Pimelic acid–urea (1/2)

Xu, W.; Huang, W.; Chen, H.

doi:10.1107/S1600536811023439

organic compounds

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ISSN: 2056-9890

Volume 67| Part 7| July 2011| Page o1795

doi:10.1107/S1600536811023439

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Pimelic acid–urea (1/2)

Wei Xu,^a ^* Wen-xiang Huang ^a and Hong-yan Chen ^a

^aCenter of Applied Solid State Chemistry Research, Ningbo University, Ningbo, Zhejiang 315211, People's Republic of China
^*Correspondence e-mail: xuwei@nbu.edu.cn

(Received 27 May 2011; accepted 16 June 2011; online 25 June 2011)

The asymmetric unit, 2CH₄N₂O·C₇H₁₂O₄, of the title cocrystal contains one urea molecule and a half-molecule of pimelic acid; the latter, together with a second urea molecule, are completed by symmetry, with the central atom of the whole pimelic acid moiety placed on a twofold crystallographic axis. The crystal packing is stabilized by O—H⋯O and N—H⋯O hydrogen-bond, generating a chain along [10 $[\overline{1}]$ ]. Additionally, the chains are assembled into a three-dimensional framework via weak N—H⋯O interchain interactions.

Related literature

For urea inclusion compounds, see: Videnova-Adrabińska (1996a ); Harris & Thomas (1990 ); Yeo et al. (1997 ). For urea-dicarboxylic acid co-crystal engineering with predesigned crystal building blocks, see: Videnova-Adrabińska (1996b ); Chadwick et al. (2009 ); Chang & Lin (2011 ).

Experimental

Crystal data

2CH₄N₂O·C₇H₁₂O₄
M_r = 280.29
Monoclinic, C 2/c
a = 15.103 (3) Å
b = 11.073 (2) Å
c = 9.1660 (18) Å
β = 112.72 (3)°
V = 1413.9 (6) Å³
Z = 4
Mo Kα radiation
μ = 0.11 mm⁻¹
T = 293 K
0.14 × 0.12 × 0.10 mm

Data collection

Rigaku R-AXIS RAPID diffractometer
Absorption correction: multi-scan (ABSCOR; Higashi, 1995 ) T_min = 0.989, T_max = 0.989
6742 measured reflections
1609 independent reflections
1084 reflections with I > 2σ(I)
R_int = 0.028

Refinement

R[F² > 2σ(F²)] = 0.043
wR(F²) = 0.135
S = 1.14
1609 reflections
87 parameters
H-atom parameters constrained
Δρ_max = 0.18 e Å⁻³
Δρ_min = −0.17 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
O1—H1⋯O3	0.88	1.72	2.584 (2)	168
N1—H1A⋯O2	0.86	2.24	3.038 (2)	154
N1—H1B⋯O2ⁱ	0.86	2.24	3.016 (2)	151
N2—H2C⋯O3ⁱⁱ	0.86	2.11	2.952 (2)	167
N2—H2D⋯O2ⁱ	0.86	2.49	3.211 (2)	142
Symmetry codes: (i) $[x, -y+1, z-{\script{1\over 2}}]$ ; (ii) $[-x+{\script{1\over 2}}, -y+{\script{1\over 2}}, -z]$ .

Data collection: RAPID-AUTO (Rigaku, 1998 ); cell refinement: RAPID-AUTO; data reduction: CrystalStructure (Rigaku/MSC, 2004 ); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEPII (Johnson, 1976 ); software used to prepare material for publication: SHELXL97.

Supporting information

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536811023439/lr2013sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536811023439/lr2013Isup2.hkl

Supporting information file. DOI: 10.1107/S1600536811023439/lr2013Isup3.cml

checkCIF report

Comment top

This crystal structure study is part of a broader program of urea-dicarboxylic acid co-crystal engineering with predesigned crystal building blocks (Videnova-Adrabińska, 1996a,b; Chang & Lin, 2011). In these solids, the urea molecules form an extensively hydrogen-bonded host structure (Harris & Thomas,1990), containing linear, parallel tunnels with guest molecules packed densely along these tunnels (Yeo et al., 1997). The phase diagram of a related urea- dicarboxylic acid co-crystal has also been reported (Chadwick et al. 2009). In this contribution, we present the crystal structure of the 2:1 urea/pimelic acid co-crystal.

The asymmetric unit of the title co-crystal, CH₄N₂O. 0.5(C₇H₁₂O₄), contains one urea molecule and a half-molecule of pimelic acid, with the complete pimelic acid molecule and the additional urea unit generated via crystallographic rotation symmetry, with the central carbon atom of the whole pimelic acid molecule positioned on a twofold axis (Fig. 1).

Five different hydrogen-bond interactions (Table.1), organize the parent molecules in a well developed three-dimensional crystal structure. The carboxylic groups of the acid connect with the corresponding urea and inter-urea molecules through O1—H1··· O3, N1—H1A .. .O2 and N2—H2C ···O3 hydrogen bonds (Table 1), generating a one dimensional chain along [101] (Figure 2). Additional weak inter-chain N—H···O intermolecular interactions (Table 1) generated a three-dimensional network, which stabilizes the crystal packing (Figure 3).

Related literature top

For urea inclusion compounds, see: Videnova-Adrabińska (1996a); Harris & Thomas (1990); Yeo et al. (1997). For urea-dicarboxylic acid co-crystal engineering with predesigned crystal building blocks, see: Videnova-Adrabińska (1996b); Chadwick et al. (2009); Chang & Lin (2011).

Experimental top

Pimelic acid acid (0.0815 g, 0.5 mmol) and urea (0.0316 g, 0.05 mmol) were dissolved in 15 ml of water (pH = 3.23) under stirring. After slow evaporation of the solution for one week at 50°C, colorless block sized crystals were obtained.

Computing details top

Data collection: RAPID-AUTO (Rigaku, 1998); cell refinement: RAPID-AUTO (Rigaku, 1998); data reduction: CrystalStructure (Rigaku/MSC, 2004); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEPII (Johnson, 1976); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008).

Figures top

	Fig. 1. ORTEP view of the title co-crystal. The displacement ellipsoids are drawn at 35% probability level. (# = -x, y, -z + 3/2)
	Fig. 2. One-dimensional chain of the title co-crystal viewed along [101] direction.O—H···O and N—H···O hydrogen bonds are shown as dashed line.
	Fig. 3. A view of the three-dimensional crystal structure of the title co-crystal viewed down the c axis.

Heptanedioic acid–urea (1/2) top

Crystal data top

2CH₄N₂O·C₇H₁₂O₄	F(000) = 600
M_r = 280.29	D_x = 1.317 Mg m⁻³
Monoclinic, C2/c	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -C 2yc	Cell parameters from 6742 reflections
a = 15.103 (3) Å	θ = 3.7–27.4°
b = 11.073 (2) Å	µ = 0.11 mm⁻¹
c = 9.1660 (18) Å	T = 293 K
β = 112.72 (3)°	Block, colorless
V = 1413.9 (6) Å³	0.14 × 0.12 × 0.10 mm
Z = 4

Data collection top

Rigaku R-AXIS RAPID diffractometer	1609 independent reflections
Radiation source: fine-focus sealed tube	1084 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.028
Detector resolution: 0 pixels mm^-1	θ_max = 27.4°, θ_min = 3.7°
ω scans	h = −19→18
Absorption correction: multi-scan (ABSCOR; Higashi, 1995)	k = 0→14
T_min = 0.989, T_max = 0.989	l = 0→11
6742 measured reflections

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)] = 0.043	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.135	H-atom parameters constrained
S = 1.14	w = 1/[σ²(F_o²) + (0.0612P)² + 0.4165P] where P = (F_o² + 2F_c²)/3
1609 reflections	(Δ/σ)_max < 0.001
87 parameters	Δρ_max = 0.18 e Å⁻³
0 restraints	Δρ_min = −0.17 e Å⁻³

Crystal data top

2CH₄N₂O·C₇H₁₂O₄	V = 1413.9 (6) Å³
M_r = 280.29	Z = 4
Monoclinic, C2/c	Mo Kα radiation
a = 15.103 (3) Å	µ = 0.11 mm⁻¹
b = 11.073 (2) Å	T = 293 K
c = 9.1660 (18) Å	0.14 × 0.12 × 0.10 mm
β = 112.72 (3)°

Data collection top

Rigaku R-AXIS RAPID diffractometer	1609 independent reflections
Absorption correction: multi-scan (ABSCOR; Higashi, 1995)	1084 reflections with I > 2σ(I)
T_min = 0.989, T_max = 0.989	R_int = 0.028
6742 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.043	0 restraints
wR(F²) = 0.135	H-atom parameters constrained
S = 1.14	Δρ_max = 0.18 e Å⁻³
1609 reflections	Δρ_min = −0.17 e Å⁻³
87 parameters

Special details top

Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds 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	Occ. (<1)
O1	0.13778 (11)	0.15952 (10)	0.34879 (17)	0.0693 (5)
H1	0.1579	0.2051	0.2889	0.104*
O2	0.11144 (11)	0.33586 (10)	0.43696 (16)	0.0690 (5)
C1	0.10938 (12)	0.22682 (14)	0.4400 (2)	0.0449 (4)
C2	0.07317 (13)	0.15469 (14)	0.5438 (2)	0.0502 (4)
H2A	0.1236	0.1001	0.6073	0.060*
H2B	0.0195	0.1058	0.4771	0.060*
C3	0.04121 (12)	0.22885 (14)	0.6531 (2)	0.0445 (4)
H3A	−0.0070	0.2863	0.5906	0.053*
H3B	0.0956	0.2743	0.7244	0.053*
C4	0.0000	0.1528 (2)	0.7500	0.0470 (6)
H4A	−0.0501	0.1012	0.6793	0.056*	0.50
H4B	0.0501	0.1012	0.8207	0.056*	0.50
O3	0.19575 (9)	0.26507 (10)	0.15014 (14)	0.0545 (4)
N1	0.13952 (13)	0.45279 (13)	0.1580 (2)	0.0679 (5)
H1A	0.1134	0.4302	0.2218	0.082*
H1B	0.1347	0.5267	0.1270	0.082*
N2	0.22675 (12)	0.41306 (13)	0.00916 (19)	0.0613 (5)
H2C	0.2583	0.3644	−0.0257	0.074*
H2D	0.2205	0.4876	−0.0194	0.074*
C5	0.18758 (12)	0.37311 (14)	0.10736 (19)	0.0449 (4)

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
O1	0.1148 (12)	0.0399 (7)	0.0885 (10)	0.0013 (7)	0.0783 (10)	−0.0003 (6)
O2	0.1195 (12)	0.0373 (7)	0.0791 (10)	−0.0059 (7)	0.0702 (9)	−0.0022 (6)
C1	0.0563 (10)	0.0379 (8)	0.0491 (9)	−0.0027 (7)	0.0299 (8)	−0.0030 (7)
C2	0.0674 (11)	0.0394 (8)	0.0559 (10)	−0.0036 (7)	0.0370 (9)	−0.0001 (7)
C3	0.0529 (10)	0.0399 (8)	0.0483 (9)	−0.0007 (7)	0.0280 (8)	−0.0001 (7)
C4	0.0575 (14)	0.0411 (12)	0.0520 (13)	0.000	0.0319 (12)	0.000
O3	0.0794 (9)	0.0391 (6)	0.0644 (8)	0.0060 (6)	0.0493 (7)	0.0062 (5)
N1	0.1134 (14)	0.0391 (8)	0.0793 (11)	0.0103 (8)	0.0681 (11)	0.0039 (7)
N2	0.0924 (12)	0.0416 (8)	0.0735 (11)	0.0023 (7)	0.0579 (10)	0.0069 (7)
C5	0.0588 (10)	0.0376 (8)	0.0447 (9)	−0.0023 (7)	0.0270 (8)	−0.0024 (7)

Geometric parameters (Å, º) top

O1—C1	1.3099 (19)	C4—C3ⁱ	1.5208 (19)
O1—H1	0.8820	C4—H4A	0.9700
O2—C1	1.2085 (19)	C4—H4B	0.9700
C1—C2	1.498 (2)	O3—C5	1.2501 (18)
C2—C3	1.512 (2)	N1—C5	1.335 (2)
C2—H2A	0.9700	N1—H1A	0.8592
C2—H2B	0.9700	N1—H1B	0.8599
C3—C4	1.5208 (19)	N2—C5	1.329 (2)
C3—H3A	0.9700	N2—H2C	0.8592
C3—H3B	0.9700	N2—H2D	0.8600

C1—O1—H1	110.4	C3ⁱ—C4—C3	112.75 (18)
O2—C1—O1	122.40 (15)	C3ⁱ—C4—H4A	109.0
O2—C1—C2	124.51 (14)	C3—C4—H4A	109.0
O1—C1—C2	113.08 (13)	C3ⁱ—C4—H4B	109.0
C1—C2—C3	114.81 (13)	C3—C4—H4B	109.0
C1—C2—H2A	108.6	H4A—C4—H4B	107.8
C3—C2—H2A	108.6	C5—N1—H1A	119.9
C1—C2—H2B	108.6	C5—N1—H1B	120.1
C3—C2—H2B	108.6	H1A—N1—H1B	120.0
H2A—C2—H2B	107.5	C5—N2—H2C	120.0
C2—C3—C4	113.19 (13)	C5—N2—H2D	120.1
C2—C3—H3A	108.9	H2C—N2—H2D	120.0
C4—C3—H3A	108.9	O3—C5—N2	120.99 (15)
C2—C3—H3B	108.9	O3—C5—N1	121.64 (15)
C4—C3—H3B	108.9	N2—C5—N1	117.36 (15)
H3A—C3—H3B	107.8

O2—C1—C2—C3	−2.1 (3)	C1—C2—C3—C4	176.91 (13)
O1—C1—C2—C3	179.01 (16)	C2—C3—C4—C3ⁱ	−174.14 (17)

Symmetry code: (i) −x, y, −z+3/2.

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
O1—H1···O3	0.88	1.72	2.584 (2)	168
N1—H1A···O2	0.86	2.24	3.038 (2)	154
N1—H1B···O2ⁱⁱ	0.86	2.24	3.016 (2)	151
N2—H2C···O3ⁱⁱⁱ	0.86	2.11	2.952 (2)	167
N2—H2D···O2ⁱⁱ	0.86	2.49	3.211 (2)	142

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

Experimental details

Crystal data
Chemical formula	2CH₄N₂O·C₇H₁₂O₄
M_r	280.29
Crystal system, space group	Monoclinic, C2/c
Temperature (K)	293
a, b, c (Å)	15.103 (3), 11.073 (2), 9.1660 (18)
β (°)	112.72 (3)
V (Å³)	1413.9 (6)
Z	4
Radiation type	Mo Kα
µ (mm⁻¹)	0.11
Crystal size (mm)	0.14 × 0.12 × 0.10

Data collection
Diffractometer	Rigaku R-AXIS RAPID diffractometer
Absorption correction	Multi-scan (ABSCOR; Higashi, 1995)
T_min, T_max	0.989, 0.989
No. of measured, independent and observed [I > 2σ(I)] reflections	6742, 1609, 1084
R_int	0.028
(sin θ/λ)_max (Å⁻¹)	0.648

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.043, 0.135, 1.14
No. of reflections	1609
No. of parameters	87
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.18, −0.17

Computer programs: RAPID-AUTO (Rigaku, 1998), CrystalStructure (Rigaku/MSC, 2004), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), ORTEPII (Johnson, 1976).

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
O1—H1···O3	0.88	1.72	2.584 (2)	167.5
N1—H1A···O2	0.86	2.24	3.038 (2)	154.1
N1—H1B···O2ⁱ	0.86	2.24	3.016 (2)	150.8
N2—H2C···O3ⁱⁱ	0.86	2.11	2.952 (2)	166.8
N2—H2D···O2ⁱ	0.86	2.49	3.211 (2)	142.2

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

Acknowledgements

This project was supported by the Scientific Research Fund of Zhejiang Provincial Education Department (grant No. Y201017782)and the Scientific Research Fund of Ningbo University (grant No. XKL09078). Sincere thanks are also extended to the K. C. Wong Magna Fund in Ningbo University.

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