Home Crystal structure of 1,1′,1″-(nitrilotris(ethane-2,1-diyl))tris(3-(4-(((E)-pyridin-2-ylmethylene)amino)phenyl)urea), C45H47N13O4
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Crystal structure of 1,1′,1″-(nitrilotris(ethane-2,1-diyl))tris(3-(4-(((E)-pyridin-2-ylmethylene)amino)phenyl)urea), C45H47N13O4

  • Jie Li ORCID logo EMAIL logo , Yinghan Dong , Mengying Qiu , Haiwei Han and Xiaoyan Pei
Published/Copyright: September 6, 2024

Abstract

C45H47N13O4, triclinic, P1̄ (no. 2), a = 10.242(6) Å, b = 14.766(15) Å, c = 15.503(8) Å, α = 70.91(2)°, β = 88.052(16)°, γ = 74.13(3)°, V = 2127(3) Å3, Z = 2, R gt (F) = 0.0411, wR ref (F 2) = 0.1059, T = 120(2) K.

CCDC no.: 2224443

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: Yellow block
Size: 0.33 × 0.29 × 0.21 mm
Wavelength:

μ:
Mo Kα radiation (0.71073 Å)

0.09 mm−1
Diffractometer, scan mode:

θ max, completeness:
Bruker APEX-II, φ and ω

25.4°, >99 %
N(hkl)measured, N(hkl)unique, R int: 52751, 7782, 0.050
Criterion for I obs, N(hkl)gt: I obs > 2σ(I obs), 6364
N(param)refined: 567
Programs: Bruker, 1 SHELX, 2 , 3 , 4 Diamond 5
Table 2:

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

Atom x y z U iso*/U eq
C1 0.1229 (2) 0.57380 (16) 0.89109 (14) 0.0480 (5)
H1 0.1185 0.5069 0.9170 0.058*
C2 0.0670 (2) 0.63972 (16) 0.93716 (14) 0.0463 (5)
H2 0.0255 0.6187 0.9932 0.056*
C3 0.0731 (2) 0.73690 (15) 0.89974 (13) 0.0409 (5)
H3A 0.0351 0.7843 0.9294 0.049*
C4 0.13507 (18) 0.76437 (14) 0.81866 (13) 0.0344 (4)
H4A 0.1407 0.8309 0.7918 0.041*
C5 0.18915 (17) 0.69335 (13) 0.77670 (12) 0.0286 (4)
C6 0.26186 (16) 0.71486 (12) 0.69186 (11) 0.0271 (4)
H6 0.2786 0.6692 0.6588 0.032*
C7 0.37492 (16) 0.81085 (11) 0.58017 (11) 0.0241 (3)
C8 0.47468 (16) 0.86042 (12) 0.57503 (11) 0.0259 (4)
H8A 0.4911 0.8811 0.6246 0.031*
C9 0.54994 (16) 0.87982 (11) 0.49854 (11) 0.0253 (4)
H9 0.6200 0.9111 0.4973 0.030*
C10 0.52385 (16) 0.85388 (11) 0.42338 (11) 0.0242 (3)
C11 0.42126 (16) 0.80661 (12) 0.42711 (11) 0.0257 (4)
H11A 0.4010 0.7898 0.3760 0.031*
C12 0.34909 (16) 0.78423 (12) 0.50502 (11) 0.0256 (4)
H12A 0.2815 0.7505 0.5074 0.031*
C13 0.63265 (15) 0.83286 (11) 0.28296 (11) 0.0231 (3)
C14 0.74692 (16) 0.83580 (12) 0.13970 (11) 0.0254 (4)
H14A 0.7114 0.8892 0.0809 0.030*
H14B 0.7054 0.7811 0.1454 0.030*
C15 0.89992 (16) 0.79658 (12) 0.13731 (10) 0.0244 (3)
H15A 0.9203 0.7812 0.0799 0.029*
H15B 0.9423 0.8496 0.1365 0.029*
C16 0.3423 (2) 0.24864 (14) 1.05648 (12) 0.0372 (4)
H16 0.2784 0.2106 1.0693 0.045*
C17 0.4215 (2) 0.24448 (16) 1.12856 (13) 0.0415 (5)
H17 0.4151 0.2024 1.1889 0.050*
C18 0.5101 (2) 0.30298 (18) 1.11089 (13) 0.0471 (5)
H18 0.5629 0.3043 1.1595 0.057*
C19 0.52137 (19) 0.35978 (15) 1.02157 (13) 0.0380 (4)
H19 0.5819 0.4005 1.0077 0.046*
C20 0.44196 (17) 0.35580 (13) 0.95284 (12) 0.0290 (4)
C21 0.45851 (17) 0.40499 (13) 0.85516 (12) 0.0303 (4)
H21 0.4000 0.4029 0.8100 0.036*
C22 0.57436 (16) 0.48457 (12) 0.73628 (11) 0.0273 (4)
C23 0.61822 (18) 0.57036 (13) 0.70348 (12) 0.0310 (4)
H23 0.6231 0.6071 0.7428 0.037*
C24 0.65458 (17) 0.60251 (12) 0.61459 (12) 0.0295 (4)
H24 0.6805 0.6627 0.5924 0.035*
C25 0.65363 (16) 0.54762 (12) 0.55702 (11) 0.0253 (4)
C26 0.61028 (16) 0.46152 (12) 0.58894 (11) 0.0262 (4)
H26 0.6089 0.4237 0.5500 0.031*
C27 0.56915 (16) 0.43083 (12) 0.67754 (11) 0.0271 (4)
H27 0.5373 0.3731 0.6984 0.033*
C28 0.79690 (17) 0.52882 (12) 0.42935 (11) 0.0275 (4)
C29 0.93707 (17) 0.53848 (12) 0.29665 (11) 0.0272 (4)
H29A 0.9317 0.4763 0.2876 0.033*
H29B 1.0214 0.5233 0.3343 0.033*
C30 0.93950 (17) 0.61702 (12) 0.20476 (11) 0.0251 (4)
H30A 1.0130 0.5889 0.1699 0.030*
H30B 0.8521 0.6349 0.1694 0.030*
C31 0.8287 (2) 1.07287 (14) 0.97354 (13) 0.0376 (4)
H31 0.8962 1.0826 1.0074 0.045*
C32 0.6957 (2) 1.10197 (14) 0.99386 (14) 0.0391 (4)
H32 0.6717 1.1328 1.0394 0.047*
C33 0.5976 (2) 1.08547 (15) 0.94679 (15) 0.0448 (5)
H33 0.5046 1.1047 0.9595 0.054*
C34 0.63602 (19) 1.04073 (14) 0.88102 (13) 0.0380 (4)
H34 0.5705 1.0273 0.8486 0.046*
C35 0.77240 (18) 1.01576 (12) 0.86316 (12) 0.0295 (4)
C36 0.82269 (19) 0.97185 (13) 0.79089 (12) 0.0329 (4)
H36 0.9039 0.9821 0.7631 0.039*
C37 0.81548 (17) 0.88400 (13) 0.69330 (12) 0.0297 (4)
C38 0.85181 (19) 0.94384 (13) 0.61197 (12) 0.0331 (4)
H38 0.8391 1.0126 0.6028 0.040*
C39 0.90614 (19) 0.90572 (13) 0.54384 (12) 0.0327 (4)
H39 0.9285 0.9484 0.4883 0.039*
C40 0.92789 (16) 0.80457 (12) 0.55697 (12) 0.0269 (4)
C41 0.88951 (17) 0.74470 (12) 0.63807 (12) 0.0301 (4)
H41 0.9025 0.6759 0.6475 0.036*
C42 0.83304 (17) 0.78349 (13) 0.70487 (12) 0.0314 (4)
H42 0.8060 0.7416 0.7590 0.038*
C43 1.02303 (17) 0.80029 (12) 0.40722 (11) 0.0267 (4)
C44 1.13525 (18) 0.76380 (12) 0.27554 (11) 0.0288 (4)
H44A 1.2328 0.7615 0.2728 0.035*
H44B 1.0815 0.8332 0.2431 0.035*
C45 1.10698 (16) 0.69522 (12) 0.22837 (11) 0.0250 (4)
H45A 1.1476 0.7087 0.1682 0.030*
H45B 1.1516 0.6252 0.2655 0.030*
N1 0.18307 (16) 0.59884 (11) 0.81175 (11) 0.0375 (4)
N2 0.30294 (13) 0.79322 (10) 0.66151 (9) 0.0256 (3)
N3 0.59786 (14) 0.88215 (10) 0.34524 (9) 0.0275 (3)
H3 0.6241 0.9364 0.3356 0.033*
N4 0.70468 (14) 0.87530 (10) 0.21420 (9) 0.0256 (3)
H4 0.7268 0.9287 0.2145 0.031*
N5 0.35014 (15) 0.30280 (11) 0.96983 (10) 0.0336 (3)
N6 0.54983 (15) 0.45011 (11) 0.83051 (10) 0.0305 (3)
N7 0.69215 (14) 0.58263 (10) 0.46540 (9) 0.0300 (3)
H7 0.6460 0.6423 0.4299 0.036*
N8 0.81914 (14) 0.57647 (10) 0.34294 (9) 0.0296 (3)
H8 0.7599 0.6333 0.3128 0.036*
N9 0.86900 (15) 1.03132 (12) 0.90843 (11) 0.0365 (4)
N10 0.76015 (15) 0.92080 (11) 0.76502 (10) 0.0325 (3)
N11 0.98874 (15) 0.75750 (10) 0.49445 (10) 0.0302 (3)
H11 1.0073 0.6920 0.5138 0.036*
N12 1.10057 (15) 0.73460 (10) 0.37031 (9) 0.0302 (3)
H12 1.1313 0.6717 0.4049 0.036*
N13 0.96127 (13) 0.70735 (9) 0.21468 (9) 0.0216 (3)
O1 0.60037 (11) 0.75569 (8) 0.28979 (7) 0.0256 (3)
O2 0.86489 (14) 0.44333 (9) 0.47375 (8) 0.0397 (3)
O3 0.98820 (13) 0.89132 (8) 0.36622 (8) 0.0342 (3)
O4 0.75066 (14) 0.02647 (10) 0.28975 (9) 0.0341 (3)
H4B 0.735 (2) 0.0799 (18) 0.3028 (15) 0.057 (7)*
H4C 0.831 (3) −0.016 (2) 0.3181 (17) 0.074 (8)*

1 Source of material

The target compound was synthesized in three synthetic steps. Fistly, a solution of tris(2-aminoethyl) amine (0.7 g, 4.79 mmol) in 15 mL of THF was added dropwise to a solution of p-nitroisocyanate(2.15 g, 13.10 mmol) in THF (15 mL). After refluxing under intensive stirring for 4 h, the precipitate was filtered off and washed several times with THF and diethyl ether and then dried in vacuum to yield analytically pure 1,1′,1″-(nitrilotris (ethane-2,1-diyl))tris(3-(4-nitrophenyl)urea) (La) as a yellow solid. Secondly, hydrazine monohydrate (11 mL) was added dropwise to the suspension of La and Pd/C 10 % (0.2 g, cat.) in ethanol (70 mL). After refluxing under stirring for 12 h, the solid was filtered off via suction filtration and dissolved in DMF (10 mL) and filtered through Celite to remove Pd/C. The DMF solution was poured in water (150 mL), and the precipitate thus obtained was filtered off, washed several times with ethanol and diethyl ether and dried to give analytically pure 1,1′,1″-(nitrilotris(ethane-2,1-diyl))tris(3-(4-aminophenyl)urea) (Lb) as a white solid. Lastly, 2-pyridylaldehyde was added to a solution of Lb in 5 mL of DMSO stirring at room temperature for 12 h. Subsequently, the precipitate was filtered, and washed several times with acetonitrile and diethyl ether, and dried over vacuum to get the target compound (L) as a yellow solid (0.48 g, 0.59 mmol, 80 %). At room temperature, yellow block crystals of L were obtained by ether diffusion method.

2 Experimental details

Hydrogen atoms were placed in their geometrically idealized positions and constrained to ride on their parent atoms, with C–H = 0.96 Å (methyl), U iso (H) = 1.5 U eq (C), C–H = 0.98 Å (methine), U iso (H) = 1.2 U eq (C), C–H = 0.93 Å (aromatic and alkenyl), U iso (H) = 1.2 U eq (C), and O–H = 0.82 Å (hydroxyl), U iso (H) = 1.5 U eq (O).

3 Comment

Over the past few decades, tripodal urea derivatives have been proved to be a class of excellent anion receptors since the tripodal framework offers a greater opportunity for the spatially adaptive encapsulation of anions with size- and shape-complementarity than linear receptors. 6 , 7 , 8 , 9 , 10 , 11 , 12 , 13 , 14 Such receptors typically contain three or six urea units, which can effectively bind with anions through multiple hydrogen bonds, making them valuable in various applications including anion extraction, 8 , 9 anion recognition 10 , 11 , 12 and transmembrane transport. 13 In this study, a novel imine-pyridine-functionalized tripodal tris(urea) receptor was prepared and its structure confirmed by single crystal X-ray diffraction.

The asymmetric structural unit contains one title molecule (see left part of the figure) and one lattice water molecule. In the tripodal structure, NH groups on two urea units point towards the outside of the cavity, while NH groups on the other urea unit point towards the inside of the cavity. The two urea groups pointing in the same direction form two intramolecular hydrogen bonds of N7–H7···O1(dN7···O1 = 3.020 Å, 148.49°), and N8–H8···O1(dN8···O2 = 2.854 Å, 159.04°). Moreover, there are six intermolecular hydrogen bonds formed by three urea units and the water molecule. Among them, O4 atom from lattice water takes part in four intermolecular hydrogen bonds with three urea units, viz. N3 ii  – H3 ii ···O4, N4 ii  – H4 ii ···O4, O4–H4C···O3 ii and O4–H4B···N2 iii (symmetry code: (ii) x, y + 1, z; (iii) −x + 2, −y + 1, −z + 1). Meanwhile, O2 atom from one urea unit takes part in two intermolecular hydrogen bonds with another urea unit from the adjacent molecule, viz. N11 i  – H11 i ···O2 and N12 i  – H12 i ···O2 (symmetry code: (i) −x + 2, −y + 1, −z + 1). The distance of N7···O1 is in the range of 2.702–2.984 Å and the angle of the intermolecular hydrogen bonds is in the range of 148.91–177.43°. The intermolecular hydrogen bonds contribute to the formation of a one-dimensional chain in the crystal structure (right part of the structure).


