Literature DB >> 22719583

N-[2,4-Dioxo-3-aza-tricyclo-[7.3.1.0(5,13)]trideca-1(13),5,7,9,11-pentaen-3-yl]thio-urea.

Rashad Al-Salahi, Mohamed Al-Omar, Mohamed Marzouk, Seik Weng Ng.   

Abstract

In the two independent mol-ecules in the asymmetric unit of the title compound, C(13)H(9)N(3)O(2)S, the aza-tricyclo-trideca-penta-ene ring system is approximately planar with r.m.s. deviations of 0.022 and 0.033 Å. The urea unit connected to the fused rings is approximately perpendicular [dihedral angles = 82.4 (1) and 82.7 (1)°]. In the crystal, the mol-ecules associate by N-H⋯O hydrogen bonds, forming a chain running along the a axis. The crystal studied was a non-merohedral twin with a fractional contribution of 49.6 (1)% for the minor domain.

Entities:  

Year:  2012        PMID: 22719583      PMCID: PMC3379385          DOI: 10.1107/S1600536812021812

Source DB:  PubMed          Journal:  Acta Crystallogr Sect E Struct Rep Online        ISSN: 1600-5368


Related literature

For background to the class of anti­tumor drugs, see; Pessoa et al. (2010 ▶).

Experimental

Crystal data

C13H9N3O2S M = 271.29 Triclinic, a = 4.5861 (2) Å b = 11.0475 (4) Å c = 22.5594 (9) Å α = 89.196 (3)° β = 88.073 (3)° γ = 81.128 (3)° V = 1128.61 (8) Å3 Z = 4 Cu Kα radiation μ = 2.58 mm−1 T = 100 K 0.25 × 0.10 × 0.03 mm

Data collection

Agilent SuperNova Dual diffractometer with an Atlas detector Absorption correction: multi-scan (CrysAlis PRO; Agilent, 2012 ▶) T min = 0.565, T max = 0.927 14869 measured reflections 7974 independent reflections 7060 reflections with I > 2σ(I) R int = 0.076

Refinement

R[F 2 > 2σ(F 2)] = 0.065 wR(F 2) = 0.196 S = 1.11 7974 reflections 345 parameters H-atom parameters constrained Δρmax = 0.47 e Å−3 Δρmin = −0.73 e Å−3 Data collection: CrysAlis PRO (Agilent, 2012 ▶); cell refinement: CrysAlis PRO; data reduction: CrysAlis PRO; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ▶); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 ▶); molecular graphics: X-SEED (Barbour, 2001 ▶); software used to prepare material for publication: publCIF (Westrip, 2010 ▶). Crystal structure: contains datablock(s) global, I. DOI: 10.1107/S1600536812021812/bt5920sup1.cif Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536812021812/bt5920Isup2.hkl Supplementary material file. DOI: 10.1107/S1600536812021812/bt5920Isup3.cml Additional supplementary materials: crystallographic information; 3D view; checkCIF report
C13H9N3O2SZ = 4
Mr = 271.29F(000) = 560
Triclinic, P1Dx = 1.597 Mg m3
Hall symbol: -P 1Cu Kα radiation, λ = 1.54184 Å
a = 4.5861 (2) ÅCell parameters from 6016 reflections
b = 11.0475 (4) Åθ = 3.9–76.4°
c = 22.5594 (9) ŵ = 2.58 mm1
α = 89.196 (3)°T = 100 K
β = 88.073 (3)°Plate, colorless
γ = 81.128 (3)°0.25 × 0.10 × 0.03 mm
V = 1128.61 (8) Å3
Agilent SuperNova Dual diffractometer with an Atlas detector7974 independent reflections
Radiation source: SuperNova (Cu) X-ray Source7060 reflections with I > 2σ(I)
Mirror monochromatorRint = 0.076
Detector resolution: 10.4041 pixels mm-1θmax = 77.5°, θmin = 3.9°
ω scanh = −5→5
Absorption correction: multi-scan (CrysAlis PRO; Agilent, 2012)k = −13→13
Tmin = 0.565, Tmax = 0.927l = −28→24
14869 measured reflections
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.065H-atom parameters constrained
wR(F2) = 0.196w = 1/[σ2(Fo2) + (0.1312P)2 + 0.6561P] where P = (Fo2 + 2Fc2)/3
S = 1.11(Δ/σ)max = 0.001
7974 reflectionsΔρmax = 0.47 e Å3
345 parametersΔρmin = −0.73 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: 0.007 (1)
xyzUiso*/Ueq
S1−0.00401 (14)0.90107 (6)0.35711 (3)0.02668 (18)
S21.03964 (15)0.64485 (7)−0.15038 (3)0.03115 (19)
O10.3711 (4)0.91572 (19)0.53190 (8)0.0280 (4)
O2−0.2323 (4)0.63074 (18)0.50792 (8)0.0247 (4)
O30.6884 (5)0.5699 (2)0.02003 (9)0.0315 (4)
O41.2207 (4)0.88347 (18)0.01639 (9)0.0268 (4)
N10.0726 (5)0.7727 (2)0.52057 (9)0.0235 (4)
N2−0.0298 (5)0.8305 (2)0.46861 (10)0.0243 (5)
H2−0.20800.87360.46890.029*
N30.3931 (5)0.7492 (2)0.41554 (10)0.0255 (5)
