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Nguyen, T. B. T., Huynh, T. M. H., Dang, M. T., & Pham, V. N. (2025). The impact of ligands on oligo(phenylene ethynylene) stability: a first-principles investigation. Dong Thap University Journal of Science, 14(04S), 418-434. https://doi.org/10.52714/dthu.14.04S.2025.1611
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The impact of ligands on oligo(phenylene ethynylene) stability: a first-principles investigation
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Abstract
This study utilizes density functional theory (DFT) calculations at the B3LYP/6-311++G(2df,2p)//B3LYP/6-31G(d,p) level to assess the stability and infrared (IR) spectral characteristics of oligo(phenylene ethynylene) (OPE) and its derivatives, which include substituents such as -CH3, -NH2, -Cl, -CN, and -NO2. The results of structural optimization reveal that OPE and its derivatives are stable, as evidenced by the absence of imaginary frequencies. This confirms that the optimized molecular structures correspond to minima on the potential energy surface. Molecules containing -NH2 and -NO2 ligands displayed multiple stable symmetry point groups. Specifically, -NH2 exhibits C2v symmetry, while -NO2 showed C1 symmetry, both of which demonstrates the lowest energies and, consequently, the highest structural stability. This finding highlights that the careful selection and attachment of ligands not only optimize electronic properties but also significantly enhance structural stability, thereby increasing the practical applicability of OPE molecular dimers in molecular electronic devices. Additionally, the computed IR spectra reveal distinctive vibrational modes for each substituent, with notable increases in vibrational intensities occurring upon the incorporation of substituents into OPE. Overall, these results confirm the structural robustness of OPE molecules and aid in the identification of characteristic functional groups within the oligo structures.
Keywords
density functional theory DFT, ligand, Oligo (phenylene ethynylene – OPE)
Article Details
This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.
References
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Gahungu, G., & Zhang, J. (2008). Shedding light on octathio[8]circulene and some of its plate-like derivatives. Physical Chemistry Chemical Physics : PCCP, 10, 1743–1747. https://doi.org/10.1039/b800685g
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Huong, V. T. T., Tai, T. B., & Nguyen, M. T. (2012). The π-conjugated P-flowers C16(PH)8 and C16(PF)8 are potential materials for organic n-type semiconductors. Physical Chemistry Chemical Physics, 14(43), 14832–14841. https://doi.org/10.1039/C2CP42474F
Jasmin Finkelmeyer, S., Mankel, C., Ansay, G., Elmanova, A., Zechel, S., Martin, D. H., Schubert, U. S., & Presselt, M. (2025). Filling the gaps: Introducing plasticizers into π-conjugated OPE-NH2 Langmuir layers for defect-free anisotropic interfaces and membranes towards unidirectional mass, charge, or energy transfer. Journal of Colloid and Interface Science, 680, 1090–1100. https://doi.org/10.1016/J.JCIS.2024.11.020
Kim, E. G., Coropceanu, V., Gruhn, N. E., Sánchez-Carrera, R. S., Snoeberger, R., Matzger, A. J., & Brédas, J. L. (2007). Charge transport parameters of the pentathienoacene crystal. Journal of the American Chemical Society, 129(43), 13072–13081. https://doi.org/10.1021/ja073587r
Li, H., Zheng, R., & Shi, Q. (2012). Theoretical Study of Charge Carrier Transport in Organic Semiconductors of Tetrathiafulvalene Derivatives. The Journal of Physical Chemistry C, 116, 11886–11894. https://doi.org/10.1021/jp301536z
Li, X.-Y., Tong, J., & He, F.-C. (2000). Ab initio calculation for inner reorganization energy of gas-phase electron transfer in organic molecule–ion systems. Chemical Physics - CHEM PHYS, 260, 283–294. https://doi.org/10.1016/S0301-0104(00)00283-4
Li, Y., Zhao, J., & Yin, G. (2007). Theoretical investigations of oligo(phenylene ethylene) molecular wire: Effects from substituents and external electric field. Computational Materials Science, 39, 775–781. https://doi.org/10.1016/j.commatsci.2006.09.010
Marcus, R. (2020). Electron transfer reactions in chemistry. Theory and experiment* (pp. 249–272). https://doi.org/10.1201/9781003076803-10
Marcus, R. A. (1993). Electron Transfer Reactions in Chemistry: Theory and Experiment (Nobel Lecture). Angewandte Chemie International Edition in English, 32(8), 1111–1121. https://doi.org/https://doi.org/10.1002/anie.199311113
Mas-Torrent, M., Hadley, P., & Rovira, C. (2004). Importance of Intermolecular Interactions in Assessing Hopping Mobilities in Organic Field Effect Transistors: Pentacene versus Dithiophene-tetrathiafulvalene. Journal of the American Chemical Society, 126, 6544–6545. https://doi.org/10.1021/ja049762a
Mowbray, D. J., Jones, G., & Thygesen, K. S. (2008). Influence of functional groups on charge transport in molecular junctions. Journal of Chemical Physics, 128(11). https://doi.org/10.1063/1.2894544/898427
Nan, G., Sci, G., Chem）, I., Yang, Sci, X., Wang, Sci, L., Shuai, Sci, Z., Zhao, Y., & 赵仪. (2009). Nuclear tunneling effects of charge transport in rubrene, tetracene, and pentacene.