Corresponding author: Jie Li, College of Chemistry and Chemical Engineering, Xinyang Normal University, Xinyang, Henan 464000, P.R. China, E-mail:

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

  2. Competing interests: The authors declare no conflicts of interest regarding this article.

  3. Research funding: The work was supported by National Natural Science Foundation of China (22003055) and Nanhu Scholars Program for Young Scholars of the Xinyang Normal University.

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Received: 2024-07-01
Accepted: 2024-08-19
Published Online: 2024-09-06
Published in Print: 2024-12-17

© 2024 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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  41. Crystal structure of 2-(2,3-bis(4-methoxyphenyl)-1H-pyrrolo[2,3-b]quinoxalin-1-yl)anilin, C30H24N4O2
  42. Crystal structure of 5,7-dihydroxy-2-phenyl-4H-chromen-4-one–N,N-dimethylformamide(1/1), C18H17NO5
  43. The crystal structure of bis(μ 2-biphenyl-2,2′-dicarboxylato)-diaqua-bis(nitrato)-bis(2,2′:6′,2′′-terpyridine)dineodymium(III), C46H32I2N8Nd2O16
  44. Crystal structure of (Z)-4-amino-N -((4-chlorophenyl)(phenyl)methylene)benzohydrazide, C20H16ClN3O
  45. Crystal structure of (E)-6,8-dimethoxy-4-(4-morpholinobenzylidene)-3,4-dihydro-1-benzoxepin-5(2H)-one, C23H25NO5
  46. Crystal structure of (R)-2-((3-(3-aminopiperidin-1-yl)-6-methyl-5-oxo-1,2,4-triazin-4(5H)-yl) methyl)-4-fluorobenzonitrile benzoate monohydrate, C24H27FN6O4
  47. The crystal structure of [triaqua-(8-carboxymethoxy-quinoline-2-carboxylato-κ 3 N,O,O)copper(II)]monohydrate, C12H15NO9Cu
  48. Crystal structure of (((4-chlorophenyl)sulfonyl)glycinato-κ 2 N,O)bis(1,10-phenanthroline-κ 2 N,N′)cobalt(II) tetrahydrate, C32H30ClCoN5O8S
  49. Crystal structure of (((3-nitrophenyl)sulfonyl)-β-alaninato-κO)bis(2,2′-bipyridine-κ 2 N, N′)copper(II) 3-nitrobenzenesulfonate, C35H29CuN7O11S2
  50. Crystal structure of 3-phenoxybenzyl 2-(6-methoxynaphthalen-2-yl)propanoate, C27H24O4
  51. 6-(2′,3′-Dihydroxy-3′-methylbutyl)-7-methoxy-8-(3″-methylbut-2″-en-1″-yl)-2H-chromen-2-one, C20H26O5
  52. Crystal structure of bromido-(2,2′:6′,2″-terpyridine-4′-onato-κ3N)palladium(II) methanol solvate
  53. The crystal structure of ethyl 2-amino-(4-nitrophenyl)-5-oxo-5,6,7,8-tetrahydro-4H-chromene-3-carboxylate, C20H22N2O6
  54. Crystal structure of (1E,3E,5E)-1,6-bis(4-(pentyloxy)phenyl)hexa-1,3,5-triene, C28H36O2
  55. The crystal structure of tris(2-bromo-4-methylphenyl)amine, C21H18Br3N
  56. The crystal structure of 3-(2,5-dimethylanilino)-1-(2,5-dimethylphenyl)-4-methyl-1H-pyrrole-2,5-dione, C21H22N2O2
  57. Crystal structure of dicarbonyl (μ2-indole-2-carboxylato κ2 O:O′)tris(triphenylarsine-κAs)dirhodium(I) acetone solvate, C68H56As3NO5Rh2
  58. The crystal structure of 4-chloro-2-formylphenyl 4-methylbenzenesulfonate, C14H11ClO4S
  59. Crystal structure of 4-iodobenzyl 2-(6-methoxynaphthalen-2-yl) propanoate, C21H19IO3
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