The effect of macromolecular architecture in nanomaterials: a comparison of site isolation in porphyrin core dendrimers and their isomeric linear analogues

The influence of macromolecular architecture on the physical properties of polymeric materials has been studied by comparing poly(benzyl ether) dendrons with their exact linear analogues. The results clearly confirm the anticipation that dendrimers are unique when compared to other architectures. Physical properties, from hydrodynamic volume to crystallinity, were shown to be different, and in a comparative study of core encapsulation in macromolecules of different architecture, energy transduction from the polymer backbone to a porphyrin core was shown to be different for dendrimers as compared to that of isomeric four- or eight-arm star polymers. Fluorescence excitation revealed strong, morphology dependent intramolecular energy transfer in the three macromolecular isomers investigated. Even at high generations, the dendrimers exhibited the most efficient energy transfer, thereby indicating that the dendritic architecture affords superior site isolation to the central porphyrin it surrounds.     

Using free energy of binding calculations to improve the accuracy of virtual screening predictions

Virtual screening of small molecule databases against macromolecular targets was used to identify binding ligands and predict their lowest energy bound conformation (i.e., pose). AutoDock4-generated poses were rescored using mean-field pathway decoupling free energy of binding calculations and evaluated if these calculations improved virtual screening discrimination between bound and nonbound ligands. Two small molecule databases were used to evaluate the effectiveness of the rescoring algorithm in correctly identifying binders of L99A T4 lysozyme. Self-dock calculations of a database containing compounds with known binding free energies and cocrystal structures largely reproduced experimental measurements, although the mean difference between calculated and experimental binding free energies increased as the predicted bound poses diverged from the experimental poses. In addition, free energy rescoring was more accurate than AutoDock4 scores in discriminating between known binders and nonbinders, suggesting free energy rescoring could be a useful approach to reduce false positive predictions in virtual screening experiments.     

The crystal and molecular structure of phenothiazine-10-propionic acid

The crystal structure of phenothiazine-10-propionic acid, C₁₂H₈SNC₂H₄COOH, was determined from three-dimensional X-ray diffraction data collected with a manual diffractomer using MoKα (λ 0.71069 Å) radiation. The space group is P2₁/c with a = 7.888 (2)Å, b = 8.703 (2)Å, c = 19.700 (8)Å, β = 101.42 (1)°, Z = 4, D_meas = 1.35(2) g. cm^?3 and D_calc = 1.36 g. cm^?3 at 23°. The structure was determined by the direct method and refined with 500 observed reflections by full-matrix least squares to an R of 0.072. The molecule is folded along the S-N axis and the dihedral angle is 136.5°. The C-S-C angle is 98.5(7)° and the average C-S bond is 1.77(2)Å. The shortening of the C-S bond, the small value of the C-S-C angle and the folding of the molecule are typical of the phenothiazine class of compounds and are assumed to be due to sulfur d orbital participation in ring bonding.     

The crystal and molecular structure of phenothiazine-10-propionitrile. The effect of crystal packing on the dihedral angle of phenothiazine heterocycles

Phenothiazine-10-propionitrile, C₁₂H₈SNC₂H₄CN, crystallizes in the centrosymmetric monoclinic space group P2₁/n, with a = 5.785(1)Å, b = 15.427(3)Å, c = 14.497(4)Å, β = 92.50(1)°, Z = 4, D_meas = 1.29(1) g cm³ and D_calc = 1.28 g cm³ at 23°. Three dimensional X-ray data were collected with a manual diffractometer using MoKα (λ 0.71069Å) radiation and by multiple film Weissenberg techniques using CuKα (λ 1.5418Å) radiation. The structure was determined by Patterson and Fourier methods and refined with 519 observed reflections by full matrix least-squares methods to an R of 0.077. The dihedral angle between the two planes of the o-phenylene rings is 135.4(3)°. In the folded heterocyclic ring the C-S-C angle is 97.8(7)° and the average C? S bond is 1.76(1)Å. A comparison of this structure to that of phenothiazine-10-propionic acid shows the two chemically similar molecules have the same dihedral angles in spite of completely different solid state packing patterns.