PMCCPMCCPMCC

Search tips
Search criteria 

Advanced

 
Logo of actaeInternational Union of Crystallographysearchopen accessarticle submissionjournal home pagethis article
 
Acta Crystallogr Sect E Struct Rep Online. 2010 March 1; 66(Pt 3): o518.
Published online 2010 February 3. doi:  10.1107/S1600536810003089
PMCID: PMC2983532

2-[(2,6-Dichloro­benz­yl)amino]-N-(4-methyl­thia­zol-2-yl)acetamide

Abstract

In the title compound, C13H13Cl2N3OS, the thia­zole and benzene rings are roughly parallel to one another in two layers [dihedral angle = 5.08 (2)°] because the N—C—C—N—C chain that links the two rings is folded [N—C—C—N torsion angle = 12.0 (2)°] rather than fully extended. An intra­molecular N—H(...)N inter­action occurs. In the crystal, weak inter­molecular N—H(...)N and C—H(...)O inter­actions are present and π–π inter­actions are indicated by the short distances [3.507 (3)–3.665 (2) Å] between the centroids of the thia­zole and benzene rings.

Related literature

For details of the biological activity of Dipeptidyl peptidase IV (DPP-IV) inhibitors, see: Cheon et al. (2005 [triangle]); Kondo et al. (2007 [triangle]); Sakashita et al. (2006 [triangle]); Zhan et al. (2009 [triangle]). For bond-length data, see: Allen et al. (1987 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-66-0o518-scheme1.jpg

Experimental

Crystal data

  • C13H13Cl2N3OS
  • M r = 330.22
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-66-0o518-efi1.jpg
  • a = 14.008 (4) Å
  • b = 18.133 (5) Å
  • c = 11.390 (3) Å
  • β = 97.341 (3)°
  • V = 2869.4 (14) Å3
  • Z = 8
  • Mo Kα radiation
  • μ = 0.60 mm−1
  • T = 113 K
  • 0.22 × 0.18 × 0.16 mm

Data collection

  • Rigaku Saturn diffractometer
  • Absorption correction: multi-scan (CrystalClear; Rigaku, 2007 [triangle]) T min = 0.880, T max = 0.911
  • 11103 measured reflections
  • 3371 independent reflections
  • 3150 reflections with I > 2σ(I)
  • R int = 0.036

Refinement

  • R[F 2 > 2σ(F 2)] = 0.056
  • wR(F 2) = 0.131
  • S = 1.20
  • 3371 reflections
  • 191 parameters
  • H atoms treated by a mixture of independent and constrained refinement
  • Δρmax = 0.65 e Å−3
  • Δρmin = −0.83 e Å−3

Data collection: CrystalClear (Rigaku, 2007 [triangle]); cell refinement: CrystalClear; data reduction: CrystalClear; 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 I, global. DOI: 10.1107/S1600536810003089/fl2286sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536810003089/fl2286Isup2.hkl

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

supplementary crystallographic information

Comment

Dipeptidyl peptidase IV (DPP-IV) inhibitors are a new class of antidiabetic agents (Cheon et al., 2005; Kondo et al., 2007; Sakashita et al., 2006) and the title compound was prepared as a novel DPP-IV inhibitor (Zhan et al., 2009). We reported the crystal structure here.

In title compound, all bond lengths in the molecular are normal (Allen et al., 1987). Atoms C4—C6/N2/N3/O1 lie in thiazole (C1—C3/N1/S1) plane with maximun least squares plane deviation for C4 0.065 (2) Å. Thiazole ring (C1—C3/N1/S1) and benzene ring (C8—C13) are essentially parallel to one another (dihedral angle of 5.08 (2) °) because the N—C—C—N—C chain that links the two rings is folded ((N—C—C—N torsion angle of 12.0 (2) °) rather than fully extended. π—π interactions are indicated by the short distance (Cg1···Cg1 distance of 3.665 (2) Å, symmetry code: 1-x,y,1/2-z; Cg1···Cg2 distance of 3.766 (3) Å, symmetry code: 1/2-x,1/2-y,-z; Cg1···Cg2 distance of 3.507 (3) Å, symmetry code: 1-x,y,-1/2-z) between the centroids of the thiazole rings C1—C3/N1/S1 (Cg1) and benzene rings C8—C13 (Cg2) (Table 1). There are intramolecular interaction and weaker N—H···N, C—H···O intermolecular interactions, which stabilized the structure (Table 1).

