxygen isotopic composition of barium sulfate induced by coprecipitation of nitrate

Coprecipitation of nitrate and sulfate by barium has probably resulted in significant error in numerous studies dealing with the oxygen isotopic composition of natural sulfates using chemical/thermal conversion of BaSO(4) and analysis by isotope ratio mass spectrometry. In solutions where NO(3) (-)/SO(4) (2-) molar ratios are above 2 the amount of nitrate coprecipitated with BaSO(4) reaches a maximum of approximately 7% and decreases roughly linearly as the molar ratio decreases. The fraction of coprecipitated nitrate appears to increase with decreasing pH and is also affected by the nature of the cations in the precipitating solution. The size of the oxygen isotope artifact in sulfate depends both on the amount of coprecipitated nitrate and the delta(18)O and Delta(17)O values of the nitrate, both of which can be highly variable. The oxygen isotopic composition of sulfate extracted from atmospheric aerosols or rain waters are probably severely biased because photochemical nitrate is usually also present and it is highly enriched in (18)O (delta(18)O approximately 50-90 per thousand) and has a large mass-independent isotopic composition (Delta(17)O approximately 20-32 per thousand). The sulfate delta(18)O error can be 2-5 per thousand with Delta(17)O artifacts reaching as high as 4.0 per thousand. Copyright (c) 2008 John Wiley & Sons, Ltd.     

Multispectral and hyperspectral image analysis of elemental and micro-Raman maps of cross-sections from a 16th century painting

Spectroscopic imaging is well suited to the study of micro-samples from artworks, where the sample material is limited and the maximum amount of information needs to be obtained. In this study, a new approach to imaging elemental data from energy dispersive X-ray analysis maps was used in conjunction with micro-Raman spectroscopic imaging to characterise the paint layers within micro-samples. Cross-sections from the 16th century painting Portrait of a Youth were found to contain vermilion, lead-tin yellow type 1 and a blue-green pigment consistent with terre-verte. The mid-preparatory layer (imprimatura) contains a high proportion of elements and mineral inclusions that indicates a clay-type composition. The ground layer was identified as anhydrite with large gypsum inclusions. The pigments and composition of the preparatory layers are consistent with those used by Italian Renaissance artist Dosso Dossi.     

Luminescence of LnIII dithiocarbamate complexes (Ln = La, Pr, Sm, Eu, Gd, Tb, Dy)

We have discovered room temperature photoluminescence in Sm3+ and Pr3+ dithiocarbamate complexes. Surprisingly, these complexes exhibit more intense emission than those of the Eu3+, Tb3+, and Dy3+ analogues. The electronic absorption, excitation, and emission spectra are reported for the complexes [Ln(S2CNR2)3L] and NH2Et2[Ln(S2CNEt2)4], where Ln = Sm, Pr; R = ethyl, ibutyl, benzyl; and L = 1,10-phenanthroline, 2,2'-bipyridine, and 5-chloro-1,10-phenanthroline. The lowest ligand-localized triplet energy level (T1) of the complexes are determined from the phosphorescence spectra of analogous La3+ and Gd3+ chelates. The luminescence decay curves were measured to determine the excited-state lifetimes for the Pr3+ and Sm3+ complexes. X-ray crystal structures of Sm(S2CNiBu2)3phen, Pr(S2CNEt2)3phen, and Pr(S2CNiBu2)3phen are also reported.     

Mixed thread/paper‐based microfluidic chips as a platform for glucose assays

A novel microfluidic thread/paper‐based analytical device (μTPAD) to detect glucose through a colorimetric assay is described. The μTPAD was fabricated from nylon thread trifurcated into three channels terminating at analysis sites comprised of circular zones of chromatography paper, which have previously been spotted with glucose of different concentrations. A solution of glucose oxidase (GOx), horseradish peroxidase (HRP), and potassium iodide (KI) is transported via capillary action to the analysis sites where a yellow‐brown color is observed indicating oxidation of iodide to iodine. The device was then dried, scanned, and analyzed yielding a correlation between yellow intensity and glucose concentrations. Both a flat platform constructed mainly of tape, and a cone platform constructed from tape and polyvinyl chloride, are described. Studies to quantitate glucose in artificial urine showed good correlation using the μTPAD.     

