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In the title compound, C17H18N2O3S2, the pyrimidine ring adopts a shallow sofa conformation, with the C atom bearing the axially-oriented thio­phene ring as the flap [deviation = 0.439 (3) Å]. The plane of the thio­phene ring lies almost normal to the pyrimidine ring, making a dihedral angle of 79.36 (19)°. In the crystal, pairs of very weak C—H...O hydrogen bonds link the mol­ecules related by twofold rotation axes, forming R22(18) rings, which are in turn linked by another C—H...O inter­action, forming chains of rings along [010]. In addition, weak C—H...π(thio­phene) inter­actions link the chains into layers parallel to [001] and π–π inter­actions with a centroid–centroid distance of 3.772 (10) Å connect these layers into a three-dimensional network.

Supporting information

cif

Crystallographic Information File (CIF) https://doi.org/10.1107/S2056989015010981/hb7433sup1.cif
Contains datablocks global, I

hkl

Structure factor file (CIF format) https://doi.org/10.1107/S2056989015010981/hb7433Isup2.hkl
Contains datablock I

cml

Chemical Markup Language (CML) file https://doi.org/10.1107/S2056989015010981/hb7433Isup3.cml
Supplementary material

CCDC reference: 1405373

Key indicators

  • Single-crystal X-ray study
  • T = 100 K
  • Mean [sigma](C-C) = 0.006 Å
  • R factor = 0.065
  • wR factor = 0.189
  • Data-to-parameter ratio = 13.7

checkCIF/PLATON results

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Alert level A PLAT222_ALERT_3_A Large Non-Solvent H Uiso(max)/Uiso(min) ... 10.0 Ratio
Author Response: This structure contains ester groups. The thermal parameters for one of the carbon atom 'C11' is very high. This was attempted to be modeled as disorder but the refinement was not successful.

Alert level C PLAT220_ALERT_2_C Large Non-Solvent C Ueq(max)/Ueq(min) Range 3.2 Ratio PLAT340_ALERT_3_C Low Bond Precision on C-C Bonds ............... 0.0062 Ang. PLAT360_ALERT_2_C Short C(sp3)-C(sp3) Bond C10 - C11 ... 1.43 Ang. PLAT480_ALERT_4_C Long H...A H-Bond Reported H1C .. O1 .. 2.64 Ang. PLAT480_ALERT_4_C Long H...A H-Bond Reported H13 .. O2 .. 2.63 Ang. PLAT906_ALERT_3_C Large K value in the Analysis of Variance ...... 8.660 Check PLAT906_ALERT_3_C Large K value in the Analysis of Variance ...... 2.310 Check
Alert level G PLAT005_ALERT_5_G No _iucr_refine_instructions_details in the CIF Please Do ! PLAT066_ALERT_1_G Predicted and Reported Tmin&Tmax Range Identical ? Check PLAT072_ALERT_2_G SHELXL First Parameter in WGHT Unusually Large. 0.11 Report PLAT793_ALERT_4_G The Model has Chirality at C5 (Centro SPGR) R Verify PLAT899_ALERT_4_G SHELXL97 is Deprecated and Succeeded by SHELXL 2014 Note PLAT909_ALERT_3_G Percentage of Observed Data at Theta(Max) still 33 % PLAT910_ALERT_3_G Missing # of FCF Reflection(s) Below Th(Min) ... 1 Report PLAT961_ALERT_5_G Dataset Contains no Negative Intensities ....... Please Check
1 ALERT level A = Most likely a serious problem - resolve or explain 0 ALERT level B = A potentially serious problem, consider carefully 7 ALERT level C = Check. Ensure it is not caused by an omission or oversight 8 ALERT level G = General information/check it is not something unexpected 1 ALERT type 1 CIF construction/syntax error, inconsistent or missing data 3 ALERT type 2 Indicator that the structure model may be wrong or deficient 6 ALERT type 3 Indicator that the structure quality may be low 4 ALERT type 4 Improvement, methodology, query or suggestion 2 ALERT type 5 Informative message, check

