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Infrared signatures of the peptide dynamical transition: A molecular dynamics simulation study
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10.1063/1.3462961
/content/aip/journal/jcp/133/3/10.1063/1.3462961
http://aip.metastore.ingenta.com/content/aip/journal/jcp/133/3/10.1063/1.3462961
View: Figures

Figures

Image of FIG. 1.
FIG. 1.

Temperature dependence of the rms fluctuations of the backbone dihedral angles and (in degrees) pertaining to the residue of the Aib peptide.

Image of FIG. 2.
FIG. 2.

Free energy landscape (in kJ/mol) along the inner backbone dihedral angles and of the Aib peptide, obtained for 220 and 300 K.

Image of FIG. 3.
FIG. 3.

(a) One-dimensional representation of the energy landscapes shown in Fig. 2, see text for details. (b) Temperature dependence of the minimum free energies and of the excited states 1 and 2 as well as the barrier heights and .

Image of FIG. 4.
FIG. 4.

Temperature dependence of the rms fluctuations (a) of the state-averaged (red) and (green) dihedral angles and (b) of the frequency shifts (red), (green), and (blue).

Image of FIG. 5.
FIG. 5.

(a) Probability distribution of the instantaneous frequency of a single Aib unit. Panels (b), (c), and (d) show the distribution of the contributions , , and , which represent the shift of the gas-phase frequency due to the interaction with the neighboring peptide units, the remaining peptide units, and the solvent, respectively.

Image of FIG. 6.
FIG. 6.

Normalized correlation functions of the frequency fluctuations caused by the neighboring peptide units (, red), the remaining peptide units (, blue), the solvent (, green), and all interactions (, magenta), as obtained for the Aib peptide at 220 and 300 K.

Image of FIG. 7.
FIG. 7.

(a) Short-time evolution of the total frequency fluctuation correlation function at 220 K (red) and 300 K (green). The curves are fitted by an exponential function, , the weight (green) and decay time (red) of which are shown in panel (b) as a function of temperature. The resulting total homogeneous dephasing rate (red) is shown in (c) together with the antidiagonal width of the 2D-IR spectra (green).

Image of FIG. 8.
FIG. 8.

Calculated 2D-IR spectra of the vibration of the Aib peptide at 220 and 300 K, as well as antidiagonal cuts of the 2D-IR spectra at various temperatures.

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/content/aip/journal/jcp/133/3/10.1063/1.3462961
2010-07-20
2014-04-21
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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: Infrared signatures of the peptide dynamical transition: A molecular dynamics simulation study
http://aip.metastore.ingenta.com/content/aip/journal/jcp/133/3/10.1063/1.3462961
10.1063/1.3462961
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