organic compounds
Z)-3,5-dioxo-1-phenylpyrazolidin-4-ylidene]methyl}amino)acetate
of ethyl 2-({[(4aChemistry and Environmental Division, Manchester Metropolitan University, Manchester M1 5GD, England, bChemistry Department, Faculty of Science, Minia University, 61519 El-Minia, Egypt, cDepartment of Physics, Faculty of Sciences, Erciyes University, 38039 Kayseri, Turkey, dDepartment of Chemistry, Tulane University, New Orleans, LA 70118, USA, eChemistry Department, Faculty of Science, Sohag University, 82524 Sohag, Egypt, and fKirkuk University, College of Science, Department of Chemistry, Kirkuk, Iraq
*Correspondence e-mail: shaabankamel@yahoo.com
The title compound, C14H15N3O4, is nearly planar, the dihedral angle between the planes of the phenyl and pyrazolidine rings being 1.13 (7) Å, and that between the plane of the pyrazolidine ring and the mean plane of the side chain [C—N—C–C(=O)—O; r.m.s. deviation = 0.024 Å] being 2.52 (7)°. This is due in large part to the presence of the intramolecular N—H⋯O and C—H⋯O hydrogen bonds. In the crystal, pairwise N—H⋯O hydrogen bonds form inversion dimers, which are further associated into layers, lying very close to plane (-120), via pairwise C—H⋯O hydrogen bonds. The layers are then weakly connected through C—H⋯O hydrogen bonds, forming a three-dimensional structure.
Keywords: crystal structure; hydrogen bonding; hydrogen-bonded dimers; pyrazolidine-3,5-dione; aminoacetic acid ester.
CCDC reference: 1015152
1. Related literature
For the synthesis of compounds containing the pyrazolidinone nucleus and their biological activity, see: Ismail et al. (2012); Khodairy (2007); Khloya et al. (2013). For biologically active synthetic containing the pyrazol-5(4H)-one core scaffold and displaying some interesting pharmaceutical properties, see: Uramaru et al. (2010) for analgesic; Thaker et al. (2011) and Chande et al. (2007) for antimicrobial; Mariappan et al. (2010) and Nishikimi et al. (2012) for anti-inflammatory; Chen et al. (2012) for cytotoxicity.
2. Experimental
2.1. Crystal data
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2.3. Refinement
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Data collection: APEX2 (Bruker, 2013); cell SAINT (Bruker, 2013); data reduction: SAINT; program(s) used to solve structure: SHELXT (Sheldrick, 2008); program(s) used to refine structure: SHELXL2014 (Sheldrick, 2008); molecular graphics: DIAMOND (Brandenburg & Putz, 2012); software used to prepare material for publication: SHELXTL (Sheldrick, 2008).
Supporting information
CCDC reference: 1015152
10.1107/S1600536814016766/su2759sup1.cif
contains datablocks global, I. DOI:Structure factors: contains datablock I. DOI: 10.1107/S1600536814016766/su2759Isup2.hkl
Supporting information file. DOI: 10.1107/S1600536814016766/su2759Isup3.cml
A mixture of 1 mmol (231 mg) of (4Z)-4-[(dimethylamino)methylene]-1-phenylpyrazolidine-3,5-dione and 1 mmol (140 mg) of ethyl aminoacetate hydrochloride and few drops of triethylamine (TEA) as a catalyst in 30 ml 1,4-dioxane was refluxed for 6 h. On cooling the solid product deposited, was filtered off, washed with cold ethanol and dried under vacuum. Crystals of the title compound were obtained as yellow needles by recrystallization of the crude product from dimethyl sulfoxide; M.p. 489–491 K.
The N-bound H atoms were located in a Fourier difference map and freely refined. The C-bound H atoms were placed in calculated positions and treated as riding atoms: C—H = 0.95 - 0.99 Å with Uiso(H) = 1.5Ueq(C-methyl) and = 1.2Ueq(C) for other H atoms. The crystal did not diffract well, hence the lower than desirable value for θfull.
Data collection: APEX2 (Bruker, 2013); cell
SAINT (Bruker, 2013); data reduction: SAINT (Bruker, 2013); program(s) used to solve structure: SHELXT (Sheldrick, 2008); program(s) used to refine structure: SHELXL2014 (Sheldrick, 2008); molecular graphics: DIAMOND (Brandenburg & Putz, 2012); software used to prepare material for publication: SHELXTL (Sheldrick, 2008).Fig. 1. The molecular structure of the title molecule, with atom labelling. Displacement ellipsoids are drawn at the 50% probability level. | |
Fig. 2. The crystal packing viewed along the b axis of the title compound. N—H···O and C—H···O hydrogen bonds are shown, respectively, as purple and black dotted lines (see Table 1 for details). | |
Fig. 3. The crystal packing of the title compound, showing the layer structure and the weak C—H···O interlayer hydrogen bonds (black dotted lines; see Table 1 for details). |
C14H15N3O4 | Z = 2 |
Mr = 289.29 | F(000) = 304 |
Triclinic, P1 | Dx = 1.462 Mg m−3 |
a = 5.4984 (1) Å | Cu Kα radiation, λ = 1.54178 Å |
b = 7.3585 (2) Å | Cell parameters from 3908 reflections |
c = 16.6265 (4) Å | θ = 2.7–72.2° |
α = 91.3290 (9)° | µ = 0.91 mm−1 |
β = 97.325 (1)° | T = 100 K |
γ = 99.562 (1)° | Needle, yellow |
V = 657.27 (3) Å3 | 0.27 × 0.09 × 0.04 mm |
Bruker D8 VENTURE PHOTON 100 CMOS diffractometer | 2450 independent reflections |
Radiation source: INCOATEC IµS micro-focus source | 2171 reflections with I > 2σ(I) |
Mirror monochromator | Rint = 0.019 |
Detector resolution: 10.4167 pixels mm-1 | θmax = 72.2°, θmin = 5.4° |
ω scans | h = −6→6 |
Absorption correction: multi-scan (SADABS; Bruker, 2013) | k = −9→8 |
Tmin = 0.91, Tmax = 0.96 | l = −20→20 |
5108 measured reflections |
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)] = 0.033 | Hydrogen site location: mixed |
wR(F2) = 0.089 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.02 | w = 1/[σ2(Fo2) + (0.0471P)2 + 0.2143P] where P = (Fo2 + 2Fc2)/3 |
2450 reflections | (Δ/σ)max < 0.001 |
199 parameters | Δρmax = 0.22 e Å−3 |
0 restraints | Δρmin = −0.19 e Å−3 |
C14H15N3O4 | γ = 99.562 (1)° |
Mr = 289.29 | V = 657.27 (3) Å3 |
Triclinic, P1 | Z = 2 |
a = 5.4984 (1) Å | Cu Kα radiation |
b = 7.3585 (2) Å | µ = 0.91 mm−1 |
c = 16.6265 (4) Å | T = 100 K |
α = 91.3290 (9)° | 0.27 × 0.09 × 0.04 mm |
