Grid-based dynamic electronic publication: A case study using combined experiment and simulation studies of crown ethers at the air/water interface.
Esther R Rousay, Hongchen Fu, Jamie M Robinson, Jeremy G Frey, Jonathan W Essex
School of Chemistry, University of Southampton,
Highfield, Southampton, SO17 1BJ, UK

Abstract The Publication@Source Paradigm and Challenges Body Molecular Dynamics Simulations Comparisons and Conclusions Acknowledgements Appendix:The TriScapeRDF browser References Glossary Search
Introduction Introduction - Compute Facility Figures Density Profiles Orientational Distribution

Density Profiles

In the analysis of the SHG, it is necessary to know, or assume, the value of the refractive index of the interfacial layer33. This is often taken as being the average of the refractive indices of the two bulk phases. This would suggest that the chromophore is positioned exactly between the phases. It is more likely that the chromophore will prefer one bulk phase to the other, and therefore, a weighted average is probably a better way of estimating the interfacial refractive index, nint. The position of the centre of the benzene ring throughout the simulation has been monitored to help determine the value to for the interfacial refractive index, nint. Figure 11 shows the positions of the benzene ring over 10 ns plotted alongside the profile of the water.

Figure 11. Plot shows the profile of the slab, along with the distributions of the benzene centre position of each crown over the 10ns simulation. Thgis data for this plot and the trajectories that give rise to it are available by links to the figure.

From the plot in figure 10, it can be judged that the preferred position of the benzene centre lies about 35% in the water phase, and 65% in the air. Thus, a more realistic value of nint than nint= (nsol- nwat)/2 used previously is nint= 0.35 nwat+ 0.65 nwat = nint= 1.12. Using the simulation derived nint, to recalculate the experimental value of D, we get D=0.62 instead of D=0.65 which is closer to the weak limit value of D = 0.6. It is useful therefore to investigate the tilt angle distribution to verify whether the chromophore is randomly aligned, or preferentially aligned with a wide distribution to further clarify the experimental results from the SHG.

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