PMCCPMCCPMCC

Search tips
Search criteria 

Advanced

 
Logo of actaeInternational Union of Crystallographysearchopen accessarticle submissionjournal home pagethis article
 
Acta Crystallogr Sect E Struct Rep Online. 2008 September 1; 64(Pt 9): o1666.
Published online 2008 August 6. doi:  10.1107/S160053680802401X
PMCID: PMC2960738

7-(Benzyl­sulfan­yl)-5-(2-methoxy­phen­yl)-1,3-dimethyl-5,6-dihydro­pyrimido[4,5-d]pyrimidine-2,4(1H,3H)-dione

Abstract

In the mol­ecule of the title compound, C22H22N4O3S, the benzene and phenyl rings are oriented at a dihedral angle of 88.72 (4)°. The other two rings have flattened-boat conformations. In the crystal structure, inter­molecular N—H(...)O hydrogen bonds link the mol­ecules.

Related literature

For general background, see: Sharma et al. (2004 [triangle]); Quiroga et al. (2002 [triangle]); Devi et al. (2003 [triangle]). For bond-length data, see: Allen et al. (1987 [triangle]). For ring conformation puckering parameters, see: Cremer & Pople (1975 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-64-o1666-scheme1.jpg

Experimental

Crystal data

  • C22H22N4O3S
  • M r = 422.51
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-64-o1666-efi1.jpg
  • a = 10.9216 (9) Å
  • b = 8.8528 (5) Å
  • c = 20.7263 (15) Å
  • β = 90.638 (6)°
  • V = 2003.8 (2) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 0.20 mm−1
  • T = 294 (2) K
  • 0.4 × 0.3 × 0.05 mm

Data collection

  • Bruker SMART CCD area-detector diffractometer
  • Absorption correction: multi-scan (SADABS; Sheldrick, 1998 [triangle]) T min = 0.928, T max = 0.985
  • 23191 measured reflections
  • 5394 independent reflections
  • 4510 reflections with I > 2σ(I)
  • R int = 0.063

Refinement

  • R[F 2 > 2σ(F 2)] = 0.055
  • wR(F 2) = 0.135
  • S = 1.15
  • 5394 reflections
  • 278 parameters
  • H atoms treated by a mixture of independent and constrained refinement
  • Δρmax = 0.32 e Å−3
  • Δρmin = −0.25 e Å−3

Data collection: SMART (Bruker, 1998 [triangle]); cell refinement: SAINT (Bruker, 1998 [triangle]); data reduction: SAINT; program(s) used to solve structure: SHELXTL (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXTL; molecular graphics: ORTEP-3 for Windows (Farrugia, 1997 [triangle]); software used to prepare material for publication: WinGX (Farrugia, 1999 [triangle]).

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S160053680802401X/hk2501sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S160053680802401X/hk2501Isup2.hkl

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

Acknowledgments

AB is grateful to the Islamic Azad University, Dorood Branch, for financial support.

supplementary crystallographic information

Comment

The importance of fused pyrimidines, common source for the development of new potential therapeutic agents (Sharma et al., 2004), is well known. Among them, the pyrimido[2,3-d]pyrimidines are an important class of annulated uracils with biological significance because of their connection with purine pteridine system (Quiroga et al., 2002). Numerous reports delineate the antitumor, antivial, antioxidant, antifungal and hepatoprotective activities of these compounds (Devi et al., 2003). Therefore, for the preparation of these complex molecules large efforts have been directed towards the synthetic manipulation of uracils. We report herein the synthesis and crystal structure of the title compound.

In the molecule of the title compound (Fig. 1), the bond lengths (Allen et al., 1987) and angles are within normal ranges. Rings A (C1-C6) and D (C16-C21) are, of course, planar and they are oriented at a dihedral angle of A/D = 88.72 (4)°. Rings B (N2/N3/C9/C11/C13/C14) and C (N1/N4/C8/C9/C14/C15) have flattened-boat [[var phi] = 105.63 (2)°, θ = 100.53 (3)° (for ring B) and [var phi] = 29.58 (3)°, θ = 58.23 (3)° (for ring C)] conformations, having total puckering amplitudes, QT, of 0.120 (3) and 0.364 (3) Å, respectively (Cremer & Pople, 1975).