H310.45320.70660.44730.031*
H320.50370.74290.38280.031*
N40.9302 (5)0.7334 (2)0.01767 (9)0.0231 (4)
N51.0573 (5)0.6935 (2)−0.03728 (10)0.0248 (5)
H51.24220.6574−0.03980.030*
N60.6345 (5)0.7835 (2)−0.08405 (10)0.0288 (5)
H610.57140.8196−0.05050.035*
H620.52600.7957−0.11560.035*
C10.1363 (6)0.8228 (2)0.41709 (11)0.0231 (5)
C20.2727 (5)0.8289 (3)0.55335 (11)0.0237 (5)
C30.3503 (5)0.7740 (2)0.61137 (11)0.0228 (5)
C40.5301 (6)0.8282 (3)0.64730 (12)0.0257 (5)
H40.60020.90120.63470.031*
C50.6094 (6)0.7749 (3)0.70274 (12)0.0288 (6)
H5A0.73240.81270.72740.035*
C60.5111 (6)0.6693 (3)0.72147 (12)0.0277 (6)
H60.56660.63470.75900.033*
C70.3271 (5)0.6110 (3)0.68538 (11)0.0241 (5)
C80.2256 (6)0.5010 (3)0.70251 (12)0.0264 (5)
H80.28030.46390.73960.032*
C90.0490 (6)0.4467 (3)0.66639 (12)0.0258 (5)
H9−0.01410.37180.67830.031*
C10−0.0390 (6)0.5017 (3)0.61165 (12)0.0255 (5)
H10−0.16470.46490.58720.031*
C110.0577 (5)0.6086 (2)0.59394 (11)0.0222 (5)
C120.2453 (5)0.6650 (2)0.62956 (11)0.0224 (5)
C13−0.0487 (5)0.6671 (2)0.53792 (11)0.0222 (5)
C140.8931 (6)0.7108 (3)−0.08703 (12)0.0254 (5)
C150.7413 (6)0.6591 (3)0.04568 (12)0.0254 (5)
C160.6217 (6)0.6980 (3)0.10479 (12)0.0249 (5)
C170.4327 (6)0.6302 (3)0.13435 (13)0.0294 (6)
H170.38490.55830.11690.035*
C180.3116 (6)0.6675 (3)0.19013 (13)0.0330 (6)
H180.17870.62150.21000.040*
C190.3827 (6)0.7698 (3)0.21630 (13)0.0325 (6)
H190.30230.79280.25460.039*
C200.5755 (6)0.8421 (3)0.18675 (12)0.0286 (6)
C210.6513 (6)0.9491 (3)0.21190 (13)0.0328 (6)
H210.57460.97370.25020.039*
C220.8338 (7)1.0178 (3)0.18183 (14)0.0341 (6)
H220.87771.09070.19900.041*
C230.9566 (6)0.9808 (3)0.12557 (12)0.0295 (6)
H231.08531.02810.10520.035*
C240.8896 (6)0.8757 (3)0.10003 (12)0.0249 (5)
C250.6951 (6)0.8056 (3)0.12967 (12)0.0258 (5)
C261.0303 (6)0.8364 (3)0.04201 (12)0.0243 (5)
U11U22U33U12U13U23
S10.0238 (3)0.0370 (3)0.0193 (3)−0.0052 (2)0.0006 (2)0.0020 (2)
S20.0249 (3)0.0490 (4)0.0204 (3)−0.0084 (3)0.0019 (2)−0.0066 (3)
O10.0271 (9)0.0336 (10)0.0251 (10)−0.0113 (8)0.0060 (7)−0.0019 (8)
O20.0200 (9)0.0343 (10)0.0213 (9)−0.0089 (7)−0.0012 (7)−0.0016 (7)
O30.0315 (10)0.0392 (11)0.0280 (10)−0.0190 (8)0.0005 (8)−0.0043 (8)
O40.0201 (8)0.0343 (10)0.0275 (9)−0.0092 (7)0.0010 (7)−0.0001 (8)
N10.0203 (10)0.0334 (11)0.0179 (10)−0.0078 (9)0.0001 (8)0.0010 (9)
N20.0177 (10)0.0338 (11)0.0210 (10)−0.0037 (8)0.0010 (8)0.0030 (9)
N30.0182 (10)0.0368 (12)0.0216 (11)−0.0051 (9)0.0017 (8)−0.0020 (9)
