Publications

An up-to-date list of all my publications can be accessed at ORCiD: 0000-0002-4243-6078

Highlights

T. J. Summers, J. A. Sobrinho, A. de Bettencourt-Dias, S. D. Kelly, J. L. Fulton, and D. C. Cantu, Solution Structures of Europium Terpyridyl Complexes with Nitrate and Triflate Counterions in Acetonitrile, Inorg. Chem (2023)

Lanthanide–ligand complexes are key components of technological applications, and their properties depend on their structures in the solution phase, which are challenging to resolve experimentally or computationally. The coordination structure of the Eu³⁺ ion in different coordination environments in acetonitrile is examined using ab initio molecular dynamics (AIMD) simulations and extended X-ray absorption fine structure (EXAFS) spectroscopy. AIMD simulations are conducted for the solvated Eu³⁺ ion in acetonitrile, both with or without a terpyridyl ligand, and in the presence of either triflate or nitrate counterions. EXAFS spectra are calculated directly from AIMD simulations and then compared to experimentally measured EXAFS spectra. In acetonitrile solution, both nitrate and triflate anions are shown to coordinate directly to the Eu³⁺ ion forming either ten- or eight-coordinate solvent complexes where the counterions are binding as bidentate or monodentate structures, respectively. Coordination of a terpyridyl ligand to the Eu³⁺ ion limits the available binding sites for the solvent and anions. In certain cases, the terpyridyl ligand excludes any solvent binding and limits the number of coordinated anions. The solution structure of the Eu-terpyridyl complex with nitrate counterions is shown to have a similar arrangement of Eu³⁺ coordinating molecules as the crystal structure. This study illustrates how a combination of AIMD and EXAFS can be used to determine how ligands, solvent, and counterions coordinate with the lanthanide ions in solution.
DOI: 10.1021/acs.inorgchem.3c00199

T. J. Summers, Q. Cheng, M. A. Palma, D.-T. Pham, D. K. Kelso III, C. E. Webster, and N. J. DeYonker, Cheminformatic Quantum Mechanical Enzyme Model Design: a Catechol-O-methyltransferase Case Study , Biophys. J. (2021)

To accurately simulate the inner workings of an enzyme active site with quantum mechanics (QM), not only must the reactive species be included in the model but also important surrounding residues, solvent, or coenzymes involved in crafting the microenvironment. Our lab has been developing the Residue Interaction Network Residue Selector (RINRUS) toolkit to utilize interatomic contact network information for automated, rational residue selection and QM-cluster model generation. Starting from an x-ray crystal structure of catechol-O-methyltransferase, RINRUS was used to construct a series of QM-cluster models. The reactant, product, and transition state of the methyl transfer reaction were computed for a total of 550 models, and the resulting free energies of activation and reaction were used to evaluate model convergence. RINRUS-designed models with only 200–300 atoms are shown to converge. RINRUS will serve as a cornerstone for improved and automated cheminformatics-based enzyme model design.
DOI: 10.1016/j.bpj.2021.07.029

T. J. Summers, B. P. Daniel, Q. Cheng, and N. J. DeYonker, Quantifying Inter-Residue Contacts through Interaction Energies , J. Chem. Inf. Model. (2019)

The validity and accuracy of protein modeling is dependent on constructing models that account for the inter-residue interactions crucial for protein structure and function. Residue interaction networks derived from interatomic van der Waals contacts have previously demonstrated usefulness toward designing protein models, but there has not yet been evidence of a connection between network-predicted interaction strength and quantitative interaction energies. This work evaluates the intraprotein contact networks of five proteins against ab initio interaction energies computed using symmetry-adapted perturbation theory. To more appropriately capture the local chemistry of the protein, we deviate from traditional protein network analysis to redefine the interacting nodes in terms of main chain and side chain functional groups rather than complete amino acids. While there is no simple correspondence between the features of the contact network and actual interaction strength, random forest models constructed from minimal structural, network, and chemical descriptors are capable of accurately predicting interaction energy. The results of this work serve as a foundation for the development and improvement of functional group-based contact networks.
DOI: 10.1021/acs.jcim.9b00804

Cover Articles

Open Access Articles and Preprints

Article	DOI
T. J. Summers, R. Hemmati, J. E. Miller, D. A. Agbaglo, Q. Cheng, and N. J. DeYonker. Evaluating the Active Site-Substrate Interplay Between X-ray Crystal Structure and Molecular Dynamics in Chorismate Mutase, J. Chem. Phys. (2023)	10.1063/5.0127106
T. J. Summers, Q. Cheng, M. A. Palma, D.-T. Pham, D. K. Kelso III, C. E. Webster, and N. J. DeYonker. Cheminformatic Quantum Mechanical Enzyme Model Design: a Catechol-O-methyltransferase Case Study, Biophys. J. (2021)	10.1016/j.bpj.2021.07.029
T. J. Summers, H. Tupkar, T. M. Ozvat, Z. Tregillus, K. A. Miller, and N. J. DeYonker. Computational Insight into the Rope-skipping Isomerization of Diarylether Cyclophanes, Symmetry (2021)	10.3390/sym13112127