Nelsen, S. F., & Blomgren, F. (2001). Estimation of electron transfer parameters from AM1 calculations. Journal of Organic Chemistry, 66(20), 6551–6559. https://doi.org/10.1021/jo001705m
Nelsen, S., Trieber, D., Ismagilov, R., & Teki, Y. (2001). Solvent Effects on Charge Transfer Bands of Nitrogen-Centered Intervalence Compounds. Journal of the American Chemical Society, 123, 5684–5694. https://doi.org/10.1021/ja003436n
O’Driscoll, L. J., & Bryce, M. R. (2021). A review of oligo(arylene ethynylene) derivatives in molecular junctions. Nanoscale, 13(24), 10668–10711. https://doi.org/10.1039/D1NR02023D
Peercy, P. (2000). The Drive to Miniaturization. Nature, 406, 1023–1026. https://doi.org/10.1038/35023223
Radula-Janik, K., Kupka, T., Ejsmont, K., Daszkiewicz, Z., & Sauer, S. P. A. (2015). Molecular modeling and experimental studies on structure and NMR parameters of 9-benzyl-3,6-diiodo-9H-carbazole. Structural Chemistry, 26. https://doi.org/10.1007/s11224-014-0554-8
Robey, S. W., Ciszek, J. W., & Tour, J. M. (2007). Effects of substitution on reorganization energies in oligo(-phenylene ethynylene) molecular wires. Journal of Physical Chemistry C, 111(46), 17206–17212. https://doi.org/10.1021/JP0750396;CTYPE:STRING:JOURNAL
Sakanoue, K., Motoda, M., Sugimoto, M., & Sakaki, S. (1999). A Molecular Orbital Study on the Hole Transport Property of Organic Amine Compounds. The Journal of Physical Chemistry A, 103(28), 5551–5556. https://doi.org/10.1021/jp990206q
Seminario, J. M., & Derosa, P. A. (2001). Molecular gain in a thiotolane system. In Journal of the American Chemical Society (Vol. 123, Issue 49, pp. 12418–12419). https://doi.org/10.1021/ja0162313
Sutton, C., Sears, J., Coropceanu, V., & Brédas, J.-L. (2013). Understanding the Density Functional Dependence of DFT-Calculated Electronic Couplings in Organic Semiconductors. The Journal of Physical Chemistry Letters, 4, 919–924. https://doi.org/10.1021/jz3021292
Tang, X.-D., Liao, Y., Gao, H.-Z., Geng, Y., & Su, Z.-M. (2012). Theoretical study of the bridging effect on the charge carrier transport properties of cyclooctatetrathiophene and its derivatives. Journal of Materials Chemistry, 22(14), 6907–6918. https://doi.org/10.1039/C2JM14871D
Taylor, J., Brandbyge, M., & Stokbro, K. (2002). Theory of Rectification in Tour Wires: The Role of Electrode Coupling. Physical Review Letters, 89, 138301. https://doi.org/10.1103/PhysRevLett.89.138301
Troisi, A., & Orlandi, G. (2001). The hole transfer in DNA: calculation of electron coupling between close bases. Chemical Physics Letters, 344(5), 509–518. https://doi.org/https://doi.org/10.1016/S0009-2614(01)00792-8
Troisi, A., & Orlandi, G. (2006). Dynamics of the intermolecular transfer integral in crystalline organic semiconductors. Journal of Physical Chemistry A, 110(11), 4065–4070. https://doi.org/10.1021/jp055432g
Wang, L., Chen, W., Huang, C., Chen, Z.-K., & Wee, A. (2006). Ultrafast Electron Transfer from Oligo( p -phenylene-ethynylene)thiol to Gold. The Journal of Physical Chemistry. B, 110, 674–676. https://doi.org/10.1021/jp056478c
