Literature DB >> 21200820

2,3,4,6,7,8,9,10-Octa-hydro-pyrimido[1,2-a]azepin-1-ium 2-cyano-1-(2,6-dimethylanilino)-2-(phenyl-sulfonyl)ethenethiol-ate.

Svetlana V Shishkina, Oleg V Shishkin, Yuriy D Vlasenko, Oleksiy O Parkhomenko, Sergey M Kovalenko.   

Abstract

In the title compound, C(9)H(17)N(2) (+)·C(17)H(15)N(2)O(2)S(2) (-), the Csp(2)-N bonds in the tetra-hydro-pyrimidine ring of the cation are delocalized. The negative charge is localized on the S atom of the thione group. Cations and anions are linked by N-H⋯S inter-molecular hydrogen bonds.

Entities:  

Year:  2007        PMID: 21200820      PMCID: PMC2915312          DOI: 10.1107/S1600536807065518

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


Related literature

For related literature, see: Bürgi & Dunitz (1994 ▶); Fadda et al. (2000 ▶); Dorwald (2000 ▶); Lindeman et al. (2003 ▶); Perez et al. (2004 ▶); Zefirov et al. (1990 ▶).

Experimental

Crystal data

C9H17N2 +·C17H15N2O2S2 − M = 496.68 Triclinic, a = 8.3278 (5) Å b = 11.348 (4) Å c = 13.661 (3) Å α = 104.03 (2)° β = 92.517 (9)° γ = 90.635 (12)° V = 1250.9 (5) Å3 Z = 2 Mo Kα radiation μ = 0.24 mm−1 T = 293 (2) K 0.20 × 0.20 × 0.20 mm

Data collection

Oxford Diffraction Xcalibur3 diffractometer Absorption correction: none 11732 measured reflections 4319 independent reflections 3564 reflections with I > 2σ(I) R int = 0.014

