Mechanisms and underlying thermodynamic determinants of translocation of charged cationic peptides such as cell-penetrating peptides across the cellular membrane continue to receive much attention. Two widely-held views include endocytotic and non-endocytotic (diffusive) processes of permeant transfer across the bilayer. Considering a purely diffusive process, we consider the free energetics of translocation of a mono-arginine peptide mimic across a model DMPC bilayer. We compute potentials of mean force for the transfer of a charged mono-arginine peptide unit from water to the center of a 1,2-Dimyristoyl-sn-Glycero-3-Phosphocholine (DMPC) model lipid bilayer. We use fully atomistic molecular dynamics simulations coupled with the adaptive biasing force (ABF) method for free energy estimation. The estimated potential of mean force difference from bulk to bilayer center is 6.94 ± 0.28 kcal/mol. The order of magnitude of this prediction is consistent with past experimental estimates of arginine partitioning into physiological bilayers in the context of translocon-based experiments, though the correlation between the bench and computer experiments is not unambiguous. Moreover, the present value is roughly one-half of previous estimates based on all-atom molecular dynamics free energy calculations. We trace the differences between the present and earlier calculations to system sizes used in the simulations, and the dependence of the contributions to the free energy from various system components (water, lipids, ions, peptide) on overall system size. By varying the bilayer lateral dimensions in simulations using only sufficient numbers of counterions to maintain overall system charge neutrality, we find the possibility of an inherent convergent transfer free energy value.

We investigate temperature-dependence of free energetics with two single halide anions, I− and Cl−, crossing the aqueous liquid-vapor interface through molecular dynamics simulations. The result shows that I− has a modest surface stability of 0.5 kcal/mol at 300 K and the stability decreases as the temperature increases, indicating the surface adsorption process for the anion is entropically disfavored. In contrast, Cl− shows no such surface state at all temperatures. Decomposition of free energetics reveals that water-water interactions provide a favorable enthalpic contribution, while the desolvation of ion induces an increase in free energy. Calculations of surface fluctuations demonstrate that I− generates significantly greater interfacial fluctuations compared to Cl−. The fluctuation is attributed to the malleability of the solvation shells, which allows for more long-ranged perturbations and solvent density redistribution induced by I− as the anion approaches the liquid-vapor interface. The increase in temperature of the solvent enhances the inherent thermally-excited fluctuations and consequently reduces the relative contribution from anion to surface fluctuations, which is consistent with the decrease in surface-stability of I−. Our results indicate a strong correlation with induced interfacial fluctuations and anion surface stability; moreover, resulting temperature dependent behavior of induced fluctuations suggests the possibility of a critical level of induced fluctuations associated with surface stability.

Ion-specific interfacial behaviors of monovalent halides impact processes such as protein denaturation, interfacial stability, surface tension modulation, and as such, their molecular and thermodynamic underpinnings garner much attention. We use molecular dynamics simulations of monovalent anions in water to explore effects on distant interfaces. We observe long-ranged ion-induced perturbations of the aqueous environment as suggested by experiment and theory. Surface stable ions, characterized as such by minima in potentials of mean force computed using umbrella sampling MD simulations, induce larger interfacial fluctuations compared to non-surface active species, conferring more entropy approaching the interface. Smaller anions and cations show no interfacial potential of mean force minima. The difference is traced to hydration shell properties of the anions, and the coupling of these shells with distant solvent. The effects correlate with the positions of the anions in the Hofmeister series (acknowledging variations in force field ability to recapitulate essential underlying physics), suggesting how differences in induced, non-local perturbations of interfaces may be related to different specific-ion effects in dilute biophysical and nanomaterial systems.

Combining umbrella sampling molecular dynamics (MD) simulations, the weighted histogram analysis method (WHAM) for unbiasing probabilities, and polarizable charge equilibration force fields, we compute the potential of mean force for the reversible transfer of methyl guanidinium from bulk solution to the center of a model DPPC bilayer. A 5 kcal/mol minimum in the potential of mean force profile for membrane permeation suggests that the analogue will preferentially reside in the headgroup region of the lipid, qualitatively in agreement with previously published results. We find the potential of mean force for permeation to be approximately 28 kcal/mol (relative to the minimum in the headgroups), within the range of values reported for similar types of simulations using fixed-charge force fields. From analysis of the lipid structure, we find that the lipid deformation leads to a substantial destabilizing contribution to the free energy of the methyl guanidinium as it resides in the bilayer center, though this deformation allows more efficient stabilization by water defects and transient pores. Water in the bilayer core stabilizes the charged residue. The role of water in stabilizing or destabilizing the solute as it crosses the bilayer depends on bulk electrolyte concentration. In 1 M KCl solution, the water contribution to the potential of mean force is stabilizing over the entire range of the permeation coordinate, with the sole destabilizing force originating from the anionic species in solution. Conversely, methyl guanidinium experiences net destabilization from water in the absence of electrolyte. The difference in solvent contributions to permeation free energy is traced to a local effect arising from differences in water density in the bilayer-water solution interface, thus leading to starkly opposite net forces on the permeant. The origin of the local water density differential rests with the penetration of hydrated chloride anions into the solution-bilayer interface. Finally, water permeation into the bilayer is required for the deformation of individual lipid molecules and permeation of ions into the membrane. From simulations where water is first excluded from the bilayer center where methyl guanidinium is restrained and then, after equilibration, allowed to enter the bilayer, we find that in the absence of any water defects/permeation into the bilayer, the lipid headgroups do not follow the methyl guanidinium. Only when water enters the bilayer do we see deformation of individual lipid molecules to associate with the amino acid analogue at bilayer center.

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