Department of Chemistry & Biochemistry

Biography

2019-present

Associate Dean for Interdisciplinary Studies and Faculty Development, University of Notre Dame

2017-present

Professor, University of Notre Dame

2011-present

Associate Professor, University of Notre Dame

2005-2011

Assistant Professor, University of Notre Dame

2002-2005

Postdoctoral Research Associate, University of Wisconsin

2001

Ph.D. in Chemistry, Yale University

1997

Sc.B. in Chemistry, Brown University

Selected Awards

2020

Thomas P. Madden Award

2019, 2012

Rev. Edmund P. Joyce, C.S.C. Award for Excellence in Undergraduate Teaching

2016

Fellow, American Chemical Society

2015

Director of Graduate Studies, University of Notre Dame

2011

Kavli Fellow, National Academies of Science and Alexander von Humboldt Foundation

2009

Sloan Research Fellowship

2009

NSF CAREER Award

2005

Camille and Henry Dreyfus New Faculty Award

2003-2005

Ruth L. Kirchstein National Research Service Award

Curriculum Vitae

Research Interests

Dynamics of water at DNA interfaces: The objective of this project is to characterize water dynamics at DNA interfaces. While it is well established that hydration is essential to the stability and function of biomolecules, its role as an active player in important biological processes, such as allosteric regulation, folding, reaction mechanisms, and molecular recognition, is not fully understood. We are investigating the solvation response in DNA of Hoechst 33258, a minor-groove binder, and Coumarin 102 a guanine-cytosine base-pair analogue. Decompositions of the computed solvation response into contributions from water, DNA, and ions will greatly aid in the interpretation of time-dependent fluorescence measurements for these systems.

Infrared probes of biomolecular structure and dynamics: We are developing robust computational protocols for the simulation of infrared spectra of site-specific carbon-deuterium (C-D) and nitrile (C≡N) probes in biological contexts. The objective of these studies is to connect the information contained in the experimentally measured infrared absorption spectra to local conformational structure and flexibility. We are also ultimately interested in developing methods to calculate chemical-exchange two-dimensional infrared spectra to aid in the interpretation of novel experiments that employ C≡N labels as probes of hydrogen-bond dynamics. Such probes could be used to measure local hydration dynamics at biomolecular interfaces.

Solvation dynmaics in ionic liquids: Ionic liquids have attracted tremendous attention because of their attractive properties as environmentally friendly alternatives to volatile organic solvents. Despite tremendous experimental and theoretical effort, solvation dynamics in ionic liquids is not nearly as well understood as in traditional polar solvents. By applying the methodologies developed to study solvation dynamics in complex biological environments, we are elucidating motions present in ionic liquids and how they influence preferential solvation and reactivity.

Nonadiabatic transition path sampling: We are developing a new theoretical and computational framework for the study of charge transfer reactions in the condensed-phase. This new method, nonadiabatic transition path sampling (NAPS), combines features of transition path sampling (TPS) and the molecular dynamics with quantum transitions (MDQT) surface-hopping algorithm. By combining TPS with MDQT, chemical reactions involving multiple electronic states that are dominated by rare but important events can be studied within the powerful TPS framework. By focusing specifically on reactive trajectories, TPS can infer detailed reaction mechanisms for processes whose timescales are outside of the range of direct simulation.

Recent Publications

• De Oliveira, D. M., Bredt, A. J., Miller, T. C., Corcelli, S. A., Ben-Amotz, D. "Spectroscopic and Structural Characterization of Water-Shared Ion-Pairs in Aqueous Sodium and Lithium Hydroxide" 2021 Journal of Physical Chemistry B, 125 (5), pp. 1439-1446. DOI:10.1021/acs.jpcb.0c10564.
• Baiz, C. R., Błasiak, B., Bredenbeck, J., Cho, M., Choi, J. -., Corcelli, S. A., Dijkstra, A. G., Feng, C. -., Garrett-Roe, S., Ge, N. -., Hanson-Heine, M. W. D., Hirst, J. D., Jansen, T. L. C., Kwac, K., Kubarych, K. J., Londergan, C. H., Maekawa, H., Reppert, M., Saito, S., Roy, S., Skinner, J. L., Stock, G., Straub, J. E., Thielges, M. C., Tominaga, K., Tokmakoff, A., Torii, H., Wang, L., Webb, L. J., Zanni, M. T. "Vibrational Spectroscopic Map, Vibrational Spectroscopy, and Intermolecular Interaction" 2020 Chemical Reviews, 120 (15), pp. 7152-7218. DOI:10.1021/acs.chemrev.9b00813.
• Cracchiolo, O. M., Geremia, D. K., Corcelli, S. A., Serrano, A. L. "Hydrogen Bond Exchange and Ca²⁺Binding of Aqueous N-Methylacetamide Revealed by 2DIR Spectroscopy" 2020 Journal of Physical Chemistry B, 124 (32), pp. 6947-6954. DOI:10.1021/acs.jpcb.0c02444.
• 4. Silski-Devlin, A. M., Petersen, J. P., Liu, J., Corcelli, S. A., Kandel, S. A. "Methylisatin Structural Isomers Have Different Kinetic Pathways to Self-Assembly" 2020 Journal of Physical Chemistry C, 124 (32), pp. 17717-17725. DOI:10.1021/acs.jpcc.0c05456.
• 5. Zhang, X. -., Brantley, S. L., Corcelli, S. A., Tokmakoff, A. "DNA minor-groove binder Hoechst 33258 destabilizes base-pairing adjacent to its binding site" 2020 Communications Biology, 3 (1), DOI:10.1038/s42003-020-01241-4.
• 6. Kananenka, A. A., Yao, K., Corcelli, S. A., Skinner, J. L. "Machine Learning for Vibrational Spectroscopic Maps" 2019 Journal of Chemical Theory and Computation, 15 (12), pp. 6850-6858. DOI:10.1021/acs.jctc.9b00698.