Structural Dependence of Extended Amide~III Vibrations in Two-Dimensional Infrared Spectra

05 July 2023, Version 1
This content is a preprint and has not undergone peer review at the time of posting.


Two-dimensional infrared (2D-IR) spectroscopy is a powerful experimental method for probing the structure and dynamics of proteins in aqueous solution. So far, most experimental studies focus on the amide I vibrations, for which empirical vibrational exciton models provide a means of interpreting such experiments. However, such models are largely lacking for other regions of the vibrational spectrum. To close this gap, we employ an efficient quantum-chemical methodology for the calculation of 2D-IR spectra, which is based on anharmonic theoretical vibrational spectroscopy with localized modes. We apply this approach to explore the potential of 2D-IR spectroscopy in the extended amide III region. Using calculations for a dipeptide model as well as alanine polypeptides, we show that distinct 2D-IR cross-peaks in the extended amide~III region can potentially be used to distinguish \alpha-helix and \beta-strand structures. We propose that the extended amide III region could be a promising target for future 2D-IR experiments.


quantum chemistry
theoretical spectroscopy
vibrational spectroscopy
2D IR spectroscopy
anharmonic theoretical vibrational spectroscopy
amide III

Supplementary materials

Supporting Information
Additional computational details and description of the computational methodology, additional calculated one-dimensional infrared and 2D-IR spectra for all 50 considered dipeptides, additional calculated 2D-IR spectra for snapshots of polyalanine-15.

Supplementary weblinks


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