Home Crystal structure of 2-((2-chloropyridin-3-ylamino)methylene)malononitrile, C9H5ClN4
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Crystal structure of 2-((2-chloropyridin-3-ylamino)methylene)malononitrile, C9H5ClN4

  • Mostafa M. Ghorab , Mansour S. Alsaid , Abdullah A. Al-Mishari , Obaid S. AlRuqi and Hazem A. Ghabbour EMAIL logo
Published/Copyright: April 2, 2016

Abstract

C9H5ClN4, monoclinic, P21/c (no. 14), a = 8.1178(4) Å, b = 7.2367(4) Å, c = 15.2585(8) Å, β = 101.506(2)°, V = 878.36(8) Å3, Z = 4, Rgt(F) = 0.0466, wRref(F2) = 0.1170, T = 100 K.

CCDC no.:: 1431816

Tables 13 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, block, size 0.158×0.368×0.415 mm
Wavelength:Mo Kα radiation (0.71073 Å)
μ:3.93 cm−1
Diffractometer, scan mode:Bruker APEX-II, φ and ω scans
2θmax:55°
N(hkl)measured, N(hkl)unique:7339, 2002
N(param)refined:135
Programs:SHELX [11], Bruker programs [12]
Table 2:

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

AtomSitexyzUiso
H(4A)4e0.68460.84700.54110.018
H(5A)4e0.86710.89710.44450.016
H(6A)4e0.21390.54440.42880.013
H(3A)4e0.415(3)0.718(3)0.487(2)0.015(6)
H(1N2)4e0.277(4)0.577(4)0.264(2)0.025(7)
Table 3:

Fractional coordinates and atomic displacement parameters (Å2).

AtomSitexyzU11U22U33U12U13U23
Cl(1)4e0.51976(6)0.67648(7)0.19164(3)0.0131(3)0.0206(3)0.0080(2)−0.0055(2)0.0043(2)−0.0017(2)
N(1)4e0.7187(2)0.8003(2)0.3346(1)0.0069(8)0.0141(8)0.0120(8)0.0005(6)0.0020(7)0.0009(7)
N(2)4e0.2987(2)0.6011(2)0.3197(1)0.0078(8)0.0140(8)0.0092(8)−0.0015(7)0.0034(7)−0.0021(7)
N(3)4e−0.1660(2)0.3525(3)0.4286(1)0.0164(9)0.031(1)0.0175(9)−0.0093(8)0.0069(8)−0.0028(8)
N(4)4e−0.0895(2)0.4870(3)0.1578(1)0.0103(9)0.025(1)0.020(1)0.0014(8)0.0014(7)0.0023(8)
C(1)4e0.5709(2)0.7225(3)0.3058(1)0.0066(9)0.0098(9)0.0090(9)0.0015(7)0.0028(7)0.0012(7)
C(2)4e0.4524(2)0.6831(3)0.3583(1)0.0063(9)0.0101(9)0.0107(9)−0.0004(7)0.0034(7)−0.0003(7)
C(3)4e0.4957(3)0.7335(3)0.4483(1)0.013(1)0.018(1)0.0100(9)−0.0024(8)0.0056(8)−0.0010(8)
C(4)4e0.6522(3)0.8134(3)0.4799(1)0.014(1)0.021(1)0.0088(9)−0.0024(9)0.0013(8)−0.0015(8)
C(5)4e0.7601(3)0.8438(3)0.4220(1)0.0093(9)0.018(1)0.012(1)−0.0025(8)−0.0003(8)0.0006(8)
C(6)4e0.1844(2)0.5410(3)0.3654(1)0.0093(9)0.0115(9)0.0120(9)0.0009(8)0.0041(7)0.0009(7)
C(7)4e0.0287(3)0.4752(3)0.3278(1)0.0092(9)0.0123(9)0.015(1)0.0002(8)0.0046(8)0.0002(8)
C(8)4e−0.0788(3)0.4075(3)0.3837(1)0.0099(9)0.018(1)0.014(1)−0.0019(8)0.0023(8)−0.0030(8)
C(9)4e−0.0362(2)0.4800(3)0.2333(1)0.0047(9)0.013(1)0.019(1)−0.0008(7)0.0034(8)0.0007(8)

Source of material

Method A: a mixture of 3-amino-2-chloropyridine (1.28 g, 0.01 mol), malononitrile (0.66 g, 0.01 mol), triethylorthoformate (1.48 g, 0.01 mol), and methanol (30 mL) containing acetic acid (1 mL) was refluxed for 8 h, the reaction mixture was filtered, the filtered solid was crystallized from ethanol. Method B: a mixture of 3-amino-2-chloropyridine (1.28 g, 0.01 mol) and 2-(ethoxymethylene)malononitrile (1.22 g, 0.01 mole) in methanol (20 mL) containing acetic acid (1 mL) was refluxed for 12 h, the reaction mixture was filtered off, the filtered solid was crystallized from ethanol to give: Yield: 89%, m.p. = 193.4°C; IR: cm−1: 3215 (NH), 3079 (CH arom.), 2975, 2864 (CH aliph.), 2218 (CN), 1614 (C = N), 759 (C—Cl) 1H—NMR (DMSO-d6, ppm): 7.2, 8.0 [m, 3H, Ar—H], 8.1 [s, 1H, CH, D2O-exchangeable], 10.9 [s, 1H, NH, D2O-exchangeable]. 13C—NMR (DMSO-d6, ppm): 55.6, 113.7(2), 122.1, 124.8, 136.7, 140.3, 146.9, 160.4. Anal. Calcd. for C9H5ClN4 (204.62, %): C, 52.83; H, 2.46; N, 27.38. Found (%): C, 52.48; H, 2.13; N, 27.71.

