A monoclinic polymorph of 4,4′-dichloro-2,2′-(piperazine-1,4-diyl­dimethyl­ene)diphenol

Kubono, K.; Tsuno, Y.; Tani, K.; Yokoi, K.

doi:10.1107/S1600536808038750

organic compounds

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Volume 64| Part 12| December 2008| Page o2446

doi:10.1107/S1600536808038750

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A monoclinic polymorph of 4,4′-dichloro-2,2′-(piperazine-1,4-diyldimethylene)diphenol

Koji Kubono,^a ^* Yuki Tsuno,^a Keita Tani ^a and Kunihiko Yokoi ^a

^aDivision of Natural Sciences, Osaka Kyoiku University, Kashiwara, Osaka 582-8582, Japan
^*Correspondence e-mail: kubono@cc.osaka-kyoiku.ac.jp

(Received 7 November 2008; accepted 19 November 2008; online 26 November 2008)

The titile compound, C₁₈H₂₀Cl₂N₂O₂, crystallizes as a monoclinic form in the space group P2₁/n, with Z′ = 1/2. It is polymorphic with the previously reported orthorhombic form [Kubono, Tsuno, Tani & Yokoi (2008). Acta Cryst. E64, o2309]. In the present polymorph, the molecule lies on a crystallographic inversion centre at the piperazine ring centroid. An intramolecular O—H⋯N hydrogen bond forms an S(6) ring motif. Intermolecular C—H⋯O hydrogen bonding generates a C(5) chain motif propagating along the b axis, forming sheets parallel to ( $[\overline{2}]$ 02) with a first-level graph set S(6)C(5)R₆⁶(34).

Related literature

For the Pbca polymorph, see: Kubono et al. (2008 ). For graph-set notation in hydrogen bonds, see: Bernstein et al. (1995 ). For the synthesis of a ligand with two piperazine arms, see: Bharathi et al. (2006 ). For the monoclinic and orthorhombic polymorphs of a tetrachloro-2,2′-(piperazine-1,4-diyldimethylene)diphenol, see: Kubono & Yokoi (2007 ). For the structure of 1,4-bis(2-hydroxy-5-methylbenzyl)piperazine, see: Kuppayee et al. (1999 ).

Experimental

Crystal data

C₁₈H₂₀Cl₂N₂O₂
M_r = 367.26
Monoclinic, P 2₁ /n
a = 15.755 (4) Å
b = 9.2667 (17) Å
c = 5.9771 (19) Å
β = 96.45 (2)°
V = 867.1 (4) Å³
Z = 2
Mo Kα radiation
μ = 0.39 mm⁻¹
T = 298.1 K
0.35 × 0.15 × 0.15 mm

Data collection

Rigaku AFC-7R diffractometer
Absorption correction: none
2462 measured reflections
1994 independent reflections
1316 reflections with F² > 2σ(F²)
R_int = 0.020
3 standard reflections every 150 reflections intensity decay: 0.3%

Refinement

R[F² > 2σ(F²)] = 0.041
wR(F²) = 0.149
S = 1.01
1994 reflections
119 parameters
All H-atom parameters refined
Δρ_max = 0.54 e Å⁻³
Δρ_min = −0.52 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
O1—H1⋯N1	0.83	1.85	2.604 (2)	150
C3—H3⋯O1ⁱ	0.95	2.60	3.547 (2)	175
Symmetry code: (i) $[-x+{\script{3\over 2}}, y+{\script{1\over 2}}, -z+{\script{5\over 2}}]$ .

Data collection: WinAFC (Rigaku/MSC, 2006 ); cell refinement: WinAFC; data reduction: CrystalStructure (Rigaku/MSC, 2006); program(s) used to solve structure: SIR92 (Altomare et al., 1993 ); program(s) used to refine structure: CRYSTALS (Betteridge et al., 2003 ); molecular graphics: PLATON (Spek, 2003 ); software used to prepare material for publication: CrystalStructure.

