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

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ISSN: 2056-9890

cis-1,2-Bis{[4-(4-pyrid­yl)pyrimidin-2-yl]sulfanylmeth­yl}benzene

aDeparment of Chemistry and Chemical Engineering, Hefei Normal University, Hefei 230061, People's Republic of China, and bSchool of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, People's Republic of China
*Correspondence e-mail: dapdong@163.com

(Received 25 October 2009; accepted 29 October 2009; online 4 November 2009)

The mol­ecular skeleton of the title mol­ecule, C26H20N6S2, adopts a cis conformation with the two arms positioned on one side of the benzene ring plane. Intra­molecular ππ inter­actions between the pyrimidine rings [centroid–centroid distance = 3.654 (2) Å] and between the pyridine rings [centroid–centroid distance = 3.775 (2) Å] help to set the mol­ecular conformation; the pyrimidine rings, as well as the pyridine rings, are nearly parallel, forming dihedral angles of 4.12 (14) and 2.46 (14)°, respectively.

Related literature

For related compounds, see: Dong et al. (2008[Dong, H. Z., Zhu, H. B., Tong, T. F. & Gou, S. H. (2008). J. Mol. Struct. 891, 266-271.], 2009[Dong, H. Z., Zhao, J., Zhu, H. B. & Gou, S. H. (2009). Polyhedron, 28, 1040-1048.]); Huang et al. (2007[Huang, C. H., Gou, S. H., Zhu, H. B. & Huang, W. (2007). Inorg. Chem. 46, 5537-5543.]).

[Scheme 1]

Experimental

Crystal data
  • C26H20N6S2

  • Mr = 480.62

  • Monoclinic, P 21 /n

  • a = 8.6078 (11) Å

  • b = 27.102 (3) Å

  • c = 10.0282 (12) Å

  • β = 103.661 (2)°

  • V = 2273.3 (5) Å3

  • Z = 4

  • Mo Kα radiation

  • μ = 0.26 mm−1

  • T = 291 K

  • 0.32 × 0.18 × 0.16 mm

Data collection
  • Bruker SMART CCD area-detector diffractometer

  • Absorption correction: multi-scan (SADABS; Bruker, 2000[Bruker (2000). SADABS, SMART and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]) Tmin = 0.917, Tmax = 0.966

  • 13064 measured reflections

  • 4903 independent reflections

  • 3067 reflections with I > 2σ(I)

  • Rint = 0.052

Refinement
  • R[F2 > 2σ(F2)] = 0.052

  • wR(F2) = 0.108

  • S = 0.90

  • 4903 reflections

  • 307 parameters

  • H-atom parameters constrained

  • Δρmax = 0.32 e Å−3

  • Δρmin = −0.22 e Å−3

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

Supporting information


Comment top

Remarkable attention has been paid to the rational design and assembly of new coordination polymers with heterocyclic thiolates or thioethers in recent years. In our previous work, we reported aserials dithioether ligands (Dong et al., 2008; 2009; Huang et al., 2007). As our continuing study, herein we report the molecular structure of the title compound - the newly synthesized ligand derived from 4-(4-pyridinyl)pyrimidine-2-thiol.

The molecular structure of the title compound is shown in Fig. 1. The molecule adopts a cis conformation with two arms positioned on one side of the benzene ring plane. It is noted that intramolecular π-π interactions between the pyrimidinyl rings [centroid-centroid distance of 3.654 (2) Å] and between the pyridinyl rings [centroid-centroid distance of 3.775 (2) Å] set the molecular conformation - the pyrimidinyl rings, as well as the pyridinyl ones, are nearly parallel forming dihedral angles of 4.12 (14)° and 2.46 (14)°, respectively.

Related literature top

For related compounds, see: Dong et al. (2008, 2009); Huang et al. (2007).

