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

Journal logoCRYSTALLOGRAPHIC
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ISSN: 2056-9890
Volume 71| Part 7| July 2015| Pages o440-o441

Crystal structure of (4Z)-4-[(di­methyl­amino)­methyl­­idene]-3,5-dioxo-2-phenyl­pyrazolidine-1-carbaldehyde

CROSSMARK_Color_square_no_text.svg

aDepartment of Chemistry, Tulane University, New Orleans, LA 70118, USA, bChemistry and Environmental Division, Manchester Metropolitan University, Manchester M1 5GD, England, cChemistry Department, Faculty of Science, Minia University, 61519 El-Minia, Egypt, dDepartment of Physics, Faculty of Sciences, Erciyes University, 38039 Kayseri, Turkey, and eChemistry Department, Faculty of Science, Sohag University, 82524 Sohag, Egypt
*Correspondence e-mail: abdala_15@yahoo.com

Edited by W. T. A. Harrison, University of Aberdeen, Scotland (Received 12 May 2015; accepted 23 May 2015; online 3 June 2015)

In the title compound, C13H13N3O3, the pyrazolidine ring adopts a shallow envelope conformation, with the carbonyl C atom closest to the benzene ring as the flap [deviation of 0.126 (1) Å from the plane through the remaining atoms (r.m.s. deviation = 0.011 Å)]. The dihedral angle between the pyrazolidine ring (all atoms) and the benzene ring is 51.09 (4)°. An extremely short (2.08 Å) intra­molecular C—H⋯O contact is seen. In the crystal, mol­ecules are linked by C—H⋯O bonds, generating [010] chains. Extremely weak C—H⋯π inter­actions are also observed.

1. Related literature

For biological studies of azole compounds, see: Patel et al. (2012[Patel, P., Gor, D. & Patel, P. S. (2012). Journal of Chemical and Pharmaceutical Research, 4, 2906-2910.]); Vijesh et al. (2011[Vijesh, A. M., Isloor, A. M., Telkar, S., Peethambar, S. K., Rai, S. & Isloor, N. (2011). Eur. J. Med. Chem. 46, 3531-3536.]). For various medicinal and industrial applications of pyrrazole-containing compounds, see: Jin et al. (2011[Jin, C. H., Krishnaiah, M., Sreenu, D., Rao, K. S., Subrahmanyam, V. B., Park, C.-Y., Son, J.-Y., Sheen, Y. Y. & Kim, D.-K. (2011). Bioorg. Med. Chem. 19, 2633-2640.]); Zhang et al. (2010[Zhang, C.-Y., Liu, X.-H., Wang, B.-L., Wang, S.-H. & Li, Z.-M. (2010). Chem. Biol. Drug Des. 75, 489-493.]); El-Sabbagh et al. (2009[El-Sabbagh, O. I., Baraka, M. M., Ibrahim, S. M., Pannecouque, C., Andrei, G., Snoeck, R., Balzarini, J. & Rashad, A. A. (2009). Eur. J. Med. Chem. 44, 3746-3753.]); Dekhane et al. (2011[Dekhane, D. V., Pawar, S. S., Gupta, S., Shingare, M. S., Patil, C. R. & Thore, S. N. (2011). Bioorg. Med. Chem. Lett. 21, 6527-6532.]); Rostom et al. (2003[Rostom, S. A. F., Shalaby, M. A. & El-Demellawy, M. A. (2003). Eur. J. Med. Chem. 38, 959-974.]); Zhou et al. (2010[Zhou, Y., Xue, N., Wang, G. & Qu, J. (2010). J. Chem. Res. (S), 34, 684-688.]); Finkelstein & Strock (1997[Finkelstein, B. L. & Strock, C. J. (1997). Pestic. Sci. 50, 324-328.]).

[Scheme 1]

2. Experimental

2.1. Crystal data

  • C13H13N3O3

  • Mr = 259.26

  • Monoclinic, C 2/c

  • a = 26.4235 (9) Å

  • b = 6.1033 (2) Å

  • c = 16.8611 (6) Å

  • β = 113.272 (1)°

  • V = 2497.96 (15) Å3

  • Z = 8

  • Cu Kα radiation

  • μ = 0.84 mm−1

  • T = 150 K

  • 0.24 × 0.15 × 0.05 mm

2.2. Data collection

  • Bruker D8 VENTURE PHOTON 100 CMOS diffractometer

  • Absorption correction: multi-scan (TWINABS; Sheldrick, 2009[Sheldrick, G. M. (2009). TWINABS. University of Göttingen, Germany.]) Tmin = 0.82, Tmax = 0.96

  • 26486 measured reflections

  • 4565 independent reflections

  • 3979 reflections with I > 2σ(I)

  • Rint = 0.021

2.3. Refinement

  • R[F2 > 2σ(F2)] = 0.037

  • wR(F2) = 0.104

  • S = 1.04

  • 4565 reflections

  • 175 parameters

  • H-atom parameters constrained

  • Δρmax = 0.26 e Å−3

  • Δρmin = −0.20 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

Cg1 is the centroid of the C1/C2/C3/N1/N2 ring.

