Recent work: Positioning and reactivity in SyrB2

Reactivity in SyrB2

SyrB2 is a non-heme Fe(II) halogenase in the syringomycin biosynthetic pathway that chlorinates a methyl group of L-Thr. Halogenation at typically unreactive alkanes is important as a source for mimics useful in drug design and to enhance understanding of how antibiotics are synthesized naturally. Importantly, substrate delivery to the SyrB2 active site is dictated by whether or not the substrate can bind to a long, prosthetic phosphopantetheine tether. In that sense, the catalytic mechanism is no longer defined simply by the energetics of the substrate and the catalyst but also by the mechanical properties of phosphopantetheine.  In order to elucidate these structure-function relationships at a quantum mechanical level, we have extended previous work that only focused on a free substrate to now look at how placement of phosphopantetheine and substrate with respect to the catalytic center alters reaction energetics.  We elucidate energy profiles that, when used in concert with biochemical observations, can help us to determine where the substrate is most likely to be when it is functionalized in the enzyme. Future work will focus on developing large-scale QM/MM studies of the full enzyme complex.

 

Past work: Properties of confined water

Spectroscopic properties of confined salt water

X-ray absorption spectroscopy is a valuable tool for examining the local electronic and geometric structural properties of materials.  We simulate theoretical x-ray absorption spectra for K-edge oxygen in a variety of salt solutions (e.g. MgCl2, CaCl2, and NaCl) to elucidate how ions alter the hydrogen bonding of water in a charge and species-specific manner.

Quantum-ESPRESSO Tutorials

Quantum Chemistry with Quantum-ESPRESSO

Quantum Chemistry for Quantum-ESPRESSO tutorials have been running roughly monthly for the past two years. They have covered a wide range of topics, and we'll be migrating some of the best ones to this new site over the next couple of months. In the meantime, you can look at the old tutorial site here.

Past work: Unexpected spin profile of TBrPP-Co

Unexpected spin and charge transfer of TBrPP-Co

The properties of molecules on solid surfaces are strongly modulated by the extent of charge transfer between the molecule and the surface. However, self-interaction errors in DFT often restrict us from obtaining qualitatively and quantitatively accurate descriptions of charge transfer. We employed DFT+U to provide quantitative descriptions of the spin density of tetrabromophenyl cobalt porphyrins on Cu(111) surface that was consistent with experimental observations.

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About Us

The Kulik group focuses on the development and application of new electronic structure methods and atomistic simulations tools in the broad area of catalysis.

Our Interests

We are interested in transition metal chemistry, with applications from biological systems (i.e. enzymes) to nonbiological applications in surface science and molecular catalysis.

Our Focus

A key focus of our group is to understand mechanistic features of complex catalysts and to facilitate and develop tools for computationally driven design.

Contact Us

Questions or comments? Let us know! Contact Dr. Kulik: