Home Physical Sciences Crystal structure of ajacisine D monohydrate, C30H44N2O9
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Crystal structure of ajacisine D monohydrate, C30H44N2O9

  • Guo-Qiang Li EMAIL logo , Qing-Peng Xu , Yi-Ting Zhao , Yun-Yi Li , Yao-Lan Li and Guo-Cai Wang
Published/Copyright: February 1, 2019

Abstract

C30H44N2O9, monoclinic, P21 (no. 4), a = 7.9827(3) Å, b = 12.6787(6) Å, c = 14.0183(9) Å, β = 90.903(5)°, V = 1418.62(13) Å3, Z = 2, Rgt(F) = 0.0607, wRref(F2) = 0.1298, T = 298(2) K.

CCDC no.: 1890792

The title crystal structure (systematic name: N-ethyl-18β-(o-aminobenzoyl)-6β,16β-dimethoxy-aconitane-1α,7β,8β,14α-tetraol) is shown in the figure. Tables 1 and 2 contain details on crystal structure and measurement conditions and a list of the atoms including atomic coordinates and displacement parameters.

Table 1:

Data collection and handling.

Crystal:Yellow block
Size:0.26 × 0.25 × 0.25 mm
Wavelength:Mo Kα radiation (0.71073 Å)
μ:0.10 mm−1
Diffractometer, scan mode:Gemini S ultra, ω
θmax, completeness:32.8°, >99%
N(hkl)measured, N(hkl)unique, Rint:19473, 9362, 0.043
Criterion for Iobs, N(hkl)gt:Iobs > 2 σ(Iobs), 6262
N(param)refined:386
Programs:CrysAlisPRO [1], SHELX [2]
Table 2:

