SUPPLEMENTARY INFORMATION

SUPPLEMENTARY INFORMATION doi:10.1038/nature11990 I. Materials and Methods Chemicals: Solvents and reagents were purchased from TCI Co., Ltd., WAKO Pure Chemical Industries Ltd., and Sigma-Aldrich Co. and used without any further purification except where noted. Glassware: Micro vials for this research were purchased from Waters (Deactivated Clear Glass 12 x 32mm Screw Neck Max Recovery Vial, 1.5 ml Volume). Syringe needle, TERUMO NN-2116R (φ = 0.80 mm), was used as an exhaust outlet for the cap of the micro vial. An incubator Fine FF-12 was used to maintain the temperature during guest inclusion. Equipment: HPLC separation of micro-gram scale natural products was performed on a JASCO UV-970 spectrometer equipped with a JASCO PU-980 pump and an ODS column DEVELOSIL ODS-5, Nomura Chemical Co., LTD. Elemental analysis was performed on a CHN/O/S elemental analyzer CE-440, Exeter Analytical, Inc. Mass spectra were recorded on a Bruker maxis spectrometer. Single crystal X-ray diffraction data were collected on a Bruker APEX-II CCD diffractometer equipped with a focusing mirror (MoK a radiation λ = 0.71073 Å) and a N 2 generator (Japan Thermal Eng. Co., Ltd.) or Rigaku VariMax with RAPID (CuK a radiation λ = 1.54187 Å). Microscopic IR spectra were recorded on a Varian DIGILAB Scimitar instrument. For X-ray diffraction and microscopic IR measurements, fluorolube was used as a protectant for the single crystals. X-ray structural analysis: The structures were solved by direct methods and refined by full-matrix least-squares calculations on F 2 using the SHELX 97 program 1. Residual electron densities in the solvent-accessible void due to disordered solvent molecules were treated with the PLATON SQUEEZE program 2. The quite large (3 9 e/å 3 ) residual electron density peaks causing the Checkcif B level alerts are all located near the iodine atoms in the corresponding structures and could not be modelled with reasonable disordered atoms. Plant Material: C. Unshiu was cultivated in Nishi-Uwajima, Ehime prefecture, Japan in 2011. The peel of C. Unshiu was air-dried at room temperature over 1 week and ground into a fine powder with a lab mixer. WWW.NATURE.COM/NATURE 1

RESEARCH SUPPLEMENTARY INFORMATION II. Guest inclusion into Crystalline Sponges II-1. Host crystals Coordination networks [(Co(NCS) 2 ) 3 (1) 4 x(toluene)] n (2) and [(ZnI 2 ) 3 (1) 2 y(nitrobenzene)] n (3) for guest inclusion were synthesized according to the reported procedures 3,4. For zinc complex 3, the initial nitrobenzene guest was exchanged for cyclohexane in advance of guest inclusion by immersing the crystals in cyclohexane (ca. 10 mg/10 ml) at 45 ºC for 1 week 5. II-2. Inclusion of liquid guests Inclusion of cyclohexanone (5) into a crystal of 2 On a glass plate, a crystal of 2 (280 280 200 µm 3 ) was soaked in a drop of cyclohexanone (5) (5 µl) at room temperature. After standing for 2 d, the crystal was picked using a protectant and mounted onto the X-ray diffractometer. After collection of the diffraction data, the same crystal was subsequently analyzed by microscopic FT-IR spectroscopy. Inclusion complex 2 5: IR (single crystal, fluorolube) 2941 (s), 2865 (m) 2053 (s, NCS st.), 1713 (s, C=O st.), 1522(m) and 1375 (m) cm 1. Crystallographic data: C 39 H 24 N 15 Co 1.5 S 3 (C 6 H 10 O), M r = 985.45, crystal dimensions 0.28 0.28 0.20 mm 3, Monoclinic, space group, C2/m, a = 37.218(6), b = 37.293(6), c = 26.388(5) Å, β = 134.988(2)º, V = 25974(8) Å 3, T = 93 K, Z = 8, 11134 unique reflections out of 23220 with I > 2σ(I), 908 parameters, 0.95 < θ < 25.00, final R factors R 1 = 0.0822 and wr 2 = 0.2430 for all data. CCDC deposit number 910380. Inclusion of isoprene (6) into a crystal of 3 In a micro vial, a crystal of 3 (80 50 50 µm 3 ) was soaked in a drop of isoprene (6) (5 µl). Then the vial was sealed with a screw cap and allowed to stand for 2 d at room temperature. The crystal was then analyzed as described above. Inclusion complex 3 6: IR (single crystal, fluorolube) 3084 (m), 3055 (m), 2970 (m), 2926 (s), 2851 (m), 1595 (m), 1510 (m), and 1424 (m) cm 1. Crystallographic data: C 36 H 24 N 12 Zn 3 I 6 0.6(C 5 H 8 ), M r =1623.05, crystal dimensions 0.08 0.05 0.05 mm 3, Monoclinic, space group, C2/c, a = 35.060(4), b = 14.7672(16), c = 30.527(3) Å, β = 101.0880(10)º, V = 15510(3) Å 3, T = 90 K, Z = 8, 10907 unique reflections out of 16083 with I > 2σ(I), 561 parameters, 1.36 < θ < 26.53, final R factors R 1 = 0.0532 and wr 2 = 0.1664 for all data. CCDC deposit number 910381. 2 WWW.NATURE.COM/NATURE

SUPPLEMENTARY INFORMATION RESEARCH II-3. Nano-to-micro gram scale guest inclusion Nano-gram scale inclusion of guaiazulene (7) To a micro vial containing a single crystal of 3 (approximately 80 80 80 µm 3 ) and cyclohexane (45 µl), a dichloromethane solution of guaiazulene (7) (80 ng/5 µl or 500 ng/5 µl) was added. The crystal was heated at 45 ºC for 2 d, as described in the general procedure. Supplementary Fig. 1. a, Network structure of guaiazulene (7) included crystalline sponge 3 prepared from 80 ng of the guest 7. Guests 7 are drawn as CPK models. b, Electron density map (2F o F c ; contour: 0.5) superimposed on the guaiazulene (7). Inclusion complex 3 7: IR (single crystal, fluorolube) 3098 (m), 3054 (m), 2924 (m), 2856 (m) 1514 (m), 1464 (m), 1425 (m), and 1369 (m) cm 1. Crystallographic data of the inclusion complex 3 7 prepared from 500 ng of guest 7 Crystallographic data: C 36 H 24 N 12 Zn 3 I 6 0.6(C 15 H 18 ), M r = 1701.16, crystal dimensions 0.07 0.06 0.06 mm 3, Monoclinic, space group, C2/c, a = 34.644(6), b = 14.879(3), c = 30.836(6) Å, β = 101.787(2)º, V = 15560(5) Å 3, T = 90 K, Z = 8, 7948 unique reflections out of 15819 with I > 2σ(I), 649 parameters, 1.20 < θ < 26.39, final R factors R 1 = 0.0859 and wr 2 = 0.3021 for all data. CCDC deposit number 910382. Crystallographic data of the inclusion complex 3 7 prepared from 80 ng of guest 7 Crystallographic data: C 72 H 48 N 24 Zn 6 I 12 0.8(C 15 H 18 ), M r = 3323.00, crystal dimensions 0.08 0.08 0.08 mm 3, Monoclinic, space group, Cc, a = 34.576, b = 14.884, c = 30.646 Å, β = 101.17º, V = 15472.5 Å 3, T = 90 K, Z = 4, 9613 unique reflections out of 25857 with I > 2σ(I), 1088 parameters, 2.61 < θ < 68.05, final R factors R 1 = 0.0993 and wr 2 = 0.3190 for all data. CCDC deposit number 910383. WWW.NATURE.COM/NATURE 3

RESEARCH SUPPLEMENTARY INFORMATION II-4. A simplified blind test Six compounds (B1-B6; 5 µg each) were analyzed only once by one of the authors (S.Y.) using the general procedure shown in the main text. Samples were provided as their CH 2 Cl 2 solutions (5 µg/5 µl). In the first phase, he was asked to solve the structures of guests without any other molecular information. Then the mass spectra of the guests were provided and the diffraction data were re-examined based on the molecular formula. Supplementary Fig. 2. Results of the blind test. For guests B1, B3 and B4, structures were correctly determined in the first phase. B2 was misassigned as a phenol because of the similar peak intensity between N and O atoms. Guest B5 was initially solved as a disordered model. Guest B6 was found on a plane of symmetry in the original space group C2/c. Taking into account the mass data, the structure was re-examined in the space group P-1. 4 WWW.NATURE.COM/NATURE

SUPPLEMENTARY INFORMATION RESEARCH Supplementary Fig. 3. Network structures of crystalline sponge 3 including guests B1 6 (from a to f), viewed from the b-axis of the original unit cell of 3. The guest molecules are represented as CPK models (C: orange, O: red, N: blue, Br: brown, and H: white). 6 W W W. N A T U R E. C O M / N A T U R E 5

RESEARCH SUPPLEMENTARY INFORMATION Inclusion complex 3 B1: IR (single crystal, fluorolube) 3101 (m), 3068 (m), 3056 (m), 2923 (m), 2851 (m), 1703 (s, C=O st.), 1524 (m) 1377 (m), and 1340 (m, NO 2 ) cm 1. Crystallographic data: C 36 H 24 N 12 Zn 3 I 6 (C 7 H 5 NO 3 ), M r = 1733.3, crystal dimensions 0.07 0.06 0.05 mm 3, Monoclinic, space group, C2/c, a = 35.602(11), b = 14.879(5), c = 30.538(10) Å, β = 103.153(4)º V = 15752(9) Å 3, T = 90 K, Z = 8, 8514 unique reflections out of 13831 with I > 2σ(I), 713 parameters, 1.37 < θ < 25.00, final R factors R 1 = 0.1130 and wr 2 = 0.3380 for all data. CCDC deposit number 910384. Inclusion complex 3 B2: IR (single crystal, fluorolube) 3091 (m), 3051 (m), 2955 (m), 2867 (m), 1617(m, NH 2 ) 1513 (m), 1457 (m), 1440 (m), and 1377 (m) cm 1 Crystallographic data: C 36 H 24 N 12 Zn 3 I 6 0.76(C 12 H 19 N), M r = 1716.27, crystal dimensions 0.06 0.05 0.04 mm 3, Monoclinic, space group, C2/c, a = 35.752(9), b = 14.774(4), c = 30.594(7) Å, β = 101.647(4)º, V = 15828(7) Å 3, T = 90 K, Z = 8, 11927 unique reflections out of 16106 with I > 2σ(I), 632 parameters, 1.16 < θ < 26.62, final R factors R 1 = 0.1182 and wr 2 = 0.3520 for all data. CCDC deposit number 910385. Inclusion complex 3 B3: IR (single crystal, fluorolube) 3082 (m), 3057 (m), 2937 (m), 2849 (m), 1683 (s, C=O st.), 1627 (m), 1519 (m), 1449 (m), and 1363 (m) cm 1. Crystallographic data: C 36 H 24 N 12 Zn 3 I 6 0.5(C 9 H 8 O), M r = 1648.26, crystal dimensions 0.17 0.07 0.05 mm 3, Monoclinic, space group, C2/c, a = 34.847(4), b = 14.7560(16), c = 30.740(4) Å, β = 102.007(2)º, V = 15461(3) Å 3, T = 90 K, Z = 8, 10901 unique reflections out of 15196 with I > 2σ(I), 604 parameters, 1.19 < θ < 26.00, final R factors R 1 = 0.0750 and wr 2 = 0.2631 for all data. CCDC deposit number 910386. Inclusion complex 3 B4: IR (single crystal, fluorolube) 3410 (m, OH st.), 3099 (m), 3058 (m), 1686 (s, C=O st.), 1613 (m), 1590 (m), 1518 (m), 1428 (m), and 1376 (m) cm 1. Crystallographic data: C 72 H 48 N 24 Zn 6 I 12 2(C 8 H 8 O 3 ), M r = 3468.65, crystal dimensions 0.05 0.08 0.10 mm 3, Triclinic, space group, P-1, a = 14.907(5), b = 18.608(6), c = 32.920(11) Å, α = 103.269(4)º, β = 93.089(4)º, γ = 108.970(4)º, V = 8323(5) Å 3, T = 90 K, Z = 2, 16584 unique reflections out of 28540 with I > 2σ(I), 1227 parameters, 0.64 < θ < 25.00, final R factors R 1 = 0.1103 and wr 2 = 0.3402 for all data. CCDC deposit number 910387. 6 WWW.NATURE.COM/NATURE