In the crystal structure, intermolecular N-H···O hydrogen bonds (Table 1) link the molecules (Fig. 2), in which they may be effective in the stabilization of the structure.

Experimental

For the preparation of the title compound, 6-amino-1,3-dimethyluracil (0.15 g, 1 mmol), 2-methylbenzaldehyde (0.12 g, 1 mmol), 2-benzylthiourea hydrochloride (0.30 g, 1.5 mmol) and p-toluenesulfonic acid (0.1 g) were mixed. The reaction mixture was placed in a screw capped vial and irradiated for 5 min with a power of 700 W microwave irradiation. After cooling, the reaction mixture was washed with water, and then recrystallized from ethyl acetate to afford the title compound (yield; 0.25 g. 65%, m.p. 519-521 K).

Refinement

H4B atom (for NH) was located in difference syntheses and refined isotropically [N-H = 0.85 (3) Å and Uiso(H) = 0.049 (6) Å2]. The remaining H atoms were positioned geometrically, with C-H = 0.93, 0.98, 0.97 and 0.96 Å for aromatic, methine, methylene and methyl H, respectively, and constrained to ride on their parent atoms with Uiso(H) = xUeq(C), where x = 1.5 for methyl H and x = 1.2 for all other H atoms.

Figures

Fig. 1.
The molecular structure of the title molecule, with the atom-numbering scheme. Displacement ellipsoids are drawn at the 30% probability level.
Fig. 2.
A packing diagram of the title compound. Hydrogen bonds are shown as dashed lines.

Crystal data

C22H22N4O3SF000 = 888
Mr = 422.51Dx = 1.401 Mg m3
Monoclinic, P21/nMo Kα radiation λ = 0.71073 Å
Hall symbol: -P 2ynCell parameters from 2175 reflections
a = 10.9216 (9) Åθ = 2.1–29.3º
b = 8.8528 (5) ŵ = 0.20 mm1
c = 20.7263 (15) ÅT = 294 (2) K
β = 90.638 (6)ºPlate, colorless
V = 2003.8 (2) Å30.4 × 0.3 × 0.05 mm
Z = 4

Data collection

Bruker SMART CCD area-detector diffractometerRint = 0.063
[var phi] and ω scansθmax = 29.3º
Absorption correction: multi-scan(SADABS; Sheldrick, 1998)θmin = 2.1º
Tmin = 0.928, Tmax = 0.985h = −14→15
23191 measured reflectionsk = −11→12
5394 independent reflectionsl = −28→28
4510 reflections with I > 2σ(I)

Refinement

Refinement on F2H atoms treated by a mixture of independent and constrained refinement
Least-squares matrix: full  w = 1/[σ2(Fo2) + (0.0538P)2 + 0.6815P] where P = (Fo2 + 2Fc2)/3
R[F2 > 2σ(F2)] = 0.055(Δ/σ)max = 0.038
wR(F2) = 0.135Δρmax = 0.32 e Å3
S = 1.15Δρmin = −0.25 e Å3
5394 reflectionsExtinction correction: none
278 parameters

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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2)

