Computational Spectroscopy and Reaction Dynamics

Abstract

Physico- and bio-chemical processes on the femto- to picosecond time scale are ideally suited to be investigated with all-atom simulations. They include, amongst others, vibrational relaxation, ligand migration in sterically demanding environments (proteins, ices), or vibrational spectra. By comparing with experimental data, the results can be used to obtain an understanding of the mechanisms underlying the observations. Furthermore, most of these processes are sensitive to the intermolecular interactions. Therefore, detailed refinement of such interaction potentials is possible. Keywords: Computational spectroscopy · Molecular dynamics simulations · Reaction dynamicsThe classification of fast and ultrafast time scales in atoms and molecules depends to some extent on the process and property considered. For example, the electronic degrees of freedom change on considerably more rapid time scales than the nuclear motions. This is the basis of the Born-Oppenheimer approximation which is valid in many cases. In proteins, on the other hand, vibrations are much more rapid than changes in the secondary structure. Typical time scales for electronic motion in molecules are attoseconds, whereas vibrations are associated with femto-and pico-second time scales. In the following, ultrafast time scales in molecular systems -which are at the focus of the NCCR Molecular and Ultrafast Science and Technology (MUST) -will be associated with atto-to picosecond processes.Understanding ultrafast processes in molecular systems requires multi-faceted approaches, including experiment, theory and computation. A typical example is the vibrational relaxation of a solvated diatomic molecule, e.g. cyanide (CN − ) in water. [1,2] Although time scales of vibrational relaxation can be reliably measured using modern laser techniques, understanding the relaxation mechanism in molecular detail is much more difficult as it includes coupling and energy transfer to solvent modes. Another example is allostery which is the regulation of a protein by binding a small molecule at the allosteric site. An allosteric activator will enhance the activity of the protein. The most widely known but still incompletely understood allosteric protein is hemoglobin. Here, four binding sites for the ligand (O 2 ) exist. Binding of the first O 2 molecule increases the protein's affinity for binding the second O 2 molecule, etc. However, the molecular details underlying the enhanced affinity for subsequent O 2 ligands is still unexplained. Finally, one purpose of high-resolution spectroscopy is to understand the bonding pattern and geometrical details of a molecule by recording and analyzing spectroscopic signatures. As the size of the molecule grows, directly determining the structure of the molecule from the spectroscopic data becomes increasingly difficult. Even more difficult is the situation in proteins where spectroscopic features of small probe molecules such as CO or NO can be recorded but the splitting patterns of the vibrational spectra are difficult ...