Abstract
The crystal structure of a polynuclear metallamacrocyclic β-alanine hydroxymate complex of copper with dicyanamide (DCA) Cu5(β-alaha)4(DCA)2(H2O)2·H2O (I) is determined by SC-XRD. Due to intermolecular O–H…N interactions, the neighboring molecules form infinite 1D chains linked together by π…π interactions of two cyano groups. An analysis of the electron density topology in Cu5(β-alaha)4(DCA)2(H2O)2 and the molecular electrostatic potential, performed on the basis of DFT calculations, shows that the coordination of dicyanamide leads to the formation of intramolecular non-covalent interactions of DCA with the copper atoms of the metallacrown and the water molecule coordinated on Cu3.
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REFERENCES
G. Mezei, C. M. Zaleski, and V. L. Pecoraro. Structural and functional evolution of metallacrowns. Chem. Rev., 2007, 107, 4933-5003. https://doi.org/10.1021/cr078200h
M. Tegoni and M. Remelli. Metallacrowns of copper(II) and aminohydroxamates: Thermodynamics of self assembly and host–guest equilibria. Coord. Chem. Rev., 2012, 256, 289-315. https://doi.org/10.1016/j.ccr.2011.06.007
M. Ostrowska, I. O. Fritsky, E. Gumienna-Kontecka, and A. V. Pavlishchuk. Metallacrown-based compounds: Applications in catalysis, luminescence, molecular magnetism, and adsorption. Coord. Chem. Rev., 2016, 327/328, 304-332. https://doi.org/10.1016/j.ccr.2016.04.017
Y. Pavlyukh, E. Rentschler, H. J. Elmers, W. Hubner, and G. Lefkidis. Magnetism of metallacrown single-molecule magnets: From a simplest model to realistic systems. Phys. Rev. B, 2018, 97, 214408. https://doi.org/10.1103/PhysRevB.97.214408
M. A. Katkova. Water-soluble polynuclear metallamacrocyclic copper(II) and lanthanide(III) complexes based on amino hydroxamic acids. Russ. J. Coord. Chem., 2018, 44, 284-300. https://doi.org/10.1134/S107032841804005X
B. L. Schneider and V. L. Pecoraro. Host–guest chemistry of metallacrowns. In: Advances in Metallacrown Chemistry / Ed. C. M. Zaleski. Cham, Switzerland: Springer, 2022, 1-36. https://doi.org/10.1007/978-3-031-08576-5_1
S. R. Batten and K. S. Murray. Structure and magnetism of coordination polymers containing dicyanamide and tricyanomethanide. Coord. Chem. Rev., 2003, 246, 103-130. https://doi.org/10.1016/S0010-8545(03)00119-X
L. Merabet, A. V. Vologzhanina, Z. Setifi, L. Kabouba, and F. Setifi. Topological motifs in dicyanamides of transition metals. CrystEngComm, 2022, 24, 4740-4747. https://doi.org/10.1039/D2CE00485B
G. V. Romanenko, E. Yu. Fursova, G. A. Letyagin, A. S. Bogomyakov, M. V. Petrova, V. A. Morozov, and V. I. Ovcharenko. Crystal structure of metal complexes with 2-imidazoline nitroxides and dicyanamide. J. Struct. Chem., 2018, 59, 1412-1420. https://doi.org/10.1134/S0022476618060239
J. Legendziewicz, M. Puchalska, Z. Ciunik, and W. Wojciechowski. The new decanuclear copper(II) cluster [Cu5(β-alaha)4Cl2]2·2HCl·15H2O, its structure, spectroscopy and magnetism. Polyhedron, 2007, 26, 1331-1337. https://doi.org/10.1016/j.poly.2006.11.002
A. V. Pavlishchuk, S. V. Kolotilov, M. Zeller, O. V. Shvets, I. O. Fritsky, S. E. Lofland, A. W. Addison, and A. D. Hunter. Magnetic and sorption properties of supramolecular systems based on pentanuclear copper(II) 12-metallacrown-4 complexes and isomeric phthalates: Structural modeling of the different stages of alcohol sorption. Eur. J. Inorg. Chem., 2011, 2011, 4826-4836. https://doi.org/10.1002/ejic.201100790
SAINT: Data reduction and correction program. Madison, WI, USA: Bruker AXS, 2014.
