N1,N3-Bis(pyridin-3-ylmeth­yl)isophthalamide dihydrate

Dong, Y.; Cao, X.

doi:10.1107/S1600536811031965

organic compounds

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Volume 67| Part 9| September 2011| Page o2339

doi:10.1107/S1600536811031965

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N¹,N³-Bis(pyridin-3-ylmethyl)isophthalamide dihydrate

Ying-ying Dong ^a and Xi-chuan Cao ^a ^*

^aSchool of Materials Science and Engineering, China University of Mining and Technology, Xuzhou, Jiangsu Province 221008, People's Republic of China
^*Correspondence e-mail: dongxiaoyingzi@163.com

(Received 25 July 2011; accepted 7 August 2011; online 17 August 2011)

The complete organic molecule in the title dihydrate, C₂₀H₂₂N₄O₄, is generated by crystallographic twofold symmetry, with two C atoms lying on the rotation axis. The symmetry unique pyridine ring forms a dihedral angle of 83.16 (8)° with the central benzene ring. In the crystal, intermolecular N—H⋯O, O—H⋯N and O—H⋯O hydrogen bonds connect the components into a two-dimensional network lying parallel to (101).

Related literature

For information on amide derivatives used in the construction of metal-organic frameworks, see: Luo et al. (2007 , 2009 ).

Experimental

Crystal data

C₂₀H₁₈N₄O₂·2H₂O
M_r = 382.42
Monoclinic, C 2/c
a = 23.0097 (8) Å
b = 7.0040 (2) Å
c = 12.4483 (4) Å
β = 107.493 (2)°
V = 1913.39 (11) Å³
Z = 4
Mo Kα radiation
μ = 0.10 mm⁻¹
T = 296 K
0.20 × 0.20 × 0.15 mm

Data collection

Bruker SMART CCD diffractometer
Absorption correction: multi-scan (SADADS; Sheldrick, 1996 ) T_min = 0.981, T_max = 0.986
7105 measured reflections
1687 independent reflections
1350 reflections with I > 2σ(I)
R_int = 0.026

Refinement

R[F² > 2σ(F²)] = 0.039
wR(F²) = 0.113
S = 1.02
1687 reflections
137 parameters
H atoms treated by a mixture of independent and constrained refinement
Δρ_max = 0.17 e Å⁻³
Δρ_min = −0.14 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N1—H1A⋯O2ⁱ	0.86	2.05	2.859 (2)	156
O2—H2W⋯O1ⁱⁱ	0.95 (3)	1.94 (3)	2.875 (2)	169 (3)
O2—H1W⋯N2	0.95 (3)	1.90 (3)	2.849 (2)	178 (3)
Symmetry codes: (i) $[-x+{\script{1\over 2}}, -y+{\script{3\over 2}}, -z+1]$ ; (ii) $[-x+{\script{1\over 2}}, -y+{\script{1\over 2}}, -z+1]$ .

Data collection: SMART (Bruker, 1998 ); cell refinement: SAINT (Bruker, 1998); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: DIAMOND (Brandenburg, 1999 ); software used to prepare material for publication: SHELXTL (Sheldrick, 2008).

Supporting information

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536811031965/lh5294sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536811031965/lh5294Isup2.hkl

Supporting information file. DOI: 10.1107/S1600536811031965/lh5294Isup3.cml

checkCIF report

Comment top

Amides are useful to construct long ligands for building porous metal-organic frameworks (Luo et al., 2007;2009). We synthesized the title compound in the hope of using it as a ligand for constructing metal-organic frameworks. The crystal structure of the title compound is presented herein.

The molecular structure of the title compound is shown in Fig. 1. The molecule lies on a twofold rotation axis. The symmetry unique pyridine ring forms a dihedral angle of 83.16 (8)° with the central benzene ring. In the crystal, intermolecular N—H···O, O—H···N and O—H···O hydrogen bonds connect the components of the structure into a two-dimensional network parallel to (101) (Fig. 2).

Related literature top

For information on amide derivatives used in the construction of metal-organic frameworks, see: Luo et al. (2007, 2009).

Experimental top

Thionyl chloride (10 mL, 99.0%) and isophthalic acid (10 mmol) in a round bottomflask was refluxed for 2 h. After the reaction was complete, dichloromethane (30 mL), triethylamine (4.2 mL) and pyridin-3-ylmethanamine (20 mmol) were added to the solution, and stired for 2 h in an ice bath. The mixture was refluxed for 3 hr. The solvent was evaporated in vacuo and the residue was washed with water. The title compound was dissolved in N,N-dimethylformamide and single crystals were obtained by slow evaporation.

