Literature DB >> 22220079

1,1'-[(2,3,3a,4,5,6,7,7a-Octa-hydro-1H-1,3-benzimidazole-1,3-di-yl)bis-(methyl-ene)]bis-(1H-benzotriazole).

Augusto Rivera, Dency José Pacheco, Jaime Ríos-Motta, Michaela Pojarová, Michal Dušek.   

Abstract

The cyclo-hexane ring in the title compound, C(21)H(24)N(8), adopts a chair conformation and the five-membered heterocyclic ring to which it is fused adopts a twist conformation on their common C-C bond. The substituents on the N atoms of the central five-membered heterocycle are arranged trans with respect to the central ring. The terminal n class="Chemical">benzotriazole rings are oriented at angles of 74.66 (8) and 84.18 (8)° with respect to the mean plane of the central heterocycle. The angle between the two benzotriazole rings is 30.80 (9)°. The bond lengths and angles are within normal ranges; the largest deviation from expecta-tion is for a long N-CH(2) bond length [1.476 (2) Å] as a consequence of an anomeric effect. In the crystal, mol-ecules are connected by C-H⋯N hydrogen bonds.

Entities:  

Year:  2011        PMID: 22220079      PMCID: PMC3247461          DOI: 10.1107/S160053681104044X

Source DB:  PubMed          Journal:  Acta Crystallogr Sect E Struct Rep Online        ISSN: 1600-5368


Related literature

For general background to anomeric effects, see: Carey & Sundberg (2000 ▶). For related structures see: Rivera et al. (2011 ▶); Wang et al. (2008 ▶). For ring conformations, see: Cremer & Pople (1975 ▶). For standard bond lengths, see: Allen et al. (1987 ▶).

Experimental

Crystal data

C21H24N8 M = 388.48 Monoclinic, a = 11.9474 (2) Å b = 5.9406 (1) Å c = 27.3861 (4) Å β = 90.861 (1)° V = 1943.50 (5) Å3 Z = 4 Cu Kα radiation μ = 0.68 mm−1 T = 120 K 0.31 × 0.18 × 0.11 mm

Data collection

Oxford Diffraction Xcalibur Atlas Gemini ultra diffractometer 37999 measured reflections 3461 independent reflections 2990 reflections with I > 2σ(I) R int = 0.172

