Crystal structure of tetra­kis­(1-oxidopyridin-2-yl)methane methanol tetra­solvate

Matsumoto, K.; Kawashita, K.; Kannami, M.; Oda, M.

doi:10.1107/S2056989015016862

organic compounds

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Volume 71| Part 10| October 2015| Pages o754-o755

doi:10.1107/S2056989015016862

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Crystal structure of tetrakis(1-oxidopyridin-2-yl)methane methanol tetrasolvate

Kouzou Matsumoto,^a ^* Kazuaki Kawashita,^b Masaki Kannami ^b and Masaji Oda ^b

^aInstitute of Natural Sciences, Senshu University, Higashimita 2-1-1, Kawasaki, Kanagawa 214-8580, Japan, and ^bDepartment of Chemistry, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
^*Correspondence e-mail: matsumoto@isc.senshu-u.ac.jp

Edited by H. Ishida, Okayama University, Japan (Received 31 August 2015; accepted 9 September 2015; online 12 September 2015)

The asymmetric unit of the title compound, C₂₁H₁₆N₄O₄·4CH₃OH, consists of a quarter molecule of tetrakis(1-oxidopyridin-2-yl)methane and one methanol solvent molecule. In the crystal, the pyridine N-oxide derivative is located about a fourfold rotoinversion axis and exhibits S₄ symmetry along the c axis. An intermolecular O—H⋯O hydrogen bond is observed between the O atom of the pyridine N-oxide and the OH group of the methanol. An intermolecular C—H⋯O bond is also observed between adjacent pyridine N-oxide rings.

Keywords: crystal structure; pyridine N-oxide; S4 symmetry; hydrogen bonding.

CCDC reference: 1423138

1. Related literature

For aspects of pyridine N-oxides, see: Katritzky & Lagowski (1971 ). For reviews of metal complexes of pyridine N-oxides, see: Orchin & Schmidt (1968 ); Carlin & De Jongh (1986 ). For the synthesis of the title compound, see: Matsumoto et al. (2003 ). For coordination polymers of pyridine N-oxides, see: Henkelis et al. (2012 ). For structures of related molecules, see: Betz et al. (2011 ); Matsumoto et al. (2014 ). For the effect of the formation of hydrogen bonds on the N—O bond length of pyridine N-oxides, see: Eichhorn (1987 ).

2. Experimental

2.1. Crystal data

C₂₁H₁₆N₄O₄·4CH₄O
M_r = 516.54
Tetragonal, I 4₁ /a
a = 14.4474 (4) Å
c = 12.2965 (5) Å
V = 2566.62 (18) Å³
Z = 4
Mo Kα radiation
μ = 0.10 mm⁻¹
T = 200 K
0.2 × 0.2 × 0.1 mm

2.2. Data collection

Rigaku R-AXIS RAPID diffractometer
12321 measured reflections
1470 independent reflections
1289 reflections with I > 2σ(I)
R_int = 0.031

2.3. Refinement

R[F² > 2σ(F²)] = 0.049
wR(F²) = 0.138
S = 1.07
1470 reflections
86 parameters
H-atom parameters constrained
Δρ_max = 0.40 e Å⁻³
Δρ_min = −0.25 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
O2—H5⋯O1	0.84	1.90	2.7285 (15)	169
C4—H2⋯O1ⁱ	0.95	2.37	3.290 (2)	163
Symmetry code: (i) $[x-{\script{1\over 2}}, y, -z+{\script{3\over 2}}]$ .

Data collection: PROCESS-AUTO (Rigaku, 1998 ); cell refinement: PROCESS-AUTO; data reduction: PROCESS-AUTO; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ); program(s) used to refine structure: SHELXL2014 (Sheldrick, 2015 ); molecular graphics: Yadokari-XG 2009 (Wakita, 2001 ) and ORTEP-3 for Windows (Farrugia, 2012 ); software used to prepare material for publication: Yadokari-XG 2009 and publCIF (Westrip, 2010 ).

