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Acta Crystallogr Sect E Struct Rep Online. 2010 August 1; 66(Pt 8): o2181.
Published online 2010 July 31. doi:  10.1107/S1600536810029788
PMCID: PMC3007268

1-[5-(Dimethyl­amino)-1-naphthylsulfon­yl]imidazolidine-2-thione

Abstract

In the title mol­ecule, C15H17N3O2S2, the dihedral angle between the naphthalene ring system and the imidazole ring is 89.63 (2)°. The crystal structure is stablized by weak inter­molecuar C—H(...)π and N—H(...)π inter­actions.

Related literature

For the applications of compounds containing a 5-(dimethyl­amino)­naphthalene-1-sulfonyl group, see: Corradini et al. (1996 [triangle], 1997 [triangle]); Christoforou et al. (2006 [triangle]). For a related structure, see: Zhang et al. (2009 [triangle]). For the synthetic procedure, see: Corradini et al. (1996 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-66-o2181-scheme1.jpg

Experimental

Crystal data

  • C15H17N3O2S2
  • M r = 335.44
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-66-o2181-efi1.jpg
  • a = 15.364 (4) Å
  • b = 6.9814 (18) Å
  • c = 15.470 (4) Å
  • β = 113.967 (4)°
  • V = 1516.3 (7) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 0.36 mm−1
  • T = 298 K
  • 0.33 × 0.32 × 0.28 mm

Data collection

  • Bruker SMART CCD diffractometer
  • Absorption correction: multi-scan (SADABS; Sheldrick, 1997 [triangle]) T min = 0.955, T max = 0.965
  • 8935 measured reflections
  • 3302 independent reflections
  • 2605 reflections with I > 2σ(I)
  • R int = 0.104

Refinement

  • R[F 2 > 2σ(F 2)] = 0.056
  • wR(F 2) = 0.145
  • S = 1.04
  • 3302 reflections
  • 204 parameters
  • H atoms treated by a mixture of independent and constrained refinement
  • Δρmax = 0.50 e Å−3
  • Δρmin = −0.35 e Å−3

Data collection: SMART (Bruker, 2007 [triangle]); cell refinement: SAINT (Bruker, 2007 [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, 2009 [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/S1600536810029788/lh5094sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536810029788/lh5094Isup2.hkl

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

supplementary crystallographic information

Comment

The dansyl (5-(dimethylamino)naphthalene-1-sulfonyl) group has been widely used as a fluorophore due to its good fluorescent properties. Recently many dansyl derivatives have been reported (Corradini et al., 1996,1997; Christoforou et al., 2006). We show great interest in preparing fluorescent probes that are expected to bind to hydrophobic sites in proteins or membranes and have recently published a structure reslted to the title compound (Zhang et al., 2009). With this in mind, the title compound, (I), was prepared and we report herein the crystal stucture.

In the molecular structure (Fig. 1), the dihedral angle between the naphthalene ring and five-membered heterocyclic ring is 89.63 (2)°. The crystal structure is stablized by weak intermolecuar C—H···π and N—H···π interactions.

Experimental

The intermediate N-(2-Aminoethyl)-5-(dimethylamino)naphthalene-1-sulfonamide was synthesized according to a literature procedure (Corradini et al., 1996). Carbon bisulfide (0.76 g, 10 mmol) and sodium hydroxide(0.40 g, 10 mmol) were added into a stirred solution of the above intermediate (1.47 g, 5 mmol) in dry methanol (20 ml).The reaction mixture was allowed to stir for 24 hr at 293 K. The progress of the reaction was monitored by TLC, untill the completion of reaction. The solvent was evaporated and the residue was purified by column chromatography (dichloromethane-ethyl acetate,1:8 v/v) to afford the title compound as a yellow solid. Single crystals suitable for X-ray diffraction were prepared by slow evaporation of a solution of the title compound in dichloromethane at room temperature.

Refinement

All H atoms were placed in idealized positions [CH(methyl)=0.96 Å, 0.97Å (methylene) and 0.93 Å (aromatic),with Uiso(H)= 1.5Ueq(methyl C) 1.2Ueq(other C). N-bounded hydrogen atom was found from the difference map and refined with the restraint of N—H = 0.88 (3)Å and Uiso(H) = 1.2 Ueq(N).

Figures

Fig. 1.
The molecular structure of (I), with displacement ellipsoids drawn at the 50% probability level.