Experimental top

All solvents and chemicals were of analytical grade and were used without further purification. The title compound was prepared by similar procedure reported in the literature (Dong et al., 2008; 2009), To a solution of 4-(4-pyridinyl)pyrimidine-2-thiol (3.78 g, 20 mmol) and sodium hydroxide (0.80 g, 20 mmol) in dry ethanol (300 ml), 1,2-bis(bromomethyl)benzene (2.64 g, 10 mmol) in CCl4 (30 ml) was added. The mixture was stirred and refluxed for 8 h. After cooling, precipitates were filtered, washed in water and ethanol, and dried in vacuum. Anal. Calcd for C26H20N6S2: C, 64.98; H, 4.19; N, 17.49%. Found: C, 65.07; H, 4.52; N, 17.34%. Single crystals of ligang suitable for X-ray diffraction were grown from methanol solution by slow evaporation in air at room temperature.

Refinement top

All hydrogen atoms were geometrically positioned (C—H 0.93–0.97 Å) and refined as riding, with Uiso(H)=1.2Ueq(C).

Computing details top

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

Figures top
[Figure 1] Fig. 1. The molecular structure of the title compound showing 30% probability displacement ellipsoids and the atom-numbering scheme.
cis-1,2-Bis{[4-(4-pyridyl)pyrimidin-2-yl]sulfanylmethyl}benzene top
Crystal data top
C26H20N6S2F(000) = 1000.0
Mr = 480.62Dx = 1.404 Mg m3
Monoclinic, P21/nMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ynCell parameters from 4903 reflections
a = 8.6078 (11) Åθ = 2.2–27.0°
b = 27.102 (3) ŵ = 0.26 mm1
c = 10.0282 (12) ÅT = 291 K
β = 103.661 (2)°Block, pale yellow
V = 2273.3 (5) Å30.32 × 0.18 × 0.16 mm
Z = 4
Data collection top
Bruker SMART CCD area-detector
diffractometer
4903 independent reflections
Radiation source: fine-focus sealed tube3067 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.052
ϕ and ω scansθmax = 27.0°, θmin = 2.2°
Absorption correction: multi-scan
(SADABS; Bruker, 2000)
h = 108
Tmin = 0.917, Tmax = 0.966k = 3431
13064 measured reflectionsl = 1212
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)] = 0.052Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.108H-atom parameters constrained
S = 0.90 w = 1/[σ2(Fo2) + (0.0421P)2]
where P = (Fo2 + 2Fc2)/3
4903 reflections(Δ/σ)max = 0.001
307 parametersΔρmax = 0.32 e Å3
0 restraintsΔρmin = 0.22 e Å3
Crystal data top
C26H20N6S2V = 2273.3 (5) Å3
Mr = 480.62Z = 4
Monoclinic, P21/nMo Kα radiation
a = 8.6078 (11) ŵ = 0.26 mm1
b = 27.102 (3) ÅT = 291 K
c = 10.0282 (12) Å0.32 × 0.18 × 0.16 mm
β = 103.661 (2)°
Data collection top
Bruker SMART CCD area-detector
diffractometer
4903 independent reflections
Absorption correction: multi-scan
(SADABS; Bruker, 2000)
3067 reflections with I > 2σ(I)
Tmin = 0.917, Tmax = 0.966Rint = 0.052
13064 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0520 restraints
