3,4-Di-2-pyridyl-1,2,5-oxadiazole and its perchlorate salt

In 3,4-di-2-pyridyl-1,2,5-oxadiazole (dpo), C₁₂H₈N₄O, each mol­ecule resides on a twofold axis and inter­acts with eight neighbours via four C—H...N and four C—H...O inter­actions to generate a three-dimensional hydrogen-bonded architecture. In the perchlorate analogue, 2-[3-(2-pyrid­yl)-1,2,5-oxadiazol-4-yl]pyridinium perchlorate, C₁₂H₉N₄O⁺·ClO₄⁻ or [Hdpo]ClO₄, the [Hdpo]⁺ cation is bisected by a crystallographic mirror plane, and the additional H atom in the cation is shared by the two pyridyl N atoms to form a symmetrical intra­molecular N...H...N hydrogen bond. The cations and perchlorate anions are linked through C—H...O hydrogen bonds and π–π stacking inter­actions to form one-dimensional tubes along the b-axis direction.

S1. Comment

Because of the well known importance of D—H···A hydrogen bonds in supramolecular, biological and materials systems (Steiner, 2002), these non-covalent interactions, ranging from strong ones involving O—H and N—H to weak ones involving C—H, continue to be the subject of intense studies, as well as a putative tool for engineering organic and organometallic solids (Desiraju & Steiner, 1999; Desiraju, 1996; Braga & Grepioni, 2000; Baures et al., 2006; Maly et al., 2006). In this paper, we report the structures of an oxadiazole compound, 3,4-di(2'-pyridyl)-1,2,5-oxadiazole (dpo), (I), and its perchlorate, [Hdpo]ClO₄, (II).

The molecular structure of dpo is shown in Fig. 1. The molecule resides on a twofold axis that passes through the O atom and the middle of the C—C bond in the oxadiazole ring. The dihedral angle between the oxadiazole ring and the pyridyl ring is 140.1 (1)°, and that between the two pyridyl rings is 56.78 (7)°, indicating a significant deviation of the molecule from planarity.

In the crystal structure, dpo molecules interact through weak C—H···O and C—H···N intermolecular hydrogen bonds (Fig. 2 and Table 1). Each pyridyl group participates in C—H···O, C—H···N and N···H—C hydrogen bonds through C3—H3A, C4—H4A and N1, respectively, to three adjacent molecules, and the oxadiazole atom O1 acts as a bifurcated acceptor in two O···H—C hydrogen bonds with the pyridyl C3—H3A groups of two adjacent molecules. Thus, each dpo molecule is linked to eight adjacent molecules through four C—H···O and four C—H···N hydrogen bonds, generating a three-dimensional supramolecular structure.

The molecular structure of [Hdpo]ClO₄ is shown in Fig. 3. A difference Fourier map indicated that the additional H atom (H1N) in the [Hdpo]⁺ cation is shared by the two pyridyl N atoms with identical N···H distances, suggesting a symmetrical intramolecular N···H···N hydrogen bond (Table 2). Nearly symmetrical N···H···N hydrogen bonds, with differences in the N···H distances in the range 0.05–0.11 Å, have been reported for several pyridinium–pyridine systems (Bock et al., 1992; Amoedo-Portela et al., 2002; Wang et al., 2003; Alfonso et al., 2001; Brammer & Zhao, 1995; Fu et al., 2004). Symmetrical hydrogen bonds have also been recognized for neutral O···H···O (e.g. Cheng & Lin, 2006; Macdonald et al., 1972). The [Hdpo]⁺ cation is bisected by a crystallographic mirror plane that passes through atoms O1 and H1N. We note that the planarity of [Hdpo]⁺ is significantly improved compared with that of the neutral dpo molecule, due to the formation of the intramolecular N···H···N hydrogen bond: The dihedral angle between the oxadiazole ring and the pyridyl ring is 12.8 (3)°, and that between the two pyridyl rings is 19.9 (2)°.

As expected, the supramolecular structure of [Hdpo]ClO₄ is distinct from that of dpo. As shown in Fig. 4(a), each [Hdpo]⁺ cation is linked to three perchlorate anions through four C—H···O hydrogen bonds (Table 2), and each perchlorate anion is linked to three [Hdpo]⁺ cations. This leads to hydrogen-bonded supramolecular tubes parallel to the b direction (Fig. 4b). The tube is further stabilized by π–π stacking interactions involving two neighbouring pyridyl rings [at (x, y, z) and (1 - x, 1 - y, 1 - z)] from different [Hdpo]⁺ cations. The interacting rings are parallel, with a centre-to-centre separation of 3.66 Å and an interplanar separation of 3.48 Å (Fig. 4a).

