Derivatives of pyrimidine-2(1
H)-selenone are a group of compounds with very strong antimicrobial activity. In order to study the effect of the position of the methoxy substituent on biological activity, molecular geometry and intermolecular interactions in the crystal, three derivatives were prepared and evaluated with respect to their antimicrobial activities, and their crystal structures were determined by X-ray diffraction. The investigated compounds, namely, 1-(
X-methoxyphenyl)-4-methyl-6-phenylpyrimidine-2(1
H)-selenones (
X = 2, 3 and 4 for
1,
2 and
3, respectively), C
18H
16N
2OSe, showed very strong activity against selected strains of Gram-positive bacteria and fungi. Two compounds,
1 and
2, crystallize in the monoclinic space group
P2
1/
c, while
3 crystallizes in the space group
P2
1/
n;
1 has two molecules in the asymmetric unit and the other two (
2 and
3) have one molecule. The geometries of the investigated compounds differ slightly in the mutual orientations of the aromatic and pyrimidineselenone rings. The O atom in
1 stabilizes the conformation of the molecules
via intramolecular C—H
O hydrogen bonding. The packing of molecules is determined by weak C—H
N and C—H
Se intermolecular interactions and additionally in
1 and
2 by C—H
O intermolecular interactions. The introduction of the methoxy substituent results in greater selectivity of the investigated compounds.
Supporting information
CCDC references: 1992163; 1992162; 1992161
For all structures, data collection: COLLECT (Bruker, 2004); cell refinement: SCALEPACK (Otwinowski & Minor, 1997); data reduction: DENZO and SCALEPACK (Otwinowski & Minor, 1997). Program(s) used to solve structure: SHELXS97 (Sheldrick, 2008) for (1), (3); SIR2014 (Burla et al., 2015) and SHELXS97 (Sheldrick, 2008) for (2). For all structures, program(s) used to refine structure: SHELXL2018 (Sheldrick, 2015); molecular graphics: ORTEP-3 (Farrugia, 2012) and Mercury (Macrae et al., 2020); software used to prepare material for publication: publCIF (Westrip, 2010).
4-Methyl-1-(2-methoxyphenyl)-6-phenylpyrimidine-2(1
H)-selenone (1)
top
Crystal data top
C18H16N2OSe | F(000) = 1440 |
Mr = 355.29 | Dx = 1.49 Mg m−3 |
Monoclinic, P21/c | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: -P 2ybc | Cell parameters from 13681 reflections |
a = 14.8080 (2) Å | θ = 1.0–27.5° |
b = 15.6970 (2) Å | µ = 2.37 mm−1 |
c = 14.9770 (2) Å | T = 100 K |
β = 114.482 (1)° | Prism, red |
V = 3168.27 (8) Å3 | 0.52 × 0.34 × 0.23 mm |
Z = 8 | |
Data collection top
Bruker KappaCCD diffractometer | 7239 independent reflections |
Horizonally mounted graphite crystal monochromator | 6200 reflections with I > 2σ(I) |
Detector resolution: 9 pixels mm-1 | Rint = 0.028 |
CCD scans | θmax = 27.5°, θmin = 2.7° |
Absorption correction: multi-scan (DENZO-SMN; Otwinowski & Minor, 1997) | h = −19→18 |
Tmin = 0.915, Tmax = 1.000 | k = −20→20 |
24786 measured reflections | l = −19→19 |
Refinement top
Refinement on F2 | Hydrogen site location: inferred from neighbouring sites |
Least-squares matrix: full | H-atom parameters constrained |
R[F2 > 2σ(F2)] = 0.026 | w = 1/[σ2(Fo2) + (0.0285P)2 + 2.5089P] where P = (Fo2 + 2Fc2)/3 |
wR(F2) = 0.064 | (Δ/σ)max = 0.001 |
S = 1.02 | Δρmax = 0.37 e Å−3 |
7239 reflections | Δρmin = −0.53 e Å−3 |
402 parameters | Extinction correction: SHELXL2018 (Sheldrick, 2015), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4 |
0 restraints | Extinction coefficient: 0.00245 (19) |
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 | |
C2A | 0.14233 (13) | 0.57910 (11) | 0.26337 (12) | 0.0139 (3) | |
N3A | 0.23808 (11) | 0.58675 (10) | 0.32912 (11) | 0.0161 (3) | |
C4A | 0.29094 (13) | 0.65440 (12) | 0.32716 (13) | 0.0163 (4) | |
C5A | 0.24940 (13) | 0.72129 (11) | 0.25984 (13) | 0.0167 (4) | |
H5A | 0.288275 | 0.769446 | 0.259874 | 0.02* | |
C6A | 0.15239 (13) | 0.71582 (11) | 0.19457 (12) | 0.0141 (3) | |
N1A | 0.09897 (11) | 0.64468 (9) | 0.19643 (10) | 0.0134 (3) | |
C19A | 0.39787 (14) | 0.65545 (13) | 0.39780 (15) | 0.0241 (4) | |
H19A | 0.409208 | 0.612592 | 0.448918 | 0.036* | |
H19B | 0.415114 | 0.71195 | 0.427987 | 0.036* | |
H19C | 0.439328 | 0.642508 | 0.362771 | 0.036* | |
C13A | 0.10486 (13) | 0.78098 (11) | 0.11746 (13) | 0.0160 (3) | |
C18A | 0.14401 (14) | 0.79467 (13) | 0.04894 (14) | 0.0221 (4) | |
H18A | 0.201453 | 0.764315 | 0.054068 | 0.027* | |
C17A | 0.09978 (16) | 0.85237 (14) | −0.02692 (15) | 0.0274 (4) | |
H17A | 0.126957 | 0.861393 | −0.073544 | 0.033* | |
C16A | 0.01616 (15) | 0.89679 (13) | −0.03478 (14) | 0.0245 (4) | |
H16A | −0.015044 | 0.935213 | −0.087738 | 0.029* | |
C15A | −0.02210 (16) | 0.88529 (12) | 0.03451 (15) | 0.0241 (4) | |
H15A | −0.078756 | 0.916699 | 0.02975 | 0.029* | |
C14A | 0.02218 (15) | 0.82794 (12) | 0.11092 (15) | 0.0218 (4) | |
H14A | −0.003754 | 0.820632 | 0.158783 | 0.026* | |
C7A | −0.00353 (13) | 0.63678 (11) | 0.12675 (12) | 0.0138 (3) | |
C12A | −0.02640 (13) | 0.60530 (11) | 0.03389 (13) | 0.0163 (3) | |
H12A | 0.024999 | 0.58772 | 0.015648 | 0.02* | |
C11A | −0.12517 (14) | 0.59943 (12) | −0.03291 (13) | 0.0198 (4) | |
H11A | −0.141727 | 0.578108 | −0.09716 | 0.024* | |
C10A | −0.19921 (14) | 0.62498 (13) | −0.00482 (14) | 0.0218 (4) | |
H10A | −0.266726 | 0.620373 | −0.050062 | 0.026* | |
C9A | −0.17604 (14) | 0.65737 (12) | 0.08892 (14) | 0.0205 (4) | |
H9A | −0.227525 | 0.674691 | 0.107163 | 0.025* | |
C8A | −0.07774 (13) | 0.66419 (11) | 0.15526 (13) | 0.0164 (4) | |
O1A | −0.04479 (10) | 0.69747 (9) | 0.24753 (9) | 0.0202 (3) | |
C20A | −0.11766 (16) | 0.73463 (15) | 0.27567 (16) | 0.0280 (5) | |
H20A | −0.153246 | 0.779751 | 0.229166 | 0.042* | |
H20B | −0.084703 | 0.758822 | 0.341703 | 0.042* | |
H20C | −0.164792 | 0.690679 | 0.275372 | 0.042* | |
C2B | 0.56860 (13) | 0.39704 (11) | 0.07566 (12) | 0.0138 (3) | |
N3B | 0.64735 (11) | 0.38649 (10) | 0.05278 (11) | 0.0162 (3) | |
C4B | 0.73440 (13) | 0.42058 (12) | 0.10926 (14) | 0.0178 (4) | |
C5B | 0.74847 (13) | 0.47022 (12) | 0.19206 (13) | 0.0179 (4) | |
H5B | 0.810321 | 0.497181 | 0.228706 | 0.021* | |
C6B | 0.67088 (13) | 0.47883 (11) | 0.21869 (12) | 0.0141 (3) | |
N1B | 0.58261 (10) | 0.43953 (9) | 0.16222 (10) | 0.0128 (3) | |
C19B | 0.81883 (14) | 0.40302 (14) | 0.08134 (16) | 0.0260 (4) | |
H19D | 0.849615 | 0.348446 | 0.109527 | 0.039* | |
H19E | 0.868181 | 0.448634 | 0.106526 | 0.039* | |
H19F | 0.793902 | 0.400509 | 0.009713 | 0.039* | |
C13B | 0.67699 (13) | 0.53107 (11) | 0.30397 (13) | 0.0153 (3) | |
C18B | 0.66280 (16) | 0.61843 (13) | 0.29220 (14) | 0.0244 (4) | |
H18B | 0.649733 | 0.643817 | 0.23048 | 0.029* | |
C17B | 0.66757 (18) | 0.66889 (14) | 0.37003 (15) | 0.0298 (5) | |
H17B | 0.657081 | 0.728593 | 0.361452 | 0.036* | |
C16B | 0.68769 (16) | 0.63200 (14) | 0.46033 (14) | 0.0259 (4) | |
H16B | 0.69122 | 0.666584 | 0.513734 | 0.031* | |
C15B | 0.70250 (17) | 0.54590 (14) | 0.47298 (14) | 0.0292 (5) | |
H15B | 0.716468 | 0.520997 | 0.535129 | 0.035* | |
C14B | 0.69715 (16) | 0.49488 (13) | 0.39509 (14) | 0.0265 (4) | |
H14B | 0.70728 | 0.435169 | 0.40408 | 0.032* | |
C7B | 0.50342 (12) | 0.44033 (11) | 0.19531 (12) | 0.0137 (3) | |
C12B | 0.43394 (13) | 0.50503 (12) | 0.16678 (13) | 0.0161 (4) | |
H12B | 0.436474 | 0.549019 | 0.124304 | 0.019* | |
C11B | 0.35993 (14) | 0.50443 (12) | 0.20166 (14) | 0.0192 (4) | |
H11B | 0.311393 | 0.548312 | 0.18277 | 0.023* | |
C10B | 0.35698 (14) | 0.44025 (13) | 0.26357 (14) | 0.0201 (4) | |
H10B | 0.306382 | 0.440527 | 0.286994 | 0.024* | |
C9B | 0.42718 (13) | 0.37523 (12) | 0.29204 (13) | 0.0180 (4) | |
H9B | 0.424586 | 0.33145 | 0.334705 | 0.022* | |
C8B | 0.50126 (13) | 0.37480 (11) | 0.25754 (13) | 0.0147 (3) | |
O1B | 0.57416 (9) | 0.31483 (8) | 0.27973 (9) | 0.0174 (3) | |
C20B | 0.57406 (15) | 0.24727 (13) | 0.34408 (15) | 0.0243 (4) | |
H20D | 0.583724 | 0.271066 | 0.407899 | 0.036* | |
H20E | 0.627982 | 0.207397 | 0.352693 | 0.036* | |
H20F | 0.510423 | 0.217148 | 0.315626 | 0.036* | |
Se1A | 0.07334 (2) | 0.48228 (2) | 0.26267 (2) | 0.01922 (6) | |
Se1B | 0.44599 (2) | 0.35690 (2) | −0.00581 (2) | 0.01773 (6) | |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
C2A | 0.0179 (8) | 0.0131 (8) | 0.0147 (8) | 0.0018 (6) | 0.0106 (7) | −0.0011 (6) |
N3A | 0.0170 (7) | 0.0168 (8) | 0.0167 (7) | 0.0005 (6) | 0.0092 (6) | −0.0014 (6) |
C4A | 0.0179 (9) | 0.0175 (9) | 0.0164 (8) | −0.0003 (7) | 0.0099 (7) | −0.0046 (7) |
C5A | 0.0185 (9) | 0.0137 (9) | 0.0211 (9) | −0.0050 (7) | 0.0114 (7) | −0.0040 (7) |
C6A | 0.0199 (9) | 0.0113 (8) | 0.0162 (8) | −0.0011 (6) | 0.0124 (7) | −0.0026 (7) |
N1A | 0.0153 (7) | 0.0127 (7) | 0.0147 (7) | −0.0017 (5) | 0.0086 (6) | −0.0011 (6) |
C19A | 0.0178 (9) | 0.0259 (10) | 0.0240 (9) | −0.0032 (8) | 0.0040 (8) | −0.0024 (8) |
C13A | 0.0183 (9) | 0.0131 (8) | 0.0174 (8) | −0.0035 (7) | 0.0081 (7) | −0.0018 (7) |
C18A | 0.0203 (9) | 0.0262 (10) | 0.0227 (9) | 0.0002 (8) | 0.0118 (8) | 0.0038 (8) |
C17A | 0.0305 (11) | 0.0344 (12) | 0.0226 (9) | 0.0003 (9) | 0.0163 (9) | 0.0073 (9) |
C16A | 0.0307 (11) | 0.0194 (10) | 0.0210 (9) | 0.0005 (8) | 0.0081 (8) | 0.0046 (8) |
C15A | 0.0295 (11) | 0.0153 (9) | 0.0303 (10) | 0.0046 (8) | 0.0150 (9) | 0.0016 (8) |
C14A | 0.0305 (11) | 0.0150 (9) | 0.0265 (10) | 0.0014 (8) | 0.0185 (8) | 0.0014 (8) |