wR(F2) = 0.108H-atom parameters constrained
S = 0.90Δρmax = 0.32 e Å3
4903 reflectionsΔρmin = 0.22 e Å3
307 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
C10.7345 (3)0.22381 (8)0.8229 (2)0.0384 (5)
C20.9748 (3)0.25202 (9)0.9324 (2)0.0494 (6)
H21.07990.24690.98070.059*
C30.9230 (3)0.29935 (8)0.9059 (2)0.0474 (6)
H30.99090.32590.93510.057*
C40.7668 (3)0.30680 (8)0.8343 (2)0.0411 (6)
C50.6967 (3)0.35654 (8)0.8048 (2)0.0436 (6)
C60.7521 (3)0.39620 (9)0.8867 (3)0.0623 (8)
H60.83550.39220.96400.075*
C70.6845 (4)0.44177 (10)0.8545 (3)0.0774 (9)
H70.72400.46800.91250.093*
C80.5126 (3)0.41215 (9)0.6685 (3)0.0690 (8)
H80.42910.41720.59190.083*
C90.5716 (3)0.36519 (8)0.6935 (3)0.0529 (7)
H90.52750.33940.63570.063*
C100.6875 (3)0.12421 (7)0.8693 (2)0.0472 (6)
H10A0.78170.11240.84180.057*
H10B0.71880.13420.96480.057*
C110.5630 (3)0.08400 (8)0.8510 (2)0.0443 (6)
C120.5488 (3)0.05264 (9)0.7392 (3)0.0592 (7)
H120.61830.05600.68150.071*
C130.4334 (4)0.01686 (9)0.7133 (3)0.0687 (8)
H130.42480.00380.63790.082*
C140.3317 (3)0.01133 (9)0.7966 (3)0.0660 (8)
H140.25190.01260.77770.079*
C150.3473 (3)0.04123 (8)0.9091 (3)0.0566 (7)
H150.27940.03670.96770.068*
C160.4617 (3)0.07813 (8)0.9376 (2)0.0446 (6)
C170.4698 (3)0.11019 (7)1.0609 (2)0.0502 (6)
H17A0.58050.11841.10170.060*
H17B0.42830.09211.12850.060*
C180.4950 (3)0.21357 (8)1.0767 (2)0.0380 (5)
C190.7376 (3)0.24131 (9)1.1805 (2)0.0484 (6)
H190.84420.23581.22380.058*
C200.6847 (3)0.28872 (8)1.1637 (2)0.0446 (6)
H200.75230.31511.19550.053*
C210.5267 (3)0.29608 (8)1.0977 (2)0.0393 (5)
C220.4562 (3)0.34572 (8)1.0709 (2)0.0399 (5)
C230.5154 (3)0.38590 (9)1.1509 (3)0.0589 (7)
H230.60240.38231.22530.071*
C240.4452 (4)0.43133 (9)1.1201 (3)0.0701 (9)
H240.48680.45791.17610.084*
C250.3284 (3)0.35403 (8)0.9626 (2)0.0497 (6)
H250.28350.32820.90520.060*
C260.2679 (3)0.40072 (9)0.9402 (3)0.0597 (7)
H260.18160.40540.86560.072*
N10.8822 (2)0.21295 (7)0.89261 (18)0.0458 (5)
N20.6713 (2)0.26820 (6)0.79073 (17)0.0405 (5)
N30.5667 (3)0.45081 (8)0.7465 (3)0.0771 (8)
N40.6443 (2)0.20240 (7)1.13813 (19)0.0463 (5)
N50.4294 (2)0.25802 (6)1.05275 (17)0.0394 (5)
N60.3221 (3)0.43947 (7)1.0157 (2)0.0640 (6)
S10.60063 (8)0.17575 (2)0.76342 (6)0.04810 (19)
S20.35623 (8)0.16649 (2)1.01669 (6)0.04634 (19)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
C10.0353 (14)0.0411 (13)0.0382 (13)0.0043 (11)0.0074 (11)0.0000 (10)
C20.0363 (16)0.0586 (16)0.0487 (15)0.0038 (12)0.0005 (12)0.0005 (12)
C30.0409 (16)0.0496 (15)0.0480 (15)0.0112 (12)0.0031 (12)0.0033 (11)
C40.0424 (15)0.0443 (13)0.0377 (13)0.0058 (12)0.0116 (11)0.0023 (10)
C50.0423 (16)0.0436 (14)0.0462 (14)0.0055 (11)0.0131 (12)0.0066 (11)
C60.068 (2)0.0518 (16)0.0583 (17)0.0030 (15)0.0019 (14)0.0126 (13)