xyzUiso*/Ueq
S10.34470 (5)0.84201 (5)0.12120 (2)0.04173 (13)
O10.34328 (15)0.11232 (15)−0.03830 (7)0.0508 (4)
O20.32309 (14)0.52289 (16)−0.17071 (6)0.0469 (3)
O30.08733 (11)0.71339 (19)0.00741 (7)0.0502 (4)
N10.33713 (13)0.57943 (16)0.05837 (7)0.0322 (3)
N20.34856 (13)0.34559 (15)0.00770 (7)0.0320 (3)
N30.32991 (14)0.31591 (16)−0.10452 (7)0.0349 (3)
N40.33864 (13)0.80243 (16)−0.00370 (7)0.0326 (3)
H4B0.341 (2)0.898 (3)−0.0043 (11)0.049 (6)*
C10.15207 (19)0.5279 (2)0.18010 (10)0.0459 (4)
H10.19820.46320.15470.055*
C20.0325 (2)0.4896 (3)0.19479 (10)0.0509 (5)
H2−0.00110.40020.1790.061*
C3−0.0368 (2)0.5839 (3)0.23278 (10)0.0526 (5)
H3−0.11690.55820.24290.063*
C40.0136 (2)0.7165 (3)0.25561 (11)0.0592 (6)
H4−0.03280.78070.28110.071*
C50.1329 (2)0.7546 (3)0.24080 (10)0.0525 (5)
H50.16590.84430.25660.063*
C60.20406 (17)0.6607 (2)0.20257 (8)0.0388 (4)
C70.33376 (18)0.7042 (2)0.18617 (9)0.0432 (4)
H7A0.37820.61390.17390.052*
H7B0.37330.74530.22450.052*
C80.33809 (14)0.72697 (18)0.05202 (8)0.0300 (3)
C90.33441 (13)0.50102 (17)0.00128 (8)0.0288 (3)
C100.37101 (17)0.2765 (2)0.07119 (9)0.0382 (4)
H10A0.29420.25320.09090.057*
H10B0.41590.34580.09810.057*
H10C0.41760.18540.0660.057*
C110.34047 (15)0.25006 (18)−0.04476 (9)0.0345 (3)
C120.3234 (2)0.2154 (2)−0.16086 (10)0.0483 (5)
H12A0.37850.1321−0.15460.072*
H12B0.34610.2704−0.19880.072*
H12C0.24140.178−0.1660.072*
C130.32425 (15)0.47335 (19)−0.11530 (8)0.0331 (3)
C140.31967 (14)0.56353 (17)−0.05833 (8)0.0293 (3)
C150.30427 (14)0.73269 (17)−0.06556 (8)0.0287 (3)
H150.36440.7662−0.09730.034*
C160.17931 (14)0.78714 (18)−0.08936 (8)0.0301 (3)
C170.16945 (17)0.8519 (2)−0.15010 (9)0.0378 (4)
H170.23810.8546−0.17620.045*
C180.0604 (2)0.9128 (2)−0.17325 (10)0.0469 (5)
H180.05590.9551−0.21430.056*
C19−0.0411 (2)0.9096 (3)−0.13438 (11)0.0532 (5)
H19−0.11430.9515−0.14910.064*
C20−0.03502 (18)0.8450 (3)−0.07381 (10)0.0493 (5)
H20−0.10410.8439−0.0480.059*
C210.07381 (16)0.7812 (2)−0.05109 (9)0.0371 (4)
C22−0.0178 (2)0.7044 (4)0.04781 (13)0.0771 (9)
H22A−0.05160.80350.05350.116*
H22B0.00570.66360.0890.116*
H22C−0.07810.640.0280.116*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
C10.0512 (11)0.0413 (10)0.0454 (10)0.0063 (8)0.0071 (8)−0.0019 (8)
C20.0550 (12)0.0452 (11)0.0528 (11)−0.0047 (9)0.0061 (9)0.0045 (9)
C30.0478 (11)0.0587 (13)0.0515 (11)0.0019 (10)0.0107 (9)0.0136 (10)
C40.0607 (14)0.0600 (14)0.0573 (13)0.0121 (11)0.0216 (11)−0.0024 (11)
C50.0591 (13)0.0489 (12)0.0495 (11)−0.0002 (9)0.0081 (9)−0.0100 (9)
C60.0425 (9)0.0429 (10)0.0311 (8)0.0043 (7)−0.0013 (7)0.0027 (7)
C70.0402 (9)0.0522 (11)0.0372 (9)0.0014 (8)−0.0051 (7)−0.0013 (8)
C80.0233 (7)0.0286 (7)0.0383 (8)0.0005 (5)0.0010 (6)−0.0006 (6)
C90.0228 (7)0.0239 (7)0.0398 (8)0.0006 (5)0.0039 (6)0.0030 (6)
C100.0377 (9)0.0320 (8)0.0447 (9)0.0034 (7)0.0009 (7)0.0115 (7)
C110.0318 (8)0.0251 (7)0.0467 (9)−0.0018 (6)0.0029 (7)0.0016 (7)
C120.0609 (12)0.0340 (9)0.0501 (11)−0.0013 (9)−0.0015 (9)−0.0085 (8)
C130.0302 (8)0.0285 (7)0.0407 (8)−0.0014 (6)0.0046 (6)0.0017 (7)
C140.0258 (7)0.0242 (7)0.0381 (8)−0.0002 (5)0.0027 (6)0.0029 (6)
C150.0262 (7)0.0242 (7)0.0356 (8)−0.0012 (5)0.0034 (6)0.0052 (6)
C160.0287 (7)0.0246 (7)0.0369 (8)−0.0004 (6)0.0005 (6)0.0034 (6)
C170.0413 (9)0.0327 (8)0.0395 (9)−0.0009 (7)0.0007 (7)0.0054 (7)
C180.0540 (12)0.0421 (10)0.0444 (10)0.0064 (9)−0.0092 (8)0.0101 (8)
C190.0440 (11)0.0559 (12)0.0593 (12)0.0163 (9)−0.0118 (9)0.0057 (10)
C200.0320 (9)0.0632 (13)0.0525 (11)0.0102 (9)0.0007 (8)0.0039 (10)
C210.0303 (8)0.0393 (9)0.0415 (9)0.0023 (7)0.0007 (6)0.0042 (7)
C220.0416 (12)0.127 (3)0.0628 (15)0.0041 (14)0.0173 (10)0.0345 (16)
N10.0338 (7)0.0268 (6)0.0361 (7)0.0024 (5)0.0011 (5)0.0018 (5)
N20.0324 (7)0.0240 (6)0.0396 (7)0.0015 (5)0.0024 (5)0.0056 (5)
N30.0379 (7)0.0257 (7)0.0411 (7)−0.0017 (5)0.0034 (6)−0.0025 (6)
N40.0340 (7)0.0220 (6)0.0418 (8)−0.0020 (5)−0.0016 (6)0.0017 (6)
O10.0688 (10)0.0210 (6)0.0624 (9)−0.0018 (6)−0.0002 (7)0.0037 (6)
O20.0654 (9)0.0384 (7)0.0371 (6)−0.0033 (6)0.0075 (6)0.0023 (6)
O30.0279 (6)0.0759 (10)0.0468 (7)0.0022 (6)0.0057 (5)0.0226 (7)
S10.0468 (3)0.0340 (2)0.0444 (2)−0.00253 (18)0.00230 (19)−0.00687 (18)

