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

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ISSN: 2056-9890

2-[3-Meth­­oxy-5-(pyrimidin-2-yl)phen­yl]pyrimidine

aCollege of Chemistry, Chemical Engineering and Biotechnology, Donghua University, 2999 North Renmin Road, Songjiang, Shanghai 201620, People's Republic of China, and bSchool of Environmental Science and Engineering, Donghua University, 2999 North Renmin Road, Songjiang, Shanghai 201620, People's Republic of China
*Correspondence e-mail: wsjin@dhu.edu.cn, dqzhang@dhu.edu.cn

(Received 17 January 2013; accepted 27 January 2013; online 2 February 2013)

The title compound, C15H12N4O, was synthesized by a standard Suzuki cross-coupling reaction. The terminal pyrim­idine rings are rotated at dihedral angles of 12.06 (4) and −13.13 (4)° with respect to the central benzene ring. In the crystal, the mol­ecules are connected by two kinds of C—H⋯N hydrogen bonds, forming zigzag chains along the c axis. Weak ππ inter­actions between the benzene and one of the pyrimidine rings are also found and stack the mol­ecules along the b axis [centroid–centroid distance = 4.112 (3) Å].

Related literature

For general background to the chemistry of tridentate NCN ligands, see: Pugh & Danopoulos (2007[Pugh, D. & Danopoulos, A. A. (2007). Coord. Chem. Rev. 251, 610-641.]); Wu et al. (2009[Wu, L. Y., Hao, X. Q., Xu, Y. X., Jia, M. Q., Wang, Y. N., Gong, J. F. & Song, M. P. (2009). Organometallics, 28, 3369-3380.], 2012[Wu, Y., Xie, D., Zhang, D., Li, X. & Jin, W. (2012). Acta Cryst. E68, m1210-m1211.]); Williams (2009[Williams, J. A. G. (2009). Chem. Soc. Rev. 38, 1783-1801.]); Wang et al. (2010[Wang, Z., Turner, E., Mahoney, V., Madakuni, S., Groy, T. & Li, A. (2010). Inorg. Chem. 49, 11276-11286.]). For the synthesis of the title compound, see: Avitia et al. (2011[Avitia, B., MacIntosh, E., Muhia, S. & Kelson, E. (2011). Tetrahedron Lett. 52, 1631-1634.]); Wakioka et al. (2010[Wakioka, M., Ikegami, M. & Ozawa, F. (2010). Macromolecules, 43, 6980-6985.]); Cardenas & Echavarren (1999[Cardenas, D. J. & Echavarren, A. M. (1999). Organometallics, 18, 3337-3341.]).

[Scheme 1]

Experimental

Crystal data
  • C15H12N4O

  • Mr = 264.29

  • Orthorhombic, P b c a

  • a = 11.3779 (8) Å

  • b = 8.0954 (6) Å

  • c = 27.3371 (18) Å

  • V = 2518.0 (3) Å3

  • Z = 8

  • Mo Kα radiation

  • μ = 0.09 mm−1

  • T = 293 K

  • 0.28 × 0.21 × 0.07 mm

Data collection
  • Bruker SMART CCD area-detector diffractometer

  • Absorption correction: multi-scan (SADABS; Bruker, 2000[Bruker (2000). SMART, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]) Tmin = 0.800, Tmax = 1.000

  • 14088 measured reflections

  • 2461 independent reflections

  • 2059 reflections with I > 2σ(I)

  • Rint = 0.030

Refinement
  • R[F2 > 2σ(F2)] = 0.044

  • wR(F2) = 0.123

  • S = 1.04

  • 2461 reflections

  • 182 parameters

  • H-atom parameters constrained

  • Δρmax = 0.16 e Å−3

  • Δρmin = −0.21 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
C9—H9⋯N4i 0.93 2.69 3.597 (2) 166
C15—H15B⋯N3ii 0.96 2.69 3.547 (2) 149
Symmetry codes: (i) [-x+2, y+{\script{1\over 2}}, -z+{\script{1\over 2}}]; (ii) [x+{\script{1\over 2}}, -y-{\script{1\over 2}}, -z+1].

