Capillary electrophoretic separation-based approach to determine the labeling kinetics of oligodeoxynucleotides.

With the recent advances in electron microscopy (EM), computation, and nanofabrication, the original idea of reading DNA sequence directly from an image can now be tested. One approach is to develop heavy atom labels that can provide the contrast required for EM imaging. While evaluating tentative labels for the respective nucleobases in synthetic oligodeoxynucleotides (oligos), we developed a streamlined CE protocol to assess the label stability, reactivity, and selectivity. We report our protocol using osmium tetroxide 2,2'-bipyridine (Osbipy) as a thymidine (T) specific label. The observed rates show that the labeling process is kinetically independent of both the oligo length, and the base composition. The conditions, i.e. temperature, optimal Osbipy concentration, and molar ratio of reagents, to promote 100% conversion of the starting oligo to labeled product were established. Hence, the optimized conditions developed with the oligos could be leveraged to allow osmylation of effectively all Ts in ssDNA, while achieving minimal mislabeling. In addition, the approach and methods employed here may be adapted to the evaluation of other prospective contrasting agents/labels to facilitate next-generation DNA sequencing by EM.

Solution interaction of potassium and calcium bis(trimethylsilyl)amides; preparation of Ca[N(SiMe3)2]2 from dibenzylcalcium.

Ca[N(SiMe(3))(2)](2) (1) is isolated in nearly quantitative yield from the room temperature reaction of Ca(CH(2)Ph)(2)(THF) and HN(SiMe(3))(2) in toluene. A commonly used preparation of 1 involving the reaction of potassium bis(trimethylsilyl)amide, K[N(SiMe(3))(2)] (2), with CaI(2) can produce material that contains substantial amounts of potassium, probably in the form of a calciate such as K[Ca{N(SiMe(3))(2)}(3)]. The favorable formation of K[Ca{N(SiMe(3))(2)}(3)] from 1 and 2 was confirmed with density functional theory calculations. Deliberate doping of solutions of 1 with 2 initially causes only an upfield shift in the single (1)H NMR resonance observed for 1; not until K/Ca ratios exceed 1:1 is the presence of the added potassium obvious by the appearance of an additional peak in the spectrum.

Copper complexes of anionic nitrogen ligands in the amidation and imidation of aryl halides.

Copper(I) imidate and amidate complexes of chelating N,N-donor ligands, which are proposed intermediates in copper-catalyzed amidations of aryl halides, have been synthesized and characterized by X-ray diffraction and detailed solution-phase methods. In some cases, the complexes adopt neutral, three-coordinate trigonal planar structures in the solid state, but in other cases they adopt an ionic form consisting of an L 2Cu (+) cation and a CuX 2 (-) anion. A tetraalkylammonium salt of the CuX 2 (-) anion in which X = phthalimidate was also isolated. Conductivity measurements and (1)H NMR spectra of mixtures of two complexes all indicate that the complexes exist predominantly in the ionic form in DMSO and DMF solutions. One complex was sufficiently soluble for conductance measurements in less polar solvents and was shown to adopt some degree of the ionic form in THF and predominantly the neutral form in benzene. The complexes containing dative nitrogen ligands reacted with iodoarenes and bromoarenes to form products from C-N coupling, but the ammonium salt of [Cu(phth) 2] (-) did not. Similar selectivities for stoichiometric and catalytic reactions with two different iodoarenes and faster rates for the stoichiometric reactions implied that the isolated amidate and imidate complexes are intermediates in the reactions of amides and imides with haloarenes catalyzed by copper complexes containing dative N,N ligands. These amidates and imidates reacted much more slowly with chloroarenes, including chloroarenes that possess more favorable reduction potentials than some bromoarenes and that are known to undergo fast dissociation of chloride from the chloroarene radical anion. The reaction of o-(allyloxy)iodobenzene with [(phen) 2Cu][Cu(pyrr) 2] results in formation of the C-N coupled product in high yield and no detectable amount of the 3-methyl-2,3-dihydrobenzofuran or 3-methylene-2,3-dihydrobenzofuran products that would be expected from a reaction that generated free radicals. These data and computed reaction barriers argue against mechanisms in which the haloarene reacts with a two-coordinate anionic copper species and mechanisms that start with electron transfer to generate a free iodoarene radical anion. Instead, these data are more consistent with mechanisms involving cleavage of the carbon-halogen bond within the coordination sphere of the metal.

High Trans Kinetic Selectivity in Ruthenium-Based Olefin Cross-Metathesis through Stereoretention.

