Literature DB >> 21587898

3,6,14,17-Tetramethoxy-22,23-diphenyl-1,10,12,21-tetraazahexacyclo[19.2.1.0.0.0.0]tetracosa-2(7),3,5,13(18),14,16-hexaene-11,24-di-thione.

Yan Yang1.   

Abstract

The title compound, C(36)H(34)N(4)O(4)S(2), is a thio-glycoluril derivative, which bears two phenyl substituents on its convex face and two meth-oxy substituted o-xylylenes as sidewalls of the molecular clip. There is one half-mol-ecule in the asymmetric unit: a crystallographic twofold axis generates the complete molecule. The non-planar seven-membered rings adopt chair conformations, while the two five-membered rings exhibit envelope conformations and make a dihedral angle of 68.46 (12)°. The O atoms of the meth-oxy groups are coplanar with the six-membered o-xylylene sidewalls.

Entities:  

Year:  2010        PMID: 21587898      PMCID: PMC3006729          DOI: 10.1107/S160053681002204X

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


Related literature

For related structures, see: Broan et al. (1989 ▶); Cao et al. (2009 ▶); Wang et al. (2006 ▶); Wang & Xi (2009 ▶); Wu & Sun, (2009 ▶). For further synthetic details, see: Broan et al. (1989 ▶); Wu et al. (2002 ▶). The rigid concave shape of glycoluril makes it a versatile building block in supramolecular chemistry, see: Gao et al. (2009 ▶); Rowan et al. (1999 ▶); Hof et al. (2002 ▶); Kolbel & Menger (2001 ▶); Wu et al. (2002 ▶); Kang et al. (2004 ▶).

Experimental

Crystal data

C36H34N4O4S2 M = 650.79 Monoclinic, a = 17.9993 (15) Å b = 12.5069 (11) Å c = 16.0934 (12) Å β = 115.961 (3)° V = 3257.3 (5) Å3 Z = 4 Mo Kα radiation μ = 0.21 mm−1 T = 298 K 0.23 × 0.20 × 0.10 mm

Data collection

Bruker SMART CCD area-detector diffractometer 13570 measured reflections 3546 independent reflections 2279 reflections with I > 2σ(I) R int = 0.067

