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Acta Crystallogr Sect E Struct Rep Online. 2011 June 1; 67(Pt 6): o1413.
Published online 2011 May 14. doi:  10.1107/S1600536811017132
PMCID: PMC3120595

Ethyl 5-{[(E)-2-(isonicotinoyl)hydrazinyl­idene]methyl}-3,4-dimethyl-1H-pyrrole-2-carboxyl­ate dihydrate

Abstract

In the title compound, C16H18N4O3·2H2O, the dihedral angle between the pyrrole and pyridine rings in the hydrazone mol­ecule is 7.12 (3)°. In the crystal structure, inter­molecular N—H(...)O, O—H(...)N and O—H(...)O hydrogen bonds link the hydrazone and water mol­ecules into double layers parallel to (101). The crystal packing exhibits weak π–π inter­actions between the pyrrole and pyridine rings of neighbouring hydrazone mol­ecules [centroid–centroid distance = 3.777 (3) Å]. The crystal studied was a non-merohedral twin, the refined ratio of twin domains being 0.73 (3):0.27 (3).

Related literature

For the anti­oxidant and DNA-binding properties of hydrazone complexes, see: Liu & Yang (2009 [triangle]). For the synthesis and structure of 5-formyl-3,4-dimethyl-1H-pyrrole-2-carboxyl­ate, see: Wu et al. (2009 [triangle]). For the similar structure of ethyl 5-[(3,4-dimethyl-1H-pyrrole-2-carboxyl­imino)-meth­yl]-3,4-dimethyl-1H-pyrrole-2-carboxyl­ate monohydrate, see: Wang et al. (2009 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-67-o1413-scheme1.jpg

Experimental

Crystal data

  • C16H18N4O3·2H2O
  • M r = 350.38
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-67-o1413-efi1.jpg
  • a = 8.297 (4) Å
  • b = 18.120 (6) Å
  • c = 11.834 (4) Å
  • β = 91.814 (4)°
  • V = 1778.3 (11) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 0.10 mm−1
  • T = 296 K
  • 0.23 × 0.21 × 0.16 mm

Data collection

  • Bruker SMART APEX CCD diffractometer
  • Absorption correction: multi-scan (SADABS; Bruker, 2007 [triangle]) T min = 0.977, T max = 0.984
  • 10998 measured reflections
  • 3839 independent reflections
  • 2671 reflections with I > 2σ(I)
  • R int = 0.037

Refinement

  • R[F 2 > 2σ(F 2)] = 0.074
  • wR(F 2) = 0.176
  • S = 1.02
  • 3839 reflections
  • 241 parameters
  • H atoms treated by a mixture of independent and constrained refinement
  • Δρmax = 0.41 e Å−3
  • Δρmin = −0.27 e Å−3

Data collection: APEX2 (Bruker, 2007 [triangle]); cell refinement: SAINT (Bruker, 2007 [triangle]); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 [triangle]); molecular graphics: SHELXTL (Sheldrick, 2008 [triangle]); software used to prepare material for publication: SHELXTL.

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536811017132/cv5084sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536811017132/cv5084Isup2.hkl

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

Acknowledgments

The authors are grateful to the National Natural Science Foundation of China for financial support (grant No. 21001040).

supplementary crystallographic information

Comment

In recent years, hydrazone complexes have received extensive attention due to their biological and pharmaceutical activities (Liu et al., 2009). As a part of our studies of hydrazone ligands bearing pyrrole unit (Wang et al., 2009), we present here the crystal structure of the title compound.

In the title compound (Fig. 1), the imine C=N double bond has an E configuration. The dihedral angle between pyrrole (N4/C8–C11, r.m.s. deviation 0.0030 Å) and pyridine rings (N1/C1–C5, r.m.s. deviation 0.0038 Å) in the hydrazone molecule is 7.12 (3)°. In the crystal structure, intermolecular N—H···O, O—H···N and O—H···O hydrogen bonds link the hydrazone and water molecules into doubled layers parallel to (101) plane. The crystal packing exhibits weak π–π interactions between the pyrrole and pyridine rings from the neighbouring hydrazone molecules [centroid-to-centroid distance of 3.777 (3) Å].

