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The main goal of our research proposal is to simulate self-assembly of covalent organic frameworks containing boroxine cores, formed by condensation of boronic acid monomers. This past summer, Lorenzo Bautista used density functional theory calculations on small molecules to obtain parameters required by the Reactive Force Field (ReaxFF) that can make and break chemical bonds. (Conventional force fields cannot do this!) Lorenzo was able to finish all the quantum calculations required (bond stretching and compression, angle bending, and torsional rotations, proton transfers). He is now partially through the difficult work of parameterizing the force field. We decided to divide this gargantuan task into two stages. Lorenzo has almost completed the first stage involving getting first pass reasonable values for the equilibrium geometries and bond dissociation energies of boroxines, and then carefully parameterizing the torsional energies in the B-C bonds. Lorenzo had previously calculated the torsional barriers for rotating these bonds in ortho-substituted phenylboroxines to force the phenyl rings to rotate 90 degrees to the boroxine ring thus placing the steric groups above and below the plane of the ring and protect them from hydrolysis. I expect he will complete the parameterization in the next month and then run molecular dynamics (MD) simulations of these substituted phenylboroxines in water to study the dynamic accessibility of water towards hydrolyzing the boroxine back to its monomeric boronic acids. This semester Lorenzo is enrolled in our Research Methods class that involves substantial writing. His goal will be to write a complete draft of the manuscript for this project, and we expect to submit it in the coming spring (acknowledging PRF support). The second more difficult stage of this project will involve parameterizing the proton transfer reactions for self-assembling boronic acids into boroxines. Lorenzo, is starting his junior year, and is interested in going to graduate school when he graduates in 2011.

This past year, I embarked on a second project involving self-assembly of a covalent-organic framework. This system is based on the trimerization reaction of monomers containing CN groups to form a triazine ring catalyzed by zinc chloride. The architecture of the covalent organic framework, with hexagonal pores, is analogous to the boroxine systems we have been working on thus far. Elizabeth Cummings, who is just starting her senior year, worked on this project last summer and is continuing this work in her last year at USD. She is using density functional theory calculations to elucidate the reaction mechanism (unknown as far as we know). She has also started some preliminary calculations to obtain parameters for a ReaxFF simulation. This project still has far to go before we reach a publishable unit. Elizabeth is planning on enrolling in a masters program in the health sciences before she applies to medical school.

To familiarize ourselves with the ins-and-outs of using ReaxFF to study self-assembly, we embarked on two projects. (1) The self-assembly of antimony trichloride and 1,4-dioxane forms an interpenetrating cubic structure with very weak bonds. We were finally able to finish a full study including parameterization, and running and analyzing many MD simulation trajectories. This project took ~2.5 years. Keaton Tomlin (graduated in 2008) began the project and Rowena Daly (graduating this December) was able to finish the project. The finished manuscript is now in press (we got the galley proofs two days ago) and acknowledges PRF support. (2) The self-assembly of titanium and benzene forms multi-decker sandwich complexes rather than rice-ball complexes. Calvin Schneider worked the last 1.5 years to parameterize ReaxFF (this was a very difficult task due to the non-directional nature of metal-metal bonds and the non-covalent metal-benzene bonds). He was able to complete the parameterization and start running MD simulations (and has some promising results). Calvin graduated this past May and is continuing to work on this project part-time. He has just started graduated school at UC-Irvine doing computational research in neuroscience. I am going to see how far he gets in this project by December, and will probably have another student finish up his project next spring. I expect to be able to submit a manuscript (acknowledging PRF support) sometime next summer.

Hadley Krizner is just starting her senior year. She started doing research with me in the summer of 2008 and in early 2009 she finished writing up a manuscript detailing her calculations on all the reactions (hydration, dimerization, ring closure) of methylglyoxal, an important molecule in the study of secondary organic aerosol formation. The manuscript, acknowledging PRF support, was published earlier this year in the Journal of Physical Chemistry A. Hadley is clearly interested in graduate school and scientific research as part of her future career. The manuscript, acknowledging PRF support, was published earlier this year in the Journal of Physical Chemistry A. Hadley did not work for me this summer because I persuaded her to apply for a fellowship allowing her to get a summer research experience in a large research university so that she knows what she’s getting into when she goes to graduate school. She did research at UCSD in the laboratory of Mark Thiemens doing experimental isotope work in atmospheric chemistry. (She has good hands in lab.) Hadley is continuing to work with me in her senior year, calculating the reactions of glyoxal and selected amino acids to help explain interesting observations made by our experimental collaborators.

Three of the students mentioned were funded by PRF this past summer: Lorenzo Bautista, Elizabeth Cummings and Rowena Daly. To date our group has four manuscripts published or in press that acknowledge PRF support. I am expecting at least two more manuscripts to be completed in the next year that will acknowledge PRF support. I’ve had a fantastic time mentoring my students through the research process, and am grateful for the funding received through this ACS-PRF grant. I plan to use the remaining funds to bring my students to the Spring ACS meeting in San Francisco this March.