Data collection: SMART (Bruker, 2000[Bruker (2000). SMART, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]); cell refinement: SAINT (Bruker, 2000[Bruker (2000). SMART, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); molecular graphics: SHELXTL (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); software used to prepare material for publication: SHELXTL.

Supporting information


Comment top

Pincer compounds have extensive applications in the coordination chemistry and material science (Pugh & Danopoulos, 2007). The most widely-used pincer ligand is terpyridine. Meanwhile, some tridentate NCN ligands with similar structures to terpyridine have also been reported (Williams, 2009; Wang et al., 2010; Wu et al., 2009). As part of our ongoing studies in this field (Wu et al., 2012), we report here the crystal structure of a new pincer compound 1,3-di(pyrimin-2-yl)-5-methoxybenzene.

The molecular structure of the title compound is shown in Figure 1. The three aryl rings of the title compound are not coplanar, but dihedral angles of 12.06 (4)° and -13.13 (4)° are found between the terminal pyrimidine rings and central phenyl ring, respectively. In the crystal, intermolecular C9–H8···N4 and C15–H15B···N3 hydrogen bonds (Table 1) form zig-zag chains along c. The molecules stack along the b axis in such a way that the same pyrimidine-phenyl segment of two neighboring molecules overlap in opposite directions with a centroid-centroid distance of 4.112 (3) Å.

Related literature top

For general background to the chemistry of tridentate NCN ligands, see: Pugh & Danopoulos (2007); Wu et al. (2009, 2012); Williams (2009); Wang et al. (2010). For the synthesis of the title compound, see: Avitia et al. (2011); Wakioka et al. (2010); Cardenas & Echavarren (1999).

Experimental top

The compound was prepared using methods described in the literature (Avitia et al., 2011; Wakioka et al., 2010; Cardenas & Echavarren, 1999). A mixture of 1,3-bis(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-5-methoxybenzene (600 mg, 1.67 mmol), 2-bromopyrimidine (800 mg, 5.03 mmol), K2CO3 aq (2.0 M, 8.40 ml) and Pd(PPh3)4 (390 mg, 0.251 mmol) in toluene (30 ml) was stirred at 110°C for 48 h under an argon atmosphere. After cooling to room temperature, the reaction mixture was poured into water, and extracted with CH2Cl2. The combined organic phase was washed with water and dried over anhydrous magnesium sulfate. After filtration and evaporation, the residue was purified with flash column chromatography (SiO2, eluted with CH2Cl2/petroleum ether = 1:5) to obtain the 1,3-di(pyrimidin-2-yl)-5-methoxybenzene as a white powder (353 mg) in 80% yield. 1H NMR (400 MHz, CDCl3) δ 9.16 (s, 1H), 8.83 (d, J = 4.8 Hz, 4H), 8.14 (d, J = 1.5 Hz, 2H), 7.20 (t, J = 4.8 Hz, 2H), 3.99 (s, 3H). 13C NMR(100 MHz, CDCl3) δ 164.30, 160.51, 157.23, 139.36, 120.85, 119.32, 115.95, 55.74. MS(EI): m/z= 263.95. A single-crystal was obtained by slow evaporation of an acetonitrile solution of the title compound.

Refinement top

All H atoms were placed geometrically and treated as riding on their parent atoms with C—H = 0.96 (methyl) Å [U iso (H) = 1.5U eq (C)], and C—H = 0.93 (aromatic) Å [U iso (H) = 1.2U eq (C)].

Computing details top

Data collection: SMART (Bruker, 2000); cell refinement: SAINT (Bruker, 2000); data reduction: SAINT (Sheldrick, 2008); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL (Sheldrick, 2008).

Figures top
[Figure 1] Fig. 1. A perspective view of the title compound with displacement ellipsoids drawn at the 30% probability level.
[Figure 2] Fig. 2. A view of the unit-cell contents of the title compound along the b axis.
2-[3-Methoxy-5-(pyrimidin-2-yl)phenyl]pyrimidine top
Crystal data top
C15H12N4OF(000) = 1104
Mr = 264.29Dx = 1.394 Mg m3
Orthorhombic, PbcaMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ac 2abCell parameters from 4404 reflections
a = 11.3779 (8) Åθ = 4.7–56.5°
b = 8.0954 (6) ŵ = 0.09 mm1
c = 27.3371 (18) ÅT = 293 K
V = 2518.0 (3) Å3Prismatic, colourless
Z = 80.28 × 0.21 × 0.07 mm
Data collection top
Bruker SMART CCD area-detector
diffractometer
2461 independent reflections
Radiation source: fine-focus sealed tube2059 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.030
ϕ and ω scansθmax = 26.0°, θmin = 1.5°
Absorption correction: multi-scan
(SADABS; Bruker, 2000)
h = 1412
Tmin = 0.800, Tmax = 1.000k = 89
14088 measured reflectionsl = 3331
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.044Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.123H-atom parameters constrained
S = 1.04 w = 1/[σ2(Fo2) + (0.0665P)2 + 0.4657P]
where P = (Fo2 + 2Fc2)/3
2461 reflections(Δ/σ)max = 0.001
182 parametersΔρmax = 0.16 e Å3
0 restraintsΔρmin = 0.21 e Å3
Crystal data top
C15H12N4OV = 2518.0 (3) Å3
Mr = 264.29Z = 8
Orthorhombic, PbcaMo Kα radiation
a = 11.3779 (8) ŵ = 0.09 mm1
b = 8.0954 (6) ÅT = 293 K
c = 27.3371 (18) Å0.28 × 0.21 × 0.07 mm
Data collection top
Bruker SMART CCD area-detector
diffractometer
2461 independent reflections
Absorption correction: multi-scan
(SADABS; Bruker, 2000)
2059 reflections with I > 2σ(I)
Tmin = 0.800, Tmax = 1.000Rint = 0.030
14088 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0440 restraints
wR(F2) = 0.123H-atom parameters constrained
S = 1.04Δρmax = 0.16 e Å3
2461 reflectionsΔρmin = 0.21 e Å3
182 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
xyzUiso*/Ueq
N11.03793 (11)0.23473 (17)0.28017 (4)0.0556 (4)
N21.20879 (9)0.20037 (16)0.32842 (4)0.0508 (3)
N30.65549 (10)0.04972 (17)0.43132 (4)0.0550 (3)
N40.65653 (10)0.05619 (16)0.35048 (4)0.0519 (3)
O11.07030 (9)0.16817 (14)0.46649 (3)0.0572 (3)
C11.02113 (12)0.07963 (17)0.42928 (4)0.0434 (3)
C20.89954 (12)0.07835 (17)0.42817 (5)0.0444 (3)
H20.85740.13400.45220.053*
C30.84023 (11)0.00505 (16)0.39159 (4)0.0394 (3)
C40.90336 (11)0.08851 (16)0.35561 (4)0.0387 (3)
H40.86390.14400.33080.046*
C51.02519 (11)0.08866 (16)0.35693 (4)0.0380 (3)
C61.08424 (11)0.00412 (16)0.39390 (4)0.0415 (3)
H61.16600.00400.39480.050*
C71.09451 (11)0.17957 (16)0.31955 (4)0.0392 (3)
C81.10177 (14)0.3194 (2)0.24815 (6)0.0609 (4)
H81.06440.36160.22060.073*
C91.21922 (13)0.3476 (2)0.25355 (6)0.0554 (4)
H91.26260.40640.23060.067*
C101.26891 (12)0.2841 (2)0.29482 (6)0.0567 (4)
H101.34900.30010.29980.068*
C110.70953 (11)0.00467 (17)0.39113 (4)0.0417 (3)
C120.53848 (13)0.0495 (2)0.43016 (6)0.0627 (5)
H120.49770.08750.45740.075*
C130.47587 (13)0.0040 (2)0.39070 (6)0.0609 (4)
H130.39410.00560.39070.073*
C140.53930 (13)0.0549 (2)0.35126 (6)0.0589 (4)
H140.49910.09050.32360.071*
C151.19460 (14)0.1760 (2)0.46883 (6)0.0639 (5)
H15A1.22460.22210.43900.096*
H15B1.21770.24430.49590.096*
H15C1.22580.06680.47320.096*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
N10.0475 (6)0.0735 (9)0.0457 (6)0.0099 (6)0.0043 (5)0.0165 (6)
N20.0395 (6)0.0582 (8)0.0548 (7)0.0046 (5)0.0003 (5)0.0092 (6)
N30.0450 (7)0.0736 (9)0.0466 (7)0.0109 (6)0.0072 (5)0.0010 (6)
N40.0403 (6)0.0610 (8)0.0542 (7)0.0031 (5)0.0002 (5)0.0046 (6)
