Startseite Crystal structure of dinitrato-κO-bis(tris((1H-benzo[d]imidazol-2-yl)methyl)amine-κ4N,N′,N′′,N′′′)-(μ2-cyclohexane-1,4-dicarboxylato-κ4O,O′:O′′,O′′′)dimanganese(II) – methanol – water (1/6/2), C62H80Mn2N16O18
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Crystal structure of dinitrato-κO-bis(tris((1H-benzo[d]imidazol-2-yl)methyl)amine-κ4N,N′,N′′,N′′′)-(μ2-cyclohexane-1,4-dicarboxylato-κ4O,O′:O′′,O′′′)dimanganese(II) – methanol – water (1/6/2), C62H80Mn2N16O18

  • Chen Jing EMAIL logo und Zhang Haodong
Veröffentlicht/Copyright: 27. Juli 2017

Abstract

C62H80Mn2N16O18, triclinic, P1̅ (no. 2), a = 11.3232(10) Å, b = 12.879(2) Å, c = 13.035(2) Å, α = 84.854(17)°, β = 69.317(16)°, γ = 73.929(13)°, V = 1708.8(4) Å3, Z = 1, Rgt(F) = 0.0320, wRref(F2) = 0.0860, T = 113 K.

CCDC no.: 1561965

The title complex is shown in the figure. Tables 1 and 2 contain details of the measurement method and a list of the atoms including atomic coordinates and displacement parameters.

Table 1

Data collection and handling.

Crystal:Colourless prism
Size:0.20 × 0.18 × 0.12 mm
Wavelength:Mo Kα radiation (0.71073 Å)
μ:4.5 cm−1
Diffractometer, scan mode:Rigaku XtaLAB P200, φ and ω
2θmax, completeness:55.0°, 98%
N(hkl)measured, N(hkl)unique, Rint:21912, 7697, 0.033
Criterion for Iobs, N(hkl)gt:Iobs > 2 σ(Iobs), 6684
N(param)refined:463
Programs:Rigaku [1], SHELX [2]
Table 2

