Startseite Naturwissenschaften Crystal structure of [tris(2-benzimidazolylmethyl)amine-κ4N,N′,N′′,N′′′]-[(pyridine-2,6-dicarboxylato-κ2O,N)]cadmium(II)–methanol (1:3) C34H36CdN8O7
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Crystal structure of [tris(2-benzimidazolylmethyl)amine-κ4N,N′,N′′,N′′′]-[(pyridine-2,6-dicarboxylato-κ2O,N)]cadmium(II)–methanol (1:3) C34H36CdN8O7

  • Chen Jing EMAIL logo , Zhang Lingcong , Chen Jingwen und Zhang Haodong
Veröffentlicht/Copyright: 5. September 2018

Abstract

C34H36CdN8O7, monoclinic, P21/n (no. 14), a = 14.863(3) Å, b = 13.184(3) Å, c = 17.202(3) Å, β = 91.33(3)°, V = 3369.8(12) Å3, Z = 4, Rgt(F) = 0.0311, wRref(F2) = 0.0825, T = 113(2) K.

CCDC no.: 1812742

The title complex is shown in the figure. Hydrogen atoms and the solvent molecules are omitted in the figure for clarity. Tables 1 and 2 contain details of the measurement method and a list of the atoms including atomic coordinates and displacement parameters.

Table 1:

Crystal collection and handling.

Crystal:Block, colorless
Size:0.20 × 0.18 × 0.12 mm
Wavelength:Mo Kα radiation (λ = 0.71073 Å)
μ:0.71 mm−1
Diffractometer, scan mode:Rigaku Saturn, ω-scans
θmax, completeness:25.0°, >99%
N(hkl)measured, N(hkl)unique, Rint:26169, 5942, 0.0418
Criterion for Iobs, N(hkl)gt:Iobs > 2σ(Iobs), 5322
N(param)refined:470
Programs:CrystalClear [1], OLEX2 [2], SHELX [3]
Table 2:

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

AtomxyzUiso*/Ueq
Cd10.45533(2)0.66299(2)0.19391(2)0.01846(9)
O10.42429(12)0.83302(12)0.22599(12)0.0266(4)
O20.48056(12)0.98530(12)0.25336(11)0.0258(4)
O30.59558(12)0.57476(13)0.12598(11)0.0266(4)
O40.74589(13)0.57663(14)0.13254(13)0.0348(5)
O50.51552(18)0.16590(14)0.32849(14)0.0435(6)
H5B0.5092520.1177000.2968920.065
O60.81779(17)0.45483(17)0.01979(13)0.0458(6)
H6A0.7963940.4930150.0538050.069
O70.2559(2)0.3689(3)0.3279(2)0.0882(11)
H7B0.2032860.3495670.3167330.132
N10.37136(14)0.49860(15)0.15055(12)0.0208(5)
N20.40522(14)0.67795(14)0.06861(12)0.0191(5)
N30.39026(15)0.60436(17)−0.04767(13)0.0229(5)
H30.389(2)0.547(3)−0.077(2)0.055(11)
N40.32154(15)0.64542(15)0.26295(13)0.0210(5)
N50.18698(16)0.57512(17)0.27714(13)0.0230(5)
H50.143(2)0.545(2)0.2665(17)0.024(8)
N60.50089(14)0.53459(15)0.27323(13)0.0225(5)
N70.50273(16)0.37580(17)0.31344(14)0.0269(5)
H70.491(2)0.317(2)0.3146(19)0.031(9)
N80.58794(14)0.75823(14)0.19662(11)0.0168(4)
C10.39067(18)0.48901(18)0.06741(15)0.0222(6)
H1A0.3429630.4481770.0412620.027
H1B0.4487280.4534180.0612780.027
C20.39515(16)0.59158(18)0.03011(15)0.0199(5)
C30.40705(17)0.75294(18)0.01157(15)0.0200(5)
C40.41311(19)0.8586(2)0.01843(17)0.0271(6)
H40.4193530.8904750.0677710.033
C50.40963(19)0.9145(2)−0.04952(18)0.0304(6)
H5A0.4128880.986331−0.0466020.037
C60.4014(2)0.8679(2)−0.12273(18)0.0313(6)
H60.3994080.909062−0.1680790.038
C70.39622(18)0.7639(2)−0.13043(16)0.0278(6)
H7A0.3916400.732307−0.1799790.033
C80.39803(17)0.70762(19)−0.06180(15)0.0217(5)
C90.27525(17)0.5200(2)0.16188(15)0.0226(6)
H9A0.2417710.4552880.1651210.027
H9B0.2508500.5583900.1166370.027
C100.26185(17)0.58023(18)0.23468(15)0.0209(5)
C110.28341(18)0.68408(19)0.32997(15)0.0211(5)
C120.31704(19)0.75318(19)0.38503(16)0.0250(6)
H120.3741970.7842520.3794300.030
C130.2640(2)0.7746(2)0.44797(16)0.0290(6)
H130.2855030.8211460.4862540.035
C140.1799(2)0.7300(2)0.45682(16)0.0307(7)
H140.1456980.7467510.5009840.037
C150.1451(2)0.66212(19)0.40311(17)0.0266(6)
H150.0877580.6316810.4091250.032
C160.19834(18)0.64034(19)0.33945(15)0.0218(5)
C170.4044(2)0.41187(19)0.19722(17)0.0289(6)
H17A0.4340230.3628030.1625510.035
H17B0.3524920.3772730.2206240.035
C180.46970(18)0.44257(18)0.26067(15)0.0220(6)
C190.55817(18)0.5276(2)0.33790(16)0.0242(6)
C200.6115(2)0.6014(2)0.37436(18)0.0325(7)
H200.6121500.6693930.3559920.039
C210.6633(2)0.5722(2)0.4380(2)0.0439(8)
H210.7005460.6207670.4639160.053
C220.6619(2)0.4721(3)0.4649(2)0.0497(9)
H220.6975950.4544310.5093530.060
C230.6101(2)0.3984(2)0.4287(2)0.0427(8)
H230.6097670.3304670.4470610.051
C240.55882(19)0.4278(2)0.36453(17)0.0274(6)
C250.48851(16)0.89342(17)0.23674(14)0.0177(5)
C260.58303(17)0.85247(17)0.22608(14)0.0172(5)
C270.65886(17)0.90985(19)0.24322(15)0.0222(6)
H270.6538950.9759770.2646320.027
C280.74233(19)0.8681(2)0.22826(18)0.0292(6)
H280.7957470.9051760.2399700.035
C290.74734(18)0.7722(2)0.19622(17)0.0272(6)
H290.8040700.7432640.1848730.033
C300.66892(17)0.71907(18)0.18091(14)0.0189(5)
C310.67039(18)0.61376(18)0.14363(15)0.0215(6)
C320.5106(3)0.1287(3)0.4049(2)0.0645(11)
H32A0.5664130.0926620.4187280.097
H32B0.4595450.0819740.4084040.097
H32C0.5024340.1853960.4408830.097
C330.8446(3)0.3624(3)0.0542(2)0.0490(9)
H33A0.9021750.3716950.0822540.073
H33B0.8513820.3108450.0137420.073
H33C0.7988680.3402470.0907190.073
C340.2974(3)0.2989(4)0.3697(3)0.0702(13)
H34A0.3410500.3312360.4053640.105
H34B0.3288050.2523120.3352310.105
H34C0.2532370.2611420.3996520.105

Source of material

Tris(2-benzimidazolylmethyl)amine (ntb) was prepared according to the literature method [1]. To a stirred methanol solution (20 mL) containing cadmium perchlorate hexahydrate (0.066 g, 0.2 mmol) and ntb (0.08 g, 0.2 mmol), a methanol solution (10 mL) of 2,6-pyridinedicarboxylic acid (H2dipic, 0.033 g, 0.2 mmol) and triethylamine (0.022 g, 0.2 mmol) was added dropwise. After stirring for 3 h, the filtrate of the resulting solution was allowed to stand at room temperature for several weeks to give colorless crystals of the title compound, in a yield of 55%.

Experimental details

The crystal structure was refined using the SHELX-18/3 package [3, 4] . Hydrogen atoms were positioned geometrically and allowed to ride on their parent atoms. The Uiso values of the hydrogen atoms of methyl groups were set to 1.5Ueq(C) and the Uiso values of all other hydrogen atoms were set to 1.2Ueq(C).

