Computational Studies on Organic Framework Materials as Absorbants and Sensors

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Organic frameworks are a diverse class of crystalline materials with a regular porous structure on the order of nanometers. They include covalent organic frameworks (COFs), which are linked entirely via covalent bonds, and metal organic frameworks (MOFs), which consist of organic units linked via dative bonds to metal ions. Due to their diverse and highly regular porous structures, they have found use in sundry applications including semiconductors, gas storage, purification, chemical sensing, and decontamination. In the studies described hereafter, we study the application of framework materials to a few of these applications. We begin with an investigation of the nucleation and growth mechanisms of a typical COF known as COF-5. This is of interest as crystal sizes, and therefore growth mechanistics, can affect the performance of COFs in semiconductor applications. I performed studies on the stacking behavior, reaction mechanism, and surface diffusion in the system as part of a joint article with Brian Koo. Next, we look at the use of MOFs for detecting nitroaromatic explosives. Many MOFs and COFs have been discovered that exhibit fluorescence quenching in response to trace amounts of nitroaromatic compounds. Although considerable experimental work has been done on the phenomenon, there are surprisingly few computational studies. We use molecular dynamics and density functional theory to investigate binding configurations of picric acid molecules to these materials, and to seek a relationship between these configurations and sensitivity towards picric acid. We then look at a system, consisting of palladium nanocrystals embedded in a MOF, that has shown an unprecedented ability to absorb hydrogen. The hydrogen is primarily absorbed into the palladium crystals, but the phenomenon is enhanced by the surrounding MOF. We investigate the structure of the MOF/Pd interface, and its relationship with absorption enhancement. Although it was already known that the MOF withdraws electron density from the palladium, we found that it also produces a region of negative charge in the palladium that likely contributes to high absorption. Lastly, we look at the applicability of MOFs for the decontamination of chemical warfare agents (CWAs). Although they have been banned in most countries by the Chemical Weapons Convention, CWAs such as sarin are still frequently used in terrorist attacks due to their high toxicity and relative ease of synthesis. Consequently, there is great desire to develop techniques to remove them from the environment. Metal Organic Frameworks have garnered attention for this purpose due to their regular nanoporous structure. We develop a model capable of screening MOFs for this purpose. In the process, we developed a novel kernel function that we show is useful for predicting blood brain barrier penetration and mutagenicity as well.

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COF; framework; kernel; MOF; simulation


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Union Local


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Clancy, Paulette

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Frazier, Peter
Hanrath, Tobias

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Chemical Engineering

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Ph. D., Chemical Engineering

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Doctor of Philosophy

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Government Document




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Attribution-NonCommercial-ShareAlike 4.0 International


dissertation or thesis

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