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!

Sampling and QM region are equally important

Quantum-mechanical/molecular-mechanical (QM/MM) methods are essential to the study of metalloproteins, but the relative importance of sampling and degree of QM treatment in achieving quantitative predictions is poorly understood. We study the relative magnitude of configurational and QM-region sensitivity of energetic and electronic properties in a representative Zn2+ metal binding site of a DNA methyltransferase. To quantify property variations, we analyze snapshots extracted from 250 ns of molecular dynamics simulation.

Predicting experimental spin states with an ANN

Determination of ground-state spins of open-shell transition metal complexes is critical to understanding catalytic and materials properties but also challenging with approximate electronic structure methods. As an alternative approach, we demonstrate how structure alone can be used to guide assignment of ground-state spin from experimentally determined crystal structures of transition metal complexes. We first identify the limits of distance-based heuristics from distributions of metal–ligand bond lengths of over 2,000 unique mononuclear Fe(II)/Fe(III) transition metal complexes.

Accelerating practical materials design

The accelerated discovery of materials for real world applications requires the achievement of multiple design objectives. The multi-dimensional nature of the search necessitates exploration of multi-million compound libraries over which even density-functional theory (DFT) screening is intractable. Machine learning (ML, e.g., artificial neural network, ANN, or Gaussian process, GP) models for this task are limited by training data availability and predictive uncertainty quantification (UQ).

DFT density delocalization error on the PES

For approximate density functional theory (DFT) to be useful in catalytic applications of transition metal complexes, modeling strategies must simultaneously address electronic, geometric, and energetic properties of the relevant species. We show that for representative transition metal triatomics (MO2, where M = Cr, Mn, Fe, Co, or Ni) and related diatomics the incorporation of Hartree–Fock (HF) exchange in most cases improves the properties of the Born–Oppenheimer potential energy surface (PES) with respect to accurate experimental or CCSD(T) references.

Improving DFT descriptions of surface chemistry

Approximate, semi-local density functional theory (DFT) suffers from delocalization error that can lead to a paradoxical model of catalytic surfaces that both overbind adsorbates yet are also too stable. We investigate the effect of two widely applied approaches for delocalization error correction, i) affordable DFT+U (i.e., semi-local DFT augmented with a Hubbard U) and ii) hybrid functionals with an admixture of Hartree-Fock (HF) exchange, on surface and adsorbate energies across a range of rutile transition metal oxides widely studied for their promise as water splitting catalysts.

Machine learning spin-state-dependent catalysis

Metal–oxo moieties are important catalytic intermediates in the selective partial oxidation of hydrocarbons and in water splitting. Stable metal–oxo species have reactive properties that vary depending on the spin state of the metal, complicating the development of structure–property relationships. To overcome these challenges, we train machine-learning (ML) models capable of predicting metal–oxo formation energies across a range of first-row metals, oxidation states, and spin states.

Improved uncertainty quantification for discovery

Machine learning (ML) models, such as artificial neural networks, have emerged as a complement to high-throughput screening, enabling characterization of new compounds in seconds instead of hours. The promise of ML models to enable large-scale, chemical space exploration can only be realized if it is straightforward to identify when molecules and materials are outside the model’s domain of applicability.

Enumeration for de novo inorganic chemistry

Despite being attractive targets for functional materials, the discovery of transition metal complexes with high-throughput computational screening is challenged by the amount of feasible coordination numbers, spin states, or oxidation states and the potentially large sizes of ligands. To overcome these limitations, we take inspiration from organic chemistry where full enumeration of neutral, closed shell molecules under the constraint of size has enriched discovery efforts.

Universal QM features of methyltransferases

Methyltransferases (MTases) are among the most ubiquitous regulatory enzymes in the cell, catalyzing gene signaling, protein repair, neurotransmitter regulation, and natural product biosynthesis. Despite being extensively investigated, competing enzymatic enhancement mechanisms have been suggested, ranging from structural methyl group C–H···X hydrogen bonds (HBs) to electrostatic- and charge-transfer-driven stabilization of the transition state (TS). No broad conclusion can be reached because each study is typically carried out on a single MTase and associated substrate.

WIRES Outlook on the future of ML

As machine learning has matured, it has opened a new frontier in theoretical and computational chemistry by offering the promise of simultaneous paradigm shifts in accuracy and efficiency. Nowhere is this advance more needed, but also more challenging to achieve, than in the discovery of open shell transition metal complexes where localized d or f electrons exhibit variable bonding that is challenging to capture even with the most computationally demanding methods.

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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: