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High-throughput density functional theory (DFT) has been widely utilized to study a variety of materials and molecular properties. However, its application to complex molecular systems, including those relevant to electrochemical reactivity and decomposition, has been limited by insufficient automation.Here, we report a broadly applicable, automated framework for the accurate and robust DFT calculation of molecules, capable of addressing species relevant to electrochemistry. This framework is specifically designed to study molecules with different charge states, open-shell electronic structure, metal coordination, and implicit solvation. We first identify appropriate levels of theory that avoid calculation failures and accurately predict molecular redox potentials. We then describe our framework, including methods to automatically detect and correct errors and to optimize structures from saddle points to potential energy surface minima. To demonstrate the efficacy of this framework, we examine a case study including over 12,000 calculations of reactive molecular fragments. This framework is able to reduce the rate of failure for DFT calculations from 25.1% to 1.2%, significantly improving the degree of automation possible for high-throughput molecular DFT.