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By the reaction of urea or thio­urea, acetyl­acetone and hydrogen halide (HF, HBr or HI), we have obtained seven new 4,6-dimethyl-2-pyrimido(thio)­nium salts, which were characterized by single-crystal X-ray diffraction, namely, 4,6-dimethyl-2-oxo-2,3-di­hydro­pyrimidin-1-ium bifluoride, C6H9N2O+·HF2 or (dmpH)F2H, 4,6-dimethyl-2-oxo-2,3-di­hydro­pyrimidin-1-ium bromide, C6H9N2O+·Br or (dmpH)Br, 4,6-dimethyl-2-oxo-2,3-di­hydro­pyrimidin-1-ium iodide, C6H9N2O+·I or (dmpH)I, 4,6-dimethyl-2-oxo-2,3-di­hydro­pyrimidin-1-ium iodide–urea (1/1), C6H9N2O+·I·CH4N2O or (dmpH)I·ur, 4,6-dimethyl-2-sul­fan­yl­idene-2,3-di­hydro­pyrimidin-1-ium bifluoride–thio­urea (1/1), C6H9N2S+·HF2·CH4N2S or (dmptH)F2H·tu, 4,6-dimethyl-2-sulfanyl­idene-2,3-di­hydro­pyrimidin-1-ium bromide, C6H9N2S+·Br or (dmptH)Br, and 4,6-dimethyl-2-sulfanyl­idene-2,3-di­hydro­pyrimidin-1-ium iodide, C6H9N2S+·I or (dmptH)I. Three HCl derivatives were described previously in the literature, namely, 4,6-dimethyl-2-oxo-2,3-di­hydro­pyrimidin-1-ium chloride, (dmpH)Cl, 4,6-dimethyl-2-sulfanyl­idene-2,3-di­hydro­pyrimidin-1-ium chloride monohydrate, (dmptH)Cl·H2O, and 4,6-dimethyl-2-sulfanyl­idene-2,3-di­hydro­pyrimidin-1-ium chloride–thio­urea (1/1), (dmptH)Cl·tu. Structural analysis shows that in 9 out of 10 of these com­pounds, the ions form one-dimensional chains or ribbons stabilized by hydrogen bonds. Only in one com­pound are parallel planes present. In all the structures, there are charge-assisted N+—H...X hydrogen bonds, as well as weaker CAr+—H...X and π+...X inter­actions. The structures can be divided into five types according to their hydrogen-bond patterns. All the com­pounds undergo thermal decom­position at relatively high temperatures (150–300 °C) without melting. Four oxopyrimidinium salts containing a π+...X...π+ sandwich-like structural motif exhibit luminescent properties.

Supporting information

cif

Crystallographic Information File (CIF) https://doi.org/10.1107/S2053229620005525/wp3004sup1.cif
Contains datablocks 1, 3, 4, 5, 6, 9, 10, global

hkl

Structure factor file (CIF format) https://doi.org/10.1107/S2053229620005525/wp30041sup2.hkl
Contains datablock 1

hkl

Structure factor file (CIF format) https://doi.org/10.1107/S2053229620005525/wp30043sup3.hkl
Contains datablock 3

cml

Chemical Markup Language (CML) file https://doi.org/10.1107/S2053229620005525/wp30043sup9.cml
Supplementary material

cml

Chemical Markup Language (CML) file https://doi.org/10.1107/S2053229620005525/wp30044sup10.cml
Supplementary material

hkl

Structure factor file (CIF format) https://doi.org/10.1107/S2053229620005525/wp30044sup4.hkl
Contains datablock 4

cml

Chemical Markup Language (CML) file https://doi.org/10.1107/S2053229620005525/wp30045sup11.cml
Supplementary material

hkl

Structure factor file (CIF format) https://doi.org/10.1107/S2053229620005525/wp30045sup5.hkl
Contains datablock 5

hkl

Structure factor file (CIF format) https://doi.org/10.1107/S2053229620005525/wp30046sup6.hkl
Contains datablock 6

cml

Chemical Markup Language (CML) file https://doi.org/10.1107/S2053229620005525/wp30049sup12.cml
Supplementary material

hkl

Structure factor file (CIF format) https://doi.org/10.1107/S2053229620005525/wp30049sup7.hkl
Contains datablock 9

cml

Chemical Markup Language (CML) file https://doi.org/10.1107/S2053229620005525/wp300410sup13.cml
Supplementary material

hkl

Structure factor file (CIF format) https://doi.org/10.1107/S2053229620005525/wp300410sup8.hkl
Contains datablock 10

CCDC references: 1998106; 1998105; 1998104; 1998103; 1998102; 1998101; 1998100

Computing details top

For all structures, data collection: X-AREA (Stoe & Cie, 2009); cell refinement: X-AREA (Stoe & Cie, 2009); data reduction: X-RED32 (Stoe & Cie, 2009); program(s) used to solve structure: SHELXT (Sheldrick, 2015a); program(s) used to refine structure: SHELXL2018 (Sheldrick, 2015b); molecular graphics: OLEX2 (Dolomanov et al., 2009); software used to prepare material for publication: OLEX2 (Dolomanov et al., 2009).

