|Ph.D Thesis||Department of Chemistry|
|Supervisors:||Assoc. Prof. Eichen Yoav|
|Assoc. Prof. Peskin Uri|
Processes in a single molecule within a well defined molecular environment are of fundamental and technological interest. Such processes are often controlled by the supramolecular environment. In this research new approaches were developed for quantifying these effects for chemical reactions taking place in a crystalline environment and for molecules in metal-molecule-metal junctions.
In chapter A thermal ring closures in the crystals of N-(propyl)-nitrospiropyran are studied. Experimental investigation of the ring closure revealed the existence of two different first order processes, which were attributed to two non equivalent molecules in the crystal. A compact theoretical model was developed for modeling the differences in the molecular environments in the two processes, and its effect on the measured rates.
In chapter B the relative stability of three tautomeric states of 1,3-bis(pyridin-2-yl)propan-2-one: ketopyridine(CH), enolpyridine(OH), and ketoenamine(NH), was studied. While the CH tautomer is the most stable in solution, only the other tautomers are observed in the crystalline state. Strong temperature dependence of the populations of these two tautomers was found by temperature dependent X-ray diffractometery. This observation was rationalized by electronic structure calculations for compact models of the crystal, suggesting that a dimeric packing of the molecules reduces the free energy differences between the tautomeric states in consistency with the measured thermal populations.
In chapter C’ a theoretical formulation of molecular conductance is introduced. Electronic resonance energies were calculated combining standard basis set calculations with complex absorbing potentials, and effective single-electron potentials, calculated by novel Poisson solver. This approach was demonstrated for two-electron model systems.