Comparison of Experimental and Theoretical Structures of a Transition State Analogue Used for the Induction of Anti-Cocaine Catalytic Antibodies

Comparison of the crystal structure of a transition state analogue that was used to raise catalytic antibodies for the benzoyl ester hydrolysis of cocaine with structures calculated by ab initio, semiempirical, and solvation semiempirical methods reveals that modeling of solvation is crucial for replicating the crystal structure geometry. Both SM3 and SM2 calculations, starting from the crystal structure TSA I, converged on structures similar to the crystal structure. The 3-21G(*)/HF, 6-31G*/HF, PM3, and AM1 calculations converged on structures similar to each other, but these gas-phase structures were significantly extended relative to the condensed phase structures. Two transition states for the hydrolysis of the benzoyl ester of cocaine were located with the SM3 method. The gas phase calculations failed to locate reasonable transition state structures for this reaction. These results imply that accurate modeling of the potential energy surfaces for the hydrolysis of cocaine requires solvation methods.

Structures of Cage, Prism, and Book Isomers of Water Hexamer from Broadband Rotational Spectroscopy

Theory predicts the water hexamer to be the smallest water cluster with a three-dimensional hydrogen-bonding network as its minimum energy structure. There are several possible low-energy isomers, and calculations with different methods and basis sets assign them different relative stabilities. Previous experimental work has provided evidence for the cage, book, and cyclic isomers, but no experiment has identified multiple coexisting structures. Here, we report that broadband rotational spectroscopy in a pulsed supersonic expansion unambiguously identifies all three isomers; we determined their oxygen framework structures by means of oxygen-18–substituted water (H218O). Relative isomer populations at different expansion conditions establish that the cage isomer is the minimum energy structure. Rotational spectra consistent with predicted heptamer and nonamer structures have also been identified.

Characterization of vascular cavity coatings and microscopic tube-shaped structures from Upper Cretaceous dinosaur bone: evidence of a bacterial origin for dinosaur blood vessels""

Recent claims of blood vessels extracted from dinosaur fossils challenge classical views of soft-tissue preservation. Alternatively, these structures may represent postdepositional,diagenetic biofilms that grew on vascular cavity surfaces within the fossil. Similar red, hollow, tube-shaped structures were recovered from well-preserved and poorly-preserved (abraded, desiccated, exposed) Upper Cretaceous dinosaur fossils in this study. Integration of light microscopy, scanning electron microscopy, and energy dispersive x-ray spectroscopy was used to compare these vessel structures to the fossils from which they are derived. Vessel structures are typically 100-400 μm long, 0.5-1.5 μm thick, 10-40 μm in diameter and take on a wide range of straight, curved, andbranching morphologies. Interior surfaces vary from smooth to globular and typically contain spheres, rods, and fibrous structures (< 2 μm in diameter) incorporated into the surface. Exterior surfaces exhibit 2-μm-tall converging ridges, spaced 1-3 μm apart, that are sub-parallel to the long axis of the vessel structure. Fossil vascular cavities are typically coated with a smooth or grainy orange layer that shows a wide range of textures including smooth, globular, rough, ropy, and combinations thereof. Coatings tend to overlay secondary mineral crystals and framboids, confirming they are not primary structures of the fossil. For some cavity coatings, the surface that had been in contact with the bone exhibits a ridged texture, similar to that of vessel structures, having formed as a mold of the intravascular bone surface. Thus, vessel structures are interpreted as intact cavity coatings isolated after the fossil is demineralized. The presence of framboids and structures consistent in size and shape with bacteria cells, the abundance of iron in cavity coatings, and the growth of biofilms directly from the fossil that resemble respective cavity coatings support the hypothesis that vessel structures result from ironconsuming bacteria that form biofilms on the intravascular bone surfaces of fossil dinosaur bone. This also accounts for microstructures resembling osteocytes as some fossil lacunae are filled with the same iron oxide that comprises vessel structures andcoatings. Results of this study show that systematic, high-resolution SEM analyses of vertebrate fossils can provide improved insight on microtaphonomic processes, including the role of bacteria in diagenesis. These results conflict with earlier claims of dinosaurblood vessels and osteocytes.