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Acta Crystallogr Sect E Struct Rep Online. 2009 November 1; 65(Pt 11): o2628.
Published online 2009 October 3. doi:  10.1107/S1600536809039105
PMCID: PMC2971116

6-Amino-8-(2-bromo­phen­yl)-1,7,8,8a-tetrahydro-3H-isothio­chromene-5,7,7-tricarbonitrile dimethyl­formamide solvate

Abstract

In the title compound, C18H13BrN4S·C3H7NO, the thio­pyran ring and the adjacent six-numbered ring adopt distorted boat conformations. The mol­ecules, lying about inversion centers, form hydrogen-bonded dimers involving one of the H atoms on the amino group with the N atom of a cyano group of an adjacent mol­ecule, resulting in a 12-membered ring system [R 2 2(12) ring motif]. The other H atom of the amino group forms an inter­molecular hydrogen bond with the O atom of the dimethyl­formamide (DMF) mol­ecule. Another lone pair of electrons on the same carbonyl O atom of DMF mol­ecule forms a non-classical C—H(...)O inter­molecular hydrogen bond, resulting in a chain of mol­ecules.

Related literature

For the biological activity of related compounds, see: Karsten & Krisztina (2007 [triangle]); Wang et al. (1998 [triangle], 2006 [triangle]); Zhang et al. (2008 [triangle]). For a related structure, see: (Mereiter et al. 2000 [triangle]). For graph-set notation, see: Bernstein et al. (1994 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-65-o2628-scheme1.jpg

Experimental

Crystal data

  • C18H13BrN4S·C3H7NO
  • M r = 470.39
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-65-o2628-efi1.jpg
  • a = 14.7733 (4) Å
  • b = 9.1710 (3) Å
  • c = 15.7897 (4) Å
  • β = 92.478 (2)°
  • V = 2137.28 (11) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 2.04 mm−1
  • T = 296 K
  • 0.44 × 0.36 × 0.05 mm

Data collection

  • Bruker SMART CCD area-detector diffractometer
  • Absorption correction: multi-scan (SADABS; Sheldrick, 1996 [triangle]) T min = 0.422, T max = 0.900
  • 13894 measured reflections
  • 3841 independent reflections
  • 2723 reflections with I > 2σ(I)
  • R int = 0.032

Refinement

  • R[F 2 > 2σ(F 2)] = 0.036
  • wR(F 2) = 0.098
  • S = 1.04
  • 3841 reflections
  • 270 parameters
  • H atoms treated by a mixture of independent and constrained refinement
  • Δρmax = 0.32 e Å−3
  • Δρmin = −0.23 e Å−3

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: SHELXTL (Sheldrick, 2008 [triangle]); software used to prepare material for publication: SHELXTL.

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536809039105/pv2211sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536809039105/pv2211Isup2.hkl

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

Acknowledgments

We are grateful to the Natural Science Foundation (08KJD150019) and the Qing Lan Project (08QLT001) of the Jiangsu Education Committee for financial support.

supplementary crystallographic information

Comment

Iso(thio)chromene derivatives are important and useful skeletons in organic synthesis. For example, it was reported that many isochromene derivatives displayed a wide range of biological activities, such as antiinflammatory activity (Wang et al. 2006), antitumor activity (Wang et al. 1998), antiviral activity (Karsten & Krisztina, 2007), and anti-apoptotic activity (Zhang, et al. 2008). We report here the crystal structure of the title compound, (I).

In the crystal structure of (I) (Fig. 1), the thiopyran ring adopts a distorted boat conformation: the atoms C5—C6, C8—C9 are coplanar, while the atoms C7 and S1 deviate from the plane by 0.332 (6) and -0.628 (6) Å, respectively. The adjacent six-numbered ring (C1—C6) also adopts a distorted boat conformation, with the atoms C1 and C6 deviating from the plane defined by atoms C2—C5 by 0.330 (5) and -0.404 (5) Å, respectively. The basal plane of the ring C1—C6 forms a dihedral angle of 16.5 (2) ° to the thiopyran ring and is nearly perpendicular to the benzene ring (C13—C18), forming a dihedral angle of 86.8 (1) °

The classical (N—H···O and N—H···N) and non-classical (C—H···O) inter-molecular hydrogen bonds are present in the crystal structure of (I). The molecules of (I) lying about inversion centers form hydrogen bonded dimers involving one of the hydrogen atoms (H3A) on the amino group with the atom N4 of the cyano group of an adjacent molecule, resulting in a twelve membered ring system which may be described in terms of graph set notation (Bernstein et al. 1994) as R22(12) ring motif; details are given in Table 1 and Figure 2. The other hydrogen atom (H3B) of the amino group forms an intermolecular hydrogen bond with atom O1 of the DMF molecule. An other lone pair of electrons on the same carbonyl O1 atom of DMF molecule form a non-classical intermolecular (C15—H15A···O1) hydrogen bond, thus resulting in a chain of molecules.