Refinement

R[F 2 > 2σ(F 2)] = 0.032 wR(F 2) = 0.090 S = 1.10 4319 reflections 317 parameters H atoms treated by a mixture of independent and constrained refinement Δρmax = 0.33 e Å−3 Δρmin = −0.26 e Å−3 Data collection: CrysAlis CCD (Oxford Diffraction, 2007 ▶); cell refinement: CrysAlis RED (Oxford Diffraction, 2007 ▶); data reduction: CrysAlis RED; program(s) used to solve structure: SHELXTL-Plus (Sheldrick, 1998 ▶); program(s) used to refine structure: SHELXTL-Plus; molecular graphics: XP (Siemens, 1998 ▶); software used to prepare material for publication: SHELXTL-Plus. Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536807065518/av2006sup1.cif Structure factors: contains datablocks I. DOI: 10.1107/S1600536807065518/av2006Isup2.hkl Additional supplementary materials: crystallographic information; 3D view; checkCIF report
C9H17N2+·C17H15N2O2S2Z = 2
Mr = 496.68F000 = 528
Triclinic, P1Dx = 1.319 Mg m3
a = 8.3278 (5) ÅMo Kα radiation λ = 0.71073 Å
b = 11.348 (4) ÅCell parameters from 9472 reflections
c = 13.661 (3) Åθ = 2.8–31.9º
α = 104.03 (2)ºµ = 0.24 mm1
β = 92.517 (9)ºT = 293 (2) K
γ = 90.635 (12)ºBlock, colourless
V = 1250.9 (5) Å30.20 × 0.20 × 0.20 mm
Oxford Diffraction Xcalibur3 diffractometer4319 independent reflections
Radiation source: Enhance (Mo) X-ray Source3564 reflections with I > 2σ(I)
Monochromator: graphiteRint = 0.014
Detector resolution: 16.1827 pixels mm-1θmax = 25.0º
T = 293(2) Kθmin = 3.0º
ω–scansh = −9→9
Absorption correction: nonek = −13→13
11732 measured reflectionsl = −16→16
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.032H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.090  w = 1/[σ2(Fo2) + (0.043P)2 + 0.3755P] where P = (Fo2 + 2Fc2)/3
S = 1.10(Δ/σ)max = 0.001
4319 reflectionsΔρmax = 0.33 e Å3
317 parametersΔρmin = −0.26 e Å3
Primary atom site location: structure-invariant direct methodsExtinction correction: none
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*/Ueq
S10.12739 (5)0.23234 (3)0.07779 (3)0.03153 (12)
S20.32290 (6)0.09686 (4)0.32967 (3)0.04391 (14)
O10.21822 (14)0.32333 (11)0.04679 (9)0.0437 (3)
O20.10480 (15)0.11538 (10)0.00763 (9)0.0420 (3)
N10.17889 (17)−0.00391 (12)0.15248 (11)0.0365 (3)
H1N0.136 (2)0.0021 (17)0.0957 (16)0.045 (5)*
N20.2919 (2)0.41319 (14)0.31254 (12)0.0506 (4)
N30.40259 (16)0.72438 (12)0.50300 (10)0.0363 (3)
N40.42004 (19)0.85309 (15)0.39899 (13)0.0459 (4)
H4N0.376 (3)0.904 (2)0.3749 (16)0.057 (6)*
C10.21102 (18)0.21136 (14)0.19027 (12)0.0309 (3)
C20.23091 (17)0.09922 (14)0.21630 (12)0.0303 (3)
C30.20953 (19)−0.12349 (14)0.16308 (12)0.0323 (3)
C40.3526 (2)−0.17697 (15)0.12811 (13)0.0382 (4)
C50.3722 (3)−0.29728 (17)0.12940 (15)0.0524 (5)
H50.4660−0.33600.10620.063*
C60.2562 (3)−0.35999 (17)0.16407 (17)0.0586 (6)
H60.2713−0.44120.16370.070*
C70.1188 (3)−0.30538 (17)0.19914 (15)0.0532 (5)
H70.0420−0.34920.22390.064*
C80.0913 (2)−0.18553 (16)0.19868 (13)0.0393 (4)