Crystal data

C15H17N3O2S2F(000) = 700
Mr = 335.44Dx = 1.465 Mg m3
Monoclinic, P21/nMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ynCell parameters from 2682 reflections
a = 15.364 (4) Åθ = 2.4–28.1°
b = 6.9814 (18) ŵ = 0.36 mm1
c = 15.470 (4) ÅT = 298 K
β = 113.967 (4)°Block, yellow
V = 1516.3 (7) Å30.33 × 0.32 × 0.28 mm
Z = 4

Data collection

Bruker SMART CCD diffractometer3302 independent reflections
Radiation source: fine-focus sealed tube2605 reflections with I > 2σ(I)
graphiteRint = 0.104
[var phi] and ω scansθmax = 27.0°, θmin = 2.4°
Absorption correction: multi-scan (SADABS; Sheldrick, 1997)h = −17→19
Tmin = 0.955, Tmax = 0.965k = −8→8
8935 measured reflectionsl = −19→19

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)] = 0.056Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.145H atoms treated by a mixture of independent and constrained refinement
S = 1.04w = 1/[σ2(Fo2) + (0.071P)2] where P = (Fo2 + 2Fc2)/3
3302 reflections(Δ/σ)max = 0.001
204 parametersΔρmax = 0.50 e Å3
0 restraintsΔρmin = −0.35 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
C10.61885 (15)0.6070 (3)0.72722 (15)0.0306 (5)
C20.68621 (19)0.7474 (3)0.76019 (18)0.0379 (6)
H20.68680.84660.72030.045*
C30.75453 (19)0.7430 (3)0.85392 (19)0.0434 (6)
H30.80110.83750.87460.052*
C40.75429 (17)0.6051 (3)0.91479 (17)0.0384 (6)
H40.79830.60990.97740.046*
C50.68768 (15)0.4529 (3)0.88431 (15)0.0271 (5)
C60.68432 (16)0.2951 (3)0.94243 (16)0.0299 (5)
C70.62594 (17)0.1403 (3)0.90561 (16)0.0342 (5)
H70.62530.03980.94480.041*
C80.56701 (17)0.1343 (3)0.80839 (17)0.0370 (6)
H80.52980.02670.78280.044*
C90.56426 (17)0.2841 (3)0.75203 (17)0.0336 (5)
H90.52350.27920.68830.040*
C100.62191 (14)0.4484 (3)0.78765 (15)0.0271 (5)
C110.45077 (18)0.6337 (5)0.6290 (2)0.0536 (7)
H11A0.44250.55780.67690.080*
H11B0.40510.59530.56780.080*
H11C0.44160.76650.63910.080*
C120.5635 (2)0.7304 (4)0.5667 (2)0.0576 (8)
H12A0.56040.86160.58370.086*
H12B0.51570.70720.50430.086*
H12C0.62530.70460.56770.086*
C130.7299 (2)0.6395 (4)1.1372 (2)0.0589 (8)
H13A0.73910.70551.08630.071*
H13B0.78960.63941.19290.071*
C140.6522 (2)0.7308 (4)1.1575 (2)0.0515 (7)
H14A0.67640.78061.22160.062*
H14B0.62230.83411.11350.062*
C150.60716 (16)0.4138 (3)1.11357 (15)0.0336 (5)
N10.54715 (14)0.6055 (3)0.63401 (13)0.0381 (5)
N20.69536 (13)0.4434 (3)1.10932 (13)0.0328 (4)
N30.58699 (18)0.5772 (3)1.14554 (17)0.0496 (6)
H3A0.534 (2)0.590 (4)1.154 (2)0.059*
O10.74468 (12)0.1037 (2)1.09977 (12)0.0422 (4)
O20.84230 (11)0.3748 (3)1.09114 (11)0.0414 (4)
S10.75069 (4)0.29031 (8)1.06638 (4)0.03206 (19)
S20.53971 (5)0.22082 (10)1.08475 (6)0.0524 (2)

