Pyridine-2,6-dicarbaldehyde bis­(benzyl­idenehydrazone) monohydrate

Cheng, C.-X.; Liu, H.-W.; Luo, F.-H.; Cao, M.-N.; Hu, Z.-Q.

doi:10.1107/S1600536807022635

Pyridine-2,6-dicarbaldehyde bis(benzylidenehydrazone) monohydrate

C.-X. Cheng, H.-W. Liu, F.-H. Luo, M.-N. Cao and Z.-Q. Hu

The crystal structure of the title compound, C₂₁H₁₇N₅O₂·H₂O, is stabilized by intermolecular hydrogen bonds.

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Supporting information

	Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536807022635/bt2363sup1.cif Contains datablocks global, I
	Structure factor file (CIF format) https://doi.org/10.1107/S1600536807022635/bt2363Isup2.hkl Contains datablock I

CCDC reference: 651435

checkCIF report

Key indicators

Single-crystal X-ray study
T = 298 K
Mean (C-C) = 0.005 Å
R factor = 0.048
wR factor = 0.108
Data-to-parameter ratio = 8.3

checkCIF/PLATON results

No syntax errors found



Alert level C
PLAT125_ALERT_4_C No _symmetry_space_group_name_Hall Given .......          ?
PLAT340_ALERT_3_C Low Bond Precision on C-C Bonds (x 1000) Ang ...          5

Alert level G
REFLT03_ALERT_4_G Please check that the estimate of the number of Friedel pairs is
            correct. If it is not, please give the correct count in the
            _publ_section_exptl_refinement section of the submitted CIF.
           From the CIF: _diffrn_reflns_theta_max           27.00
           From the CIF: _reflns_number_total               2278
           Count of symmetry unique reflns         2278
           Completeness (_total/calc)            100.00%
           TEST3: Check Friedels for noncentro structure
           Estimate of Friedel pairs measured         0
           Fraction of Friedel pairs measured     0.000
           Are heavy atom types Z>Si present         no
PLAT860_ALERT_3_G Note: Number of Least-Squares Restraints .......          1

   0 ALERT level A = In general: serious problem
   0 ALERT level B = Potentially serious problem
   2 ALERT level C = Check and explain
   2 ALERT level G = General alerts; check

   0 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
   0 ALERT type 2 Indicator that the structure model may be wrong or deficient
   2 ALERT type 3 Indicator that the structure quality may be low
   2 ALERT type 4 Improvement, methodology, query or suggestion
   0 ALERT type 5 Informative message, check

Comment top

Tridentate ligands containing the 2,6-dipicolinoyhydrazone moiety have been intensively studied due to their interesting coordination mode (Chen et al., 1997; Thompson et al.,2002; Zhao et al., 2004).

The molecules are linked into a three dimensional framework by a combination of N–H···O C—H···O and O—H···O hydrogen bonds.

Related literature top

For related literature, see: Chen et al. (1997); Thompson (2002); Zhao et al. (2004).

Experimental top

To a solution of benzaldehyde (1.166 g, 11 mmol) in absolute ethanol (40 ml) a suspension of 2,6-dipicolinoyhydrazine in the same solvent (50 ml) was added at 353 K. The mixture was left to react at reflux for 8 h. Then, the white product was filtered, washed with hot ethanol (20 ml) three times and dried in vacuo. Crystals suitable for X-ray diffraction were obtained from dimethylformamide–methanol (3:1 v/v) over a period of about three weeks.

Structure description top

The molecules are linked into a three dimensional framework by a combination of N–H···O C—H···O and O—H···O hydrogen bonds.

For related literature, see: Chen et al. (1997); Thompson (2002); Zhao et al. (2004).

Computing details top

Data collection: SMART (Bruker, 2001); cell refinement: SMART-Plus (Bruker, 2001); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: PLATON (Spek, 2003); software used to prepare material for publication: SHELXTL.

Figures top

Fig. 1. The molecular structure of the title compound with atom labels and 50% probability displacement ellipsoids. Hydrogen bonds are shown as dashed lines.

