5-[(4,6-Dimethylpyrimidin-2-ylsulfanyl)methyl]-3-(morpholinomethyl)-1,3,4-oxadiazole-2(3H)-thione
Supporting information
Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536807032448/wn2165sup1.cif | |
Structure factor file (CIF format) https://doi.org/10.1107/S1600536807032448/wn2165Isup2.hkl |
CCDC reference: 657708
Key indicators
- Single-crystal X-ray study
- T = 160 K
- Mean (C-C) = 0.004 Å
- R factor = 0.057
- wR factor = 0.177
- Data-to-parameter ratio = 24.7
checkCIF/PLATON results
No syntax errors found
Alert level B DIFMX01_ALERT_2_B The maximum difference density is > 0.1*ZMAX*1.00 _refine_diff_density_max given = 1.981 Test value = 1.600 PLAT094_ALERT_2_B Ratio of Maximum / Minimum Residual Density .... 4.76 PLAT097_ALERT_2_B Maximum (Positive) Residual Density ............ 1.98 e/A
Alert level C DIFMX02_ALERT_1_C The maximum difference density is > 0.1*ZMAX*0.75 The relevant atom site should be identified. PLAT062_ALERT_4_C Rescale T(min) & T(max) by ..................... 0.97 PLAT154_ALERT_1_C The su's on the Cell Angles are Equal (x 10000) 200 Deg. PLAT432_ALERT_2_C Short Inter X...Y Contact O21 .. C2 .. 2.94 Ang. PLAT601_ALERT_2_C Structure Contains Solvent Accessible VOIDS of . 82.00 A 3
0 ALERT level A = In general: serious problem 3 ALERT level B = Potentially serious problem 5 ALERT level C = Check and explain 0 ALERT level G = General alerts; check 2 ALERT type 1 CIF construction/syntax error, inconsistent or missing data 5 ALERT type 2 Indicator that the structure model may be wrong or deficient 0 ALERT type 3 Indicator that the structure quality may be low 1 ALERT type 4 Improvement, methodology, query or suggestion 0 ALERT type 5 Informative message, check
For related literature, see: Wichmann et al. (1999); El-Bendary et al. (1998); Kirpal (1999); Tsuji & Ishikawa (1994); Mohan et al. (1989); Baraldi et al. (1996, 2003); Sanjay et al. (2006); Thiruvalluvar, Subramanyam, Kalluraya & Lingappa (2007); Thiruvalluvar, Subramanyam, Lingappa & Kalluraya (2007).
A solution of 5-(4,6-dimethyl-2-thiomethyl pyrimidyl)-1,3,4-oxadiazole-2-thione (2.56 g, 0.01 mol) in absolute ethanol (20 ml) was placed in a round-bottomed flask and treated with formaldehyde (40%, 3.0 ml). Later, morpholine (0.87 g, 0.01 mol) in ethanol (10 ml) was added with stirring and the reaction mixture was stirred overnight. The precipitated yellow solid was collected by filtration, dried and recrystallized from chloroform to give white crystals (1.64 g, 46%).
H atoms were positioned geometrically and allowed to ride on their parent atoms, with C—H = 0.95, 0.98 and 0.99 Å for Csp2, methyl and methylene, respectively. Uiso(H) = xUeq(C), where x = 1.5 for methyl and 1.2 for all other H atoms. The maximum residual electron-density peak is located 2.79 Å from atom H23B.
A literature survey shows that large numbers of simple, N-bridged, nitrogen- and sulfur-containing heterocyclic compounds containing the pyrimidine unit have diverse biological activities (Wichmann et al., 1999; El-Bendary et al., 1998; Kirpal, 1999; Tsuji & Ishikawa, 1994). In the light of this significant importance of pyrimidine compounds, and as a continuation of our work on the study of pyrimidine derivatives (Thiruvalluvaret al., 2007a,b), an X-ray crystallographic structure determination of the title compound was undertaken and the results are presented here.
