Atomic-scale determination of DNA conformational response to strained furanose: a static mode approach

An original approach of macromolecular ‘induced-fit’ flexibility, namely the static modes, is applied to shed light on some fundamental mechanisms impacting DNA conformations. We first investigate a constrained nucleic acid of the D-CNA family, in which some backbone torsional angles are conformationally restricted by a dioxaphosphorinane ring structure. We take a special interest in α,β-D-CNA, in which α and β angles are restricted to the canonical conformation. We used the static mode method to evaluate the impact of the insertion of modified nucleotides on the stability of DNA/DNA and DNA/RNA duplexes. Although our approach authorizes the design of complex excitation modes on a specific molecule, we here establish with an atomic precision how a DNA south to north transition can be optimally operated through C5′ and O5′ single excitations.     

Surface and interfacial structural characterization of MBE grown Si/Ge multilayers

Si/Ge multilayer structures have been grown by solid source molecular beam epitaxy (MBE) on Si (1 1 1) and (1 0 0) substrates and were characterized by high-resolution X-ray diffraction (XRD), atomic force microscopy (AFM), high-depth-resolution secondary ion mass spectroscopy (SIMS) and cross-section high-resolution transmission electron microscopy (HRTEM). A reasonably good agreement has been obtained for layer thickness, interfacial structure and diffusion between SIMS and HRTEM measurements. Epitaxial growth and crystalline nature of the individual layer have been probed using cross-sectional HRTEM and XRD measurements. Surface and interface morphological studies by AFM and HRTEM show island-like growth of both Si and Ge nanostructures.     

Sensitivity of the resonant ultrasound spectroscopy to weak gradients of elastic properties

The applicability of resonant ultrasound spectroscopy on materials with weak spatial gradients in elastic coefficients and density is analyzed. It is shown that such gradients do not affect measurably the resonant spectrum but have a significant impact on the modal shapes. A numerical inverse procedure is proposed to explore the possibility of reconstructing the gradients from experimentally obtained modal shapes. This procedure is tested on synthetic data and applied to determine the gradient of the shear modulus in a continuously graded silicon nitride ceramic material. The results are in a good agreement with the gradient calculated for the examined material theoretically as well as with the results of other experimental methods.     

A simple asymmetric organocatalytic approach to optically active cyclohexenones

Optically active 2,5-disubstituted-cyclohexen-2-one derivatives have been prepared in a one-pot process consisting of five reaction steps: an organocatalytic asymmetric conjugated addition of beta-ketoesters to alpha,beta-unsaturated aldehydes that proceeds in aqueous solutions or under solvent-free conditions has been implemented in a multi-step process.     

Development and validation of an enantioselective LC‐MS/MS method to quantify enantiomers of (±)‐TAK‐700 in rat plasma: lack of in vivo inversion of (+)‐TAK‐700 (Orteronel) to its antipode

A highly sensitive, specific and enantioselective assay has been developed and validated for the estimation of TAK‐700 enantiomers [(+)‐TAK‐700 and (?)‐TAK‐700] in rat plasma on LC‐MS/MS‐ESI in the positive‐ion mode. Liquid–liquid extraction was used to extract (±)‐TAK‐700 enantiomers and IS (phenacetin) from rat plasma. TAK‐700 enantiomers were separated using methanol and 5 mm ammonium acetate (80:20, v/v) at a flow rate of 0.7 mL/min on a Chiralcel OJ‐RH column. The total run time was 7.0 min and the elution of (+)‐TAK‐700, (?)‐TAK‐700 and IS occurred at 3.71, 4.45 and 4.33 min, respectively. The MS/MS ion transitions monitored were m/z 308.2 → 95.0 for TAK‐700 and m/z 180.2 → 110.1 for IS. The standard curves for TAK‐700 enantiomers were linear (r² > 0.998) in the concentration range 2.01–2015 ng/mL for each enantiomer. The inter‐ and intra‐day precisions were in the ranges 3.74–7.61 and 2.06–8.71% and 3.59–9.00 and 2.32–11.0% for (+)‐TAK‐700 and (?)‐TAK‐700, respectively. Both the enantiomers were found to be stable in a battery of stability studies. This novel method was applied to the study of stereoselective oral pharmacokinetics of (+)‐TAK‐700 and it was unequivocally demonstrated that (+)‐TAK‐700 does not undergo chiral inversion to its antipode in vivo. Copyright © 2012 John Wiley & Sons, Ltd.     

Chemoselective and Site‐Selective Lysine‐Directed Lysine Modification Enables Single‐Site Labeling of Native Proteins

The necessity for precision labeling of proteins emerged during the efforts to understand and regulate their structure and function. It demands selective attachment of tags such as affinity probes, fluorophores, and potent cytotoxins. Here, we report a method that enables single‐site labeling of a high‐frequency Lys residue in the native proteins. At first, the enabling reagent forms stabilized imines with multiple solvent‐accessible Lys residues chemoselectively. These linchpins create the opportunity to regulate the position of a second Lys‐selective electrophile connected by a spacer. Consequently, it enables the irreversible single‐site labeling of a Lys residue independent of its place in the reactivity order. The user‐friendly protocol involves a series of steps to deconvolute and address chemoselectivity, site‐selectivity, and modularity. Also, it delivers ordered immobilization and analytically pure probe‐tagged proteins. Besides, the methodology provides access to antibody‐drug conjugate (ADC), which exhibits highly selective anti‐proliferative activity towards HER‐2 expressing SKBR‐3 breast cancer cells.     

Synthesis and Modeling of Acridine Dyes as Potential Photosensitizers for Dye‐Sensitized Photovoltaic Applications †

We have synthesized novel aromatic amine‐substituted acridine dyes as potential candidates for the photosensitizers in dye sensitized nanocrystalline semiconductor based solar cells (DSSC) cells. The protonation and quaternization of the acridine nitrogen led to acridine dyes with extended absorption from 400–800 nm. Computational modeling was used to evaluate a variety of structures to achieve insights for correlating these types of molecular structures with predicted absorption spectra. Pertinent dihedral angles as well as bond lengths were evaluated to assess and compare planarity and conjugation for these dyes. Other predictions include plots of the HOMO and LUMO levels to qualitatively examine electron distributions and the potential for electron injection. The results from modeling along with the experimental data consisting of synthesis, characterization and UV‐visible absorption properties of the selected dyes are presented.     

A kinetic Monte Carlo study of the initial stage of silicon oxidation: Basic mechanisms-induced partial ordering of the oxide interfacial layer

A kinetic Monte Carlo study of the early stage of silicon oxidation is presented. The model assembles the most recently published dedicated surface mechanisms: oxygen incorporations, migrations, charge transfer effects. Simulations of the thermal oxidation at typical manufacturing temperature and pressure conditions are discussed. As revealed recently through Density Functional Theory investigations, we observe hexagonal patterns that can be here extended over the surface giving rise to a new model system of the Si/SiO₂ interface as well as new associated specific defects. We show that our simulator is able to reproduce correctly the oxidation states of the silicon atoms which are specific of the Si/SiO₂ interface.