C9−0.0614 (2)−0.1257 (2)0.23623 (17)0.0623 (6)
H9C−0.1219−0.17880.26650.093*
H9B−0.1239−0.10880.18070.093*
H9A−0.0361−0.05110.28550.093*
C100.4806 (2)−0.1070 (2)0.09221 (17)0.0587 (5)
H10C0.5594−0.16190.05910.088*
H10B0.5311−0.04950.14880.088*
H10A0.4337−0.06460.04560.088*
C110.25701 (19)0.32106 (14)0.25980 (12)0.0337 (4)
C12−0.06628 (19)0.29086 (15)0.10429 (12)0.0343 (4)
C13−0.1846 (2)0.21876 (18)0.12817 (14)0.0472 (4)
H13−0.16360.13920.13060.057*
C14−0.3353 (2)0.2659 (2)0.14860 (16)0.0600 (6)
H14−0.41580.21810.16570.072*
C15−0.3663 (3)0.3824 (2)0.14384 (17)0.0665 (6)
H15−0.46790.41360.15730.080*
C16−0.2487 (3)0.4526 (2)0.11951 (19)0.0653 (6)
H16−0.27060.53190.11660.078*
C17−0.0964 (2)0.40779 (17)0.09902 (15)0.0473 (4)
H17−0.01630.45600.08200.057*
C180.3354 (2)0.69195 (18)0.59082 (14)0.0473 (4)
H18B0.32270.76560.64330.057*
H18A0.41100.64140.61700.057*
C190.1752 (2)0.6252 (2)0.56735 (18)0.0589 (5)
H19B0.17870.56670.50270.071*
H19A0.15770.58060.61830.071*
C200.0358 (2)0.7076 (2)0.56372 (19)0.0656 (6)
H20A0.02820.76240.62990.079*
H20B−0.06240.65850.54920.079*
C210.0472 (2)0.7822 (2)0.48615 (18)0.0639 (6)
H21B−0.05020.82830.48650.077*
H21A0.05150.72710.41990.077*
C220.1902 (2)0.86958 (18)0.50166 (17)0.0547 (5)
H22B0.16660.93220.46620.066*
H22A0.20400.90880.57300.066*
C230.3450 (2)0.81263 (15)0.46655 (13)0.0376 (4)
C240.5760 (2)0.80974 (19)0.36486 (16)0.0527 (5)
H24B0.66040.85440.41050.063*
H24A0.59100.82210.29800.063*
C250.5840 (2)0.67836 (19)0.36216 (15)0.0529 (5)
H25B0.69140.65000.34600.063*
H25A0.50910.63290.30980.063*
C260.5433 (2)0.65656 (16)0.46223 (14)0.0429 (4)
H26B0.52230.57040.45450.051*
H26A0.63470.68050.50970.051*
U11U22U33U12U13U23
S10.0346 (2)0.0303 (2)0.0314 (2)0.00208 (15)0.00147 (16)0.01090 (16)
S20.0605 (3)0.0321 (2)0.0387 (3)0.0009 (2)−0.0147 (2)0.01085 (18)
O10.0424 (6)0.0452 (7)0.0508 (7)−0.0001 (5)0.0073 (6)0.0248 (6)
O20.0575 (7)0.0361 (6)0.0312 (6)0.0053 (5)−0.0030 (5)0.0065 (5)
N10.0487 (8)0.0268 (7)0.0335 (8)0.0009 (6)−0.0098 (7)0.0083 (6)
N20.0681 (11)0.0335 (8)0.0479 (9)−0.0050 (7)−0.0077 (8)0.0076 (7)
N30.0370 (7)0.0378 (8)0.0365 (8)0.0020 (6)−0.0005 (6)0.0143 (6)
N40.0464 (9)0.0440 (9)0.0553 (10)0.0043 (7)0.0041 (7)0.0271 (8)
C10.0332 (8)0.0278 (8)0.0323 (8)0.0011 (6)−0.0026 (6)0.0093 (7)
C20.0283 (7)0.0293 (8)0.0338 (8)0.0014 (6)0.0003 (6)0.0085 (7)
C30.0404 (9)0.0257 (8)0.0303 (8)−0.0013 (6)−0.0055 (7)0.0073 (6)
C40.0399 (9)0.0380 (9)0.0353 (9)0.0024 (7)−0.0031 (7)0.0067 (7)
C50.0583 (12)0.0405 (10)0.0526 (12)0.0158 (9)−0.0086 (9)0.0014 (9)
C60.0874 (16)0.0262 (9)0.0608 (13)−0.0007 (10)−0.0164 (12)0.0114 (9)
C70.0717 (13)0.0409 (10)0.0488 (11)−0.0194 (10)−0.0084 (10)0.0174 (9)
C80.0444 (9)0.0403 (9)0.0327 (9)−0.0070 (7)−0.0024 (7)0.0086 (7)
C90.0500 (11)0.0808 (15)0.0576 (13)−0.0012 (11)0.0125 (10)0.0184 (12)
C100.0486 (11)0.0661 (13)0.0597 (13)−0.0044 (10)0.0123 (10)0.0107 (11)
C110.0370 (8)0.0302 (9)0.0356 (9)0.0019 (7)−0.0024 (7)0.0122 (7)
