Molecular structure determination: solid-state NMR applications
Abstract
Solid-state Nuclear Magnetic Resonance (ssNMR) has become one of the best
techniques to determine molecular structure via inter/intra-molecular interactions.
Unlike the well-known solution state NMR, solid-state NMR primarily elucidates the
structural information by chemical shift anisotropy and dipolar coupling regardless of
the solubility, crystallinity, and amorphousness of the target samples. This method has
been applied in studying lyophilized samples, non-crystalline solids, insoluble
aggregates, and biopolymer frozen solutions to determine their physical, chemical, and
biological properties. This dissertation focuses on the applications of a variety of techniques of ssNMR
spectroscopy in combination with other techniques to understand the molecular
structures of substances of different kinds. The theoretical bases and the experimental
introduction are reviewed first, and then experimental design and results are provided
for the three projects separately: (1) The molecular structure of thin-film Boron carbide
and the intermediate “X” in the PECVD fabrication process are elucidated mainly
through ssNMR. Both13C and 11B direct excitation and cross polarization (CP)
experiments, correlation experiments (13C-1H and 11B-1H), and 13C-11B distance measurements (REDOR) are applied to obtain connectivity information. FT-IR,
elemental analysis, and ab initio calculations are used in addition to confirm the NMR
results. The structure model of the intermediate “X” is proposed which is distinguished
from the structure of the thin-film boron carbide, however, the structure model of the
thin-film has not yet generated due to the weak signal from the natural abundance
product. (2) The non-fibrillar and fibrillar C-terminal and K3 fragments of beta 2
microglobulin are evaluated. The homonuclear distances (CT-fpRFDR) measurements
for the singly isotopically labeled protein samples are determined by comparing NMR
results of the fibrillized fragments with the beta amyloid (G9V12) measurement
standard. The fibril formation information is suggested by TEM, UV-Vis, and
Fluorescence spectra. The CT and K3 fragments of beta 2 microglobulin are proved to
form fibrils via parallel beta sheet structure. (3) The binding sites and/or the relative
orientation of the dissociation drug of beta amyloid aggregates are investigated by
ssNMR. Heteronuclear measurements (13C-2H REDOR) are mainly used to determine the
distance between the deuterium label on the drug and the carbon label on Aβ1-42. The
method upper limit is confirmed by lab made distance measurement standards,anthracene derivatives. However, the negative result is obtained from the triple labeled
protein and singly labeled drug complex is not able to locate the drug-protein bound
positions clearly. Therefore, different labeling schemes are also proposed for further
confirm the assumption of binding sites.
Table of Contents
Introduction -- NMR basics -- Solid-state NMR experiments -- Structure determination of amorphous hydrogenated boron carbides -- Structure determination of beta-2 microglobulin protein fragments -- Structure determination of drug bound beta amyloid oligomer complex -- Appendix I. ab initio calculations and results -- Appendix II. REDOR measurement confirmation
Degree
Ph.D.