In the title compound, Fig.1, the pyrimidine ring makes a dihedral angle of 82.8 (1)° with the oxadiazole ring. The morpholine ring adopts a chair conformation. There is a short intermolecular contact between O21 and C2 [2.938 (3) Å; -x, -y, -z + 1]. The molecules are linked by C—H···S hydrogen bonds (Fig. 2); an intramolecular C—H···N hydrogen bond is also present.
For related literature, see: Wichmann et al. (1999); El-Bendary et al. (1998); Kirpal (1999); Tsuji & Ishikawa (1994); Mohan et al. (1989); Baraldi et al. (1996, 2003); Sanjay et al. (2006); Thiruvalluvar, Subramanyam, Kalluraya & Lingappa (2007); Thiruvalluvar, Subramanyam, Lingappa & Kalluraya (2007).
Data collection: COLLECT (Nonius, 2000); cell refinement: DENZO-SMN (Otwinowski & Minor, 1997); data reduction: DENZO-SMN and SCALEPACK (Otwinowski & Minor, 1997); program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: ORTEP-3 (Farrugia, 1997); software used to prepare material for publication: PLATON (Spek, 2003).
C14H19N5O2S2 | Z = 2 |
Mr = 353.48 | F(000) = 372 |
Triclinic, P1 | Dx = 1.311 Mg m−3 |
Hall symbol: -P 1 | Melting point: 378(1) K |
a = 7.1250 (3) Å | Mo Kα radiation, λ = 0.71073 Å |
b = 10.6735 (3) Å | Cell parameters from 32939 reflections |
c = 12.3740 (5) Å | θ = 2.0–30.0° |
α = 93.607 (2)° | µ = 0.31 mm−1 |
β = 90.561 (2)° | T = 160 K |
γ = 107.474 (2)° | Block, light_brown |
V = 895.42 (6) Å3 | 0.28 × 0.23 × 0.20 mm |
Nonius KappaCCD area-detector diffractometer | 5188 independent reflections |
Radiation source: Nonius FR590 sealed tube generator | 3963 reflections with I > 2σ(I) |
Horizontally mounted graphite crystal monochromator | Rint = 0.062 |
Detector resolution: 9 pixels mm-1 | θmax = 30.0°, θmin = 2.0° |
φ and ω scans with κ offsets | h = −10→10 |
Absorption correction: multi-scan (Blessing, 1995) | k = −15→15 |
Tmin = 0.892, Tmax = 0.964 | l = −17→17 |
25642 measured reflections |
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)] = 0.057 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.177 | H-atom parameters constrained |
S = 1.06 | w = 1/[σ2(Fo2) + (0.0975P)2 + 0.7899P] where P = (Fo2 + 2Fc2)/3 |
5188 reflections | (Δ/σ)max < 0.001 |
210 parameters | Δρmax = 1.98 e Å−3 |
0 restraints | Δρmin = −0.42 e Å−3 |
C14H19N5O2S2 | γ = 107.474 (2)° |
Mr = 353.48 | V = 895.42 (6) Å3 |
Triclinic, P1 | Z = 2 |
a = 7.1250 (3) Å | Mo Kα radiation |
b = 10.6735 (3) Å | µ = 0.31 mm−1 |
