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Oil/water transfer is partly driven by molecular shape, not just size.

ABSTRACT: We present a new approach to computer modeling of solvation free energies of oil in water. In Semi-Explicit Assembly, we first precompute structural and thermal properties of TIP3P waters around different Lennard-Jones spheres. This tabulated information is then used to compute the nonpolar solvation properties of arbitrary solutes. By accumulating interactions from whole regions of the solute molecule, Semi-Explicit Assembly more properly accounts for effects of solute shape and solves problems that appear as nonadditivities in traditional gammaA approaches. Semi-Explicit Assembly involves little parameter fitting because the solute and water properties are taken from existing force fields. We tested the predictions on alkanes, alkynes, linear and planar polyaromatic hydrocarbons, and on a diverse set of 504 molecules previously explored by explicit solvent simulations. We found that not all hydrocarbons are the same. Hydrocarbons have "hot spots", places where first-shell waters interact more strongly with the molecule than at other locations. For example, waters are more attracted to hover over hydrocarbon rings than at the edges. By accounting for these collective regional effects, Semi-Explicit Assembly approaches the physical accuracies of explicit solvent models in computing nonpolar solvation free energies, but because of the precomputations and the regional additivities, it is nearly as fast to compute as gammaA methods.

SUBMITTER: Fennell CJ

PROVIDER: S-EPMC2810857 | biostudies-literature | 2010 Jan

REPOSITORIES: biostudies-literature

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Oil/water transfer is partly driven by molecular shape, not just size.

Fennell Christopher J CJ Kehoe Charlie C Dill Ken A KA

Journal of the American Chemical Society 20100101 1

We present a new approach to computer modeling of solvation free energies of oil in water. In Semi-Explicit Assembly, we first precompute structural and thermal properties of TIP3P waters around different Lennard-Jones spheres. This tabulated information is then used to compute the nonpolar solvation properties of arbitrary solutes. By accumulating interactions from whole regions of the solute molecule, Semi-Explicit Assembly more properly accounts for effects of solute shape and solves problems ...[more]

PMID: 19961159

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Project description:The molecular characteristics of soluble extensin from tomato have been investigated. An apparent molecular mass greater than 240 kDa has been previously observed with the shape-dependent method of gel-filtration chromatography [Brownleader and Dey (1993) Planta (Berlin) 191, 457-469]. Tomato extensin is a heavily glycosylated protein that does not migrate into SDS/polyacrylamide gels. This shape-dependent behaviour raises doubts about agreement between the observed apparent mass and the absolute value. The molecular mass measured with matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF MS) was 72.3 kDa, with no evidence of any other species except a doubly charged ion. The sample was therefore considered to be monodisperse under the conditions used. Electron microscopy of soluble extensin showed the presence of particles 40-50 nm in length and 2.0-2.5 nm in width. A minority of these particles showed a central 'kink'. A number of smaller and generally wider particles (20 nm x 2-4 nm) were considered to be folded monomers and larger particles were thought to be dimers. Sedimentation analysis showed that extensin exists in a rapid monomer-dimer equilibrium in the concentration range and buffer used. Sedimentation equilibrium data gave a Kd of 8.5 microM and sedimentation velocity data generated a Kd between 1 and 10 microM. The concentration dependence of the measured sedimentation coefficient was used, together with hydrodynamic bead modelling, to define plausible shapes for monomer and dimer. This suggests that monomeric extensin is an elongated rod of length 40 nm and width 2 nm, which forms staggered dimers of average length 50 nm and width 3 nm. Extensin is an integral component of the primary cell wall. The physical characteristics (size, shape and form) of the rod-like extensin have been evaluated in this paper so that the role that extensin plays in primary cell wall architecture and during plant disease resistance can be more fully understood.

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Oil/water transfer is partly driven by molecular shape, not just size.

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Oil/water transfer is partly driven by molecular shape, not just size.

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