Home Physical Sciences Crystal structure of 4-(3-(pyridin-3-yl)ureido)benzoic acid — adipic acid (2/1), C16H16N3O5
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Crystal structure of 4-(3-(pyridin-3-yl)ureido)benzoic acid — adipic acid (2/1), C16H16N3O5

  • Chong Wu , Shou-Ting Wu , Qi-Long Zhang ORCID logo EMAIL logo and Juan Zou
Published/Copyright: June 18, 2020

Abstract

C13H11N3O3 ⋅ C3H5O2, triclinic, P1̄ (no. 2), a = 9.6481(6) Å, b = 10.0123(6) Å, c = 10.1667(6) Å, α = 116.680(2)°, β = 113.268(2)°, γ = 95.809(2)°, V = 758.31(8) Å3, Z = 2, Rgt(F) = 0.0426, wRref(F2) = 0.1212, T = 293(2) K.

CCDC no.: 2003127

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:Colorless block
Size:0.25 × 0.24 × 0.21 mm
Wavelength:Mo Kα radiation (0.71073 Å)
μ:0.11 mm−1
Diffractometer, scan mode:D8/APEX2, φ and ω
θmax, completeness:25.0°, >99%
N(hkl)measured, N(hkl)unique, Rint:4933, 2663, 0.016
Criterion for Iobs, N(hkl)gt:Iobs > 2 σ(Iobs), 2131
N(param)refined:217
Programs:Olex2 [1], Bruker [2], SHELX [3], Diamond [4]
Table 2:

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

AtomxyzUiso*/Ueq
C10.9537(2)0.3885(2)0.0968(2)0.0416(5)
C20.9199(2)0.3146(2)0.1820(2)0.0397(4)
C30.7715(2)0.2072(2)0.1142(2)0.0423(5)
H30.68920.17750.00850.051*
C40.7439(2)0.1438(2)0.2007(2)0.0440(5)
H40.64360.07260.15420.053*
C50.8681(2)0.1875(2)0.3590(2)0.0399(4)
C61.0166(2)0.2942(2)0.4263(2)0.0472(5)
H61.09980.32290.53110.057*
C71.0421(2)0.3579(2)0.3402(3)0.0476(5)
H71.14180.43060.38780.057*
C80.7317(2)0.0177(2)0.4217(2)0.0411(5)
C90.6736(2)−0.1015(2)0.5708(2)0.0389(4)
C100.5186(2)−0.2033(2)0.4473(2)0.0457(5)
H100.4685−0.20740.34570.055*
C110.7411(2)−0.1003(2)0.7199(2)0.0446(5)
H110.8451−0.03140.80380.053*
C120.4403(3)−0.2983(3)0.4787(3)0.0525(5)
H120.3361−0.36810.39750.063*
C130.5152(3)−0.2905(2)0.6288(3)0.0499(5)
H130.4602−0.35570.64750.060*
C140.8047(2)−0.2519(2)0.0846(2)0.0431(5)
C150.6331(2)−0.3584(2)−0.0187(2)0.0414(5)
H15A0.6118−0.4346−0.13180.050*
H15B0.5649−0.2946−0.02880.050*
C160.5873(2)−0.4482(2)0.0530(2)0.0435(5)
H16A0.6533−0.51420.06080.052*
H16B0.6097−0.37250.16680.052*
N10.7691(2)0.0014(2)0.5581(2)0.0487(5)
H10.86210.06190.64570.058*
N20.8551(2)0.1330(2)0.4592(2)0.0500(5)
H20.93670.17870.55920.060*
N30.6643(2)−0.19289(19)0.7491(2)0.0460(4)
O10.60740(17)−0.06004(16)0.28759(16)0.0515(4)
O20.83928(17)0.33400(17)−0.05790(17)0.0523(4)
H2A0.86760.3811−0.09620.078*
O31.08046(18)0.49416(18)0.16600(18)0.0582(4)
O40.85402(16)−0.17033(17)0.03139(18)0.0519(4)
H4A0.7919−0.12380.00900.078*
O50.89897(18)−0.2404(2)0.21382(19)0.0677(5)

Source of material

A solution of pyridine-3-isocyanate (8 mmol) in ethanol (25 mL) was added to a stirred ethanol solution (30 mL) of p-aminobenzoic acid (8 mmol) in a three-necked flask. The reaction mixture was refluxed for 7 h, after that the solution was cooled to room temperature. The white precipitated residue was washed with ether and ethanol 3 times. The white solids (0.2 mmol) were dissolved in 15 mL methanol. The adipic acid (0.1 mmol) was added. Single crystals were obtained from methanol by slow evaporation at room temperature.

