Molecular dynamics simulations in drug delivery research: Calcium chelation of G3.5 PAMAM dendrimers

Figures & data

Figure 1. Average of the radial distributions of the Ca²⁺ and Cl⁻ ions over the three runs performed for the EDTA and Ca²⁺ system in water.

Table 1. Average distance and average minimum distance from the van der Waals surface of the EDTA molecule and average percentage dwell time of the counter ions (Cl⁻ and Ca²⁺) included in this simulation

Counter ion	Average distance (Å)	Average minimum distance (Å)	Average (%) dwell time
Cl^−	15.89 (0.47)	2.95 (0.21)	0.00 (0.0)
Ca^2+	10.34 (5.70)	2.86 (0.58)	0.39 (0.42)

Standard deviations, over the three independent runs of the EDTA and Ca²⁺ in water MD simulations, given between parentheses.

Table 2. Average distance and average minimum distance from the van der Waals surface of the EDTA molecule and average percentage dwell time of the counter ions (Cl⁻, Na⁺, and Ca²⁺) included in this simulation

Counter ion	Average distance (Å)	Average minimum distance (Å)	Average (%) dwell time
Cl^−	15.84 (0.43)	3.05 (0.26)	0.00 (0.0)
Na^+	12.26 (4.04)	2.02 (0.09)	0.24 (0.29)
Ca^2+	9.05 (4.96)	2.54 (0.40)	0.47 (0.37)

Note: Standard deviations, over the three independent runs of the EDTA and Ca²⁺ in a buffer MD simulation, given between parentheses.

Figure 2. Three-dimensional representation of the final recorded step of one of the MD simulations of the G3.5 PAMAM dendrimer and Ca²⁺ in water.

Note: The blue spheres represent Ca²⁺ ions present in close proximity to the G3.5 PAMAM dendrimer.

Table 3. Average distance and average minimum distance from the van der Waals surface of the G3.5 PAMAM molecule and average percentage dwell time of the counter ions (Ca²⁺) included in this simulation

Counter ion	Average distance (Å)	Average minimum distance (Å)	Average (%) dwell time
Ca^2+	4.13 (2.83)	2.40 (0.02)	0.86 (0.22)

Note: Standard deviations, over the three independent runs of the G3.5 PAMAM dendrimer and Ca²⁺ in water MD simulation, given between parentheses.

Table 4. Average distance and average minimum distance from the van der Waals surface of the G3.5 PAMAM molecule and average percentage dwell time of the counter ions (Na⁺ and Ca²⁺) included in this simulation

Counter ion	Average distance (Å)	Average minimum distance (Å)	Average (%) dwell time
Na^+	7.50 (3.13)	2.02 (0.05)	0.60 (0.20)
Ca^2+	3.55 (2.20)	2.40 (0.01)	0.91 (0.13)

Note: Standard deviations, over the three independent runs of the G3.5 PAMAM dendrimer and Ca²⁺ in a buffer MD simulation, given between parentheses.

Figure 3. Average of the radial distribution functions of the Ca²⁺ ions over the three runs performed for the G3.5 PAMAM dendrimer and Ca²⁺ system in water (top) and the Ca²⁺ and Na⁺ ions over the three runs performed for the G3.5 PAMAM dendrimer in a buffer solution (bottom).