Toshiko Ichiye
Professor, William G. McGowan Chair in Chemistry  

Department of Chemistry 
Georgetown University
37th and O Streets NW
Washington, DC 20057-1227

[cv]

Statistical Mechanics, Physical Chemistry II, Computational Methods for Biomacromolecules

Physical Chemistry & Biophysics
Our research involves theoretical studies of biological macromolecules and other condensed matter systems at a molecular level. We are interested in problems such as how the structure of a given protein promotes its biological function and how solvent influences structure and function of proteins, as well as general problems in solution theory. 

We use a variety of theoretical and computational tools in our research. One approach is molecular dynamics simulations, especially molecular dynamics simulations, in which the motions of the individual atoms comprising the molecules are modeled. This type of computer simulation has provided insights into many physical, chemical and biochemical problems, and is particularly useful in studying complex biological molecules. Other tools include electronic structure calculations, continuum dielectrics and statistical mechanical theory. 

One research area involves electron transfer, a crucial process in both respiration and photosynthesis. We use molecular dynamics simulations to understand at a molecular level how the protein environment influences the transfer process. Our focus is on the iron-sulfur proteins, particularly rubredoxin. 

Another research area is in liquid state theory, using both statistical mechanical theories and computer simulations. We are formulating molecular theories of solvation for macromolecules such as proteins and DNA. This work has ranged from studies of water and aqueous solutions to proteins in solution. The goal of this work is to include solvent effects efficiently into computer simulations of proteins and nucleic acids which is currently a major stumbling block. 

Tan, M.-L.; Dolan, E. A.; Ichiye, T. Understanding intramolecular electron transfer in ferredoxin: A molecular dynamics study. J. Phys. Chem. B 2004, 108, 20435-20441.

Chowdhuri, S.; Tan, M.-L.; Ichiye, T. Dynamical properties of the soft sticky dipole-quadrupole-octupole water model: A molecular dynamics study. J. Chem. Phys. 2006, 125, 144513-144520.

Xiao, Y.; Tan, M.-L.; Ichiye, T.; Wang, H.; Smith, M. C.; Meyer, J.; Sturhahn, W.; Alp, E. E.; Zhao, J.; Yoda, Y.; Cramer, S. P. Dynamics of Rhodobacter capsulatus [2Fe-2S] ferredoxin VI and Aquifex aeolicus ferredoxin 5 via nuclear resonance vibrational spectroscopy (NRVS) and resonance Raman spectroscopy. Biochem. 2008, 47, 6612-6627.

Niu, S.; Ichiye, T. Cleavage of [4Fe-4S]-type clusters: Breaking the symmetry. J. Phys. Chem. A, Articles ASAP April 20, 2009.

Niu, S.; Ichiye, T. Insight into environmental effects on bonding and redox properties of [4Fe-4S] clusters in proteins. J. Am. Chem. Soc., Articles ASAP April 2, 2009.

[complete list]