journal menuBuy article online - an online subscription or single-article purchase is required to access this article.
research papers
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+—HX− 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.
X− hydrogen bonds, as well as weaker CAr+—HX− 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.Keywords: pyrimidone; pyrimidinethione; anion–π interactions; chalcogen interactions; halides; crystal structure.
Supporting information
 | Crystallographic Information File (CIF) https://doi.org/10.1107/S2053229620005525/wp3004sup1.cif |
 | Structure factor file (CIF format) https://doi.org/10.1107/S2053229620005525/wp30041sup2.hkl |
| Structure factor file (CIF format) https://doi.org/10.1107/S2053229620005525/wp30043sup3.hkl |
 | Chemical Markup Language (CML) file https://doi.org/10.1107/S2053229620005525/wp30043sup9.cml |
| Chemical Markup Language (CML) file https://doi.org/10.1107/S2053229620005525/wp30044sup10.cml |
| Structure factor file (CIF format) https://doi.org/10.1107/S2053229620005525/wp30044sup4.hkl |
| Chemical Markup Language (CML) file https://doi.org/10.1107/S2053229620005525/wp30045sup11.cml |
| Structure factor file (CIF format) https://doi.org/10.1107/S2053229620005525/wp30045sup5.hkl |
| Structure factor file (CIF format) https://doi.org/10.1107/S2053229620005525/wp30046sup6.hkl |
| Chemical Markup Language (CML) file https://doi.org/10.1107/S2053229620005525/wp30049sup12.cml |
| Structure factor file (CIF format) https://doi.org/10.1107/S2053229620005525/wp30049sup7.hkl |
| Chemical Markup Language (CML) file https://doi.org/10.1107/S2053229620005525/wp300410sup13.cml |
| Structure factor file (CIF format) https://doi.org/10.1107/S2053229620005525/wp300410sup8.hkl |
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+·HF2− | F(000) = 172 |
| Mr = 164.16 | Dx = 1.484 Mg m−3 |
| Monoclinic, P21/m | Mo Kα radiation, λ = 0.71073 Å |
| a = 7.9253 (16) Å | Cell parameters from 1096 reflections |
| b = 5.9962 (14) Å | θ = 3.0–29.4° |
| c = 8.433 (2) Å | µ = 0.14 mm−1 |
| β = 113.551 (18)° | T = 120 K |
| V = 367.39 (16) Å3 | Block, colourless |
| Z = 2 | 0.25 × 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 mm2 | 1009 reflections with I > 2σ(I) |
| Parabolic x-ray mirror monochromator | Rint = 0.028 |
| Detector resolution: 6.67 pixels mm-1 | θmax = 29.3°, θmin = 4.3° |
| rotation method scans | h = −10→10 |
| Absorption correction: integration [X-RED32 (Stoe & Cie, 2009), analogous to Coppens (1970)] | k = −8→8 |
| Tmin = 0.949, Tmax = 0.983 | l = −11→11 |
| 6035 measured reflections |
Refinement top
| Refinement on F2 | Primary atom site location: dual |
| Least-squares matrix: full | Hydrogen site location: mixed |
| R[F2 > 2σ(F2)] = 0.035 | H 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 reflections | Δρmax = 0.39 e Å−3 |
| 84 parameters | Δρmin = −0.32 e Å−3 |
| 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
| x | y | z | Uiso*/Ueq | ||
| O1 | 0.71017 (14) | 0.250000 | 0.91063 (13) | 0.0205 (2) | |
| N2 | 0.72246 (15) | 0.250000 | 0.64423 (14) | 0.0140 (2) | |
| H2 | 0.601583 | 0.250000 | 0.592192 | 0.017* | |
| N6 | 0.99054 (14) | 0.250000 | 0.89619 (14) | 0.0137 (2) | |
| H6 | 1.046662 | 0.250000 | 1.009730 | 0.016* | |
| C1 | 0.80061 (17) | 0.250000 | 0.82331 (16) | 0.0140 (3) | |
| C3 | 0.81877 (18) | 0.250000 | 0.54510 (16) | 0.0142 (3) | |
| C4 | 1.00892 (18) | 0.250000 | 0.62426 (16) | 0.0155 (3) | |
| H4 | 1.080338 | 0.250000 | 0.556716 | 0.019* | |
| C5 | 1.09434 (17) | 0.250000 | 0.80387 (17) | 0.0142 (3) | |
| C7 | 0.7107 (2) | 0.250000 | 0.35340 (17) | 0.0196 (3) | |
| C8 | 1.29731 (18) | 0.250000 | 0.90421 (19) | 0.0192 (3) | |
| F1 | 0.36129 (11) | 0.250000 | 0.50873 (11) | 0.0214 (2) | |
| H1 | 0.255 (2) | 0.250000 | 0.3699 (12) | 0.064 (9)* | |
| F2 | 0.13833 (15) | 0.250000 | 0.23660 (11) | 0.0316 (3) | |
| H7A | 0.790 (3) | 0.250000 | 0.294 (3) | 0.030 (5)* | |
| H8A | 1.362 (3) | 0.250000 | 0.827 (3) | 0.032 (6)* | |
| H8B | 1.331 (2) | 0.120 (3) | 0.9768 (18) | 0.031 (4)* | |