C7A | 0.0148 (8) | 0.0114 (8) | 0.0160 (8) | −0.0011 (6) | 0.0070 (7) | 0.0014 (6) |
C12A | 0.0196 (9) | 0.0135 (8) | 0.0192 (8) | −0.0002 (7) | 0.0114 (7) | 0.0011 (7) |
C11A | 0.0221 (9) | 0.0189 (9) | 0.0169 (8) | −0.0007 (7) | 0.0067 (7) | −0.0020 (7) |
C10A | 0.0161 (9) | 0.0227 (10) | 0.0231 (9) | 0.0009 (7) | 0.0047 (7) | 0.0003 (8) |
C9A | 0.0185 (9) | 0.0208 (10) | 0.0252 (9) | 0.0035 (7) | 0.0121 (8) | 0.0012 (8) |
C8A | 0.0200 (9) | 0.0145 (8) | 0.0175 (8) | 0.0005 (7) | 0.0106 (7) | 0.0015 (7) |
O1A | 0.0223 (7) | 0.0233 (7) | 0.0192 (6) | 0.0019 (5) | 0.0130 (5) | −0.0044 (5) |
C20A | 0.0315 (11) | 0.0297 (11) | 0.0308 (11) | 0.0092 (9) | 0.0210 (9) | −0.0025 (9) |
C2B | 0.0162 (8) | 0.0119 (8) | 0.0150 (8) | 0.0023 (6) | 0.0083 (7) | 0.0026 (6) |
N3B | 0.0160 (7) | 0.0162 (8) | 0.0193 (7) | 0.0010 (6) | 0.0103 (6) | 0.0007 (6) |
C4B | 0.0177 (9) | 0.0159 (9) | 0.0229 (9) | 0.0024 (7) | 0.0115 (7) | 0.0038 (7) |
C5B | 0.0144 (8) | 0.0196 (9) | 0.0204 (9) | −0.0013 (7) | 0.0081 (7) | 0.0006 (7) |
C6B | 0.0147 (8) | 0.0110 (8) | 0.0153 (8) | 0.0008 (6) | 0.0048 (7) | 0.0027 (6) |
N1B | 0.0123 (7) | 0.0127 (7) | 0.0147 (7) | 0.0002 (5) | 0.0067 (6) | 0.0006 (6) |
C19B | 0.0186 (9) | 0.0324 (12) | 0.0335 (11) | −0.0020 (8) | 0.0172 (8) | −0.0049 (9) |
C13B | 0.0121 (8) | 0.0172 (9) | 0.0149 (8) | −0.0021 (6) | 0.0038 (7) | −0.0012 (7) |
C18B | 0.0359 (11) | 0.0196 (10) | 0.0175 (9) | 0.0028 (8) | 0.0107 (8) | 0.0029 (8) |
C17B | 0.0446 (13) | 0.0188 (10) | 0.0238 (10) | 0.0070 (9) | 0.0121 (9) | −0.0012 (8) |
C16B | 0.0296 (11) | 0.0283 (11) | 0.0182 (9) | −0.0040 (8) | 0.0084 (8) | −0.0063 (8) |
C15B | 0.0409 (12) | 0.0274 (11) | 0.0150 (9) | −0.0064 (9) | 0.0072 (9) | 0.0011 (8) |
C14B | 0.0377 (12) | 0.0179 (10) | 0.0181 (9) | −0.0023 (8) | 0.0057 (8) | 0.0012 (8) |
C7B | 0.0125 (8) | 0.0163 (9) | 0.0141 (8) | −0.0015 (6) | 0.0073 (6) | −0.0041 (7) |
C12B | 0.0175 (9) | 0.0145 (9) | 0.0166 (8) | 0.0006 (7) | 0.0073 (7) | −0.0025 (7) |
C11B | 0.0177 (9) | 0.0197 (9) | 0.0209 (9) | 0.0047 (7) | 0.0087 (7) | −0.0040 (7) |
C10B | 0.0175 (9) | 0.0250 (10) | 0.0223 (9) | −0.0012 (7) | 0.0129 (7) | −0.0073 (8) |
C9B | 0.0189 (9) | 0.0194 (9) | 0.0193 (9) | −0.0011 (7) | 0.0116 (7) | −0.0013 (7) |
C8B | 0.0141 (8) | 0.0155 (9) | 0.0152 (8) | −0.0002 (6) | 0.0067 (7) | −0.0025 (7) |
O1B | 0.0181 (6) | 0.0163 (6) | 0.0224 (6) | 0.0038 (5) | 0.0130 (5) | 0.0050 (5) |
C20B | 0.0266 (10) | 0.0211 (10) | 0.0303 (10) | 0.0050 (8) | 0.0168 (8) | 0.0108 (8) |
Se1A | 0.02195 (10) | 0.01511 (10) | 0.02205 (10) | −0.00360 (7) | 0.01054 (8) | 0.00195 (7) |
Se1B | 0.01455 (9) | 0.02195 (10) | 0.01731 (9) | −0.00183 (7) | 0.00721 (7) | −0.00489 (7) |
Geometric parameters (Å, º) top
C2A—N3A | 1.355 (2) | C2B—N3B | 1.355 (2) |
C2A—N1A | 1.394 (2) | C2B—N1B | 1.395 (2) |
C2A—Se1A | 1.8287 (18) | C2B—Se1B | 1.8292 (17) |
N3A—C4A | 1.327 (2) | N3B—C4B | 1.327 (2) |
C4A—C5A | 1.408 (3) | C4B—C5B | 1.405 (3) |
C4A—C19A | 1.496 (3) | C4B—C19B | 1.499 (2) |
C5A—C6A | 1.365 (3) | C5B—C6B | 1.370 (3) |
C5A—H5A | 0.95 | C5B—H5B | 0.95 |
C6A—N1A | 1.375 (2) | C6B—N1B | 1.374 (2) |