Computing details top

Data collection: SMART (Bruker, 1998); cell refinement: SAINT (Bruker, 1998); data reduction: SAINT (Bruker, 1998); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: DIAMOND (Brandenburg, 1999); software used to prepare material for publication: SHELXTL (Sheldrick, 2008).

Figures top

	Fig. 1. The molecular structure of the title compound with displacement ellipsoids drawn at the 50% probability level (symmetry code; (A) -x+1, y, -z+1/2). Only the symmetry unique water molecule is shown.
	Fig. 2. Part of the crystal structure with hydrogen bonds shown as dashed lines. Only H atoms involved in hydrogen bonds are shown.

N¹,N³-Bis(pyridin-3-ylmethyl)isophthalamide dihydrate top

Crystal data top

C₂₀H₁₈N₄O₂·2H₂O	F(000) = 808
M_r = 382.42	D_x = 1.328 Mg m⁻³
Monoclinic, C2/c	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -C 2yc	Cell parameters from 2484 reflections
a = 23.0097 (8) Å	θ = 3.1–27.3°
b = 7.0040 (2) Å	µ = 0.10 mm⁻¹
c = 12.4483 (4) Å	T = 296 K
β = 107.493 (2)°	Block, colorless
V = 1913.39 (11) Å³	0.20 × 0.20 × 0.15 mm
Z = 4

Data collection top

Bruker SMART CCD diffractometer	1687 independent reflections
Radiation source: fine-focus sealed tube	1350 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.026
ϕ and ω scans	θ_max = 25.0°, θ_min = 1.9°
Absorption correction: multi-scan (SADADS; Sheldrick, 1996)	h = −27→27
T_min = 0.981, T_max = 0.986	k = −8→8
7105 measured reflections	l = −14→14

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)] = 0.039	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.113	H atoms treated by a mixture of independent and constrained refinement
S = 1.02	w = 1/[σ²(F_o²) + (0.0574P)² + 0.8895P] where P = (F_o² + 2F_c²)/3
1687 reflections	(Δ/σ)_max < 0.001
137 parameters	Δρ_max = 0.17 e Å⁻³
0 restraints	Δρ_min = −0.14 e Å⁻³

Crystal data top

C₂₀H₁₈N₄O₂·2H₂O	V = 1913.39 (11) Å³
M_r = 382.42	Z = 4
Monoclinic, C2/c	Mo Kα radiation
a = 23.0097 (8) Å	µ = 0.10 mm⁻¹
b = 7.0040 (2) Å	T = 296 K
c = 12.4483 (4) Å	0.20 × 0.20 × 0.15 mm
β = 107.493 (2)°

Data collection top

Bruker SMART CCD diffractometer	1687 independent reflections
Absorption correction: multi-scan (SADADS; Sheldrick, 1996)	1350 reflections with I > 2σ(I)
T_min = 0.981, T_max = 0.986	R_int = 0.026
7105 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.039	0 restraints
wR(F²) = 0.113	H atoms treated by a mixture of independent and constrained refinement
S = 1.02	Δρ_max = 0.17 e Å⁻³
1687 reflections	Δρ_min = −0.14 e Å⁻³
137 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	0.26370 (7)	0.5013 (2)	0.48897 (15)	0.0532 (5)
H1	0.2776	0.5491	0.5619	0.064*
C2	0.30590 (7)	0.4263 (2)	0.44286 (13)	0.0440 (4)
C3	0.28433 (8)	0.3535 (3)	0.33491 (15)	0.0614 (5)
H3	0.3112	0.3006	0.3004	0.074*
C4	0.22323 (9)	0.3594 (3)	0.27895 (16)	0.0706 (6)
H4	0.2081	0.3095	0.2067	0.085*
C5	0.18480 (8)	0.4404 (3)	0.33149 (19)	0.0681 (6)
H5	0.1435	0.4469	0.2924	0.082*
C6	0.37282 (7)	0.4242 (3)	0.50748 (13)	0.0500 (4)
H6A	0.3792	0.4938	0.5774	0.060*
H6B	0.3858	0.2933	0.5262	0.060*
C7	0.43779 (6)	0.4081 (2)	0.38248 (13)	0.0442 (4)
C8	0.47085 (6)	0.5210 (2)	0.31622 (12)	0.0402 (4)
C9	0.5000	0.4233 (3)	0.2500	0.0402 (5)
H9	0.5000	0.2905	0.2500	0.048*
C10	0.47222 (7)	0.7191 (3)	0.31698 (14)	0.0544 (5)
H10	0.4542	0.7863	0.3631	0.065*
C11	0.5000	0.8164 (4)	0.2500	0.0655 (8)
H11	0.5000	0.9492	0.2500	0.079*
H1W	0.1383 (14)	0.563 (4)	0.494 (2)	0.126 (10)*
H2W	0.0893 (14)	0.482 (5)	0.548 (3)	0.141 (11)*
N1	0.40984 (5)	0.5090 (2)	0.44382 (11)	0.0470 (4)
H1A	0.4140	0.6311	0.4457	0.056*
N2	0.20366 (7)	0.5099 (2)	0.43535 (15)	0.0662 (5)
O1	0.43603 (5)	0.23240 (18)	0.37774 (11)	0.0644 (4)
O2	0.10649 (7)	0.5921 (2)	0.52588 (15)	0.0810 (5)