c = 12.3740 (5) Å | T = 160 K |
α = 93.607 (2)° | 0.28 × 0.23 × 0.20 mm |
β = 90.561 (2)° |
Nonius KappaCCD area-detector diffractometer | 5188 independent reflections |
Absorption correction: multi-scan (Blessing, 1995) | 3963 reflections with I > 2σ(I) |
Tmin = 0.892, Tmax = 0.964 | Rint = 0.062 |
25642 measured reflections |
R[F2 > 2σ(F2)] = 0.057 | 0 restraints |
wR(F2) = 0.177 | H-atom parameters constrained |
S = 1.06 | Δρmax = 1.98 e Å−3 |
5188 reflections | Δρmin = −0.42 e Å−3 |
210 parameters |
Experimental. Solvent used: Chloroform Cooling Device: Oxford Cryosystems Cryostream 700 Crystal mount: glued on a glass fibre Mosaicity (°.): 1.041 (2) Frames collected: 408 Seconds exposure per frame: 44 Degrees rotation per frame: 2.0 Crystal-Detector distance (mm): 32.0 |
Geometry. Bond distances, angles etc. have been calculated using the rounded fractional coordinates. All su's are estimated from the variances of the (full) variance-covariance matrix. The cell e.s.d.'s are taken into account in the estimation of distances, angles and torsion angles |
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. |
x | y | z | Uiso*/Ueq | ||
S5 | 0.62058 (8) | 0.31119 (6) | 0.52324 (5) | 0.02696 (16) | |
S21 | 0.20019 (9) | 0.59892 (5) | 0.76795 (4) | 0.02255 (15) | |
O1 | 0.3493 (2) | 0.38961 (15) | 0.63170 (13) | 0.0208 (3) | |
O21 | −0.0632 (3) | −0.12209 (17) | 0.34104 (17) | 0.0383 (5) | |
N3 | 0.1046 (3) | 0.36310 (18) | 0.51156 (15) | 0.0197 (4) | |
N4 | 0.2574 (3) | 0.32370 (17) | 0.46596 (14) | 0.0186 (4) | |
N11 | 0.3236 (3) | 0.65029 (19) | 0.96765 (15) | 0.0222 (4) | |
N13 | 0.1632 (3) | 0.42186 (19) | 0.91862 (15) | 0.0229 (4) | |
N24 | 0.1471 (3) | 0.14660 (18) | 0.32052 (15) | 0.0222 (4) | |
C2 | 0.1660 (3) | 0.3999 (2) | 0.60967 (17) | 0.0190 (4) | |
C4 | 0.2486 (3) | 0.2826 (2) | 0.34962 (17) | 0.0216 (4) | |
H4A | 0.1837 | 0.3370 | 0.3103 | 0.026* | |
H4B | 0.3849 | 0.3022 | 0.3241 | 0.026* | |
C5 | 0.4063 (3) | 0.3393 (2) | 0.53748 (18) | 0.0197 (4) | |
C12 | 0.2297 (3) | 0.5477 (2) | 0.89887 (18) | 0.0201 (4) | |
C14 | 0.1957 (3) | 0.3923 (2) | 1.02001 (19) | 0.0249 (5) | |
C15 | 0.2942 (4) | 0.4908 (3) | 1.09725 (19) | 0.0264 (5) | |
H15 | 0.3198 | 0.4700 | 1.1683 | 0.032* | |
C16 | 0.3544 (3) | 0.6198 (2) | 1.06892 (19) | 0.0248 (5) | |
C21 | 0.0579 (3) | 0.4458 (2) | 0.69701 (19) | 0.0240 (5) | |
H21A | 0.0182 | 0.3772 | 0.7497 | 0.029* | |
