Startseite Crystal structure of (2,2′-((naphthalen-1-ylmethyl)azanediyl)diacetato-κ3 N,O,O′)-(1,10-phenanthroline-κ2 N,N′)-copper(II) trihydrate, CuC27H27N3O7
Artikel Open Access

Crystal structure of (2,2′-((naphthalen-1-ylmethyl)azanediyl)diacetato-κ3 N,O,O′)-(1,10-phenanthroline-κ2 N,N′)-copper(II) trihydrate, CuC27H27N3O7

  • Xingman Xu ORCID logo EMAIL logo und Renqiang Sun
Veröffentlicht/Copyright: 22. März 2022

Abstract

CuC27H27N3O7, orthorhombic, Pca21 (no. 29), a = 22.9142(18) Å, b = 7.3271(6) Å, c = 14.7386(11) Å, V = 2474.5(3) Å3, Z = 4, R gt (F) = 0.0443, wR ref (F 2) = 0.0990, T = 294(2) K.

CCDC no.: 2144403

The asymmetric unit of the title crystal structure is shown in the figure. Table 1 contains crystallographic data and Table 2 contains the list of the atoms including atomic coordinates and displacement parameters.

Table 1:

Data collection and handling.

Crystal: Blue block
Size: 0.12 × 0.10 × 0.10 mm
Wavelength: Mo Kα radiation (0.71073 Å)
μ: 0.94 mm−1
Diffractometer, scan mode: φ and ω
θ max, completeness: 28.3°, >99%
N(hkl)measured, N(hkl)unique, R int: 16,736, 5352, 0.044
Criterion for I obs, N(hkl)gt: I obs > 2 σ(I obs), 4224
N(param)refined: 352
Programs: Bruker [1], SHELX [2], [3], [4], Diamond [5], Olex2 [6], PLATON [7]
Table 2:

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2).

Atom x y z U iso*/U eq
C1 0.79889 (19) 0.0923 (6) 0.7026 (3) 0.0415 (10)
H1A 0.796156 0.103621 0.768000 0.050*
H1B 0.831649 0.165665 0.682380 0.050*
C2 0.80975 (17) −0.1037 (6) 0.6783 (4) 0.0407 (13)
C3 0.7529 (2) 0.1837 (7) 0.5623 (3) 0.0471 (11)
H3A 0.790791 0.134267 0.546237 0.057*
H3B 0.753626 0.313105 0.548430 0.057*
C4 0.7082 (2) 0.0957 (7) 0.5034 (3) 0.0503 (12)
C5 0.72674 (19) 0.3387 (6) 0.7046 (4) 0.0447 (11)
H5A 0.748847 0.438085 0.677900 0.054*
H5B 0.735941 0.334250 0.768755 0.054*
C6 0.6621 (2) 0.3763 (6) 0.6930 (4) 0.0454 (12)
C7 0.6413 (3) 0.4520 (7) 0.6144 (4) 0.0565 (14)
H7 0.668053 0.483274 0.569552 0.068*
C8 0.5816 (3) 0.4851 (8) 0.5976 (4) 0.0612 (14)
H8 0.569028 0.531602 0.542281 0.073*
C9 0.5430 (2) 0.4465 (6) 0.6653 (6) 0.0600 (12)
H9 0.503533 0.469497 0.656043 0.072*
C10 0.5613 (2) 0.3725 (6) 0.7492 (4) 0.0471 (12)
C11 0.62194 (19) 0.3358 (6) 0.7624 (4) 0.0459 (11)
C12 0.6385 (2) 0.2628 (7) 0.8493 (4) 0.0513 (12)
H12 0.677440 0.234785 0.860642 0.062*
C13 0.5979 (3) 0.2347 (7) 0.9148 (4) 0.0594 (14)
H13 0.609583 0.189958 0.970977 0.071*
C14 0.5394 (3) 0.2713 (8) 0.8995 (5) 0.0668 (16)
H14 0.512392 0.249521 0.945380 0.080*
C15 0.5211 (2) 0.3376 (8) 0.8198 (5) 0.0637 (16)
H15 0.481668 0.360990 0.810825 0.076*
C16 0.5594 (2) −0.0296 (7) 0.6214 (4) 0.0520 (12)
H16 0.570885 0.009587 0.564113 0.062*
C17 0.4999 (2) −0.0310 (8) 0.6431 (4) 0.0612 (17)
H17 0.472371 0.006018 0.600509 0.073*
C18 0.4824 (2) −0.0871 (7) 0.7274 (5) 0.0650 (17)
H18 0.442959 −0.087960 0.742080 0.078*
C19 0.5238 (2) −0.1434 (7) 0.7916 (4) 0.0516 (13)
C20 0.5114 (3) −0.2058 (8) 0.8812 (5) 0.0674 (17)
H20 0.472947 −0.207897 0.901185 0.081*
C21 0.5543 (3) −0.2623 (8) 0.9383 (4) 0.0654 (16)
H21 0.544662 −0.302776 0.996143 0.078*
C22 0.6135 (2) −0.2604 (7) 0.9110 (3) 0.0478 (12)
C23 0.6606 (3) −0.3184 (7) 0.9660 (3) 0.0560 (13)
H23 0.653960 −0.360566 1.024601 0.067*
C24 0.7149 (3) −0.3116 (7) 0.9323 (4) 0.0574 (13)
H24 0.746119 −0.348886 0.968119 0.069*
C25 0.7251 (2) −0.2501 (7) 0.8455 (3) 0.0464 (11)
H25 0.763284 −0.248458 0.824130 0.056*
C26 0.62714 (19) −0.1986 (6) 0.8241 (3) 0.0377 (10)
C27 0.58245 (18) −0.1398 (6) 0.7638 (3) 0.0395 (10)
Cu1 0.68688 (2) −0.09753 (6) 0.66375 (4) 0.03550 (14)
N1 0.74485 (13) 0.1624 (4) 0.6610 (3) 0.0365 (7)
N2 0.59960 (14) −0.0822 (4) 0.6798 (3) 0.0380 (10)
N3 0.68280 (14) −0.1932 (5) 0.7912 (2) 0.0361 (8)
O1 0.76685 (11) −0.1993 (4) 0.6493 (2) 0.0406 (7)
O2 0.85943 (14) −0.1634 (5) 0.6899 (3) 0.0609 (11)
O3 0.67791 (14) −0.0349 (6) 0.5360 (2) 0.0523 (9)
O4 0.7047 (2) 0.1460 (6) 0.4242 (3) 0.0796 (12)
O5 0.3772 (3) 0.6113 (7) 0.8548 (4) 0.0957 (15)
H5C 0.341481 0.602977 0.853320 0.143*
H5D 0.387848 0.521768 0.883678 0.143*
O6 0.3787 (2) 0.2318 (7) 0.8910 (4) 0.0844 (14)
H6A 0.375941 0.177076 0.842656 0.127*
H6B 0.366220 0.160028 0.928970 0.127*
O7 0.3900 (2) 0.5306 (5) 0.6648 (4) 0.0810 (10)
H7A 0.386941 0.420147 0.672546 0.121*
H7B 0.391386 0.573174 0.716178 0.121*

Source of material

All the reagents and solvents were used as obtained without further purification. N-(1-naphtylmethyl)iminodiacetic acid (H2NamIDA) was prepared in its acid form according to an earlier reported method [8]. A small amounts of Cu2CO3(OH)2 (0.44 g, 2.0 mmol), 1,10-phenanthroline (0.36 g, 2.0 mmol) and H2NamIDA (0.6 g, 2.2 mmol) were added into a flask in 50.0 mL distilled water. The solution was heated (50 °C) and stirred for 2 h. The residue was filtered and stood at room temperature for three days. Block blue crystals are formed (Yield: 60%, 0.683 g, based on metal salt).

Experimental details

H atoms were treated as riding, with C–H distances of 0.93 Å (aromatic) and 0.97 Å (methylene); U iso(H) = 1.2U eq (aromatic and methylene C). H atoms bonded to water O atoms were initially found in difference maps, and refined with constraint of O–H = 0.82 Å and U iso(H) values were set equal to 1.5 times of their parent atoms.

