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Acta Crystallographica Section E: Structure Reports Online logoLink to Acta Crystallographica Section E: Structure Reports Online
. 2012 Dec 8;69(Pt 1):o49. doi: 10.1107/S1600536812049707

1,3-Diethyl-2-sulfanyl­idene-5-(2,4,5-trimeth­oxy­benzyl­idene)-1,3-diazinane-4,6-dione

Abdullah M Asiri a,b,*, Muhammad Nadeem Arshad a,b, Muhammad Zia-ur-Rehman c,*, Tariq R Sobahi a
PMCID: PMC3588229  PMID: 23476432

Abstract

The title compound, C18H22N2O5S, is largely planar, with an r.m.s. deviation of 0.0546 (1) Å of atoms from the mean plane through all non-H atoms except for the methyl groups. The benzene and pyrimidine­dione rings are inclined to one another at a dihedral angle of 1.41 (7)°. In the crystal, weak C—H⋯O inter­actions connect the mol­ecules into chains propagating along the b-axis direction.

Related literature  

For the synthesis of the title compound, see: Asiri et al. (2004). For a related structure, see: Asiri et al. (2009).graphic file with name e-69-00o49-scheme1.jpg

Experimental  

Crystal data  

  • C18H22N2O5S

  • M r = 378.44

  • Monoclinic, Inline graphic

  • a = 7.9711 (1) Å

  • b = 17.4106 (3) Å

  • c = 13.5265 (2) Å

  • β = 99.237 (2)°

  • V = 1852.89 (5) Å3

  • Z = 4

  • Cu Kα radiation

  • μ = 1.83 mm−1

  • T = 296 K

  • 0.29 × 0.10 × 0.09 mm

Data collection  

  • Agilent SuperNova (Dual, Cu at zero, Atlas, CCD) diffractometer

  • Absorption correction: multi-scan (CrysAlis PRO; Agilent, 2012) T min = 0.875, T max = 1.000

  • 14850 measured reflections

  • 3777 independent reflections

  • 3083 reflections with I > 2σ(I)

  • R int = 0.027

Refinement  

  • R[F 2 > 2σ(F 2)] = 0.041

  • wR(F 2) = 0.121

  • S = 1.05

  • 3777 reflections

  • 240 parameters

  • H-atom parameters constrained

  • Δρmax = 0.25 e Å−3

  • Δρmin = −0.20 e Å−3

Data collection: CrysAlis PRO (Agilent, 2012); 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: PLATON (Spek, 2009); software used to prepare material for publication: WinGX (Farrugia, 2012) and X-SEED (Barbour, 2001).

Supplementary Material

Crystal structure: contains datablock(s) I, global. DOI: 10.1107/S1600536812049707/sj5286sup1.cif

e-69-00o49-sup1.cif (26.2KB, cif)

Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536812049707/sj5286Isup2.hkl

e-69-00o49-Isup2.hkl (185.2KB, hkl)

Supplementary material file. DOI: 10.1107/S1600536812049707/sj5286Isup3.cml

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

Table 1. Hydrogen-bond geometry (Å, °).

D—H⋯A D—H H⋯A DA D—H⋯A
C13—H13C⋯O2i 0.96 2.58 3.455 (2) 152

Symmetry code: (i) Inline graphic.

Acknowledgments

The authors would like to thank the Deanship of Scientific Research at King Abdulaziz University for the support of this research via the Research Group Track (grant No. 3-102/428).

supplementary crystallographic information

Comment

The title compound is related to the arylidene 5-[3-(2,5-dimethoxyphenyl)prop- 2-enylidene]-1,3-diethyl-2-thioxohexahydropyrimidine-4,6-dione (II) already reported by our group (Asiri et al., 2009). The molecule is largely planar with a dihedral angle between the benzene and pyrimidine dione rings of 1.41 (7)°. The r. m. s. deviation of atoms from the best fit plane through the non-hydrogen atoms C1/N1/C2/C3/C4/N2/S1/O1/O2/C5/C6/C7/C8/C9/C10/C11/C12/ C14/O3/O4/O5) is 0.0546 (1) Å. Atoms S1 and O1 are displaced from this plane by -0.1187 (1) Å and 0.1131 (2) Å respectively. Non-classical C13–H13C···O2 hydrogen bonds connect the molecule into chains along the b axis (Table. 1, Fig. 2).

Experimental

1,3-Diethyl-2-thiobarbituric acid (0.005 mol) and 2,4,5-trimethoxybenzaldehyde (0.005 mol) were heated in ethanol (15 ml) for 3 h; several drops of diethylamine were added. The progress of reaction was monitored by TLC. The mixture was cooled and the resulting solid was recrystallized from methanol (Asiri et al. 2004) by slow evaporation at room temperature.

