Literature DB >> 23723844

3-[(4-Phenyl-piperazin-1-yl)meth-yl]-5-(thio-phen-2-yl)-2,3-di-hydro-1,3,4-oxa-diazole-2-thione.

Ali A El-Emam1, Mohamed A Al-Omar, Abdul-Rahman M Al-Obaid, Seik Weng Ng, Edward R T Tiekink.   

Abstract

In the title compound, C17H18N4OS2, the 2-thienyl ring is disordered over two co-planar, opposite orientations in a 0.684 (2): 0.316 ratio. The 1,3,4-oxa-diazole ring is almost co-planar with the attached 2-thienyl ring [dihedral angles of 5.34 (19) and 4.8 (5)° for the major and minor components, respectively]. The relative disposition of the thione- and ring-S atoms is anti for the major orientation of the 2-thienyl residue. Overall, the shape of the mol-ecule approximates the letter V. In the crystal, a three-dimensional architecture is consolidated by a combination of weak C-H⋯S and C-H⋯π contacts.

Entities:  

Year:  2013        PMID: 23723844      PMCID: PMC3647878          DOI: 10.1107/S1600536813009252

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


Related literature

For background to the biological properties of 1,3,4-oxa­diazole derivatives, see: Al-Omar (2010 ▶). For a related structure, see: El-Emam et al. (2012 ▶).

Experimental

Crystal data

C17H18N4OS2 M = 358.47 Monoclinic, a = 26.1721 (17) Å b = 5.7253 (3) Å c = 23.7008 (18) Å β = 97.802 (6)° V = 3518.5 (4) Å3 Z = 8 Mo Kα radiation μ = 0.31 mm−1 T = 295 K 0.40 × 0.30 × 0.20 mm

Data collection

Agilent SuperNova Dual diffractometer with Atlas detector Absorption correction: multi-scan (CrysAlis PRO; Agilent, 2011 ▶) T min = 0.887, T max = 1.000 9546 measured reflections 4083 independent reflections 2797 reflections with I > 2σ(I) R int = 0.025