C120.0326 (8)0.0403 (9)0.0295 (8)0.0017 (7)−0.0024 (6)0.0080 (7)
C130.0432 (10)0.0556 (11)0.0466 (11)−0.0027 (8)0.0015 (8)0.0199 (9)
C140.0379 (10)0.0952 (18)0.0475 (11)−0.0059 (11)0.0051 (9)0.0184 (11)
C150.0423 (11)0.0912 (18)0.0594 (14)0.0203 (12)0.0024 (10)0.0045 (12)
C160.0546 (12)0.0571 (13)0.0788 (16)0.0213 (10)−0.0019 (11)0.0063 (12)
C170.0441 (10)0.0400 (10)0.0564 (12)0.0035 (8)−0.0029 (9)0.0103 (9)
C180.0533 (11)0.0528 (11)0.0413 (10)0.0029 (9)0.0040 (8)0.0220 (9)
C190.0607 (12)0.0579 (13)0.0649 (13)−0.0064 (10)0.0129 (10)0.0266 (11)
C200.0470 (11)0.0824 (16)0.0721 (15)−0.0043 (11)0.0142 (11)0.0263 (13)
C210.0391 (10)0.0882 (16)0.0709 (15)0.0131 (10)0.0090 (10)0.0305 (13)
C220.0573 (12)0.0495 (11)0.0635 (13)0.0199 (9)0.0147 (10)0.0232 (10)
C230.0400 (9)0.0339 (9)0.0399 (9)0.0001 (7)−0.0008 (7)0.0113 (7)
C240.0401 (10)0.0677 (13)0.0576 (12)0.0005 (9)0.0076 (9)0.0284 (11)
C250.0489 (11)0.0609 (12)0.0489 (11)0.0122 (9)0.0076 (9)0.0121 (10)
C260.0446 (10)0.0385 (9)0.0465 (10)0.0094 (8)0.0007 (8)0.0122 (8)
S1—O11.4285 (12)C12—C171.371 (2)
S1—O21.4413 (13)C12—C131.373 (2)
S1—C11.7291 (16)C13—C141.383 (3)
S1—C121.7697 (16)C13—H130.9300
S2—C21.7037 (16)C14—C151.366 (3)
N1—C21.334 (2)C14—H140.9300
N1—C31.424 (2)C15—C161.358 (3)
N1—H1N0.86 (2)C15—H150.9300
N2—C111.143 (2)C16—C171.387 (3)
N3—C231.308 (2)C16—H160.9300
N3—C261.465 (2)C17—H170.9300
N3—C181.469 (2)C18—C191.509 (3)
N4—C231.305 (2)C18—H18B0.9700
N4—C241.450 (2)C18—H18A0.9700
N4—H4N0.82 (2)C19—C201.505 (3)
C1—C111.408 (2)C19—H19B0.9700
C1—C21.411 (2)C19—H19A0.9700
C3—C81.377 (2)C20—C211.514 (3)
C3—C41.393 (2)C20—H20A0.9700
C4—C51.381 (3)C20—H20B0.9700
C4—C101.491 (3)C21—C221.515 (3)
C5—C61.361 (3)C21—H21B0.9700
C5—H50.9300C21—H21A0.9700
C6—C71.358 (3)C22—C231.494 (2)
C6—H60.9300C22—H22B0.9700
C7—C81.383 (3)C22—H22A0.9700
C7—H70.9300C24—C251.485 (3)
C8—C91.500 (3)C24—H24B0.9700
C9—H9C0.9600C24—H24A0.9700
C9—H9B0.9600C25—C261.499 (3)
C9—H9A0.9600C25—H25B0.9700
C10—H10C0.9600C25—H25A0.9700
C10—H10B0.9600C26—H26B0.9700
C10—H10A0.9600C26—H26A0.9700
O1—S1—O2117.84 (8)C16—C15—C14120.04 (19)
O1—S1—C1109.46 (8)C16—C15—H15120.0
O2—S1—C1108.65 (7)C14—C15—H15120.0
O1—S1—C12107.00 (8)C15—C16—C17120.9 (2)
O2—S1—C12106.90 (8)C15—C16—H16119.5
C1—S1—C12106.39 (8)C17—C16—H16119.5
C2—N1—C3125.95 (14)C12—C17—C16118.62 (19)
C2—N1—H1N116.6 (13)C12—C17—H17120.7
C3—N1—H1N116.7 (13)C16—C17—H17120.7
C23—N3—C26122.01 (14)N3—C18—C19113.53 (16)
C23—N3—C18121.92 (15)N3—C18—H18B108.9
C26—N3—C18115.99 (14)C19—C18—H18B108.9
C23—N4—C24122.62 (16)N3—C18—H18A108.9
C23—N4—H4N118.0 (15)C19—C18—H18A108.9
C24—N4—H4N119.4 (15)H18B—C18—H18A107.7
C11—C1—C2120.44 (14)C20—C19—C18113.49 (18)
C11—C1—S1113.16 (11)C20—C19—H19B108.9
C2—C1—S1126.38 (12)C18—C19—H19B108.9
N1—C2—C1120.26 (14)C20—C19—H19A108.9
N1—C2—S2120.37 (12)C18—C19—H19A108.9
C1—C2—S2119.37 (12)H19B—C19—H19A107.7
C8—C3—C4122.55 (15)C19—C20—C21114.37 (18)