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

AtomxyzUiso*/Ueq
Mn10.21115(2)0.694694(16)0.256283(16)0.01324(6)
O10.05032(10)0.87599(8)0.27014(8)0.0198(2)
O20.16460(10)0.78056(8)0.11962(8)0.0183(2)
N10.37957(11)0.55528(9)0.32723(9)0.0144(2)
N20.30654(11)0.54827(9)0.14608(9)0.0146(2)
N30.44956(11)0.38684(9)0.09640(9)0.0156(2)
H30.5211(12)0.3339(11)0.0949(14)0.019*
N40.36001(11)0.76995(9)0.26991(9)0.0154(2)
N50.53332(12)0.77207(10)0.31315(10)0.0173(2)
H50.6009(13)0.7453(13)0.3345(14)0.021*
N60.11428(11)0.64874(9)0.42388(9)0.0158(2)
N70.09927(12)0.53849(10)0.56724(10)0.0173(2)
H70.1232(16)0.4817(10)0.6054(13)0.021*
C10.47872(13)0.49409(11)0.23124(11)0.0156(3)
H1A0.52440.42360.25410.019*
H1B0.54420.53470.19280.019*
C20.41079(13)0.47708(11)0.15718(11)0.0144(3)
C30.27590(13)0.50067(11)0.06935(11)0.0152(3)
C40.17654(14)0.53760(12)0.02454(12)0.0195(3)
H40.11680.60700.04260.023*
C50.16878(15)0.46865(14)−0.04741(12)0.0238(3)
H5A0.10320.4924−0.08020.029*
C60.25472(15)0.36491(13)−0.07330(12)0.0237(3)
H60.24390.3194−0.12090.028*
C70.35479(14)0.32779(12)−0.03080(12)0.0205(3)
H7B0.41380.2580−0.04850.025*
C80.36446(13)0.39825(11)0.03944(11)0.0160(3)
C90.43506(14)0.61566(11)0.38008(12)0.0172(3)
H9C0.52320.57270.37800.021*
H9D0.37860.63100.45770.021*
C100.44363(13)0.71921(11)0.31950(11)0.0154(3)
C110.39856(13)0.86402(11)0.22803(11)0.0157(3)
C120.34815(15)0.94645(11)0.16619(12)0.0199(3)
H120.27430.94610.14770.024*
C130.40969(15)1.02870(12)0.13282(13)0.0226(3)
H130.37721.08590.09050.027*
C140.51893(15)1.02999(12)0.15970(13)0.0237(3)
H140.55861.08800.13520.028*
C150.56991(15)0.94889(12)0.22087(13)0.0225(3)
H150.64370.94960.23930.027*
C160.50786(14)0.86559(11)0.25439(12)0.0173(3)
C170.30344(13)0.48782(11)0.40446(11)0.0158(3)
H17A0.34830.45300.45640.019*
H17B0.29430.43060.36420.019*
C180.17171(14)0.55918(11)0.46528(11)0.0153(3)
C19−0.00552(14)0.68930(11)0.50692(11)0.0167(3)
C20−0.10481(14)0.78350(12)0.51140(13)0.0214(3)
H20−0.10110.82980.45000.026*
C21−0.20906(15)0.80657(13)0.60937(14)0.0253(3)
H21−0.27720.87090.61560.030*
C22−0.21651(15)0.73731(13)0.69977(13)0.0247(3)
H22−0.28960.75610.76550.030*
C23−0.12055(15)0.64278(12)0.69562(12)0.0215(3)
H23−0.12590.59550.75640.026*
C24−0.01524(14)0.62051(11)0.59729(12)0.0172(3)
C250.07500(13)0.86226(11)0.16962(11)0.0156(3)
C260.00474(13)0.94399(11)0.10449(11)0.0158(3)
H26−0.08160.98440.15650.019*
C27−0.02012(14)0.89042(11)0.01658(12)0.0174(3)
H27A−0.07680.84170.05220.021*
H27B0.06410.8461−0.03280.021*
C280.08584(14)1.02552(11)0.05105(12)0.0169(3)
H28A0.09671.06280.10900.020*
H28B0.17390.98610.00290.020*
O30.76893(11)0.64776(9)0.34751(10)0.0282(3)
O40.97589(11)0.63672(9)0.26736(9)0.0291(3)
O50.82973(12)0.78146(9)0.25057(11)0.0341(3)
N80.85978(13)0.69016(10)0.28720(10)0.0216(3)
O60.85550(15)0.05328(11)0.36219(11)0.0465(4)
H6A0.92160.00080.33880.070*
C290.8445(2)0.08450(15)0.46705(16)0.0405(5)
H29A0.92560.10080.46300.061*
H29B0.82910.02550.51870.061*
H29C0.77110.14890.49220.061*
O70.44194(14)0.71153(11)0.58787(12)0.0421(3)
H7A0.36930.72150.63890.063*
C300.4965(2)0.7970(2)0.5864(2)0.0546(6)
H30A0.44510.86310.56300.082*
H30B0.58680.77990.53500.082*
H30C0.49580.80790.66000.082*
O80.20492(13)0.77757(10)0.75540(10)0.0336(3)
H80.18390.83520.72280.050*
C310.1151(3)0.71489(19)0.7676(2)0.0552(6)
H31A0.05500.72000.84370.083*
H31B0.16330.63920.74910.083*
H31C0.06510.74240.71850.083*
O90.67037(10)0.23401(9)0.09111(9)0.0207(2)
H9A0.7072(15)0.2303(14)0.1400(10)0.025*
H9B0.7257(14)0.2288(14)0.0257(7)0.025*

Source of material

Tris(2-benzimidazolylmethyl)amine (ntb) was prepared according to the literature [3]. To a stirred methanol solution (20 mL) containing manganese(II) nitrate hexahydrate (0.057 g, 0.2 mmol) and ntb (0.08 g, 0.2 mmol), a methanol solution (10 mL) of 1,4-cyclohexanedicarboxylic acid (1,4-chdc, 0.017 g, 0.1 mmol) and triethylamine (0.022 g, 0.2 mmol) was added dropwise. After stirring for 2 hours, the filtrate of the resulting solution was allowed to stand at room temperature for several weeks to give light brown crystals, in a yield of 58%.

Experimental details

Hydrogen atoms were positioned geometrically and allowed to ride on their parent atoms. H atoms of water molecule were initially found in the difference Fourier map and were refined with restraint O⋯H distance of 0.86 Å. The Uiso values of the hydrogen atoms were set to 1.2 Ueq(C).

Discussion

Superoxide dismutases (SODs) can catalyze the conversion of superoxide to hydrogen peroxide and dioxygen via redox active metals [3, 4] . Mn-SOD is found in eukaryotic cell, prokaryotic cell and stroma of mitochondria. It has been proven by X-ray crystallography that the manganese in the Mn-SODs from Bacillus stearothermophilus [5], Thermus thermophilus [6] and humans [7] is five-coordinated in a trigonal-bipyramidal geometry with a N3O2 coordination sphere and is ligated by three histidine residues, one aspartic acid residue and a water molecule [8].

