organic compounds
of 3-[4-(pyrimidin-2-yl)piperazin-1-ium-1-yl]butanoate
aDepartment of Studies in Chemistry, University of Mysore, Manasagangotri, Mysore 570 006, India, and bDepartment of Chemistry, Keene State College, 229 Main Street, Keene, NH 03435-2001, USA
*Correspondence e-mail: jjasinski@keene.edu
The title compound, C12H18N4O2, crystallizes in the zwitterionic form with protonation at the N atom of the piperazine ring bearing the carboxylate group. The piperazine ring adopts a slightly distorted chair conformation. In the crystal, N—H⋯O hydrogen bonds are observed, forming chains along [010]. The packing is consolidated by C—H⋯O interactions, which generate a three-dimensional network.
Keywords: crystal structure; 3-(piperazin-1-ium-1-yl)butanoate; zwitterionic form; fused heterocyclic derivatives; aza-Michael reactions.
CCDC reference: 1020635
1. Related literature
For general background and pharmacological properties of fused heterocyclic derivatives, see: Amin et al. (2009); Ibrahim & El-Metwally (2010); Kuyper et al. (1996); Onal & Yıldırım (2007); Padmaja et al. (2009); Tollefson et al. (1991). For pharmacological properties of pyrimidines, see: Burdge (2000). For background to aza-Michael reactions, see: Arend et al.(1998); Vicario et al. (2005); Xu & Xia (2005). For related structures, see: Jin et al. (2012); Parvez et al. (2004); Yamuna et al. (2014a,b).
2. Experimental
2.1. Crystal data
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2.1.3. Refinement
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Data collection: CrysAlis PRO (Agilent, 2012); cell CrysAlis PRO; data reduction: CrysAlis RED; program(s) used to solve structure: SUPERFLIP (Palatinus & Chapuis, 2007); program(s) used to refine structure: SHELXL2012 (Sheldrick, 2008); molecular graphics: OLEX2 (Dolomanov et al., 2009); software used to prepare material for publication: OLEX2.
Supporting information
CCDC reference: 1020635
10.1107/S1600536814018972/bt6993sup1.cif
contains datablock I. DOI:Structure factors: contains datablock I. DOI: 10.1107/S1600536814018972/bt6993Isup2.hkl
Supporting information file. DOI: 10.1107/S1600536814018972/bt6993Isup3.cml
A mixture of 1-(2-pyrimidyl)piperazine, from sigma-aldrich (0.2 g, 1.22 mmol) and crotonic acid (but-2-enoic acid) (0.1048 g, 1.22 mmol ) were dissolved in DMSO, stirred well and warmed at 343 K for 20 minutes. After few days, X-ray quality crystals were obtained on slow evaporation (m.p.: 411-418 K).
H3 was refined isotropically and all of the remaining H atoms were placed in their calculated positions and then refined using the riding model with Atom—H lengths of 0.95Å (CH); 0.99Å (CH2); 0.98Å (CH3) or 1.00Å (NH). Isotropic displacement parameters for these atoms were set to 1.2 (CH, CH2, NH) or 1.5 (CH3) times Ueq of the parent atom. Idealised Me was refined as a rotating group. The title compound was refined as a twin with BASF = 0.41572.
Data collection: CrysAlis PRO (Agilent, 2012); cell
CrysAlis PRO (Agilent, 2012); data reduction: CrysAlis RED (Agilent, 2012); program(s) used to solve structure: SUPERFLIP (Palatinus & Chapuis, 2007); program(s) used to refine structure: SHELXL2012 (Sheldrick, 2008); molecular graphics: OLEX2 (Dolomanov et al., 2009); software used to prepare material for publication: OLEX2 (Dolomanov et al., 2009).Fig. 1. ORTEP drawing of (C12H18N4O2) showing the labeling scheme of the asymmetric unit of the title compound with 30% probability displacement ellipsoids. | |
Fig. 2. Molecular packing for (I), viewed along the b axis. Dashed lines indicate weak C—H···O intermolecular interactions in addition to N—H···O intermolecular hydrogen bonds which together form an extended three-dimensional supramolecular network structure. H atoms not involved in hydrogen bonding have been removed for clarity. |
C12H18N4O2 | F(000) = 536 |
Mr = 250.30 | Dx = 1.341 Mg m−3 |
Monoclinic, P21/c | Cu Kα radiation, λ = 1.54184 Å |
a = 13.5157 (6) Å | Cell parameters from 5404 reflections |
b = 7.8454 (3) Å | θ = 3.8–71.4° |
c = 12.2147 (5) Å | µ = 0.77 mm−1 |
β = 106.884 (5)° | T = 173 K |
V = 1239.36 (9) Å3 | Irregular, colourless |
Z = 4 | 0.32 × 0.22 × 0.06 mm |
Agilent Eos Gemini diffractometer | 3995 independent reflections |
Radiation source: Enhance (Cu) X-ray Source | 3668 reflections with I > 2σ(I) |
Detector resolution: 16.0416 pixels mm-1 | θmax = 71.2°, θmin = 3.4° |
ω scans | h = −16→16 |
Absorption correction: multi-scan (CrysAlis PRO and CrysAlis RED; Agilent, 2012) | k = −9→9 |
Tmin = 0.854, Tmax = 1.000 | l = −13→14 |
3995 measured reflections |
Refinement on F2 | Primary atom site location: structure-invariant direct methods |
Least-squares matrix: full | Hydrogen site location: mixed |
R[F2 > 2σ(F2)] = 0.053 | H atoms treated by a mixture of independent and constrained refinement |
wR(F2) = 0.149 | w = 1/[σ2(Fo2) + (0.0768P)2 + 0.6386P] where P = (Fo2 + 2Fc2)/3 |
S = 1.06 | (Δ/σ)max < 0.001 |
3995 reflections | Δρmax = 0.36 e Å−3 |
169 parameters | Δρmin = −0.27 e Å−3 |
0 restraints |
C12H18N4O2 | V = 1239.36 (9) Å3 |
Mr = 250.30 | Z = 4 |
Monoclinic, P21/c | Cu Kα radiation |
a = 13.5157 (6) Å | µ = 0.77 mm−1 |
b = 7.8454 (3) Å | T = 173 K |
c = 12.2147 (5) Å | 0.32 × 0.22 × 0.06 mm |
β = 106.884 (5)° |
Agilent Eos Gemini diffractometer | 3995 measured reflections |
Absorption correction: multi-scan (CrysAlis PRO and CrysAlis RED; Agilent, 2012) | 3995 independent reflections |
Tmin = 0.854, Tmax = 1.000 | 3668 reflections with I > 2σ(I) |
R[F2 > 2σ(F2)] = 0.053 | 0 restraints |
wR(F2) = 0.149 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.06 | Δρmax = 0.36 e Å−3 |
3995 reflections | Δρmin = −0.27 e Å−3 |
169 parameters |
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. Refined as a 2-component twin. |
x | y | z | Uiso*/Ueq | ||
O1 | −0.15848 (13) | 0.4680 (3) | 0.29107 (16) | 0.0449 (5) | |
O2 | −0.05978 (12) | 0.4109 (2) | 0.17822 (15) | 0.0339 (4) | |
N1 | 0.16438 (12) | 0.1694 (2) | 0.44116 (14) | 0.0217 (4) | |
H1 | 0.1313 | 0.0618 | 0.4040 | 0.026* | |
N2 | 0.32869 (12) | 0.0043 (3) | 0.60849 (16) | 0.0287 (4) | |
N3 | 0.40034 (14) | 0.0836 (3) | 0.79721 (17) | 0.0324 (5) | |
N4 | 0.50457 (13) | 0.0549 (3) | 0.66957 (17) | 0.0336 (5) | |
C1 | −0.08258 (15) | 0.4025 (3) | 0.2726 (2) | 0.0277 (5) | |
C2 | −0.00940 (16) | 0.2979 (3) | 0.3691 (2) | 0.0308 (5) | |
H2A | −0.0174 | 0.3357 | 0.4434 | 0.037* | |
H2B | −0.0296 | 0.1763 | 0.3588 | 0.037* | |
C3 | 0.10322 (15) | 0.3150 (3) | 0.3722 (2) | 0.0260 (5) | |
H3 | 0.098 (2) | 0.289 (4) | 0.289 (3) | 0.041 (8)* | |
C4 | 0.16425 (15) | 0.1604 (3) | 0.56333 (18) | 0.0261 (5) | |
H4A | 0.0922 | 0.1532 | 0.5671 | 0.031* | |
H4B | 0.1959 | 0.2650 | 0.6040 | 0.031* | |
C5 | 0.22479 (15) | 0.0048 (3) | 0.6211 (2) | 0.0290 (5) | |
H5A | 0.2291 | 0.0053 | 0.7034 | 0.035* | |
H5B | 0.1880 | −0.1001 | 0.5866 | 0.035* | |
C6 | 0.32772 (15) | 0.0092 (3) | 0.48941 (19) | 0.0276 (5) | |
H6A | 0.2918 | −0.0928 | 0.4491 | 0.033* | |
H6B | 0.3995 | 0.0084 | 0.4845 | 0.033* | |
C7 | 0.27285 (14) | 0.1685 (3) | 0.43312 (18) | 0.0243 (4) | |
H7A | 0.3102 | 0.2707 | 0.4716 | 0.029* | |
H7B | 0.2719 | 0.1716 | 0.3518 | 0.029* | |
C8 | 0.41389 (15) | 0.0508 (3) | 0.69526 (18) | 0.0248 (4) | |
C9 | 0.48642 (19) | 0.1182 (3) | 0.8810 (2) | 0.0359 (5) | |
H9 | 0.4802 | 0.1456 | 0.9545 | 0.043* | |
C10 | 0.58388 (18) | 0.1162 (3) | 0.8665 (2) | 0.0372 (6) | |
H10 | 0.6444 | 0.1349 | 0.9284 | 0.045* | |
C11 | 0.58837 (17) | 0.0857 (3) | 0.7574 (2) | 0.0376 (6) | |
H11 | 0.6540 | 0.0864 | 0.7436 | 0.045* | |
C12 | 0.14735 (18) | 0.4895 (3) | 0.4145 (2) | 0.0329 (5) | |
H12A | 0.1545 | 0.4997 | 0.4964 | 0.049* | |
H12B | 0.1007 | 0.5784 | 0.3725 | 0.049* | |
H12C | 0.2153 | 0.5026 | 0.4019 | 0.049* |
U11 | U22 | U33 | U12 | U13 | U23 | |
O1 | 0.0322 (9) | 0.0605 (12) | 0.0415 (11) | 0.0190 (8) | 0.0099 (8) | 0.0110 (9) |
O2 | 0.0282 (8) | 0.0318 (8) | 0.0409 (10) | 0.0066 (6) | 0.0087 (7) | 0.0019 (7) |
N1 | 0.0143 (7) | 0.0280 (9) | 0.0214 (9) | 0.0003 (6) | 0.0028 (6) | 0.0038 (7) |
N2 | 0.0138 (8) | 0.0488 (11) | 0.0234 (9) | 0.0065 (7) | 0.0053 (7) | 0.0076 (8) |
N3 | 0.0284 (9) | 0.0427 (11) | 0.0266 (10) | 0.0100 (8) | 0.0088 (8) | 0.0026 (8) |
N4 | 0.0184 (8) | 0.0522 (12) | 0.0303 (10) | 0.0007 (8) | 0.0070 (8) | −0.0065 (9) |
C1 | 0.0200 (9) | 0.0303 (11) | 0.0295 (11) | −0.0011 (8) | 0.0018 (8) | 0.0025 (9) |
C2 | 0.0222 (10) | 0.0364 (12) | 0.0335 (12) | 0.0054 (9) | 0.0078 (9) | 0.0073 (10) |
C3 | 0.0200 (9) | 0.0287 (10) | 0.0259 (10) | 0.0018 (8) | 0.0014 (8) | 0.0052 (9) |
C4 | 0.0166 (9) | 0.0379 (12) | 0.0245 (10) | 0.0041 (8) | 0.0072 (8) | 0.0033 (9) |
C5 | 0.0158 (9) | 0.0441 (13) | 0.0282 (11) | 0.0042 (8) | 0.0084 (8) | 0.0112 (10) |
C6 | 0.0169 (9) | 0.0424 (13) | 0.0233 (10) | 0.0046 (8) | 0.0059 (8) | 0.0012 (9) |
C7 | 0.0154 (9) | 0.0373 (11) | 0.0204 (10) | −0.0038 (8) | 0.0055 (7) | 0.0012 (9) |
C8 | 0.0184 (9) | 0.0304 (10) | 0.0254 (11) | 0.0077 (8) | 0.0062 (8) | 0.0044 (9) |
C9 | 0.0359 (12) | 0.0428 (13) | 0.0264 (12) | 0.0102 (10) | 0.0051 (10) | −0.0020 (10) |
C10 | 0.0297 (11) | 0.0408 (13) | 0.0336 (13) | 0.0035 (10) | −0.0027 (10) | −0.0052 (10) |
C11 | 0.0199 (10) | 0.0495 (14) | 0.0407 (14) | 0.0000 (10) | 0.0046 (9) | −0.0103 (11) |
C12 | 0.0322 (11) | 0.0287 (11) | 0.0337 (13) | −0.0001 (9) | 0.0032 (10) | 0.0024 (10) |
O1—C1 | 1.226 (3) | C4—H4A | 0.9900 |
O2—C1 | 1.278 (3) | C4—H4B | 0.9900 |
N1—H1 | 1.0000 | C4—C5 | 1.524 (3) |
N1—C3 | 1.514 (2) | C5—H5A | 0.9900 |
N1—C4 | 1.494 (3) | C5—H5B | 0.9900 |
N1—C7 | 1.498 (2) | C6—H6A | 0.9900 |
N2—C5 | 1.457 (2) | C6—H6B | 0.9900 |
N2—C6 | 1.451 (3) | C6—C7 | 1.513 (3) |
N2—C8 | 1.369 (3) | C7—H7A | 0.9900 |
N3—C8 | 1.335 (3) | C7—H7B | 0.9900 |
N3—C9 | 1.335 (3) | C9—H9 | 0.9500 |
N4—C8 | 1.351 (3) | C9—C10 | 1.379 (3) |
N4—C11 | 1.336 (3) | C10—H10 | 0.9500 |
C1—C2 | 1.538 (3) | C10—C11 | 1.373 (4) |
C2—H2A | 0.9900 | C11—H11 | 0.9500 |
C2—H2B | 0.9900 | C12—H12A | 0.9800 |
C2—C3 | 1.518 (3) | C12—H12B | 0.9800 |
C3—H3 | 1.01 (3) | C12—H12C | 0.9800 |
C3—C12 | 1.523 (3) | ||
C3—N1—H1 | 106.5 | N2—C5—H5B | 109.4 |
C4—N1—H1 | 106.5 | C4—C5—H5A | 109.4 |
C4—N1—C3 | 115.63 (17) | C4—C5—H5B | 109.4 |
C4—N1—C7 | 110.51 (15) | H5A—C5—H5B | 108.0 |
C7—N1—H1 | 106.5 | N2—C6—H6A | 109.7 |
C7—N1—C3 | 110.70 (15) | N2—C6—H6B | 109.7 |
C6—N2—C5 | 112.18 (17) | N2—C6—C7 | 109.75 (18) |
C8—N2—C5 | 122.52 (19) | H6A—C6—H6B | 108.2 |
C8—N2—C6 | 121.99 (18) | C7—C6—H6A | 109.7 |
C8—N3—C9 | 115.4 (2) | C7—C6—H6B | 109.7 |
C11—N4—C8 | 115.6 (2) | N1—C7—C6 | 109.51 (16) |
O1—C1—O2 | 125.4 (2) | N1—C7—H7A | 109.8 |
O1—C1—C2 | 118.0 (2) | N1—C7—H7B | 109.8 |
O2—C1—C2 | 116.65 (19) | C6—C7—H7A | 109.8 |
C1—C2—H2A | 109.0 | C6—C7—H7B | 109.8 |
C1—C2—H2B | 109.0 | H7A—C7—H7B | 108.2 |
H2A—C2—H2B | 107.8 | N3—C8—N2 | 117.45 (18) |
C3—C2—C1 | 112.91 (18) | N3—C8—N4 | 126.3 (2) |
C3—C2—H2A | 109.0 | N4—C8—N2 | 116.26 (19) |
C3—C2—H2B | 109.0 | N3—C9—H9 | 118.3 |
N1—C3—C2 | 109.19 (17) | N3—C9—C10 | 123.5 (2) |
N1—C3—H3 | 105.9 (16) | C10—C9—H9 | 118.3 |
N1—C3—C12 | 113.11 (17) | C9—C10—H10 | 122.0 |
C2—C3—H3 | 100.5 (16) | C11—C10—C9 | 116.1 (2) |
C2—C3—C12 | 112.28 (19) | C11—C10—H10 | 122.0 |
C12—C3—H3 | 115.0 (17) | N4—C11—C10 | 123.0 (2) |
N1—C4—H4A | 109.6 | N4—C11—H11 | 118.5 |
N1—C4—H4B | 109.6 | C10—C11—H11 | 118.5 |
N1—C4—C5 | 110.12 (17) | C3—C12—H12A | 109.5 |
H4A—C4—H4B | 108.1 | C3—C12—H12B | 109.5 |
C5—C4—H4A | 109.6 | C3—C12—H12C | 109.5 |
C5—C4—H4B | 109.6 | H12A—C12—H12B | 109.5 |
N2—C5—C4 | 110.96 (17) | H12A—C12—H12C | 109.5 |
N2—C5—H5A | 109.4 | H12B—C12—H12C | 109.5 |
O1—C1—C2—C3 | −144.6 (2) | C6—N2—C5—C4 | −57.3 (3) |
O2—C1—C2—C3 | 36.8 (3) | C6—N2—C8—N3 | 163.5 (2) |
N1—C4—C5—N2 | 54.5 (2) | C6—N2—C8—N4 | −18.1 (3) |
N2—C6—C7—N1 | −59.2 (2) | C7—N1—C3—C2 | 172.41 (18) |
N3—C9—C10—C11 | 3.7 (4) | C7—N1—C3—C12 | −61.8 (2) |
C1—C2—C3—N1 | −161.91 (18) | C7—N1—C4—C5 | −55.5 (2) |
C1—C2—C3—C12 | 71.8 (3) | C8—N2—C5—C4 | 102.5 (2) |
C3—N1—C4—C5 | 177.77 (16) | C8—N2—C6—C7 | −100.4 (2) |
C3—N1—C7—C6 | −172.54 (17) | C8—N3—C9—C10 | −1.8 (4) |
C4—N1—C3—C2 | −61.0 (2) | C8—N4—C11—C10 | −1.8 (4) |
C4—N1—C3—C12 | 64.8 (2) | C9—N3—C8—N2 | 176.1 (2) |
C4—N1—C7—C6 | 58.0 (2) | C9—N3—C8—N4 | −2.2 (3) |
C5—N2—C6—C7 | 59.5 (2) | C9—C10—C11—N4 | −1.7 (4) |
C5—N2—C8—N3 | 5.7 (3) | C11—N4—C8—N2 | −174.3 (2) |
C5—N2—C8—N4 | −175.9 (2) | C11—N4—C8—N3 | 4.0 (4) |
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1···O2i | 1.00 | 1.67 | 2.653 (2) | 168 |
C2—H2B···O2i | 0.99 | 2.51 | 3.277 (3) | 134 |
C4—H4B···O1ii | 0.99 | 2.58 | 3.428 (3) | 144 |
C7—H7B···O1i | 0.99 | 2.53 | 3.147 (3) | 120 |
C11—H11···O1iii | 0.95 | 2.47 | 3.352 (3) | 155 |
Symmetry codes: (i) −x, y−1/2, −z+1/2; (ii) −x, −y+1, −z+1; (iii) x+1, −y+1/2, z+1/2. |
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1···O2i | 1.00 | 1.67 | 2.653 (2) | 167.7 |
C2—H2B···O2i | 0.99 | 2.51 | 3.277 (3) | 133.8 |
C4—H4B···O1ii | 0.99 | 2.58 | 3.428 (3) | 143.5 |
C7—H7B···O1i | 0.99 | 2.53 | 3.147 (3) | 120.3 |
C11—H11···O1iii | 0.95 | 2.47 | 3.352 (3) | 155.0 |
Symmetry codes: (i) −x, y−1/2, −z+1/2; (ii) −x, −y+1, −z+1; (iii) x+1, −y+1/2, z+1/2. |
Acknowledgements
TSY thanks University of Mysore for research facilities and also grateful to the Principal, Maharani's Science College for Women, Mysore, for giving permission to do research. JPJ acknowledges the NSF–MRI program (grant No. CHE-1039027) for funds to purchase the X-ray diffractometer.
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Pyrimidines in general have been of much interest for biological and medical reasons and thus their chemistry has been investigated extensively (Onal & Yıldırım, 2007) and in many drugs used for the treatment of hypothyroidism and hypertension, in cancer chemotherapy or HIV infections (Burdge, 2000) and with related fused heterocyclic compounds that exhibit biological activities such as anticancer (Amin et al., 2009), antiviral (Ibrahim & El-Metwally, 2010), antibacterial (Kuyper et al., 1996) and antioxidant (Padmaja et al., 2009). Some pyrimidinylpiperazinyl compounds like buspirone and BuSpar (Tollefson et al., 1991) are used to treat anxiety. The incorporation of two moieties increases biological activity of both the molecules. Aza-Michael addition reaction has been extensively studied using a variety of catalysts as well as solvents and various researchers have also reported the utility of aza-Michael addition towards the synthesis of various pharmacological active compounds and proved useful in the synthesis of core intermediates of many natural products (Arend et al., 1998). The role of aza-Michael reaction in the synthesis of pharmacologically important families of β-amino carbonyl compounds and its derivatives is well documented in the literature (Vicario et al., 2005; Xu & Xia, 2005). Our research group has published many papers on incorporated heterocyclic ring structures, viz; 4-(pyrimidin-2-yl)piperazin-1-ium (E)-3-carboxyprop-2-enoate (Yamuna et al., 2014a); flupentixol tartarate (Yamuna et al., 2014b). Some related zwitterion structures are: 3,3'-(piperazine-1,4-diium-1,4-diyl)dipropionate dihydrate (Jin et al., 2012), enoxacin trihydrate[1-ethyl-6-fluoro-1,4-dihydro-4-oxo-7-(piperazin-4-ium-1-yl)-1,8- naphthyridine-3-carboxylate trihydrate] (Parvez et al., 2004). In view of the importance of derivatives of the incorporated heterocyclic pyrimidylpiperazines, this paper reports the crystal structure of the title zwitterionic compound, (I), 3-(4-Pyrimidin-2-yl-piperazin-1-ium-1-yl)-butanoate, C12H18N4O2 prepared from 2-(piperazin-1-yl)pyrimidine and but-2-enoic acid by aza-Michael addition reaction.
The title compound, (I), C12H18N4O2 crystallizes in the zwitterionic form with protonation on the N1 nitrogen atom of the piperazine ring (Fig. 1). In the compound, the piperazine ring adopts a slightly disordered chair conformation (puckering parameters Q, θ, and ϕ = 0.576 (2)Å, 3.0 (2)° and 282 (4)°, respectively. Bond lengths are in normal ranges. In the crystal, N—H···O intermolecular hydrogen bonds are observed forming 1D chains along [0 1 0] (Fig. 2). The packing is consolidated by weak C—H···O interactions which generate a three-dimensional network.