N40.0168 (9)0.0354 (11)0.0184 (10)−0.0090 (8)0.0036 (8)−0.0053 (9)
N50.0195 (10)0.0359 (12)0.0195 (10)−0.0066 (8)0.0028 (8)−0.0043 (9)
N60.0195 (10)0.0457 (13)0.0212 (11)−0.0053 (9)0.0004 (8)−0.0001 (10)
C10.0198 (11)0.0286 (12)0.0227 (12)−0.0097 (9)0.0007 (9)−0.0034 (10)
C20.0172 (11)0.0340 (13)0.0209 (12)−0.0079 (10)0.0050 (9)−0.0040 (10)
C30.0169 (11)0.0310 (12)0.0207 (12)−0.0053 (9)0.0029 (9)−0.0031 (10)
C40.0193 (11)0.0338 (13)0.0254 (13)−0.0083 (10)0.0019 (10)−0.0050 (10)
C50.0202 (12)0.0404 (15)0.0266 (13)−0.0065 (11)−0.0012 (10)−0.0081 (11)
C60.0189 (12)0.0444 (16)0.0199 (12)−0.0047 (11)0.0004 (9)−0.0052 (11)
C70.0184 (11)0.0326 (13)0.0212 (12)−0.0044 (10)0.0029 (9)−0.0014 (10)
C80.0223 (12)0.0344 (13)0.0212 (12)−0.0014 (10)0.0038 (10)0.0021 (10)
C90.0259 (12)0.0283 (12)0.0236 (12)−0.0066 (10)0.0052 (10)0.0013 (10)
C100.0223 (12)0.0342 (13)0.0210 (12)−0.0086 (10)0.0034 (9)−0.0025 (10)
C110.0181 (11)0.0306 (12)0.0188 (11)−0.0078 (9)0.0040 (9)−0.0017 (10)
C120.0174 (11)0.0303 (12)0.0204 (12)−0.0066 (9)0.0009 (9)−0.0003 (10)
C130.0163 (11)0.0310 (12)0.0201 (12)−0.0071 (9)0.0042 (9)−0.0010 (10)
C140.0197 (12)0.0358 (13)0.0229 (12)−0.0121 (10)0.0015 (9)−0.0007 (10)
C150.0201 (11)0.0351 (13)0.0224 (13)−0.0083 (10)−0.0025 (10)−0.0006 (10)
C160.0183 (11)0.0365 (13)0.0208 (12)−0.0074 (10)−0.0006 (9)0.0018 (10)
C170.0211 (12)0.0403 (15)0.0276 (14)−0.0080 (11)−0.0008 (10)0.0057 (11)
C180.0205 (12)0.0484 (17)0.0293 (14)−0.0048 (11)0.0031 (10)0.0120 (12)
C190.0228 (13)0.0507 (17)0.0218 (13)0.0007 (12)0.0019 (10)0.0040 (12)
C200.0216 (12)0.0405 (15)0.0220 (13)0.0002 (11)−0.0009 (10)0.0007 (11)
C210.0269 (13)0.0474 (17)0.0217 (13)0.0027 (12)−0.0036 (10)−0.0064 (12)
C220.0346 (15)0.0380 (15)0.0288 (14)−0.0008 (12)−0.0082 (12)−0.0079 (12)
C230.0271 (13)0.0381 (15)0.0242 (13)−0.0069 (11)−0.0036 (11)−0.0028 (11)
C240.0213 (12)0.0332 (13)0.0212 (12)−0.0068 (10)−0.0016 (10)−0.0035 (10)
C250.0174 (11)0.0388 (14)0.0214 (12)−0.0045 (10)−0.0017 (9)−0.0006 (11)
C260.0189 (11)0.0344 (13)0.0207 (12)−0.0074 (10)−0.0019 (9)−0.0010 (10)
S1—C11.687 (3)C6—H60.9500
S2—C141.685 (3)C7—C81.411 (4)
O1—C21.210 (3)C7—C121.423 (4)
O2—C131.216 (3)C8—C91.374 (4)
O3—C151.210 (3)C8—H80.9500
O4—C261.210 (3)C9—C101.412 (4)
N1—N21.388 (3)C9—H90.9500
N1—C131.413 (3)C10—C111.374 (4)
N1—C21.417 (3)C10—H100.9500
N2—C11.364 (3)C11—C121.414 (3)
N2—H20.8800C11—C131.475 (4)
