Title

Study of hydrogen bonding properties with ab initio calculations, neutron scattering spectroscopy and 1H NMR

Date of Award

2007

Degree Type

Dissertation

Degree Name

Doctor of Philosophy (PhD)

Department

Biology

Advisor(s)

Bruce S. Hudson

Keywords

Hydrogen bonding, Ab initio calculation, 1H NMR, Neutron scattering spectroscopy, Aggregation, Cooperative hydrogen bonding

Subject Categories

Biology

Abstract

The H-bond is known to be very importance in solid aggregation, molecular biology, and medicine. It is also very important in proteins and nucleic acids and therefore in life-sustaining processes. The understanding and control of non-covalent interactions, such as H-bonding, will be very helpful to the assembly of functional nano-systems with a precision analogous to that found in the natural world. This thesis is to investigate H-bond properties of small organic molecules with neutron scattering spectroscopy (INS), ab initio calculations, and 1 H NMR. I first show the results of the theoretical and experimental study of INS vibrational spectra of a moderate H-bonding system. The calculation methods are correctly used to simulate the vibrational spectra of the system. I also show a detailed study on 1,3-cyclohexanedione (CHD) and its methylated analogues that exhibit cooperative, resonance assisted H-bonding (RAHB) in solid state. INS simulations with hartree fork (HF) and density functional theory (DFT) are carried out for non-deuterated and deuterated species, with results in good agreement with experiment. 1 H NMR experimental methods are used in connection with HF and DFT calculations. The results of gas phase calculations on theoretical energy of a monomer, dimer, and trimer of CHD and its analogues indicate that cooperative behavior is expected with aggregation. Evidence from the comparison of crystal structure with the structure calculated for several aggregates also suggests a basis for such cooperative behavior. Measures of the association equilibria of CHD, however, provide no evidence for cooperativity due to a large effect of the CDCl 3 solvent. Calculations of CHD in CHCl 3 medium using Onsager Spherical Model indicate that the polar solvent has a big effect on the H-bonding equilibrium of CHD. The cooperative energy on going from dimer to trimer is compensated in the free energy by a change in the enthalpy and entropy so the cooperative effect is not reflected in the equilibrium constants. This thesis first solved the problem of the keto-enol equilibrium of CHD and its aggregations in solution. This is a new method that combines both experiment and theory to examine the hydrogen bonding properties of CHD in solution.

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