M.Sc Thesis

M.Sc StudentBen Shir Herbet Irina
SubjectCucurbituril Based Complexes as Components of Molecular
DepartmentDepartment of Chemistry
Supervisor PROFESSOR EMERITUS Ehud Keinan


In light of the worldwide trend towards miniaturization of macroscopic systems down to the molecular scale, the design and synthesis of molecular machines is of particular significance.

Our long term goal is the rational design and synthesis of rotaxane-type, low-friction rotary motors. These systems consist of a linear component, such as a polyalkyne rod, which is terminated by two bulky anchor groups, and a macrocyclic component, such as the cucurbituril (CB[6]) cavitand (Scheme 1).

Scheme 1: General synthesis of CB[6].

 The Cucurbit[6]uril (CB) is a macrocyclic cavitand that able to host molecules and cations. The construction of the linear axle on the basis of a polyalkyne chain is expected to provide frictionless motion due to the floatation of the CB wheel on repulsive interactions with the polyalkyne rod.

Scheme 2: List of polyalkyne diamines.

Several polyalkynyl diamines (Scheme 2) and their binding properties to CB[6] were characterized using X-ray crystallography, microcalorimetry and NMR.

The crystal structures show that the diacetylene rod indeed floats at the center of CB. Several hydrogen-bonded water molecules, as well as the counteranions and the ammonium cations, are positioned near the polar CB portals.

Isothermal Titration Calorimetry (ITC) was used for measurement of binding constants between CB[6] and the diamine ligands. The binding constants were found to be within the same order of magnitude as the reference ligand, 7 (Ka ~105).

Host-guest inclusion complexe was investigated by multi-nuclear solid-state and solution NMR spectroscopies. Assignment of the 13C NMR resonances utilized both solid-state and solution NMR techniques. The solid-state NMR results provide clear experimental evidence that the molecular mobility of the guest exceeds that of the host, basing on greater cross-polarization efficiency, significantly weaker 13C-1H dipole-dipole interaction the methylene moiety of the guest revealed by interrupted decoupling experiments and different 13C T1’s.

2H NMR spectroscopy the free deuterated ligands revealed fast molecular motion. Line-shape analysis was preformed and fast rotation of ammonium group over two axles was concluded. 2H NMR study of CB[6] complexes with these ligands identified an efficient anisotropy averaging due to the fast molecular motion. This molecular motion could arise ether from the enhanced dynamics of a ligand molecule inside CB[6], from motion of ordered water molecules in the crystal, or from both. Further experiments, including alternative sample preparation techniques and varied temperature NMR, as well as computational methods, could shed more light on the dynamics of these molecular rotors.