2. Density Functional Theory (DFT) Calculations
3. Molecular Dynamic (MD) Simulation Procedures and Results
- A MD simulation box with 5 × 5 × 5 = 125 molecules was built by the intrinsic tools in the Gromacs software, as shown in Figure 2a.
- We boxed those stable structures and set the distances from molecules to the boundaries of the simulation boxes to about +3 nm. In this manner we could build simulation systems with reasonable densities which were in the range of their gas states and also made the systems isolated from the adjacent simulation boxes under the periodic boundary conditions, as shown in Figure 2c.
- Longer (more than 1,000 picoseconds) equilibrating simulations were performed in the NVT ensembles, and we applied the PME method with the cut-off at 2.0 nm and high temperatures (in the range of 500–700 K) in order to make sure the entire system went to the gaseous state, i.e., all the molecules separated from each other and distributed randomly in the simulation box as shown in Figure 2d.By applying the above four-step procedure we could equilibrate the system in a gas state. As a result, we eliminated the problem due to directly equilibrating the initially prepared molecular system, Figure 2a, at high temperatures. The equilibrated and stable-structure gaseous state, Figure 2d, was then ready for cooling down towards the self-assembly.
- Further cooling down of the system resulted in the complete self-assembly of all the molecules (to solid state) as shown in Figure 2f.
3.1. Adamantane and ADM•Na
3.2. Diamantane and DIM•Na
3.3. Amantadine, Rimantadine and Memantine
- . Since there are nitrogen ions in the structure of amantadine, rimantadine and memantine, which makes their attractive intermolecular forces much larger than that of adamantane, higher temperatures should be applied to these systems in order to obtain initial gas state structures in the step d of Figure 2.
- . During the cooling down process of amantadine, rimantadine and memantine, hydrogen-bonds are formed which, as expected, increases their phase transition temperatures compared to that of adamantane.
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|Group 1||Group 2||Group 3|
|Adamantane||Diamantane||Amantadine||Rimantadine||Memantine||Optimized ADM•Na||Optimized DIM•Na|
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