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Direct calculation of 1-octanol–water partition coefficients from adaptive biasing force molecular dynamics simulations
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10.1063/1.4730040
/content/aip/journal/jcp/137/1/10.1063/1.4730040
http://aip.metastore.ingenta.com/content/aip/journal/jcp/137/1/10.1063/1.4730040

Figures

Image of FIG. 1.
FIG. 1.

Schematic of the system used for the calculation of ΔG via the method of direct transfer (system S3). The solute n-butane was placed initially at the center of water box. During the simulation, the solute diffused from the water rich phase to the 1-octanol rich phase. A, B, C, D, E, F, G, H, and I correspond to the midpoint of the 9 ABF windows along the reaction coordinate. The corresponding average free energy for each of the 9 windows is shown as filled circles on the PMF profile. Arrow shows the direction of solute transfer from water into 1-octanol.

Image of FIG. 2.
FIG. 2.

Hydration free energy profile generated with ABF-MD method for n-alkane transfer from water to vacuum (system S1). Dashed line denotes the location of the interface. Data shown are from calculations performed with a 14 Å LJ cutoff.

Image of FIG. 3.
FIG. 3.

Hydration free energy for n-alkanes as predicted by adaptive biasing force molecular dynamics simulations with a LJ cutoff of 14.0 Å (red diamonds); thermodynamic integration (green squares); experiment70,75 (black circles).

Image of FIG. 4.
FIG. 4.

Solvation free energy profile generated with ABF method for n-alkane transfer from 1-octanol to vacuum (system S2). Dashed line denotes the location of the interface. Data shown are from calculations performed with a 14 Å LJ cutoff.

Image of FIG. 5.
FIG. 5.

Solvation free energy for transfer of n-alkanes from vacuum into 1-octanol predicted by adaptive biasing force molecular dynamics using a Lennard-Jones cutoff of 14 Å for the TraPPE-UA force field (red diamonds); thermodynamic integration (green squares); GEMC (blue triangles); experiment (black circles).

Image of FIG. 6.
FIG. 6.

Octanol–water partition coefficient for n-alkanes predicted by adaptive force bias molecular dynamics simulations using a 14 Å LJ cutoff: direct transfer for 30 Å (red diamond) and 100 Å (orange triangles) 1-octanol box; indirect transfer (blue triangles); thermodynamic integration (green squares); experiment (black circles).

Image of FIG. 7.
FIG. 7.

Density profiles for system S3. The density has been normalized by average bulk density of each component: water (green), 1-octanol CH2 (black), 1-octanol oxygen (red). Dashed blue line represents position of the interface.

Image of FIG. 8.
FIG. 8.

Free energy profile generated with ABF method for ethane (red), butane (orange), hexane (green), and octane (blue) transfer in system S3 from water to 1-octanol (dry) phase. Data shown are from calculations performed with a 14 Å LJ cutoff. Dashed black line marks the location of the interface.

Image of FIG. 9.
FIG. 9.

Free energy profile generated with ABF method for n-alkane transfer from water to 1-octanol (dry) phase in system S4. Data shown are from calculations performed with a 14 Å LJ cutoff.

Image of FIG. 10.
FIG. 10.

(Top panel) Number integrals for interactions between CH2 (octane) and O (1-octanol). (Bottom panel) Number integrals for interactions between CH2(octane) and CH2(1-octanol). System S3 (black line), system S4 (red line).

Image of FIG. 11.
FIG. 11.

Distribution of samples along the reaction coordinate from 8 ns ABF-MD simulations for the transfer of n-pentane from water to vacuum (red) and from 1-octanol to vacuum (black). Distribution was constructed by combining data from the 5 individual simulations.

Image of FIG. 12.
FIG. 12.

Evolution of sampling histogram from 0.02 ns to 1.0 ns during 1.0 ns ABF-MD simulation.

Image of FIG. 13.
FIG. 13.

Evolution of max-min ratio during 1 ns ABF MD simulation.

Tables

Generic image for table
Table I.

Hydration free energies ΔG HYD for n-alkanes predicted by TraPPE-UA force field.

Generic image for table
Table II.

Comparison of free energies of hydration and log Kow for n-alkanes predicted using SPC/E and TIP4P water models. Data are shown for simulations using a 14.0 Å LJ cutoff.

Generic image for table
Table III.

Solvation free energies (ΔG SOLV ) for n-alkanes in 1-octanol predicted using TraPPE-UA force field.

Generic image for table
Table IV.

Effect of water saturation of the octanol phase on the free energies of solvation and partition coefficients for n-alkanes. Data shown are for simulations using a 14.0 Å LJ cutoff.

Generic image for table
Table V.

Octanol–water partition coefficients (log KOW) predicted by the TraPPE-UA force field for n-alkanes.

Generic image for table
Table VI.

Sampling efficiency and max-min ratio at the end of ABF simulations. Data shown are for the case of n-pentane transfer from 1-octanol to vacuum (system S1), n-pentane transfer from water to vacuum (system S2), and of n-pentane transfer from water to 1-octanol (system S4).

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/content/aip/journal/jcp/137/1/10.1063/1.4730040
2012-07-03
2014-04-20
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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: Direct calculation of 1-octanol–water partition coefficients from adaptive biasing force molecular dynamics simulations
http://aip.metastore.ingenta.com/content/aip/journal/jcp/137/1/10.1063/1.4730040
10.1063/1.4730040
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