Research in the Computational Biochemistry Group

The computational biochemistry group simulates chemical and biochemical reactions under consideration of environmental effects. We complement experiment and provide answers where experiment alone is not able to do so. We study enzymes, biological receptors, astrochemistry, materials science, and catalysis. Many of the projects make use of the QM/MM method, the combination of quantum mechanics (QM) and empirical force fields (MM).

We develop methods that allow us to investigate these kinds of problems in innovative ways. The program package ChemShell is co-authored by us and we lead the development of the optimization library DL-FIND. Our group extends the capabilities of geometry optimization in systems with many thousand degrees of freedom and developed methods to calculate tunneling processes in large systems as well as free-energy sampling techniques using molecular dynamics.

Method Development

	Umbrella Integration: a novel analysis method for umbrella sampling simulations. Sampling free-energy changes is becoming more and more important in the simulation of large systems. Umbrella Integration allows to derive the free-energy change as well as its statistical error from umbrella sampling simulations. Umbrella Integration, in conjuction with our geometry optimizer DL-FIND is used in our project umbrella sampling simulations in the Collaborative Research Center 716 .
	QM/MM method development: QM treats the chemically active center of a system (enzyme, surface, solid state) with highly accurate quantum mechanical methods, and includes the environment using efficient force field methods. We use the modular package ChemShell for QM/MM simulations. However, there is more to QM/MM than just sticking a QM and an MM code together: we implemented a microiterative QM/MM geometry optimization scheme as well as QM/MM free-energy perturbation.
	Transition-state search, conical intersections, parallel geometry optimization: The PI developed the modular geometry optimization library DL-FIND. It can be interfaced to atomistic simulation codes. We use it in conjunction with ChemShell. This is a collaboration with Daresbury Laboratory, UK.
	Tunneling rates in large systems: Instanton theory allows to calculate the rate of tunneling of atoms in chemical reactions. Since the efficiency of tunneling depends on the width of a barrier as well as its height, the optimal tunneling path (shown in red in the Figure on the left) often differs from the dominant classical path (black).

Applications

	The peptide-bond in the ribosome is formed in an environment of chemically inert substances. We used QM/MM calculations and found out how the ribosome is still able to accelerate the reaction by more than 6 orders of magnitude.
	Signaling of the Epidermal Growth Factor Receptor is induced by ligand binding. This, in turn, induces oligomerization of the receptor. In collaboration with experimentalists (FRET measurements) we investigated the alignment of the receptor on the cell membrane. This induces changes in the ligand binding affinity.
	Catalytic mechanism of nitrogenase: Nitrogenase is able to break the strongest covalent bond in nature: the N-N triple bond in dinitrogen. We investigated how the enzyme manages this extraordinary task by means of density functional (DFT) calculations.