Supporting information

CCDC reference: 1423138

Crystal structure: contains datablocks I, Global. DOI: 10.1107/S2056989015016862/is5417sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S2056989015016862/is5417Isup2.hkl

Supporting information file. DOI: 10.1107/S2056989015016862/is5417Isup3.cml

checkCIF report

Comment top

Pyridine N-oxides are one of the most common heterocyclic N-oxides and their physical and chemical properties are studied in detail (Katritzky & Lagowski, 1971). Pyridine N-oxides are the important compounds not only as the precursors of the substituted pyridine derivatives but also as the ligand molecules for the metal complexes (Orchin & Schmidt, 1968; Carlin & De Jongh, 1986). Recently, the bridging ligands containing more than two pyridine N-oxide groups were explored (Henkelis et al., 2012). In the course of our investigation of tetrakis(pyridin-2-yl)methane (Matsumoto et al., 2003), we are interested in the corresponding N-oxides as the bridging ligand and now we report the crystal structure of the title compound (Fig. 1). The bond lengths and angles of pyridine rings are similar to those of 2-methylpyridine N-oxide (Betz et al., 2011). The C1—C2 bond length [1.5472 (11) Å] is similar to that of tetrakis(pyridin-2-yl)methane [1.545 (2) Å] (Matsumoto et al., 2014) and the prominent C1—C2 bond elongation by N-oxidation is not observed. The N—O bond length [1.3174 (14) Å] is also normal value in considering the formation of hydrogen bond with methanol molecule (Eichhorn, 1987). The interatomic distance of hydrogen bond is O1···H5 = 1.90 Å [O1···O2 = 2.7285 (15) Å]. An intermolecular C—H···O bond is also observed between the adjacent pyridine N-oxide rings [C4···H2 = 2.37 Å, O1···O2 = 3.290 (2) Å; Table 1].

Related literature top

For aspects of pyridine N-oxides, see: Katritzky & Lagowski (1971). For reviews of metal complexes of pyridine N-oxides, see: Orchin & Schmidt (1968); Carlin & De Jongh (1986). For the synthesis of the title compound, see: Matsumoto et al. (2003). For coordination polymers of pyridine N-oxides, see: Henkelis et al. (2012). For structures of related molecules, see: Betz et al. (2011); Matsumoto et al. (2014). For the effect of the formation of hydrogen bonds on the N—O bond length of pyridine N-oxides, see: Eichhorn (1987).

Experimental top

To a solution of tetrakis(pyridin-2-yl)methane (100 mg, 0.3 mmol) in acetic acid (4.5 mL) was added 30% aqueous solution of hydrogen peroxide (66 mmol). The mixture was heated to 90 °C for 2.5 hours. After cooling to room temperature, acetone (20 mL) was added. When the mixture was stirred a few minutes, white precipitates appeared. Collection of the precipitate by filtration gave the title compound (120 mg, 46%) as colourless solid. The single crystals were prepared by slow evaporation of a solution of the title compound in methanol. The obtained single crystals were highly efflorescent and the exposure of the crystal to the air should be avoided.

Computing details top

Data collection: PROCESS-AUTO (Rigaku, 1998); cell refinement: PROCESS-AUTO (Rigaku, 1998); data reduction: PROCESS-AUTO (Rigaku, 1998); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL2014 (Sheldrick, 2015); molecular graphics: Yadokari-XG 2009 (Wakita, 2001) and ORTEP-3 for Windows (Farrugia, 2012); software used to prepare material for publication: Yadokari-XG 2009 (Wakita, 2001) and publCIF (Westrip, 2010).

Figures top

Fig. 1. ORTEP drawing of the title compound (viewed along the b axis). Displacement ellipsoids are drawn at the 50% probability level. The hydrogen bonds are shown in the dashed lines. [Symmetry codes: (i) -x, 1/2 - y, z; (ii) -1/4 + y, 1/4 - x, 5/4 - z; (iii) 1/4 - y, 1/4 + x, 5/4 - z.]

Tetrakis(1-oxidopyridin-2-yl)methane methanol tetrasolvate top

Crystal data top

C₂₁H₁₆N₄O₄·4CH₄O	D_x = 1.337 Mg m⁻³
M_r = 516.54	Mo Kα radiation, λ = 0.71075 Å
Tetragonal, I4₁/a	Cell parameters from 9662 reflections
a = 14.4474 (4) Å	θ = 3.6–27.4°
c = 12.2965 (5) Å	µ = 0.10 mm⁻¹
V = 2566.62 (18) Å³	T = 200 K
Z = 4	Prism, colourless
F(000) = 1096	0.2 × 0.2 × 0.1 mm

Data collection top

Rigaku R-AXIS RAPID diffractometer	R_int = 0.031
Detector resolution: 10.00 pixels mm^-1	θ_max = 27.4°, θ_min = 3.6°
ω scans	h = −18→18
12321 measured reflections	k = −18→18
1470 independent reflections	l = −15→15
1289 reflections with I > 2σ(I)

