organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

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ISSN: 2056-9890

3-Amino-4,6-di­methyl­thieno[2,3-b]pyridine-2-carbo­nitrile

aDepartment of Pharmaceutical and Bioengineering, School of Chemical Engineering, Sichuan University, Chengdu 610065, People's Republic of China, and bState Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, People's Republic of China
*Correspondence e-mail: yangli@scu.edu.cn

(Received 5 November 2009; accepted 13 November 2009; online 21 November 2009)

The mol­ecule of the title compound, C10H9N3S, is almost planar, with a dihedral angle of 1.38 (4)° between the thio­phene and pyridine rings. In the crystal packing, mol­ecules are linked into layers parallel to the ab plane by inter­molecular N—H⋯N hydrogen bonds and by ππ stacking inter­actions involving adjacent pyridine and thio­phene rings with a centroid–centroid distance of 3.537 (3) Å.

Related literature

For the biological properties of thieno[2,3-b]pyridine derivatives, see: Litvinov et al. (2005[Litvinov, V. P., Dotsenko, V. V. & Krivokolysko, S. G. (2005). Russ. Chem. Bull. 54, 864-904.]).

[Scheme 1]

Experimental

Crystal data
  • C10H9N3S

  • Mr = 203.26

  • Orthorhombic, P b c a

  • a = 14.562 (3) Å

  • b = 8.1252 (16) Å

  • c = 16.211 (3) Å

  • V = 1918.1 (7) Å3

  • Z = 8

  • Mo Kα radiation

  • μ = 0.30 mm−1

  • T = 113 K

  • 0.26 × 0.25 × 0.20 mm

Data collection
  • Rigaku Saturn CCD area detector diffractometer

  • Absorption correction: multi-scan (ABSCOR; Higashi, 1995[Higashi, T. (1995). ABSCOR, Rigaku Corporation, Tokyo, Japan.]) Tmin = 0.927, Tmax = 0.943

  • 16095 measured reflections

  • 2280 independent reflections

  • 2047 reflections with I > 2σ(I)

  • Rint = 0.038

Refinement
  • R[F2 > 2σ(F2)] = 0.037

  • wR(F2) = 0.101

  • S = 1.04

  • 2280 reflections

  • 137 parameters

  • H atoms treated by a mixture of independent and constrained refinement

  • Δρmax = 0.33 e Å−3

  • Δρmin = −0.34 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
N2—H1N⋯N1i 0.881 (19) 2.180 (19) 3.0361 (17) 163.9 (17)
N2—H2N⋯N3ii 0.89 (2) 2.35 (2) 3.0900 (18) 141.1 (16)
Symmetry codes: (i) [x+{\script{1\over 2}}, y, -z+{\script{3\over 2}}]; (ii) [-x+1, y-{\script{1\over 2}}, -z+{\script{3\over 2}}].

Data collection: CrystalClear (Rigaku/MSC,2005[Rigaku/MSC (2005). CrystalClear. Rigaku/MSC, The Woodlands, Texas, USA. ]); cell refinement: CrystalClear; data reduction: CrystalClear; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); molecular graphics: ORTEPIII (Burnett & Johnson, 1996[Burnett, M. N. & Johnson, C. K. (1996). ORTEPIII. Report ORNL-6895. Oak Ridge National Laboratory, Tennessee, USA.]); software used to prepare material for publication: PLATON (Spek, 2009[Spek, A. L. (2009). Acta Cryst. D65, 148-155.]).

Supporting information


Comment top

Thieno[2,3-b]pyridine derivatives are of great importance owing to their wide biological properties (Litvinov et al., 2005). The title compound is one of the key intermediates in our research aimed at the synthesis and investigation of new antitumor drugs. We report here its crystal structure.

The thieno[2,3-b]pyridine ring system of the title molecule (Fig. 1) is almost planar, the dihedral angle formed by the thiophene and pyridine rings being 1.38 (4)°. The N2 amine atom, the C8/N3 nitrile atoms and the C9/C10 methyl atoms are displaced from the mean plane through the dimethylthieno[2,3-b]pyridine ring system by 0.0761 (13), 0.0478 (14), 0.0922 (13), 0.0934 (15) and 0.0680 (15) Å, respectively. In the crystal structure (Fig. 2), the molecules are linked into layers parallel to the ab plane by intermolecular N—H···N hydrogen bonds (Table 1) and by π···π stacking interactions involving adjacent pyridine and thiophene rings, with a centroid-to-centroid distance of 3.537 (3) Å.

Related literature top

For the biological properties of thieno[2,3-b]pyridine derivatives, see: Litvinov et al. (2005).