Exponential growth rates of free and amalgamated products

We prove that there is a gap between \(\sqrt 2 and\left( {1 + \sqrt 5 } \right)/2\) for the exponential growth rate of nontrivial free products. For amalgamated products G = A_*CB with ([A: C] ? 1)([B: C] ? 1) ≥ 2, we show that an exponential growth rate lower than \(\sqrt 2 \) can be achieved. Indeed, there are infinitely many amalgamated products for which the exponential growth rate is equal to ψ ≈ 1.325, where ψ is the unique positive root of the polynomial z³?z?1. One of these groups is \(PGL\left( {2,\mathbb{Z}} \right) \cong \left( {{C_2} \times {C_2}} \right){*_{{C_2}}}{D_6}\). However, under some natural conditions the lower bound can be put up to \(\sqrt 2 \). This answers two questions by Avinoam Mann [The growth of free products, Journal of Algebra 326, no. 1 (2011), 208–217]. We also prove that ψ is a lower bound for the minimal growth rates of a large class of Coxeter groups, including cofinite non-cocompact planar hyperbolic groups, which strengthens a result obtained earlier by William Floyd, who considered only standard Coxeter generators.     

Energy-directed tree search: an efficient systematic algorithm for finding the lowest energy conformation of molecules

We present a new systematic algorithm, energy-directed tree search (EDTS), for exploring the conformational space of molecules. The algorithm has been designed to reliably locate the global minimum (or, in the worst case, a structure within 4 kJ mol(-1) of this species) at a fraction of the cost of a full conformational search, and in this way extend the range of chemical systems for which accurate thermochemistry can be studied. The algorithm is inspired by the build-up approach but is performed on the original molecule as a whole, and objectively determines the combinations of torsional angles to optimise using a learning process. The algorithm was tested for a set of 22 large molecules, including open- and closed-shell species, stable structures and transition structures, and neutral and charged species, incorporating a range of functional groups (such as phenyl rings, esters, thioesters and phosphines), and covering polymers, peptides, drugs, and natural products. For most of the species studied the global minimum energy structure was obtained; for the rest the EDTS algorithm found conformations whose total electronic energies are within chemical accuracy from the true global minima. When the conformational space is searched at a resolution of 120 degrees , the cost of the EDTS algorithm (in its worst-case scenario) scales as 2(N) for large N (where N is the number of rotatable bonds), compared with 3(N) for the corresponding systematic search.     

Single-cell electroporation arrays with real-time monitoring and feedback control

Rapid well-controlled intracellular delivery of drug compounds, RNA, or DNA into a cell--without permanent damage to the cell--is a pervasive challenge in basic cell biology research, drug discovery, and gene delivery. To address this challenge, we have developed a bench-top system comprised of a control interface, that mates to disposable 96-well-formatted microfluidic devices, enabling the individual manipulation, electroporation and real-time monitoring of each cell in suspension. This is the first demonstrated real-time feedback-controlled electroporation of an array of single-cells. Our computer program automatically detects electroporation events and subsequently releases the electric field, precluding continued field-induced damage of the cell, to allow for membrane resealing. Using this novel set-up, we demonstrate the reliable electroporation of an array (n = 15) of individual cells in suspension, using low applied electric fields (<1 V) and the rapid and localized intracellular delivery of otherwise impermeable compounds (Calcein and Orange Green Dextran). Such multiplexed electrical and optical measurements as a function of time are not attainable with typical electroporation setups. This system, which mounts on an inverted microscope, obviates many issues typically associated with prototypical microfluidic chip setups and, more importantly, offers well-controlled and reproducible parallel pressure and electrical application to individual cells for repeatability.