## 3 Results and Discussions
### Molecular Dynamics Simulations
Otherwise, the difference could stem from the higher hydrophobicity of L-D-L phenylalanine residues of D-Phes. Figure 4: The last snapshots of the second type of simulations of L- (left) and D-Phes (right) (**a**) and corresponding secondary structure profiles during the simulations (**b**). Water molecules and ions were omitted for the clarity. Charged and three phenylalanine residues are shown by licorice model. Orange balls show phosphorus atoms of DMPC membrane. We surveyed the Lennard-Jones interaction term of the three phenylalanine residues with the hydrophobic tail of DMPC membrane to estimate hydrophobicity of N-terminal parts of the peptides. Figure 7 shows the average interaction energies between the three phenylalanine residues and the hydrophobic tails of DMPC membrane. The three Phe residues of L-Phe exhibited slightly more rapid and favorable interaction with the membrane than those of D-Phe did in the first 30 ns. Then, the  
Figure 5: The last snapshots of the third type of simulations of L- (left) and D-Phes (right). Water molecules and ions were omitted for the clarity. Charged and three-phenylalanine residues are shown by licorice model. Orange balls show phosphorus atoms of DMPC membrane. [PERSON] and yellow balls represent the sodium and chloride ions respectively  
Figure 6: Secondary structure profiles during the third type of simulations (MD3). residues of D-Phes showed slightly more interaction compared to the residues of L-Phes during the period from 30 ns to 200 ns. These data suggest that the higher hydrophobicity of D-Phes, which was also observed in our HPLC results, facilitated interactions with the membrane. Furthermore, we analyzed the center of mass distances between the phenyl rings during the last 100 ns simulations. There was a lack of difference between the distributions of the first two rings. Figure 8 shows the distribution of the center of mass distances between the second and third phenyl rings. The distribution of D-Phes was smaller than that of L-Phes. The distances in L-Phes showed broader distribution than 6 A. When the distance between two phenyl rings was less than 6 A, \(\pi\)-\(\pi\) stacking could occur between them [50]. In Figure 8, we observed a population of D-Phes smaller than 6 A. When the peptides form oligomeric state in solution [3], the second and the third rings of b-Phes could with stack each other. Stacking of the phenyl rings are important for the self-assembly of short peptides, and phenylalanine tripeptides consisting of l- and d- amino acids have been shown to self-assemble into nanostructures [51]. Although we did not consider peptide-peptide interactions in this work, the higher probability of the packing in D-Phes could affect the association of the peptides and thus affect its interactions with membrane. Figure 8: Distribution of the center of mass distance between second and third phenyl rings during the last 100 ns of all three runs. Figure 7: Lennard–Jones interaction components between the three phenylalanine residues and the hydrophobic tails of DMPC membrane. Three different runs of the peptides averaged, and the running average values are shown in this figure for every 1 ns.