Comment

2,2′-(1-naphthylmethyl)iminodiacetic acid (H2NamIDA) is a frequently used organic starting material in the synthesis of metal-organic compounds as supra-molecular building blocks or as biological probe [9], [10], [11], [12]. As the continuation of our earlier work aiming to design new useful DNA cleaving agents [13, 14], we have synthesized new mixed ligated copper(II) complexes formed by NamIDA and 1,10-phenanthroline.

The title compound was crystallized in the orthorhombic acentric Pca21 space group. In its asymmetric unit, there is a neutral metal coordination ion and three free water molecules. The central copper (II) is five-coordinated by a {N3O2} donor set from each one NamIDA dianionic ligands and one phenanthroline molecule. The coordination configuration around Cu(II) center can be best described as a distorted square pyramidal polyhedron with a τ parameter of 0.13 [15]. The square plane is constituted by each two carboxylate oxygen and two phenanthroline nitrogen atoms, and the aliphatic amine N1 atom resides at the axial position. The Cu–O (1.990(3) Å and 1.949(3) Å) bond distances are slightly shorter than the Cu–N bond lengths (2.017(3) Å and 2.008(4) Å). The axial Cu1–N1 bond (2.323(3) Å) are apparently longer than the four basal Cu–O and Cu–N bond which is similar to some analogs [9, 11].

In the crystal, the coordination ions are linked into a two-dimensional network parallel to the (100) plane by six O–H⃛O hydrogen bonds. Due to the two aromatic naphthyl and phenanthroline rings existing in the molecular structure, there are also strong π⃛π stacking interactions, which further consolidated the crystal packing. For instance, the centroid-to-centroid distance between the six-numbered C16–C19/C27/N2 and C10–C15 rings is only 3.525(2) Å with a dihedral angle of 3.3(1)°. There is also another π⃛π stacking interaction between the C19–C22/C26/C27 and C10–C15 rings with the centroid-to-centroid distance and dihedral angle of 3.653(3) Å and 2.4(1)°, respectively [7].


Corresponding author: Xingman Xu, College of Chemistry, Central China Normal Univeristy, Wuhan 430079, P. R. China, E-mail:

Funding source: Central China Normal University http://dx.doi.org/10.13039/501100005234

Award Identifier / Grant number: No. CCNU18QN010

  1. Author contributions: All the authors have accepted responsibility for the entire content of this submitted manuscript and approved submission.

  2. Research funding: This work was financially supported by Central China Normal University (No. CCNU18QN010).

  3. Conflict of interest statement: The authors declare no conflicts of interest regarding this article.

References

1. Bruker. SMART and SAINT; Bruker AXS Inc.: Madison, WI, USA, 2003.Suche in Google Scholar

2. Sheldrick, G. M. SHELXTL – integrated space-group and crystal-structure determination. Acta Crystallogr. 2015, A71, 3–8; https://doi.org/10.1107/s2053273314026370.Suche in Google Scholar

3. Sheldrick, G. M. Crystal structure refinement with SHELXL. Acta Crystallogr. 2015, C71, 3–8; https://doi.org/10.1107/s2053229614024218.Suche in Google Scholar

4. Sheldrick, G. M. A short history of SHELX. Acta Crystallogr. 2008, A64, 112–122; https://doi.org/10.1107/s0108767307043930.Suche in Google Scholar

5. Brandenburg, K. DIAMOND; Crystal Impact GbR: Bonn, Germany, 2006.Suche in Google Scholar

6. Dolomanov, O. V., Bourhis, L. J., Gildea, R. J., Howard, J. A. K., Puschmann, H. OLEX2: a complete structure solution, refinement and analysis program. J. Appl. Crystallogr. 2009, 42, 339–341; https://doi.org/10.1107/s0021889808042726.Suche in Google Scholar

7. Spek, A. L. Structure validation in chemical crystallography. Acta Crystallogr. 2009, D65, 148–155; https://doi.org/10.1107/s090744490804362x.Suche in Google Scholar

