Abstract
Hydrophobicity is a phenomenon of great importance in biology, chemistry, and biochemistry. It is defined as the interaction between nonpolar molecules or groups in water and their low solubility. Hydrophobic interactions affect many processes in water, for example, complexation, surfactant aggregation, and coagulation. These interactions play a pivotal role in the formation and stability of proteins or biological membranes. In the present study, we assessed the effect of ionic strength, solute size, and shape on hydrophobic interactions between pairs of nonpolar particles. Pairs of methane, neopentane, adamantane, fullerene, ethane, propane, butane, hexane, octane, and decane were simulated by molecular dynamics in AMBER 16.0 force field. As a solvent, TIP3P and TIP4PEW water models were used. Potential of mean force (PMF) plots of these dimers were determined at four values of ionic strength, 0, 0.04, 0.08, and 0.40 mol/dm3, to observe its impact on hydrophobic interactions. The characteristic shape of PMFs with three extrema (contact minimum, solvent-separated minimum, and desolvation maximum) was observed for most of the compounds for hydrophobic interactions. Ionic strength affected hydrophobic interactions. We observed a tendency to deepen contact minima with an increase in ionic strength value in the case of spherical and spheroidal molecules. Additionally, two-dimensional distribution functions describing water density and average number of hydrogen bonds between water molecules were calculated in both water models for adamantane and hexane. It was observed that the density of water did not significantly change with the increase in ionic strength, but the average number of hydrogen bonds changed. The latter tendency strongly depends on the water model used for simulations.
Highlights
Hydrophobicity is a property of considerable importance in biology, chemistry, and biochemistry
Hydrophobic effects have a significant effect on molecular recognition, detergency, and formation of gas clathrates.[1,3−5] It is hypothesized that hydrophobic interactions play a pivotal role in the initiation of protein-folding process.[6−8] It is assumed that one of the initial steps of this process occurs in the protein fragment with the greatest number of nonpolar residues and that hydrophobic interactions lead to protein folding.[6−8]
The deepest contact minimum (CM) for nearly spherical particles is observed for fullerene with a depth of around −3.5 to −3.94 kcal/mol depending on the ionic strength value in the TIP3P model and −2.84 to −4.93 kcal/mol in the TIP4PEW model (Figure S3)
Summary
Hydrophobicity is a property of considerable importance in biology, chemistry, and biochemistry It is defined as low affinity for water or even the avoidance of water by certain molecules or substances. Once the molecules come closer to each other, the number of water particles in contact with them decreases. These structural changes significantly contribute to free energy.[1] Hydrophobic interactions are categorized as solvent-induced interactions.[3,5,9] In this context, hydrophobicity could be characterized by the free energy of association or alternatively by changes in the free energy as a function of the distance between a pair of nonpolar molecules in an aqueous solution.[1,3]
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