20Control
7.1.6. Molecular dynamics simulation
Figure 7.1.12: Snapshot of the simulation box at the end of 4 ns NVT run. Water molecules (green color), methanol molecules (red color), and HPBI molecules (blue).
Molecular simulation technique is a powerful tool to follow the aggregation process.
However, such studies were limited [330]. Tang et al. preformed simulation of polyacetylenes without solvent molecules and they predicted the formation of aggregates by simulation [330]. Here, to comprehend the molecular aggregation of HPBI, simulation was performed with 5 HPBI molecules in methanol-water system and observed that 3 HPBI molecules aggregate to form a cluster [Figure 7.1.12].
Classical molecular dynamics using NAMD [331] simulation engine was performed to simulate the aggregation process of HPBI molecules in water-methanol mixture at atomistic level. Initially 5 HPBI molecules were placed randomly in methanol solvent and performed short equilibration run. This system was merged with pre-equilibrated water box and then the overlapping water molecules were removed. The ratio of methanol and water
106 Facile synthesis of spindles, rods and niddles from HPBI analogues: AIEE from ESIPT
molecules was maintained carefully as that of experimental condition. Total system (5 HPBI, 267 methanol and 20000 water molecules) consisting of 61750 atoms, was equilibrated in isothermal- isobaric (NPT) ensemble for 2 ns and production run was performed for 5 ns in canonical (NVT) ensemble. All the bonded and non-bonded interactions between the atoms of the present simulation system were described by OPLS (Optimized Potentials for Liquid Simulations) force field [332] which is of the form given below
………..…7.1.1 where Etotal is the total energy of the system. Simple harmonic functions were used to represent bond stretching and angle bending with force constants (Kr, Kθ) and equilibr ium bond lengths (r0) and angles (θ0). Van der Waals (Vdw) interactions were computed with Lennard-Jones potential with Aij and Cij as the parameters. These parameters between the atoms of different types were obtained as Aij = sqrt(AiiAjj) and Cij= sqrt(CiiCjj). Coulomb’s law was used for electrostatic interactions as shown above, where qi and qj are the partial charges present on the atoms. The simulation box after aggregate formation is shown in Figure 7.1.12. Temperature and pressure was maintained at 300 K and 1 atm respectively by Langevin piston Nose-Hoover method [333, 334]. Particle Mesh Ewald method [335, 336] was used for the computation of electrostatic interactions with grid spacing of 1 Å with periodic boundary conditions in all the dimensions. TIP3P model [337] was used for water molecule and the bonds involving hydrogen were constrained by settle algorithm. Time step was 1 fs in all the simulations performed. The final equilibrated box length was found to be 85.66 Å. All the visualizations were done using Visual Molecular Dynamics (VMD) [338].
To obtain further insight into the aggregation phenomena, one of the HPBI molecule is followed. Here onwards referred as HPBI8, where "8" is its residue number which was far in the beginning from the aggregate of two HPBI molecules [HPBI1, HPBI6], but
(
0)
2(
0)
2total r
bonds angles
E =
∑
K r−r +∑
Kθθ θ
− 2n 1 cos( )
torsoins
V n
φ γ
+
∑
± − 12 6
ij ij i j
non bonded ij ij ij
A C q q
r r r
−
+ − +
∑
Chapter 7 107
reached them in less than 1 ns of simulation time to be in the aggregate and lasts till the end of the simulation run. For analyzing the hydrogen bond formation, the criterion that the distance between the donor and acceptor should be less than 3.0 Å and the donor-hydroge n- acceptor (D-H-A) angle should be less than 20° as mentioned in the hydrogen bond analys is plugin of VMD is used [338, 328]. In all the HPBI molecules, the intramolecular hydrogen bond was present between O1 (OH) and N1. Donor-Acceptor pairs between HPBI8 and the rest of the system, from this analysis are summarized in Table 7.1.2.
Table 7.1.2: List of possible intermolecular hydrogen bond Donor-Acceptor pairs from VMD analysis. For atoms refer Figure 10 (f).
Donor Acceptor
N2 of HPBI8 O of water O of water O1 of HPBI8 O of water N1 of HPBI8 O1 of HPBI8 O of water
O of water C1 of HBPI8 O of Methanol N1 of HPBI8 N2 of HPBI8 N1 of HPBI6 N2 of HPBI1 N1 of HPBI8 O of Methanol O1 of HPBI8 O of Water C2 of HPBI8 O of water C10 of HPBI8 N2 of HPBI8 O1 of HPBI6 O of Water C3 of HPBI8
In addition to solvent molecules, HPBI form hydrogen bond with other HPBI molecules. These intermolecular hydrogen bonds are through N2 (NH) with N1 and N2 (NH) with O1. Sekiya et al. investigated the crystals of HPBI and reported HPBI in two polymorphs [326]. They also showed the N2 (NH) with O1 intermolecular hydrogen bond between HPBI molecules interconnect the HPBI molecules in both the polymorp hs.
Interestingly neither their crystal structure nor the present simulation of aggregates predict
108 Facile synthesis of spindles, rods and niddles from HPBI analogues: AIEE from ESIPT
any intermolecular O1 (OH) and N1 hydrogen bond between HPBI molecules. This advocates that excited state proton transfer of HPBI is an intramolecular process in aggregates/crystals also. The water molecules around HPBI8 were tracked throughout the simulation run and it was observed that there was no water molecules between HPBI8 and other HPBI molecules in the aggregate as shown in Figure 7.1.13 (e). This suggest some hydrophobic interactions between the HPBI molecules. The representative orientations of the HPBI molecules in the aggregate are as shown in Figure 7.1.13 (a), (b), (c), (d). It is clear from the molecular orientation that the molecules are not in the planar conformat io n and the individual HPBI molecules embrace twisted conformations. To summar ize, molecular dynamics simulation study provides an explanation for aggregation of HPBI molecules in the presence of water-methanol mixture. The hydrophobic induced attraction, in addition to the existence of hydrogen bonds between the atoms of HPBI molecules could be playing an important role in the aggregation process. The twisted conformations of the molecules present in the aggregates precludes the π-π stacking which lead to fluorescence quenching.
Figure 7.1.13: Orientation of HPBI molecules in aggregates from molecular dynamics simulation at various time steps in the “BONDS” representation of VMD.
Chapter 7 109