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Acta Cryst. (2009). E65, o41    [ doi:10.1107/S1600536808040075 ]

1,3-Dimethoxy-2,3-dihydro-1H-isoindole-2-carbothioamide

B. Maliha, M. I. Tariq, M. N. Tahir, I. Hussain and M. Ali

Abstract top

In the molecule of the title compound, C11H14N2O2S, the five-membered ring adopts an envelope conformation and an intramolecular N-H...O hydrogen bond occurs. Intramolecular N-H...O, C-H...S and C-H...N hydrogen bonds result in the formation of two five- and one six-membered rings, having twisted conformations. In the crystal structure, intermolecular N-H...O, N-H...S and C-H...S hydrogen bonds link the molecules, forming polymeric sheets. The [pi]-[pi] contacts between the isoindole ring systems, [centroid-centroid distances = 3.5883 (8) and 4.0619 (8) Å] may further stabilize the structure. A C-H...[pi] interactions also occur.

Comment top

Isoindoles and their derivatives are of great pharmaceutical importance (Mancilla et al., 2007). Certain derivatives of isoindoles have shown a wide range of herbicidal activities (Toru et al., 1986). The title compound is in continuation of the syntheses of isoindoles along with their derivatives and characterizations with the help of X-ray crystallography (Maliha et al., 2007; Maliha, Hussain et al., 2008; Maliha, Tariq et al., 2008).

In the molecule of title compound (Fig 1), the bond lengths (Allen et al., 1987) and angles are within normal ranges. Ring A (C2-C7) is, of course, planar, while the five-membered ring B (N1/C1/C2/C7/C8) adopts envelope conformation with C8 atom displaced by 0.141 (3) Å from the plane of the other ring atoms. The intramolecular N-H···O, C-H···S and C-H···N hydrogen bonds (Table 1) result in the formation of two five- and one six-membered rings: C (N1/S1/C8/C11/H8), D (O1/N1/N2/C1/C11/H2N) and E (O1/N1/C1/C9/H9C), respectively, having twisted conformations.

In the crystal structure, intermolecular N-H···O, N-H···S and C-H···S hydrogen bonds (Table 1) link the molecules to form polymeric sheets, in which the orientations of O—CH3 groups cause to the R and S-configurations at the carbon atoms, C1 and C8, respectively. The behaviour of the O—CH3 groups are not identical, because only opposite of S-atom is involved in intramolecular H-bonding. The π-π contacts between the isoindole ring systems, CgB—CgBi and CgB—CgAi [symmetry code: (i) -x, y, 1/2 - z, where CgA and CgB are centroids of the rings A (C2-C7) and B (N1/C1/C2/C7/C8)] may further stabilize the structure, with centroid-centroid distances of 3.5883 (8) Å and 4.0619 (8) Å. There also exist two C–H···π interactions (Table 1).

Related literature top

For general background to isoindoles and their derivative, see: Mancilla et al. (2007); Toru et al. (1986). For relatesd structures, see: Maliha et al. (2007); Maliha, Hussain et al. (2008); Maliha, Tariq et al. (2008). For bond-length data, see: Allen et al. (1987). CgA and CgB are centroids of the C2–C7 andN1/C1/C2/C7/C8 rings, respectively.

Experimental top

For the preparation of the title conpound, ortho-phthaldehyde (1.34 g, 200 mmol) and thiourea (0.76 g, 200 mmol) were added to distilled water (250 ml), and aqueous NaOH (5 ml, 5%) was added dropwise with constant stirring. After 3 h, a colorless precipitate was obtained, which was washed with hexane, ethanol, acetone and methanol, respectively. Then, it was further refluxed in methanol for 2 h, and left to stand overnight. The deep red tiny crystals settled down, which were washed with ether, hexane and cold methanol, respectively. Crystals suitable for X-ray analysis were obtained from a solution of acetone/methanol mixture by slow evaporation at room temperature.

Refinement top

H1, H8 (for CH) and H1N, H2N (for NH2) atoms were located in difference syntheses and refined [C-H = 0.972 (17) and 0.979 (16) Å, N-H = 0.891 (17) and 0.826 (17) Å; Uiso(H) = 1.2Ueq(C,N). The remaining H atoms were positioned geometrically, with C-H = 0.95 and 0.98 Å for aromatic 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 aromatic H atoms.

Computing details top

Data collection: APEX2 (Bruker, 2007); cell refinement: SAINT (Bruker, 2007); data reduction: SAINT (Bruker, 2007); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 for Windows (Farrugia, 1997) and PLATON (Spek, 2003); software used to prepare material for publication: 'WinGX publication routines (Farrugia, 1999) and PLATON'.

Figures top
[Figure 1] Fig. 1. The molecular structure of the title molecule, with the atom-numbering scheme. Displacement ellipsoids are drawn at the 50% probability level. Hydrogen bonds are shown as dashed lines.
[Figure 2] Fig. 2. A partial packing diagram of the title compound. Hydrogen bonds are shown as dashed lines.
(1R,3S)-1,3-dimethoxy-2,3-dihydro-1H-isoindole-2-carbothioamide top
Crystal data top
C11H14N2O2SF(000) = 1008
Mr = 238.30Dx = 1.362 Mg m−3
Monoclinic, C2/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -C 2ycCell parameters from 1295 reflections
a = 15.4577 (8) Åθ = 2.3–28.3°
b = 8.6455 (5) ŵ = 0.27 mm−1
c = 18.2184 (10) ÅT = 100 K
β = 107.322 (2)°Prismatic, red
V = 2324.3 (2) Å30.20 × 0.16 × 0.12 mm
Z = 8
Data collection top
Bruker Kappa APEXII CCD
diffractometer		2894 independent reflections
Radiation source: fine-focus sealed tube2471 reflections with I > 2σ(I)
graphiteRint = 0.032
Detector resolution: 7.40 pixels mm-1θmax = 28.3°, θmin = 2.3°
ω scansh = −20→20
Absorption correction: multi-scan
(SADABS; Bruker, 2005)		k = −11→11
Tmin = 0.945, Tmax = 0.969l = −24→23
18083 measured reflections
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.032Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.110H atoms treated by a mixture of independent and constrained refinement
S = 1.01 w = 1/[σ2(Fo2) + (0.0799P)2 + 0.660P]
where P = (Fo2 + 2Fc2)/3
2894 reflections(Δ/σ)max = 0.002
159 parametersΔρmax = 0.44 e Å−3
0 restraintsΔρmin = −0.37 e Å−3
Crystal data top
C11H14N2O2SV = 2324.3 (2) Å3
Mr = 238.30Z = 8
Monoclinic, C2/cMo Kα radiation
a = 15.4577 (8) ŵ = 0.27 mm−1
b = 8.6455 (5) ÅT = 100 K
c = 18.2184 (10) Å0.20 × 0.16 × 0.12 mm
β = 107.322 (2)°
Data collection top
Bruker Kappa APEXII CCD
diffractometer		2894 independent reflections
Absorption correction: multi-scan
(SADABS; Bruker, 2005)		2471 reflections with I > 2σ(I)
Tmin = 0.945, Tmax = 0.969Rint = 0.032
18083 measured reflectionsθmax = 28.3°
Refinement top
R[F2 > 2σ(F2)] = 0.032H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.110Δρmax = 0.44 e Å−3
S = 1.01Δρmin = −0.37 e Å−3
2894 reflectionsAbsolute structure:
159 parametersFlack parameter: ?
0 restraintsRogers parameter: ?
Special details top

