4,4′-Dichloro-2,2′-[(3aR,7aR/3aS,7aS)-2,3,3a,4,5,6,7,7a-octa­hydro-1H-1,3-benzimidazole-1,3-di­yl)bis­(methyl­ene)]diphenol

Rivera, A.; Quiroga, D.; Ríos-Motta, J.; Dušek, M.; Fejfarová, K.

doi:10.1107/S160053681003792X

organic compounds

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Volume 66| Part 10| October 2010| Page o2643

doi:10.1107/S160053681003792X

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4,4′-Dichloro-2,2′-[(3aR,7aR/3aS,7aS)-2,3,3a,4,5,6,7,7a-octahydro-1H-1,3-benzimidazole-1,3-diyl)bis(methylene)]diphenol

Augusto Rivera,^a ^* Diego Quiroga,^a Jaime Ríos-Motta,^a Michal Dušek ^b and Karla Fejfarová ^b

^aDepartamento de Química, Universidad Nacional de Colombia, Bogotá, AA 14490, Colombia, and ^bInstitute of Physics, Na Slovance 2, 182 21 Praha 8, Czech Republic
^*Correspondence e-mail: ariverau@unal.edu.co

(Received 20 August 2010; accepted 22 September 2010; online 30 September 2010)

Molecules of the the title compound, C₂₁H₂₄Cl₂N₂O₂, are located on a twofold rotation axis, which passes through the C atom linking the two N atoms. Two intramolecular O—H⋯N hydrogen bonds were observed. In the crystal, non-classical intermolecular C—H⋯O hydrogen bonds link the molecules into chains along the a axis. The crystal studied was a racemic twin.

Related literature

For related structures, see: Rivera et al. (2009 , 2010 ). For uses of di-Mannich bases, see: Mitra et al. (2006 ); Elias et al. (1997 ). For the antimalarial activity of di-Mannich bases, see: Shanks & Edstein (2005 ).

Experimental

Crystal data

C₂₁H₂₄Cl₂N₂O₂
M_r = 407.3
Orthorhombic, P 2₁ 2₁ 2
a = 5.9529 (2) Å
b = 18.3846 (5) Å
c = 8.9704 (3) Å
V = 981.74 (5) Å³
Z = 2
Cu Kα radiation
μ = 3.11 mm⁻¹
T = 120 K
0.36 × 0.21 × 0.12 mm

Data collection

Oxford Diffraction Xcalibur diffractometer with an Atlas (Gemini ultra Cu) detector
Absorption correction: analytical [CrysAlis PRO (Oxford Diffraction, 2009 $[Oxford Diffraction (2009). CrysAlis PRO, CrysAlis CCD and CrysAlis RED. Oxford Diffraction Ltd, Yarnton, England.]$ ), based on expressions derived by Clark & Reid (1995 )] T_min = 0.518, T_max = 0.773
12720 measured reflections
1566 independent reflections
1517 reflections with I > 3σ(I)
R_int = 0.027

Refinement

R[F² > 2σ(F²)] = 0.022
wR(F²) = 0.068
S = 1.50
1566 reflections
127 parameters
H atoms treated by a mixture of independent and constrained refinement
Δρ_max = 0.11 e Å⁻³
Δρ_min = −0.11 e Å⁻³
Absolute structure: Flack (1983 ), 615 Friedel pairs
Flack parameter: 0.32 (1)

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
C1—H1a⋯O1ⁱ	0.95	2.56	3.3398 (11)	137.58
O1—H1o⋯N1	0.91 (2)	1.83 (2)	2.6515 (13)	149.3 (18)
Symmetry code: (i) x-1, y, z.

Data collection: CrysAlis CCD (Oxford Diffraction, 2009 $[Oxford Diffraction (2009). CrysAlis PRO, CrysAlis CCD and CrysAlis RED. Oxford Diffraction Ltd, Yarnton, England.]$ ); cell refinement: CrysAlis RED (Oxford Diffraction, 2009 $[Oxford Diffraction (2009). CrysAlis PRO, CrysAlis CCD and CrysAlis RED. Oxford Diffraction Ltd, Yarnton, England.]$ ); data reduction: CrysAlis RED; program(s) used to solve structure: SIR2002 (Burla et al., 2003 ); program(s) used to refine structure: JANA2006 (Petříček et al., 2006 ); molecular graphics: DIAMOND (Brandenburg & Putz, 2005 ); software used to prepare material for publication: JANA2006.

Supporting information

Crystal structure: contains datablocks global, I. DOI: 10.1107/S160053681003792X/bt5333sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S160053681003792X/bt5333Isup2.hkl

checkCIF report

Comment top

It is interesting to notice that two types of non-classical intermolecular hydrogen bonds of C—H···O and C—H···Cl were found according to crystallographic data. The molecular structure and atom-numbering scheme for (I) are shown in Fig. 1. Its X-ray structure confirms the presence of intramolecular hydrogen bonds between the phenolic hydroxyl groups and nitrogen atoms [N—H, 1.83 (2) Å), whereas the N···O distances [2.652 (2) Å,] is significantly shorter than the corresponding N···O bond in related structures [2.70 (1) Å]. Furthermore the observed C—O bond length [1.354 (2) Å] is considerably shortened in relation to related structures [1.364 (2) Å] (Rivera et al., 2010) and [1.365 (2) Å] (Rivera et al., 2009). This additional H-bonding does not influence the H—O distance, which shows (as a result of unrestrained refinement) a typical separation of 0.91 (2) Å. Thus, these results indicate an increase in hydrogen-bonding strength due to the presence of chlorine atom. In fact, the presence of the chlorine atom favours the formation of weak intermolecular C—H···O interactions between neighboring molecules, which link them into 1-D extended chains along the a axis and help to stabilize the chain.

The chains are linked along the c direction by C—H···Cl interactions [2.902 (2) Å]. This interaction involves contacts between an apparently electron deficient aromatic C6—H6 and the chlorine atom from a second molecule. The phenyl group in both molecules lies in an orientation which favours hydrogen bond formation.

In the title compound, C₂₁H₂₄Cl₂N₂O₂,the asymmetric unit contains one-half of the molecule, which is related to the other half by a twofold rotation axis [symmetry code: - x, y, -z] passing through C1 (Figure 1). Unlike the related structures Rivera et al. (2010, 2009), the title compound crystallizes in a different crystal system and it has a chiral space group. The compound is a racemic twin and the absolute structure was determined on the basis of that of the starting amine whose stereochemistry is: trans-(rac)-1,2-cyclohexanediamine and the chiral centers were not affected when reacted.

Related literature top

For related structures, see: Rivera et al. (2009, 2010). For uses of di-Mannich bases, see: Mitra et al. (2006); Elias et al. (1997). For the antimalarial activity of di-Mannich bases, see: Shanks & Edstein (2005).

Experimental top

Preparation of title compound (I)

A solution of (2R,7R,11S,16S)-1,8,10,17-tetraazapentacyclo[8.8.1.18,17.0^2,7.0^11,16] icosane (276 mg, 1.00 mmol) in dioxane (3 ml) and water (4 ml), prepared beforehand following previously described procedures, was added dropwise in a dioxane solution (3 ml) containing two equivalents of p-chlorophenol (257 mg, 2.00 mmol) in a two-necked round-bottomed flask. The mixture was refluxed for about 6 h until precipitation of a colourless solid. The resulting solid was collected by filtration, washed with cool methanol and dried under vacuum (yield 30%, m.p. = 490–492 K). Next, the racemic product (100 mg, 0.246 mmol) was dissolved in 5 ml of a 4:1 mixture of chloroform: methanol. Single crystals of title compound (I) suitable for X-ray analysis were grown by slow evaporation of the solvent at room temperature over a period of about 2 weeks in a preferential crystallization (yield 46%). 1H NMR (CDCl₃, 400 MHz): δ 1.29 (4H, m), 1.85 (2H, m), 2.04 (2H, m), 2.34 (2H, m), 3.42 (2H, d, J = 14.0 Hz, ArCH₂N), 3.51 (2H, s, NCH₂N), 4.14 (2H, d, J = 14.0 Hz, ArCH₂N), 6.74 (2H, d, J = 8.8 Hz), 6.92 (2H, s), 7.10 (2H, d, J = 8.8 Hz).

Computing details top

Data collection: CrysAlis CCD (Oxford Diffraction, 2009); cell refinement: CrysAlis RED (Oxford Diffraction, 2009); data reduction: CrysAlis RED (Oxford Diffraction, 2009); program(s) used to solve structure: SIR2002 (Burla et al., 2003); program(s) used to refine structure: JANA2006 (Petříček et al., 2006); molecular graphics: DIAMOND (Brandenburg & Putz, 2005); software used to prepare material for publication: JANA2006 (Petříček et al., 2006).

Figures top

	Fig. 1. Molecule of the title compound with atom-labeling scheme. Displacement elipsoids are drawn at 50% probability level.
	Fig. 2. Hydrogen bonding of the molecules of the title compound in a direction.

4,4'-Dichloro-2,2'-[(3aR,7aR/3aS,7aS)- 2,3,3a,4,5,6,7,7a-octahydro-1H-1,3-benzimidazole-1,3- diyl)bis(methylene)]diphenol top

Crystal data top

C₂₁H₂₄Cl₂N₂O₂	F(000) = 428
M_r = 407.3	D_x = 1.378 Mg m⁻³
Orthorhombic, P2₁2₁2	Cu Kα radiation, λ = 1.54184 Å
Hall symbol: P 2 2ab	Cell parameters from 10371 reflections
a = 5.9529 (2) Å	θ = 4.8–62.4°
b = 18.3846 (5) Å	µ = 3.11 mm⁻¹
c = 8.9704 (3) Å	T = 120 K
V = 981.74 (5) Å³	Irregular shape, colorless
Z = 2	0.36 × 0.21 × 0.12 mm

Data collection top

Oxford Diffraction Xcalibur diffractometer with an Atlas (Gemini ultra Cu) detector	1566 independent reflections
Radiation source: X-ray tube	1517 reflections with I > 3σ(I)
Mirror monochromator	R_int = 0.027
Detector resolution: 10.3784 pixels mm^-1	θ_max = 62.5°, θ_min = 4.8°
Rotation method data acquisition using ω scans	h = −6→6
Absorption correction: analytical [CrysAlis PRO (Oxford Diffraction, 2009), based on expressions derived by Clark & Reid (1995)]	k = −21→20
T_min = 0.518, T_max = 0.773	l = −10→10
12720 measured reflections

Refinement top

Refinement on F²	H atoms treated by a mixture of independent and constrained refinement
R[F² > 2σ(F²)] = 0.022	Weighting scheme based on measured s.u.'s w = 1/[σ²(I) + 0.0016I²]
wR(F²) = 0.068	(Δ/σ)_max = 0.010
S = 1.50	Δρ_max = 0.11 e Å⁻³
1566 reflections	Δρ_min = −0.11 e Å⁻³
127 parameters	Absolute structure: Flack (1983), 615 Friedel pairs
0 restraints	Absolute structure parameter: 0.32 (1)
45 constraints

Crystal data top

C₂₁H₂₄Cl₂N₂O₂	V = 981.74 (5) Å³
M_r = 407.3	Z = 2
Orthorhombic, P2₁2₁2	Cu Kα radiation
a = 5.9529 (2) Å	µ = 3.11 mm⁻¹
b = 18.3846 (5) Å	T = 120 K
c = 8.9704 (3) Å	0.36 × 0.21 × 0.12 mm