β = 97.325 (1)° |
Bruker D8 VENTURE PHOTON 100 CMOS diffractometer | 2450 independent reflections |
Absorption correction: multi-scan (SADABS; Bruker, 2013) | 2171 reflections with I > 2σ(I) |
Tmin = 0.91, Tmax = 0.96 | Rint = 0.019 |
5108 measured reflections |
R[F2 > 2σ(F2)] = 0.033 | 0 restraints |
wR(F2) = 0.089 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.02 | Δρmax = 0.22 e Å−3 |
2450 reflections | Δρmin = −0.19 e Å−3 |
199 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. H-atoms attached to carbon were placed in calculated positions (C—H = 0.95 - 0.99 Å) and included as riding contributions with isotropic displacement parameters 1.2 - 1.5 times those of the attached carbon atoms. H-atoms attached to nitrogen were refined independently. |
x | y | z | Uiso*/Ueq | ||
O1 | 0.81993 (17) | 0.91924 (12) | 0.58190 (5) | 0.0208 (2) | |
O2 | 0.18424 (17) | 0.56447 (13) | 0.39606 (5) | 0.0232 (2) | |
O3 | 0.56220 (17) | 0.89351 (13) | 0.80229 (5) | 0.0238 (2) | |
O4 | 0.20347 (17) | 0.77726 (12) | 0.84951 (5) | 0.0214 (2) | |
N1 | 0.7714 (2) | 0.82957 (15) | 0.44586 (6) | 0.0193 (2) | |
N2 | 0.5788 (2) | 0.73223 (15) | 0.38878 (6) | 0.0182 (2) | |
N3 | 0.3705 (2) | 0.76426 (15) | 0.64837 (6) | 0.0185 (2) | |
C1 | 0.6132 (2) | 0.71090 (16) | 0.30668 (7) | 0.0171 (3) | |
C2 | 0.8342 (2) | 0.79219 (17) | 0.27959 (7) | 0.0187 (3) | |
H2 | 0.9640 | 0.8617 | 0.3167 | 0.022* | |
C3 | 0.8642 (3) | 0.77134 (18) | 0.19820 (8) | 0.0221 (3) | |
H3 | 1.0142 | 0.8281 | 0.1799 | 0.026* | |
C4 | 0.6776 (3) | 0.66856 (18) | 0.14350 (8) | 0.0224 (3) | |
H4 | 0.6992 | 0.6543 | 0.0881 | 0.027* | |
C5 | 0.4589 (3) | 0.58691 (18) | 0.17083 (8) | 0.0224 (3) | |
H5 | 0.3308 | 0.5160 | 0.1336 | 0.027* | |
C6 | 0.4240 (2) | 0.60707 (17) | 0.25156 (7) | 0.0203 (3) | |
H6 | 0.2729 | 0.5509 | 0.2693 | 0.024* | |
C7 | 0.3762 (2) | 0.66257 (17) | 0.42850 (7) | 0.0177 (3) | |
C8 | 0.4474 (2) | 0.72955 (16) | 0.51201 (7) | 0.0173 (3) | |
C9 | 0.6925 (2) | 0.83530 (17) | 0.51974 (7) | 0.0175 (3) | |
C10 | 0.3003 (2) | 0.69795 (17) | 0.57301 (7) | 0.0172 (3) | |
H10 | 0.1399 | 0.6246 | 0.5602 | 0.021* | |
C11 | 0.2115 (2) | 0.73107 (18) | 0.71157 (7) | 0.0187 (3) | |
H11A | 0.1573 | 0.5967 | 0.7154 | 0.022* | |