N3—C11.324 (3)C15—C161.469 (4)
N3—H310.8800C16—C171.380 (4)
N3—H320.8800C16—C251.413 (4)
N4—N51.399 (3)C17—C181.400 (4)
N4—C151.412 (3)C17—H170.9500
N4—C261.414 (3)C18—C191.370 (5)
N5—C141.367 (3)C18—H180.9500
N5—H50.8800C19—C201.423 (4)
N6—C141.326 (4)C19—H190.9500
N6—H610.8800C20—C211.414 (4)
N6—H620.8800C20—C251.422 (4)
C2—C31.466 (4)C21—C221.372 (5)
C3—C41.381 (3)C21—H210.9500
C3—C121.415 (4)C22—C231.411 (4)
C4—C51.409 (4)C22—H220.9500
C4—H40.9500C23—C241.384 (4)
C5—C61.371 (4)C23—H230.9500
C5—H5A0.9500C24—C251.415 (4)
C6—C71.421 (4)C24—C261.480 (4)
N2—N1—C13116.5 (2)C10—C11—C12121.2 (2)
N2—N1—C2117.5 (2)C10—C11—C13118.6 (2)
C13—N1—C2125.9 (2)C12—C11—C13120.1 (2)
C1—N2—N1122.3 (2)C11—C12—C3121.7 (2)
C1—N2—H2118.9C11—C12—C7118.8 (2)
N1—N2—H2118.9C3—C12—C7119.4 (2)
C1—N3—H31120.0O2—C13—N1120.4 (2)
C1—N3—H32120.0O2—C13—C11123.9 (2)
H31—N3—H32120.0N1—C13—C11115.7 (2)
N5—N4—C15116.5 (2)N6—C14—N5118.8 (2)
N5—N4—C26116.2 (2)N6—C14—S2123.1 (2)
C15—N4—C26126.9 (2)N5—C14—S2118.0 (2)
C14—N5—N4119.8 (2)O3—C15—N4118.9 (2)
C14—N5—H5120.1O3—C15—C16124.9 (3)
N4—N5—H5120.1N4—C15—C16116.2 (2)
C14—N6—H61120.0C17—C16—C25121.2 (3)
C14—N6—H62120.0C17—C16—C15119.2 (3)
H61—N6—H62120.0C25—C16—C15119.7 (2)
N3—C1—N2118.5 (2)C16—C17—C18119.9 (3)
N3—C1—S1122.9 (2)C16—C17—H17120.1
N2—C1—S1118.5 (2)C18—C17—H17120.1
O1—C2—N1119.1 (2)C19—C18—C17120.7 (3)
O1—C2—C3124.6 (2)C19—C18—H18119.7
N1—C2—C3116.3 (2)C17—C18—H18119.7
C4—C3—C12120.6 (2)C18—C19—C20120.8 (3)
C4—C3—C2119.5 (2)C18—C19—H19119.6
C12—C3—C2119.9 (2)C20—C19—H19119.6
C3—C4—C5119.9 (3)C21—C20—C25118.8 (3)
C3—C4—H4120.1C21—C20—C19122.5 (3)
C5—C4—H4120.1C25—C20—C19118.7 (3)
C6—C5—C4120.8 (2)C22—C21—C20121.1 (3)
C6—C5—H5A119.6C22—C21—H21119.5
C4—C5—H5A119.6C20—C21—H21119.5
C5—C6—C7120.7 (3)C21—C22—C23120.3 (3)
C5—C6—H6119.6C21—C22—H22119.8
C7—C6—H6119.6C23—C22—H22119.8
C8—C7—C6122.5 (2)C24—C23—C22120.0 (3)
C8—C7—C12118.9 (2)C24—C23—H23120.0
C6—C7—C12118.6 (2)C22—C23—H23120.0
C9—C8—C7121.0 (2)C23—C24—C25120.4 (2)
C9—C8—H8119.5C23—C24—C26119.0 (2)
C7—C8—H8119.5C25—C24—C26120.6 (2)
C8—C9—C10120.3 (2)C16—C25—C24121.8 (2)
C8—C9—H9119.9C16—C25—C20118.8 (3)
C10—C9—H9119.9C24—C25—C20119.4 (3)
C11—C10—C9119.8 (2)O4—C26—N4120.4 (2)
C11—C10—H10120.1O4—C26—C24125.1 (2)
C9—C10—H10120.1N4—C26—C24114.5 (2)
C13—N1—N2—C1−105.9 (3)C10—C11—C13—N1−176.4 (2)
C2—N1—N2—C178.2 (3)C12—C11—C13—N16.3 (3)
C15—N4—N5—C1477.9 (3)N4—N5—C14—N611.6 (4)
