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Acta Crystallogr Sect E Struct Rep Online. 2008 December 1; 64(Pt 12): o2404.
Published online 2008 November 22. doi:  10.1107/S160053680803732X
PMCID: PMC2960130

2-(4-Bromo­phen­oxy)-3-isopropyl-5,6,7,8-tetra­hydro-1-benzothieno[2,3-d]pyrimidin-4(3H)-one

Abstract

In the title compound, C19H19BrN2O2S, the central thieno­pyrim­idine ring system is essentially planar, with a maximum displacement of 0.068 (3) Å. The attached cyclo­hexene ring adopts a half-chair conformation. The molecular conformation and crystal packing are stabilized by three intra­molecular C—H(...)O hydrogen bonds and two C—H(...)π inter­actions.

Related literature

For background to the use of pyrimidine derivatives as drugs, see: Ding et al. (2004 [triangle]). For a description of the Cambridge Structural Database, see: Allen (2002 [triangle]). For a related structure, see: Zeng et al. (2006 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-64-o2404-scheme1.jpg

Experimental

Crystal data

  • C19H19BrN2O2S
  • M r = 418.32
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-64-o2404-efi1.jpg
  • a = 13.3957 (7) Å
  • b = 5.7366 (3) Å
  • c = 13.3956 (7) Å
  • β = 115.5410 (10)°
  • V = 928.81 (8) Å3
  • Z = 2
  • Mo Kα radiation
  • μ = 2.34 mm−1
  • T = 298 (2) K
  • 0.20 × 0.10 × 0.10 mm

Data collection

  • Bruker SMART CCD area-detector diffractometer
  • Absorption correction: multi-scan (SADABS; Sheldrick, 1996 [triangle]) T min = 0.652, T max = 0.800
  • 5798 measured reflections
  • 3228 independent reflections
  • 2346 reflections with I > 2σ(I)
  • R int = 0.106

Refinement

  • R[F 2 > 2σ(F 2)] = 0.067
  • wR(F 2) = 0.204
  • S = 1.07
  • 3228 reflections
  • 228 parameters
  • 1 restraint
  • H-atom parameters constrained
  • Δρmax = 7.69 e Å−3
  • Δρmin = −2.63 e Å−3
  • Absolute structure: Flack (1983 [triangle]), 1424 Freidel pairs
  • Flack parameter: 0.00 (8)

Data collection: SMART (Bruker, 2001 [triangle]); cell refinement: SAINT (Bruker, 2001 [triangle]); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 [triangle]); molecular graphics: PLATON (Spek, 2003 [triangle]); software used to prepare material for publication: SHELXTL (Sheldrick, 2008 [triangle]).

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S160053680803732X/at2674sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S160053680803732X/at2674Isup2.hkl

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

Acknowledgments

We gratefully acknowledge financial support of this work by the Research Foundation for Students and Teachers of Yunyang Medical College (grant Nos. 2007QDJ15, 2007ZQB19, 2007ZQB20).

supplementary crystallographic information

Comment

Pyrimidine derivatives are attracting the increasing attention of synthetic community because of the important role played by such systems in many natural products, antibiotics and drugs (Ding et al., 2004). In recent years, we have been engaged in the preparation of the derivatives of heterocycles via aza-Wittig reaction. The title compound, (I), was synthesized and structurally characterized in this context.

The molecular structure indicates that the thieno[2,3-d]pyrimidine moiety is a conjugated system (Fig. 1). All ring atoms in thieno[2,3-d]pyrimidine are essentially coplanar (Zeng et al., 2006). The bond lengths and angles are within experimental error, in the ranges of values in previously reported structures in the Cambridge Structural Database (Version 5.26; Allen, 2002).

The cyclohexene ring adopts a half-chair conformation. The crystal packing is stabilized by three intramolecular C—H···O hydrogen bonds and two C—H···π interactions (Table 1). There exist no intermolecular hydrogen bonding interactions and no π-π stackings.

