Pyridine-4-carboxamidoxime N-oxide

Padgett, C.W.; Sheriff, K.; Lynch, W.E.

doi:10.1107/S2414314620013358

organic compounds

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ISSN: 2414-3146

Volume 5| Part 10| October 2020| x201335

https://doi.org/10.1107/S2414314620013358

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Pyridine-4-carboxamidoxime N-oxide

Clifford W. Padgett,^a ^* Kirkland Sheriff ^a and Will E. Lynch ^a

^aGeorgia Southern University, 11935 Abercorn St., Department of Chemistry and Biochemistry, Savannah GA 31419, USA
^*Correspondence e-mail: cpadgett@georgiasouthern.edu

Edited by S. Bernès, Benemérita Universidad Autónoma de Puebla, México (Received 9 September 2020; accepted 5 October 2020; online 9 October 2020)

Our work in the area of synthesis of metal–organic frameworks (MOFs) based on organic N-oxides led to the crystallization of pyridine-4-carboxamidoxime N-oxide. Herein we report the first crystal structure of the title compound, C₆H₇N₃O₂ [systematic name: (Z)-4-(N′-hydroxycarbamimidoyl)pyridine N-oxide]. The hydroxycarbamimidoyl group is essentially coplanar with the aromatic ring, r.m.s.d. = 0.112 Å. The compound crystallizes in hydrogen-bonding layers built from the formation of strong O—H⋯O hydrogen bonds between the oxime oxygen atom and the oxygen atom of the N-oxide, and the formation of N—H⋯O hydrogen bonds between one amine nitrogen atom and the N-oxide oxygen atom. These combined build R³₄(24) ring motifs in the crystal. The crystal structure has no π–π interactions.

Keywords: crystal structure; N-oxide; oxime; hydrogen bonding; supramolecular structure.

CCDC reference: 2035503

Structure description

Since their first reported syntheses (Meisenheimer et al., 1926 ), pyridine N-oxide and related compounds have garnered much interest in chemistry. We are particularly interested in their uses in coordination polymers and as potential catalysts. The utility of these aromatic N-oxides to facilitate organic oxotransfer reactions has been well documented over the years (see, for example: Espenson, 2003 ). Many of these reactions are actually catalyzed by transition-metal interactions with the N-oxide ligands (see, for example: Moustafa et al., 2014 ). Others have reported their use as coordination polymers (Ren et al., 2018 ). We have also previously reported N-oxides used in coordination polymers of Mn (Kang et al., 2017 and Lynch et al., 2018 ). In this work, the syntheses of metal complexes of the title compound were attempted (Mn, Cu, Ce, Nd, Er, and Pr) by mixing the halide or nitrate salts of the metals with the title compound in methanol; unfortunately, all resulting crystals were of the uncomplexed ligand.

Herein we report the first crystal structure of pyridine-4-carboxamidoxime N-oxide (Fig. 1), which crystallizes in the monoclinic space group P2₁/c. The molecule is nearly planar with a r.m.s.d. of 0.112 Å for all non-hydrogen atoms, with the carbamimidoyl group slightly rotated by 15.09 (8)° with respect to the pyridine ring plane. N1—O1 has a distance of 1.3226 (18) Å and is consistent with normal N-oxide distances. The crystal structure contains a strong intermolecular hydrogen bond between O2⋯O1ⁱ which forms a chain running parallel to the b axis; the O2⋯O1ⁱ separation is 2.6747 (19) Å. Another hydrogen bond is formed between N3⋯O1ⁱⁱ which links neighboring chains together; the N3⋯O1ⁱⁱ separation is 2.899 (2) Å [symmetry codes: (i) x, y + 1, z; (ii) x, −y + $[{1\over 2}]$ , z + $[{1\over 2}]$ , see Table 1].

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
O2—H2A⋯O1ⁱ	0.91 (3)	1.77 (3)	2.6747 (19)	172 (2)
N3—H3A⋯O1ⁱⁱ	0.91 (2)	2.00 (2)	2.899 (2)	167 (2)
Symmetry codes: (i) x, y+1, z; (ii) $[x, -y+{\script{1\over 2}}, z+{\script{1\over 2}}]$ .

Figure 1
A view of the molecular structure of the title compound, with the atom-labeling scheme. Displacement ellipsoids are drawn at the 50% probability level.

These hydrogen bonds link four molecules together and form an R₄³(24) ring motif in the crystal. Each molecule is also part of four different R(24) synthons, generating sheets of hydrogen-bonding molecules parallel to the (100) face of the unit cell (Fig. 2). There are no other short contacts or π–π interactions observed in the crystal.

Figure 2
Crystal packing diagram of title compound viewed along [100]. Hydrogen bonds are colored red.

Synthesis and crystallization

An amount of 0.025 g of pyridine-4-carboxamidoxime N-oxide (Alfa Aesar) was weighed and dissolved in a 25 ml beaker in enough methanol to form a solution that allowed to slowly evaporate at room temperature. The clear crystals were analyzed on a Rigaku Xtal Miniflex.

Refinement

Crystal data, data collection and structure refinement details are summarized in Table 2.

Table 2
Experimental details

Crystal data
Chemical formula	C₆H₇N₃O₂
M_r	153.15
Crystal system, space group	Monoclinic, P2₁/c
Temperature (K)	170
a, b, c (Å)	7.4130 (8), 9.2858 (7), 10.1238 (10)
β (°)	102.841 (10)
V (Å³)	679.45 (11)
Z	4
Radiation type	Mo Kα
μ (mm⁻¹)	0.12
Crystal size (mm)	0.35 × 0.2 × 0.2

Data collection
Diffractometer	Rigaku XtaLAB mini
Absorption correction	Multi-scan (CrysAlis PRO; Rigaku OD, 2018 $[Rigaku OD (2018). CrysAlis PRO. Rigaku Oxford Diffraction, Yarnton, England.]$ )
T_min, T_max	0.940, 1.000
No. of measured, independent and observed [I > 2σ(I)] reflections	5858, 1238, 961
R_int	0.034
(sin θ/λ)_max (Å⁻¹)	0.602

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.039, 0.101, 1.04
No. of reflections	1238
No. of parameters	113
No. of restraints	3
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
Δρ_max, Δρ_min (e Å⁻³)	0.17, −0.15
Computer programs: CrysAlis PRO (Rigaku OD, 2018 $[Rigaku OD (2018). CrysAlis PRO. Rigaku Oxford Diffraction, Yarnton, England.]$ ), SHELXT (Sheldrick, 2015a ), SHELXL (Sheldrick, 2015b ) and OLEX2 (Dolomanov et al., 2009 ).

Structural data

CCDC reference: 2035503

Crystal structure: contains datablock I. DOI: https://doi.org/10.1107/S2414314620013358/bh4056sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2414314620013358/bh4056Isup2.hkl

checkCIF report

Computing details top

Data collection: CrysAlis PRO (Rigaku OD, 2018); cell refinement: CrysAlis PRO (Rigaku OD, 2018); data reduction: CrysAlis PRO (Rigaku OD, 2018); program(s) used to solve structure: ShelXT (Sheldrick, 2015a); program(s) used to refine structure: SHELXL (Sheldrick, 2015b); molecular graphics: OLEX2 (Dolomanov et al., 2009); software used to prepare material for publication: OLEX2 (Dolomanov et al., 2009).

(Z)-4-(N'-Hydroxycarbamimidoyl)pyridine N-oxide top

Crystal data top

C₆H₇N₃O₂	F(000) = 320
M_r = 153.15	D_x = 1.497 Mg m⁻³
Monoclinic, P2₁/c	Mo Kα radiation, λ = 0.71073 Å
a = 7.4130 (8) Å	Cell parameters from 3017 reflections
b = 9.2858 (7) Å	θ = 2.1–32.6°
c = 10.1238 (10) Å	µ = 0.12 mm⁻¹
β = 102.841 (10)°	T = 170 K
V = 679.45 (11) Å³	Block, clear dark colourless
Z = 4	0.35 × 0.2 × 0.2 mm

