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Author ORCID Identifier

Document Type

Open Access Dissertation

Degree Name

Doctor of Philosophy (PhD)

Degree Program


Year Degree Awarded


Month Degree Awarded


First Advisor

Scott M. Auerbach

Subject Categories

Physical Chemistry


Our research attention is focused on the development of new fuel cell membrane materials and new zeolites which improve biomass conversion rate to meet the increasing demand of renewable and sustainable energy. We have simulated the dynamics of amphiprotic groups (pyrazole, imidazole, 1,2,3-triazole, 1,2,4-triazole, and tetrazole, acetic acid, formic acid, sulfuric acid, and phosphoric acid) as neat liquids and tethered via linkers to aliphatic backbones, to determine how tethering and varying functional groups affect hydrogen bond networks and reorientation dynamics, both factors thought to influence proton conduction. We used the DL_Poly_2 molecular dynamics code with the GAFF force field to simulate tethered systems over the temperature range 200−900 K, and to simulate the corresponding neat liquids under liquid state temperatures at standard pressure. We computed hydrogen-bond cluster sizes; orientational order parameters and orientational correlation functions associated with functional groups, linkers, and backbones; and time scales and activation energies associated with orientational randomization. Regarding neat phosphoric acid, we find that anomalously large hydrogen-bond clusters provide a neutral-system signature of the high experimental proton conductivity in neat phosphoric acid. Regarding tethered oligomer systems, all exhibited a liquid to glassy-solid transition upon cooling, with the formic-, and acetic-based oligomers retaining liquid behavior to relatively low temperatures (~400 K); while azoles- and phosphonic-oligomers formed glassy solids around 500-600 K; and sulfonic-pentamers lost motion around 900 K as evidenced by orientational order parameters and correlation functions. Hydrogen bond cluster sizes in tethered phosphonic acid (T ≤ 500 K) remain orders of magnitude above all other tethered systems, suggesting tethered phosphonic oligomers as promising targets for new PEMs. Tethering the azoles was generally found to produce hydrogen-bond cluster sizes similar to those in untethered liquids, and to produce longer hydrogen-bond lifetimes than those in liquids. The simulated rates of functional group reorientation decreased dramatically upon tethering. The activation energies associated with orientational randomization agree well with NMR data for tethered imidazole systems at lower temperatures, and for tethered 1,2,3-triazole systems at both low- and high-temperature ranges. Overall, our simulations corroborate the notion that tethering functional groups dramatically slows the process of reorientation. We found a linear correlation between gas-phase hydrogen-bond energies and tethered-functional-group reorientation barriers for all azoles except for imidazole, which acts as an outlier because of both atomic charges and molecular structure.

We have performed density functional theory (DFT) calculations to investigate the convergence of reaction barriers with respect to zeolite cluster size, for multi-step reactions catalyzed in HZSM-5 zeolite. We have constructed cluster models of HZSM-5 using the delta-cluster approach reported previously by us [ACS Catalysis 5, 2859 (2015)], which systematically treats zeolite confinement using a single neighbor-list radius. We computed barriers for several different reaction types, and with a range of reactant sizes from 2 to 13 heavy (non-hydrogen) atoms, to determine the cluster sizes and neighbor-list radii needed to fully treat zeolite confinement effects. To establish barrier convergence, we studied the acid-zeolite-catalyzed aldol reactions of acetone with aldehydes of increasing size (formaldehyde, furfural, and hydroxymethyl-furfural), modeling the acid-catalyzed aldol reaction in three steps: keto/enol tautomerization of acetone, bimolecular combination between each aldehyde and the enol, and aldol dehydration. We found that the delta cluster neighbor-list radius of 4 Å is sufficient to converge barriers with respect to cluster size for all reaction steps considered, yielding complete treatments of confinement in HZSM-5 with clusters containing up to 99 (Si, Al, O) framework atoms. For comparison, periodic DFT calculations on HZSM-5 include 288 framework atoms, requiring 19 times more CPU time in our head-to-head comparisons on a single processor. The converged acetone/formaldehyde dehydration barrier from our cluster calculations agrees quantitatively with a comparable barrier obtained by Curtiss and coworkers with periodic DFT, showing that cluster calculations can converge properties with respect to system size at a fraction of the cost of periodic DFT. Interestingly, we found that the bulkier, furan-containing aldehydes exhibit faster aldol reactivity because of charge delocalization from their aromatic rings, which significantly speeds up aldol dehydration.