Experimental

To a solution of iminophosphorane (1.45 g, 3 mmol) in anhydrous dichloromethane (15 ml) was added iso-propyl isocyanate (3 mmol) under dry nitrogen at room temperature. After the reaction mixture was left unstirred for 48 h at room temperature, the solvent was removed off under reduced pressure and ether/petroleum ether (1:2 v/v, 20 ml) was added to precipitate triphenylphosphine oxide. After filtration, the solvent was removed, and the residue was dissolved in CH3CN (15 ml). After adding 4-Br-PhOH (3.1 mmol) and excess K2CO3 to the solution of carbodiimide, The mixture was stirred for 24 h at room temperature, the solution was condensed and the residue was recrystallized by EtOH to give the title compound, (I), in yield of 80% (m.p. 478 K). Elemental analysis calculated for C19H19BrN2O2S: C 54.42, H 4.57, N 6.68. Found: C 54.56, H 4.42, N 6.53. Crystals suitable for single crystal X-ray diffraction were obtained by vapor diffusion of hexane and dichloromethane (1:3 v/v) at room temperature.

Refinement

H atoms were placed at calculated positions and treated as riding atoms, with C—H = 0.93–0.98 Å, and Uiso(H) = 1.2Ueq(C) for CH or 1.5Ueq(C) for CH3.

Figures

Fig. 1.
View of the molecule of (I) showing the atom-labeling scheme. Displacement ellipsoids are drawn at 50% probability level. H-atoms are represented by circles of arbitrary size.

Crystal data

C19H19BrN2O2SF000 = 428
Mr = 419.33Dx = 1.499 Mg m3
Monoclinic, P21Melting point: 478K K
Hall symbol: P 2ybMo Kα radiation λ = 0.71073 Å
a = 13.3957 (7) ÅCell parameters from 2048 reflections
b = 5.7366 (3) Åθ = 2.9–24.5º
c = 13.3956 (7) ŵ = 2.34 mm1
β = 115.5410 (10)ºT = 298 (2) K
V = 928.81 (8) Å3Block, colorless
Z = 20.20 × 0.10 × 0.10 mm

Data collection

Bruker SMART CCD area-detector diffractometer3228 independent reflections
Radiation source: fine-focus sealed tube2346 reflections with I > 2σ(I)
Monochromator: graphiteRint = 0.106
T = 298(2) Kθmax = 25.0º
[var phi] and ω scansθmin = 1.7º
Absorption correction: multi-scan(SADABS; Sheldrick, 1996)h = −13→15
Tmin = 0.652, Tmax = 0.800k = −6→6
5798 measured reflectionsl = −15→15

Refinement

Refinement on F2Hydrogen site location: inferred from neighbouring sites
Least-squares matrix: fullH-atom parameters constrained
R[F2 > 2σ(F2)] = 0.067  w = 1/[σ2(Fo2) + (0.1151P)2] where P = (Fo2 + 2Fc2)/3
wR(F2) = 0.204(Δ/σ)max = 0.001
S = 1.07Δρmax = 0.67 e Å3
3228 reflectionsΔρmin = −0.62 e Å3
228 parametersExtinction correction: none
1 restraintAbsolute structure: Flack (1983), 1424 Friedel pairs
Primary atom site location: structure-invariant direct methodsFlack parameter: 0.00 (8)
Secondary atom site location: difference Fourier map

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)