SUPPLEMENTARY INFORMATION RESEARCH Inclusion complex 3 B5: IR (single crystal, fluorolube) 3097 (m), 3053 (m), 2923 (m), 2846 (m), 1515 (m), 1448 (m), and 1378 (m) cm 1. Crystallographic data: C 36 H 24 N 12 Zn 3 I 6 0.68(C 14 H 9 Br), M r = 1756.82, crystal dimensions 0.07 0.05 0.05 mm 3, Monoclinic, space group, C2/c, a = 35.862(5), b = 14.902(2), c = 31.358(5) Å, β = 102.694(2)º, V = 16349(4) Å 3, T = 90 K, Z = 8, 9795 unique reflections out of 14400 with I > 2σ(I), 650 parameters, 1.33 < θ < 25.00, final R factors R 1 = 0.1162 and wr 2 = 0.3753 for all data. CCDC deposit number 910388. Inclusion complex 3 B6: IR (single crystal, fluorolube) 3099 (m), 3052 (m), 2929 (m), 2850 (m), 1710 (s, C=O st.), 1516 (m), and 1376 (m) cm 1. Crystallographic data: C 72 H 48 N 24 Zn 6 I 12 0.7(C 6 H 6 O 2 ), M r = 3241.44, crystal dimensions 0.14 0.04 0.04 mm 3, Triclinic, space group, P-1, a = 14.952(9), b = 18.584(11), c = 32.756(19) Å, α = 104.933(8)º, β = 102.349(7)º, γ = 111.615(8)º, V = 7678(8) Å 3, T = 90 K, Z = 2, 8761 unique reflections out of 2911 with I > 2σ(I), 1099 parameters, 0.69 < θ < 25.00, final R factors R 1 = 0.1345 and wr 2 = 0.3775 for all data. CCDC deposit number 910389. II-5. Inclusion of a chiral guest According to the general procedure, santonin (8) (5 µg) was included into a crystal of 3. Inclusion complex 3 8: IR (single crystal, fluorolube) 3081 (m), 3061 (m), 2926 (m), 2854 (m), 1780 (s, C=O st.), 1630 (s, C=O st.), 1514 (m) and 1370 (m) cm 1. Crystallographic data: C 144 H 96 N 48 Zn 12 I 24 5(C 15 H 16 O 3 ) 6(C 6 H 12 ), M r = 8065.13, crystal dimensions 0.15 0.05 0.04 mm 3, Monoclinic, space group, P2 1, a = 32.866(5), b = 14.853(2), c = 34.850(6) Å, β = 105.848(2)º, V = 16366(5) Å 3, T = 90 K, Z = 2, 48049 unique reflections out of 60731 with I > 2σ(I), 3187 parameters, 0.75 < θ < 25.50, final R factors R 1 = 0.0827 and wr 2 = 0.1813 for all data. CCDC deposit number 910390. WWW.NATURE.COM/NATURE 7