Refinement

R[F 2 > 2σ(F 2)] = 0.047 wR(F 2) = 0.123 S = 1.06 4083 reflections 230 parameters 33 restraints H-atom parameters constrained Δρmax = 0.25 e Å−3 Δρmin = −0.26 e Å−3 Data collection: CrysAlis PRO (Agilent, 2011 ▶); 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: ORTEP-3 for Windows (Farrugia, 2012 ▶) and DIAMOND (Brandenburg, 2006 ▶); software used to prepare material for publication: publCIF (Westrip, 2010 ▶). Click here for additional data file. Crystal structure: contains datablock(s) global, I. DOI: 10.1107/S1600536813009252/hb7064sup1.cif Click here for additional data file. Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536813009252/hb7064Isup2.hkl Click here for additional data file. Supplementary material file. DOI: 10.1107/S1600536813009252/hb7064Isup3.cml Additional supplementary materials: crystallographic information; 3D view; checkCIF report
C17H18N4OS2F(000) = 1504
Mr = 358.47Dx = 1.353 Mg m3
Monoclinic, C2/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -C 2ycCell parameters from 2605 reflections
a = 26.1721 (17) Åθ = 3.1–27.5°
b = 5.7253 (3) ŵ = 0.31 mm1
c = 23.7008 (18) ÅT = 295 K
β = 97.802 (6)°Prism, light-brown
V = 3518.5 (4) Å30.40 × 0.30 × 0.20 mm
Z = 8
Agilent SuperNova Dual diffractometer with Atlas detector4083 independent reflections
Radiation source: SuperNova (Mo) X-ray Source2797 reflections with I > 2σ(I)
Mirror monochromatorRint = 0.025
Detector resolution: 10.4041 pixels mm-1θmax = 27.6°, θmin = 3.1°
ω scanh = −32→34
Absorption correction: multi-scan (CrysAlis PRO; Agilent, 2011)k = −7→5
Tmin = 0.887, Tmax = 1.000l = −16→30
9546 measured reflections
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.047Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.123H-atom parameters constrained
S = 1.06w = 1/[σ2(Fo2) + (0.0496P)2 + 0.9031P] where P = (Fo2 + 2Fc2)/3
4083 reflections(Δ/σ)max = 0.001
230 parametersΔρmax = 0.25 e Å3
33 restraintsΔρmin = −0.26 e Å3
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.
xyzUiso*/UeqOcc. (<1)
S10.51012 (6)0.4713 (3)0.35472 (6)0.0619 (3)0.684 (2)
S1'0.51936 (13)0.8668 (6)0.43201 (16)0.0619 (3)0.316
S20.35703 (2)0.65396 (10)0.54603 (3)0.0727 (2)
O10.43151 (5)0.6708 (2)0.47998 (5)0.0534 (3)
N10.41826 (6)0.3583 (3)0.42460 (7)0.0522 (4)
N20.38163 (6)0.3737 (3)0.46156 (7)0.0509 (4)
N30.29660 (6)0.2250 (3)0.41864 (7)0.0556 (4)
N40.22283 (6)0.3760 (2)0.32601 (6)0.0489 (4)
C10.55629 (17)0.6849 (7)0.3488 (3)0.0629 (13)0.684 (2)
H10.57860.67990.32150.076*0.684 (2)
C20.5569 (3)0.8585 (13)0.3874 (2)0.0655 (13)0.684 (2)
H20.57830.98890.38990.079*0.684 (2)
C30.5214 (2)0.8105 (7)0.4216 (2)0.0673 (14)0.684 (2)
H30.51800.90640.45260.081*0.684 (2)
C1'0.5583 (6)0.821 (3)0.3787 (6)0.0629 (13)0.316 (2)
H1'0.58440.92500.37260.076*0.316 (2)
C2'0.5483 (5)0.627 (2)0.3469 (7)0.0655 (13)0.316 (2)
H2'0.56490.58260.31630.079*0.316 (2)
C3'0.5102 (5)0.509 (2)0.3670 (6)0.0673 (14)0.316 (2)
H3'0.49840.36490.35240.081*0.316 (2)
C40.49000 (7)0.6179 (3)0.41049 (8)0.0506 (4)
C50.44667 (7)0.5396 (3)0.43703 (8)0.0481 (4)
C60.38888 (7)0.5603 (3)0.49568 (8)0.0524 (5)
C70.34040 (8)0.1950 (3)0.46076 (10)0.0613 (5)
H7A0.35540.04310.45520.074*
H7B0.32870.19340.49790.074*
C80.26756 (8)0.4377 (4)0.42299 (9)0.0685 (6)
H8A0.28690.56980.41150.082*
H8B0.26190.46160.46220.082*
C90.21648 (8)0.4220 (5)0.38539 (9)0.0721 (6)
H9A0.19610.29800.39910.086*
H9B0.19780.56750.38760.086*
C100.25448 (8)0.1688 (3)0.32178 (10)0.0628 (5)
H10A0.26080.14900.28270.075*
H10B0.23620.03200.33250.075*
C110.30534 (8)0.1901 (4)0.36017 (9)0.0632 (6)
H11A0.32550.04930.35750.076*
H11B0.32470.32090.34800.076*
C120.17704 (7)0.3921 (3)0.28724 (8)0.0473 (4)
C130.14489 (8)0.5860 (3)0.28800 (9)0.0573 (5)
H130.15360.70330.31470.069*
C140.10056 (9)0.6071 (4)0.25001 (10)0.0654 (6)
H140.07990.73840.25150.078*
C150.08620 (9)0.4380 (4)0.20978 (10)0.0670 (6)
H150.05600.45280.18430.080*
C160.11754 (9)0.2471 (4)0.20823 (9)0.0658 (6)
H160.10850.13140.18120.079*
C170.16222 (8)0.2226 (3)0.24588 (9)0.0579 (5)
H170.18280.09130.24370.069*
U11U22U33U12U13U23
S10.0542 (5)0.0638 (7)0.0700 (7)−0.0048 (4)0.0171 (5)−0.0069 (5)
S1'0.0542 (5)0.0638 (7)0.0700 (7)−0.0048 (4)0.0171 (5)−0.0069 (5)
S20.0815 (4)0.0786 (4)0.0626 (4)0.0100 (3)0.0265 (3)0.0018 (3)
O10.0542 (8)0.0540 (7)0.0521 (8)−0.0023 (6)0.0082 (6)0.0000 (6)
N10.0470 (9)0.0554 (9)0.0546 (10)−0.0002 (7)0.0086 (7)0.0011 (7)
N20.0456 (9)0.0535 (8)0.0541 (9)0.0008 (7)0.0089 (7)0.0064 (7)
N30.0471 (9)0.0608 (9)0.0604 (10)−0.0044 (8)0.0124 (8)0.0048 (8)
N40.0457 (8)0.0541 (8)0.0491 (9)−0.0023 (7)0.0142 (7)−0.0106 (7)
C10.052 (2)0.058 (3)0.083 (3)−0.0088 (18)0.025 (2)0.003 (2)
C20.061 (2)0.062 (3)0.075 (3)−0.0087 (19)0.015 (2)0.0010 (19)
C30.078 (3)0.056 (3)0.068 (3)0.006 (2)0.011 (2)−0.0046 (19)
C1'0.052 (2)0.058 (3)0.083 (3)−0.0088 (18)0.025 (2)0.003 (2)
C2'0.061 (2)0.062 (3)0.075 (3)−0.0087 (19)0.015 (2)0.0010 (19)
C3'0.078 (3)0.056 (3)0.068 (3)0.006 (2)0.011 (2)−0.0046 (19)
C40.0448 (10)0.0544 (10)0.0516 (11)0.0005 (8)0.0032 (8)0.0050 (8)
C50.0453 (10)0.0513 (10)0.0464 (10)0.0046 (8)0.0018 (8)0.0041 (8)
C60.0522 (11)0.0542 (10)0.0505 (11)0.0052 (9)0.0065 (9)0.0097 (9)
C70.0594 (13)0.0566 (11)0.0689 (14)−0.0061 (10)0.0121 (10)0.0156 (10)
C80.0593 (13)0.0951 (15)0.0518 (12)0.0152 (12)0.0097 (10)−0.0165 (11)
C90.0537 (12)0.1097 (17)0.0543 (13)0.0173 (12)0.0127 (10)−0.0143 (12)
C100.0535 (12)0.0641 (12)0.0714 (14)0.0021 (10)0.0102 (10)−0.0198 (10)
C110.0507 (12)0.0677 (12)0.0729 (15)0.0054 (10)0.0142 (10)−0.0162 (10)
C120.0469 (10)0.0488 (9)0.0491 (10)−0.0100 (8)0.0165 (8)−0.0018 (8)
C130.0612 (12)0.0507 (10)0.0609 (13)−0.0047 (10)0.0120 (10)−0.0051 (9)
C140.0651 (14)0.0591 (12)0.0713 (15)0.0052 (10)0.0072 (11)0.0040 (11)
C150.0656 (14)0.0697 (13)0.0628 (14)−0.0044 (11)−0.0026 (11)0.0052 (11)
C160.0708 (14)0.0665 (13)0.0575 (13)−0.0078 (11)−0.0003 (11)−0.0100 (10)
C170.0606 (12)0.0551 (10)0.0585 (12)−0.0020 (9)0.0098 (10)−0.0077 (9)
S1—C41.708 (2)C3'—C41.371 (9)
S1—C11.738 (3)C3'—H3'0.9300
S1'—C41.666 (3)C4—C51.441 (3)
S1'—C1'1.748 (9)C7—H7A0.9700
S2—C61.636 (2)C7—H7B0.9700
O1—C51.367 (2)C8—C91.505 (3)
O1—C61.377 (2)C8—H8A0.9700
N1—C51.288 (2)C8—H8B0.9700
N1—N21.386 (2)C9—H9A0.9700
N2—C61.338 (2)C9—H9B0.9700
N2—C71.485 (2)C10—C111.512 (3)
N3—C71.425 (3)C10—H10A0.9700
N3—C81.447 (3)C10—H10B0.9700
N3—C111.449 (3)C11—H11A0.9700
N4—C121.411 (2)C11—H11B0.9700
N4—C101.458 (2)C12—C131.395 (3)
N4—C91.463 (2)C12—C171.396 (3)
C1—C21.349 (5)C13—C141.374 (3)
C1—H10.9300C13—H130.9300
C2—C31.342 (7)C14—C151.375 (3)
C2—H20.9300C14—H140.9300
C3—C41.379 (5)C15—C161.370 (3)
C3—H30.9300C15—H150.9300
C1'—C2'1.349 (8)C16—C171.379 (3)
C1'—H1'0.9300C16—H160.9300
C2'—C3'1.344 (10)C17—H170.9300
