Crystal structure of a second polymorph of tetra­kis­(pyridin-2-yl)methane

Matsumoto, K.; Kannami, M.; Fuyuhiro, A.; Oda, M.

doi:10.1107/S1600536814025057

organic compounds

CRYSTALLOGRAPHIC
COMMUNICATIONS

ISSN: 2056-9890

Volume 70| Part 12| December 2014| Pages o1277-o1278

doi:10.1107/S1600536814025057

Open

access

Crystal structure of a second polymorph of tetrakis(pyridin-2-yl)methane

Kouzou Matsumoto,^a ^* Masaki Kannami,^b Akira Fuyuhiro ^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 S. Parkin, University of Kentucky, USA (Received 31 October 2014; accepted 15 November 2014; online 21 November 2014)

A second polymorph of the title compound, C₂₁H₁₆N₄, is reported. The original polymorph was solved by our group [Matsumoto et al. (2003 ). Tetrahedron Lett. 44, 2861–2864] in the monoclinic space group C2/c and refined to R = 0.050. Now the crystal structure of a tetragonal polymorph (space group P-42₁c) has been solved and refined to R = 0.036. In the crystal, there are no strong intermolecular interactions. Reflecting the high symmetry of the molecular structure, the asymmetric unit is a quarter of the molecule, and the molecule exhibits S4 symmetry along the c axis in the crystal.

Keywords: crystal structure; pyridine; bridging ligands; S4 symmetry; polymorph.

CCDC reference: 1034349

1. Related literature

For a recent review on related bridging ligands, see: Sumby (2011 ). For the synthesis of the title compound, see: Matsumoto et al. (2003); Abu-Shanab (2007 ). For transition metal complexes of the title compound, see: Matsumoto et al. (2004 ); Okazawa et al. (2004 , 2005 , 2006 ); Ishikawa et al. (2009 ); Hirosawa et al. (2012 ).

2. Experimental

2.1. Crystal data

C₂₁H₁₆N₄
M_r = 324.38
Tetragonal, $[P \overline 42_1 c ]$
a = 10.60 (1) Å
c = 7.03 (1) Å
V = 790 (2) Å³
Z = 2
Mo Kα radiation
μ = 0.08 mm⁻¹
T = 200 K
0.5 × 0.5 × 0.4 mm

2.2. Data collection

Rigaku R-AXIS RAPID imaging plate diffractometer
7257 measured reflections
904 independent reflections
858 reflections with I > 2σ(I)
R_int = 0.046

2.3. Refinement

R[F² > 2σ(F²)] = 0.036
wR(F²) = 0.090
S = 1.07
904 reflections
57 parameters
H-atom parameters constrained
Δρ_max = 0.14 e Å⁻³
Δρ_min = −0.24 e Å⁻³

Data collection: PROCESS-AUTO (Rigaku, 1998 ); cell refinement: PROCESS-AUTO; data reduction: PROCESS-AUTO; program(s) used to solve structure: SIR2014 (Burla et al., 2012 , 2014 ); program(s) used to refine structure: SHELXL2014 (Sheldrick, 2008 ); molecular graphics: Yadokari-XG 2009 (Wakita, 2001 ; Kabuto et al., 2009 ) 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: 1034349

Crystal structure: contains datablock I. DOI: 10.1107/S1600536814025057/pk2537sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536814025057/pk2537Isup2.hkl

Supporting information file. DOI: 10.1107/S1600536814025057/pk2537Isup3.cml

checkCIF report

Comment top

Bridging ligands that possess more than one coordination site have attracted considerable attention in relation to multinuclear metallosupramolecular assemblies and coordination polymers (Sumby, 2011). The title compound (Fig. 1) is a typical tetrahedral bridging ligand when it binds to two metal ions in a two-fold bidentate fashion (Fig. 2a). The title compound was first synthesized by the reaction of tris(pyridin-2-yl)methyl anion with 2-chloropyridine (Matsumoto et al., 2003). More recently, Abu-Shanab reported that the treatment of 2-picoline with excess of lithium diisopropylamide followed by 2-bromopyridine yielded the title compound as the main product (Abu-Shanab, 2007). The title compound takes on S4 symmetry along the c axis in the crystal (Fig. 1), reflecting the highly symmetric molecular structure.

The silver complex of the title compound forms a one-dimensional coordination polymer in which the title compound acts as a two-fold bidentate bridging ligand (Matsumoto et al., 2004). This coordination pattern was also observed in a dinuclear Mn(II) complex (Okazawa et al., 2004) and dinuclear Ni(II) complex (Okazawa et al., 2006). On the other hand, the title compound often takes bidentate (Fig. 2b) or tripodal coordination patterns (Fig. 2c) to bind only one metal ion. The bidentate coordination pattern was observed in the Cu(II) complexes of the title compound (Matsumoto et al., 2004; Okazawa et al., 2005) and tripodal coordination patterns were observed in Cu(II), Fe(II), and Co(II) complexes (Matsumoto et al., 2004; Ishikawa et al., 2009; Hirosawa et al., 2012).

Related literature top

For a recent review on related bridging ligands, see: Sumby (2011). For the synthesis of the title compound, see: Matsumoto et al. (2003); Abu-Shanab (2007). For transition metal complexes of the title compound, see: Matsumoto et al. (2004); Okazawa et al. (2004, 2005, 2006); Ishikawa et al. (2009); Hirosawa et al. (2012).

Experimental top

The title compound was synthesized by the reported procedure (Matsumoto et al., 2003). Crystallization from methanol/chloroform (1/1) gave colorless crystals, which were used for X-ray analysis.

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: SIR2014 (Burla et al., 2012, 2014); program(s) used to refine structure: SHELXL2014 (Sheldrick, 2008); molecular graphics: Yadokari-XG 2009 (Wakita, 2001; Kabuto et al., 2009) and ORTEP-3 for Windows (Farrugia, 2012); software used to prepare material for publication: Yadokari-XG 2009 (Wakita, 2001; Kabuto et al., 2009) and publCIF (Westrip, 2010).

Figures top

An ellipsoid plot of the title compound (viewed down the c axis). Displacement ellipsoids are drawn at the 50% probability level. Symmetry codes: (i) y, -x, -z + 1; (ii) -x, -y, z; (iii) -y, x, -z + 1.

Three kinds of coordination patterns of the title compound. (a) Two-fold bidentate, (b) bidentate, and (c) tripodal. M represents a transition metal ion.

Tetrakis(pyridin-2-yl)methane top

Crystal data top

C₂₁H₁₆N₄	Melting point: 259 K
M_r = 324.38	Mo Kα radiation, λ = 0.71075 Å
Tetragonal, P42₁c	Cell parameters from 6223 reflections
a = 10.60 (1) Å	θ = 3.5–27.5°
c = 7.03 (1) Å	µ = 0.08 mm⁻¹
V = 790 (2) Å³	T = 200 K
Z = 2	Prism, colourless
F(000) = 340	0.5 × 0.5 × 0.4 mm
D_x = 1.364 Mg m⁻³

Data collection top

Rigaku R-AXIS RAPID imaging plate diffractometer	R_int = 0.046
Detector resolution: 10.00 pixels mm^-1	θ_max = 27.5°, θ_min = 3.5°
ω scans	h = −10→13
7257 measured reflections	k = −12→13
904 independent reflections	l = −9→9
858 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)] = 0.036	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.090	H-atom parameters constrained
S = 1.07	w = 1/[σ²(F_o²) + (0.0438P)² + 0.1368P] where P = (F_o² + 2F_c²)/3
904 reflections	(Δ/σ)_max < 0.001
57 parameters	Δρ_max = 0.14 e Å⁻³
0 restraints	Δρ_min = −0.24 e Å⁻³

Crystal data top

C₂₁H₁₆N₄	Z = 2
M_r = 324.38	Mo Kα radiation
Tetragonal, P42₁c	µ = 0.08 mm⁻¹
a = 10.60 (1) Å	T = 200 K
c = 7.03 (1) Å	0.5 × 0.5 × 0.4 mm
V = 790 (2) Å³

Data collection top

Rigaku R-AXIS RAPID imaging plate diffractometer	858 reflections with I > 2σ(I)
7257 measured reflections	R_int = 0.046
904 independent reflections

Refinement top

R[F² > 2σ(F²)] = 0.036	0 restraints
wR(F²) = 0.090	H-atom parameters constrained
S = 1.07	Δρ_max = 0.14 e Å⁻³
904 reflections	Δρ_min = −0.24 e Å⁻³
57 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.