Wartelle, C., Viruela, R., Viruela, P. M., Sauvage, F. X., Sallé, M., Ortí, E., Levillain, E., & Le Derf, F. (2003). First signals of electrochemically oxidized species of TTF and TTM-TTF: A study by in situ spectroelectrochemical FTIR and DFT calculations. Physical Chemistry Chemical Physics, 5(20), 4672–4679. https://doi.org/10.1039/b307552d
Yang, X., Li, Q., & Shuai, Z. (2007). Theoretical modelling of carrier transports in molecular semiconductors: Molecular design of triphenylamine dimer systems. Nanotechnology, 18, 424029. https://doi.org/10.1088/0957-4484/18/42/424029
Yin, S., Yi, Y., Li, Q., Yu, G., Liu, Y., & Shuai, Z. (2006). Balanced carrier transports of electrons and holes in silole-based compounds - A theoretical study. Journal of Physical Chemistry A, 110(22), 7138–7143. https://doi.org/10.1021/jp057291o
Chai, S., Wen, S., Huang, J.-D., & Han, K.-L. (2011). Density Functional Theory Study on Electron and Hole Transport Properties of Organic Pentacene Derivatives with Electron-Withdrawing Substituent. Journal of Computational Chemistry, 32, 3218–3225. https://doi.org/10.1002/jcc.21904
Chen, H., Sangtarash, S., Li, G., Gantenbein, M., Cao, W., Alqorashi, A., Liu, J., Zhang, C., Zhang, Y., Chen, L., Chen, Y., Olsen, G., Sadeghi, H., Bryce, M. R., Lambert, C. J., & Hong, W. (2020). Exploring the thermoelectric properties of oligo(phenylene-ethynylene) derivatives. Nanoscale, 12(28), 15150–15156. https://doi.org/10.1039/D0NR03303K
Chen, J., & Reed, M. A. (2002). Reed MA: Electronic transport of molecular systems, Chem Phys 281:127. Chemical Physics, 281, 127–145. https://doi.org/10.1016/S0301-0104(02)00616-X
Chen, X.-K., Zou, L.-Y., Guo, J.-F., & Ren, A.-M. (2012). An efficient strategy for designing n-type organic semiconductor materials—introducing a six-membered imide ring into aromatic diimides. Journal of Materials Chemistry, 22(13), 6471–6484. https://doi.org/10.1039/C2JM15935J
Francl, M. M., Pietro, W. J., Hehre, W. J., Binkley, J. S., Gordon, M. S., DeFrees, D. J., & Pople, J. A. (1982). Self‐consistent molecular orbital methods. XXIII. A polarization‐type basis set for second‐row elements. The Journal of Chemical Physics, 77(7), 3654–3665. https://doi.org/10.1063/1.444267
Frisch, M. J. ea, Trucks, G. W., Schlegel, H. B., Scuseria, G. E., Robb, Ma., Cheeseman, J. R., Scalmani, G., Barone, V., Petersson, G. A., & Nakatsuji, H. (2016). Gaussian 16. Gaussian, Inc. Wallingford, CT.
Gahungu, G., Zhang, B., & Zhang, J. (2006). Design of TTF-based phosphazenes combining a good electron-donor capacity and possible inclusion adduct formation. Journal of Physical Chemistry B, 110(34), 16852–16859. https://doi.org/10.1021/jp062629f
Gahungu, G., & Zhang, J. (2008). Shedding light on octathio[8]circulene and some of its plate-like derivatives. Physical Chemistry Chemical Physics : PCCP, 10, 1743–1747. https://doi.org/10.1039/b800685g
Hariharan, P. C., & Pople, J. A. (1973). The Influence of Polarization Functions on Molecular Orbital Hydrogenation Energies. In Theoret. chim. Acta (Berl.) (Vol. 28). Springer-Verlag.
