This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. Two-dimensional infrared (2D IR) spectroscopy in conjunction with ab initio quantum computations and molecular dynamics simulations is a promising approach to determining the dynamics of structure changes of peptides. However, in order to allow this novel approach to reach its full potential, there is a great need for predictive theories of the vibrational spectra of the peptide backbone in the presence of water. It is now evident that calculations of spectra that do not incorporate specific solvent effects on the frequencies and transition dipoles of the amide unit will not be successful in predicting many essential details of the spectra of peptides. The dynamic shifts caused by hydrogen bonding and other charge effects are substantial and need to be combined with computations of intermode coupling to predict the characteristic infrared spectra of the various secondary structure motifs. It has been shown through numerous experiments using FTIR and 2D IR experiments that isotope selective labeling of many types of peptide environments can permit structure and dynamics to be examined on a residue-by-residue basis. One of the main goals of 2D IR methods is to simplify the broadband spectra of peptides and define more clearly the underlying features and their interactions with water. However, the amide vibrations of peptides form groups of modes, each having a near degeneracy of the number of residues, and the modes in these groups are not normally identified separately in solution phase experiments. Even very simplified empirical theories of peptide IR spectra often capture approximately the spectral shapes for particular secondary structures if the coupling constants happen to be very large and of the easily manageable dipole-dipole type. However, such approaches do not claim to predict the correct spectral shifts from isolated molecule states, and they contain arbitrariness in the choice of their line shapes, zero-order frequencies and fluctuations, prior to any coupling, for modes from different residues that might be experiencing very different hydrogen bonding or electric fields from the remaining secondary structure or the solvent. The computation of linear and 2D IR spectra of individual residues shifted by isotope replacement would constitute a much more stringent test of the theoretical methods.
Showing the most recent 10 out of 128 publications
