Home Crystal structure of (E)-N-((3R,5S,10S, 13S,14S,17S)-17-((S)-1-(dimethylamino)ethyl)-10,13-dimethylhexadecahydro-1H-cyclopenta[a]phenanthren-3-yl)-2-methylbut-2-enamide – water – methanol (1/1/1), C29H54N2O3
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Crystal structure of (E)-N-((3R,5S,10S, 13S,14S,17S)-17-((S)-1-(dimethylamino)ethyl)-10,13-dimethylhexadecahydro-1H-cyclopenta[a]phenanthren-3-yl)-2-methylbut-2-enamide – water – methanol (1/1/1), C29H54N2O3

  • Bo Tan , Qi-Yun Wu , Ji-Chun Wu , Shao-Jie Huo , Xi-Cheng He and Jiang Du EMAIL logo
Published/Copyright: April 27, 2019

Abstract

C29H54N2O3, monoclinic, P21 (no. 4), a = 9.8091(11) Å, b = 7.6661(8) Å, c = 19.095(2) Å, β = 93.171(4)°, V = 1433.7(3) Å3, Z = 2, Rgt(F) = 0.0657, wRref(F2) = 0.1362, T = 250 K.

CCDC no.: 1892028

The molecular 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:Colourless block
Size:0.19 × 0.08 × 0.05 mm
Wavelength:Mo Kα radiation (0.71073 Å)
μ:0.07 mm−1
Diffractometer, scan mode:Bruker APEX-II, φ and ω
θmax, completeness:27.9°, >99%
N(hkl)measured, N(hkl)unique, Rint:14394, 6775, 0.058
Criterion for Iobs, N(hkl)gt:Iobs > 2 σ(Iobs), 3520
N(param)refined:320
Programs:Bruker [1], Olex2 [2], SHELX [3], [4]
Table 2:

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

AtomxyzUiso*/Ueq
O10.7378(3)0.5316(5)0.85083(14)0.0681(9)
N10.5101(3)0.5420(5)0.84832(14)0.0471(9)
H10.4375620.5439570.8725480.056*
N20.0938(4)0.5137(5)0.21028(17)0.0526(9)
C10.2116(4)0.2185(5)0.40154(19)0.0382(10)
H1A0.1316200.1657000.4216260.046*
H1B0.2837510.1304340.3996980.046*
C20.1744(4)0.2938(5)0.3274(2)0.0403(11)
H2A0.2351720.2460060.2931700.048*
H2B0.0800610.2639940.3125430.048*
C190.0978(4)0.5952(5)0.28057(19)0.0405(11)
H190.0043360.5871700.2973700.049*
C30.1914(4)0.4925(5)0.33275(18)0.0305(9)
H30.2867230.5200110.3222820.037*
C40.1766(3)0.5295(6)0.41217(17)0.0278(8)
C50.2392(4)0.6967(5)0.44215(19)0.0408(11)
H5A0.1845450.7964240.4249050.049*
H5B0.3314720.7101820.4257280.049*
C60.2461(5)0.6967(5)0.5222(2)0.0482(13)
H6A0.1528630.7022580.5380390.058*
H6B0.2938840.8023710.5388210.058*
C70.3179(3)0.5380(5)0.55608(16)0.0285(8)
H70.4146490.5457850.5441830.034*
C80.2629(4)0.3661(5)0.52405(19)0.0271(9)
H80.1678610.3503960.5378340.032*
C90.2611(4)0.3761(5)0.44422(18)0.0268(8)
H90.3566510.3967860.4322040.032*
C100.3475(4)0.2129(5)0.55287(18)0.0381(10)
H10A0.3045750.1038840.5364170.046*
H10B0.4386130.2184720.5343430.046*
C110.3619(4)0.2107(5)0.63262(19)0.0407(11)
H11A0.2733930.1816290.6509780.049*
H11B0.4267670.1191040.6477230.049*
C120.4105(4)0.3827(5)0.66347(18)0.0303(9)
H120.5015250.4044080.6453200.036*
C130.3184(3)0.5365(5)0.63746(16)0.0294(8)
C140.3831(5)0.7052(6)0.6678(2)0.0456(11)
H14A0.4704480.7244940.6464710.055*
H14B0.3232070.8036230.6546660.055*
C150.4077(5)0.7033(6)0.7476(2)0.0500(12)
H15A0.4542700.8110840.7627650.060*
H15B0.3197470.6991300.7695130.060*
C160.4933(4)0.5482(6)0.77190(18)0.0411(10)
H160.5849500.5613150.7532310.049*
C170.4311(4)0.3776(6)0.74303(19)0.0385(10)
H17A0.4914910.2801330.7567300.046*
H17B0.3429870.3577470.7635300.046*
C180.1736(4)0.5190(6)0.66259(19)0.0466(11)
H18A0.1315070.4142080.6428480.070*
H18B0.1201160.6199480.6474840.070*
H18C0.1774460.5117600.7133810.070*
C200.1347(5)0.7895(6)0.2792(2)0.0554(13)
H20A0.2295130.8024840.2681840.083*
H20B0.1211010.8406990.3247200.083*
H20C0.0767380.8482100.2437430.083*
C230.0261(3)0.5178(6)0.42891(19)0.0406(10)
H23A−0.0166450.4214160.4031690.061*
H23B−0.0198130.6257280.4153490.061*
H23C0.0193080.4989980.4788320.061*
C22−0.0156(6)0.5910(8)0.1634(3)0.097(2)
H22A−0.1026120.5793100.1847320.145*
H22B−0.0195660.5306400.1186420.145*
H22C0.0036900.7135050.1560360.145*
C210.2242(5)0.5226(8)0.1760(2)0.0726(15)
H21A0.2180520.4535770.1333230.109*
H21B0.2967330.4772280.2074100.109*
H21C0.2438020.6429710.1644750.109*
C240.6322(4)0.5336(6)0.88238(19)0.0415(10)
C250.6400(4)0.5170(6)0.9607(2)0.0492(11)
C260.5445(5)0.5769(7)0.9983(2)0.0576(13)
H260.4680010.6275800.9743870.069*
C270.5460(6)0.5719(8)1.0781(2)0.0866(18)
H27A0.5387670.4519081.0936070.130*
H27B0.4695060.6385411.0939020.130*
H27C0.6306990.6218761.0974930.130*
C280.7707(5)0.4354(8)0.9917(3)0.0827(19)
H28A0.7884540.3276490.9671420.124*
H28B0.7610270.4107951.0409910.124*
H28C0.8461060.5154490.9867350.124*
O20.9965(3)0.6660(5)0.8360(2)0.0778(12)
H2C0.9772590.7589860.8123090.117*
H2D0.9194880.6319220.8505820.117*
O31.2276(3)0.5247(7)0.89842(17)0.0837(11)
H3A1.1610220.5561220.8727760.126*
C291.1818(6)0.4456(8)0.9585(3)0.0805(18)
H29A1.1091550.3641390.9454470.121*
H29B1.1477180.5340760.9893860.121*
H29C1.2567920.3835120.9826060.121*

