Introduction

The Tokmakoff group uses ultrafast vibrational spectroscopy to study the molecular dynamics of chemical and biological processes in solution. We are interested in revealing the time-scale and mechanism by which the molecular structure of water, peptides, proteins, and other macromolecules change; how the dynamical nature of hydrogen bonds influence proton transfer processes; and the details of molecular recognition, interaction, and binding. These questions all involve understanding the molecular details of competing non-covalent interactions, such as repulsion, electrostatics, and hydrogen bonding. We try to reduce the large number of variables that describe molecules in solution to the few dominant effects 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 involves development of new structurally sensitive femtosecond vibrational spectroscopies that can be used to follow the time-evolution of molecular structure. The most sensitive and broadly applicable tool is two-dimensional infrared spectroscopy, which we developed to capture information on transient molecular structure and characterize structural variation. Experiments are complemented by theoretical work on nonlinear spectroscopy, statistical mechanical modeling of dynamics and relaxation, and molecular dynamics computer simulations.

For further details you can read about:

2D IR Spectroscopy

The structure and dynamics of water

Proton transfer along hydrogen bonds

Protein folding and self-assembly