3,5,6-Trimethyl­thieno[2,3-d]pyrimidin-4(3H)-one

Khatamov, K.; Saitqulov, F.; Ashurov, J.; Shakhidoyatov, K.

doi:10.1107/S1600536812035416

organic compounds

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ISSN: 2056-9890

Volume 68| Part 9| September 2012| Page o2740

doi:10.1107/S1600536812035416

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3,5,6-Trimethylthieno[2,3-d]pyrimidin-4(3H)-one

Khamroqul Khatamov,^a ^* Fozil Saitqulov,^a Jamshid Ashurov ^b and Khusnutdin Shakhidoyatov ^c

^aA. Navoiy Samarkand State University. University Avenue 15, Samarkand, Uzbekistan, ^bInstitute of Bioorganic Chemistry, Academy of Sciences of Uzbekistan, H. Abdullaev Str. 83, Tashkent 100125, Uzbekistan, and ^cS. Yunusov Institute of the Chemistry of Plant Substances, Academy of Sciences of Uzbekistan, H. Abdullaev Str. 83, Tashkent 100125, Uzbekistan
^*Correspondence e-mail: crystal_uz@rambler.ru

(Received 14 May 2012; accepted 10 August 2012; online 23 August 2012)

In the title compound, C₉H₁₀N₂OS, the thienopyrimidine ring system is almost planar [greatest deviation from the mean plane = 0.0318 (13) Å for the S atom]. The crystal packing features C—H⋯O hydrogen bonds and π–π stacking interactions between inversion-related pairs of molecules with a centroid–centroid distance of 3.530 (3) Å.

Related literature

For the synthesis, properties and biological activity of pyrimidinone derivatives, see: Litvinov (2004 ); Al-Taisan et al. (2010 ). For the crystal and molecular structures of related compounds, see: Tashkhodzhaev et al. (2002 ).

Experimental

Crystal data

C₉H₁₀N₂OS
M_r = 194.25
Monoclinic, P 2₁ /c
a = 8.027 (3) Å
b = 10.706 (5) Å
c = 10.907 (3) Å
β = 97.333 (3)°
V = 929.7 (6) Å³
Z = 4
Cu Kα radiation
μ = 2.77 mm⁻¹
T = 293 K
0.42 × 0.36 × 0.28 mm

Data collection

Oxford Diffraction Xcalibur Ruby diffractometer
Absorption correction: multi-scan (CrysAlis PRO; Oxford Diffraction, 2009 $[Oxford Diffraction (2009). CrysAlis PRO. Oxford Diffraction Ltd, Yarnton, England.]$ ) T_min = 0.324, T_max = 1.000
2983 measured reflections
1588 independent reflections
1208 reflections with I > 2σ(I)
R_int = 0.029

Refinement

R[F² > 2σ(F²)] = 0.050
wR(F²) = 0.151
S = 1.05
1588 reflections
122 parameters
H-atom parameters constrained
Δρ_max = 0.27 e Å⁻³
Δρ_min = −0.22 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
C2—H2⋯O1ⁱ	0.93	2.32	3.250 (4)	173
Symmetry code: (i) $[-x+1, y+{\script{1\over 2}}, -z+{\script{3\over 2}}]$ .

Data collection: CrysAlis PRO (Oxford Diffraction, 2009 $[Oxford Diffraction (2009). CrysAlis PRO. Oxford Diffraction Ltd, Yarnton, England.]$ ); cell refinement: CrysAlis PRO; data reduction: CrysAlis PRO; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: XP in SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXL97.

Supporting information

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536812035416/aa2064sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536812035416/aa2064Isup2.hkl

Supporting information file. DOI: 10.1107/S1600536812035416/aa2064Isup3.cml

checkCIF report

Comment top

The derivatives of thienopyrimidine are of interest because of their interesting pharmacological and biological activities (Litvinov, 2004). The title compound, C₉H₁₀N₂OS, may be used for obtaining bioactive molecules. The asymmetric unit of the title compound consists of a single molecule (Fig.1). The thienopyrimidine ring system (N1/C2/N3/C4/C5/C6/C7/C8/S1) is ideal planar with greatest deviation from mean plane 0.0318 (12) Å for the S1). The crystal packing is stabilized by intermolecular hydrogen bonds (Table 1) and π-π stacking interactions between inversion-related pair of molecules with a centroid-centroid (N1/C2/N3/C4/C5/C6/C7/C8/S1) distance of 3.530 (3) Å.

