2.3 MD simulation.
The GROMACS package at 2019.3 version41 with OPLS-AA
force field applied for both EG and BUT was applied in the simulation.
According to the temperature effect in experiment, the simulation was
simulated at both temperature 295.15K, 337.15K. During the simulation,
the velocity-rescale method was used to maintain the equilibrium
temperature, and Berendsen barostat was applied to control the pressure.
The particle mesh-Ewald method was used to maintain the long-range
electrostatics with a cutoff of 1.0 nm. The packmol42software was applied to load the molecules into the simulation box. The
box size is set to be 4.5nm in all three orthogonal directions at the
very beginning. The energy of the simulation box was minimized by the
steepest descent algorithm. The NVT simulation for 1ns and NPT
simulation for 1ns was carried out after that to allow the system to
achieve the relaxation state. After that, the box was added two vacuum
volume and generating two vapor/liquid interfaces by changing Z
direction length of the simulation box into three times the original
length. An NVT simulation for 10ns at a temporal step of 2 fs was
performed and the trajectories are generated for further discussion. The
coordinates of the simulation results are acquired treated by program
written with python 3.7, which is used to analyze the orientation of the
group and hydrogen bonds between molecules.
To illustrate the molecular orientation informed from the MD simulation,
the directions of chemical bonds of BUT and EG are calculated from the
simulated results. As shown in Figure 1, θ1refers to the angle formed by the positive directions of the vectors of
C3-C4 chemical bond which are those to be pointing from C3 to C4, of all
the BUT molecules and positive direction of the Z axis which is
perpendicular to the vapor/liquid interface. In the same way we can
defined θ2 is the angle between the C2=O2 bonds
and Z axis. θ3 is the angle formed by the C5-C6
bonds in the EG molecules and positive Z axis. θ4 is the angle formed by the angular bisector of CH2 group of C6 and
positive Z axis. If the tilt angle θ ranging between 0° to 90°,
the corresponding group is pointing to the vapor side. And a θranging between 90° to 180° means a downward orientation.