Abstract
Four novel complexes of 2,4-dithiouracil (pyrimidine-2,4(1H,3H)-dithione, DTU) with 18-membered benzo- and dibenzo-crown ethers were synthesized in approximately the same conditions and studied by single crystal diffraction. Hydrogen bonding was observed to be the most important for the complexation in the solid state but π–π interactions also contribute to it. The crystalline monohydrates of the 1:1:1 stoichiometry are recorded for 4-bromo- and 4-nitrobenzo-18-crown-6 (complexes 1 and 2), while complexes with [2.4]dibenzo- and thia[1.5]dibenzo-18-crown-6 (complexes 3 and 4) represent anhydrous adducts of the 2:2 ratio. The crystal structures reveal three supramolecular structural motifs: the alternative chain for the ternary complex 1 and two types of capsules for complexes 2−4 where the DTU dimers are encapsulated inside the space restricted by two crown molecules.
Similar content being viewed by others
References
Pedersen, C.J.: Cyclic polyethers and their complexes with metal salts. J. Am. Chem. Soc. 89, 7017–7036 (1967)
Pedersen, C.J.: The discovery of crown ethers (noble lecture). Angew. Chem. Int. Ed. Engl. 27, 1021–1027 (1988)
(a) Bradshaw, J.S., Krakowiak, K.E., Izatt, R.M.: Aza-Crown Compounds, vol. 51, 885 pp. Wiley, New York (1993); (b) Gokel, G.W., Leevy, W.M., Weber, M.E.: Crown ethers: sensors for ions and molecular scaffolds for materials and biological models. Chem. Rev. 104, 2723–2750 (2004); (c) Gokel, G.W., Carasel, I.A.: Biologically active, synthetic ion transporters. Chem. Soc. Rev. 36, 378–389 (2007); (d) Steed, J.W.: First- and second-sphere coordination chemistry of alkali metal crown ether complexes. Coord. Chem. Rev. 215, 171–221 (2001); (e) Bond, A.H., Dietz, M.L., Chiarizia, R.: Incorporating size selectivity into synergistic solvent extraction: a review of crown ether-containing systems. Ind. Eng. Chem. Res. 39(10), 3442–3464 (2000); (f) Cusack, P.A., Smith, P.J.: Crown ethers in tin chemistry. Appl. Organometal. Chem. 4, 311–317 (1990)
(a) Simonov, Yu.A., Fonari, M.S., Zaworotko, M.J., Abourahma, H., Lipkowski, J., Ganin, E.V., Yavolovskii, A.A.: From 1D strands to extended supramolecular assemblies in the binary compounds of dithiooxamide and dithiobiurea with crown ethers. Org. Biomol. Chem. 1, 2922–2929 (2003); (b) Fonari, M.S., Simonov, Yu.A., Kravtsov, V.Ch., Lipkowski, J., Ganin, E.V., Yavolovskii, A.A.: Hydrogen bonding assemblies in the host-guest complexes with 18-crown-6. J. Mol. Struct. 647(1–3), 129–140 (2003)
(a) Ganin, E.V., Fonari, M.S., Simonov, Yu.A., Bocelli, G., Basok, S.S., Tkachuk, V.V., Kotlyar, S.A., Kamalov, G.L.: Structure of dibenzocrown ethers and their H-bonded adducts. 2. [1.5]Dibenzo-18-crown-6, a suitable building block to modulate the supramolecular assemblages sustained by conventional and weak hydrogen bonds. J. Incl. Phenom. 52, 63–74 (2005); (b) Kotlyar, S.A., Fonari, M.S., Simonov, Yu.A., Bocelli, G., Shishkin, O.V., Shishkina, S.V., Tkachuk, V.V., Grigorash, R.Ya., Kamalov, G.L.: Structure of dibenzocrownethers and their H-bonded adducts. 1. [1.5]Dibenzo-18-crown-6 and biphenyl-20-crown-6: complexes with amidosulfuric acid. J. Incl. Phenom. 52, 75–84 (2005)
Kiviniemi, S., Nissinen, M., Kolli, T., Jalonen, J., Rissanen, K., Pursiainen, J.: Crown ether complexes of six-membered N-heteroaromatic cations. J. Incl. Phenom. 40, 153–159 (2001)