RESEARCH SUPPLEMENTARY INFORMATION III. LC-SCD analysis III-1. Extraction of PMFs Dried and ground peel of C. Unshiu (20 g) was extracted with CHCl 3 (100 ml 2 times) at room temperature. After filtration of insoluble materials, the solvent was evaporated to leave an orange oil. The residue was chromatographed on silica gel first with CH 2 Cl 2 as eluent to remove oily fractions, and then with CH 2 Cl 2 /ethyl acetate (9:1) to give a crude mixture of PMFs (20 mg). III-2. LC-SCD analysis of PMFs The mixture of PMFs was dissolved in THF (30 µg/5 µl) and separated by analytical HPLC (eluent: acetonitrile/water = 52:48, flow rate: 1 ml/min.). Three main fractions eluted at 5.1, 5.9 and 7.0 min (fractions A, B, and C, respectively) were each collected in a separate vial. After removal of the solvent under reduced pressure, each residue was transferred into a micro vial containing a crystal of 3 and cyclohexane (45 µl) using 5 µl of CH 2 Cl 2. Incubation of the samples was performed at 45 ºC for 1 week. Supplementary Fig. 4. The electron density maps (2F o F c ; contour: 0.5) overlaid on the refined structures of the PMFs 9 11. 8 WWW.NATURE.COM/NATURE

SUPPLEMENTARY INFORMATION RESEARCH Crystallographic data obtained by LC-SCD analysis: Inclusion complex 3 9: IR (single crystal, fluorolube) 3075 (m), 3052(m), 2925 (m), 2852 (m), 1618 (s, C=O st.), 1577 (m), 1529 (m), 1513 (m), and 1371 (m) cm 1. Crystallographic data: C 36 H 24 N 12 Zn 3 I 6 0.5(C 21 H 22 O 8 ), M r = 1783.38, crystal dimensions 0.12 0.1 0.07 mm 3, Monoclinic, space group, C2/c, a = 34.562(8), b = 14.950(4), c = 30.348(7) Å, β = 100.119(3)º, V = 15437(6) Å 3, T = 93 K, Z = 8, 10259 unique reflections out of 13534 with I > 2σ(I), 780 parameters, 1.20 < θ < 25.00, final R factors R 1 = 0.1065 and wr 2 = 0.2915 for all data. CCDC deposit number 910391. Inclusion complex 3 10: IR (single crystal, fluorolube) 3076 (m), 3053 (m), 2924 (m), 2851 (m), 1616 (s, C=O st.), 1578 (m), 1525 (m), 1514 (m), and 1371 (m) cm 1. Crystallographic data: C 72 H 48 N 24 Zn 6 I 12 0.5(C 22 H 24 O 9 ), M r = 3380.57, crystal dimensions 0.08 0.05 0.04 mm 3, Monoclinic, space group, Cc, a = 34.534(6), b = 15.028(3), c = 31.197(6) Å, β = 101.215(3)º, V = 15881(5) Å 3, T = 90 K, Z = 4, 10274 unique reflections out of 31029 with I > 2σ(I), 1151 parameters, 1.20 < θ < 26.00, final R factors R 1 = 0.0730 and wr 2 = 0.2184 for all data. CCDC deposit number 910392. Inclusion complex 3 11: IR (single crystal, fluorolube) 3080 (m), 3055 (m), 2929 (m), 2854 (m), 1620 (s, C=O st.), 1576 (m), 1525 (m) and 1375 (m) cm 1. Crystallographic data: C 36 H 24 N 12 Zn 3 I 6 0.94(C 20 H 20 O 7 ), M r = 1930.40, crystal dimensions 0.15 0.05 0.05 mm 3, Monoclinic, space group, C2/c, a = 34.103(6), b = 14.767(3), c = 30.700(6) Å, β = 99.802(2)º, V = 15234(5) Å 3, T = 93 K, Z = 8, 9422 unique reflections out of 12914 with I > 2σ(I), 758 parameters, 1.21 < θ < 24.71, final R factors R 1 = 0.0823 and wr 2 = 0.2283 for all data. CCDC deposit number 910393. Characterization of PMFs: Fraction A: nobiletin (9) HR-ESI TOF-MS m/z = 403.1403 (calcd. for C 21 H 23 O 9 = 403.1393 [M+H] + ) Fraction B: 3,5,6,7,8,3,4 -heptamethoxyflavone (10) HR-ESI TOF-MS m/z = 433.1482 (calcd. for C 22 H 25 O 9 = 433.1499 [M+H] + ) Fraction C: tangeritin (11) HR-ESI TOF-MS m/z = 373.1283 (calcd. for C 20 H 21 O 7 = 373.1289 [M+H] + ) After the isolation on a large scale (~5 mg), we also confirmed that the 1 H NMR spectrum of each fraction was identical to the reported spectrum 6. WWW.NATURE.COM/NATURE 9