D—H⋯A D—H H⋯A DA D—H⋯A
C6—H6A⋯O2 0.98 2.08 3.016 (2) 160
C5—H5C⋯O3i 0.98 2.52 3.1803 (19) 124
C7—H7⋯O2ii 0.95 2.29 3.0663 (16) 139
C5—H5BCg1iii 0.98 2.98 3.8823 (18) 153
Symmetry codes: (i) -x+1, -y+1, -z+1; (ii) -x+1, -y, -z+1; (iii) [-x+1, y, -z+{\script{1\over 2}}].

Data collection: APEX2 (Bruker, 2014[Bruker (2014). APEX2 and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]); cell refinement: SAINT (Bruker, 2014[Bruker (2014). APEX2 and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]); data reduction: SAINT; program(s) used to solve structure: SHELXT (Sheldrick, 2015a[Sheldrick, G. M. (2015a). Acta Cryst. A71, 3-8.]); program(s) used to refine structure: SHELXL2014 (Sheldrick, 2015b[Sheldrick, G. M. (2015b). Acta Cryst. C71, 3-8.]); molecular graphics: DIAMOND (Brandenburg & Putz, 2012[Brandenburg, K. & Putz, H. (2012). DIAMOND. Crystal Impact GbR, Bonn, Germany.]); software used to prepare material for publication: SHELXTL (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]).

Supporting information


Comment top

Azole compounds are extensively studied and widely used as anti-microbial agents (Patel et al., 2012; Vijesh et al., 2011). Recently, urea derivatives of pyrazole have been reported as potent inhibitors of p38 kinase (Jin et al., 2011). Many of other pyrazole scaffold compounds are reported to have broad spectra of biological activities, such as anti-fungal (Zhang et al., 2010), anti-viral (El-Sabbagh et al., 2009), anti-inflammatory (Dekhane et al., 2011), anti-tumor, anti-HCV (Rostom et al., 2003), herbicidal (Zhou et al., 2010) and insecticidal activities (Finkelstein & Strock, 1997). In view of such findings and as a continuation of our study on the synthesis of potential bio-active heterocyclic molecules, we report here the synthesis and crystal structure of the title compound.

In the title compound, the pyrazolidine ring is slightly twisted with an r.m.s. deviation from the mean plane of the 5 atoms forming the ring of 0.036 Å. The dihedral angle between this plane and that of the phenyl ring is 51.09 (4)° (Fig. 1).

Related literature top

For biological studies of azole compounds, see: Patel et al. (2012); Vijesh et al. (2011). For various medicinal and industrial applications of pyrrazole-containing compounds, see: Jin et al. (2011); Zhang et al. (2010); El-Sabbagh et al. (2009); Dekhane et al. (2011); Rostom et al. (2003); Zhou et al. (2010); Finkelstein & Strock (1997).

Experimental top

To phosphorous oxychloride (0.1 mol, 10 ml), in a conical flask with a magnetic stirrer, dry dimethylformamide (35 ml) was added drop-wise with stirring at 303–308 K for 30 min. Then a solution of 1-phenylpyrazolidine-3,5-dione (0.05 mol, 8.8 g) in dimethylformamide (15 ml), was added drop-wise with continuous stirring while ensuring that the temperature did not exceed 318 K. The reaction mixture was stirred overnight and poured onto crushed ice. The solid product was collected by filtration and recrystallized from ethanol to give colourless crystals in 75% yield (m. p. 453–455 K).

Refinement top

H-atoms were placed in calculated positions (C—H = 0.95 - 0.98 Å) and included as riding contributions with isotropic displacement parameters 1.2 - 1.5 times those of the attached carbon atoms. The model was refined as a 2-component twin.

Computing details top

Data collection: APEX2 (Bruker, 2014); cell refinement: SAINT (Bruker, 2014); data reduction: SAINT (Bruker, 2014); program(s) used to solve structure: SHELXT (Sheldrick, 2015a); program(s) used to refine structure: SHELXL2014 (Sheldrick, 2015b); molecular graphics: DIAMOND (Brandenburg & Putz, 2012); software used to prepare material for publication: SHELXTL (Sheldrick, 2008).