Data collection top

Oxford Diffraction Xcalibur diffractometer with an Atlas (Gemini ultra Cu) detector	1566 independent reflections
Absorption correction: analytical [CrysAlis PRO (Oxford Diffraction, 2009), based on expressions derived by Clark & Reid (1995)]	1517 reflections with I > 3σ(I)
T_min = 0.518, T_max = 0.773	R_int = 0.027
12720 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.022	H atoms treated by a mixture of independent and constrained refinement
wR(F²) = 0.068	Δρ_max = 0.11 e Å⁻³
S = 1.50	Δρ_min = −0.11 e Å⁻³
1566 reflections	Absolute structure: Flack (1983), 615 Friedel pairs
127 parameters	Absolute structure parameter: 0.32 (1)
0 restraints

Special details top

Experimental. CrysAlisPro, Oxford Diffraction Ltd., Version 1.171.33.51 (release 27-10-2009 CrysAlis171 .NET) Analytical numeric absorption correction using a multifaceted crystal model based on expressions derived by Clark & Reid (1995)

Physical Measurements

The melting point was determined with an Electrothermal apparatus, and it has not been corrected. IR spectrum was recorded as KBr pellets at 292 K on a Perkin-Elmer Paragon FT-IR instrument. NMR spectra were performed in CDCl₃ at room temperature on a Bruker AMX 400 Advance spectrometer.

Refinement. The refinement was carried out against all reflections. The conventional R-factor is always based on F. The goodness of fit as well as the weighted R-factor are based on F and F² for refinement carried out on F and F², respectively. The threshold expression is used only for calculating R-factors etc. and it is not relevant to the choice of reflections for refinement.

The program used for refinement, Jana2006, uses the weighting scheme based on the experimental expectations, see _refine_ls_weighting_details, that does not force S to be one. Therefore the values of S are usually larger than the ones from the SHELX program.

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

	x	y	z	U_iso*/U_eq
Cl1	0.56453 (8)	0.22892 (2)	0.85004 (4)	0.03657 (14)
O1	0.99889 (19)	0.41865 (6)	0.41066 (13)	0.0278 (3)
N1	0.59603 (9)	0.44360 (5)	0.29542 (10)	0.0191 (4)
C1	0.5	0.5	0.39535 (12)	0.0190 (6)
C2	0.5511 (3)	0.36844 (7)	0.34499 (16)	0.0207 (4)
C3	0.6738 (3)	0.34996 (7)	0.48640 (16)	0.0188 (4)
C4	0.8923 (2)	0.37633 (8)	0.51184 (18)	0.0208 (4)
C5	1.0043 (3)	0.35815 (8)	0.64297 (17)	0.0260 (5)
C6	0.9061 (3)	0.31220 (8)	0.74665 (18)	0.0266 (5)
C7	0.6930 (3)	0.28560 (8)	0.71952 (17)	0.0244 (5)
C8	0.5774 (3)	0.30421 (7)	0.59086 (16)	0.0204 (4)
C9	0.5027 (2)	0.45884 (7)	0.14700 (16)	0.0214 (4)
C10	0.6300 (3)	0.43023 (9)	0.01323 (18)	0.0313 (5)
C11	0.5134 (3)	0.45859 (9)	−0.12729 (18)	0.0387 (6)
H1a	0.382262	0.478981	0.454451	0.0228*
H2a	0.392563	0.362122	0.359869	0.0249*
H2b	0.594229	0.335034	0.267886	0.0249*
H5	1.151137	0.37767	0.661739	0.0312*
H6	0.984963	0.299065	0.836016	0.0319*
H8	0.429374	0.285198	0.574125	0.0245*
H9	0.361614	0.434259	0.134648	0.0257*
H10a	0.626351	0.378021	0.013612	0.0375*
H10b	0.781744	0.447839	0.016012	0.0375*
H11a	0.368381	0.436182	−0.136609	0.0464*
H11b	0.597131	0.443924	−0.213654	0.0464*
H1o	0.893 (3)	0.4356 (10)	0.347 (2)	0.0334*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
Cl1	0.0514 (3)	0.0328 (2)	0.0254 (2)	−0.00039 (19)	0.00732 (18)	0.00639 (15)
O1	0.0191 (5)	0.0233 (5)	0.0410 (6)	−0.0026 (4)	0.0007 (5)	0.0049 (5)
N1	0.0231 (6)	0.0132 (6)	0.0208 (6)	0.0018 (5)	0.0003 (5)	0.0012 (5)
C1	0.0188 (10)	0.0153 (9)	0.0231 (10)	−0.0004 (8)	0	0
C2	0.0217 (7)	0.0140 (6)	0.0264 (8)	−0.0016 (6)	−0.0020 (7)	−0.0004 (6)
C3	0.0200 (7)	0.0116 (6)	0.0249 (8)	0.0028 (6)	−0.0009 (6)	−0.0019 (6)
C4	0.0173 (7)	0.0150 (6)	0.0300 (9)	0.0027 (5)	0.0017 (6)	−0.0035 (6)
C5	0.0200 (8)	0.0239 (7)	0.0341 (9)	0.0039 (6)	−0.0053 (7)	−0.0055 (7)
C6	0.0314 (9)	0.0230 (7)	0.0253 (8)	0.0095 (7)	−0.0050 (7)	−0.0058 (6)
C7	0.0339 (9)	0.0179 (7)	0.0213 (8)	0.0045 (7)	0.0050 (7)	−0.0005 (6)
C8	0.0204 (7)	0.0142 (6)	0.0267 (7)	0.0010 (6)	0.0021 (6)	−0.0023 (6)
C9	0.0246 (8)	0.0177 (8)	0.0218 (7)	0.0029 (5)	−0.0014 (6)	−0.0014 (6)
C10	0.0446 (10)	0.0239 (8)	0.0253 (9)	0.0088 (7)	0.0027 (8)	−0.0020 (7)
C11	0.0611 (13)	0.0322 (10)	0.0229 (8)	0.0134 (8)	−0.0012 (9)	−0.0039 (7)

