Diatomic Molecules as Spectroscopic Probes for Protein Interiors With recent advances in both, experiment and computer simulations, it has become possible to investigate the dynamics of small molecules in heterogeneous environments. This is of particular interest because small ligands can be used as an experimental probe to investigate the interior - especially electrical fields - of proteins. Atomistic Simulations are an established computational method to investigate gas- and condensed-phase systems. Recent extensions to force fields incorporate more details in better representing electrostatic interactions and allow to more quantitatively understand particular processes. In this seminar I will describe some of these methods and their use to understand the energetics and vibrational spectroscopy of diatomic spectroscopic probes in biological and physico-chemical systems. In particular, I will show how and to what extent results from infrared spectroscopy can be related to three dimensional structure. This is a difficult and challenging problem in the characterization of complex systems which can be addressed by using a combination of experiment and computation.