(a) Simonov, Yu.A., Fonari, M.S., Lipkowski, J., Yavolovskii, A.A., Ganin, E.V.: Preparation and X-ray study of inclusion complexes of (4Z,5E)-pyrimidine-2,4,5,6(1H, 3H)-tetraone 4,5-dioxime and the product of its cyclization, (1,2,5)-oxadiazolo(3,4-d)-pyrimidine-5,7(4H,6H)-dione with two 18-membered macrocycles. J. Incl. Phenom. 46(1–2), 27–36 (2003); (b) Fonari, M.S., Simonov, Yu.A., Chumakov, Yu.M., Bocelli, G., Ganin, Ed.V., Yavolovskii, A.A.: The dihydropyrimidine-2,4-(1H,3H)-dione functionality: a suitable module for novel crown-containing hydrogen-bonded supramolecular assemblies. Supramol. Chem. 16(1), 23–30 (2004)
(a) Rostkowska, H., Szczepaniak, K., Nowak, M.J., Leszczynski, J., KuBulat, K., Person, W.B.: Thiouracils. 2. Tautomerism and infrared spectra of thiouracils. Matrix-isolation and ab initio studies. J. Am. Chem. Soc. 112, 2147–2160 (1990); (b) Leszczynski, J., Lammertsma, K.: 2,4-Dithiouracil tautomers: structures and energies. J. Phys. Chem. 95, 3128–3132 (1991); (c) Leš, A., Adamowicz, L.: Tautomerism of 2- and 4-thiouracil. Ab initio theoretical study. J. Am. Chem. Soc. 112, 1504–1509 (1990); (d) Lapinski, L., Rostkowska, H., Nowak, M., Kwiatkowski, J., Leszczynski, J.: Infrared spectra of thiouracils: experimental matrix isolation and ab initio Hartree-Fock, post-Hartree-Fock and density functional theory studies. Vib. Spectrosc. 13, 23–40 (1996); (e) Yekeler, H.: Ab initio study on tautomerism of 2-thiouracil in the gas phase and in solution. J. Comput. Aided Mol. Des. 14, 243–250 (2000); (f) Wang, H., Meng, F., Xu, W., Liu, C.: The effects of incorporating 2,4-dithiouracil into uracil tetrad: a theoretical study. J. Mol. Struct. THEOCHEM 716, 137–141 (2005); (g) Gomzi, V., Herak, J.N.: Ionization potentials of nucleobase analogs using partial third-order electron propagator method. J. Mol. Struct. THEOCHEM 683, 155–157 (2004); (h) Yang, Z., Rodgers, M.T.: Influence of thioketo substitution on the properties of uracil and its noncovalent interactions with alkali metal ions: threshold collision-induced dissociation and theoretical studies. J. Phys. Chem. A 110(4), 1455–1468 (2006)
(a) Shefter, E. Mautner, H.G.: The crystal and molecular structure of 2,4-dithiouracil. J. Am. Chem. Soc. 89, 1249–1253 (1967); (b) Tiekink, E.R.T.: Crystal structure of 2-thiouracil. Z. Kristallogr. 187, 79–84 (1989); (c) Fonari, M.S., Simonov, Yu.A., Ganin, E.V., Yavolowski, A.A., Luboradzki, R.: Crystal and molecular structures of the 1:2 “host-guest” complex between cis-anti-cis isomer of dicyclohexano-18-crown-6 and 2-thiouracil. Crystallogr. Rep. 44, 1006–1009 (1999)
Wang, W.-J., Ganin, E.V., Fonari, M.S., Simonov, Yu.A., Bocelli, G.: 2,4-Dithiouracil: the reproducible H-bonded structural motifs in the complexes with 18-membered crown ethers. Org. Biomol. Chem. 3, 3054–3058 (2005)
Etter, M.C., Frankenbach, G.A.: Hydrogen-bond directed cocrystallization as a tool for designing acentric organic solids. Chem. Mater. 1, 10–12 (1989)
Allen, F.N.: The Cambridge Structural Database: a quarter of a million crystal structures and rising. Acta Crystallogr. B58, 380–388 (2002)