Comment top

Pyrimidine derivatives are important class of compounds which display number of pharmacological properties including antiviral, antitumour, antibacterial and antihypertensive effects (Atwal et al., 1991; Kappe et al., 1997). Pyrimidine has been subjected to a large variety of structural modifications in order to synthesize derivatives (Singh et al., 2011) with different biological properties, among which, thiazole ring fused to pyrimidine ring resulting in thiazolopyrimidine is found to be more active (Ozair et al., 2010; Hayam et al., 2010). Herein, we report the crystal structure of the title compound (1). The bond lengths and angles in the title compound are in good agreement with the corresponding bond distances and angles reported in closely related structures (Nagarajaiah et al., 2012; Prasad et al., 2014). The molecular structure of the compound C17H18N2O3S2 is shown in Fig. 1. The thiophenyl ring at chiral carbon C5 is positioned axially and exactly bisects the pyrimidine ring with a dihedral angle of 82.973 (1)°. The thiazine and pyrimidine ring form a dihedral angle of 5.975 (1)°. In the central pyrimidine ring, the chiral carbon atom C6 is displaced by 0.3130 (4) Å and adopts a flattened sofa conformation. The exocyclic ester group at C6 adopts cis orientation with respect to C6=C7 double bond and the carboxyl group (C11/C10/O3/C16) is slightly deviating from the thiozolopyrimidine plane at -87.946 (6)°. The crystal structure is mainly stabilized by a variety of intermolecular C—H···O interactions. C1—H1C···O1 hydrogen bonds link the molecules related by twofold rotation axes, forming R22(18) loops, which are in turn linked by C13—H13···O2 interactions to form chains of rings along [010] (Table.1; Fig. 2). In addition, weak C—H···π (thiophene) interactions of the type C11—H11A···Cg link the chains into layers parallel to [001] and ππ interactions between inversion-related thiazolopyrimidine rings with a centroid—centroid distance of 3.772 (10) Å connect these layers into a three-dimensional network (Fig. 3).

Related literature top

For the biological activities of fused pyrimidine derivatives, see: Atwal et al. (1991); Kappe et al. (1997); Singh et al. (2011); Ozair et al. (2010); Hayam et al. (2010). For related structures, see: Prasad et al. (2014); Nagarajaiah et al. (2012).

Experimental top

A mixture of 6-methyl-4-thiophen-2-yl-2-thioxo-1,2,3,4-tetrahydro-pyrimidine-5- carboxylic acid ethyl ester (10 mmol) and 3-chloro-2,4-pentanedione (10 mmol) was refluxed in dry ethanol (20 mmol) for 12 h. The excess of solvent was distilled off and the solid hydrochloride salt that separated was collected by filtration, suspended in water and neutralized by aqueous sodium carbonate solution to yield the free base. The solution was filtered, the solid washed with water, dried and recrystallized from ethyl acetate to give the title compound (74% yield, mp 385 K). The compound was recrystallized by slow evaporation from 1:1 mixture of ethyl acetate and methanol, yielding pale- yellow blocks of the title compound.

Refinement top

The H atoms were placed at calculated positions in the riding-model approximation with C—H = 0.95 Å, 1.00 Å and 0.96 Å for aromatic, methyne and methyl H-atoms respectively, with Uiso(H) = 1.5Ueq(C) for methyl H atoms and Uiso(H) = 1.2Ueq(C) for other hydrogen atoms.

Computing details top

Data collection: SMART (Bruker,1998); cell refinement: SAINT-Plus (Bruker,1998); data reduction: SAINT-Plus (Bruker,1998); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 for Windows (Farrugia, 2012) and CAMERON (Watkin et al., 1996); software used to prepare material for publication: WinGX (Farrugia, 2012).

