1,3-Bis[4-(4-pyrid­yl)pyrimidin-2-ylsulfan­yl]propane

Sun, Y.-Y.; Dong, H.-Z.; Cheng, L.

doi:10.1107/S1600536808010854

organic compounds

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ISSN: 2056-9890

Volume 64| Part 5| May 2008| Page o901

doi:10.1107/S1600536808010854

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1,3-Bis[4-(4-pyridyl)pyrimidin-2-ylsulfanyl]propane

Yan-Yan Sun,^a Hua-Ze Dong ^b and Lin Cheng ^a ^*

^aDepartment of Chemistry and Chemical Engineering, Southeast University, Nanjing, People's Republic of China, and ^bDepartment of Chemistry and Chemical Engineering, State Key Laboratory of Coordination Chemistry, Nanjing University, Nanjing, People's Republic of China
^*Correspondence e-mail: cep02chl@yahoo.com.cn

(Received 8 April 2008; accepted 18 April 2008; online 23 April 2008)

In the title compound, C₂₁H₁₈N₆S₂, the dihedral angles between the aromatic rings in the two 4-(4-pyridyl)pyrimidine residues are 23.45 (13) and 2.67 (14)°. Whereas one of the C—S—C—C torsion angles corresponds to a staggered conformation, the other is gauche.

Related literature

For related structures, see: Awaleh et al. (2005 ); Xie et al. (2005 ).

Experimental

Crystal data

C₂₁H₁₈N₆S₂
M_r = 418.55
Triclinic, $[P \overline 1]$
a = 9.986 (3) Å
b = 10.057 (3) Å
c = 10.645 (3) Å
α = 98.972 (5)°
β = 90.688 (5)°
γ = 112.632 (5)°
V = 971.6 (5) Å³
Z = 2
Mo Kα radiation
μ = 0.29 mm⁻¹
T = 291 (2) K
0.30 × 0.20 × 0.20 mm

Data collection

Bruker SMART CCD area-detector diffractometer
Absorption correction: multi-scan (SADABS; Bruker, 2000 ) T_min = 0.915, T_max = 0.943
5163 measured reflections
3720 independent reflections
2986 reflections with I > 2σ(I)
R_int = 0.028

Refinement

R[F² > 2σ(F²)] = 0.059
wR(F²) = 0.156
S = 1.02
3720 reflections
262 parameters
H-atom parameters constrained
Δρ_max = 0.52 e Å⁻³
Δρ_min = −0.46 e Å⁻³

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

Supporting information

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536808010854/bt2695sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536808010854/bt2695Isup2.hkl

checkCIF report

Comment top

In the title compound, the dihedral angles between the aromatic rings in the two(4-pyridyl)-pyrimidine residues are 23.45 (13)° and 2.67 (14)°. Whereas one of the C-S-C-C torsion angles adopts a staggered conformation [-176.74 (17)°], the other one is gauche [87.6 (2)°].

Related literature top

For related structures, see: Awaleh et al. (2005); Xie et al. (2005).

Experimental top

NaOH (0.80 g, 20 mmol) in ethanol (10 mL) was added with stirring to a solution of 4-(pyridin-4-yl)pyrimidine-2-thiol (3.78 g, 20 mmol) in acetone (30 mL) at ambient temperature for 20 min. A solution of 1,3-dibromopropane (2.00 g, 10.0 mmol) was added slowly over 1 h, and the resulting mixture was further refluxed for 6 h. The solids isolated from the reaction mixture were washed with water and acetone. The yellow products were obtained by vacuum dryness in 91% yield (3.80 g). The filtrate was allowed to evaporate slowly at room temperature. After several days, yellow block shaped crystals suitable for X-ray diffraction analyses were obtained.

Computing details top

Data collection: SMART (Bruker, 2000); cell refinement: SMART (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

Fig. 1. The molecular structure of the title compound.

