Modeling two-dimensional infrared spectroscopy of hydrogen bonded systems

The focus of this thesis is to study the dynamics of hydrogen bonds using computational simulations with the aim to reveal the properties of molecular structures. Hydrogen bonds are chemical bonds, but, unlike other bonds, they can break and form very fast while having enough strength to hold a system together. One example of the importance of hydrogen bonds is proteins where long chains of aminoacids are folded up into functional structures largely determined by these bonds. This interaction has an average length of 0.15 nanometer, and a duration (lifetime) in the order of picoseconds. Comparing with the human scale this bond is one million times smaller than a grain of sand, and its lifetime is in the order of a trillionth of a second. To measure how fast dynamical changes occur, femtosecond time-resolved spectroscopy methods were invented. In other words, we can capture in real time the evolution of a system even if fast changes are occurring. These studies can be performed with the aid of computers, which allow us to see more of the microscopic world. Thus, overcoming experimental limitations. Each of the studied hydrogen bonding systems shows specific properties of hydrogen bonds. Remarkably one of the presented studies shows that some liquids organize due to hydrogen bonding structures, and this information can be used to mimic very labile protein structures with important biological functions.