We use ultrafast vibrational spectroscopy to study molecular dynamics of water and biological processes.
Research Interests:
The Tokmakoff group studies the molecular dynamics of aqueous solutions and biophysical processes. We wish to understand how the hydrogen bond network of water changes with time, how it accommodates and interacts with different solutes, and how it mediates the transport of protons. We are interested in understanding the molecular details of how proteins fold, how they recognize and bind to a target, and how DNA oligonucleotides hybridize.
These questions all involve understanding the interplay of numerous 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. 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 spectrometers, and close work with theorists on computational modeling tools and molecular dynamics simulations.
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.