C6A—C13A | 1.484 (2) | C6B—C13B | 1.489 (2) |
N1A—C7A | 1.448 (2) | N1B—C7B | 1.450 (2) |
C19A—H19A | 0.98 | C19B—H19D | 0.98 |
C19A—H19B | 0.98 | C19B—H19E | 0.98 |
C19A—H19C | 0.98 | C19B—H19F | 0.98 |
C13A—C18A | 1.389 (3) | C13B—C18B | 1.387 (3) |
C13A—C14A | 1.397 (3) | C13B—C14B | 1.392 (3) |
C18A—C17A | 1.387 (3) | C18B—C17B | 1.387 (3) |
C18A—H18A | 0.95 | C18B—H18B | 0.95 |
C17A—C16A | 1.383 (3) | C17B—C16B | 1.385 (3) |
C17A—H17A | 0.95 | C17B—H17B | 0.95 |
C16A—C15A | 1.385 (3) | C16B—C15B | 1.370 (3) |
C16A—H16A | 0.95 | C16B—H16B | 0.95 |
C15A—C14A | 1.389 (3) | C15B—C14B | 1.390 (3) |
C15A—H15A | 0.95 | C15B—H15B | 0.95 |
C14A—H14A | 0.95 | C14B—H14B | 0.95 |
C7A—C12A | 1.379 (2) | C7B—C12B | 1.381 (2) |
C7A—C8A | 1.401 (2) | C7B—C8B | 1.397 (2) |
C12A—C11A | 1.391 (3) | C12B—C11B | 1.396 (3) |
C12A—H12A | 0.95 | C12B—H12B | 0.95 |
C11A—C10A | 1.386 (3) | C11B—C10B | 1.382 (3) |
C11A—H11A | 0.95 | C11B—H11B | 0.95 |
C10A—C9A | 1.396 (3) | C10B—C9B | 1.392 (3) |
C10A—H10A | 0.95 | C10B—H10B | 0.95 |
C9A—C8A | 1.385 (3) | C9B—C8B | 1.393 (2) |
C9A—H9A | 0.95 | C9B—H9B | 0.95 |
C8A—O1A | 1.364 (2) | C8B—O1B | 1.365 (2) |
O1A—C20A | 1.435 (2) | O1B—C20B | 1.433 (2) |
C20A—H20A | 0.98 | C20B—H20D | 0.98 |
C20A—H20B | 0.98 | C20B—H20E | 0.98 |
C20A—H20C | 0.98 | C20B—H20F | 0.98 |
| | | |
N3A—C2A—N1A | 119.23 (15) | N3B—C2B—N1B | 118.78 (15) |
N3A—C2A—Se1A | 119.44 (13) | N3B—C2B—Se1B | 120.64 (13) |
N1A—C2A—Se1A | 121.32 (13) | N1B—C2B—Se1B | 120.58 (12) |
C4A—N3A—C2A | 120.26 (16) | C4B—N3B—C2B | 120.01 (16) |
N3A—C4A—C5A | 121.73 (17) | N3B—C4B—C5B | 122.41 (16) |
N3A—C4A—C19A | 117.03 (16) | N3B—C4B—C19B | 116.76 (17) |
C5A—C4A—C19A | 121.21 (17) | C5B—C4B—C19B | 120.82 (17) |
C6A—C5A—C4A | 118.92 (16) | C6B—C5B—C4B | 118.43 (17) |
C6A—C5A—H5A | 120.5 | C6B—C5B—H5B | 120.8 |
C4A—C5A—H5A | 120.5 | C4B—C5B—H5B | 120.8 |
C5A—C6A—N1A | 118.69 (16) | C5B—C6B—N1B | 118.36 (16) |
C5A—C6A—C13A | 122.22 (16) | C5B—C6B—C13B | 122.95 (16) |
N1A—C6A—C13A | 118.95 (15) | N1B—C6B—C13B | 118.65 (15) |
C6A—N1A—C2A | 121.11 (15) | C6B—N1B—C2B | 121.59 (14) |
C6A—N1A—C7A | 119.67 (14) | C6B—N1B—C7B | 118.91 (14) |
C2A—N1A—C7A | 119.21 (14) | C2B—N1B—C7B | 119.47 (14) |
C4A—C19A—H19A | 109.5 | C4B—C19B—H19D | 109.5 |
C4A—C19A—H19B | 109.5 | C4B—C19B—H19E | 109.5 |
H19A—C19A—H19B | 109.5 | H19D—C19B—H19E | 109.5 |
C4A—C19A—H19C | 109.5 | C4B—C19B—H19F | 109.5 |
H19A—C19A—H19C | 109.5 | H19D—C19B—H19F | 109.5 |
H19B—C19A—H19C | 109.5 | H19E—C19B—H19F | 109.5 |
C18A—C13A—C14A | 119.25 (17) | C18B—C13B—C14B | 119.18 (17) |
C18A—C13A—C6A | 118.24 (16) | C18B—C13B—C6B | 118.90 (16) |
C14A—C13A—C6A | 122.51 (16) | C14B—C13B—C6B | 121.92 (17) |
C17A—C18A—C13A | 120.43 (18) | C17B—C18B—C13B | 120.36 (18) |
C17A—C18A—H18A | 119.8 | C17B—C18B—H18B | 119.8 |
C13A—C18A—H18A | 119.8 | C13B—C18B—H18B | 119.8 |
C16A—C17A—C18A | 120.08 (18) | C16B—C17B—C18B | 119.8 (2) |
C16A—C17A—H17A | 120 | C16B—C17B—H17B | 120.1 |
C18A—C17A—H17A | 120 | C18B—C17B—H17B | 120.1 |
C17A—C16A—C15A | 120.03 (18) | C15B—C16B—C17B | 120.31 (19) |
C17A—C16A—H16A | 120 | C15B—C16B—H16B | 119.8 |