The crystal structure of a closely related compound has been reported (Mereiter et al. 2000).

Experimental

The title compound, (I), was prepared by the reaction of 2-bromobenzaldehyde (1 mmol, 0.185 g), malononitrile (1.2 mmol, 0.079 g) and 2-(tetrahydrothiopyran-4-ylidene)malononitrile (1 mmol, 0.164 g) in 1-butyl-3-methylimidazolium fluoroborate (20 ml) at 353 K. The single crystals suitable for X-ray diffraction were obtained by slow evaporation from a DMF solution.

Refinement

The H atoms bonded to C atoms were included at geometrically calculated positions and in riding mode at C—H distances 0.93, 0.96, 0.97 and 0.98 Å for aryl, methyl, methine and methylene type H-atoms, respectively, with Uiso(H) = 1.5Ueq(methyl C-atoms) and 1.2Ueq(non-methyl C-atoms). The H-atoms bonded to N3 were allowed to refine with isotropic displacement parameters.

Figures

Fig. 1.
The molecular structure of (I) showing 50% probability of displacement ellipsoids and the atom-numbering scheme.
Fig. 2.
The molecular packing diagram showing the hydrogen bonds in the crystal of (I).

Crystal data

C18H13BrN4S·C3H7NOF(000) = 960
Mr = 470.39Dx = 1.462 Mg m3
Monoclinic, P21/cMelting point = 530–532 K
Hall symbol: -P 2ybcMo Kα radiation, λ = 0.71073 Å
a = 14.7733 (4) ÅCell parameters from 4434 reflections
b = 9.1710 (3) Åθ = 2.6–22.6°
c = 15.7897 (4) ŵ = 2.04 mm1
β = 92.478 (2)°T = 296 K
V = 2137.28 (11) Å3Plate, colourless
Z = 40.44 × 0.36 × 0.05 mm

Data collection

Bruker SMART CCD area-detector diffractometer3841 independent reflections
Radiation source: fine-focus sealed tube2723 reflections with I > 2σ(I)
graphiteRint = 0.032
[var phi] and ω scansθmax = 25.2°, θmin = 1.4°
Absorption correction: multi-scan (SADABS; Sheldrick, 1996)h = −14→17
Tmin = 0.422, Tmax = 0.900k = −9→10
13894 measured reflectionsl = −18→16

Refinement

Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.036Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.098H atoms treated by a mixture of independent and constrained refinement
S = 1.04w = 1/[σ2(Fo2) + (0.0486P)2 + 0.4516P] where P = (Fo2 + 2Fc2)/3
3841 reflections(Δ/σ)max = 0.001
270 parametersΔρmax = 0.32 e Å3
0 restraintsΔρmin = −0.23 e Å3

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.
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.

