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


Distinguished Alumni Service Award, California State University Sacramento  2017

Ahmed Zewail Award in Ultrafast Science and Technology  2016

Ernest Plyler Prize (American Physical Society)  2012

Fellow, Optical Society of America  2009

National Fresenius Award (Phi Lambda Upsilon)  2002

Alfred P. Sloan Fellowship  2002

Coblentz Award  2002

David and Lucile Packard Fellowship  2000

Research Corporation Research Innovation Award  1999

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

Preface: Special Topic on Biological Water,”Gerhard Hummer and Andrei Tokmakoff, J. Chem. Phys., 141 (2014) 22D101-1-2.

“Ultrafast 2D IR spectroscopy of the excess proton in liquid water,” Martin Thämer, Luigi De Marco, Krupa Ramasesha, Aritra Mandal, and Andrei Tokmakoff, Science, 350 (2015) 78–82.

“Anharmonic exciton dynamics and energy dissipation in liquid water from two-dimensional infrared spectroscopy,”Luigi De Marco, Joseph A. Fournier, Martin Thämer, William Carpenter, and Andrei Tokmakoff, J. Chem. Phys., 145 (2016) 094501-1-13.

“The interplay of ion–water and water–water interactions within the hydration shells of nitrate and carbonate directly probed with 2D IR spectroscopy,”J. Am. Chem. Soc., 138 (2016), 9634–9645.

“Ultrafast 2D IR microscopy,” Carlos R. Baiz, Denise Schach, and Andrei Tokmakoff, Opt. Express, 22 (2014) 18724–18735.

“Studying protein–protein binding through T-Jump induced dissociation: Transient 2D IR spectroscopy of insulin dimer,” Xin-Xing Zhang, Kevin C. Jones, Ann Fitzpatrick, Chunte Sam Peng, Chi-Jui Feng, Carlos Baiz, and Andrei Tokmakoff, J. Phys. Chem. B,120 (2016) 5134–5145.

“Sequence dependent mechanism of DNA oligonucleotide dehybridization resolved through infrared spectroscopy,”Paul J. Sanstead, Paul Stevenson, and Andrei Tokmakoff, J. Am. Chem. Soc., Article ASAP.

“Computational amide I 2D IR spectroscopy as a probe of protein structure and dynamics,” Mike Reppert and Andrei Tokmakoff, Annu. Rev. of Phys. Chem., 67 (2016) 359–386.

“Visualizing KcsA conformational changes upon ion binding by atomistic modeling of infrared spectroscopy,”Paul Stevenson, Christoph Götz, Carlos R. Baiz, Jasper Akerboom, Andrei Tokmakoff, and Alipasha Vaziri, J. Phys. Chem. B, 119 (2015), 5824–5831.

“Structural disorder of folded proteins: Isotope-edited 2D IR spectroscopy and Markov state modeling,”Carlos Baiz and Andrei Tokmakoff, Biophys. J., 108 (2015) 1747–1757.