| H7B | 0.631 (2) | 0.121 (3) | 0.3222 (19) | 0.033 (4)* |
Atomic displacement parameters (Å2) top
| U11 | U22 | U33 | U12 | U13 | U23 | |
| O1 | 0.0167 (5) | 0.0302 (6) | 0.0178 (5) | 0.000 | 0.0102 (4) | 0.000 |
| N2 | 0.0121 (5) | 0.0156 (5) | 0.0135 (5) | 0.000 | 0.0044 (4) | 0.000 |
| N6 | 0.0122 (5) | 0.0164 (5) | 0.0120 (4) | 0.000 | 0.0041 (4) | 0.000 |
| C1 | 0.0134 (6) | 0.0147 (6) | 0.0144 (6) | 0.000 | 0.0059 (4) | 0.000 |
| C3 | 0.0184 (6) | 0.0111 (5) | 0.0138 (5) | 0.000 | 0.0071 (5) | 0.000 |
| C4 | 0.0172 (6) | 0.0159 (6) | 0.0164 (6) | 0.000 | 0.0100 (5) | 0.000 |
| C5 | 0.0136 (5) | 0.0122 (5) | 0.0175 (6) | 0.000 | 0.0071 (5) | 0.000 |
| C7 | 0.0244 (7) | 0.0204 (6) | 0.0122 (6) | 0.000 | 0.0055 (5) | 0.000 |
| C8 | 0.0123 (6) | 0.0229 (7) | 0.0218 (6) | 0.000 | 0.0062 (5) | 0.000 |
| F1 | 0.0143 (4) | 0.0300 (5) | 0.0168 (4) | 0.000 | 0.0029 (3) | 0.000 |
| F2 | 0.0386 (6) | 0.0322 (5) | 0.0140 (4) | 0.000 | 0.0001 (4) | 0.000 |
Geometric parameters (Å, º) top
| O1—C1 | 1.2156 (16) | C4—C5 | 1.3904 (18) |
| N2—H2 | 0.8800 | C5—C8 | 1.4886 (18) |
| N2—C1 | 1.3846 (16) | C7—H7A | 0.95 (2) |
| N2—C3 | 1.3385 (16) | C7—H7B | 0.967 (16) |
| N6—H6 | 0.8800 | C7—H7Bi | 0.967 (16) |
| N6—C1 | 1.3800 (16) | C8—H8A | 0.98 (2) |
| N6—C5 | 1.3396 (16) | C8—H8B | 0.962 (16) |
| C3—C4 | 1.3831 (18) | C8—H8Bi | 0.962 (16) |
| C3—C7 | 1.4968 (18) | F1—H1 | 1.1360 (15) |
| C4—H4 | 0.9500 | F2—H1 | 1.1360 (15) |
| C1—N2—H2 | 117.9 | N6—C5—C4 | 119.24 (12) |
| C3—N2—H2 | 117.9 | N6—C5—C8 | 116.40 (12) |
| C3—N2—C1 | 124.28 (11) | C4—C5—C8 | 124.36 (12) |
| C1—N6—H6 | 118.1 | C3—C7—H7A | 111.2 (13) |
| C5—N6—H6 | 118.1 | C3—C7—H7B | 108.9 (9) |
| C5—N6—C1 | 123.71 (11) | C3—C7—H7Bi | 108.9 (9) |
| O1—C1—N2 | 123.07 (12) | H7A—C7—H7B | 110.5 (11) |
| O1—C1—N6 | 122.18 (12) | H7A—C7—H7Bi | 110.5 (11) |
| N6—C1—N2 | 114.75 (11) | H7B—C7—H7Bi | 106.7 (18) |
| N2—C3—C4 | 118.80 (12) | C5—C8—H8A | 111.1 (13) |
| N2—C3—C7 | 116.86 (12) | C5—C8—H8Bi | 109.1 (9) |
| C4—C3—C7 | 124.34 (12) | C5—C8—H8B | 109.1 (9) |
| C3—C4—H4 | 120.4 | H8A—C8—H8Bi | 109.5 (11) |
| C3—C4—C5 | 119.22 (12) | H8A—C8—H8B | 109.5 (11) |
| C5—C4—H4 | 120.4 | H8B—C8—H8Bi | 108.5 (17) |
| Symmetry code: (i) x, −y+1/2, z. |
4,6-Dimethyl-2-oxo-2,3-dihydropyrimidin-1-ium bromide (3) top
Crystal data top
| C6H9N2O+·Br− | Dx = 1.723 Mg m−3 |
| Mr = 205.06 | Mo Kα radiation, λ = 0.71073 Å |
| Orthorhombic, Pnma | Cell parameters from 16240 reflections |
| a = 14.4984 (18) Å | θ = 3.8–29.7° |
| b = 6.722 (2) Å | µ = 5.13 mm−1 |
| c = 8.113 (7) Å | T = 120 K |
| V = 790.6 (7) Å3 | Plate, colourless |
| Z = 4 | 0.35 × 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 mm2 | 971 reflections with I > 2σ(I) |
| Parabolic x-ray mirror monochromator | Rint = 0.050 |
| Detector resolution: 6.67 pixels mm-1 | θmax = 29.0°, θmin = 3.8° |
| rotation method scans | h = −19→19 |
| Absorption correction: integration [X-RED32 (Stoe & Cie, 2009), analogous to Coppens (1970)] | k = −9→8 |
| Tmin = 0.639, Tmax = 0.905 | l = −11→11 |
| 10482 measured reflections |
Refinement top
| Refinement on F2 | Primary atom site location: dual |
| Least-squares matrix: full | Hydrogen site location: mixed |
| R[F2 > 2σ(F2)] = 0.031 | H 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 reflections | Δρmax = 0.74 e Å−3 |
| 75 parameters | Δρmin = −0.59 e Å−3 |
| 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
| x | y | z | Uiso*/Ueq | ||
| Br1 | 0.35196 (2) | 0.250000 | 0.50127 (2) | 0.02388 (16) | |
| O1 | 0.58317 (14) | 0.250000 | 0.8135 (2) | 0.0371 (5) | |
| N2 | 0.57782 (16) | 0.250000 | 0.5322 (3) | 0.0226 (4) | |
| H2 | 0.517129 | 0.250000 | 0.532890 | 0.027* | |
| N6 | 0.71848 (15) | 0.250000 | 0.6681 (3) | 0.0248 (4) | |
| H6 | 0.751254 | 0.250000 | 0.759377 | 0.030* | |
| C3 | 0.6210 (2) | 0.250000 | 0.3855 (3) | 0.0245 (5) | |
| C5 | 0.7641 (2) | 0.250000 | 0.5243 (3) | 0.0242 (5) | |
| C4 | 0.71538 (19) | 0.250000 | 0.3791 (3) | 0.0254 (5) | |
| H4 | 0.746603 | 0.250000 | 0.276126 | 0.031* | |