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
C1	0.0526 (10)	0.0520 (10)	0.0644 (11)	−0.0028 (8)	0.0316 (8)	−0.0020 (8)
C2	0.0488 (8)	0.0400 (9)	0.0508 (9)	−0.0032 (7)	0.0263 (7)	0.0027 (7)
C3	0.0595 (10)	0.0687 (13)	0.0624 (11)	−0.0019 (9)	0.0282 (9)	−0.0078 (9)
C4	0.0648 (12)	0.0808 (15)	0.0648 (12)	−0.0124 (10)	0.0173 (10)	−0.0058 (11)
C5	0.0477 (10)	0.0721 (13)	0.0825 (14)	−0.0080 (9)	0.0167 (9)	0.0105 (11)
C6	0.0495 (9)	0.0574 (11)	0.0509 (9)	0.0000 (8)	0.0271 (7)	0.0031 (8)
C7	0.0406 (8)	0.0453 (10)	0.0512 (9)	0.0011 (7)	0.0205 (7)	0.0030 (7)
C8	0.0335 (7)	0.0442 (9)	0.0459 (8)	0.0006 (6)	0.0163 (6)	0.0010 (7)
C9	0.0361 (10)	0.0374 (11)	0.0496 (12)	0.000	0.0167 (9)	0.000
C10	0.0614 (10)	0.0458 (10)	0.0700 (11)	0.0029 (8)	0.0410 (9)	−0.0033 (8)
C11	0.0823 (18)	0.0390 (13)	0.097 (2)	0.000	0.0606 (16)	0.000
N1	0.0461 (7)	0.0473 (8)	0.0568 (8)	−0.0013 (6)	0.0295 (6)	0.0014 (6)
N2	0.0513 (9)	0.0639 (10)	0.0945 (13)	0.0020 (7)	0.0388 (8)	0.0039 (9)
O1	0.0800 (9)	0.0451 (8)	0.0886 (9)	0.0000 (6)	0.0566 (7)	0.0049 (6)
O2	0.0929 (10)	0.0548 (9)	0.1232 (13)	0.0019 (7)	0.0745 (10)	−0.0074 (8)

Geometric parameters (Å, º) top

C1—N2	1.343 (2)	C7—O1	1.232 (2)
C1—C2	1.372 (2)	C7—N1	1.3383 (19)
C1—H1	0.9300	C7—C8	1.504 (2)
C2—C3	1.383 (2)	C8—C10	1.388 (2)
C2—C6	1.508 (2)	C8—C9	1.3892 (17)
C3—C4	1.369 (3)	C9—C8ⁱ	1.3892 (17)
C3—H3	0.9300	C9—H9	0.9300
C4—C5	1.371 (3)	C10—C11	1.374 (2)
C4—H4	0.9300	C10—H10	0.9300
C5—N2	1.326 (3)	C11—C10ⁱ	1.374 (2)
C5—H5	0.9300	C11—H11	0.9300
C6—N1	1.4534 (18)	N1—H1A	0.8600
C6—H6A	0.9700	O2—H1W	0.95 (3)
C6—H6B	0.9700	O2—H2W	0.95 (3)

N2—C1—C2	124.12 (17)	O1—C7—N1	122.70 (14)
N2—C1—H1	117.9	O1—C7—C8	120.90 (14)
C2—C1—H1	117.9	N1—C7—C8	116.38 (14)
C1—C2—C3	117.08 (15)	C10—C8—C9	118.85 (14)
C1—C2—C6	121.21 (14)	C10—C8—C7	122.41 (13)
C3—C2—C6	121.70 (14)	C9—C8—C7	118.72 (14)
C4—C3—C2	119.80 (17)	C8ⁱ—C9—C8	121.0 (2)
C4—C3—H3	120.1	C8ⁱ—C9—H9	119.5
C2—C3—H3	120.1	C8—C9—H9	119.5
C3—C4—C5	118.73 (18)	C11—C10—C8	120.36 (15)
C3—C4—H4	120.6	C11—C10—H10	119.8
C5—C4—H4	120.6	C8—C10—H10	119.8
N2—C5—C4	123.23 (17)	C10ⁱ—C11—C10	120.5 (2)
N2—C5—H5	118.4	C10ⁱ—C11—H11	119.7
C4—C5—H5	118.4	C10—C11—H11	119.7
N1—C6—C2	112.14 (12)	C7—N1—C6	123.79 (14)
N1—C6—H6A	109.2	C7—N1—H1A	118.1
C2—C6—H6A	109.2	C6—N1—H1A	118.1
N1—C6—H6B	109.2	C5—N2—C1	117.01 (15)
C2—C6—H6B	109.2	H1W—O2—H2W	113 (2)
H6A—C6—H6B	107.9