C8—C3—N1118.90 (15)C19—C20—H20A108.7
C4—C3—N1118.28 (15)C21—C20—H20A108.7
C5—C4—C3117.24 (17)C19—C20—H20B108.7
C5—C4—C10121.19 (18)C21—C20—H20B108.7
C3—C4—C10121.56 (16)H20A—C20—H20B107.6
C6—C5—C4120.93 (19)C20—C21—C22115.35 (19)
C6—C5—H5119.5C20—C21—H21B108.4
C4—C5—H5119.5C22—C21—H21B108.4
C7—C6—C5120.74 (18)C20—C21—H21A108.4
C7—C6—H6119.6C22—C21—H21A108.4
C5—C6—H6119.6H21B—C21—H21A107.5
C6—C7—C8121.06 (19)C23—C22—C21114.77 (17)
C6—C7—H7119.5C23—C22—H22B108.6
C8—C7—H7119.5C21—C22—H22B108.6
C3—C8—C7117.46 (17)C23—C22—H22A108.6
C3—C8—C9121.48 (17)C21—C22—H22A108.6
C7—C8—C9121.06 (18)H22B—C22—H22A107.6
C8—C9—H9C109.5N4—C23—N3121.38 (16)
C8—C9—H9B109.5N4—C23—C22118.27 (16)
H9C—C9—H9B109.5N3—C23—C22120.34 (16)
C8—C9—H9A109.5N4—C24—C25108.70 (16)
H9C—C9—H9A109.5N4—C24—H24B110.0
H9B—C9—H9A109.5C25—C24—H24B110.0
C4—C10—H10C109.5N4—C24—H24A110.0
C4—C10—H10B109.5C25—C24—H24A110.0
H10C—C10—H10B109.5H24B—C24—H24A108.3
C4—C10—H10A109.5C24—C25—C26110.45 (17)
H10C—C10—H10A109.5C24—C25—H25B109.6
H10B—C10—H10A109.5C26—C25—H25B109.6
N2—C11—C1176.46 (17)C24—C25—H25A109.6
C17—C12—C13120.95 (17)C26—C25—H25A109.6
C17—C12—S1119.06 (13)H25B—C25—H25A108.1
C13—C12—S1119.98 (14)N3—C26—C25112.07 (14)
C12—C13—C14119.24 (19)N3—C26—H26B109.2
C12—C13—H13120.4C25—C26—H26B109.2
C14—C13—H13120.4N3—C26—H26A109.2
C15—C14—C13120.2 (2)C25—C26—H26A109.2
C15—C14—H14119.9H26B—C26—H26A107.9
C13—C14—H14119.9
O1—S1—C1—C1142.43 (14)O1—S1—C12—C13174.72 (14)
O2—S1—C1—C11172.37 (11)O2—S1—C12—C1347.62 (16)
C12—S1—C1—C11−72.86 (13)C1—S1—C12—C13−68.34 (16)
O1—S1—C1—C2−139.31 (14)C17—C12—C13—C14−1.0 (3)
O2—S1—C1—C2−9.36 (17)S1—C12—C13—C14−179.96 (14)
C12—S1—C1—C2105.41 (15)C12—C13—C14—C150.8 (3)
C3—N1—C2—C1171.24 (15)C13—C14—C15—C16−0.4 (3)
C3—N1—C2—S2−8.4 (2)C14—C15—C16—C170.1 (4)
C11—C1—C2—N1176.19 (14)C13—C12—C17—C160.8 (3)
S1—C1—C2—N1−2.0 (2)S1—C12—C17—C16179.74 (15)
C11—C1—C2—S2−4.2 (2)C15—C16—C17—C12−0.3 (3)
S1—C1—C2—S2177.69 (9)C23—N3—C18—C1974.2 (2)
C2—N1—C3—C8101.1 (2)C26—N3—C18—C19−109.05 (18)
C2—N1—C3—C4−84.8 (2)N3—C18—C19—C20−80.1 (2)
C8—C3—C4—C50.6 (2)C18—C19—C20—C2159.1 (3)
N1—C3—C4—C5−173.36 (15)C19—C20—C21—C22−61.7 (3)
C8—C3—C4—C10−178.51 (17)C20—C21—C22—C2379.5 (2)
N1—C3—C4—C107.6 (2)C24—N4—C23—N3−4.3 (3)
C3—C4—C5—C6−0.4 (3)C24—N4—C23—C22175.81 (18)
C10—C4—C5—C6178.72 (19)C26—N3—C23—N4−7.3 (3)
C4—C5—C6—C7−0.6 (3)C18—N3—C23—N4169.31 (17)
C5—C6—C7—C81.4 (3)C26—N3—C23—C22172.61 (16)
C4—C3—C8—C70.2 (2)C18—N3—C23—C22−10.8 (3)
N1—C3—C8—C7174.06 (16)C21—C22—C23—N4122.0 (2)
C4—C3—C8—C9179.79 (17)C21—C22—C23—N3−57.8 (3)
N1—C3—C8—C9−6.3 (2)C23—N4—C24—C2535.4 (3)
C6—C7—C8—C3−1.2 (3)N4—C24—C25—C26−53.5 (2)
C6—C7—C8—C9179.24 (18)C23—N3—C26—C25−14.2 (2)
O1—S1—C12—C17−4.27 (16)C18—N3—C26—C25169.07 (16)
O2—S1—C12—C17−131.37 (14)C24—C25—C26—N344.5 (2)
C1—S1—C12—C17112.67 (15)
D—H···AD—HH···AD···AD—H···A
N1—H1N···O20.86 (2)1.98 (2)2.7091 (19)143 (2)
N4—H4N···S2i0.82 (2)2.45 (2)3.2335 (19)161 (2)
Table 1