C2'—H2'0.9300
C4—S1—C190.4 (2)N2—C7—H7A108.3
C4—S1'—C1'86.7 (6)N3—C7—H7B108.3
C5—O1—C6106.05 (14)N2—C7—H7B108.3
C5—N1—N2103.39 (14)H7A—C7—H7B107.4
C6—N2—N1112.28 (15)N3—C8—C9109.90 (18)
C6—N2—C7126.94 (16)N3—C8—H8A109.7
N1—N2—C7120.78 (15)C9—C8—H8A109.7
C7—N3—C8115.60 (17)N3—C8—H8B109.7
C7—N3—C11115.92 (16)C9—C8—H8B109.7
C8—N3—C11109.70 (16)H8A—C8—H8B108.2
C12—N4—C10116.68 (15)N4—C9—C8111.87 (16)
C12—N4—C9114.66 (14)N4—C9—H9A109.2
C10—N4—C9110.64 (17)C8—C9—H9A109.2
C2—C1—S1114.1 (6)N4—C9—H9B109.2
C2—C1—H1122.9C8—C9—H9B109.2
S1—C1—H1122.9H9A—C9—H9B107.9
C3—C2—C1108.2 (7)N4—C10—C11110.80 (16)
C3—C2—H2125.9N4—C10—H10A109.5
C1—C2—H2125.9C11—C10—H10A109.5
C2—C3—C4119.4 (5)N4—C10—H10B109.5
C2—C3—H3120.3C11—C10—H10B109.5
C4—C3—H3120.3H10A—C10—H10B108.1
C2'—C1'—S1'115.9 (14)N3—C11—C10110.26 (16)
C2'—C1'—H1'122.0N3—C11—H11A109.6
S1'—C1'—H1'122.0C10—C11—H11A109.6
C3'—C2'—C1'108.4 (16)N3—C11—H11B109.6
C3'—C2'—H2'125.8C10—C11—H11B109.6
C1'—C2'—H2'125.8H11A—C11—H11B108.1
C2'—C3'—C4114.7 (12)C13—C12—C17116.86 (19)
C2'—C3'—H3'122.7C13—C12—N4120.30 (16)
C4—C3'—H3'122.7C17—C12—N4122.82 (17)
C3'—C4—C3103.2 (6)C14—C13—C12121.24 (19)
C3'—C4—C5126.4 (6)C14—C13—H13119.4
C3—C4—C5130.4 (2)C12—C13—H13119.4
C3'—C4—S1'114.2 (6)C13—C14—C15121.3 (2)
C5—C4—S1'119.33 (17)C13—C14—H14119.3
C3—C4—S1107.6 (2)C15—C14—H14119.3
C5—C4—S1121.91 (15)C16—C15—C14118.2 (2)
S1'—C4—S1118.65 (15)C16—C15—H15120.9
N1—C5—O1113.36 (16)C14—C15—H15120.9
N1—C5—C4127.95 (17)C15—C16—C17121.5 (2)
O1—C5—C4118.66 (16)C15—C16—H16119.3
N2—C6—O1104.91 (15)C17—C16—H16119.3
N2—C6—S2131.15 (15)C16—C17—C12120.94 (19)
O1—C6—S2123.94 (15)C16—C17—H17119.5
N3—C7—N2116.10 (15)C12—C17—H17119.5
N3—C7—H7A108.3
C5—N1—N2—C6−0.7 (2)S1'—C4—C5—O1−1.2 (3)
C5—N1—N2—C7179.54 (16)S1—C4—C5—O1−177.46 (15)
C4—S1—C1—C20.5 (3)N1—N2—C6—O10.5 (2)
S1—C1—C2—C31.9 (5)C7—N2—C6—O1−179.85 (16)
C1—C2—C3—C4−4.4 (7)N1—N2—C6—S2−179.55 (15)
C4—S1'—C1'—C2'0.4 (9)C7—N2—C6—S20.1 (3)
S1'—C1'—C2'—C3'−2.3 (13)C5—O1—C6—N2−0.01 (18)
C1'—C2'—C3'—C43.5 (16)C5—O1—C6—S2−179.99 (14)
C2'—C3'—C4—C3−5.5 (13)C8—N3—C7—N2−61.8 (2)
C2'—C3'—C4—C5175.2 (9)C11—N3—C7—N268.7 (2)
C2'—C3'—C4—S1'−3.4 (17)C6—N2—C7—N397.8 (2)
C2'—C3'—C4—S1152 (10)N1—N2—C7—N3−82.5 (2)
C2—C3—C4—C3'6.7 (7)C7—N3—C8—C9−166.94 (17)
C2—C3—C4—C5−174.1 (4)C11—N3—C8—C959.7 (2)
C2—C3—C4—S1'−164 (2)C12—N4—C9—C8−171.40 (17)
C2—C3—C4—S14.7 (7)C10—N4—C9—C854.1 (2)
C1'—S1'—C4—C3'1.7 (11)N3—C8—C9—N4−56.9 (3)
C1'—S1'—C4—C312 (2)C12—N4—C10—C11172.40 (16)
C1'—S1'—C4—C5−177.1 (6)C9—N4—C10—C11−54.1 (2)
C1'—S1'—C4—S1−0.7 (6)C7—N3—C11—C10166.26 (16)
C1—S1—C4—C3'−26 (9)C8—N3—C11—C10−60.6 (2)
C1—S1—C4—C3−2.6 (4)N4—C10—C11—N357.9 (2)
C1—S1—C4—C5176.2 (2)C10—N4—C12—C13−179.25 (17)
C1—S1—C4—S1'−0.1 (3)C9—N4—C12—C1349.1 (2)
N2—N1—C5—O10.74 (19)C10—N4—C12—C17−1.0 (2)
N2—N1—C5—C4−177.59 (17)C9—N4—C12—C17−132.6 (2)
C6—O1—C5—N1−0.5 (2)C17—C12—C13—C140.5 (3)
C6—O1—C5—C4178.00 (15)N4—C12—C13—C14178.91 (17)
C3'—C4—C5—N1−1.5 (9)C12—C13—C14—C150.0 (3)
C3—C4—C5—N1179.4 (4)C13—C14—C15—C16−0.4 (3)
S1'—C4—C5—N1177.1 (2)C14—C15—C16—C170.3 (3)
S1—C4—C5—N10.8 (3)C15—C16—C17—C120.2 (3)
C3'—C4—C5—O1−179.8 (9)C13—C12—C17—C16−0.6 (3)
C3—C4—C5—O11.1 (4)N4—C12—C17—C16−178.96 (17)
D—H···AD—HH···AD···AD—H···A
C9—H9B···S2i0.972.773.618 (3)146
C1—H1···Cg1ii0.932.723.545 (6)148
C11—H11A···Cg1iii0.972.983.600 (2)123
C15—H15···Cg2iii0.932.953.743 (3)144
Table 1