C15A—C16A—H16A | 120 | C17B—C16B—H16B | 119.8 |
C16A—C15A—C14A | 120.14 (19) | C16B—C15B—C14B | 120.15 (19) |
C16A—C15A—H15A | 119.9 | C16B—C15B—H15B | 119.9 |
C14A—C15A—H15A | 119.9 | C14B—C15B—H15B | 119.9 |
C15A—C14A—C13A | 120.03 (18) | C15B—C14B—C13B | 120.16 (19) |
C15A—C14A—H14A | 120 | C15B—C14B—H14B | 119.9 |
C13A—C14A—H14A | 120 | C13B—C14B—H14B | 119.9 |
C12A—C7A—C8A | 121.42 (16) | C12B—C7B—C8B | 121.84 (16) |
C12A—C7A—N1A | 120.23 (16) | C12B—C7B—N1B | 120.31 (16) |
C8A—C7A—N1A | 118.32 (15) | C8B—C7B—N1B | 117.84 (15) |
C7A—C12A—C11A | 119.63 (17) | C7B—C12B—C11B | 118.61 (17) |
C7A—C12A—H12A | 120.2 | C7B—C12B—H12B | 120.7 |
C11A—C12A—H12A | 120.2 | C11B—C12B—H12B | 120.7 |
C10A—C11A—C12A | 119.37 (17) | C10B—C11B—C12B | 120.26 (17) |
C10A—C11A—H11A | 120.3 | C10B—C11B—H11B | 119.9 |
C12A—C11A—H11A | 120.3 | C12B—C11B—H11B | 119.9 |
C11A—C10A—C9A | 121.00 (17) | C11B—C10B—C9B | 120.86 (17) |
C11A—C10A—H10A | 119.5 | C11B—C10B—H10B | 119.6 |
C9A—C10A—H10A | 119.5 | C9B—C10B—H10B | 119.6 |
C8A—C9A—C10A | 119.79 (17) | C10B—C9B—C8B | 119.54 (17) |
C8A—C9A—H9A | 120.1 | C10B—C9B—H9B | 120.2 |
C10A—C9A—H9A | 120.1 | C8B—C9B—H9B | 120.2 |
O1A—C8A—C9A | 125.77 (16) | O1B—C8B—C9B | 125.30 (16) |
O1A—C8A—C7A | 115.44 (16) | O1B—C8B—C7B | 115.81 (15) |
C9A—C8A—C7A | 118.77 (16) | C9B—C8B—C7B | 118.89 (16) |
C8A—O1A—C20A | 117.14 (15) | C8B—O1B—C20B | 116.92 (14) |
O1A—C20A—H20A | 109.5 | O1B—C20B—H20D | 109.5 |
O1A—C20A—H20B | 109.5 | O1B—C20B—H20E | 109.5 |
H20A—C20A—H20B | 109.5 | H20D—C20B—H20E | 109.5 |
O1A—C20A—H20C | 109.5 | O1B—C20B—H20F | 109.5 |
H20A—C20A—H20C | 109.5 | H20D—C20B—H20F | 109.5 |
H20B—C20A—H20C | 109.5 | H20E—C20B—H20F | 109.5 |
| | | |
N1A—C2A—N3A—C4A | −2.6 (2) | N1B—C2B—N3B—C4B | −3.9 (2) |
Se1A—C2A—N3A—C4A | 176.25 (13) | Se1B—C2B—N3B—C4B | 175.73 (13) |
C2A—N3A—C4A—C5A | 2.1 (3) | C2B—N3B—C4B—C5B | −1.8 (3) |
C2A—N3A—C4A—C19A | −176.11 (16) | C2B—N3B—C4B—C19B | 177.56 (17) |
N3A—C4A—C5A—C6A | −0.5 (3) | N3B—C4B—C5B—C6B | 4.4 (3) |
C19A—C4A—C5A—C6A | 177.65 (16) | C19B—C4B—C5B—C6B | −175.00 (18) |
C4A—C5A—C6A—N1A | −0.6 (2) | C4B—C5B—C6B—N1B | −1.0 (3) |
C4A—C5A—C6A—C13A | −176.21 (16) | C4B—C5B—C6B—C13B | −178.91 (16) |
C5A—C6A—N1A—C2A | 0.0 (2) | C5B—C6B—N1B—C2B | −4.8 (2) |
C13A—C6A—N1A—C2A | 175.82 (15) | C13B—C6B—N1B—C2B | 173.28 (15) |
C5A—C6A—N1A—C7A | −178.91 (15) | C5B—C6B—N1B—C7B | 173.40 (16) |
C13A—C6A—N1A—C7A | −3.1 (2) | C13B—C6B—N1B—C7B | −8.6 (2) |
N3A—C2A—N1A—C6A | 1.6 (2) | N3B—C2B—N1B—C6B | 7.3 (2) |
Se1A—C2A—N1A—C6A | −177.27 (12) | Se1B—C2B—N1B—C6B | −172.30 (13) |
N3A—C2A—N1A—C7A | −179.50 (15) | N3B—C2B—N1B—C7B | −170.82 (15) |
Se1A—C2A—N1A—C7A | 1.7 (2) | Se1B—C2B—N1B—C7B | 9.6 (2) |
C5A—C6A—C13A—C18A | 60.2 (2) | C5B—C6B—C13B—C18B | 82.1 (2) |
N1A—C6A—C13A—C18A | −115.45 (19) | N1B—C6B—C13B—C18B | −95.9 (2) |
C5A—C6A—C13A—C14A | −120.5 (2) | C5B—C6B—C13B—C14B | −97.5 (2) |
N1A—C6A—C13A—C14A | 63.9 (2) | N1B—C6B—C13B—C14B | 84.6 (2) |
C14A—C13A—C18A—C17A | −2.0 (3) | C14B—C13B—C18B—C17B | −0.7 (3) |
C6A—C13A—C18A—C17A | 177.36 (18) | C6B—C13B—C18B—C17B | 179.72 (19) |