H11B | 0.0614 | 0.7881 | 0.6980 | 0.022* | |
C12 | 0.3509 (2) | 0.81183 (17) | 0.79164 (7) | 0.0188 (3) | |
C13 | 0.3112 (3) | 0.84585 (19) | 0.93050 (7) | 0.0239 (3) | |
H13A | 0.3525 | 0.9822 | 0.9326 | 0.029* | |
H13B | 0.4654 | 0.7958 | 0.9472 | 0.029* | |
C14 | 0.1209 (3) | 0.7838 (2) | 0.98568 (8) | 0.0326 (3) | |
H14A | −0.0333 | 0.8293 | 0.9670 | 0.049* | |
H14B | 0.1841 | 0.8327 | 1.0411 | 0.049* | |
H14C | 0.0877 | 0.6487 | 0.9850 | 0.049* | |
H1 | 0.896 (4) | 0.907 (3) | 0.4313 (10) | 0.034 (5)* | |
H3A | 0.525 (3) | 0.834 (2) | 0.6622 (10) | 0.027 (4)* |
U11 | U22 | U33 | U12 | U13 | U23 | |
O1 | 0.0191 (5) | 0.0237 (5) | 0.0168 (4) | −0.0039 (4) | 0.0017 (3) | −0.0013 (3) |
O2 | 0.0169 (5) | 0.0300 (5) | 0.0190 (4) | −0.0062 (4) | 0.0019 (3) | −0.0010 (4) |
O3 | 0.0199 (5) | 0.0270 (5) | 0.0218 (4) | −0.0024 (4) | 0.0014 (4) | −0.0012 (4) |
O4 | 0.0214 (5) | 0.0253 (5) | 0.0158 (4) | −0.0016 (4) | 0.0035 (3) | −0.0016 (3) |
N1 | 0.0157 (6) | 0.0226 (5) | 0.0166 (5) | −0.0056 (4) | 0.0023 (4) | −0.0017 (4) |
N2 | 0.0154 (5) | 0.0210 (5) | 0.0158 (5) | −0.0029 (4) | 0.0012 (4) | −0.0016 (4) |
N3 | 0.0160 (6) | 0.0208 (5) | 0.0171 (5) | −0.0018 (4) | 0.0028 (4) | 0.0003 (4) |
C1 | 0.0190 (6) | 0.0162 (6) | 0.0163 (6) | 0.0036 (5) | 0.0020 (5) | 0.0012 (5) |
C2 | 0.0182 (6) | 0.0179 (6) | 0.0193 (6) | 0.0010 (5) | 0.0023 (5) | 0.0005 (5) |
C3 | 0.0220 (7) | 0.0228 (6) | 0.0222 (6) | 0.0034 (5) | 0.0062 (5) | 0.0028 (5) |
C4 | 0.0275 (7) | 0.0245 (7) | 0.0161 (6) | 0.0062 (6) | 0.0037 (5) | 0.0009 (5) |
C5 | 0.0230 (7) | 0.0236 (7) | 0.0189 (6) | 0.0022 (5) | −0.0005 (5) | −0.0009 (5) |
C6 | 0.0181 (7) | 0.0216 (6) | 0.0197 (6) | 0.0002 (5) | 0.0018 (5) | 0.0003 (5) |
C7 | 0.0156 (6) | 0.0179 (6) | 0.0188 (6) | 0.0005 (5) | 0.0027 (5) | 0.0017 (5) |
C8 | 0.0168 (6) | 0.0166 (6) | 0.0174 (6) | 0.0009 (5) | 0.0011 (5) | 0.0009 (5) |
C9 | 0.0182 (6) | 0.0164 (6) | 0.0177 (6) | 0.0016 (5) | 0.0027 (5) | 0.0010 (4) |
C10 | 0.0149 (6) | 0.0165 (6) | 0.0189 (6) | 0.0003 (5) | 0.0009 (4) | 0.0017 (4) |
C11 | 0.0170 (6) | 0.0212 (6) | 0.0169 (6) | −0.0005 (5) | 0.0036 (5) | 0.0006 (5) |
C12 | 0.0193 (7) | 0.0177 (6) | 0.0189 (6) | 0.0022 (5) | 0.0022 (5) | 0.0015 (5) |
C13 | 0.0270 (7) | 0.0268 (7) | 0.0157 (6) | 0.0006 (6) | 0.0008 (5) | −0.0021 (5) |