Experimental

Isonicotinohydrazide (0.137 g, 1 mmol) and ethyl 5-formyl-3,4-dimethyl-1H-pyrrole-2-carboxylate (0.167 g, 1 mmol) (Wu et al., 2009) was dissolved in an ethanol solution. The mixture was stirred for 4 h at room temperture. The resulting solution was left in air for a few days, yielding yellow prism-shaped crystals.

Refinement

The water H atoms were located in a difference Fourier map and refined with Uiso(H)=1.5Ueq(O). Other H atoms were placed in calculated positions, with C—H = 0.93–0.97 Å and N—H = 0.86 Å, and were thereafter treated as riding, with Uiso(H) values of 1.5Ueq(C) for methyl groups and 1.2Ueq(C,N) for others. The crystal studied was a twin.

Figures

Fig. 1.
The title compound with the displacement ellipsoids shown at the 50% probability level.

Crystal data

C16H18N4O3·2H2OF(000) = 744
Mr = 350.38Dx = 1.309 Mg m3
Monoclinic, P21/nMo Kα radiation, λ = 0.71073 Å
a = 8.297 (4) Åθ = 2.7–25.3°
b = 18.120 (6) ŵ = 0.10 mm1
c = 11.834 (4) ÅT = 296 K
β = 91.814 (4)°Prism, yellow
V = 1778.3 (11) Å30.23 × 0.21 × 0.16 mm
Z = 4

Data collection

Bruker SMART APEX CCD diffractometer3839 independent reflections
Radiation source: fine-focus sealed tube2671 reflections with I > 2σ(I)
graphiteRint = 0.037
[var phi] and ω scansθmax = 27.0°, θmin = 2.1°
Absorption correction: multi-scan (SADABS; Bruker, 2007)h = −10→10
Tmin = 0.977, Tmax = 0.984k = −9→24
10998 measured reflectionsl = −15→15

Refinement

Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.074Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.176H atoms treated by a mixture of independent and constrained refinement
S = 1.02w = 1/[σ2(Fo2) + (0.02P)2 + 3.5P] where P = (Fo2 + 2Fc2)/3
3839 reflections(Δ/σ)max = 0.069
241 parametersΔρmax = 0.41 e Å3
0 restraintsΔρmin = −0.27 e Å3

Special details

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)

