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Improved understanding of charge-transport in single molecules is essential for harnessing the potential of molecules, e.g., as circuit components at the ultimate size limit. However, interpretation and analysis of the large, stochastic data sets produced by most quantum transport experiments remain an ongoing challenge to discovering much-needed structure–property relationships. Here, we introduce segment clustering, a novel unsupervised hypothesis generation tool for investigating single molecule break junction distance–conductance traces. In contrast to previous machine learning approaches for single molecule data, segment clustering identifies groupings of similar pieces of traces instead of entire traces. This offers a new and advantageous perspective into data set structure because it facilitates the identification of meaningful local trace behaviors that may otherwise be obscured by random fluctuations over longer distance scales. We illustrate the power and broad applicability of this approach with two case studies that address common challenges encountered in single molecule studies: First, segment clustering is used to extract primary molecular features from a varying background to increase the precision and robustness of conductance measurements, enabling small changes in conductance in response to molecular design to be identified with confidence. Second, segment clustering is applied to a known data mixture to qualitatively separate distinct molecular features in a rigorous and unbiased manner. These examples demonstrate two powerful ways in which segment clustering can aid in the development of structure–property relationships in molecular quantum transport, an outstanding challenge in the field of molecular electronics.

The rational design of single molecule electrical components requires a deep and predictive understanding of structure-function relationships. Here we explore the relationship between chemical substituents and the conductance of metal-single molecule-metal junctions, using functionalized oligophenylenevinylenes as a model system. Using a combination of mechanically controlled break-junction experiments and various levels of theory including non-equilibrium Green's functions, we demonstrate that the connection between gas-phase molecular electronic structure and in-junction molecular conductance is complicated by the involvement of multiple mutually correlated and opposing effects that contribute to energy level alignment in the junction. We propose that these opposing correlations represent powerful new "design principles," because their physical origins make them broadly applicable, and they are capable of predicting the direction and relative magnitude of observed conductance trends. In particular, we show that they are consistent with the observed conductance variability not just within our own experimental results, but also within disparate molecular series reported in literature and, crucially, with the trend in variability across these molecular series, which previous simple models fail to explain. The design principles introduced here can therefore aid in both screening and suggesting novel design strategies for maximizing conductance tunability in single-molecule systems.

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Structure–function relationships constitute an important tool to investigate the fundamental principles of molecular electronics. Most commonly, this involves identifying a potentially important molecular structural element, followed by designing and synthesizing a set of related organic molecules, and finally interpretation of their experimental and/or computational quantum transport properties in the light of this structural element. Though this has been extremely powerful in many instances, we demonstrate here the common need for more nuanced relationships even for relatively simple structures, using both experimental and computational results for a series of stilbene derivatives as a case study. In particular, we show that the presence of multiple competing and subtle structural factors can combine in unexpected ways to control quantum transport in these molecules. Our results clarify the reasons for previous widely varying and often contradictory reports on charge transport in stilbene derivatives and highlight the need for refined multidimensional structure–property relationships in single-molecule electronics.