Figures top
[Figure 1] Fig. 1. The molecular structure of the title compound with displacement ellipsoids drawn at the 50% probability level.
[Figure 2] Fig. 2. Unit-cell packing of the title compound showing C—H···O interactions as dotted lines. H atoms not involved in hydrogen bonding have been excluded.
[Figure 3] Fig. 3. Unit-cell packing depicting the C—H···π and ππ interactions with dotted lines.
Ethyl 2-acetyl-3,7-dimethyl-5-(thiophen-2-yl)-5H-thiazolo[3,2-a]pyrimidine-6-carboxylate top
Crystal data top
C17H18N2O3S2F(000) = 760
Mr = 362.45Dx = 1.397 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 3038 reflections
a = 7.8835 (10) Åθ = 2.6–25.0°
b = 14.4041 (19) ŵ = 0.33 mm1
c = 15.231 (2) ÅT = 100 K
β = 94.940 (4)°Block, yellow
V = 1723.2 (4) Å30.18 × 0.16 × 0.16 mm
Z = 4
Data collection top
Bruker SMART APEX CCD
diffractometer
3038 independent reflections
Radiation source: fine-focus sealed tube1984 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.046
ω scansθmax = 25.0°, θmin = 2.6°
Absorption correction: multi-scan
(SADABS; Bruker, 1998)
h = 99
Tmin = 0.944, Tmax = 0.950k = 1717
12021 measured reflectionsl = 1718
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)] = 0.065Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.189H-atom parameters constrained
S = 1.00 w = 1/[σ2(Fo2) + (0.1059P)2 + 1.4984P]
where P = (Fo2 + 2Fc2)/3
3038 reflections(Δ/σ)max < 0.001
221 parametersΔρmax = 0.51 e Å3
0 restraintsΔρmin = 0.28 e Å3
Crystal data top
C17H18N2O3S2V = 1723.2 (4) Å3
Mr = 362.45Z = 4
Monoclinic, P21/cMo Kα radiation
a = 7.8835 (10) ŵ = 0.33 mm1
b = 14.4041 (19) ÅT = 100 K
c = 15.231 (2) Å0.18 × 0.16 × 0.16 mm
β = 94.940 (4)°
Data collection top
Bruker SMART APEX CCD
diffractometer
3038 independent reflections
Absorption correction: multi-scan
(SADABS; Bruker, 1998)
1984 reflections with I > 2σ(I)
Tmin = 0.944, Tmax = 0.950Rint = 0.046
12021 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0650 restraints
wR(F2) = 0.189H-atom parameters constrained
S = 1.00Δρmax = 0.51 e Å3
3038 reflectionsΔρmin = 0.28 e Å3
221 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 > 2σ(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
S10.41155 (14)0.67664 (8)0.10428 (8)0.0478 (4)