xyzUiso*/Ueq
O10.6319 (3)0.46189 (12)0.4160 (2)0.0530 (6)
O21.1091 (4)0.29040 (14)0.9756 (2)0.0660 (8)
O30.9696 (3)0.27423 (12)0.8122 (2)0.0564 (7)
N10.4775 (4)0.68078 (16)0.1780 (2)0.0532 (8)
N20.7766 (3)0.55247 (14)0.5019 (2)0.0406 (6)
H2A0.80430.59820.50240.049*
N30.8374 (3)0.50452 (14)0.5828 (2)0.0420 (6)
N40.9761 (3)0.41573 (14)0.7584 (2)0.0415 (6)
H4A0.91580.38920.71410.050*
C10.4299 (4)0.6106 (2)0.1836 (3)0.0545 (9)
H10.35070.59460.13190.065*
C20.4901 (4)0.56074 (19)0.2606 (3)0.0498 (8)
H20.45220.51240.26040.060*
C30.6076 (4)0.58255 (17)0.3388 (3)0.0385 (7)
C40.6579 (5)0.65506 (18)0.3348 (3)0.0531 (9)
H40.73550.67300.38610.064*
C50.5898 (5)0.70012 (19)0.2527 (3)0.0605 (10)
H50.62670.74850.25000.073*
C60.6727 (4)0.52615 (16)0.4219 (3)0.0380 (7)
C70.9388 (4)0.53192 (17)0.6540 (3)0.0418 (7)
H7A0.96860.58110.64710.050*
C81.0084 (4)0.48875 (17)0.7448 (3)0.0412 (7)
C91.1112 (4)0.51125 (18)0.8322 (3)0.0428 (8)
C101.1406 (4)0.44984 (18)0.9021 (3)0.0423 (7)
C111.0555 (4)0.39167 (17)0.8543 (3)0.0411 (7)
C121.1778 (5)0.5870 (2)0.8501 (3)0.0654 (11)
H12A1.17540.61310.77950.098*
H12B1.28700.58370.87890.098*
H12C1.11370.61290.90330.098*
C131.2480 (5)0.4481 (2)1.0061 (3)0.0589 (10)
H13A1.18940.46541.06950.088*
H13B1.33980.47920.99540.088*
H13C1.28350.39841.02010.088*
C141.0502 (4)0.31492 (18)0.8893 (3)0.0452 (8)
C150.9548 (5)0.19650 (18)0.8342 (3)0.0609 (10)
H15A0.89780.18830.90340.073*
H15B1.06050.17380.84200.073*
C160.8642 (7)0.1652 (2)0.7371 (4)0.0830 (15)
H16A0.76230.19000.72810.125*
H16B0.84610.11350.74980.125*
H16C0.92470.17150.67000.125*
O1W0.4291 (4)0.80318 (15)0.0290 (3)0.0654 (8)
H1C0.428 (7)0.770 (3)0.059 (5)0.098*
H1D0.528 (6)0.813 (3)0.001 (4)0.098*
O2W0.7783 (3)0.34071 (15)0.5656 (2)0.0588 (7)
H2C0.704 (6)0.305 (3)0.544 (4)0.088*
H2D0.744 (6)0.380 (3)0.541 (4)0.088*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
O10.0688 (16)0.0297 (12)0.0598 (15)−0.0029 (11)−0.0066 (12)0.0035 (10)
O20.102 (2)0.0431 (14)0.0513 (15)0.0040 (14)−0.0203 (15)0.0099 (12)
O30.0790 (18)0.0327 (12)0.0562 (15)−0.0080 (12)−0.0160 (13)0.0066 (11)
N10.0622 (19)0.0453 (17)0.0512 (18)0.0079 (14)−0.0106 (15)0.0081 (14)
N20.0489 (15)0.0314 (13)0.0412 (15)0.0009 (11)−0.0045 (12)0.0071 (11)
N30.0514 (16)0.0334 (14)0.0412 (15)0.0061 (12)0.0007 (12)0.0060 (11)
N40.0479 (15)0.0373 (14)0.0388 (14)−0.0002 (12)−0.0063 (12)0.0009 (11)
C10.055 (2)0.056 (2)0.051 (2)−0.0028 (17)−0.0150 (17)0.0018 (17)
C20.053 (2)0.0374 (18)0.058 (2)−0.0064 (15)−0.0077 (17)0.0021 (16)
C30.0430 (17)0.0327 (16)0.0396 (17)0.0022 (13)0.0000 (13)−0.0006 (13)
C40.069 (2)0.0373 (18)0.052 (2)−0.0048 (16)−0.0192 (18)0.0029 (15)
C50.079 (3)0.0298 (18)0.072 (3)−0.0034 (17)−0.017 (2)0.0099 (17)
C60.0437 (17)0.0295 (16)0.0410 (17)0.0023 (13)0.0040 (14)0.0027 (13)
C70.0525 (19)0.0333 (16)0.0396 (17)0.0013 (14)0.0019 (15)0.0003 (13)
C80.0459 (18)0.0379 (17)0.0399 (17)0.0056 (14)0.0024 (14)0.0016 (14)
C90.0515 (19)0.0367 (17)0.0404 (17)0.0011 (14)0.0029 (15)−0.0014 (13)
C100.0501 (19)0.0384 (17)0.0383 (17)0.0027 (14)−0.0022 (14)−0.0018 (14)
C110.0502 (18)0.0368 (17)0.0359 (16)0.0040 (14)−0.0030 (14)0.0018 (13)
C120.092 (3)0.042 (2)0.061 (2)−0.008 (2)−0.011 (2)0.0002 (18)
C130.072 (3)0.056 (2)0.047 (2)0.0001 (19)−0.0138 (18)−0.0002 (17)
C140.057 (2)0.0384 (18)0.0404 (18)0.0043 (15)−0.0020 (15)0.0007 (14)
C150.086 (3)0.0304 (18)0.065 (2)−0.0057 (18)−0.004 (2)0.0070 (16)
C160.118 (4)0.043 (2)0.086 (3)−0.005 (2)−0.025 (3)−0.005 (2)
O1W0.0706 (18)0.0443 (16)0.081 (2)0.0111 (14)−0.0049 (16)0.0186 (14)
O2W0.0681 (18)0.0384 (14)0.0692 (18)0.0038 (12)−0.0093 (14)−0.0031 (13)

