Nanoscale Hydrophobic Interaction and Nanobubble Nucleation

Kondo, Takahiro; Yoo, Soohaeng; Yasuoka, Kenji; Zeng, Xiao Cheng; Narumi, Takatsune; Susukita, Ryutaro; Kawai, Maki; Furusawa, Hideaki; Suenaga, Atsushi; Okimoto, Noriaki; Futatsugi, Noriyuki; Ebisuzaki, Toshikazu

doi:10.1103/physrevlett.93.185701

Cited by 98 publications

(94 citation statements)

References 32 publications

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“…In light of this remarkable connection, it will be instructive to perform a quantitative analysis of the dependence of ␥ ϱ b on an extensive set of thermodynamic conditions for water and other liquids. Together, these results have implications for a fundamental understanding of solvation in condensed matter and applications, including extensions of protein pressure-temperature phase diagrams to metastable regions, phase behavior, and self-assembly in confined environments of interest to disparate fields of geochemistry, environmental sciences, and biotechnology (62)(63)(64). …”

Section: Discussionmentioning

confidence: 99%

Hydrophobic hydration from small to large lengthscales: Understanding and manipulating the crossover

Rajamani

Truskett

Garde

2005

Proc. Natl. Acad. Sci. U.S.A.

276

329

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Small and large hydrophobic solutes exhibit remarkably different hydration thermodynamics. Small solutes are accommodated in water with minor perturbations to water structure, and their hydration is captured accurately by theories that describe density fluctuations in pure water. In contrast, hydration of large solutes is accompanied by dewetting of their surfaces and requires a macroscopic thermodynamic description. A unified theoretical description of these lengthscale dependencies was presented by Lum, Chandler, and Weeks [(1999) J. Phys. Chem. B 103, 4570 -4577]. Here, we use molecular simulations to study lengthscale-dependent hydrophobic hydration under various thermodynamic conditions. We show that the hydration of small and large solutes displays disparate dependencies on thermodynamic variables, including pressure, temperature, and additive concentration. Understanding these dependencies allows manipulation of the small-tolarge crossover lengthscale, which is nanoscopic under ambient conditions. Specifically, applying hydrostatic tension or adding ethanol decreases the crossover length to molecular sizes, making it accessible to atomistic simulations. With detailed temperaturedependent studies, we further demonstrate that hydration thermodynamics changes gradually from entropic to enthalpic near the crossover. The nanoscopic lengthscale of the crossover and its sensitivity to thermodynamic variables imply that quantitative modeling of biomolecular self-assembly in aqueous solutions requires elements of both molecular and macroscopic hydration physics. We also show that the small-to-large crossover is directly related to the Egelstaff-Widom lengthscale, the product of surface tension and isothermal compressibility, which is another fundamental lengthscale in liquids. molecular dynamics ͉ salt and additive effects ͉ density fluctuations ͉ nonpolar solvation B iological self-assembly processes in aqueous solutions are driven by water-mediated interactions between constituents taking part in the assembly. Of these, hydrophobic interactions have received particular attention because of their relevance to protein folding and interactions, micelle and membrane formation, and molecular recognition (1-5). Theoretical work in this direction has been focused on the modeling of primitive hydrophobic phenomena, such as hydration and association of small hydrophobic particles in water (6-13). However, biological assembly occurs over a spectrum of lengthscales from that of an amino acid to proteins and larger. Naturally, fundamental understanding of the lengthscale dependence of hydration and association of hydrophobic solutes in water will be relevant to the quantitative modeling of realistic macromolecular processes (14,15).Small hydrophobic solutes can be accommodated into the open hydrogen-bonded network of liquid water without significant perturbations. Indeed, theories that model density fluctuations over small lengthscales in pure water provide a quantitative description of the hydration thermodynamics of small...

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Section: Discussionmentioning

confidence: 99%

Hydrophobic hydration from small to large lengthscales: Understanding and manipulating the crossover

Rajamani

Truskett

Garde

2005

Proc. Natl. Acad. Sci. U.S.A.