S20.86975 (15)0.38590 (8)0.30180 (7)0.0514 (4)
N10.6122 (4)0.5389 (2)0.11268 (19)0.0343 (8)
C60.5337 (5)0.3792 (3)0.1355 (2)0.0384 (10)
O10.8379 (4)0.7993 (2)0.0552 (2)0.0610 (9)
C90.4445 (5)0.5583 (3)0.1190 (2)0.0378 (10)
N20.3249 (4)0.5002 (3)0.1340 (2)0.0472 (9)
C30.7148 (5)0.6131 (3)0.0965 (2)0.0345 (9)
C130.6889 (5)0.5373 (3)0.2994 (2)0.0378 (10)
H130.61440.58690.28150.045*
O20.4904 (5)0.2161 (2)0.1141 (3)0.0753 (11)
C20.6282 (5)0.6938 (3)0.0902 (3)0.0386 (10)
C160.5843 (6)0.2820 (3)0.1255 (3)0.0482 (11)
C170.9012 (5)0.5964 (3)0.0884 (3)0.0521 (12)
H17A0.91510.54200.05111.000*
H17B0.95920.58550.14701.000*
H17C0.95080.65090.06181.000*
C120.7368 (5)0.4638 (3)0.2456 (2)0.0359 (9)
C70.3696 (6)0.4072 (3)0.1363 (3)0.0434 (10)
C50.6754 (5)0.4494 (3)0.1488 (2)0.0359 (9)
H50.77340.42860.11620.043*
C100.8235 (8)0.1808 (3)0.1127 (4)0.0683 (15)
H10A0.74310.14480.07240.082*
H10B0.93190.18660.08490.082*
C140.7725 (6)0.5240 (3)0.3865 (3)0.0499 (11)
H140.76020.56620.43350.060*
C40.6955 (6)0.7881 (3)0.0792 (3)0.0447 (11)
C10.2188 (6)0.3437 (3)0.1387 (3)0.0592 (13)
H1A0.11980.37960.15381.000*
H1B0.24440.29540.18321.000*
H1C0.19400.31490.08081.000*
C80.5863 (7)0.8697 (3)0.0997 (4)0.0686 (15)
H8A0.54070.85990.15691.000*
H8B0.49200.87580.05381.000*
H8C0.65520.92640.10191.000*
C150.8682 (6)0.4481 (3)0.3959 (3)0.0484 (11)
H150.92930.43060.44990.058*
O30.7530 (4)0.2735 (2)0.1262 (2)0.0560 (8)
C110.8530 (10)0.1323 (5)0.1948 (4)0.110 (3)
H11A0.89400.06940.18390.166*
H11B0.74660.12860.22350.166*
H11C0.93870.16560.23320.166*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
S10.0422 (7)0.0400 (7)0.0619 (7)0.0079 (5)0.0093 (5)0.0074 (5)
S20.0591 (8)0.0471 (7)0.0467 (7)0.0086 (5)0.0026 (5)0.0011 (5)
N10.0349 (19)0.0318 (18)0.0364 (18)0.0033 (15)0.0036 (14)0.0039 (14)
C60.043 (2)0.038 (2)0.033 (2)0.0054 (19)0.0006 (17)0.0010 (17)
O10.061 (2)0.047 (2)0.075 (2)0.0107 (16)0.0111 (18)0.0040 (16)
C90.037 (2)0.039 (2)0.037 (2)0.0067 (19)0.0031 (17)0.0017 (18)
N20.038 (2)0.048 (2)0.057 (2)0.0058 (18)0.0122 (17)0.0046 (18)
C30.038 (2)0.036 (2)0.029 (2)0.0036 (19)0.0006 (16)0.0010 (16)
C130.048 (2)0.035 (2)0.030 (2)0.0105 (18)0.0020 (18)0.0038 (17)
O20.077 (3)0.041 (2)0.106 (3)0.0134 (19)0.006 (2)0.0007 (19)
C20.041 (2)0.036 (2)0.039 (2)0.0001 (18)0.0054 (18)0.0045 (18)