Refinement

All the H-atoms bound to C were positioned with idealized geometry with C—H = 0.93 Å for aromatic, C—H = 0.97 Å for methylene & C—H = 0.96 Å for methyl groups. H-atoms were refined as riding with Uiso(H) = kUeq(C), where k = 1.5 for methyl H-atoms & k = 1.2 for other H-atoms .

Figures

Fig. 1.

Fig. 1.

The structure of (I) with 50% probability ellipsoids.

Fig. 2.

Fig. 2.

Unit cell diagram showing C—H···O hydrogen bonds, drawn as dashed lines.

Crystal data

C18H22N2O5S F(000) = 800
Mr = 378.44 Dx = 1.357 Mg m3
Monoclinic, P21/c Cu Kα radiation, λ = 1.54184 Å
Hall symbol: -P 2ybc Cell parameters from 6212 reflections
a = 7.9711 (1) Å θ = 3.3–75.4°
b = 17.4106 (3) Å µ = 1.83 mm1
c = 13.5265 (2) Å T = 296 K
β = 99.237 (2)° Needle like, red
V = 1852.89 (5) Å3 0.29 × 0.10 × 0.09 mm
Z = 4

Data collection

Agilent SuperNova (Dual, Cu at zero, Atlas, CCD) diffractometer 3777 independent reflections
Radiation source: SuperNova (Cu) X-ray Source 3083 reflections with I > 2σ(I)
Mirror monochromator Rint = 0.027
ω scans θmax = 75.6°, θmin = 4.2°
Absorption correction: multi-scan (CrysAlis PRO; Agilent, 2012) h = −9→7
Tmin = 0.875, Tmax = 1.000 k = −21→21
14850 measured reflections l = −16→16

Refinement

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)] = 0.041 Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.121 H-atom parameters constrained
S = 1.05 w = 1/[σ2(Fo2) + (0.0597P)2 + 0.385P] where P = (Fo2 + 2Fc2)/3
3777 reflections (Δ/σ)max = 0.001
240 parameters Δρmax = 0.25 e Å3
0 restraints Δρmin = −0.20 e Å3

Special details

Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds 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 > 2sigma(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)

x y z Uiso*/Ueq
S1 −0.22340 (6) 0.56530 (3) 0.08605 (3) 0.05970 (16)
O1 0.0851 (2) 0.69234 (8) 0.38430 (11) 0.0875 (5)
O2 0.10560 (19) 0.42242 (7) 0.36247 (9) 0.0651 (4)
O3 0.40703 (17) 0.63202 (7) 0.63548 (9) 0.0591 (3)
O4 0.58803 (17) 0.38883 (7) 0.78593 (9) 0.0595 (3)
O5 0.42004 (19) 0.31584 (7) 0.63615 (9) 0.0646 (4)
N1 −0.05338 (18) 0.62856 (8) 0.25049 (10) 0.0472 (3)
N2 −0.05463 (17) 0.49412 (7) 0.24558 (10) 0.0435 (3)
C1 −0.1055 (2) 0.56302 (9) 0.19924 (12) 0.0431 (4)
C2 0.0503 (2) 0.63052 (10) 0.34507 (13) 0.0527 (4)
C3 0.1117 (2) 0.55692 (9) 0.38958 (11) 0.0415 (3)
C4 0.0594 (2) 0.48671 (9) 0.33594 (11) 0.0428 (3)
C5 0.2186 (2) 0.56421 (8) 0.47980 (11) 0.0411 (3)
H5 0.2339 0.6157 0.4973 0.049*
C6 0.31256 (19) 0.51620 (9) 0.55427 (11) 0.0388 (3)
C7 0.4108 (2) 0.55426 (9) 0.63690 (11) 0.0420 (3)
C8 0.5034 (2) 0.51281 (10) 0.71486 (11) 0.0456 (4)
H8 0.5662 0.5387 0.7686 0.055*
C9 0.5032 (2) 0.43358 (10) 0.71329 (11) 0.0449 (4)
C10 0.4101 (2) 0.39422 (9) 0.63098 (11) 0.0454 (4)
C11 0.3173 (2) 0.43493 (9) 0.55483 (11) 0.0421 (3)
H11 0.2552 0.4083 0.5015 0.050*
C12 −0.1014 (3) 0.70471 (10) 0.20484 (14) 0.0615 (5)
H12A −0.1120 0.7414 0.2574 0.074*
H12B −0.2111 0.7007 0.1621 0.074*
C13 0.0275 (3) 0.73339 (11) 0.14422 (17) 0.0764 (6)
H13A 0.0335 0.6987 0.0897 0.115*
H13B 0.1367 0.7364 0.1859 0.115*
H13C −0.0052 0.7834 0.1182 0.115*
C14 −0.1166 (2) 0.42108 (10) 0.19685 (13) 0.0537 (4)
H14A −0.2290 0.4291 0.1586 0.064*
H14B −0.1263 0.3830 0.2480 0.064*
C15 −0.0014 (3) 0.39104 (12) 0.12873 (15) 0.0670 (5)
H15A 0.1113 0.3852 0.1656 0.101*
H15B 0.0009 0.4265 0.0746 0.101*
H15C −0.0425 0.3422 0.1023 0.101*
C16 0.5046 (3) 0.67409 (11) 0.71491 (15) 0.0659 (5)
H16A 0.6227 0.6615 0.7185 0.099*
H16B 0.4682 0.6610 0.7771 0.099*
H16C 0.4887 0.7281 0.7027 0.099*
C17 0.6693 (3) 0.42503 (13) 0.87605 (14) 0.0652 (5)
H17A 0.5884 0.4565 0.9028 0.098*
H17B 0.7613 0.4564 0.8616 0.098*
H17C 0.7126 0.3865 0.9241 0.098*
C18 0.3502 (4) 0.27476 (12) 0.54961 (16) 0.0889 (8)
H18A 0.3996 0.2927 0.4936 0.133*
H18B 0.2294 0.2826 0.5364 0.133*
H18C 0.3739 0.2210 0.5598 0.133*

