All structures were optimized in their ground state (Figure 1S, Supporting Information). Compounds C1, C2, C5, and C6 had adenine nucleotides as their side chains while C3, C4, C7, and C8 had guanine ones. Interestingly, some structures exhibited bending along the O-P-O-P dihedral angles of the side chains while others were more straightened (Figure 2, Table 1). The solvent and a nature of nucleotide played a major role in the bending of these compounds. Most of the polymers containing guanine displayed bending, except for C3 and C4 in gas phase and C4 in THF phase. Presumably, the oxygen atom on the guanine plays a part in the bending, especially when exposed to the solvent. In some cases, the bending of these molecules was also affected by having two benzoic acid end groups instead of one.
Table 1
O-P-O-P dihedral angles of the compounds in gas and solvent phases.
Gas
|
Water
|
C1
|
C2
|
C1
|
C2
|
φ
|
1
|
2
|
φ
|
1
|
2
|
φ
|
1
|
2
|
φ
|
1
|
2
|
156˚
|
156˚
|
157˚
|
157˚
|
105˚
|
110˚
|
104˚
|
111˚
|
C3
|
C4
|
C3
|
C4
|
φ
|
1
|
2
|
φ
|
1
|
2
|
φ
|
1
|
2
|
φ
|
1
|
2
|
156˚
|
157˚
|
158˚
|
156˚
|
130˚
|
110˚
|
113˚
|
81˚
|
C5
|
C6
|
C5
|
C6
|
φ
|
1
|
2
|
φ
|
1
|
2
|
φ
|
1
|
2
|
φ
|
1
|
2
|
156˚
|
155˚
|
156˚
|
155˚
|
66˚
|
109˚
|
126˚
|
118˚
|
3
|
4
|
3
|
4
|
3
|
4
|
3
|
4
|
155˚
|
156˚
|
157˚
|
156˚
|
107˚
|
66˚
|
108˚
|
107˚
|
C7
|
C8
|
C7
|
C8
|
φ
|
1
|
2
|
φ
|
1
|
2
|
φ
|
1
|
2
|
φ
|
1
|
2
|
156˚
|
149˚
|
156˚
|
155˚
|
106˚
|
139˚
|
57˚
|
65˚
|
3
|
4
|
3
|
4
|
3
|
4
|
3
|
4
|
60˚
|
60˚
|
140˚
|
60˚
|
65˚
|
64˚
|
136˚
|
65˚
|
THF
|
DCM
|
C1
|
C2
|
C1
|
C2
|
φ
|
1
|
2
|
φ
|
1
|
2
|
φ
|
1
|
2
|
φ
|
1
|
2
|
138˚
|
137˚
|
116˚
|
107˚
|
102˚
|
134˚
|
105˚
|
133˚
|
C3
|
C4
|
C3
|
C4
|
φ
|
1
|
2
|
φ
|
1
|
2
|
φ
|
1
|
2
|
φ
|
1
|
2
|
55˚
|
54˚
|
136˚
|
134˚
|
55˚
|
55˚
|
55˚
|
55˚
|
C5
|
C6
|
C5
|
C6
|
φ
|
1
|
2
|
φ
|
1
|
2
|
φ
|
1
|
2
|
φ
|
1
|
2
|
133˚
|
134˚
|
135˚
|
136˚
|
118˚
|
132˚
|
138˚
|
135˚
|
3
|
4
|
3
|
4
|
3
|
4
|
3
|
4
|
134˚
|
135˚
|
138˚
|
136˚
|
63˚
|
135˚
|
137˚
|
134˚
|
C7
|
C8
|
C7
|
C8
|
φ
|
1
|
2
|
φ
|
1
|
2
|
φ
|
1
|
2
|
φ
|
1
|
2
|
136˚
|
138˚
|
55˚
|
130˚
|
64˚
|
138˚
|
55˚
|
128˚
|
3
|
4
|
3
|
4
|
3
|
4
|
3
|
4
|
64˚
|
64˚
|
137˚
|
64˚
|
64˚
|
135˚
|
141˚
|
64˚
|
The absorption spectra were calculated for all studied here compounds in their gas and solvent phases (water, THF, and DCM). The charted absorption spectra for all phases are shown in Figure 3, while Table 1S (Supporting Information) displays the detailed information on maximum wavelength, excitation energy, major percent contributions, and the electronic transitions. The maximum wavelengths of absorption for the solvent phases mostly had a blue-shift (increased in excitation energy) when compared to the gas phase. However, for C2, C4, C6, and C8 in THF maximum of absorption had a similar wavelength as in gas phase, which also leaded to their excitation energy and major percent contributions being similar. None of the compounds in this study showed to absorb near the IR region of the spectrum. The electronic transitions for tmajority of the compounds were due to the HOMO to LUMO transitions, excluding C3 and C4 in the gas phase, where it was due to the HOMO-1 to LUMO transitions. These results were followed by a more extensive investigation into the molecular orbitals of these compounds.
Figure 4 displays the visualization of the molecular orbital transitions, the HOMO and LUMO energies, and the HOMO-LUMO energy gap. For all the compounds the HOMO and LUMO orbitals were located along the dibenzocyclopentadithiophene backbone, except for the HOMO orbitals of C3 and C4 which is positioned along the top side chain of the guanine molecule. The HOMO-1 molecular orbitals of C3 and C4 in the gas phase had similar orbital shapes as all the other compounds, shown in Figure 5 along with their HOMO-1 to LUMO energy gap. This explained why the major % contributions of the above-mentioned compounds are due to the HOMO-1 to LUMO transitions. The HOMO-LUMO energy difference illustrated in Figure 4 showed that C7 in the gas phase had the lowest energy gap. This structure exhibited the HOMO and LUMO orbitals different from the others, with the HOMO being located farther away from the benzoic acid end group and the LUMO being closer to the benzoic acid end group.
The reorganization energy, the ionization potential energy as well as the global chemical reactivity descriptors were calculated (Table 2S, Supporting Information). The reorganization energy for all compounds was lower in the solvent phases than in the gas phase. It was also seen that the reorganization energy of compounds containing 4 monomers was lower compared to ones made of two monomers, except for C2 and C6 in DCM phase. Having lower values of the reorganization energy, ionization potential energy, and electronegativity in solvent suggested that solvation can help improve the charge transfer properties by providing a higher charge transfer rate and a more efficient charge injection. The chemical potential calculation showed a higher tendency of electrons escaping the system when solvation model was used, which suggests better donor properties of studied compounds in solvent phase than in gas phase. The hardness was also improved in solvent phases. All these trends were illustrated in Figure 6. C7, in the gas phase, exhibited distinctive extremum properties when compared to the other compounds. It is believed that this could be caused by the delocalization of the molecular orbitals, shown in C7, resulted in lower HOMO-LUMO energy gaps.
Also, it was noted that the bending of these molecules resulted in lowering the reorganization energy and the ionization potential energy. This can signify that bending on the side chains can be associated with the reorganization energy and the ionization energy directly.
Overall, the size of the compounds increased the absorption maxima and lowers the energy for the reorganization energy, ionization potential, and the hardness. The energy gap was also lower for compounds where n = 4. While no significant changes occurred for the different side chains, in many cases the guanine side chain improved some of these properties. The choice of one or two end groups did not affect any of the properties listed above, however, it can be seen that it plays a part in the bending of the compounds.