Home Physical Sciences Crystal structure of 6-(pyridin-3-yl)-1,3,5-triazine-2,4-diamine-sebacic acid (2/1), C13H17N6O2
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Crystal structure of 6-(pyridin-3-yl)-1,3,5-triazine-2,4-diamine-sebacic acid (2/1), C13H17N6O2

  • Zhi-Yong Wang , Peng-Xin Qian , Xian-Jiong Yang , Qi-Long Zhang ORCID logo EMAIL logo , Hong Xu and Ya-Li Huang
Published/Copyright: August 11, 2023

Abstract

C8H8N6·C5H9O2, monoclinic, I2/a (no. 15), a = 13.2666(17) Å, b = 11.0435(15) Å, c = 19.778(3) Å, β = 92.707(10)°, V = 2894.4(7) Å3, Z = 8, Rgt(F) = 0.0528, wRref(F2) = 0.1511, T = 293(2) K.

CCDC no.: 2285911

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: 0.18 × 0.15 × 0.14 mm
Wavelength: Mo Kα radiation (0.71073 Å)
μ: 0.10 mm−1
Diffractometer, scan mode: φ and ω
θmax, completeness: 25.0°, >99 %
N(hkl)measured, N(hkl)unique, Rint: 9157, 2547, 0.081
Criterion for Iobs, N(hkl)gt: Iobs > 2 σ(Iobs), 1186
N(param)refined: 192
Programs: Olex2 [1], Bruker [2], SHELX [3], Diamond [4]
Table 2:

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

Atom x y z Uiso*/Ueq
C1 1.0285 (2) 0.1348 (3) 0.38777 (16) 0.0493 (8)
C2 0.8696 (2) 0.1300 (3) 0.42480 (17) 0.0520 (8)
C3 1.0022 (2) 0.1594 (2) 0.49828 (15) 0.0454 (7)
C4 1.0437 (2) 0.1748 (3) 0.56877 (15) 0.0464 (8)
C5 0.9835 (2) 0.1850 (3) 0.62318 (16) 0.0588 (9)
H5 0.9137 0.1873 0.6164 0.071*
C6 1.1476 (2) 0.1747 (3) 0.58281 (16) 0.0569 (9)
H6 1.1895 0.1692 0.5466 0.068*
C7 1.1296 (2) 0.1899 (3) 0.69621 (16) 0.0608 (9)
H7 1.1584 0.1943 0.7399 0.073*
C8 1.0266 (2) 0.1920 (3) 0.68766 (17) 0.0644 (10)
H8 0.9864 0.1980 0.7248 0.077*
C9 0.9895 (2) 0.4906 (3) 0.46228 (15) 0.0654 (9)
H9A 1.0240 0.4179 0.4484 0.079*
H9B 1.0172 0.5584 0.4381 0.079*
C10 0.8779 (2) 0.4791 (3) 0.44233 (17) 0.0688 (10)
H10A 0.8500 0.4116 0.4667 0.083*
H10B 0.8434 0.5520 0.4558 0.083*
C11 0.8578 (2) 0.4596 (3) 0.36693 (17) 0.0688 (10)
H11A 0.8856 0.5271 0.3425 0.083*
H11B 0.8922 0.3866 0.3533 0.083*
C12 0.7466 (2) 0.4484 (4) 0.34770 (17) 0.0757 (11)
H12A 0.7186 0.3833 0.3739 0.091*
H12B 0.7131 0.5227 0.3599 0.091*
C13 0.7238 (2) 0.4240 (3) 0.27420 (18) 0.0670 (10)
N1 0.92914 (16) 0.1220 (2) 0.37212 (12) 0.0528 (7)
N2 1.09129 (17) 0.1264 (2) 0.33802 (13) 0.0684 (9)
H2A 1.1552 0.1340 0.3464 0.082*
H2B 1.0683 0.1133 0.2973 0.082*
N3 1.06854 (16) 0.1552 (2) 0.45034 (12) 0.0499 (7)
N4 0.90183 (15) 0.1480 (2) 0.48956 (12) 0.0511 (7)
N5 0.77033 (16) 0.1188 (3) 0.41081 (13) 0.0691 (9)
H5A 0.7480 0.1072 0.3698 0.083*
H5B 0.7288 0.1233 0.4428 0.083*
N6 1.19039 (17) 0.1820 (3) 0.64490 (13) 0.0639 (8)
O1 0.78647 (16) 0.4182 (3) 0.23236 (12) 0.0930 (9)
O2 0.62676 (14) 0.4110 (3) 0.25933 (11) 0.0802 (8)
H2 0.6181 0.3926 0.2193 0.120*

1 Source of materials

Nicotinonitrile (1.05 g, 10 mmol), amino guanidine (1.10 g, 10 mmol) and potassium hydroxide (0.56 g, 10 mmol) are added to 80 mL 2-methoxyethanol and heated for 4 h under nitrogen protection and reflux to produce a large number of white solids, which are collected by filtration, washed with water for three times, and then dried in the vacuum. The product weighs 1.41 g and the yield rate is 75 %. 0.1 mmol of the purple solid is added to 20 mL ethanol solution and sebacic acid, dissolved by heating, and then a single crystal of an appropriate X-ray diffraction size is separated by standing the volatile solvent at room temperature for crystallization for 10 days.

2 Experimental details

Using Olex2 [1], 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).

3 Comment

The nitrogen atom on the aromatic ring contains lone pair electrons and is easy to form complexes with metal ions. Therefore, the design and synthesis of nitrogen-containing organic ligands has been a hot topic in coordination chemistry [5, 6]. The 6-(pyridin-3-yl)-1,3,5-triazine-2,4-diamine contains multiple nitrogen atoms and two amido groups, due to which it is easy to coordinate with metal ions [7]. At the same time, as proton donors, amino groups easily interact with large electronegative atoms (such as O, N, and F) to form a two-dimensional or even three-dimensional supramolecular network structure [8]. Here, we report the crystal structure of self-assembly formed by 6-(pyridin-3-yl)-1,3,5-triazine-2,4-diamine and sebacic acid. Pyridine and triazine rings are not parallel to each other and the dihedral angle between them is 173.16°. The 6-(pyridin-3-yl)-1,3,5-triazine-2,4-diamine forms a one-dimensional chain structure through interaction with hydrogen bonds of N2–H2A⋯N6 and N5–H5B⋯N4. Through interaction of sebacic acid and 6-(pyridin-3-yl)-1,3,5-triazine-2,4-diamine, hydrogen bonds of N5–H5A⋯O1 and O2–H2⋯N1 is produced, so as to expand the one-dimensional chain structure to two-dimensional structure. All geometric parameters are in the expected ranges [9].


Corresponding author: Qi-Long Zhang, School of Basic Medical Science, Guizhou Medical University, Guiyang, 550025, People’s Republic of China, E-mail:

  1. Author contributions: All the authors have accepted responsibility for the entire content of this submitted manuscript and approved submission.

  2. Research funding: Science and Technology Foundation of Guizhou Province (grant number ZK[2022]395, 19NSP042, 26222030209), the Provincial General Project of University Student Innovation and Entrepreneurship Fund, China (No. S202110660050).

  3. Conflict of interest statement: The authors declare no conflicts of interest regarding this article.

References

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Received: 2023-07-19
Accepted: 2023-08-01
Published Online: 2023-08-11
Published in Print: 2023-10-26

© 2023 the author(s), published by De Gruyter, Berlin/Boston

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

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