C14 | 0.0382 (9) | 0.0375 (8) | 0.0204 (7) | −0.0017 (7) | 0.0077 (6) | −0.0002 (6) |
O1—C9 | 1.2580 (15) | C4—C5 | 1.388 (2) |
O2—C7 | 1.2288 (16) | C4—H4 | 0.9500 |
O3—C12 | 1.2052 (17) | C5—C6 | 1.3879 (18) |
O4—C12 | 1.3378 (16) | C5—H5 | 0.9500 |
O4—C13 | 1.4438 (14) | C6—H6 | 0.9500 |
N1—C9 | 1.3557 (16) | C7—C8 | 1.4455 (17) |
N1—N2 | 1.4126 (14) | C8—C10 | 1.3764 (18) |
N1—H1 | 0.88 (2) | C8—C9 | 1.4289 (18) |
N2—C7 | 1.3975 (17) | C10—H10 | 0.9500 |
N2—C1 | 1.4105 (16) | C11—C12 | 1.5049 (16) |
N3—C10 | 1.3201 (16) | C11—H11A | 0.9900 |
N3—C11 | 1.4503 (16) | C11—H11B | 0.9900 |
N3—H3A | 0.914 (18) | C13—C14 | 1.500 (2) |
C1—C2 | 1.3958 (19) | C13—H13A | 0.9900 |
C1—C6 | 1.4023 (17) | C13—H13B | 0.9900 |
C2—C3 | 1.3920 (18) | C14—H14A | 0.9800 |
C2—H2 | 0.9500 | C14—H14B | 0.9800 |
C3—C4 | 1.3873 (18) | C14—H14C | 0.9800 |
C3—H3 | 0.9500 | ||
C12—O4—C13 | 115.89 (10) | C10—C8—C9 | 126.25 (11) |
C9—N1—N2 | 109.72 (10) | C10—C8—C7 | 125.21 (12) |
C9—N1—H1 | 124.3 (11) | C9—C8—C7 | 108.54 (11) |
N2—N1—H1 | 122.3 (11) | O1—C9—N1 | 124.26 (12) |
C7—N2—C1 | 130.04 (10) | O1—C9—C8 | 128.51 (12) |
C7—N2—N1 | 109.26 (10) | N1—C9—C8 | 107.22 (11) |
C1—N2—N1 | 120.63 (10) | N3—C10—C8 | 123.39 (12) |
C10—N3—C11 | 122.52 (11) | N3—C10—H10 | 118.3 |
C10—N3—H3A | 119.8 (10) | C8—C10—H10 | 118.3 |
C11—N3—H3A | 117.7 (10) | N3—C11—C12 | 109.81 (10) |
C2—C1—C6 | 119.51 (11) | N3—C11—H11A | 109.7 |
C2—C1—N2 | 120.64 (11) | C12—C11—H11A | 109.7 |
C6—C1—N2 | 119.86 (11) | N3—C11—H11B | 109.7 |
C3—C2—C1 | 119.92 (12) | C12—C11—H11B | 109.7 |
C3—C2—H2 | 120.0 | H11A—C11—H11B | 108.2 |
C1—C2—H2 | 120.0 | O3—C12—O4 | 125.26 (12) |
C4—C3—C2 | 120.74 (12) | O3—C12—C11 | 125.64 (12) |
C4—C3—H3 | 119.6 | O4—C12—C11 | 109.10 (10) |
C2—C3—H3 | 119.6 | O4—C13—C14 | 106.97 (11) |
C3—C4—C5 | 119.13 (12) | O4—C13—H13A | 110.3 |
C3—C4—H4 | 120.4 | C14—C13—H13A | 110.3 |
C5—C4—H4 | 120.4 | O4—C13—H13B | 110.3 |
C4—C5—C6 | 121.15 (12) | C14—C13—H13B | 110.3 |
C4—C5—H5 | 119.4 | H13A—C13—H13B | 108.6 |
C6—C5—H5 | 119.4 | C13—C14—H14A | 109.5 |
C5—C6—C1 | 119.55 (12) | C13—C14—H14B | 109.5 |
C5—C6—H6 | 120.2 | H14A—C14—H14B | 109.5 |
C1—C6—H6 | 120.2 | C13—C14—H14C | 109.5 |
O2—C7—N2 | 124.92 (11) | H14A—C14—H14C | 109.5 |