O10.0531 (6)0.0696 (7)0.0491 (6)0.0027 (5)0.0065 (4)0.0201 (5)
C10.0468 (7)0.0460 (8)0.0375 (6)0.0020 (6)0.0027 (5)0.0030 (6)
C20.0463 (8)0.0490 (8)0.0378 (6)0.0033 (6)0.0050 (5)0.0046 (6)
C30.0387 (7)0.0411 (7)0.0383 (6)0.0012 (5)0.0021 (5)0.0037 (5)
C40.0395 (7)0.0415 (7)0.0352 (6)0.0008 (5)0.0013 (5)0.0001 (5)
C50.0387 (7)0.0395 (7)0.0357 (6)0.0010 (5)0.0012 (5)0.0027 (5)
C60.0359 (6)0.0472 (8)0.0414 (7)0.0001 (5)0.0014 (5)0.0003 (6)
C70.0380 (6)0.0410 (7)0.0385 (6)0.0010 (5)0.0006 (5)0.0021 (5)
C80.0611 (9)0.0768 (11)0.0449 (8)0.0123 (8)0.0027 (7)0.0170 (8)
C90.0587 (9)0.0581 (9)0.0495 (8)0.0128 (7)0.0122 (6)0.0053 (7)
C100.0397 (7)0.0626 (10)0.0677 (10)0.0083 (7)0.0078 (6)0.0072 (8)
C110.0400 (7)0.0425 (7)0.0426 (7)0.0017 (5)0.0036 (5)0.0050 (6)
C120.0465 (8)0.0834 (12)0.0582 (9)0.0140 (8)0.0140 (7)0.0097 (8)
C130.0356 (7)0.0702 (11)0.0768 (11)0.0021 (7)0.0063 (7)0.0170 (9)
C140.0416 (8)0.0652 (10)0.0699 (10)0.0051 (7)0.0055 (7)0.0001 (8)
C150.0553 (9)0.0735 (11)0.0628 (9)0.0086 (8)0.0128 (7)0.0178 (8)
Geometric parameters (Å, º) top
N1—C81.3280 (18)C4—H40.9300
N1—C71.3316 (17)C5—C61.3934 (17)
N2—C101.3310 (18)C5—C71.4859 (17)
N2—C71.3333 (16)C6—H60.9300
N3—C121.3317 (19)C8—C91.364 (2)
N3—C111.3338 (16)C8—H80.9300
N4—C111.3311 (17)C9—C101.363 (2)
N4—C141.3340 (18)C9—H90.9300
O1—C11.3643 (15)C10—H100.9300
O1—C151.4171 (18)C12—C131.363 (2)
C1—C61.3821 (18)C12—H120.9300
C1—C21.3838 (18)C13—C141.361 (2)
C2—C31.3826 (18)C13—H130.9300
C2—H20.9300C14—H140.9300
C3—C41.3928 (17)C15—H15A0.9600
C3—C111.4872 (18)C15—H15B0.9600
C4—C51.3867 (17)C15—H15C0.9600
C8—N1—C7116.21 (12)N1—C8—H8118.3
C10—N2—C7116.10 (12)C9—C8—H8118.3
C12—N3—C11116.16 (13)C10—C9—C8115.66 (13)
C11—N4—C14115.93 (12)C10—C9—H9122.2
C1—O1—C15117.79 (11)C8—C9—H9122.2
O1—C1—C6124.49 (12)N2—C10—C9123.39 (13)
O1—C1—C2115.47 (11)N2—C10—H10118.3
C6—C1—C2120.03 (11)C9—C10—H10118.3
C3—C2—C1120.49 (12)N4—C11—N3125.60 (12)
C3—C2—H2119.8N4—C11—C3117.35 (11)
C1—C2—H2119.8N3—C11—C3117.04 (11)
C2—C3—C4119.74 (12)N3—C12—C13122.78 (14)
C2—C3—C11119.55 (11)N3—C12—H12118.6
C4—C3—C11120.71 (11)C13—C12—H12118.6
C5—C4—C3119.83 (11)C14—C13—C12116.48 (14)
C5—C4—H4120.1C14—C13—H13121.8
C3—C4—H4120.1C12—C13—H13121.8
C4—C5—C6120.04 (11)N4—C14—C13123.02 (15)
C4—C5—C7120.87 (11)N4—C14—H14118.5
C6—C5—C7119.09 (11)C13—C14—H14118.5
C1—C6—C5119.87 (12)O1—C15—H15A109.5
C1—C6—H6120.1O1—C15—H15B109.5
C5—C6—H6120.1H15A—C15—H15B109.5
N1—C7—N2125.18 (12)O1—C15—H15C109.5
N1—C7—C5117.74 (11)H15A—C15—H15C109.5
N2—C7—C5117.07 (11)H15B—C15—H15C109.5
N1—C8—C9123.44 (14)
C15—O1—C1—C60.5 (2)C6—C5—C7—N1168.58 (12)
C15—O1—C1—C2178.92 (13)C4—C5—C7—N2167.50 (12)
O1—C1—C2—C3178.88 (12)C6—C5—C7—N211.89 (18)
C6—C1—C2—C30.6 (2)C7—N1—C8—C91.4 (2)
C1—C2—C3—C40.05 (19)N1—C8—C9—C100.6 (3)
C1—C2—C3—C11179.97 (12)C7—N2—C10—C90.5 (2)
C2—C3—C4—C50.56 (18)C8—C9—C10—N20.4 (2)
C11—C3—C4—C5179.41 (11)C14—N4—C11—N31.3 (2)
C3—C4—C5—C60.63 (18)C14—N4—C11—C3179.78 (13)
C3—C4—C5—C7178.76 (11)C12—N3—C11—N40.9 (2)
O1—C1—C6—C5178.91 (12)C12—N3—C11—C3179.84 (13)
C2—C1—C6—C50.52 (19)C2—C3—C11—N4166.49 (13)
C4—C5—C6—C10.10 (18)C4—C3—C11—N413.54 (18)
C7—C5—C6—C1179.31 (12)C2—C3—C11—N312.55 (18)
C8—N1—C7—N21.3 (2)C4—C3—C11—N3167.43 (12)
C8—N1—C7—C5178.20 (13)C11—N3—C12—C130.5 (2)
C10—N2—C7—N10.4 (2)N3—C12—C13—C141.4 (3)
C10—N2—C7—C5179.09 (13)C11—N4—C14—C130.2 (2)
C4—C5—C7—N112.03 (18)C12—C13—C14—N41.0 (2)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C9—H9···N4i0.932.693.597 (2)166
C15—H15B···N3ii0.962.693.547 (2)149
Symmetry codes: (i) x+2, y+1/2, z+1/2; (ii) x+1/2, y1/2, z+1.