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

AtomxyzUiso*/Ueq
O1−0.0122(3)−0.09255(18)0.38972(17)0.0390(5)
H10.0830−0.08100.40990.059*
O20.2924(3)0.19199(16)0.11396(15)0.0342(5)
O30.5416(2)0.02230(17)0.23040(16)0.0341(5)
H30.59570.06420.19870.051*
O40.4506(3)0.02337(19)0.03575(16)0.0414(5)
H40.42510.08550.02810.062*
O50.2108(4)−0.1108(2)−0.07619(18)0.0541(7)
H50.2583−0.0555−0.08950.081*
O60.3160(3)−0.31633(17)0.06658(17)0.0422(5)
O70.0615(3)0.34374(16)0.34533(18)0.0406(5)
O80.2084(3)0.49181(19)0.3672(2)0.0544(7)
N10.3003(3)−0.0077(2)0.38030(17)0.0300(5)
N20.0477(4)0.6764(2)0.3377(2)0.0441(7)
H2A0.10400.68110.28590.053*
H2B0.01630.73870.35460.053*
C1−0.0596(3)−0.0120(3)0.3224(2)0.0316(6)
H1A−0.1507−0.04090.28270.038*
C2−0.1282(4)0.0845(3)0.3724(2)0.0367(7)
H2C−0.17800.13180.32550.044*
H2D−0.21510.06320.41600.044*
C30.0086(4)0.1414(3)0.4270(2)0.0370(7)
H3A0.04350.09830.48090.044*
H3B−0.03640.20670.45190.044*
C40.1649(3)0.1673(2)0.3664(2)0.0310(6)
C50.1353(3)0.1372(2)0.2593(2)0.0264(6)
H5A0.04970.18210.22920.032*
C60.3040(3)0.1445(2)0.2065(2)0.0275(6)
H60.38180.18640.24570.033*
C70.3700(3)0.0289(2)0.2037(2)0.0264(6)
C80.3406(3)−0.0239(2)0.1050(2)0.0290(6)
C90.1574(3)−0.0063(2)0.0715(2)0.0305(6)
H90.14580.06280.04090.037*
C100.0295(3)−0.0174(2)0.1525(2)0.0281(6)
H10−0.06870.02490.13450.034*
C110.0857(3)0.0184(2)0.2536(2)0.0255(5)
C12−0.0246(4)−0.1363(2)0.1471(2)0.0343(7)
H12A−0.0056−0.17080.20810.041*
H12B−0.1424−0.14220.13000.041*
C130.0842(4)−0.1868(3)0.0700(2)0.0351(7)
H130.0255−0.24550.03860.042*
C140.1024(4)−0.0936(3)0.0025(2)0.0378(7)
H14−0.0090−0.0756−0.02290.045*
C150.3925(4)−0.1413(2)0.1055(2)0.0334(7)
H15A0.4528−0.15520.04730.040*
H15B0.4704−0.15210.15840.040*
C160.2534(4)−0.2229(2)0.1133(2)0.0330(7)
H160.2376−0.23910.18090.040*
C170.2606(3)−0.0280(2)0.2792(2)0.0262(6)
H170.2607−0.10420.26730.031*
C180.2059(4)0.2838(2)0.3775(3)0.0367(7)
H18A0.23160.29980.44380.044*
H18B0.30260.30170.33970.044*
C190.3165(4)0.1043(2)0.4045(2)0.0331(7)
H19A0.41830.13220.37720.040*
H19B0.32490.11210.47320.040*
C200.4420(4)−0.0706(3)0.4205(3)0.0385(7)
H20A0.4812−0.03800.47930.046*
H20B0.5336−0.06980.37590.046*
C210.3944(5)−0.1821(3)0.4403(4)0.0633(12)
H21A0.3559−0.21500.38230.095*
H21B0.3066−0.18350.48630.095*
H21C0.4901−0.21960.46500.095*
C220.2951(5)0.3037(3)0.1174(3)0.0488(9)
H22A0.29120.33140.05370.073*
H22B0.39620.32680.14910.073*
H22C0.19990.32860.15190.073*
C230.2399(5)−0.4112(3)0.0995(3)0.0555(10)
H23A0.2809−0.46990.06340.083*
H23B0.1206−0.40620.09130.083*
H23C0.2672−0.42120.16580.083*
C24−0.0825(4)0.5027(2)0.3244(2)0.0344(7)
C25−0.0907(4)0.6144(3)0.3226(2)0.0365(7)
C26−0.2465(5)0.6616(3)0.3051(3)0.0545(10)
H26−0.25460.73480.30400.065*
C27−0.3867(5)0.6021(4)0.2895(4)0.0674(13)
H27−0.48850.63560.27750.081*
C28−0.3806(5)0.4931(4)0.2911(3)0.0635(11)
H28−0.47730.45340.28090.076*
C29−0.2290(4)0.4443(3)0.3082(3)0.0477(9)
H29−0.22370.37110.30890.057*
C300.0761(4)0.4492(2)0.3478(2)0.0349(7)
O90.2853(4)−0.3169(3)−0.1356(3)0.0584(7)
H9A0.301(7)−0.321(5)−0.071(5)0.11(2)*
H9B0.250(6)−0.257(4)−0.141(4)0.069(15)*

Source of material

Air-dry roots of the plant Delphinium grandiflorum were purchased from Guangzhou qingping medicine market, Guangdong, China. Powder of roots (10 kg) was extracted with 95% ethanol at room temperature. The total alkaloids (63 g) was then obtained by acid extraction and alkali precipitation method. The total alkaloids was loaded on a silica gel column chromatography and eluted with CHCl3—CH3OH solvent system (100:0–0:100) to afford six fractions (Fr. 1–6). The title compound was obtained from Fr. 5 and crystallized in a mixture of methanol and water.

Experimental details

The C-bound H atoms were positioned geometrically and were included in the refinement in the riding-model approximation. The crystal structure was solved by direct method and refined by full-matrix least-squares refinement with SHELX program [2]. The Flack parameter is not conclusive.

Comment

According to our previous work, many alkaloids have been isolated from Delphinium grandiflorum [3], [4]. The title compound, ajacisine D monohydrate, is one of the diterpenoid alkaloids which have been proved to be the main chemical components of genus Delphinium [5], [6]. These diterpenoid alkaloids have complex structure skeletons and posess multiple biological activities such as anastalsis, antibacterial activity [7], [8], [9], [10]. The single crystals were obtained by slow evaporation from a mixture of methanol and water.