Data collection top

Rigaku XtaLAB mini diffractometer	1238 independent reflections
Radiation source: fine-focus sealed X-ray tube, Enhance (Mo) X-ray Source	961 reflections with I > 2σ(I)
Graphite Monochromator monochromator	R_int = 0.034
Detector resolution: 13.6612 pixels mm^-1	θ_max = 25.4°, θ_min = 2.8°
ω–scans	h = −8→8
Absorption correction: multi-scan (CrysAlisPro; Rigaku OD, 2018)	k = −11→11
T_min = 0.940, T_max = 1.000	l = −12→12
5858 measured reflections

Refinement top

Refinement on F²	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: mixed
R[F² > 2σ(F²)] = 0.039	H atoms treated by a mixture of independent and constrained refinement
wR(F²) = 0.101	w = 1/[σ²(F_o²) + (0.0443P)² + 0.2172P] where P = (F_o² + 2F_c²)/3
S = 1.04	(Δ/σ)_max < 0.001
1238 reflections	Δρ_max = 0.17 e Å⁻³
113 parameters	Δρ_min = −0.14 e Å⁻³
3 restraints	Extinction correction: SHELXL-2018/1 (Sheldrick 2015b), Fc^*=kFc[1+0.001xFc²λ³/sin(2θ)]^-1/4
Primary atom site location: dual	Extinction coefficient: 0.007 (2)

Special details top

Refinement. All carbon-bound H atoms were positioned geometrically and refined as riding, with C—H = 0.95 Å and U_iso(H) = 1.2U_eq(C). N—H and O—H hydrogen atoms were refined with free coordinates and isotropic displacement parameters.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å²) top

	x	y	z	U_iso*/U_eq
N1	0.7185 (2)	0.20253 (15)	0.40257 (15)	0.0361 (4)
C1	0.6365 (3)	0.31255 (19)	0.32458 (18)	0.0392 (5)
H1	0.565809	0.293556	0.235921	0.047*
O1	0.6953 (2)	0.06920 (13)	0.35596 (13)	0.0498 (4)
C2	0.6543 (2)	0.45181 (18)	0.37200 (17)	0.0371 (5)
H2	0.596971	0.528186	0.315518	0.044*
N2	0.7210 (2)	0.73345 (15)	0.47364 (16)	0.0434 (4)
O2	0.7388 (2)	0.86472 (14)	0.54650 (15)	0.0628 (5)
H2A	0.713 (3)	0.933 (3)	0.481 (2)	0.084 (8)*
C3	0.7554 (2)	0.48156 (17)	0.50187 (16)	0.0311 (4)
N3	0.8319 (3)	0.64526 (18)	0.69433 (16)	0.0450 (5)
H3A	0.807 (3)	0.572 (2)	0.748 (2)	0.066 (7)*
H3B	0.805 (3)	0.7337 (18)	0.722 (2)	0.059 (7)*
C4	0.8403 (3)	0.36626 (19)	0.57809 (18)	0.0382 (5)
H4	0.912748	0.382572	0.666750	0.046*
C5	0.8210 (3)	0.22887 (19)	0.52697 (19)	0.0407 (5)
H5	0.881159	0.151356	0.580441	0.049*
C6	0.7673 (2)	0.62923 (18)	0.55763 (17)	0.0337 (4)

