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ISSN: 2056-9890

(2S,3R)-2-[(4-Ethyl-2,3-dioxopiperazin-1-yl)carbonyl­amino]-3-hy­droxy­butyric acid monohydrate

aDepartment of Applied Chemistry, College of Science, Nanjing University of Technolgy, Xinmofan Road No. 5, Nanjing 210009, People's Republic of China, and bNanjing FroChem Tech Co. Ltd., Xinmofan Road No. 36 Nanjing, Nanjing 210009, People's Republic of China
*Correspondence e-mail: guocheng@njut.edu.cn

(Received 17 April 2008; accepted 12 June 2008; online 19 June 2008)

In the title compound, C11H17N3O6·H2O, an important building block of the medicine cefbuperazone sodium, the piperazine ring adopts a screw-boat conformation. Inter­molecular O—H⋯O and intra­molecular N—H⋯O hydrogen bonds are observed. The water mol­ecule participates as both donor and acceptor in this framework.

Related literature

For related literature, see: Anger et al. (2001[Anger, T., Madge, D. J., Mulla, M. & Riddall, D. (2001). J. Med. Chem. 44, 115-137.]); Özcan et al. (2003[Özcan, Y., İde, S., Şakiyan, İ. & Logoglu, E. (2003). J. Mol. Struct. 658, 207-213.]); Rondu et al. (1997[Rondu, F., Le Bihan, G., Wang, X., Lamouri, A., Touboul, E., Dive, G., Bellahsene, T., Pfeiffer, B., Renard, P., Guardiola-Lemaitre, B. et al. (1997). J. Med. Chem. 40, 3793-3803.]); Saikawa et al. (1981[Saikawa, I., Takano, S., Imaizumi, H., Takakura, I., Ochiai, H., Yasuda, T., Taki, H., Tai, M. & Kodama, Y. (1981). US Patent No. 4 263 292.]).

[Scheme 1]

Experimental

Crystal data
  • C11H17N3O6·H2O

  • Mr = 305.29

  • Orthorhombic, P 21 21 21

  • a = 9.4640 (19) Å

  • b = 11.389 (2) Å

  • c = 13.611 (3) Å

  • V = 1467.1 (5) Å3

  • Z = 4

  • Mo Kα radiation

  • μ = 0.12 mm−1

  • T = 293 (2) K

  • 0.40 × 0.30 × 0.20 mm

Data collection
  • Enraf–Nonius CAD-4 diffractometer

  • Absorption correction: ψ scan (North et al., 1968[North, A. C. T., Phillips, D. C. & Mathews, F. S. (1968). Acta Cryst. A24, 351-359.]) Tmin = 0.955, Tmax = 0.977

  • 1519 measured reflections

  • 1519 independent reflections

  • 1287 reflections with I > 2σ(I)

  • 3 standard reflections every 200 reflections intensity decay: <1%

Refinement
  • R[F2 > 2σ(F2)] = 0.041

  • wR(F2) = 0.105

  • S = 1.04

  • 1519 reflections

  • 205 parameters

  • 2 restraints

  • H atoms treated by a mixture of independent and constrained refinement

  • Δρmax = 0.16 e Å−3

  • Δρmin = −0.16 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
N3—H3A⋯O2 0.86 1.99 2.647 (3) 132
O7—H7A⋯O2 0.85 (2) 1.98 (2) 2.817 (4) 169 (5)
O4—H4⋯O7i 0.75 (5) 1.85 (5) 2.593 (4) 170 (5)
O6—H6⋯O1ii 0.83 (4) 1.95 (4) 2.772 (3) 167 (4)
O7—H7B⋯O6iii 0.815 (19) 2.07 (3) 2.803 (4) 149 (4)
Symmetry codes: (i) [x+{\script{1\over 2}}, -y+{\script{3\over 2}}, -z+1]; (ii) [-x+2, y-{\script{1\over 2}}, -z+{\script{1\over 2}}]; (iii) [-x+2, y+{\script{1\over 2}}, -z+{\script{1\over 2}}].

Data collection: CAD-4 Software (Enraf–Nonius, 1989[Enraf-Nonius (1989). CAD-4 Software. Enraf-Nonius, Delft, The Netherlands.]); cell refinement: CAD-4 Software; data reduction: XCAD4 (Harms & Wocadlo, 1995[Harms, K. & Wocadlo, S. (1995). XCAD4. University of Marburg, Germany.]); 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: SHELXTL (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); software used to prepare material for publication: PLATON (Spek, 2003[Spek, A. L. (2003). J. Appl. Cryst. 36, 7-13.]).

Supporting information


Comment top

Some derivatives of piperazine are important chemical materials (Saikawa et al., 1981) with pharmaceutical properties (Rondu et al., 1997) for example against migraine, and are calcium channel antagonist (Anger et al., 2001). As part of our studies in this area, we report here the crystal structure of the title compound, (I).

The refined molecular structure of (I) is shown in Fig. 1. The title compound includes a piperzaine and a threonine moieties, and the asymmetric unit is completed by one lattice water molecule. The piperazine ring adopts a screw-boat conformation with atoms C4 and C6 displaced by 0.104 (8) and 0.596 (2) Å, respectively, from the mean plane through atoms N1, C3, N2 and C5. The dihedral angle between N1/C3/N2/C5 and N2/C7/N3/C8 planes is 4.1°.

The threonine molecular group has two chiral atoms, C8 and C10, and adopts a configuration in agreement with previous reports (e.g. Özcan et al., 2003). The separation O6···O1 suggests an interaction between the ketone and the carboxyl group (Table 1). The water molecule is linked to the main molecule via O—H···O hydrogen bonds. These hydrogen bonds are effective in the stabilization of the crystal structure.

Related literature top

For related literature, see: Anger et al. (2001); Özcan et al. (2003); Rondu et al. (1997); Saikawa et al. (1981).

Experimental top

To a suspension of 2.0 g of L-threonine [(2S,3R)-2-amino-3-hydroxybutanoic acid] in methylene chloride (50 ml), 6.6 ml of trimethylchlorosilane were added, after which 7.1 ml of triethylamine were added dropwise at 273 K. The mixture was heated to 293 K for 2 h, and then a mixture of 4-ethyl-2,3-dioxo-1-piperazinecarbonyl chloride and triethylamine was added to the reaction mixture. After stirring for 1 h, the solvent was removed under reduced pressure. To the residue, 30 ml of water was added, and the pH was adjusted to 8 with NaHCO3, after which the solution was washed with 50 ml of ethyl acetate. Acetonitrile (50 ml) was added to the solution. The pH of the mixture was adjusted to 1 with HCl. The mixture was then saturated with NaCl, and the acetonitrile layer was thereafter separated. The aqueous layer was extracted with acetonitrile (3 × 50 ml), the combined acetonitrile layers were washed with saturated NaCl, and then distilled in vacuo to remove the solvent. The residue was recrystallized from ethanol to obtain 3.2 g of (I). Crystals of (I) suitable for X-ray diffraction were obtained by slow evaporation of an ethanol solution. 1H NMR (DMSO): δ 3.78–4.30 (m, 4H), 3.28–3.75 (m, 4H), 1.13 (d, 3H), 1.11 (t, 3H).

Refinement top

Hydroxyl H atoms were located in a difference map and refined freely. Water H atoms were found in a difference map and refined with a restrained geometry, O—H = 0.84 (2) Å. Other H atoms were positioned geometrically and refined using a riding model, with C—H = 0.96-0.98 Å, N—H = 0.86 Å and Uiso(H) = 1.2 or 1.5 Ueq of the carrier atom. Friedel pairs were merged and the absolute configuration was assigned from starting materials.

Computing details top

Data collection: CAD–4 Software (Enraf–Nonius, 1989); cell refinement: CAD–4 Software (Enraf–Nonius, 1989); data reduction: XCAD4 (Harms & Wocadlo, 1995); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: PLATON (Spek, 2003).

Figures top
[Figure 1] Fig. 1. A view of the molecular structure of (I), showing displacement ellipsoids at the 30% probability level. Dashed lines indicate O—H···O and N—H···O hydrogen bonds.
[Figure 2] Fig. 2. A packing diagram for (I). Hydrogen bonds are shown as dashed lines.
(2S,3R)-2-[(4-Ethyl-2,3-dioxopiperazin-1-yl)carbonylamino]-3-hydroxybutyric acid monohydrate top
Crystal data top
C11H17N3O6·H2OF(000) = 648
Mr = 305.29Dx = 1.382 Mg m3
Orthorhombic, P212121Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ac 2abCell parameters from 25 reflections
a = 9.4640 (19) Åθ = 10–13°
b = 11.389 (2) ŵ = 0.12 mm1
c = 13.611 (3) ÅT = 293 K
V = 1467.1 (5) Å3Block, colourless
Z = 40.40 × 0.30 × 0.20 mm
Data collection top
Enraf–Nonius CAD-4
diffractometer
1287 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tubeRint = 0.000
Graphite monochromatorθmax = 25.1°, θmin = 2.3°
ω/2θ scansh = 011
Absorption correction: ψ scan
(North et al., 1968)
k = 013
Tmin = 0.955, Tmax = 0.977l = 016
1519 measured reflections3 standard reflections every 200 reflections
1519 independent reflections intensity decay: <1%
Refinement top
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.041H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.105 w = 1/[σ2(Fo2) + (0.0652P)2 + 0.1558P]
where P = (Fo2 + 2Fc2)/3
S = 1.04(Δ/σ)max < 0.001
1519 reflectionsΔρmax = 0.16 e Å3
205 parametersΔρmin = 0.16 e Å3
2 restraintsExtinction correction: SHELXL97 (Sheldrick, 2008), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
Primary atom site location: structure-invariant direct methodsExtinction coefficient: 0.037 (4)
Crystal data top
C11H17N3O6·H2OV = 1467.1 (5) Å3
Mr = 305.29Z = 4
Orthorhombic, P212121Mo Kα radiation
a = 9.4640 (19) ŵ = 0.12 mm1
b = 11.389 (2) ÅT = 293 K
c = 13.611 (3) Å0.40 × 0.30 × 0.20 mm
Data collection top
Enraf–Nonius CAD-4
diffractometer
1287 reflections with I > 2σ(I)
Absorption correction: ψ scan
(North et al., 1968)
Rint = 0.000
Tmin = 0.955, Tmax = 0.9773 standard reflections every 200 reflections
1519 measured reflections intensity decay: <1%
1519 independent reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0412 restraints
wR(F2) = 0.105H atoms treated by a mixture of independent and constrained refinement
S = 1.04Δρmax = 0.16 e Å3
1519 reflectionsΔρmin = 0.16 e Å3
205 parameters
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
C10.2982 (5)0.8688 (4)0.3149 (3)0.0802 (14)
H1A0.22310.90610.27930.120*
H1B0.37790.92070.31830.120*
H1C0.26660.85050.38020.120*
C20.3399 (4)0.7585 (3)0.2637 (3)0.0517 (9)
H2A0.25880.70660.26010.062*
H2B0.36830.77710.19700.062*
C30.5900 (3)0.7122 (3)0.2851 (2)0.0401 (7)
C40.7064 (3)0.6501 (3)0.3450 (2)0.0385 (7)
C50.5156 (3)0.5303 (3)0.4161 (3)0.0549 (10)
H5A0.48930.47380.36590.066*
H5B0.49970.49450.47980.066*
C60.4272 (3)0.6364 (3)0.4065 (3)0.0544 (9)
H6B0.32820.61450.40910.065*
H6C0.44610.68910.46090.065*
C70.7632 (3)0.4841 (3)0.4570 (2)0.0403 (7)
C81.0033 (3)0.4380 (3)0.5054 (2)0.0373 (7)
H8A0.95250.40060.55980.045*
C91.1128 (3)0.5210 (3)0.5489 (2)0.0390 (7)
C101.0768 (3)0.3423 (3)0.4465 (2)0.0425 (7)
H10A1.13840.29840.49130.051*
C110.9774 (4)0.2570 (3)0.3990 (3)0.0570 (9)
H11A1.03060.19920.36330.085*
H11B0.91610.29820.35470.085*
H11C0.92190.21880.44870.085*
N10.4564 (2)0.6970 (2)0.31326 (19)0.0416 (7)
N20.6683 (3)0.5610 (2)0.4054 (2)0.0397 (6)
N30.9022 (2)0.5055 (2)0.44847 (19)0.0383 (6)
H3A0.93140.55940.40910.046*
O10.6257 (2)0.7700 (3)0.21398 (19)0.0635 (8)
O20.8292 (2)0.6821 (2)0.33274 (19)0.0534 (7)
O30.7145 (3)0.4047 (2)0.5047 (2)0.0648 (8)
O41.1991 (3)0.4638 (2)0.6080 (2)0.0654 (8)
H41.254 (6)0.501 (4)0.632 (3)0.072 (15)*
O51.1208 (2)0.6236 (2)0.53094 (18)0.0506 (6)
O61.1642 (3)0.4009 (2)0.3763 (2)0.0600 (7)
H61.217 (5)0.354 (4)0.347 (3)0.064 (12)*
O70.9118 (3)0.9195 (3)0.3221 (2)0.0663 (8)
H7A0.894 (5)0.847 (2)0.332 (3)0.080*
H7B0.909 (5)0.937 (4)0.2641 (17)0.080*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
C10.071 (3)0.088 (3)0.081 (3)0.038 (3)0.034 (3)0.023 (3)
C20.0347 (16)0.063 (2)0.057 (2)0.0056 (17)0.0130 (16)0.0023 (18)
C30.0329 (15)0.0434 (17)0.0441 (17)0.0010 (14)0.0026 (14)0.0032 (15)
C40.0277 (15)0.0402 (16)0.0476 (17)0.0004 (13)0.0058 (14)0.0067 (15)
C50.0280 (15)0.056 (2)0.081 (3)0.0076 (15)0.0075 (17)0.017 (2)
C60.0271 (15)0.067 (2)0.069 (2)0.0013 (16)0.0102 (17)0.016 (2)
C70.0325 (15)0.0342 (15)0.0541 (18)0.0024 (13)0.0063 (15)0.0054 (16)
C80.0310 (14)0.0399 (15)0.0410 (15)0.0004 (14)0.0004 (13)0.0091 (15)
C90.0337 (15)0.0446 (17)0.0389 (16)0.0053 (14)0.0036 (14)0.0016 (14)
C100.0366 (15)0.0394 (16)0.0515 (17)0.0076 (15)0.0094 (16)0.0010 (15)
C110.051 (2)0.0486 (18)0.071 (2)0.0071 (17)0.016 (2)0.0059 (19)
N10.0261 (12)0.0516 (16)0.0471 (15)0.0005 (11)0.0009 (12)0.0043 (13)
N20.0228 (11)0.0387 (13)0.0577 (15)0.0007 (11)0.0055 (12)0.0078 (13)
N30.0283 (12)0.0399 (14)0.0468 (14)0.0006 (11)0.0037 (12)0.0092 (12)
O10.0382 (13)0.0902 (19)0.0622 (14)0.0059 (13)0.0057 (12)0.0350 (15)
O20.0280 (11)0.0555 (14)0.0765 (16)0.0003 (11)0.0077 (12)0.0252 (13)
O30.0400 (13)0.0541 (15)0.100 (2)0.0055 (12)0.0030 (14)0.0349 (15)
O40.0657 (18)0.0583 (16)0.0722 (18)0.0039 (15)0.0344 (16)0.0042 (14)
O50.0444 (13)0.0402 (12)0.0672 (15)0.0013 (11)0.0009 (12)0.0009 (12)
O60.0441 (13)0.0687 (17)0.0672 (16)0.0033 (14)0.0184 (13)0.0123 (14)
O70.0633 (16)0.0645 (16)0.0710 (16)0.0032 (15)0.0206 (16)0.0012 (16)
Geometric parameters (Å, º) top
C1—C21.491 (5)C7—N31.343 (4)
C1—H1A0.9600C7—N21.438 (4)
C1—H1B0.9600C8—N31.451 (4)
C1—H1C0.9600C8—C101.521 (4)
C2—N11.470 (4)C8—C91.522 (4)
C2—H2A0.9700C8—H8A0.9800
C2—H2B0.9700C9—O51.196 (4)
C3—O11.218 (4)C9—O41.319 (4)
C3—N11.333 (4)C10—O61.430 (4)
C3—C41.542 (4)C10—C111.499 (5)
C4—O21.229 (3)C10—H10A0.9800
C4—N21.354 (4)C11—H11A0.9600
C5—C61.476 (5)C11—H11B0.9600
C5—N21.495 (4)C11—H11C0.9600
C5—H5A0.9700N3—H3A0.8600
C5—H5B0.9700O4—H40.75 (5)
C6—N11.470 (4)O6—H60.83 (4)
C6—H6B0.9700O7—H7A0.85 (2)
C6—H6C0.9700O7—H7B0.815 (19)
C7—O31.205 (4)
C2—C1—H1A109.5N3—C8—C10113.6 (2)
C2—C1—H1B109.5N3—C8—C9109.1 (2)
H1A—C1—H1B109.5C10—C8—C9109.8 (2)
C2—C1—H1C109.5N3—C8—H8A108.1
H1A—C1—H1C109.5C10—C8—H8A108.1
H1B—C1—H1C109.5C9—C8—H8A108.1
N1—C2—C1112.7 (3)O5—C9—O4124.6 (3)
N1—C2—H2A109.1O5—C9—C8124.8 (3)
C1—C2—H2A109.1O4—C9—C8110.6 (3)
N1—C2—H2B109.1O6—C10—C11112.2 (3)
C1—C2—H2B109.1O6—C10—C8106.4 (3)
H2A—C2—H2B107.8C11—C10—C8113.9 (3)
O1—C3—N1124.2 (3)O6—C10—H10A108.1
O1—C3—C4118.0 (3)C11—C10—H10A108.1
N1—C3—C4117.8 (3)C8—C10—H10A108.1
O2—C4—N2123.8 (3)C10—C11—H11A109.5
O2—C4—C3117.8 (3)C10—C11—H11B109.5
N2—C4—C3118.3 (2)H11A—C11—H11B109.5
C6—C5—N2110.3 (3)C10—C11—H11C109.5
C6—C5—H5A109.6H11A—C11—H11C109.5
N2—C5—H5A109.6H11B—C11—H11C109.5
C6—C5—H5B109.6C3—N1—C2121.2 (3)
N2—C5—H5B109.6C3—N1—C6119.2 (3)
H5A—C5—H5B108.1C2—N1—C6118.6 (2)
N1—C6—C5110.7 (3)C4—N2—C7125.9 (2)
N1—C6—H6B109.5C4—N2—C5119.5 (3)
C5—C6—H6B109.5C7—N2—C5114.4 (2)
N1—C6—H6C109.5C7—N3—C8120.2 (3)
C5—C6—H6C109.5C7—N3—H3A119.9
H6B—C6—H6C108.1C8—N3—H3A119.9
O3—C7—N3123.9 (3)C9—O4—H4115 (4)
O3—C7—N2118.8 (3)C10—O6—H6111 (3)
N3—C7—N2117.3 (3)H7A—O7—H7B113 (5)
O1—C3—C4—O216.1 (5)C1—C2—N1—C672.6 (4)
N1—C3—C4—O2165.3 (3)C5—C6—N1—C344.8 (4)
O1—C3—C4—N2161.7 (3)C5—C6—N1—C2146.7 (3)
N1—C3—C4—N216.9 (4)O2—C4—N2—C76.0 (5)
N2—C5—C6—N155.3 (4)C3—C4—N2—C7171.7 (3)
N3—C8—C9—O56.4 (4)O2—C4—N2—C5179.1 (3)
C10—C8—C9—O5118.6 (3)C3—C4—N2—C53.2 (4)
N3—C8—C9—O4174.5 (3)O3—C7—N2—C4176.4 (3)
C10—C8—C9—O460.4 (3)N3—C7—N2—C43.4 (5)
N3—C8—C10—O667.5 (3)O3—C7—N2—C51.3 (5)
C9—C8—C10—O654.9 (3)N3—C7—N2—C5178.5 (3)
N3—C8—C10—C1156.5 (4)C6—C5—N2—C432.7 (5)
C9—C8—C10—C11179.0 (3)C6—C5—N2—C7151.8 (3)
O1—C3—N1—C25.0 (5)O3—C7—N3—C85.7 (5)
C4—C3—N1—C2176.5 (3)N2—C7—N3—C8174.5 (2)
O1—C3—N1—C6173.2 (3)C10—C8—N3—C7101.8 (3)
C4—C3—N1—C68.3 (4)C9—C8—N3—C7135.4 (3)
C1—C2—N1—C395.7 (4)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N3—H3A···O20.861.992.647 (3)132
O7—H7A···O20.85 (2)1.98 (2)2.817 (4)169 (5)
O4—H4···O7i0.75 (5)1.85 (5)2.593 (4)170 (5)
O6—H6···O1ii0.83 (4)1.95 (4)2.772 (3)167 (4)
O7—H7B···O6iii0.82 (2)2.07 (3)2.803 (4)149 (4)
Symmetry codes: (i) x+1/2, y+3/2, z+1; (ii) x+2, y1/2, z+1/2; (iii) x+2, y+1/2, z+1/2.

Experimental details

Crystal data
Chemical formulaC11H17N3O6·H2O
Mr305.29
Crystal system, space groupOrthorhombic, P212121
Temperature (K)293
a, b, c (Å)9.4640 (19), 11.389 (2), 13.611 (3)
V3)1467.1 (5)
Z4
Radiation typeMo Kα
µ (mm1)0.12
Crystal size (mm)0.40 × 0.30 × 0.20
Data collection
DiffractometerEnraf–Nonius CAD-4
diffractometer
Absorption correctionψ scan
(North et al., 1968)
Tmin, Tmax0.955, 0.977
No. of measured, independent and
observed [I > 2σ(I)] reflections
1519, 1519, 1287
Rint0.000
(sin θ/λ)max1)0.598
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.041, 0.105, 1.04
No. of reflections1519
No. of parameters205
No. of restraints2
H-atom treatmentH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å3)0.16, 0.16

Computer programs: CAD–4 Software (Enraf–Nonius, 1989), XCAD4 (Harms & Wocadlo, 1995), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), SHELXTL (Sheldrick, 2008), PLATON (Spek, 2003).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N3—H3A···O20.861.992.647 (3)132.0
O7—H7A···O20.85 (2)1.98 (2)2.817 (4)169 (5)
O4—H4···O7i0.75 (5)1.85 (5)2.593 (4)170 (5)
O6—H6···O1ii0.83 (4)1.95 (4)2.772 (3)167 (4)
O7—H7B···O6iii0.815 (19)2.07 (3)2.803 (4)149 (4)
Symmetry codes: (i) x+1/2, y+3/2, z+1; (ii) x+2, y1/2, z+1/2; (iii) x+2, y+1/2, z+1/2.
 

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