H21B | −0.0634 | 0.4576 | 0.6656 | 0.029* | |
C22 | 0.1393 (5) | −0.0825 (3) | 0.3129 (3) | 0.0404 (7) | |
H22A | 0.1482 | −0.0860 | 0.2330 | 0.048* | |
H22B | 0.2040 | −0.1448 | 0.3405 | 0.048* | |
C23 | 0.2460 (4) | 0.0553 (2) | 0.3594 (2) | 0.0291 (5) | |
H23A | 0.2458 | 0.0582 | 0.4395 | 0.035* | |
H23B | 0.3845 | 0.0812 | 0.3367 | 0.035* | |
C25 | −0.0601 (4) | 0.1057 (2) | 0.3506 (2) | 0.0279 (5) | |
H25A | −0.1274 | 0.1662 | 0.3224 | 0.033* | |
H25B | −0.0688 | 0.1093 | 0.4305 | 0.033* | |
C26 | −0.1592 (4) | −0.0334 (2) | 0.3035 (2) | 0.0363 (6) | |
H26A | −0.2986 | −0.0615 | 0.3245 | 0.044* | |
H26B | −0.1564 | −0.0354 | 0.2235 | 0.044* | |
C41 | 0.1210 (5) | 0.2502 (3) | 1.0433 (2) | 0.0370 (6) | |
H41A | −0.0183 | 0.2282 | 1.0612 | 0.056* | |
H41B | 0.1967 | 0.2341 | 1.1046 | 0.056* | |
H41C | 0.1356 | 0.1953 | 0.9794 | 0.056* | |
C61 | 0.4595 (4) | 0.7317 (3) | 1.1477 (2) | 0.0331 (6) | |
H61A | 0.5980 | 0.7349 | 1.1552 | 0.050* | |
H61B | 0.3981 | 0.7189 | 1.2183 | 0.050* | |
H61C | 0.4512 | 0.8146 | 1.1213 | 0.050* |
U11 | U22 | U33 | U12 | U13 | U23 | |
S5 | 0.0179 (3) | 0.0328 (3) | 0.0311 (3) | 0.0095 (2) | −0.0032 (2) | 0.0001 (2) |
S21 | 0.0281 (3) | 0.0208 (3) | 0.0185 (3) | 0.0072 (2) | −0.0025 (2) | 0.0004 (2) |
O1 | 0.0184 (7) | 0.0226 (8) | 0.0208 (7) | 0.0057 (6) | −0.0044 (6) | −0.0001 (6) |
O21 | 0.0448 (12) | 0.0190 (8) | 0.0464 (12) | 0.0026 (8) | −0.0080 (9) | 0.0037 (8) |
N3 | 0.0181 (9) | 0.0188 (8) | 0.0221 (9) | 0.0058 (7) | −0.0028 (7) | −0.0006 (7) |
N4 | 0.0172 (8) | 0.0188 (8) | 0.0190 (8) | 0.0049 (7) | −0.0022 (7) | −0.0005 (7) |
N11 | 0.0217 (9) | 0.0246 (9) | 0.0206 (9) | 0.0079 (7) | −0.0019 (7) | −0.0015 (7) |
N13 | 0.0237 (9) | 0.0229 (9) | 0.0230 (9) | 0.0079 (8) | 0.0014 (7) | 0.0025 (7) |
N24 | 0.0278 (10) | 0.0179 (9) | 0.0186 (9) | 0.0040 (7) | −0.0031 (7) | 0.0004 (7) |
C2 | 0.0171 (9) | 0.0181 (9) | 0.0206 (10) | 0.0036 (8) | −0.0042 (7) | 0.0016 (8) |
C4 | 0.0261 (11) | 0.0197 (10) | 0.0168 (10) | 0.0034 (8) | −0.0007 (8) | 0.0032 (8) |
C5 | 0.0189 (10) | 0.0161 (9) | 0.0220 (10) | 0.0020 (7) | −0.0031 (8) | 0.0021 (8) |
C12 | 0.0172 (10) | 0.0226 (10) | 0.0214 (10) | 0.0079 (8) | 0.0001 (8) | 0.0002 (8) |
C14 | 0.0248 (11) | 0.0284 (11) | 0.0248 (11) | 0.0122 (9) | 0.0051 (9) | 0.0048 (9) |
C15 | 0.0274 (12) | 0.0357 (13) | 0.0186 (10) | 0.0131 (10) | 0.0014 (8) | 0.0037 (9) |
C16 | 0.0221 (11) | 0.0312 (12) | 0.0221 (11) | 0.0103 (9) | −0.0010 (8) | −0.0029 (9) |
