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Acta Crystallogr Sect E Struct Rep Online. 2009 August 1; 65(Pt 8): o1900.
Published online 2009 July 18. doi:  10.1107/S1600536809027329
PMCID: PMC2977231

N′-[(E)-3-Indol-3-ylmethyl­ene]isonicotino­hydrazide monohydrate

Abstract

Crystals of the title compound, C15H12N4O·H2O, were obtained from a condensation reaction of isonicotinylhydrazine and 3-indolylformaldehyde. The mol­ecule assumes an E configuration, with the isonicotinoylhydrazine and indole units located on the opposite sites of the C=N double bond. In the mol­ecular structure the pyridine ring is twisted with respect to the indole ring system, forming a dihedral angle of 44.72 (7)°. Extensive classical N—H(...)N, N—H(...)O, O—H(...)O and O—H(...)N hydrogen bonding and weak C—H(...)O inter­actions are present in the crystal structure.

Related literature

For the applications of hydrazone derivatives in biology, see: Okabe et al. (1993 [triangle]). For general background to this work, see: Shan et al. (2003 [triangle]); Qiang et al. (2007 [triangle]). For the corresponding (E)-3-indolylformaldehyde isonicotinoylhydrazone methanol solvate, see: Tai et al. (2003 [triangle]), and (E)-3-indolylformaldehyde isonicotinoylhydrazone ethanol solvate, see: Jing et al. (2006 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-65-o1900-scheme1.jpg

Experimental

Crystal data

  • C15H12N4O·H2O
  • M r = 282.30
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-65-o1900-efi1.jpg
  • a = 7.1984 (11) Å
  • b = 25.327 (4) Å
  • c = 7.9811 (16) Å
  • β = 104.062 (12)°
  • V = 1411.5 (4) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 0.09 mm−1
  • T = 294 K
  • 0.40 × 0.32 × 0.28 mm

Data collection

  • Rigaku R-AXIS RAPID IP diffractometer
  • Absorption correction: none
  • 9235 measured reflections
  • 2504 independent reflections
  • 1575 reflections with I > 2σ(I)
  • R int = 0.048

Refinement

  • R[F 2 > 2σ(F 2)] = 0.055
  • wR(F 2) = 0.161
  • S = 1.07
  • 2504 reflections
  • 191 parameters
  • H-atom parameters constrained
  • Δρmax = 0.18 e Å−3
  • Δρmin = −0.20 e Å−3

Data collection: PROCESS-AUTO (Rigaku, 1998 [triangle]); cell refinement: PROCESS-AUTO; data reduction: CrystalStructure (Rigaku/MSC, 2002 [triangle]); program(s) used to solve structure: SIR92 (Altomare et al., 1993 [triangle]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 [triangle]); molecular graphics: ORTEP-3 for Windows (Farrugia, 1997 [triangle]); software used to prepare material for publication: WinGX (Farrugia, 1999 [triangle]).

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536809027329/xu2554sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536809027329/xu2554Isup2.hkl

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

Acknowledgments

The work was supported by the Natural Science Foundation of Zhejiang Province, China (No. M203027).

supplementary crystallographic information

Comment

The hydrazone derivatives has attracted our much attention because they have shown to be potential DNA damaging and mutagenic agents (Okabe et al., 1993). As part of the ongoing investigation on the relationship between structure and property of hydrazone derivatives (Shan et al., 2003; Qiang et al., 2007) the title compound has recently been prepared in our laboratory and its crystal structure is reported here.

The molecular structure of the title compound is shown in Fig. 1. The pyridine ring is twisted with respect to the indole ring system by a dihedral angle of 44.72 (7)°. The N2—C9 bond distance of 1.293 (3) Å shows a typical C═N double bond. The isonicotinoylhydrazine and indole moieties are located on the opposite sites of the CN bond, thus the molecule assumes an E configuration, which agrees with those found in ethanol solvate compound (Jing et al., 2006) and methanol solvate compound (Tai et al., 2003).

The extensive classic hydrogen bonding and weak C—H···O hydrogen bonding are present in the crystal structure (Table 1).

Experimental

Isonicotinylhydrazine (1.37 g, 0.01 mol) was dissolved in ethanol (50 ml), the solution was heated at about 333 K for several minutes until the solution cleared. An ethanol solution (20 ml) containing 3-indolylformaldehyde (1.45 g, 0.01 mol) was dropped slowly into the above solution with continuous stirring, and the mixture solution was refluxed for 1.5 h. When the solution had cooled to room temperature, colorless powder crystals appeared. The powder crystals were separated from the solution and washed with cold water three times. Recrystallization was performed twice with a mixture solvent of 2-propanol-water (1:1 v/v), to obtain single crystals of the title compound.

Refinement

Water and imino H atoms were located in a difference Fourier map and were refined as riding in as-found relative positions, Uiso(H) = 1.5Ueq(N,O). Methyl H atoms were placed in calculated positions with C—H = 0.96 Å and torsion angle was refined to fit the electron density, Uiso(H) = 1.5Ueq(C). Other H atoms were placed in calculated positions with C—H = 0.93 Å, and refined in riding mode with Uiso(H) = 1.2Ueq(C).