Related literature

For related literature, see: Alfonso et al. (2001); Amoedo-Portela, Carballo, Casas, Garcia-Martinez, Gomez-Alonso, Sanchez-Gonzalez, Sordo & Vazquez-Lopez (2002); Baures et al. (2006); Bock et al. (1992); Braga & Grepioni (2000); Brammer & Zhao (1995); Cheng & Lin (2006); Desiraju (1996); Desiraju & Steiner (1999); Fu et al. (2004); Macdonald et al. (1972); Maly et al. (2006); Richardson et al. (2002); Steiner (2002); Wang et al. (2003).

S2. Experimental

The compound dpo was synthesized according to the literature procedure of Richardson et al. (2002). Single crystals of dpo were obtained by recrystallization from petroleum ether–ethyl acetate (3:1 v/v), and crystals of [Hdpo]ClO₄ were prepared by slow evaporation of an ethanol solution of dpo and HClO₄.

S3. Refinement

All H atoms attached to C atoms were placed in calculated positions and refined using a riding model. The H atom involved in N···H···N hydrogen bonding in (II) was located in a difference map and refined isotropically. The absolute structure of (I) was not determined; because the compound is a weak anomalous scatterer (no atom heavier than Si), Friedel pairs were merged (MERG 4) before the final refinement and the meaningless absolute structure parameter has been removed from the CIF.

Computing details

For both compounds, data collection: COLLECT (Nonius, 1998); cell refinement: HKL SCALEPACK (Otwinowski & Minor, 1997); data reduction: HKL DENZO (Otwinowski & Minor, 1997) and maXus (Mackay et al., 1998); program(s) used to solve structure: SHELXS97 (Sheldrick, 1997a); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997a); molecular graphics: SHELXTL (Sheldrick, 1997b); software used to prepare material for publication: SHELXL97.

Figures

	Fig. 1. The molecular structure of (I), with the atom-numbering scheme. Displacement ellipsoids are drawn at the 25% probability level and H atoms are shown as small spheres of arbitrary radii. Atoms marked with an asterisk and unlabelled atoms? (*) are at the symmetry position (-x, -y, z).
	Fig. 2. Hydrogen bonds around a molecule of (I). H atoms not involved in hydrogen bonding have been omitted for clarity.
	Fig. 3. The molecular structure of (II), with the atom-numbering scheme. Displacement ellipsoids are drawn at the 30% probability level and H atoms are shown as small spheres of arbitrary radii. Atoms marked with an asterisk (*) and unlabelled atoms? are at the symmetry position (x, -y + 1/2, z).
	Fig. 4. (a) The one-dimensional tube-like motif in (II), showing the hydrogen bonds and π–π interactions (dashed lines) along the b direction. (b) The packing of the tube-like motifs. H atoms not involved in hydrogen bonding have been omitted for clarity.

(I) 3,4-di-2-pyridyl-1,2,5-oxadiazole

Crystal data

C12H8N4O	F(000) = 928
Mr = 224.22	Dx = 1.335 Mg m^−3
Orthorhombic, Fdd2	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: F2-2d	Cell parameters from 7309 reflections
a = 13.0702 (8) Å	θ = 3.4–27.5°
b = 21.8905 (16) Å	µ = 0.09 mm^−1
c = 7.7957 (5) Å	T = 293 K
V = 2230.5 (3) Å^3	Rod, colourless
Z = 8	0.3 × 0.2 × 0.2 mm

Data collection

Nonius KappaCCD area-detector diffractometer	398 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tube	Rint = 0.093
Graphite monochromator	θmax = 27.4°, θmin = 3.6°
Detector resolution: 0.76 pixels mm^-1	h = −16→16
ϕ and ω scans	k = −28→28
8433 measured reflections	l = −10→9
676 independent reflections

Refinement

Refinement on F^2	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F^2 > 2σ(F^2)] = 0.065	H-atom parameters constrained
wR(F^2) = 0.083	w = 1/[σ^2(Fo^2) + (0.0334P)^2] where P = (Fo^2 + 2Fc^2)/3
S = 1.10	(Δ/σ)max < 0.001
676 reflections	Δρmax = 0.13 e Å^−3
79 parameters	Δρmin = −0.17 e Å^−3
1 restraint	Extinction correction: SHELXL97 (Sheldrick, 1997a), Fc^*=kFc[1+0.001xFc^2λ^3/sin(2θ)]^-1/4
Primary atom site location: structure-invariant direct methods	Extinction coefficient: 0.0037 (6)