Huang, J., & Kertesz, M. (2004). Intermolecular transfer integrals for organic molecular materials: Can basis set convergence be achieved? Chemical Physics Letters, 390, 110–115. https://doi.org/10.1016/j.cplett.2004.03.141
Huong, V. T. T., Tai, T. B., & Nguyen, M. T. (2012). The π-conjugated P-flowers C16(PH)8 and C16(PF)8 are potential materials for organic n-type semiconductors. Physical Chemistry Chemical Physics, 14(43), 14832–14841. https://doi.org/10.1039/C2CP42474F
Jasmin Finkelmeyer, S., Mankel, C., Ansay, G., Elmanova, A., Zechel, S., Martin, D. H., Schubert, U. S., & Presselt, M. (2025). Filling the gaps: Introducing plasticizers into π-conjugated OPE-NH2 Langmuir layers for defect-free anisotropic interfaces and membranes towards unidirectional mass, charge, or energy transfer. Journal of Colloid and Interface Science, 680, 1090–1100. https://doi.org/10.1016/J.JCIS.2024.11.020
Kim, E. G., Coropceanu, V., Gruhn, N. E., Sánchez-Carrera, R. S., Snoeberger, R., Matzger, A. J., & Brédas, J. L. (2007). Charge transport parameters of the pentathienoacene crystal. Journal of the American Chemical Society, 129(43), 13072–13081. https://doi.org/10.1021/ja073587r
Li, H., Zheng, R., & Shi, Q. (2012). Theoretical Study of Charge Carrier Transport in Organic Semiconductors of Tetrathiafulvalene Derivatives. The Journal of Physical Chemistry C, 116, 11886–11894. https://doi.org/10.1021/jp301536z
Li, X.-Y., Tong, J., & He, F.-C. (2000). Ab initio calculation for inner reorganization energy of gas-phase electron transfer in organic molecule–ion systems. Chemical Physics - CHEM PHYS, 260, 283–294. https://doi.org/10.1016/S0301-0104(00)00283-4
Li, Y., Zhao, J., & Yin, G. (2007). Theoretical investigations of oligo(phenylene ethylene) molecular wire: Effects from substituents and external electric field. Computational Materials Science, 39, 775–781. https://doi.org/10.1016/j.commatsci.2006.09.010
Marcus, R. (2020). Electron transfer reactions in chemistry. Theory and experiment* (pp. 249–272). https://doi.org/10.1201/9781003076803-10
Marcus, R. A. (1993). Electron Transfer Reactions in Chemistry: Theory and Experiment (Nobel Lecture). Angewandte Chemie International Edition in English, 32(8), 1111–1121. https://doi.org/https://doi.org/10.1002/anie.199311113
Mas-Torrent, M., Hadley, P., & Rovira, C. (2004). Importance of Intermolecular Interactions in Assessing Hopping Mobilities in Organic Field Effect Transistors: Pentacene versus Dithiophene-tetrathiafulvalene. Journal of the American Chemical Society, 126, 6544–6545. https://doi.org/10.1021/ja049762a
Mowbray, D. J., Jones, G., & Thygesen, K. S. (2008). Influence of functional groups on charge transport in molecular junctions. Journal of Chemical Physics, 128(11). https://doi.org/10.1063/1.2894544/898427
Nan, G., Sci, G., Chem）, I., Yang, Sci, X., Wang, Sci, L., Shuai, Sci, Z., Zhao, Y., & 赵仪. (2009). Nuclear tunneling effects of charge transport in rubrene, tetracene, and pentacene.
