Home Crystal structure of bis((1-methylbenzimidazol-2-yl)methyl)amine, C18H19N5
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Crystal structure of bis((1-methylbenzimidazol-2-yl)methyl)amine, C18H19N5

  • Meng Gaoxiang ORCID logo EMAIL logo , Yongming Yang , Qiang Li and Zhou Li
Published/Copyright: January 4, 2022

Abstract

C18H19N5, triclinic, P 1 (no. 2), a = 6.612(4) Å, b = 8.800(5) Å, c = 13.777(8) Å, α = 83.219(7)°, β = 79.329(6)°, γ = 78.744(6)°, V = 769.8(8) Å3, Z = 2, R gt (F) = 0.0394, wR ref (F 2) = 0.0996, T = 100(2) K.

CCDC no.: 2120269

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: 0.12 × 0.10 × 0.06 mm
Wavelength: Mo Kα radiation (0.71073 Å)
μ: 0.08 mm−1
Diffractometer, scan mode: Bruker Apex II, φ and ω
θ max, completeness: 26.9°, >99%
N(hkl)measured, N(hkl)unique, R int: 8564, 3284, 0.028
Criterion for I obs, N(hkl)gt: I obs > 2 σ(I obs), 2882
N(param)refined: 213
Programs: Bruker [1], SHELX [2], [3], [4], Diamond [5], Olex2 [6]
Table 2:

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

Atom x y z U iso*/U eq
C1 0.6990 (2) 0.87744 (15) 0.38431 (9) 0.0231 (3)
H1A 0.750452 0.809345 0.329364 0.028*
H1B 0.545026 0.905601 0.390128 0.028*
C2 0.7522 (2) 0.78962 (15) 0.47868 (9) 0.0205 (3)
C3 0.9439 (2) 0.65481 (14) 0.58565 (9) 0.0209 (3)
C4 1.0994 (2) 0.57547 (15) 0.63811 (10) 0.0254 (3)
H4 1.243623 0.572320 0.612476 0.030*
C5 1.0325 (2) 0.50132 (16) 0.72976 (10) 0.0283 (3)
H5 1.133474 0.445801 0.767920 0.034*
C6 0.8193 (2) 0.50651 (15) 0.76730 (10) 0.0282 (3)
H6 0.778991 0.454756 0.830416 0.034*
C7 0.6660 (2) 0.58549 (15) 0.71432 (10) 0.0265 (3)
H7 0.521838 0.588559 0.740195 0.032*
C8 0.7301 (2) 0.66057 (14) 0.62154 (9) 0.0215 (3)
C9 1.1454 (2) 0.76232 (17) 0.42700 (10) 0.0272 (3)
H9A 1.131995 0.748151 0.359115 0.041*
H9B 1.263540 0.686814 0.446856 0.041*
H9C 1.169421 0.867948 0.430006 0.041*
C10 0.76723 (19) 1.08687 (14) 0.25882 (9) 0.0199 (3)
H10A 0.810416 1.189947 0.247988 0.024*
H10B 0.618511 1.102050 0.251113 0.024*
C11 0.89728 (19) 0.98427 (14) 0.18280 (9) 0.0179 (3)
C12 0.99944 (19) 0.82134 (14) 0.07210 (9) 0.0184 (3)
C13 1.0174 (2) 0.71265 (15) 0.00300 (9) 0.0230 (3)
H13 0.897240 0.680915 −0.011022 0.028*
C14 1.2158 (2) 0.65314 (15) −0.04409 (10) 0.0253 (3)
H14 1.231487 0.579007 −0.091015 0.030*
C15 1.3946 (2) 0.69955 (15) −0.02430 (10) 0.0250 (3)
H15 1.528120 0.656249 −0.058367 0.030*
C16 1.3814 (2) 0.80672 (15) 0.04355 (9) 0.0227 (3)
H16 1.501975 0.838268 0.057207 0.027*
C17 1.18051 (19) 0.86563 (14) 0.09066 (9) 0.0183 (3)
C18 1.2411 (2) 1.05296 (17) 0.20302 (11) 0.0275 (3)
H18A 1.243686 1.154931 0.166004 0.041*
H18B 1.383646 0.993132 0.197540 0.041*
H18C 1.183862 1.066871 0.272921 0.041*
N1 0.78974 (17) 1.01903 (13) 0.36043 (8) 0.0210 (2)
H1 0.713 (2) 1.0893 (19) 0.4025 (12) 0.025*
N2 0.95392 (16) 0.73860 (12) 0.49388 (8) 0.0208 (2)
N3 0.61208 (17) 0.74629 (13) 0.55304 (8) 0.0231 (2)
N4 1.11084 (16) 0.96983 (12) 0.16239 (8) 0.0190 (2)
N5 0.82334 (16) 0.89714 (12) 0.13125 (8) 0.0196 (2)