Refinement

R[F 2 > 2σ(F 2)] = 0.056 wR(F 2) = 0.162 S = 0.98 3546 reflections 210 parameters H-atom parameters constrained Δρmax = 0.29 e Å−3 Δρmin = −0.24 e Å−3 Data collection: SMART (Bruker, 2001 ▶); cell refinement: SAINT-Plus (Bruker, 2001 ▶); data reduction: SAINT-Plus; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ▶); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 ▶); molecular graphics: PLATON (Spek, 2009 ▶); software used to prepare material for publication: PLATON. Crystal structure: contains datablocks I, global. DOI: 10.1107/S160053681002204X/fl2304sup1.cif Structure factors: contains datablocks I. DOI: 10.1107/S160053681002204X/fl2304Isup2.hkl Additional supplementary materials: crystallographic information; 3D view; checkCIF report
C36H34N4O4S2F(000) = 1368
Mr = 650.79Dx = 1.327 Mg m3
Monoclinic, C2/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -C 2ycCell parameters from 2697 reflections
a = 17.9993 (15) Åθ = 2.5–21.3°
b = 12.5069 (11) ŵ = 0.21 mm1
c = 16.0934 (12) ÅT = 298 K
β = 115.961 (3)°Block, colorless
V = 3257.3 (5) Å30.23 × 0.20 × 0.10 mm
Z = 4
Bruker SMART CCD area-detector diffractometer2279 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tubeRint = 0.067
graphiteθmax = 27.0°, θmin = 2.1°
phi and ω scansh = −22→13
13570 measured reflectionsk = −15→15
3546 independent reflectionsl = −19→20
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) = 0.162H-atom parameters constrained
S = 0.98w = 1/[σ2(Fo2) + (0.0878P)2] where P = (Fo2 + 2Fc2)/3
3546 reflections(Δ/σ)max = 0.001
210 parametersΔρmax = 0.29 e Å3
0 restraintsΔρmin = −0.24 e Å3
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.
xyzUiso*/Ueq
S10.11451 (4)0.22118 (5)0.14339 (5)0.0528 (3)
N10.09215 (11)0.31734 (13)0.27979 (13)0.0335 (5)
N2−0.00738 (11)0.34780 (13)0.14082 (13)0.0325 (4)
C130.07957 (13)0.50126 (16)0.32973 (15)0.0343 (5)
C90.16813 (14)0.27755 (17)0.35521 (17)0.0388 (6)
H9A0.19700.33710.39490.047*
H9B0.20360.24890.32940.047*
C120.03855 (13)0.39284 (16)0.29759 (15)0.0306 (5)
C100.06573 (14)0.29489 (16)0.18917 (16)0.0326 (5)
O20.06197 (14)0.16264 (16)0.57355 (15)0.0713 (6)
O10.24132 (13)0.08009 (14)0.37734 (15)0.0683 (6)
C10.15415 (14)0.19204 (17)0.41322 (17)0.0393 (6)
C20.10798 (15)0.21274 (17)0.46227 (17)0.0406 (6)
C60.19350 (16)0.09225 (18)0.42349 (19)0.0477 (7)
C180.13789 (15)0.53676 (19)0.30210 (19)0.0497 (7)
H180.15600.49160.26880.060*
C11−0.06462 (15)0.31850 (18)0.04628 (16)0.0392 (6)
H11A−0.03430.31570.00920.047*
H11B−0.10600.37420.02090.047*
C30.10368 (17)0.1344 (2)0.52320 (19)0.0512 (7)
C140.05429 (16)0.56979 (18)0.37978 (18)0.0463 (7)
H140.01500.54690.39880.056*
C40.14195 (17)0.0364 (2)0.5309 (2)0.0578 (8)
H40.1379−0.01560.57010.069*
C170.16966 (18)0.6394 (2)0.3237 (2)0.0655 (9)
H170.20860.66310.30450.079*
C50.18588 (18)0.0156 (2)0.4811 (2)0.0564 (8)
H50.2108−0.05080.48630.068*
C150.0865 (2)0.6717 (2)0.4019 (2)0.0638 (9)
H150.06930.71700.43600.077*
C160.1438 (2)0.7055 (2)0.3733 (2)0.0731 (10)
H160.16540.77420.38780.088*
C70.2729 (2)−0.0224 (2)0.3750 (3)0.0859 (11)
H7A0.2924−0.05500.43480.129*
H7B0.3178−0.01620.35830.129*
H7C0.2301−0.06580.33020.129*
C80.0599 (2)0.0907 (3)0.6401 (2)0.0865 (11)
H8A0.02410.03190.60940.130*
H8B0.03960.12690.67870.130*
H8C0.11460.06430.67750.130*
U11U22U33U12U13U23
S10.0520 (5)0.0520 (4)0.0612 (5)0.0130 (3)0.0311 (4)−0.0081 (3)
N10.0300 (11)0.0293 (9)0.0435 (12)0.0043 (7)0.0181 (9)0.0014 (8)
N20.0341 (11)0.0273 (9)0.0390 (11)0.0020 (8)0.0189 (9)−0.0016 (8)
C130.0316 (13)0.0300 (11)0.0397 (13)−0.0029 (9)0.0141 (10)0.0006 (9)
C90.0268 (13)0.0385 (13)0.0466 (14)0.0035 (10)0.0118 (11)0.0042 (10)
C120.0317 (12)0.0264 (10)0.0391 (12)0.0013 (9)0.0205 (10)0.0006 (9)
C100.0327 (13)0.0270 (11)0.0395 (14)−0.0012 (9)0.0170 (11)0.0011 (9)
O20.0922 (16)0.0662 (13)0.0746 (14)0.0174 (11)0.0543 (13)0.0311 (11)
O10.0756 (15)0.0481 (11)0.0968 (17)0.0248 (10)0.0521 (13)0.0162 (10)
C10.0328 (14)0.0343 (12)0.0433 (14)0.0000 (10)0.0097 (11)0.0030 (10)
C20.0390 (14)0.0331 (12)0.0430 (14)−0.0015 (10)0.0118 (12)0.0037 (10)
C60.0452 (16)0.0364 (13)0.0582 (17)0.0053 (11)0.0197 (13)0.0014 (11)
C180.0428 (16)0.0428 (14)0.0692 (19)−0.0048 (11)0.0300 (14)0.0017 (12)