C160.062 (3)0.036 (2)0.045 (3)0.009 (2)0.005 (2)0.0013 (19)
C170.036 (2)0.051 (3)0.070 (3)0.001 (2)0.008 (2)0.008 (2)
C120.036 (2)0.031 (2)0.040 (2)0.0005 (17)0.0011 (17)0.0016 (17)
C70.051 (3)0.039 (3)0.041 (2)0.006 (2)0.0069 (19)0.0014 (18)
C50.042 (2)0.032 (2)0.034 (2)0.0055 (18)0.0034 (17)0.0009 (16)
C100.085 (4)0.042 (3)0.078 (4)0.013 (3)0.008 (3)0.014 (3)
C140.057 (3)0.051 (3)0.042 (2)0.000 (2)0.004 (2)0.009 (2)
C40.055 (3)0.040 (2)0.039 (2)0.004 (2)0.003 (2)0.0020 (19)
C10.051 (3)0.057 (3)0.070 (3)0.022 (2)0.013 (2)0.001 (2)
C80.087 (4)0.038 (3)0.083 (4)0.008 (3)0.019 (3)0.005 (2)
C150.052 (3)0.054 (3)0.038 (2)0.001 (2)0.0011 (19)0.003 (2)
O30.060 (2)0.0390 (18)0.067 (2)0.0087 (15)0.0048 (16)0.0080 (15)
C110.157 (7)0.091 (5)0.086 (5)0.063 (5)0.027 (4)0.017 (4)
Geometric parameters (Å, º) top
S1—C91.736 (4)C17—H17B0.9902
S1—C21.757 (4)C17—H17C0.9902
S2—C151.692 (4)C12—C51.525 (5)
S2—C121.714 (4)C7—C11.502 (6)
N1—C91.363 (5)C5—H51.0000
N1—C31.375 (5)C10—C111.433 (7)
N1—C51.471 (5)C10—O31.467 (5)
C6—C71.355 (6)C10—H10A0.9900
C6—C161.468 (6)C10—H10B0.9900
C6—C51.508 (6)C14—C151.328 (6)
O1—C41.221 (5)C14—H140.9500
C9—N21.296 (5)C4—C81.506 (6)
N2—C71.385 (5)C1—H1A0.9828
C3—C21.348 (5)C1—H1B0.9828
C3—C171.505 (6)C1—H1C0.9828
C13—C121.410 (5)C8—H8A0.9913
C13—C141.442 (6)C8—H8B0.9913
C13—H130.9500C8—H8C0.9913
O2—C161.207 (5)C15—H150.9500
C2—C41.472 (6)C11—H11A0.9800
C16—O31.335 (5)C11—H11B0.9800
C17—H17A0.9902C11—H11C0.9800
C9—S1—C291.04 (19)C6—C5—C12113.0 (3)
C15—S2—C1291.6 (2)N1—C5—H5109.1
C9—N1—C3116.3 (3)C6—C5—H5109.1
C9—N1—C5116.9 (3)C12—C5—H5109.1
C3—N1—C5124.2 (3)C11—C10—O3110.9 (4)
C7—C6—C16123.5 (4)C11—C10—H10A109.5
C7—C6—C5119.8 (4)O3—C10—H10A109.5
C16—C6—C5116.7 (4)C11—C10—H10B109.4
N2—C9—N1127.2 (4)O3—C10—H10B109.5
N2—C9—S1123.7 (3)H10A—C10—H10B108.0
N1—C9—S1109.1 (3)C15—C14—C13114.8 (4)
C9—N2—C7116.2 (4)C15—C14—H14122.6
C2—C3—N1112.4 (3)C13—C14—H14122.6
C2—C3—C17128.6 (4)O1—C4—C2120.4 (4)
N1—C3—C17119.0 (3)O1—C4—C8121.0 (4)
C12—C13—C14108.1 (4)C2—C4—C8118.6 (4)
C12—C13—H13126.0C7—C1—H1A109.8
C14—C13—H13125.9C7—C1—H1B109.7
C3—C2—C4128.2 (4)H1A—C1—H1B109.2
C3—C2—S1111.2 (3)C7—C1—H1C109.8
C4—C2—S1120.5 (3)H1A—C1—H1C109.2
O2—C16—O3121.8 (4)H1B—C1—H1C109.2
O2—C16—C6126.6 (5)C4—C8—H8A110.6
