Vibrational spectra of small protonated peptides from finite temperature MD simulations and IRMPD spectroscopy

A. Cimas, T. D. Vaden, T. S.J.A. De Boer, L. C. Snoek, M. P. Gaigeot

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Finite temperature Born-Oppenheimer DFT-based molecular dynamics simulations are presented for the vibrational spectroscopy of the prototype gas-phase Ala2H+ and Ala3H+ protonated peptides. The dynamics and the vibrational signatures are used to interpret IR-MPD spectra recorded in the NH/OH stretch region. Molecular dynamics simulations are one way to go beyond the harmonic approximations commonly applied for the calculations of infrared spectra, naturally including all anharmonicities, i.e. mode couplings, vibrational and dipole anharmonicities. The dynamics of the peptides allows understanding of the evolution of the shape and width of the N-H bands when increasing the size of the peptide, as demonstrated here with the two small prototypes Ala 2H+ and Ala3H+. Hence, the conformational dynamics of Ala2 + at room temperature participates to the broadening of the IR active bands. The complex N-H broadband of Ala3H++ is shown to result from the dynamics of the N-H groups in the different peptide families, with a special role from breaking/reforming of hydrogen bonds involving the N-H groups. Taking this dynamics into account is thus mandatory for the understanding of this band in the 300-400 K experimental spectrum.

Original languageEnglish (US)
Pages (from-to)1068-1078
Number of pages11
JournalJournal of Chemical Theory and Computation
Issue number4
StatePublished - Apr 14 2009

All Science Journal Classification (ASJC) codes

  • Computer Science Applications
  • Physical and Theoretical Chemistry


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