iMOS Master: Infrared Spectroscopy of Highly Reactive Aggregates in…

Infrared Spectroscopy of Highly Reactive Aggregates in Helium Nanodroplets

Daniel Leicht

In my master thesis I investigated the infrared (i.e. the vibrational) spectrum of helium solvated allyl radicals. The radicals were produced by pyrolysis of 1,5-hexadiene and trapped in superfluid helium nanodroplets. The helium droplet beam was overlapped by the output of a tunable infrared laser to obtain the infrared spectrum. After obtaining the experimental infrared spectrum ab initio calculations were carried out as a basis of the spectral assignment. Different DFT methods were compared with respect to their viability since open-shell species often pose a problem in such computations.

Figure_DL

Spin density surface of the allyl radical.

Based on the quantum chemical calculations five CH-stretching bands were assigned to the observed spectral features. The rotational fine-structure of the recorded spectrum was investigated as well. Due to the very low droplet temperature of 0.37 K, also weakly bound complexes can be studied using this technique. As an outlook I proposed an investigation of the allyl:HCl complex, which has been carried out and published at a later time.

After finishing his iMOS Master’s thesis Daniel Leicht started his PhD research in the group of Prof. Havenith.

Link to  Master course in Molecular Sciences and Simulation (iMOS) at Ruhr-University Bochum

iMOS Master: Correlation of solvent fluctuations with dynamics of…

Correlation of solvent fluctuations with dynamics of simple ligand binding to biomolecular surfaces

Christopher Päslack

Image1_ChristopherWe   used   classical   atomistic   molecular   dynamics   (MD) simulations  to investigate how and to what extend collective protein-water motions affect the dynamics of ligand binding to a biomolecular surface. Therefore, the free energy surface (i.e. potential  of mean  force,  PMF)  along  the  reaction  coordinate was determined via Umbrella Sampling and based on that we obtained static one-body friction/diffusion profiles of the ligand along  the  reaction  coordinate.  The  reaction  coordinate  was defined  as  the distance  between  the  hydrophobic  patch  of ubiquitin and the ligand (LJ-spere).

We could show that dynamics of the ligand are affected both by the binding affinity in terms of the PMF as well as by internal motions  of  the  protein.  Furthermore,  the  ligand couples  to solvent  fluctuations  in  the  vicinity  of  the  hydrophobic  binding patch of ubiquitin.

Folie_Christ.1024_768After finishing his iMOS Master’s thesis Christopher Päslack started his PhD research in the group of Prof. Lars Schäfer.

Link to  Master course in Molecular Sciences and Simulation (iMOS) at Ruhr-University Bochum