Strain effects in electron spin resonance spectroscopy of quintet 2,6-bis(4'-nitrenophenyl)-4-phenylpyridine

Photolysis of 2,6-bis(4'-azidophenyl)-4-phenylpyridine in 2-methyltetrahydrofuran (2MTHF) glass at 7 K leads to quintet 2,6-bis(4'-nitrenophenyl)-4-phenylpyridine as a mixture of rotational isomers. The electron spin resonance (ESR) spectrum of this mixture of rotamers shows a considerable broadening of many transitions in the range of 0-5000 G and cannot be reproduced by computer simulations solely based on the tuning of the spin Hamiltonian parameters g, D(Q), and E(Q) alone or on predictions of DFT calculations. The best modeling of the experimental ESR spectrum is obtained only when the large line-broadening parameter of Γ(E(Q)) = 1200 MHz along with the spin Hamiltonian g = 2.003, D(Q) = 0.154 cm(-1), and E(Q) = 0.050 cm(-1) is used in the spectral simulations. The most accurate theoretical estimations of the magnetic parameters of the dinitrene in a 2MTHF glass are obtained from the B3LYP/6-311+G(d,p)+PBE/DZ/COSMO calculations of the spin-spin coupling parameters D(SS) and E(SS). Such calculations overestimate the E(Q) and D(Q) values of the dinitrene just by 1% and 10%, respectively, demonstrating that contributions of the spin-orbit coupling parameters D(SOC) and E(SOC) to the total D(Q) and E(Q) values are negligibly small. The research shows that ESR studies of polynuclear high-spin nitrenes, obtained by photolysis of rotational isomers of the starting azides, can only be successful if large E(Q) strain effects are taken into account in the spectral simulations.     

Snooker: a structure-based pharmacophore generation tool applied to class A GPCRs

G-protein coupled receptors (GPCRs) are important drug targets for various diseases and of major interest to pharmaceutical companies. The function of individual members of this protein family can be modulated by the binding of small molecules at the extracellular side of the structurally conserved transmembrane (TM) domain. Here, we present Snooker, a structure-based approach to generate pharmacophore hypotheses for compounds binding to this extracellular side of the TM domain. Snooker does not require knowledge of ligands, is therefore suitable for apo-proteins, and can be applied to all receptors of the GPCR protein family. The method comprises the construction of a homology model of the TM domains and prioritization of residues on the probability of being ligand binding. Subsequently, protein properties are converted to ligand space, and pharmacophore features are generated at positions where protein ligand interactions are likely. Using this semiautomated knowledge-driven bioinformatics approach we have created pharmacophore hypotheses for 15 different GPCRs from several different subfamilies. For the beta-2-adrenergic receptor we show that ligand poses predicted by Snooker pharmacophore hypotheses reproduce literature supported binding modes for ～75% of compounds fulfilling pharmacophore constraints. All 15 pharmacophore hypotheses represent interactions with essential residues for ligand binding as observed in mutagenesis experiments and compound selections based on these hypotheses are shown to be target specific. For 8 out of 15 targets enrichment factors above 10-fold are observed in the top 0.5% ranked compounds in a virtual screen. Additionally, prospectively predicted ligand binding poses in the human dopamine D3 receptor based on Snooker pharmacophores were ranked among the best models in the community wide GPCR dock 2010.     

Electrophoresis of concentrated colloidal dispersions in low-polar solvents

We present a method to accurately measure the electrophoretic mobility of spherical colloids at high volume fractions in real space using confocal laser scanning microscopy (CLSM) and particle tracking. We show that for polymethylmethacrylate (PMMA) particles in a low-polar, density- and refractive-index-matched mixture of cyclohexylbromide and cis-decahydronaphthalene, the electrophoretic mobility decreases nonlinearly with increasing volume fraction. From the electrophoretic mobilities, we calculate the ζ-potential and the particle charge with and without correcting for volume fraction effects. For both cases, we find a decreasing particle charge as a function of volume fraction. This is in accordance with the fact that the charges originate from chemical equilibria that represent so-called weak association and/or dissociation reactions. Finally, as our methodology also provides data on particle self-diffusion in the presence of an electric field, we also analyze the diffusion at different volume fractions and identify a nonlinear decreasing trend for increasing volume fraction.     

The micromechanics of three‐dimensional collagen‐I gels

We study the micromechanics of collagen‐I gel with the goal of bridging the gap between theory and experiment in the study of biopolymer networks. Three‐dimensional images of fluorescently labeled collagen are obtained by confocal microscopy, and the network geometry is extracted using a 3D network skeletonization algorithm. Each fiber is modeled as an elastic beam that resists stretching and bending, and each crosslink is modeled as torsional spring. The stress–strain curves of networks at three different densities are compared with rheology measurements. The model shows good agreement with experiment, confirming that strain stiffening of collagen can be explained entirely by geometric realignment of the network, as opposed to entropic stiffening of individual fibers. The model also suggests that at small strains, crosslink deformation is the main contributer to network stiffness, whereas at large strains, fiber stretching dominates. As this modeling effort uses networks with realistic geometries, this analysis can ultimately serve as a tool for understanding how the mechanics of fibers and crosslinks at the microscopic level produce the macroscopic properties of the network. © 2010 Wiley Periodicals, Inc. Complexity 16: 22‐28, 2011     

Photoemission valence band spectra and electronic density of states in copper oxides and copper based ceramic super-conductors

Photoemission valence band spectra with three different photon energies (21.2 eV, 40.8 eV, 1253.6 eV) for Cu₂O and CuO and a number of copper oxide based superconducting ceramics are investigated, namely La₂CuO₄ (LCO), Y₁Ba₂Cu₃O₇ (YBCO), Bi₂Sr₂CaCu₂O₈ (BSCCO) and Tl₂Ba₂Ca₂Cu₃O₁₀ (TBCCO). From the Cu₂O data it can be infered, that the He-II (40.8 eV) spectra give a fair representation of the density of states (DOS). In addition the agreement between the calculated density of states (DOS) and the He-II photoemission spectrum is almost perfect for Cu₂O. This agreement is worse for CuO and the other materials which all have a Cu groundstate close to a 3d ⁹ configuration indicating a large contribution of thed-d correlation energy to the excitation spectra which is absent in Cu₂O because of the filled 3d-shell. In all cases the experimental DOS atE _F is very small and only the spectra of BSCCO show a well defined Fermi edge. The relevance of these findings with respect to the theoretical local functional density DOS calculations is discussed.