Geometric parameters (Å, º) top

Cl1—C7	1.7441 (16)	C5—H5	0.96
O1—C4	1.3535 (19)	C6—C7	1.381 (2)
O1—H1o	0.91 (2)	C6—H6	0.96
N1—C1	1.4850 (11)	C7—C8	1.386 (2)
N1—C2	1.4761 (16)	C8—H8	0.96
N1—C9	1.4697 (17)	C9—C9ⁱ	1.5138 (19)
C1—H1a	0.96	C9—C10	1.514 (2)
C1—H1aⁱ	0.96	C9—H9	0.96
C2—C3	1.503 (2)	C10—C11	1.531 (2)
C2—H2a	0.96	C10—H10a	0.96
C2—H2b	0.96	C10—H10b	0.96
C3—C4	1.406 (2)	C11—C11ⁱ	1.531 (2)
C3—C8	1.384 (2)	C11—H11a	0.96
C4—C5	1.393 (2)	C11—H11b	0.96
C5—C6	1.386 (2)

C4—O1—H1o	106.9 (12)	C5—C6—H6	120.4925
C1—N1—C2	113.70 (8)	C7—C6—H6	120.4933
C1—N1—C9	105.56 (8)	Cl1—C7—C6	119.74 (12)
C2—N1—C9	112.50 (9)	Cl1—C7—C8	119.24 (12)
N1—C1—N1ⁱ	105.74 (8)	C6—C7—C8	121.01 (14)
N1—C1—H1a	109.4709	C3—C8—C7	120.52 (14)
N1—C1—H1aⁱ	109.4712	C3—C8—H8	119.7416
N1ⁱ—C1—H1a	109.4713	C7—C8—H8	119.7416
N1ⁱ—C1—H1aⁱ	109.4709	N1—C9—C9ⁱ	101.45 (10)
H1a—C1—H1aⁱ	112.9619	N1—C9—C10	117.56 (12)
N1—C2—C3	112.19 (11)	N1—C9—H9	110.2149
N1—C2—H2a	109.4717	C9ⁱ—C9—C10	110.98 (12)
N1—C2—H2b	109.4705	C9ⁱ—C9—H9	116.8873
C3—C2—H2a	109.4714	C10—C9—H9	100.538
C3—C2—H2b	109.4717	C9—C10—C11	107.90 (14)
H2a—C2—H2b	106.6084	C9—C10—H10a	109.4715
C2—C3—C4	120.58 (13)	C9—C10—H10b	109.4705
C2—C3—C8	120.48 (13)	C11—C10—H10a	109.4721
C4—C3—C8	118.88 (14)	C11—C10—H10b	109.4708
O1—C4—C3	121.52 (14)	H10a—C10—H10b	110.9991
O1—C4—C5	118.68 (13)	C10—C11—C11ⁱ	112.71 (13)
C3—C4—C5	119.80 (14)	C10—C11—H11a	109.4707
C4—C5—C6	120.75 (14)	C10—C11—H11b	109.4709
C4—C5—H5	119.6278	C11ⁱ—C11—H11a	109.472
C6—C5—H5	119.6266	C11ⁱ—C11—H11b	109.4712
C5—C6—C7	119.01 (15)	H11a—C11—H11b	106.0299