Geometric parameters (Å, °)

N4—H4B0.85 (3)C11—N21.379 (2)
C1—C61.383 (3)C12—N31.469 (2)
C1—C21.387 (3)C12—H12A0.96
C1—H10.93C12—H12B0.96
C2—C31.379 (3)C12—H12C0.96
C2—H20.93C13—O21.229 (2)
C3—C41.378 (4)C13—N31.413 (2)
C3—H30.93C13—C141.427 (2)
C4—C51.383 (3)C14—C151.514 (2)
C4—H40.93C15—N41.468 (2)
C5—C61.392 (3)C15—C161.524 (2)
C5—H50.93C15—H150.98
C6—C71.510 (3)C16—C171.386 (2)
C7—S11.822 (2)C16—C211.407 (2)
C7—H7A0.97C17—C181.388 (3)
C7—H7B0.97C17—H170.93
C8—N11.313 (2)C18—C191.377 (3)
C8—N41.334 (2)C18—H180.93
C8—S11.7596 (17)C19—C201.381 (3)
C9—C141.362 (2)C19—H190.93
C9—N11.372 (2)C20—C211.393 (3)
C9—N21.3908 (19)C20—H200.93
C10—N21.469 (2)C21—O31.359 (2)
C10—H10A0.96C22—O31.431 (2)
C10—H10B0.96C22—H22A0.96
C10—H10C0.96C22—H22B0.96
C11—O11.227 (2)C22—H22C0.96
C11—N31.373 (2)
C6—C1—C2121.20 (19)N3—C13—C14115.02 (14)
C6—C1—H1119.4C9—C14—C13121.24 (14)
C2—C1—H1119.4C9—C14—C15120.24 (14)
C3—C2—C1120.1 (2)C13—C14—C15118.45 (14)
C3—C2—H2120N4—C15—C14107.61 (13)
C1—C2—H2120N4—C15—C16111.66 (13)
C4—C3—C2119.4 (2)C14—C15—C16116.28 (13)
C4—C3—H3120.3N4—C15—H15106.9
C2—C3—H3120.3C14—C15—H15106.9
C3—C4—C5120.4 (2)C16—C15—H15106.9
C3—C4—H4119.8C17—C16—C21118.14 (15)
C5—C4—H4119.8C17—C16—C15119.01 (14)
C4—C5—C6120.9 (2)C21—C16—C15122.79 (14)
C4—C5—H5119.5C16—C17—C18122.16 (17)
C6—C5—H5119.5C16—C17—H17118.9
C1—C6—C5117.99 (19)C18—C17—H17118.9
C1—C6—C7121.56 (17)C19—C18—C17118.85 (18)
C5—C6—C7120.45 (18)C19—C18—H18120.6
C6—C7—S1113.99 (13)C17—C18—H18120.6
C6—C7—H7A108.8C18—C19—C20120.64 (18)
S1—C7—H7A108.8C18—C19—H19119.7
C6—C7—H7B108.8C20—C19—H19119.7
S1—C7—H7B108.8C19—C20—C21120.48 (19)
H7A—C7—H7B107.6C19—C20—H20119.8
N1—C8—N4125.81 (15)C21—C20—H20119.8
N1—C8—S1119.63 (13)O3—C21—C20124.34 (17)
N4—C8—S1114.52 (12)O3—C21—C16115.97 (15)
C14—C9—N1125.32 (14)C20—C21—C16119.68 (17)
C14—C9—N2120.04 (15)O3—C22—H22A109.5
N1—C9—N2114.64 (14)O3—C22—H22B109.5
N2—C10—H10A109.5H22A—C22—H22B109.5
N2—C10—H10B109.5O3—C22—H22C109.5
H10A—C10—H10B109.5H22A—C22—H22C109.5
N2—C10—H10C109.5H22B—C22—H22C109.5
H10A—C10—H10C109.5C8—N1—C9114.65 (14)
