Startseite The crystal structure of 5-chloro-4,6-dimethoxypyrimidin-2-amine, C6H8ClN3O2
Artikel Open Access

The crystal structure of 5-chloro-4,6-dimethoxypyrimidin-2-amine, C6H8ClN3O2

  • Sheng Yan ORCID logo , Mei Xue ORCID logo , Xinyuan He , Chengqian Wang , Zixin Wang und Jianlong Wang EMAIL logo
Veröffentlicht/Copyright: 18. März 2020

Abstract

C6H8ClN3O2, monoclinic, P21/n (no. 14), a = 5.066(3) Å, b = 12.775(8) Å, c = 12.587(8) Å, β = 94.060(8)°, V = 812.5(9) Å3, Z = 4, Rgt(F) = 0.0597, wRref(F2) = 0.1990, T = 296(2) K.

CCDC no.: 1986382

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:White rod
Size:0.12 × 0.10 × 0.08 mm
Wavelength:Mo Kα radiation (0.71073 Å)
μ:0.43 mm−1
Diffractometer, scan mode:Bruker APEX-II, φ and ω
θmax, completeness:27.4°, >99%
N(hkl)measured, N(hkl)unique, Rint:4854, 1823, 0.057
Criterion for Iobs, N(hkl)gt:Iobs > 2 σ(Iobs), 965
N(param)refined:111
Programs:Bruker [1], SHELX [2], [3]
Table 2:

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

AtomxyzUiso*/Ueq
Cl10.1897(2)0.34398(8)0.79001(9)0.0537(4)
O10.2141(5)0.2033(2)0.6081(2)0.0493(8)
O20.5749(5)0.5083(2)0.7582(2)0.0458(7)
N20.5312(6)0.2924(2)0.5216(2)0.0371(8)
N30.7199(5)0.4496(2)0.5985(2)0.0356(7)
N60.8465(7)0.3827(3)0.4402(3)0.0478(9)
H6A0.8352920.3362950.3905490.057*
H6B0.9552660.4340730.4368200.057*
C10.3819(7)0.2849(3)0.6027(3)0.0376(9)
C20.3869(7)0.3561(3)0.6852(3)0.0357(9)
C30.5640(7)0.4385(3)0.6785(3)0.0367(9)
C40.7498(8)0.5960(3)0.7512(3)0.0529(12)
H4A0.9288610.5714400.7507130.079*
H4B0.7338510.6411450.8113250.079*
H4C0.7038220.6340260.6867180.079*
C50.2104(10)0.1284(4)0.5248(4)0.0702(15)
H5A0.1731890.1627970.4576240.105*
H5B0.0758830.0771240.5350070.105*
H5C0.3796410.0944490.5254010.105*
C60.6941(7)0.3748(3)0.5231(3)0.0362(9)

Source of material

Sodium dichloroisocyanurate (SDIC, 5.30 g) was added to deionized water (40.00 mL). The solution was stirred at 288 K to get a clear solution, after which 5.5 mL of glacial acetic acid and 2-amino-4,6-dimethoxypyrimidine aqueous solution (including 3.10 g of pyrimidine and 10 mL of deionized water) were sequentially added to the mixture. After reacting at room temperature for 4 h, the filtrate from filtering was put in the refrigerator overnight to be cooled. Colorless transparent crystals were obtained.

Experimental details

H atoms were positioned geometrically (N—H = 0.86 Å, C—H = 0.96 Å) and were included in the refinement in the riding model approximation, with Uiso(H) = 1.2Ueq(N) or 1.5Ueq(methyl C).

Comment

Aminopyrimidine derivatives have attracted extensive attention in molecular biology, as versatile intermediates in organic synthesis and because of their bactericidal action [4], [5], [6], [7], [8], [9], [10], [11], [12], [13]. The crystal structures of some 2-amino-substituted pyrimidine compounds, such as 2-amino-4,6-dimethyl pyrimidiniumbromide [8] and 5-chloro-pyrimidin-2-amine [13] have previously been elucidated.