Selected bond lengths (Å)

S1—O11.4285 (12)
S1—O21.4413 (13)
S1—C11.7291 (16)
S2—C21.7037 (16)
N3—C231.308 (2)
N4—C231.305 (2)
C1—C21.411 (2)
Table 2

Hydrogen-bond geometry (Å, °)

D—H⋯AD—HH⋯ADAD—H⋯A
N1—H1N⋯O20.86 (2)1.98 (2)2.7091 (19)143 (2)
N4—H4N⋯S2i0.82 (2)2.45 (2)3.2335 (19)161 (2)

Symmetry code: (i) .

  2 in total

1.  Activation of carbon dioxide by bicyclic amidines.

Authors:  Eduardo R Pérez; Regina H A Santos; Maria T P Gambardella; Luiz G M de Macedo; Ubirajara P Rodrigues-Filho; Jean-Claude Launay; Douglas W Franco
Journal:  J Org Chem       Date:  2004-11-12       Impact factor: 4.354

2.  The charge-transfer motif in crystal engineering. Self-assembly of acentric (diamondoid) networks from halide salts and carbon tetrabromide as electron-donor/acceptor synthons.

Authors:  Sergey V Lindeman; Jürgen Hecht; Jay K Kochi
Journal:  J Am Chem Soc       Date:  2003-09-24       Impact factor: 15.419

  2 in total

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