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)] = 0.049	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.138	H-atom parameters constrained
S = 1.07	w = 1/[σ²(F_o²) + (0.0821P)² + 1.7364P] where P = (F_o² + 2F_c²)/3
1470 reflections	(Δ/σ)_max < 0.001
86 parameters	Δρ_max = 0.40 e Å⁻³
0 restraints	Δρ_min = −0.25 e Å⁻³

Crystal data top

C₂₁H₁₆N₄O₄·4CH₄O	Z = 4
M_r = 516.54	Mo Kα radiation
Tetragonal, I4₁/a	µ = 0.10 mm⁻¹
a = 14.4474 (4) Å	T = 200 K
c = 12.2965 (5) Å	0.2 × 0.2 × 0.1 mm
V = 2566.62 (18) Å³

Data collection top

Rigaku R-AXIS RAPID diffractometer	1289 reflections with I > 2σ(I)
12321 measured reflections	R_int = 0.031
1470 independent reflections

Refinement top

R[F² > 2σ(F²)] = 0.049	0 restraints
wR(F²) = 0.138	H-atom parameters constrained
S = 1.07	Δρ_max = 0.40 e Å⁻³
1470 reflections	Δρ_min = −0.25 e Å⁻³
86 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 was performed using all reflections. The weighted R-factor (wR) and goodness of fit (S) are based on F². R-factor (gt) are based on F. The threshold expression of F² > 2.0 σ(F²) is used only for calculating R-factor (gt).

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

	x	y	z	U_iso*/U_eq
C1	0.0000	0.2500	0.6250	0.0172 (5)
C2	−0.06345 (8)	0.18960 (8)	0.69738 (9)	0.0181 (3)
C3	−0.15822 (8)	0.17917 (8)	0.68249 (10)	0.0218 (3)
H1	−0.1873	0.2091	0.6228	0.026*
C4	−0.21147 (9)	0.12608 (9)	0.75266 (11)	0.0263 (3)
H2	−0.2762	0.1198	0.7416	0.032*
C5	−0.16814 (10)	0.08235 (10)	0.83934 (12)	0.0299 (4)
H3	−0.2030	0.0458	0.8887	0.036*
C6	−0.07458 (9)	0.09250 (10)	0.85293 (11)	0.0276 (3)
H4	−0.0449	0.0623	0.9120	0.033*
C7	0.14412 (17)	0.16009 (17)	1.05514 (18)	0.0626 (6)
H6	0.0822	0.1835	1.0727	0.094*
H7	0.1792	0.2082	1.0169	0.094*
H8	0.1764	0.1433	1.1224	0.094*
N1	−0.02328 (7)	0.14510 (7)	0.78324 (8)	0.0211 (3)
O1	0.06661 (6)	0.15169 (7)	0.79946 (8)	0.0279 (3)
O2	0.13633 (12)	0.08248 (11)	0.98897 (12)	0.0639 (5)
H5	0.1193	0.0987	0.9265	0.096*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
C1	0.0179 (7)	0.0179 (7)	0.0159 (10)	0.000	0.000	0.000
C2	0.0194 (6)	0.0181 (5)	0.0167 (6)	0.0004 (4)	0.0014 (4)	0.0005 (4)
C3	0.0202 (6)	0.0224 (6)	0.0230 (6)	0.0003 (4)	−0.0006 (4)	−0.0001 (5)
C4	0.0195 (6)	0.0286 (7)	0.0308 (7)	−0.0018 (5)	0.0037 (5)	−0.0003 (5)
C5	0.0275 (7)	0.0321 (7)	0.0300 (7)	−0.0014 (5)	0.0095 (5)	0.0067 (5)
C6	0.0287 (7)	0.0315 (7)	0.0225 (6)	0.0021 (5)	0.0039 (5)	0.0091 (5)
C7	0.0630 (13)	0.0783 (15)	0.0464 (11)	−0.0129 (11)	−0.0033 (9)	−0.0051 (10)
N1	0.0194 (5)	0.0251 (5)	0.0186 (5)	0.0015 (4)	0.0009 (4)	0.0029 (4)
O1	0.0183 (5)	0.0382 (6)	0.0271 (5)	0.0004 (4)	−0.0033 (3)	0.0090 (4)
O2	0.0954 (12)	0.0553 (9)	0.0411 (8)	0.0033 (7)	−0.0273 (7)	0.0119 (6)