The title compound pyrimidine molecule (cf. the figure) has a symmetrical structure, which crystallises in space group P21/n. All the bond lengths and angles are within proper ranges and in great accord with that found for related structures [8], [14]. The two carbon atoms (C4, C5) of the methoxy substituent in the ring are 7.083 Å apart, while the chlorine atom (Cl1) and the nitrogen atom (N6) from amino are only 5.725 Å apart from each other. At the same time, all the atoms in the molecule (except the hydrogen atom) are basically in the same plane, where the dihedral angle between the planes defined by one methoxy group (C4, O2, C3, N3) and by the central ring is the largest, that is 2.6(5)°. Therefore, the title compound has an unexceptionable stacking property, which makes contributions to the packing scheme resulting in a high density and stability.

Acknowledgements

We are grateful for the support of Beijing Ernst NMR Technology Co., Ltd.

References

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Received: 2020-01-12
Accepted: 2020-02-26
Published Online: 2020-03-18
Published in Print: 2020-06-25

©2020 Sheng Yan et al., published by De Gruyter, Berlin/Boston

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

Artikel in diesem Heft

  1. Frontmatter
  2. Crystal structure of bis [1-(phenylsulfonyl)-2-(1-(pyrazin-2-yl)ethylidene)hydrazin-1-ido-κ3N,N′,O]cobalt(II), C24H22N8O4S2Co
  3. The crystal structure of 1,3-bis(4-(methoxycarbonyl)benzyl)-2-methyl-1H-benzo[d]imidazol-3-ium bromide, C26H25BrN2O4
  4. Crystal structure of {tris((1H-benzo[d]imidazol-2-yl)methyl)amine-κ4N,N′,N′′,N′′′}-(nitrito-κ2O,O′)nickel(II) perchlorate – ethanol (1/1), C26H27ClN8NiO7
  5. Crystal structure of catena-poly[aqua[(μ2-4,5-dicarboxylato-2-(2-carboxylatophenyl)imidazol-1-ido-κ4N,O,O′:N′)](μ2-4,4′-bipyridine-κ2N:N′)dicopper(II)], C22H14Cu2N4O7
  6. Crystal structure of chlorido-tris(4-methylbenzyl-κC)-(triphenylarsine oxide-κO)tin(IV), C42H42AsClOSn
  7. The crystal structure of 4,4′-bipyridinium bis(3-carboxy-2-nitrobenzoate) tetrahydrate, C13H13N2O8
  8. Crystal structure of 1-(3-chlorophenyl)-4-(4-(((2,3-dihydro-1H-inden-5-yl)oxy)methyl)phenethyl)piperazine, C28H31ClN2O
  9. Crystal structure of catena-poly[diaqua-bis(μ2-5,5′-(1H-imidazole-4,5-diyl)bis(tetrazol-2-ido)-κ4N,N′:N′′,N′′′)magnesium], C10H8N20O2Mg
  10. The crystal structure of (E)-2-((2-hydroxy-4-ethoxybenzylidene)amino)-2-methylpropane-1,3-diol monohydrate, C13H21NO5
  11. Crystal structure of catena-poly[diaqua-(μ2-bipyridine-κ2N:N′)-bis(3,5-dichloroisonicotinato-κO)cadmium(II)] dihydrate, C22H20CdCl4N4O8
  12. The crystal structure of 4-(4-chlorophenyl)cyclohexane-1-carboxylic acid, C13H15ClO2
  13. Redetermination of the crystal structure of yttrium(III) trinitrate(V) pentahydrate, Y(NO3)3 ⋅ 5 H2O, H10N3O14Y
  14. Crystal structure of catena-poly[di-μ2-chlorido-1,10-phenanthroline-κ2N,N′-cadmium(II)], C12H8Cl2CdN2
