Inelastic neutron scattering and quantum mechanical calculations of polymorphic organic crystals
Date of Award
Doctor of Philosophy (PhD)
Neutron scattering, Organic crystals, Polymorphic crystals, Glycine
Chemistry | Physical Chemistry | Physical Sciences and Mathematics
This research focuses on obtaining vibrational spectra from organic systems using inelastic neutron scattering (INS) and its reproducibility when comparing experimental data to quantum mechanical calculations via single molecule and solid state density functional theory (DFT). This information allows the investigation of hydrogen bonding polymorph thermodynamics. Other techniques, such as X-ray diffraction and terahertz (THz) spectroscopy are employed in order to further investigate phenomena of interest.
In particular, there are four different organic systems investigated in this research. The first two are aromatic hydrocarbons, triphenylene and azulene, where interest is focused on the bonding structure of the molecule upon packing. As well as, two systems that represent increasing interest in hydrogen bonded polymorphic interactions, a complex between 4-methylpyridine and pentachlorophenol (4-MPPCP) and three polymorphs of glycine.
The research regarding triphenylene provides information into a highly symmetric molecule (D 3h ) that reduces its symmetry upon packing into a lower symmetry lattice site in its monoclinic crystal structure (C 1 ). INS and solid state DMol 3 vibrational spectra support the lack of symmetry in the molecule in the crystal. It is found that a single triphenylene molecule in its crystal structure has asymmetric bond length deviations from D 3h and that these deviations are not induced by crystal packing forces which therefore means these deviations are not real. It is possible that the unequal bonds in D 3h symmetry only appear unequal because of the zero point thermal motion. It is also found that the bond lengths differ in a random way to support DMol 3 calculations providing a more accurate description of the bond lengths than X-ray diffraction when the X-ray diffraction crystal structure is provided as a starting point. Further studies using other Mills-Nixon type molecules are needed to confirm a trend in DFT bond length description. The same type of investigation is needed on different types of molecules (ie: non Mills-Nixon) to see if DFT also provides better bond lengths when the diffraction structure is used as a starting point.
Azulene continues to elude definitive single molecule and crystal structure determination. INS, THz spectroscopy and DFT calculations are performed in this research to obtain the crystal structure. Previous research concludes there are two molecules per unit cell which is represented by room temperature X-ray diffraction as if there were two azulene molecules superimposed on each site. This suggests a thermodynamically favorable 180° in plane rotation at room temperature, an even distribution of parallel and antiparallel configurations or predominantly parallel azulenes in small domains with the domain direction being random in orientation. This work continues to be a work in progress, however THz spectroscopy in combination with INS and DMol3 suggests the parallel configuration is lower in energy than the antiparallel configuration.
Two of the three polymorphs of glycine, α and γ, are extensively investigated in this research by INS and solid state DFT, DMol 3 . The third polymorph of glycine, β, has been difficult to prepare and converts to the α form when cooled; it is investigated by DMol 3 methods only. The INS data reveals differences in the anharmonic -NH 3 region of the polymorphs that are related to thermodynamics. This research has uncovered increasing isotopomeric polymorphism upon deuteration of the amino group and induced stress. γ-Glycine-ND 3 is stable under stress, while α-glycine-ND 3 converts to γ-glycine-ND 3 upon grinding and cooling. The thermodynamics of the system is also investigated. Previous research suggested α-glycine to be more stable than γ-glycine. However, it has recently been determined that γ-glycine is lower in energy than α-glycine. Calculations reported in the literature support α-glycine having a lower lattice energy than γ-glycine; therefore, this research attempts to explain why the difference occurs, how to keep track of it when performing future studies, and how to obtain the proper answer for this particular system. In short, when calculating the energies of different polymorphic forms, the zero point energy (ZPE) of the polymorphs must be taken into account. The ZPE difference calculated for γ-α glycine is 162.5 cm -1 or 1.94 kJ/mol. While this may seem alarmingly large, a proper method to calculate the difference in energies of the polymorphs is necessary, such as molecular mechanics. The ZPE difference for α-glcine-ND 3 and γ-glycine ND 3 is 135.7 cm -1 . Additional ZPE differences are reported in Chapter 5. The contribution of vibrational energy to the ZPE should not be ignored when considering polymorph stability.
4-MPPCP is known to exhibit isotopomeric polymorphism upon deuteration of the hydrogen bond between the molecules. (Abstract shortened by UMI.)
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Rivera, Sharon, "Inelastic neutron scattering and quantum mechanical calculations of polymorphic organic crystals" (2008). Chemistry - Dissertations. 29.