Experimental details

The hydrogen atoms H4A, H5A and H6A were idealized and refined using a riding model (AFIX 43 option of the SHELX program [11]).

Discussion

Pyridine derivatives were shown antibacterial [1], antimalarial [2], anticonvulsant [3], and cytotoxic agents [46]. These findings led us to continue our work on the synthesis of biologically active compounds [710]. The aim of this work was to, synthesize the corresponding compound having a biologically active methylenemalononitrile moiety. The crystal structure of target compound contains one molecule in the asymmetric unit. There is one intramolecular N—H⋯Cl hydrogen bond (figure). The crystal structure is stabilized by three intermolecular hydrogen bonds, of which N1, N3 and N4 work as hydrogen bond acceptors and N2, C6 and C4 work as hydrogen bond donors. The distance of the interactions between N2—H1N2⋯N1i is 2.51(3) Å, C4—H4A⋯N4ii is 2.58 Å and C6—H6A⋯N3iii is 2.4 Å and the angles are 138(3)°, 145° and 151°, respectively. Symmetry codes: (i) −x+1, y−1/2, −z+1/2; (ii) x+1, −y+3/2, z+1/2; (iii) −x, −y+1, −z+1.


Corresponding author: Hazem A. Ghabbour, Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, P. O. Box 2457, Riyadh 11451, Saudi Arabia; and Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt

Award Identifier / Grant number: RGP-VPP-302

Funding statement: The authors would like to extend their sincere appreciation to the Deanship of Scientific Research at King Saud University for funding of this research through the Research Group Project no. RGP-VPP-302.

Acknowledgements:

The authors would like to extend their sincere appreciation to the Deanship of Scientific Research at King Saud University for funding of this research through the Research Group Project no. RGP-VPP-302. The authors thank the responsible editor for supplying the figure.

References

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Received: 2016-2-4
Accepted: 2016-3-4
Published Online: 2016-4-2
Published in Print: 2016-9-1

©2016 Mostafa M. Ghorab et al., published by De Gruyter.

