Studies of single molecule bond rupture: Understanding interactions in biological and nanoscale materials

The reversibility of weak bonds is critical for small devices, biological or synthetic, to work. Nano-scale sensors and biological machinery rely on the ability to bind a target, effect some change, and then release the target to repeat the process again. Traditionally, experiments of molecular bonding are performed on ensembles of interacting species to extract chemical kinetics and equilibrium free energies. But with the advent of ultra-sensitive mechanical sensing devices, such as the Atomic Force Microscope (AFM), we are now able to study single bonds between a pair of interacting species, a technique formally called Dynamic Force Spectroscopy (DFS).; In this dissertation I discuss experiments on molecular bond rupture that have expanded our understanding of the way small molecules interact. I will first, give an overview of the basic physics that describes small molecule behavior in solution, and follow with theoretical models for DFS. The remainder of the dissertation will focus on specific applications of bond rupture in different systems. These experiments include: Measuring the interaction between individual functional groups with the sidewalls of carbon nanotubes; Measurements of 1, 2, and 3 bonds between the cancer marker Mucin1 and its antibody; The first demonstration and analysis of the equilibrium plateau in DFS; Studying the mechanics of binding and compaction between DNA and a mitochondrial packaging protein abf2p using optical tweezers.