The first kinetically controlled, highly trans-selective (>98%) olefin cross-metathesis reaction is demonstrated using Ru-based catalysts. Reactions with either trans or cis olefins afford products with highly trans or cis stereochemistry, respectively. This E-selective olefin cross-metathesis is shown to occur between two trans olefins and between a trans olefin and a terminal olefin. Additionally, new stereoretentive catalysts have been synthesized for improved reactivity.

Relative rates for the amination of eta3-allyl and eta3-benzyl complexes of palladium.

Reactions of nucleophiles with metal-bound hydrocarbyl pi-ligands bound in an eta3-fashion are key steps in a variety of carbon-carbon and carbon-heteroatom bond-forming reactions. To reveal factors that control the rates of reaction of nucleophiles with this type of ligand, the rates of reactions of an aromatic and an aliphatic amine with a series of eta3-allyl, eta3-benzyl, and eta3-phenethyl palladium complexes ligated by the bisphosphine (R)-BINAP to form allylic and benzylic amines were measured. These data showed that the less common addition to an eta3-benzyl complex is faster than the more common addition to an eta3-allyl complex. The relative rates of reaction followed the trend naphthylmethyl > naphthylethyl > benzyl > 1,1-dimethylallyl > allyl. Computational studies suggest that there is a correlation between the amount of positive charge at the site of nucleophilic attack and the rate of C-N bond formation.

Direct measurement of the thermodynamics of vinylarene hydroamination.

The thermodynamics for intermolecular hydroamination of vinylarenes with arylamines have been measured directly by conducting the addition processes, as well as cleavage of the addition products, under conditions in which amine, vinylarene, and phenethylamine are all present. The reaction of N-methylaniline with styrene is exothermic by about 10 kcal/mol but nearly thermoneutral in free energy. The free energies for additions of various primary arylamines to styrene and for additions of primary arylamines to indene, dihydronaphthalene, and two vinylarenes range from 1.3 to -3.5 kcal/mol (K = 0.16-155 M-1). The steric properties of the nucleophile significantly influenced the equilibrium constant for addition, but the electronic properties of the nucleophile had a minor effect on this equilibrium constant. These measurements have led to the first successful intermolecular addition of aniline to indene and 1,2-dihydronaphthalene and shed light on factors requiring consideration when choosing substrates and reaction conditions for this transformation.

A highly active palladium catalyst for intermolecular hydroamination. Factors that control reactivity and additions of functionalized anilines to dienes and vinylarenes.

We report a catalyst for intermolecular hydroamination of vinylarenes that is substantially more active for this process than catalysts published previously. With this more reactive catalyst, we demonstrate that additions of amines to vinylarenes and dienes occur in the presence of potentially reactive functional groups, such as ketones with enolizable hydrogens, free alcohols, free carboxylic acids, free amides, nitriles, and esters. The catalyst for these reactions is generated from [Pd(eta(3)-allyl)Cl](2) (with or without added AgOTf) or [Pd(CH(3)CN)(4)](BF(4))(2) and Xantphos (9,9-dimethyl-4,5-bis(diphenylphosphino)xanthene), which generates complexes with large P-Pd-P bite angles. Studies on the rate of the C-N bond-forming step that occurs by attack of amine on an eta(3)-phenethyl and an eta(3)-allyl complex were conducted to determine the effect of the bite angle on the rate of this nucleophilic attack. Studies on model eta(3)-benzyl complexes containing various bisphosphines showed that the nucleophilic attack was faster for complexes containing larger P-Pd-P bite angles. Studies of substituted unsymmetrical and unsubstituted symmetrical model eta(3)-allyl complexes showed that nucleophilic attack on complexes ligated by Xantphos was faster than on complexes bearing ligands with smaller bite angles and that nucleophilic attack on unsymmetrical allyl complexes with larger bite angle ligands was faster than on unsymmetrical allyl complexes with smaller bite angle ligands. However, monitoring of catalytic reactions of dienes by (31)P NMR spectroscopy showed that the concentration of active catalyst was the major factor that controlled rates for reactions of symmetrical dienes catalyzed by complexes of phosphines with smaller bite angles. The identity of the counterion also affected the rate of attack: reactions of allylpalladium complexes with chloride counterion occurred faster than reactions of allylpalladium complexes with triflate or tetrafluoroborate counterion. As is often observed, the dynamics of the allyl and benzyl complexes also depended on the identity of the counterion.