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A self-assembled nanodielectric (SAND) is an ultrathin film, typically with periodic layer pairs of high-k oxide and phosphonic-acid-based π-electron (PAE) molecular layers. IPAE, having a molecular structure similar to that of PAE but with an inverted dipole direction, has recently been developed for use in thin-film transistors. Here we report that replacing PAE with IPAE in SAND-based thin-film transistors induces sizable threshold and turn-on voltage shifts, indicating the flipping of the built-in SAND polarity. The bromide counteranion (Br-) associated with the cationic stilbazolium portion of PAE or IPAE is of great importance, because its relative position strongly affects the electric dipole moment of the organic layer. Hence, a set of X-ray synchrotron measurements were designed and performed to directly measure and compare the Br- distributions within the PAE and IPAE SANDs. Two trilayer SANDs, consisting of a PAE or IPAE layer sandwiched between an HfOx and a ZrOx layer, were deposited on the SiOx surface of Si substrates or periodic Si/Mo multilayer substrates for X-ray reflectivity and X-ray standing wave measurements, respectively. Along with complementary DFT simulations, the spacings, elemental (Hf, Br, and Zr) distributions, molecular orientations, and Mulliken charge distributions of the PAE and IPAE molecules within each of the SAND trilayers were determined and correlated with the dipole inversion.