3,3′-(Piperazine-1,4-diium-1,4-di­yl)di­propionate dihydrate

Jin, S.; Huang, Y.; Fang, H.; Wang, T.; Ding, L.

doi:10.1107/S1600536812037312

organic compounds

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ISSN: 2056-9890

Volume 68| Part 10| October 2012| Page o2827

https://doi.org/10.1107/S1600536812037312

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3,3′-(Piperazine-1,4-diium-1,4-diyl)dipropionate dihydrate

Shouwen Jin,^a ^* Yanfei Huang,^a Hao Fang,^a Tianyi Wang ^a and Liangliang Ding ^a

^aTianmu College of ZheJiang A & F University, Lin'An 311300, People's Republic of China
^*Correspondence e-mail: shouwenjin@yahoo.cn

(Received 20 August 2012; accepted 29 August 2012; online 1 September 2012)

During the recrystallization of 3-[4-(2-carboxyethyl)piperazin-1-yl]propionic acid, the carboxylic acid H atoms were transferred to the piperazine N atoms, forming the title compound, C₁₀H₁₈N₂O₄·2H₂O, in which the zwitterion lies about an inversion center. In the crystal, bifurcated N—H⋯(O,O) hydrogen bonds connect the zwitterions into a two-dimensional framework parallel to (-102) forming R₄⁴(30) rings. O—H⋯O hydrogen bonds involving the solvent water molecules connect the two-dimensional framework into a three-dimensional network. In addition, weak C—H⋯O hydrogen bonds are observed.

Related literature

For general background and applications of carboxylic acids, see: Jin et al. (2012 ); Grossel et al. (2006 ); Rueff et al. (2001 ); Strachan et al. (2007 ); Desiraju (2002 ). For hydrogen-bond motifs, see: Bernstein et al. (1995 ).

Experimental

Crystal data

C₁₀H₁₈N₂O₄·2H₂O
M_r = 266.30
Monoclinic, P 2₁ /c
a = 6.8028 (6) Å
b = 8.8925 (7) Å
c = 10.4301 (11) Å
β = 101.780 (1)°
V = 617.67 (10) Å³
Z = 2
Mo Kα radiation
μ = 0.12 mm⁻¹
T = 298 K
0.43 × 0.40 × 0.32 mm

Data collection

Bruker SMART CCD diffractometer
Absorption correction: multi-scan (SADABS; Bruker, 2002 ) T_min = 0.951, T_max = 0.963
2951 measured reflections
1087 independent reflections
895 reflections with I > 2σ(I)
R_int = 0.023

Refinement

R[F² > 2σ(F²)] = 0.040
wR(F²) = 0.111
S = 1.06
1087 reflections
82 parameters
H-atom parameters constrained
Δρ_max = 0.21 e Å⁻³
Δρ_min = −0.23 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
O3—H3F⋯O2ⁱ	0.85	1.93	2.776 (2)	177
O3—H3E⋯O1	0.85	2.11	2.964 (2)	177
N1—H1⋯O2ⁱⁱ	0.91	2.50	3.0577 (19)	120
N1—H1⋯O1ⁱⁱ	0.91	1.80	2.7011 (18)	172
C4—H4B⋯O3ⁱⁱⁱ	0.97	2.58	3.419 (2)	145
C4—H4B⋯O2ⁱⁱ	0.97	2.53	3.137 (2)	120
C5—H5A⋯O1^iv	0.97	2.51	3.477 (2)	172
Symmetry codes: (i) $[x, -y+{\script{1\over 2}}, z+{\script{1\over 2}}]$ ; (ii) $[-x+1, y-{\script{1\over 2}}, -z+{\script{1\over 2}}]$ ; (iii) x-1, y, z; (iv) $[x, -y+{\script{1\over 2}}, z-{\script{1\over 2}}]$ .

Data collection: SMART (Bruker, 2002); cell refinement: SAINT (Bruker, 2002); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008) and Mercury (Macrae et al., 2006 ); software used to prepare material for publication: SHELXTL.

Supporting information

Crystal structure: contains datablocks global, I. DOI: https://doi.org/10.1107/S1600536812037312/lh5520sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S1600536812037312/lh5520Isup2.hkl

Supporting information file. DOI: https://doi.org/10.1107/S1600536812037312/lh5520Isup3.cml

checkCIF report

Comment top

Carboxylic acids are important compounds, which have been widely used in various fields as coordination chemistry (Rueff et al., 2001), pharmaceutical chemistry (Strachan et al., 2007), and supramolecular chemistry (Desiraju, 2002). Recently the main focus for carboxylic acids has been in crystal engineering via hydrogen bonded assembly of organic acids and organic bases (Grossel et al., 2006). As an extension of our study concentrating on hydrogen bonded assembly of organic acids and organic bases (Jin et al., 2012), herein we report the crystal structure of the title compound (I).

During the recrystallization of 3-[4-(2-carboxy-ethyl)-piperazin-1-yl]-propionic acid the carboxylic acid H atoms were transferred to the piperazine N atoms forming (I) (Fig. 1) in which the zwitterion lies across an inversion center. In the crystal, bifurcated N—H···(O,O) hydrogen bonds connect the zwitterions a two-dimensional framework parallel to (102) forming R⁴₄(30) rings (Bernstein et al., 1995). Furthermore O—H···O hydrogen bonds involving sovent water molecules connect the two-dimensional framework into a three-dimensional network. In addition, weak C—H···O hydrogen bonds are observed (Fig. 2).

Related literature top

For general background and applications of carboxylic acids, see: Jin et al. (2012); Grossel et al. (2006); Rueff et al. (2001); Strachan et al. (2007); Desiraju (2002). For hydrogen-bond motifs, see: Bernstein et al. (1995).

Experimental top

3-[4-(2-Carboxy-ethyl)-piperazin-1-yl]-propionic acid (23.0 mg, 0.10 mmol) was dissolved in 6 ml of ethanol, and pyridine (15.8 mg, 0.2 mmol) was added to the ethanol solution. The solution was stirred for 1 h, and then filtered into a test tube. The solution was left standing at room temperature for about one week, colorless block crystals were obtained.

Structure description top

For general background and applications of carboxylic acids, see: Jin et al. (2012); Grossel et al. (2006); Rueff et al. (2001); Strachan et al. (2007); Desiraju (2002). For hydrogen-bond motifs, see: Bernstein et al. (1995).

Computing details top

Data collection: SMART (Bruker, 2002); cell refinement: SAINT (Bruker, 2002); data reduction: SAINT (Bruker, 2002); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008) and Mercury (Macrae et al., 2006); software used to prepare material for publication: SHELXTL (Sheldrick, 2008).

Figures top

	Fig. 1. The molecular structure of (I) with displacement ellipsoids drawn at the 30% probability level. Unlabeled atoms are related by the symmetry operator (-x, -y, -z). Only the symmetry unique solvent water molecule is shown.
	Fig. 2. Part of the crystal structure with hydrogen bonds shown as dotted lines.

3,3'-(Piperazine-1,4-diium-1,4-diyl)dipropionate dihydrate top

Crystal data top

C₁₀H₁₈N₂O₄·2H₂O	F(000) = 288
M_r = 266.30	D_x = 1.432 Mg m⁻³
Monoclinic, P2₁/c	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybc	Cell parameters from 1525 reflections
a = 6.8028 (6) Å	θ = 3.0–28.2°
b = 8.8925 (7) Å	µ = 0.12 mm⁻¹
c = 10.4301 (11) Å	T = 298 K
β = 101.780 (1)°	Block, colorless
V = 617.67 (10) Å³	0.43 × 0.40 × 0.32 mm
Z = 2

Data collection top

Bruker SMART CCD diffractometer	1087 independent reflections
Radiation source: fine-focus sealed tube	895 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.023
φ and ω scans	θ_max = 25.0°, θ_min = 3.0°
Absorption correction: multi-scan (SADABS; Bruker, 2002)	h = −8→7
T_min = 0.951, T_max = 0.963	k = −10→5
2951 measured reflections	l = −12→11

Refinement top

Refinement on F²	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F² > 2σ(F²)] = 0.040	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.111	H-atom parameters constrained
S = 1.06	w = 1/[σ²(F_o²) + (0.0526P)² + 0.3063P] where P = (F_o² + 2F_c²)/3
1087 reflections	(Δ/σ)_max < 0.001
82 parameters	Δρ_max = 0.21 e Å⁻³
0 restraints	Δρ_min = −0.23 e Å⁻³

Crystal data top

C₁₀H₁₈N₂O₄·2H₂O	V = 617.67 (10) Å³
M_r = 266.30	Z = 2
Monoclinic, P2₁/c	Mo Kα radiation
a = 6.8028 (6) Å	µ = 0.12 mm⁻¹
b = 8.8925 (7) Å	T = 298 K
c = 10.4301 (11) Å	0.43 × 0.40 × 0.32 mm
β = 101.780 (1)°

Data collection top

Bruker SMART CCD diffractometer	1087 independent reflections
Absorption correction: multi-scan (SADABS; Bruker, 2002)	895 reflections with I > 2σ(I)
T_min = 0.951, T_max = 0.963	R_int = 0.023
2951 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.040	0 restraints
wR(F²) = 0.111	H-atom parameters constrained
S = 1.06	Δρ_max = 0.21 e Å⁻³
1087 reflections	Δρ_min = −0.23 e Å⁻³
82 parameters

Special details top

Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell e.s.d.'s are taken into account individually in the estimation of e.s.d.'s in distances, angles and torsion angles; correlations between e.s.d.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell e.s.d.'s is used for estimating e.s.d.'s involving l.s. planes.

Refinement. Refinement of F² against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F², conventional R-factors R are based on F, with F set to zero for negative F². The threshold expression of F² > σ(F²) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F² are statistically about twice as large as those based on F, and R- factors based on ALL data will be even larger.

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

	x	y	z	U_iso*/U_eq
N1	0.15979 (19)	0.08898 (15)	0.08004 (12)	0.0204 (3)
H1	0.2428	0.0121	0.1137	0.024*
O1	0.56844 (18)	0.37957 (15)	0.31249 (12)	0.0340 (4)
O2	0.7046 (2)	0.4517 (2)	0.14744 (14)	0.0551 (5)
O3	0.8070 (2)	0.10838 (18)	0.40824 (15)	0.0541 (5)
H3E	0.7405	0.1861	0.3781	0.065*
H3F	0.7788	0.0870	0.4818	0.065*
C1	0.5838 (2)	0.3752 (2)	0.19346 (17)	0.0288 (4)
C2	0.4531 (3)	0.2636 (2)	0.10320 (18)	0.0335 (5)
H2A	0.4302	0.3019	0.0143	0.040*
H2B	0.5256	0.1694	0.1049	0.040*
C3	0.2521 (3)	0.23274 (19)	0.13874 (17)	0.0276 (4)
H3A	0.2697	0.2274	0.2333	0.033*
H3B	0.1616	0.3154	0.1084	0.033*
C4	−0.0379 (2)	0.06441 (19)	0.11862 (16)	0.0236 (4)
H4A	−0.1283	0.1462	0.0851	0.028*
H4B	−0.0187	0.0648	0.2134	0.028*
C5	0.1314 (2)	0.08320 (19)	−0.06607 (15)	0.0230 (4)
H5A	0.2604	0.0950	−0.0910	0.028*
H5B	0.0456	0.1656	−0.1042	0.028*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
N1	0.0183 (7)	0.0214 (7)	0.0211 (7)	−0.0005 (5)	0.0031 (5)	−0.0011 (6)
O1	0.0355 (7)	0.0386 (8)	0.0274 (7)	−0.0108 (6)	0.0049 (5)	−0.0046 (6)
O2	0.0584 (9)	0.0713 (11)	0.0388 (8)	−0.0414 (9)	0.0174 (7)	−0.0142 (8)
O3	0.0650 (10)	0.0500 (10)	0.0518 (10)	0.0019 (8)	0.0225 (8)	0.0053 (8)
C1	0.0261 (9)	0.0297 (9)	0.0300 (10)	−0.0040 (7)	0.0044 (7)	−0.0036 (8)
C2	0.0317 (10)	0.0379 (11)	0.0317 (10)	−0.0112 (8)	0.0084 (8)	−0.0090 (8)
C3	0.0249 (9)	0.0256 (9)	0.0317 (9)	−0.0040 (7)	0.0046 (7)	−0.0064 (7)
C4	0.0201 (8)	0.0287 (9)	0.0224 (8)	0.0000 (7)	0.0056 (6)	−0.0013 (7)
C5	0.0214 (8)	0.0279 (9)	0.0202 (8)	−0.0010 (7)	0.0050 (6)	0.0022 (7)

Geometric parameters (Å, º) top

N1—C4	1.4966 (19)	C2—H2A	0.9700
N1—C5	1.4975 (19)	C2—H2B	0.9700
N1—C3	1.499 (2)	C3—H3A	0.9700
N1—H1	0.9100	C3—H3B	0.9700
O1—C1	1.267 (2)	C4—C5ⁱ	1.512 (2)
O2—C1	1.237 (2)	C4—H4A	0.9700
O3—H3E	0.8501	C4—H4B	0.9700
O3—H3F	0.8500	C5—C4ⁱ	1.512 (2)
C1—C2	1.523 (2)	C5—H5A	0.9700
C2—C3	1.513 (2)	C5—H5B	0.9700

C4—N1—C5	109.42 (12)	N1—C3—H3A	109.2
C4—N1—C3	109.84 (12)	C2—C3—H3A	109.2
C5—N1—C3	113.65 (13)	N1—C3—H3B	109.2
C4—N1—H1	107.9	C2—C3—H3B	109.2
C5—N1—H1	107.9	H3A—C3—H3B	107.9
C3—N1—H1	107.9	N1—C4—C5ⁱ	111.35 (13)
H3E—O3—H3F	108.3	N1—C4—H4A	109.4
O2—C1—O1	123.88 (16)	C5ⁱ—C4—H4A	109.4
O2—C1—C2	117.96 (16)	N1—C4—H4B	109.4
O1—C1—C2	118.09 (15)	C5ⁱ—C4—H4B	109.4
C3—C2—C1	114.16 (15)	H4A—C4—H4B	108.0
C3—C2—H2A	108.7	N1—C5—C4ⁱ	110.85 (13)
C1—C2—H2A	108.7	N1—C5—H5A	109.5
C3—C2—H2B	108.7	C4ⁱ—C5—H5A	109.5
C1—C2—H2B	108.7	N1—C5—H5B	109.5
H2A—C2—H2B	107.6	C4ⁱ—C5—H5B	109.5
N1—C3—C2	112.25 (14)	H5A—C5—H5B	108.1

O2—C1—C2—C3	−151.50 (18)	C5—N1—C4—C5ⁱ	57.11 (18)
O1—C1—C2—C3	31.5 (2)	C3—N1—C4—C5ⁱ	−177.48 (13)
C4—N1—C3—C2	179.91 (14)	C4—N1—C5—C4ⁱ	−56.82 (18)
C5—N1—C3—C2	−57.14 (19)	C3—N1—C5—C4ⁱ	−179.99 (13)
C1—C2—C3—N1	−160.56 (15)

Symmetry code: (i) −x, −y, −z.

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
O3—H3F···O2ⁱⁱ	0.85	1.93	2.776 (2)	177
O3—H3E···O1	0.85	2.11	2.964 (2)	177
N1—H1···O2ⁱⁱⁱ	0.91	2.50	3.0577 (19)	120
N1—H1···O1ⁱⁱⁱ	0.91	1.80	2.7011 (18)	172
C4—H4B···O3^iv	0.97	2.58	3.419 (2)	145
C4—H4B···O2ⁱⁱⁱ	0.97	2.53	3.137 (2)	120
C5—H5A···O1^v	0.97	2.51	3.477 (2)	172

Symmetry codes: (ii) x, −y+1/2, z+1/2; (iii) −x+1, y−1/2, −z+1/2; (iv) x−1, y, z; (v) x, −y+1/2, z−1/2.

Experimental details

Crystal data
Chemical formula	C₁₀H₁₈N₂O₄·2H₂O
M_r	266.30
Crystal system, space group	Monoclinic, P2₁/c
Temperature (K)	298
a, b, c (Å)	6.8028 (6), 8.8925 (7), 10.4301 (11)
β (°)	101.780 (1)
V (Å³)	617.67 (10)
Z	2
Radiation type	Mo Kα
µ (mm⁻¹)	0.12
Crystal size (mm)	0.43 × 0.40 × 0.32

Data collection
Diffractometer	Bruker SMART CCD
Absorption correction	Multi-scan (SADABS; Bruker, 2002)
T_min, T_max	0.951, 0.963
No. of measured, independent and observed [I > 2σ(I)] reflections	2951, 1087, 895
R_int	0.023
(sin θ/λ)_max (Å⁻¹)	0.595

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.040, 0.111, 1.06
No. of reflections	1087
No. of parameters	82
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.21, −0.23

Computer programs: SMART (Bruker, 2002), SAINT (Bruker, 2002), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), SHELXTL (Sheldrick, 2008) and Mercury (Macrae et al., 2006), SHELXTL (Sheldrick, 2008).

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
O3—H3F···O2ⁱ	0.85	1.93	2.776 (2)	177
O3—H3E···O1	0.85	2.11	2.964 (2)	177
N1—H1···O2ⁱⁱ	0.91	2.50	3.0577 (19)	120
N1—H1···O1ⁱⁱ	0.91	1.80	2.7011 (18)	172
C4—H4B···O3ⁱⁱⁱ	0.97	2.58	3.419 (2)	145
C4—H4B···O2ⁱⁱ	0.97	2.53	3.137 (2)	120
C5—H5A···O1^iv	0.97	2.51	3.477 (2)	172

Symmetry codes: (i) x, −y+1/2, z+1/2; (ii) −x+1, y−1/2, −z+1/2; (iii) x−1, y, z; (iv) x, −y+1/2, z−1/2.

Acknowledgements

We gratefully acknowledge the financial support of the Education Office Foundation of Zhejiang Province (project No. Y201017321) and the innovation project of Zhejiang A & F University.

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