Vibrational spectroscopic characteristics of secondary structure polypeptides in liquid water: Constrained MD simulation studies

Using the constrained MD simulation method in combination with quantum chemistry calculation, Hessian matrix reconstruction, and fragmentation approximation methods, we established a computational scheme for numerical simulations of amide I IR absorption, vibrational circular dichroism (VCD), and 2D IR photon echo spectra of peptides in solution. Six different secondary structure peptides, i.e., α‐helix, 3 10 ‐helix, π‐helix, antiparallel and parallel β‐sheets, and polyproline II (P II ), are considered, and the vibrational characteristic features in their linear and nonlinear spectra in the amide I band region are discussed. Isotope‐labeling effects on IR and VCD spectra are notable only for α‐ and π‐helical peptides due to the strong vibrational couplings between two nearest neighboring amide I local oscillators. The amplitudes of difference 2D IR spectra are shown to be strongly dependent on both the extent of mode delocalization and the relative orientation of local mode transition dipoles determined by secondary structure. © 2006 Wiley Periodicals, Inc. Biopolymers 83: 519–536, 2006 This article was originally published online as an accepted preprint. The “Published Online“ date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com