The behavior of a 17-residue model peptide is analyzed by means of molecular dynamics simulations including explicitly more than a thousand water molecules. On the basis of the charge-group concept, Coulomb interactions are truncated for three values of the cutoff radius: 0.6, 1.0, and 1.4 nm. It is found that the stability of an alpha-helix, which acts as a common starting configuration, is a function of the cutoff size. While the overall stability of the helix is conserved in a simulation using a cutoff of 1.0 nm, it is lost within a very short period of 100 ps when the cutoff is increased to 1.4 nm. This demonstrates that the commonly used cutoff size of 1.0 nm is inappropriate because it does not ensure the convergence of Coulomb interactions. In order to permit an independent judgment, we have performed a 225-ps simulation using the Ewald summation technique, which is more elaborate but circumvents the problem to find an appropriate cutoff value. In contrast to the 1.4-nm cutoff trajectory, the Ewald technique simulation conserves the helical character of the peptide conformation. This demonstrates that even 1.4 nm is too short a cutoff. Due to the fundamental uncertainty introduced by the use of a simple cutoff, this truncation scheme seems questionable for molecular dynamics simulations of solvated biomolecules.

In this study we present the results of the molecular dynamics simulation of the ionic liquids: 1-butyl-3-methyl-imidazolium tetrafluoroborate and trifluoromethylacetate as well as 1-ethyl-3-methyl-imidazolium dicyanamide. Ionic liquids are characterized by both a molecular dipole moment and a net charge. Thus, in contrast to a solution of simple ions in a (non-) polar solvent, rotational and translational effects influence the very same molecule. This study works out the theoretical framework necessary to compute the conductivity spectrum and its low frequency limit of ionic liquids. Merging these computed conductivity spectra with previous simulation results on the dielectric spectra of ionic liquids yields the spectrum of the generalized dielectric constant, which may be compared to experiments. This spectrum was calculated for the three ionic liquids over six orders of magnitude in frequency ranging from 10 MHz to 50 THz. The role of rotation and translation and their coupling term on the generalized dielectric constant is discussed in detail with a special emphasis on the zero-frequency limit. Thereby, the frequency dependence of the cross correlation between the collective rotational dipole moment and the current is discussed.

We report the static and frequency-dependent dielectric properties of a 9 mmol/L ubiquitin solution based on the analysis of a 5 ns molecular dynamics (MD) simulation. In accord with available experimental results, we obtain a significant dielectric increment for the dielectric constant (DC) at low frequencies (including the static DC (ω ) 0)), but a decrement at higher frequencies. The overall dielectric properties were decomposed into the protein-protein and the water-water self-terms, as well as the protein-water cross-term. The most significant contributions arise from the two self-terms, approximately 65% from water and 21% from the protein. These two components, corresponding to what experimentalists often refer to as β-and γ-processes, also determine the bimodal shape of the dielectric loss function (χ′′(ω)). The quantitatively smallest proteinwater cross-term (14%) corresponds to the experimentally observed δ-relaxation; it accentuates the bimodal shape of χ′′(ω) even further. A finer partitioning of the solvent into two solvation shells and bulk reveals the special role and properties of the first hydration layer surrounding the protein. Our findings point to proteinwater interactions and, in particular, bound biological water as the microscopic origin of the δ-relaxation.

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