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 (Ų)

	x	y	z	Uiso*/Ueq
C1	0.1794 (2)	0.02206 (15)	0.5662 (4)	0.0768 (9)
H1A	0.1911	−0.0047	0.4756	0.092*
C2	0.2237 (2)	0.07872 (17)	0.5586 (5)	0.0843 (11)
H2A	0.2649	0.0897	0.4663	0.101*
C3	0.2060 (3)	0.11860 (15)	0.6891 (5)	0.0848 (10)
H3A	0.2345	0.1575	0.6868	0.102*
C4	0.1459 (2)	0.10073 (12)	0.8241 (4)	0.0724 (9)
H4A	0.1329	0.1271	0.9150	0.087*
C5	0.10528 (19)	0.04296 (12)	0.8215 (4)	0.0561 (8)
C6	0.0440 (2)	0.01959 (10)	0.9645 (4)	0.0584 (7)
N1	0.12092 (17)	0.00284 (11)	0.6945 (3)	0.0628 (7)
N2	0.0692 (2)	0.03188 (12)	1.1228 (3)	0.0806 (9)
O1	0.0000	0.0000	1.2239 (4)	0.0941 (10)

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
C1	0.068 (2)	0.079 (2)	0.084 (2)	0.0072 (17)	0.013 (2)	−0.0046 (18)
C2	0.066 (2)	0.084 (3)	0.102 (3)	−0.0055 (19)	0.012 (2)	0.022 (2)
C3	0.080 (2)	0.0614 (19)	0.113 (3)	−0.0144 (17)	−0.011 (2)	0.012 (2)
C4	0.084 (2)	0.0543 (19)	0.079 (2)	−0.0079 (16)	−0.0137 (19)	−0.0022 (17)
C5	0.0555 (16)	0.0478 (17)	0.065 (2)	0.0032 (13)	−0.0113 (15)	−0.0012 (17)
C6	0.0713 (19)	0.0493 (17)	0.0544 (17)	0.0095 (12)	−0.0089 (16)	−0.0064 (15)
N1	0.0584 (15)	0.0565 (13)	0.0737 (17)	−0.0007 (12)	0.0032 (14)	−0.0096 (13)
N2	0.101 (2)	0.0744 (17)	0.0664 (19)	0.0035 (15)	−0.0071 (16)	−0.0040 (14)
O1	0.131 (3)	0.093 (2)	0.0587 (19)	0.003 (2)	0.000	0.000

Geometric parameters (Å, º)

C1—N1	1.327 (4)	C4—H4A	0.9300
C1—C2	1.370 (4)	C5—N1	1.339 (3)
C1—H1A	0.9300	C5—C6	1.465 (4)
C2—C3	1.360 (5)	C6—N2	1.305 (4)
C2—H2A	0.9300	C6—C6^i	1.434 (5)
C3—C4	1.370 (5)	N2—O1	1.388 (3)
C3—H3A	0.9300	O1—N2^i	1.388 (3)
C4—C5	1.372 (4)
N1—C1—C2	124.3 (3)	C5—C4—H4A	120.9
N1—C1—H1A	117.9	N1—C5—C4	123.8 (3)
C2—C1—H1A	117.9	N1—C5—C6	114.6 (2)
C3—C2—C1	118.5 (3)	C4—C5—C6	121.5 (3)
C3—C2—H2A	120.8	N2—C6—C6^i	109.01 (18)
C1—C2—H2A	120.8	N2—C6—C5	120.6 (3)
C2—C3—C4	119.2 (3)	C6^i—C6—C5	130.32 (16)
C2—C3—H3A	120.4	C1—N1—C5	115.9 (3)
C4—C3—H3A	120.4	C6—N2—O1	105.6 (3)
C3—C4—C5	118.3 (3)	N2^i—O1—N2	110.8 (3)
C3—C4—H4A	120.9
N1—C1—C2—C3	−0.9 (5)	C4—C5—C6—C6^i	143.6 (4)
C1—C2—C3—C4	0.7 (5)	C2—C1—N1—C5	0.6 (4)
C2—C3—C4—C5	−0.3 (5)	C4—C5—N1—C1	−0.1 (4)
C3—C4—C5—N1	0.0 (4)	C6—C5—N1—C1	−177.6 (2)
C3—C4—C5—C6	177.3 (3)	C6^i—C6—N2—O1	1.3 (4)
N1—C5—C6—N2	138.2 (3)	C5—C6—N2—O1	−176.31 (19)
C4—C5—C6—N2	−39.4 (4)	C6—N2—O1—N2^i	−0.52 (14)
N1—C5—C6—C6^i	−38.8 (5)

Symmetry code: (i) −x, −y, z.