C21 | 0.0202 (10) | 0.0269 (11) | 0.0230 (11) | 0.0052 (9) | −0.0024 (8) | −0.0031 (9) |
C22 | 0.0482 (17) | 0.0235 (12) | 0.0502 (17) | 0.0136 (12) | −0.0034 (13) | −0.0040 (11) |
C23 | 0.0299 (12) | 0.0226 (11) | 0.0357 (13) | 0.0094 (9) | −0.0021 (10) | 0.0011 (9) |
C25 | 0.0254 (12) | 0.0212 (11) | 0.0337 (13) | 0.0024 (9) | −0.0076 (9) | 0.0010 (9) |
C26 | 0.0359 (14) | 0.0227 (12) | 0.0433 (15) | −0.0009 (10) | −0.0145 (12) | 0.0013 (10) |
C41 | 0.0491 (17) | 0.0289 (13) | 0.0345 (14) | 0.0125 (12) | 0.0068 (12) | 0.0091 (11) |
C61 | 0.0383 (14) | 0.0373 (14) | 0.0218 (12) | 0.0106 (11) | −0.0063 (10) | −0.0071 (10) |
S5—C5 | 1.651 (2) | C16—C61 | 1.497 (4) |
S21—C12 | 1.772 (2) | C22—C23 | 1.512 (4) |
S21—C21 | 1.810 (2) | C25—C26 | 1.515 (4) |
O1—C2 | 1.369 (3) | C4—H4A | 0.9900 |
O1—C5 | 1.369 (3) | C4—H4B | 0.9900 |
O21—C22 | 1.430 (4) | C15—H15 | 0.9500 |
O21—C26 | 1.421 (4) | C21—H21A | 0.9900 |
N3—N4 | 1.392 (3) | C21—H21B | 0.9900 |
N3—C2 | 1.283 (3) | C22—H22A | 0.9900 |
N4—C4 | 1.473 (3) | C22—H22B | 0.9900 |
N4—C5 | 1.339 (3) | C23—H23A | 0.9900 |
N11—C12 | 1.343 (3) | C23—H23B | 0.9900 |
N11—C16 | 1.347 (3) | C25—H25A | 0.9900 |
N13—C12 | 1.323 (3) | C25—H25B | 0.9900 |
N13—C14 | 1.347 (3) | C26—H26A | 0.9900 |
N24—C4 | 1.435 (3) | C26—H26B | 0.9900 |
N24—C23 | 1.464 (3) | C41—H41A | 0.9800 |
N24—C25 | 1.467 (4) | C41—H41B | 0.9800 |
C2—C21 | 1.476 (3) | C41—H41C | 0.9800 |
C14—C15 | 1.389 (4) | C61—H61A | 0.9800 |
C14—C41 | 1.497 (4) | C61—H61B | 0.9800 |
C15—C16 | 1.382 (4) | C61—H61C | 0.9800 |
S5···N3i | 3.331 (2) | C23···C5 | 3.519 (3) |
S5···C21i | 3.632 (2) | C25···N3 | 3.197 (3) |
S5···C23 | 3.676 (2) | C26···C61x | 3.547 (4) |
S5···C2ii | 3.521 (2) | C61···C26xi | 3.547 (4) |
S5···N3ii | 3.496 (2) | C4···H15ix | 3.0400 |
S21···O1 | 3.1542 (16) | C4···H41Bix | 3.0400 |
S5···H21Bi | 2.8400 | C5···H23A | 3.0400 |
S5···H4B | 2.9500 | C14···H61Aviii | 3.1000 |
S5···H22Biii | 3.0400 | C22···H21Av | 3.0500 |
S21···H4Aiv | 3.1700 | C26···H61Ax | 3.0500 |
S21···H4Bii | 3.0800 | H4A···H15ix | 2.3600 |
S21···H25Aiv | 2.9900 | H4A···H25A | 2.4200 |
O1···S21 | 3.1542 (16) | H4A···S21iv | 3.1700 |
O1···N4 | 2.155 (2) | H4A···H21Biv | 2.5800 |
O1···O21v | 3.010 (2) | H4B···S5 | 2.9500 |
O21···N24 | 2.838 (3) | H4B···H23B | 2.3700 |
O21···O1v | 3.010 (2) | H4B···S21ii | 3.0800 |
O21···N3v | 3.190 (3) | H15···C4xii | 3.0400 |