Supporting information

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536808038750/si2131sup1.cif

Structure factors: contains datablock II. DOI: 10.1107/S1600536808038750/si2131IIsup2.hkl

checkCIF report

Comment top

We have recently reported the crystal structure of 4,4'-dichloro-2,2'-(piperazine-1,4-diyldimethylene)diphenol, (I) (Kubono et al., 2008), which crystallizes as an orthorhombic form in space group Pbca with Z' = 1. (I) can act as complexing reagents (Bharathi et al., 2006), so trying to synthesize the zinc complex with this ligand. The crystalline metal complexes were not given, however, a small amount of a new polymorph of the title compound, (II), was obtained from the reaction solution. We report here the molecular and crystal structure of (II).

The molecule of (II) crystallizes in the centrosymmetric space group P2₁/n with Z' = 1/2 in the asymmetric unit. The molecular structure of (II) is shown in Fig. 1. The molecule lies on a crystallographic inversion centre at the piperazine ring centroid. It is interesting to note that in the orthorhombic form (I) (Kubono et al., 2008) the molecule has a pseudo-inversion centre. The piperazine ring adopts a chair conformation. The bond lengths and angles in (II) are normal and comparable with those in the orthorhombic form (I) (Kubono et al., 2008), in the monoclinic and orthorhombic polymorph of dichlorophenol derivative (Kubono & Yokoi, 2007) and in the p-cresol one (Kuppayee et al., 1999). The molecular structures of (I) and (II) are closely similar, so the only slight differences were observed. The maximum differences of bond distance and angle between the two polymorphs are less than 0.02 Å [C1—C2: (I) 1.377 (4) Å, (II) 1.395 (2) Å] and less than 2 ° [C7—N1—C8: (I) 110.6 (2) °, (II) 112.58 (15) °], respectively. The most obvious differences are the torsion angles C5—C6—C7—N1 [(I) 149.3 (2) °, (II) 157.10 (17) °]. The intramolecular O1—H1···N1 hydrogen bond distance is 2.604 (2) Å (Table 1), forming a S(6) ring motif (Bernstein et al., 1995).

In the crystal structure of (II), there is intermolecular C—H···O hydrogen bond, involving a aromatic H atom (Table 1). Atom C3 in the molecule at (x, y, z) acts as hydrogen bond donor to atom O1 in the molecule at (3/2 - x,1/2 + y,5/2 - z), so forming a C(5) chain running parallel to the [010] direction and generated by the n-glide plane at y = 1/4. The molecules are linked by the combination of the S(6) ring and the C(5) chain into a sheet parallel to (202) with a first level graph set S(6)C(5)R₆⁶(34) (Fig. 2). In the crystal structure of (I), intermolecular C—H···O hydrogen bonds involving methylene H atoms generate C(5) chain motifs to form a sheet with a first level graph set S(6)C(5)R₆⁶(26) (Kubono et al., 2008). Each polymorph is characterized by the hydrogen bonding network structure.

Related literature top

For the Pbca polymorph, see: Kubono et al. (2008). For graph-set notation in hydrogen bonds, see: Bernstein et al. (1995). For the synthesis of a ligand with two piperazine arms, see: Bharathi et al. (2006). For the monoclinic and orthorhombic polymorphs of a tetrachloro-2,2'-(piperazine-1,4-diyldimethylene)diphenol, see: Kubono & Yokoi (2007). For the structure of 1,4-bis(2-hydroxy-5-methylbenzyl)piperazine, see: Kuppayee et al. (1999).

Experimental top

The title compound was prepared by the reaction of 4-chlorophenol, piperazine and paraformaldehyde as described previously (Kubono et al. 2008). The orthorhombic form, (I) (36.7 mg, 0.10 mmol) was dissolved in 25 ml hot chloroform. Then 15 ml of a methanol solution of zinc acetate dihydrate (22.0 mg, 0.10 mmol) were added to this solution. The mixture was stirred for 20 min at 340 K. After a few days at room temperature, trace amount of column crystals of (II) were picked out manually in the reaction solution. Melting point: 512–514 K. ESI-Ms: m/z, 367 for [M]⁺.

Computing details top

Data collection: WinAFC (Rigaku/MSC, 2006); cell refinement: WinAFC (Rigaku/MSC, 2006); data reduction: CrystalStructure (Rigaku/MSC, 2006); program(s) used to solve structure: SIR92 (Altomare et al., 1993); program(s) used to refine structure: CRYSTALS (Betteridge et al., 2003); molecular graphics: PLATON (Spek, 2003); software used to prepare material for publication: CrystalStructure (Rigaku/MSC, 2006).

Figures top

	Fig. 1. The molecular structure of (II) with the atom-labelling scheme and displacement ellipsoids are drawn at the 50% probability level. H atoms are represented by circles of arbitrary size. [Symmetry code: (i) 1 - x, -y, 2 - z.]
	Fig. 2. The molecular packing of (II), showing the formation of a sheet with a first level graph set S(6)C(5)R₆⁶(34). The hydrogen bonds are shown as dashed lines. The H atoms not involved in the hydrogen bonds have been omitted for clarity.

4,4'-dichloro-2,2'-(piperazine-1,4-diyldimethylene)diphenol top

Crystal data top

C₁₈H₂₀Cl₂N₂O₂	F(000) = 384.00
M_r = 367.26	D_x = 1.407 Mg m⁻³
Monoclinic, P2₁/n	Mo Kα radiation, λ = 0.71069 Å
Hall symbol: -P 2yn	Cell parameters from 25 reflections
a = 15.755 (4) Å	θ = 15.2–17.3°
b = 9.2667 (17) Å	µ = 0.39 mm⁻¹
c = 5.9771 (19) Å	T = 298 K
β = 96.45 (2)°	Column, colorless
V = 867.1 (4) Å³	0.35 × 0.15 × 0.15 mm
Z = 2

Data collection top

Rigaku AFC-7R diffractometer	θ_max = 27.5°
ω–2θ scans	h = −20→20
2462 measured reflections	k = 0→12
1994 independent reflections	l = −7→4
1316 reflections with F² > 2σ(F²)	3 standard reflections every 150 reflections
R_int = 0.020	intensity decay: 0.4%

Refinement top

Refinement on F²	All H-atom parameters refined
R[F² > 2σ(F²)] = 0.041	w = 1/[0.002F_o² + σ(F_o²)]/(4F_o²)
wR(F²) = 0.149	(Δ/σ)_max < 0.001
S = 1.01	Δρ_max = 0.54 e Å⁻³
1994 reflections	Δρ_min = −0.52 e Å⁻³
119 parameters

Crystal data top

C₁₈H₂₀Cl₂N₂O₂	V = 867.1 (4) Å³
M_r = 367.26	Z = 2
Monoclinic, P2₁/n	Mo Kα radiation
a = 15.755 (4) Å	µ = 0.39 mm⁻¹
b = 9.2667 (17) Å	T = 298 K
c = 5.9771 (19) Å	0.35 × 0.15 × 0.15 mm
β = 96.45 (2)°

Data collection top

Rigaku AFC-7R diffractometer	R_int = 0.020
2462 measured reflections	3 standard reflections every 150 reflections
1994 independent reflections	intensity decay: 0.4%
1316 reflections with F² > 2σ(F²)

Refinement top

R[F² > 2σ(F²)] = 0.041	119 parameters
wR(F²) = 0.149	All H-atom parameters refined
S = 1.01	Δρ_max = 0.54 e Å⁻³
1994 reflections	Δρ_min = −0.52 e Å⁻³

Special details top

Refinement. Refinement was performed using all reflections. The weighted R-factor (wR) and goodness of fit (S) are based on F². R-factor (gt) are based on F. The threshold expression of F² > 2.0 σ(F²) is used only for calculating R-factor (gt).

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

	x	y	z	U_iso*/U_eq
Cl1	0.70334 (4)	0.71539 (6)	0.65673 (12)	0.0627 (2)
O1	0.59890 (10)	0.28682 (15)	1.2938 (2)	0.0497 (4)
N1	0.50843 (9)	0.15177 (16)	0.9674 (2)	0.0354 (3)
C1	0.62416 (12)	0.3779 (2)	1.1357 (3)	0.0378 (4)
C2	0.69309 (12)	0.4691 (2)	1.1990 (3)	0.0461 (5)
C3	0.71835 (13)	0.5701 (2)	1.0514 (4)	0.0473 (5)
C4	0.67524 (12)	0.5798 (2)	0.8384 (3)	0.0436 (5)
C5	0.60947 (12)	0.4866 (2)	0.7692 (3)	0.0385 (5)
C6	0.58325 (11)	0.38356 (19)	0.9157 (3)	0.0337 (4)
C7	0.50735 (12)	0.28755 (19)	0.8387 (3)	0.0390 (5)
C8	0.57289 (12)	0.0497 (2)	0.9043 (4)	0.0417 (5)
C9	0.57559 (11)	−0.0814 (2)	1.0552 (4)	0.0422 (5)
H1	0.5656	0.2261	1.2298	0.059*
H2	0.7224	0.4609	1.3462	0.054*
H3	0.7650	0.6328	1.0950	0.056*
H4	0.5819	0.4926	0.6198	0.047*
H5	0.5090	0.2653	0.6841	0.046*
H6	0.4562	0.3383	0.8565	0.046*
H7	0.5580	0.0195	0.7531	0.051*
H8	0.6272	0.0954	0.9174	0.051*
H9	0.6173	−0.1479	1.0157	0.051*
H10	0.5898	−0.0510	1.2065	0.051*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
Cl1	0.0679 (4)	0.0428 (3)	0.0828 (5)	−0.0173 (2)	0.0324 (3)	−0.0034 (2)
O1	0.0618 (9)	0.0389 (8)	0.0467 (9)	−0.0050 (6)	−0.0016 (7)	−0.0006 (6)
N1	0.0266 (6)	0.0258 (6)	0.0545 (10)	−0.0007 (5)	0.0077 (6)	−0.0043 (6)
C1	0.0365 (9)	0.0272 (8)	0.0493 (11)	0.0049 (7)	0.0029 (8)	−0.0052 (8)
C2	0.0383 (10)	0.0387 (10)	0.0582 (13)	0.0016 (8)	−0.0081 (9)	−0.0107 (9)
C3	0.0323 (9)	0.0367 (9)	0.0727 (15)	−0.0036 (8)	0.0044 (9)	−0.0146 (10)
C4	0.0363 (9)	0.0299 (9)	0.0670 (14)	−0.0038 (7)	0.0158 (9)	−0.0074 (8)
C5	0.0372 (9)	0.0304 (9)	0.0481 (11)	−0.0024 (7)	0.0057 (8)	−0.0045 (8)
C6	0.0295 (8)	0.0255 (7)	0.0463 (10)	0.0007 (7)	0.0043 (7)	−0.0059 (7)
C7	0.0349 (9)	0.0302 (9)	0.0510 (12)	−0.0037 (7)	0.0002 (8)	−0.0011 (8)
C8	0.0314 (8)	0.0295 (9)	0.0665 (13)	−0.0012 (7)	0.0153 (8)	−0.0067 (8)
C9	0.0286 (8)	0.0293 (8)	0.0689 (13)	−0.0005 (7)	0.0062 (8)	−0.0048 (9)

Geometric parameters (Å, º) top

Cl1—C4	1.750 (2)	C8—C9	1.510 (2)
O1—C1	1.360 (2)	O1—H1	0.832
N1—C7	1.474 (2)	C2—H2	0.950
N1—C8	1.468 (2)	C3—H3	0.950
N1—C9ⁱ	1.468 (2)	C5—H4	0.950
C1—C2	1.395 (2)	C7—H5	0.950
C1—C6	1.399 (2)	C7—H6	0.950
C2—C3	1.375 (3)	C8—H7	0.950
C3—C4	1.377 (3)	C8—H8	0.950
C4—C5	1.376 (2)	C9—H9	0.950
C5—C6	1.389 (2)	C9—H10	0.950
C6—C7	1.520 (2)

C7—N1—C8	112.58 (15)	C3—C2—H2	120.2
C7—N1—C9ⁱ	111.96 (14)	C2—C3—H3	120.7
C8—N1—C9ⁱ	109.43 (14)	C4—C3—H3	120.0
O1—C1—C2	117.87 (17)	C4—C5—H4	119.7
O1—C1—C6	122.46 (16)	C6—C5—H4	119.7
C2—C1—C6	119.67 (18)	N1—C7—H5	108.8
C1—C2—C3	120.75 (19)	N1—C7—H6	108.9
C2—C3—C4	119.27 (18)	C6—C7—H5	108.3
Cl1—C4—C3	119.17 (14)	C6—C7—H6	109.0
Cl1—C4—C5	119.92 (16)	H5—C7—H6	109.5
C3—C4—C5	120.90 (19)	N1—C8—H7	109.3
C4—C5—C6	120.60 (18)	N1—C8—H8	109.5
C1—C6—C5	118.68 (16)	C9—C8—H7	108.6
C1—C6—C7	121.77 (17)	C9—C8—H8	110.1
C5—C6—C7	119.41 (16)	H7—C8—H8	109.5
N1—C7—C6	112.28 (15)	N1ⁱ—C9—H9	109.3
N1—C8—C9	109.81 (17)	N1ⁱ—C9—H10	109.5
N1ⁱ—C9—C8	109.75 (15)	C8—C9—H9	110.4
C1—O1—H1	108.6	C8—C9—H10	108.5
C1—C2—H2	119.0	H9—C9—H10	109.5

C7—N1—C8—C9	175.34 (15)	C6—C1—C2—C3	3.6 (3)
C8—N1—C7—C6	−74.1 (2)	C1—C2—C3—C4	−0.6 (3)
C7—N1—C9ⁱ—C8ⁱ	−175.02 (17)	C2—C3—C4—Cl1	176.21 (16)
C9ⁱ—N1—C7—C6	162.11 (16)	C2—C3—C4—C5	−2.3 (3)
C8—N1—C9ⁱ—C8ⁱ	59.4 (2)	Cl1—C4—C5—C6	−176.38 (15)
C9ⁱ—N1—C8—C9	−59.5 (2)	C3—C4—C5—C6	2.1 (3)
O1—C1—C2—C3	−175.83 (18)	C4—C5—C6—C1	0.9 (2)
O1—C1—C6—C5	175.67 (17)	C4—C5—C6—C7	176.70 (17)
O1—C1—C6—C7	0.0 (2)	C1—C6—C7—N1	−27.3 (2)
C2—C1—C6—C5	−3.8 (2)	C5—C6—C7—N1	157.10 (17)
C2—C1—C6—C7	−179.42 (17)	N1—C8—C9—N1ⁱ	59.7 (2)

Symmetry code: (i) −x+1, −y, −z+2.

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
O1—H1···N1	0.83	1.85	2.604 (2)	150
C3—H3···O1ⁱⁱ	0.95	2.60	3.547 (2)	175

Symmetry code: (ii) −x+3/2, y+1/2, −z+5/2.