The tetradentate tripodal ligand, tris(2-benzimidazolylmethyl) amine (ntb), similar to the histidine imidazole in coordination aspects of Mn-SOD, shows great potential to mimic the properties of SODs. In order to model the active site structure of Mn-SOD, a novel manganese(II) complex [Mn2(ntb)2(chdc)]2(NO3)2 ⋅ 6CH3OH ⋅ 2H2O was synthesized and characterized. The two Mn atoms are bridged by 1,4-cyclohexanedicarboxylate in an asymmetrically bidetate mode (Mn-O: 2.16/2.51 Å). The distance between two Mn(II) metal centers is 11.030 Å. Each Mn is primarily five-coordinated with four nitrogen atoms from ligand of ntb and one the stronger coordinated oxygen atom from 1,4-cyclohexanedicarboxylate ligand. The O4 atom of the nitrate counter anion/anionic ligand shows a Mn-O distance of 2.91 Å. This is most probably to be seen as a coordination, as otherwise a large hole is present in the coordination sphere of the Mn(II) metal center (cf. the figure). The further discussion is focused on the five strong coordinated ligand atoms. The trigonal plane is occupied by three ligating nitrogen atoms of the benzimidazolyle groups with Mn1 being 0.0771 Å out of the plane. The bond distances are 2.2469(12) Å for Mn1-N2, 2.2269(12) Å for Mn1-N4 and 2.1819(13) Å for Mn1-N6. The angles of the trigonal plane are 104.21(5)° for N(6)-Mn(1)-N(4), 110.47(5)° for N6-Mn1-N(2) and 111.02(4)° for N4-Mn1-N2, respectively. The axial positions are occupied by one nitrogen atom N(1) from ntb and one carboxylate oxygen atom O2 of 1,4-cyclohexanedicarboxylate ligand with bond length of 2.6016(13) Å for Mn1-N1 and 2.1590(11) Å for Mn1-O2. The bond angle of O2-Mn1-N1 is 148.4(4)°. The bond length between Mn1 and the tertiary amine N1 atom is significantly longer (about 0.383 Å) than Mn-N(benzimidazole) (average 2.219 Å). This significant elongation has also been observed in other manganese complexes of tripodal tetradentate ligands with benzimidazolylmethyl group [3]. This complex can be regarded as the model complex of the active site structure of Mn-SOD.

Acknowledgement

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).

The authors express their thank to the responsible editor for providing the figure.

References

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Received: 2017-3-10
Accepted: 2017-7-14
Published Online: 2017-7-27
Published in Print: 2017-9-26

©2017 Chen Jing et al., published by De Gruyter, Berlin/Boston

This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 3.0 License.