xyzUiso*/Ueq
Br10.84533 (6)0.7555 (2)0.71718 (7)0.0762 (4)
C10.0942 (6)1.2447 (18)0.8813 (6)0.0534 (18)
H1A0.04441.31570.81180.064*
H1B0.06501.09210.88530.064*
C20.0967 (9)1.390 (3)0.9738 (10)0.103 (5)
H2A0.02311.45140.95360.124*
H2B0.11521.29081.03800.124*
C30.1719 (9)1.578 (2)1.0038 (11)0.093 (4)
H3A0.17301.64641.07040.111*
H3B0.14161.69420.94590.111*
C40.2917 (7)1.537 (2)1.0246 (7)0.067 (3)
H4A0.32341.67971.01190.081*
H4B0.33511.48851.10060.081*
C50.2930 (6)1.3513 (13)0.9472 (6)0.0460 (19)
C60.2071 (5)1.2157 (15)0.8824 (5)0.046 (2)
C70.2363 (6)1.0548 (14)0.8163 (6)0.0405 (16)
C80.3446 (6)1.0816 (16)0.8335 (6)0.052 (2)
C90.1666 (6)0.9073 (15)0.7312 (6)0.0457 (18)
C100.3302 (6)0.8295 (14)0.7015 (6)0.047 (2)
C110.1472 (6)0.6545 (14)0.5719 (6)0.0459 (18)
H110.07260.66170.56830.055*
C120.1754 (9)0.3997 (19)0.5775 (8)0.079 (3)
H12A0.19060.34060.64970.119*
H12B0.23950.37960.56380.119*
H12C0.11420.31610.52280.119*
C130.1386 (8)0.767 (2)0.4657 (6)0.071 (2)
H13A0.21040.77070.46610.107*
H13B0.11120.92330.46080.107*
H13C0.08890.67840.40330.107*
C140.4794 (6)0.7242 (18)0.6612 (7)0.055 (2)
C150.5512 (8)0.553 (2)0.7233 (8)0.073 (3)
H150.52680.43200.75360.087*
C160.6596 (8)0.563 (2)0.7394 (9)0.074 (3)
H160.70960.44980.78150.088*
C170.6938 (5)0.741 (2)0.6934 (6)0.061 (2)
C180.6221 (7)0.9049 (19)0.6317 (8)0.066 (2)
H180.64581.02450.60020.079*
C190.5134 (8)0.895 (2)0.6152 (9)0.073 (3)
H190.46341.00730.57200.088*
N10.3955 (5)0.9634 (13)0.7793 (6)0.0527 (17)
N20.2193 (4)0.7931 (13)0.6717 (4)0.0415 (13)
O10.0683 (4)0.8637 (12)0.7061 (5)0.0664 (19)
O20.3666 (4)0.7053 (13)0.6384 (5)0.072 (2)
S10.41333 (15)1.2916 (5)0.93045 (17)0.0604 (6)

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
Br10.0420 (4)0.1275 (10)0.0622 (5)−0.0010 (6)0.0253 (4)−0.0105 (6)
C10.048 (4)0.055 (5)0.061 (4)−0.001 (5)0.027 (3)0.001 (5)
C20.063 (6)0.162 (13)0.089 (8)−0.006 (7)0.037 (6)−0.052 (8)
C30.079 (7)0.105 (10)0.106 (9)−0.008 (7)0.051 (7)−0.036 (8)
C40.059 (5)0.090 (7)0.043 (4)0.009 (5)0.013 (4)−0.009 (5)
C50.045 (4)0.050 (5)0.038 (4)0.004 (3)0.014 (3)0.001 (3)
C60.039 (4)0.057 (6)0.036 (3)0.007 (4)0.011 (3)0.004 (4)
C70.032 (3)0.052 (4)0.033 (3)0.007 (3)0.010 (3)0.002 (3)
C80.033 (4)0.070 (6)0.043 (4)−0.004 (4)0.006 (3)−0.002 (4)
C90.037 (4)0.055 (5)0.040 (4)−0.004 (4)0.012 (3)0.006 (3)
C100.038 (4)0.053 (5)0.049 (4)0.004 (3)0.018 (3)−0.006 (3)
C110.037 (4)0.053 (5)0.044 (4)−0.009 (3)0.013 (3)−0.004 (3)
C120.100 (8)0.058 (6)0.061 (6)−0.002 (6)0.016 (6)0.001 (5)
C130.083 (6)0.069 (6)0.044 (4)0.001 (6)0.011 (4)0.007 (5)
C140.039 (4)0.068 (6)0.061 (4)−0.009 (4)0.024 (3)−0.022 (5)
C150.054 (5)0.088 (8)0.076 (7)−0.002 (5)0.028 (5)0.010 (6)
C160.050 (5)0.093 (8)0.076 (6)0.004 (5)0.027 (5)0.019 (6)
C170.034 (3)0.106 (7)0.043 (4)0.005 (6)0.016 (3)−0.019 (6)
C180.049 (5)0.072 (6)0.074 (6)0.000 (5)0.023 (5)0.016 (5)
C190.048 (5)0.077 (7)0.084 (7)0.011 (5)0.019 (5)0.009 (5)
N10.034 (3)0.063 (5)0.057 (4)−0.007 (3)0.016 (3)−0.022 (4)
N20.031 (3)0.049 (4)0.043 (3)−0.005 (3)0.013 (2)0.002 (3)
O10.033 (3)0.103 (6)0.062 (3)−0.012 (3)0.018 (2)−0.019 (3)
O20.039 (3)0.098 (6)0.079 (4)−0.011 (3)0.025 (3)−0.041 (4)
S10.0373 (9)0.0736 (16)0.0600 (11)−0.0053 (11)0.0114 (8)−0.0194 (12)

Geometric parameters (Å, °)

Br1—C171.916 (7)C10—O21.347 (9)
C1—C21.481 (14)C10—N21.378 (8)
C1—C61.515 (9)C11—N21.497 (9)
C1—H1A0.9700C11—C121.504 (14)
C1—H1B0.9700C11—C131.521 (12)
C2—C31.410 (18)C11—H110.9800
C2—H2A0.9700C12—H12A0.9600
C2—H2B0.9700C12—H12B0.9600
C3—C41.523 (14)C12—H12C0.9600
C3—H3A0.9700C13—H13A0.9600
C3—H3B0.9700C13—H13B0.9600
C4—C51.492 (12)C13—H13C0.9600
C4—H4A0.9700C14—C191.336 (15)
C4—H4B0.9700C14—C151.377 (15)
C5—C61.350 (11)C14—O21.412 (9)
C5—S11.754 (8)C15—C161.374 (13)
C6—C71.445 (10)C15—H150.9300
C7—C81.375 (10)C16—C171.370 (15)
C7—C91.404 (11)C16—H160.9300
C8—N11.370 (10)C17—C181.342 (14)
C8—S11.719 (9)C18—C191.377 (12)
C9—O11.236 (9)C18—H180.9300
C9—N21.431 (10)C19—H190.9300
C10—N11.287 (10)
C2—C1—C6113.0 (7)N2—C11—C12114.8 (7)
C2—C1—H1A109.0N2—C11—C13111.6 (7)
C6—C1—H1A109.0C12—C11—C13112.1 (8)
C2—C1—H1B109.0N2—C11—H11105.8
C6—C1—H1B109.0C12—C11—H11105.8
H1A—C1—H1B107.8C13—C11—H11105.8
C3—C2—C1115.1 (10)C11—C12—H12A109.5
C3—C2—H2A108.5C11—C12—H12B109.5
C1—C2—H2A108.5H12A—C12—H12B109.5
C3—C2—H2B108.5C11—C12—H12C109.5
C1—C2—H2B108.5H12A—C12—H12C109.5
H2A—C2—H2B107.5H12B—C12—H12C109.5
C2—C3—C4120.1 (11)C11—C13—H13A109.5
C2—C3—H3A107.3C11—C13—H13B109.5
C4—C3—H3A107.3H13A—C13—H13B109.5
C2—C3—H3B107.3C11—C13—H13C109.5
C4—C3—H3B107.3H13A—C13—H13C109.5
H3A—C3—H3B106.9H13B—C13—H13C109.5
C5—C4—C3108.0 (8)C19—C14—C15121.0 (8)
C5—C4—H4A110.1C19—C14—O2120.1 (9)
C3—C4—H4A110.1C15—C14—O2118.6 (9)
C5—C4—H4B110.1C16—C15—C14118.6 (10)
C3—C4—H4B110.1C16—C15—H15120.7
H4A—C4—H4B108.4C14—C15—H15120.7
C6—C5—C4126.6 (7)C17—C16—C15119.9 (10)
C6—C5—S1112.4 (5)C17—C16—H16120.1
C4—C5—S1121.0 (6)C15—C16—H16120.1
C5—C6—C7112.3 (6)C18—C17—C16120.6 (7)
C5—C6—C1120.9 (7)C18—C17—Br1119.9 (8)
C7—C6—C1126.7 (7)C16—C17—Br1119.5 (8)
C8—C7—C9119.2 (7)C17—C18—C19119.7 (10)
C8—C7—C6111.8 (7)C17—C18—H18120.1
C9—C7—C6128.4 (6)C19—C18—H18120.1
N1—C8—C7125.8 (7)C14—C19—C18120.2 (9)
N1—C8—S1121.3 (5)C14—C19—H19119.9
C7—C8—S1112.8 (6)C18—C19—H19119.9
O1—C9—C7126.9 (7)C10—N1—C8113.9 (6)
O1—C9—N2118.7 (7)C10—N2—C9119.9 (6)
C7—C9—N2114.4 (6)C10—N2—C11122.7 (6)
N1—C10—O2121.4 (6)C9—N2—C11117.2 (5)
N1—C10—N2126.6 (7)C10—O2—C14117.8 (6)