There is one ajacisine D molecule (C30H42N2O8) and one water molecule (H2O) in the asymmetric unit (cf. the figure). In the crystal structure, the typical bond lengths of C1—O1, N1—C20, O8—C30 and N2—C25 are 1.437(4) Å, 1.488(4) Å, 1.213(4) Å, 1.370(5) Å respectively. The torsion angle of O7—C30—C24—C29 is 3.7(4)°, which demonstrates that the aryl moiety (mean deviation 0.002 Å) and the ester group are not exactly coplanar. The angle of C4—C19—N1 is 110.9(2)°, which is smaller than 114.2(2)° of C17—N1—C19. Intermolecular hydrogen-bonding interactions involving the water molecule, methoxy group, the hydroxy and the phenyl amine give a three-dimensional stucture. Two short intramolecular interactions between the C1 hydroxy and N1, C8 hydroxy and methoxy O at C6 are also present [cf. the figure; O1—H1⋯N1 = 2.722(3) Å, 144°; O4—H4⋯O2 = 2.722(3) Å, 132°].

Award Identifier / Grant number: 21405013

Award Identifier / Grant number: A030310079

Funding statement: This work was supported financially by grants from the national Natural Science Foundation of China (no. 21405013), Postgraduate demonstration course construction fundation of Guangdong Education Department (2016SFKC-43), the Fundamental Research Funds for the Central Universities (Grant gg040971), the Natural Science Foundation of Guangdong Province (Grant 2016 A030310079

References

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Received: 2018-11-26
Accepted: 2019-01-14
Published Online: 2019-02-01
Published in Print: 2019-03-26

©2019 Guo-Qiang Li et al., published by De Gruyter, Berlin/Boston

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

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  62. Crystal structure of poly-[(μ2-(carboxylatomethyl)((3-nitrophenyl)sulfonyl)amido-κ3N:O:O′)(μ2-4,4′-bipyridine-κ2N:N′) nickel(II)], C18H14NiN4O6S
  63. Crystal structure of N-((3R,10S,13S,17S)-17-((S)-1-(dimethylamino)ethyl)-10,13-dimethylhexadecahydro-1H-cyclopenta[a]phenanthren-3-yl)-N-methylbenzamide, C31H48N2O
  64. The crystal structure of dichloroido(1,3-bis(2,6-dimethyl-phenyl)-1H-3l4-imidazol-2-yl)(2-methyl-4,5-dihydrooxazol-κN)palladium(IV)-water (1/1), C23H29Cl2N3O2Pd
  65. Crystal structure of catena-poly[dibromido-{μ2-1,5-dimethyl-2-phenyl-4-((pyridin-4-ylmethylene)amino)-1,2-dihydro-3H-pyrazol-3-one-κ2N:O}zinc(II)], C34H32Br4N8O2Zn2
  66. Crystal structure of diaqua-dichlorido-bis(μ2-2-(((1,5-dimethyl-3-oxo-2-phenyl-2,3-dihydro-1H-pyrazol-4-yl)imino)methyl)phenolato-κ4O:O,N,O′)dicobalt(II), C36H36Cl2N6O6Co2
  67. Crystal structure of catena-poly[diaqua-(μ2-1,2-bis(4-pyridinyl)ethyane-κ2N:N′)-(μ2–pyridazine-4,5-dicarboxylato-κ2O:O′)]dizinc(II) dihydrate, C12H12ZnN3O6
  68. The crystal structure of 2-(4-chloro-2,6-dinitrophenyl)-1-(4-chloro)diazene oxide, C12H6Cl2N4O5
  69. Crystal structure of 2-isopropylthioxanthone, C16H14OS
  70. Crystal structure of methyl 2-(4-(3-(1-methyl-1H-pyrazol-4-yl)pyrazolo[1,5-a]pyrimidin-6-yl)phenyl)acetate, C19H17N5O2
  71. Crystal structure of 4,4-dimethyl-2-(trifluoromethyl)-4,5-dihydro-1H-imidazole, C6H9F3N2
  72. Crystal structure of N-methylanilinium 5,7-dihydroxy-4-oxo-2-phenyl-4H-chromene-8-sulfonate monohydrate, C22H21NO8S
  73. Crystal structure of methyl 4-acetoxybenzoate, C10H10O4
  74. Crystal structure of catena-poly[(bis(μ-1,1′-[(5-methoxy-2,4,6-trimethyl-1,3-phenylene)bis(methylene)]bis(1H-1,2,4-triazole)-κ2N:N′)-bis(isothiocyanato-κN)manganese(II)], C34H40MnN14O2S2
  75. Crystal structure of N-(2-methylphenyl)(propan-2-yloxy)carbothioamide, C11H15NOS
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