90
D. Makieła et al.
well-characterized nanoscale pool for a range of chemistries. In recent years, the
molecular dynamics (MD) computer simulation method has become a popular way
to study micelles [5, 9–31], because of its ability to simulate phenomena at the
atomic scale on very short time periods. In this work we have used MD technique
to detailed study of the dynamics of water molecules confined in spherical reverse
micelle composed of the important living cell biomembrane constituent, namely,
1,2-dimyristoyl-sn-glycero-3phosphocholine (DMPC) molecules.
6.1.1 Simulation Details
Molecular dynamics simulations were performed with NAMD 2.8 simulations code
[32, 33], with the all-atom CHARMM27 force field [34] for modeling DMPC
phospholipid. We used VMD 1.9.2 [35] to visualize the simulated system. The
filled with water spherical reverse micelle, formed from 58 DMPC molecules,
was constructed, and the sample composed of these micelles was simulated with
the periodic boundary condition. The TIP3 [36] model of water was used. The
equilibration process was performed over 8 * 10 6 time steps with step equal to
1 fs. After that initial simulation, the “production run” was conducted, up to 8 ns.
We kept constant number of particles, constant volume, and constant temperature
(NVT ensemble) for the system studied. During this stage of research, data were
collected every 500 simulation steps for calculating physical observables and
visualization of the systems. The simulations were performed for the temperature
range 280 K ≤ T ≤ 320 K. To better assess the impact of confinement on dynamics
of water molecules, results were compared with the corresponding data for a bulk
(unconfined) water.
6.1.2 Results
In order to visualize the system studied, we present the building block of micelle,
i.e., DMPC molecule (see Fig. 6.1), and an example snapshot of the equilibrium
configuration of the micelle formed from 58 DMPC molecules and filled with water
(see Fig. 6.2).
Note that the interior of micelle happened to be approximately spherical.
First, we have calculated the radial distribution function g(r) of the center of
mass of confined water molecules. The temperature dependence of g(r) is presented
in Fig. 6.3.
Essentially, only one very sharp, pronounced peak connected with the nearest
neighbors distance appears; it is the highest at the lowest temperature. With
decreasing of temperature, the second wide peak is slowly appearing, reflecting the
gradual development of the second coordination sphere of confined water at lower
temperature, where the motion of water molecules slows down.
D. Makieła et al.
well-characterized nanoscale pool for a range of chemistries. In recent years, the
molecular dynamics (MD) computer simulation method has become a popular way
to study micelles [5, 9–31], because of its ability to simulate phenomena at the
atomic scale on very short time periods. In this work we have used MD technique
to detailed study of the dynamics of water molecules confined in spherical reverse
micelle composed of the important living cell biomembrane constituent, namely,
1,2-dimyristoyl-sn-glycero-3phosphocholine (DMPC) molecules.
6.1.1 Simulation Details
Molecular dynamics simulations were performed with NAMD 2.8 simulations code
[32, 33], with the all-atom CHARMM27 force field [34] for modeling DMPC
phospholipid. We used VMD 1.9.2 [35] to visualize the simulated system. The
filled with water spherical reverse micelle, formed from 58 DMPC molecules,
was constructed, and the sample composed of these micelles was simulated with
the periodic boundary condition. The TIP3 [36] model of water was used. The
equilibration process was performed over 8 * 10 6 time steps with step equal to
1 fs. After that initial simulation, the “production run” was conducted, up to 8 ns.
We kept constant number of particles, constant volume, and constant temperature
(NVT ensemble) for the system studied. During this stage of research, data were
collected every 500 simulation steps for calculating physical observables and
visualization of the systems. The simulations were performed for the temperature
range 280 K ≤ T ≤ 320 K. To better assess the impact of confinement on dynamics
of water molecules, results were compared with the corresponding data for a bulk
(unconfined) water.
6.1.2 Results
In order to visualize the system studied, we present the building block of micelle,
i.e., DMPC molecule (see Fig. 6.1), and an example snapshot of the equilibrium
configuration of the micelle formed from 58 DMPC molecules and filled with water
(see Fig. 6.2).
Note that the interior of micelle happened to be approximately spherical.
First, we have calculated the radial distribution function g(r) of the center of
mass of confined water molecules. The temperature dependence of g(r) is presented
in Fig. 6.3.
Essentially, only one very sharp, pronounced peak connected with the nearest
neighbors distance appears; it is the highest at the lowest temperature. With
decreasing of temperature, the second wide peak is slowly appearing, reflecting the
gradual development of the second coordination sphere of confined water at lower
temperature, where the motion of water molecules slows down.