MD simulations
Partial charges for MHC atoms and NO3-ions were obtained from density functional theory (DFT) calculations
using Gaussian 09 program. The Becke three parameters hybrid
exchange-correlation functional (B3LYP)15 and the
standard Gaussian-type basis set 6-311 G* were employed. All other force
field parameters for atoms were extracted from PLOS-AA force
field16. The initial configuration was solvated into a
cubic water box with 63 Å on each side, containing 8,000 water
molecules. The simple point charge (SPC) water model as explicit solvent
was used for solvation17. Then 15
Cl- were added to balance system charges. The system
energy was minimized for 500 steps using steepest descending method. The
initial velocities were assigned to produce a Maxwell distribution at
298 K. After a 0.2 ns equilibrium, a 1 ns simulation was carried out
with the NO3- ion frozen so that the
MHC carbon chains would reach a balance. Finally, this system perform a
3 ns MD simulation. More details are in the SI.