Molecular dynamics view on matrix isolation

Abstract

Ability to identify different molecules is one of key goals in chemistry. A common modern way is to identify molecules based on their vibrations that can be detected by infrared spectroscopy or vibrational Raman spectroscopy. This is the way how molecules are identified in matrix isolation experiments, where individual molecules or molecule clusters are enclosed in solid noble gas or nitrogen matrix, an inert environment that allows long term storage of highly reactive molecules and radicals. Surrounding matrix changes the infrared signal of the molecules enclosed within, by changing the shape of observed vibrational transtions and possibly causing extra peaks to appear. While these rarely prevent identification, it is important to understand where these effects originate, as it gives us information how the matrix atoms are positioned around the embedded molecule(s), called as local site structure. They will give information on how reactions happen in the matrix and where the extra structures in the observed spectra originate. This Thesis introduces a way to calculate these matrix effects based on molecular dynamics. The method also allows modeling of chemical reactions within the matrix. Resulting calculations present novel information about local site structures of certain molecule and some results on dynamical behavior of vibrationally induced reactions. Such insights include answers to some decades old questions on the local structures and their spectroscopic evidences in the experimental investigations. In the future the method presented here, and the suggested future developments are likely to become a standard part of matrix isolation experiments. Such an approach as presented here could open up a new era in matrix isolation field, where the matrix effects appearing and observed in experimental spectra can be consistently understood and the reactions therein may be modeled with good accuracy.