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Acta Crystallogr Sect E Struct Rep Online. 2009 October 1; 65(Pt 10): o2572.
Published online 2009 September 30. doi:  10.1107/S1600536809038562
PMCID: PMC2970259

6-Methyl­sulfanyl-4H-pyrimido[1,6-a]pyrimidin-4-one

Abstract

Reaction of 2-(methyl­sulfan­yl)pyrimidin-4-amine with the 5-(methoxy­vinyl­idene) derivative of Meldrum’s acid and subsequent heating of the product in Dowtherm fluid yielded the title compound, C8H7N3OS, which was proven to contain a bicyclic 4H-pyrimido[1,6-a]pyrimidine system. All non-H atoms of the mol­ecule are coplanar within 0.15 Å. The bond-length distribution in the bicyclic core shows localization of the double bonds. The geometry of the intra­molecular S(...)O 1,5-contact [2.534 (2) Å] is consistent with the existence of an attractive inter­action.

Related literature

For the structure of a compound with a similar bicyclic carbon–nitro­gen core, see: Olomucki et al. (1984 [triangle]). For statistical studies of the geometry of S(...)O inter­actions, see: Rosenfield et al. (1977 [triangle]); Iwaoka et al. (2002 [triangle]).

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Object name is e-65-o2572-scheme1.jpg

Experimental

Crystal data

  • C8H7N3OS
  • M r = 193.23
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-65-o2572-efi1.jpg
  • a = 9.7621 (8) Å
  • b = 4.1725 (3) Å
  • c = 20.4092 (16) Å
  • β = 100.106 (1)°
  • V = 818.42 (11) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 0.35 mm−1
  • T = 123 K
  • 0.48 × 0.14 × 0.08 mm

Data collection

  • Bruker APEXII CCD diffractometer
  • Absorption correction: multi-scan (SADABS; Bruker, 2001 [triangle]) T min = 0.849, T max = 0.972
  • 6497 measured reflections
  • 1498 independent reflections
  • 1333 reflections with I > 2σ(I)
  • R int = 0.022

Refinement

  • R[F 2 > 2σ(F 2)] = 0.035
  • wR(F 2) = 0.097
  • S = 1.13
  • 1498 reflections
  • 118 parameters
  • H-atom parameters constrained
  • Δρmax = 0.43 e Å−3
  • Δρmin = −0.19 e Å−3

Data collection: APEX2 (Bruker, 2004 [triangle]); cell refinement: SAINT (Bruker, 2004 [triangle]); data reduction: SAINT; program(s) used to solve structure: SIR2004 (Burla et al., 2005 [triangle]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 [triangle]); molecular graphics: ORTEP-32 (Farrugia, 1997 [triangle]); software used to prepare material for publication: WinGX (Farrugia, 1999 [triangle]).

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536809038562/rz2363sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536809038562/rz2363Isup2.hkl

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

supplementary crystallographic information

Comment

The title compound was obtained by reaction of 2-(methylsulfanyl)pyrimidin-4-amine with 5-(methoxyvinylidene) derivative of Meldrum's acid and subsequent heating of the product in Dowtherm fluid (Fig. 1).

All non-hydrogen atoms of the molecule of the title compound (Fig. 2) are approximately coplanar; maximum deviation of the C1 atom from the least-squares plane is 0.143 (2) Å. The bond length values indicate localization of double bonds in the bicyclic core (N1–C2, 1.298 (3) Å; N3–C5, 1.308 (3) Å; C3–C4, 1.351 (3) Å; C6–C7, 1.355 (3) Å;), which is consistent with the fact that no resonance structures can be drawn. Surprisingly, to the best of our knowledge no other isolated bicyclic carbon-nitrogen system with the same positions of the N atoms was structurally studied. Similar bond lengths were observed in dihydropyrimido(1,2 - c)purine derivative, where analogous bicyclic core makes up a part of the tricyclic system (Olomucki et al., 1984).

The S1···O1 distance [2.534 (2) Å] and the O1···S1—C1 angle [177.5 (1)°] are consistent with the existence of the intramolecular attractive interaction (Rosenfield et al., 1977; Iwaoka et al., 2002).

Experimental

A mixture of (2-methylsulfanyl)pyrimidin-4-ylamine (5.0 g, 35 mmol, 1.0 eq), 5-(methoxyvinylidene) derivative of Meldrum's acid (9.23 g, 49.6 mmol, 1.4 eq), and 2-PrOH (100 ml) was refluxed at 85°C for 1 h to reach reaction completion. The resulting suspension was cooled to 25°C, filtered, and washed with EtOH to afford 10 g of the displacement product as a yellow solid in 96% yield. LC—MS (APCI, M+1) 296.0; 1H NMR (400 MHz, DMSO-d6) δ p.p.m. 1.69 (s, 6 H) 2.55 (s, 3 H) 7.43 (d, J = 5.54 Hz, 1 H) 8.57 (d, J = 5.54 Hz, 1 H) 9.20 (s, 1 H) 11.35 (s, 1 H).