Figures

Fig. 1.
The molecular structure of the title compound with 40% probability displacement (arbitrary spheres for H atoms). Dashed line indicates the hydrogen bonding.

Crystal data

C15H12N4O·H2OF(000) = 592
Mr = 282.30Dx = 1.328 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 3236 reflections
a = 7.1984 (11) Åθ = 2.8–25.0°
b = 25.327 (4) ŵ = 0.09 mm1
c = 7.9811 (16) ÅT = 294 K
β = 104.062 (12)°Prism, colorless
V = 1411.5 (4) Å30.40 × 0.32 × 0.28 mm
Z = 4

Data collection

Rigaku R-AXIS RAPID IP diffractometer1575 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tubeRint = 0.048
graphiteθmax = 25.2°, θmin = 2.8°
Detector resolution: 10.0 pixels mm-1h = −8→8
ω scansk = −30→28
9235 measured reflectionsl = −9→9
2504 independent reflections

Refinement

Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.055H-atom parameters constrained
wR(F2) = 0.161w = 1/[σ2(Fo2) + (0.0753P)2] where P = (Fo2 + 2Fc2)/3
S = 1.07(Δ/σ)max < 0.001
2504 reflectionsΔρmax = 0.18 e Å3
191 parametersΔρmin = −0.20 e Å3
0 restraintsExtinction correction: SHELXL97 (Sheldrick, 2008), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
Primary atom site location: structure-invariant direct methodsExtinction coefficient: 0.022 (4)

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
N10.0721 (3)0.27145 (8)0.4661 (3)0.0532 (6)
H1N0.01890.23880.45180.080*
N20.2051 (3)0.44265 (8)0.6709 (3)0.0557 (6)
N30.1479 (3)0.48641 (8)0.7552 (3)0.0567 (6)
H3N0.02490.49040.75530.085*
N40.0958 (3)0.66448 (8)1.0414 (3)0.0585 (6)
O10.4458 (3)0.52331 (7)0.8055 (3)0.0778 (7)
O1W0.2725 (3)0.51295 (8)0.3543 (3)0.0717 (6)
H1A0.36800.50590.30000.108*
H2A0.29890.49270.44900.108*
C10.0052 (4)0.31058 (10)0.5519 (3)0.0524 (7)
H1−0.10420.30810.59400.063*
C20.1222 (4)0.35481 (10)0.5685 (3)0.0485 (7)
C30.4346 (4)0.36807 (10)0.4582 (3)0.0520 (7)
H30.46250.40230.49890.062*
C40.5486 (4)0.34271 (11)0.3671 (4)0.0603 (8)
H40.65180.36060.34290.072*
C50.5118 (4)0.29032 (12)0.3099 (4)0.0630 (8)
H50.59310.27410.25110.076*
C60.3582 (4)0.26257 (10)0.3389 (3)0.0546 (7)
H60.33480.22780.30190.066*
C70.2390 (4)0.28874 (9)0.4262 (3)0.0469 (6)
C80.2756 (3)0.34103 (9)0.4881 (3)0.0444 (6)
C90.0874 (4)0.40330 (10)0.6509 (3)0.0511 (7)
H9−0.02320.40630.69090.061*
C100.2762 (4)0.52496 (10)0.8150 (4)0.0539 (7)
C110.2053 (4)0.57134 (9)0.8990 (3)0.0483 (7)
C120.0156 (4)0.58804 (10)0.8584 (3)0.0587 (8)
H12−0.07850.56850.78350.070*
C13−0.0314 (4)0.63452 (10)0.9316 (4)0.0611 (8)
H13−0.15850.64540.90260.073*
C140.2765 (4)0.64680 (11)1.0837 (4)0.0629 (8)
H140.36660.66621.16320.076*
C150.3374 (4)0.60145 (10)1.0164 (4)0.0590 (8)
H150.46520.59131.04930.071*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
N10.0506 (13)0.0365 (12)0.0698 (15)−0.0060 (10)0.0094 (11)−0.0002 (11)
N20.0574 (14)0.0399 (13)0.0711 (15)0.0061 (11)0.0184 (12)−0.0088 (11)
N30.0554 (13)0.0399 (13)0.0771 (16)0.0050 (11)0.0207 (12)−0.0113 (11)
N40.0716 (16)0.0416 (13)0.0618 (14)0.0087 (12)0.0153 (12)−0.0015 (11)
O10.0638 (14)0.0592 (13)0.1204 (18)−0.0004 (11)0.0418 (13)−0.0204 (12)
O1W0.0577 (12)0.0756 (14)0.0845 (14)0.0109 (10)0.0221 (11)−0.0006 (11)
C10.0469 (15)0.0442 (15)0.0663 (17)0.0017 (13)0.0139 (13)0.0062 (13)
C20.0488 (15)0.0374 (14)0.0575 (16)0.0058 (12)0.0093 (13)0.0040 (12)
C30.0542 (16)0.0382 (14)0.0616 (17)−0.0011 (13)0.0099 (14)0.0032 (12)
C40.0524 (16)0.0555 (18)0.0711 (19)0.0016 (14)0.0111 (15)0.0059 (15)
C50.0606 (18)0.0628 (18)0.0662 (19)0.0130 (16)0.0165 (15)−0.0018 (15)
C60.0597 (17)0.0408 (15)0.0580 (17)0.0048 (13)0.0039 (14)−0.0042 (12)
C70.0464 (15)0.0369 (14)0.0524 (15)0.0020 (12)0.0021 (12)−0.0006 (12)
C80.0454 (14)0.0339 (14)0.0491 (14)0.0025 (12)0.0021 (12)0.0007 (11)
C90.0558 (16)0.0411 (15)0.0587 (16)0.0054 (13)0.0185 (13)0.0041 (12)
C100.0569 (18)0.0396 (15)0.0677 (18)0.0069 (13)0.0203 (14)0.0001 (13)
C110.0552 (16)0.0371 (14)0.0564 (16)0.0041 (12)0.0206 (13)0.0036 (12)
C120.0615 (18)0.0461 (15)0.0633 (17)0.0100 (14)0.0048 (14)−0.0080 (13)
C130.0632 (18)0.0543 (17)0.0625 (18)0.0154 (15)0.0088 (15)−0.0032 (14)
C140.0634 (19)0.0478 (17)0.076 (2)−0.0035 (15)0.0131 (16)−0.0070 (14)
C150.0500 (16)0.0466 (16)0.081 (2)0.0017 (13)0.0165 (15)−0.0072 (14)

