The vibrational spectrum of the hydrated alanine-leucine peptide in the amide region from IR experiments and first principles calculations

Hassan, Irtaza; Donati, Luca; Stensitzki, Till; Keller, Bettina; Heyne, Karsten; Imhof, Petra

doi:10.1016/j.cplett.2018.03.026

Cited by 6 publications

(2 citation statements)

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“…For example, the calculated frequency of the alanine dipeptide is 1605 cm

and the experimental value is 1635 cm

[ 79 ]. Our present results are in particular comparable to those of to the Ala-Leu peptide, with measured carbonyl vibration at 1660 cm

and a calculated frequency at ∼1600 cm

[ 14 ]. This is the same frequency that we find in this work for the central carbonyl group in a one-water state, in agreement with the one hydrogen bond (on average) observed for the carbonyl group in Ala-Leu [ 14 ], confirming again the interplay of hydrogen bonds and vibrational frequencies.…”

Section: Discussionsupporting

confidence: 88%

“…For the assignment of different conformations of a peptide, one therefore needs to rely on a set of first-principles simulations, in which each conformation, obtained, e.g., from sampling with empirical force fields, is simulated separately [ 14 ]. Such an approach is feasible if the time scale of the conformational dynamics is beyond that of the simulation time the spectra calculation is based on, and all other processes that may effect the vibrational signature are fast enough to average out.…”

Section: Introductionmentioning

confidence: 99%

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Effect of the Hydration Shell on the Carbonyl Vibration in the Ala-Leu-Ala-Leu Peptide

2021

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The vibrational spectrum of the Ala-Leu-Ala-Leu peptide in solution, computed from first-principles simulations, shows a prominent band in the amide I region that is assigned to stretching of carbonyl groups. Close inspection reveals combined but slightly different contributions by the three carbonyl groups of the peptide. The shift in their exact vibrational signature is in agreement with the different probabilities of these groups to form hydrogen bonds with the solvent. The central carbonyl group has a hydrogen bond probability intermediate to the other two groups due to interchanges between different hydrogen-bonded states. Analysis of the interaction energies of individual water molecules with that group shows that shifts in its frequency are directly related to the interactions with the water molecules in the first hydration shell. The interaction strength is well correlated with the hydrogen bond distance and hydrogen bond angle, though there is no perfect match, allowing geometrical criteria for hydrogen bonds to be used as long as the sampling is sufficient to consider averages. The hydrogen bond state of a carbonyl group can therefore serve as an indicator of the solvent’s effect on the vibrational frequency.

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