Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2011 Dec;32(16):3505-19.
doi: 10.1002/jcc.21939. Epub 2011 Sep 22.

Application of molecular dynamics simulations in molecular property prediction II: diffusion coefficient

Junmei Wang  1 , Tingjun Hou
Affiliations

Application of molecular dynamics simulations in molecular property prediction II: diffusion coefficient

Junmei Wang et al. J Comput Chem. 2011 Dec.

Abstract

In this work, we have evaluated how well the general assisted model building with energy refinement (AMBER) force field performs in studying the dynamic properties of liquids. Diffusion coefficients (D) have been predicted for 17 solvents, five organic compounds in aqueous solutions, four proteins in aqueous solutions, and nine organic compounds in nonaqueous solutions. An efficient sampling strategy has been proposed and tested in the calculation of the diffusion coefficients of solutes in solutions. There are two major findings of this study. First of all, the diffusion coefficients of organic solutes in aqueous solution can be well predicted: the average unsigned errors and the root mean square errors are 0.137 and 0.171 × 10(-5) cm(-2) s(-1), respectively. Second, although the absolute values of D cannot be predicted, good correlations have been achieved for eight organic solvents with experimental data (R(2) = 0.784), four proteins in aqueous solutions (R(2) = 0.996), and nine organic compounds in nonaqueous solutions (R(2) = 0.834). The temperature dependent behaviors of three solvents, namely, TIP3P water, dimethyl sulfoxide, and cyclohexane have been studied. The major molecular dynamics (MD) settings, such as the sizes of simulation boxes and with/without wrapping the coordinates of MD snapshots into the primary simulation boxes have been explored. We have concluded that our sampling strategy that averaging the mean square displacement collected in multiple short-MD simulations is efficient in predicting diffusion coefficients of solutes at infinite dilution.