Geometric parameters (Å, °)

O1—C61.214 (4)C7—H7A0.9300
O2—C141.204 (4)C8—C91.382 (5)
O3—C141.336 (4)C9—C101.403 (4)
O3—C151.438 (4)C9—C121.492 (5)
N1—C51.312 (5)C10—C111.380 (4)
N1—C11.334 (5)C10—C131.497 (5)
N2—C61.347 (4)C11—C141.452 (4)
N2—N31.377 (3)C12—H12A0.9600
N2—H2A0.8600C12—H12B0.9600
N3—C71.273 (4)C12—H12C0.9600
N4—C81.361 (4)C13—H13A0.9600
N4—C111.366 (4)C13—H13B0.9600
N4—H4A0.8600C13—H13C0.9600
C1—C21.366 (5)C15—C161.468 (5)
C1—H10.9300C15—H15A0.9700
C2—C31.380 (4)C15—H15B0.9700
C2—H20.9300C16—H16A0.9600
C3—C41.380 (4)C16—H16B0.9600
C3—C61.506 (4)C16—H16C0.9600
C4—C51.376 (5)O1W—H1C0.69 (5)
C4—H40.9300O1W—H1D0.91 (5)
C5—H50.9300O2W—H2C0.92 (5)
C7—C81.435 (4)O2W—H2D0.82 (5)
C14—O3—C15117.4 (3)C11—C10—C9106.7 (3)
C5—N1—C1115.2 (3)C11—C10—C13127.2 (3)
C6—N2—N3118.5 (3)C9—C10—C13126.1 (3)
C6—N2—H2A120.7N4—C11—C10108.9 (3)
N3—N2—H2A120.7N4—C11—C14121.6 (3)
C7—N3—N2115.7 (3)C10—C11—C14129.4 (3)
C8—N4—C11108.5 (3)C9—C12—H12A109.5
C8—N4—H4A125.8C9—C12—H12B109.5
C11—N4—H4A125.8H12A—C12—H12B109.5
N1—C1—C2124.1 (3)C9—C12—H12C109.5
N1—C1—H1117.9H12A—C12—H12C109.5
C2—C1—H1117.9H12B—C12—H12C109.5
C1—C2—C3119.6 (3)C10—C13—H13A109.5
C1—C2—H2120.2C10—C13—H13B109.5
C3—C2—H2120.2H13A—C13—H13B109.5
C4—C3—C2117.2 (3)C10—C13—H13C109.5
C4—C3—C6124.5 (3)H13A—C13—H13C109.5
C2—C3—C6118.3 (3)H13B—C13—H13C109.5
C3—C4—C5118.1 (3)O2—C14—O3123.9 (3)
C3—C4—H4120.9O2—C14—C11125.5 (3)
C5—C4—H4120.9O3—C14—C11110.7 (3)
N1—C5—C4125.7 (3)O3—C15—C16106.3 (3)
N1—C5—H5117.1O3—C15—H15A110.5
C4—C5—H5117.1C16—C15—H15A110.5
O1—C6—N2123.4 (3)O3—C15—H15B110.5
O1—C6—C3121.3 (3)C16—C15—H15B110.5
N2—C6—C3115.3 (3)H15A—C15—H15B108.7
N3—C7—C8121.7 (3)C15—C16—H16A109.5
N3—C7—H7A119.2C15—C16—H16B109.5
C8—C7—H7A119.2H16A—C16—H16B109.5
N4—C8—C9108.5 (3)C15—C16—H16C109.5
N4—C8—C7122.9 (3)H16A—C16—H16C109.5
C9—C8—C7128.6 (3)H16B—C16—H16C109.5
C8—C9—C10107.4 (3)H1C—O1W—H1D112 (5)
C8—C9—C12126.5 (3)H2C—O2W—H2D107 (4)