O21···C2v | 2.938 (3) | H15···H4Axii | 2.3600 |
O21···C5v | 3.274 (3) | H15···H41B | 2.4800 |
N3···S5vi | 3.331 (2) | H15···H61B | 2.5800 |
N3···O1 | 2.220 (3) | H21A···N13 | 2.2800 |
N3···N24 | 3.281 (3) | H21A···C22v | 3.0500 |
N3···C25 | 3.197 (3) | H21B···S5vi | 2.8400 |
N3···S5ii | 3.496 (2) | H21B···H4Aiv | 2.5800 |
N3···O21v | 3.190 (3) | H22A···H26B | 2.3900 |
N4···O1 | 2.155 (2) | H22B···S5iii | 3.0400 |
N24···O21 | 2.838 (3) | H23A···N4 | 2.8100 |
N24···N3 | 3.281 (3) | H23A···C5 | 3.0400 |
N3···H25B | 2.7400 | H23A···H25B | 2.4600 |
N4···H25B | 2.7400 | H23A···H25Bv | 2.5300 |
N4···H23A | 2.8100 | H23B···H4B | 2.3700 |
N11···H41Avii | 2.8800 | H25A···H4A | 2.4200 |
N13···H61Aviii | 2.8400 | H25A···S21iv | 2.9900 |
N13···H21A | 2.2800 | H25B···N3 | 2.7400 |
N24···H41Bix | 2.8800 | H25B···N4 | 2.7400 |
C2···S5ii | 3.521 (2) | H25B···H23A | 2.4600 |
C2···O21v | 2.938 (3) | H25B···H23Av | 2.5300 |
C5···O21v | 3.274 (3) | H26B···H22A | 2.3900 |
C5···C23 | 3.519 (3) | H41A···N11vii | 2.8800 |
C5···C5ii | 3.476 (3) | H41B···N24xii | 2.8800 |
C12···C15viii | 3.538 (4) | H41B···C4xii | 3.0400 |
C12···C14vii | 3.428 (3) | H41B···H15 | 2.4800 |
C14···C12vii | 3.428 (3) | H41C···H61Aviii | 2.5100 |
C14···C16viii | 3.436 (3) | H61A···C26xi | 3.0500 |
C15···C12viii | 3.538 (4) | H61A···N13viii | 2.8400 |
C16···C14viii | 3.436 (3) | H61A···C14viii | 3.1000 |
C21···S5vi | 3.632 (2) | H61A···H41Cviii | 2.5100 |
C23···S5 | 3.676 (2) | H61B···H15 | 2.5800 |
C12—S21—C21 | 101.70 (10) | C14—C15—H15 | 121.00 |
C2—O1—C5 | 105.80 (17) | C16—C15—H15 | 121.00 |
C22—O21—C26 | 110.5 (2) | S21—C21—H21A | 109.00 |
N4—N3—C2 | 103.32 (19) | S21—C21—H21B | 109.00 |
N3—N4—C4 | 120.00 (18) | C2—C21—H21A | 109.00 |
N3—N4—C5 | 111.76 (17) | C2—C21—H21B | 109.00 |
C4—N4—C5 | 128.0 (2) | H21A—C21—H21B | 108.00 |
C12—N11—C16 | 115.25 (19) | O21—C22—H22A | 109.00 |
C12—N13—C14 | 116.15 (19) | O21—C22—H22B | 109.00 |
C4—N24—C23 | 114.03 (19) | C23—C22—H22A | 109.00 |
C4—N24—C25 | 113.83 (18) | C23—C22—H22B | 109.00 |
C23—N24—C25 | 110.01 (18) | H22A—C22—H22B | 108.00 |
O1—C2—N3 | 113.6 (2) | N24—C23—H23A | 110.00 |
O1—C2—C21 | 119.51 (18) | N24—C23—H23B | 110.00 |
N3—C2—C21 | 126.8 (2) | C22—C23—H23A | 110.00 |
N4—C4—N24 | 115.98 (17) | C22—C23—H23B | 110.00 |
S5—C5—O1 | 123.87 (16) | H23A—C23—H23B | 108.00 |
S5—C5—N4 | 130.65 (18) | N24—C25—H25A | 110.00 |
O1—C5—N4 | 105.47 (18) | N24—C25—H25B | 110.00 |