Geometric parameters (Å, °)

N1—C11.358 (3)C3—H30.9300
N1—C71.387 (3)C4—C51.407 (4)
N1—H1N0.9057C4—H40.9300
N2—C91.293 (3)C5—C61.376 (4)
N2—N31.409 (3)C5—H50.9300
N3—C101.349 (3)C6—C71.397 (3)
N3—H3N0.8916C6—H60.9300
N4—C131.338 (3)C7—C81.416 (3)
N4—C141.339 (3)C9—H90.9300
O1—C101.242 (3)C10—C111.502 (3)
O1W—H1A0.9147C11—C151.389 (3)
O1W—H2A0.8945C11—C121.391 (4)
C1—C21.388 (3)C12—C131.392 (3)
C1—H10.9300C12—H120.9300
C2—C91.444 (3)C13—H130.9300
C2—C81.449 (3)C14—C151.384 (4)
C3—C41.380 (4)C14—H140.9300
C3—C81.403 (3)C15—H150.9300
C1—N1—C7108.6 (2)N1—C7—C6129.5 (2)
C1—N1—H1N122.6N1—C7—C8108.3 (2)
C7—N1—H1N128.5C6—C7—C8122.2 (2)
C9—N2—N3114.0 (2)C3—C8—C7119.2 (2)
C10—N3—N2118.9 (2)C3—C8—C2134.4 (2)
C10—N3—H3N120.8C7—C8—C2106.4 (2)
N2—N3—H3N119.7N2—C9—C2122.1 (2)
C13—N4—C14116.3 (2)N2—C9—H9119.0
H1A—O1W—H2A105.0C2—C9—H9119.0
N1—C1—C2110.9 (2)O1—C10—N3123.6 (2)
N1—C1—H1124.6O1—C10—C11119.9 (2)
C2—C1—H1124.6N3—C10—C11116.5 (2)
C1—C2—C9124.2 (2)C15—C11—C12117.6 (2)
C1—C2—C8105.9 (2)C15—C11—C10118.6 (2)
C9—C2—C8130.0 (2)C12—C11—C10123.7 (2)
C4—C3—C8118.4 (2)C11—C12—C13119.0 (3)
C4—C3—H3120.8C11—C12—H12120.5
C8—C3—H3120.8C13—C12—H12120.5
C3—C4—C5121.4 (3)N4—C13—C12123.9 (3)
C3—C4—H4119.3N4—C13—H13118.1
C5—C4—H4119.3C12—C13—H13118.1
C6—C5—C4121.5 (3)N4—C14—C15124.0 (3)
C6—C5—H5119.3N4—C14—H14118.0
C4—C5—H5119.3C15—C14—H14118.0
C5—C6—C7117.2 (2)C14—C15—C11119.2 (3)
C5—C6—H6121.4C14—C15—H15120.4
C7—C6—H6121.4C11—C15—H15120.4

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
N1—H1N···N4i0.912.062.961 (3)171
N3—H3N···O1Wii0.892.112.939 (3)155
O1W—H1A···O1iii0.911.902.800 (3)168
O1W—H2A···N20.892.403.223 (3)152
C12—H12···O1Wii0.932.583.466 (3)159

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

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: XU2554).

References

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