The Anharmonic Vibrational Potential and Relaxation Pathways of the Amide I and II Modes of N-Methylacetamide

Abstract

We investigate the influence of isotopic substitution and solvation of N-methylacetamide (NMA) on anharmonic vibrational coupling and vibrational relaxation of the amide I and amide II modes. Differences in the anharmonic potential of isotopic derivatives of NMA in D2O and DMSO-d6 are quantified by extraction of the anharmonic parameters and the transition dipole moment angles from cross-peaks in the two-dimensional infrared (2D-IR) spectra. To interpret the effects of isotopic substitution and solvent interaction on the anharmonic potential, density functional theory and potential energy distribution calculations are performed. It is shown that the origin of anharmonic variation arises from differing local mode contributions to the normal modes of the NMA isotopologues, particularly in amide II. The time domain manifestation of the coupling is the coherent exchange of excitation between amide modes seen as the quantum beats in femtosecond pump-probes. The biphasic behavior of population relaxation of the pump-probe and 2D-IR experiments can be understood by the rapid exchange of strongly coupled modes within the peptide backbone, followed by picosecond dissipation into weakly coupled modes of the bath.

Two-dimensional vibrational lineshapes of amide III, II, I and A bands in a helical peptide

“…We found that higher multipoles of the electric field make significant contributions to the frequency fluctuations and line broadening [24]. The EDM reproduces the experimental amide I and II anharmonicities [13].…”

“…Coherent ultrafast infrared spectroscopy has been applied to probe protein structure [8][9][10]. Two-dimensional infrared cross-peaks of amide I with other amide modes (A and II) have been reported in model systems of the amide bond [11][12][13]. Recent simulations [14] showed that the cross-peak bandshapes are sensitive to the correlated hydrogen bond dynamics at the two atom sites where the two amide vibrations reside.…”

Two-Dimensional Spectroscopy of Extended Molecular Systems: Applications to Energy Transport and Relaxation in an α-Helix

“…In particular, the analogues of the NOESY variant of 2DNMR allow for the study of dynamics, because they involve a waiting time t 2 that may be controlled at the femtosecond time scales, thus allowing one to take snapshots of a system while it evolves. 2,3 Examples of systems that have been studied using 2DIR or 2Dvis spectroscopies with nonzero waiting times include relatively simple few-level systems, such as the coupled amide I and amide II vibrations in N-methylacetamide (NMA) 4 and vibrations in other small organic molecules, 5 as well as extended systems with a multitude of levels, such as the amide I band in polypeptides or proteins, 6,7 the excitonic transitions in the photosynthetic Fenna-Matthew-Olsen complex, 8 and the excitonic transitions in double-wall molecular nanotubes. 9 In the simplest situation, with only two interacting vibrational or electronic states of interest, it is rather straightforward to obtain information about their coupled dynamics from the waiting time dependence of the 2D spectrum.…”

Vibrational−Exciton Couplings for the Amide I, II, III, and A Modes of Peptides

“…This Hamiltonian is in good agreement with the recent experiment of the amide I and II cross peak. 31 In this Article, we provide the other necessary ingredient of the effective Hamiltonian for larger peptides, the intermode couplings. Torii and Tasumi had constructed a map of amide I couplings between neighboring amide units starting with ab initio calculations of a glycine dipeptide (GLDP) for various Ramachandran angles (ψ and φ) at the Hartree-Fock level.…”