Pyridine-2,6-dicarbaldehyde bis(benzylidenehydrazone) monohydrate top

Crystal data top

C₂₁H₁₇N₅O₂·H₂O	D_x = 1.297 Mg m⁻³
M_r = 389.41	Mo Kα radiation, λ = 0.71073 Å
Orthorhombic, Pna2₁	Cell parameters from 1982 reflections
a = 10.3490 (8) Å	θ = 2.5–21.4°
b = 16.2487 (12) Å	µ = 0.09 mm⁻¹
c = 11.8556 (9) Å	T = 298 K
V = 1993.6 (3) Å³	Block, colourless
Z = 4	0.20 × 0.10 × 0.10 mm
F(000) = 816

Data collection top

Bruker SMART CCD area-detector diffractometer	1653 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tube	R_int = 0.077
Graphite monochromator	θ_max = 27.0°, θ_min = 2.1°
φ and ω scans	h = −9→13
11761 measured reflections	k = −20→20
2278 independent reflections	l = −12→15

Refinement top

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)] = 0.048	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.108	H atoms treated by a mixture of independent and constrained refinement
S = 0.98	w = 1/[σ²(F_o²) + (0.0503P)²] where P = (F_o² + 2F_c²)/3
2278 reflections	(Δ/σ)_max < 0.001
274 parameters	Δρ_max = 0.14 e Å⁻³
1 restraint	Δρ_min = −0.16 e Å⁻³

Crystal data top

C₂₁H₁₇N₅O₂·H₂O	V = 1993.6 (3) Å³
M_r = 389.41	Z = 4
Orthorhombic, Pna2₁	Mo Kα radiation
a = 10.3490 (8) Å	µ = 0.09 mm⁻¹
b = 16.2487 (12) Å	T = 298 K
c = 11.8556 (9) Å	0.20 × 0.10 × 0.10 mm

Data collection top

Bruker SMART CCD area-detector diffractometer	1653 reflections with I > 2σ(I)
11761 measured reflections	R_int = 0.077
2278 independent reflections

Refinement top

R[F² > 2σ(F²)] = 0.048	1 restraint
wR(F²) = 0.108	H atoms treated by a mixture of independent and constrained refinement
S = 0.98	Δρ_max = 0.14 e Å⁻³
2278 reflections	Δρ_min = −0.16 e Å⁻³
274 parameters