C70.090 (3)0.0455 (17)0.086 (2)0.0035 (16)0.001 (2)0.0243 (15)
C80.063 (2)0.0504 (16)0.081 (2)0.0088 (14)0.0070 (16)0.0122 (15)
C90.0461 (17)0.0422 (14)0.0656 (17)0.0020 (12)0.0036 (14)0.0122 (12)
C100.0394 (15)0.0401 (13)0.0559 (15)0.0036 (11)0.0010 (12)0.0066 (11)
C110.0447 (16)0.0305 (12)0.0509 (15)0.0019 (11)0.0025 (12)0.0012 (11)
C120.064 (2)0.0480 (15)0.0640 (18)0.0002 (14)0.0131 (15)0.0030 (13)
C130.079 (2)0.0455 (16)0.072 (2)0.0027 (15)0.0014 (18)0.0151 (14)
C140.058 (2)0.0367 (15)0.094 (2)0.0075 (13)0.0005 (17)0.0006 (15)
C150.0512 (18)0.0380 (14)0.079 (2)0.0012 (12)0.0129 (15)0.0064 (13)
C160.0457 (16)0.0304 (12)0.0526 (15)0.0027 (11)0.0016 (12)0.0056 (11)
C170.0563 (17)0.0387 (13)0.0527 (16)0.0057 (12)0.0071 (13)0.0101 (11)
C180.0354 (15)0.0429 (13)0.0355 (13)0.0000 (11)0.0084 (11)0.0030 (10)
C190.0335 (15)0.0601 (16)0.0471 (15)0.0018 (13)0.0005 (12)0.0007 (12)
C200.0357 (15)0.0464 (14)0.0473 (14)0.0037 (11)0.0014 (12)0.0047 (11)
C210.0379 (14)0.0453 (13)0.0340 (13)0.0012 (11)0.0070 (11)0.0043 (10)
C220.0364 (14)0.0410 (13)0.0417 (13)0.0033 (11)0.0080 (11)0.0054 (10)
C230.0475 (17)0.0524 (16)0.0654 (18)0.0002 (13)0.0096 (14)0.0141 (13)
C240.065 (2)0.0455 (16)0.088 (2)0.0040 (14)0.0062 (17)0.0218 (14)
C250.0514 (17)0.0407 (14)0.0511 (15)0.0003 (12)0.0003 (13)0.0089 (11)
C260.0584 (19)0.0521 (16)0.0590 (17)0.0073 (14)0.0057 (14)0.0017 (13)
N10.0354 (13)0.0505 (12)0.0475 (12)0.0011 (10)0.0016 (10)0.0037 (9)
N20.0357 (12)0.0397 (11)0.0440 (11)0.0041 (9)0.0054 (9)0.0016 (9)
N30.079 (2)0.0508 (14)0.0889 (19)0.0089 (13)0.0057 (15)0.0148 (13)
N40.0392 (13)0.0472 (11)0.0494 (12)0.0050 (10)0.0041 (10)0.0038 (9)
N50.0350 (12)0.0394 (11)0.0420 (11)0.0016 (9)0.0053 (9)0.0027 (8)
N60.0645 (17)0.0434 (13)0.0754 (16)0.0052 (11)0.0007 (13)0.0055 (11)
S10.0409 (4)0.0417 (3)0.0538 (4)0.0057 (3)0.0044 (3)0.0051 (3)
S20.0425 (4)0.0402 (3)0.0539 (4)0.0003 (3)0.0067 (3)0.0024 (3)
Geometric parameters (Å, º) top
C1—N21.328 (2)C13—H130.9300
C1—N11.331 (3)C14—C151.369 (3)
C1—S11.748 (2)C14—H140.9300
C2—N11.329 (3)C15—C161.385 (3)
C2—C31.364 (3)C15—H150.9300
C2—H20.9300C16—C171.500 (3)
C3—C41.381 (3)C17—S21.810 (2)
C3—H30.9300C17—H17A0.9700
C4—N21.338 (2)C17—H17B0.9700
C4—C51.478 (3)C18—N41.323 (3)
C5—C61.369 (3)C18—N51.328 (2)
C5—C91.375 (3)C18—S21.754 (2)
C6—C71.371 (3)C19—N41.333 (3)
C6—H60.9300C19—C201.360 (3)
C7—N31.320 (3)C19—H190.9300
C7—H70.9300C20—C211.379 (3)
C8—N31.324 (3)C20—H200.9300
C8—C91.372 (3)C21—N51.339 (2)
C8—H80.9300C21—C221.474 (3)
C9—H90.9300C22—C251.369 (3)
C10—C111.509 (3)C22—C231.377 (3)
C10—S11.807 (2)C23—C241.374 (3)
C10—H10A0.9700C23—H230.9300
C10—H10B0.9700C24—N61.321 (3)
C11—C161.377 (3)C24—H240.9300
C11—C121.389 (3)C25—C261.367 (3)
C12—C131.368 (3)C25—H250.9300
C12—H120.9300C26—N61.314 (3)
C13—C141.354 (4)C26—H260.9300