Figures top
[Figure 1] Fig. 1. The title molecule with 50% probability ellipsoids.
[Figure 2] Fig. 2. Packing viewed down the b axis. C—H···π interactions are shown by dotted lines.
(4Z)-4-[(Dimethylamino)methylidene]-3,5-dioxo-2-phenylpyrazolidine-1-carbaldehyde top
Crystal data top
C13H13N3O3F(000) = 1088
Mr = 259.26Dx = 1.379 Mg m3
Monoclinic, C2/cCu Kα radiation, λ = 1.54178 Å
a = 26.4235 (9) ÅCell parameters from 9978 reflections
b = 6.1033 (2) Åθ = 3.6–72.3°
c = 16.8611 (6) ŵ = 0.84 mm1
β = 113.272 (1)°T = 150 K
V = 2497.96 (15) Å3Rod, colourless
Z = 80.24 × 0.15 × 0.05 mm
Data collection top
Bruker D8 VENTURE PHOTON 100 CMOS
diffractometer
4565 independent reflections
Radiation source: INCOATEC IµS micro–focus source3979 reflections with I > 2σ(I)
Mirror monochromatorRint = 0.021
Detector resolution: 10.4167 pixels mm-1θmax = 72.3°, θmin = 3.6°
ω scansh = 3230
Absorption correction: multi-scan
(TWINABS; Sheldrick, 2009)
k = 77
Tmin = 0.82, Tmax = 0.96l = 2020
26486 measured 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)] = 0.037Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.104H-atom parameters constrained
S = 1.04 w = 1/[σ2(Fo2) + (0.0577P)2 + 0.7347P]
where P = (Fo2 + 2Fc2)/3
4565 reflections(Δ/σ)max < 0.001
175 parametersΔρmax = 0.26 e Å3
0 restraintsΔρmin = 0.20 e Å3
Crystal data top
C13H13N3O3V = 2497.96 (15) Å3
Mr = 259.26Z = 8
Monoclinic, C2/cCu Kα radiation
a = 26.4235 (9) ŵ = 0.84 mm1
b = 6.1033 (2) ÅT = 150 K
c = 16.8611 (6) Å0.24 × 0.15 × 0.05 mm
β = 113.272 (1)°
Data collection top
Bruker D8 VENTURE PHOTON 100 CMOS
diffractometer
4565 independent reflections
Absorption correction: multi-scan
(TWINABS; Sheldrick, 2009)
3979 reflections with I > 2σ(I)
Tmin = 0.82, Tmax = 0.96Rint = 0.021
26486 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0370 restraints
wR(F2) = 0.104H-atom parameters constrained
S = 1.04Δρmax = 0.26 e Å3
4565 reflectionsΔρmin = 0.20 e Å3
175 parameters
Special details top

Experimental. Analysis of 3764 reflections having I/σ(I) > 12 and chosen from

the full data set with CELL_NOW (Sheldrick, 2008) showed

the crystal to belong to the monoclinic system and to be twinned

by a 180° rotation about the c* axis. The raw data were

processed using the multi-component version of SAINT under

control of the two-component orientation file generated by

CELL_NOW.