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

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  72. Crystal structure of ent-1β,7α,11α-trihydroxy-7β,20-epoxykaur-16-en-15-one, C20H28O5
  73. Crystal structure of poly-[tetraaquabis(μ8-benzene-1,2,4,5-tetracarboxylato-1κ3O4:O6:O8:2κ4O2:O2:O5:O5:3κ4O1:O3:O5:O7)(di-μ3-hydroxido)-pentazinc(II)] decahydrate, C20H34O32Zn5
  74. Crystal structure of 1-(4-methylthiazol-2-yl)-3-propylthiourea, C8H13N3S2
  75. Crystal structure of 2-((dimethylamino)methylene)-5,5-Dimethylcyclohexane-1,3-dione, C11H17NO2
  76. Crystal structure of poly[1,4-bis(2-methylbenzimidazol)butane-κ2N:N′)bis(4,4′-oxybis(benzoato-κ4O,O′:O′′,O′′′)dicadmium] monohydrate, C48H38Cd2N4O10
  77. Crystal structure of 2-(3-(benzofuran-2-yl)-5-(4-fluorophenyl)-4,5-dihydro-1H-pyrazol-1-yl)-4-(4-chlorophenyl)thiazole, C26H17ClFN3OS
  78. Crystal structure of bis(μ3-isophthalato-κ3O:O′:O′′)(μ2-1,4-\ bis((2-propyl-1H-benzo[d]imidazol-1-yl)methyl)benzene-κ2N:N′)dizinc(II), C22H19N2O4Zn
  79. Crystal structure of poly[bis(adipate-κ4O,O′:O′′, O′′′)(1,4-bis(2-methyl-1H-benzo[d]imidazol-1-yl)benzene-κ2N:N′)dizinc(II), C36H38N4O8Zn2
  80. Crystal structure of N-(2-(2-oxoindolin-4-yl)ethyl)-N-propylpropan-1-aminium tetraphenylborate, C40H45BN2O
  81. Crystal structure of 1-(2,3-dihydro-4-methyl-3-phenyl-2-thioxothiazol-5-yl)-1-ethanone, C12H11NOS2
  82. Crystal structure of 3-(adamantan-1-yl)-1-[(4-benzylpiperazin-1-yl)methyl]-4-[(E)-(2,6-difluorobenzylidene)amino]-1H-1,2,4-triazole-5(4H)-thione, C31H36F2N6S
  83. Crystal structure of 6-(4-chlorophenyl)-3-(thiophen-2-yl)-[1,2,4]triazolo[3,4-b][1,3,4]-thiadiazole, C13H7ClN4S2
  84. Crystal structure of bis(ethanaminium) poly[bis(hexaselenido-κ2Se1,Se6)palladate(II)], C4H16N2PdSe12
  85. Crystal structure of 2-(3-(benzofuran-2-yl)-5-phenyl-4,5-dihydro-1H-pyrazol-1-yl)-4-phenylthiazole, C26H19N3OS
  86. Crystal structure of poly-[bis(μ3-5-hydroxyisophtalato-κ3O:O′:O′′)(μ2-1,4-bis(2-ethylbenzimidazol-1-ylmethyl)benzene-κ2N:N′)dizinc(II)], C40H30N4O5Zn2
  87. Crystal structure of poly-[(μ-1,4-bis(2-ethylbenzimidazol-1-ylmethyl)benzene-κ2N:N′)-bis(μ4-2,2′-(1,3-phenylene)diacetate-κ4O:O′:O′′:O′′′)dizinc(II)], C44H38N4O8Zn2
  88. Crystal structure of 5,17-bis-cyano-25,26,27,28-tetrapropyloxy-calix[4]arene, C42H46N2O4
  89. Crystal structure of poly-[μ-1,4-bis(2-ethylbenzimidazol-1-ylmethyl)benzene-κ2N:N′)-bis(μ3-5-hydroxyisophthalate(2–)-κ3O,O′:O′′)dicadmium(II)] monohydrate, C64H54N8O11Cd2
  90. Crystal structure of poly-[μ-1,4-bis(2-ethylbenzimidazol-1-ylmethyl)benzene-κ2N:N′)-bis(μ4-4,4′-sulfonyldibenzoato-κ4O:O′:O′′:O′′′)dicadmium(II)] monohydrate, C52H42N4O14Cd2
  91. Crystal structure of poly-[bis(μ4-adipato-κ4O:O′:O′′:O′′′)(μ2-1,4-bis((2-ethyl-1H-benzo[d]imidazol-1-yl)methyl)benzene-κ2N:N′)dizinc(II)], C38H42N4O8Zn2
  92. Crystal structure of (2-(2-chlorophenyl)-5-methyl-1,3-dioxan-5-yl)methanol, C12H15ClO3
  93. Crystal structure of 2-(4-Bromophenyl)-5-ethyl-1,3-dioxane-5-carboxylic acid, C13H15BrO4
  94. Crystal structure of (2-(4-bromophenyl)-5-ethyl-1,3-dioxan-5-yl)methanol, C13H17BrO3
  95. Crystal structure of 3-((1,3,5,7-tetraoxo-6-(pyridin-3-ylmethyl)-3,3a,4,4a,5,6,7,7a,8,8a-decahydro-4,8-ethenopyrrolo[3,4-f]isoindol-2(1H)-yl)methyl)pyridin-1-ium-κN-trichloridocobalt(II) hemihydrate, C24H22Cl3CoN4O4.5
  96. Crystal structure of 4-chloro-4′,6′-dichloro-2,2′-[propane-1,3-diyldioxybis(nitrilomethylidyne)]-diphenol, C17H14Cl3N2O4
  97. Crystal structure of 2-amino-4-(3-trifluoromethylphenyl)-5-oxo-5,6,7,8-tetrahydro-4H-chromene-3-carbonitrile, C17H13F3N2O2
  98. Crystal structure of bis(benzoato-κO)bis(4,4′-((1H-1,2,4-triazol-1-yl)methylene)dibenzonitrile-κN)zinc(II), C48H32N10O4Zn
  99. Crystal structure of 3-methyl-2H-chromen-2-one, C10H8O2
  100. Crystal structure of catena-poly-[aqua-(2-carboxy-5-(3-carboxy-5-carboxylatophenoxy)benzoato-κO)(μ2-4,4′-di(1H-imidazol-1-yl)-1,1′-biphenyl-κ2N:N′)cobalt(II)], C34H24N4O10Co
  101. Crystal structure of 4,4′-di(1H-imidazol-1-yl)-1,1′-biphenyl, C36H28N8
  102. Crystal structure of 1-(3-chloropropyl)piperidin-1-ium tetraphenylborate, C32H37BClN
  103. Crystal structure of dimethyl 5-(benzylamino)isophthalate, C17H17NO4
  104. Crystal structure of dimethyl 5-(dibenzylamino)isophthalate, C24H23NO4
  105. Crystal structure of N-(adamantan-1-yl)-4-phenylpiperazine-1-carbothioamide, C21H29N3S
  106. Crystal structure of (2,2′(cyclohexane-1,2-diylbis(nitrilo(E)methylylidene))diphenolato-κ4O,O′,N,N′)dimethanolmanganese(III) bromide, C22H28BrMnN2O4
  107. Crystal structure of 3,5,7-tris(morpholinomethyl)tropolone·0.67 hydrate, C22H33N3O5·0.67H2O
  108. Crystal structure of biphenyl-2,3′,5,5′-tetracarboxylic acid – 4,4′-biphenyl-4,4′-diyldipyridine (3/2), C49H34N3O8
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