4,6-Dimethyl-2-oxo-2,3-dihydropyrimidin-1-ium bifluoride (1) top
Crystal data top
C6H9N2O+·HF2F(000) = 172
Mr = 164.16Dx = 1.484 Mg m3
Monoclinic, P21/mMo Kα radiation, λ = 0.71073 Å
a = 7.9253 (16) ÅCell parameters from 1096 reflections
b = 5.9962 (14) Åθ = 3.0–29.4°
c = 8.433 (2) ŵ = 0.14 mm1
β = 113.551 (18)°T = 120 K
V = 367.39 (16) Å3Block, colourless
Z = 20.25 × 0.04 × 0.04 mm
Data collection top
Stoe IPDS 2T
diffractometer
1075 independent reflections
Radiation source: microfocus sealed X-ray tube, GeniX Mo, 0.05 x 0.05 mm21009 reflections with I > 2σ(I)
Parabolic x-ray mirror monochromatorRint = 0.028
Detector resolution: 6.67 pixels mm-1θmax = 29.3°, θmin = 4.3°
rotation method scansh = 1010
Absorption correction: integration
[X-RED32 (Stoe & Cie, 2009), analogous to Coppens (1970)]
k = 88
Tmin = 0.949, Tmax = 0.983l = 1111
6035 measured reflections
Refinement top
Refinement on F2Primary atom site location: dual
Least-squares matrix: fullHydrogen site location: mixed
R[F2 > 2σ(F2)] = 0.035H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.096 w = 1/[σ2(Fo2) + (0.0471P)2 + 0.1674P]
where P = (Fo2 + 2Fc2)/3
S = 1.05(Δ/σ)max < 0.001
1075 reflectionsΔρmax = 0.39 e Å3
84 parametersΔρmin = 0.32 e Å3
1 restraint
Special details top

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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
O10.71017 (14)0.2500000.91063 (13)0.0205 (2)
N20.72246 (15)0.2500000.64423 (14)0.0140 (2)
H20.6015830.2500000.5921920.017*
N60.99054 (14)0.2500000.89619 (14)0.0137 (2)
H61.0466620.2500001.0097300.016*
C10.80061 (17)0.2500000.82331 (16)0.0140 (3)
C30.81877 (18)0.2500000.54510 (16)0.0142 (3)
C41.00892 (18)0.2500000.62426 (16)0.0155 (3)
H41.0803380.2500000.5567160.019*
C51.09434 (17)0.2500000.80387 (17)0.0142 (3)
C70.7107 (2)0.2500000.35340 (17)0.0196 (3)
C81.29731 (18)0.2500000.90421 (19)0.0192 (3)
F10.36129 (11)0.2500000.50873 (11)0.0214 (2)
H10.255 (2)0.2500000.3699 (12)0.064 (9)*
F20.13833 (15)0.2500000.23660 (11)0.0316 (3)
H7A0.790 (3)0.2500000.294 (3)0.030 (5)*
H8A1.362 (3)0.2500000.827 (3)0.032 (6)*
H8B1.331 (2)0.120 (3)0.9768 (18)0.031 (4)*
H7B0.631 (2)0.121 (3)0.3222 (19)0.033 (4)*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O10.0167 (5)0.0302 (6)0.0178 (5)0.0000.0102 (4)0.000
N20.0121 (5)0.0156 (5)0.0135 (5)0.0000.0044 (4)0.000
N60.0122 (5)0.0164 (5)0.0120 (4)0.0000.0041 (4)0.000
C10.0134 (6)0.0147 (6)0.0144 (6)0.0000.0059 (4)0.000
C30.0184 (6)0.0111 (5)0.0138 (5)0.0000.0071 (5)0.000
C40.0172 (6)0.0159 (6)0.0164 (6)0.0000.0100 (5)0.000
C50.0136 (5)0.0122 (5)0.0175 (6)0.0000.0071 (5)0.000
C70.0244 (7)0.0204 (6)0.0122 (6)0.0000.0055 (5)0.000
C80.0123 (6)0.0229 (7)0.0218 (6)0.0000.0062 (5)0.000
F10.0143 (4)0.0300 (5)0.0168 (4)0.0000.0029 (3)0.000
F20.0386 (6)0.0322 (5)0.0140 (4)0.0000.0001 (4)0.000
Geometric parameters (Å, º) top
O1—C11.2156 (16)C4—C51.3904 (18)
N2—H20.8800C5—C81.4886 (18)
N2—C11.3846 (16)C7—H7A0.95 (2)
N2—C31.3385 (16)C7—H7B0.967 (16)
N6—H60.8800C7—H7Bi0.967 (16)
N6—C11.3800 (16)C8—H8A0.98 (2)
N6—C51.3396 (16)C8—H8B0.962 (16)
C3—C41.3831 (18)C8—H8Bi0.962 (16)
C3—C71.4968 (18)F1—H11.1360 (15)
C4—H40.9500F2—H11.1360 (15)
C1—N2—H2117.9N6—C5—C4119.24 (12)
C3—N2—H2117.9N6—C5—C8116.40 (12)
C3—N2—C1124.28 (11)C4—C5—C8124.36 (12)
C1—N6—H6118.1C3—C7—H7A111.2 (13)
C5—N6—H6118.1C3—C7—H7B108.9 (9)
C5—N6—C1123.71 (11)C3—C7—H7Bi108.9 (9)
O1—C1—N2123.07 (12)H7A—C7—H7B110.5 (11)
O1—C1—N6122.18 (12)H7A—C7—H7Bi110.5 (11)
N6—C1—N2114.75 (11)H7B—C7—H7Bi106.7 (18)
N2—C3—C4118.80 (12)C5—C8—H8A111.1 (13)
N2—C3—C7116.86 (12)C5—C8—H8Bi109.1 (9)
C4—C3—C7124.34 (12)C5—C8—H8B109.1 (9)
C3—C4—H4120.4H8A—C8—H8Bi109.5 (11)
C3—C4—C5119.22 (12)H8A—C8—H8B109.5 (11)
C5—C4—H4120.4H8B—C8—H8Bi108.5 (17)
Symmetry code: (i) x, y+1/2, z.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N2—H2···F10.881.752.6240 (15)175
4,6-Dimethyl-2-oxo-2,3-dihydropyrimidin-1-ium bromide (3) top
Crystal data top
C6H9N2O+·BrDx = 1.723 Mg m3
Mr = 205.06Mo Kα radiation, λ = 0.71073 Å
Orthorhombic, PnmaCell parameters from 16240 reflections
a = 14.4984 (18) Åθ = 3.8–29.7°
b = 6.722 (2) ŵ = 5.13 mm1
c = 8.113 (7) ÅT = 120 K
V = 790.6 (7) Å3Plate, colourless
Z = 40.35 × 0.20 × 0.03 mm
F(000) = 408
Data collection top
Stoe IPDS 2T
diffractometer
1130 independent reflections
Radiation source: microfocus sealed X-ray tube, GeniX Mo, 0.05 x 0.05 mm2971 reflections with I > 2σ(I)
Parabolic x-ray mirror monochromatorRint = 0.050
Detector resolution: 6.67 pixels mm-1θmax = 29.0°, θmin = 3.8°
rotation method scansh = 1919
Absorption correction: integration
[X-RED32 (Stoe & Cie, 2009), analogous to Coppens (1970)]
k = 98
Tmin = 0.639, Tmax = 0.905l = 1111
10482 measured reflections
Refinement top
Refinement on F2Primary atom site location: dual
Least-squares matrix: fullHydrogen site location: mixed
R[F2 > 2σ(F2)] = 0.031H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.096 w = 1/[σ2(Fo2) + (0.0666P)2 + 0.2083P]
where P = (Fo2 + 2Fc2)/3
S = 1.09(Δ/σ)max = 0.001
1130 reflectionsΔρmax = 0.74 e Å3
75 parametersΔρmin = 0.59 e Å3
12 restraints
Special details top

