Silicon (Si) is the most commonly and widely used semiconductor device component in commercial microelectronics due to its high stability, abundance, and technological readiness. To achieve efficient device performance for optoelectronic and electronic applications such as solar cells [1] and field-effect transistors, [2] appropriate energy level alignment and effective charge carrier transport across p-n junction structures are necessary. In particular, atomic arrangements and charge redistribution at interfaces are crucial design parameters for high-quality devices. [3] However, the design and performance of classical Si-based p-n junctions are limited in terms of length scale: Significant degradation of the device performance caused by short-channel effects, e.g., tunneling-induced leakage currents or draininduced barrier lowering, can occur when approaching the nanoscale. [4] To overcome such drawbacks, hybrid organic/inorganic systems can be a good alternative for Si-based nanoscale optoelectronic/electronic devices. Designing hybrid heterojunctions with specific electronic properties requires, primarily, the achievement of an appropriate energy level alignment of the comprising materials. In this respect, H-Si(111) surface, with its work function (Φ) of about 4.3 eV, [5,6] can be generally regarded as an anode material, when interfaced with charge acceptor layers having typically higher Φ. To control the level alignment, one may add interlayers of molecular units. If these are composed of strong electron acceptors, there will be electron transfer to the molecular layer (ML) and hole accumulation in the Si anode layer. Good candidates for the organic electron acceptor component are 2,3,5,6-tetrafluoro-7,7,8,8-tetracyano-quinodi-methane (F4-TCNQ) and 1,3,4,5,7,8-hexafluorotetracyano-naphthoquinodimethane (F6-TCNNQ) due to their high electron affinity of 5.24 [7] and 5.60 eV, [8] respectively, as measured in neat molecular thin films.The quantitative tuning of the properties of such interfaces depends critically on the structure of the organic/inorganic interface, which is an aspect that is rarely properly modeled or measured under realistic device conditions. [9][10][11][12] In this contribution, we report an experimental and theoretical analysis of the interface between F4-TCNQ (F6-TCNNQ) and the well-defined Advances in hybrid organic/inorganic architectures for optoelectronics can be achieved by understanding how the atomic and electronic degrees of freedom cooperate or compete to yield the desired functional properties. Here, how work function changes are modulated by the structure of the organic components in model hybrid systems is shown. Two cyanoquinodimethane derivatives (F4-TCNQ and F6-TCNNQ), which are strong electron-acceptor molecules, adsorbed on H-Si(111) are considered. From systematic structure searches employing the range-separated hybrid HSE06 functional including many-body van der Waals (vdW) contributions, it is predicted that, despite their similar composition, these molecules ads...