O3—C16—C6111.5 (4)C4—C8—H8B110.6
C3—C17—H17A110.5H8A—C8—H8B108.3
C3—C17—H17B110.5C4—C8—H8C110.6
H17A—C17—H17B108.4H8A—C8—H8C108.3
C3—C17—H17C110.5H8B—C8—H8C108.3
H17A—C17—H17C108.4C14—C15—S2112.9 (3)
H17B—C17—H17C108.4C14—C15—H15123.5
C13—C12—C5125.8 (3)S2—C15—H15123.5
C13—C12—S2112.6 (3)C16—O3—C10118.1 (4)
C5—C12—S2121.6 (3)C10—C11—H11A109.5
C6—C7—N2121.9 (4)C10—C11—H11B109.5
C6—C7—C1125.3 (4)H11A—C11—H11B109.5
N2—C7—C1112.8 (4)C10—C11—H11C109.5
N1—C5—C6108.3 (3)H11A—C11—H11C109.5
N1—C5—C12108.2 (3)H11B—C11—H11C109.5
C3—N1—C9—N2179.9 (4)C5—C6—C7—N211.1 (6)
C5—N1—C9—N217.4 (6)C16—C6—C7—C18.2 (6)
C3—N1—C9—S10.2 (4)C5—C6—C7—C1169.4 (4)
C5—N1—C9—S1162.2 (2)C9—N2—C7—C69.1 (6)
C2—S1—C9—N2179.7 (4)C9—N2—C7—C1170.4 (4)
C2—S1—C9—N10.0 (3)C9—N1—C5—C633.4 (4)
N1—C9—N2—C76.0 (6)C3—N1—C5—C6165.7 (3)
S1—C9—N2—C7174.4 (3)C9—N1—C5—C1289.4 (4)
C9—N1—C3—C20.4 (5)C3—N1—C5—C1271.5 (4)
C5—N1—C3—C2160.6 (3)C7—C6—C5—N131.2 (5)
C9—N1—C3—C17179.8 (3)C16—C6—C5—N1151.0 (3)
C5—N1—C3—C1719.2 (5)C7—C6—C5—C1288.6 (4)
N1—C3—C2—C4175.6 (4)C16—C6—C5—C1289.2 (4)
C17—C3—C2—C44.2 (7)C13—C12—C5—N120.6 (5)
N1—C3—C2—S10.4 (4)S2—C12—C5—N1162.0 (3)
C17—C3—C2—S1179.8 (3)C13—C12—C5—C699.3 (4)
C9—S1—C2—C30.2 (3)S2—C12—C5—C678.1 (4)
C9—S1—C2—C4176.1 (3)C12—C13—C14—C151.3 (5)
C7—C6—C16—O22.5 (7)C3—C2—C4—O116.3 (7)
C5—C6—C16—O2179.8 (4)S1—C2—C4—O1168.1 (3)
C7—C6—C16—O3179.4 (4)C3—C2—C4—C8162.5 (4)
C5—C6—C16—O32.8 (5)S1—C2—C4—C813.1 (5)
C14—C13—C12—C5178.8 (4)C13—C14—C15—S20.7 (5)
C14—C13—C12—S21.3 (4)C12—S2—C15—C140.1 (4)
C15—S2—C12—C130.8 (3)O2—C16—O3—C100.2 (6)
C15—S2—C12—C5178.5 (3)C6—C16—O3—C10177.3 (3)
C16—C6—C7—N2171.2 (4)C11—C10—O3—C1687.9 (6)
Hydrogen-bond geometry (Å, º) top
Cg1 is the centroid of the S2/C12–C15 ring.
D—H···AD—HH···AD···AD—H···A
C1—H1C···O1i0.982.643.598 (6)166
C13—H13···O2ii0.952.633.269 (8)125
C11—H11A···Cg1iii0.982.893.693 (2)139
Symmetry codes: (i) x+1, y+1, z; (ii) x+1, y+1/2, z+1/2; (iii) x, y+1, z.
Hydrogen-bond geometry (Å, º) top
Cg1 is the centroid of the S2/C12–C15 ring.
D—H···AD—HH···AD···AD—H···A
C1—H1C···O1i0.982.643.598 (6)166
C13—H13···O2ii0.952.633.269 (8)125
C11—H11A···Cg1iii0.982.893.693 (2)139
Symmetry codes: (i) x+1, y+1, z; (ii) x+1, y+1/2, z+1/2; (iii) x, y+1, z.
 

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