Semiclassical variational transition state calculations for the reactions of H and D with thermal and vibrationally excited H2

We present calculations of the rate constants for the title reactions on a new accurate potential energy surface with a 9.65 kcal mol^?1 barrier and a carefully fitted long-range attraction. The low-temperature thermal rate constant decreases from the previously calculated value, corresponding to a surface with a barrier of 9.80 kcal mol^?1, which is opposite to the direction of change expectedbecause of the change in barrier height. This demonstrates the sensitivity of tunneling contributions to more global characteristics of the surface. The excited-state (n = 1) rate constants alsochange slightly, but not nearly enough to settle the controversial disagreement of theory with experiment for these rate constants.     

Circle packings and polyhedral surfaces

Given a triangulated surface, a euclidean or hyperbolic polyhedral surface can be constructed by assigning radii to the vertices of the triangulation. We develop necessary and sufficient conditions for the existence of such a polyhedral surface having specified characteristics. The results in this paper are included in the author's doctoral dissertation [12].     

Automated docking of ligands to an artificial active site: augmenting crystallographic analysis with computer modeling

The W191G cavity of cytochrome c peroxidase is useful as a model system for introducing small molecule oxidation in an artificially created cavity. A set of small, cyclic, organic cations was previously shown to bind in the buried, solvent-filled pocket created by the W191G mutation. We docked these ligands and a set of non-binders in the W191G cavity using AutoDock 3.0. For the ligands, we compared docking predictions with experimentally determined binding energies and X-ray crystal structure complexes. For the ligands, predicted binding energies differed from measured values by +/- 0.8 kcal/mol. For most ligands, the docking simulation clearly predicted a single binding mode that matched the crystallographic binding mode within 1.0 A RMSD. For 2 ligands, where the docking procedure yielded an ambiguous result, solutions matching the crystallographic result could be obtained by including an additional crystallographically observed water molecule in the protein model. For the remaining 2 ligands, docking indicated multiple binding modes, consistent with the original electron density, suggesting disordered binding of these ligands. Visual inspection of the atomic affinity grid maps used in docking calculations revealed two patches of high affinity for hydrogen bond donating groups. Multiple solutions are predicted as these two sites compete for polar hydrogens in the ligand during the docking simulation. Ligands could be distinguished, to some extent, from non-binders using a combination of two trends: predicted binding energy and level of clustering. In summary, AutoDock 3.0 appears to be useful in predicting key structural and energetic features of ligand binding in the W191G cavity.     

Theoretical studies of diamagnetic properties of the hydrogen molecule ion II. Effect of varying internuclear separation

The diamagnetic susceptibility χ and magnetic shielding σ for H are investigated in the range of internuclear separations R = 1.6 a.u. to R = 2.4 a.u. according to a previously reported technique. From this data values of 〈χ〉 and 〈σ〉, for which nuclear motion due to zero-point vibration and centrifugal stretching is taken into account, are calculated at 300°K. These averages are 〈χ〉 = ?0.3902 α²a and 〈σ〉 = 1.096 × 10^?5 c.g.s. units which are approximately 3.1% and 1.4% respectively, smaller than the equilibrium values.     

Imaging of small molecules in tissue sections with a new intermediate-pressure MALDI linear ion trap mass spectrometer

We describe a new intermediate-pressure MALDI linear ion trap mass spectrometer and its capabilities for imaging mass spectrometry. The instrument design is described and is characterized in terms of four performance issues (1) MALDI performance at intermediate pressure; (2) analysis of samples on non-conductive and conductive glass slides; (3) critical importance of tandem mass spectrometry (both MS² and MS³) for identification of analyte species and imaging of isobaric species; (4) capability for repeated analysis of the same tissue section. Application of the new instrument to imaging phospholipids in rat brain sections is described in detail.