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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
Br10.35196 (2)0.2500000.50127 (2)0.02388 (16)
O10.58317 (14)0.2500000.8135 (2)0.0371 (5)
N20.57782 (16)0.2500000.5322 (3)0.0226 (4)
H20.5171290.2500000.5328900.027*
N60.71848 (15)0.2500000.6681 (3)0.0248 (4)
H60.7512540.2500000.7593770.030*
C30.6210 (2)0.2500000.3855 (3)0.0245 (5)
C50.7641 (2)0.2500000.5243 (3)0.0242 (5)
C40.71538 (19)0.2500000.3791 (3)0.0254 (5)
H40.7466030.2500000.2761260.031*
C10.62334 (19)0.2500000.6826 (3)0.0266 (5)
C70.5611 (2)0.2500000.2362 (3)0.0326 (6)
C80.8668 (2)0.2500000.5294 (4)0.0360 (7)
H7A0.5971 (13)0.2500000.1340 (16)0.049 (12)*
H7B0.5221 (2)0.13098 (8)0.2398 (17)0.068 (8)*
H8A0.8902 (18)0.2500000.6427 (11)0.057 (11)*
H8B0.8890 (9)0.13099 (8)0.4719 (10)0.054 (9)*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Br10.0223 (2)0.0298 (2)0.0195 (2)0.0000.00044 (6)0.000
O10.0251 (9)0.0693 (15)0.0169 (9)0.0000.0028 (7)0.000
N20.0199 (10)0.0304 (11)0.0176 (7)0.0000.0006 (8)0.000
N60.0217 (9)0.0374 (12)0.0151 (8)0.0000.0005 (7)0.000
C30.0306 (13)0.0276 (12)0.0152 (10)0.0000.0005 (10)0.000
C50.0230 (13)0.0293 (12)0.0204 (9)0.0000.0048 (9)0.000
C40.0272 (12)0.0328 (13)0.0163 (10)0.0000.0024 (9)0.000
C10.0243 (11)0.0367 (14)0.0188 (11)0.0000.0009 (10)0.000
C70.0327 (14)0.0472 (16)0.0179 (11)0.0000.0034 (10)0.000
C80.0241 (12)0.057 (2)0.0273 (11)0.0000.0020 (12)0.000
Geometric parameters (Å, º) top
O1—C11.211 (3)C5—C41.373 (4)
N2—H20.8800C5—C81.490 (4)
N2—C31.345 (3)C4—H40.9500
N2—C11.387 (3)C7—H7A0.9799 (12)
N6—H60.8800C7—H7Bi0.9800 (8)
N6—C51.340 (3)C7—H7B0.9800 (8)
N6—C11.384 (3)C8—H8A0.9802 (12)
C3—C41.369 (3)C8—H8Bi0.9802 (8)
C3—C71.490 (4)C8—H8B0.9802 (8)
C3—N2—H2118.1O1—C1—N2122.8 (3)
C3—N2—C1123.9 (2)O1—C1—N6123.6 (3)
C1—N2—H2118.1N6—C1—N2113.5 (2)
C5—N6—H6117.8C3—C7—H7A112.1 (14)
C5—N6—C1124.4 (2)C3—C7—H7B108.2 (7)
C1—N6—H6117.8C3—C7—H7Bi108.2 (7)
N2—C3—C4119.9 (2)H7A—C7—H7B109.44 (13)
N2—C3—C7116.6 (3)H7A—C7—H7Bi109.44 (13)
C4—C3—C7123.5 (2)H7B—C7—H7Bi109.43 (16)
N6—C5—C4119.5 (3)C5—C8—H8A111.8 (16)
N6—C5—C8118.0 (3)C5—C8—H8Bi108.4 (8)
C4—C5—C8122.5 (2)C5—C8—H8B108.4 (8)
C3—C4—C5118.8 (2)H8A—C8—H8Bi109.39 (13)
C3—C4—H4120.6H8A—C8—H8B109.39 (13)
C5—C4—H4120.6H8B—C8—H8Bi109.40 (16)
Symmetry code: (i) x, y+1/2, z.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N2—H2···Br10.882.413.284 (2)174
N6—H6···Br1ii0.882.433.308 (3)176
Symmetry code: (ii) x+1/2, y, z+3/2.
4,6-Dimethyl-2-oxo-2,3-dihydropyrimidin-1-ium iodide (4) top
Crystal data top
C6H9N2O+·IF(000) = 240
Mr = 252.05Dx = 1.899 Mg m3
Monoclinic, P2/nMo Kα radiation, λ = 0.71073 Å
a = 7.1803 (10) ÅCell parameters from 1779 reflections
b = 7.2139 (18) Åθ = 3.4–27.7°
c = 8.6574 (12) ŵ = 3.57 mm1
β = 100.603 (11)°T = 120 K
V = 440.78 (14) Å3Needles, colourless
Z = 20.66 × 0.37 × 0.14 mm
Data collection top
Stoe IPDS 2T
diffractometer
1166 independent reflections
Radiation source: microfocus sealed X-ray tube, GeniX Mo, 0.05 x 0.05 mm21143 reflections with I > 2σ(I)
Parabolic x-ray mirror monochromatorRint = 0.066
Detector resolution: 6.67 pixels mm-1θmax = 29.0°, θmin = 3.4°
rotation method scansh = 99
Absorption correction: integration
[X-RED32 (Stoe & Cie, 2009), analogous to Coppens (1970)]
k = 99
Tmin = 0.274, Tmax = 0.624l = 1011
5622 measured reflections
Refinement top
Refinement on F20 restraints
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.059H-atom parameters constrained
wR(F2) = 0.165 w = 1/[σ2(Fo2) + (0.0966P)2 + 2.7212P]
where P = (Fo2 + 2Fc2)/3
S = 1.09(Δ/σ)max < 0.001
1166 reflectionsΔρmax = 1.55 e Å3
49 parametersΔρmin = 1.29 e Å3
Special details top