C13A—C18A—C17A—C16A | 0.0 (3) | C13B—C18B—C17B—C16B | 0.7 (3) |
C18A—C17A—C16A—C15A | 1.6 (3) | C18B—C17B—C16B—C15B | −0.2 (3) |
C17A—C16A—C15A—C14A | −1.3 (3) | C17B—C16B—C15B—C14B | −0.2 (3) |
C16A—C15A—C14A—C13A | −0.7 (3) | C16B—C15B—C14B—C13B | 0.2 (3) |
C18A—C13A—C14A—C15A | 2.3 (3) | C18B—C13B—C14B—C15B | 0.3 (3) |
C6A—C13A—C14A—C15A | −176.99 (18) | C6B—C13B—C14B—C15B | 179.83 (19) |
C6A—N1A—C7A—C12A | 84.2 (2) | C6B—N1B—C7B—C12B | 91.0 (2) |
C2A—N1A—C7A—C12A | −94.7 (2) | C2B—N1B—C7B—C12B | −90.8 (2) |
C6A—N1A—C7A—C8A | −93.92 (19) | C6B—N1B—C7B—C8B | −88.0 (2) |
C2A—N1A—C7A—C8A | 87.1 (2) | C2B—N1B—C7B—C8B | 90.18 (19) |
C8A—C7A—C12A—C11A | −0.8 (3) | C8B—C7B—C12B—C11B | 0.1 (3) |
N1A—C7A—C12A—C11A | −178.89 (16) | N1B—C7B—C12B—C11B | −178.81 (16) |
C7A—C12A—C11A—C10A | −0.3 (3) | C7B—C12B—C11B—C10B | 0.1 (3) |
C12A—C11A—C10A—C9A | 0.8 (3) | C12B—C11B—C10B—C9B | −0.1 (3) |
C11A—C10A—C9A—C8A | −0.1 (3) | C11B—C10B—C9B—C8B | −0.1 (3) |
C10A—C9A—C8A—O1A | 177.46 (18) | C10B—C9B—C8B—O1B | −179.90 (17) |
C10A—C9A—C8A—C7A | −1.1 (3) | C10B—C9B—C8B—C7B | 0.3 (3) |
C12A—C7A—C8A—O1A | −177.15 (16) | C12B—C7B—C8B—O1B | 179.85 (16) |
N1A—C7A—C8A—O1A | 0.9 (2) | N1B—C7B—C8B—O1B | −1.2 (2) |
C12A—C7A—C8A—C9A | 1.5 (3) | C12B—C7B—C8B—C9B | −0.4 (3) |
N1A—C7A—C8A—C9A | 179.62 (16) | N1B—C7B—C8B—C9B | 178.60 (15) |
C9A—C8A—O1A—C20A | −5.1 (3) | C9B—C8B—O1B—C20B | −0.2 (3) |
C7A—C8A—O1A—C20A | 173.46 (16) | C7B—C8B—O1B—C20B | 179.52 (16) |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
C5A—H5A···O1Bi | 0.95 | 2.45 | 3.258 (2) | 143 |
C9A—H9A···Se1Bii | 0.95 | 2.99 | 3.6681 (19) | 129 |
C17A—H17A···N3Aiii | 0.95 | 2.74 | 3.663 (2) | 165 |
C19A—H19B···Se1Bi | 0.98 | 2.96 | 3.855 (2) | 152 |
C12B—H12B···N3Biv | 0.95 | 2.62 | 3.447 (2) | 146 |
C15B—H15B···N3Av | 0.95 | 2.51 | 3.425 (3) | 161 |
C18B—H18B···Se1Biv | 0.95 | 3.06 | 3.9263 (19) | 152 |
C19B—H19E···Se1Avi | 0.98 | 3.01 | 3.827 (2) | 141 |
Symmetry codes: (i) −x+1, y+1/2, −z+1/2; (ii) −x, −y+1, −z; (iii) x, −y+3/2, z−1/2; (iv) −x+1, −y+1, −z; (v) −x+1, −y+1, −z+1; (vi) x+1, y, z. |
4-Methyl-1-(3-methoxyphenyl)-6-phenylpyrimidine-2(1
H)-selenone (2)
top
Crystal data top
C18H16N2OSe | F(000) = 720 |
Mr = 355.29 | Dx = 1.521 Mg m−3 |
Monoclinic, P21/c | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: -P 2ybc | Cell parameters from 6409 reflections |
a = 9.4670 (6) Å | θ = 1.0–27.5° |
b = 10.3070 (7) Å | µ = 2.42 mm−1 |
c = 16.6150 (9) Å | T = 293 K |
β = 106.887 (4)° | Block, orange |
V = 1551.32 (17) Å3 | 0.28 × 0.09 × 0.04 mm |
Z = 4 | |
Data collection top
Bruker KappaCCD diffractometer | 3562 independent reflections |
Horizonally mounted graphite crystal monochromator | 2778 reflections with I > 2σ(I) |
Detector resolution: 9 pixels mm-1 | Rint = 0.065 |
CCD scans | θmax = 27.5°, θmin = 3.0° |
Absorption correction: multi-scan (DENZO-SMN; Otwinowski & Minor, 1997) | h = −12→12 |
Tmin = 0.743, Tmax = 1.000 | k = −13→13 |
11675 measured reflections | l = −21→21 |
Refinement top
Refinement on F2 | Hydrogen site location: inferred from neighbouring sites |