Source of material

All the reagents and solvents were used as obtained without further purification. Bis((1-methylbenzimidazol-2-yl)methyl)amine (MeIDB) was prepared according to a slightly modified method described by Adams et al. [7] in which only the raw material o-phenylenediamine was changed to be N,N′-dimethyl-1,2-phenylenediamine. Crystals of MeIDB were obtained three days later by slow evaporation in methanol (95%) at room temperature.

Experimental details

Hydrogen atoms bonded to carbon atoms were placed in their geometrically idealized positions and constrained to ride on their parent atoms with C–H = 0.95 Å (aromatic), 0.99 Å (methylene), 0.98 Å (methyl) U iso(H) = 1.2U eq (aromatic and methylene) and 1.5U eq (methyl). The H atom at N1 was found from the difference maps, which was refined freely and the U iso value set to 1.2 times of U eq(N1).

Comment

Multi-benzimidazole ligands have been often used in the synthesis of various metal-organic complexes or modelling the biomimetic coordination environment around the enzymatic active site [7]. For instance, by employing a tripodal bis(benzimidazole) ligand bis((1-methylbenzimidazol-2-yl)methyl)amine(MeIDB) and its derivative as the main ligand, a series of nickel and copper complexes were synthesized which allow a systematic investigation of a biomimetic chemistry [8, 9]. However, up to now the detailed crystallization properties of MeIDB has been not reported which can be helpful for the design of various multifunctional compounds due to its central acyclic –CH2–N–CH2– linkage moiety, making the ligand possess various steric arrangements. We have also synthesized some complexes involving tetrazole ligands, to get fluorescent materials [1011].

The titled compound was crystallized as one anhydrous form in the triclinic P 1 space group with only one MeIDB molecule in its asymmetric unit. The MeIDB molecule adopts a nearly V-shaped conformation which is reflected by the torsion angle of –C2–C1–N1–C10– (169.6(1)°), –C1–N1–C10–C11 (−67.3(1)°) and the dihedral angle between two benzimidazole groups (74.4(1)°) which is apparently distinct from most of its analogs [7]. The single bonds C2–N2 and C11–N4 are respectively about 0.05 Å longer than the neighboring C2–N3 and C11–N5 double bonds, indicating their potentially donating electron ability.

In the crystal packing, the MeIDB molecules are linked mainly by a: one N1–H1⃛N3 hydrogen bond (d N1⃛N3 = 3.164(1) Å), 146.4(1)°, symmetry code: 1−x, 2−y, 1−z); b: one π⃛π stacking between imidazole group (N4/N5/C11/C12/C17) and the symmetry related benzene rings (C12–C17, symmetry code: 2−x, 2−y, −z) with a centroid-to-centroid distance of 3.569(2) Å; c: one C–H⃛π interaction (C6–H6⃛Cg (Cg is the centroid of phenyl C12–C17, symmetry code: 2−x, 1−y, 1−z) connecting molecules into a two-dimensional network parallel to the [111] plane. There are no specific directional intermolecular interactions between these adjacent two dimensional layers PLATON [12]. Finally it should be mentioned that the title molecule has been used as a ligand [13].


Corresponding author: Meng Gaoxiang, School of Advanced Materials and Mechatronic Engineering, Hubei Minzu University , Enshi 445000, Hubei, P. R. China, E-mail:

Funding source: Hubei Minzu University Null

Award Identifier / Grant number: PY21016

Award Identifier / Grant number: PY21016

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

  2. Research funding: This work is supported by High Level Scientific Research Achievements In-school Cultivation Project of Hubei Minzu University (PY21016).

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

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Received: 2021-11-04
Accepted: 2021-12-14
Published Online: 2022-01-04
Published in Print: 2022-04-26

© 2021 Meng Gaoxiang 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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