Source of material

The stems and roots of Sarcococcahookeriana (14.5 kg) collected from Hezhang country, Guizhou province, were extracted by methanol with ultrasonic three times. The extract was concentrated and then partitioned between EtOAc and 1% aq. H2SO4. The acid-soluble fraction was alkalinized with aq. Na2CO3 to pH 9 and followed by exhaustive extraction with CH2Cl2 to afford crude alkaloids. The crude alkaloids were roughly divided into five fractions: Frs. A—E. Subsequently, fraction A was separated by silica gel column chromatography using petroleum ether/ethylacetate/diethylamine (50:1:1) as the eluent and then recrystallized with dichloromethane to get the title compound as colorless crystals.

Experimental details

The crystal structure was solved by direct methods and refined by full-matrix least-squares methods on F2 using Olex2 [3]. All hydrogen atoms were positioned geometrically, with the d(C—H) = 0.95–1.00 Å. The Uiso(H) were set to 1.2 times Ueq(C) for the methylene groups as well as methenyl groups, at 1.5 times Ueq(C) for the methyl groups.

Comment

The S. hookeriana possesses a variety of bioactivities. Experimental study shows that the main chemical compositions of S. hookeriana are pregnane-type steroidal alkaloids [4]. These compounds have cholinesterase inhibition [5], antileishmanial [6], antibacterial [7] and estrogen biosynthesis-promoting [8] activities. Besides, as a folk prescription in miao area of Guizhou province, S. hookeriana is used to treat Alzheimer’s diseases and other diseases.

The space group in which the title compound crystallizes is monoclinic P21. Geometric parameters of the title structure are in the usual ranges [10]. The compound contains one amide group, one five-membered ring, three six-membered rings, and one dimethylamino group. The dimethylamino group was confirmed by the distance of 1.470(5) Å, 1.483(5) Å (C21—N2 and C22—N2), respectively. Then the amide group was confirmed by the distance of 1.226(4) Å, 1.460(4) Å, 1.332(4) Å (C24—O1, C16—N1 and C24—N1).

In this crystal exist additionally one water and one MeOH molecule. Actually, because of the water and MeOH it makes this crystal existent. There is intermolecular hydrogen bond between the O1 atom and the oxygen of water (O2). There is a hydrogen bond between the O1 and H2D. And also O2 forms the hydrogen bond with the hydrogen of MeOH (H3A). Finally, the O3 is involved in a hydrogen bond.

