Unallowed Transitions: An Experimental Projection of Practical Knowledge into the Lab Frame

摘要

Chapter 1 is an introduction to me and what I've studied. It describes both the fundamental ideas of physical chemistry as well as a philosophical overview of how I see the sciences and mathematics correlated. It also lays out my major contributions in the fields of nuclear magnetic resonance (NMR) and computational chemistry in addition to acknowledging my time spent working to involve the blind and visually impaired community into the sciences.;Chapter 2 focuses on the relevant theories associated with NMR and computational chemistry. For NMR the early experiments from Stern, Gerlach, Rabi, and others are briefly discussed, and a more rigorous discussion of the mathematics behind the principles behind the scenes is given. Without getting as deeply into mathematics as many other books are already written explicitly for explaining, it is instead mentioned what an actual NMR experimentalist encounters in the lab. This chapter also delves into the ideas and general mechanics behind computational chemistry. The underlying quantum mechanics of a multi-body system is briefly considered and the concepts of utilizing the variational principle to seek out energetic minima are discussed. Also, the real life experience of employing computational chemistry to solve a problem is written to give the reader a reality check into how the science is done these days without most users ever performing multiple integrals and matrix diagonalization by hand.;Chapter 3 is a reworked version of a soon to be submitted manuscript detailing the investigation of the lanthanide doped up-converting nanoparticle phosphor NaY1-x-yYbxEryF4. Solid State NMR was used to investigate the relaxation properties of optical up-converting nanoparticle phosphors doped with various trivalent lanthanide cations. This work probed the Yb3+ - Er3+ interaction which is central to optical up-conversion.;Chapter 4 is the story of the development of AsteriX BVI starting from AsteriX itself as a crawler for the protein databank used to extract individual images, and eventually becoming a free and open platform where anyone, including blind or visually impaired researchers, could generate input structures for computational chemistry experiments. This work was published in the Journal of Computer Aided Molecular Design. The discussion includes how we chose to represent different atom types, bond types, and the difficulties with surface tiling of 3-D objects for eventual 3-D printing. There is also a listing of details regarding the various functions of the software and eventually the development of the Molecular Fabricator itself which is a software implementing an accessible text based input language for accurate 3-D molecule generation for use with Gaussian software packages.;Chapter 5 details the computational investigation of a unique decarboxylation mechanism that appears energetically unfavorable at first. This work was published in the Journal of Natural Products. The most interesting part of the decarboxylation is that it absolutely requires a full carbocationic rearrangement prior to decarboxylation and then it again becomes energetically favorable to return to the original geometry sans carboxylate. There are numerous energies calculated regarding the process which starts with a protonation, and then goes through multiple alkyl shifts, the decarboxylation itself, additional alkyl shifting, and finally a deprotonation event returning the molecule to an overall lower energy state than where it started all to release CO2 from a difficult site. The process ultimately validates the assumption that during the distillation of vetiver oil, zizanoic acid is capable of being converted in high yield to noriso-ziza-5-ene by a mechanism supported by investigations of other similar terpenoid systems and computationally energetic favorability.