Supporting information for: BOCS: Bottom-up Open-source Coarse-graining. Software

Transcription

1 Supporting information for: BOCS: Bottom-up Open-source Coarse-graining Software Nicholas J. H. Dunn,, Kathryn M. Lebold, Michael R. DeLyser, Joseph F. Rudzinski,, and W.G. Noid, Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 1682 Current Address: Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN Current Address: Max Planck Institute for Polymer Research, Mainz, Germany S1

2 This document provides supporting information for the manuscript: BOCS: Bottomup Open-source Coarse-graining Software by Nicholas J. H. Dunn, Kathryn M. Lebold, Michael R. Delyser, Joseph F. Rudzinski, and W. G. Noid. In particular, this document provides additional potentials, structural distribution functions, and volume distributions to supplement the results of the main text. Radial Distribution Functions Figure 5 of the main text presents CT-CT radial distribution functions (rdfs) from simulations of pure butane, pure heptane, and pure decane. Figures S1 and S2 present CM-CM and CT-CM rdfs from the same simulations. In both figures, panels a and b present results from simulations of pure heptane and pure decane, respectively. The dashed black curves present results for the mapped AA ensemble, while the solid blue and solid red curves present results for the system-specific MS-CG and transferable extended ensemble () models, respectively. As observed for the CT-CT distributions in Figure 5 of the main text, the CM-CM and CT-CM distributions for the two CG models are nearly identical and agree well with the distributions for the mapped AA ensemble. Intramolecular Potentials Figures S3 and S4 present the intramolecular potentials calculated for the CG alkane models. In these figures, the dashed black curves present transferable potentials, while the solid colored curves present the system-specific MS-CG potentials. Note that the and system-specific MS-CG potentials are very similar in all cases. This is expected because the intramolecular interactions are relatively decoupled from the intermolecular interactions and because, with the exception of the CT-CM bond, each of these intramolecular potentials is unique to a single alkane molecule in the parameterization extended ensemble. S2

3 Intramolecular Distribution Functions Figures S5, S6 and S7 present the simulated intramolecular probability distributions for butane, heptane, and decane, respectively. The curves in these figures are labeled the same as in Fig. S1. Both of the CG models accurately reproduce the mapped AA distributions for bonds. However, the CG models significantly underestimate the tendency of the AA models to sample large angles in heptane and decane. Panel d) of Fig. S7 demonstrates that the AA mapped distribution for the decane dihedral demonstrates relatively little structure. (Note the scale of the y-axis.) Accordingly, the CG models did not include a potential for modeling this degree of freedom. Consequently, it is unsurprising that the CG models do not accurately reproduce the fine details of this distribution. Volume Distributions Figure S8 presents the simulated volume distributions for the pure alkane systems. Each panel corresponds to a different system. The curves are color coded according to the same scheme as Fig. S1. In all cases, the CG distribution very closely matches the AA distribution. This accuracy is also reflected in the PV curves presented in Fig. 7 of the main text. The self-consistent pressure-matching approach ensures this level of accuracy. 5:5 Butane:Decane Mixture Figures S9 and S1 present results from simulations of the 5:5 butane:decane mixture with the AA model and with the transferable potentials. Both figures employ the same color scheme as Figure S1. Figure S9 presents the rdfs for the pair interactions that are not shown in the main text. Each panel corresponds to a different pair interaction. In all cases, the rdfs agree well with the rdfs for the mapped ensemble. Figure S1 compares the volume distributions for the AA and models. As expected, the distributions match very closely, S3

4 as indicated by the PV curves in Fig. 9 of the main text. Supporting Information Figure Captions S1 Radial distribution functions for the CM-CM nonbonded pair interactions for heptane and decane. The dashed black curves present results for the mapped AA ensemble, while the solid blue and solid red curves present results for the system-specific MS-CG and transferable potentials, respectively. S2 Radial distribution functions for the CT-CM nonbonded pair interactions for heptane and decane. The dashed black curves present results for the mapped AA ensemble, while the solid blue and solid red curves present results for the system-specific MS-CG and transferable potentials, respectively. S3 Bond stretching potentials for CT-CT, CT-CM, and c) CM-CM bonds. The dashed black curves present transferable potentials, while the solid red, blue, and green curves present system-specific MS-CG potentials for butane, heptane, and decane, respectively. S4 Angle potentials for CT-CM-CT and CT-CM-CM angles. The dashed black curves present transferable potentials, while the solid blue and green curves present system-specific MS-CG potentials for heptane and decane, respectively. S5 Bond stretching distribution for the CT-CT bond in butane. The dashed black curves present results for the mapped AA ensemble, while the solid blue and solid red curves present results for the system-specific MS-CG and transferable models, respectively. S6 Probability distributions for the CT-CM bond and the CT-CM-CT angle in heptane. The dashed black curves present results for the mapped AA ensemble, while the solid blue and solid red curves present results for the system-specific MS-CG and transferable models, respectively. S4

