Research in the Kulik group

Research in the Kulik group leverages computational modeling to aid the discovery of new materials and mechanisms. Our group uses first-principles modeling to unearth fundamental aspects of structure-property relationships in catalysts and materials. By taking a computational approach, we carry out studies that allow us to make connections across a wide range of catalytic systems from biological enzymes to emerging heterogeneous single-atom catalysts. We develop computational software and machine learning models that accelerate the discovery of new materials and design rules. This approach enables the prediction of new materials properties in seconds, the exploration of million-compound design spaces, and the identification of design rules and exceptions that go beyond intuition. To ensure the predictive power of our approach, our group develops new methods to increase the accuracy of density functional theory especially for materials with challenging electronic structure such as transition metal complexes and solids.

Read more about our group’s work in the recently published papers below!

Amorphous nanostructures from AIMD

Semiconducting quantum dots (QDs) have a broad number of applications due to their unique size- and shape- dependent electronic and optical properties. When people use first-principles simulations to study structure-property relationships in QDs, the experimental bulk crystal structure is the most commonly used model. However, experiments show QDs may possess distinct, amorphous structures.

Exploring the role of exchange in transition metal complex properties

Spin crossover complexes are transition metal complexes that undergo a transition in spin or magnetic moment when a stimulus such as increasing temperature, pressure, or light is applied. Many catalysts of interest also possess multiple closely spaced spin states. In all of these cases, robust prediction of ground state spin is a profound challenge for almost all electronic structure methods, especially density functional theory. One challenge for DFT is self-interaction error, in which electrons are repelled by their own image.

Studying depolymerization dynamics of lignin from first-principles

Lignin is a highly heterogeneous biopolymer that makes up about 35% of biomass by weight. While lignin monomers are relatively homogeneous aromatic compounds, e.g. coniferyl alcohol, they link together to form at least 8 different kinds of linkages. In order to depolymerize lignin into useful products, it is necessary to understand how it can be broken down in order to turn it into valuable products.

Understanding nanoparticle growth

Indium phosphide (InP) quantum dots (QDs) have a wide range of applications due to their unique size- and shape-dependent electronic and optical properties. In this project, we aim to understand InP QDs core structure and surface ligand morphology through ab initio simulations. We investigate the interaction between indium phosphide nanoparticle surfaces and precursors using techniques such as ab initio molecular dynamics.

Catalyst design and discovery

Efficient design and discovery of catalysts is central to solving modern challenges in energy and resource utilization. Effective catalyst design, however, is a multi-step process that includes the generation of candidate catalytic materials followed by evaluation and modification of their properties with the ultimate goal of maximizing the catalytic activity for a specific reaction or reaction network. Often these improvements are carried out in an ad hoc manner. Instead, we are developing systematic workflows that streamline this process by combining first principles calculations, chemical intuition, cheminformatics and evaluation of catalytic properties. Here, we target single-site catalysts that provide exquisite control and selectivity but are supported on hetereogeneous substrates, allowing us to overcome the challenges associated with separation and recovery of molecular catalysts.

Recent work: Quantum chemistry for proteins

Proteins are large biological macromolecules that play a pivotal role in the function of all living things.  Because of the large size of proteins (most are at least several hundred to thousands of atoms in size), study of their structure and function has been largely limited to empirical force fields.  While these force fields can reproduce many basic structural properties of proteins as observed experimentally by NMR or X-ray crystallography, typical force fields cannot accurately describe bond-rearrangement, polarization, and charge transfer, all of which are key for understanding protein function.  We recently investigated whether GPU-accelerated quantum chemistry approaches could provide additional insight into protein structure-function relationships by examining a vast test set of over 55 proteins with a variety of DFT, HF, and force field methods.  

Recent work: DFT+U(R) for accurate energetics

Despite the importance of transition metals in a variety of biological and inorganic systems, density functional theory calculations often fail quantitatively in describing these systems.  We first showed that a DFT+U approach improves upon standard density-functionals in transition metal systems of both small and large size over both standard pure and hybrid functionals. However, one major shortcoming of this approach remains: we must use a calculated average of the values of Hubbard U when comparing points along a potential energy surface.

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.

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.


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: