organic compounds
Ethyl 4-(3-bromophenyl)-6-methyl-2-oxo-1,2,3,4-tetrahydropyrimidine-5-carboxylate
aSchool of Display and Chemical Engineering, Yeungnam University, Gyeongsan, Gyeongbuk 712-749, Republic of Korea, bCentre of Advanced Study in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai 600 025, India, and cDepartment of Chemistry, Karnatak Universitys Karnatak Science College, Dharwad 580 001, Karnataka, India
*Correspondence e-mail: yuvraj_pd@yahoo.co.in
In the title compound, C14H15BrN2O3, the dihydropyrimidinone ring adopts a boat conformation. In the crystal, adjacent molecules are linked through N—H⋯O hydrogen bonds forming an R22(8) ring motif and generating a zigzag chain extending in [010].
Related literature
For general background to and the pharmaceutical applications of pyrimidinones, see: Biginelli (1891); Atwal (1990); Kappe (2000). For a related structure, see: Fun et al. (2009). For ring conformations, see: Cremer & Pople (1975). For hydrogen-bond motifs, see: Bernstein et al. (1995).
Experimental
Crystal data
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Refinement
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Data collection: APEX2 (Bruker, 2008); cell SAINT (Bruker, 2008); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 (Farrugia, 1997); software used to prepare material for publication: SHELXL97 and PLATON (Spek, 2009).
Supporting information
https://doi.org/10.1107/S1600536810049019/bt5419sup1.cif
contains datablocks global, I. DOI:Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S1600536810049019/bt5419Isup2.hkl
A mixture of ethylacetoacetate (5 mmol), 3-bromobenzaldehyde (5 mmol) and urea (6 mmol) was refluxed in ethanol in the presence of concentrated hydrochloric acid as catalyst. After the completion of reaction, it was quenched in ice cold water and the obtained precipitate was filtered, dried and crystallized from ethanol to obtain the title compound.
All H atoms were positioned geometrically (N—H = 0.86 Å, C—H = 0.93–0.98 Å) and allowed to ride on their parent atoms, with 1.5Ueq(C) for methyl H and 1.2 Ueq(C,N) for other H atoms.
In recent years, acid-catalyzed cyclocondensation of β-ketoesters with aromatic and ureas, known as the Biginelli reaction, has attracted remarkable attention. The resulting dihydropyrimidinones (DHPM) have drawn wide-spread interest due to their broad range of therapeutic and pharmacological properties (Kappe, 2000). Owing to this background and in order to obtain detailed information on its the x-ray structure of the title compound has been determined and is discussed here.
The ORTEP plot of the title molecule is shown in Fig.1. In the present structure dihydropyrimidinone ring adopts a boat conformation with atoms N2 and C7 deviating by 0.159 (2) and 0.214 (2) Å, respectively from the least square plane defined by the remaining atoms N1/C8/C9/C10 in the ring.
The puckering parameters (Cremer & Pople, 1975) are Q = 0.339 (2) Å;Θ = 74.9 (3)° and φ = 50.2 (3)°. Atom Br1 deviates from the plane of the C1—C6 benzene ring by -0.024 (1) Å. The ethyl acetate group shows an extended conformation [C11—O3—C12—C13] = 174.7 (2)°. In the the molecules at (x, y, z), -x,-1/2 + y,1/2 - z,and -x,1/2 + y,1/2 - z are linked by N(1)—H(1 A)···O(1) and N(2)—H(2 A)···O(1) hydrogen bonds and forming a ring motif R22(8) and generating a one dimensional chain extending in [010] direction.
For general background and the pharmaceutical applications of pyrimidinones, see: Biginelli (1891); Atwal (1990); Kappe (2000). For a related structure, see: Fun et al. (2009). For ring conformations, see: Cremer & Pople (1975). For hydrogen-bond motifs, see: Bernstein et al. (1995).
Data collection: APEX2 (Bruker, 2008); cell
SAINT (Bruker, 2008); data reduction: SAINT (Bruker, 2008); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 (Farrugia, 1997); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008) and PLATON (Spek, 2009).C14H15BrN2O3 | F(000) = 688 |
Mr = 339.19 | Dx = 1.588 Mg m−3 |
Monoclinic, P21/c | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: -P 2ybc | Cell parameters from 754 reflections |
a = 12.5184 (11) Å | θ = 1.8–28.4° |
b = 7.3412 (5) Å | µ = 2.91 mm−1 |
c = 17.0426 (15) Å | T = 293 K |
β = 115.086 (6)° | Block, colourless |
V = 1418.5 (2) Å3 | 0.25 × 0.23 × 0.2 mm |
Z = 4 |
Bruker SMART APEXII area-detector diffractometer | 3541 independent reflections |
Radiation source: fine-focus sealed tube | 2597 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.033 |
ω and φ scans | θmax = 28.4°, θmin = 1.8° |
Absorption correction: multi-scan (SADABS; Bruker, 2008) | h = −16→14 |
Tmin = 0.488, Tmax = 0.559 | k = −9→9 |
13419 measured reflections | l = −22→22 |
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)] = 0.034 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.092 | H-atom parameters constrained |
S = 1.02 | w = 1/[σ2(Fo2) + (0.0446P)2 + 0.4545P] where P = (Fo2 + 2Fc2)/3 |
3541 reflections | (Δ/σ)max = 0.001 |
183 parameters | Δρmax = 0.32 e Å−3 |
0 restraints | Δρmin = −0.57 e Å−3 |
C14H15BrN2O3 | V = 1418.5 (2) Å3 |
Mr = 339.19 | Z = 4 |
Monoclinic, P21/c | Mo Kα radiation |
a = 12.5184 (11) Å | µ = 2.91 mm−1 |
b = 7.3412 (5) Å | T = 293 K |
c = 17.0426 (15) Å | 0.25 × 0.23 × 0.2 mm |
β = 115.086 (6)° |
Bruker SMART APEXII area-detector diffractometer | 3541 independent reflections |
Absorption correction: multi-scan (SADABS; Bruker, 2008) | 2597 reflections with I > 2σ(I) |
Tmin = 0.488, Tmax = 0.559 | Rint = 0.033 |
13419 measured reflections |
R[F2 > 2σ(F2)] = 0.034 | 0 restraints |
wR(F2) = 0.092 | H-atom parameters constrained |
S = 1.02 | Δρmax = 0.32 e Å−3 |
3541 reflections | Δρmin = −0.57 e Å−3 |
183 parameters |
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. |
x | y | z | Uiso*/Ueq | ||
Br1 | 0.44441 (3) | −0.16428 (4) | 0.393184 (18) | 0.06851 (13) | |
O1 | −0.01129 (13) | 0.45992 (18) | 0.25987 (9) | 0.0366 (3) | |
O2 | 0.19555 (17) | 0.5721 (2) | −0.01580 (10) | 0.0542 (4) | |
O3 | 0.20747 (13) | 0.2739 (2) | 0.01176 (9) | 0.0398 (3) | |
N1 | 0.07460 (14) | 0.3000 (2) | 0.18856 (10) | 0.0300 (3) | |
H1A | 0.0413 | 0.2007 | 0.1932 | 0.036* | |
N2 | 0.07540 (15) | 0.6114 (2) | 0.18553 (10) | 0.0328 (4) | |
H2A | 0.0724 | 0.7129 | 0.2097 | 0.039* | |
C1 | 0.37388 (19) | 0.3902 (3) | 0.25000 (14) | 0.0394 (5) | |
H1 | 0.3602 | 0.5013 | 0.2212 | 0.047* | |
C2 | 0.4823 (2) | 0.3559 (3) | 0.31773 (15) | 0.0471 (5) | |
H2 | 0.5408 | 0.4446 | 0.3338 | 0.056* | |
C3 | 0.5056 (2) | 0.1925 (3) | 0.36196 (14) | 0.0455 (5) | |
H3 | 0.5785 | 0.1701 | 0.4077 | 0.055* | |
C4 | 0.41681 (19) | 0.0634 (3) | 0.33589 (13) | 0.0390 (5) | |
C5 | 0.30810 (18) | 0.0945 (3) | 0.26915 (12) | 0.0349 (4) | |
H5 | 0.2498 | 0.0056 | 0.2536 | 0.042* | |
C6 | 0.28529 (16) | 0.2598 (3) | 0.22473 (11) | 0.0287 (4) | |
C7 | 0.16221 (16) | 0.2905 (2) | 0.15251 (11) | 0.0271 (4) | |
H7 | 0.1428 | 0.1848 | 0.1138 | 0.033* | |
C8 | 0.04431 (16) | 0.4545 (2) | 0.21425 (11) | 0.0285 (4) | |
C9 | 0.11175 (17) | 0.6132 (2) | 0.11857 (11) | 0.0293 (4) | |
C10 | 0.15120 (16) | 0.4584 (2) | 0.09844 (11) | 0.0281 (4) | |
C11 | 0.18583 (17) | 0.4468 (3) | 0.02604 (11) | 0.0329 (4) | |
C12 | 0.2432 (2) | 0.2459 (4) | −0.05813 (13) | 0.0446 (5) | |
H12A | 0.3109 | 0.3214 | −0.0493 | 0.054* | |
H12B | 0.1793 | 0.2784 | −0.1132 | 0.054* | |
C13 | 0.2736 (3) | 0.0503 (4) | −0.05805 (18) | 0.0688 (8) | |
H13A | 0.3368 | 0.0196 | −0.0033 | 0.103* | |
H13B | 0.2979 | 0.0279 | −0.1036 | 0.103* | |
H13C | 0.2059 | −0.0231 | −0.0672 | 0.103* | |
C14 | 0.1005 (2) | 0.7953 (3) | 0.07619 (13) | 0.0397 (5) | |
H14A | 0.1762 | 0.8535 | 0.0982 | 0.060* | |
H14B | 0.0463 | 0.8696 | 0.0885 | 0.060* | |
H14C | 0.0716 | 0.7794 | 0.0147 | 0.060* |
U11 | U22 | U33 | U12 | U13 | U23 | |
Br1 | 0.0843 (2) | 0.04469 (16) | 0.06112 (18) | 0.01772 (13) | 0.01586 (15) | 0.02071 (12) |
O1 | 0.0494 (8) | 0.0265 (7) | 0.0486 (8) | 0.0023 (6) | 0.0348 (7) | 0.0010 (6) |
O2 | 0.0830 (12) | 0.0447 (10) | 0.0545 (9) | 0.0032 (8) | 0.0483 (9) | 0.0133 (8) |
O3 | 0.0568 (9) | 0.0381 (8) | 0.0374 (7) | −0.0002 (7) | 0.0322 (7) | −0.0014 (6) |
N1 | 0.0377 (8) | 0.0216 (7) | 0.0397 (8) | −0.0004 (6) | 0.0250 (7) | 0.0030 (6) |
N2 | 0.0496 (10) | 0.0197 (7) | 0.0374 (8) | −0.0007 (6) | 0.0267 (8) | −0.0020 (6) |
C1 | 0.0426 (11) | 0.0347 (10) | 0.0429 (11) | −0.0015 (9) | 0.0202 (9) | 0.0064 (9) |
C2 | 0.0382 (11) | 0.0504 (14) | 0.0514 (12) | −0.0075 (10) | 0.0178 (10) | 0.0000 (10) |
C3 | 0.0401 (11) | 0.0548 (14) | 0.0389 (11) | 0.0097 (10) | 0.0140 (9) | 0.0021 (10) |
C4 | 0.0519 (12) | 0.0331 (11) | 0.0352 (9) | 0.0121 (9) | 0.0216 (9) | 0.0059 (8) |
C5 | 0.0441 (11) | 0.0278 (9) | 0.0354 (9) | 0.0015 (8) | 0.0195 (9) | −0.0002 (8) |
C6 | 0.0362 (9) | 0.0273 (9) | 0.0291 (8) | 0.0036 (7) | 0.0202 (8) | 0.0001 (7) |
C7 | 0.0356 (9) | 0.0219 (8) | 0.0289 (8) | −0.0002 (7) | 0.0186 (7) | −0.0004 (7) |
C8 | 0.0327 (9) | 0.0247 (9) | 0.0312 (8) | 0.0001 (7) | 0.0165 (8) | 0.0016 (7) |
C9 | 0.0334 (9) | 0.0258 (9) | 0.0289 (8) | −0.0037 (7) | 0.0133 (7) | 0.0021 (7) |
C10 | 0.0330 (9) | 0.0269 (9) | 0.0261 (8) | −0.0017 (7) | 0.0142 (7) | 0.0019 (7) |
C11 | 0.0358 (10) | 0.0356 (10) | 0.0284 (8) | −0.0012 (8) | 0.0146 (8) | 0.0015 (8) |
C12 | 0.0493 (12) | 0.0619 (15) | 0.0323 (10) | 0.0057 (11) | 0.0266 (9) | −0.0014 (10) |
C13 | 0.099 (2) | 0.0677 (19) | 0.0591 (15) | 0.0209 (16) | 0.0522 (16) | −0.0020 (14) |
C14 | 0.0533 (12) | 0.0255 (9) | 0.0433 (11) | 0.0000 (8) | 0.0235 (10) | 0.0065 (8) |
Br1—C4 | 1.892 (2) | C4—C5 | 1.373 (3) |
O1—C8 | 1.245 (2) | C5—C6 | 1.394 (3) |
O2—C11 | 1.202 (2) | C5—H5 | 0.9300 |
O3—C11 | 1.341 (2) | C6—C7 | 1.527 (3) |
O3—C12 | 1.453 (2) | C7—C10 | 1.510 (2) |
N1—C8 | 1.328 (2) | C7—H7 | 0.9800 |
N1—C7 | 1.469 (2) | C9—C10 | 1.340 (3) |
N1—H1A | 0.8600 | C9—C14 | 1.497 (3) |
N2—C8 | 1.371 (2) | C10—C11 | 1.474 (2) |
N2—C9 | 1.396 (2) | C12—C13 | 1.486 (4) |
N2—H2A | 0.8600 | C12—H12A | 0.9700 |
C1—C2 | 1.382 (3) | C12—H12B | 0.9700 |
C1—C6 | 1.388 (3) | C13—H13A | 0.9600 |
C1—H1 | 0.9300 | C13—H13B | 0.9600 |
C2—C3 | 1.380 (3) | C13—H13C | 0.9600 |
C2—H2 | 0.9300 | C14—H14A | 0.9600 |
C3—C4 | 1.383 (3) | C14—H14B | 0.9600 |
C3—H3 | 0.9300 | C14—H14C | 0.9600 |
C11—O3—C12 | 116.02 (16) | O1—C8—N1 | 123.16 (16) |
C8—N1—C7 | 123.15 (15) | O1—C8—N2 | 120.97 (16) |
C8—N1—H1A | 118.4 | N1—C8—N2 | 115.85 (16) |
C7—N1—H1A | 118.4 | C10—C9—N2 | 118.96 (16) |
C8—N2—C9 | 122.68 (15) | C10—C9—C14 | 127.08 (17) |
C8—N2—H2A | 118.7 | N2—C9—C14 | 113.95 (17) |
C9—N2—H2A | 118.7 | C9—C10—C11 | 122.34 (16) |
C2—C1—C6 | 120.4 (2) | C9—C10—C7 | 118.95 (15) |
C2—C1—H1 | 119.8 | C11—C10—C7 | 118.71 (16) |
C6—C1—H1 | 119.8 | O2—C11—O3 | 122.56 (17) |
C3—C2—C1 | 121.3 (2) | O2—C11—C10 | 126.29 (19) |
C3—C2—H2 | 119.3 | O3—C11—C10 | 111.15 (16) |
C1—C2—H2 | 119.3 | O3—C12—C13 | 107.72 (19) |
C2—C3—C4 | 117.7 (2) | O3—C12—H12A | 110.2 |
C2—C3—H3 | 121.1 | C13—C12—H12A | 110.2 |
C4—C3—H3 | 121.1 | O3—C12—H12B | 110.2 |
C5—C4—C3 | 122.09 (19) | C13—C12—H12B | 110.2 |
C5—C4—Br1 | 118.33 (17) | H12A—C12—H12B | 108.5 |
C3—C4—Br1 | 119.58 (16) | C12—C13—H13A | 109.5 |
C4—C5—C6 | 119.84 (19) | C12—C13—H13B | 109.5 |
C4—C5—H5 | 120.1 | H13A—C13—H13B | 109.5 |
C6—C5—H5 | 120.1 | C12—C13—H13C | 109.5 |
C1—C6—C5 | 118.62 (18) | H13A—C13—H13C | 109.5 |
C1—C6—C7 | 123.28 (17) | H13B—C13—H13C | 109.5 |
C5—C6—C7 | 118.07 (17) | C9—C14—H14A | 109.5 |
N1—C7—C10 | 109.00 (14) | C9—C14—H14B | 109.5 |
N1—C7—C6 | 110.31 (14) | H14A—C14—H14B | 109.5 |
C10—C7—C6 | 114.35 (15) | C9—C14—H14C | 109.5 |
N1—C7—H7 | 107.6 | H14A—C14—H14C | 109.5 |
C10—C7—H7 | 107.6 | H14B—C14—H14C | 109.5 |
C6—C7—H7 | 107.6 | ||
C6—C1—C2—C3 | −0.1 (3) | C9—N2—C8—N1 | 14.2 (3) |
C1—C2—C3—C4 | 0.4 (4) | C8—N2—C9—C10 | −20.2 (3) |
C2—C3—C4—C5 | −0.8 (3) | C8—N2—C9—C14 | 159.42 (18) |
C2—C3—C4—Br1 | 179.20 (17) | N2—C9—C10—C11 | 177.02 (16) |
C3—C4—C5—C6 | 0.8 (3) | C14—C9—C10—C11 | −2.5 (3) |
Br1—C4—C5—C6 | −179.11 (14) | N2—C9—C10—C7 | −3.8 (3) |
C2—C1—C6—C5 | 0.1 (3) | C14—C9—C10—C7 | 176.64 (18) |
C2—C1—C6—C7 | 177.96 (19) | N1—C7—C10—C9 | 28.6 (2) |
C4—C5—C6—C1 | −0.5 (3) | C6—C7—C10—C9 | −95.4 (2) |
C4—C5—C6—C7 | −178.46 (17) | N1—C7—C10—C11 | −152.22 (15) |
C8—N1—C7—C10 | −36.2 (2) | C6—C7—C10—C11 | 83.8 (2) |
C8—N1—C7—C6 | 90.2 (2) | C12—O3—C11—O2 | −0.3 (3) |
C1—C6—C7—N1 | −111.5 (2) | C12—O3—C11—C10 | −179.66 (16) |
C5—C6—C7—N1 | 66.4 (2) | C9—C10—C11—O2 | 8.7 (3) |
C1—C6—C7—C10 | 11.8 (2) | C7—C10—C11—O2 | −170.5 (2) |
C5—C6—C7—C10 | −170.39 (16) | C9—C10—C11—O3 | −171.96 (17) |
C7—N1—C8—O1 | −165.42 (17) | C7—C10—C11—O3 | 8.9 (2) |
C7—N1—C8—N2 | 16.2 (2) | C11—O3—C12—C13 | 174.7 (2) |
C9—N2—C8—O1 | −164.23 (17) |
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1A···O1i | 0.86 | 2.04 | 2.868 (2) | 161 |
N2—H2A···O1ii | 0.86 | 2.12 | 2.948 (2) | 162 |
Symmetry codes: (i) −x, y−1/2, −z+1/2; (ii) −x, y+1/2, −z+1/2. |
Experimental details
Crystal data | |
Chemical formula | C14H15BrN2O3 |
Mr | 339.19 |
Crystal system, space group | Monoclinic, P21/c |
Temperature (K) | 293 |
a, b, c (Å) | 12.5184 (11), 7.3412 (5), 17.0426 (15) |
β (°) | 115.086 (6) |
V (Å3) | 1418.5 (2) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 2.91 |
Crystal size (mm) | 0.25 × 0.23 × 0.2 |
Data collection | |
Diffractometer | Bruker SMART APEXII area-detector |
Absorption correction | Multi-scan (SADABS; Bruker, 2008) |
