Quantum decoherence plays an important role in the charge transport characteristics of molecular wires at room temperature. In this paper we propose a generalization of an electron-phonon dephasing model to non orthogonal LCAO basis. We implemented the model in combination with a density functional-based tight binding (DFTB) theory framework and utilized it to model charge transport characteristics of an anthraquinone (AQ) based molecular wire. We demonstrate a modulation of Quantum Interference (QI) effects compatible with experiments and confirm the robustness of QI signatures with respect to dephasing. An analysis of the spatial localization of the dephasing process reveals that both the QI and the dephasing process are localized in the AQ region, hence justifying the general robustness of the transmission temperature dependence in different AQ-based systems.
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