256
D. Makieła and Z. Gburski
2 Calculation Details
The NAMD 2.11 software [29] was used to perform the molecular dynamics
(MD) computer simulations with the periodic boundary conditions. The common
CHARMM interaction potential [30] was used with VMD 1.9.2 [31] software for
visualization of the time evolution of the studied ensemble. The system was placed
in 66 × 68 × 140 Å cuboid simulation box. The β-cyclodextrins were located on
the graphene in the following manners, (a) OH group (first order) of βCD (site 1)
opposite the graphene layer, (b) OH group (second order) of βCD (site 2) opposite
the graphene surface, and (c) both first and second order–OH groups of βCD settled
alternately down (site 3) opposite the graphene sheet. The two densities of βCD
were investigated, low (nine β-cyclodextrins) and high with sixteen β-cyclodextrin
molecules. The ensembles were studied at six temperatures T = 280, 290, 300, 310,
320, and 330 K. The temperature was controlled via Langevin thermostat, a damping
coefficient of 1 ps
−1 was applied. The non-bonding interactions were cut off at 10 Å.
The Particle Mesh Ewald method was used to calculate the contribution of long-range
electrostatic interactions. The time step of the integration of equations of motion was
t = 1.0 fs for all calculations. The system was equilibrate in NVT [29] ensemble.
The equilibration phase was conducted up to 5 × 10
6 time steps, then the simulation
data were collected over the 30 ns, i.e., 30 × 10
6 integration time steps. The NAMD
software integration procedure based on BBK algorithm [32] was applied. The data
were collected in the “production” phase of simulation, every 2000 integration time
steps (2 ps).
3 Results
Figure 1 shows an instantaneous settlement of β-cyclodextrins on graphene honeycomb lattice.
The inspection of the simulated trajectories of β-cyclodextrin molecules indicates
that they are pretty mobile, can migrate all over a graphene layer. Nonetheless,
βCDs move only in near proximity of graphene, and they do not escape up or out
of the graphene surface. The motion of β-cyclodextrin molecules, perpendicular to
graphene sheet, is restricted by the attractive influence of graphene. In addition, the
characteristics of the movement of molecules depend on whether these molecules
point toward the plain of graphene with: site (1) OH group of the first order, or site
(2) OH group of the second order (Fig. 2). The above statements find justification
while inspecting the forthcoming figure.
The next figure (Fig. 3) shows the calculated mean square displacement
| r ⊥ (t)|
2 of the center of mass of βCD molecule, where r ⊥ (t) = =
r ⊥ (t) − −
r ⊥ (0)
and
r ⊥ is the component of the total displacement vector, perpendicular to graphene
plane.
D. Makieła and Z. Gburski
2 Calculation Details
The NAMD 2.11 software [29] was used to perform the molecular dynamics
(MD) computer simulations with the periodic boundary conditions. The common
CHARMM interaction potential [30] was used with VMD 1.9.2 [31] software for
visualization of the time evolution of the studied ensemble. The system was placed
in 66 × 68 × 140 Å cuboid simulation box. The β-cyclodextrins were located on
the graphene in the following manners, (a) OH group (first order) of βCD (site 1)
opposite the graphene layer, (b) OH group (second order) of βCD (site 2) opposite
the graphene surface, and (c) both first and second order–OH groups of βCD settled
alternately down (site 3) opposite the graphene sheet. The two densities of βCD
were investigated, low (nine β-cyclodextrins) and high with sixteen β-cyclodextrin
molecules. The ensembles were studied at six temperatures T = 280, 290, 300, 310,
320, and 330 K. The temperature was controlled via Langevin thermostat, a damping
coefficient of 1 ps
−1 was applied. The non-bonding interactions were cut off at 10 Å.
The Particle Mesh Ewald method was used to calculate the contribution of long-range
electrostatic interactions. The time step of the integration of equations of motion was
t = 1.0 fs for all calculations. The system was equilibrate in NVT [29] ensemble.
The equilibration phase was conducted up to 5 × 10
6 time steps, then the simulation
data were collected over the 30 ns, i.e., 30 × 10
6 integration time steps. The NAMD
software integration procedure based on BBK algorithm [32] was applied. The data
were collected in the “production” phase of simulation, every 2000 integration time
steps (2 ps).
3 Results
Figure 1 shows an instantaneous settlement of β-cyclodextrins on graphene honeycomb lattice.
The inspection of the simulated trajectories of β-cyclodextrin molecules indicates
that they are pretty mobile, can migrate all over a graphene layer. Nonetheless,
βCDs move only in near proximity of graphene, and they do not escape up or out
of the graphene surface. The motion of β-cyclodextrin molecules, perpendicular to
graphene sheet, is restricted by the attractive influence of graphene. In addition, the
characteristics of the movement of molecules depend on whether these molecules
point toward the plain of graphene with: site (1) OH group of the first order, or site
(2) OH group of the second order (Fig. 2). The above statements find justification
while inspecting the forthcoming figure.
The next figure (Fig. 3) shows the calculated mean square displacement
| r ⊥ (t)|
2 of the center of mass of βCD molecule, where r ⊥ (t) = =
r ⊥ (t) − −
r ⊥ (0)
and
r ⊥ is the component of the total displacement vector, perpendicular to graphene
plane.