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
C10.0297 (12)0.0365 (13)0.0286 (12)0.0012 (10)0.0150 (9)0.0006 (9)
C20.0425 (14)0.0352 (13)0.0384 (13)−0.0015 (10)0.0190 (11)0.0049 (10)
C30.0452 (16)0.0396 (14)0.0437 (15)−0.0167 (11)0.0165 (12)−0.0017 (11)
C40.0372 (14)0.0423 (14)0.0316 (12)−0.0092 (11)0.0097 (10)−0.0028 (10)
C50.0263 (11)0.0309 (11)0.0263 (11)0.0000 (9)0.0129 (8)−0.0013 (9)
C60.0266 (11)0.0343 (12)0.0291 (11)0.0026 (9)0.0118 (9)0.0001 (9)
C70.0402 (13)0.0308 (12)0.0339 (12)−0.0022 (10)0.0173 (10)−0.0006 (10)
C80.0413 (14)0.0339 (13)0.0393 (13)−0.0111 (11)0.0200 (11)−0.0103 (10)
C90.0303 (12)0.0416 (13)0.0295 (12)−0.0041 (10)0.0126 (9)−0.0060 (10)
C100.0232 (10)0.0328 (12)0.0280 (11)0.0021 (9)0.0130 (9)−0.0015 (9)
C110.0345 (15)0.072 (2)0.0477 (16)0.0080 (14)0.0092 (12)0.0107 (14)
C120.0583 (19)0.073 (2)0.0356 (15)−0.0115 (15)0.0130 (13)0.0146 (13)
C130.0640 (19)0.0383 (15)0.083 (2)−0.0096 (14)0.0386 (17)−0.0153 (15)
C140.070 (2)0.0387 (15)0.0469 (16)0.0002 (13)0.0246 (15)−0.0069 (12)
C150.0395 (13)0.0371 (13)0.0266 (11)0.0071 (10)0.0158 (10)0.0067 (10)
N10.0322 (11)0.0490 (12)0.0302 (10)0.0000 (9)0.0099 (8)0.0070 (9)
N20.0342 (11)0.0307 (10)0.0343 (11)−0.0012 (8)0.0145 (8)−0.0036 (8)
N30.0595 (15)0.0440 (13)0.0595 (15)0.0068 (11)0.0389 (13)−0.0025 (11)
O10.0509 (11)0.0343 (9)0.0399 (10)0.0105 (8)0.0169 (8)0.0090 (7)
O20.0284 (9)0.0521 (11)0.0391 (10)0.0026 (8)0.0092 (7)0.0035 (8)
S10.0314 (3)0.0339 (3)0.0303 (3)0.0052 (2)0.0119 (2)0.0030 (2)
S20.0465 (4)0.0484 (4)0.0687 (5)−0.0096 (3)0.0300 (4)0.0000 (3)

Geometric parameters (Å, °)

