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Open Positions

Simulation of Nonlinear Infrared Spectra of [NiFe] Hydrogenase Models to Understand Cofactor-Environment Interactions (Master's Project)

[NiFe] Hydrogenases are complex metalloenzymes that catalyse the cleavage and evolution of molecular hydrogen, an ideally clean fuel that releases large amounts of energy but no greenhouse gases upon combustion. To accomplish this kinetically demanding reaction, [NiFe] hydrogenases feature a unique catalytic site containing one nickel (Ni) and one iron (Fe) ion, the latter of which is coordinated by three biologically uncommon ligands, one carbon monoxide (CO) and two cyanides (CN). These diatomics ligands are highly important, because they (1) tune the electronic properties of the catalytic metal site and (2) can serve as site-selective and highly sensitive structural probes in infrared (IR) spectroscopic studies. As a consequence, IR spectroscopy has long been used as a key technique in hydrogenase research, but electronic and structural insights by conventional IR absorption experiments are limited.

To overcome this limitation, we have recently introduced advanced variants of IR spectroscopy like IRpump-IRprobe and two-dimensional techniques to hydrogenase research. These techniques provide otherwise inaccessible insights into molecular bonding, equilibrium dynamics, energy transfer phenomena, coherent atom motions, and interactions of the catalytic metal site with the functional protein environment. So far, however, understanding of the experimental data is limited by their inherent complexity and a lack of suitable theoretical strategies for modelling the spectroscopic properties.

The offered Master’s project will address these challenges by calculating nonlinear IR spectra of a synthetic model complex that mimics the unique Fe(CO)(CN)2 motif of [NiFe] hydrogenases and its spectroscopic properties. This approach has two advantages: First, the molecular model lacks the complexity of the enzymatic analogue. Second, influences of the protein environment can be systematically studied by exploring the impact of different strongly or weakly interacting solvents. Using density functional theory and vibrational perturbation theory together with explicit and implicit solvent modelling, this project will complement experimental studies, thereby contributing greatly to the understanding of [NiFe] hydrogenases and the unique spectroscopic properties of metal carbonyl and cyanido complexes in general.

The suitable candidate should have a background in physics or physical/theoretical chemistry. General chemical knowledge and previous experience with electronic structure calculations, vibrational analysis, and/or IR spectroscopy is highly beneficial. In case of questions, don’t hesitate to send a message to Marius Horch.

M. Horch, J. Schoknecht, S. L. D. Wrathall, G. M. Greetham, O. Lenz, N. T. Hunt, “Understanding the Structure and Dynamics of Hydrogenases by Ultrafast and Two-Dimensional Infrared Spectroscopy“ Chem. Sci. 2019, 10, 8981–8989.

https://doi.org/10.1039/C9SC02851J


Insights Into Unusual Fluorine-Mediated Hydrogen Bonds by Computational Nonlinear Infrared Spectroscopy (Master's Project)

Fluorinated compounds play a key role in pure and applied chemistry, including various applications in medicine, pharmacy, and material science. This key role is related to the unique properties of fluorine, e.g. its high electronegativity and small atomic radius, which lead to fluorine-specific interactions like unusual hydrogen bonding and the formation of hydrogen-bond networks. For instance, the strongest hydrogen bond known to date is formed in bifluoride, which features three-centre two-electron bonding at the tip of covalent and hydrogen bonding.

Understanding unusual hydrogen bonding involving fluorinated compounds requires spectroscopic techniques that provide insights into the potential energy surfaces (PES) of the relevant molecular adducts. Nonlinear infrared (IR) spectroscopic techniques yield detailed information on the shape of the PES by probing transitions between multiple vibrational energy levels of a molecule. In the case of bifluoride, such studies have recently revealed a highly anharmonic PES with strong interactions between different vibrational degrees of freedom and a seamless transition between strongly anharmonic and superharmonic bond potentials.

Understanding these phenomena, the associated nonlinear IR spectra, and the relation of these aspects to the unique bonding properties of fluorinated compounds requires the simulation of vibrational transitions beyond the harmonic approximation and a detailed modelling of intermolecular interactions – within and between individual hydrogen-bonded adducts. The offered Master’s project will address these challenges by using density functional theory, vibrational perturbation theory, and a combination of explicit and implicit solvent modelling. Focussing on hydrogen fluoride adducts of small organic molecules, these theoretical studies will guide planned experiments and provide a basis for future work dedicated to synthetic and bio-inspired catalysts featuring fluorine-mediated hydrogen-bond networks.

The suitable candidate should have a background in physics or physical/theoretical chemistry. General chemical knowledge and previous experience with electronic structure calculations, vibrational analysis, and/or IR spectroscopy is highly beneficial. In case of questions, don’t hesitate to send a message to Marius Horch.

B. Dereka, Q. Yu, N. H. C. Lewis, W. B. Carpenter, J. L. Bowman, A. Tokmakoff, “Crossover from Hydrogen to Chemical Bonding” Science 2021, 371, 160–164.

https://doi.org/10.1126/science.abe1951


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