Experimental details

Crystal data
Chemical formula	C₁₈H₂₀Cl₂N₂O₂
M_r	367.26
Crystal system, space group	Monoclinic, P2₁/n
Temperature (K)	298
a, b, c (Å)	15.755 (4), 9.2667 (17), 5.9771 (19)
β (°)	96.45 (2)
V (Å³)	867.1 (4)
Z	2
Radiation type	Mo Kα
µ (mm⁻¹)	0.39
Crystal size (mm)	0.35 × 0.15 × 0.15

Data collection
Diffractometer	Rigaku AFC-7R diffractometer
Absorption correction	–
No. of measured, independent and observed [F² > 2σ(F²)] reflections	2462, 1994, 1316
R_int	0.020
(sin θ/λ)_max (Å⁻¹)	0.650

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.041, 0.149, 1.01
No. of reflections	1994
No. of parameters	119
No. of restraints	?
H-atom treatment	All H-atom parameters refined
Δρ_max, Δρ_min (e Å⁻³)	0.54, −0.52

Computer programs: WinAFC (Rigaku/MSC, 2006), CrystalStructure (Rigaku/MSC, 2006), SIR92 (Altomare et al., 1993), CRYSTALS (Betteridge et al., 2003), PLATON (Spek, 2003).

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
O1—H1···N1	0.832	1.852	2.604 (2)	149.6
C3—H3···O1ⁱ	0.95	2.599	3.547 (2)	175.3

Symmetry code: (i) −x+3/2, y+1/2, −z+5/2.

Acknowledgements

This study was supported financially in part by Grants-in-Aid (Nos. 19550040 and 20550075) from the Ministry of Education, Culture, Sports, Science, and Technology, Japan.

References

Altomare, A., Cascarano, G., Giacovazzo, C. & Guagliardi, A. (1993). J. Appl. Cryst. 26, 343–350. CrossRef Web of Science IUCr Journals Google Scholar
Bernstein, J., Davis, R. E., Shimoni, L. & Chang, N.-L. (1995). Angew. Chem. Int. Ed. Engl. 34, 1555–1573. CrossRef CAS Web of Science Google Scholar
Betteridge, P. W., Carruthers, J. R., Cooper, R. I., Prout, K. & Watkin, D. J. (2003). J. Appl. Cryst. 36, 1487. Web of Science CrossRef IUCr Journals Google Scholar
Bharathi, K. S., Rahiman, A. K., Rajesh, K., Sreedaran, S., Aravindan, P. G., Velmurugan, D. & Narayanan, V. (2006). Polyhedron, 25, 2859–2868. Web of Science CSD CrossRef CAS Google Scholar
Kubono, K., Tsuno, Y., Tani, K. & Yokoi, K. (2008). Acta Cryst. E64, o2309. Web of Science CSD CrossRef IUCr Journals Google Scholar
Kubono, K. & Yokoi, K. (2007). Acta Cryst. C63, o535–o537. Web of Science CSD CrossRef IUCr Journals Google Scholar
Kuppayee, M., Kumaran, D., Ponnuswamy, M. N., Kandaswamy, M., Violet, M. J., Chinnakali, K. & Fun, H.-K. (1999). Acta Cryst. C55, 2147–2149. Web of Science CSD CrossRef CAS IUCr Journals Google Scholar
Rigaku/MSC (2006). WinAFC and CrystalStructure. Rigaku/MSC, The Woodlands, Texas, USA. Google Scholar
Spek, A. L. (2003). J. Appl. Cryst. 36, 7–13. Web of Science CrossRef CAS IUCr Journals Google Scholar

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

A monoclinic polymorph of 4,4′-di­chloro-2,2′-(piperazine-1,4-diyl­di­methyl­ene)diphenol

Related literature

Experimental

Crystal data

Data collection

Refinement

Supporting information

Acknowledgements

References

organic compounds

A monoclinic polymorph of 4,4′-dichloro-2,2′-(piperazine-1,4-diyldimethylene)diphenol