Artikel in diesem Heft

  1. Cover and Frontmatter
  2. Crystal structure of 2-(2-ethoxyphenyl)-7-propyl-5-methylimidazo[5,1-f][1,2,4]triazin-4(3H)-one, C17H20N4O2
  3. Crystal structure of catena-poly[aqua-(μ3-1,3,5-benzenetricarboxylato-κ3O:O′:O′′)-[μ3hydroxy-(1,3-di-(μ2-1,2,4-triazole-4-yl)benzoato-κ2N:N′)copper(II)], C19H16Cu2N6O9
  4. Crystal structure of poly[aqua-(μ3-3,5-di(4H-1,2,4-triazolyl-4-κ3N,N′:N′′)benzenecarboxylato)silver(I)], C11H9AgN6O3
  5. Crystal structure of tetrapropylammonium hydrogen carbonate, C13H29NO3
  6. Crystal structure of poly[μ2-acetato-κ3-O,O′:O′)diaqua(μ3-isophthalato-κ4O,O′:O′′:O′′′)yttrium(III)] monohydrate, C20H24O17Y2
  7. Crystal structure of catena-poly[dichlorido-(μ2-4-(1H-pyrazol-3-yl)-pyridine-κ2N,N′)]cadmium(II), C48H42Cd3Cl16N18
  8. Crystal structure of bis(tetraethylammonium) [1,1′-biphenyl]-2,2′-dicarboxylate trihydrate, C30H54N2O7
  9. Crystal structure of poly[(thiophene-3,4-dicarboxylato-κ1O)bis[1,2-bis(4-pyridyl)ethane-κ2N:N′]silver(I)] octahydrate, C30H42Ag2N4O12S
  10. The crystal structure of amine-(4-(1H-1,2,4-triazol-1-yl)benzoato-κN)silver(I) dihydrate, C9H13AgN4O4
  11. Crystal structure of poly[tetrakis(μ2-cyanido-κ2N:O)-cyanido-tris(pyridine)dicobalt(II/III)], C20H15Co2N8
  12. Crystal structure of bis(pyridine)-bis(2-formyl-4,6-dichlorophenolato)cobalt(II), C24H16Cl4CoN2O4
  13. Crystal structure of (E)-1-(4-(((E)-5-bromo-2-hydroxybenzylidene)amino)phenyl)ethan-1-one O-methyl oxime, C16H15BrN2O2
  14. Crystal structure of catena-poly[(μ2-3-(1H-pyrazol-4-yl)-5-(pyridin-4-yl)-1,2,4-triazole-κ N:N′)-bis(benzoato-κO)zinc(II)], C24H18N6O4Zn
  15. Hydrothermal synthesis and crystal structure of a poly[aqua-(μ4-4-(carboxylatomethyl)benzoato-κ4O:O′:O′′:O′′′)-(μ2-1-(4-(1H-imidazol-1-yl)benzyl)-1H-1,2,4-triazole-κ2N:N′) dimanganese(II)], [Mn2(C9H6O4)2(C12H11N5)(H2O)]
  16. Crystal structure of diaqua-catena-poly[diaqua-bis(μ2-5-(4-(1H-1,2,4-triazol-1-yl)phenyl)tetrazol-2-ido-κ2N:N′)cobalt(II)] dihydrate, C20H24CoN14O4
  17. Crystal structure of bis(μ3-2,2′-azanediylbis(ethan-1-olato)-κ5O:O,N,O′:O′)-tetrachlorido-bis(μ2-2-((2-hydroxyethyl)amino)ethan-1-olato-κ3N,O:O)dicobalt(II)dicobalt(III), C16H38Cl4Co4N4O8
  18. Crystal structure of poly[μ4-(4-(carboxylatomethyl)benzoato-κ4O:O′:O′′:O′′′)-(2-(4-(1H-imidazol-1-yl)phenyl)-1H-benzo[d]imidazole-κN)manganese(II)] [Mn(C9H6O4)(C16H12N4)]
  19. Crystal structure of 4-chloro-6-phenylpyrimidine, C10H7ClN2
  20. The crystal structure of [6-methoxy-2-(2,2,2-trifluoroacetyl)-3,4-dihydronaphthalen-1(2H)-one]difluoroborane, C13H10BF5O3
  21. Crystal structure of 3,3′-(butane-1,4-diylbis(azanylylidene))bis(1-phenylbut-1-en-1-olato)-κ4N,N′,O,O′]copper(II), C24H26N2O2Cu
  22. Crystal structure of tetraaqua-bis((E)-N′-(2-bromobenzylidene)isonicotinohydrazide-κN)zinc(II) dinitrate, C26H28N8O12Br2Zn
  23. Crystal structure of 2-amino-4-(4-bromophenyl)-5-oxo-5,6,7,8-tetrahydro-4H-chromene-3-carbonitrile, C16H13BrN2O2
  24. A single crystal study on tert-butyl-4-((4-(4-bromo-2-fluorophenylamino)-6-methoxyquinazolin-7-yloxy)methyl)piperidine-1-carboxylate, C26H30BrFN4O4
  25. Crystal structure of 1,1′-((1E,1′E)-(((ethane-1,2-diylbis(oxy))bis(2,1-phenylene))bis(azanylylidene))bis(methanylylidene))bis(naphthalen-2-olato-κ3O,O′,N)zinc(II), C36H26N2O4Zn