| C1 | 0.62334 (19) | 0.250000 | 0.6826 (3) | 0.0266 (5) | |
| C7 | 0.5611 (2) | 0.250000 | 0.2362 (3) | 0.0326 (6) | |
| C8 | 0.8668 (2) | 0.250000 | 0.5294 (4) | 0.0360 (7) | |
| H7A | 0.5971 (13) | 0.250000 | 0.1340 (16) | 0.049 (12)* | |
| H7B | 0.5221 (2) | 0.13098 (8) | 0.2398 (17) | 0.068 (8)* | |
| H8A | 0.8902 (18) | 0.250000 | 0.6427 (11) | 0.057 (11)* | |
| H8B | 0.8890 (9) | 0.13099 (8) | 0.4719 (10) | 0.054 (9)* |
Atomic displacement parameters (Å2) top
| U11 | U22 | U33 | U12 | U13 | U23 | |
| Br1 | 0.0223 (2) | 0.0298 (2) | 0.0195 (2) | 0.000 | −0.00044 (6) | 0.000 |
| O1 | 0.0251 (9) | 0.0693 (15) | 0.0169 (9) | 0.000 | 0.0028 (7) | 0.000 |
| N2 | 0.0199 (10) | 0.0304 (11) | 0.0176 (7) | 0.000 | 0.0006 (8) | 0.000 |
| N6 | 0.0217 (9) | 0.0374 (12) | 0.0151 (8) | 0.000 | −0.0005 (7) | 0.000 |
| C3 | 0.0306 (13) | 0.0276 (12) | 0.0152 (10) | 0.000 | 0.0005 (10) | 0.000 |
| C5 | 0.0230 (13) | 0.0293 (12) | 0.0204 (9) | 0.000 | 0.0048 (9) | 0.000 |
| C4 | 0.0272 (12) | 0.0328 (13) | 0.0163 (10) | 0.000 | 0.0024 (9) | 0.000 |
| C1 | 0.0243 (11) | 0.0367 (14) | 0.0188 (11) | 0.000 | −0.0009 (10) | 0.000 |
| C7 | 0.0327 (14) | 0.0472 (16) | 0.0179 (11) | 0.000 | −0.0034 (10) | 0.000 |
| C8 | 0.0241 (12) | 0.057 (2) | 0.0273 (11) | 0.000 | 0.0020 (12) | 0.000 |
Geometric parameters (Å, º) top
| O1—C1 | 1.211 (3) | C5—C4 | 1.373 (4) |
| N2—H2 | 0.8800 | C5—C8 | 1.490 (4) |
| N2—C3 | 1.345 (3) | C4—H4 | 0.9500 |
| N2—C1 | 1.387 (3) | C7—H7A | 0.9799 (12) |
| N6—H6 | 0.8800 | C7—H7Bi | 0.9800 (8) |
| N6—C5 | 1.340 (3) | C7—H7B | 0.9800 (8) |
| N6—C1 | 1.384 (3) | C8—H8A | 0.9802 (12) |
| C3—C4 | 1.369 (3) | C8—H8Bi | 0.9802 (8) |
| C3—C7 | 1.490 (4) | C8—H8B | 0.9802 (8) |
| C3—N2—H2 | 118.1 | O1—C1—N2 | 122.8 (3) |
| C3—N2—C1 | 123.9 (2) | O1—C1—N6 | 123.6 (3) |
| C1—N2—H2 | 118.1 | N6—C1—N2 | 113.5 (2) |
| C5—N6—H6 | 117.8 | C3—C7—H7A | 112.1 (14) |
| C5—N6—C1 | 124.4 (2) | C3—C7—H7B | 108.2 (7) |
| C1—N6—H6 | 117.8 | C3—C7—H7Bi | 108.2 (7) |
| N2—C3—C4 | 119.9 (2) | H7A—C7—H7B | 109.44 (13) |
| N2—C3—C7 | 116.6 (3) | H7A—C7—H7Bi | 109.44 (13) |
| C4—C3—C7 | 123.5 (2) | H7B—C7—H7Bi | 109.43 (16) |
| N6—C5—C4 | 119.5 (3) | C5—C8—H8A | 111.8 (16) |
| N6—C5—C8 | 118.0 (3) | C5—C8—H8Bi | 108.4 (8) |
| C4—C5—C8 | 122.5 (2) | C5—C8—H8B | 108.4 (8) |
| C3—C4—C5 | 118.8 (2) | H8A—C8—H8Bi | 109.39 (13) |
| C3—C4—H4 | 120.6 | H8A—C8—H8B | 109.39 (13) |
| C5—C4—H4 | 120.6 | H8B—C8—H8Bi | 109.40 (16) |
| Symmetry code: (i) x, −y+1/2, z. |
Hydrogen-bond geometry (Å, º) top
| D—H···A | D—H | H···A | D···A | D—H···A |
| N2—H2···Br1 | 0.88 | 2.41 | 3.284 (2) | 174 |
| N6—H6···Br1ii | 0.88 | 2.43 | 3.308 (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+·I− | F(000) = 240 |
| Mr = 252.05 | Dx = 1.899 Mg m−3 |
| Monoclinic, P2/n | Mo Kα radiation, λ = 0.71073 Å |
| a = 7.1803 (10) Å | Cell parameters from 1779 reflections |
| b = 7.2139 (18) Å | θ = 3.4–27.7° |
| c = 8.6574 (12) Å | µ = 3.57 mm−1 |
| β = 100.603 (11)° | T = 120 K |
| V = 440.78 (14) Å3 | Needles, colourless |
| Z = 2 | 0.66 × 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 mm2 | 1143 reflections with I > 2σ(I) |
| Parabolic x-ray mirror monochromator | Rint = 0.066 |
| Detector resolution: 6.67 pixels mm-1 | θmax = 29.0°, θmin = 3.4° |
| rotation method scans | h = −9→9 |
| Absorption correction: integration [X-RED32 (Stoe & Cie, 2009), analogous to Coppens (1970)] | k = −9→9 |
| Tmin = 0.274, Tmax = 0.624 | l = −10→11 |
| 5622 measured reflections |
Refinement top
| Refinement on F2 | 0 restraints |
| Least-squares matrix: full | Hydrogen site location: inferred from neighbouring sites |
| R[F2 > 2σ(F2)] = 0.059 | H-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 reflections | Δρmax = 1.55 e Å−3 |
| 49 parameters | Δρmin = −1.29 e Å−3 |
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
| x | y | z | Uiso*/Ueq | ||
| I1 | 0.250000 | 0.36113 (8) | 0.750000 | 0.0398 (3) | |
| C1 | 0.250000 | 0.4775 (14) | 0.250000 | 0.0394 (19) | |
| C3 | 0.2593 (9) | 0.7723 (10) | 0.3881 (9) | 0.0394 (13) | |