O2—C10—N2112.0 (6)C8—S1—C590.6 (4)
C6—C1—C2—C336.3 (16)Br1—C17—C18—C19−179.7 (8)
C1—C2—C3—C4−50.1 (18)C15—C14—C19—C18−1.6 (16)
C2—C3—C4—C534.6 (16)O2—C14—C19—C18−175.9 (9)
C3—C4—C5—C6−9.8 (13)C17—C18—C19—C140.5 (16)
C3—C4—C5—S1169.1 (8)O2—C10—N1—C8178.4 (7)
C4—C5—C6—C7179.3 (8)N2—C10—N1—C8−1.7 (13)
S1—C5—C6—C70.4 (8)C7—C8—N1—C104.8 (13)
C4—C5—C6—C11.0 (12)S1—C8—N1—C10−173.3 (6)
S1—C5—C6—C1−177.9 (6)N1—C10—N2—C9−1.2 (12)
C2—C1—C6—C5−13.3 (13)O2—C10—N2—C9178.8 (7)
C2—C1—C6—C7168.6 (10)N1—C10—N2—C11173.0 (8)
C5—C6—C7—C8−1.3 (10)O2—C10—N2—C11−7.0 (10)
C1—C6—C7—C8176.9 (7)O1—C9—N2—C10−176.8 (7)
C5—C6—C7—C9−172.1 (8)C7—C9—N2—C101.2 (10)
C1—C6—C7—C96.1 (13)O1—C9—N2—C118.7 (10)
C9—C7—C8—N1−4.8 (13)C7—C9—N2—C11−173.3 (7)
C6—C7—C8—N1−176.6 (8)C12—C11—N2—C1066.0 (10)
C9—C7—C8—S1173.4 (6)C13—C11—N2—C10−63.0 (10)
C6—C7—C8—S11.6 (9)C12—C11—N2—C9−119.6 (9)
C8—C7—C9—O1179.4 (8)C13—C11—N2—C9111.4 (8)
C6—C7—C9—O1−10.4 (14)N1—C10—O2—C140.8 (13)
C8—C7—C9—N21.5 (11)N2—C10—O2—C14−179.2 (7)
C6—C7—C9—N2171.7 (7)C19—C14—O2—C10−86.5 (11)
C19—C14—C15—C161.5 (15)C15—C14—O2—C1099.1 (10)
O2—C14—C15—C16175.9 (9)N1—C8—S1—C5177.1 (8)
C14—C15—C16—C17−0.4 (16)C7—C8—S1—C5−1.2 (7)
C15—C16—C17—C18−0.6 (16)C6—C5—S1—C80.4 (6)
C15—C16—C17—Br1179.7 (8)C4—C5—S1—C8−178.6 (7)
C16—C17—C18—C190.6 (15)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
C11—H11···O10.982.202.726 (10)112
C12—H12B···O20.962.432.915 (13)111
C13—H13A···O20.962.382.951 (10)117
C12—H12B···Cg10.962.923.854 (11)165
C12—H12B···Cg20.962.713.434 (11)133

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: AT2674).

References

  • Allen, F. H. (2002). Acta Cryst. B58, 380–388. [PubMed]
  • Bruker (2001). SMART and SAINT Bruker AXS Inc., Madison, Wisconsin, USA.
  • Ding, M. W., Xu, S. Z. & Zhao, J. F. (2004). J. Org. Chem.69, 8366–8371. [PubMed]
  • Flack, H. D. (1983). Acta Cryst. A39, 876–881.
  • Sheldrick, G. M. (1996). SADABS University of Göttingen, Germany.
  • Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. [PubMed]
  • Spek, A. L. (2003). J. Appl. Cryst.36, 7–13.
  • Zeng, X.-H., Ding, M.-W. & He, H.-W. (2006). Acta Cryst. E62, o731–o732.

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