Model building, equilibration and
validation of a 105 lipid Nonoxynol 10 micelle
Nonyl phenol ethoxylated decyl ether (also Nonoxynol 10, or Tergitol NP-10) is a nonionic, water
soluble surfactant. An aggregation number of 105 lipids and an ellipsoidal
shape has been reported (Zhang R., Somasundaran P., Langmuir. 2004 Sep 28;20(20):8552-8,
doi:10.1021/la049295a [Reference]).
Molecule:
The initial model building and subsequent equilibration were performed with Micelle
Maker.
Because of the enormous size of the system (291229 atoms, box size 147^3 Å) and the resulting high
computational costs, Nonoxynol 10 is not available in the Micelle Maker web
service. However, we provide the parameter files for AMBER and the Micelle
Maker results instead.
Parameters:
The nonionic head group of Nonoxynol 10 was described by the GAFF2 force
field as implemented in AMBER16, the hydrophobic tail was described by the
GLYCAM library similar to all other lipids available in the Micelle Maker web
service. Partial charges were calculated in the gas-phase at the
HF/6-31G* level of theory, using Gaussian09 rev. D.01 and the standard RESP
fitting procedure.
LEaP parameter files for Nonoxynol 10:
Download library file
Download frcmod file
Micelle after equilibration:
Results from initial model building and
equilibration:
Download here
Molecular dynamics simulation (MD):
The validation simulation and subsequent analysis was done in the same way as described for all
other lipids described in the Micelle Maker reference.
Micelle after 100ns MD simulation:
Radius of Gyration:
Eccentricity:
Calculated micelle parameters:
Please also see Table S1 in the Micelle Maker reference for comparison.
No. lipids
105
Salt c
0.15
Tail carbons
10
Rs
34.611 ± 0.266
ROG
26.809 ± 0.206
ROG max.
49.29 ± 2.244
SASA
59508 ± 1462
l ratio
1.185 ± 0.066
ecc
0.088 ± 0.032
Dc_h
1.834
Dc_t
0.651
If you use any data obtained from this site in your publication, please
cite:
Krüger, D. M., Kamerlin, S. C. L., Micelle Maker: An Online Tool for
Generating Equilibrated Micelles as Direct Input for Molecular Dynamics
Simulations, ACS Omega, 2017, 2 (8), pp 4524–4530, DOI:
10.1021/acsomega.7b00820.
[Reference]