Related literature top

For the synthesis, properties and biological activity of pyrimidinone derivatives, see: Litvinov (2004); Al-Taisan et al. (2010). For the crystal and molecular structures of related compounds, see: Tashkhodzhaev et al. (2002).

Experimental top

To a suspension of 5,6-trimethylthieno(2,3 - d)pyrimidin-4-one (181 mg, 0.1 mmol) in 50 ml e thanol sodium hydride (24 mg, 1 mmol) was added. The mixture was stirred at room temperature for 30 min. Then a solution of methyl iodide(142 mg, 1 mmol) in ethanol was added drop wise. The solution was stirred at 353–363 K for 4 h, then the solution was evaporated under reduced pressure and the residue was treated by distilled water. The precipitate was filtered and dried. Yield of 84% (174 mg). Crystals suitable for single-crystal X-ray diffraction were obtained by recrystallization from chloroform at room temperature.

Computing details top

Data collection: CrysAlis PRO (Oxford Diffraction, 2009); cell refinement: CrysAlis PRO (Oxford Diffraction, 2009); data reduction: CrysAlis PRO (Oxford Diffraction, 2009); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: XP in SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008).

Figures top

The molecular structure of the title compound, showing 30% probability displacement ellipsoids and the atom numbering scheme.

A packing diagram for title compound. C—H···O hydrogen bonds are shown as dashed lines.

3,5,6-Trimethylthieno[2,3-d]pyrimidin-4(3H)-one top

Crystal data top

C₉H₁₀N₂OS	F(000) = 408
M_r = 194.25	D_x = 1.388 Mg m⁻³
Monoclinic, P2₁/c	Cu Kα radiation, λ = 1.54184 Å
Hall symbol: -P 2ybc	Cell parameters from 185 reflections
a = 8.027 (3) Å	θ = 4.1–43.7°
b = 10.706 (5) Å	µ = 2.77 mm⁻¹
c = 10.907 (3) Å	T = 293 K
β = 97.333 (3)°	Block, colourless
V = 929.7 (6) Å³	0.42 × 0.36 × 0.28 mm
Z = 4

Data collection top

Oxford Diffraction Xcalibur Ruby diffractometer	1588 independent reflections
Radiation source: fine-focus sealed tube	1208 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.029
Detector resolution: 10.2576 pixels mm^-1	θ_max = 67.2°, θ_min = 5.6°
ω scans	h = −8→9
Absorption correction: multi-scan (CrysAlis PRO; Oxford Diffraction, 2009)	k = −12→12
T_min = 0.324, T_max = 1.000	l = −13→11
2983 measured reflections

Refinement top

Refinement on F²	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F² > 2σ(F²)] = 0.050	H-atom parameters constrained
wR(F²) = 0.151	w = 1/[σ²(F_o²) + (0.1022P)² + 0.0132P] where P = (F_o² + 2F_c²)/3
S = 1.05	(Δ/σ)_max < 0.001
1588 reflections	Δρ_max = 0.27 e Å⁻³
122 parameters	Δρ_min = −0.22 e Å⁻³
0 restraints	Extinction correction: SHELXL97 (Sheldrick, 2008), Fc^*=kFc[1+0.001xFc²λ³/sin(2θ)]^-1/4
Primary atom site location: structure-invariant direct methods	Extinction coefficient: 0.0070 (14)

Crystal data top

C₉H₁₀N₂OS	V = 929.7 (6) Å³
M_r = 194.25	Z = 4
Monoclinic, P2₁/c	Cu Kα radiation
a = 8.027 (3) Å	µ = 2.77 mm⁻¹
b = 10.706 (5) Å	T = 293 K
c = 10.907 (3) Å	0.42 × 0.36 × 0.28 mm
β = 97.333 (3)°