Special details top

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) top

	x	y	z	U_iso*/U_eq
C1	0.1229 (3)	0.68779 (19)	0.7135 (3)	0.0417 (7)
C2	0.0307 (3)	0.6861 (2)	0.7975 (3)	0.0560 (9)
H2	−0.0476	0.7133	0.7885	0.067*
C3	0.0570 (4)	0.6437 (2)	0.8943 (3)	0.0674 (10)
H3	−0.0035	0.6416	0.9522	0.081*
C4	0.1735 (3)	0.6041 (2)	0.9053 (3)	0.0575 (9)
H4	0.1934	0.5748	0.9704	0.069*
C5	0.2607 (3)	0.60884 (18)	0.8169 (3)	0.0426 (7)
C6	0.0924 (3)	0.73123 (18)	0.6064 (3)	0.0456 (7)
C7	0.2320 (4)	0.7503 (2)	0.3423 (3)	0.0591 (10)
H7	0.3023	0.7157	0.3541	0.071*
C8	0.2124 (3)	0.7865 (2)	0.2314 (3)	0.0538 (8)
C9	0.2824 (4)	0.7571 (2)	0.1402 (3)	0.0693 (11)
H9	0.3439	0.7161	0.1512	0.083*
C10	0.2617 (4)	0.7881 (3)	0.0331 (3)	0.0757 (12)
H10	0.3082	0.7673	−0.0277	0.091*
C11	0.1732 (4)	0.8494 (3)	0.0162 (4)	0.0751 (12)
H11	0.1598	0.8704	−0.0558	0.090*
C12	0.1055 (4)	0.8790 (2)	0.1043 (3)	0.0689 (11)
H12	0.0455	0.9208	0.0923	0.083*
C13	0.1232 (3)	0.8489 (2)	0.2117 (3)	0.0597 (9)
H13	0.0753	0.8703	0.2712	0.072*
C14	0.3879 (3)	0.56512 (19)	0.8299 (3)	0.0463 (8)
C15	0.6689 (3)	0.5587 (2)	0.6706 (3)	0.0515 (8)
H15	0.6409	0.5909	0.6106	0.062*
C16	0.8009 (3)	0.5264 (2)	0.6703 (3)	0.0546 (9)
C17	0.8874 (3)	0.5537 (2)	0.5896 (3)	0.0621 (9)
H17	0.8617	0.5924	0.5365	0.075*
C18	1.0127 (4)	0.5230 (3)	0.5881 (4)	0.0775 (13)
H18	1.0708	0.5413	0.5337	0.093*
C19	1.0508 (4)	0.4663 (3)	0.6659 (5)	0.0834 (14)
H19	1.1349	0.4461	0.6649	0.100*
C20	0.9653 (4)	0.4391 (3)	0.7455 (5)	0.0863 (13)
H20	0.9915	0.4002	0.7982	0.104*
C21	0.8410 (3)	0.4687 (2)	0.7486 (4)	0.0705 (11)
H21	0.7837	0.4498	0.8032	0.085*
N1	0.2374 (2)	0.64974 (15)	0.7219 (2)	0.0418 (6)
N2	0.1809 (3)	0.72613 (19)	0.5239 (3)	0.0575 (8)
N3	0.1550 (2)	0.76508 (16)	0.4236 (2)	0.0553 (7)
N4	0.4704 (3)	0.57779 (18)	0.7442 (2)	0.0497 (7)
N5	0.5920 (2)	0.54337 (16)	0.7514 (2)	0.0514 (7)
O1	−0.0089 (2)	0.76993 (14)	0.5958 (2)	0.0605 (6)
O2	0.4109 (2)	0.52270 (15)	0.9118 (2)	0.0654 (7)
O3	0.3994 (3)	0.60103 (18)	0.4627 (3)	0.0724 (8)
H4A	0.454 (4)	0.605 (2)	0.683 (4)	0.087*
H2A	0.244 (4)	0.693 (3)	0.535 (4)	0.087*
H3B	0.431 (4)	0.551 (3)	0.445 (4)	0.109*
H3A	0.458 (4)	0.637 (3)	0.470 (5)	0.109*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
C1	0.0390 (16)	0.0443 (16)	0.0419 (18)	0.0012 (13)	0.0026 (13)	0.0021 (13)
C2	0.051 (2)	0.063 (2)	0.054 (2)	0.0104 (16)	0.0116 (17)	0.0085 (18)
C3	0.061 (2)	0.088 (3)	0.053 (2)	0.0149 (19)	0.0240 (18)	0.017 (2)
C4	0.064 (2)	0.064 (2)	0.044 (2)	0.0074 (17)	0.0107 (16)	0.0135 (17)
C5	0.0456 (18)	0.0419 (16)	0.0403 (18)	−0.0040 (13)	0.0027 (14)	0.0041 (14)
C6	0.0435 (17)	0.0439 (17)	0.0495 (19)	0.0039 (14)	0.0022 (15)	0.0026 (15)
C7	0.055 (2)	0.065 (2)	0.057 (2)	0.0169 (17)	0.0111 (17)	0.0182 (19)
C8	0.0539 (19)	0.057 (2)	0.051 (2)	0.0010 (16)	0.0118 (16)	0.0071 (17)
C9	0.075 (3)	0.066 (2)	0.067 (3)	−0.002 (2)	0.023 (2)	0.000 (2)
C10	0.092 (3)	0.085 (3)	0.049 (2)	−0.026 (3)	0.026 (2)	−0.014 (2)
C11	0.085 (3)	0.094 (3)	0.046 (2)	−0.025 (3)	−0.004 (2)	0.012 (2)
C12	0.067 (2)	0.085 (3)	0.055 (2)	0.0016 (19)	−0.004 (2)	0.018 (2)
C13	0.059 (2)	0.072 (2)	0.048 (2)	0.0052 (18)	0.0053 (17)	0.0113 (18)
C14	0.0490 (19)	0.0480 (18)	0.0418 (18)	−0.0008 (14)	−0.0016 (14)	0.0046 (15)
C15	0.0486 (19)	0.0551 (19)	0.051 (2)	0.0092 (15)	−0.0054 (16)	−0.0033 (17)
C16	0.0448 (18)	0.055 (2)	0.064 (2)	0.0056 (15)	−0.0024 (17)	−0.0187 (18)
C17	0.053 (2)	0.064 (2)	0.069 (3)	−0.0008 (17)	0.0032 (18)	−0.016 (2)
C18	0.056 (2)	0.084 (3)	0.093 (3)	−0.011 (2)	0.020 (2)	−0.034 (3)
C19	0.052 (2)	0.087 (3)	0.112 (4)	0.017 (2)	−0.012 (3)	−0.033 (3)
C20	0.062 (2)	0.094 (3)	0.102 (4)	0.024 (2)	−0.010 (3)	−0.003 (3)
C21	0.055 (2)	0.082 (3)	0.074 (3)	0.0168 (19)	0.003 (2)	−0.001 (2)
N1	0.0399 (13)	0.0447 (13)	0.0409 (15)	−0.0007 (11)	0.0034 (11)	0.0062 (12)
N2	0.0509 (17)	0.072 (2)	0.0499 (17)	0.0186 (14)	0.0112 (14)	0.0248 (15)
N3	0.0534 (16)	0.0626 (17)	0.0498 (18)	0.0096 (13)	0.0082 (14)	0.0172 (15)
N4	0.0430 (14)	0.0621 (17)	0.0441 (16)	0.0105 (12)	−0.0008 (12)	0.0084 (13)
N5	0.0440 (15)	0.0594 (16)	0.0508 (17)	0.0110 (12)	−0.0021 (13)	0.0029 (14)
O1	0.0526 (13)	0.0707 (15)	0.0581 (15)	0.0241 (11)	0.0065 (12)	0.0106 (13)
O2	0.0650 (15)	0.0791 (16)	0.0521 (15)	0.0141 (12)	0.0000 (11)	0.0228 (14)
O3	0.0643 (17)	0.0628 (16)	0.090 (2)	0.0070 (13)	0.0042 (14)	−0.0171 (15)

Geometric parameters (Å, º) top

C1—N1	1.340 (4)	C12—H12	0.9300
C1—C2	1.380 (4)	C13—H13	0.9300
C1—C6	1.486 (4)	C14—O2	1.214 (4)
C2—C3	1.366 (5)	C14—N4	1.343 (4)
C2—H2	0.9300	C15—N5	1.271 (4)
C3—C4	1.373 (5)	C15—C16	1.463 (4)
C3—H3	0.9300	C15—H15	0.9300
C4—C5	1.385 (4)	C16—C17	1.383 (5)
C4—H4	0.9300	C16—C21	1.383 (5)
C5—N1	1.330 (4)	C17—C18	1.389 (5)
C5—C14	1.504 (4)	C17—H17	0.9300
C6—O1	1.229 (3)	C18—C19	1.363 (7)
C6—N2	1.343 (4)	C18—H18	0.9300
C7—N3	1.274 (4)	C19—C20	1.367 (7)
C7—C8	1.454 (5)	C19—H19	0.9300
C7—H7	0.9300	C20—C21	1.373 (5)
C8—C9	1.387 (5)	C20—H20	0.9300
C8—C13	1.391 (5)	C21—H21	0.9300
C9—C10	1.383 (6)	N2—N3	1.374 (4)
C9—H9	0.9300	N2—H2A	0.86 (4)
C10—C11	1.367 (6)	N4—N5	1.380 (3)
C10—H10	0.9300	N4—H4A	0.87 (4)
C11—C12	1.347 (6)	O3—H3B	0.90 (4)
C11—H11	0.9300	O3—H3A	0.85 (5)
C12—C13	1.376 (5)

N1—C1—C2	123.2 (3)	C12—C13—H13	119.9
N1—C1—C6	118.1 (2)	C8—C13—H13	119.9
C2—C1—C6	118.6 (3)	O2—C14—N4	124.6 (3)
C3—C2—C1	118.6 (3)	O2—C14—C5	121.5 (3)
C3—C2—H2	120.7	N4—C14—C5	114.0 (3)
C1—C2—H2	120.7	N5—C15—C16	121.1 (3)
C2—C3—C4	119.4 (3)	N5—C15—H15	119.4
C2—C3—H3	120.3	C16—C15—H15	119.4
C4—C3—H3	120.3	C17—C16—C21	119.2 (3)
C3—C4—C5	118.3 (3)	C17—C16—C15	119.4 (3)
C3—C4—H4	120.9	C21—C16—C15	121.4 (3)
C5—C4—H4	120.9	C16—C17—C18	119.9 (4)
N1—C5—C4	123.4 (3)	C16—C17—H17	120.0
N1—C5—C14	118.8 (3)	C18—C17—H17	120.0
C4—C5—C14	117.8 (3)	C19—C18—C17	120.2 (4)
O1—C6—N2	122.6 (3)	C19—C18—H18	119.9
O1—C6—C1	120.8 (3)	C17—C18—H18	119.9
N2—C6—C1	116.6 (3)	C18—C19—C20	119.9 (4)
N3—C7—C8	121.4 (3)	C18—C19—H19	120.0
N3—C7—H7	119.3	C20—C19—H19	120.0
C8—C7—H7	119.3	C19—C20—C21	120.8 (5)
C9—C8—C13	117.8 (3)	C19—C20—H20	119.6
C9—C8—C7	119.5 (3)	C21—C20—H20	119.6
C13—C8—C7	122.6 (3)	C20—C21—C16	120.0 (4)
C10—C9—C8	120.6 (4)	C20—C21—H21	120.0
C10—C9—H9	119.7	C16—C21—H21	120.0
C8—C9—H9	119.7	C5—N1—C1	117.0 (2)
C11—C10—C9	120.3 (4)	C6—N2—N3	118.0 (3)
C11—C10—H10	119.9	C6—N2—H2A	117 (3)
C9—C10—H10	119.9	N3—N2—H2A	125 (3)
C12—C11—C10	119.7 (4)	C7—N3—N2	116.5 (3)
C12—C11—H11	120.2	C14—N4—N5	118.1 (3)
C10—C11—H11	120.2	C14—N4—H4A	126 (3)
C11—C12—C13	121.4 (4)	N5—N4—H4A	116 (3)
C11—C12—H12	119.3	C15—N5—N4	116.5 (3)
C13—C12—H12	119.3	H3B—O3—H3A	113 (4)
C12—C13—C8	120.2 (3)