L. Krause, R. Herbst-Irmer, G. M. Sheldrick, and D. Stalke. Comparison of silver and molybdenum microfocus X-ray sources for single-crystal structure determination. J. Appl. Crystallogr., 2015, 48, 3-10. https://doi.org/10.1107/S1600576714022985
G. M. Sheldrick. SHELXT - Integrated space-group and crystal-structure determination. Acta Crystallogr., Sect. A: Found. Adv., 2015, 71, 3-8. https://doi.org/10.1107/S2053273314026370
G. M. Sheldrick. Crystal structure refinement with SHELXL. Acta Crystallogr., Sect. C: Struct. Chem., 2015, 71, 3-8. https://doi.org/10.1107/S2053229614024218
M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, M. A. Robb, J. R. Cheeseman, G. Scalmani, V. Barone, B. Mennucci, G. A. Petersson, H. Nakatsuji, M. Caricato, X. Li, H. P. Hratchian, A. F. Izmaylov, J. Bloino, G. Zheng, J. L. Sonnenberg, M. Hada, M. Ehara, K. Toyota, R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, H. Nakai, T. Vreven, J. A. Montgomery Jr., J. E. Peralta, F. Ogliaro, M. Bearpark, J. J. Heyd, E. Brothers, K. N. Kudin, V. N. Staroverov, T. Keith, R. Kobayashi, J. Normand, K. Raghavachari, A. Rendell, J. C. Burant, S. S. Iyengar, J. Tomasi, M. Cossi, N. Rega, J. M. Millam, M. Klene, J. E. Knox, J. B. Cross, V. Bakken, C. Adamo, J. Jaramillo, R. Gomperts, R. E. Stratmann, O. Yazyev, A. J. Austin, R. Cammi, C. Pomelli, J. W. Ochterski, R. L. Martin, K. Morokuma, V. G. Zakrzewski, G. A. Voth, P. Salvador, J. J. Dannenberg, S. Dapprich, A. D. Daniels, O. Farkas, J. B. Foresman, J. V. Ortiz, J. Cioslowski, and D. J. Fox. Gaussian09, Revision D.01. Wallingford, CT, USA: Gaussian, 2013.
A. D. Becke. Density-functional thermochemistry. III. The role of exact exchange. J. Chem. Phys., 1993, 98, 5648-5652. https://doi.org/10.1063/1.464913
C. Lee, W. Yang, and R. G. Parr. Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density. Phys. Rev., 1988, 37, 785-789. https://doi.org/10.1103/PhysRevB.37.785
P. J. Stephens, F. J. Devlin, C. F. Chabalowski, and M. J. Frisch. Ab initio calculation of vibrational absorption and circular dichroism spectra using density functional force fields. J. Phys. Chem., 1994, 98, 11623-11627. https://doi.org/10.1021/j100096a001
B. P. Pritchard, D. Altarawy, B. Didier, T. D. Gibson, and T. L. Windus. New basis set exchange: An open, up-to-date resource for the molecular sciences community. J. Chem. Inf. Model., 2019, 59, 4814-4820. https://doi.org/10.1021/acs.jcim.9b00725
G. G. Camiletti, S. F. Machado, and F. E. Jorge. Gaussian basis set of double zeta quality for atoms K through Kr: Application in DFT calculations of molecular properties. J. Comput. Chem., 2008, 29, 2434-2444. https://doi.org/10.1002/jcc.20996
A. Canal Neto, E. P. Muniz, R. Centoducatte, and F. E. Jorge. Gaussian basis sets for correlated wave functions. Hydrogen, helium, first- and second-row atoms. J. Mol. Struc.: THEOCHEM, 2005, 718, 219-224. https://doi.org/10.1016/j.theochem.2004.11.037
J. Tomasi, B. Mennucci, and R. Cammi. Quantum mechanical continuum solvation models. Chem. Rev., 2005, 105, 2999-3094. https://doi.org/10.1021/cr9904009
