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

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Pimelic acid–urea (1/2)

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[Videnova-Adrabińska, V. (1996a). Acta Cryst. B52, 1048-1056.]); Harris & Thomas (1990[Harris, K. D. M. & Thomas, J. M. (1990). J. Chem. Soc. Faraday Trans. pp. 2985-2996.]); Yeo et al. (1997[Yeo, L., Harris, K. D. M. & Guillaume, F. (1997). J. Solid State Chem. 128, 273-281.]). For urea-dicarb­oxy­lic acid co-crystal engineering with predesigned crystal building blocks, see: Videnova-Adrabińska (1996b[Videnova-Adrabińska, V. (1996b). J. Mol. Struct. 374, 199-222.]); Chadwick et al. (2009[Chadwick, K., Davey, R., Sadiq, G., Cross, W. & Pritchard, R. (2009). CrystEngComm, 11, 412-414.]); Chang & Lin (2011[Chang, H.-S. & Lin, J.-L. (2011). Acta Cryst. E67, o1317.]).

[Scheme 1]

Experimental

Crystal data
  • 2CH4N2O·C7H12O4

  • Mr = 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[Higashi, T. (1995). ABSCOR. Rigaku Corporation, Tokyo, Japan.]) Tmin = 0.989, Tmax = 0.989

  • 6742 measured reflections

  • 1609 independent reflections

  • 1084 reflections with I > 2σ(I)

  • Rint = 0.028

Refinement
  • R[F2 > 2σ(F2)] = 0.043

  • wR(F2) = 0.135

  • S = 1.14

  • 1609 reflections

  • 87 parameters

  • H-atom parameters constrained

  • Δρmax = 0.18 e Å−3

  • Δρmin = −0.17 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA 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[Rigaku (1998). RAPID-AUTO. Rigaku Corporation, Tokyo, Japan.]); cell refinement: RAPID-AUTO; data reduction: CrystalStructure (Rigaku/MSC, 2004[Rigaku/MSC (2004). CrystalStructure. Rigaku/MSC Inc., The Woodlands, Texas, USA.]); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); molecular graphics: ORTEPII (Johnson, 1976[Johnson, C. K. (1976). ORTEPII. Report ORNL-5138. Oak Ridge National Laboratory, Tennessee, USA.]); software used to prepare material for publication: SHELXL97.

Supporting information


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.

Refinement top

H atoms bonded to C and N atoms were placed in their geometrically calculated position and refined using a riding model, with C-H distances 0.97 Å and N-H distances 0.86 Å and Uiso(H) = 1.2 Ueq(C,N). H atoms attached to O atoms were found in a difference Fourier synthesis and refined using a riding model, with the O—H distances fixed as initially found and with Uiso(H) values set at 1.2 Ueq(O).

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
[Figure 1] Fig. 1. ORTEP view of the title co-crystal. The displacement ellipsoids are drawn at 35% probability level. (# = -x, y, -z + 3/2)
[Figure 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.
[Figure 3] 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·C7H12O4F(000) = 600
Mr = 280.29Dx = 1.317 Mg m3
Monoclinic, C2/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -C 2ycCell parameters from 6742 reflections
a = 15.103 (3) Åθ = 3.7–27.4°
b = 11.073 (2) ŵ = 0.11 mm1
c = 9.1660 (18) ÅT = 293 K
β = 112.72 (3)°Block, colorless
V = 1413.9 (6) Å30.14 × 0.12 × 0.10 mm
Z = 4
Data collection top
Rigaku R-AXIS RAPID
diffractometer
1609 independent reflections
Radiation source: fine-focus sealed tube1084 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.028
Detector resolution: 0 pixels mm-1θmax = 27.4°, θmin = 3.7°
ω scansh = 1918
Absorption correction: multi-scan
(ABSCOR; Higashi, 1995)
k = 014
Tmin = 0.989, Tmax = 0.989l = 011
6742 measured reflections
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.043Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.135H-atom parameters constrained
S = 1.14 w = 1/[σ2(Fo2) + (0.0612P)2 + 0.4165P]
where P = (Fo2 + 2Fc2)/3
1609 reflections(Δ/σ)max < 0.001
87 parametersΔρmax = 0.18 e Å3
0 restraintsΔρmin = 0.17 e Å3
Crystal data top
2CH4N2O·C7H12O4V = 1413.9 (6) Å3
Mr = 280.29Z = 4
Monoclinic, C2/cMo Kα radiation
a = 15.103 (3) ŵ = 0.11 mm1
b = 11.073 (2) ÅT = 293 K
c = 9.1660 (18) Å0.14 × 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)
Tmin = 0.989, Tmax = 0.989Rint = 0.028
6742 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0430 restraints
wR(F2) = 0.135H-atom parameters constrained
S = 1.14Δρmax = 0.18 e Å3
1609 reflectionsΔρmin = 0.17 e Å3
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
xyzUiso*/UeqOcc. (<1)
O10.13778 (11)0.15952 (10)0.34879 (17)0.0693 (5)
H10.15790.20510.28890.104*
O20.11144 (11)0.33586 (10)0.43696 (16)0.0690 (5)
C10.10938 (12)0.22682 (14)0.4400 (2)0.0449 (4)
C20.07317 (13)0.15469 (14)0.5438 (2)0.0502 (4)
H2A0.12360.10010.60730.060*
H2B0.01950.10580.47710.060*
C30.04121 (12)0.22885 (14)0.6531 (2)0.0445 (4)
H3A0.00700.28630.59060.053*
H3B0.09560.27430.72440.053*
C40.00000.1528 (2)0.75000.0470 (6)
H4A0.05010.10120.67930.056*0.50
H4B0.05010.10120.82070.056*0.50
O30.19575 (9)0.26507 (10)0.15014 (14)0.0545 (4)
N10.13952 (13)0.45279 (13)0.1580 (2)0.0679 (5)
H1A0.11340.43020.22180.082*
H1B0.13470.52670.12700.082*
N20.22675 (12)0.41306 (13)0.00916 (19)0.0613 (5)
H2C0.25830.36440.02570.074*
H2D0.22050.48760.01940.074*
C50.18758 (12)0.37311 (14)0.10736 (19)0.0449 (4)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O10.1148 (12)0.0399 (7)0.0885 (10)0.0013 (7)0.0783 (10)0.0003 (6)
O20.1195 (12)0.0373 (7)0.0791 (10)0.0059 (7)0.0702 (9)0.0022 (6)
C10.0563 (10)0.0379 (8)0.0491 (9)0.0027 (7)0.0299 (8)0.0030 (7)
C20.0674 (11)0.0394 (8)0.0559 (10)0.0036 (7)0.0370 (9)0.0001 (7)
C30.0529 (10)0.0399 (8)0.0483 (9)0.0007 (7)0.0280 (8)0.0001 (7)
C40.0575 (14)0.0411 (12)0.0520 (13)0.0000.0319 (12)0.000
O30.0794 (9)0.0391 (6)0.0644 (8)0.0060 (6)0.0493 (7)0.0062 (5)
N10.1134 (14)0.0391 (8)0.0793 (11)0.0103 (8)0.0681 (11)0.0039 (7)
N20.0924 (12)0.0416 (8)0.0735 (11)0.0023 (7)0.0579 (10)0.0069 (7)
C50.0588 (10)0.0376 (8)0.0447 (9)0.0023 (7)0.0270 (8)0.0024 (7)
Geometric parameters (Å, º) top
O1—C11.3099 (19)C4—C3i1.5208 (19)
O1—H10.8820C4—H4A0.9700
O2—C11.2085 (19)C4—H4B0.9700
C1—C21.498 (2)O3—C51.2501 (18)
C2—C31.512 (2)N1—C51.335 (2)
C2—H2A0.9700N1—H1A0.8592
C2—H2B0.9700N1—H1B0.8599
C3—C41.5208 (19)N2—C51.329 (2)
C3—H3A0.9700N2—H2C0.8592
C3—H3B0.9700N2—H2D0.8600
C1—O1—H1110.4C3i—C4—C3112.75 (18)
O2—C1—O1122.40 (15)C3i—C4—H4A109.0
O2—C1—C2124.51 (14)C3—C4—H4A109.0
O1—C1—C2113.08 (13)C3i—C4—H4B109.0
C1—C2—C3114.81 (13)C3—C4—H4B109.0
C1—C2—H2A108.6H4A—C4—H4B107.8
C3—C2—H2A108.6C5—N1—H1A119.9
C1—C2—H2B108.6C5—N1—H1B120.1
C3—C2—H2B108.6H1A—N1—H1B120.0
H2A—C2—H2B107.5C5—N2—H2C120.0
C2—C3—C4113.19 (13)C5—N2—H2D120.1
C2—C3—H3A108.9H2C—N2—H2D120.0
C4—C3—H3A108.9O3—C5—N2120.99 (15)
C2—C3—H3B108.9O3—C5—N1121.64 (15)
C4—C3—H3B108.9N2—C5—N1117.36 (15)
H3A—C3—H3B107.8
O2—C1—C2—C32.1 (3)C1—C2—C3—C4176.91 (13)
O1—C1—C2—C3179.01 (16)C2—C3—C4—C3i174.14 (17)
Symmetry code: (i) x, y, z+3/2.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O1—H1···O30.881.722.584 (2)168
N1—H1A···O20.862.243.038 (2)154
N1—H1B···O2ii0.862.243.016 (2)151
N2—H2C···O3iii0.862.112.952 (2)167
N2—H2D···O2ii0.862.493.211 (2)142
Symmetry codes: (ii) x, y+1, z1/2; (iii) x+1/2, y+1/2, z.

Experimental details

Crystal data
Chemical formula2CH4N2O·C7H12O4
Mr280.29
Crystal system, space groupMonoclinic, C2/c
Temperature (K)293
a, b, c (Å)15.103 (3), 11.073 (2), 9.1660 (18)
β (°) 112.72 (3)
V3)1413.9 (6)
Z4
Radiation typeMo Kα
µ (mm1)0.11
Crystal size (mm)0.14 × 0.12 × 0.10
Data collection
DiffractometerRigaku R-AXIS RAPID
diffractometer
Absorption correctionMulti-scan
(ABSCOR; Higashi, 1995)
Tmin, Tmax0.989, 0.989
No. of measured, independent and
observed [I > 2σ(I)] reflections
6742, 1609, 1084
Rint0.028
(sin θ/λ)max1)0.648
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.043, 0.135, 1.14
No. of reflections1609
No. of parameters87
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)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···AD—HH···AD···AD—H···A
O1—H1···O30.881.722.584 (2)167.5
N1—H1A···O20.862.243.038 (2)154.1
N1—H1B···O2i0.862.243.016 (2)150.8
N2—H2C···O3ii0.862.112.952 (2)166.8
N2—H2D···O2i0.862.493.211 (2)142.2
Symmetry codes: (i) x, y+1, z1/2; (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.

References

First citationChadwick, K., Davey, R., Sadiq, G., Cross, W. & Pritchard, R. (2009). CrystEngComm, 11, 412–414.  Web of Science CSD CrossRef CAS Google Scholar
First citationChang, H.-S. & Lin, J.-L. (2011). Acta Cryst. E67, o1317.  Web of Science CSD CrossRef IUCr Journals Google Scholar
First citationHarris, K. D. M. & Thomas, J. M. (1990). J. Chem. Soc. Faraday Trans. pp. 2985–2996.  CrossRef Google Scholar
First citationHigashi, T. (1995). ABSCOR. Rigaku Corporation, Tokyo, Japan.  Google Scholar
First citationJohnson, C. K. (1976). ORTEPII. Report ORNL-5138. Oak Ridge National Laboratory, Tennessee, USA.  Google Scholar
First citationRigaku (1998). RAPID-AUTO. Rigaku Corporation, Tokyo, Japan.  Google Scholar
First citationRigaku/MSC (2004). CrystalStructure. Rigaku/MSC Inc., The Woodlands, Texas, USA.  Google Scholar
First citationSheldrick, G. M. (2008). Acta Cryst. A64, 112–122.  Web of Science CrossRef CAS IUCr Journals Google Scholar
First citationVidenova-Adrabińska, V. (1996a). Acta Cryst. B52, 1048–1056.  CSD CrossRef Web of Science IUCr Journals Google Scholar
First citationVidenova-Adrabińska, V. (1996b). J. Mol. Struct. 374, 199–222.  Google Scholar
First citationYeo, L., Harris, K. D. M. & Guillaume, F. (1997). J. Solid State Chem. 128, 273–281.  CSD CrossRef CAS Web of Science Google Scholar

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