| N2 | 0.2632 (9) | 0.5837 (9) | 0.3837 (7) | 0.0411 (12) | |
| H2 | 0.275074 | 0.524688 | 0.473976 | 0.049* | |
| C7 | 0.2664 (18) | 0.8639 (11) | 0.5416 (12) | 0.056 (2) | |
| H7A | 0.143381 | 0.851002 | 0.574207 | 0.085* | |
| H7B | 0.295644 | 0.995667 | 0.532394 | 0.085* | |
| H7C | 0.364872 | 0.805749 | 0.620039 | 0.085* | |
| O1 | 0.250000 | 0.3089 (13) | 0.250000 | 0.058 (2) | |
| C4 | 0.250000 | 0.8710 (12) | 0.250000 | 0.041 (2) | |
| H4 | 0.249999 | 1.002703 | 0.250000 | 0.049* |
Atomic displacement parameters (Å2) top
| U11 | U22 | U33 | U12 | U13 | U23 | |
| I1 | 0.0384 (4) | 0.0395 (4) | 0.0419 (4) | 0.000 | 0.0083 (2) | 0.000 |
| C1 | 0.038 (4) | 0.031 (4) | 0.048 (5) | 0.000 | 0.006 (4) | 0.000 |
| C3 | 0.034 (3) | 0.033 (3) | 0.049 (3) | −0.003 (2) | 0.003 (2) | 0.003 (3) |
| N2 | 0.042 (3) | 0.042 (3) | 0.039 (3) | 0.006 (2) | 0.005 (2) | 0.001 (2) |
| C7 | 0.074 (6) | 0.045 (5) | 0.050 (5) | −0.006 (3) | 0.008 (4) | −0.003 (3) |
| O1 | 0.089 (7) | 0.033 (4) | 0.056 (5) | 0.000 | 0.021 (4) | 0.000 |
| C4 | 0.042 (5) | 0.025 (4) | 0.053 (6) | 0.000 | 0.004 (4) | 0.000 |
Geometric parameters (Å, º) top
| C1—N2 | 1.377 (8) | N2—H2 | 0.8800 |
| C1—N2i | 1.377 (8) | C7—H7A | 0.9800 |
| C1—O1 | 1.216 (14) | C7—H7B | 0.9800 |
| C3—N2 | 1.362 (9) | C7—H7C | 0.9800 |
| C3—C7 | 1.477 (12) | C4—H4 | 0.9500 |
| C3—C4 | 1.382 (8) | ||
| N2i—C1—N2 | 112.4 (9) | C3—C7—H7A | 109.5 |
| O1—C1—N2i | 123.8 (4) | C3—C7—H7B | 109.5 |
| O1—C1—N2 | 123.8 (4) | C3—C7—H7C | 109.5 |
| N2—C3—C7 | 118.3 (7) | H7A—C7—H7B | 109.5 |
| N2—C3—C4 | 119.3 (7) | H7A—C7—H7C | 109.5 |
| C4—C3—C7 | 122.4 (7) | H7B—C7—H7C | 109.5 |
| C1—N2—H2 | 117.3 | C3i—C4—C3 | 118.0 (9) |
| C3—N2—C1 | 125.5 (7) | C3—C4—H4 | 121.0 |
| C3—N2—H2 | 117.3 | C3i—C4—H4 | 121.0 |
| Symmetry code: (i) −x+1/2, y, −z+1/2. |
4,6-Dimethyl-2-oxo-2,3-dihydropyrimidin-1-ium iodide–urea (1/1) (5) top
Crystal data top
| C6H9N2O+·I−·CH4N2O | F(000) = 608 |
| Mr = 312.11 | Dx = 1.829 Mg m−3 |
| Monoclinic, P21/c | Mo Kα radiation, λ = 0.71073 Å |
| a = 8.772 (1) Å | Cell parameters from 3188 reflections |
| b = 11.5579 (10) Å | θ = 3.0–29.4° |
| c = 14.0700 (16) Å | µ = 2.81 mm−1 |
| β = 127.378 (7)° | T = 120 K |
| V = 1133.6 (2) Å3 | Prism, colourless |
| Z = 4 | 0.49 × 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 mm2 | 2800 reflections with I > 2σ(I) |
| Parabolic x-ray mirror monochromator | Rint = 0.050 |
| Detector resolution: 6.67 pixels mm-1 | θmax = 29.0°, θmin = 3.4° |
| rotation method scans | h = −11→11 |
| Absorption correction: integration [X-RED32 (Stoe & Cie, 2009), analogous to Coppens (1970)] | k = −15→15 |
| Tmin = 0.258, Tmax = 0.579 | l = −19→19 |
| 16324 measured reflections |
Refinement top
| Refinement on F2 | Primary atom site location: dual |
| Least-squares matrix: full | Hydrogen site location: inferred from neighbouring sites |
| R[F2 > 2σ(F2)] = 0.032 | H-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 reflections | Δρmax = 0.84 e Å−3 |
| 129 parameters | Δρmin = −1.25 e Å−3 |
| 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
| x | y | z | Uiso*/Ueq | ||
| I1 | 0.83377 (2) | 0.74469 (2) | 0.35562 (2) | 0.02789 (9) | |
| O1U | 0.5613 (2) | 0.14468 (14) | 0.46992 (15) | 0.0333 (3) | |
| O1 | 0.6489 (3) | 0.44215 (14) | 0.44055 (16) | 0.0342 (4) | |
| N2 | 0.7967 (3) | 0.44561 (16) | 0.35149 (17) | 0.0288 (4) | |
| H2 | 0.809381 | 0.521263 | 0.359539 | 0.035* | |
| N6 | 0.6879 (3) | 0.27280 (16) | 0.37324 (18) | 0.0269 (4) | |
| H6 | 0.627973 | 0.233371 | 0.395104 | 0.032* | |
| N1U | 0.4346 (3) | 0.29408 (18) | 0.5062 (2) | 0.0337 (4) | |
| H1UA | 0.485102 | 0.345600 | 0.486678 | 0.040* | |
| H1UB | 0.365183 | 0.316836 | 0.528741 | 0.040* | |
| C1 | 0.7072 (3) | 0.39069 (18) | 0.39252 (19) | 0.0274 (4) | |
| C5 | 0.7551 (3) | 0.21480 (19) | 0.32306 (19) | 0.0279 (4) | |
| C3 | 0.8663 (3) | 0.39169 (18) | 0.29974 (19) | 0.0281 (4) | |
| C1U | 0.4631 (4) | 0.1814 (2) | 0.5016 (2) | 0.0303 (5) | |
| N2U | 0.3831 (3) | 0.10581 (18) | 0.5326 (2) | 0.0411 (5) | |
| H2UA | 0.399411 | 0.030962 | 0.530629 | 0.049* | |