N2—C1—C2—C3	−0.9 (3)	N1—C7—C8—C9	−179.21 (11)
N2—C1—C2—C6	179.05 (15)	C10—C8—C9—C8ⁱ	−1.20 (11)
C1—C2—C3—C4	0.4 (3)	C7—C8—C9—C8ⁱ	177.47 (14)
C6—C2—C3—C4	−179.58 (17)	C9—C8—C10—C11	2.4 (2)
C2—C3—C4—C5	0.8 (3)	C7—C8—C10—C11	−176.19 (12)
C3—C4—C5—N2	−1.6 (3)	C8—C10—C11—C10ⁱ	−1.24 (11)
C1—C2—C6—N1	−127.37 (16)	O1—C7—N1—C6	−2.4 (2)
C3—C2—C6—N1	52.6 (2)	C8—C7—N1—C6	176.18 (13)
O1—C7—C8—C10	178.05 (16)	C2—C6—N1—C7	−95.97 (18)
N1—C7—C8—C10	−0.6 (2)	C4—C5—N2—C1	1.1 (3)
O1—C7—C8—C9	−0.6 (2)	C2—C1—N2—C5	0.2 (3)

Symmetry code: (i) −x+1, y, −z+1/2.

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1A···O2ⁱⁱ	0.86	2.05	2.859 (2)	156
O2—H2W···O1ⁱⁱⁱ	0.95 (3)	1.94 (3)	2.875 (2)	169 (3)
O2—H1W···N2	0.95 (3)	1.90 (3)	2.849 (2)	178 (3)

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

Experimental details

Crystal data
Chemical formula	C₂₀H₁₈N₄O₂·2H₂O
M_r	382.42
Crystal system, space group	Monoclinic, C2/c
Temperature (K)	296
a, b, c (Å)	23.0097 (8), 7.0040 (2), 12.4483 (4)
β (°)	107.493 (2)
V (Å³)	1913.39 (11)
Z	4
Radiation type	Mo Kα
µ (mm⁻¹)	0.10
Crystal size (mm)	0.20 × 0.20 × 0.15

Data collection
Diffractometer	Bruker SMART CCD diffractometer
Absorption correction	Multi-scan (SADADS; Sheldrick, 1996)
T_min, T_max	0.981, 0.986
No. of measured, independent and observed [I > 2σ(I)] reflections	7105, 1687, 1350
R_int	0.026
(sin θ/λ)_max (Å⁻¹)	0.595

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.039, 0.113, 1.02
No. of reflections	1687
No. of parameters	137
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
Δρ_max, Δρ_min (e Å⁻³)	0.17, −0.14

Computer programs: SMART (Bruker, 1998), SAINT (Bruker, 1998), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), DIAMOND (Brandenburg, 1999), SHELXTL (Sheldrick, 2008).

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1A···O2ⁱ	0.86	2.05	2.859 (2)	156.1
O2—H2W···O1ⁱⁱ	0.95 (3)	1.94 (3)	2.875 (2)	169 (3)
O2—H1W···N2	0.95 (3)	1.90 (3)	2.849 (2)	178 (3)

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

References

Brandenburg, K. (1999). DIAMOND. Crystal Impact GbR, Bonn, Germany. Google Scholar
Bruker (1998). SMART and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA Google Scholar
Luo, F., Che, Y. X. & Zheng, J. M. (2009). Micropor. Mesopor. Mater. A117, 486–489. Google Scholar
Luo, F., Zheng, J. M. & Batten, S. R. (2007). Chem. Commun. 36, 3744–3746. Web of Science CSD CrossRef Google Scholar
Sheldrick, G. M. (1996). SADABS. University of Göttingen, Germany. Google Scholar
Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. Web of Science CrossRef CAS IUCr Journals Google Scholar

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CRYSTALLOGRAPHIC
COMMUNICATIONS

ISSN: 2056-9890

Volume 67| Part 9| September 2011| Page o2339

doi:10.1107/S1600536811031965

Open

access