Experimental top

To a suspension of 4,6-dimethyl-3-cyanopyridine-2-(1H)-thione (1.7 g, 10 mmol) in DMF (20 ml) was added a 10% aqueous KOH solution (5.6 ml,10 mmol) followed by the addition of chloroacetonitrile (0.8 g, 10 mmol) at room temperature. After stirring for 10–15 min at r.t., a 10% aqueous KOH solution (5.6 ml,10 mmol) was added and the mixture heated to 358 K for 6 h. The reaction mixture was then allowed to cool to r.t., the precipitate was collected by filtration and washed with cold ethanol, then it was recrystallized from ethanol to give a white solid (1.6 g, 80% yield). Crystals suitable for X-ray analysis were obtained by slow evaporation of a methanol/dichloromethane (1:2 v/v) solution.

Refinement top

H atoms of the amino group were located in a difference map and refined freely. All other H atoms were positioned geometrically and refined using a riding model, with C—H = 0.93–0.97 Å and with Uiso(H) = 1.2 Ueq(C) or 1.5 Ueq(C) for methyl H atoms.

Computing details top

Data collection: CrystalClear (Rigaku/MSC,2005); cell refinement: CrystalClear (Rigaku/MSC,2005); data reduction: CrystalClear (Rigaku/MSC,2005); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEPIII (Burnett & Johnson, 1996); software used to prepare material for publication: PLATON (Spek, 2009).

Figures top
[Figure 1] Fig. 1. The molecular structure of the title compound, with displacement ellipsoids drawn at the 30% probability level.
[Figure 2] Fig. 2. Packing diagram of the title compound. Hydrogen bonds are shown as dotted lines.
3-amino-4,6-dimethylthieno[2,3-b]pyridine-2-carbonitrile top
Crystal data top
C10H9N3SF(000) = 848
Mr = 203.26Dx = 1.408 Mg m3
Orthorhombic, PbcaMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ac 2abCell parameters from 5470 reflections
a = 14.562 (3) Åθ = 2.5–27.9°
b = 8.1252 (16) ŵ = 0.30 mm1
c = 16.211 (3) ÅT = 113 K
V = 1918.1 (7) Å3Block, colourless
Z = 80.26 × 0.25 × 0.20 mm
Data collection top
Rigaku Saturn CCD area detector
diffractometer
2280 independent reflections
Radiation source: rotating anode2047 reflections with I > 2σ(I)
Confocal monochromatorRint = 0.038
Detector resolution: 7.31 pixels mm-1θmax = 27.9°, θmin = 3.1°
ω and ϕ scansh = 1918
Absorption correction: multi-scan
(ABSCOR; Higashi, 1995)
k = 108
Tmin = 0.927, Tmax = 0.943l = 2121
16095 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)] = 0.037Hydrogen site location: mixed
wR(F2) = 0.101H atoms treated by a mixture of independent and constrained refinement
S = 1.04 w = 1/[σ2(Fo2) + (0.0627P)2 + 0.6561P]
where P = (Fo2 + 2Fc2)/3
2280 reflections(Δ/σ)max = 0.001
137 parametersΔρmax = 0.33 e Å3
0 restraintsΔρmin = 0.34 e Å3
Crystal data top
C10H9N3SV = 1918.1 (7) Å3
Mr = 203.26Z = 8
Orthorhombic, PbcaMo Kα radiation
a = 14.562 (3) ŵ = 0.30 mm1
b = 8.1252 (16) ÅT = 113 K
c = 16.211 (3) Å0.26 × 0.25 × 0.20 mm
Data collection top
Rigaku Saturn CCD area detector
diffractometer
2280 independent reflections
Absorption correction: multi-scan
(ABSCOR; Higashi, 1995)
2047 reflections with I > 2σ(I)
Tmin = 0.927, Tmax = 0.943Rint = 0.038
16095 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0370 restraints
wR(F2) = 0.101H atoms treated by a mixture of independent and constrained refinement
S = 1.04Δρmax = 0.33 e Å3
2280 reflectionsΔρmin = 0.34 e Å3
137 parameters
Special details top

