Potential of Mean Force (PMFs) for Zerovalent Iron (Fe (100-110-111)) NanoParticles

The data is potential of mean force for three fcc configurations of  zero valent iron, (100), (110) and (111) nano particles interacting with side chain analugos of 22 different amino acids that are the building blocks of the proteins. We used adaptive Well-Tempered Metadynamics method to calculate the adsorption free energies that has previously been described for measuring the adsorption of the biomolecules for TiO2 and Ag. GROMACS and plumed softwares were used to carry out the simulations and the CHARMM-GUI/Nanomaterial Modeler was used create the iron slabs.  

The system was solvated using the original form of TIP3 water model . It was then neutralized by NaCl regarding the charge of the whole system. In the MD calculation the energy of the system has been minimized by Verlet particle-based cut-off scheme using charge groups and steepest gradient method for 1000 steps. The system was equilibrated under constant pressure, particles and temperature (300 K) condition (NPT) using Berendsen weak coupling or 1.0 ns. The component of the pressure tensor were set to 1.0 bar. The thermostat and the barostat for the relaxation time was 1.0 ps. The system underwent another more unbiased equilibrations for 10 ns in the NVT ensemble conditions. The Nose-Hoover thermostat’s relaxation time constant for the NVT ensemble was 5 ps. The cut-off distance was set to 1.0 nm for the VdW short range interactions. In the metadynamics biased simulation, the Surface Separation Distance (SSD) describes the reaction coordinates. This SSD measures the minimum distance of the center-of-mass (COMs) of the SCA Rmol and the surface atoms ri along the z coordinate.