Synthesis,characterization and metal ion complexation and extraction capabilities of calix[4]arene Schiff base compounds

The syntheses, characterization and metal ion complexation and extraction capabilities of six new calix[4]arene Schiff base compounds, 5–10, are reported. The preparation of the compounds was achieved by the condensation of 5,17-diamino-11,23-di-tert-butyl-25,27-di-n-butoxy-26,28-dihydroxycalix[4]arene with the appropriate aldehyde (5-bromosalicylaldehyde for 5, 4-anisaldehyde for 6, 4-(dimethylamino)benzaldehyde for 7, 9-anthracenecarboxaldehyde for 8, 1-pyrenecarboxaldehyde for 9, and 9-fluorenecarboxaldehyde for 10) in refluxing ethanol. The compounds were characterized by ¹H and ¹³C NMR spectroscopy, IR spectroscopy, high-resolution mass spectrometry and elemental analysis. The X-ray crystal structures of 7, 8 and 9 (as dichloromethane solvates) revealed that the calixarene molecules adopt H-bond stabilized, distorted-cone conformations and form centrosymmetric dimers in the solid state. Compounds 5–10 did not form host–guest complexes with NEt₄[(bdt)MoO₂(OSiPh₃)] (bdt^2–=benzene-1,2-dithiolate), a potential precursor for biologically relevant oxosulfido-Mo(VI/V) enzyme models; such host–guest complexes have the potential to stabilize these sought-after but highly reactive model compounds. In addition, the capabilities of 5–10 to extract selected metal ions (Ni²⁺, Co²⁺, Cu²⁺, Zn²⁺, Ag⁺, Pb²⁺, Cd²⁺ and Hg²⁺) from an aqueous into an organic phase have been assessed by picrate extraction experiments. Compound 5 displayed exceptional selectivity towards Ni²⁺, compound 7 exhibited enhanced extraction towards all of the metal ions tested and compounds 6, 9 and 10 showed very high selectivity towards Hg²⁺. On the other hand, compound 8 exhibited negligible capacity to extract any of the metal ions tested.     

Dicarboxylated ethynylarenes as buffer-dependent chemosensors for Cd(II), Pb(II), and Zn(II)

Two dicarboxylated ethynylarenes were prepared efficiently from condensation of 1,3-bis(3-aminophenylethynyl)benzene with 2 equiv of either succinic anhydride or glutaric anhydride. These compounds behave as fluorescent chemosensors selective for Cd(II), Pb(II), and Zn(II) cations under buffered aqueous conditions, with analyte binding observed as bathochromically shifted, intensified fluorescence. It was noteworthy that the fluorescence responses varied significantly with buffer identity. A conformational restriction mechanism involving reversible interactions between the fluorophore, metal cation, and buffer itself is proposed.     

A scalable process for the synthesis of (E)-pterostilbene involving aqueous Wittig olefination chemistry

A synthetic approach toward the pharmacologically active (E)-stilbene pterostilbene is described using a Wittig reaction conducted under mildly basic, aqueous conditions. A surprising, non-intuitive difference in (E)/(Z) stereoselectivity was observed comparing the two possible isomeric Wittig routes, allowing for the development of a highly efficient process to access the title stilbene derivative through a one-pot olefination deprotection sequence.     

Application of isotopic labeling,and gas chromatography mass spectrometry,to understanding degradation products and pathways in the thermal-oxidative aging of Nylon 6.6

Nylon 6.6 containing ¹³C isotopic labels at specific positions along the macromolecular backbone has been subjected to extensive thermal-oxidative aging at 138 °C for time periods up to 243 days. In complementary experiments, unlabeled Nylon 6.6 was subjected to the same aging conditions under an atmosphere of ¹⁸O₂. Volatile organic degradation products were analyzed by cryofocusing gas chromatography mass spectrometry (cryo-GC/MS) to identify the isotopic labeling. The labeling results, combined with basic considerations of free radical reaction chemistry, provided insights to the origin of degradation species, with respect to the macromolecular structure. A number of inferences on chemical mechanisms were drawn, based on 1) the presence (or absence) of the isotopic labels in the various products, 2) the location of the isotope within the product molecule, and 3) the relative abundance of products as indicated by large differences in peak intensities in the gas chromatogram. The overall degradation results can be understood in terms of free radical pathways originating from initial attacks on three different positions along the nylon chain which include hydrogen abstraction from: the (CH₂) group adjacent to the nitrogen atom, at the (CH₂) adjacent the carbonyl group, and direct radical attack on the carbonyl. Understanding the pathways which lead to Nylon 6.6 degradation ultimately provides new insight into changes that can be leveraged to detect and reduce early aging and minimize problems associated with material degradation.     