(a) Goldberg, I.: Geometry of the ether, sulphide and hydroxyl Groups and structural chemistry of macrocyclic and non-cyclic polyether compounds. In: Patai, S., Rappaport, Z. (eds.) Crown Ethers and Analogs, pp. 359–476. Wiley (1989); (b) Abramson, S., Berkovich-Berger, D., Dagan, S., Goldberg, I., Golender, L., Grabarnik, M., Lemcoff, N.G., Weinman, S., Fuchs, B.: Polythiacrown macro- and gigantocycles with chiral diacetal cores. Eur. J. Org. Chem. 1957–1975 (2007)
Kotlyar, S.A., Pluzhnik-Gladyr, S.M.: The development of convenient synthesis methods of halogenosubstituted benzo- and dibenzocrown ethers. In: Monomers for Thermotolerant Polymers (Russ.). Moscow. NIITECHIM, 74–80 (1990)
Ivanov, O.V., Markovich, I.S., Blokhina, L.I., Nikolaenko, S.P., Filatova, M.P.: The method of nitration of benzocrown ethers. Patent USSR, № 1544754 (1990). Bull. 1990, №7
Gorodnuyk, V.P., Ivanov, O.V., Kotlyar, S.A.: Simple synthesis of unsymmetrical dibenzocrown ethers. Chem. Heterocycl. Comp. (Russ.). 26, 1414–1415 (1990) (translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 12, pp. 1697–1698, 1990)
Sheldrick, G.M.: SHELXS97 and SHELXL97. Programs for Crystal Structure Solution and Refinement. University of Göttingen, Germany (1997)
(a) Kotlyar, S.A., Shishkina, S.V., Shishkin, O.V., Pluzhnik-Gladyr, S.M., Kiriyak, A.V., Chuprin, G.N., Kamalov, G.L.: (4-Bromobenzo-18-crown-6)potassium chlorochromate. Acta Crystallogr. E62, m120–m122 (2006); (b) Hlavata, D., Hasek, J., Huml, K.: The crystal and molecular structure of 4-nitrobenzo-1,4,7,10,13,16-hexaoxacyclooctadecane. RbSCN, C17H23O8N2SRb. Acta Crystallogr. B34, 416–420 (1978); (c) Hasek, J., Hlavata, D., Huml, K.: Crystal and molecular structure of a complex formed by caesium thiocyanate and 4-nitrobenzo-1,4,7,10,13,16-hexaoxacyclooctadecane (4-nitrobenzo-18-crown-6). Acta Crystallogr. B33, 3372–3376 (1977); (d) Calleja, M., Johnson, K., Belcher, W.J., Steed, J.W.: Oxonium ions from aqua regia: isolation by hydrogen bonding to crown ethers. Inorg. Chem. 40, 4978–4985, (2001); (e) Talanova, G.G., Elkarim, N.S.A., Talanov, V.S., Hanes Junior, R.E., Hwang, H.-S., Bartsch, R.A., Rogers, R.D.: The “picrate effect” on extraction selectivities of aromatic group-containing crown ethers for alkali metal cations. J. Am. Chem. Soc. 121, 11281–11290 (1999); (f) Fonari, M.S., Ganin, E.V., Gelmboldt, V.O., Lipkowski, J., Kotlyar, S.A., Kamalov, G.L.: The 1:1 adduct of antimony trifluoride with [1.5]dibenzothia-18-crown-6. Acta Crystallogr. E62, m1021–m1023 (2006)
(a) Brewer, A.D., Ferguson, G., Parvez, M.: Triethylammonium salt of 1,2,3,4-tetrahydro-6-hydroxy-4-oxo-N-phenyl-2-thio-5-pyrimidinecarboxamide, ethanol solvate. Acta Crystallogr. C43, 144–147 (1987); (b) Tiekink, E.R.T.: Crystal and molecular structure of 5-carboxy-2-thiouracil monohydrate. Z. Kristallogr. 216, 122–125 (2001)
Author information
Authors and Affiliations
Corresponding author
Additional information
For part 3 see JIPh., 56, 345 (2006).
Rights and permissions
About this article
Cite this article
Fonari, M.S., Simonov, Y.A., Bocelli, G. et al. Structure of benzo- and dibenzocrown ethers and their H-bonded adducts. 4. Structural motifs in the 2,4-dithiouracil complexes with 4-bromo- and 4-nitrobenzo-18-crown-6, [2.4]dibenzo- and thia[1.5]dibenzo-18-crown-6. J Incl Phenom Macrocycl Chem 61, 367–375 (2008). https://doi.org/10.1007/s10847-008-9431-7
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s10847-008-9431-7