Effect of doped H, Br, Cu, Kr, Ge, As and Fe on structural features and bandgap of poly C13H8OS-X: a DFT calculation

ABSTRACT Structural features such as the shape, the lattice constant, the bond length, the total energy per cell, and the energy bandgap (Eg) of C13H8OS-X are studied by the calculating Partial Density Of States (PDOS), and DOS package of the Material Studio (MS) software. Calculations show that the bond length and the bond angle between atoms insignificant change as 1.316 Å to 1.514 Å for C-C, 1.211 Å for C-O, 1.077 Å to 1.105 Å for C-H; bond angle of round one changes from 118.883° to 121.107° for C-C-C, from 117.199° to 122.635° for H-C-C, from 119.554° to 123.147° for C-C-O and from 109.956° to 117.537° for C-C-H. When C13H8OS-X doped in the order of -Br, -Cu, -Kr, -Ge, -As, and -Fe then bond lengths, bond angles between atoms have a nearly constant value. Particularly for links C-X, there is a huge change in value, respectively 1.876, 1.909, 10.675, 2.025, 2.016, 2.014 Å; the total energy change from Etot = −121,794 eV to Etot = −202,859 eV, and the energy band gap decreases from Eg = 2.001 eV to Eg = 0.915 eV. The obtained results are useful and serve as a basis for future experimental research.

The reason is that these polymers can assemble spontaneously through intermolecular bonds under the action of a suitable solvent or medium [26][27][28][29][30][31][32]. On the other hand, Cui et Kertesz [33] showed the existence of helix polythiophene by the semi-experimental method [33] and other scientific groups showed the existence of polymeric helix [34].
One group of researchers [35][36][37] has found a polymeric helix structure after the polythiophenes completed bonding with the client molecules and polymers. Other groups of researchers also suggested that non-ionic polythiophenes could fold in hydrophobic solvents [38,39]. These results are determined through Scanning Electron Microscopy (SEM) but they did not observe the diversity of materials [40].
Also, when studying the effect of doped or solvent on the bond lengths of polymer materials, it cannot be studied by X-ray diffraction method or SEM method [41,42].
In this article, we continue to doped atoms of cycle 4 including -H, -Br, -Cu, -Kr, -Ge, -As, and -Fe with the desire to synthesize new polythiophenes with the ability to improve their treatment, environmental stability, and electrical properties. Figure 1 shows the synthesizing process of poly (C 13 H 8 OS-X) (X = -H, -Br, -Cu, -Kr, -Ge, -As, -Fe). The structural and electronic structural properties of poly[3-(3-phenyl prop-1-ene-3-one-1-yl) thiophene] by the calculating Partial Density Of States (PDOS), DOS package of the Material Studio (MS) software, and their transition temperatures were simulated using DFT [65][66][67][68] in the framework of DMol3 module [67] in the copyrighted Material Studio software, installed at the Center for Computational Science of the Hanoi National University of Education HNUE (Hanoi, Vietnam). The Generalized Gradient Approximation (GGA) package [69] with the PW91 parametrization for the exchange-correlation function [70,71] and the Monkhorst-Pack [72] k-point sampling were applied into a three-dimensional (3-D) unit cell of poly C 13 H 8 OS-H, C 13 H 8 OS-Br, C 13 H 8 OS-Cu, C 13 H 8 OS-Kr, C 13 H 8 OS-Ge, C 13 H 8 OS-As, C 13 H 8 OS-Fe with the lattice constants a = 27 Å, b = 13 Å, c = 6 Å, and the bond angles α = β = γ = 90°. The electron-electrons interaction was described by the Density Function Semicore Pseudo-Potential [73] and to be considered as a homogeneous electron gas. The tolerance for energy was set at 1 × 10 −6 eV, the displacement during the geometry optimization is at level 1 × 10 −5 Ha/integer and 5 × 10 −3 Å. The synthesis procedure of poly (C 13 H 8 OS-X) was shown in Figure 1.

Structural property of C 13 H 8 OS-H
The optimized structures of poly (C 13 H 8 OS-H) 2 are shown in Figure 2.
The stable structure of C 13 H 8 OS-H after running the NVE ( Figure 2). The final shape of C 13 H 8 OS-H has C 13 H 8 OS-H poly structures with all C, H, S, O atoms are distributed in a unit cell of the triclinic system with the corresponding cell sizes a = 27.0951 Å, b = 11.5351 Å, c = 6.1176 Å, α = β = 90° and γ = 94.42°. The distance between atoms in round one changes from 1.380 Å to 1.41 Å for C-C, and from 1.060 Å to 1.119 Å for C-H. The distance between round one and round two changes from 1.316 Å to 1.514 Å for C-C, 1.211 Å for C-O, and from 1.077 Å to 1.105 Å for C-H. The obtained results are in good agreement with the structural determination [57,64] for which C-C = 1.33 Å, C-O = 1.23 Å, and previous calculation [57,64]. The bond length in round two changes from 1.372 Å to 1.399 Å for C-C, 1.722 Å for C-S, and from 1.106 Å to 1.148 Å for C-H. The bond angle of round one changes from 118.883° to 121.107° for C-C-C, from 117.199° to 122.635° for H-C-C, from 119.554° to 123.147° for C-C-O, and from 109.956° to 117.537° for C-C-H. The bond angle of round two changes from 111.186° to 115.008° for C-C-C, from 122.321° to 124.347° for H-C-C, 89.695° for C-S-C, from 109.929° to 114.042° for S-C-C, and 122.983° for S-C-H.