Discussion

Imidazole is a typical heterocyclic ligand as a component of biologically important molecules [5]. Moreover, the derivates of imidazole have long been used in coordination chemistry [6]. For example, tris(2-benzimidazylmethyl)amine (ntb) was used in the coordination of transition metals to mimic the active sites of superoxide dismutase by Nie’s group [7]. The tetradentate tripodal ligand ntb contains three aromatic N-donors on its arms, which can each rotate freely around an N(apical)-C bond. Thus, multicomponent complexes or coordination polymeric networks can be formed from this ligand with metal ions of low coordination number [8]. Compared to other metal complexes, cadmium complexes of ntb are rarely reported [9, 10] . On the other hand cadmium(II) complexes of ntb using 2,6-pyridinedicarboxylate as coligand have never been reported. In this article, we report the structures of a new 2,6-pyridinedicarboxylate-containing cadmium(II) complex of ntb, which exhibits hydrogen-bonding forming a chain structure.

The title compound consists of one [Cd(ntb)(dipic)] complex, and three methanol molecules. The Cd(II) ion is octahedrally coordinated by four N atoms of ntb, one carboxylate oxygen and pyridine nitrogen of the 2,6-pyridinedicarboxylate ligand. The equatorial plane is defined by three benzimidazoles N(1), N(2), N(6) of ntb and one carboxylate oxygen atom O(1). Equatorial bond angles are ranging from 69.7° to 139.8°. The bond distance of Cd(1)—N(1) = 2.602(2) Å, lies trans-to O(1) atom, is significantly longer than Cd(1)—N(2) = 2.272(2) Å, Cd(1)—N(6) = 2.268(2) Å, and Cd(1)—O(1) = 2.3571(19) Å. The axial positions are occupied by N(4) and N(8) with N(4)—Cd(1)—N(8) angle of 139.91°. The bond length of Cd(1)—N(4) is 2.352(3) Å and the distance of Cd(1)—N(8) is 2.336(2) Å. The bond distance Cd(1)—N(1) and the angle N(4)—Cd(1)—N(8) reflect the distortions of the coordination octahedron. Other significant distortions are observed in the angles, N(1)—Cd(1)—O(1) = 139.82°, N(2)—Cd(1)—N(6) = 136.32°. In addition, intermolecular H-bond of type N—H⋯O [N(3)H(3)⋯O(3) = 2.72 Å N(3)H(3)⋯O(3) 168°] between the NH group of ntb and the uncoordinated carboxylate oxygen atom of pyridinedicarboxylate anion bridges adjacent molecules to form a dimeric unit. These dimers are further connected via two hydrogen bonds: one between the NH group of ntb and methanol oxygen N—H⋯O [N(7)—H(7 A)⋯O(5) = 2.775 Å N(7)—H(7 A)⋯O(5) 152.94°] and the other between OH of methanol and the uncoordinated carboxylate oxygen of the picolinato ligand O—H⋯O [O(5)—H(5 A)⋯O(2) = 2.752 Å O(5)—H(5 A)⋯O(2) 161.23°] to form two antiparallel chains. Geometric parameters of the ligands and coordination modes are in perfect accord with the literature [11].

Acknowledgements

The authors are grateful for the financial support from National Natural Science Foundation of China (Grant No. 21404081), and Beijing National Laboratory for Molecular Sciences (BNLMS) (20140149).

References

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Received: 2018-06-14
Accepted: 2018-08-21
Published Online: 2018-09-05
Published in Print: 2018-11-27

©2018 Chen Jing et al., published by De Gruyter, Berlin/Boston

This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 License.