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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
I10.2500000.36113 (8)0.7500000.0398 (3)
C10.2500000.4775 (14)0.2500000.0394 (19)
C30.2593 (9)0.7723 (10)0.3881 (9)0.0394 (13)
N20.2632 (9)0.5837 (9)0.3837 (7)0.0411 (12)
H20.2750740.5246880.4739760.049*
C70.2664 (18)0.8639 (11)0.5416 (12)0.056 (2)
H7A0.1433810.8510020.5742070.085*
H7B0.2956440.9956670.5323940.085*
H7C0.3648720.8057490.6200390.085*
O10.2500000.3089 (13)0.2500000.058 (2)
C40.2500000.8710 (12)0.2500000.041 (2)
H40.2499991.0027030.2500000.049*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
I10.0384 (4)0.0395 (4)0.0419 (4)0.0000.0083 (2)0.000
C10.038 (4)0.031 (4)0.048 (5)0.0000.006 (4)0.000
C30.034 (3)0.033 (3)0.049 (3)0.003 (2)0.003 (2)0.003 (3)
N20.042 (3)0.042 (3)0.039 (3)0.006 (2)0.005 (2)0.001 (2)
C70.074 (6)0.045 (5)0.050 (5)0.006 (3)0.008 (4)0.003 (3)
O10.089 (7)0.033 (4)0.056 (5)0.0000.021 (4)0.000
C40.042 (5)0.025 (4)0.053 (6)0.0000.004 (4)0.000
Geometric parameters (Å, º) top
C1—N21.377 (8)N2—H20.8800
C1—N2i1.377 (8)C7—H7A0.9800
C1—O11.216 (14)C7—H7B0.9800
C3—N21.362 (9)C7—H7C0.9800
C3—C71.477 (12)C4—H40.9500
C3—C41.382 (8)
N2i—C1—N2112.4 (9)C3—C7—H7A109.5
O1—C1—N2i123.8 (4)C3—C7—H7B109.5
O1—C1—N2123.8 (4)C3—C7—H7C109.5
N2—C3—C7118.3 (7)H7A—C7—H7B109.5
N2—C3—C4119.3 (7)H7A—C7—H7C109.5
C4—C3—C7122.4 (7)H7B—C7—H7C109.5
C1—N2—H2117.3C3i—C4—C3118.0 (9)
C3—N2—C1125.5 (7)C3—C4—H4121.0
C3—N2—H2117.3C3i—C4—H4121.0
Symmetry code: (i) x+1/2, y, z+1/2.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N2—H2···I10.882.703.571 (7)170
4,6-Dimethyl-2-oxo-2,3-dihydropyrimidin-1-ium iodide–urea (1/1) (5) top
Crystal data top
C6H9N2O+·I·CH4N2OF(000) = 608
Mr = 312.11Dx = 1.829 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
a = 8.772 (1) ÅCell parameters from 3188 reflections
b = 11.5579 (10) Åθ = 3.0–29.4°
c = 14.0700 (16) ŵ = 2.81 mm1
β = 127.378 (7)°T = 120 K
V = 1133.6 (2) Å3Prism, colourless
Z = 40.49 × 0.42 × 0.19 mm
Data collection top
Stoe IPDS 2T
diffractometer
2995 independent reflections
Radiation source: microfocus sealed X-ray tube, GeniX Mo, 0.05 x 0.05 mm22800 reflections with I > 2σ(I)
Parabolic x-ray mirror monochromatorRint = 0.050
Detector resolution: 6.67 pixels mm-1θmax = 29.0°, θmin = 3.4°
rotation method scansh = 1111
Absorption correction: integration
[X-RED32 (Stoe & Cie, 2009), analogous to Coppens (1970)]
k = 1515
Tmin = 0.258, Tmax = 0.579l = 1919
16324 measured reflections
Refinement top
Refinement on F2Primary atom site location: dual
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.032H-atom parameters constrained
wR(F2) = 0.093 w = 1/[σ2(Fo2) + (0.061P)2 + 0.6546P]
where P = (Fo2 + 2Fc2)/3
S = 1.07(Δ/σ)max = 0.001
2995 reflectionsΔρmax = 0.84 e Å3
129 parametersΔρmin = 1.25 e Å3
0 restraints
Special details top