8. El Bakkali, H., Choquesillo-Lazarte, D., Domínguez-Martín, A., Pérez-Toro, M. I., Lezama, L., González-Pérez, J. M., Castiñeiras, A., Niclós-Gutiérrez, J. Cocrystallization of mononuclear and trinuclear metallacycle molecules from an aqueous mixed-ligand copper(II) solution. Cryst. Growth Des. 2014, 14, 889–892; https://doi.org/10.1021/cg4015898.Suche in Google Scholar

9. Schmitt, W., Hill, J. P., Juanico, M. P., Caneschi, A., Costantino, F., Anson, C. E., Powell, A. K. Supramolecular coordination assemblies of dinuclear FeIII complexes. Angew. Chem. Int. Ed. 2005, 44, 4187–4192; https://doi.org/10.1002/anie.200500516.Suche in Google Scholar

10. Xu, J.-Y., Xie, C.-Z., Xue, F., Hao, L.-F., Ma, Z.-Y., Liao, D.-Z., Yan, S.-P. Directed assembly and characterization of 1D polymers based on [MII(BMA)]2+ node (M = Cu, Mn, Ni and Zn; BMA = N,N-bis (benzimidazol-2-yl-methyl)amine) with linear bridging dicyanamide and terephthalate ligands. Dalton Trans. 2010, 39, 7159–7166; https://doi.org/10.1039/c003226c.Suche in Google Scholar

11. Sánchez-Moreno, M. J., Choquesillo-Lazarte, D., González-Pérez, J. M., Carballo, R., Castiñeiras, A., Niclós-Gutiérrez, J. Inter-ligand interactions and the selective formation of the unusual metal—N3(adenine) bond in ternary copper(II) complexes with N-benzyliminodiacetato(2-) ligands. Inorg. Chem. Commun. 2002, 5, 800–802.10.1016/S1387-7003(02)00559-2Suche in Google Scholar

12. García-Rubiño, M. E., Barceló-Oliver, M., Castiñeiras, A., Domínguez-Martín, A. Probing the effect of N-alkylation on the molecular recognition abilities of the major groove N7-binding site of purine ligands. J. Inorg. Biochem. 2019, 200, 110801.10.1016/j.jinorgbio.2019.110801Suche in Google Scholar PubMed

13. Xu, X.-M., Mao, Z.-W., Ji, L.-N., Yao, J.-H., Li, H. Syntheses, characterization and DNA cleavage studies of acyclic copper(II) complexes. Transition Met. Chem. 2004, 29, 658–662; https://doi.org/10.1007/s11243-004-4997-4.Suche in Google Scholar

14. Xu, X.-M., Yao, J.-H., Mao, Z.-W., Yu, K.-B., Ji, L.-N. DNA cleavage by a novel acyclic copper(II) complex. Inorg. Chem. Commun. 2004, 7, 803–805; https://doi.org/10.1016/j.inoche.2004.04.014.Suche in Google Scholar

15. Addison, A. W., Rao, T. N., Reedijk, J., van Rijn, J., Verschoor, G. C. Synthesis, structure, and spectroscopic properties of copper(II) compounds containing nitrogen–sulphur donor ligands; The crystal and molecular structure of aqua [1,7-bis(N-methylbenzimidazol-2′-yl)-2,6-dithiaheptane]copper(II) perchlorate. J. Chem. Soc., Dalton Trans. 1984, 1349–1356; https://doi.org/10.1039/dt9840001349.Suche in Google Scholar

Received: 2022-01-25
Accepted: 2022-03-11
Published Online: 2022-03-22
Published in Print: 2022-06-27

© 2022 Xingman Xu and Renqiang Sun, published by De Gruyter, Berlin/Boston

This work is licensed under the Creative Commons Attribution 4.0 International License.

