# Predicting Melting Points of Biofriendly Choline-Based Ionic Liquids with Molecular Dynamics
## 2 Materials and Methods
### Solid Phase Structures  
The starting structures were generated randomly with the Packmol (Packmol 1.1.2.272, University of Campinas, Sao Paulo, Brazil, 2009) algorithm [26]. First, these structures were equilibriated in a short MD run with the steep integrator. Subsequently, the solid phases were obtained in 200 ps \(NVT\) simulations, where the temperature was changed from 1000 K to 1 K in 100 ps and then kept at 1 K for 100 ps.  
200 ps, or even 200 us, is too short timescale for the formation of a realistic solid phase--a process that is known to be problematic and time-consuming for the ILs in experiments. The necessary macroscopic timescales are practically unreachable in simulations. Thus, Coulombic potentials wells were added to the system to facilitate the generation of more ordered solid phase structures. Similar approach was used in the PSCP method by [PERSON] et al. to obtain a single known solid phase during a cycle of simulations for the purposes of melting point prediction [19; 20].  
In contrast to the PSCP method, in this work, as the placement of ions in the real solid phase was unknown for our ILs, eight different potential well lattices were constructed for each IL. Different lattices were generated by the combination of CsCl and NaCl ionic lattices with 3:2:2, 3:3:2, 3:3:3 and 4:3:2 lattice vector ratios. Thus, all subsequent simulations were conducted with eight differently  
Figure 2: Schematical workflow of the developed melting point prediction method. Ionic liquids are packed, structurized with Coulombic potential wells, heated from 175 to 475 K and the melting points are then estimated from diffusion coefficient (\(D\)) temperature (\(T\)) dependence.  
packed systems for each IL. Even though cubic or orthorombic initial lattices were used, the ions were not explicitly restricted to be at the centers of potential wells even if it was the most energetically favored. Also ions were allowed to relax prior to annealing simulations, so that the IL lattice could adapt any of the Bravais lattices.  
A potential well is a virtual site which interacts with the rest of the system only through a linear Coulombic potential. The linear potential scaling from distance is important to avoid the forces to approach infinity at close distances since they have no Lennard-Jones repulsion. The presence of the potential wells enable the use of elevated temperatures without the decomposition of an ordered lattice. The elevated temperatures are beneficial for allowing ions to overcome rotational energy barriers in short amounts of time, after which the system is cooled down.  
After the initial structuring, six subsequent 500 ps-long \(NVT\) simulations were run again with potential wells. In simulations one, three and five only the anions were allowed to move while the positions of the cations were restrained. In simulations two, four and six the cations moved while the anions were restrained. The temperature control was similar to the initial potential well simulation: the temperature was decreased from 1000 K to 1 K within 400 ps and was kept there for the final 100 ps. However, weaker potential wells were used in each consecutive simulation so that the yielded solid phase structure could improve iteratively as the perturbation from the potential wells was weaker. An iterative approach and using position restrictions is necessary for obtaining a more organized solid phase, because the position of every ion in the system depends on all other ions.