Experimental

A round-bottomed flask was charged with [(2,6-dichlorophenyl)methyl]amine (1.76 g, 10 mmol), 2-[(2-chloroacetyl)amino]-4-methylthiazole (1.91 g, 10 mmol), triethylamine (1.21 g, 12 mmol) and THF (20 ml), and the resulting mixture was stirred at room temperature over night. The reaction mixture was concentrated on a rotary evaporator and diluted with 100 ml of dichloromethane, and the organic solution thus obtained was washed with saturated brine, dried over sodium sulfate and evaporated on a rotary evaporator to afford a solid residue, which was triturated with a mixed solvent consisting of 5 ml of dichloromethane and 10 ml of ethyl acetate and filtered. The crystals were collected and dried to yield the title compound as colorless crystals 2.51 g (Yield 76.1%). Crystals suitable for single-crystal X-ray diffraction were obtained via slow evaporation at room temperature of a solution of the pure title compound in dichloromethane.

Refinement

All H atoms were found on difference maps. The H atoms of secondary amine were refined freely, giveing 0.84 or 0.89 Å, and C—H hyrdogens in the final cycles of refinement using a riding model, giveing 0.95-0.99 Å, with Uiso(H) = 1.2Ueq(C) and 1.5Ueq(C) for the methyl H atoms.

Figures

Fig. 1.
The molecular structure of (I), with atom labels and 40% probability displacement ellipsoids for non-H atoms.
Fig. 2.
A packing diagram of the molecule of the title compound, view down b axis. Hydrogen bonds are shown as dashed lines.

Crystal data

C13H13Cl2N3OSF(000) = 1360
Mr = 330.22Dx = 1.529 Mg m3
Monoclinic, C2/cMo Kα radiation, λ = 0.71075 Å
Hall symbol: -C 2ycCell parameters from 5153 reflections
a = 14.008 (4) Åθ = 1.8–27.9°
b = 18.133 (5) ŵ = 0.60 mm1
c = 11.390 (3) ÅT = 113 K
β = 97.341 (3)°Prism, colorless
V = 2869.4 (14) Å30.22 × 0.18 × 0.16 mm
Z = 8

Data collection

Rigaku Saturn diffractometer3371 independent reflections
Radiation source: rotating anode3150 reflections with I > 2σ(I)
multilayerRint = 0.036
Detector resolution: 14.63 pixels mm-1θmax = 27.9°, θmin = 1.9°
ω and [var phi] scansh = −18→18
Absorption correction: multi-scan (CrystalClear; Rigaku, 2007)k = −23→18
Tmin = 0.880, Tmax = 0.911l = −13→14
11103 measured reflections

Refinement

Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.056H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.131w = 1/[σ2(Fo2) + (0.0837P)2 + 0.6909P] where P = (Fo2 + 2Fc2)/3
S = 1.20(Δ/σ)max < 0.001
3371 reflectionsΔρmax = 0.65 e Å3
191 parametersΔρmin = −0.83 e Å3
0 restraintsExtinction correction: SHELXL97 (Sheldrick, 2008), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
Primary atom site location: structure-invariant direct methodsExtinction coefficient: 0.086 (3)

