Cellular uptake through endocytosis is crucial for drug delivery and nanomedicine. However, the conditions under which passive endocytosis (i.e., not ATP driven) takes place are not well understood. We report MD simulations of the passive uptake of ligand-coated nanoparticles with varying size, shape, coverage, and membrane-binding strength. We find that the efficiency of passive endocytosis is higher for spherocylindrical particles than for spheres and that endocytosis is suppressed for particles with sharp edges.

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Water autoionization reaction 2H2O 3 H3O ؊ ؉ OH ؊ is a textbook process of basic importance, resulting in pH ‫؍‬ 7 for pure water. However, pH of pure water surface is shown to be significantly lower, the reduction being caused by proton stabilization at the surface. The evidence presented here includes ab initio and classical molecular dynamics simulations of water slabs with solvated H3O ؉ and OH ؊ ions, density functional studies of (H2O)48H ؉ clusters, and spectroscopic isotopic-exchange data for D2O substitutional impurities at the surface and in the interior of ice nanocrystals. Because H3O ؉ does, but OH ؊ does not, display preference for surface sites, the H2O surface is predicted to be acidic with pH < 4.8. For similar reasons, the strength of some weak acids, such as carbonic acid, is expected to increase at the surface. Enhanced surface acidity can have a significant impact on aqueous surface chemistry, e.g., in the atmosphere.density functional theory ͉ IR spectroscopy ͉ molecular dynamics ͉ water autoionization ͉ ice nanocrystals I n room-temperature liquid, one in 6 ϫ 10 8 water molecules is autoionized, yielding the standard value of pH ϭ 7. Autoionization in crystal ice should be less favorable, because, in contrast to water, ice is a very poor solvent of ionic and polar substances (1). As recently realized (2-5), the chemistry and composition of aqueous surfaces are quite distinct from that of the bulk; therefore, autoionization behavior should be reexamined at the surface.A number of recent computations (6-8) indicated the preference of hydronium cations for surface positions. Surface propensity of H 3 O ϩ was also deduced from vibrational spectroscopy of large protonated water clusters (6), as well as vibrational sum frequency generation (8, 9) and second harmonic generation (10) spectroscopic experiments probing extended aqueous interfaces. Interestingly, zeta potential measurements and titration experiments on oil droplets dispersed in water indicated the presence of negative charges at the interface, interpreted as adsorbed OH Ϫ ions (11). Similar conclusions have also been drawn from zeta potentials of air bubbles in water (12). More work is clearly needed to reconcile this apparent discord between predictions of surface-selective spectroscopies and molecular simulations on one side and electrochemical measurements on the other side.H 3 O ϩ forms three strong proton-donor bonds to H 2 O, but acts as a poor proton acceptor. A surface position with only H atoms hydrogen-bonded is preferred to interior positions, because the latter are associated with disruption of the approximately tetrahedral hydrogen-bond network in water (10). The present work focuses on the effect of surface stabilization of hydronium on water autoionization and surface pH. CalculationsOverview. Modeling of proton-tranfer systems is a nontrivial problem, because standard (empirical) potential energy surfaces do not include a possibility of proton hopping between different water molecules or transitions between the two li...

Phospholipid force fields are of ample importance for the simulation of artificial bilayers, membranes, and also for the simulation of integral membrane proteins. Here, we compare the two most applied atomic force fields for phospholipids, the all-atom CHARMM27 and the united atom Berger force field, with a newly developed all-atom generalized AMBER force field (GAFF) for dioleoylphosphatidylcholine molecules. Only the latter displays the experimentally observed difference in the order of the C2 atom between the two acyl chains. The interfacial water dynamics is smoothly increased between the lipid carbonyl region and the bulk water phase for all force fields; however, the water order and with it the electrostatic potential across the bilayer showed distinct differences between the force fields. Both Berger and GAFF underestimate the lipid self-diffusion. GAFF offers a consistent force field for the atomic scale simulation of biomembranes.

We established the charge and structure of the oil/water interface by combining ζ-potential measurements, sum frequency scattering (SFS) and molecular dynamics simulations. The SFS experiments show that the orientation of water molecules can be followed on the oil droplet/water interface. The average water orientation on a neat oil droplet/water interface is the same as the water orientation on a negatively charged interface. pH dependent experiments show, however, that there is no sign of selective adsorption of hydroxide ions. Molecular dynamics simulations, both with and without intermolecular charge transfer, show that the balance of accepting and donating hydrogen bonds is broken in the interfacial layer, leading to surface charging. This can account for the negative surface charge that is found in experiments.