N2—C1—N1127.8 (2)C14—C15—H15119.2
N2—C1—S1113.12 (17)C16—C15—H15119.2
N1—C1—S1119.04 (17)C11—C16—C15118.6 (2)
N1—C2—C3123.0 (2)C11—C16—C17122.7 (2)
N1—C2—H2118.5C15—C16—C17118.7 (2)
C3—C2—H2118.5C16—C17—S2111.68 (15)
C2—C3—C4118.2 (2)C16—C17—H17A109.3
C2—C3—H3120.9S2—C17—H17A109.3
C4—C3—H3120.9C16—C17—H17B109.3
N2—C4—C3120.2 (2)S2—C17—H17B109.3
N2—C4—C5117.2 (2)H17A—C17—H17B107.9
C3—C4—C5122.6 (2)N4—C18—N5128.1 (2)
C6—C5—C9116.6 (2)N4—C18—S2120.10 (17)
C6—C5—C4121.9 (2)N5—C18—S2111.83 (17)
C9—C5—C4121.5 (2)N4—C19—C20123.3 (2)
C5—C6—C7119.8 (2)N4—C19—H19118.4
C5—C6—H6120.1C20—C19—H19118.4
C7—C6—H6120.1C19—C20—C21117.4 (2)
N3—C7—C6124.2 (2)C19—C20—H20121.3
N3—C7—H7117.9C21—C20—H20121.3
C6—C7—H7117.9N5—C21—C20121.2 (2)
N3—C8—C9124.2 (2)N5—C21—C22116.3 (2)
N3—C8—H8117.9C20—C21—C22122.4 (2)
C9—C8—H8117.9C25—C22—C23116.7 (2)
C8—C9—C5119.5 (2)C25—C22—C21120.9 (2)
C8—C9—H9120.3C23—C22—C21122.4 (2)
C5—C9—H9120.3C24—C23—C22119.7 (2)
C11—C10—S1107.66 (15)C24—C23—H23120.1
C11—C10—H10A110.2C22—C23—H23120.1
S1—C10—H10A110.2N6—C24—C23123.7 (2)
C11—C10—H10B110.2N6—C24—H24118.1
S1—C10—H10B110.2C23—C24—H24118.1
H10A—C10—H10B108.5C26—C25—C22119.1 (2)
C16—C11—C12119.3 (2)C26—C25—H25120.4
C16—C11—C10122.9 (2)C22—C25—H25120.4
C12—C11—C10117.7 (2)N6—C26—C25125.1 (2)
C13—C12—C11120.6 (3)N6—C26—H26117.4
C13—C12—H12119.7C25—C26—H26117.4
C11—C12—H12119.7C2—N1—C1114.35 (19)
C14—C13—C12120.5 (3)C1—N2—C4116.4 (2)
C14—C13—H13119.8C7—N3—C8115.6 (2)
C12—C13—H13119.8C18—N4—C19114.42 (19)
C13—C14—C15119.4 (3)C18—N5—C21115.62 (19)
C13—C14—H14120.3C26—N6—C24115.6 (2)
C15—C14—H14120.3C1—S1—C10103.16 (11)
C14—C15—C16121.6 (3)C18—S2—C17104.16 (11)

Experimental details

Crystal data
Chemical formulaC26H20N6S2
Mr480.62
Crystal system, space groupMonoclinic, P21/n
Temperature (K)291
a, b, c (Å)8.6078 (11), 27.102 (3), 10.0282 (12)
β (°) 103.661 (2)
V3)2273.3 (5)
Z4
Radiation typeMo Kα
µ (mm1)0.26
Crystal size (mm)0.32 × 0.18 × 0.16
Data collection
DiffractometerBruker SMART CCD area-detector
diffractometer
Absorption correctionMulti-scan
(SADABS; Bruker, 2000)
Tmin, Tmax0.917, 0.966
No. of measured, independent and
observed [I > 2σ(I)] reflections
13064, 4903, 3067
Rint0.052
(sin θ/λ)max1)0.639
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.052, 0.108, 0.90
No. of reflections4903
No. of parameters307
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)0.32, 0.22

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

 

Acknowledgements

The authors are indebted to the National Natural Science Foundationof China (grant No. 20801011) for financial support.

References

First citationBruker (2000). SADABS, SMART and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.  Google Scholar
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