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 > 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
Cl10.59889 (3)0.30694 (2)0.64087 (4)0.03507 (18)
Cl20.60026 (3)0.00844 (2)0.65202 (3)0.03000 (17)
S10.60179 (3)0.37651 (2)0.15270 (3)0.02879 (17)
O10.59946 (9)0.22476 (8)0.16770 (10)0.0371 (3)
N20.65223 (10)0.28348 (8)0.33975 (11)0.0262 (3)
N10.66017 (10)0.41118 (7)0.37000 (11)0.0260 (3)
N30.66669 (9)0.15932 (7)0.46748 (11)0.0244 (3)
C10.64101 (10)0.35505 (9)0.29875 (12)0.0242 (3)
C20.64316 (12)0.47666 (9)0.30816 (14)0.0284 (3)
C30.61282 (13)0.46827 (10)0.19104 (15)0.0325 (4)
H3A0.59940.50800.13700.039*
C40.65614 (15)0.54732 (10)0.37486 (15)0.0368 (4)
H4A0.67020.58690.32110.055*
H4B0.70970.54250.43870.055*
H4C0.59710.55900.40870.055*
C50.63006 (11)0.22221 (9)0.27318 (13)0.0282 (4)
C60.64796 (12)0.15012 (9)0.33971 (13)0.0290 (4)
H6A0.59110.11780.32070.035*
H6B0.70370.12500.31190.035*
C70.57765 (11)0.15610 (8)0.52297 (13)0.0239 (3)
H7A0.54210.11030.49860.029*
H7B0.53600.19860.49640.029*
C80.60135 (10)0.15779 (8)0.65549 (12)0.0216 (3)
C90.61402 (11)0.22376 (8)0.71857 (13)0.0251 (3)
C100.63758 (11)0.22652 (10)0.84107 (14)0.0299 (4)
H100.64540.27260.88090.036*
C110.64947 (12)0.16110 (10)0.90375 (14)0.0299 (4)
H110.66550.16220.98730.036*
C120.63813 (11)0.09389 (9)0.84525 (14)0.0275 (3)
H120.64620.04880.88800.033*
C130.61481 (10)0.09381 (8)0.72306 (13)0.0232 (3)
H20.6752 (16)0.2782 (14)0.411 (2)0.049 (6)*
H30.7065 (14)0.1245 (11)0.5004 (18)0.030 (5)*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
Cl10.0473 (3)0.0242 (2)0.0324 (3)−0.00894 (14)−0.0001 (2)0.00170 (13)
Cl20.0396 (3)0.0237 (3)0.0275 (3)−0.00282 (13)0.00714 (17)0.00110 (12)
S10.0322 (3)0.0420 (3)0.0119 (2)−0.00337 (14)0.00174 (16)0.00325 (13)
O10.0493 (8)0.0486 (8)0.0121 (5)−0.0193 (5)−0.0016 (5)−0.0025 (5)
N20.0355 (7)0.0315 (7)0.0105 (6)−0.0120 (5)−0.0011 (5)0.0016 (5)
N10.0302 (7)0.0323 (7)0.0157 (6)−0.0046 (5)0.0031 (5)0.0022 (5)
N30.0305 (7)0.0278 (7)0.0147 (6)−0.0082 (5)0.0028 (5)−0.0007 (4)
C10.0244 (7)0.0353 (8)0.0131 (7)−0.0071 (6)0.0029 (5)0.0024 (5)
C20.0309 (8)0.0345 (8)0.0211 (8)0.0034 (6)0.0079 (6)0.0043 (6)
C30.0397 (9)0.0384 (9)0.0200 (8)0.0065 (7)0.0066 (6)0.0064 (6)
C40.0546 (11)0.0321 (8)0.0253 (8)0.0080 (7)0.0110 (7)0.0037 (6)
C50.0331 (8)0.0380 (8)0.0134 (7)−0.0158 (6)0.0027 (6)−0.0025 (6)
C60.0411 (9)0.0298 (8)0.0161 (8)−0.0137 (6)0.0033 (6)−0.0048 (6)
C70.0282 (7)0.0285 (8)0.0146 (7)−0.0088 (5)0.0007 (5)0.0015 (5)
C80.0222 (7)0.0265 (8)0.0160 (7)−0.0061 (5)0.0016 (5)0.0002 (5)
C90.0271 (7)0.0277 (7)0.0201 (7)−0.0056 (5)0.0008 (6)0.0005 (5)
C100.0297 (8)0.0367 (8)0.0226 (8)−0.0045 (6)0.0007 (6)−0.0084 (6)
C110.0273 (8)0.0471 (10)0.0147 (7)−0.0007 (6)0.0007 (6)−0.0007 (6)
C120.0262 (7)0.0378 (9)0.0190 (7)0.0009 (6)0.0042 (6)0.0064 (6)
C130.0236 (7)0.0272 (7)0.0192 (7)−0.0035 (5)0.0044 (5)0.0009 (5)

Geometric parameters (Å, °)