| H2UB | 0.314446 | 0.131331 | 0.554735 | 0.049* | |
| C4 | 0.8454 (4) | 0.2744 (2) | 0.2849 (2) | 0.0297 (4) | |
| H4 | 0.892487 | 0.234216 | 0.248637 | 0.036* | |
| C8 | 0.7286 (4) | 0.08672 (19) | 0.3136 (2) | 0.0347 (5) | |
| H8A | 0.844970 | 0.049635 | 0.382072 | 0.052* | |
| H8B | 0.703908 | 0.059710 | 0.239327 | 0.052* | |
| H8C | 0.619515 | 0.066691 | 0.313008 | 0.052* | |
| C7 | 0.9637 (4) | 0.4651 (2) | 0.2641 (2) | 0.0354 (5) | |
| H7A | 0.877315 | 0.527494 | 0.211581 | 0.053* | |
| H7B | 0.997284 | 0.417626 | 0.221505 | 0.053* | |
| H7C | 1.080603 | 0.498420 | 0.335673 | 0.053* |
Atomic displacement parameters (Å2) top
| U11 | U22 | U33 | U12 | U13 | U23 | |
| I1 | 0.03397 (14) | 0.01755 (12) | 0.03683 (14) | 0.00064 (4) | 0.02392 (11) | 0.00024 (4) |
| O1U | 0.0442 (9) | 0.0230 (8) | 0.0462 (9) | 0.0034 (6) | 0.0344 (8) | 0.0025 (6) |
| O1 | 0.0461 (9) | 0.0230 (8) | 0.0480 (9) | 0.0021 (6) | 0.0360 (8) | −0.0009 (6) |
| N2 | 0.0394 (9) | 0.0168 (8) | 0.0387 (10) | 0.0001 (7) | 0.0282 (8) | −0.0003 (6) |
| N6 | 0.0320 (9) | 0.0184 (7) | 0.0359 (9) | −0.0007 (7) | 0.0235 (8) | 0.0006 (7) |
| N1U | 0.0496 (12) | 0.0185 (9) | 0.0459 (11) | 0.0028 (8) | 0.0358 (10) | 0.0011 (8) |
| C1 | 0.0304 (9) | 0.0197 (9) | 0.0350 (10) | 0.0006 (7) | 0.0215 (8) | 0.0004 (7) |
| C5 | 0.0337 (10) | 0.0193 (9) | 0.0329 (10) | 0.0011 (8) | 0.0214 (9) | −0.0012 (8) |
| C3 | 0.0335 (10) | 0.0221 (10) | 0.0328 (10) | 0.0011 (7) | 0.0223 (8) | −0.0001 (7) |
| C1U | 0.0362 (11) | 0.0247 (11) | 0.0363 (11) | 0.0012 (8) | 0.0253 (9) | 0.0013 (8) |
| N2U | 0.0621 (14) | 0.0225 (9) | 0.0674 (14) | −0.0010 (9) | 0.0542 (12) | −0.0022 (9) |
| C4 | 0.0385 (12) | 0.0209 (9) | 0.0370 (11) | 0.0014 (9) | 0.0267 (10) | −0.0025 (9) |
| C8 | 0.0476 (13) | 0.0187 (10) | 0.0486 (13) | −0.0008 (9) | 0.0348 (11) | −0.0020 (8) |
| C7 | 0.0512 (13) | 0.0225 (10) | 0.0482 (12) | −0.0027 (9) | 0.0382 (11) | −0.0019 (9) |
Geometric parameters (Å, º) top
| O1U—C1U | 1.260 (3) | C3—C4 | 1.367 (3) |
| O1—C1 | 1.221 (3) | C3—C7 | 1.491 (3) |
| N2—H2 | 0.8800 | C1U—N2U | 1.348 (3) |
| N2—C1 | 1.379 (3) | N2U—H2UA | 0.8800 |
| N2—C3 | 1.353 (3) | N2U—H2UB | 0.8800 |
| N6—H6 | 0.8800 | C4—H4 | 0.9500 |
| N6—C1 | 1.379 (3) | C8—H8A | 0.9800 |
| N6—C5 | 1.342 (3) | C8—H8B | 0.9800 |
| N1U—H1UA | 0.8800 | C8—H8C | 0.9800 |
| N1U—H1UB | 0.8800 | C7—H7A | 0.9800 |
| N1U—C1U | 1.336 (3) | C7—H7B | 0.9800 |
| C5—C4 | 1.381 (3) | C7—H7C | 0.9800 |
| C5—C8 | 1.492 (3) | ||
| C1—N2—H2 | 117.6 | N1U—C1U—N2U | 117.8 (2) |
| C3—N2—H2 | 117.6 | C1U—N2U—H2UA | 120.0 |
| C3—N2—C1 | 124.78 (19) | C1U—N2U—H2UB | 120.0 |
| C1—N6—H6 | 118.1 | H2UA—N2U—H2UB | 120.0 |
| C5—N6—H6 | 118.1 | C5—C4—H4 | 120.3 |
| C5—N6—C1 | 123.8 (2) | C3—C4—C5 | 119.4 (2) |
| H1UA—N1U—H1UB | 120.0 | C3—C4—H4 | 120.3 |
| C1U—N1U—H1UA | 120.0 | C5—C8—H8A | 109.5 |
| C1U—N1U—H1UB | 120.0 | C5—C8—H8B | 109.5 |
| O1—C1—N2 | 122.90 (19) | C5—C8—H8C | 109.5 |
| O1—C1—N6 | 123.1 (2) | H8A—C8—H8B | 109.5 |
| N2—C1—N6 | 113.95 (18) | H8A—C8—H8C | 109.5 |
| N6—C5—C4 | 119.6 (2) | H8B—C8—H8C | 109.5 |
| N6—C5—C8 | 116.7 (2) | C3—C7—H7A | 109.5 |
| C4—C5—C8 | 123.7 (2) | C3—C7—H7B | 109.5 |
| N2—C3—C4 | 118.4 (2) | C3—C7—H7C | 109.5 |
| N2—C3—C7 | 117.21 (19) | H7A—C7—H7B | 109.5 |
| C4—C3—C7 | 124.4 (2) | H7A—C7—H7C | 109.5 |
| O1U—C1U—N1U | 122.3 (2) | H7B—C7—H7C | 109.5 |
| O1U—C1U—N2U | 119.9 (2) |
Hydrogen-bond geometry (Å, º) top
| D—H···A | D—H | H···A | D···A | D—H···A |
| N2—H2···I1 | 0.88 | 2.59 | 3.4692 (19) | 173 |
| N6—H6···O1U | 0.88 | 1.80 | 2.666 (3) | 167 |
| N1U—H1UA···O1 | 0.88 | 2.21 | 3.070 (3) | 167 |
| N1U—H1UB···I1i | 0.88 | 3.11 | 3.883 (2) | 148 |
| N2U—H2UA···O1Uii | 0.88 | 2.06 | 2.940 (3) | 179 |
| N2U—H2UB···I1i | 0.88 | 2.71 | 3.565 (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−·CH4N2S | F(000) = 268 |
| Mr = 256.34 | Dx = 1.457 Mg m−3 |
| Monoclinic, P21/m | Mo Kα radiation, λ = 0.71073 Å |
| a = 6.3876 (11) Å | Cell parameters from 1229 reflections |
| b = 8.8268 (13) Å | θ = 3.1–28.7° |
| c = 10.500 (2) Å | µ = 0.46 mm−1 |