Atomic displacement parameters (Å2)

U11 U22 U33 U12 U13 U23
S1 0.0627 (3) 0.0666 (3) 0.0436 (2) 0.0013 (2) −0.01048 (19) 0.00529 (18)
O1 0.1387 (15) 0.0401 (7) 0.0671 (9) 0.0214 (8) −0.0336 (9) −0.0107 (6)
O2 0.0932 (10) 0.0372 (6) 0.0533 (7) −0.0014 (6) −0.0234 (7) 0.0007 (5)
O3 0.0709 (8) 0.0411 (6) 0.0572 (7) −0.0051 (6) −0.0145 (6) −0.0083 (5)
O4 0.0676 (8) 0.0606 (7) 0.0434 (6) 0.0106 (6) −0.0122 (5) 0.0023 (5)
O5 0.0981 (10) 0.0408 (6) 0.0467 (7) 0.0036 (6) −0.0128 (6) 0.0039 (5)
N1 0.0545 (8) 0.0427 (7) 0.0412 (7) 0.0128 (6) −0.0015 (6) −0.0003 (5)
N2 0.0476 (7) 0.0419 (7) 0.0382 (6) −0.0027 (6) −0.0019 (5) −0.0003 (5)
C1 0.0397 (8) 0.0492 (9) 0.0399 (8) 0.0026 (6) 0.0047 (6) 0.0014 (6)
C2 0.0670 (11) 0.0424 (9) 0.0441 (8) 0.0112 (8) −0.0048 (8) −0.0045 (7)
C3 0.0467 (8) 0.0389 (8) 0.0374 (7) 0.0037 (6) 0.0023 (6) −0.0004 (6)
C4 0.0481 (9) 0.0403 (8) 0.0377 (7) −0.0016 (6) −0.0005 (6) 0.0020 (6)
C5 0.0459 (8) 0.0370 (7) 0.0394 (8) 0.0006 (6) 0.0037 (6) −0.0036 (6)
C6 0.0391 (7) 0.0413 (8) 0.0352 (7) −0.0016 (6) 0.0033 (6) −0.0020 (6)
C7 0.0412 (8) 0.0420 (8) 0.0417 (8) −0.0030 (6) 0.0033 (6) −0.0041 (6)
C8 0.0417 (8) 0.0520 (9) 0.0401 (8) −0.0026 (7) −0.0027 (6) −0.0073 (6)
C9 0.0427 (8) 0.0536 (9) 0.0363 (8) 0.0034 (7) −0.0002 (6) 0.0023 (6)
C10 0.0538 (9) 0.0413 (8) 0.0390 (8) 0.0000 (7) 0.0009 (7) 0.0013 (6)
C11 0.0485 (9) 0.0412 (8) 0.0343 (7) −0.0030 (6) −0.0001 (6) −0.0009 (6)
C12 0.0780 (13) 0.0455 (9) 0.0548 (10) 0.0238 (9) −0.0076 (9) −0.0010 (8)
C13 0.1027 (17) 0.0430 (10) 0.0783 (14) 0.0035 (11) −0.0015 (12) 0.0120 (9)
C14 0.0613 (11) 0.0513 (9) 0.0444 (9) −0.0132 (8) −0.0039 (8) 0.0005 (7)
C15 0.0834 (15) 0.0549 (11) 0.0608 (11) −0.0030 (10) 0.0053 (10) −0.0092 (9)
C16 0.0708 (12) 0.0523 (11) 0.0663 (12) −0.0143 (9) −0.0142 (10) −0.0139 (9)
C17 0.0611 (11) 0.0810 (14) 0.0456 (10) 0.0059 (10) −0.0158 (8) −0.0016 (9)
C18 0.157 (2) 0.0432 (10) 0.0560 (11) 0.0000 (13) −0.0162 (13) −0.0037 (9)

