Rapid Arene Triazene Chemistry for Macrocyclization

Here, we report a novel rapid arene triazene strategy for the macrocyclization of peptides that generates an inbuilt chromophoric triazene moiety at the site of cyclization within a minute. The rapid arene triazene chemistry is chemoselective for secondary amines and p-amino phenylalanine. Importantly, the resulting triazene cyclic peptide is highly stable at neutral pH and under harsh conditions but rapidly responds to various external stimuli such as UV radiations and acidic conditions, resulting in the ring opening to generate the linear peptides in an unchanged form, which further cyclizes under neutral pH conditions. This method works with completely unprotected peptides and has been applied for the synthesis of 18- to 66-membered monocycles and bicycles with various amino acid compositions in one pot under neutral pH conditions. Due to the high stability of triazene cyclic peptides, the postcyclization modification was carried out with various functional groups. This rapid, macrocyclization strategy featuring a triazene scaffold, amenable to late-stage diversification and responsive to external stimuli, should find application in various fields of chemical biology, selective drug delivery, and identification of cyclic peptide hits after library screening.

Charge Transfer Tuned by the Surrounding Dielectrics in TiO₂-Ag Composite Arrays

TiO₂/Ag bilayer films sputtered onto a 2D polystyrene (PS) bead array in a magnetron sputtering system were found to form a nanocap-shaped nanostructure composed of a TiO₂-Ag composite on each PS bead, in which the Ag nanoparticles were trapped partially or fully in the TiO₂ matrix, depending on the TiO₂ thickness. X-ray Photoelectron Spectroscopy (XPS) results showed the opposite shifts of binding energy for Ti 2p and Ag 3d, indicating the transfer of electrons from metallic Ag to TiO₂ owing to the Ag-O-TiO₂ composite formation. UV-Vis absorption spectra showed the blue shifts of the surface plasma resonance peaks, and the maximum absorption peak intensity was obtained for TiO₂ at 30 nm. The surface-enhanced Raman scattering (SERS) peak intensity first increased and then decreased when the TiO₂ thickness changed. The observations of SERS, XPS, and UV-Vis absorption spectra were explained by the dependency of the charge-transfer process on TiO₂ thickness, which was ascribed to the changing dielectric properties in the metal/semiconductor system.

Avogadro: an advanced semantic chemical editor, visualization, and analysis platform

Background

The Avogadro project has developed an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible, high quality rendering, and a powerful plugin architecture. Typical uses include building molecular structures, formatting input files, and analyzing output of a wide variety of computational chemistry packages. By using the CML file format as its native document type, Avogadro seeks to enhance the semantic accessibility of chemical data types.

Results

The work presented here details the Avogadro library, which is a framework providing a code library and application programming interface (API) with three-dimensional visualization capabilities; and has direct applications to research and education in the fields of chemistry, physics, materials science, and biology. The Avogadro application provides a rich graphical interface using dynamically loaded plugins through the library itself. The application and library can each be extended by implementing a plugin module in C++ or Python to explore different visualization techniques, build/manipulate molecular structures, and interact with other programs. We describe some example extensions, one which uses a genetic algorithm to find stable crystal structures, and one which interfaces with the PackMol program to create packed, solvated structures for molecular dynamics simulations. The 1.0 release series of Avogadro is the main focus of the results discussed here.

Conclusions

Avogadro offers a semantic chemical builder and platform for visualization and analysis. For users, it offers an easy-to-use builder, integrated support for downloading from common databases such as PubChem and the Protein Data Bank, extracting chemical data from a wide variety of formats, including computational chemistry output, and native, semantic support for the CML file format. For developers, it can be easily extended via a powerful plugin mechanism to support new features in organic chemistry, inorganic complexes, drug design, materials, biomolecules, and simulations. Avogadro is freely available under an open-source license from http://avogadro.openmolecules.net.