1,3-Bis[4-(4-pyridyl)pyrimidin-2-ylsulfanyl]propane top

Crystal data top

C₂₁H₁₈N₆S₂	Z = 2
M_r = 418.55	F(000) = 436.0
Triclinic, P1	D_x = 1.431 Mg m⁻³
Hall symbol: -P 1	Mo Kα radiation, λ = 0.71073 Å
a = 9.986 (3) Å	Cell parameters from 765 reflections
b = 10.057 (3) Å	θ = 2.5–28.0°
c = 10.645 (3) Å	µ = 0.30 mm⁻¹
α = 98.972 (5)°	T = 291 K
β = 90.688 (5)°	Block, yellow
γ = 112.632 (5)°	0.30 × 0.20 × 0.20 mm
V = 971.6 (5) Å³

Data collection top

Bruker CCD area-detector diffractometer	3720 independent reflections
Radiation source: fine-focus sealed tube	2986 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.028
ϕ and ω scans	θ_max = 26.0°, θ_min = 1.9°
Absorption correction: multi-scan (SADABS; Bruker, 2000)	h = −12→11
T_min = 0.915, T_max = 0.943	k = −12→10
5163 measured reflections	l = −12→13

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)] = 0.059	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.156	H-atom parameters constrained
S = 1.02	w = 1/[σ²(F_o²) + (0.1031P)²] where P = (F_o² + 2F_c²)/3
3720 reflections	(Δ/σ)_max < 0.001
262 parameters	Δρ_max = 0.52 e Å⁻³
0 restraints	Δρ_min = −0.46 e Å⁻³

Crystal data top

C₂₁H₁₈N₆S₂	γ = 112.632 (5)°
M_r = 418.55	V = 971.6 (5) Å³
Triclinic, P1	Z = 2
a = 9.986 (3) Å	Mo Kα radiation
b = 10.057 (3) Å	µ = 0.30 mm⁻¹
c = 10.645 (3) Å	T = 291 K
α = 98.972 (5)°	0.30 × 0.20 × 0.20 mm
β = 90.688 (5)°

Data collection top

Bruker CCD area-detector diffractometer	3720 independent reflections
Absorption correction: multi-scan (SADABS; Bruker, 2000)	2986 reflections with I > 2σ(I)
T_min = 0.915, T_max = 0.943	R_int = 0.028
5163 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.059	0 restraints
wR(F²) = 0.156	H-atom parameters constrained
S = 1.02	Δρ_max = 0.52 e Å⁻³
3720 reflections	Δρ_min = −0.46 e Å⁻³
262 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

	x	y	z	U_iso*/U_eq
S1	0.66814 (7)	0.18543 (8)	0.02844 (6)	0.0501 (2)
S2	0.31122 (8)	0.33035 (8)	0.24761 (7)	0.0551 (2)
N1	0.9037 (2)	0.1412 (2)	−0.0039 (2)	0.0484 (5)
N2	0.88209 (19)	0.3272 (2)	−0.10815 (17)	0.0362 (4)
N3	1.1505 (2)	0.6455 (2)	−0.4191 (2)	0.0517 (6)
N4	0.1388 (2)	0.1026 (2)	0.3337 (2)	0.0516 (5)
N5	0.3748 (2)	0.1065 (2)	0.29548 (17)	0.0394 (5)
N6	0.6716 (3)	−0.1928 (3)	0.3320 (2)	0.0558 (6)
C1	0.8365 (2)	0.2254 (3)	−0.0352 (2)	0.0374 (5)
C2	1.0326 (3)	0.1682 (3)	−0.0486 (2)	0.0488 (6)
H2	1.0859	0.1158	−0.0270	0.059*
C3	1.0916 (3)	0.2709 (3)	−0.1260 (2)	0.0449 (6)
H3	1.1826	0.2879	−0.1565	0.054*
C4	1.0107 (2)	0.3474 (2)	−0.1565 (2)	0.0346 (5)
C5	1.0584 (2)	0.4510 (2)	−0.2471 (2)	0.0355 (5)
C6	1.1556 (3)	0.4399 (3)	−0.3360 (2)	0.0438 (6)
H6	1.1925	0.3676	−0.3397	0.053*
C7	1.1961 (3)	0.5387 (3)	−0.4185 (3)	0.0520 (7)
H7	1.2605	0.5294	−0.4784	0.062*
C8	1.0070 (3)	0.5595 (3)	−0.2489 (2)	0.0423 (6)
H8	0.9392	0.5687	−0.1928	0.051*
C9	1.0560 (3)	0.6538 (3)	−0.3333 (3)	0.0504 (6)
H9	1.0216	0.7279	−0.3311	0.061*
C10	0.6054 (3)	0.3160 (3)	−0.0212 (2)	0.0454 (6)
H10A	0.6765	0.4146	0.0080	0.055*
H10B	0.5920	0.2998	−0.1135	0.055*
C11	0.4614 (3)	0.2964 (3)	0.0364 (2)	0.0475 (6)
H11A	0.4109	0.3412	−0.0101	0.057*
H11B	0.4011	0.1928	0.0263	0.057*
C12	0.4802 (3)	0.3627 (3)	0.1758 (2)	0.0446 (6)
H12A	0.5352	0.4674	0.1852	0.054*
H12B	0.5367	0.3228	0.2213	0.054*
C13	0.2733 (3)	0.1608 (3)	0.2964 (2)	0.0416 (5)
C14	0.1092 (3)	−0.0215 (3)	0.3770 (2)	0.0519 (7)
H14	0.0168	−0.0673	0.4037	0.062*
C15	0.2062 (3)	−0.0862 (3)	0.3847 (2)	0.0464 (6)
H15	0.1824	−0.1720	0.4179	0.056*
C16	0.3416 (3)	−0.0181 (2)	0.3409 (2)	0.0373 (5)
C17	0.4557 (3)	−0.0781 (2)	0.3402 (2)	0.0373 (5)
C18	0.4364 (3)	−0.2049 (3)	0.3858 (2)	0.0491 (6)
H18	0.3500	−0.2550	0.4204	0.059*
C19	0.5447 (3)	−0.2568 (3)	0.3800 (2)	0.0546 (7)
H19	0.5286	−0.3423	0.4117	0.066*
C20	0.5885 (3)	−0.0082 (3)	0.2938 (2)	0.0443 (6)
H20	0.6092	0.0798	0.2650	0.053*
C21	0.6903 (3)	−0.0697 (3)	0.2905 (3)	0.0536 (7)
H21	0.7781	−0.0217	0.2569	0.064*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
S1	0.0461 (4)	0.0571 (4)	0.0600 (4)	0.0260 (3)	0.0245 (3)	0.0303 (3)
S2	0.0617 (5)	0.0605 (4)	0.0689 (5)	0.0449 (4)	0.0295 (4)	0.0283 (4)
N1	0.0516 (13)	0.0521 (12)	0.0558 (13)	0.0287 (10)	0.0163 (10)	0.0272 (10)
N2	0.0346 (10)	0.0392 (10)	0.0392 (10)	0.0173 (8)	0.0077 (8)	0.0118 (8)
N3	0.0481 (13)	0.0537 (13)	0.0615 (14)	0.0215 (10)	0.0138 (10)	0.0283 (11)
N4	0.0447 (12)	0.0597 (14)	0.0598 (13)	0.0287 (11)	0.0183 (10)	0.0142 (11)
N5	0.0438 (11)	0.0451 (11)	0.0400 (10)	0.0264 (9)	0.0124 (8)	0.0134 (8)
N6	0.0701 (16)	0.0584 (13)	0.0590 (14)	0.0434 (12)	0.0147 (12)	0.0192 (11)
C1	0.0389 (12)	0.0410 (12)	0.0381 (12)	0.0193 (10)	0.0083 (10)	0.0132 (10)
C2	0.0470 (14)	0.0536 (15)	0.0620 (16)	0.0306 (12)	0.0109 (12)	0.0270 (12)
C3	0.0391 (13)	0.0505 (14)	0.0575 (15)	0.0257 (11)	0.0139 (11)	0.0226 (12)
C4	0.0326 (11)	0.0355 (11)	0.0385 (12)	0.0148 (9)	0.0052 (9)	0.0103 (9)
C5	0.0296 (11)	0.0382 (12)	0.0414 (12)	0.0145 (9)	0.0036 (9)	0.0113 (9)
C6	0.0381 (13)	0.0482 (14)	0.0553 (14)	0.0232 (11)	0.0144 (11)	0.0206 (11)
C7	0.0458 (15)	0.0595 (16)	0.0604 (16)	0.0242 (13)	0.0210 (12)	0.0277 (13)
C8	0.0409 (13)	0.0445 (13)	0.0485 (13)	0.0219 (11)	0.0099 (10)	0.0139 (11)
C9	0.0516 (15)	0.0439 (14)	0.0654 (16)	0.0244 (12)	0.0104 (13)	0.0218 (12)
C10	0.0450 (14)	0.0548 (15)	0.0446 (13)	0.0251 (12)	0.0125 (11)	0.0164 (11)
C11	0.0392 (13)	0.0628 (16)	0.0494 (14)	0.0265 (12)	0.0092 (11)	0.0172 (12)
C12	0.0447 (14)	0.0477 (13)	0.0508 (14)	0.0251 (11)	0.0122 (11)	0.0160 (11)
C13	0.0477 (14)	0.0485 (13)	0.0392 (12)	0.0294 (11)	0.0123 (10)	0.0097 (10)
C14	0.0455 (15)	0.0552 (15)	0.0556 (15)	0.0197 (12)	0.0189 (12)	0.0098 (12)
C15	0.0501 (15)	0.0438 (13)	0.0455 (14)	0.0172 (12)	0.0153 (11)	0.0109 (11)
C16	0.0441 (13)	0.0399 (12)	0.0309 (11)	0.0200 (10)	0.0073 (9)	0.0057 (9)
C17	0.0488 (14)	0.0389 (12)	0.0299 (11)	0.0226 (10)	0.0091 (9)	0.0077 (9)
C18	0.0627 (16)	0.0483 (14)	0.0488 (14)	0.0303 (13)	0.0199 (12)	0.0201 (11)
C19	0.080 (2)	0.0489 (15)	0.0537 (15)	0.0400 (14)	0.0211 (14)	0.0233 (12)
C20	0.0506 (15)	0.0425 (13)	0.0508 (14)	0.0256 (11)	0.0134 (11)	0.0193 (11)
C21	0.0560 (16)	0.0590 (16)	0.0627 (16)	0.0353 (14)	0.0207 (13)	0.0242 (13)