C26—N4—N5—C14−108.8 (3)N4—N5—C14—S2−171.95 (18)
N1—N2—C1—N35.9 (4)N5—N4—C15—O3−3.5 (4)
N1—N2—C1—S1−177.69 (19)C26—N4—C15—O3−176.0 (2)
N2—N1—C2—O1−8.2 (4)N5—N4—C15—C16176.8 (2)
C13—N1—C2—O1176.4 (2)C26—N4—C15—C164.3 (4)
N2—N1—C2—C3173.1 (2)O3—C15—C16—C17−0.5 (4)
C13—N1—C2—C3−2.4 (4)N4—C15—C16—C17179.2 (2)
O1—C2—C3—C45.2 (4)O3—C15—C16—C25−178.7 (3)
N1—C2—C3—C4−176.2 (2)N4—C15—C16—C251.0 (4)
O1—C2—C3—C12−173.6 (2)C25—C16—C17—C18−0.3 (4)
N1—C2—C3—C125.1 (4)C15—C16—C17—C18−178.6 (3)
C12—C3—C4—C5−0.3 (4)C16—C17—C18—C19−1.1 (4)
C2—C3—C4—C5−179.0 (2)C17—C18—C19—C201.5 (4)
C3—C4—C5—C60.3 (4)C18—C19—C20—C21179.2 (3)
C4—C5—C6—C70.1 (4)C18—C19—C20—C25−0.5 (4)
C5—C6—C7—C8178.8 (2)C25—C20—C21—C220.8 (4)
C5—C6—C7—C12−0.5 (4)C19—C20—C21—C22−178.9 (3)
C6—C7—C8—C9−179.7 (2)C20—C21—C22—C23−1.8 (5)
C12—C7—C8—C9−0.4 (4)C21—C22—C23—C241.0 (4)
C7—C8—C9—C10−1.2 (4)C22—C23—C24—C250.8 (4)
C8—C9—C10—C111.4 (4)C22—C23—C24—C26−177.7 (2)
C9—C10—C11—C120.1 (4)C17—C16—C25—C24179.7 (3)
C9—C10—C11—C13−177.2 (2)C15—C16—C25—C24−2.1 (4)
C10—C11—C12—C3179.0 (2)C17—C16—C25—C201.4 (4)
C13—C11—C12—C3−3.8 (4)C15—C16—C25—C20179.6 (2)
C10—C11—C12—C7−1.7 (4)C23—C24—C25—C16179.9 (3)
C13—C11—C12—C7175.5 (2)C26—C24—C25—C16−1.6 (4)
C4—C3—C12—C11179.1 (2)C23—C24—C25—C20−1.8 (4)
C2—C3—C12—C11−2.1 (4)C26—C24—C25—C20176.7 (2)
C4—C3—C12—C7−0.2 (4)C21—C20—C25—C16179.4 (2)
C2—C3—C12—C7178.6 (2)C19—C20—C25—C16−0.9 (4)
C8—C7—C12—C111.9 (4)C21—C20—C25—C241.0 (4)
C6—C7—C12—C11−178.8 (2)C19—C20—C25—C24−179.3 (3)
C8—C7—C12—C3−178.8 (2)N5—N4—C26—O4−1.8 (4)
C6—C7—C12—C30.5 (4)C15—N4—C26—O4170.8 (3)
N2—N1—C13—O20.2 (4)N5—N4—C26—C24179.8 (2)
C2—N1—C13—O2175.7 (2)C15—N4—C26—C24−7.7 (4)
N2—N1—C13—C11−178.7 (2)C23—C24—C26—O46.3 (4)
C2—N1—C13—C11−3.2 (4)C25—C24—C26—O4−172.3 (3)
C10—C11—C13—O24.8 (4)C23—C24—C26—N4−175.4 (2)
C12—C11—C13—O2−172.6 (2)C25—C24—C26—N46.1 (4)
D—H···AD—HH···AD···AD—H···A
N2—H2···O1i0.882.353.074 (3)140
N2—H2···O1ii0.882.332.993 (3)132
N3—H31···O2iii0.882.092.912 (3)154
N5—H5···O3iii0.882.553.301 (3)144
N5—H5···O3iv0.882.522.988 (3)114
N6—H61···O4i0.882.213.015 (3)152
Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯AD—HH⋯ADAD—H⋯A
N2—H2⋯O1i0.882.353.074 (3)140
N2—H2⋯O1ii0.882.332.993 (3)132
N3—H31⋯O2iii0.882.092.912 (3)154
N5—H5⋯O3iii0.882.553.301 (3)144
N5—H5⋯O3iv0.882.522.988 (3)114
N6—H61⋯O4i0.882.213.015 (3)152

Symmetry codes: (i) ; (ii) ; (iii) ; (iv) .

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