Data collection top

Oxford Diffraction Xcalibur Ruby diffractometer	1588 independent reflections
Absorption correction: multi-scan (CrysAlis PRO; Oxford Diffraction, 2009)	1208 reflections with I > 2σ(I)
T_min = 0.324, T_max = 1.000	R_int = 0.029
2983 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.050	0 restraints
wR(F²) = 0.151	H-atom parameters constrained
S = 1.05	Δρ_max = 0.27 e Å⁻³
1588 reflections	Δρ_min = −0.22 e Å⁻³
122 parameters

Special details top

Geometry. All s.u.'s (except the s.u. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell s.u.'s are taken into account individually in the estimation of s.u.'s in distances, angles and torsion angles; correlations between s.u.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell s.u.'s is used for estimating s.u.'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
C1	0.3074 (3)	0.1156 (2)	0.4761 (3)	0.0448 (7)
C2	0.4524 (4)	0.1684 (3)	0.6555 (3)	0.0559 (8)
H2	0.5198	0.2239	0.7052	0.067*
C3	0.3198 (3)	−0.0372 (3)	0.6401 (2)	0.0467 (7)
C4	0.2664 (3)	−0.0020 (2)	0.5153 (2)	0.0396 (6)
C5	0.1683 (3)	−0.0728 (2)	0.4196 (2)	0.0446 (7)
C6	0.1362 (4)	−0.0066 (3)	0.3125 (2)	0.0498 (7)
C7	0.4735 (4)	0.0352 (4)	0.8380 (3)	0.0693 (10)
H7A	0.3808	0.0084	0.8791	0.104*
H7B	0.5195	0.1109	0.8754	0.104*
H7C	0.5584	−0.0285	0.8454	0.104*
C8	0.1125 (4)	−0.2045 (3)	0.4345 (3)	0.0615 (8)
H8A	0.0263	−0.2062	0.4879	0.092*
H8B	0.2062	−0.2539	0.4699	0.092*
H8C	0.0690	−0.2379	0.3551	0.092*
C9	0.0413 (4)	−0.0454 (4)	0.1917 (3)	0.0694 (9)
H9A	−0.0690	−0.0091	0.1831	0.104*
H9B	0.0319	−0.1348	0.1890	0.104*
H9C	0.0998	−0.0173	0.1254	0.104*
N1	0.4025 (3)	0.2028 (2)	0.5443 (2)	0.0537 (6)
N2	0.4153 (3)	0.0576 (2)	0.7075 (2)	0.0505 (6)
O1	0.2922 (3)	−0.13487 (19)	0.69116 (18)	0.0595 (6)
S1	0.22443 (10)	0.14187 (7)	0.32561 (6)	0.0543 (3)

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
C1	0.0458 (16)	0.0418 (14)	0.0482 (15)	0.0049 (11)	0.0116 (12)	−0.0006 (11)
C2	0.0553 (19)	0.0501 (17)	0.062 (2)	0.0007 (13)	0.0055 (14)	−0.0163 (14)
C3	0.0443 (16)	0.0495 (16)	0.0468 (15)	0.0075 (12)	0.0074 (12)	−0.0022 (12)
C4	0.0368 (14)	0.0398 (14)	0.0430 (14)	0.0064 (10)	0.0081 (11)	0.0000 (10)
C5	0.0427 (16)	0.0448 (15)	0.0470 (15)	0.0027 (11)	0.0083 (12)	−0.0010 (11)
C6	0.0476 (17)	0.0553 (17)	0.0458 (15)	0.0063 (13)	0.0036 (12)	−0.0013 (12)
C7	0.073 (2)	0.088 (3)	0.0436 (17)	0.0157 (18)	−0.0037 (15)	−0.0115 (15)
C8	0.067 (2)	0.0505 (17)	0.067 (2)	−0.0105 (14)	0.0080 (16)	−0.0035 (14)
C9	0.072 (2)	0.083 (2)	0.0512 (18)	−0.0023 (18)	−0.0023 (15)	−0.0075 (16)
N1	0.0568 (15)	0.0428 (13)	0.0613 (16)	0.0001 (11)	0.0071 (12)	−0.0060 (11)
N2	0.0519 (14)	0.0564 (15)	0.0419 (13)	0.0091 (11)	0.0006 (10)	−0.0089 (10)
O1	0.0688 (15)	0.0553 (13)	0.0531 (12)	0.0013 (10)	0.0025 (10)	0.0164 (9)
S1	0.0631 (6)	0.0502 (5)	0.0493 (5)	0.0040 (3)	0.0068 (3)	0.0099 (3)