Geometric parameters (Å, º) top

S1—C1	1.743 (2)	C7—H7	0.9300
S1—C10	1.799 (3)	C8—C9	1.365 (3)
S2—C13	1.762 (3)	C8—H8	0.9300
S2—C12	1.796 (2)	C9—H9	0.9300
N1—C2	1.320 (3)	C10—C11	1.525 (3)
N1—C1	1.342 (3)	C10—H10A	0.9700
N2—C1	1.325 (3)	C10—H10B	0.9700
N2—C4	1.343 (3)	C11—C12	1.507 (3)
N3—C7	1.320 (3)	C11—H11A	0.9700
N3—C9	1.338 (3)	C11—H11B	0.9700
N4—C14	1.325 (3)	C12—H12A	0.9700
N4—C13	1.336 (3)	C12—H12B	0.9700
N5—C13	1.323 (3)	C14—C15	1.367 (4)
N5—C16	1.337 (3)	C14—H14	0.9300
N6—C21	1.326 (3)	C15—C16	1.385 (3)
N6—C19	1.330 (4)	C15—H15	0.9300
C2—C3	1.379 (3)	C16—C17	1.480 (3)
C2—H2	0.9300	C17—C18	1.381 (3)
C3—C4	1.379 (3)	C17—C20	1.380 (3)
C3—H3	0.9300	C18—C19	1.368 (4)
C4—C5	1.478 (3)	C18—H18	0.9300
C5—C8	1.376 (3)	C19—H19	0.9300
C5—C6	1.386 (3)	C20—C21	1.377 (4)
C6—C7	1.376 (3)	C20—H20	0.9300
C6—H6	0.9300	C21—H21	0.9300

