The boundaries between traditional disciplines are eroding, and some of the most exciting and important discoveries are taking place at the intersections of historically distinct fields. Our group embraces this shift by investigating fundamental questions of chemical and biological structure and dynamics from an essentially physical perspective. Biological systems such as proteins, nucleic acids, membranes, cells, and organelles present spectacular challenges to our understanding of chemical dynamics and structure in complicated heterogeneous environments. Most protein molecules have reasonably well-defined structures to the extent that they can be characterized by X-ray diffraction and NMR spectroscopy. These structures, though, must necessarily respond to their environments, which can range from surfaces to solids to water to oily membranes. Globular proteins, for example, are nearly solid density, and yet to function they must often be flexible. One of the distinguishing features of many biological molecules is that they are not neatly categorized as solids or liquids, but rather something in between.
In order to push towards a detailed microscopic description of these hard-to-classify biological systems, we are developing an array of optical spectroscopy tools that will complement the already commonly used X-ray and NMR techniques. We rely heavily on state-of-the-art femtosecond (1 fs = 10 -15 sec) laser pulses. Through various nonlinear optical processes we are able to generate significantly intense pulses at any wavelength from the ultraviolet to the infrared. Our main approach is to take advantage of the rich chemical specificity and well-developed intuition of vibrational transitions in order to track the course of chemical events. Vibrational transitions can be excited through infrared absorption, and the information content relates directly to the displacement of atoms, thus limiting our reliance on the complicated dynamics of electronic transitions.
Our experimental approach is based on the workhorse of multidimensional IR spectroscopy. This new technique allows us to find out how different motions are coupled together. In particular we are using these powerful new spectroscopic probes to address nonequilibrium dynamical questions. Phototriggered chemical reactions often take place on the femtosecond to picosecond time scale, and by using multidimensional IR as a probe we can directly map the reactant vibrations to those of the product, giving a bond-by-bond view of the reaction's progress with femtosecond resolution.
J. A. Dunbar, E. J. Arthur, A. M. White, K. J. Kubarych “Ultrafast 2D-IR and Simulation Investigations of Preferential Solvation and Cosolvent Exchange Dynamics,” J. Phys. Chem. B 119 (2015) 6271-6279.
L. M. Kiefer, J. T. King, K. J. Kubarych, “Multidimensional Ultrafast Snapshots of Carbon Dioxide Photocatalyst Dynamics,” Acc. Chem. Res. 48 (2015) 1123-1130.
L. M. Kiefer, K. J. Kubarych, “Solvent-Dependent Dynamics of a Series of Rhenium Photo-Activated Catalysts Measured with Ultrafast 2DIR,” J. Phys. Chem. A 119 (2015) 959-965.
L. M. Kiefer, J. T. King, K. J. Kubarych, “Equilibrium Excited State Dynamics of a Photo-Activated Catalyst Measured with Ultrafast Transient 2DIR,” J. Phys. Chem. B 118 (2014) 9853-9860.
J. T. King, E. J. Arthur, C. L. Brooks, K. J. Kubarych, “Crowding induced collective hydration of biological macromolecules over extended distances,” J. Am. Chem. Soc. 136 (2014) 188-194.
D. G. Osborne, J. A. Dunbar, J. G. Lapping, A. M. White, K. J. Kubarych, “Site-Specific Measurements of Lipid Membrane Interfacial Water Dynamics with Multidimensional Infrared Spectroscopy,” J. Phys. Chem. B 117 (2013) 15407-15414.
D. G. Osborne, J. T. King, J. A. Dunbar, A. M. White, K. J. Kubarych, “Ultrafast 2DIR Probe of a Host-Guest Inclusion Complex: Structural and Dynamical Constraints of Nanoconfinement,” J. Chem. Phys. 138 (2013) 144501.
J. T. King, K. J. Kubarych, “Site-specific coupling of hydration water and protein flexibility studied in solution with ultrafast 2D-IR spectroscopy,” J. Am. Chem. Soc. 134 (2012) 18705-18712.