276

329

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“…Due to its unique geometrical features, such and similar systems have been used extensively to study the hydrophobic interaction and charge effect. 41,43,54,55,58,61,65,67,82,108 The specific two-plate system we study here is the same as that studied by MD simulations in Ref. 41 ξ = 1.…”

Section: B Two Charged Parallel Plates: Potential Of Mean Forcementioning

confidence: 94%

“…Experiment and molecular dynamics (MD) simulations have suggested that such pockets and the associated dry-wet transitions are crucial in proteinligand binding, and molecular recognition in general. [39][40][41][42][43][44][45][46][47][48][49][50][51][52][53][54][55][56][57][58] As the size of such a pocket is large enough to contain a few water molecules, it is evident that the fluctuating pocket surface can be hardly described by any kinds of fixed surfaces.…”

Section: Introductionmentioning

confidence: 99%

“…Moreover, it is clear that the PF-VISM with tight and loose initials predict wet and dry states, respectively, and that the electrostatics wets the inter-plate region, agreeing with MD simulations and previous level-set VISM calculations. 41,43,61,65,67,82,108 Note that the dielectric boundary force always directs from the high dielectric solvent region to the low dielectric solute region, and the PB based continuum electrostatics theory predicts such a force direction. 105,[109][110][111] This is the reason that with the solute partial charges, the dielectric boundary is pushed in to wet the system.…”

Section: B Two Charged Parallel Plates: Potential Of Mean Forcementioning

confidence: 99%

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A self-consistent phase-field approach to implicit solvation of charged molecules with Poisson–Boltzmann electrostatics

Sun

Wen

Zhao³

et al. 2015

The Journal of Chemical Physics

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Dielectric boundary based implicit-solvent models provide efficient descriptions of coarse-grained effects, particularly the electrostatic effect, of aqueous solvent. Recent years have seen the initial success of a new such model, variational implicit-solvent model (VISM) McCammon Phys. Rev. Lett. 96, 087802 (2006) and J. Chem. Phys. 124, 084905 (2006)], in capturing multiple dry and wet hydration states, describing the subtle electrostatic effect in hydrophobic interactions, and providing qualitatively good estimates of solvation free energies. Here, we develop a phase-field VISM to the solvation of charged molecules in aqueous solvent to include more flexibility. In this approach, a stable equilibrium molecular system is described by a phase field that takes one constant value in the solute region and a different constant value in the solvent region, and smoothly changes its value on a thin transition layer representing a smeared solute-solvent interface or dielectric boundary. Such a phase field minimizes an effective solvation free-energy functional that consists of the solute-solvent interfacial energy, solute-solvent van der Waals interaction energy, and electrostatic free energy described by the Poisson-Boltzmann theory. We apply our model and methods to the solvation of single ions, two parallel plates, and protein complexes BphC and p53/MDM2 to demonstrate the capability and efficiency of our approach at different levels. With a diffuse dielectric boundary, our new approach can describe the dielectric asymmetry in the solute-solvent interfacial region. Our theory is developed based on rigorous mathematical studies and is also connected to the Lum-Chandler-Weeks theory (1999). We discuss these connections and possible extensions of our theory and methods. C 2015 AIP Publishing LLC. [http://dx

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“…3 Furthermore, water, which is close to the liquid-vapor transition at normal conditions, can minimize interface area by locally evaporating and forming a 'nanobubble' within hydrophobic confinement. Evidence of bubble formation in confined geometry has been given early by computer simulations of smooth plate-like solutes, 4 but more recently it has been demonstrated in varying degrees in atomistically resolved plate-like solutes, 5,6 hydrophobic tubes and ion channels, 7,8 and in the collapse of proteins, 9,10 suggesting that it plays a key role in the stabilization and folding dynamics of certain classes of biomolecules. 11,12 Experimental evidence of nanobubbles in strong confinement (in contrast to bubbles at a single planar surface 3 ) has been given for instance in studies of water between hydrophobic surfaces, 13 in zeolites and silica nanotubes, 14,15 and on a subnanometer scale in nonpolar protein cavities.…”

Section: Introductionmentioning

confidence: 99%

Interface dynamics of microscopic cavities in water

Dzubiella

2007

The Journal of Chemical Physics

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An analytical description of the interface motion of a collapsing nanometer-sized spherical cavity in water is presented by a modification of the Rayleigh-Plesset equation in conjunction with explicit solvent molecular dynamics simulations. Quantitative agreement is found between the two approaches for the time-dependent cavity radius R(t) at different solvent conditions while in the continuum picture the solvent viscosity has to be corrected for curvature effects. The typical magnitude of the interface or collapse velocity is found to be given by the ratio of surface tension and fluid viscosity, v ≃ γ/η, while the curvature correction accelerates collapse dynamics on length scales below the equilibrium crossover scales (∼1nm). The study offers a starting point for an efficient implicit modeling of water dynamics in aqueous nanoassembly and protein systems in nonequilibrium.

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Nanoscale Hydrophobic Interaction and Nanobubble Nucleation

Cited by 98 publications

References 32 publications

Hydrophobic hydration from small to large lengthscales: Understanding and manipulating the crossover

Hydrophobic hydration from small to large lengthscales: Understanding and manipulating the crossover

A self-consistent phase-field approach to implicit solvation of charged molecules with Poisson–Boltzmann electrostatics

Interface dynamics of microscopic cavities in water

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