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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
I10.83377 (2)0.74469 (2)0.35562 (2)0.02789 (9)
O1U0.5613 (2)0.14468 (14)0.46992 (15)0.0333 (3)
O10.6489 (3)0.44215 (14)0.44055 (16)0.0342 (4)
N20.7967 (3)0.44561 (16)0.35149 (17)0.0288 (4)
H20.8093810.5212630.3595390.035*
N60.6879 (3)0.27280 (16)0.37324 (18)0.0269 (4)
H60.6279730.2333710.3951040.032*
N1U0.4346 (3)0.29408 (18)0.5062 (2)0.0337 (4)
H1UA0.4851020.3456000.4866780.040*
H1UB0.3651830.3168360.5287410.040*
C10.7072 (3)0.39069 (18)0.39252 (19)0.0274 (4)
C50.7551 (3)0.21480 (19)0.32306 (19)0.0279 (4)
C30.8663 (3)0.39169 (18)0.29974 (19)0.0281 (4)
C1U0.4631 (4)0.1814 (2)0.5016 (2)0.0303 (5)
N2U0.3831 (3)0.10581 (18)0.5326 (2)0.0411 (5)
H2UA0.3994110.0309620.5306290.049*
H2UB0.3144460.1313310.5547350.049*
C40.8454 (4)0.2744 (2)0.2849 (2)0.0297 (4)
H40.8924870.2342160.2486370.036*
C80.7286 (4)0.08672 (19)0.3136 (2)0.0347 (5)
H8A0.8449700.0496350.3820720.052*
H8B0.7039080.0597100.2393270.052*
H8C0.6195150.0666910.3130080.052*
C70.9637 (4)0.4651 (2)0.2641 (2)0.0354 (5)
H7A0.8773150.5274940.2115810.053*
H7B0.9972840.4176260.2215050.053*
H7C1.0806030.4984200.3356730.053*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
I10.03397 (14)0.01755 (12)0.03683 (14)0.00064 (4)0.02392 (11)0.00024 (4)
O1U0.0442 (9)0.0230 (8)0.0462 (9)0.0034 (6)0.0344 (8)0.0025 (6)
O10.0461 (9)0.0230 (8)0.0480 (9)0.0021 (6)0.0360 (8)0.0009 (6)
N20.0394 (9)0.0168 (8)0.0387 (10)0.0001 (7)0.0282 (8)0.0003 (6)
N60.0320 (9)0.0184 (7)0.0359 (9)0.0007 (7)0.0235 (8)0.0006 (7)
N1U0.0496 (12)0.0185 (9)0.0459 (11)0.0028 (8)0.0358 (10)0.0011 (8)
C10.0304 (9)0.0197 (9)0.0350 (10)0.0006 (7)0.0215 (8)0.0004 (7)
C50.0337 (10)0.0193 (9)0.0329 (10)0.0011 (8)0.0214 (9)0.0012 (8)
C30.0335 (10)0.0221 (10)0.0328 (10)0.0011 (7)0.0223 (8)0.0001 (7)
C1U0.0362 (11)0.0247 (11)0.0363 (11)0.0012 (8)0.0253 (9)0.0013 (8)
N2U0.0621 (14)0.0225 (9)0.0674 (14)0.0010 (9)0.0542 (12)0.0022 (9)
C40.0385 (12)0.0209 (9)0.0370 (11)0.0014 (9)0.0267 (10)0.0025 (9)
C80.0476 (13)0.0187 (10)0.0486 (13)0.0008 (9)0.0348 (11)0.0020 (8)
C70.0512 (13)0.0225 (10)0.0482 (12)0.0027 (9)0.0382 (11)0.0019 (9)
Geometric parameters (Å, º) top
O1U—C1U1.260 (3)C3—C41.367 (3)
O1—C11.221 (3)C3—C71.491 (3)
N2—H20.8800C1U—N2U1.348 (3)
N2—C11.379 (3)N2U—H2UA0.8800
N2—C31.353 (3)N2U—H2UB0.8800
N6—H60.8800C4—H40.9500
N6—C11.379 (3)C8—H8A0.9800
N6—C51.342 (3)C8—H8B0.9800
N1U—H1UA0.8800C8—H8C0.9800
N1U—H1UB0.8800C7—H7A0.9800
N1U—C1U1.336 (3)C7—H7B0.9800
C5—C41.381 (3)C7—H7C0.9800
C5—C81.492 (3)
C1—N2—H2117.6N1U—C1U—N2U117.8 (2)
C3—N2—H2117.6C1U—N2U—H2UA120.0
C3—N2—C1124.78 (19)C1U—N2U—H2UB120.0
C1—N6—H6118.1H2UA—N2U—H2UB120.0
C5—N6—H6118.1C5—C4—H4120.3
C5—N6—C1123.8 (2)C3—C4—C5119.4 (2)
H1UA—N1U—H1UB120.0C3—C4—H4120.3
C1U—N1U—H1UA120.0C5—C8—H8A109.5
C1U—N1U—H1UB120.0C5—C8—H8B109.5
O1—C1—N2122.90 (19)C5—C8—H8C109.5
O1—C1—N6123.1 (2)H8A—C8—H8B109.5
N2—C1—N6113.95 (18)H8A—C8—H8C109.5
N6—C5—C4119.6 (2)H8B—C8—H8C109.5
N6—C5—C8116.7 (2)C3—C7—H7A109.5
C4—C5—C8123.7 (2)C3—C7—H7B109.5
N2—C3—C4118.4 (2)C3—C7—H7C109.5
N2—C3—C7117.21 (19)H7A—C7—H7B109.5
C4—C3—C7124.4 (2)H7A—C7—H7C109.5
O1U—C1U—N1U122.3 (2)H7B—C7—H7C109.5
O1U—C1U—N2U119.9 (2)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N2—H2···I10.882.593.4692 (19)173
N6—H6···O1U0.881.802.666 (3)167
N1U—H1UA···O10.882.213.070 (3)167
N1U—H1UB···I1i0.883.113.883 (2)148
N2U—H2UA···O1Uii0.882.062.940 (3)179
N2U—H2UB···I1i0.882.713.565 (2)166
Symmetry codes: (i) x+1, y+1, z+1; (ii) x+1, y, z+1.
4,6-Dimethyl-2-sulfanylidene-2,3-dihydropyrimidin-1-ium bifluoride–thiourea (1/1) (6) top
Crystal data top
C6H9N2S+·F2H·CH4N2SF(000) = 268
Mr = 256.34Dx = 1.457 Mg m3
Monoclinic, P21/mMo Kα radiation, λ = 0.71073 Å
a = 6.3876 (11) ÅCell parameters from 1229 reflections
b = 8.8268 (13) Åθ = 3.1–28.7°
c = 10.500 (2) ŵ = 0.46 mm1
β = 99.355 (15)°T = 120 K
V = 584.15 (17) Å3Plate, yellow
Z = 20.32 × 0.2 × 0.07 mm
Data collection top
Stoe IPDS 2T
diffractometer
1532 independent reflections
Radiation source: microfocus sealed X-ray tube, GeniX Mo, 0.05 x 0.05 mm21375 reflections with I > 2σ(I)
Parabolic x-ray mirror monochromatorRint = 0.047
Detector resolution: 6.67 pixels mm-1θmax = 28.4°, θmin = 3.9°
rotation method scansh = 78
Absorption correction: integration
[X-RED32 (Stoe & Cie, 2009), analogous to Coppens (1970)]
k = 1011
Tmin = 0.853, Tmax = 0.967l = 1313
3316 measured reflections
Refinement top
Refinement on F2Primary atom site location: dual
Least-squares matrix: fullHydrogen site location: mixed
R[F2 > 2σ(F2)] = 0.071H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.220 w = 1/[σ2(Fo2) + (0.0998P)2 + 1.0253P]
where P = (Fo2 + 2Fc2)/3
S = 1.18(Δ/σ)max < 0.001
1532 reflectionsΔρmax = 0.55 e Å3
80 parametersΔρmin = 0.49 e Å3
0 restraints
Special details top