C110.0397 (14)0.0408 (13)0.0357 (13)0.0020 (10)0.0153 (11)−0.0017 (10)
C30.0549 (18)0.0474 (15)0.0536 (17)−0.0009 (13)0.0259 (14)0.0083 (12)
C140.0582 (17)0.0334 (13)0.0518 (16)−0.0035 (11)0.0284 (14)−0.0037 (11)
C40.063 (2)0.0437 (15)0.0596 (18)0.0013 (13)0.0207 (16)0.0190 (13)
C170.0486 (18)0.0531 (17)0.091 (2)−0.0183 (14)0.0267 (17)0.0117 (16)
C50.065 (2)0.0345 (14)0.0639 (19)0.0073 (12)0.0226 (16)0.0073 (13)
C150.090 (2)0.0359 (14)0.0624 (19)−0.0065 (15)0.0304 (17)−0.0115 (13)
C160.084 (3)0.0387 (16)0.080 (2)−0.0232 (16)0.021 (2)−0.0042 (15)
C70.112 (3)0.055 (2)0.113 (3)0.0199 (19)0.070 (3)−0.0035 (18)
C80.099 (3)0.095 (3)0.076 (2)0.009 (2)0.048 (2)0.036 (2)
S1—C101.652 (2)C6—C51.381 (4)
N1—C101.351 (3)C18—C171.386 (4)
N1—C91.462 (3)C18—H180.9300
N1—C121.465 (3)C11—C2i1.511 (3)
N2—C101.371 (3)C11—H11A0.9700
N2—C12i1.450 (3)C11—H11B0.9700
N2—C111.462 (3)C3—C41.384 (4)
C13—C181.381 (3)C14—C151.381 (3)
C13—C141.382 (3)C14—H140.9300
C13—C121.522 (3)C4—C51.375 (4)
C9—C11.511 (3)C4—H40.9300
C9—H9A0.9700C17—C161.364 (4)
C9—H9B0.9700C17—H170.9300
C12—N2i1.450 (3)C5—H50.9300
C12—C12i1.553 (4)C15—C161.369 (4)
O2—C31.370 (3)C15—H150.9300
O2—C81.412 (3)C16—H160.9300
O1—C61.369 (3)C7—H7A0.9600
O1—C71.410 (3)C7—H7B0.9600
C1—C21.398 (3)C7—H7C0.9600
C1—C61.409 (3)C8—H8A0.9600
C2—C31.412 (3)C8—H8B0.9600
C2—C11i1.511 (3)C8—H8C0.9600
C10—N1—C9125.79 (19)N2—C11—H11A108.6
C10—N1—C12113.23 (17)C2i—C11—H11A108.6
C9—N1—C12120.91 (18)N2—C11—H11B108.6
C10—N2—C12i111.24 (18)C2i—C11—H11B108.6
C10—N2—C11122.26 (18)H11A—C11—H11B107.6
C12i—N2—C11120.09 (18)O2—C3—C4123.7 (2)
C18—C13—C14118.6 (2)O2—C3—C2116.3 (2)
C18—C13—C12120.1 (2)C4—C3—C2120.0 (3)
C14—C13—C12121.1 (2)C15—C14—C13121.0 (3)
N1—C9—C1113.92 (19)C15—C14—H14119.5
N1—C9—H9A108.8C13—C14—H14119.5
C1—C9—H9A108.8C5—C4—C3120.4 (2)
N1—C9—H9B108.8C5—C4—H4119.8
C1—C9—H9B108.8C3—C4—H4119.8
H9A—C9—H9B107.7C16—C17—C18120.0 (3)
N2i—C12—N1111.61 (16)C16—C17—H17120.0
N2i—C12—C13112.90 (18)C18—C17—H17120.0
N1—C12—C13112.20 (18)C4—C5—C6120.8 (2)
N2i—C12—C12i103.2 (2)C4—C5—H5119.6
N1—C12—C12i100.82 (17)C6—C5—H5119.6
C13—C12—C12i115.23 (12)C16—C15—C14119.4 (3)
N1—C10—N2108.02 (18)C16—C15—H15120.3
N1—C10—S1126.35 (17)C14—C15—H15120.3
N2—C10—S1125.57 (17)C17—C16—C15120.7 (3)
C3—O2—C8119.2 (2)C17—C16—H16119.7
C6—O1—C7118.2 (2)C15—C16—H16119.7
C2—C1—C6119.4 (2)O1—C7—H7A109.5
C2—C1—C9121.2 (2)O1—C7—H7B109.5
C6—C1—C9119.2 (2)H7A—C7—H7B109.5
C1—C2—C3119.4 (2)O1—C7—H7C109.5
C1—C2—C11i121.4 (2)H7A—C7—H7C109.5
C3—C2—C11i119.2 (2)H7B—C7—H7C109.5
O1—C6—C5123.9 (2)O2—C8—H8A109.5
O1—C6—C1116.0 (2)O2—C8—H8B109.5
C5—C6—C1120.0 (3)H8A—C8—H8B109.5
C13—C18—C17120.3 (3)O2—C8—H8C109.5
C13—C18—H18119.8H8A—C8—H8C109.5
C17—C18—H18119.8H8B—C8—H8C109.5
N2—C11—C2i114.50 (19)
C10—N1—C9—C1−106.3 (3)C7—O1—C6—C511.7 (4)
C12—N1—C9—C177.1 (3)C7—O1—C6—C1−171.6 (3)
C10—N1—C12—N2i122.1 (2)C2—C1—C6—O1−176.5 (2)
C9—N1—C12—N2i−60.9 (2)C9—C1—C6—O1−1.2 (3)
C10—N1—C12—C13−110.1 (2)C2—C1—C6—C50.4 (4)
C9—N1—C12—C1366.9 (2)C9—C1—C6—C5175.7 (2)
C10—N1—C12—C12i13.1 (2)C14—C13—C18—C17−0.5 (4)
C9—N1—C12—C12i−169.92 (18)C12—C13—C18—C17173.8 (2)
C18—C13—C12—N2i155.7 (2)C10—N2—C11—C2i70.0 (3)
C14—C13—C12—N2i−30.1 (3)C12i—N2—C11—C2i−79.4 (2)
C18—C13—C12—N128.6 (3)C8—O2—C3—C42.6 (4)
C14—C13—C12—N1−157.3 (2)C8—O2—C3—C2−175.9 (3)
C18—C13—C12—C12i−86.0 (3)C1—C2—C3—O2175.8 (2)
C14—C13—C12—C12i88.1 (3)C11i—C2—C3—O2−2.3 (4)
C9—N1—C10—N2−179.57 (19)C1—C2—C3—C4−2.8 (4)
C12—N1—C10—N2−2.7 (2)C11i—C2—C3—C4179.0 (2)
C9—N1—C10—S1−2.1 (3)C18—C13—C14—C150.0 (4)
C12—N1—C10—S1174.75 (16)C12—C13—C14—C15−174.3 (2)
C12i—N2—C10—N1−10.2 (2)O2—C3—C4—C5−177.0 (3)
C11—N2—C10—N1−162.05 (19)C2—C3—C4—C51.5 (4)
C12i—N2—C10—S1172.29 (15)C13—C18—C17—C160.6 (4)
C11—N2—C10—S120.5 (3)C3—C4—C5—C60.8 (4)
N1—C9—C1—C2−61.3 (3)O1—C6—C5—C4174.9 (2)
N1—C9—C1—C6123.5 (2)C1—C6—C5—C4−1.8 (4)
C6—C1—C2—C31.8 (4)C13—C14—C15—C160.5 (4)
C9—C1—C2—C3−173.4 (2)C18—C17—C16—C15−0.2 (5)
C6—C1—C2—C11i180.0 (2)C14—C15—C16—C17−0.4 (5)
C9—C1—C2—C11i4.8 (3)
Cg1 is the centroid of the C1–C6 ring.
D—H···AD—HH···AD···AD—H···A
C9—H9A···Cg1ii0.972.703.540145
C11—H11A···O2ii0.972.262.757 (3)111
C14—H14···N2ii0.932.562.879 (3)101
C18—H18···N10.932.512.842 (3)102
C9—H9B···S10.972.733.189 (3)110
C9—H9B···O10.972.252.748 (3)111
  7 in total

