The static and dynamic properties of matter depend largely on its inherent heterogeneity in the mass, charge, and spin distributions. Excitations within and coupling of matter to its environment would be expected to exhibit spatial and temporal dependences. Because matter is assembled from individual atoms and molecules, a viable approach in obtaining a basic understanding starts by examining excitations at different length scales from single atoms to molecules and interactions driving their self-assembly. Inelastic electron tunneling spectroscopy (IETS) and microscopy with a scanning tunneling microscope (STM) provides versatile measurement of the excitations within and between molecules adsorbed on a solid surface with sub-Ångstróm resolution. This talk illustrates by three examples the use of STM-IETS to probe the nature of the chemical bond in molecular structure and intermolecular interactions, exchange interaction and spin-vibration coupling in single magnetic molecules, and single molecule vibration and dynamics in the joint space-time domain.