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) top
xyzUiso*/Ueq
S10.20101 (2)0.66501 (4)0.69746 (2)0.01744 (13)
N10.09825 (8)0.51450 (14)0.81134 (7)0.0168 (3)
N20.43428 (8)0.53762 (16)0.80376 (7)0.0197 (3)
H1N0.4779 (13)0.550 (2)0.7666 (11)0.030 (5)*
H2N0.4479 (13)0.463 (2)0.8416 (12)0.032 (5)*
N30.42910 (9)0.79977 (16)0.61222 (7)0.0231 (3)
C10.09139 (9)0.42573 (17)0.88087 (8)0.0175 (3)
C20.16908 (9)0.37944 (17)0.92658 (8)0.0179 (3)
H20.16080.31890.97620.021*
C30.25762 (9)0.41919 (17)0.90166 (8)0.0163 (3)
C40.26566 (9)0.50818 (16)0.82730 (8)0.0150 (3)
C50.34563 (9)0.56490 (16)0.78168 (8)0.0154 (3)
C60.31997 (10)0.65374 (17)0.71273 (9)0.0170 (3)
C70.18349 (9)0.55260 (17)0.78720 (8)0.0151 (3)
C80.38019 (9)0.73372 (17)0.65747 (8)0.0175 (3)
C90.00311 (9)0.37597 (18)0.90758 (9)0.0222 (3)
H9A0.03520.47160.93050.033*
H9B0.00130.28990.94970.033*
H9C0.03730.33380.86000.033*
C100.33843 (10)0.36632 (19)0.95308 (8)0.0225 (3)
H10A0.31650.30991.00270.034*
H10B0.37430.46330.96900.034*
H10C0.37720.29130.92100.034*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
S10.0131 (2)0.0222 (2)0.0170 (2)0.00032 (12)0.00226 (11)0.00211 (12)
N10.0128 (6)0.0185 (6)0.0190 (5)0.0002 (4)0.0006 (4)0.0026 (4)
N20.0116 (6)0.0276 (7)0.0198 (6)0.0016 (5)0.0007 (4)0.0031 (5)
N30.0209 (6)0.0269 (7)0.0217 (6)0.0034 (5)0.0009 (5)0.0004 (5)
C10.0153 (7)0.0178 (6)0.0194 (6)0.0003 (5)0.0022 (5)0.0038 (5)
C20.0175 (7)0.0198 (7)0.0165 (6)0.0004 (5)0.0025 (5)0.0011 (5)
C30.0154 (6)0.0175 (6)0.0159 (6)0.0016 (5)0.0006 (5)0.0035 (5)
C40.0127 (6)0.0158 (6)0.0165 (6)0.0001 (5)0.0000 (5)0.0032 (5)
C50.0129 (6)0.0166 (6)0.0166 (6)0.0003 (5)0.0008 (5)0.0031 (5)
C60.0131 (6)0.0201 (7)0.0178 (6)0.0005 (5)0.0003 (5)0.0011 (5)
C70.0140 (6)0.0155 (6)0.0157 (6)0.0004 (5)0.0012 (5)0.0023 (5)
C80.0156 (6)0.0194 (6)0.0175 (6)0.0004 (5)0.0026 (5)0.0019 (5)
C90.0141 (7)0.0269 (8)0.0255 (7)0.0019 (5)0.0028 (5)0.0012 (6)
C100.0180 (7)0.0316 (8)0.0179 (6)0.0027 (6)0.0012 (5)0.0037 (6)
Geometric parameters (Å, º) top
S1—C71.7366 (14)C3—C41.4104 (18)
S1—C61.7522 (15)C3—C101.5047 (19)
N1—C71.3377 (17)C4—C71.4088 (18)
N1—C11.3419 (17)C4—C51.4546 (18)
N2—C51.3579 (17)C5—C61.3820 (19)
N2—H1N0.881 (19)C6—C81.4121 (19)
N2—H2N0.89 (2)C9—H9A0.9800
N3—C81.1547 (18)C9—H9B0.9800
C1—C21.4038 (19)C9—H9C0.9800
C1—C91.4982 (18)C10—H10A0.9800
C2—C31.3892 (19)C10—H10B0.9800
C2—H20.9500C10—H10C0.9800
C7—S1—C689.97 (7)C5—C6—C8125.84 (13)
C7—N1—C1116.05 (11)C5—C6—S1114.14 (10)
C5—N2—H1N119.1 (12)C8—C6—S1120.02 (11)
C5—N2—H2N120.5 (12)N1—C7—C4126.42 (12)
H1N—N2—H2N112.9 (16)N1—C7—S1120.21 (10)
N1—C1—C2121.83 (12)C4—C7—S1113.36 (10)
N1—C1—C9117.14 (12)N3—C8—C6179.64 (15)
C2—C1—C9121.03 (12)C1—C9—H9A109.5
C3—C2—C1122.15 (13)C1—C9—H9B109.5
C3—C2—H2118.9H9A—C9—H9B109.5
C1—C2—H2118.9C1—C9—H9C109.5
C2—C3—C4116.41 (12)H9A—C9—H9C109.5
C2—C3—C10119.88 (12)H9B—C9—H9C109.5
C4—C3—C10123.71 (12)C3—C10—H10A109.5
C7—C4—C3117.08 (12)C3—C10—H10B109.5
C7—C4—C5111.36 (12)H10A—C10—H10B109.5
C3—C4—C5131.56 (12)C3—C10—H10C109.5
N2—C5—C6123.75 (13)H10A—C10—H10C109.5
N2—C5—C4125.13 (12)H10B—C10—H10C109.5
C6—C5—C4111.11 (12)
C7—N1—C1—C21.59 (19)N2—C5—C6—C82.6 (2)
C7—N1—C1—C9177.76 (12)C4—C5—C6—C8176.41 (13)
N1—C1—C2—C31.6 (2)N2—C5—C6—S1178.35 (11)
C9—C1—C2—C3177.76 (13)C4—C5—C6—S12.65 (15)
C1—C2—C3—C40.4 (2)C7—S1—C6—C51.57 (11)
C1—C2—C3—C10179.98 (13)C7—S1—C6—C8177.55 (12)
C2—C3—C4—C72.05 (18)C1—N1—C7—C40.3 (2)
C10—C3—C4—C7178.37 (12)C1—N1—C7—S1179.24 (10)
C2—C3—C4—C5177.59 (13)C3—C4—C7—N12.2 (2)
C10—C3—C4—C52.0 (2)C5—C4—C7—N1177.56 (13)
C7—C4—C5—N2178.43 (13)C3—C4—C7—S1178.83 (10)
C3—C4—C5—N21.2 (2)C5—C4—C7—S11.46 (15)
C7—C4—C5—C62.60 (16)C6—S1—C7—N1179.09 (12)
C3—C4—C5—C6177.75 (14)C6—S1—C7—C40.00 (11)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N2—H1N···N1i0.881 (19)2.180 (19)3.0361 (17)163.9 (17)
N2—H2N···N3ii0.89 (2)2.35 (2)3.0900 (18)141.1 (16)
Symmetry codes: (i) x+1/2, y, z+3/2; (ii) x+1, y1/2, z+3/2.