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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
S1T0.5456 (2)0.7500001.04796 (11)0.0367 (4)
S10.3578 (2)0.2500000.63525 (12)0.0424 (4)
F10.2389 (4)0.6231 (2)0.5513 (2)0.0494 (6)
N1T0.4051 (4)0.6196 (3)0.8226 (3)0.0321 (6)
H1TA0.3553870.6208290.7394090.038*
H1TB0.4294120.5325800.8633190.038*
N20.2256 (4)0.3803 (3)0.4084 (3)0.0343 (6)
H20.2522360.4669340.4492530.041*
C1T0.4438 (6)0.7500000.8874 (4)0.0281 (8)
C40.1035 (6)0.2500000.2147 (4)0.0299 (9)
H40.0463470.2500000.1253520.036*
C30.1457 (5)0.3849 (4)0.2805 (3)0.0312 (7)
C70.1049 (5)0.5375 (4)0.2222 (4)0.0377 (7)
H7A0.0017660.5898390.2634140.056*
H7B0.0527060.5271840.1295690.056*
H7C0.2368500.5962550.2351860.056*
C10.2672 (7)0.2500000.4777 (5)0.0357 (10)
H10.261 (15)0.7500000.545 (8)0.08 (3)*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
S1T0.0486 (7)0.0226 (6)0.0379 (6)0.0000.0044 (5)0.000
S10.0433 (7)0.0448 (8)0.0376 (6)0.0000.0023 (5)0.000
F10.0736 (16)0.0302 (11)0.0444 (12)0.0082 (11)0.0092 (10)0.0031 (9)
N1T0.0333 (13)0.0207 (12)0.0411 (14)0.0006 (10)0.0031 (10)0.0007 (10)
N20.0333 (13)0.0276 (14)0.0421 (14)0.0011 (10)0.0066 (11)0.0023 (10)
C1T0.0260 (18)0.0223 (19)0.035 (2)0.0000.0037 (15)0.000
C40.0264 (18)0.024 (2)0.039 (2)0.0000.0062 (16)0.000
C30.0273 (13)0.0259 (15)0.0414 (16)0.0020 (11)0.0083 (11)0.0001 (11)
C70.0381 (16)0.0232 (15)0.0515 (19)0.0008 (12)0.0068 (13)0.0017 (13)
C10.033 (2)0.036 (2)0.038 (2)0.0000.0056 (17)0.000
Geometric parameters (Å, º) top
S1T—C1T1.706 (4)N2—C11.363 (4)
S1—C11.662 (5)C4—H40.9500
F1—H11.132 (14)C4—C3i1.381 (4)
N1T—H1TA0.8800C4—C31.381 (4)
N1T—H1TB0.8800C3—C71.485 (4)
N1T—C1T1.340 (3)C7—H7A0.9800
N2—H20.8800C7—H7B0.9800
N2—C31.357 (4)C7—H7C0.9800
H1TA—N1T—H1TB120.0N2—C3—C4118.7 (3)
C1T—N1T—H1TA120.0N2—C3—C7116.6 (3)
C1T—N1T—H1TB120.0C4—C3—C7124.7 (3)
C3—N2—H2117.9C3—C7—H7A109.5
C3—N2—C1124.2 (3)C3—C7—H7B109.5
C1—N2—H2117.9C3—C7—H7C109.5
N1T—C1T—S1T120.7 (2)H7A—C7—H7B109.5
N1Tii—C1T—S1T120.7 (2)H7A—C7—H7C109.5
N1Tii—C1T—N1T118.5 (4)H7B—C7—H7C109.5
C3i—C4—H4120.4N2i—C1—S1122.5 (2)
C3—C4—H4120.4N2—C1—S1122.5 (2)
C3i—C4—C3119.1 (4)N2—C1—N2i115.0 (4)
Symmetry codes: (i) x, y+1/2, z; (ii) x, y+3/2, z.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1T—H1TA···F10.881.992.874 (4)179
N1T—H1TB···S1Tiii0.882.663.528 (3)170
N2—H2···F10.881.762.610 (4)163
Symmetry code: (iii) x+1, y+1, z+2.
4,6-Dimethyl-2-sulfanylidene-2,3-dihydropyrimidin-1-ium bromide (9) top
Crystal data top
C6H9N2S+·BrF(000) = 440
Mr = 221.12Dx = 1.725 Mg m3
Monoclinic, C2/cMo Kα radiation, λ = 0.71073 Å
a = 8.4675 (11) ÅCell parameters from 2102 reflections
b = 14.9142 (19) Åθ = 3.8–28.8°
c = 6.8814 (9) ŵ = 5.02 mm1
β = 101.575 (10)°T = 120 K
V = 851.35 (19) Å3Prism, yellow
Z = 40.21 × 0.14 × 0.04 mm
Data collection top
Stoe IPDS 2T
diffractometer
933 independent reflections
Radiation source: microfocus sealed X-ray tube, GeniX Mo, 0.05 x 0.05 mm2871 reflections with I > 2σ(I)
Parabolic x-ray mirror monochromatorRint = 0.118
Detector resolution: 6.67 pixels mm-1θmax = 27.0°, θmin = 3.8°
rotation method scansh = 1010
Absorption correction: integration
[X-RED32 (Stoe & Cie, 2009), analogous to Coppens (1970)]
k = 1818
Tmin = 0.262, Tmax = 0.740l = 88
5070 measured reflections
Refinement top
Refinement on F2Primary atom site location: dual
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.064H-atom parameters constrained
wR(F2) = 0.168 w = 1/[σ2(Fo2) + (0.1393P)2]
where P = (Fo2 + 2Fc2)/3
S = 1.05(Δ/σ)max < 0.001
933 reflectionsΔρmax = 2.21 e Å3
49 parametersΔρmin = 1.62 e Å3
0 restraints
Special details top