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
N1	0.0481 (9)	0.0226 (7)	0.0376 (8)	0.0000 (7)	0.0092 (7)	−0.0035 (6)
C1	0.0496 (11)	0.0309 (10)	0.0334 (9)	0.0011 (8)	0.0016 (8)	−0.0018 (8)
O1	0.0790 (10)	0.0213 (7)	0.0470 (8)	−0.0002 (6)	0.0098 (7)	−0.0077 (6)
C2	0.0468 (11)	0.0263 (9)	0.0359 (10)	0.0036 (8)	0.0044 (8)	0.0038 (7)
N2	0.0670 (11)	0.0213 (8)	0.0419 (9)	−0.0020 (7)	0.0119 (8)	−0.0021 (7)
O2	0.1140 (14)	0.0213 (7)	0.0520 (9)	−0.0023 (8)	0.0158 (9)	−0.0038 (7)
C3	0.0334 (9)	0.0255 (9)	0.0348 (9)	−0.0015 (7)	0.0083 (8)	−0.0008 (7)
N3	0.0656 (11)	0.0286 (9)	0.0387 (9)	−0.0060 (8)	0.0068 (8)	−0.0042 (7)
C4	0.0446 (11)	0.0299 (9)	0.0360 (10)	0.0018 (8)	0.0002 (8)	−0.0005 (8)
C5	0.0517 (11)	0.0288 (10)	0.0377 (10)	0.0064 (8)	0.0018 (9)	0.0036 (8)
C6	0.0382 (10)	0.0265 (9)	0.0365 (10)	−0.0046 (7)	0.0088 (8)	−0.0013 (8)

Geometric parameters (Å, º) top

N1—C1	1.350 (2)	O2—H2A	0.91 (3)
N1—O1	1.3226 (18)	C3—C4	1.386 (2)
N1—C5	1.341 (2)	C3—C6	1.478 (2)
C1—H1	0.9500	N3—H3A	0.912 (16)
C1—C2	1.376 (2)	N3—H3B	0.903 (15)
C2—H2	0.9500	N3—C6	1.368 (2)
C2—C3	1.389 (2)	C4—H4	0.9500
N2—O2	1.4156 (19)	C4—C5	1.372 (2)
N2—C6	1.284 (2)	C5—H5	0.9500

O1—N1—C1	119.59 (15)	C4—C3—C6	121.51 (15)
O1—N1—C5	120.50 (15)	H3A—N3—H3B	114 (2)
C5—N1—C1	119.91 (15)	C6—N3—H3A	116.5 (14)
N1—C1—H1	119.6	C6—N3—H3B	111.1 (14)
N1—C1—C2	120.77 (16)	C3—C4—H4	119.6
C2—C1—H1	119.6	C5—C4—C3	120.77 (16)
C1—C2—H2	119.8	C5—C4—H4	119.6
C1—C2—C3	120.47 (16)	N1—C5—C4	120.90 (16)
C3—C2—H2	119.8	N1—C5—H5	119.5
C6—N2—O2	108.89 (15)	C4—C5—H5	119.5
N2—O2—H2A	103.8 (16)	N2—C6—C3	117.52 (15)
C2—C3—C6	121.33 (15)	N2—C6—N3	124.75 (16)
C4—C3—C2	117.14 (16)	N3—C6—C3	117.71 (15)

N1—C1—C2—C3	−0.7 (3)	C2—C3—C6—N3	165.27 (17)
C1—N1—C5—C4	1.7 (3)	O2—N2—C6—C3	179.01 (15)
C1—C2—C3—C4	1.8 (3)	O2—N2—C6—N3	−3.0 (3)
C1—C2—C3—C6	−176.45 (16)	C3—C4—C5—N1	−0.5 (3)
O1—N1—C1—C2	178.21 (17)	C4—C3—C6—N2	165.18 (17)
O1—N1—C5—C4	−177.58 (17)	C4—C3—C6—N3	−13.0 (3)
C2—C3—C4—C5	−1.2 (3)	C5—N1—C1—C2	−1.1 (3)
C2—C3—C6—N2	−16.6 (3)	C6—C3—C4—C5	177.05 (17)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
O2—H2A···O1ⁱ	0.91 (3)	1.77 (3)	2.6747 (19)	172 (2)
N3—H3A···O1ⁱⁱ	0.91 (2)	2.00 (2)	2.899 (2)	167 (2)

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

Acknowledgements

The authors wish to thank Georgia Southern University and the Department of Chemistry and Biochemistry for financial support of the department X–ray facility.

References

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IUCrDATA

ISSN: 2414-3146

Volume 5| Part 10| October 2020| x201335

https://doi.org/10.1107/S2414314620013358

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Pyridine-4-carboxamidoxime N-oxide

Structure description

Synthesis and crystallization

Refinement

Structural data

Acknowledgements

References

organic compounds