Hydrogen-bond geometry (Å, °)

Cg1 is the centroid of the O1,N1,N2,C5,C6 ring

D—H⋯A D—HH⋯A DA D—H⋯A
C9—H9B⋯S2i 0.972.773.618 (3)146
C1—H1⋯Cg1ii 0.932.723.545 (6)148
C11—H11ACg1iii 0.972.983.600 (2)123
C15—H15⋯Cg2iii 0.932.953.743 (3)144

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

  3 in total

1.  A short history of SHELX.

Authors:  George M Sheldrick
Journal:  Acta Crystallogr A       Date:  2007-12-21       Impact factor: 2.290

2.  3-[(N-Methyl-anilino)meth-yl]-5-(thio-phen-2-yl)-1,3,4-oxadiazole-2(3H)-thione.

Authors:  Ali A El-Emam; Mohamed A Al-Omar; Hazem A Ghabbour; Hoong-Kun Fun; Tze Shyang Chia
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2012-04-13

3.  Synthesis and antimicrobial activity of new 5-(2-thienyl)-1,2,4-triazoles and 5-(2-thienyl)-1,3,4-oxadiazoles and related derivatives.

Authors:  Mohamed A Al-Omar
Journal:  Molecules       Date:  2010-01-22       Impact factor: 4.411

  3 in total
  3 in total

1.  2,9-Bis(5-sulfanylidene-4,5-di-hydro-1,3,4-oxa-diazol-2-yl)-1,10-phenanthroline dimethyl sulfoxide disolvate.

Authors:  Md A Rahman; Mohammad Karim; Md Arifuzzaman; Tasneem Siddiquee; Lee M Daniels
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2014-02-22

2.  Crystal structure of 3-[(4-benzyl-piperazin-1-yl)meth-yl]-5-(thio-phen-2-yl)-2,3-di-hydro-1,3,4-oxa-diazole-2-thione.

Authors:  Fatmah A M Al-Omary; Ali A El-Emam; Hazem A Ghabbour; C S Chidan Kumar; Ching Kheng Quah; Hoong-Kun Fun
Journal:  Acta Crystallogr E Crystallogr Commun       Date:  2015-02-13

3.  Crystal structure of 3-{[4-(2-meth-oxy-phen-yl)piperazin-1-yl]meth-yl}-5-(thio-phen-2-yl)-1,3,4-oxa-diazole-2(3H)-thione.

Authors:  Monirah A Al-Alshaikh; Hatem A Abuelizz; Ali A El-Emam; Mohammed S M Abdelbaky; Santiago Garcia-Granda
Journal:  Acta Crystallogr E Crystallogr Commun       Date:  2016-01-30
  3 in total

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