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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
S10.11517 (2)0.49877 (3)0.21266 (2)0.0204 (1)
O10.14785 (6)−0.02891 (10)0.15401 (5)0.0138 (2)
O2−0.01835 (6)0.30468 (10)0.05803 (5)0.0171 (2)
N10.07220 (7)0.20405 (11)0.17484 (6)0.0120 (3)
N20.21825 (7)0.25081 (12)0.24928 (6)0.0148 (3)
C10.08273 (8)0.03577 (13)0.18556 (7)0.0110 (3)
C2−0.01336 (8)−0.02006 (14)0.15260 (7)0.0117 (3)
C3−0.04573 (8)−0.17035 (14)0.15157 (7)0.0154 (3)
C4−0.13922 (9)−0.19328 (15)0.12533 (8)0.0174 (3)
C5−0.19841 (9)−0.06902 (15)0.10138 (7)0.0167 (3)
C6−0.16516 (8)0.08113 (14)0.10175 (7)0.0141 (3)
C7−0.07174 (8)0.10380 (13)0.12693 (7)0.0119 (3)
C8−0.01925 (8)0.25238 (13)0.13215 (7)0.0128 (3)
C90.12812 (10)−0.01421 (17)0.07232 (8)0.0221 (4)
C10−0.08727 (10)0.41497 (17)0.02569 (9)0.0275 (4)
C110.13705 (8)0.30768 (14)0.21217 (7)0.0125 (3)
H10.1091 (11)0.0123 (16)0.2398 (10)0.0132*
H1N0.2602 (11)0.318 (2)0.2748 (9)0.0178*
H2N0.2325 (11)0.160 (2)0.2447 (9)0.0178*
H3−0.00537−0.254870.168250.0184*
H4−0.16291−0.295030.123740.0208*
H5−0.26194−0.086730.084670.0201*
H6−0.205330.165940.085190.0169*
H8−0.0393 (10)0.3344 (18)0.1604 (9)0.0153*
H9A0.07524−0.077790.046760.0265*
H9B0.18042−0.049090.056810.0265*
H9C0.115200.094290.057530.0265*
H10A−0.146790.368070.019250.0330*
H10B−0.082900.44837−0.024490.0330*
H10C−0.079670.504560.059980.0330*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
S10.0134 (2)0.0095 (2)0.0347 (2)0.0004 (1)0.0018 (2)−0.0017 (1)
O10.0126 (4)0.0154 (4)0.0131 (4)0.0039 (3)0.0032 (3)−0.0015 (3)
O20.0180 (4)0.0163 (4)0.0155 (4)0.0019 (3)0.0025 (4)0.0062 (3)
N10.0103 (5)0.0095 (4)0.0144 (5)0.0014 (3)0.0010 (4)0.0007 (4)
N20.0121 (5)0.0107 (5)0.0195 (5)0.0001 (4)0.0013 (4)−0.0006 (4)
C10.0115 (5)0.0089 (5)0.0119 (5)0.0016 (4)0.0024 (4)0.0000 (4)
C20.0105 (5)0.0133 (5)0.0109 (5)0.0006 (4)0.0025 (4)−0.0007 (4)
C30.0161 (6)0.0124 (5)0.0162 (6)0.0005 (4)0.0026 (5)−0.0008 (4)
C40.0182 (6)0.0145 (6)0.0184 (6)−0.0043 (4)0.0040 (5)−0.0014 (5)
C50.0123 (5)0.0208 (6)0.0160 (6)−0.0035 (5)0.0027 (5)−0.0001 (5)
C60.0126 (5)0.0160 (6)0.0130 (6)0.0016 (4)0.0027 (4)0.0011 (4)
C70.0134 (5)0.0121 (5)0.0098 (5)0.0006 (4)0.0030 (4)−0.0004 (4)
C80.0113 (5)0.0116 (5)0.0138 (5)0.0013 (4)0.0013 (4)0.0011 (4)
C90.0224 (7)0.0315 (8)0.0134 (6)0.0055 (5)0.0069 (5)−0.0018 (5)
C100.0194 (6)0.0282 (7)0.0313 (8)0.0045 (5)0.0021 (6)0.0163 (6)
C110.0127 (5)0.0127 (5)0.0126 (5)−0.0006 (4)0.0046 (4)0.0003 (4)
Geometric parameters (Å, °) top
S1—C111.6869 (12)C5—C61.3954 (18)
