Modelling of Spectroscopic and Structural Properties using Molecular Dynamics

The following dissertation is about the study that I performed at the Chemistry Department of the University of Florence and at the European Laboratory for Non- Linear Spectroscopy (LENS) to recover and elucidate structural, dynamical, and spectroscopic molecular features adopting computer simulations. In particular, here ab initio molecular dynamics simulations and time-frequency analysis are the most employed “tools”, in order to have a better understanding of the origins of vibrational features. Hydrogen-bonding is the main type of inter-molecular interaction that can af- fect the vibrational spectra, and occurs in all the systems studied here. It is shown how the hydrogen-bonding usually induces a redshift on the vibrational frequen- cies of the groups engaged in it, and how this redshift nicely correlates with the strength of this type of bond, as obtained from (so-called) “first principles simulations”. While the hydrogen-bond induced redshift is the most common occurrence, I’ve also studied a system where a blueshift can be found. Recovering and ex- plaining this somewhat unusual effect, well established in the literature, required particular computational efforts. Hydrogen-bonding can manifest itself also as a bifurcated interaction between one donor and two acceptor centres. This bifurcated configuration is usually seen just as a very brief intermediate step occurring in water during breaking and cre- ation of “true” hydrogen-bonds, but, in confined water, it has longer lifetimes al- lowing it to be studied by both spectroscopic and computational means. The computational protocols implemented and adopted in this dissertation allow a direct comparison between structural features and vibrational spectrum, highlighting how the formers influence the latter.