  26. Crystal structure of diaqua-bis(5′-(pyridin-1-ium-4-yl)-1H-[3,3′-bi(1,2,4-triazol)]-2′-ide-κ2N,N′)cobalt(II) — bis(5-(pyridin-4-yl-κN)-1H,1′H-3,3′-bi(1,2,4-triazole))octamolybdate – water (2/1/8), C27H33CoMo4N21O19
  27. Crystal structure of 3-cyclohexyl-2-(cyclohexylimino)-2,3-dihydro-6,8-diiodo-4H-1,3-benzoxazin-4-one, C20H24I2N2O2
  28. Crystal structure of dinitrato-κO-bis(tris((1H-benzo[d]imidazol-2-yl)methyl)amine-κ4N,N′,N′′,N′′′)-(μ2-cyclohexane-1,4-dicarboxylato-κ4O,O′:O′′,O′′′)dimanganese(II) – methanol – water (1/6/2), C62H80Mn2N16O18
  29. Crystal structure of bis(2-hydroxyethyl(phenyl)carbamodithioate)nickel(II), C18H20N2NiO2S4
  30. Crystal structure of methyl 1-(4-fluorobenzyl)-4-methoxy-5-oxopyrrolidine-3-carboxylate, C14H16FNO4
  31. Crystal structure of di-μ-iodido-bis(6-(p-tolyl)-2,2′-bipyridine-κ2N,N′)dicopper(I) — 2-(diphenylphosphoryl)benzoic acid (1/2), C36H29CuIN2O3P
  32. Crystal structure of 2-amino-4-(3-bromo-4-fluoro-phenyl)-7,7-dimethyl-5-oxo-5,6,7,8-tetrahydro-4H-chromene-3-carbonitrile, C18H16BrFN2O2
  33. Crystal structure of bis(μ2-2-chlorobenzoato-κ3O,O′:O′)-(2-chlorobenzoato-κO)-(2-chlorobenzoato-κO,O′)-bis(1,10-phenanthroline-κ2N,N′)-dicadmium(II) monohydrate, C52H36Cd2Cl4N4O10
  34. Crystal structure of 2-(8a-methyl-5-oxo-hexahydroimidazo [1,2-a]pyridin-1(5H)-yl)-2-oxoethyl acetate, C12H18N2O4
  35. Crystal structure of (E)-N,N-diethyl-2-(5-nitrothiazol-2-yl)-1-phenylethen-1-amine, C15H17N3O2S
  36. Crystal structure of diazido-dimethanolato-bis(μ2-2-(((3-oxidopropyl)imino)methyl)phenolato-κ4O:O,O′,N)dimanganese(III), C22H28Mn2N8O6
  37. The crystal structure of bis(2-(2,2,2-trifluoroacetyl)-3,4-dihydronaphthalen-1-olato-κ2O,O′)copper(II), C24H16CuF6O4
  38. Crystal structure of hexaaquanickel(II) bis((E)-4-((4-(dimethylamino)phenyl)diazenyl)benzenesulfonate), C28H40N6NiO12S2
  39. Crystal structure of catena-poly[aqua-(μ2-hexamethylenetetramine-κ2N:N′)-bis(2,6-difluorobenzoato-κ2O:O′)cadmium(II)]monohydrate, C20H22CdF4N4O6
  40. Crystal structure of 3-benzyl-2,3-dihydro-2-thioxoquinazolin-4(1H)-one, C15H12N2OS
  41. Crystal structure of bis(μ2-ferrocenecarboxylato-κ2O:O′)-bis(1,10-phenanthroline-κ2N,N′)-(μ2-methanolato2O,O)dicopper(II) tetrafluoroborate – acetonitrile (1/1), C49H40BCu2F4Fe2N5O5
  42. The crystal structure of tetrakis(1,3,5-triaza-7-phosphatricyclo[3.3.1.13,7]decane-κP)silver(I) chloride dihydrate, C24H60AgClN12O6P4
  43. Crystal structure of 5-ethyl-2-(p-tolyl)-1,3-dioxane-5-carboxylic acid, C14H18O4
  44. Crystal structure of 2-(4-fluorophenyl)-1,3-dimethyl-1H-perimidin-3-ium iodide, C19H16ClIN2
  45. Crystal structure of catena-poly[(μ2-hexamethylenetetramine-κ2N:N′)-tetrakis(μ2-2,6-difluorobenzoato-κ2O:O′)dicopper(II)], C34H24Cu2F8N4O8
  46. Crystal structure of ethyl 3-hydroxy-5-methyl-2-(4-(m-tolyl)-1H-1,2,3-triazol-1-yl)-[1,1′-biphenyl]-4- carboxylate, C25H24N3O3
  47. The crystal structure of carbonyl(2-oxopyridin-1(2H)-olato-κ2O,O′)-(diphenylcyclohexylphosphine-κP)rhodium(I), C24H25NO3PRh
  48. Crystal structure of bis((pyrazin-2-ylmethyl)(pyrazine-2-carbonyl)amido-κ3N,N′,N′′)copper(II), C20H16CuN10O2
  49. Crystal structure of catena-poly[tetraaqua-(μ2-succinonitrile-κ2N:N′)cobalt(II)] dinitrate, C4H12CoN4O10
  50. The crystal structure of 1,1′-bisisoquinoline, C18H12N2
  51. Crystal structure of bis(hydroxydi(pyridin-2-yl)methanolato-κ3N,N′,O)cobalt(III) perchlorate dihydrate, C22H22ClCoN4O10
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