O1—C11.4145 (16)C6—C71.3927 (18)
O1—C91.4331 (16)C7—C81.5072 (17)
O2—C81.4280 (15)C1—H10.972 (17)
O2—C101.4204 (18)C3—H30.9500
N1—C11.4705 (15)C4—H40.9500
N1—C81.4571 (17)C5—H50.9500
N1—C111.3653 (16)C6—H60.9500
N2—C111.3300 (17)C8—H80.979 (16)
N2—H1N0.891 (17)C9—H9A0.9800
N2—H2N0.826 (17)C9—H9B0.9800
C1—C21.5062 (18)C9—H9C0.9800
C2—C71.3887 (17)C10—H10A0.9800
C2—C31.3905 (17)C10—H10B0.9800
C3—C41.3946 (19)C10—H10C0.9800
C4—C51.3942 (19)
S1···O23.3984 (10)C6···H10A2.9600
S1···N2i3.2857 (11)C6···H1vi2.819 (17)
S1···H3ii2.7900C6···H9Biv2.8400
S1···H82.697 (16)C7···H1vi2.773 (17)
S1···H2Ni2.646 (17)C7···H10A3.0100
O1···N22.9867 (14)C10···H10Bv2.8900
O1···N2iii2.9738 (14)C10···H5vii2.9800
O2···S13.3984 (10)H1···N22.637 (16)
O1···H1Niii2.087 (17)H1···H2N2.28 (2)
O1···H2N2.413 (17)H1···C2vi2.800 (18)
O2···H9C2.7500H1···C3vi2.920 (17)
O2···H9Aiv2.7000H1···C4vi2.955 (16)
O2···H10Bv2.8200H1···C5vi2.897 (17)
N2···C6vi3.3938 (16)H1···C6vi2.819 (17)
N2···O12.9867 (14)H1···C7vi2.773 (17)
N2···O1i2.9738 (14)H1N···O1i2.087 (17)
N2···S1iii3.2857 (11)H1N···C1i2.986 (17)
N1···H9C2.6000H2N···O12.413 (17)
N2···H12.637 (16)H2N···C12.488 (17)
C1···C2vi3.4582 (18)H2N···H12.28 (2)
C1···C7vi3.5200 (17)H2N···S1iii2.646 (17)
C2···C2vi3.4486 (17)H3···S1viii2.7900
C2···C1vi3.4582 (18)H5···C10vii2.9800
C3···C3vi3.4413 (17)H6···H10A2.4400
C6···N2vi3.3938 (16)H6···H10Avii2.5200
C6···C9iv3.4352 (19)H8···S12.697 (16)
C6···C103.563 (2)H8···H10C2.2800
C7···C1vi3.5200 (17)H9A···C22.7200
C7···C9iv3.5571 (19)H9A···O2iv2.7000
C9···C7iv3.5571 (19)H9B···C6iv2.8400
C9···C6iv3.4352 (19)H9C···O22.7500
C10···C10v3.438 (2)H9C···N12.6000
C10···C63.563 (2)H10A···C62.9600
C1···H1Niii2.986 (17)H10A···C73.0100
C1···H2N2.488 (17)H10A···H62.4400
C2···H9A2.7200H10A···H6vii2.5200
C2···H1vi2.800 (18)H10B···O2v2.8200
C3···H1vi2.920 (17)H10B···C10v2.8900
C4···H1vi2.955 (16)H10C···H82.2800
C5···H1vi2.897 (17)
C1—O1—C9115.45 (10)O1—C1—H1101.4 (10)
C8—O2—C10112.80 (10)N1—C1—H1109.8 (8)
C1—N1—C8113.96 (10)C2—C1—H1113.8 (10)
C1—N1—C11123.18 (10)C2—C3—H3121.00
C8—N1—C11121.97 (10)C4—C3—H3121.00
H1N—N2—H2N119.8 (16)C3—C4—H4120.00
C11—N2—H1N117.0 (11)C5—C4—H4120.00
C11—N2—H2N122.7 (12)C4—C5—H5120.00
O1—C1—N1113.65 (10)C6—C5—H5120.00
O1—C1—C2116.61 (10)C5—C6—H6121.00
N1—C1—C2101.95 (10)C7—C6—H6121.00
C1—C2—C3127.81 (11)O2—C8—H8111.2 (9)
C3—C2—C7121.39 (12)N1—C8—H8109.6 (9)
C1—C2—C7110.61 (10)C7—C8—H8113.7 (9)
C2—C3—C4118.00 (12)O1—C9—H9A109.00
C3—C4—C5120.95 (12)O1—C9—H9B109.00
C4—C5—C6120.59 (13)O1—C9—H9C109.00