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
C3—H3A···O1^ii	0.93	2.63	3.379 (4)	139
C4—H4A···N1^iii	0.93	2.76	3.467 (3)	133

Symmetry codes: (ii) x+1/4, −y+1/4, z−3/4; (iii) −x+1/4, y+1/4, z+1/4.

(II) 2-[3-(2-pyridyl)-1,2,5-oxadiazol-4-yl]pyridinium perchlorate

Crystal data

C12H9N4O^+·ClO4^−	F(000) = 664
Mr = 324.68	Dx = 1.575 Mg m^−3
Orthorhombic, Pnma	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P2ac2n	Cell parameters from 11064 reflections
a = 13.5254 (4) Å	θ = 3.4–27.5°
b = 13.1646 (4) Å	µ = 0.31 mm^−1
c = 7.6908 (2) Å	T = 293 K
V = 1369.40 (7) Å^3	Rod, colourless
Z = 4	0.2 × 0.1 × 0.1 mm

Data collection

Nonius KappaCCD area-detector diffractometer	905 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tube	Rint = 0.088
Graphite monochromator	θmax = 27.5°, θmin = 3.4°
Detector resolution: 0.76 pixels mm^-1	h = −17→17
ϕ and ω scans	k = −16→17
21299 measured reflections	l = −9→9
1631 independent reflections

Refinement

Refinement on F^2	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F^2 > 2σ(F^2)] = 0.064	Hydrogen site location: inferred from neighbouring sites
wR(F^2) = 0.221	H atoms treated by a mixture of independent and constrained refinement
S = 1.03	w = 1/[σ^2(Fo^2) + (0.1422P)^2] where P = (Fo^2 + 2Fc^2)/3
1631 reflections	(Δ/σ)max < 0.001
109 parameters	Δρmax = 0.79 e Å^−3
0 restraints	Δρmin = −0.56 e Å^−3

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 (Ų)

	x	y	z	Uiso*/Ueq
C1	0.3280 (2)	0.4164 (2)	0.5158 (4)	0.0513 (8)
H1A	0.2805	0.3936	0.4375	0.062*
C2	0.3307 (3)	0.5179 (3)	0.5597 (5)	0.0616 (10)
H2A	0.2854	0.5634	0.5125	0.074*
C3	0.4016 (3)	0.5503 (3)	0.6747 (5)	0.0679 (11)
H3A	0.4046	0.6185	0.7056	0.082*
C4	0.4683 (3)	0.4828 (2)	0.7445 (5)	0.0600 (10)
H4A	0.5166	0.5045	0.8221	0.072*
C5	0.4616 (2)	0.3813 (2)	0.6963 (4)	0.0466 (8)
C6	0.5299 (2)	0.3052 (2)	0.7661 (4)	0.0539 (9)
N1	0.39250 (18)	0.34969 (17)	0.5834 (3)	0.0450 (7)
H1N	0.360 (4)	0.2500	0.584 (7)	0.084 (18)*
N2	0.6075 (2)	0.3354 (3)	0.8499 (5)	0.0770 (10)
O1	0.6562 (3)	0.2500	0.9015 (6)	0.0887 (14)
O2	0.3937 (4)	0.3369 (4)	0.1146 (7)	0.189 (3)
O3	0.2627 (3)	0.2500	0.2196 (5)	0.0722 (11)
O4	0.3063 (5)	0.2500	−0.0716 (6)	0.143 (2)
Cl1	0.34351 (10)	0.2500	0.10130 (15)	0.0582 (5)