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

xyzUiso*/Ueq
Br10.26620 (2)0.56202 (4)0.85086 (2)0.06278 (16)
S1−0.08662 (5)0.75087 (9)0.66332 (5)0.0568 (2)
C9−0.08406 (19)0.4522 (3)0.65402 (18)0.0437 (7)
H9A−0.11630.36540.64810.052*
C10.15871 (17)0.5338 (3)0.66735 (17)0.0353 (6)
H1A0.15050.49010.72310.042*
C50.00049 (18)0.4509 (3)0.62871 (16)0.0347 (6)
C60.06373 (18)0.5807 (3)0.63235 (17)0.0361 (6)
H6A0.06940.61790.57460.043*
C40.03938 (18)0.3190 (3)0.59218 (15)0.0341 (6)
N30.1653 (2)0.1753 (3)0.54913 (17)0.0465 (7)
C20.19932 (18)0.4123 (3)0.61042 (17)0.0347 (6)
C10−0.02003 (18)0.2040 (3)0.56411 (17)0.0400 (7)
C30.12949 (18)0.2955 (3)0.58223 (16)0.0351 (6)
C110.2753 (2)0.3418 (3)0.66002 (19)0.0447 (7)
N4−0.06658 (17)0.1117 (3)0.53989 (18)0.0582 (7)
C120.2385 (2)0.4739 (3)0.5331 (2)0.0428 (7)
C130.22316 (18)0.6621 (3)0.68104 (17)0.0379 (6)
C180.27173 (19)0.6886 (3)0.75675 (17)0.0431 (7)
C70.02957 (19)0.7038 (3)0.6874 (2)0.0506 (8)
H7A0.06700.78930.67990.061*
H7B0.03610.67490.74650.061*
N10.2686 (2)0.5194 (3)0.47443 (19)0.0646 (8)
N20.3323 (2)0.2913 (3)0.69975 (19)0.0716 (8)
C140.2323 (2)0.7653 (3)0.6164 (2)0.0489 (8)
H14A0.20020.75270.56500.059*
C8−0.1330 (2)0.5780 (3)0.6909 (2)0.0555 (8)
H8A−0.13090.56870.75220.067*
H8B−0.19610.57450.67130.067*
C150.2877 (2)0.8846 (3)0.6273 (2)0.0628 (9)
H15A0.29390.94980.58290.075*
C170.3260 (2)0.8109 (4)0.7679 (2)0.0633 (9)
H17A0.35700.82700.81960.076*
C160.3338 (3)0.9082 (4)0.7027 (3)0.0738 (11)
H16A0.37040.99010.70990.089*
O10.65268 (16)0.8365 (3)0.50459 (17)0.0758 (7)
N50.53153 (19)0.7245 (3)0.55611 (19)0.0675 (8)
C190.6160 (2)0.7654 (4)0.5584 (3)0.0671 (10)
H19A0.65170.73760.60560.081*
C200.4938 (3)0.6366 (6)0.6229 (3)0.1171 (17)
H20A0.53990.61790.66620.176*
H20B0.47210.54580.59950.176*
H20C0.44450.68820.64690.176*
C210.4730 (3)0.7652 (6)0.4850 (3)0.1229 (18)
H21A0.50640.82200.44600.184*
H21B0.42330.82180.50440.184*
H21C0.45010.67900.45710.184*
H3A0.131 (2)0.119 (3)0.5268 (18)0.042 (9)*
H3B0.222 (3)0.169 (4)0.533 (2)0.074 (12)*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
Br10.0733 (3)0.0739 (3)0.0399 (2)−0.01304 (18)−0.01097 (16)0.00090 (16)
S10.0557 (5)0.0529 (5)0.0613 (5)0.0176 (4)−0.0045 (4)−0.0084 (4)
C90.0404 (18)0.0459 (17)0.0447 (17)−0.0014 (14)0.0006 (14)−0.0004 (13)
C10.0387 (15)0.0341 (15)0.0329 (15)−0.0012 (12)−0.0014 (12)0.0010 (12)
C50.0372 (16)0.0374 (16)0.0289 (14)0.0018 (12)−0.0060 (12)0.0021 (11)
C60.0403 (16)0.0359 (16)0.0317 (15)0.0042 (12)−0.0025 (12)−0.0003 (12)
C40.0368 (16)0.0320 (14)0.0333 (14)−0.0021 (12)−0.0014 (12)0.0026 (12)
N30.0385 (16)0.0382 (16)0.0624 (18)−0.0015 (13)−0.0031 (14)−0.0120 (13)
C20.0353 (15)0.0323 (15)0.0359 (15)0.0021 (12)−0.0037 (12)0.0026 (12)
C100.0356 (16)0.0396 (17)0.0450 (17)0.0027 (14)0.0039 (13)0.0003 (13)
C30.0416 (17)0.0286 (15)0.0343 (15)0.0002 (12)−0.0055 (12)0.0018 (12)
C110.0474 (18)0.0373 (17)0.0487 (18)0.0025 (14)−0.0066 (14)−0.0090 (14)
N40.0469 (16)0.0502 (16)0.077 (2)−0.0109 (14)0.0022 (14)−0.0160 (14)
C120.0422 (17)0.0393 (17)0.0467 (19)−0.0041 (13)−0.0005 (15)−0.0043 (14)
C130.0391 (16)0.0300 (15)0.0444 (16)0.0005 (12)−0.0024 (13)−0.0013 (13)
C180.0443 (17)0.0378 (16)0.0468 (17)−0.0017 (13)−0.0022 (14)−0.0030 (13)
C70.0465 (18)0.0455 (17)0.059 (2)0.0053 (14)−0.0028 (15)−0.0130 (15)
N10.075 (2)0.0656 (19)0.0541 (18)−0.0172 (15)0.0148 (16)−0.0007 (15)
N20.070 (2)0.0647 (19)0.077 (2)0.0193 (16)−0.0305 (16)−0.0106 (16)
C140.0499 (19)0.0363 (17)0.0597 (19)−0.0021 (14)−0.0066 (15)0.0070 (15)
C80.0440 (18)0.066 (2)0.057 (2)0.0067 (15)0.0035 (15)−0.0056 (16)
C150.063 (2)0.0366 (18)0.089 (3)0.0007 (17)0.005 (2)0.0175 (18)
C170.060 (2)0.053 (2)0.076 (2)−0.0118 (17)−0.0147 (18)−0.0157 (19)
C160.071 (3)0.040 (2)0.109 (3)−0.0164 (17)−0.012 (2)−0.004 (2)
O10.0585 (16)0.0812 (18)0.0890 (19)−0.0077 (13)0.0197 (14)−0.0008 (15)
N50.0437 (17)0.084 (2)0.075 (2)0.0016 (15)0.0046 (15)0.0082 (17)
C190.054 (2)0.074 (3)0.073 (3)0.0110 (19)−0.0049 (19)−0.013 (2)
C200.099 (4)0.121 (4)0.135 (4)0.020 (3)0.041 (3)0.047 (3)
C210.074 (3)0.190 (5)0.103 (4)−0.014 (3)−0.022 (3)0.025 (4)