S21—C12—N11 | 111.36 (15) | C26—C25—H25A | 110.00 |
S21—C12—N13 | 120.50 (17) | C26—C25—H25B | 110.00 |
N11—C12—N13 | 128.1 (2) | H25A—C25—H25B | 108.00 |
N13—C14—C15 | 120.4 (2) | O21—C26—H26A | 109.00 |
N13—C14—C41 | 116.6 (2) | O21—C26—H26B | 109.00 |
C15—C14—C41 | 123.0 (2) | C25—C26—H26A | 109.00 |
C14—C15—C16 | 118.9 (2) | C25—C26—H26B | 109.00 |
N11—C16—C15 | 121.1 (2) | H26A—C26—H26B | 108.00 |
N11—C16—C61 | 116.7 (2) | C14—C41—H41A | 109.00 |
C15—C16—C61 | 122.1 (2) | C14—C41—H41B | 109.00 |
S21—C21—C2 | 113.27 (15) | C14—C41—H41C | 109.00 |
O21—C22—C23 | 111.6 (3) | H41A—C41—H41B | 109.00 |
N24—C23—C22 | 109.2 (2) | H41A—C41—H41C | 109.00 |
N24—C25—C26 | 109.3 (2) | H41B—C41—H41C | 110.00 |
O21—C26—C25 | 111.0 (2) | C16—C61—H61A | 109.00 |
N4—C4—H4A | 108.00 | C16—C61—H61B | 109.00 |
N4—C4—H4B | 108.00 | C16—C61—H61C | 109.00 |
N24—C4—H4A | 108.00 | H61A—C61—H61B | 109.00 |
N24—C4—H4B | 108.00 | H61A—C61—H61C | 109.00 |
H4A—C4—H4B | 107.00 | H61B—C61—H61C | 109.00 |
C21—S21—C12—N11 | −176.28 (17) | C12—N11—C16—C15 | 0.8 (3) |
C21—S21—C12—N13 | 3.9 (2) | C12—N11—C16—C61 | 179.8 (2) |
C12—S21—C21—C2 | −113.85 (17) | C14—N13—C12—S21 | 178.84 (17) |
C5—O1—C2—N3 | −0.9 (2) | C14—N13—C12—N11 | −0.9 (4) |
C5—O1—C2—C21 | 177.15 (18) | C12—N13—C14—C15 | −0.1 (3) |
C2—O1—C5—S5 | 179.02 (16) | C12—N13—C14—C41 | 180.0 (2) |
C2—O1—C5—N4 | 0.4 (2) | C23—N24—C4—N4 | −67.3 (3) |
C26—O21—C22—C23 | 58.3 (3) | C25—N24—C4—N4 | 60.1 (3) |
C22—O21—C26—C25 | −58.4 (3) | C4—N24—C23—C22 | −173.3 (2) |
C2—N3—N4—C4 | −175.71 (18) | C25—N24—C23—C22 | 57.4 (3) |
C2—N3—N4—C5 | −0.7 (2) | C4—N24—C25—C26 | 172.7 (2) |
N4—N3—C2—O1 | 1.0 (2) | C23—N24—C25—C26 | −57.9 (3) |
N4—N3—C2—C21 | −176.9 (2) | O1—C2—C21—S21 | 51.9 (2) |
N3—N4—C4—N24 | −86.7 (2) | N3—C2—C21—S21 | −130.3 (2) |
C5—N4—C4—N24 | 99.1 (3) | N13—C14—C15—C16 | 1.4 (4) |
N3—N4—C5—S5 | −178.33 (17) | C41—C14—C15—C16 | −178.7 (3) |
N3—N4—C5—O1 | 0.1 (2) | C14—C15—C16—N11 | −1.7 (4) |
C4—N4—C5—S5 | −3.8 (3) | C14—C15—C16—C61 | 179.4 (2) |
C4—N4—C5—O1 | 174.69 (18) | O21—C22—C23—N24 | −57.6 (3) |
C16—N11—C12—S21 | −179.21 (17) | N24—C25—C26—O21 | 58.4 (3) |
C16—N11—C12—N13 | 0.6 (4) |
Symmetry codes: (i) x+1, y, z; (ii) −x+1, −y+1, −z+1; (iii) −x+1, −y, −z+1; (iv) −x, −y+1, −z+1; (v) −x, −y, −z+1; (vi) x−1, y, z; (vii) −x, −y+1, −z+2; (viii) −x+1, −y+1, −z+2; (ix) x, y, z−1; (x) x−1, y−1, z−1; (xi) x+1, y+1, z+1; (xii) x, y, z+1. |