  15. Crystal structure of 4-((2-methyl-6-(trifluoromethyl)pyrimidin-4-yl)oxy)benzoic acid, C13H9F3N2O3
  16. Crystal structure of 3-acetyl-4-hydroxybenzoic acid, C18H16O8
  17. Crystal structure of bis(N,2-bis(4-ethoxybenzylidene)hydrazine-1-carbohydrazonothioato-κ2N,S)nickel(II) — N,N-dimethylformamide (1/2), C44H56N10S2O6Ni
  18. The crystal structure of 5-chloro-4,6-dimethoxypyrimidin-2-amine, C6H8ClN3O2
  19. Crystal structure of poly[aqua-(μ4-benzene-1,2,4,5-tetracarboxylato-κ4O,O′,O′′,O′′′)bis(μ2-1-(4-(1H-imidazol-1-yl)benzyl)-1H-1,2,4-triazole-κ2N:N)dinickel(II)], NiC17H14N5O5
  20. Crystal structure of poly[aqua(5-dimethylamino)naphthalene-1-sulfonato-κ2N:O)(μ2-4,4′-bipyridyl -κ2N:N′)silver(I)], C44H44Ag2N6O8S2
  21. Crystal structure of 1-[3-(trifluoromethyl)cinnamoyl]-3-(pyridin-2-yl-κN)pyrazole-κ2N-bis(2-phenylpyridinato-k2C,N)iridium(III) hexafluorophosphate complex, [C40H28F3IrN5O]PF6
  22. Crystal structure of catena-poly[aqua(μ6-piperazine-1,4-bisethanesulfonato-κ6N:N′:O:O′:O′′:O′′′)(μ2-pyrazinyl-κ2N:N′)disilver(I)sesquihydrate], C12H30Ag2N4O11S2
  23. Crystal structure of (E)-1-(2-nitrophenyl)-N-(o-tolyl)methanimine, C14H12N2O2
  24. Crystal structure of 4′-amino-3′,5′-diisopropyl-(1,1′-biphenyl)-4-carbonitrile, C19H22N2
  25. The crystal structure of poly[bis(N,N-dimethylformamide-κ1O)-tetrakis(μ2-cyanido-κ2C:N)dinickel(II)], C10H14N6O2Ni2
  26. Crystal structure of rac-trans-N,N′-bis(3-bromo-5-chlorosalicylidene)-1,2-cyclohexanediamine, C20H18Br2Cl2N2O2
  27. Crystal structure of rac-trans-N,N′-bis(3,5-dibromosalicylidene)-1,2-cyclohexanediamine, C20H18Br4N2O2
  28. The crystal structure of (dichromato-κ2O,O′)bis(1,10-phenanthroline-κ2N,N′)nickel(II), C12H16N4O7Cr2Ni
  29. The crystal structure of 3-((1R,2S)-1-methylpyrrolidin-1-ium-2-yl)pyridin-1-ium tetrachloridozincate(II) monohydrate, C10H18Cl4ZnN2O
  30. Crystal structure of bis(μ2-azido-k2N,N)-bis(2-amino-1-(N-(3-bromosalicylaldiminato))ethane)-dicopper(II), C20H18Br4N2O2
  31. Crystal structure of (η6-1-methyl-4-isopropylbenzene)-[5-bromo-2-(2-pyridyl)phenyl-κ2C,N]-chloro-ruthenium(II), C21H21BrClNRu
  32. Crystal structure of N-(methyl(oxo)(1-(6-(trifluoromethyl)pyridin-3-yl)ethyl)-λ6-sulfanylidene)cyanamide, C10H10F3N3OS
  33. Crystal structure of 6,6′-((cyclohexane-1,2-diylbis(azanylylidene))bis(methanylylidene))bis(2-bromo-4-chlorophenolato-κ4N,N′,O,O′)nickel(II), C20H16Br2Cl2NiN2O2
  34. Redetermination of the crystal structure of catena-poly[aqua-(1,10-phenanthroline-κ2N,N′)-(μ2-tetraoxidomolybdato(VI)-κ2O:O′)manganese(II) monohydrate, C12H12N2O6MoMn
  35. The crystal structure tetrakis(μ2-o-chlorobenzoato-κ2O:O′)-bis(methanol-κ1O)dirhodium(II), C30H24Cl4O10Rh2
  36. Crystal structure of bis(2,3-diphenyltetrazolidine-5-thione-κ1S)-(nitrato-κ1O)-(nitrato-κ2O,O′)lead(II), C26H20N10O6S2Pb
  37. Crystal structure of bis(3-bromo-N-(1-(3-methylpyrazin-2-yl)ethylidene)benzohydrazonato-κ3O,N,N′)cadmium(II) hemihydrate, C28H25N8O2.5Br2Cd
