46700-GB10
Boron-Containing Covalent Organic Frameworks: Simulating Dynamics of Self-Assembly
The goal of our research proposal is to simulate self-assembly of covalent organic frameworks containing boroxine cores, formed by condensation of boronic acid monomers. Such a simulation requires a method that can both handle hundreds to thousands of atoms and make/break covalent bonds. (Most conventional force fields cannot do this.) We have opted to use the Reactive Force Field (ReaxFF) developed by van Duin and co-workers. They have already parameterized terms for C, H, O but lack the parameters for boron. This past summer, two undergraduates (Kelly Nesseth and Lorenzo Bautista) used density functional theory calculations on small molecules to obtain parameters required by ReaxFF. They were able to finish calculating all the bond stretch/compression terms, torsional rotation terms, and most of the angle bend terms. This semester Lorenzo is continuing the project by finishing the angle bend terms, and then calculating the terms required to handle the proton transfers required for the condensation reaction to proceed. Kelly wrote a proposal to the Summer Undergraduate Research Experience (SURE) program funded through the University of San Diego (USD); she was successful and only needed minimal support through PRF. Lorenzo was funded through the SUMR award. Kelly is applying to Pharmacy school so I’m not sure if computational chemistry will be in her future. Lorenzo, however, is only just starting his sophomore year and is continuing this research. He is still interested in going to graduate school.
One offshoot of our proposal was to explore the feasibility of forming heterotrimeric boroxine cores. Based on our prior computational work, we were able to design a system that would favor the heterotrimer over homotrimers in a one-pot reaction with different monomers present. The strategy used was to include an internal Lewis base that would stabilize the boroxine core on one monomer, and to add electron withdrawing groups to the other monomer. The design was successful! Our collaborators were able to synthesize the heterotrimer and characterize it via 1H NMR and x-ray crystallography. Both papers (one mainly experimental with our supporting computational results, the other is the full computational paper exploring the phase space for heterotrimer formation) have either been published or are in press. Most of the calculations were preformed by an undergraduate, Charles Gyselbrecht, this past academic year. I am planning to (1) extend the phase space of heterotrimer formation to include ABC heterotrimers with three different monomers, and (2) find a way to estimate the entropic contribution in solution for these condensation reactions. The entropic contribution is a nagging problem in all small molecule electronic structure calculations involving an implicit solvent, and it is not unique to our system. Charles was unable to continue his research this summer so I used the remaining student stipends to support two excellent students making great progress in projects of interest to PRF.
Calvin Schneider worked for me last Spring and this past summer to parameterize ReaxFF to simulate the self-assembly of metal-benzene complexes. He has finished all the quantum calculations and is now going through the difficult process of conducting a multidimensional parameterization. In the meantime, he has found some interesting trends in how the ground spin states change (due to curve-crossing) as he stretches the metallic bonds. When Calvin first came to USD, he was planning on going to medical school to eventually become a neurosurgeon. Since taking up computational research he has decided to go to graduate school instead and do research in computation and neural networks. In fact, he is taking a whole range of upper division mathematics classes right now in his senior year to prepare himself for graduate school. He is hoping to take his projects to completion (and eventual publication that will acknowledge PRF support) before he graduates, and is continuing his research throughout his final year here.
Hadley Krizner is just starting her junior year. She started doing research with me over the summer and did such a fantastic job that she is now writing up a manuscript to be submitted by the end of the semester. (All the calculations have been completed. I’ve decided to mentor her through the writing process instead of just writing it myself. This work will acknowledge PRF support.) Hadley calculated all the reactions (hydration, dimerization, ring closure) of methylglyoxal, an important molecule in the study of secondary organic aerosol formation, and all the necessary transition states and energy barriers. Hadley is clearly interested in graduate school and scientific research as part of her future career. This semester she will also be calculating the reactions of glyoxal and selected amino acids to help explain interesting observations made by our experimental collaborators.
I’ve had a fantastic time mentoring my students through the research process, and I’m looking forward to shepherding them through this academic year.