D—H···A | D—H | H···A | D···A | D—H···A |
C21—H21A···N13 | 0.99 | 2.28 | 2.883 (3) | 118 |
C21—H21B···S5vi | 0.99 | 2.84 | 3.632 (2) | 137 |
Symmetry code: (vi) x−1, y, z. |
Experimental details
Crystal data | |
Chemical formula | C14H19N5O2S2 |
Mr | 353.48 |
Crystal system, space group | Triclinic, P1 |
Temperature (K) | 160 |
a, b, c (Å) | 7.1250 (3), 10.6735 (3), 12.3740 (5) |
α, β, γ (°) | 93.607 (2), 90.561 (2), 107.474 (2) |
V (Å3) | 895.42 (6) |
Z | 2 |
Radiation type | Mo Kα |
µ (mm−1) | 0.31 |
Crystal size (mm) | 0.28 × 0.23 × 0.20 |
Data collection | |
Diffractometer | Nonius KappaCCD area-detector |
Absorption correction | Multi-scan (Blessing, 1995) |
Tmin, Tmax | 0.892, 0.964 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 25642, 5188, 3963 |
Rint | 0.062 |
(sin θ/λ)max (Å−1) | 0.704 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.057, 0.177, 1.06 |
No. of reflections | 5188 |
No. of parameters | 210 |
H-atom treatment | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 1.98, −0.42 |
Computer programs: COLLECT (Nonius, 2000), DENZO-SMN (Otwinowski & Minor, 1997), DENZO-SMN and SCALEPACK (Otwinowski & Minor, 1997), SHELXS97 (Sheldrick, 1997), SHELXL97 (Sheldrick, 1997), ORTEP-3 (Farrugia, 1997), PLATON (Spek, 2003).
D—H···A | D—H | H···A | D···A | D—H···A |
C21—H21A···N13 | 0.99 | 2.28 | 2.883 (3) | 118 |
C21—H21B···S5i | 0.99 | 2.84 | 3.632 (2) | 137 |
Symmetry code: (i) x−1, y, z. |
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A literature survey shows that large numbers of simple, N-bridged, nitrogen- and sulfur-containing heterocyclic compounds containing the pyrimidine unit have diverse biological activities (Wichmann et al., 1999; El-Bendary et al., 1998; Kirpal, 1999; Tsuji & Ishikawa, 1994). In the light of this significant importance of pyrimidine compounds, and as a continuation of our work on the study of pyrimidine derivatives (Thiruvalluvaret al., 2007a,b), an X-ray crystallographic structure determination of the title compound was undertaken and the results are presented here.
In the title compound, Fig.1, the pyrimidine ring makes a dihedral angle of 82.8 (1)° with the oxadiazole ring. The morpholine ring adopts a chair conformation. There is a short intermolecular contact between O21 and C2 [2.938 (3) Å; -x, -y, -z + 1]. The molecules are linked by C—H···S hydrogen bonds (Fig. 2); an intramolecular C—H···N hydrogen bond is also present.