Acknowledgements

The authors gratefully acknowledge support from The National Natural Science Foundation of China [No. 30960529] and the Science and Technology Project of Guizhou Province [No. 2016–1015].

References

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Received: 2019-02-18
Accepted: 2019-03-29
Published Online: 2019-04-27
Published in Print: 2019-06-26

© 2019 Bo Tan 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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  61. Crystal structure of cyclo-[octaaqua-tetrakis(μ2-5,5′-(1H-imidazole-4,5-diyl)bis(tetrazol-2-ido)-κ4N,N′,N′′,N′′′)tetramagnesium(II)], C20H24N40O8Mg4
  62. The crystal structure of a matrine derivative, 13-(4-Cl-pyrrole)-matrine, C18H26ClN4O
  63. Crystal structure of (dibenzyl sulphoxide-κO)bis(2-chlorobenzyl-κC1)dichloridotin(IV), C28H26Cl4OSSn
  64. Crystal structure of catena-poly[(μ2-azido-κ2N:N)(μ2-4-cyanobenzoato-κ2O:O′)-(μ2-methanol-κ2O:O)copper(II)], C9H8CuN4O3
  65. Crystal structure of 1,1′-dibenzyl-3,3′-dicyano-1,1′,4,4′-tetrahydro-4,4′-bipyridine, C26H22N4
  66. Crystal structure of (2-bromobenzyl)((1-bromonaphthalen-2-yl)methyl)sulfane, C18H14Br2S
  67. Crystal structure of 2-(4-ammoniocyclohexyl)-3-(pyridin-2-yl)imidazo[1,5-a]pyridin-2-ium 2-[(2-carboxylatophenyl)disulfanyl]benzoate dihydrate, [C18H22N4][C14H8O4S2] ⋅ 2H2O
  68. Crystal structure of (E)-N-((3R,5S,10S, 13S,14S,17S)-17-((S)-1-(dimethylamino)ethyl)-10,13-dimethylhexadecahydro-1H-cyclopenta[a]phenanthren-3-yl)-2-methylbut-2-enamide – water – methanol (1/1/1), C29H54N2O3
  69. Crystal structure of methyl 2-(4-(3-(2,4-difluorophenyl)pyrazolo[1,5-a]pyrimidin-6-yl)phenyl)acetate, C21H15F2N3O2
  70. Crystal structure of poly[triaqua-(μ4-benzene-1,3,5-tricarboxylato-κ5O1,O2:O3:O4:O5)-(μ2-5-(3-pyridyl)tetrazolato-κ2N1:N3)dizinc(II)], C15H13N5O9Zn2
  71. Crystal structure of N-(3-methylphenyl)(propan-2-yloxy)carbothioamide, C11H15NOS
  72. Crystal structure of poly[(μ2-1,3-bis(imidazol-1-ylmethyl)benzene-κ2N:N′)(nitrato-κ1O)cadmium(II)] — water (2/1), C28H32CdN10O7
  73. Crystal structure of 4-phenyl-2,4-dihydro-3H-1,2,4-triazole-3-thione, C8H7N3S
  74. Crystal structure of benzyltrichloridobis(1H-pyrazole-κ2N)tin(IV), C13H15Cl3N4Sn
  75. Crystal structure of chlorido-4-fluorobenzyl-bis(2-methylquinolin-8-olato-κ2N,O)tin(IV), C27H22ClFN2O2Sn
  76. Crystal structure of tetrakis(O,O′-diisopropyldithiophosphato-κ2S,S′)-(μ2-1,2-bis(4-pyridylmethylene)hydrazine-κ2N:N′)zinc(II), C36H66N4O8P4S8Zn2
  77. Crystal structure of tetrabutylammonium 4,4-oxydibenzoate – boric acid – water (1/2/6) C46H98B2N2O17
  78. Redetermination of the crystal structure of catena-poly[[tribenzyltin(IV)]-(μ2-pyridine-4-carboxylato-κ2N:O)], C27H25NO2Sn
  79. The synthysis and crystal structure of cyclohexyl 5-amino-1-(2,6-dichloro-4-(trifluoromethyl)phenyl)-4-((trifluoromethyl)sulfinyl)-1H-pyrazole-3-carboxylate, C18H15N3Cl2F6O3S
  80. The crystal structure of 5,7-bis(2-hydroxyethoxy)-2-phenyl-4H-chromen-4-one, C19H18O6
  81. Synthesis and crystal structure of (±)-Ethyl 5′-(difluoromethyl)-2-oxo-4′,5′-dihydrospiro[indoline-3,3′-pyrazole]-4′-carboxylate, C14H13F2N3O3
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