Geometric parameters (Å, °)

Br1—C181.890 (3)C13—C181.389 (4)
S1—C81.788 (3)C13—C141.402 (4)
S1—C71.795 (3)C18—C171.385 (4)
C9—C51.328 (4)C7—H7A0.9700
C9—C81.494 (4)C7—H7B0.9700
C9—H9A0.9300C14—C151.372 (4)
C1—C131.523 (4)C14—H14A0.9300
C1—C61.546 (4)C8—H8A0.9700
C1—C21.568 (4)C8—H8B0.9700
C1—H1A0.9800C15—C161.363 (5)
C5—C41.468 (4)C15—H15A0.9300
C5—C61.512 (4)C17—C161.371 (5)
C6—C71.525 (4)C17—H17A0.9300
C6—H6A0.9800C16—H16A0.9300
C4—C31.364 (4)O1—C191.216 (4)
C4—C101.431 (4)N5—C191.302 (4)
N3—C31.339 (4)N5—C211.436 (5)
N3—H3A0.79 (3)N5—C201.457 (5)
N3—H3B0.89 (4)C19—H19A0.9300
C2—C121.485 (4)C20—H20A0.9600
C2—C111.488 (4)C20—H20B0.9600
C2—C31.539 (4)C20—H20C0.9600
C10—N41.145 (3)C21—H21A0.9600
C11—N21.128 (4)C21—H21B0.9600
C12—N11.126 (4)C21—H21C0.9600
C8—S1—C796.21 (14)C6—C7—S1113.2 (2)
C5—C9—C8127.0 (3)C6—C7—H7A108.9
C5—C9—H9A116.5S1—C7—H7A108.9
C8—C9—H9A116.5C6—C7—H7B108.9
C13—C1—C6112.8 (2)S1—C7—H7B108.9
C13—C1—C2112.2 (2)H7A—C7—H7B107.7
C6—C1—C2110.9 (2)C15—C14—C13121.5 (3)
C13—C1—H1A106.8C15—C14—H14A119.2
C6—C1—H1A106.8C13—C14—H14A119.2
C2—C1—H1A106.8C9—C8—S1113.1 (2)
C9—C5—C4121.0 (2)C9—C8—H8A109.0
C9—C5—C6124.7 (2)S1—C8—H8A109.0
C4—C5—C6114.3 (2)C9—C8—H8B109.0
C5—C6—C7112.7 (2)S1—C8—H8B109.0
C5—C6—C1110.2 (2)H8A—C8—H8B107.8
C7—C6—C1108.6 (2)C16—C15—C14120.6 (3)
C5—C6—H6A108.4C16—C15—H15A119.7
C7—C6—H6A108.4C14—C15—H15A119.7
C1—C6—H6A108.4C16—C17—C18119.9 (3)
C3—C4—C10115.9 (2)C16—C17—H17A120.1
C3—C4—C5125.2 (2)C18—C17—H17A120.1
C10—C4—C5119.0 (2)C15—C16—C17119.8 (3)
C3—N3—H3A117 (2)C15—C16—H16A120.1
C3—N3—H3B124 (2)C17—C16—H16A120.1
H3A—N3—H3B115 (3)C19—N5—C21119.4 (3)
C12—C2—C11106.6 (2)C19—N5—C20122.4 (4)
C12—C2—C3107.9 (2)C21—N5—C20118.2 (3)
C11—C2—C3109.3 (2)O1—C19—N5126.2 (4)
C12—C2—C1111.9 (2)O1—C19—H19A116.9
C11—C2—C1107.8 (2)N5—C19—H19A116.9
C3—C2—C1113.1 (2)N5—C20—H20A109.5
N4—C10—C4178.4 (3)N5—C20—H20B109.5
N3—C3—C4125.4 (3)H20A—C20—H20B109.5
N3—C3—C2114.5 (2)N5—C20—H20C109.5
C4—C3—C2120.1 (2)H20A—C20—H20C109.5
