Urea-Induced Drying of Hydrophobic Nanotubes: Comparison of Different Urea Models

Abstract

In a previous study, we performed the molecular dynamics (MD) simulations of various carbon nanotubes solvated in 8 M urea and observed a striking phenomenon of urea-induced drying of hydrophobic nanotubes, which resulted from the stronger dispersion interaction of urea than water with nanotube (Das, P.; Zhou, R. H. J. Phys. Chem. B2010, 114, 5427-5430). In this paper, we have compared five different urea models to investigate if the above phenomenon is sensitive to the urea models used. We demonstrate through MD simulations that the drying phenomenon and its physical mechanism are qualitatively independent of the urea models. Consistent with our previous study, our current analyses with both interaction potential energy and association free energy indicate that there is a "dry state" inside the carbon nanotubes, which is caused by the urea's preferential binding to nanotubes through stronger dispersion interactions. These results also have implications for understanding the urea-induced protein denaturation by providing further evidence of the potential existence of a "dry globule"-like transient state during protein unfolding and the "direct interaction mechanism" (whereby urea attacks protein directly, rather than disrupts water structure as a "water breaker"). In addition, our study highlights the crucial role of dispersion interaction in the selective absorption of molecules in hydrophobic nanopores and may have significance for nanoscience and nanotechnology.

Toward an atomistic description of the urea-denatured state of proteins

“…After test calculations with different urea force-field models, we selected the widely used refined parameters from the Optimized Potentials for Liquid Simulations (OPLS) forcefield, (5, 8-11, 13, 15, 20, 28). Note, however, that although incorrect models can yield to biased results (9, 33) most current urea models provide very similar results (34,35). Chloride ions were added to keep electroneutrality.…”

Small Molecules and Peptides Inside Carbon Nanotubes: Impact of Nanoscale Confinement

“…Second, we find a striking phenomen that urea can induce the drying of CNTs and result in single-file urea wires. The unique properties of a urea wire as well as its biological and technological implications are discussed [22,23]. Third, we show that nanoscale confinement can catalyze the chiral transition of chiral molecules.…”

“…To answer this, we performed MD simulations of (17, 8) SWNT (1.73 nm in diameter, it can accommodate several layers of urea and water) immersed in 8 M urea solution. Considering that there are some urea models commonly used in literature whose charge distributions are quite different [22], herein we have used five different urea models to test if the drying phenomenon is sensitive to force fields used.…”

“…In this book chapter, we review some of our recent works [21][22][23][24], with large scale molecular dynamics (MD) simulations using massively parallel supercomputers such as IBM Blue Gene, on the nanoscale confinement of both small molecules and peptides inside the CNT, which demonstrate wide implications in nanoscale signal processing, single-file transportation, drug delivery, and even cytotoxicity. The structure of this chapter will be organized as following.…”

Probing cellulose amphiphilicity

“…For instance, urea inhibits hydrophobic association of surfactants, which consequently results in an increase in critical micelle concentration. Obviously, as briefly mentioned above, the key point here is the amphiphilic nature of urea which has been additionally demonstrated by molecular modeling; enhancement of its concentration close to model hydrophobic surfaces (Koishi et al 2010) and inside hydrophobic nanotubes (Xiu et al 2011). Its amphiphilic nature makes it act like a surfactant molecule capable of forming hydrogen bonds with the solvent while, at the same time, having the ability of solvating the hydrophobic sides of cellulose.…”