Refinement

R[F 2 > 2σ(F 2)] = 0.052 wR(F 2) = 0.137 S = 1.06 3461 reflections 262 parameters H-atom parameters constrained Δρmax = 0.23 e Å−3 Δρmin = −0.31 e Å−3 Data collection: CrysAlis PRO (Oxford Diffraction, 2010 ▶); cell refinement: CrysAlis PRO; data reduction: CrysAlis PRO; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ▶); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 ▶); molecular graphics: DIAMOND (Brandenburg & Putz, 2005 ▶); software used to prepare material for publication: publCIF (Westrip, 2010 ▶). Crystal structure: contains datablock(s) I, global. DOI: 10.1107/S160053681104044X/bh2381sup1.cif Structure factors: contains datablock(s) I. DOI: 10.1107/S160053681104044X/bh2381Isup2.hkl Supplementary material file. DOI: 10.1107/S160053681104044X/bh2381Isup3.cml Additional supplementary materials: crystallographic information; 3D view; checkCIF report
C21H24N8F(000) = 824
Mr = 388.48Dx = 1.328 Mg m3
Monoclinic, P21/cMelting point: 424 K
Hall symbol: -P 2ybcCu Kα radiation, λ = 1.5418 Å
a = 11.9474 (2) ÅCell parameters from 13493 reflections
b = 5.9406 (1) Åθ = 3.2°
c = 27.3861 (4) ŵ = 0.68 mm1
β = 90.861 (1)°T = 120 K
V = 1943.50 (5) Å3Plate, colourless
Z = 40.31 × 0.18 × 0.11 mm
Oxford Diffraction Xcalibur Atlas Gemini ultra diffractometer2990 reflections with I > 2σ(I)
Radiation source: Enhance Ultra (Cu) X-ray SourceRint = 0.172
mirrorθmax = 67.1°, θmin = 3.2°
Detector resolution: 10.3784 pixels mm-1h = −14→14
Rotation method data acquisition using ω scansk = −7→7
37999 measured reflectionsl = −32→32
3461 independent reflections
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.052Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.137H-atom parameters constrained
S = 1.06w = 1/[σ2(Fo2) + (0.0756P)2 + 0.4705P] where P = (Fo2 + 2Fc2)/3
3461 reflections(Δ/σ)max < 0.001
262 parametersΔρmax = 0.23 e Å3
0 restraintsΔρmin = −0.31 e Å3
0 constraints
xyzUiso*/Ueq
N10.06576 (12)1.3038 (2)0.03014 (5)0.0301 (4)
N20.06561 (12)1.1599 (2)0.06570 (5)0.0298 (3)
N30.12624 (11)0.9755 (2)0.05292 (5)0.0256 (3)
N40.21777 (12)0.7711 (2)0.12114 (5)0.0277 (3)
N50.34776 (11)0.9703 (2)0.16832 (5)0.0250 (3)
N60.31150 (11)0.9133 (2)0.25550 (5)0.0240 (3)
N70.34948 (11)0.7097 (3)0.27089 (5)0.0296 (4)
N80.27753 (12)0.6222 (3)0.30094 (5)0.0302 (3)
C10.12747 (13)1.2136 (3)−0.00732 (6)0.0249 (4)
C20.14940 (14)1.3000 (3)−0.05407 (6)0.0293 (4)
H20.12331.4406−0.06390.035*
C30.21134 (15)1.1660 (3)−0.08439 (7)0.0332 (4)
H30.22661.2157−0.11580.040*
C40.25227 (15)0.9548 (3)−0.06892 (7)0.0334 (4)
H40.29490.8705−0.09040.040*
C50.23166 (14)0.8690 (3)−0.02351 (7)0.0299 (4)
H50.25910.7296−0.01360.036*
C60.16690 (13)1.0034 (3)0.00695 (6)0.0239 (4)
C70.12758 (14)0.7809 (3)0.08616 (7)0.0288 (4)
H7A0.05770.77970.10380.035*
H7B0.12960.64500.06660.035*
C80.22853 (13)0.9669 (3)0.15340 (6)0.0270 (4)
H8A0.18100.95090.18160.032*
H8B0.20831.10410.13620.032*
C90.33087 (14)0.7201 (3)0.10497 (6)0.0265 (4)
H90.35410.83390.08130.032*
C100.35246 (16)0.4874 (3)0.08427 (7)0.0350 (4)
H10A0.31260.46910.05340.042*
H10B0.32650.37300.10670.042*
C110.47850 (16)0.4632 (3)0.07680 (8)0.0391 (5)
H11A0.50170.56700.05150.047*
H11B0.49450.31170.06570.047*
C120.54586 (16)0.5107 (3)0.12368 (8)0.0391 (5)
H12A0.62510.50200.11670.047*
H12B0.52920.39560.14760.047*