| β = 99.355 (15)° | T = 120 K |
| V = 584.15 (17) Å3 | Plate, yellow |
| Z = 2 | 0.32 × 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 mm2 | 1375 reflections with I > 2σ(I) |
| Parabolic x-ray mirror monochromator | Rint = 0.047 |
| Detector resolution: 6.67 pixels mm-1 | θmax = 28.4°, θmin = 3.9° |
| rotation method scans | h = −7→8 |
| Absorption correction: integration [X-RED32 (Stoe & Cie, 2009), analogous to Coppens (1970)] | k = −10→11 |
| Tmin = 0.853, Tmax = 0.967 | l = −13→13 |
| 3316 measured reflections |
Refinement top
| Refinement on F2 | Primary atom site location: dual |
| Least-squares matrix: full | Hydrogen site location: mixed |
| R[F2 > 2σ(F2)] = 0.071 | H 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 reflections | Δρmax = 0.55 e Å−3 |
| 80 parameters | Δρmin = −0.49 e Å−3 |
| 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
| x | y | z | Uiso*/Ueq | ||
| S1T | 0.5456 (2) | 0.750000 | 1.04796 (11) | 0.0367 (4) | |
| S1 | 0.3578 (2) | 0.250000 | 0.63525 (12) | 0.0424 (4) | |
| F1 | 0.2389 (4) | 0.6231 (2) | 0.5513 (2) | 0.0494 (6) | |
| N1T | 0.4051 (4) | 0.6196 (3) | 0.8226 (3) | 0.0321 (6) | |
| H1TA | 0.355387 | 0.620829 | 0.739409 | 0.038* | |
| H1TB | 0.429412 | 0.532580 | 0.863319 | 0.038* | |
| N2 | 0.2256 (4) | 0.3803 (3) | 0.4084 (3) | 0.0343 (6) | |
| H2 | 0.252236 | 0.466934 | 0.449253 | 0.041* | |
| C1T | 0.4438 (6) | 0.750000 | 0.8874 (4) | 0.0281 (8) | |
| C4 | 0.1035 (6) | 0.250000 | 0.2147 (4) | 0.0299 (9) | |
| H4 | 0.046347 | 0.250000 | 0.125352 | 0.036* | |
| C3 | 0.1457 (5) | 0.3849 (4) | 0.2805 (3) | 0.0312 (7) | |
| C7 | 0.1049 (5) | 0.5375 (4) | 0.2222 (4) | 0.0377 (7) | |
| H7A | −0.001766 | 0.589839 | 0.263414 | 0.056* | |
| H7B | 0.052706 | 0.527184 | 0.129569 | 0.056* | |
| H7C | 0.236850 | 0.596255 | 0.235186 | 0.056* | |
| C1 | 0.2672 (7) | 0.250000 | 0.4777 (5) | 0.0357 (10) | |
| H1 | 0.261 (15) | 0.750000 | 0.545 (8) | 0.08 (3)* |
Atomic displacement parameters (Å2) top
| U11 | U22 | U33 | U12 | U13 | U23 | |
| S1T | 0.0486 (7) | 0.0226 (6) | 0.0379 (6) | 0.000 | 0.0044 (5) | 0.000 |
| S1 | 0.0433 (7) | 0.0448 (8) | 0.0376 (6) | 0.000 | 0.0023 (5) | 0.000 |
| F1 | 0.0736 (16) | 0.0302 (11) | 0.0444 (12) | −0.0082 (11) | 0.0092 (10) | −0.0031 (9) |
| N1T | 0.0333 (13) | 0.0207 (12) | 0.0411 (14) | −0.0006 (10) | 0.0031 (10) | −0.0007 (10) |
| N2 | 0.0333 (13) | 0.0276 (14) | 0.0421 (14) | −0.0011 (10) | 0.0066 (11) | −0.0023 (10) |
| C1T | 0.0260 (18) | 0.0223 (19) | 0.035 (2) | 0.000 | 0.0037 (15) | 0.000 |
| C4 | 0.0264 (18) | 0.024 (2) | 0.039 (2) | 0.000 | 0.0062 (16) | 0.000 |
| C3 | 0.0273 (13) | 0.0259 (15) | 0.0414 (16) | −0.0020 (11) | 0.0083 (11) | 0.0001 (11) |
| C7 | 0.0381 (16) | 0.0232 (15) | 0.0515 (19) | −0.0008 (12) | 0.0068 (13) | 0.0017 (13) |
| C1 | 0.033 (2) | 0.036 (2) | 0.038 (2) | 0.000 | 0.0056 (17) | 0.000 |
Geometric parameters (Å, º) top
| S1T—C1T | 1.706 (4) | N2—C1 | 1.363 (4) |
| S1—C1 | 1.662 (5) | C4—H4 | 0.9500 |
| F1—H1 | 1.132 (14) | C4—C3i | 1.381 (4) |
| N1T—H1TA | 0.8800 | C4—C3 | 1.381 (4) |
| N1T—H1TB | 0.8800 | C3—C7 | 1.485 (4) |
| N1T—C1T | 1.340 (3) | C7—H7A | 0.9800 |
| N2—H2 | 0.8800 | C7—H7B | 0.9800 |
| N2—C3 | 1.357 (4) | C7—H7C | 0.9800 |
| H1TA—N1T—H1TB | 120.0 | N2—C3—C4 | 118.7 (3) |
| C1T—N1T—H1TA | 120.0 | N2—C3—C7 | 116.6 (3) |
| C1T—N1T—H1TB | 120.0 | C4—C3—C7 | 124.7 (3) |
| C3—N2—H2 | 117.9 | C3—C7—H7A | 109.5 |
| C3—N2—C1 | 124.2 (3) | C3—C7—H7B | 109.5 |
| C1—N2—H2 | 117.9 | C3—C7—H7C | 109.5 |
| N1T—C1T—S1T | 120.7 (2) | H7A—C7—H7B | 109.5 |
| N1Tii—C1T—S1T | 120.7 (2) | H7A—C7—H7C | 109.5 |
| N1Tii—C1T—N1T | 118.5 (4) | H7B—C7—H7C | 109.5 |
| C3i—C4—H4 | 120.4 | N2i—C1—S1 | 122.5 (2) |
| C3—C4—H4 | 120.4 | N2—C1—S1 | 122.5 (2) |
| C3i—C4—C3 | 119.1 (4) | N2—C1—N2i | 115.0 (4) |
| Symmetry codes: (i) x, −y+1/2, z; (ii) x, −y+3/2, z. |
Hydrogen-bond geometry (Å, º) top
| D—H···A | D—H | H···A | D···A | D—H···A |
| N1T—H1TA···F1 | 0.88 | 1.99 | 2.874 (4) | 179 |
| N1T—H1TB···S1Tiii | 0.88 | 2.66 | 3.528 (3) | 170 |
