Paper Citing NAMD - Abstract
Waegele, Matthias M.; Gai, Feng
Computational Modeling of the Nitrile Stretching Vibration of 5-Cyanoindole in Water
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 1:781-786, FEB 18 2010
The bandwidth of the nitrite (C N) stretching vibration of 5-cyanotryptophan shows. a significant broadening upon hydration. Thus, it has been proposed to be a useful infrared probe of the local hydration environment,of proteins. However, the molecular mechanism underlying this hydration induced spectral broadening is not known, making interpretation of the experimental results difficult. Herein, we investigate how interactions of water with various sites. of 5-cyanoindole the side chain of 5-cyanotryptophan, affect its C N stretching vibration via a combined electronic structure/molecular dynamics approach. It is found that, besides those interactions with the nitrite group, interactions of water with the indole ring also play a significant role in mediating the C N stretching frequency. Thus, this study provides a molecular basis for understanding how hydration affects the C N stretching band of 5-cyanotryptophan. In addition, an empirical model, which includes interactions of water with both the nitrite and indole groups, is developed for predicting the C N stretching vibrational band via molecular dynamics simulations.
