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. Vibrational spectroscopy of proteins labeled with site-specific carbon-deuterium (CD) bonds is emerging as a powerful experimental technique for investigating protein structure, dynamics, and function. To fully establish a quantitative connection between CD infrared line shapes and the local structure and dynamics of proteins, I propose to utilize a mixed quantum-classical approach for the computation of infrared (IR) line shapes. The IR line shapes are obtained from the power spectrum of the fluctuating electric dipole moment of the deuterated amino acid solute. The dynamics of the entire system are propagated with molecular dynamics, but the dipole moment of the solute is computed with quantum mechanics/molecular mechanics (QM/MM) methods and contains the effects of polarization by the solvent. If granted, this allocation of computing resources will primarily be used to learn about how the TeraGrid systems can be integrated into our research program.
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