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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
Br10.0000000.19294 (3)0.2500000.0325 (3)
S10.5000000.12830 (11)0.2500000.0368 (5)
N20.3645 (5)0.2889 (2)0.2528 (6)0.0310 (8)
H20.2733490.2599500.2485040.037*
C10.5000000.2400 (4)0.2500000.0296 (12)
C30.3622 (5)0.3795 (3)0.2619 (5)0.0307 (8)
C40.5000000.4264 (4)0.2500000.0327 (12)
H40.5000010.4900540.2499970.039*
C70.2091 (6)0.4223 (3)0.2835 (7)0.0381 (9)
H7A0.1260720.4100190.1652950.057*
H7B0.2249630.4871660.2988730.057*
H7C0.1749210.3979570.4008120.057*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Br10.0298 (5)0.0429 (5)0.0265 (5)0.0000.0095 (3)0.000
S10.0363 (8)0.0359 (9)0.0419 (9)0.0000.0168 (7)0.000
N20.0274 (17)0.0390 (16)0.0292 (19)0.0001 (15)0.0117 (15)0.0000 (14)
C10.026 (2)0.033 (3)0.032 (3)0.0000.011 (2)0.000
C30.0262 (17)0.041 (2)0.0255 (18)0.0037 (16)0.0081 (14)0.0010 (15)
C40.035 (3)0.039 (3)0.025 (3)0.0000.008 (2)0.000
C70.031 (2)0.046 (2)0.039 (2)0.0046 (17)0.0114 (19)0.0009 (17)
Geometric parameters (Å, º) top
S1—C11.665 (6)C3—C71.479 (6)
N2—H20.8800C4—H40.9500
N2—C11.363 (5)C7—H7A0.9800
N2—C31.352 (5)C7—H7B0.9800
C3—C41.377 (5)C7—H7C0.9800
C1—N2—H2118.1C3i—C4—C3119.0 (6)
C3—N2—H2118.1C3—C4—H4120.5
C3—N2—C1123.8 (4)C3i—C4—H4120.5
N2—C1—S1122.4 (3)C3—C7—H7A109.5
N2i—C1—S1122.4 (3)C3—C7—H7B109.5
N2—C1—N2i115.2 (5)C3—C7—H7C109.5
N2—C3—C4118.9 (4)H7A—C7—H7B109.5
N2—C3—C7117.2 (4)H7A—C7—H7C109.5
C4—C3—C7123.9 (4)H7B—C7—H7C109.5
Symmetry code: (i) x+1, y, z+1/2.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N2—H2···Br10.882.523.399 (4)174
4,6-Dimethyl-2-sulfanylidene-2,3-dihydropyrimidin-1-ium iodide (10) top
Crystal data top
C6H9N2S+·IDx = 1.913 Mg m3
Mr = 268.11Mo Kα radiation, λ = 0.71073 Å
Orthorhombic, CmcmCell parameters from 1294 reflections
a = 8.7198 (14) Åθ = 3.9–26.7°
b = 15.095 (3) ŵ = 3.60 mm1
c = 7.0716 (11) ÅT = 120 K
V = 930.8 (3) Å3Plate, yellow
Z = 40.17 × 0.12 × 0.05 mm
F(000) = 512
Data collection top
Stoe IPDS 2T
diffractometer
708 independent reflections
Radiation source: microfocus sealed X-ray tube, GeniX Mo, 0.05 x 0.05 mm2661 reflections with I > 2σ(I)
Parabolic x-ray mirror monochromatorRint = 0.058
Detector resolution: 6.67 pixels mm-1θmax = 28.9°, θmin = 4.0°
rotation method scansh = 1111
Absorption correction: integration
[X-RED32 (Stoe & Cie, 2009), analogous to Coppens (1970)]
k = 2020
Tmin = 0.520, Tmax = 0.837l = 99
7434 measured reflections
Refinement top
Refinement on F2Primary atom site location: dual
Least-squares matrix: fullHydrogen site location: mixed
R[F2 > 2σ(F2)] = 0.025H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.060 w = 1/[σ2(Fo2) + (0.0431P)2]
where P = (Fo2 + 2Fc2)/3
S = 1.07(Δ/σ)max < 0.001
708 reflectionsΔρmax = 1.10 e Å3
42 parametersΔρmin = 0.88 e Å3
6 restraints
Special details top