1.  Substituent effects control the self-association of molecular clips in the crystalline state.

Authors:  Zhi-Guo Wang; Bao-Han Zhou; Yun-Feng Chen; Guo-Dong Yin; Yi-Tao Li; An-Xin Wu; Lyle Isaacs
Journal:  J Org Chem       Date:  2006-06-09       Impact factor: 4.354

2.  A short history of SHELX.

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

Review 3.  Molecular encapsulation.

Authors:  Fraser Hof; Stephen L Craig; Colin Nuckolls; Julius Rebek
Journal:  Angew Chem Int Ed Engl       Date:  2002-05-03       Impact factor: 15.336

4.  2,6-Bis(2-hydroxy-ethyl)-8b,8c-diphenyl-perhydro-2,3a,4a,6,7a,8a-hexa-azacyclo-penta-[def]fluorene-4,8-dithione.

Authors:  Zihua Wang; Hailing Xi
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2009-05-29

5.  2,6-Bis(2-chloro-ethyl)-8b,8c-diphenyl-perhydro-2,3a,4a,6,7a,8a-hexa-azacyclo-penta-[def]fluorene-4,8-dithione.

Authors:  Yandong Wu; Yichong Sun
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2009-06-27

6.  Methylene-bridged glycoluril dimers: synthetic methods.

Authors:  Anxin Wu; Arindam Chakraborty; Dariusz Witt; Jason Lagona; Fehmi Damkaci; Marie A Ofori; Jessica K Chiles; James C Fettinger; Lyle Isaacs
Journal:  J Org Chem       Date:  2002-08-09       Impact factor: 4.354

7.  Structure validation in chemical crystallography.

Authors:  Anthony L Spek
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2009-01-20
  7 in total

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