O2—C7—C8 | 129.97 (12) | H14B—C14—H14C | 109.5 |
N2—C7—C8 | 105.10 (10) | ||
C9—N1—N2—C7 | −4.17 (14) | N2—C7—C8—C10 | 178.32 (11) |
C9—N1—N2—C1 | 178.53 (10) | O2—C7—C8—C9 | 178.57 (13) |
C7—N2—C1—C2 | −179.41 (12) | N2—C7—C8—C9 | −0.82 (13) |
N1—N2—C1—C2 | −2.73 (17) | N2—N1—C9—O1 | −176.95 (11) |
C7—N2—C1—C6 | 0.56 (19) | N2—N1—C9—C8 | 3.52 (13) |
N1—N2—C1—C6 | 177.24 (11) | C10—C8—C9—O1 | −0.3 (2) |
C6—C1—C2—C3 | 0.66 (18) | C7—C8—C9—O1 | 178.83 (12) |
N2—C1—C2—C3 | −179.37 (11) | C10—C8—C9—N1 | 179.20 (12) |
C1—C2—C3—C4 | −0.74 (19) | C7—C8—C9—N1 | −1.67 (14) |
C2—C3—C4—C5 | 0.28 (19) | C11—N3—C10—C8 | 179.28 (12) |
C3—C4—C5—C6 | 0.26 (19) | C9—C8—C10—N3 | 0.2 (2) |
C4—C5—C6—C1 | −0.33 (19) | C7—C8—C10—N3 | −178.81 (11) |
C2—C1—C6—C5 | −0.13 (19) | C10—N3—C11—C12 | 175.64 (11) |
N2—C1—C6—C5 | 179.90 (11) | C13—O4—C12—O3 | 0.30 (18) |
C1—N2—C7—O2 | 0.5 (2) | C13—O4—C12—C11 | 179.81 (10) |
N1—N2—C7—O2 | −176.50 (12) | N3—C11—C12—O3 | 0.61 (18) |
C1—N2—C7—C8 | 179.91 (11) | N3—C11—C12—O4 | −178.90 (10) |
N1—N2—C7—C8 | 2.93 (13) | C12—O4—C13—C14 | −177.08 (11) |
O2—C7—C8—C10 | −2.3 (2) |
D—H···A | D—H | H···A | D···A | D—H···A |
N3—H3A···O1 | 0.914 (18) | 2.250 (17) | 2.9062 (14) | 128.3 (13) |
C6—H6···O2 | 0.95 | 2.23 | 2.8833 (16) | 126 |
N1—H1···O1i | 0.88 (2) | 1.89 (2) | 2.7573 (14) | 170.7 (16) |
C2—H2···O1i | 0.95 | 2.36 | 3.2777 (15) | 162 |
C10—H10···O2ii | 0.95 | 2.28 | 3.1268 (16) | 148 |
C11—H11A···O2ii | 0.99 | 2.58 | 3.1498 (15) | 117 |
C11—H11B···O1iii | 0.99 | 2.51 | 3.3386 (15) | 142 |
Symmetry codes: (i) −x+2, −y+2, −z+1; (ii) −x, −y+1, −z+1; (iii) x−1, y, z. |
D—H···A | D—H | H···A | D···A | D—H···A |
N3—H3A···O1 | 0.914 (18) | 2.250 (17) | 2.9062 (14) | 128.3 (13) |
C6—H6···O2 | 0.95 | 2.23 | 2.8833 (16) | 126 |
N1—H1···O1i | 0.88 (2) | 1.89 (2) | 2.7573 (14) | 170.7 (16) |
C2—H2···O1i | 0.95 | 2.36 | 3.2777 (15) | 162 |
C10—H10···O2ii | 0.95 | 2.28 | 3.1268 (16) | 148 |
C11—H11A···O2ii | 0.99 | 2.58 | 3.1498 (15) | 117 |
C11—H11B···O1iii | 0.99 | 2.51 | 3.3386 (15) | 142 |
Symmetry codes: (i) −x+2, −y+2, −z+1; (ii) −x, −y+1, −z+1; (iii) x−1, y, z. |
Acknowledgements
The support of NSF–MRI grant No. 1228232 for the purchase of the diffractometer is gratefully acknowledged.
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