Geometric parameters (Å, º) top

C1—C2	1.5472 (11)	C5—C6	1.3698 (19)
C1—C2ⁱ	1.5472 (11)	C5—H3	0.9500
C1—C2ⁱⁱ	1.5472 (11)	C6—N1	1.3643 (16)
C1—C2ⁱⁱⁱ	1.5472 (11)	C6—H4	0.9500
C2—N1	1.3656 (16)	C7—O2	1.390 (3)
C2—C3	1.3895 (16)	C7—H6	0.9800
C3—C4	1.3874 (18)	C7—H7	0.9800
C3—H1	0.9500	C7—H8	0.9800
C4—C5	1.3881 (19)	N1—O1	1.3174 (14)
C4—H2	0.9500	O2—H5	0.8400

C2—C1—C2ⁱ	109.77 (9)	C6—C5—H3	120.3
C2—C1—C2ⁱⁱ	109.32 (4)	C4—C5—H3	120.3
C2ⁱ—C1—C2ⁱⁱ	109.32 (4)	N1—C6—C5	121.26 (12)
C2—C1—C2ⁱⁱⁱ	109.32 (4)	N1—C6—H4	119.4
C2ⁱ—C1—C2ⁱⁱⁱ	109.32 (4)	C5—C6—H4	119.4
C2ⁱⁱ—C1—C2ⁱⁱⁱ	109.77 (9)	O2—C7—H6	109.5
N1—C2—C3	118.00 (11)	O2—C7—H7	109.5
N1—C2—C1	117.29 (9)	H6—C7—H7	109.5
C3—C2—C1	124.69 (10)	O2—C7—H8	109.5
C4—C3—C2	121.63 (11)	H6—C7—H8	109.5
C4—C3—H1	119.2	H7—C7—H8	109.5
C2—C3—H1	119.2	O1—N1—C6	118.73 (10)
C3—C4—C5	118.62 (12)	O1—N1—C2	120.13 (10)
C3—C4—H2	120.7	C6—N1—C2	121.13 (11)
C5—C4—H2	120.7	C7—O2—H5	109.5
C6—C5—C4	119.34 (12)

C2ⁱ—C1—C2—N1	−45.51 (8)	C3—C4—C5—C6	−0.2 (2)
C2ⁱⁱ—C1—C2—N1	74.40 (6)	C4—C5—C6—N1	0.3 (2)
C2ⁱⁱⁱ—C1—C2—N1	−165.42 (10)	C5—C6—N1—O1	−179.29 (12)
C2ⁱ—C1—C2—C3	133.05 (13)	C5—C6—N1—C2	0.0 (2)
C2ⁱⁱ—C1—C2—C3	−107.04 (14)	C3—C2—N1—O1	178.83 (10)
C2ⁱⁱⁱ—C1—C2—C3	13.14 (11)	C1—C2—N1—O1	−2.51 (15)
N1—C2—C3—C4	0.59 (18)	C3—C2—N1—C6	−0.48 (18)
C1—C2—C3—C4	−177.96 (10)	C1—C2—N1—C6	178.18 (10)
C2—C3—C4—C5	−0.2 (2)

Symmetry codes: (i) −x, −y+1/2, z; (ii) −y+1/4, x+1/4, −z+5/4; (iii) y−1/4, −x+1/4, −z+5/4.

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
O2—H5···O1	0.84	1.90	2.7285 (15)	169
C4—H2···O1^iv	0.95	2.37	3.290 (2)	163

Symmetry code: (iv) x−1/2, y, −z+3/2.

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
O2—H5···O1	0.84	1.90	2.7285 (15)	169
C4—H2···O1ⁱ	0.95	2.37	3.290 (2)	163

Symmetry code: (i) x−1/2, y, −z+3/2.

Acknowledgements

This work was supported by a Grant-in-Aid for Scientific Research (No. 24550049) from the Japan Society for the Promotion of Science.

References

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doi:10.1107/S2056989015016862

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organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

Crystal structure of tetra­kis­(1-oxidopyridin-2-yl)methane methanol tetra­solvate

1. Related literature

2. Experimental

2.1. Crystal data

2.2. Data collection

2.3. Refinement

Supporting information

Acknowledgements

References

organic compounds

Crystal structure of tetrakis(1-oxidopyridin-2-yl)methane methanol tetrasolvate