C10—C9—C12126.1 (3)
C6—N2—N3—C7177.9 (3)C7—C8—C9—C10177.6 (3)
C5—N1—C1—C20.3 (6)N4—C8—C9—C12179.8 (3)
N1—C1—C2—C30.1 (6)C7—C8—C9—C12−1.8 (6)
C1—C2—C3—C40.3 (5)C8—C9—C10—C110.4 (4)
C1—C2—C3—C6−179.4 (3)C12—C9—C10—C11179.9 (3)
C2—C3—C4—C5−1.0 (5)C8—C9—C10—C13178.8 (3)
C6—C3—C4—C5178.7 (3)C12—C9—C10—C13−1.8 (6)
C1—N1—C5—C4−1.1 (6)C8—N4—C11—C10−0.5 (4)
C3—C4—C5—N11.5 (7)C8—N4—C11—C14−177.4 (3)
N3—N2—C6—O1−1.4 (5)C9—C10—C11—N40.0 (4)
N3—N2—C6—C3178.1 (3)C13—C10—C11—N4−178.3 (3)
C4—C3—C6—O1−174.7 (3)C9—C10—C11—C14176.6 (3)
C2—C3—C6—O15.0 (5)C13—C10—C11—C14−1.7 (6)
C4—C3—C6—N25.8 (5)C15—O3—C14—O2−0.7 (5)
C2—C3—C6—N2−174.5 (3)C15—O3—C14—C11179.5 (3)
N2—N3—C7—C8178.2 (3)N4—C11—C14—O2−175.6 (3)
C11—N4—C8—C90.8 (4)C10—C11—C14—O28.2 (6)
C11—N4—C8—C7−177.7 (3)N4—C11—C14—O34.3 (5)
N3—C7—C8—N42.6 (5)C10—C11—C14—O3−172.0 (3)
N3—C7—C8—C9−175.5 (3)C14—O3—C15—C16−179.3 (4)
N4—C8—C9—C10−0.8 (4)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
N2—H2A···O1Wi0.862.082.919 (4)164
N4—H4A···O2W0.862.243.084 (4)165
O1W—H1C···N10.69 (5)2.18 (5)2.854 (4)164 (6)
O1W—H1D···O2Wii0.91 (5)1.88 (5)2.790 (5)174 (5)
O2W—H2C···O2iii0.92 (5)2.06 (5)2.941 (4)160 (4)
O2W—H2D···O10.82 (5)2.27 (5)3.048 (4)159 (5)
O2W—H2D···N30.82 (5)2.43 (5)3.014 (4)129 (4)

Symmetry codes: (i) x+1/2, −y+3/2, z+1/2; (ii) −x+3/2, y+1/2, −z+1/2; (iii) x−1/2, −y+1/2, z−1/2.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: CV5084).

References

  • Bruker (2007). APEX2, SAINT and SADABS Bruker AXS Inc., Madison, Wisconsin, USA .
  • Liu, Y.-C. & Yang, Z.-Y. (2009). J. Inorg. Biochem. 103, 1014–1022. [PubMed]
  • Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. [PubMed]
  • Wang, Y., Wu, W.-N., Zhao, R.-Q., Wang, Q.-F. & Qin, B.-F. (2009). Z. Kristallogr. New Cryst. Struct. 224, 625–626.
  • Wu, W.-N., Wang, Y. & Wang, Q.-F. (2009). Acta Cryst. E65, o1661. [PMC free article] [PubMed]

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