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Water properties and potential of mean force for hydrophobic interactions of methane and nanoscopic pockets studied by computer simulations
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10.1063/1.2749250
/content/aip/journal/jcp/127/5/10.1063/1.2749250
http://aip.metastore.ingenta.com/content/aip/journal/jcp/127/5/10.1063/1.2749250

Figures

Image of FIG. 1.
FIG. 1.

Simulated system: hydrophobic walls, 1030 water molecules and two methanelike particles.

Image of FIG. 2.
FIG. 2.

Pocket intersection: effective radius and effective volume, measured from the pocket entrance (defined as a surface containing the first layer of wall molecules) to border, where water-wall interaction energy was greater that , Me: methane molecule, and : reaction coordinate used in PMF calculations.

Image of FIG. 3.
FIG. 3.

Spatial distribution of: wall-solvent energy , solvent-solvent energy , water density , and solvent energy density . These and all other contour maps were generated with the XFARBE program (Ref. 81).

Image of FIG. 4.
FIG. 4.

PMF curves for considered systems. Plots resulting from increasing number of simulation data are shown. Note that base lines are shifted for each plot except the R8.

Image of FIG. 5.
FIG. 5.

sPMFs plots (solid line), work component (dotted line), and their difference (dashed line), accompanied by solvent density and solvent energy density contour maps for selected values of the reaction coordinate. Grayscale legends inserted in R8 and R5 plots are common for all cases.

Image of FIG. 6.
FIG. 6.

Schematic representation of the molecular surface (MS: thick line) and the solvent accessible surface (SAS: dashed line) of two atoms (gray). An empty circle denotes a solvent sphere used for surface construction.

Image of FIG. 7.
FIG. 7.

Comparison of sPMFs (solid lines) with estimations based on SASA and MSA approaches (dashed lines). Note that base lines are shifted for each plot except the R8.

Image of FIG. 8.
FIG. 8.

RMSD values for predictions in relation to sPMF for each system.

Tables

Generic image for table
Table I.

Force field parameters. (m)—modified parameters for grid. LJ potential from is .

Generic image for table
Table II.

Properties of systems used in PMF calculation. : effective pocket volume; : effective pocket radius; : number of water molecules occupying a pocket volume when standard density is assumed; and : distance between walls.

Generic image for table
Table III.

Detailed values for extrema in PMF curves. CM: PMF value at contact minimum; sCM: solvent induced contribution to CM; DB: solvent induced contribution of PMF at desolvation barrier.

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/content/aip/journal/jcp/127/5/10.1063/1.2749250
2007-08-02
2014-04-19
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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: Water properties and potential of mean force for hydrophobic interactions of methane and nanoscopic pockets studied by computer simulations
http://aip.metastore.ingenta.com/content/aip/journal/jcp/127/5/10.1063/1.2749250
10.1063/1.2749250
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