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

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ISSN: 2056-9890

2-[3,5-Dioxo-4-(pyridin-3-yl)piperazin-1-yl]acetic acid

aDepartment of Chemistry, Yazd Branch, Islamic Azad University, PO Box 89195-155, Yazd, Iran
*Correspondence e-mail: mhmosslemin@yahoo.com

(Received 21 January 2012; accepted 26 January 2012; online 4 February 2012)

In the title compound, C11H11N3O4, the 3,5-dioxopiperazine ring adopts an envelope conformation, with the N atom connecting to the –CH2COOH group on the flap. In the crystal, mol­ecules are linked by O—H⋯N hydrogen bonds to produce a linear chain running along the c axis. ππ stacking is observed between parallel pyridine rings of adjacent mol­ecules, the centroid–centroid distance being 3.834 (2) Å.

Related literature

For the pharmaceutical activity, see: Parcel (1961[Parcel, R. F. (1961). US Patent 2976290.]); Creighton et al. (1969[Creighton, A. M., Hellmann, K. & Whitecross, S. (1969). Nature (London), 222, 384-385.]); Hasinoff et al. (1998[Hasinoff, B. B., Hellmann, K., Herman, E. H. & Ferrans, V. J. (1998). Curr. Med. Chem. 5, 1-28.]). For related structures, see: Hasinoff et al. (2004[Hasinoff, B. B., Wu, X. & Yang, Y. (2004). J. Inorg. Biochem. 98, 616-624.]); Mancilla et al. (2002[Mancilla, T., Carrillo, L., Zamudio-Rivera, L. S., Beltran, H. I. & Farfan, N. (2002). Org. Prep. Proced. Int. 34, 87-94.]); Skrzypczak-Jankun et al. (1999[Skrzypczak-Jankun, E., Sucheck, S. & Smith, D. A. (1999). Private communication (refcode GOTSOX). CCDC, Cambridge, England.]); Hempel et al. (1981[Hempel, A., Camerman, N. & Camerman, A. (1981). Acta Cryst. A37, C58.]); Jolley et al. (1999[Jolley, J., Campbell, C. J., Castineiras, A., Yanovsky, A. I. & Nolan, K. B. (1999). Polyhedron, 18, 49-53.]); Liu et al. (1998[Liu, Q., Zhang, S.-W. & Shao, M.-C. (1998). Acta Cryst. C54, 439-440.]); Davies et al. (1998[Davies, H. O., Brown, D. A., Yanovsky, A. I. & Nolan, K. B. (1998). Inorg. Chim. Acta, 268, 313-316.]); Smith et al. (1992[Smith, D. A., Cramer, S., Sucheck, S. & Skrzypczak-Jankun, E. (1992). Tetrahedron Lett. 33, 7765-7768.]).

[Scheme 1]

Experimental

Crystal data
  • C11H11N3O4

  • Mr = 249.23

  • Orthorhombic, P b c a

  • a = 12.762 (2) Å

  • b = 7.9495 (10) Å

  • c = 22.218 (3) Å

  • V = 2254.0 (6) Å3

  • Z = 8

  • Mo Kα radiation

  • μ = 0.11 mm−1

  • T = 298 K

  • 0.3 × 0.07 × 0.06 mm

Data collection
  • Bruker SMART 1000 CCD diffractometer

  • Absorption correction: multi-scan (SADABS; Bruker, 2001[Bruker (2001). SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]) Tmin = 0.986, Tmax = 0.996

  • 5235 measured reflections

  • 2181 independent reflections

  • 1355 reflections with I > 2σ(I)

  • Rint = 0.082

Refinement
  • R[F2 > 2σ(F2)] = 0.083

  • wR(F2) = 0.139

  • S = 1.13

  • 2181 reflections

  • 167 parameters

  • 1 restraint

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

  • Δρmax = 0.19 e Å−3

  • Δρmin = −0.18 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
O4—H4⋯N1i 0.83 (3) 1.83 (3) 2.655 (4) 173 (5)
Symmetry code: (i) [x, -y+{\script{5\over 2}}, z+{\script{1\over 2}}].

Data collection: SMART (Bruker, 2007[Bruker (2007). SMART and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]); cell refinement: SAINT (Bruker, 2007[Bruker (2007). SMART and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]); data reduction: SAINT; program(s) used to solve structure: SHELXTL (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXTL; molecular graphics: ORTEP-3 for Windows (Farrugia, 1997[Farrugia, L. J. (1997). J. Appl. Cryst. 30, 565.]); software used to prepare material for publication: WinGX (Farrugia, 1999[Farrugia, L. J. (1999). J. Appl. Cryst. 32, 837-838.]).

Supporting information


Comment top

The interest in derivatives of piperazine-2,6-dione has significantly increased because of their practical usage. Some piperazine-2,6-diones were found to have pharmaceutical activity (Parcel, 1961). In this regard, piperazine-2,6-diones have been studied for the anticancerous activity, an interaction with other anticancerous drugs and sensitivity to radiation (Creighton et al., 1969; Hasinoff, et al., 1998). In spite of the importance of these compounds, at present, only 12 crystal structures of piperazines are available in the literature, (Hasinoff et al., 2004; Mancilla et al., 2002; Skrzypczak-Jankun et al., 1999; Hempel et al., 1981; Jolley et al., 1999; Liu et al., 1998; Davies et al., 1998 and Smith et al., 1992). Here, we report the synthesis and characterization of the title compound, I.

In this molecule, the six membered piperazine-2,6-dionering has an envelope conformation with the N3 atom out of plane. The dihedral angle between the pyridine ring and the five-atom planar portion of the piperazine-2,6-dione ring is 77.9 (9)°. Also, the angle between mean plane containing acetic acid moiety and pyridine ring is 15.7 (8)°. As it is clear from figure 2, in the crystal packing of title molecule, the intermolecular O—H···N hydrogen bonds (Table 1) seem to be effective in the stabilization of the crystal structure.

Related literature top

For the pharmaceutical activity, see: Parcel (1961); Creighton et al. (1969); Hasinoff et al. (1998). For related structures, see: Hasinoff et al. (2004); Mancilla et al. (2002); Skrzypczak-Jankun et al. (1999); Hempel et al. (1981); Jolley et al. (1999); Liu et al. (1998); Davies et al. (1998); Smith et al. (1992).

Experimental top

A solution of 3-aminopyridine (0.94 gr, 0.01 mole) in 20 ml pyridine was added to a solution of 1.91 gr (0.01 mole) nitrilotriacetic acid in 20 ml pyridine. The resulting solution was stirred at 313 K for 1 h, then 2.6 ml triphenyl phosphite was added dropwise, and the reaction mixture was stirred at 373 K for 10 h and at ambient temperature for 48 h. the product was obtained by addition of cold water to oyridine solution. X-ray quality crystals were obtained by slow diffusion of diethyl ether into a CH2Cl2 solution at room temperature.

Refinement top

The carboxyl H atom was located in a difference Fourier map and refined isotropically. Other H atoms were positioned geometrically with C—H = 0.93 and 0.97 Å for aromatic H and methylene H atoms, respectively, and constrained to ride on their parent atoms with Uiso(H) = 1.2Ueq(C).

Computing details top

Data collection: SMART (Bruker, 2007); cell refinement: SAINT (Bruker, 2007); data reduction: SAINT (Bruker, 2007); program(s) used to solve structure: SHELXTL (Sheldrick, 2008); program(s) used to refine structure: SHELXTL (Sheldrick, 2008); molecular graphics: ORTEP-3 for Windows (Farrugia, 1997); software used to prepare material for publication: WinGX (Farrugia, 1999).

Figures top
[Figure 1] Fig. 1. The molecular structure of the title molecule, with the atom-numbering scheme. Displacement ellipsoids are drawn at the 50% probability level.
[Figure 2] Fig. 2. Unit-cell packing diagram for (I).
2-[3,5-Dioxo-4-(pyridin-3-yl)piperazin-1-yl]acetic acid top
Crystal data top
C11H11N3O4F(000) = 1040
Mr = 249.23Dx = 1.469 Mg m3
Orthorhombic, PbcaMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ac 2abCell parameters from 5235 reflections
a = 12.762 (2) Åθ = 2.4–26°
b = 7.9495 (10) ŵ = 0.11 mm1
c = 22.218 (3) ÅT = 298 K
V = 2254.0 (6) Å3Block, colorless
Z = 80.3 × 0.07 × 0.06 mm
Data collection top
Bruker SMART 1000 CCD
diffractometer
1355 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.082
ϕ and ω scansθmax = 26.0°, θmin = 2.4°
Absorption correction: multi-scan
(SADABS; Bruker, 2001)
h = 1513
Tmin = 0.986, Tmax = 0.996k = 98
5235 measured reflectionsl = 2718
2181 independent 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)] = 0.083Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.139H atoms treated by a mixture of independent and constrained refinement
S = 1.13 w = 1/[σ2(Fo2) + (0.0234P)2 + 2.3505P]
where P = (Fo2 + 2Fc2)/3
2181 reflections(Δ/σ)max = 0.003
167 parametersΔρmax = 0.19 e Å3
1 restraintΔρmin = 0.18 e Å3
Crystal data top
C11H11N3O4V = 2254.0 (6) Å3
Mr = 249.23Z = 8
Orthorhombic, PbcaMo Kα radiation
a = 12.762 (2) ŵ = 0.11 mm1
b = 7.9495 (10) ÅT = 298 K
c = 22.218 (3) Å0.3 × 0.07 × 0.06 mm
Data collection top
Bruker SMART 1000 CCD
diffractometer
2181 independent reflections
Absorption correction: multi-scan
(SADABS; Bruker, 2001)
1355 reflections with I > 2σ(I)
Tmin = 0.986, Tmax = 0.996Rint = 0.082
5235 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0831 restraint
wR(F2) = 0.139H atoms treated by a mixture of independent and constrained refinement
S = 1.13Δρmax = 0.19 e Å3
2181 reflectionsΔρmin = 0.18 e Å3
167 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
xyzUiso*/Ueq
C10.6306 (3)0.9688 (5)0.48064 (15)0.0465 (10)
H10.63050.96350.43880.056*
C20.6268 (3)0.8204 (5)0.51293 (17)0.0468 (10)
H20.6240.71740.49320.056*
C30.6274 (3)0.8274 (5)0.57515 (16)0.0409 (9)
H30.62430.72960.5980.049*
C40.6326 (3)0.9824 (4)0.60224 (14)0.0352 (8)
C50.6357 (3)1.1239 (5)0.56714 (15)0.0420 (9)
H50.63881.22820.58610.05*
C60.5383 (3)1.0558 (4)0.69368 (15)0.0353 (8)
C70.5406 (3)1.0795 (5)0.76080 (15)0.0429 (9)
H7A0.55731.19570.77010.051*
H7B0.47211.05470.77740.051*
C80.7256 (3)0.9787 (5)0.69787 (16)0.0396 (9)
C90.7218 (3)1.0056 (5)0.76503 (15)0.0422 (9)
H9A0.77220.93240.78450.051*
H9B0.74041.12110.77420.051*
C100.6095 (4)0.9576 (4)0.85320 (15)0.0459 (10)
H10A0.65850.87230.86680.055*
H10B0.53960.91840.86290.055*
C110.6299 (3)1.1167 (5)0.88859 (15)0.0403 (9)
N10.6345 (3)1.1197 (4)0.50719 (13)0.0436 (8)
N20.6320 (2)1.0005 (4)0.66694 (11)0.0347 (7)
N30.6179 (2)0.9703 (3)0.78789 (11)0.0368 (7)
O10.4629 (2)1.0852 (4)0.66345 (12)0.0542 (8)
O20.8058 (2)0.9448 (4)0.67151 (13)0.0665 (9)
O30.6582 (3)1.2471 (3)0.86656 (12)0.0666 (9)
O40.6119 (3)1.0957 (4)0.94599 (11)0.0555 (8)
H40.624 (4)1.184 (3)0.9643 (18)0.075 (16)*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
C10.046 (2)0.073 (3)0.0202 (16)0.001 (2)0.0019 (16)0.0060 (17)
C20.047 (2)0.054 (2)0.039 (2)0.005 (2)0.0012 (18)0.0145 (18)
C30.048 (2)0.040 (2)0.0349 (19)0.003 (2)0.0048 (18)0.0003 (15)
C40.0376 (19)0.042 (2)0.0254 (17)0.0002 (17)0.0022 (15)0.0012 (15)
C50.050 (2)0.045 (2)0.032 (2)0.0020 (19)0.0027 (17)0.0003 (16)
C60.043 (2)0.0343 (18)0.0291 (17)0.0007 (17)0.0040 (15)0.0005 (15)
C70.042 (2)0.057 (2)0.0298 (19)0.002 (2)0.0034 (16)0.0072 (17)
C80.039 (2)0.049 (2)0.0312 (19)0.0054 (18)0.0010 (16)0.0000 (16)
C90.048 (2)0.055 (2)0.0230 (17)0.011 (2)0.0047 (15)0.0000 (16)
C100.069 (3)0.041 (2)0.0267 (19)0.002 (2)0.0033 (18)0.0004 (15)
C110.047 (2)0.047 (2)0.0272 (18)0.0006 (19)0.0003 (16)0.0007 (16)
N10.0453 (19)0.059 (2)0.0262 (16)0.0008 (17)0.0003 (14)0.0072 (14)
N20.0394 (16)0.0410 (17)0.0237 (14)0.0048 (14)0.0025 (12)0.0010 (12)
N30.053 (2)0.0360 (15)0.0218 (14)0.0003 (15)0.0027 (13)0.0013 (11)
O10.0466 (16)0.077 (2)0.0385 (15)0.0163 (16)0.0113 (12)0.0093 (14)
O20.0398 (16)0.121 (3)0.0391 (17)0.0152 (18)0.0009 (13)0.0150 (17)
O30.112 (3)0.0494 (16)0.0379 (15)0.0274 (19)0.0120 (17)0.0063 (14)
O40.091 (2)0.0530 (18)0.0222 (13)0.0052 (18)0.0078 (14)0.0028 (12)
Geometric parameters (Å, º) top
C1—N11.338 (5)C7—H7A0.97
C1—C21.381 (5)C7—H7B0.97
C1—H10.93C8—O21.210 (4)
C2—C31.383 (5)C8—N21.389 (4)
C2—H20.93C8—C91.508 (5)
C3—C41.373 (5)C9—N31.446 (4)
C3—H30.93C9—H9A0.97
C4—C51.369 (5)C9—H9B0.97
C4—N21.445 (4)C10—N31.459 (4)
C5—N11.332 (4)C10—C111.511 (5)
C5—H50.93C10—H10A0.97
C6—O11.197 (4)C10—H10B0.97
C6—N21.406 (4)C11—O31.202 (4)
C6—C71.504 (4)C11—O41.307 (4)
C7—N31.446 (4)O4—H40.829 (10)
N1—C1—C2122.5 (3)O2—C8—C9122.5 (3)
N1—C1—H1118.7N2—C8—C9116.4 (3)
C2—C1—H1118.7N3—C9—C8110.4 (3)
C1—C2—C3119.0 (4)N3—C9—H9A109.6
C1—C2—H2120.5C8—C9—H9A109.6
C3—C2—H2120.5N3—C9—H9B109.6
C4—C3—C2118.3 (4)C8—C9—H9B109.6
C4—C3—H3120.8H9A—C9—H9B108.1
C2—C3—H3120.8N3—C10—C11116.6 (3)
C5—C4—C3119.3 (3)N3—C10—H10A108.1
C5—C4—N2119.0 (3)C11—C10—H10A108.1
C3—C4—N2121.7 (3)N3—C10—H10B108.1
N1—C5—C4123.2 (4)C11—C10—H10B108.1
N1—C5—H5118.4H10A—C10—H10B107.3
C4—C5—H5118.4O3—C11—O4124.1 (4)
O1—C6—N2120.5 (3)O3—C11—C10124.2 (3)
O1—C6—C7123.3 (3)O4—C11—C10111.8 (3)
N2—C6—C7116.2 (3)C5—N1—C1117.7 (3)
N3—C7—C6110.6 (3)C8—N2—C6124.2 (3)
N3—C7—H7A109.5C8—N2—C4118.4 (3)
C6—C7—H7A109.5C6—N2—C4117.1 (3)
N3—C7—H7B109.5C7—N3—C9111.2 (3)
C6—C7—H7B109.5C7—N3—C10113.9 (3)
H7A—C7—H7B108.1C9—N3—C10115.5 (3)
O2—C8—N2121.1 (3)C11—O4—H4110 (3)
N1—C1—C2—C30.2 (6)O2—C8—N2—C40.3 (6)
C1—C2—C3—C40.5 (6)C9—C8—N2—C4177.6 (3)
C2—C3—C4—C50.8 (6)O1—C6—N2—C8173.7 (3)
C2—C3—C4—N2179.1 (3)C7—C6—N2—C84.6 (5)
C3—C4—C5—N10.4 (6)O1—C6—N2—C40.4 (5)
N2—C4—C5—N1178.7 (3)C7—C6—N2—C4177.9 (3)
O1—C6—C7—N3154.6 (3)C5—C4—N2—C899.6 (4)
N2—C6—C7—N327.2 (5)C3—C4—N2—C882.1 (5)
O2—C8—C9—N3154.6 (4)C5—C4—N2—C674.1 (4)
N2—C8—C9—N327.5 (5)C3—C4—N2—C6104.2 (4)
N3—C10—C11—O34.7 (6)C6—C7—N3—C960.3 (4)
N3—C10—C11—O4174.7 (4)C6—C7—N3—C10167.1 (3)
C4—C5—N1—C10.4 (6)C8—C9—N3—C760.4 (4)
C2—C1—N1—C50.7 (6)C8—C9—N3—C10167.8 (3)
O2—C8—N2—C6173.6 (4)C11—C10—N3—C764.7 (5)
C9—C8—N2—C64.4 (5)C11—C10—N3—C965.9 (5)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O4—H4···N1i0.83 (3)1.83 (3)2.655 (4)173 (5)
Symmetry code: (i) x, y+5/2, z+1/2.

Experimental details

Crystal data
Chemical formulaC11H11N3O4
Mr249.23
Crystal system, space groupOrthorhombic, Pbca
Temperature (K)298
a, b, c (Å)12.762 (2), 7.9495 (10), 22.218 (3)
V3)2254.0 (6)
Z8
Radiation typeMo Kα
µ (mm1)0.11
Crystal size (mm)0.3 × 0.07 × 0.06
Data collection
DiffractometerBruker SMART 1000 CCD
diffractometer
Absorption correctionMulti-scan
(SADABS; Bruker, 2001)
Tmin, Tmax0.986, 0.996
No. of measured, independent and
observed [I > 2σ(I)] reflections
5235, 2181, 1355
Rint0.082
(sin θ/λ)max1)0.617
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.083, 0.139, 1.13
No. of reflections2181
No. of parameters167
No. of restraints1
H-atom treatmentH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å3)0.19, 0.18

Computer programs: SMART (Bruker, 2007), SAINT (Bruker, 2007), SHELXTL (Sheldrick, 2008), ORTEP-3 for Windows (Farrugia, 1997), WinGX (Farrugia, 1999).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O4—H4···N1i0.83 (3)1.83 (3)2.655 (4)173 (5)
Symmetry code: (i) x, y+5/2, z+1/2.
 

Acknowledgements

The author is grateful to the Islamic Azad University, Yazd Branch, for financial support.

References

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