C1—S1—C10	103.68 (11)	H10A—C10—H10B	108.4
C13—S2—C12	102.41 (11)	C12—C11—C10	113.0 (2)
C2—N1—C1	114.9 (2)	C12—C11—H11A	109.0
C1—N2—C4	115.73 (19)	C10—C11—H11A	109.0
C7—N3—C9	115.9 (2)	C12—C11—H11B	109.0
C14—N4—C13	114.3 (2)	C10—C11—H11B	109.0
C13—N5—C16	116.7 (2)	H11A—C11—H11B	107.8
C21—N6—C19	115.5 (2)	C11—C12—S2	113.52 (17)
N2—C1—N1	127.7 (2)	C11—C12—H12A	108.9
N2—C1—S1	119.77 (17)	S2—C12—H12A	108.9
N1—C1—S1	112.50 (17)	C11—C12—H12B	108.9
N1—C2—C3	122.8 (2)	S2—C12—H12B	108.9
N1—C2—H2	118.6	H12A—C12—H12B	107.7
C3—C2—H2	118.6	N5—C13—N4	127.3 (2)
C4—C3—C2	117.5 (2)	N5—C13—S2	119.94 (18)
C4—C3—H3	121.2	N4—C13—S2	112.72 (18)
C2—C3—H3	121.2	N4—C14—C15	124.0 (2)
N2—C4—C3	121.2 (2)	N4—C14—H14	118.0
N2—C4—C5	116.95 (19)	C15—C14—H14	118.0
C3—C4—C5	121.8 (2)	C14—C15—C16	116.9 (2)
C8—C5—C6	117.4 (2)	C14—C15—H15	121.6
C8—C5—C4	122.0 (2)	C16—C15—H15	121.6
C6—C5—C4	120.6 (2)	N5—C16—C15	120.7 (2)
C7—C6—C5	118.4 (2)	N5—C16—C17	116.6 (2)
C7—C6—H6	120.8	C15—C16—C17	122.7 (2)
C5—C6—H6	120.8	C18—C17—C20	116.4 (2)
N3—C7—C6	124.9 (2)	C18—C17—C16	122.6 (2)
N3—C7—H7	117.6	C20—C17—C16	121.0 (2)
C6—C7—H7	117.6	C19—C18—C17	119.9 (2)
C9—C8—C5	119.8 (2)	C19—C18—H18	120.1
C9—C8—H8	120.1	C17—C18—H18	120.1
C5—C8—H8	120.1	N6—C19—C18	124.3 (2)
N3—C9—C8	123.7 (2)	N6—C19—H19	117.8
N3—C9—H9	118.1	C18—C19—H19	117.8
C8—C9—H9	118.1	C21—C20—C17	119.5 (2)
C11—C10—S1	108.09 (17)	C21—C20—H20	120.3
C11—C10—H10A	110.1	C17—C20—H20	120.3
S1—C10—H10A	110.1	N6—C21—C20	124.4 (2)
C11—C10—H10B	110.1	N6—C21—H21	117.8
S1—C10—H10B	110.1	C20—C21—H21	117.8

Experimental details

Crystal data
Chemical formula	C₂₁H₁₈N₆S₂
M_r	418.55
Crystal system, space group	Triclinic, P1
Temperature (K)	291
a, b, c (Å)	9.986 (3), 10.057 (3), 10.645 (3)
α, β, γ (°)	98.972 (5), 90.688 (5), 112.632 (5)
V (Å³)	971.6 (5)
Z	2
Radiation type	Mo Kα
µ (mm⁻¹)	0.30
Crystal size (mm)	0.30 × 0.20 × 0.20

Data collection
Diffractometer	Bruker CCD area-detector diffractometer
Absorption correction	Multi-scan (SADABS; Bruker, 2000)
T_min, T_max	0.915, 0.943
No. of measured, independent and observed [I > 2σ(I)] reflections	5163, 3720, 2986
R_int	0.028
(sin θ/λ)_max (Å⁻¹)	0.617

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.059, 0.156, 1.02
No. of reflections	3720
No. of parameters	262
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.52, −0.46

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

Acknowledgements

The authors thank the Program for Excellent Talents Introduction of Southeast University for financial support.

References

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