Scientific Publications 2006
2006. "Characterization of Exciton Self-trapping in Amorphous Silica." Journal of Non-crystalline Solids 352(23-25):2589-2595. doi:10.1016/j.jnoncrysol.2006.01.095 Abstract Triplet electron-hole excitations were introduced into amorphous silica to study self-trapping (localization) and damage formation using density functional theory. Multiple self-trapped exciton (STE) states are found that can be differentiated based on the luminescence energy, the localization and distribution of the excess spin density of the triplet state, and relevant structural data, including the presence or absence of broken bonds. The trapping is shown to be affected by the relaxation response of the silica network, and by comparing results of quartz and amorphous silica systems the effects of the inherent disordered structures on exciton self-trapping are revealed. A key result is that during the process of the exciton trapping, point defects are formed as a result of a non-activated damage mechanism where the triplet energy surface and the corresponding ground state singlet surface come into close proximity. This work was supported by the Office of Basic Energy Sciences of the Department of Energy, in part by the Chemical Sciences program and in part by the Engineering and Geosciences Division. The Pacific Northwest National Laboratory is operated by Battelle for the US Department of Energy under contract DE-AC05-76RL01830.
2006. "Theoretical Study of Helium Insertion and Diffusion in 3C-SiC." Journal of Nuclear Materials 348(1-2):51-59. Abstract Insertion and diffusion of helium in cubic silicon carbide have been investigated by means of density functional theory. That method has first been assessed by calculating relevant properties for the perfect crystal along with point defect formation energies. Results are consistent with available theoretical as well as experimental data. Helium insertion energies have been calculated to be lower for divacancy and silicon vacancy defects compared to the other mono-vacancies and interstitial sites considered. Migration barriers for helium have been determined by using the nudged elastic band method. Calculated activation energies for migration in and around vacancies (silicon vacancy, carbon vacancy or divacancy) range from 0.6 to 1.0 eV. The activation energy for interstitial migration is calculated to be 2.5 eV. These values are discussed and related to recent experimental activation energies for migration that range from 1.1 to 3.2 eV, depending on the SiC samples used and on helium implantation conditions.
2006. "Enzyme-amplified protein micorarray and a fluidic renewable surface fluorescence immunoassay for botulinum neurotoxin detection using high-affinity recombinant antibodies." Analytica Chimica Acta 570(2):137-143. Abstract With the use of high-affinity recombinant monoclonal antibodies against the receptor binding domain of botulinum neurotoxin A (BoNT/A), two separate immunoassay platforms were developed for either the sensitive or the rapid detection of BoNT/A. An enzyme-linked immunosorbent assay (ELISA) microarray was developed for the specific and sensitive detection of BoNT in buffer and clinical fluids. This assay has the sensitivity to detect BoNT in diverse samples down to 14 fM (1.4 pg/mL). Using the recombinant monoclonal antibodies, a renewable surface microcolumn sensor was developed for the rapid detection of BoNT/A in an automated fluidic system. While the ELISA microarray assay, because of its sensitivity, offers an alternative to the mouse bioassay, the renewable surface assay has potential as a rapid screening assay for the analysis of complex environmental samples.
2006. " Ab Initio and Analytic Intermolecular Potentials for Ar-CF₄." Journal of Physical Chemistry A 110(9):3174-3178. doi:10.1021/jp054592p Abstract Ab initio calculations at the CCSD(T) level of theory are performed to characterize the Ar ﹢ CF ₄ intermolecular potential. Extensive calculations, with and without a correction for basis set superposition error (BSSE), are performed with the cc-pVTZ basis set. Additional calculations are performed with other correlation consistent (cc) basis sets to extrapolate the Ar---CF₄potential energy minimum to the complete basis set (CBS) limit. Both the size of the basis set and BSSE have substantial effects on the Ar + CF₄ potential. Calculations with the cc-pVTZ basis set and without a BSSE correction, appear to give a good representation of the potential at the CBS limit and with a BSSE correction. In addition, MP2 theory is found to give potential energies in very good agreement with those determined by the much higher level CCSD(T) theory. Two analytic potential energy functions were determined for Ar ﹢ CF₄by fitting the cc-pVTZ calculations both with and without a BSSE correction. These analytic functions were written as a sum of two body potentials and excellent fits to the ab initio potentials were obtained by representing each two body interaction as a Buckingham potential.
2006. "Post-transition State Dynamics for Propene Ozonolysis:Intramolecular and Unimolecular Dynamics of Molozonide." Journal of Chemical Physics 125:014317 1-16. doi:10.1063/1.2206785 Abstract The research described in this product was performed in part in the Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by the Department of Energy's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory. A direct chemical dynamics simulation, at the B3LYP/6-31G(d) level of theory, was used to study the post-transition state intramolecular and unimolecular dynamics for the O₃+propene reaction. Comparisons of B3LYP/6-31G(d) with CCSD(T)/cc-pVTZ and other levels of theory show that the former gives accurate structures and energies for the reaction’s stationary points. The direct dynamics simulations are initiated at the anti and syn O₃+propene transition states (TSs) and the TS symmetries are preserved in forming the molozonide intermediates. Anti↔syn molozonide isomerization has a very low barrier of 2–3 kcal/mol and its Rice-Ramsperger-Kassel-Marcus (RRKM) lifetime is 0.3 ps. However, the trajectory isomerization is slower and it is unclear whether this anti↔syn equilibration is complete when the trajectories are terminated at 1.6 ps. The syn (anti) molozonides dissociate to CH₃CHO+H₂COO and H₂CO+syn (anti) CH₃CHOO. The kinetics for the latter reactions are in overall good agreement with RRKM theory, but there is a symmetry preserving non-RRKM dynamical constraint for the former. Dissociation of anti molozonide to CH₃CHO+H₂COO is enhanced and suppressed, respectively, for the trajectory ensembles initiated at the anti and syn O₃+propene TSs. The dissociation of syn molozonide to CH₃CHO+H₂COO may also be enhanced for trajectories initiated at the syn O₃+propene TS. At the time the trajectories are terminated at 1.6 ps, the ratio of the trajectory and RRKM values of the CH₃CHO+H₂COO product yield is 1.6 if the symmetries of the initiation and dissociation TSs are the same and 0.6 if their symmetries are different. There are coherences in the intramolecular energy flow, which depend on molozonide’s symmetry (i.e., anti or syn). This symmetry related dynamics is not completely understood, but it is clearly related to the non-RRKM dynamics for anti↔syn isomerization and anti molozonide dissociation to CH₃CHO+H₂COO. Correlations are found between the stretching motions of molozonide, indicative of nonchaotic and non-RRKM dynamics. The non-RRKM dynamics of molozonide dissociation partitions vibration energy to H₂COO that is larger than statistical partitioning. Though the direct dynamics simulations are classical, better agreement is obtained using quantum instead of classical harmonic RRKM theory. This may result from the neglect of anharmonicity in the RRKM calculations, the non-RRKM dynamics of the classical trajectories, or a combination of these two effects. The trajectories suggest that the equilibrium syn/anti molozonide ratio is approximately 1.1–1.2 times larger than that predicted by the harmonic densities of state, indicating an anharmonic correction.