The generated 5-[(2-methylsulfanyl)pyrimidin-4-ylaminovinylidene] derivative of Meldrum's acid (6.5 g, 22 mmol, 1.0 eq) was added portionwise to 130 ml of preheated Dowtherm A at 220°C (inner temperature). After being reacted at 220°C for 10 min, LC—MS indicated that reaction was complete. The reaction mixture was cooled to 25°C and diluted with 1 L heptane. The resulting suspension was left to stand overnight. The solid was filtered, washed with heptane, and dried under vacuum to afford 3.4 g of the target compound as a yellow solid in (80% yield). LC—MS (APCI, M+1) 194.0; 1H NMR (400 MHz, DMSO-d6) δ p.p.m. 2.40 (s, 3 H) 6.35 (d, J = 6.55 Hz, 1 H) 7.04 (d, J = 6.29 Hz, 1 H) 8.08 (t, J = 6.55 Hz, 2 H). The product was recrystallized from EtOAc/hexane to yield single crystals suitable for X-ray diffraction studies.

Refinement

All H atoms were placed in geometrically calculated positions (C—H = 0.95 Å and 0.98 Å for aromatic and methyl H atoms respectively) and included in the refinement in riding motion approximation. The Uiso(H) were set to 1.2Ueq(C) or 1.5Ueq(C) for methyl H atoms.

Figures

Fig. 1.
Synthesis of the title compound.
Fig. 2.
Molecular structure of the title compound, showing 50% probability displacement ellipsoids and atom numbering scheme. H atoms are drawn as circles with arbitrary small radius.

Crystal data

C8H7N3OSF(000) = 400
Mr = 193.23Dx = 1.568 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 4134 reflections
a = 9.7621 (8) Åθ = 3.2–25.4°
b = 4.1725 (3) ŵ = 0.35 mm1
c = 20.4092 (16) ÅT = 123 K
β = 100.106 (1)°Blade, brown
V = 818.42 (11) Å30.48 × 0.14 × 0.08 mm
Z = 4

Data collection

Bruker APEXII CCD diffractometer1498 independent reflections
Radiation source: fine-focus sealed tube1333 reflections with I > 2σ(I)
graphiteRint = 0.022
[var phi] and ω scansθmax = 25.4°, θmin = 2.1°
Absorption correction: multi-scan (SADABS; Bruker, 2001)h = −11→11
Tmin = 0.849, Tmax = 0.972k = −4→5
6497 measured reflectionsl = −24→24

Refinement

Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.035Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.097H-atom parameters constrained
S = 1.13w = 1/[σ2(Fo2) + (0.045P)2 + 0.5615P] where P = (Fo2 + 2Fc2)/3
1498 reflections(Δ/σ)max = 0.001
118 parametersΔρmax = 0.43 e Å3
0 restraintsΔρmin = −0.19 e Å3

Special details

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)

xyzUiso*/Ueq
S10.56563 (5)0.91748 (12)0.81678 (2)0.02069 (19)
O10.80408 (15)0.9008 (4)0.78390 (7)0.0276 (4)
N10.59517 (17)0.5753 (4)0.92701 (8)0.0203 (4)
N20.79659 (16)0.5851 (4)0.87620 (7)0.0172 (4)
N30.99408 (17)0.2689 (4)0.92351 (8)0.0238 (4)
C10.3990 (2)0.9169 (5)0.84302 (11)0.0280 (5)
H1A0.33331.04740.81230.042*
H1B0.40891.00640.88800.042*
H1C0.36420.69660.84310.042*
C20.65797 (19)0.6714 (5)0.87950 (9)0.0183 (4)
C30.6652 (2)0.3762 (5)0.97497 (10)0.0209 (4)
H3B0.61930.30941.01000.025*
C40.7959 (2)0.2700 (5)0.97507 (9)0.0203 (4)
H4A0.83920.12841.00890.024*
C50.8678 (2)0.3717 (5)0.92427 (9)0.0186 (4)
C61.0583 (2)0.3766 (5)0.87347 (11)0.0254 (5)
H6A1.14950.30100.87190.030*
C70.9993 (2)0.5853 (5)0.82589 (9)0.0199 (4)
H7A1.05060.65120.79270.024*
C80.8652 (2)0.7063 (5)0.82424 (9)0.0219 (4)