Tmin, Tmax | 0.488, 0.559 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 13419, 3541, 2597 |
Rint | 0.033 |
(sin θ/λ)max (Å−1) | 0.669 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.034, 0.092, 1.02 |
No. of reflections | 3541 |
No. of parameters | 183 |
H-atom treatment | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 0.32, −0.57 |
Computer programs: APEX2 (Bruker, 2008), SAINT (Bruker, 2008), SHELXS97 (Sheldrick, 2008), ORTEP-3 (Farrugia, 1997), SHELXL97 (Sheldrick, 2008) and PLATON (Spek, 2009).
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1A···O1i | 0.86 | 2.04 | 2.868 (2) | 161 |
N2—H2A···O1ii | 0.86 | 2.12 | 2.948 (2) | 162 |
Symmetry codes: (i) −x, y−1/2, −z+1/2; (ii) −x, y+1/2, −z+1/2. |
Acknowledgements
HY gratefully acknowledges Yeungnam University for offering the opportunity to work as a Full-Time Foreign Instructor. SS and DV thank the TBI X-ray Facility, CAS in Crystallography and Biophysics, University of Madras, India, for the data collection and the University Grants Commission (UGC&SAP) for financial support.
References
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In recent years, acid-catalyzed cyclocondensation of β-ketoesters with aromatic aldehydes and ureas, known as the Biginelli reaction, has attracted remarkable attention. The resulting dihydropyrimidinones (DHPM) have drawn wide-spread interest due to their broad range of therapeutic and pharmacological properties (Kappe, 2000). Owing to this background and in order to obtain detailed information on its molecular conformation, the x-ray structure of the title compound has been determined and is discussed here.
The ORTEP plot of the title molecule is shown in Fig.1. In the present structure dihydropyrimidinone ring adopts a boat conformation with atoms N2 and C7 deviating by 0.159 (2) and 0.214 (2) Å, respectively from the least square plane defined by the remaining atoms N1/C8/C9/C10 in the ring.
The puckering parameters (Cremer & Pople, 1975) are Q = 0.339 (2) Å;Θ = 74.9 (3)° and φ = 50.2 (3)°. Atom Br1 deviates from the plane of the C1—C6 benzene ring by -0.024 (1) Å. The ethyl acetate group shows an extended conformation [C11—O3—C12—C13] = 174.7 (2)°. In the crystal structure, the molecules at (x, y, z), -x,-1/2 + y,1/2 - z,and -x,1/2 + y,1/2 - z are linked by N(1)—H(1 A)···O(1) and N(2)—H(2 A)···O(1) hydrogen bonds and forming a ring motif R22(8) and generating a one dimensional chain extending in [010] direction.