PubMed Disclaimer

Figures

Figure 1
Figure 1
Calculations of diffusion coefficients of solutes in solvation that need long time MD simulations. (a) benzene in ethanol solution (b) phenol in aqueous solution
Figure 1
Figure 1
Calculations of diffusion coefficients of solutes in solvation that need long time MD simulations. (a) benzene in ethanol solution (b) phenol in aqueous solution
Figure 2
Figure 2
Prediction of diffusion coefficients of two solvents using the slope of mean square displacements (MSD) ~ simulation time plot. (a) TIP3P water at 298 K and (b) methanol at 298 K. Left panel: calculated D ~ simulation time plot; right panel: correlation between MSD and simulation time.
Figure 2
Figure 2
Prediction of diffusion coefficients of two solvents using the slope of mean square displacements (MSD) ~ simulation time plot. (a) TIP3P water at 298 K and (b) methanol at 298 K. Left panel: calculated D ~ simulation time plot; right panel: correlation between MSD and simulation time.
Figure 3
Figure 3
Correlation between calculated and experimental diffusion coefficients for the organic solvents
Figure 4
Figure 4
Correlation between mean squared displacement (MSD) and simulation time for representing solvents. (a) acetic acid, (b) DMSO, (c) CCl4, (d) cyclohexane, (e) NMA.
Figure 4
Figure 4
Correlation between mean squared displacement (MSD) and simulation time for representing solvents. (a) acetic acid, (b) DMSO, (c) CCl4, (d) cyclohexane, (e) NMA.
Figure 4
Figure 4
Correlation between mean squared displacement (MSD) and simulation time for representing solvents. (a) acetic acid, (b) DMSO, (c) CCl4, (d) cyclohexane, (e) NMA.
Figure 4
Figure 4
Correlation between mean squared displacement (MSD) and simulation time for representing solvents. (a) acetic acid, (b) DMSO, (c) CCl4, (d) cyclohexane, (e) NMA.
Figure 4
Figure 4
Correlation between mean squared displacement (MSD) and simulation time for representing solvents. (a) acetic acid, (b) DMSO, (c) CCl4, (d) cyclohexane, (e) NMA.
Figure 5
Figure 5
The temperature dependence of diffusion coefficient of TIP3P water
Figure 6
Figure 6
Performance of predicting diffusion coefficients at different temperatures for (a) cyclohexane and (b) DMSO
Figure 6
Figure 6
Performance of predicting diffusion coefficients at different temperatures for (a) cyclohexane and (b) DMSO
Figure 7
Figure 7
Calculations of diffusion coefficients for organic solutes in solutions using the strategy of averaging MSD of multiple independent MD runs. Left panel: MSD ~ simulation time plots for 20 MD runs; right panel: correlation between mean MSD ~ simulation time. (a) water in acetone, (b) aniline in benzene, (c) CHCl3 in CCl4, (d) benzene in cyclohexane, (e) pyridine in ethanol, (f) cyclohexane in water, (g) diethylamine in water, and (h) phenol in water
Figure 7
Figure 7
Calculations of diffusion coefficients for organic solutes in solutions using the strategy of averaging MSD of multiple independent MD runs. Left panel: MSD ~ simulation time plots for 20 MD runs; right panel: correlation between mean MSD ~ simulation time. (a) water in acetone, (b) aniline in benzene, (c) CHCl3 in CCl4, (d) benzene in cyclohexane, (e) pyridine in ethanol, (f) cyclohexane in water, (g) diethylamine in water, and (h) phenol in water
Figure 7
Figure 7
Calculations of diffusion coefficients for organic solutes in solutions using the strategy of averaging MSD of multiple independent MD runs. Left panel: MSD ~ simulation time plots for 20 MD runs; right panel: correlation between mean MSD ~ simulation time. (a) water in acetone, (b) aniline in benzene, (c) CHCl3 in CCl4, (d) benzene in cyclohexane, (e) pyridine in ethanol, (f) cyclohexane in water, (g) diethylamine in water, and (h) phenol in water
Figure 7
Figure 7
Calculations of diffusion coefficients for organic solutes in solutions using the strategy of averaging MSD of multiple independent MD runs. Left panel: MSD ~ simulation time plots for 20 MD runs; right panel: correlation between mean MSD ~ simulation time. (a) water in acetone, (b) aniline in benzene, (c) CHCl3 in CCl4, (d) benzene in cyclohexane, (e) pyridine in ethanol, (f) cyclohexane in water, (g) diethylamine in water, and (h) phenol in water
Figure 7
Figure 7
Calculations of diffusion coefficients for organic solutes in solutions using the strategy of averaging MSD of multiple independent MD runs. Left panel: MSD ~ simulation time plots for 20 MD runs; right panel: correlation between mean MSD ~ simulation time. (a) water in acetone, (b) aniline in benzene, (c) CHCl3 in CCl4, (d) benzene in cyclohexane, (e) pyridine in ethanol, (f) cyclohexane in water, (g) diethylamine in water, and (h) phenol in water
Figure 7
Figure 7
Calculations of diffusion coefficients for organic solutes in solutions using the strategy of averaging MSD of multiple independent MD runs. Left panel: MSD ~ simulation time plots for 20 MD runs; right panel: correlation between mean MSD ~ simulation time. (a) water in acetone, (b) aniline in benzene, (c) CHCl3 in CCl4, (d) benzene in cyclohexane, (e) pyridine in ethanol, (f) cyclohexane in water, (g) diethylamine in water, and (h) phenol in water
Figure 7
Figure 7
Calculations of diffusion coefficients for organic solutes in solutions using the strategy of averaging MSD of multiple independent MD runs. Left panel: MSD ~ simulation time plots for 20 MD runs; right panel: correlation between mean MSD ~ simulation time. (a) water in acetone, (b) aniline in benzene, (c) CHCl3 in CCl4, (d) benzene in cyclohexane, (e) pyridine in ethanol, (f) cyclohexane in water, (g) diethylamine in water, and (h) phenol in water
Figure 7
Figure 7
Calculations of diffusion coefficients for organic solutes in solutions using the strategy of averaging MSD of multiple independent MD runs. Left panel: MSD ~ simulation time plots for 20 MD runs; right panel: correlation between mean MSD ~ simulation time. (a) water in acetone, (b) aniline in benzene, (c) CHCl3 in CCl4, (d) benzene in cyclohexane, (e) pyridine in ethanol, (f) cyclohexane in water, (g) diethylamine in water, and (h) phenol in water
Figure 8
Figure 8
Correlations between the calculated and the experimental diffusion coefficients of nine solutes in organic solvents
Figure 9
Figure 9
Calculations of diffusion coefficients for proteins in aqueous solution using the strategy of averaging MSD of multiple independent MD runs. Left panel: MSD ~ simulation time plots for 20 MD runs; right panel: correlation between mean MSD ~ simulation time. (a) 1BWI, (b) 1EX3, (c) 1HRC, and (d) 1OVA
Figure 9
Figure 9
Calculations of diffusion coefficients for proteins in aqueous solution using the strategy of averaging MSD of multiple independent MD runs. Left panel: MSD ~ simulation time plots for 20 MD runs; right panel: correlation between mean MSD ~ simulation time. (a) 1BWI, (b) 1EX3, (c) 1HRC, and (d) 1OVA
Figure 9
Figure 9
Calculations of diffusion coefficients for proteins in aqueous solution using the strategy of averaging MSD of multiple independent MD runs. Left panel: MSD ~ simulation time plots for 20 MD runs; right panel: correlation between mean MSD ~ simulation time. (a) 1BWI, (b) 1EX3, (c) 1HRC, and (d) 1OVA
Figure 9
Figure 9
Calculations of diffusion coefficients for proteins in aqueous solution using the strategy of averaging MSD of multiple independent MD runs. Left panel: MSD ~ simulation time plots for 20 MD runs; right panel: correlation between mean MSD ~ simulation time. (a) 1BWI, (b) 1EX3, (c) 1HRC, and (d) 1OVA
Figure 10
Figure 10
Correlations between the calculated and the experimental diffusion coefficients of four proteins
See this image and copyright information in PMC

References

    1. Wang JM, Hou TJ. J Chem Theory Comput. 2011 ePub, ahead of print.
    1. Georgalis Y, Starikov EB, Hollenbach B, Lurz R, Scherzinger E, Saenger W, Lehrach H, Wanker EE. Proc Natl Acad Sci U S A. 1998;95(11):6118–6121. - PMC - PubMed
    1. Krewson CE, Saltzman WM. Brain Res. 1996;727(1-2):169–181. - PubMed
    1. Tellez CM, Cole KD. Electrophoresis. 2000;21(5):1001–1009. - PubMed
    1. Yu HB, Hansson T, van Gunsteren WF. Journal Of Chemical Physics. 2003;118(1):221–234.

Publication types

LinkOut - more resources