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
S10.0177 (3)0.0225 (3)0.0219 (3)0.00111 (19)0.0038 (2)0.0028 (2)
O10.0237 (8)0.0363 (9)0.0241 (7)0.0002 (7)0.0079 (6)0.0095 (7)
N10.0196 (8)0.0199 (9)0.0220 (8)−0.0009 (7)0.0053 (7)−0.0002 (7)
N20.0184 (8)0.0176 (8)0.0164 (8)−0.0021 (6)0.0050 (6)−0.0017 (6)
N30.0199 (8)0.0240 (9)0.0278 (9)0.0015 (7)0.0047 (7)−0.0014 (8)
C10.0201 (11)0.0335 (12)0.0312 (11)0.0032 (9)0.0068 (9)0.0059 (10)
C20.0169 (9)0.0178 (9)0.0201 (10)−0.0015 (8)0.0026 (8)−0.0037 (8)
C30.0211 (10)0.0232 (10)0.0190 (10)−0.0025 (8)0.0052 (8)0.0004 (8)
C40.0233 (10)0.0189 (10)0.0184 (10)−0.0007 (8)0.0026 (8)0.0006 (8)
C50.0179 (10)0.0173 (9)0.0200 (10)−0.0016 (8)0.0022 (8)−0.0041 (8)
C60.0180 (10)0.0264 (11)0.0326 (11)−0.0005 (9)0.0068 (9)−0.0070 (9)
C70.0253 (11)0.0186 (10)0.0183 (10)−0.0042 (8)0.0108 (8)−0.0040 (8)
C80.0234 (10)0.0245 (11)0.0186 (10)−0.0066 (9)0.0059 (8)−0.0026 (9)

Geometric parameters (Å, °)

S1—C21.761 (2)C1—H1B0.9800
S1—C11.799 (2)C1—H1C0.9800
O1—C81.233 (2)C3—C41.351 (3)
N1—C21.298 (3)C3—H3B0.9500
N1—C31.371 (3)C4—C51.415 (3)
N2—C21.413 (2)C4—H4A0.9500
N2—C51.414 (2)C6—C71.355 (3)
N2—C81.442 (2)C6—H6A0.9500
N3—C51.308 (3)C7—C81.398 (3)
N3—C61.365 (3)C7—H7A0.9500
C1—H1A0.9800
C2—S1—C199.03 (9)N1—C3—H3B118.2
C2—N1—C3118.60 (17)C3—C4—C5119.37 (18)
C2—N2—C5119.08 (16)C3—C4—H4A120.3
C2—N2—C8121.20 (16)C5—C4—H4A120.3
C5—N2—C8119.70 (16)N3—C5—N2123.26 (18)
C5—N3—C6117.29 (18)N3—C5—C4119.98 (18)
S1—C1—H1A109.5N2—C5—C4116.76 (17)
S1—C1—H1B109.5C7—C6—N3123.66 (19)
H1A—C1—H1B109.5C7—C6—H6A118.2
S1—C1—H1C109.5N3—C6—H6A118.2
H1A—C1—H1C109.5C6—C7—C8121.85 (18)
H1B—C1—H1C109.5C6—C7—H7A119.1
N1—C2—N2122.57 (17)C8—C7—H7A119.1
N1—C2—S1118.33 (15)O1—C8—C7126.55 (18)
N2—C2—S1119.10 (14)O1—C8—N2119.26 (18)
C4—C3—N1123.53 (18)C7—C8—N2114.19 (17)
C4—C3—H3B118.2

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: RZ2363).

References

  • Bruker (2001). SADABS Bruker AXS Inc., Madison, Wisconsin, USA.
  • Bruker (2004). APEX2 and SAINT Bruker AXS Inc., Madison, Wisconsin, USA.
  • Burla, M. C., Caliandro, R., Camalli, M., Carrozzini, B., Cascarano, G. L., De Caro, L., Giacovazzo, C., Polidori, G. & Spagna, R. (2005). J. Appl. Cryst.38, 381–388.
  • Farrugia, L. J. (1997). J. Appl. Cryst.30, 565.
  • Farrugia, L. J. (1999). J. Appl. Cryst.32, 837–838.
  • Iwaoka, M., Takemoto, S. & Tomoda, S. (2002). J. Am. Chem. Soc.124, 10613–10620. [PubMed]
  • Olomucki, M., Le Gall, J. Y., Colinart, S., Durant, F., Norberg, B. & Evrard, G. (1984). Tetrahedron Lett.25, 3471–3474.
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