N2—C11—C2177.7 (3)H20B—C20—H20C109.5
N1—C12—C2179.4 (3)N5—C21—H21A109.5
C18—C13—C14116.4 (2)N5—C21—H21B109.5
C18—C13—C1123.6 (2)H21A—C21—H21B109.5
C14—C13—C1119.9 (2)N5—C21—H21C109.5
C17—C18—C13121.7 (3)H21A—C21—H21C109.5
C17—C18—Br1116.2 (2)H21B—C21—H21C109.5
C13—C18—Br1122.1 (2)
C8—C9—C5—C4−179.0 (3)C11—C2—C3—C4133.3 (3)
C8—C9—C5—C6−0.4 (5)C1—C2—C3—C413.2 (3)
C9—C5—C6—C713.9 (4)C12—C2—C11—N2121 (9)
C4—C5—C6—C7−167.4 (2)C3—C2—C11—N2−123 (9)
C9—C5—C6—C1135.4 (3)C1—C2—C11—N21(9)
C4—C5—C6—C1−46.0 (3)C11—C2—C12—N140 (33)
C13—C1—C6—C5−174.2 (2)C3—C2—C12—N1−77 (33)
C2—C1—C6—C558.9 (3)C1—C2—C12—N1158 (100)
C13—C1—C6—C7−50.4 (3)C6—C1—C13—C18127.9 (3)
C2—C1—C6—C7−177.3 (2)C2—C1—C13—C18−106.0 (3)
C9—C5—C4—C3−164.3 (3)C6—C1—C13—C14−48.9 (3)
C6—C5—C4—C317.0 (4)C2—C1—C13—C1477.3 (3)
C9—C5—C4—C1015.7 (4)C14—C13—C18—C170.3 (4)
C6—C5—C4—C10−163.0 (2)C1—C13—C18—C17−176.5 (3)
C13—C1—C2—C12−47.4 (3)C14—C13—C18—Br1179.3 (2)
C6—C1—C2—C1279.8 (3)C1—C13—C18—Br12.4 (4)
C13—C1—C2—C1169.6 (3)C5—C6—C7—S1−49.2 (3)
C6—C1—C2—C11−163.2 (2)C1—C6—C7—S1−171.53 (19)
C13—C1—C2—C3−169.4 (2)C8—S1—C7—C662.6 (2)
C6—C1—C2—C3−42.2 (3)C18—C13—C14—C151.1 (4)
C3—C4—C10—N4−48 (11)C1—C13—C14—C15178.1 (3)
C5—C4—C10—N4131 (11)C5—C9—C8—S122.8 (4)
C10—C4—C3—N3−0.2 (4)C7—S1—C8—C9−47.3 (3)
C5—C4—C3—N3179.8 (3)C13—C14—C15—C16−1.8 (5)
C10—C4—C3—C2−179.9 (2)C13—C18—C17—C16−1.1 (5)
C5—C4—C3—C20.1 (4)Br1—C18—C17—C16179.9 (3)
C12—C2—C3—N369.1 (3)C14—C15—C16—C171.0 (5)
C11—C2—C3—N3−46.5 (3)C18—C17—C16—C150.4 (5)
C1—C2—C3—N3−166.6 (2)C21—N5—C19—O1−0.4 (6)
C12—C2—C3—C4−111.2 (3)C20—N5—C19—O1178.7 (4)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
N3—H3B···O1i0.89 (4)1.96 (4)2.856 (4)178 (3)
N3—H3A···N4ii0.79 (3)2.54 (3)3.294 (4)162 (3)
C15—H15A···O1iii0.932.543.438 (4)162

Symmetry codes: (i) −x+1, −y+1, −z+1; (ii) −x, −y, −z+1; (iii) −x+1, −y+2, −z+1.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: PV2211).

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