C130.51985 (14)0.7429 (3)0.14530 (7)0.0338 (4)
H13A0.55900.76210.17630.041*
H13B0.54370.86070.12330.041*
C140.39463 (14)0.7551 (3)0.15242 (6)0.0265 (4)
H140.37280.63770.17550.032*
C150.37030 (13)1.0415 (3)0.21750 (6)0.0270 (4)
H15A0.34981.19890.22040.032*
H15B0.45021.03020.22380.032*
C160.21029 (13)0.9579 (3)0.27606 (6)0.0235 (4)
C170.13513 (14)1.1384 (3)0.27189 (6)0.0284 (4)
H170.14971.26360.25260.034*
C180.03858 (15)1.1180 (3)0.29813 (7)0.0333 (4)
H18−0.01441.23240.29600.040*
C190.01666 (14)0.9313 (3)0.32806 (6)0.0313 (4)
H19−0.04970.92670.34540.038*
C200.09064 (14)0.7563 (3)0.33234 (6)0.0297 (4)
H200.07620.63330.35230.036*
C210.18967 (14)0.7708 (3)0.30514 (6)0.0255 (4)
U11U22U33U12U13U23
N10.0331 (8)0.0264 (8)0.0309 (8)0.0061 (6)−0.0009 (6)−0.0036 (6)
N20.0288 (7)0.0288 (8)0.0320 (8)0.0062 (6)0.0007 (6)−0.0046 (6)
N30.0240 (7)0.0252 (7)0.0275 (8)0.0008 (5)0.0001 (6)−0.0031 (6)
N40.0231 (7)0.0284 (8)0.0316 (8)−0.0020 (5)−0.0018 (6)0.0023 (6)
N50.0199 (7)0.0294 (8)0.0258 (8)−0.0033 (5)0.0033 (5)0.0013 (6)
N60.0203 (6)0.0282 (7)0.0233 (7)−0.0007 (5)0.0004 (5)0.0026 (5)
N70.0238 (7)0.0329 (8)0.0320 (8)0.0046 (6)0.0004 (6)0.0050 (6)
N80.0263 (7)0.0314 (8)0.0329 (8)0.0032 (6)0.0028 (6)0.0057 (6)
C10.0228 (8)0.0221 (8)0.0298 (9)−0.0012 (6)−0.0019 (6)−0.0047 (6)
C20.0281 (8)0.0257 (9)0.0338 (10)−0.0039 (7)−0.0051 (7)0.0021 (7)
C30.0281 (9)0.0409 (10)0.0308 (9)−0.0068 (7)0.0025 (7)0.0020 (8)
C40.0283 (9)0.0375 (10)0.0345 (10)0.0027 (7)0.0063 (7)−0.0074 (8)
C50.0267 (8)0.0271 (9)0.0361 (10)0.0033 (7)0.0018 (7)−0.0047 (7)
C60.0204 (7)0.0258 (8)0.0255 (9)−0.0025 (6)−0.0025 (6)−0.0034 (6)
C70.0256 (8)0.0261 (9)0.0345 (10)−0.0034 (6)−0.0024 (7)0.0021 (7)
C80.0218 (8)0.0345 (9)0.0247 (9)−0.0010 (7)0.0016 (6)0.0004 (7)
C90.0249 (8)0.0247 (9)0.0299 (9)−0.0019 (6)0.0020 (7)0.0035 (7)
C100.0373 (10)0.0263 (9)0.0412 (11)0.0003 (7)−0.0049 (8)−0.0014 (8)
C110.0403 (11)0.0298 (10)0.0473 (12)0.0066 (8)0.0055 (9)−0.0036 (8)
C120.0282 (9)0.0362 (11)0.0530 (13)0.0040 (8)0.0008 (8)0.0004 (9)
C130.0230 (9)0.0353 (10)0.0431 (11)−0.0004 (7)0.0007 (7)0.0002 (8)
C140.0236 (8)0.0259 (9)0.0299 (9)−0.0024 (6)0.0028 (7)0.0046 (7)
C150.0223 (8)0.0304 (9)0.0283 (9)−0.0073 (6)0.0021 (6)0.0022 (7)
C160.0204 (8)0.0276 (9)0.0225 (8)−0.0011 (6)−0.0003 (6)−0.0027 (6)
C170.0319 (9)0.0243 (9)0.0291 (9)0.0023 (7)0.0012 (7)−0.0005 (7)
C180.0324 (9)0.0346 (10)0.0330 (10)0.0088 (7)0.0013 (7)−0.0074 (7)
C190.0252 (8)0.0393 (10)0.0297 (10)−0.0011 (7)0.0067 (7)−0.0085 (7)
C200.0284 (9)0.0333 (10)0.0274 (9)−0.0055 (7)0.0037 (7)0.0010 (7)
C210.0247 (8)0.0268 (9)0.0250 (9)0.0005 (6)0.0006 (6)0.0004 (6)
N1—N21.296 (2)C8—H8B0.9700
N1—C11.380 (2)C9—C141.511 (2)
N2—N31.3619 (19)C9—C101.517 (2)
N3—C61.366 (2)C9—H90.9800
N3—C71.471 (2)C10—C111.529 (3)
N4—C71.432 (2)C10—H10A0.9700
N4—C91.460 (2)C10—H10B0.9700
N4—C81.465 (2)C11—C121.531 (3)
N5—C151.433 (2)C11—H11A0.9700
N5—C141.464 (2)C11—H11B0.9700
N5—C81.476 (2)C12—C131.535 (3)
N6—N71.357 (2)C12—H12A0.9700
N6—C161.367 (2)C12—H12B0.9700
N6—C151.476 (2)C13—C141.513 (2)
N7—N81.307 (2)C13—H13A0.9700
N8—C211.378 (2)C13—H13B0.9700
C1—C61.389 (2)C14—H140.9800
C1—C21.408 (2)C15—H15A0.9700
C2—C31.375 (3)C15—H15B0.9700
C2—H20.9300C16—C211.391 (2)
C3—C41.409 (3)C16—C171.402 (2)
C3—H30.9300C17—C181.374 (2)
C4—C51.370 (3)C17—H170.9300
C4—H40.9300C18—C191.406 (3)