H10B—C10—H10C109.5C11—N2—C9121.68 (14)
O1—C11—N3121.48 (17)C11—N2—C10117.34 (14)
O1—C11—N2121.47 (17)C9—N2—C10120.98 (14)
N3—C11—N2117.05 (14)C11—N3—C13124.39 (14)
N3—C12—H12A109.5C11—N3—C12117.56 (15)
N3—C12—H12B109.5C13—N3—C12118.05 (15)
H12A—C12—H12B109.5C8—N4—C15122.81 (14)
N3—C12—H12C109.5C8—N4—H4B120.9 (16)
H12A—C12—H12C109.5C15—N4—H4B114.5 (16)
H12B—C12—H12C109.5C21—O3—C22117.82 (16)
O2—C13—N3119.99 (16)C8—S1—C7102.25 (9)
O2—C13—C14124.99 (16)
C6—C1—C2—C3−0.4 (3)C17—C16—C21—O3178.46 (16)
C1—C2—C3—C40.3 (3)C15—C16—C21—O3−4.6 (3)
C2—C3—C4—C5−0.2 (4)C17—C16—C21—C20−2.5 (3)
C3—C4—C5—C60.2 (4)C15—C16—C21—C20174.39 (17)
C2—C1—C6—C50.4 (3)N4—C8—N1—C9−1.1 (2)
C2—C1—C6—C7−179.27 (18)S1—C8—N1—C9−178.71 (11)
C4—C5—C6—C1−0.2 (3)C14—C9—N1—C8−7.4 (2)
C4—C5—C6—C7179.4 (2)N2—C9—N1—C8172.47 (14)
C1—C6—C7—S1100.2 (2)O1—C11—N2—C9−174.13 (16)
C5—C6—C7—S1−79.5 (2)N3—C11—N2—C96.3 (2)
N1—C9—C14—C13176.78 (15)O1—C11—N2—C105.0 (2)
N2—C9—C14—C13−3.1 (2)N3—C11—N2—C10−174.62 (14)
N1—C9—C14—C15−0.1 (2)C14—C9—N2—C11−4.1 (2)
N2—C9—C14—C15−179.98 (13)N1—C9—N2—C11175.99 (14)
O2—C13—C14—C9−172.94 (17)C14—C9—N2—C10176.78 (15)
N3—C13—C14—C97.4 (2)N1—C9—N2—C10−3.1 (2)
O2—C13—C14—C154.0 (2)O1—C11—N3—C13178.99 (17)
N3—C13—C14—C15−175.67 (14)N2—C11—N3—C13−1.4 (2)
C9—C14—C15—N413.62 (19)O1—C11—N3—C12−0.7 (3)
C13—C14—C15—N4−163.38 (13)N2—C11—N3—C12178.94 (16)
C9—C14—C15—C16−112.44 (17)O2—C13—N3—C11175.12 (16)
C13—C14—C15—C1670.56 (19)C14—C13—N3—C11−5.2 (2)
N4—C15—C16—C17124.18 (16)O2—C13—N3—C12−5.2 (2)
C14—C15—C16—C17−111.82 (17)C14—C13—N3—C12174.47 (15)
N4—C15—C16—C21−52.7 (2)N1—C8—N4—C1517.5 (2)
C14—C15—C16—C2171.3 (2)S1—C8—N4—C15−164.81 (11)
C21—C16—C17—C181.3 (3)C14—C15—N4—C8−21.9 (2)
C15—C16—C17—C18−175.73 (17)C16—C15—N4—C8106.81 (17)
C16—C17—C18—C190.4 (3)C20—C21—O3—C221.3 (3)
C17—C18—C19—C20−1.0 (3)C16—C21—O3—C22−179.8 (2)
C18—C19—C20—C21−0.3 (4)N1—C8—S1—C7−5.17 (15)
C19—C20—C21—O3−179.0 (2)N4—C8—S1—C7176.99 (12)
C19—C20—C21—C162.1 (3)C6—C7—S1—C8−84.81 (15)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
N4—H4B···O1i0.85 (3)2.02 (3)2.836 (2)161 (2)