Artikel in diesem Heft

  1. Frontmatter
  2. New Crystal Structures
  3. Crystal structure of (E)-(4-imidazol-1-yl-phenyl)-(2-methoxy-benzylidene)-amine monohydrate, C17H17N3O2
  4. Crystal structure of 6-methyl-3-(pyrrolidine-1-carbonyl)-2H-chromen-2-one, C15H15N1O3
  5. Crystal structure of 4-methyl-4-nitropentanoic acid, C6H11NO4
  6. The crystal structure of (E)-3-(furan-2-yl)acrylonitrile, C7H5NO
  7. Crystal structure of 3-(difluoromethyl)-1-methyl-N-(4,11,11-trimethyl-1,2,3,4-tetrahydro-1,4-methanoacridin-9-yl)-1H-pyrazole-4-carboxamide monohydrate, C23H26F2N4O3
  8. Crystal structure of 2-(4-bromobenzyloxy)-6-chloropyridine, C12H9BrClNO
  9. Crystal structure of N-(4-bromo-2,6-dichloro-phenyl)pyrazin-2-amine, C10H6BrCl2N3
  10. Crystal structure of (E)-1-(2–nitrophenyl)-3-phenylprop-2-en-1-one, C15H11NO3
  11. The crystal structure of (E)-3-chloro-2-(2-(4-fluorobenzylidene)hydrazinyl)pyridine, C12H9ClFN3
  12. Crystal structure of (E)-amino(2-(thiazol-2-ylmethylene)hydrazineyl)methaniminium nitrate, C10H16N12O6S2
  13. Crystal structure of 9-methoxy-2,3,4,4a,5,6-hexahydro-1H-pyrido [1′,2′:1,6]pyrazino[2,3-b]quinoxaline, C15H18N4O
  14. The crystal structure bis(dimethylsulfoxide-κ1O)-dipyridine-κ1 N-bis(m2-(Z)-3-methyl-2-oxido-N-((Z)-oxido(phenyl)methylene)benzohydrazonato-κ5)trinickel(II) - dimethylsulfoxide (1/2), C48H56N6Ni3O10S4
  15. Crystal structure of bis(bis(triphenylphosphine)iminium) tetradecacarbonyltetratelluridopentaferrate(2-), (PPN)2[Fe5Te4(CO)14]
  16. Crystal structure of 4-Hydroxy-3-(naphthalen-2-ylthio)pent-3-en-2-one, C15H14O2S
  17. The crystal structure of [(1,10-phenanthroline-κ2 N,N)-bis(6-phenylpyridine-2-carboxylate-κ2 N,O)nickel(II)] monohydrate, C36H26N4O5Ni
  18. Crystal structure of 3,3′-(pyridine-2,6-diylbis(methylene))bis(1-propyl-1H-imidazol-3-ium) ditetrafluoroborate, C19H27B2F8N5
  19. The crystal structure of (E)-1-(4-aminophenyl)-3-(p-tolyl)prop-2-en-1-one, C16H15NO
  20. The crystal structure of poly[(μ2-terephthalato-κ4O,O′: O″,O‴)-(μ4-terephthalato-κ4O:O′:O″:O‴)-{μ4-(1,2,4,5-tetrakis(1,2,4-triazol-1-ylmethyl)-benzene-κ4O:O′:O″,O‴)}dicadmium(II)] – water – acetronitrile (1/2/2), C38H36N14O10Cd2
  21. The crystal structure of diaqua-bis(6-phenylpyridine-2-carboxylato-κ2 N,O)cobalt(II)–water–N,N-dimethylformamide(1/2/1), C27H31N3O9Co
  22. The co-crystal structure of 4-hydroxy-3-methoxybenzoic acid – 4,4′-bipyridine, C8H8O4·C10H8N2
  23. Crystal structure of catena-poly[(μ2-1,1′-(biphenyl-4,4′-diyl)bis(1H-imidazol)-κ2N:N′)-bis(4-bromobenzoate-κ1O)cobalt(II)], C32H22Br2CoN4O4
  24. Crystal structure of (E)-5-propyl-4-((pyridin-2-ylmethylene)amino)-2,4-dihydro-3H-1,2,4-triazole-3-thione – methanol (1/1), C11H13N5S
  25. The crystal structure of (Z)-4-bromo-6-(((1,3-dihydroxy-2-(hydroxymethyl)propan-2-yl)amino)methylene)cyclohexa-2,4-dien-1-one monohydrate, C11H16BrNO5