N1—C1—C2—C3	0.0 (5)	C4—C5—C14—N4	−175.4 (3)
C6—C1—C2—C3	177.6 (3)	N5—C15—C16—C17	−170.8 (3)
C1—C2—C3—C4	0.0 (6)	N5—C15—C16—C21	9.7 (5)
C2—C3—C4—C5	0.0 (6)	C21—C16—C17—C18	−0.1 (5)
C3—C4—C5—N1	0.0 (5)	C15—C16—C17—C18	−179.6 (3)
C3—C4—C5—C14	−179.9 (3)	C16—C17—C18—C19	−0.1 (6)
N1—C1—C6—O1	−177.0 (3)	C17—C18—C19—C20	0.3 (6)
C2—C1—C6—O1	5.2 (4)	C18—C19—C20—C21	−0.4 (7)
N1—C1—C6—N2	2.6 (4)	C19—C20—C21—C16	0.2 (7)
C2—C1—C6—N2	−175.2 (3)	C17—C16—C21—C20	0.0 (6)
N3—C7—C8—C9	−167.6 (4)	C15—C16—C21—C20	179.5 (4)
N3—C7—C8—C13	10.9 (6)	C4—C5—N1—C1	0.0 (4)
C13—C8—C9—C10	−1.2 (6)	C14—C5—N1—C1	179.9 (3)
C7—C8—C9—C10	177.3 (4)	C2—C1—N1—C5	0.0 (4)
C8—C9—C10—C11	1.1 (6)	C6—C1—N1—C5	−177.7 (3)
C9—C10—C11—C12	−0.4 (6)	O1—C6—N2—N3	−0.9 (5)
C10—C11—C12—C13	−0.1 (6)	C1—C6—N2—N3	179.5 (3)
C11—C12—C13—C8	0.0 (6)	C8—C7—N3—N2	178.5 (3)
C9—C8—C13—C12	0.7 (5)	C6—N2—N3—C7	−171.0 (3)
C7—C8—C13—C12	−177.8 (4)	O2—C14—N4—N5	−3.0 (5)
N1—C5—C14—O2	−175.3 (3)	C5—C14—N4—N5	176.9 (3)
C4—C5—C14—O2	4.6 (5)	C16—C15—N5—N4	179.0 (3)
N1—C5—C14—N4	4.7 (4)	C14—N4—N5—C15	−177.9 (3)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
C7—H7···O3	0.93	2.48	3.305 (5)	148
N2—H2A···O3	0.86 (4)	2.35 (4)	3.126 (4)	150 (4)
O3—H3B···O2ⁱ	0.90 (4)	2.06 (4)	2.874 (3)	149 (4)
N4—H4A···O1ⁱⁱ	0.87 (4)	2.32 (4)	3.044 (4)	142 (4)
O3—H3A···O1ⁱⁱ	0.85 (5)	2.14 (5)	2.790 (4)	133 (5)

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

Experimental details

Crystal data
Chemical formula	C₂₁H₁₇N₅O₂·H₂O
M_r	389.41
Crystal system, space group	Orthorhombic, Pna2₁
Temperature (K)	298
a, b, c (Å)	10.3490 (8), 16.2487 (12), 11.8556 (9)
V (Å³)	1993.6 (3)
Z	4
Radiation type	Mo Kα
µ (mm⁻¹)	0.09
Crystal size (mm)	0.20 × 0.10 × 0.10

Data collection
Diffractometer	Bruker SMART CCD area-detector
Absorption correction	–
No. of measured, independent and observed [I > 2σ(I)] reflections	11761, 2278, 1653
R_int	0.077
(sin θ/λ)_max (Å⁻¹)	0.639

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.048, 0.108, 0.98
No. of reflections	2278
No. of parameters	274
No. of restraints	1
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
Δρ_max, Δρ_min (e Å⁻³)	0.14, −0.16

Computer programs: SMART (Bruker, 2001), SMART-Plus (Bruker, 2001), SAINT, SHELXS97 (Sheldrick, 1997), SHELXL97 (Sheldrick, 1997), PLATON (Spek, 2003), SHELXTL.