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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
I10.0000000.18528 (2)0.7500000.02004 (12)
S10.5000000.12787 (8)0.7500000.0258 (3)
N20.3682 (3)0.28725 (19)0.7500000.0195 (6)
H20.2801270.2587950.7500000.023*
C10.5000000.2378 (3)0.7500000.0198 (9)
C40.5000000.4226 (3)0.7500000.0201 (9)
H40.4999990.4855350.7500000.024*
C30.3643 (4)0.3766 (2)0.7500000.0201 (6)
C70.2109 (5)0.4189 (2)0.7500000.0298 (8)
H7A0.220 (4)0.4836 (3)0.7500000.062 (18)*
H7B0.1549 (12)0.3999 (11)0.63687 (7)0.049 (11)*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
I10.01939 (17)0.01578 (17)0.02494 (19)0.0000.0000.000
S10.0231 (6)0.0113 (5)0.0429 (8)0.0000.0000.000
N20.0177 (12)0.0140 (12)0.0267 (15)0.0014 (10)0.0000.000
C10.021 (2)0.015 (2)0.024 (2)0.0000.0000.000
C40.020 (2)0.014 (2)0.026 (3)0.0000.0000.000
C30.0229 (15)0.0128 (14)0.0246 (17)0.0039 (12)0.0000.000
C70.0262 (17)0.0175 (15)0.046 (3)0.0071 (13)0.0000.000
Geometric parameters (Å, º) top
S1—C11.659 (5)C4—C3i1.372 (4)
N2—H20.8800C3—C71.482 (5)
N2—C11.371 (4)C7—H7A0.9800 (11)
N2—C31.350 (4)C7—H7B0.9800 (7)
C4—H40.9500C7—H7Bii0.9800 (7)
C4—C31.372 (4)
C1—N2—H2117.8N2—C3—C4118.9 (3)
C3—N2—H2117.8N2—C3—C7117.0 (3)
C3—N2—C1124.5 (3)C4—C3—C7124.1 (3)
N2i—C1—S1123.0 (2)C3—C7—H7A111 (2)
N2—C1—S1123.0 (2)C3—C7—H7B108.9 (10)
N2i—C1—N2113.9 (4)C3—C7—H7Bii108.9 (10)
C3—C4—H4120.4H7A—C7—H7B109.43 (13)
C3i—C4—H4120.4H7A—C7—H7Bii109.43 (13)
C3—C4—C3i119.2 (4)H7B—C7—H7Bii109.43 (16)
Symmetry codes: (i) x+1, y, z+3/2; (ii) x, y, z+3/2.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N2—H2···I10.882.683.561 (3)175
Compounds under consideration. For explanation of symbols, see Fig. 1. top
GX-YReference
(1)OF2H--This work
(2)OCl--Lee et al. (1984)
(3)OBr--This work
(4)OI--This work
(5)OI-OC(NH2)2This work
(6)SF2H-SC(NH2)2This work
(7)SCl-H2OBattaglia et al. (1986) and Seth et al. (1996)
(8)SCl-SC(NH2)2Gaye et al. (2009)
(9)SBr--This work
(10)SI--This work
Distances between halogen and the mean ring planes (p) and centroids (d) of dmpH (or dmptH). Structure (7) was excluded since it has no sandwich feature. When parameters for the upper and lower plane differ, two values are provided. Hydrogen-bonding motif R22(8) is regarded as the upper ring of the sandwich in structure (5). The shift was calculated using a Pythagorean equation based on the distance to the centroid, d, and the distance perpendicular to the mean plane, p: shift = sqrt(d2 - p2). All values are in Å. top
Compound(1)(2)(3)(4)(5)(6)(8)(9)(10)
XF2HClBrIIF2HClBrI
Distance X···p2.9983.3343.3613.5663.559, 3.6323.188, 3.0513.3233.4643.536
Distance X···d3.0543.3663.3853.6013.515, 3.5303.828, 3.2793.4903.3383.545
Typeaaabcddaa
Symmetrym on ringm on ringm on ring2 on I1 (none)vertical m on F2Hm on ring & mm2 on Cl2 on Brm on ring & mm2 on I
RvdW(X) (Mantina et al., 2009)1.401.741.821.991.991.401.741.821.99
Plane proximity1.5981.5941.5411.5761.569, 1.6421.788, 1.6511.5831.6441.546
Shift0.5820.4630.4020.5010.558, 0.8542.119, 1.2011.0670.9260.252
 

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