Doctoral Dissertations
Date of Award
5-2005
Degree Type
Dissertation
Degree Name
Doctor of Philosophy
Major
Chemistry
Major Professor
John F. C. Turner
Committee Members
Crag E. Barnes, Fred M. Schell, Claudia J. Rawn, Chick C. Wilson, Bryan Chakoumakos
Abstract
The purpose of this study was two fold. The determination of hydrogen atom positions by X-ray diffraction methods is widely underused. With advances in instrument and computing technology, the use of X-ray diffraction experiments to accurately image the electron density associated with a hydrogen bond has become feasible. Secondly, general crystallographic computing programs analyze diffraction data by employing a spherical atom model. However, no such atom can be defined solely by a sphere when bound in a molecule. The use of spherical harmonics to model diffraction data enables a more complete description of the electron density in a molecular system. The use of these types of programs has allowed a detailed analysis of a variety of both hydrogen bonded and non-hydrogen bonded system.
This dissertation details the experimental information for charge density and hydrogen bonding studies. The experimental results are analyzed in depth to yield a more complete understanding of a variety of bonding motifs. In some cases, the DFT calculations were performed to augment the experimental results. A series of other experimental components are added to yield a more complete structural model of each molecular system.
Chapter one presents a solid background to X-ray diffraction and the solid state. The information presented in the chapter describes the development of X-ray diffraction, various techniques and the experimental methods available to model diffraction data. Chapter one also develops the basic concepts for understanding the crystalline sold state.
Chapter two gives a detailed introduction to hydrogen bonding and the use of diffraction technique to model the electron and nuclear density as well as define the distribution of these densities in a three-center four-electron bond. The first molecule analyzed is urotropine-N-oxide∙formic acid, which consists of a short, strong, symmetric hydrogen bond. Variable temperature X-ray diffraction studies were used to model the total electron density in the hydrogen bond through the use of Fourier difference maps, while neutron diffraction experiments were used to confirm the proton position in the hydrogen bond. The second system analyzed was para-iodobenzoic acid. Variable temperature X-ray diffraction experiments revealed a split-site population of the electron density associated with the proton position, as is evident by the use of difference Fourier maps.
Chapter three contains the detailed charge density analysis of a material containing a short, strong, asymmetric hydrogen bond, namely cobaltocenium 3,5 bis(trifluoromethyl)phenoxide 3,5-bis(trifluoromethyl)phenol. High resolution X-ray diffraction data were collected to give insight into the chemical bonding both in the hydrogen bond as well as in the organometallic segment.
Chapter four focuses on the charge density studies on a novel heterocyclic alkene, 1,2,3,4,5,6,7,8-octahydro-2a,4a,6a,8a-tetraaza-cyclopenta[fg]acenaphthylene. Accurate determination of the electron density in this system demonstrates a delocalization of the electron density on the p orbitals on nitrogen over the π system.
Chapter five is a detailed experimental section for all material covered in this body of work.
Recommended Citation
Nygren, Cara Lynn, "Experimental studies of intra- and intermolecular chemical structure. " PhD diss., University of Tennessee, 2005.
https://trace.tennessee.edu/utk_graddiss/4372