A molecular dynamics study of the dielectric properties of aqueous solutions of alanine and alanine dipeptide

Abstract

Molecular dynamics simulations were used to compute the frequency-dependent dielectric susceptibility of aqueous solutions of alanine and alanine dipeptide. We studied four alanine solutions, ranging in concentration from 0.13-0.55 mol/liter, and two solutions of alanine dipeptide (0.13 and 0.27 mol/liter). In accord with experiment we find a strong dielectric increment for both solutes, whose molecular origin is shown to be the zwitterionic nature of the solutes. The dynamic properties were analyzed based on a dielectric component analysis into solute, a first hydration shell, and all remaining (bulk) waters. The results of this three component decomposition were interpreted directly, as well as by uniting the solute and hydration shell component to a "suprasolute" component. In both approaches three contributions to the frequency-dependent dielectric properties can be discerned. The quantitatively largest and fastest component arises from bulk water [i.e., water not influenced by the solute(s)]. The interaction between waters surrounding the solute(s) (the hydration shell) and bulk water molecules leads to a relaxation process occurring on an intermediate time scale. The slowest relaxation process originates from the solute(s) and the interaction of the solute(s) with the first hydration shell and bulk water. The primary importance of the hydration shell is the exchange of shell and bulk waters; the self-contribution from bound water molecules is comparatively small. While in the alanine solutions the solute-water cross-terms are more important than the solute self-term, the solute contribution is larger in the dipeptide solutions. In the latter systems a much clearer separation of time scales between water and alanine dipeptide related properties is observed. The similarities and differences of the dielectric properties of the amino acid/peptide solutions studied in this work and of solutions of mono- and disaccharides and of the protein ubiquitin are discussed.

Molecular Dynamics Simulations of Highly Crowded Amino Acid Solutions: Comparisons of Eight Different Force Field Combinations with Experiment and with Each Other

“…This result is again consistent with experimental observations for amino acids 66 and with a previous study that measured the dielectric increments of alanine solutions using MD simulations similar to those carried out here. 67 …”

Implementation of the SCC-DFTB Method for Hybrid QM/MM Simulations within the Amber Molecular Dynamics Package

“…Recent experimental results suggest that the backbone preferences in proteins are already present in blocked aminoacids. 55,56 A number of experimental 55,[57][58][59][60] and theoretical, [61][62][63][64][65][66][67][68][69][70][71][72][73][74][75][76][77][78] studies indicate that the potential energy surface for AD in vacuum and in solution are considerably different: While in the gas-phase the global minimum is believed to be a C7 eq structure (ϕ− 83°, ψ~73°), 70 interaction with water favors the polyproline-II (P II , (ϕ~−75°, ψ~150°) conformation. 60 AD has also been used previously to investigate the performance of the SCC-DFTB method as compared to different classical force fields.…”

Hydration Dynamics of Water near an Amphiphilic Model Peptide at Low Hydration Levels: A Dielectric Relaxation Study

“…Phenomenological interpretations ignore this cross term, but its relevance has been shown in several MD simulations and MD-assisted interpretations of experimental data. [16,29,30,37,38] The high-frequency mode (2) on the 10 ps timescale evolves from the Debye relaxation of neat water. Upon addition of NALA this mode largely broadens, which indicates that the dynamics becomes widely distributed.…”