Experimental details

Crystal data
Chemical formulaC10H9N3S
Mr203.26
Crystal system, space groupOrthorhombic, Pbca
Temperature (K)113
a, b, c (Å)14.562 (3), 8.1252 (16), 16.211 (3)
V3)1918.1 (7)
Z8
Radiation typeMo Kα
µ (mm1)0.30
Crystal size (mm)0.26 × 0.25 × 0.20
Data collection
DiffractometerRigaku Saturn CCD area detector
diffractometer
Absorption correctionMulti-scan
(ABSCOR; Higashi, 1995)
Tmin, Tmax0.927, 0.943
No. of measured, independent and
observed [I > 2σ(I)] reflections
16095, 2280, 2047
Rint0.038
(sin θ/λ)max1)0.658
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.037, 0.101, 1.04
No. of reflections2280
No. of parameters137
H-atom treatmentH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å3)0.33, 0.34

Computer programs: CrystalClear (Rigaku/MSC,2005), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), ORTEPIII (Burnett & Johnson, 1996), PLATON (Spek, 2009).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N2—H1N···N1i0.881 (19)2.180 (19)3.0361 (17)163.9 (17)
N2—H2N···N3ii0.89 (2)2.35 (2)3.0900 (18)141.1 (16)
Symmetry codes: (i) x+1/2, y, z+3/2; (ii) x+1, y1/2, z+3/2.
 

Acknowledgements

The project was sponsored by the Scientific Research Foundation for Returned Overseas Chinese Scholars (No. 20071108–18-14), State Education Ministry. We thank the Analytical and Testing Center of Sichuan University for the X-ray measurements.

References

First citationBurnett, M. N. & Johnson, C. K. (1996). ORTEPIII. Report ORNL-6895. Oak Ridge National Laboratory, Tennessee, USA.  Google Scholar
First citationHigashi, T. (1995). ABSCOR, Rigaku Corporation, Tokyo, Japan.  Google Scholar
First citationLitvinov, V. P., Dotsenko, V. V. & Krivokolysko, S. G. (2005). Russ. Chem. Bull. 54, 864–904.  Web of Science CrossRef CAS Google Scholar
First citationRigaku/MSC (2005). CrystalClear. Rigaku/MSC, The Woodlands, Texas, USA.  Google Scholar
First citationSheldrick, G. M. (2008). Acta Cryst. A64, 112–122.  Web of Science CrossRef CAS IUCr Journals Google Scholar
First citationSpek, A. L. (2009). Acta Cryst. D65, 148–155.  Web of Science CrossRef CAS IUCr Journals Google Scholar

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