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

	x	y	z	U_iso*/U_eq
C1	0.0000	0.0000	0.5000	0.0209 (6)
C2	−0.02294 (14)	0.11449 (14)	0.3685 (2)	0.0224 (4)
C3	−0.11972 (16)	0.10889 (16)	0.2328 (3)	0.0290 (4)
H1	−0.1706	0.0355	0.2218	0.035*
C4	−0.14016 (17)	0.21120 (17)	0.1155 (3)	0.0340 (4)
H2	−0.2061	0.2101	0.0241	0.041*
C5	−0.06207 (18)	0.31595 (17)	0.1342 (3)	0.0337 (4)
H3	−0.0741	0.3884	0.0567	0.040*
C6	0.03280 (17)	0.31239 (17)	0.2670 (3)	0.0345 (5)
H4	0.0873	0.3833	0.2765	0.041*
N1	0.05294 (13)	0.21395 (13)	0.3845 (2)	0.0283 (4)

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
C1	0.0205 (9)	0.0205 (9)	0.0216 (14)	0.000	0.000	0.000
C2	0.0216 (7)	0.0233 (7)	0.0222 (7)	0.0020 (5)	0.0033 (6)	0.0006 (7)
C3	0.0279 (8)	0.0315 (8)	0.0275 (8)	−0.0007 (6)	−0.0028 (7)	0.0007 (7)
C4	0.0310 (9)	0.0430 (10)	0.0280 (8)	0.0076 (7)	−0.0026 (8)	0.0038 (8)
C5	0.0393 (9)	0.0316 (9)	0.0302 (9)	0.0077 (7)	0.0046 (8)	0.0093 (8)
C6	0.0382 (10)	0.0268 (9)	0.0386 (10)	−0.0028 (7)	0.0025 (8)	0.0075 (7)
N1	0.0294 (7)	0.0257 (7)	0.0299 (7)	−0.0022 (5)	−0.0014 (6)	0.0039 (6)

Geometric parameters (Å, º) top

C1—C2ⁱ	1.545 (2)	C3—H1	0.9500
C1—C2ⁱⁱ	1.545 (2)	C4—C5	1.391 (3)
C1—C2ⁱⁱⁱ	1.545 (2)	C4—H2	0.9500
C1—C2	1.545 (2)	C5—C6	1.373 (3)
C2—N1	1.330 (3)	C5—H3	0.9500
C2—C3	1.402 (3)	C6—N1	1.348 (3)
C3—C4	1.380 (3)	C6—H4	0.9500

C2ⁱ—C1—C2ⁱⁱ	111.01 (8)	C2—C3—H1	120.4
C2ⁱ—C1—C2ⁱⁱⁱ	106.43 (16)	C3—C4—C5	118.52 (16)
C2ⁱⁱ—C1—C2ⁱⁱⁱ	111.01 (8)	C3—C4—H2	120.7
C2ⁱ—C1—C2	111.01 (8)	C5—C4—H2	120.7
C2ⁱⁱ—C1—C2	106.43 (16)	C6—C5—C4	118.55 (15)
C2ⁱⁱⁱ—C1—C2	111.01 (8)	C6—C5—H3	120.7
N1—C2—C3	122.22 (15)	C4—C5—H3	120.7
N1—C2—C1	118.44 (13)	N1—C6—C5	123.68 (17)
C3—C2—C1	119.30 (14)	N1—C6—H4	118.2
C4—C3—C2	119.26 (17)	C5—C6—H4	118.2
C4—C3—H1	120.4	C2—N1—C6	117.72 (15)

C2ⁱ—C1—C2—N1	−0.78 (13)	C1—C2—C3—C4	179.97 (14)
C2ⁱⁱ—C1—C2—N1	−121.70 (15)	C2—C3—C4—C5	1.1 (3)
C2ⁱⁱⁱ—C1—C2—N1	117.39 (18)	C3—C4—C5—C6	0.7 (3)
C2ⁱ—C1—C2—C3	177.21 (14)	C4—C5—C6—N1	−1.8 (3)
C2ⁱⁱ—C1—C2—C3	56.30 (12)	C3—C2—N1—C6	1.2 (2)
C2ⁱⁱⁱ—C1—C2—C3	−64.62 (12)	C1—C2—N1—C6	179.09 (13)
N1—C2—C3—C4	−2.1 (2)	C5—C6—N1—C2	0.8 (3)