C1—C21.365 (3)C11—H11B0.9600
C1—N11.415 (3)C11—H11C0.9600
C1—C101.437 (3)C12—N11.456 (3)
C2—C31.403 (4)C12—H12A0.9600
C2—H20.9300C12—H12B0.9600
C3—C41.348 (3)C12—H12C0.9600
C3—H30.9300C13—N21.468 (3)
C4—C51.417 (3)C13—C141.496 (4)
C4—H40.9300C13—H13A0.9700
C5—C101.425 (3)C13—H13B0.9700
C5—C61.436 (3)C14—N31.428 (3)
C6—C71.372 (3)C14—H14A0.9700
C6—S11.769 (2)C14—H14B0.9700
C7—C81.406 (3)C15—N31.329 (3)
C7—H70.9300C15—N21.398 (3)
C8—C91.351 (3)C15—S21.647 (2)
C8—H80.9300N2—S11.6628 (19)
C9—C101.417 (3)N3—H3A0.88 (3)
C9—H90.9300O1—S11.4182 (17)
C11—N11.464 (3)O2—S11.4275 (17)
C11—H11A0.9600
C2—C1—N1123.0 (2)N1—C12—H12A109.5
C2—C1—C10119.4 (2)N1—C12—H12B109.5
N1—C1—C10117.6 (2)H12A—C12—H12B109.5
C1—C2—C3120.4 (2)N1—C12—H12C109.5
C1—C2—H2119.8H12A—C12—H12C109.5
C3—C2—H2119.8H12B—C12—H12C109.5
C4—C3—C2121.7 (2)N2—C13—C14103.6 (2)
C4—C3—H3119.2N2—C13—H13A111.0
C2—C3—H3119.2C14—C13—H13A111.0
C3—C4—C5120.7 (2)N2—C13—H13B111.0
C3—C4—H4119.7C14—C13—H13B111.0
C5—C4—H4119.7H13A—C13—H13B109.0
C4—C5—C10118.31 (19)N3—C14—C13103.3 (2)
C4—C5—C6124.9 (2)N3—C14—H14A111.1
C10—C5—C6116.72 (19)C13—C14—H14A111.1
C7—C6—C5121.9 (2)N3—C14—H14B111.1
C7—C6—S1115.27 (17)C13—C14—H14B111.1
C5—C6—S1122.80 (17)H14A—C14—H14B109.1
C6—C7—C8119.7 (2)N3—C15—N2105.5 (2)
C6—C7—H7120.1N3—C15—S2125.9 (2)
C8—C7—H7120.1N2—C15—S2128.54 (17)
C9—C8—C7120.3 (2)C1—N1—C12115.8 (2)
C9—C8—H8119.8C1—N1—C11113.87 (19)
C7—C8—H8119.8C12—N1—C11110.3 (2)
C8—C9—C10121.7 (2)C15—N2—C13111.46 (19)
C8—C9—H9119.2C15—N2—S1125.90 (16)
C10—C9—H9119.2C13—N2—S1122.26 (17)
C9—C10—C5119.38 (19)C15—N3—C14115.8 (2)
C9—C10—C1121.37 (19)C15—N3—H3A121 (2)
C5—C10—C1119.17 (19)C14—N3—H3A123.1 (19)
N1—C11—H11A109.5O1—S1—O2119.00 (10)
N1—C11—H11B109.5O1—S1—N2108.99 (10)
H11A—C11—H11B109.5O2—S1—N2103.62 (10)
N1—C11—H11C109.5O1—S1—C6108.55 (11)
H11A—C11—H11C109.5O2—S1—C6110.75 (10)
H11B—C11—H11C109.5N2—S1—C6104.94 (10)
N1—C1—C2—C3178.9 (2)C2—C1—N1—C1216.4 (3)
C10—C1—C2—C3−3.7 (4)C10—C1—N1—C12−161.2 (2)
C1—C2—C3—C4−2.1 (4)C2—C1—N1—C11−113.0 (3)
C2—C3—C4—C53.6 (4)C10—C1—N1—C1169.5 (3)
C3—C4—C5—C100.7 (3)N3—C15—N2—C13−2.2 (3)
C3—C4—C5—C6177.1 (2)S2—C15—N2—C13177.2 (2)
C4—C5—C6—C7−171.7 (2)N3—C15—N2—S1−175.13 (17)
C10—C5—C6—C74.8 (3)S2—C15—N2—S14.3 (3)
C4—C5—C6—S111.1 (3)C14—C13—N2—C15−1.1 (3)
C10—C5—C6—S1−172.47 (15)C14—C13—N2—S1172.14 (18)
C5—C6—C7—C8−0.3 (3)N2—C15—N3—C145.0 (3)
S1—C6—C7—C8177.21 (17)S2—C15—N3—C14−174.4 (2)
C6—C7—C8—C9−3.2 (3)C13—C14—N3—C15−5.7 (3)
C7—C8—C9—C101.9 (4)C15—N2—S1—O1−44.0 (2)
C8—C9—C10—C52.9 (3)C13—N2—S1—O1143.8 (2)
C8—C9—C10—C1179.8 (2)C15—N2—S1—O2−171.64 (17)
C4—C5—C10—C9170.7 (2)C13—N2—S1—O216.1 (2)
C6—C5—C10—C9−6.0 (3)C15—N2—S1—C672.1 (2)
C4—C5—C10—C1−6.3 (3)C13—N2—S1—C6−100.1 (2)
C6—C5—C10—C1177.01 (18)C7—C6—S1—O112.6 (2)
C2—C1—C10—C9−169.1 (2)C5—C6—S1—O1−169.92 (17)
N1—C1—C10—C98.5 (3)C7—C6—S1—O2145.02 (18)
C2—C1—C10—C57.8 (3)C5—C6—S1—O2−37.5 (2)
N1—C1—C10—C5−174.59 (19)C7—C6—S1—N2−103.77 (18)
N2—C13—C14—N33.7 (3)C5—C6—S1—N273.67 (19)

Hydrogen-bond geometry (Å, °)

Cg1 and Cg2 are the centroids of the C1–C5/C10 and C5–C10 rings, respectively.
D—H···AD—HH···AD···AD—H···A
C2—H2···Cg1i0.932.883.667 (3)143
N3—H3A···Cg2ii0.88 (3)2.58 (3)3.433 (3)165 (2)

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

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: LH5094).

References

  • Bruker (2007). SAINT-Plus and SMART Bruker AXS Inc., Madison, Wisconsin, USA.
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  • Corradini, R., Dossena, A., Galaverna, G., Marchelli, R., Panagia, A. & Sarto, G. (1997). J. Org. Chem.62, 6283–6289.
  • Corradini, R., Dossena, A., Marchelli, R., Panagia, A., Sartor, G., Saviano, M., Lombardi, A. & Pavone, V. (1996). Chem. Eur. J.2, 373–381.
  • Sheldrick, G. M. (1997). SADABS University of Göttingen, Germany.
  • Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. [PubMed]
  • Spek, A. L. (2009). Acta Cryst. D65, 148–155. [PMC free article] [PubMed]
  • Zhang, Y., Qu, Y. & Liu, T. (2009). Acta Cryst. E65, o2752. [PMC free article] [PubMed]

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