  38. Crystal structure of catena-poly[tetrakis(μ2-trifluoroacetato-κ2O:O′)(μ2-2,5-dimethylpyrazine-κ2N,N′)dicopper(II)], C7H4CuF6NO4
  39. The crystal structure of catena-poly[bis[3-azoniapentane-1,5-diammonium][bis(μ4-oxo)-tetrakis(μ3-oxo)-heptakis(μ2-oxo)-tetradecaoxo-octa-molybdenum] dihydrate], (C8H36N6O29Mo8)n
  40. Crystal structure of tetraaqua-bis(2-((3,5,6-trichloropyridin-2-yl)oxy)acetato-κO)-nickel(II)—diaqua-bis(2-((3,5,6-trichloropyridin-2-yl)oxy)acetato-nickel(II), C28H24Cl12N4Ni2O18
  41. The crystal structure of bis(2-hydroxypyrimidinium) pentachloridobismuthate(III), (C4N2H5O)2BiCl5
  42. The crystal structure of catena-poly[(μ2-4,4′-dipyridine-κ2N,N′)-bis(3,5,6-trichloropyridine-2-oxyacetato-κO)-bis(ethanol-κO)nickel(II)], C28H26Cl6N4NiO8
  43. Crystal structure and anti-inflammatory activity of (3E,5E)-1-((4-chlorophenyl)sulfonyl)-3,5-bis(4-fluorobenzylidene)piperidin-4-one-dichloromethane (1/1), C26H20Cl3F2NO3S
  44. The crystal structure of 5-bromopicolinic acid monohydrate, C6H6BrNO3
  45. The crystal structure of 2-(3-(4-bromophenyl)-5-(4-fluorophenyl)-4,5-dihydro-1H-pyrazol-1-yl)-8H-indeno[1,2-d]thiazole, C25H17BrFN3S
  46. The crystal structure of catena-poly[(μ2-2-((3-bromo-2-oxidobenzylidene)amino)acetato-κ4O,N,O′:O′′)-(dimethylformamide-κ1O)]zinc(II), C12H13N2O4BrZn
  47. Crystal structure of aqua-azido-κ1N-(6,6′-((propane-1,3-diylbis(azanylylidene))bis(methanylylidene))bis(3-bromophenolato)-κ4N,N′,O,O′iron(III), C17H16Br2FeN5O3
  48. The crystal structure of tris(1-ethylimidazole-κ1N)-(sulfato-κ2O,O′)vanadium(IV), C15H24N6O5SV
  49. Crystal structure of (E)-3-methoxy-N′-(1-(pyridin-2-yl)ethylidene)benzohydrazide, C15H15N3O2
  50. Crystal structure of dichloro-bis-(1-butyl-1H-benzo[d]imidazole)-nickel(II), C22H28Cl2N4Ni
  51. The crystal structure of 2-(2,3-dimethoxyphenyl)-3-hydroxy-4H-chromen-4-one, C17H14O5
  52. The crystal structure of 5-(2-(4-fluorophenyl)hydrazono)-4-methyl-2-((3-(5-methyl-1-(4-methylphenyl)-1H-1,2,3-triazol-4-yl)-1-phenyl-1H-pyrazol-4-yl)methylene) hydrazono)-2,5-dihydrothiazole dimethylformamide monosolvate, C30H25FN10S⋅C3H7NO
  53. The crystal structure of 1,8-bis(pyridin-4-ylethynyl)anthracene-1,2,4,5-tetrafluoro-3,6-diiodobenzene (2/1), C62H32F4I2N4
  54. The crystal structure of 3,6-di-tert-butyl-1,8-diiodo-9-methyl-9H-carbazole, C21H25I2N
  55. The crystal structure of 8-((4-chlorophenylamino)methylene)-6,10-dioxaspiro[4.5]decane-7,9-dione, C15H14ClNO4
  56. The crystal structure of catena-poly[oktaaqua-bis(μ2-4,4′-ethene-1,2-diyldipyridine-κ2N:N′)-(μ2-3,3′-(1-oxidodiazene-1,2-diyl)diphthalato-κ2O:O′)dicobalt(II)] dihydrate, C28H36N4O19Co2
  57. Crystal structure of (E)-1-(2-cyano-3-oxo-1-phenylprop-1-en-1-yl)-3,7-diphenylindolizine-6-carbonitrile, C31H19N3O
  58. Crystal structure of 1,1′-bis(diphenylphosphino)ferrocene-(1,1′-bis(diphenylphosphino)ferrocene-κ2P,P′)-(O-isobutyl sulfurodithioito-κ2S,S′)copper(I), C39H37CuFeOP2S2