Free energy profiles associated with moving atmospheric gases or radicals across the air/water interface were calculated as potentials of mean force by classical molecular dynamics simulations. With the employed force field, the experimental hydration free energies are satisfactorily reproduced. The main finding is that both hydrophobic gases (nitrogen, oxygen, and ozone) and hydrophilic species (hydroxyl radical, hydroperoxy radical, or hydrogen peroxide) have a free energy minimum at the air/water interface. As a consequence, it is inferred that atmospheric gases, with the exception of water vapor, exhibit enhanced concentrations at surfaces of aqueous aerosols. This has important implications for understanding heterogeneous chemical processes in the troposphere.

For a series of different proteins, including a structural protein, enzyme, inhibitor, protein marker, and a charge-transfer system, we have quantified the higher affinity of Na ؉ over K ؉ to the protein surface by means of molecular dynamics simulations and conductivity measurements. Both approaches show that sodium binds at least twice as strongly to the protein surface than potassium does with this effect being present in all proteins under study. Different parts of the protein exterior are responsible to a varying degree for the higher surface affinity of sodium, with the charged carboxylic groups of aspartate and glutamate playing the most important role. Therefore, local ion pairing is the key to the surface preference of sodium over potassium, which is further demonstrated and quantified by simulations of glutamate and aspartate in the form of isolated amino acids as well as short oligopeptides. As a matter of fact, the effect is already present at the level of preferential pairing of the smallest carboxylate anions, formate or acetate, with Na ؉ versus K ؉ , as shown by molecular dynamics and ab initio quantum chemical calculations. By quantifying and rationalizing the higher preference of sodium over potassium to protein surfaces, the present study opens a way to molecular understanding of many ion-specific (Hofmeister) phenomena involving protein interactions in salt solutions.ion-protein interaction ͉ molecular dynamics ͉ cell environment ͉ protein function ͉ Hofmeister series S odium and potassium represent the two most abundant monovalent cations in living organisms. Despite the fact that they possess the same charge and differ only in size [Na ϩ having a smaller ionic radius but a larger hydrated radius than K ϩ (1)], sodium versus potassium ion specificity plays a crucial role in many biochemical processes. More than 100 years ago, Hofmeister discovered that Na ϩ destabilizes (''salts out'') hens' egg white protein more efficiently than K ϩ does (2), analogous behavior being later shown also for other proteins (3). In a similar way, sodium was found to be significantly more efficient than potassium, e.g., in enhancing polymerization of rat brain tubulin (4). 23 Na NMR studies also were used to characterize cation-binding sites in proteins (5). The vital biological relevance of the difference between Na ϩ and K ϩ is exemplified by the low intracellular and high extracellular sodium͞potassium ratio maintained in living cells by ion pumps at a considerable energy cost (6). The principal goal of this article is to quantify and rationalize the different affinities of sodium and potassium to protein surfaces by means of molecular dynamics (MD) simulations, quantum chemistry calculations, and conductivity measurements for a series of proteins and protein fragments in aqueous solutions. Our effort, which is aimed at understanding the generic, thermodynamic Na ϩ ͞K ϩ ion specificity at protein surfaces, is thus complementary to recent computational studies of ion selectivity during active transport across ...

By means of molecular dynamics simulations with an all-atom force field, we investigated the affinities of alkali cations and halide anions for the dioleoylphosphatidylcholine lipid membrane in aqueous salt solutions. In addition, changes in phospholipid lateral diffusion and in headgroup mobility upon adding NaCl were observed using fluorescence spectroscopy. The simulations revealed that sodium is attracted to the headgroup region with its concentration being maximal in the vicinity of the phosphate groups. Potassium and cesium, however, do not preferentially adsorb to the membrane. Similarly, halide anions do not exhibit a strong affinity for the lipid headgroups but merely compensate for the positive charge of the sodium countercations. Nevertheless, larger halides such as bromide and iodide penetrate deeper into the headgroup region toward the boundary with the hydrophobic alkyl chain, this effect being likely underestimated within the present nonpolarizable force field. Addition of alkali halide salts modifies physical properties of the bilayer including the electronic density profiles, the electrostatic potential, and the area per lipid headgroup.