Artikel in diesem Heft

  1. Cover and Frontmatter
  2. Crystal structure of di-μ2-aqua-tetraaqua-bis(4-(1H-1,2,4-triazol-1-yl)benzoato-κN)disodium(I) C18H24N6Na2O10
  3. Crystal structure of diaqua-bis(2-bromo-4-chloro-6-formylphenolato-κ2O,O′)cobalt(II), C16H16Cl2CrN3O7
  4. Crystal structure of catena-poly[(μ2-1-(4-(1H-pyrazol-1-yl)phenyl)ethan-1-one-κ2N:O)-bis(1,1,1-trifluoro-4-oxo-4-(thiophen-2-yl)but-2-en-2-olato-κ2O,O′)copper(II)], C27H18CuF6N2O5S2
  5. Crystal structure of ethyl 2-amino-4-(3,5-difluorophenyl)-7-methyl-5-oxo-4H,5H-pyrano[4,3-b]pyran-3-carboxylate, C18H15F2NO5
  6. Crystal structure of 5,5′-dimethoxy-2,2′-[1,1′-(ethylenedioxydinitrilo)diethylidyne]diphenol, C20H24N2O6
  7. Crystal structure of (E)-1-(4-(((E)-3,5-dichloro-2-hydroxybenzylidene)amino)phenyl)ethan-1-one O-methyl oxime, C16H14Cl2N2O2
  8. Crystal structure of 2,3,9,10,16,17,23,24-octakis(2,6-dimethylphenoxy)phthalocyanine - trichloromethane (1/2), C98H84Cl6N8O8
  9. Crystal structure of methyl 2-((1-(2-(methoxycarbonyl)benzyl)-1H-1,2,3-triazol-4-yl)methoxy)-1-naphthoate, C24H21N3O5
  10. Crystal structure of catena-poly[(μ2-3,3′-thiodipropionato-κ2O:O′)-(bipyridine-κ2N,N′)copper(II)] C16H16CuN2O4S
  11. Crystal structure of [4-chloro-2-(((2-((3-ethoxy-2-oxidobenzylidene)amino)phenyl)imino)(phenyl)methyl)phenolato-κ4N,N′,O,O′}nickel(II) - ethyl acetate (1/1), C32H29ClN2NiO5
  12. Crystal structure of (4-(4-chlorophenyl)-5-ethyl-1,3-dioxane-5-carboxylato-κ2O,O′)-(5,5,7,12,12,14-hexamethyl-1,4,8,11-tetraazacyclotetradecane-κ4N,N′,N′′,N′′′)nickel(II) perchlorate monohydrate, C29H52Cl2N4NiO9
  13. Crystal structure of ethyl 2-amino-4-(3,4-dimethylphenyl)-7-methyl-5-oxo-4H,5H-pyrano[4,3-b]pyran-3-carboxylate, C20H21NO5
  14. Structure and photochromism of 1,2-bis[2-methyl-5-(3-quinolyl)-3-thienyl]-3,3,4,4,5,5-hexafluorocyclopent-1-ene, C33H20F6N2S2
  15. Crystal structure of catena-poly[diaqua-bis(μ2-3,5-di(1H-1,2,4-triazol-1-yl)benzoate-κ2N:N′)cobalt(II))] 2.5 hydrate, C22H23CoN12O8.50
  16. The crystal structure of dichlorido(1,3-dimesityl-1H-3λ4-imidazol-2-yl)(morpholine-κN)palladium(IV), C25H33Cl2N3OPd
  17. Crystal structure of catena-poly[bis(4,4′-dipyridylaminium-kN)-(μ2-germanowolframato-κ2O:O′)-(2,2′-bipyridine-κ2N,N′)copper(II)] with a Keggin-type heteropolyoxoanion, [Cu(C10H8N2)(C10H10N3)2][GeW12O40] ⋅ H2O
  18. Crystal structure of diaqua-(N-(1-(pyrazin-2-yl)ethylidene)pyridin-1-ium-4-carbohydrazonate-κ3N,N′,O)-tris[nitrato-κ2O,O′)lanthanum(III), C12H15N8O12La
  19. The crystal structure of 2-hydroxy-4-((2-hydroxy-4-methoxy-3,6-dimethylbenzoyl)oxy)-3,6-dimethylbenzoic acid–methanol (1/1), C20H24O8
  20. Crystal structure of guanidinium tetrapropylammonium bis(hydrogencarbonate) dihydrate, C15H40N4O8
  21. Crystal structure of (Z)-2-bromo-3-(3,5-di-tert-butyl-4-hydroxyphenyl)-1-phenylprop-2-en-1-one, C23H27BrO2
  22. Crystal structure of 2-(4-(4H-1,2,4-triazol-4-yl)phenyl)acetic acid, C10H9N3O4
  23. Crystal structure of 4,4′-(1,4-phenylene)bis(1H-imidazol-3-ium)bis(2-carboxybenzoate), C30H26N4O8