  59. Crystal structure of poly[(5-bimethylamino-1-naphthalenesulfonato-κO)-(μ3-hexamethylenetetramino-κ3N:N′:N′′)silver(I)] dihydrate, C36H52Ag2N10O8S2
  60. Crystal structure of poly[μ2-diaqua-(μ2-2-amino-4,5-dicyano-κ2N:N′-imidazol-1-ide)sodium(I)], C5H6N5O2Na
  61. Crystal structure of (1,3-propanediamine-κ2N,N′)(N-(3-aminopropyl)-α-methyl aspartato-κ4N,N′,O,O′)cobalt(III) chloride, C11H24ClCoN4O4
  62. Crystal structure and anti-inflammatory activity of (3E,5E)-3,5-bis(4-fluorobenzylidene)-1-((4-fluorophenyl)sulfonyl)piperidin-4-one-dichloromethane (1/1), C26H20Cl2F3NO3S
  63. Crystal structure of (S)-(+)-1-cyclohexylethylaminium chloride, C8H18NCl
  64. The crystal structure of tris(nitrato-κ2O,O′)-bis(4,4,5,5-tetramethyl-2-(o-pyridyl)imidazoline-1-oxyl 3-oxide-κ2N,O)yttrium(III), C24H32N9O13Y
  65. Hydrogen bonding versus packing effects in the crystal structure of 3-((1R,2S)-1-methylpyrrolidin-1-ium-2-yl)pyridin-1-ium tetraiodidozincate(II), C10H16I4ZnN2
  66. Dimerization of 2-[(2-((2-aminophenyl)thio)phenyl)amino]-cyclohepta-2,4,6-trien-1-one through hydrogen bonding, C19H16N2OS
  67. Crystal structure of 1-(4-chloro-phenyl)-7-ethoxyl-6,8-difluoro-4-oxo-1,4-dihydro-quinoline-3-carboxylic acid, C18H12ClF2NO4
  68. Crystal structure of 7-ethoxy-6,8-difluoro-4-oxo-1-pyridin-2-ylmethyl-1,4-dihydro-quinoline-3-carboxylic acid, C18H14F2N2O4
  69. Crystal structure of octahydro-7aR,8′R-dimethylspiro[isobenzofuran-4(1H), 4′ (3′H)-[1H-7,9a]methanocyclohepta[c]pyran]-1′,3, 9′ (3aH,4′aH)-trione, C20H26O5
  70. Crystal structure of bis(5-ethoxy-2-(((1-hydroxy-2-methyl-3-oxidopropan-2-yl)imino)methyl)phenolato-κ3N,O,O’)manganese(IV) – methanol (1/1), C27H38MnN2O9
  71. Crystal structure of 8a,8a′′-oxybis(8aH-8,9-dioxa-3a1λ4-aza-8aλ4-borabenzo[fg]tetracene), C34H22B2N2O5
  72. Crystal structure of bromido-triphenyl-(triphenylarsine oxide-κO)tin(IV), C36H30AsBrOSn
  73. Crystal structure of catena-poly[chlorido-(μ2-formato-κ2O:O′)-(1,10-phenathroline-κ2N,N′)copper(II)], C26H18Cl2Cu2N4O4
  74. The crystal structure of poly[(μ10-5-carboxyisophthalato-κ10O)disodium], C9H4Na2O6
  75. The crystal structure of 3,5-difluoroisonicotinic acid, C6H3F2NO2
  76. The crystal structure of ethyl-1-(N-(adamantan-1-yl)-carbamothioyl)piperidine-4-carboxylate, C19H30N2O2S
  77. Crystal structure of 5-methyl-3-phenyl-1-tosyl-1,2,3,4-tetrahydropyridine, C19H21NO2S
  78. Crystal structure of bis((3-chlorosalicylidene)-ethylenediaminato-κ4N,N′,O,O′)nickel (II), C16H12Cl2NiN2O2
  79. Crystal structure of (E)-N′-(2-chloro-6-hydroxybenzylidene)-4-hydroxybenzohydrazide — dihydrofuran-2(3H)-one (1/1), C18H17ClN2O5
  80. Crystal structure of bis((3-bromosalicylidene)-ethylenediaminato-κ4N,N′,O,O′) nickel (II), C16H12Br2NiN2O2
  81. Crystal structure of trimethylsulfoxonium tetrachloridocobaltate(II) [(CH3)3SO]2CoCl4
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