Symmetry codes: (i) x, y+1, z.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: HK2501).

References

  • Allen, F. H., Kennard, O., Watson, D. G., Brammer, L., Orpen, A. G. & Taylor, R. (1987). J. Chem. Soc. Perkin Trans. 2, pp. S1–19.
  • Bruker (1998). SMART and SAINT Bruker AXS Inc., Madison, Wisconsin, USA.
  • Cremer, D. & Pople, J. A. (1975). J. Am. Chem. Soc.97, 1354–1358.
  • Devi, I., Kumar, B. S. D. & Bhuyan, P. J. (2003). Tetrahedron Lett.44, 8307–8310.
  • Farrugia, L. J. (1997). J. Appl. Cryst.30, 565.
  • Farrugia, L. J. (1999). J. Appl. Cryst.32, 837–838.
  • Quiroga, J., Insuasty, H., Insuasty, B., Abonia, R., Cobo, J., Sanchez, A. & Nogueras, M. (2002). Tetrahedron, 58, 4873–4877.
  • Sharma, P., Rane, N. & Gurram, V. K. (2004). Bioorg. Med. Chem. Lett.14, 4185–4190. [PubMed]
  • Sheldrick, G. M. (1998). SADABS Bruker AXS Inc., Madison, Wisconsin, USA.
  • Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. [PubMed]

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