Cl1—C91.7480 (16)C4—H4B0.9800
Cl2—C131.7465 (16)C4—H4C0.9800
S1—C31.7222 (19)C5—C61.516 (2)
S1—C11.7282 (15)C6—H6A0.9900
O1—C51.2238 (19)C6—H6B0.9900
N2—C51.359 (2)C7—C81.5038 (19)
N2—C11.381 (2)C7—H7A0.9900
N2—H20.84 (2)C7—H7B0.9900
N1—C11.308 (2)C8—C131.392 (2)
N1—C21.385 (2)C8—C91.395 (2)
N3—C61.4550 (19)C9—C101.393 (2)
N3—C71.470 (2)C10—C111.384 (3)
N3—H30.89 (2)C10—H100.9500
C2—C31.356 (2)C11—C121.388 (2)
C2—C41.489 (3)C11—H110.9500
C3—H3A0.9500C12—C131.388 (2)
C4—H4A0.9800C12—H120.9500
C3—S1—C188.07 (8)C5—C6—H6A108.9
C5—N2—C1124.86 (13)N3—C6—H6B108.9
C5—N2—H2118.5 (17)C5—C6—H6B108.9
C1—N2—H2116.6 (17)H6A—C6—H6B107.7
C1—N1—C2110.07 (13)N3—C7—C8109.89 (11)
C6—N3—C7111.78 (12)N3—C7—H7A109.7
C6—N3—H3111.3 (13)C8—C7—H7A109.7
C7—N3—H3108.1 (13)N3—C7—H7B109.7
N1—C1—N2121.05 (13)C8—C7—H7B109.7
N1—C1—S1115.90 (12)H7A—C7—H7B108.2
N2—C1—S1123.05 (11)C13—C8—C9115.51 (13)
C3—C2—N1114.58 (15)C13—C8—C7122.35 (13)
C3—C2—C4126.94 (15)C9—C8—C7122.11 (13)
N1—C2—C4118.44 (14)C10—C9—C8123.02 (14)
C2—C3—S1111.37 (12)C10—C9—Cl1118.29 (12)
C2—C3—H3A124.3C8—C9—Cl1118.69 (11)
S1—C3—H3A124.3C11—C10—C9118.91 (15)
C2—C4—H4A109.5C11—C10—H10120.5
C2—C4—H4B109.5C9—C10—H10120.5
H4A—C4—H4B109.5C10—C11—C12120.41 (15)
C2—C4—H4C109.5C10—C11—H11119.8
H4A—C4—H4C109.5C12—C11—H11119.8
H4B—C4—H4C109.5C11—C12—C13118.67 (14)
O1—C5—N2122.92 (15)C11—C12—H12120.7
O1—C5—C6122.55 (14)C13—C12—H12120.7
N2—C5—C6114.51 (13)C12—C13—C8123.46 (14)
N3—C6—C5113.47 (13)C12—C13—Cl2117.64 (12)
N3—C6—H6A108.9C8—C13—Cl2118.89 (11)
C2—N1—C1—N2−179.90 (14)N3—C7—C8—C13−91.91 (15)
C2—N1—C1—S10.25 (17)N3—C7—C8—C986.22 (17)
C5—N2—C1—N1176.97 (15)C13—C8—C9—C10−0.6 (2)
C5—N2—C1—S1−3.2 (2)C7—C8—C9—C10−178.88 (14)
C3—S1—C1—N10.33 (13)C13—C8—C9—Cl1179.82 (11)
C3—S1—C1—N2−179.52 (14)C7—C8—C9—Cl11.57 (19)
C1—N1—C2—C3−0.9 (2)C8—C9—C10—C110.3 (2)
C1—N1—C2—C4177.06 (14)Cl1—C9—C10—C11179.80 (12)
N1—C2—C3—S11.16 (19)C9—C10—C11—C120.1 (2)
C4—C2—C3—S1−176.61 (15)C10—C11—C12—C130.1 (2)
C1—S1—C3—C2−0.81 (13)C11—C12—C13—C8−0.5 (2)
C1—N2—C5—O11.8 (3)C11—C12—C13—Cl2−179.61 (12)
C1—N2—C5—C6−179.27 (14)C9—C8—C13—C120.8 (2)
C7—N3—C6—C590.42 (15)C7—C8—C13—C12179.01 (14)
O1—C5—C6—N3−169.05 (15)C9—C8—C13—Cl2179.86 (11)
N2—C5—C6—N312.0 (2)C7—C8—C13—Cl2−1.90 (19)
C6—N3—C7—C8174.04 (12)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
N3—H3···N1i0.89 (2)2.32 (2)3.130 (2)150.9 (17)
C7—H7B···O1ii0.992.533.3233 (19)137
N2—H2···N30.84 (2)2.26 (2)2.6742 (19)111 (2)
Cg1—···.Cg1ii..3.665 (2).
Cg1—···.Cg2iii..3.766 (3).
Cg2—···.Cg2iv..3.507 (3).

Symmetry codes: (i) −x+3/2, −y+1/2, −z+1; (ii) −x+1, y, −z+1/2; (iii) −x+1/2, −y+1/2, −z; (iv) −x+1, y, −z−1/2.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: FL2286).

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.
  • Cheon, H. G., Kim, S.-S., Kim, K.-R., Rhee, S. D., Yang, S.-D., Ahn, J. H., Park, S.-D., Lee, J. M., Jung, W. H., Lee, H. S. & Kim, H. Y. (2005). Biochem. Pharmacol 70, 22–29. [PubMed]
  • Kondo, T., Sugimoto, I., Nekado, T., Ochi, K., Ohtani, T., Tajima, Y., Yamamoto, S., Kawabata, K., Nakai, H. & Toda, M. (2007). Bioorg. Med. Chem 15, 2715–2735. [PubMed]
  • Rigaku (2007). CrystalClear Rigaku Corporation, Tokyo, Japan.
  • Sakashita, H., Akahoshi, F., Kitajima, H., Tsutsumiuchi, R. & Hayashi, Y. (2006). Bioorg. Med. Chem 14, 3662–3671. [PubMed]
  • Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. [PubMed]
  • Zhan, F. X., Wang, Y. L., Zhao, G. L., Xu, W. R., Li, Y. L., Zou, M. X., Tang, L. D. & Wang, J. W. (2009). Chin. J. Org. Chem 29, 1236–1242

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