5 S7 Probability distributions for the CT-CM bond, CM-CM bond, c) CT-CM-CM angle, and d) CT-CM-CM-CT dihedral in decane. The dashed black curves present results for the mapped AA ensemble, while the solid blue and solid red curves present results for the system-specific MS-CG and transferable models, respectively. S8 Volume distributions from simulations of pure butane, pure heptane, and c) pure decane. The dashed black curves present results for the AA model, while the solid blue and solid red curves present results for the system-specific MS-CG and transferable models, respectively. S9 Radial distribution functions from simulations of the 5:5 butane:decane mixture. Panels a, b, and c present distributions for butane-ct-decane-cm pairs, decane-ctdecane-cm pairs, and decane-cm-decane-cm pairs. The dashed black and solid red curves correspond to distributions for the mapped AA ensemble and simulated model, respectively. S1 Volume distributions for the simulated 5:5 butane:decane mixture. The dashed black and solid red curves correspond to distributions for the AA and simulated models, respectively. S5

6 Supporting Information Figures g(r).8 MSCG g(r).8 r (nm) Figure S1 Radial distribution functions for the CM-CM nonbonded pair interactions for heptane and decane. The dashed black curves present results for the mapped AA ensemble, while the solid blue and solid red curves present results for the system-specific MS-CG and transferable potentials, respectively. S6

7 g(r).8 MSCG g(r).8 r (nm) Figure S2 Radial distribution functions for the CT-CM nonbonded pair interactions for heptane and decane. The dashed black curves present results for the mapped AA ensemble, while the solid blue and solid red curves present results for the system-specific MS-CG and transferable potentials, respectively. S7

8 4 Butane Heptane Decane 2 U (kj mol -1 ) c).3.4 Bond length (nm) Figure S3 Bond stretching potentials for CT-CT, CT-CM, and c) CM-CM bonds. The dashed black curves present transferable potentials, while the solid red, blue, and green curves present system-specific MS-CG potentials for butane, heptane, and decane, respectively. S8

9 U (kj mol -1 ) U (kj mol -1 ) Heptane Decane Figure S4 Angle potentials for CT-CM-CT and CT-CM-CM angles. The dashed black curves present transferable potentials, while the solid blue and green curves present system-specific MS-CG potentials for heptane and decane, respectively. S9

10 6 3 MSCG bond length (nm) Figure S5 Bond stretching distribution for the CT-CT bond in butane. The dashed black curves present results for the mapped AA ensemble, while the solid blue and solid red curves present results for the system-specific MS-CG and transferable models, respectively. S1

11 3 MSCG bond length (nm) angle (degrees) Figure S6 Probability distributions for the CT-CM bond and the CT-CM-CT angle in heptane. The dashed black curves present results for the mapped AA ensemble, while the solid blue and solid red curves present results for the system-specific MS-CG and transferable models, respectively. S11

12 3 MSCG.3 c) bond length (nm) angle (deg) 4.28 d) bond length (nm) dihedral (deg) Figure S7 Probability distributions for the CT-CM bond, CM-CM bond, c) CT-CM-CM angle, and d) CT-CM-CM-CT dihedral in decane. The dashed black curves present results for the mapped AA ensemble, while the solid blue and solid red curves present results for the system-specific MS-CG and transferable models, respectively. S12

13 .4.2 Probability density (nm -3 ) MSCG c) Volume (nm 3 ) Figure S8 Volume distributions from simulations of pure butane, pure heptane, and c) pure decane. The dashed black curves present results for the AA model, while the solid blue and solid red curves present results for the system-specific MS-CG and transferable models, respectively. S13

14 1.6 g(r) g(r) c) g(r) r (nm) Figure S9 Radial distribution functions from simulations of the 5:5 butane:decane mixture. Panels a, b, and c present distributions for butane-ct-decane-cm pairs, decane-ct-decane-cm pairs, and decane-cm-decane-cm pairs. The dashed black and solid red curves correspond to distributions for the mapped AA ensemble and simulated model, respectively. S14

15 Probability density (nm -3 ) Figure S1 Volume distributions for the simulated 5:5 butane:decane mixture. The dashed black and solid red curves correspond to distributions for the AA and simulated models, respectively. S15