C5—C6—C7118.48 (11)H9A—C9—H9B109.00
C2—C7—C6120.56 (11)H9A—C9—H9C109.00
C2—C7—C8110.63 (11)H9B—C9—H9C109.00
C6—C7—C8128.80 (11)O2—C10—H10A109.00
N1—C8—C7101.99 (9)O2—C10—H10B109.00
O2—C8—N1108.33 (10)O2—C10—H10C109.00
O2—C8—C7111.52 (10)H10A—C10—H10B109.00
S1—C11—N1121.78 (10)H10A—C10—H10C109.00
S1—C11—N2121.31 (10)H10B—C10—H10C109.00
N1—C11—N2116.90 (11)
C9—O1—C1—N1−62.73 (14)N1—C1—C2—C3−175.58 (12)
C9—O1—C1—C255.45 (14)N1—C1—C2—C7−0.62 (13)
C10—O2—C8—N1−153.14 (10)C1—C2—C3—C4173.19 (12)
C10—O2—C8—C795.39 (12)C7—C2—C3—C4−1.28 (19)
C8—N1—C1—O1120.77 (11)C1—C2—C7—C6−173.11 (11)
C8—N1—C1—C2−5.57 (13)C1—C2—C7—C86.27 (14)
C11—N1—C1—O1−69.90 (15)C3—C2—C7—C62.22 (19)
C11—N1—C1—C2163.77 (11)C3—C2—C7—C8−178.40 (11)
C1—N1—C8—O2−108.78 (11)C2—C3—C4—C5−0.45 (19)
C1—N1—C8—C78.96 (13)C3—C4—C5—C61.3 (2)
C11—N1—C8—O281.74 (13)C4—C5—C6—C7−0.33 (19)
C11—N1—C8—C7−160.52 (11)C5—C6—C7—C2−1.37 (18)
C1—N1—C11—S1−167.45 (9)C5—C6—C7—C8179.37 (12)
C1—N1—C11—N211.57 (18)C2—C7—C8—O2106.35 (12)
C8—N1—C11—S11.05 (17)C2—C7—C8—N1−9.08 (13)
C8—N1—C11—N2−179.93 (11)C6—C7—C8—O2−74.34 (16)
O1—C1—C2—C360.04 (17)C6—C7—C8—N1170.24 (12)
O1—C1—C2—C7−125.00 (11)
Symmetry codes: (i) −x+1/2, y+1/2, −z+1/2; (ii) x, y+1, z; (iii) −x+1/2, y−1/2, −z+1/2; (iv) −x, −y, −z; (v) −x, −y+1, −z; (vi) −x, y, −z+1/2; (vii) −x−1/2, −y+1/2, −z; (viii) x, y−1, z.
Hydrogen-bond geometry (Å, °) top
D—H···AD—HH···AD···AD—H···A
N2—H1N···O1i0.891 (17)2.087 (17)2.9738 (14)172.9 (15)
N2—H2N···O10.826 (17)2.413 (17)2.9867 (14)127.3 (14)
N2—H2N···S1iii0.826 (17)2.646 (17)3.2857 (11)135.4 (15)
C3—H3···S1viii0.95002.79003.7362 (13)178.00
C8—H8···S10.979 (16)2.697 (16)3.0318 (12)100.5 (11)
C9—H9C···N10.98002.60002.9593 (18)102.00
C1—H1···CgBvi0.98002.500 (17)3.4059 (13)155.1 (1)
C9—H9C···CgA0.98002.742.9052 (16)90
Symmetry codes: (i) −x+1/2, y+1/2, −z+1/2; (iii) −x+1/2, y−1/2, −z+1/2; (viii) x, y−1, z; (vi) −x, y, −z+1/2.
Table 1
Hydrogen-bond geometry (Å, °) top
D—H···AD—HH···AD···AD—H···A
N2—H1N···O1i0.891 (17)2.087 (17)2.9738 (14)172.9 (15)
N2—H2N···O10.826 (17)2.413 (17)2.9867 (14)127.3 (14)
N2—H2N···S1ii0.826 (17)2.646 (17)3.2857 (11)135.4 (15)
C3—H3···S1iii0.95002.79003.7362 (13)178.00
C8—H8···S10.979 (16)2.697 (16)3.0318 (12)100.5 (11)
C9—H9C···N10.98002.60002.9593 (18)102.00
C1—H1···CgBiv0.98002.500 (17)3.4059 (13)155.1 (1)
C9—H9C···CgA0.98002.742.9052 (16)90
Symmetry codes: (i) −x+1/2, y+1/2, −z+1/2; (ii) −x+1/2, y−1/2, −z+1/2; (iii) x, y−1, z; (iv) −x, y, −z+1/2.
references
References top

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