Nelsen, S. F., & Blomgren, F. (2001). Estimation of electron transfer parameters from AM1 calculations. Journal of Organic Chemistry, 66(20), 6551–6559. https://doi.org/10.1021/jo001705m
Nelsen, S., Trieber, D., Ismagilov, R., & Teki, Y. (2001). Solvent Effects on Charge Transfer Bands of Nitrogen-Centered Intervalence Compounds. Journal of the American Chemical Society, 123, 5684–5694. https://doi.org/10.1021/ja003436n
O’Driscoll, L. J., & Bryce, M. R. (2021). A review of oligo(arylene ethynylene) derivatives in molecular junctions. Nanoscale, 13(24), 10668–10711. https://doi.org/10.1039/D1NR02023D
Peercy, P. (2000). The Drive to Miniaturization. Nature, 406, 1023–1026. https://doi.org/10.1038/35023223
Radula-Janik, K., Kupka, T., Ejsmont, K., Daszkiewicz, Z., & Sauer, S. P. A. (2015). Molecular modeling and experimental studies on structure and NMR parameters of 9-benzyl-3,6-diiodo-9H-carbazole. Structural Chemistry, 26. https://doi.org/10.1007/s11224-014-0554-8
Robey, S. W., Ciszek, J. W., & Tour, J. M. (2007). Effects of substitution on reorganization energies in oligo(-phenylene ethynylene) molecular wires. Journal of Physical Chemistry C, 111(46), 17206–17212. https://doi.org/10.1021/JP0750396;CTYPE:STRING:JOURNAL
Sakanoue, K., Motoda, M., Sugimoto, M., & Sakaki, S. (1999). A Molecular Orbital Study on the Hole Transport Property of Organic Amine Compounds. The Journal of Physical Chemistry A, 103(28), 5551–5556. https://doi.org/10.1021/jp990206q
Seminario, J. M., & Derosa, P. A. (2001). Molecular gain in a thiotolane system. In Journal of the American Chemical Society (Vol. 123, Issue 49, pp. 12418–12419). https://doi.org/10.1021/ja0162313
Sutton, C., Sears, J., Coropceanu, V., & Brédas, J.-L. (2013). Understanding the Density Functional Dependence of DFT-Calculated Electronic Couplings in Organic Semiconductors. The Journal of Physical Chemistry Letters, 4, 919–924. https://doi.org/10.1021/jz3021292
Tang, X.-D., Liao, Y., Gao, H.-Z., Geng, Y., & Su, Z.-M. (2012). Theoretical study of the bridging effect on the charge carrier transport properties of cyclooctatetrathiophene and its derivatives. Journal of Materials Chemistry, 22(14), 6907–6918. https://doi.org/10.1039/C2JM14871D
Taylor, J., Brandbyge, M., & Stokbro, K. (2002). Theory of Rectification in Tour Wires: The Role of Electrode Coupling. Physical Review Letters, 89, 138301. https://doi.org/10.1103/PhysRevLett.89.138301
Troisi, A., & Orlandi, G. (2001). The hole transfer in DNA: calculation of electron coupling between close bases. Chemical Physics Letters, 344(5), 509–518. https://doi.org/https://doi.org/10.1016/S0009-2614(01)00792-8
Troisi, A., & Orlandi, G. (2006). Dynamics of the intermolecular transfer integral in crystalline organic semiconductors. Journal of Physical Chemistry A, 110(11), 4065–4070. https://doi.org/10.1021/jp055432g
Wang, L., Chen, W., Huang, C., Chen, Z.-K., & Wee, A. (2006). Ultrafast Electron Transfer from Oligo( p -phenylene-ethynylene)thiol to Gold. The Journal of Physical Chemistry. B, 110, 674–676. https://doi.org/10.1021/jp056478c
Wartelle, C., Viruela, R., Viruela, P. M., Sauvage, F. X., Sallé, M., Ortí, E., Levillain, E., & Le Derf, F. (2003). First signals of electrochemically oxidized species of TTF and TTM-TTF: A study by in situ spectroelectrochemical FTIR and DFT calculations. Physical Chemistry Chemical Physics, 5(20), 4672–4679. https://doi.org/10.1039/b307552d
Yang, X., Li, Q., & Shuai, Z. (2007). Theoretical modelling of carrier transports in molecular semiconductors: Molecular design of triphenylamine dimer systems. Nanotechnology, 18, 424029. https://doi.org/10.1088/0957-4484/18/42/424029
Yin, S., Yi, Y., Li, Q., Yu, G., Liu, Y., & Shuai, Z. (2006). Balanced carrier transports of electrons and holes in silole-based compounds - A theoretical study. Journal of Physical Chemistry A, 110(22), 7138–7143. https://doi.org/10.1021/jp057291o
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