Experimental details

Crystal data
Chemical formulaC15H12N4O
Mr264.29
Crystal system, space groupOrthorhombic, Pbca
Temperature (K)293
a, b, c (Å)11.3779 (8), 8.0954 (6), 27.3371 (18)
V3)2518.0 (3)
Z8
Radiation typeMo Kα
µ (mm1)0.09
Crystal size (mm)0.28 × 0.21 × 0.07
Data collection
DiffractometerBruker SMART CCD area-detector
diffractometer
Absorption correctionMulti-scan
(SADABS; Bruker, 2000)
Tmin, Tmax0.800, 1.000
No. of measured, independent and
observed [I > 2σ(I)] reflections
14088, 2461, 2059
Rint0.030
(sin θ/λ)max1)0.617
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.044, 0.123, 1.04
No. of reflections2461
No. of parameters182
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)0.16, 0.21

Computer programs: SMART (Bruker, 2000), SAINT (Bruker, 2000), SAINT (Sheldrick, 2008), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), SHELXTL (Sheldrick, 2008).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C9—H9···N4i0.932.693.597 (2)166
C15—H15B···N3ii0.962.693.547 (2)149
Symmetry codes: (i) x+2, y+1/2, z+1/2; (ii) x+1/2, y1/2, z+1.
 

Acknowledgements

This work was supported by STCSM (12JC1400200).

References

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