Experimental details

The structure was solved using Charge Flipping and refined with the ShelXL [3] refinement. All hydrogen atoms were positioned geometrically, with the d(C—H) = 0.97–0.99 Å, Uiso(H) = 1.2 times Ueq(C) and Uiso(H) = 1.5 times Ueq(O).

Comment

As a double hydrogen bond donor, ureido derivatives may form double hydrogen bonds to a Y-type hydrogen bond binding site for example acetate or tetrahedral anions (such as SO42−) [5]. It is more likely that a hydrogen bond may be formed between ureido and ureido, or between ureido and other molecules, etc., which may assemble into supramolecular compounds. This phenomenon has caused some attention [6].

In the crystal structure of the title compound, the asymmetric unit of the title compound consists of one formula unit of 4-(3-(pyridin-3-yl)ureido) benzoic acid and one half adipic acid (see the figure). The pyridine ring and benzoic acid fragment are linked by an ureido moiety, forming a non-coplanar structure. The dihedral angle between the rings is 176.04°. The bond lengths and bond angles are in the normal ranges [7], [8]. There are some weak non-classical intramolecular hydrogen bonds (for example: C4—H4⋯O1, C10—H10⋯O1) in the molecules. The carboxyl group and carboxyl group of the title compound form a dimer through the double hydrogen bond (O2—H2A⋯O3), and the nitrogen atom on the urea group and the nitrogen atom on the pyridine ring form a hydrogen bond (N1—H1⋯O5, N2—H1⋯O5 and O4—H4A⋯N3) with the carboxyl group of adipic acid respectively to expand into a two-dimensional network structure.

Acknowledgements

This work was supported by the Science and Technology Foundation of Guizhou Province (grant number [2019]2792, grant number [2018]5779-14, grant number 2019[1032], 2014[7334]).

References

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2. Bruker. APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, WI, USA (2012).Search in Google Scholar

3. Sheldrick, G. M.: Crystal structure refinement with SHELXL. Acta Crystallogr. C71 (2015) 3–8.10.1107/S2053229614024218Search in Google Scholar PubMed PubMed Central

4. Brandenburg, K.: DIAMOND. Visual Crystal Structure Information System. Ver. 4.0. Crystal Impact, Bonn, Germany (2015).Search in Google Scholar

5. Zuo, W.; Jia, C. D.; Zhang, H. Z.; Zhao, Y. X.; Yang, X. J.; Wu, B.: Selective recognition of choline phosphate by tripodal hexa-urea receptors with dual binding sites: crystal and solution evidence. Chem. Sci. 10 (2019) 2483–2488.10.1039/C8SC04338HSearch in Google Scholar

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8. Zhang, Q.-L.; Xie, H.-F.; Yu, Q.; Yang, X.-S.: Crystal structure of 3-(3-(pyridin-3-yl)ureido)benzoic acid, C13H11N3O3. Z. Kristallogr. NCS 235 (2019) 35–36.10.1515/ncrs-2019-0454Search in Google Scholar

Received: 2020-04-24
Accepted: 2020-05-11
Published Online: 2020-06-18
Published in Print: 2020-08-26

©2020 Chong Wu et al., published by De Gruyter, Berlin/Boston

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

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  74. Crystal structure of chloridotris(4-chlorophenyl)(dimethyl sulfoxide-κO)tin(IV), C20H18Cl4OSSn
  75. Crystal structure of catena{di-aqua-sodium-[N-(hydroxyethyl), N-isopropyl-dithiocarbamato]}n, [C6H16NNaO2S2]n
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  78. Crystal structure of hexanedihydrazide, C6H14N4O2
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