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The structure of zeolite SSZ‐43 was determined by 3D electron diffraction, synchrotron X‐ray powder diffraction, and high‐resolution transmission electron microscopy. The SSZ‐43 framework forms one‐dimensional, sinusoidal 12‐ring channels from 5461butterfly units commonly found in other zeolites, but with unique 6.5×6.5 Å apertures and 12‐ring 6.5×8.9 Å windows perpendicular to the channels. SSZ‐43 crystals are intergrowths of two polytypes: ≈90 % orthorhombic polytype A with ABAB stacking of the 12‐rings, and ≈10 % monoclinic polytype B with ABCABC stacking. Molecular modeling performed on the idealized Si‐SSZ‐43 structure along with empirical relationships for zeolite selectivity in boron‐ and aluminum‐containing synthesis gels were used in a combined approach to design new di‐quaternary ammonium organic structure‐directing agents (OSDAs). Experimental trials demonstrated that the new OSDAs produced SSZ‐43 over a broader range of compositions than previous mono‐quaternary OSDAs. [ABSTRACT FROM AUTHOR]