| N2—H2···F1 | 0.88 | 1.76 | 2.610 (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+·Br− | F(000) = 440 |
| Mr = 221.12 | Dx = 1.725 Mg m−3 |
| Monoclinic, C2/c | Mo Kα radiation, λ = 0.71073 Å |
| a = 8.4675 (11) Å | Cell parameters from 2102 reflections |
| b = 14.9142 (19) Å | θ = 3.8–28.8° |
| c = 6.8814 (9) Å | µ = 5.02 mm−1 |
| β = 101.575 (10)° | T = 120 K |
| V = 851.35 (19) Å3 | Prism, yellow |
| Z = 4 | 0.21 × 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 mm2 | 871 reflections with I > 2σ(I) |
| Parabolic x-ray mirror monochromator | Rint = 0.118 |
| Detector resolution: 6.67 pixels mm-1 | θmax = 27.0°, θmin = 3.8° |
| rotation method scans | h = −10→10 |
| Absorption correction: integration [X-RED32 (Stoe & Cie, 2009), analogous to Coppens (1970)] | k = −18→18 |
| Tmin = 0.262, Tmax = 0.740 | l = −8→8 |
| 5070 measured reflections |
Refinement top
| Refinement on F2 | Primary atom site location: dual |
| Least-squares matrix: full | Hydrogen site location: inferred from neighbouring sites |
| R[F2 > 2σ(F2)] = 0.064 | H-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 reflections | Δρmax = 2.21 e Å−3 |
| 49 parameters | Δρmin = −1.62 e Å−3 |
| 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
| x | y | z | Uiso*/Ueq | ||
| Br1 | 0.000000 | 0.19294 (3) | 0.250000 | 0.0325 (3) | |
| S1 | 0.500000 | 0.12830 (11) | 0.250000 | 0.0368 (5) | |
| N2 | 0.3645 (5) | 0.2889 (2) | 0.2528 (6) | 0.0310 (8) | |
| H2 | 0.273349 | 0.259950 | 0.248504 | 0.037* | |
| C1 | 0.500000 | 0.2400 (4) | 0.250000 | 0.0296 (12) | |
| C3 | 0.3622 (5) | 0.3795 (3) | 0.2619 (5) | 0.0307 (8) | |
| C4 | 0.500000 | 0.4264 (4) | 0.250000 | 0.0327 (12) | |
| H4 | 0.500001 | 0.490054 | 0.249997 | 0.039* | |
| C7 | 0.2091 (6) | 0.4223 (3) | 0.2835 (7) | 0.0381 (9) | |
| H7A | 0.126072 | 0.410019 | 0.165295 | 0.057* | |
| H7B | 0.224963 | 0.487166 | 0.298873 | 0.057* | |
| H7C | 0.174921 | 0.397957 | 0.400812 | 0.057* |
Atomic displacement parameters (Å2) top
| U11 | U22 | U33 | U12 | U13 | U23 | |
| Br1 | 0.0298 (5) | 0.0429 (5) | 0.0265 (5) | 0.000 | 0.0095 (3) | 0.000 |
| S1 | 0.0363 (8) | 0.0359 (9) | 0.0419 (9) | 0.000 | 0.0168 (7) | 0.000 |
| N2 | 0.0274 (17) | 0.0390 (16) | 0.0292 (19) | 0.0001 (15) | 0.0117 (15) | 0.0000 (14) |
| C1 | 0.026 (2) | 0.033 (3) | 0.032 (3) | 0.000 | 0.011 (2) | 0.000 |
| C3 | 0.0262 (17) | 0.041 (2) | 0.0255 (18) | 0.0037 (16) | 0.0081 (14) | −0.0010 (15) |
| C4 | 0.035 (3) | 0.039 (3) | 0.025 (3) | 0.000 | 0.008 (2) | 0.000 |
| C7 | 0.031 (2) | 0.046 (2) | 0.039 (2) | 0.0046 (17) | 0.0114 (19) | −0.0009 (17) |
Geometric parameters (Å, º) top
| S1—C1 | 1.665 (6) | C3—C7 | 1.479 (6) |
| N2—H2 | 0.8800 | C4—H4 | 0.9500 |
| N2—C1 | 1.363 (5) | C7—H7A | 0.9800 |
| N2—C3 | 1.352 (5) | C7—H7B | 0.9800 |
| C3—C4 | 1.377 (5) | C7—H7C | 0.9800 |
| C1—N2—H2 | 118.1 | C3i—C4—C3 | 119.0 (6) |
| C3—N2—H2 | 118.1 | C3—C4—H4 | 120.5 |
| C3—N2—C1 | 123.8 (4) | C3i—C4—H4 | 120.5 |
| N2—C1—S1 | 122.4 (3) | C3—C7—H7A | 109.5 |
| N2i—C1—S1 | 122.4 (3) | C3—C7—H7B | 109.5 |
| N2—C1—N2i | 115.2 (5) | C3—C7—H7C | 109.5 |
| N2—C3—C4 | 118.9 (4) | H7A—C7—H7B | 109.5 |
| N2—C3—C7 | 117.2 (4) | H7A—C7—H7C | 109.5 |
| C4—C3—C7 | 123.9 (4) | H7B—C7—H7C | 109.5 |
| Symmetry code: (i) −x+1, y, −z+1/2. |
4,6-Dimethyl-2-sulfanylidene-2,3-dihydropyrimidin-1-ium iodide (10) top
Crystal data top
| C6H9N2S+·I− | Dx = 1.913 Mg m−3 |
| Mr = 268.11 | Mo Kα radiation, λ = 0.71073 Å |
| Orthorhombic, Cmcm | Cell parameters from 1294 reflections |
| a = 8.7198 (14) Å | θ = 3.9–26.7° |
| b = 15.095 (3) Å | µ = 3.60 mm−1 |
| c = 7.0716 (11) Å | T = 120 K |
| V = 930.8 (3) Å3 | Plate, yellow |
| Z = 4 | 0.17 × 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 mm2 | 661 reflections with I > 2σ(I) |
| Parabolic x-ray mirror monochromator | Rint = 0.058 |
| Detector resolution: 6.67 pixels mm-1 | θmax = 28.9°, θmin = 4.0° |
| rotation method scans | h = −11→11 |
| Absorption correction: integration [X-RED32 (Stoe & Cie, 2009), analogous to Coppens (1970)] | k = −20→20 |
| Tmin = 0.520, Tmax = 0.837 | l = −9→9 |