RESEARCH SUPPLEMENTARY INFORMATION IV. Structural analysis of Miyakosyne A Inclusion of Miyakosyne A According to the general procedure, miyakosyne A (12) (5 µg) was included into a crystal of 3. Inclusion complex 3 12: IR (single crystal, fluorolube) 3474 (m, OH st.), 3279 (m), 3098 (m), 3054 (m), 2924 (m), 2851 (m), 1620 (m), 1576 (m), 1515 (m), 1375 (m) and 1317 (m) cm 1. Crystallographic data: C 36 H 24 N 12 Zn 3 I 6 0.5(C 29 H 24 O 2 ), M r = 3378.70, crystal dimensions 0.11 0.09 0.08 mm 3, Monoclinic, space group, C2, a = 34.804(3), b = 14.8607(11), c = 31.624(2) Å, β = 102.0830(10)º, V = 15994(2) Å 3, T = 90 K, Z = 4, 11126 unique reflections out of 14697 with I > 2σ(I), 1350 parameters, 1.20 < θ < 25.00, final R factors R 1 = 0.0725 and wr 2 = 0.2478 for all data. CCDC deposit number 910394. Supplementary Fig. 5. Electron density map (2F o F c ; contour: 0.25) superimposed on the refined structure of Miyakosyne A. 10 WWW.NATURE.COM/NATURE

SUPPLEMENTARY INFORMATION RESEARCH V. References 1. Sheldrick, G. M. SHELX97 Programs for Crystal Structure Analysis (Release 97-2). (Univ. of Göttingen, 1997). 2. Sluis, P. & Spek A. L. BYPASS: an effective method for the refinement of crystal structures containing disordered solvent regions. Acta Cryst. A46, 194-201 (1990). 3. Inokuma, Y., Arai, T. & Fujita, M. Networked molecular cages as crystalline sponges for fullerenes and other guests. Nat. Chem. 2, 780-783 (2010). 4. Biradha, K. & Fujita, M. A springlike 3D-coordination network that shrinks or swells in a crystal-to-crystal manner upon guest removal or readsorption. Angew. Chem. Int. Ed. 41, 3392-3395 (2002). 5. Ohara, K., Kawano, M., Inokuma, Y. & Fujita, M. A porous coordination network catalyzes an olefin isomerization reaction in the pore. J. Am. Chem. Soc. 132, 30-31 (2010). 6. Han, S., Kim, H. M., Lee, J. M., Mok. S., & Lee, S. Isolation and identification of polymethoxyflavones from the hybrid citrus, hallabong. J. Agric. Food Chem. 58, 9488-9491 (2010). WWW.NATURE.COM/NATURE 11