Geometric parameters (Å, º) top

C1—N1	1.365 (4)	C6—C9	1.494 (4)
C1—C4	1.382 (4)	C6—S1	1.739 (3)
C1—S1	1.714 (3)	C7—N2	1.461 (4)
C2—N1	1.282 (4)	C7—H7A	0.9600
C2—N2	1.364 (4)	C7—H7B	0.9600
C2—H2	0.9300	C7—H7C	0.9600
C3—O1	1.218 (3)	C8—H8A	0.9600
C3—N2	1.419 (4)	C8—H8B	0.9600
C3—C4	1.424 (4)	C8—H8C	0.9600
C4—C5	1.441 (3)	C9—H9A	0.9600
C5—C6	1.362 (4)	C9—H9B	0.9600
C5—C8	1.495 (4)	C9—H9C	0.9600

N1—C1—C4	126.3 (3)	N2—C7—H7C	109.5
N1—C1—S1	122.1 (2)	H7A—C7—H7C	109.5
C4—C1—S1	111.6 (2)	H7B—C7—H7C	109.5
N1—C2—N2	125.8 (3)	C5—C8—H8A	109.5
N1—C2—H2	117.1	C5—C8—H8B	109.5
N2—C2—H2	117.1	H8A—C8—H8B	109.5
O1—C3—N2	119.6 (3)	C5—C8—H8C	109.5
O1—C3—C4	127.9 (3)	H8A—C8—H8C	109.5
N2—C3—C4	112.4 (2)	H8B—C8—H8C	109.5
C1—C4—C3	118.9 (2)	C6—C9—H9A	109.5
C1—C4—C5	112.6 (2)	C6—C9—H9B	109.5
C3—C4—C5	128.5 (2)	H9A—C9—H9B	109.5
C6—C5—C4	112.0 (2)	C6—C9—H9C	109.5
C6—C5—C8	123.8 (3)	H9A—C9—H9C	109.5
C4—C5—C8	124.2 (2)	H9B—C9—H9C	109.5
C5—C6—C9	129.1 (3)	C2—N1—C1	113.8 (3)
C5—C6—S1	112.0 (2)	C2—N2—C3	122.6 (2)
C9—C6—S1	118.9 (2)	C2—N2—C7	119.2 (3)
N2—C7—H7A	109.5	C3—N2—C7	118.2 (3)
N2—C7—H7B	109.5	C1—S1—C6	91.90 (13)
H7A—C7—H7B	109.5

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
C2—H2···O1ⁱ	0.93	2.32	3.250 (4)	173

Symmetry code: (i) −x+1, y+1/2, −z+3/2.

Experimental details

Crystal data
Chemical formula	C₉H₁₀N₂OS
M_r	194.25
Crystal system, space group	Monoclinic, P2₁/c
Temperature (K)	293
a, b, c (Å)	8.027 (3), 10.706 (5), 10.907 (3)
β (°)	97.333 (3)
V (Å³)	929.7 (6)
Z	4
Radiation type	Cu Kα
µ (mm⁻¹)	2.77
Crystal size (mm)	0.42 × 0.36 × 0.28

Data collection
Diffractometer	Oxford Diffraction Xcalibur Ruby diffractometer
Absorption correction	Multi-scan (CrysAlis PRO; Oxford Diffraction, 2009)
T_min, T_max	0.324, 1.000
No. of measured, independent and observed [I > 2σ(I)] reflections	2983, 1588, 1208
R_int	0.029
(sin θ/λ)_max (Å⁻¹)	0.598

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.050, 0.151, 1.05
No. of reflections	1588
No. of parameters	122
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.27, −0.22

Computer programs: CrysAlis PRO (Oxford Diffraction, 2009), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), XP in SHELXTL (Sheldrick, 2008).

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
C2—H2···O1ⁱ	0.93	2.32	3.250 (4)	172.9

Symmetry code: (i) −x+1, y+1/2, −z+3/2.

Acknowledgements

We thank the Academy of Sciences of the Republic of Uzbekistan for supporting this study (grants FA–F3–T045 and FA–F3–T047)

References

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