| 7434 measured reflections |
Refinement top
| Refinement on F2 | Primary atom site location: dual |
| Least-squares matrix: full | Hydrogen site location: mixed |
| R[F2 > 2σ(F2)] = 0.025 | H 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 reflections | Δρmax = 1.10 e Å−3 |
| 42 parameters | Δρmin = −0.88 e Å−3 |
| 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
| x | y | z | Uiso*/Ueq | ||
| I1 | 0.000000 | 0.18528 (2) | 0.750000 | 0.02004 (12) | |
| S1 | 0.500000 | 0.12787 (8) | 0.750000 | 0.0258 (3) | |
| N2 | 0.3682 (3) | 0.28725 (19) | 0.750000 | 0.0195 (6) | |
| H2 | 0.280127 | 0.258795 | 0.750000 | 0.023* | |
| C1 | 0.500000 | 0.2378 (3) | 0.750000 | 0.0198 (9) | |
| C4 | 0.500000 | 0.4226 (3) | 0.750000 | 0.0201 (9) | |
| H4 | 0.499999 | 0.485535 | 0.750000 | 0.024* | |
| C3 | 0.3643 (4) | 0.3766 (2) | 0.750000 | 0.0201 (6) | |
| C7 | 0.2109 (5) | 0.4189 (2) | 0.750000 | 0.0298 (8) | |
| H7A | 0.220 (4) | 0.4836 (3) | 0.750000 | 0.062 (18)* | |
| H7B | 0.1549 (12) | 0.3999 (11) | 0.63687 (7) | 0.049 (11)* |
Atomic displacement parameters (Å2) top
| U11 | U22 | U33 | U12 | U13 | U23 | |
| I1 | 0.01939 (17) | 0.01578 (17) | 0.02494 (19) | 0.000 | 0.000 | 0.000 |
| S1 | 0.0231 (6) | 0.0113 (5) | 0.0429 (8) | 0.000 | 0.000 | 0.000 |
| N2 | 0.0177 (12) | 0.0140 (12) | 0.0267 (15) | −0.0014 (10) | 0.000 | 0.000 |
| C1 | 0.021 (2) | 0.015 (2) | 0.024 (2) | 0.000 | 0.000 | 0.000 |
| C4 | 0.020 (2) | 0.014 (2) | 0.026 (3) | 0.000 | 0.000 | 0.000 |
| C3 | 0.0229 (15) | 0.0128 (14) | 0.0246 (17) | 0.0039 (12) | 0.000 | 0.000 |
| C7 | 0.0262 (17) | 0.0175 (15) | 0.046 (3) | 0.0071 (13) | 0.000 | 0.000 |
Geometric parameters (Å, º) top
| S1—C1 | 1.659 (5) | C4—C3i | 1.372 (4) |
| N2—H2 | 0.8800 | C3—C7 | 1.482 (5) |
| N2—C1 | 1.371 (4) | C7—H7A | 0.9800 (11) |
| N2—C3 | 1.350 (4) | C7—H7B | 0.9800 (7) |
| C4—H4 | 0.9500 | C7—H7Bii | 0.9800 (7) |
| C4—C3 | 1.372 (4) | ||
| C1—N2—H2 | 117.8 | N2—C3—C4 | 118.9 (3) |
| C3—N2—H2 | 117.8 | N2—C3—C7 | 117.0 (3) |
| C3—N2—C1 | 124.5 (3) | C4—C3—C7 | 124.1 (3) |
| N2i—C1—S1 | 123.0 (2) | C3—C7—H7A | 111 (2) |
| N2—C1—S1 | 123.0 (2) | C3—C7—H7B | 108.9 (10) |
| N2i—C1—N2 | 113.9 (4) | C3—C7—H7Bii | 108.9 (10) |
| C3—C4—H4 | 120.4 | H7A—C7—H7B | 109.43 (13) |
| C3i—C4—H4 | 120.4 | H7A—C7—H7Bii | 109.43 (13) |
| C3—C4—C3i | 119.2 (4) | H7B—C7—H7Bii | 109.43 (16) |
| Symmetry codes: (i) −x+1, y, −z+3/2; (ii) x, y, −z+3/2. |
Compounds under consideration. For explanation of symbols, see Fig. 1. top
| G | X- | Y | Reference | |
| (1) | O | F2H- | - | This work |
| (2) | O | Cl- | - | Lee et al. (1984) |
| (3) | O | Br- | - | This work |
| (4) | O | I- | - | This work |
| (5) | O | I- | OC(NH2)2 | This work |
| (6) | S | F2H- | SC(NH2)2 | This work |
| (7) | S | Cl- | H2O | Battaglia et al. (1986) and Seth et al. (1996) |
| (8) | S | Cl- | SC(NH2)2 | Gaye et al. (2009) |
| (9) | S | Br- | - | This work |
| (10) | S | I- | - | 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) |
| X | F2H | Cl | Br | I | I | F2H | Cl | Br | I |
| Distance X···p | 2.998 | 3.334 | 3.361 | 3.566 | 3.559, 3.632 | 3.188, 3.051 | 3.323 | 3.464 | 3.536 |
| Distance X···d | 3.054 | 3.366 | 3.385 | 3.601 | 3.515, 3.530 | 3.828, 3.279 | 3.490 | 3.338 | 3.545 |
| Type | a | a | a | b | c | d | d | a | a |
| Symmetry | m on ring | m on ring | m on ring | 2 on I | 1 (none) | vertical m on F2H | m on ring & mm2 on Cl | 2 on Br | m on ring & mm2 on I |
| RvdW(X) (Mantina et al., 2009) | 1.40 | 1.74 | 1.82 | 1.99 | 1.99 | 1.40 | 1.74 | 1.82 | 1.99 |
| Plane proximity | 1.598 | 1.594 | 1.541 | 1.576 | 1.569, 1.642 | 1.788, 1.651 | 1.583 | 1.644 | 1.546 |
| Shift | 0.582 | 0.463 | 0.402 | 0.501 | 0.558, 0.854 | 2.119, 1.201 | 1.067 | 0.926 | 0.252 |
Subscribe to Acta Crystallographica Section C: Structural Chemistry
The full text of this article is available to subscribers to the journal.
- Information on subscribing
- Sample issue
- Purchase subscription
- Reduced-price subscriptions
- If you have already subscribed, you may need to register
