Atom labeling of the Ac-Lys-Glu-NHMe model peptide, restricted just to groups that can form hydrogen bonds.
Details of the model peptide Ac-Lys-Glu-NHMe side chain termini. Top: Dipeptide in neutral form with one (left: contact) and with two water (right: solvent shared) molecules attached. Center: Zwitterionic contact pair with one (left) or two (right) water molecules attached. Bottom: Solvent shared ion pairs involving one (left) or two (right) oxygen atoms of the carboxyl group.
Proton transfer mechanisms from a 4 ps part of a BOMD trajectory for Ac-Lys-Glu-NHMe(H2O)2. The figure shows the heavy-heavy atom distance vs. the corresponding proton asymmetry variable δ (see text) for three different transfer scenarios: Proton transferred between amino nitrogen and carboxylic oxygen (black) or water oxygen (red), or between water and carboxylic oxygen (green).
Smeared number of hydrogen bonds additionally stabilizing the side chain termini and proton asymmetry coordinate δ = rNH−rOH.
Normalized distributions of CN distances for the COO−⋅⋅⋅NH3 + side chain termini from 200 ns/300 K simulation for Ac-Lys-Glu-NHMe dipeptide solvated in water clusters of different sizes.
Fractions of contact, solvent shared, and solvent separated ion pairs obtained from 200 ns/300 K direct MD simulations as a function of the number of water molecules attached to the Ac-Lys-Glu-NHMe dipeptide. Dashed lines serve to guide the eye.
Free energy profile of NH4 +⋅⋅⋅HCOO− ion pair dissociation in water clusters of different sizes obtained by umbrella sampling.
Free energy profile of Ac-Lys-Glu-NHMe dipeptide salt bridge opening in water clusters of different sizes obtained by umbrella sampling.
Lifetimes (ps) from linear fitting of logarithm of probability of staying in particular state. The lifetime is calculated as τ = −1/k, where k is the slope of the line, the shortest times were omitted from the fit in order to reduce the influence of recrossings. For details see Fig. S4. 28
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