C5—C61.397 (2)C18—H180.9300
C5—H50.9300C19—C201.369 (3)
C7—H7A0.9700C19—H190.9300
C7—H7B0.9700C20—C211.410 (2)
C8—H8A0.9700C20—H200.9300
N2—N1—C1108.00 (14)C9—C10—H10A110.1
N1—N2—N3109.32 (13)C11—C10—H10A110.1
N2—N3—C6109.70 (13)C9—C10—H10B110.1
N2—N3—C7118.30 (13)C11—C10—H10B110.1
C6—N3—C7131.64 (14)H10A—C10—H10B108.4
C7—N4—C9119.73 (14)C10—C11—C12112.13 (16)
C7—N4—C8115.44 (13)C10—C11—H11A109.2
C9—N4—C8105.94 (13)C12—C11—H11A109.2
C15—N5—C14118.03 (14)C10—C11—H11B109.2
C15—N5—C8115.53 (13)C12—C11—H11B109.2
C14—N5—C8106.11 (13)H11A—C11—H11B107.9
N7—N6—C16109.79 (13)C11—C12—C13112.45 (16)
N7—N6—C15121.24 (13)C11—C12—H12A109.1
C16—N6—C15128.57 (14)C13—C12—H12A109.1
N8—N7—N6109.28 (13)C11—C12—H12B109.1
N7—N8—C21107.87 (14)C13—C12—H12B109.1
N1—C1—C6108.83 (15)H12A—C12—H12B107.8
N1—C1—C2130.01 (16)C14—C13—C12107.41 (14)
C6—C1—C2121.12 (16)C14—C13—H13A110.2
C3—C2—C1116.57 (16)C12—C13—H13A110.2
C3—C2—H2121.7C14—C13—H13B110.2
C1—C2—H2121.7C12—C13—H13B110.2
C2—C3—C4121.44 (17)H13A—C13—H13B108.5
C2—C3—H3119.3N5—C14—C9100.73 (13)
C4—C3—H3119.3N5—C14—C13117.62 (14)
C5—C4—C3122.54 (17)C9—C14—C13111.67 (14)
C5—C4—H4118.7N5—C14—H14108.8
C3—C4—H4118.7C9—C14—H14108.8
C4—C5—C6115.99 (16)C13—C14—H14108.8
C4—C5—H5122.0N5—C15—N6115.18 (13)
C6—C5—H5122.0N5—C15—H15A108.5
N3—C6—C1104.14 (14)N6—C15—H15A108.5
N3—C6—C5133.54 (16)N5—C15—H15B108.5
C1—C6—C5122.31 (16)N6—C15—H15B108.5
N4—C7—N3116.54 (13)H15A—C15—H15B107.5
N4—C7—H7A108.2N6—C16—C21104.25 (14)
N3—C7—H7A108.2N6—C16—C17133.15 (15)
N4—C7—H7B108.2C21—C16—C17122.59 (15)
N3—C7—H7B108.2C18—C17—C16115.60 (16)
H7A—C7—H7B107.3C18—C17—H17122.2
N4—C8—N5104.68 (13)C16—C17—H17122.2
N4—C8—H8A110.8C17—C18—C19122.65 (16)
N5—C8—H8A110.8C17—C18—H18118.7
N4—C8—H8B110.8C19—C18—H18118.7
N5—C8—H8B110.8C20—C19—C18121.58 (16)
H8A—C8—H8B108.9C20—C19—H19119.2
N4—C9—C1499.64 (13)C18—C19—H19119.2
N4—C9—C10117.77 (14)C19—C20—C21117.01 (16)
C14—C9—C10111.14 (14)C19—C20—H20121.5
N4—C9—H9109.3C21—C20—H20121.5
C14—C9—H9109.3N8—C21—C16108.80 (14)
C10—C9—H9109.3N8—C21—C20130.64 (16)
C9—C10—C11107.98 (15)C16—C21—C20120.56 (15)
N3—C7—N4—C856.8 (4)C8—N5—C15—N655.5 (4)
D—H···AD—HH···AD···AD—H···A
C8—H8a···N60.972.552.970 (2)106
C8—H8b···N30.972.582.995 (2)106
C7—H7b···N1i0.972.383.301 (2)159
C15—H15b···N7ii0.972.623.504 (2)151
Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯AD—HH⋯ADAD—H⋯A
C7—H7b⋯N1i0.972.383.301 (2)159
C15—H15b⋯N7ii0.972.623.504 (2)151

Symmetry codes: (i) ; (ii) .

  3 in total

1.  A short history of SHELX.

Authors:  George M Sheldrick
Journal:  Acta Crystallogr A       Date:  2007-12-21       Impact factor: 2.290

2.  2-(Benzotriazol-1-ylmethyl-amino)-benzoic acid.

Authors:  Yao Wang; Mai-Hua Yin; Guo-Fang Zhang
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2008-03-20

3.  1,3-Bis[(1H-benzotriazol-1-yl)meth-yl]-2,3-dihydro-1H-benzimidazole.

Authors:  Augusto Rivera; Mauricio Maldonado; José Luis Casas; Michal Dušek; Karla Fejfarová
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2011-03-26
  3 in total
  1 in total

1.  1,1'-[Imidazolidine-1,3-diylbis(methyl-ene)]bis-(1H-benzotriazole).

Authors:  Augusto Rivera; Diego Quiroga; Jaime Ríos-Motta; Karla Fejfarová; Michal Dušek
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2012-01-11
  1 in total

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