Impact of the Crystal Structure of Silica Nanoparticles on Rhodamine 6G Adsorption: A Molecular Dynamics Study

Abstract

Understanding the mechanism of adsorption of Rhodamine 6G (R6G) to various crystal structures of silica nanoparticles (SNPs) is important to elucidate the impact of dye size when measuring the size of the dye-SNP complex via the time-resolved fluorescence anisotropy method. In this work, molecular dynamics (MD) simulations were used to get an insight into the R6G adsorption process, which cannot be observed using experimental methods. It was found that at low pH, α-Cristobalite structured SNPs have a strong affinity to R6G; however, at high pH, more surface silanol groups undergo ionization when compared with α-Quartz, preventing the adsorption. Therefore, α-Quartz structured SNPs are more suitable for R6G adsorption at high pH than the α-Cristobalite ones. Furthermore, it was found that stable adsorption can occur only when the R6G xanthene core is oriented flat with respect to the SNP surface, indicating that the dye size does not contribute significantly to the measured size of the dye-SNP complex. The requirement of correct dipole moment orientation indicates that only one R6G molecule can adsorb on any sized SNP, and the R6G layer formation on SNP is not possible. Moreover, the dimerization process of R6G and its competition with the adsorption has been explored. It has been shown that the highest stable R6G aggregate is a dimer, and in this form, R6G does not adsorb to SNPs. Finally, using steered molecular dynamics (SMD) with constant-velocity pulling, the binding energies of R6G dimers and R6G complexes with both α-Quartz and α-Cristobalite SNPs of 40 Å diameter were estimated. These confirm that R6G adsorption is most stable on 40 Å α-Quartz at pH 7, although dimerization is equally possible.

Figure 1

R6G structure from 2v3l.pdb (left) and the structure after modification, most commonly used in experiments (right) and therefore used in all MD simulations. Modified parts are circled in red.

Figure 2

Initial system setup. (a) Example of 40 Å SNP system containing one SNP and six R6G molecules; (b) example of 20 Å system containing three SNPs and six R6G. Water is indicated by the transparent film, while oxygen (red), silica (yellow), hydrogen (white), carbon (cyan), chlorine (ice blue), and sodium ions (tan) are indicated by VdW spheres. Note the scale of each system.

Figure 3

Silanol groups on the SNP surface. (a) Estimated number of surface silanol groups per unit area (Ų) and (b) number of ionized silanol groups per Ų at different pH values. The figures were created by using the SNP structures at different degrees of ionization built by CHARMM–GUI. Afterward, by calculating the volume of the SNP of a specific size, the values per Ų were estimated. Finally, the SNP sizes for both crystal structures were normalized to 40 and 20 Å to allow objective comparison.

Figure 4

COM distance plots for (a) 40qSNP7 and (b) 40qSNP12. Fluctuating colored lines represent COM distances from each R6G molecule to the SNP COM, while the gray line represents the adsorption threshold, which is set as a 5 Å distance between the SNP surface and the R6G molecule.

Figure 5

R6G adsorption process. (a) Simplified COM distance plot for two best adsorbing R6G molecules, R6G_4 (blue) and R6G_5 (red). The gray line marks the 5 Å distance from the SNP surface and (b) angle (θ) between SNP and R6G_5 dipole moments. The red line represents the average θ when R6G_5 is adsorbed. Inset in panel (b) shows how the θ angle was measured.

Figure 6

40qSNP7-R6G complex with visualized dipole moments. As predicted, in the case of state A, dipole moments are roughly in antiparallel orientation.

Figure 7

COM distance plots for (a) 40cSNP7 and (b) 40cSNP12. Fluctuating colored lines represent COM distances from each R6G molecule to SNP COM, the gray line marks the 5 Å distance from the SNP surface.

Figure 8

R6G adsorption on 40cSNP7. (a) Simplified COM distance plot for two best adsorbing R6G molecules, R6G_3 (blue) and R6G_4 (red); the gray line marks the 5 Å distance from the SNP surface. (b) 40cSNP7-R6G complex with visualized dipole moments.

Figure 9

COM distance plots for 20qSNPs. (a) Simplified COM distance plot for two best adsorbing R6G molecules, R6G_1 (blue) and R6G_2 (red) for 20qSNP7 and (b) simplified COM distance plot for two best adsorbing R6G molecules, R6G_1 (blue) and R6G_2 (red) for 20qSNP12. The gray line marks the 5 Å distance from the SNP surface.

Figure 10

R6G Dimer: (a) top view of the dimer with visualized dipole moments and (b) side view of the dimer.

Figure 11

Force and displacement as a function of time for the R6G pulled from 40qSNP7 with constant velocity. Desorption steps (A–E, red lines) are labeled.