Geometric parameters (Å, º)

S1—C1 1.6634 (16) C9—C10 1.412 (2)
O1—C2 1.212 (2) C10—C11 1.366 (2)
O2—C4 1.2145 (19) C11—H11 0.9300
O3—C7 1.3542 (19) C12—C13 1.499 (3)
O3—C16 1.424 (2) C12—H12A 0.9700
O4—C9 1.3478 (19) C12—H12B 0.9700
O4—C17 1.431 (2) C13—H13A 0.9600
O5—C10 1.368 (2) C13—H13B 0.9600
O5—C18 1.408 (2) C13—H13C 0.9600
N1—C1 1.365 (2) C14—C15 1.496 (3)
N1—C2 1.407 (2) C14—H14A 0.9700
N1—C12 1.487 (2) C14—H14B 0.9700
N2—C1 1.384 (2) C15—H15A 0.9600
N2—C4 1.407 (2) C15—H15B 0.9600
N2—C14 1.480 (2) C15—H15C 0.9600
C2—C3 1.466 (2) C16—H16A 0.9600
C3—C5 1.377 (2) C16—H16B 0.9600
C3—C4 1.448 (2) C16—H16C 0.9600
C5—C6 1.426 (2) C17—H17A 0.9600
C5—H5 0.9300 C17—H17B 0.9600
C6—C11 1.415 (2) C17—H17C 0.9600
C6—C7 1.421 (2) C18—H18A 0.9600
C7—C8 1.389 (2) C18—H18B 0.9600
C8—C9 1.380 (2) C18—H18C 0.9600
C8—H8 0.9300
C7—O3—C16 119.70 (14) N1—C12—C13 111.77 (15)
C9—O4—C17 118.14 (15) N1—C12—H12A 109.3
C10—O5—C18 116.88 (14) C13—C12—H12A 109.3
C1—N1—C2 124.63 (13) N1—C12—H12B 109.3
C1—N1—C12 119.84 (14) C13—C12—H12B 109.3
C2—N1—C12 115.49 (14) H12A—C12—H12B 107.9
C1—N2—C4 125.06 (13) C12—C13—H13A 109.5
C1—N2—C14 119.37 (13) C12—C13—H13B 109.5
C4—N2—C14 115.52 (13) H13A—C13—H13B 109.5
N1—C1—N2 116.84 (14) C12—C13—H13C 109.5
N1—C1—S1 121.91 (12) H13A—C13—H13C 109.5
N2—C1—S1 121.25 (12) H13B—C13—H13C 109.5
O1—C2—N1 118.63 (15) N2—C14—C15 112.36 (15)
O1—C2—C3 123.93 (16) N2—C14—H14A 109.1
N1—C2—C3 117.44 (14) C15—C14—H14A 109.1
C5—C3—C4 127.53 (14) N2—C14—H14B 109.1
C5—C3—C2 113.68 (14) C15—C14—H14B 109.1
C4—C3—C2 118.78 (14) H14A—C14—H14B 107.9
O2—C4—N2 117.66 (14) C14—C15—H15A 109.5
O2—C4—C3 125.48 (15) C14—C15—H15B 109.5
N2—C4—C3 116.85 (13) H15A—C15—H15B 109.5
C3—C5—C6 138.77 (14) C14—C15—H15C 109.5
C3—C5—H5 110.6 H15A—C15—H15C 109.5
C6—C5—H5 110.6 H15B—C15—H15C 109.5
C11—C6—C7 116.80 (14) O3—C16—H16A 109.5
C11—C6—C5 126.91 (14) O3—C16—H16B 109.5
C7—C6—C5 116.29 (14) H16A—C16—H16B 109.5
O3—C7—C8 122.56 (14) O3—C16—H16C 109.5
O3—C7—C6 116.54 (14) H16A—C16—H16C 109.5
C8—C7—C6 120.90 (15) H16B—C16—H16C 109.5
C9—C8—C7 120.58 (14) O4—C17—H17A 109.5
C9—C8—H8 119.7 O4—C17—H17B 109.5
C7—C8—H8 119.7 H17A—C17—H17B 109.5
O4—C9—C8 124.58 (15) O4—C17—H17C 109.5
O4—C9—C10 115.65 (15) H17A—C17—H17C 109.5
C8—C9—C10 119.77 (14) H17B—C17—H17C 109.5
C11—C10—O5 125.18 (15) O5—C18—H18A 109.5
C11—C10—C9 119.67 (15) O5—C18—H18B 109.5