High–quality protein backbone reconstruction from alpha carbons using Gaussian mixture models

Coarse‐grained protein structure models offer increased efficiency in structural modeling, but these must be coupled with fast and accurate methods to revert to a full‐atom structure. Here, we present a novel algorithm to reconstruct mainchain models from C traces. This has been parameterized by fitting Gaussian mixture models (GMMs) to short backbone fragments centered on idealized peptide bonds. The method we have developed is statistically significantly more accurate than several competing methods, both in terms of RMSD values and dihedral angle differences. The method produced Ramachandran dihedral angle distributions that are closer to that observed in real proteins and better Phaser molecular replacement log‐likelihood gains. Amino acid residue sidechain reconstruction accuracy using SCWRL4 was found to be statistically significantly correlated to backbone reconstruction accuracy. Finally, the PD2 method was found to produce significantly lower energy full‐atom models using Rosetta which has implications for multiscale protein modeling using coarse‐grained models. A webserver and C++ source code is freely available for noncommercial use from: http://www.sbg.bio.ic.ac.uk/phyre2/PD2_ca2main/ . © 2013 Wiley Periodicals, Inc.     

An assessment of pure,hybrid, meta,and hybrid‐meta GGA density functional theory methods for open‐shell systems: The case of the nonheme iron enzyme 8R–LOX

The performance of a range density functional theory functionals combined in a quantum mechanical (QM)/molecular mechanical (MM) approach was investigated in their ability to reliably provide geometries, electronic distributions, and relative energies of a multicentered open‐shell mechanistic intermediate in the mechanism 8R–Lipoxygenase. With the use of large QM/MM active site chemical models, the smallest average differences in geometries between the catalytically relevant quartet and sextet complexes were obtained with the B3LYP^* functional. Moreover, in the case of the relative energies between ⁴II and ⁶II , the use of the B3LYP^* functional provided a difference of 0.0 kcal mol^–1. However, B3LYP^± and B3LYP also predicted differences in energies of less than 1 kcal mol^–1. In the case of describing the electronic distribution (i.e., spin density), the B3LYP^*, B3LYP, or M06‐L functionals appeared to be the most suitable. Overall, the results obtained suggest that for systems with multiple centers having unpaired electrons, the B3LYP^* appears most well rounded to provide reliable geometries, electronic structures, and relative energies. © 2012 Wiley Periodicals, Inc.     

Rapid parameterization of small molecules using the force field toolkit

The inability to rapidly generate accurate and robust parameters for novel chemical matter continues to severely limit the application of molecular dynamics simulations to many biological systems of interest, especially in fields such as drug discovery. Although the release of generalized versions of common classical force fields, for example, General Amber Force Field and CHARMM General Force Field, have posited guidelines for parameterization of small molecules, many technical challenges remain that have hampered their wide‐scale extension. The Force Field Toolkit (ffTK), described herein, minimizes common barriers to ligand parameterization through algorithm and method development, automation of tedious and error‐prone tasks, and graphical user interface design. Distributed as a VMD plugin, ffTK facilitates the traversal of a clear and organized workflow resulting in a complete set of CHARMM‐compatible parameters. A variety of tools are provided to generate quantum mechanical target data, setup multidimensional optimization routines, and analyze parameter performance. Parameters developed for a small test set of molecules using ffTK were comparable to existing CGenFF parameters in their ability to reproduce experimentally measured values for pure‐solvent properties (<15% error from experiment) and free energy of solvation (±0.5 kcal/mol from experiment). © 2013 Wiley Periodicals, Inc.