R. F. W. Bader. Atoms in Molecules: A Quantum Theory. Oxford: Oxford Univ., 1990.
F. Cortes-Guzman and R. F. W. Bader. Complementarity of QTAIM and MO theory in the study of bonding in donor–acceptor complexes. Coord. Chem. Rev., 2005, 249, 633-662. https://doi.org/10.1016/j.ccr.2004.08.022
T. A. Keith. AIMAll (Version 17.11.14). Overland Park, KS, USA: TK Gristmill Software, 2017, http://aim.tkgristmill.com/
T. Lu and F. Chen. Multiwfn: A multifunctional wavefunction analyzer. J. Comput. Chem., 2012, 33, 580-592. https://doi.org/10.1002/jcc.22885
I. A. Guzei and M. Wendt. An improved method for the computation of ligand steric effects based on solid angles. Dalton Trans., 2006, 3991-3999. https://doi.org/10.1039/B605102B
L. Yang, D. R. Powell, and R. P. Houser. Structural variation in copper(I) complexes with pyridylmethylamide ligands: structural analysis with a new four-coordinate geometry index, τ4. Dalton Trans., 2007, 955-964. https://doi.org/10.1039/B617136B
J. A. Halfen, J. J. Bodwin, and V. L. Pecoraro. Preparation and characterization of chiral copper 12-metallacrown-4 complexes, inorganic analogues of tetraphenylporphyrinatocopper(II). Inorg. Chem., 1998, 37, 5416/5417. https://doi.org/10.1021/ic9807386
C. McDonald, T. Whyte, S. M. Taylor, S. Sanz, E. K. Brechin, D. Gaynor, and L. F. Jones. Progressive decoration of pentanuclear Cu(II) 12-metallacrown-4 nodes towards targeted 1- and 2D extended networks. CrystEngComm, 2013, 15, 6672-6681. https://doi.org/10.1039/C3CE40859K
I. J. Bruno, J. C. Cole, P. R. Edgington, M. Kessler, C. F. Macrae, P. McCabe, J. Pearson, and R. Taylor. New software for searching the Cambridge Structural Database and visualizing crystal structures. Acta Crystallogr., Sect. B: Struct. Sci., 2002, 58, 389-397. https://doi.org/10.1107/S0108768102003324
S. S. Batsanov. Van der Waals radii of elements. Inorg. Mater., 2001, 37, 871-885. https://doi.org/10.1023/A:1011625728803
Yu. V. Zefirov and P. M. Zorky. New applications of van der Waals radii in chemistry. Russ. Chem. Rev., 1995, 64, 415-428. https://doi.org/10.1070/RC1995v064n05ABEH000157
P. A. Wood, S. J. Borwick, D. J. Watkin, W. D. S. Motherwell, and F. H. Allen. Dipolar C≡N…C≡N interactions in organic crystal structures: database analysis and calculation of interaction energies. Acta Crystallogr., Sect. B: Struct. Sci., 2008, 64, 393-396. https://doi.org/10.1107/S0108768108010239
E. Espinosa, E. Molins, and C. Lecomte. Hydrogen bond strengths revealed by topological analyses of experimentally observed electron densities. Chem. Phys. Lett., 1998, 285, 170-173. https://doi.org/10.1016/S0009-2614(98)00036-0
Funding
This work was funded by the Russian Science Foundation (project No. 23-13-00139, https://rscf.ru/project/23-13-00139/).
The SC-XRD studies were performed using equipment of the Analytical Center of IOMC RAS.
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Russian Text © The Author(s), 2023, published in Zhurnal Strukturnoi Khimii, 2023, Vol. 64, No. 9, 115665.https://doi.org/10.26902/JSC_id115665
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Rumyantsev, R.V., Katkova, M.A., Zabrodina, G.S. et al. FEATURES OF DICYANAMIDE BINDING TO A POLYNUCLEAR METALLAMACROCYCLIC COPPER COMPLEX. J Struct Chem 64, 1635–1643 (2023). https://doi.org/10.1134/S002247662309007X
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DOI: https://doi.org/10.1134/S002247662309007X