The Tokmakoff group uses ultrafast vibrational spectroscopy to study the molecular dynamics of chemical reactions in solution and biological processes. We are interested in revealing the time-scale and mechanism by which the hydrogen bond network of water changes, the mechanism of protein folding; how the dynamical nature of water’s hydrogen bonds influence processes such as charge transfer, hydrophobicity, and self-assembly; how hydrogen bonding mediates proton transfer; and the details of molecular recognition, interaction, and binding. These questions all involve understanding the details of competing non-covalent interactions, such as repulsion, electrostatics, and hydrogen bonding. Our aim is to reveal the few dominant variables that capture the relevant chemistry for the system, and thereby gain insight into the appropriate reaction coordinate for chemical and biological processes.

Our experimental approach is to develop and use structure-sensitive femtosecond vibrational spectroscopies to follow the time-evolution of molecular structure. The most sensitive and broadly applicable tool is two-dimensional infrared spectroscopy, which we use to capture information on transient molecular structure and structural variation.  Our experiments are complemented by theoretical work on nonlinear spectroscopy, statistical mechanical modeling of dynamics and relaxation, and molecular dynamics computer simulations. More details of our work are described on our web site.

REPRESENTATIVE PUBLICATIONS

• “Coherent 2D IR Spectroscopy: Molecular structure and dynamics in solution,” M. Khalil, N. Demirdöven and A. Tokmakoff, Journal of Physical Chemistry A, 107 (2003) 5258.
• “Hydrogen bonds in liquid water are broken only fleetingly,” J. D. Eaves*, J. J. Loparo*, C. J. Fecko, S. T. Roberts, A. Tokmakoff and P. L. Geissler, Proceedings of the National Academy of Sciences, USA, 102 (2005) 13019.
• “Amide I two-dimensional infrared spectroscopy of proteins,” Ziad Ganim, Hoi Sung Chung, Adam W. Smith, Lauren P. DeFlores, Kevin C. Jones, and Andrei Tokmakoff, Accounts of Chemical Research, (2008).
• “Conformational changes during the nanosecond to millisecond unfolding of ubiquitin,” Hoi Sung Chung, Munira Khalil, Adam W. Smith, Ziad Ganim and Andrei Tokmakoff, Proceedings of the National Academy of Sciences, USA, 102 (2005) 612.
• “Transient 2D IR spectroscopy of ubiquitin unfolding dynamics,” Hoi Sung Chung*, Ziad Ganim*, Kevin C. Jones, and Andrei Tokmakoff, Proceedings of the National Academy of Sciences, USA, 104 (2007) 14237.
• “Water penetration into protein secondary structure revealed by hydrogen-deuterium exchange 2D IR spectroscopy,” Lauren P. DeFlores and Andrei Tokmakoff, Journal of the American Chemical Society, 128 (2006) 16520.
• “Probing local structural events in β-hairpin unfolding with transient nonlinear infrared spectroscopy ,” Adam W. Smith and Andrei Tokmakoff, Angewandte Chemie, International Edition, 46 (2007) 7984.