Electronic Structure of C 13 H 8 OS-H
The bandgap is E g = 2.255 eV (Figure 3a1) and the density of electrons of C 13 H 8 OS-H ( Figure 3a2) has a maximum value of 23.5%. The density of electrons for C 13 H 8 OS-H is shown in Table 1.
The results of Figure 3b show that the phase transition temperature zone of C 13 H 8 OS-H ranges from 567.5 K to 611.1 K, where the glass temperature T g = 567.5 K and melting temperature T m = 611.1 K. These values are larger than values obtained in [57,64]. The reason for this phenomenon is that we put the material into a force field with boundary conditions different from initial boundary conditions. The obtained density of electrons for C 13 H 8 OS-H is shown in Table 1.

The effect of doped on structural features of C 13 H 8 OS-X
The obtained results show that the distance between the atoms and the bond angle does not change significantly, and that is completely consistent with  previous simulations [57,64]. However, the distance between the doped atoms changes strongly for poly(C 13 Table 2, respectively. Table 3 gives the valence electrons and the value of bandgap energy for doped C 13 H 8 OS-X. The bandgap energy for C 13      The density of electrons for C 13 H 8 OS-X doped the functional groups -Br, -Cu, -Kr, -Ge, -As, -Fe changes greatly. For example when the energy level at −20 eV, the density of electrons is 4.099% for C 13 H 8 OS-X doped -H, 3.262% for C 13 H 8 OS-X doped -Br,4.071% for C 13 H 8 OS-X doped -Cu, 0,014% for C 13 H 8 OS-X doped -Kr, 0% for C 13 H 8 OS-X doped -Ge and -As, 0.063% for C 13 H 8 OS-X doped -Fe. At −15 eV, the corresponding densities of electrons are 3.110%, 10.772%, 6.619%, 2.511%, 11.541%, 9.02% and 3.785%. At −10 eV, the corresponding densities of electrons are 5.631%, 11.681%, 8.704%, 10.836%, 7.388%, 3.312% and 7.529%. At-5 eV, the corresponding densities of electrons are 16.394%, 18.743%, 21.630%, 17.866%, 17.608%, 17.583% and 15.650%; At −2.5 eV, the corresponding densities of electrons are 5.606%, 3.954%, 9.327%, 3.585%, 15.764%, 12.443% and 11.425%. At 0, the corresponding densities of electrons are 9.703%, 6.343%, 7.909%, 7.806%, 12.238%, 15.230% and 7.020%. At 2.5 eV, the corresponding densities of electrons are 6.044%, 3.857%, 5.089%, 6.786%, 12.214%, 2.208% and 6.016%. At 5 eV, the corresponding densities of electrons are 5.684%, 6.493%, 3.290%, 3.903%, 0, 0 and 0. This shows that in the valence region, the density of electrons has the largest percentage extending the maximum value at the energy range of −5 eV. Also, the bandgap E g decreases for the doped in the order of -Br, -Cu, -Kr, -Ge, -As, and -Fe. Besides, the total energy E tot of the system decreases suddenly at -Kr, which shows that the E tot of the −4p subclass of the material decreases for increasing the subclass from −4p 2 to −4p 3 , −4p 5 , and −4p 6 . The obtained results are used as the basis for future experimental research and used to predict the structural features and electronic structure of C 13 H 8 OS-X doped.

Conclusion
The effects of doped -H, -Br, -Cu, -Kr, -Ge, -As, and -Fe on structural features and the electronic structure of C 13 H 8 OS-X are studied by the GGA package PW91 of the Material Studio software copyrighted based on the DFT method. Structural features such as the lengths of the bonds C-H, C-Fe, C-Ge, C-C, C-Br, C-O, C-Cu, C-Kr, C-As and the bond angles H-C-H, H-C-C, C-C-C, C-Fe-H, C-Ge-C, C-Br-C, C-O-C, Cu-C-C, Kr-C-C, As-C-C do not change significantly. However, when  then total energy change of system decrease from E tot = −121,794 eV to E tot = −202,859 eV; and the total energy and the bandgap of C 13 H 8 OS-X doped in the order of -H, -Br, -Cu, -Kr, -Ge, -As and -Fe decrease from E tot = -121,794 eV to E tot = -202,859 eV and from E g = 2.001 eV to E g = 0.915 eV respectively. This shows that the influence of benzene ring and impurities on electronic structure features and the bandgap of poly materials is important and these results are considered as a basis for future experimental research.

Disclosure statement
The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper. The funders had no role in the design of the study and the authors declare no conflict of interest.

Data Availability Statement
The data that support the findings of this study are available from the corresponding author upon reasonable request.