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 were placed in

calculated positions (C—H = 0.95 - 0.98 Å) and included as riding

contributions with isotropic displacement parameters 1.2 - 1.5 times those

of the attached carbon atoms. The model was refined as a 2-component twin.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
O10.43175 (4)0.79022 (16)0.28697 (7)0.0296 (2)
O20.52891 (4)0.15926 (16)0.42906 (7)0.0324 (3)
O30.37052 (4)0.10698 (18)0.39957 (6)0.0316 (3)
N10.40831 (4)0.46179 (18)0.33205 (7)0.0236 (3)
N20.43832 (4)0.26978 (18)0.36829 (7)0.0239 (3)
N30.59876 (5)0.64368 (19)0.42207 (8)0.0265 (3)
C10.44610 (5)0.6170 (2)0.32599 (8)0.0233 (3)
C20.50109 (5)0.5284 (2)0.37179 (8)0.0235 (3)
C30.49589 (5)0.3060 (2)0.39467 (8)0.0242 (3)
C40.54556 (5)0.6654 (2)0.38045 (9)0.0249 (3)
H40.53490.80010.35020.030*
C50.63539 (6)0.8195 (3)0.41755 (10)0.0344 (3)
H5A0.61330.94450.38610.052*
H5B0.65800.76610.38740.052*
H5C0.65940.86520.47610.052*
C60.62712 (6)0.4598 (3)0.47712 (10)0.0344 (3)
H6A0.60020.34710.47500.052*
H6B0.64620.51090.53670.052*
H6C0.65400.39780.45660.052*
C70.41757 (5)0.1104 (2)0.40511 (8)0.0255 (3)
H70.44160.00340.43670.031*
C80.35475 (5)0.4373 (2)0.26388 (8)0.0235 (3)
C90.34078 (5)0.2502 (2)0.21315 (9)0.0275 (3)
H90.36670.13490.22270.033*
C100.28831 (6)0.2336 (3)0.14813 (9)0.0311 (3)
H100.27830.10620.11290.037*
C110.25040 (6)0.4019 (3)0.13433 (9)0.0311 (3)
H110.21460.38990.08970.037*
C120.26490 (6)0.5880 (2)0.18593 (10)0.0308 (3)
H120.23900.70310.17650.037*
C130.31717 (5)0.6066 (2)0.25127 (9)0.0271 (3)
H130.32710.73330.28680.033*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O10.0274 (5)0.0239 (5)0.0339 (5)0.0033 (4)0.0083 (4)0.0053 (4)
O20.0221 (5)0.0284 (5)0.0409 (6)0.0034 (4)0.0063 (4)0.0100 (4)
O30.0259 (5)0.0404 (6)0.0290 (5)0.0054 (4)0.0115 (4)0.0019 (4)
N10.0201 (5)0.0227 (6)0.0262 (6)0.0027 (4)0.0072 (4)0.0031 (4)
N20.0190 (5)0.0234 (6)0.0267 (6)0.0013 (4)0.0062 (4)0.0053 (4)
N30.0232 (5)0.0306 (6)0.0260 (6)0.0047 (4)0.0099 (4)0.0026 (5)
C10.0241 (6)0.0232 (6)0.0227 (6)0.0005 (5)0.0093 (5)0.0009 (5)
C20.0211 (6)0.0252 (7)0.0233 (6)0.0009 (5)0.0077 (5)0.0017 (5)
C30.0206 (6)0.0268 (6)0.0231 (6)0.0003 (5)0.0063 (5)0.0013 (5)
C40.0266 (6)0.0250 (6)0.0233 (6)0.0015 (5)0.0102 (5)0.0005 (5)
C50.0296 (7)0.0432 (8)0.0314 (7)0.0132 (6)0.0132 (6)0.0043 (7)
C60.0237 (6)0.0348 (8)0.0386 (8)0.0007 (6)0.0059 (6)0.0005 (6)
C70.0254 (6)0.0271 (7)0.0216 (6)0.0029 (5)0.0066 (5)0.0022 (5)
C80.0195 (6)0.0289 (7)0.0227 (6)0.0010 (5)0.0090 (5)0.0033 (5)
C90.0247 (6)0.0310 (7)0.0258 (7)0.0054 (5)0.0089 (5)0.0001 (5)
C100.0289 (7)0.0344 (8)0.0273 (7)0.0001 (6)0.0082 (6)0.0029 (6)
C110.0212 (6)0.0397 (8)0.0281 (7)0.0010 (6)0.0053 (5)0.0056 (6)
C120.0222 (6)0.0319 (7)0.0383 (8)0.0060 (5)0.0121 (6)0.0072 (6)
C130.0240 (6)0.0263 (7)0.0326 (7)0.0018 (5)0.0128 (6)0.0007 (5)
Geometric parameters (Å, º) top
O1—C11.2234 (17)C5—H5C0.9800
O2—C31.2247 (17)C6—H6A0.9800
O3—C71.2096 (17)C6—H6B0.9800
N1—C11.4094 (17)C6—H6C0.9800
N1—N21.4116 (15)C7—H70.9500
N1—C81.4356 (16)C8—C91.387 (2)
N2—C71.3789 (17)C8—C131.3898 (18)
