Illustration of the atom movement in the (a) amide-1 and (b) amide-2 modes and the dominant resonance structure (c) in NMA (Ref. 45).
The double-sided Feynman diagrams that contribute to the two-dimensional infrared signal. Diagram (a) rephasing ground state bleach, (b) rephasing stimulated emission, (c) rephasing induced absorption, (d) nonrephasing ground state bleach, (e) nonrephasing stimulated emission, and (f) nonrephasing induced absorption.
(Color online) Histograms of the fluctuations in the (a) amide-1 frequency, (b) amide-2 frequency, and (c) coupling obtained from the molecular dynamics trajectory. The solid lines are Gaussian functions; their widths are equal to the standard deviations calculated from the trajectories.
(Color online) Correlation functions and spectral densities for the system parameters, obtained using an electrostatic map in combination with molecular dynamics simulations (Ref. 44). Panel (a) shows the autocorrelation functions for the amide-1 and amide-2 frequencies and the cross-correlation function between these two parameters. Panel (b) shows the correlation functions that involve the coupling. Panels (c) and (d) show the corresponding spectral densities.
(Color online) Calculated spectra [panel (a)] obtained from the full calculation (solid line), and from three simplified models: neglecting anticorrelation between the fluctuations in the amide-1 and amide-2 frequencies (dashed line), neglecting fluctuations in the coupling (dotted line), and neglecting both the anticorrelation between the amide-1 and amide-2 fluctuations and the fluctuations in the coupling (dash-dotted line). Panel (b) shows the full calculation (solid line) together with the experimental spectrum from Ref. 12 (dashed line). All spectra are normalized to the same integrated intensity.
(Color) Calculated 2DIR spectra for [(a) and (b)] , [(c) and (d)] , [(e) and (f)] , and [(g) and (h)] . 26 Equidistant contours were drawn from to of the maximum in the spectrum. Solid contours filled with red and yellow show the bleaching and stimulated emission peaks; induced absorption peaks are plotted in blue with dashed contours.
(Color online) Amplitude of the bleaching part of the cross peak (dots) and calculated amide-I population following amide-II excitation (solid line). The cross peak amplitude was measured in the perpendicular polarization spectrum as the local maximum in a slice at equal to the maximum of the amide-II peak . The inset shows the cross peak intensity for short waiting times. The dashed line is a fit of the amide-I population to Eq. (30), which hardly deviates from the calculated population.
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