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
C1	0.0514 (18)	0.0446 (17)	0.0578 (19)	−0.0014 (14)	0.0048 (15)	0.0022 (15)
C2	0.068 (2)	0.0418 (17)	0.075 (2)	0.0089 (17)	0.0126 (19)	0.0031 (17)
C3	0.086 (3)	0.0409 (18)	0.077 (2)	−0.0003 (19)	0.021 (2)	−0.0077 (18)
C4	0.072 (2)	0.0499 (19)	0.058 (2)	−0.0138 (18)	0.0043 (18)	−0.0073 (16)
C5	0.0466 (18)	0.0449 (17)	0.0483 (16)	−0.0076 (14)	0.0067 (14)	−0.0017 (13)
C6	0.0493 (18)	0.061 (2)	0.0518 (18)	−0.0033 (16)	−0.0036 (15)	−0.0030 (15)
N1	0.0455 (14)	0.0402 (14)	0.0493 (14)	−0.0025 (12)	0.0025 (11)	−0.0005 (11)
N2	0.063 (2)	0.078 (2)	0.090 (2)	−0.0046 (18)	−0.0242 (18)	−0.0054 (18)
O1	0.074 (3)	0.085 (3)	0.107 (3)	0.000	−0.039 (2)	0.000
O2	0.179 (4)	0.173 (4)	0.215 (5)	−0.130 (4)	0.107 (4)	−0.106 (4)
O3	0.082 (3)	0.064 (2)	0.071 (2)	0.000	0.026 (2)	0.000
O4	0.155 (5)	0.216 (7)	0.058 (3)	0.000	0.005 (3)	0.000
Cl1	0.0744 (9)	0.0454 (7)	0.0549 (7)	0.000	0.0141 (6)	0.000

Geometric parameters (Å, º)

C1—N1	1.342 (4)	C5—C6	1.464 (4)
C1—C2	1.379 (5)	C6—N2	1.294 (4)
C1—H1A	0.9300	C6—C6^i	1.453 (6)
C2—C3	1.372 (6)	N1—H1N	1.382 (19)
C2—H2A	0.9300	N2—O1	1.362 (4)
C3—C4	1.375 (5)	O1—N2^i	1.362 (4)
C3—H3A	0.9300	O2—Cl1	1.334 (4)
C4—C5	1.390 (4)	O3—Cl1	1.422 (4)
C4—H4A	0.9300	O4—Cl1	1.422 (5)
C5—N1	1.342 (4)	Cl1—O2^i	1.334 (4)
N1—C1—C2	121.5 (3)	N2—C6—C6^i	107.9 (2)
N1—C1—H1A	119.3	N2—C6—C5	118.9 (3)
C2—C1—H1A	119.3	C6^i—C6—C5	133.16 (17)
C3—C2—C1	118.5 (4)	C5—N1—C1	120.0 (3)
C3—C2—H2A	120.8	C5—N1—H1N	121 (2)
C1—C2—H2A	120.8	C1—N1—H1N	115 (2)
C2—C3—C4	120.6 (3)	C6—N2—O1	106.5 (3)
C2—C3—H3A	119.7	N2^i—O1—N2	111.2 (4)
C4—C3—H3A	119.7	O2—Cl1—O2^i	118.1 (6)
C3—C4—C5	118.3 (3)	O2—Cl1—O4	104.6 (3)
C3—C4—H4A	120.8	O2^i—Cl1—O4	104.6 (3)
C5—C4—H4A	120.8	O2—Cl1—O3	110.0 (2)
N1—C5—C4	121.0 (3)	O2^i—Cl1—O3	110.0 (2)
N1—C5—C6	117.7 (3)	O4—Cl1—O3	109.0 (3)
C4—C5—C6	121.3 (3)
N1—C1—C2—C3	0.3 (5)	C4—C5—C6—C6^i	166.6 (2)
C1—C2—C3—C4	−0.2 (5)	C4—C5—N1—C1	−0.3 (4)
C2—C3—C4—C5	−0.3 (5)	C6—C5—N1—C1	179.9 (3)
C3—C4—C5—N1	0.5 (5)	C2—C1—N1—C5	−0.1 (5)
C3—C4—C5—C6	−179.7 (3)	C6^i—C6—N2—O1	0.3 (4)
N1—C5—C6—N2	167.8 (3)	C5—C6—N2—O1	179.2 (3)
C4—C5—C6—N2	−11.9 (5)	C6—N2—O1—N2^i	−0.5 (6)
N1—C5—C6—C6^i	−13.6 (4)

Symmetry code: (i) x, −y+1/2, z.

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1N···N1^i	1.38 (2)	1.38 (2)	2.625 (5)	143 (5)
C1—H1A···O3	0.93	2.54	3.281 (4)	137
C4—H4A···O2^ii	0.93	2.46	3.209 (5)	137

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