N2—C31.4236 (16)C9—C101.3903 (19)
N3—C41.3064 (17)C9—H90.9500
N3—C61.4607 (19)C10—C111.389 (2)
N3—C51.4669 (18)C10—H100.9500
C1—C21.4538 (17)C11—C121.389 (2)
C2—C41.4019 (18)C11—H110.9500
C2—C31.4324 (19)C12—C131.390 (2)
C4—H40.9500C12—H120.9500
C5—H5A0.9800C13—H130.9500
C5—H5B0.9800
C1—N1—N2107.25 (10)N3—C6—H6A109.5
C1—N1—C8120.96 (11)N3—C6—H6B109.5
N2—N1—C8117.89 (10)H6A—C6—H6B109.5
C7—N2—N1121.70 (11)N3—C6—H6C109.5
C7—N2—C3122.33 (11)H6A—C6—H6C109.5
N1—N2—C3110.76 (10)H6B—C6—H6C109.5
C4—N3—C6126.32 (12)O3—C7—N2123.82 (13)
C4—N3—C5119.34 (12)O3—C7—H7118.1
C6—N3—C5114.31 (12)N2—C7—H7118.1
O1—C1—N1122.81 (12)C9—C8—C13121.19 (12)
O1—C1—C2129.76 (12)C9—C8—N1121.16 (11)
N1—C1—C2107.42 (11)C13—C8—N1117.64 (12)
C4—C2—C3134.64 (12)C8—C9—C10119.07 (13)
C4—C2—C1117.00 (12)C8—C9—H9120.5
C3—C2—C1108.28 (11)C10—C9—H9120.5
O2—C3—N2120.52 (12)C11—C10—C9120.43 (14)
O2—C3—C2133.97 (12)C11—C10—H10119.8
N2—C3—C2105.51 (11)C9—C10—H10119.8
N3—C4—C2132.47 (13)C10—C11—C12119.85 (13)
N3—C4—H4113.8C10—C11—H11120.1
C2—C4—H4113.8C12—C11—H11120.1
N3—C5—H5A109.5C11—C12—C13120.33 (13)
N3—C5—H5B109.5C11—C12—H12119.8
H5A—C5—H5B109.5C13—C12—H12119.8
N3—C5—H5C109.5C8—C13—C12119.12 (13)
H5A—C5—H5C109.5C8—C13—H13120.4
H5B—C5—H5C109.5C12—C13—H13120.4
C1—N1—N2—C7161.44 (12)C1—C2—C3—N24.26 (14)
C8—N1—N2—C757.85 (16)C6—N3—C4—C22.8 (2)
C1—N1—N2—C36.44 (14)C5—N3—C4—C2179.28 (14)
C8—N1—N2—C3147.14 (11)C3—C2—C4—N39.4 (3)
N2—N1—C1—O1170.26 (12)C1—C2—C4—N3174.34 (14)
C8—N1—C1—O131.01 (19)N1—N2—C7—O310.0 (2)
N2—N1—C1—C28.87 (14)C3—N2—C7—O3162.12 (13)
C8—N1—C1—C2148.12 (11)C1—N1—C8—C9111.30 (15)
O1—C1—C2—C46.4 (2)N2—N1—C8—C923.84 (17)
N1—C1—C2—C4174.52 (11)C1—N1—C8—C1369.53 (16)
O1—C1—C2—C3170.80 (13)N2—N1—C8—C13155.33 (12)
N1—C1—C2—C38.25 (14)C13—C8—C9—C100.6 (2)
C7—N2—C3—O224.0 (2)N1—C8—C9—C10179.72 (13)
N1—N2—C3—O2178.78 (12)C8—C9—C10—C110.2 (2)
C7—N2—C3—C2156.09 (12)C9—C10—C11—C120.2 (2)
N1—N2—C3—C21.27 (14)C10—C11—C12—C130.0 (2)
C4—C2—C3—O20.8 (3)C9—C8—C13—C120.7 (2)
C1—C2—C3—O2175.68 (15)N1—C8—C13—C12179.87 (12)
C4—C2—C3—N2179.21 (14)C11—C12—C13—C80.4 (2)
Hydrogen-bond geometry (Å, º) top
Cg1 is the centroid of the C1/C2/C3/N1/N2 ring.
D—H···AD—HH···AD···AD—H···A
C6—H6A···O20.982.083.016 (2)160
C5—H5C···O3i0.982.523.1803 (19)124
C7—H7···O2ii0.952.293.0663 (16)139
C5—H5B···Cg1iii0.982.983.8823 (18)153
Symmetry codes: (i) x+1, y+1, z+1; (ii) x+1, y, z+1; (iii) x+1, y, z+1/2.
Hydrogen-bond geometry (Å, º) top
Cg1 is the centroid of the C1/C2/C3/N1/N2 ring.
D—H···AD—HH···AD···AD—H···A
C6—H6A···O20.982.083.016 (2)160
C5—H5C···O3i0.982.523.1803 (19)124
C7—H7···O2ii0.952.293.0663 (16)139
C5—H5B···Cg1iii0.982.983.8823 (18)153
Symmetry codes: (i) x+1, y+1, z+1; (ii) x+1, y, z+1; (iii) x+1, y, z+1/2.
 

Acknowledgements

The support of NSF–MRI grant No. 1228232 for the purchase of the diffractometer and Tulane University for support of the Tulane Crystallography Laboratory are gratefully acknowledged.

References

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Volume 71| Part 7| July 2015| Pages o440-o441
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