Kevin Alan Walker and Dr. David Dearden, Chemistry and Biochemistry
Nanotechnology offers the potential of creating machines the size of molecules. Such machines have limitless possibilities in numerous fields: chemistry, computer science, technology, and medicine, to name a few. Molecular machines could be instrumental in creating computers millions of times faster than our present computers. These machines could catalyze or inhibit a variety of chemical reactions. Such machines could be instrumental in altering and fixing an individual’s genetic makeup to successfully combat disease and illness. However, because nanotechnology is a relatively new field of study, science has yet to scratch the surface of the implications molecular machines may have in the future. Dr. David Dearden’s research group is currently utilizing molecular studies performed in the gas phase to better understand molecular machine components and probe the fundamental processes behind the working of these devices. As a member of Dr. Dearden’s research group, I exclusively focused on the ability of cucurbiturils to form molecular machine components, specifically pseudorotaxanes.
Before I delve into a discussion of my research results, let me briefly explain what cucurbiturils are, what pseudorotaxanes are, and how gas phase studies are performed. Cucurbiturils are molecules in the shape of hollow containers; their shape is comparable to a pumpkin with both ends cut off. The basic building block of cucurbiturils is two fused pentagonal rings with carbonyl oxygens extending from both ends of the fused ring system. Cucurbiturils vary in size depending on the number of these building blocks, and the numerical name reflects the size, i.e. cucurbituril is composed of five building blocks.
Rotaxanes are molecules with a “wheel” and “axle” structure – a relatively linear molecule threads through the center of a cyclic molecule. Rotaxanes have bulky groups at the ends of the linear axle molecule that prevents the cyclic wheel molecule from coming off. Pseudorotaxanes are similar to rotaxanes, but pseudorotaxanes lack the bulky groups at the ends of the axle molecule. How does the structure stay together? Other interactions between the two molecules prevent the wheel from coming off. In the case of cucurbiturils, the carbonyl oxygens extending from the ends of the building blocks provide sufficient binding to hold the structure together.
Most chemical reactions are studied in solution. This often presents variables that may affect the results and interfere with data. Studying reactions and obtaining data in the gas phase removes variables that are present in solution. In my research cucurbiturils of various size were mixed with 1,4-diaminobutane (DAB) in solution where the DAB was ionized for labeling purposes. The dissolved ions were then sprayed into the gas phase to remove extraneous material. The ions were trapped in an electromagnetic test tube. A mass spectrum presenting a series of peaks corresponding to the masses of the tube’s contents was produced. Data from gas phase experiments using mass spectrometry suggest that DAB and cucurbit[n]uril (n=5, 6, 7, and 8) form two types of complexes that are dependent on the cucurbituril size.
Cucurbiturils produce only one peak in the mass spectrum corresponding to one cucurbituril and two singly-protonated DABs bound together. When these complexes were isolated and subjected to collision-induced dissociation experiments, the DABs were easily removed and/or displaced by other molecules. This led to the conclusion that the two singly-protonated DAB molecules bind to the carbonyl rims of the cucurbituril, with the hydrocarbon tails pointing away from the cucurbituril. The relatively weak binding that occurs between the two molecules in this conformation allows for easy dissociation of the complex.
Like cucurbiturils, cucurbiturils also produce only one peak in the mass spectrum. However, the mass of this peak represents the cucurbituril bound to a single doubly-protonated DAB. Collision-induced dissociation attempts failed to dissociate this complex, leading to the conclusion that much stronger binding occurs in this complex than in the cucurbituril-DAB complex. This strong binding occurs because the complex is a pseudorotaxane. The cucurbituril is sufficiently large for the DAB to thread through the cavity. The protonated ends of the DAB bind with the carbonyl oxygens around the rims of the cavity opening – it is this binding that holds the complex together in a wheel and axle conformation.
Cucurbit[7 and 8]urils produced peaks on the mass spectrum corresponding to both conformations: one doubly-protonated DAB threaded through the cavity and two singlyprotonated DABs bound to the rims of the cucurbituril. Dr. Dearden is continuing research with the larger cucurbiturils to determine the exact conformation of these complexes.
In conclusion, it is apparent that the cucurbituril cavity is too small for the DAB to enter. However, the other cucurbiturils have sufficiently large cavities to allow the diammonium ion to enter and create a pseudorotaxane. Pseudorotaxanes are one component of larger molecular machines. Understanding that these molecules are capable of forming such components is an essential step in developing the ability to create molecular machines capable of greatly enhancing our lives.