The Faculty


Ultrafast vibrational spectroscopy to study the molecular dynamics of chemical reactions in solution and biological processes


Born: Sacramento, CA, 1967.
Cal. State Univ., Sacramento, B.S., 1989
Stanford University, M.S. 1992
Stanford University, Ph.D. 1995
A.v.Humboldt Postdoctoral Fellow, Technical Univ. Munich, 1995
NSF Postdoctoral Fellow, Univ. Chicago (1996-7) and UC Berkeley (1997-8)
Massachusetts Institute of Technology, Professor, 1998-2012.
University of Chicago, Professor, 2013-present


  • 2012 Ernest Plyler Prize (American Physical Society)
  • 2009 Fellow, Optical Society of America
  • 2002 National Fresenius Award (Phi Lambda Upsilon)
  • 2002 Alfred P. Sloan Fellowship
  • 2002 Coblentz Award
  • 2000 David and Lucile Packard Fellowship
  • 1999 Research Corporation Research Innovation Award

Research Interests

The Tokmakoff group uses ultrafast vibrational spectroscopy to study the molecular dynamics of chemical reactions in solution and biological processes. We seek to provide insight into the mechanism by which the hydrogen bond network of water changes, the mechanism of protein and DNA aptamer 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; the conformational preferences of disordered proteins, and the details of molecular recognition, interaction, and binding with proteins and DNA. 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 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 ultrafast vibrational spectroscopy as a tool for following the time-evolution of molecular structure. Our primary method is two-dimensional infrared spectroscopy, which we use to capture information on transient molecular structure and structural variation. This work involves the design and construction of new ultrafast infrared optics and spectrometers, and the development and use of mixed quantum-classical computational modeling tools to extract structural and dynamic information. The details of our work are described on our web site.

Selected References

“An Introduction to Protein 2D IR Spectroscopy,” C. Baiz, M. Reppert, A. Tokmakoff, in Ultrafast Infrared Vibrational Spectroscopy, ed. by M. D. Fayer (Taylor & Francis, New York).

“Structural Rearrangements in Water Viewed Through Two-Dimensional Infrared Spectroscopy,” S. T. Roberts, K. Ramasesha, and A. Tokmakoff, Acc. Chem. Res., 42 (2009) 1239-1249.

“Amide I two-dimensional infrared spectroscopy of proteins,” Z. Ganim, H. S. Chung, A. W. Smith, L. P. DeFlores, K. C. Jones, and A.Tokmakoff, Acc. Chem. Res., 41 (2008) 432-441.

“Identifying residual structure in intrinsically disordered systems: A 2D IR spectroscopic study of the GVGXPGVG peptide,” J. Lessing, S. Roy, M. Reppert, M. Baer, D. Marx, T.L.C.Jansen, J. Knoester, and A.Tokmakoff, J. Am. Chem. Soc., 134 (2012) 5032–5035.

“Identification of lactam-lactim tautomers of aromatic heterocycles in aqueous solution using 2D IR spectroscopy,” C. S. Peng and A.Tokmakoff, J.Phys.Chem.Lett., 3 (2012) 3302–3306.

“Ultrafast 2D IR Anisotropy of Water Reveals Reorientation during Hydrogen-Bond Switching,” K. Ramasesha, S. T. Roberts, R. A. Nicodemus, A. Mandal and A.Tokmakoff, J. Chem. Phys., 135 (2011) 054509.

“A Source for Ultrafast Continuum Infrared and Terahertz Radiation,” Poul B. Petersen and Andrei Tokmakoff, Optics Lett., 35 (2010) 1962-1964.

“Melting of a β-hairpin peptide using isotope-edited 2D IR spectroscopy and simulations,” A. W. Smith, J. Lessing, Z. Ganim, C. S. Peng, A. Tokmakoff, S. Roy, T. L. C. Jansen, and J. Knoester, J. Phys. Chem. B, 114 (2010) 10913–10924.

“Insulin Dimer Dissociation and Unfolding Revealed by Amide I Two-Dimensional Infrared Spectroscopy,” Ziad Ganim, Kevin C. Jones, and Andrei Tokmakoff, Phys.Chem. Chem. Phys., 12, (2010) 3579–3588.

“Observation of a Zundel-like transition state during proton transfer in aqueous hydroxide solutions,” S. T. Roberts, P. B. Petersen, K. Ramasesha, A. Tokmakoff, I.S. Ufimtsev, and T. J. Martinez, Proc. Nat’l Acad. Sci., USA, 106 (2009) 15154-15159.