  24. Crystal structure of 4,4′-(4,10-diphenyl-4,10-dihydropyreno[4,5-d:9,10-d′]diimidazole-5,11-diyl)bis(N,N-diphenylaniline), C66H44N6
  25. Crystal structure of catena-poly[diaqua-bis(μ2-5-(3-(1H-imidazol-5-yl)phenyl)tetrazol-2-ido-κ2N:N′)cobalt(II)], C20H18CoN12O2
  26. Crystal structure of 1,3-dimethyl-2-(p-tolyl)-1H-perimidin-3-ium iodide 1.5 hydrate, C20H22IN2O1.5
  27. Crystal structure of 2-(4-methoxyphenyl)chromane, C16H16O2
  28. Crystal structure of poly[(μ2-2-carboxy-5-nitroisophthalato-κ2O:O′)-(μ2-4-((1H-imidazol-1-yl)methyl)pyridine-κ2N:N′)zinc(II)], C18H12N4O8Zn
  29. Crystal structure of bis(1-((2-ethyl-4-methyl-1H-imidazol-1-yl)methyl)-1H-benzo[d][1,2,3]triazole-κ2N:N′)tetraiodidodicadmium(II), [Cd2(C13H15N5)2I4]
  30. Crystal structure of tetramethylammonium bis(acetato-κ1O)-tetrakis(μ3-3-((hydroxyimino)methyl)-5-methoxy-2-oxidobenzoate-κ5O,O′:O′,N:O′′)tetrazinc(II) — N,N′-dimethylformamide — water (1/2/2), C62H96Zn4N10O28
  31. Crystal structure of poly[(μ4-5-tert-butylisophthalato-κ4O:O′:O′′:O′′′)-(1,3-dimethyl-2-imidazolidinone-κO)zinc(II)] C17H22N2O5Zn
  32. Crystal structure of [tris(2-benzimidazolylmethyl)amine-κ4N,N′,N′′,N′′′]-[(pyridine-2,6-dicarboxylato-κ2O,N)]cadmium(II)–methanol (1:3) C34H36CdN8O7
  33. The crystal structure of bis(1H-benzo[d]imidazol-2-amine-κN)-diiodidocadmium(II), C14H14CdI2N6
  34. Crystal structure of tetrakis(1H-benzimidazol-2-amine)-κN)-bis(μ2-sulfonato-κ2O:O′)dizinc(II) - methanol (1/1), C30H36N12O10S2Zn2
  35. Crystal structure of 3β-methoxy-20α-dimethylamino-pregn-5-ene, C24H41NO
  36. Crystal structure of dimethyl 4,4′-oxydibenzoate, C16H14O5
  37. Crystal structure of catena-poly[diiodido-(μ2-1,5-dimethyl-2-phenyl-4-((pyridin-3-ylmethylene)amino)-1,2-dihydro-3H-pyrazol-3-one-κ2N:O)zinc(II)], C17H16I2N4OZn
  38. Crystal structure of 4-((E)-((E)-5-(2-fluorobenzylidene)-1-((4-fluorophenyl)sulfonyl)-4-oxopiperidin-3-ylidene)methyl)benzonitrile, C26H18F2N2O3S
  39. Crystal structure of bis(acetato-κ1O)-bis(1-(pyridin-2-yl)ethan-1-one oxime-κ2N,N′)zinc(II), C18H22N4O6Zn
  40. The crystal structure of 9-butoxy-2-(hydroxymethyl)-2H-imidazo[1,5-a]quinolin-10-ium bromide, C17H21O2N2Br
  41. Crystal stucture of 2-(tert-butyl)-6-(hydroxymethyl)-4-methylphenol, C12H18O2
  42. Crystal structure of catena-poly[(2-(5-chloroquinolin-8-yloxy)-1-(pyrrolidin-1-yl)ethan-1-one-κ3N,O,O′)-(dinitrato-κ2O,O′)mercury(II)], C15H15N4O8ClHg
  43. Crystal structure of dimethyl (3aS,6R,6aS,7S)-1H,3H,6H,7H-3a,6:7,9a-diepoxybenzo[de]isochromene-3a1,6a-dicarboxylate, C16H16O7
  44. The crystal structure of 2-(dimethoxymethyl)-4-(4-methylphenyl)-1H-imidazole—petroleum ether-chloroform (3/1), C27H33Cl3N4O4
  45. Crystal structure of 8-(trifluoromethyl)imidazo[1,2-a]pyridine-3-carbaldehyde, C9H5F3N2O
  46. The crystal structure of N,N-diethyl-4,6-bis(naphthalen-2-yloxy)-1,3,5-triazin-2-amine, C27H24N4O2
  47. Crystal structure of 5-bromo-7-chloro-3,3a-dihydrocyclopenta[b]chromen-1(2H)-one, C12H8BrClO2
  48. Crystal structure of 2-(bis(4-fluorophenyl)methylene)hydrazine-1-carbothioamide, C14H11F2N3S
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