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We have used the quantitative polymerase chain reaction (qPCR) to measure the extent of oxidative DNA damage under varying reaction conditions used for copper(I)-catalyzed click chemistry. We systematically studied how the damage depends on a number of key reaction parameters, including the amounts of copper, ascorbate, and ligand used, and found that the damage is significant under nearly all conditions tested, including those commonly used for bioconjugation. Furthermore, we discovered that the addition of dimethyl sulfoxide, a known radical scavenger, into the aqueous mixture dramatically suppresses DNA damage during the reaction. We also measured the efficiency of cross-linking two short synthetic oligonucleotides via click chemistry, and found that the reaction could proceed reasonably efficiently even with DMSO present. This approach for screening both DNA damage and reactivity under a range of reaction conditions will be valuable for improving the biocompatibility of click chemistry, and should help to extend this powerful synthetic tool for both in vitro and in vivo applications.

This article describes the aza-Piancatelli rearrangement with hydroxylamines to 4-aminocyclopentenones and subsequent transformations that highlight the versatility of the cyclopentene scaffold and the value of the hydroxylamine nucleophile in this transformation.

Continuing developments in the elucidation techniques of complex catalytic processes is of foremost importance to modern synthetic chemistry, and the identification of efficient synthetic techniques relies on precise, reliable, and adaptable methods to dissect the mechanism of a given transformation. Currently, methods of reaction development are grounded upon the systematic modification of specific variables - such as temperature, time, concentration, etc. - to account for and control the dynamic series of coupled equilibria within a catalytic environment. On the other hand, tandem reaction analytical methods that involve the concomitant use of different instruments to probe a reaction can provide time-resolved information regarding active chemical species and facilitate the interrogation and optimization of the system. Herein, we report our study applying tandem in situ ReactIR and HPLC-MS monitoring to the dysprosium(III) triflate-catalyzed aza-Piancatelli rearrangement of 2-furylcarbinols, a reaction that grants access to trans-4,5-disubstituted cyclopentenones - common motifs in important biologically relevant and natural compounds. With a prototype automated sampling apparatus, information was obtained about the intrinsic chemoselectivity of the reaction, and previously unseen intermediates were observed, allowing for a more detailed reaction mechanism to be substantiated. The advantages of applying this type of tandem measurement to study these types of systems are also discussed. (Figure Presented).

A current goal in nanotechnology focuses on the assembly of different nanoparticle types into 3D organized structures. In this paper we report the use of a liquid crystal host phase in a new process for the generation of micron-scale vesicle-like nanoparticle shells stabilized by ligand-ligand interactions. The constructs formed consist of a robust, thin spherical layer, composed of closely packed quantum dots (QDs) and stabilized by local crystallization of the mesogenic ligands. Ligand structure can be tuned to vary QD packing within the shell and made UV cross-linkable to allow for intact shell extraction into toluene. The assembly method we describe could be extended to other nanoparticle types (metallic, magnetic etc.), where hollow shell formation is controlled by thermally sorting mesogen-functionalized nanoparticles in a liquid crystalline host material at the isotropic to nematic transition. This process represents a versatile method for making non-planar 3D nano-assemblies.

We present a novel method that covalently and sequence-specifically attaches long DNA molecules to a surface that is compatible with high-resolution atomic force microscopy (AFM) imaging. Surfaces prepared with this approach are ideally suited for performing biophysical experiments on single DNA molecules.

Mesogenic ligands have the potential to provide control over the dispersion and stabilization of nanoparticles in liquid crystal (LC) phases. The creation of such hybrid materials is an important goal for the creation of soft tunable photonic devices, such as the LC laser. Herein, we present a comparison of isotropic and mesogenic ligands attached to the surface of CdSe (core-only) and CdSe/ZnS (core/shell) quantum dots (QDs). The mesogenic ligand's flexible arm structure enhances ligand alignment, with the local LC director promoting QD dispersion in the isotropic and nematic phases. To characterize QD dispersion on different length scales, we apply fluorescence microscopy, X-ray scattering, and scanning confocal photoluminescent imaging. These combined techniques demonstrate that the LC-modified QDs do not aggregate into the dense clusters observed for dots with simple isotropic ligands when dispersed in liquid crystal, but loosely associate in a fluid-like droplet with an average interparticle spacing >10 nm. Embedding the QDs in a cholesteric cavity, we observe comparable coupling effects to those reported for more closely packed isotropic ligands.

The observed rate of reaction in the dysprosium triflate catalyzed aza-Piancatelli rearrangement is controlled by a key off-cycle binding between aniline and catalyst. Deconvoluting the role of these ancillary species greatly broadens our understanding of factors affecting the productive catalytic pathway. We demonstrate that the rate of reaction is controlled by initial competitive binding between the furylcarbinol and nitrogen nucleophile using either a Brønsted or Lewis acid catalyst and that the resulting rearrangement proceeds without involving the Brønsted and Lewis acid catalyst. This shows conclusively that the rate-controlling step and selectivity of reaction are decoupled.

A facile and efficient resolution of omeprazole as the monopotassium salt diethanol solvate using coupled preferential crystallization has been developed. This approach uses small perturbations in solution-phase concentration to control the competing process of selective crystal growth while suppressing unwanted primary nucleation. The result is a selective crystallization technique that replaces the traditional batch-type isolation with a continuous process amenable to scale, which provides easy access to enantiopure conglomerate crystals.