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As an alternative technology to energy intensive distillations, adsorptive separation by porous solids offers lower energy cost and higher efficiency. Herein we report a topology-directed design and synthesis of a series of Zr-based metal-organic frameworks with optimized pore structure for efficient separation of C6 alkane isomers, a critical step in the petroleum refining process to produce gasoline with high octane rating. Zr6O4(OH)4(bptc)3 adsorbs a large amount of n-hexane but excluding branched isomers. The n-hexane uptake is ~70% higher than that of a benchmark adsorbent, zeolite-5A. A derivative structure, Zr6O4(OH)8(H2O)4(abtc)2, is capable of discriminating all three C6 isomers and yielding a high separation factor for 3-methylpentane over 2,3-dimethylbutane. This property is critical for producing gasoline with further improved quality. Multicomponent breakthrough experiments provide a quantitative measure of the capability of these materials for separation of C6 alkane isomers. A detailed structural analysis reveals the unique topology, connectivity and relationship of these compounds. ; We would like to thank the financial support from the Materials Sciences and Engineering Division, Office of Basic Research Energy Sciences of the U.S. Department of Energy through Grant no. DE-FG02-08ER-46491. Y.H. acknowledges the KAUST CCF fund for supporting this study. The Advanced Light Source is supported by the Director, Office of Science, Office of Basic Energy Sciences, of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. T.T. acknowledges generous support from the Simons Foundation through Grant no. 391888, which endowed his sabbatical at MIT. D.M.P. thanks the Russian Government (Grant 14.B25.31.0005). E.V.A. is grateful to the Russian Science Foundation (Grant no. 16-13-10158). The RU team would also like to acknowledge Micromeritics Instrument Corp. for the award of a 3Flex system through its Instrument Grant program. H.W. would like to thank Ever Velasco for helpful discussions.