  26. Crystal structure of bis(tetrapropylammonium) nonaselenidotetrastannate(IV), (Pr4N)2[Sn4Se9]
  27. Crystal structure of 2,6-di-tert-butyl-4-(4-chlorobenzylidene)cyclohexa-2,5-dien-1-one, C21H25ClO
  28. Crystal structure of (2,2′-((naphthalen-1-ylmethyl)azanediyl)diacetato-κ3 N,O,O′)-(1,10-phenanthroline-κ2 N,N′)-copper(II) trihydrate, CuC27H27N3O7
  29. The crystal structure of tetrakis(6-phenylpyridine-2-carboxylato-κ2N,O)-bis(1H-pyrazol-3-ylamine-κ2 N:N)dicobalt(II) dihydrate, C27H23N5O5Co
  30. The crystal structure of bis((E)-2-((tert-butylimino)methyl)-4-chlorophenolato-κ2N,O)zinc(II), C22H26Cl2N2O2Zn
  31. The crystal structure of poly[diaqua-(μ3-5-nitrobenzene-1,2,3-tricarboxylato-κ3O:O′:O′)-(μ2-4,4′-dipyridylamine-κ2N:N′)copper(II)], C38H30Cu3N8O20
  32. The crystal structure of (E)-1-ferrocenyl-3-(naphthalen-1-yl)prop-2-en-1-one, C23H18FeO
  33. The crystal structure of (E)-1-ferrocenyl-3-(4-isopropylphenyl)prop-2-en-1-one, C22H22FeO
  34. Crystal structure of 6-hydroxy-2,2-dimethyl-4Hbenzo[d][1,3]dioxin-4-one, C10H10O4
  35. The crystal structure of (2E,4E)-1-ferrocenyl-5-phenylpenta-2,4-dien-1-one, C21H18FeO
  36. Crystal structure of alaninato-κ2N,O-bis(hydroxylamido-κ2N,O)-oxido-vanadium(V), C3H10N3O5V
  37. Crystal structure of catena-poly[aqua-bis[μ2-6-(1H-imidazol-1-yl)nicotinato-κ2 N,O]copper(II)], C18H14N6O5Cu
  38. Crystal structure of diethyl 4,6-diphenyl-1,9-di-p-tolylhexahydro-3H-2,7,3,5-(epimethanetriyliminomethanetriyl)cyclopenta[b]pyridine-3,5(2H)-dicarboxylate, C42H42N2O4
  39. The crystal structure of cobalt cadmium bis(hydrogenphosphate) bis(phosphate(V)) tetrahydrate, H10O20P4Co3.14Cd1.86
  40. Crystal structure of dimethyl 1,4,6,9-tetraphenylhexahydro-3H-2,7,3,5-(epimethanetriyliminomethanetriyl)cyclopenta[b]pyridine-3,7(2H)-dicarboxylate, C38H34N2O4
  41. Crystal structure of (Z)-4-(furan-2-yl((4-iodophenyl)amino)methylene)-5-methyl-2(p-tolyl)-2,4-dihydro-3H-pyrazol-3-one, C21H16I N3O2
  42. Crystal structure of (E)-1-(4-(3,5-dimethoxystyryl)phenyl)-7-ethylheptanedioate, C25H30O6
  43. Crystal structure of 6-bromo-2-(4-chlorophenyl)chroman-4-one (6-bromo-4′-chloroflavanone), C15H10BrClO2
  44. The crystal structure of 2-(benzhydryloxy)-3-nitropyridine, C18H14N2O3
  45. The crystal structure of 1,3(4,1)-dipyridin-1-iuma-2(1,8)-diethynylanthracena-5(1,3)-benzenacyclohexaphane-11,31-diium bis(hexafluoridophosphate), C36H24F12N2P2
  46. Crystal structure of 3,6-di-tert-butyl-1-iodo-9-methyl-8-(pyren-1-ylethynyl)-9H-carbazole, C39H34IN
  47. The cocrystal 2-(dimethylammonio)-5-nitrobenzoate – 2-(dimethylamino)-5-nitrobenzoic acid, C9H10N2O4
  48. Crystal structure of 5-nitroquinazolin-4(3H)-one, C8H5N3O3
Heruntergeladen am 5.9.2025 von https://www.degruyterbrill.com/document/doi/10.1515/ncrs-2022-0050/html
Button zum nach oben scrollen