O5—C10—C9 115.14 (14) H18A—C18—H18B 109.5
C10—C11—C6 122.25 (14) O5—C18—H18C 109.5
C10—C11—H11 118.9 H18A—C18—H18C 109.5
C6—C11—H11 118.9 H18B—C18—H18C 109.5
C2—N1—C1—N2 1.4 (2) C3—C5—C6—C7 178.82 (18)
C12—N1—C1—N2 179.25 (15) C16—O3—C7—C8 1.8 (3)
C2—N1—C1—S1 −178.14 (14) C16—O3—C7—C6 −178.93 (16)
C12—N1—C1—S1 −0.3 (2) C11—C6—C7—O3 179.37 (14)
C4—N2—C1—N1 −6.7 (2) C5—C6—C7—O3 −1.0 (2)
C14—N2—C1—N1 175.91 (14) C11—C6—C7—C8 −1.3 (2)
C4—N2—C1—S1 172.90 (12) C5—C6—C7—C8 178.27 (14)
C14—N2—C1—S1 −4.5 (2) O3—C7—C8—C9 179.83 (15)
C1—N1—C2—O1 −178.32 (19) C6—C7—C8—C9 0.6 (2)
C12—N1—C2—O1 3.8 (3) C17—O4—C9—C8 7.1 (3)
C1—N1—C2—C3 2.5 (3) C17—O4—C9—C10 −173.28 (16)
C12—N1—C2—C3 −175.38 (16) C7—C8—C9—O4 −179.43 (15)
O1—C2—C3—C5 −2.0 (3) C7—C8—C9—C10 1.0 (2)
N1—C2—C3—C5 177.12 (15) C18—O5—C10—C11 10.0 (3)
O1—C2—C3—C4 179.2 (2) C18—O5—C10—C9 −171.0 (2)
N1—C2—C3—C4 −1.7 (3) O4—C9—C10—C11 178.64 (15)
C1—N2—C4—O2 −172.69 (16) C8—C9—C10—C11 −1.7 (2)
C14—N2—C4—O2 4.8 (2) O4—C9—C10—O5 −0.4 (2)
C1—N2—C4—C3 7.3 (2) C8—C9—C10—O5 179.17 (15)
C14—N2—C4—C3 −175.18 (14) O5—C10—C11—C6 179.94 (16)
C5—C3—C4—O2 −1.4 (3) C9—C10—C11—C6 1.0 (2)
C2—C3—C4—O2 177.22 (18) C7—C6—C11—C10 0.5 (2)
C5—C3—C4—N2 178.57 (15) C5—C6—C11—C10 −178.98 (16)
C2—C3—C4—N2 −2.8 (2) C1—N1—C12—C13 −89.7 (2)
C4—C3—C5—C6 −1.4 (3) C2—N1—C12—C13 88.3 (2)
C2—C3—C5—C6 179.87 (18) C1—N2—C14—C15 90.12 (19)
C3—C5—C6—C11 −1.6 (3) C4—N2—C14—C15 −87.55 (18)

Hydrogen-bond geometry (Å, º)

D—H···A D—H H···A D···A D—H···A
C13—H13C···O2i 0.96 2.58 3.455 (2) 152

Symmetry code: (i) −x, y+1/2, −z+1/2.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: SJ5286).

References

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Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Supplementary Materials

Crystal structure: contains datablock(s) I, global. DOI: 10.1107/S1600536812049707/sj5286sup1.cif

e-69-00o49-sup1.cif (26.2KB, cif)

Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536812049707/sj5286Isup2.hkl

e-69-00o49-Isup2.hkl (185.2KB, hkl)

Supplementary material file. DOI: 10.1107/S1600536812049707/sj5286Isup3.cml

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


Articles from Acta Crystallographica Section E: Structure Reports Online are provided here courtesy of International Union of Crystallography

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