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

Experimental details

Crystal data
Chemical formula	C₂₁H₁₆N₄
M_r	324.38
Crystal system, space group	Tetragonal, P42₁c
Temperature (K)	200
a, c (Å)	10.60 (1), 7.03 (1)
V (Å³)	790 (2)
Z	2
Radiation type	Mo Kα
µ (mm⁻¹)	0.08
Crystal size (mm)	0.5 × 0.5 × 0.4

Data collection
Diffractometer	Rigaku R-AXIS RAPID imaging plate diffractometer
Absorption correction	–
No. of measured, independent and observed [I > 2σ(I)] reflections	7257, 904, 858
R_int	0.046
(sin θ/λ)_max (Å⁻¹)	0.649

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.036, 0.090, 1.07
No. of reflections	904
No. of parameters	57
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.14, −0.24

Computer programs: PROCESS-AUTO (Rigaku, 1998), SIR2014 (Burla et al., 2012, 2014), SHELXL2014 (Sheldrick, 2008), Yadokari-XG 2009 (Wakita, 2001; Kabuto et al., 2009) and ORTEP-3 for Windows (Farrugia, 2012), Yadokari-XG 2009 (Wakita, 2001; Kabuto et al., 2009) and publCIF (Westrip, 2010).

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

Abu-Shanab, F. A. (2007). J. Sulfur Chem. 28, 519–526. CAS Google Scholar
Burla, M. C., Caliandro, R., Camalli, M., Carrozzini, B., Cascarano, G. L., Giacovazzo, C., Mallamo, M., Mazzone, A., Polidori, G. & Spagna, R. (2012). J. Appl. Cryst. 45, 357–361. Web of Science CrossRef CAS IUCr Journals Google Scholar
Burla, M. C., Caliandro, R., Carrozzini, B., Cascarano, G. L., Giacovazzo, C., Mallamo, M., Mazzone, A. & Polidori, G. (2014). J. Appl. Cryst. Submitted. CrossRef IUCr Journals Google Scholar
Farrugia, L. J. (2012). J. Appl. Cryst. 45, 849–854. Web of Science CrossRef CAS IUCr Journals Google Scholar
Hirosawa, N., Oso, Y. & Ishida, T. (2012). Chem. Lett. 41, 716–718. Web of Science CSD CrossRef CAS Google Scholar
Ishikawa, R., Matsumoto, K., Onishi, K., Kubo, T., Fuyuhiro, A., Hayami, S., Inoue, K., Kaizaki, S. & Kawata, S. (2009). Chem. Lett. 38, 620–621. Web of Science CSD CrossRef CAS Google Scholar
Kabuto, C., Akine, S., Nemoto, T. & Kwon, E. (2009). J. Crystallogr. Soc. Jpn, 51, 218–224. CrossRef Google Scholar
Matsumoto, K., Kannami, M. & Oda, M. (2003). Tetrahedron Lett. 44, 2861–2864. Web of Science CSD CrossRef CAS Google Scholar
Matsumoto, K., Kannami, M. & Oda, M. (2004). Chem. Lett. 33, 1096–1097. Web of Science CSD CrossRef CAS Google Scholar
Okazawa, A., Ishida, T. & Nogami, T. (2004). Chem. Lett. 33, 1478–1479. Web of Science CSD CrossRef CAS Google Scholar
Okazawa, A., Ishida, T. & Nogami, T. (2005). Polyhedron, 24, 2584–2587. Web of Science CSD CrossRef CAS Google Scholar
Okazawa, A., Nogami, T. & Ishida, T. (2006). Chem. Phys. Lett. 427, 333–337. Web of Science CSD CrossRef CAS Google Scholar
Rigaku (1998). PROCESS-AUTO. Rigaku Corporation, Tokyo, Japan. Google Scholar
Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. Web of Science CrossRef CAS IUCr Journals Google Scholar
Sumby, C. J. (2011). Coord. Chem. Rev. 255, 1937–1967. Web of Science CrossRef CAS Google Scholar
Wakita, K. (2001). Yadokari-XG. http://www.hat.hi-ho.ne.jp/k-wakita/yadokari . Google Scholar
Westrip, S. P. (2010). J. Appl. Cryst. 43, 920–925. Web of Science CrossRef CAS IUCr Journals Google Scholar