Symmetry code: (i) −x+1, −y+1, z.

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
C1—H1a···O1ⁱⁱ	0.95	2.56	3.3398 (11)	137.58
O1—H1o···N1	0.91 (2)	1.83 (2)	2.6515 (13)	149.3 (18)

Symmetry code: (ii) x−1, y, z.

Experimental details

Crystal data
Chemical formula	C₂₁H₂₄Cl₂N₂O₂
M_r	407.3
Crystal system, space group	Orthorhombic, P2₁2₁2
Temperature (K)	120
a, b, c (Å)	5.9529 (2), 18.3846 (5), 8.9704 (3)
V (Å³)	981.74 (5)
Z	2
Radiation type	Cu Kα
µ (mm⁻¹)	3.11
Crystal size (mm)	0.36 × 0.21 × 0.12

Data collection
Diffractometer	Oxford Diffraction Xcalibur diffractometer with an Atlas (Gemini ultra Cu) detector
Absorption correction	Analytical [CrysAlis PRO (Oxford Diffraction, 2009), based on expressions derived by Clark & Reid (1995)]
T_min, T_max	0.518, 0.773
No. of measured, independent and observed [I > 3σ(I)] reflections	12720, 1566, 1517
R_int	0.027
(sin θ/λ)_max (Å⁻¹)	0.575

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.022, 0.068, 1.50
No. of reflections	1566
No. of parameters	127
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
Δρ_max, Δρ_min (e Å⁻³)	0.11, −0.11
Absolute structure	Flack (1983), 615 Friedel pairs
Absolute structure parameter	0.32 (1)

Computer programs: CrysAlis CCD (Oxford Diffraction, 2009), CrysAlis RED (Oxford Diffraction, 2009), SIR2002 (Burla et al., 2003), JANA2006 (Petříček et al., 2006), DIAMOND (Brandenburg & Putz, 2005).

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
C1—H1a···O1ⁱ	0.95	2.56	3.3398 (11)	137.58
O1—H1o···N1	0.91 (2)	1.83 (2)	2.6515 (13)	149.3 (18)

Symmetry code: (i) x−1, y, z.

Acknowledgements

We acknowledge the Dirección de Investigaciones Sede Bogotá (DIB) of the Universidad Nacional de Colombia for financial support of this work, the Institutional research plan No. AVOZ10100521 of the Institute of Physics and the project Praemium Academiae of the Academy of Sciences (ASCR).

References

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ISSN: 2056-9890

Volume 66| Part 10| October 2010| Page o2643

doi:10.1107/S160053681003792X

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organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

4,4′-Di­chloro-2,2′-[(3aR,7aR/3aS,7aS)-2,3,3a,4,5,6,7,7a-octa­hydro-1H-1,3-benzimidazole-1,3-di­yl)bis­­(methyl­ene)]diphenol

Related literature

Experimental

Crystal data

Data collection

Refinement

Supporting information

Acknowledgements

References

organic compounds

4,4′-Dichloro-2,2′-[(3aR,7aR/3aS,7aS)-2,3,3a,4,5,6,7,7a-octahydro-1H-1,3-benzimidazole-1,3-diyl)bis(methylene)]diphenol