Least-squares matrix: full | H-atom parameters constrained |
R[F2 > 2σ(F2)] = 0.050 | w = 1/[σ2(Fo2) + (0.0216P)2 + 3.2907P] where P = (Fo2 + 2Fc2)/3 |
wR(F2) = 0.100 | (Δ/σ)max < 0.001 |
S = 1.11 | Δρmax = 0.87 e Å−3 |
3562 reflections | Δρmin = −0.66 e Å−3 |
202 parameters | Extinction correction: SHELXL2018 (Sheldrick, 2015), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4 |
0 restraints | Extinction coefficient: 0.0024 (5) |
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 | |
C2 | 0.1813 (4) | 0.5822 (3) | 0.5281 (2) | 0.0223 (7) | |
N3 | 0.1369 (3) | 0.6656 (3) | 0.46276 (18) | 0.0244 (6) | |
C4 | 0.1464 (4) | 0.6313 (4) | 0.3872 (2) | 0.0260 (7) | |
C5 | 0.2033 (4) | 0.5115 (3) | 0.3723 (2) | 0.0237 (7) | |
H5 | 0.205001 | 0.488716 | 0.318403 | 0.028* | |
C6 | 0.2561 (4) | 0.4289 (3) | 0.4381 (2) | 0.0212 (7) | |
N1 | 0.2475 (3) | 0.4652 (3) | 0.51637 (17) | 0.0210 (6) | |
C19 | 0.0951 (5) | 0.7282 (4) | 0.3183 (2) | 0.0388 (10) | |
H19A | −0.009262 | 0.741422 | 0.306893 | 0.058* | |
H19B | 0.115694 | 0.696748 | 0.268472 | 0.058* | |
H19C | 0.145761 | 0.808907 | 0.335035 | 0.058* | |
C13 | 0.3230 (4) | 0.3019 (3) | 0.4265 (2) | 0.0227 (7) | |
C14 | 0.2362 (5) | 0.2122 (4) | 0.3720 (2) | 0.0316 (8) | |
H14 | 0.136785 | 0.229841 | 0.346736 | 0.038* | |
C15 | 0.2959 (5) | 0.0967 (4) | 0.3550 (3) | 0.0397 (10) | |
H15 | 0.236877 | 0.036854 | 0.318355 | 0.048* | |
C16 | 0.4446 (5) | 0.0702 (4) | 0.3928 (3) | 0.0378 (10) | |
H16 | 0.485068 | −0.007745 | 0.38196 | 0.045* | |
C17 | 0.5319 (5) | 0.1601 (4) | 0.4466 (2) | 0.0342 (9) | |
H17 | 0.631556 | 0.142863 | 0.471193 | 0.041* | |
C18 | 0.4722 (4) | 0.2754 (4) | 0.4641 (2) | 0.0278 (8) | |
H18 | 0.531297 | 0.335073 | 0.500786 | 0.033* | |
C7 | 0.3074 (4) | 0.3784 (3) | 0.5877 (2) | 0.0241 (7) | |
C8 | 0.2319 (4) | 0.2664 (3) | 0.5924 (2) | 0.0251 (7) | |
H8 | 0.141241 | 0.248609 | 0.553637 | 0.03* | |
C9 | 0.2965 (4) | 0.1796 (3) | 0.6580 (2) | 0.0275 (8) | |
C10 | 0.4311 (4) | 0.2092 (3) | 0.7155 (2) | 0.0303 (8) | |
H10 | 0.473019 | 0.151385 | 0.758826 | 0.036* | |
C11 | 0.5036 (4) | 0.3229 (4) | 0.7093 (2) | 0.0293 (8) | |
H11 | 0.593516 | 0.341646 | 0.748582 | 0.035* | |
C12 | 0.4421 (4) | 0.4100 (3) | 0.6443 (2) | 0.0251 (8) | |
H12 | 0.49016 | 0.486834 | 0.639024 | 0.03* | |
O1 | 0.2341 (3) | 0.0635 (3) | 0.66904 (17) | 0.0352 (6) | |
C20 | 0.1217 (5) | 0.0147 (4) | 0.5977 (3) | 0.0385 (10) | |
H20A | 0.034797 | 0.067495 | 0.588149 | 0.058* | |
H20B | 0.098418 | −0.073087 | 0.608365 | 0.058* | |
H20C | 0.156591 | 0.017174 | 0.548991 | 0.058* | |
Se1 | 0.15424 (5) | 0.62264 (4) | 0.62984 (2) | 0.02975 (13) | |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
C2 | 0.0255 (17) | 0.0178 (15) | 0.0271 (18) | 0.0009 (14) | 0.0130 (14) | −0.0004 (13) |
N3 | 0.0275 (15) | 0.0212 (14) | 0.0261 (15) | 0.0032 (12) | 0.0104 (13) | 0.0036 (11) |
C4 | 0.0282 (18) | 0.0247 (17) | 0.0267 (17) | 0.0033 (16) | 0.0103 (14) | 0.0037 (15) |
C5 | 0.0283 (19) | 0.0232 (17) | 0.0217 (17) | 0.0014 (15) | 0.0104 (15) | 0.0006 (13) |
C6 | 0.0229 (17) | 0.0206 (16) | 0.0226 (17) | −0.0015 (14) | 0.0104 (14) | −0.0003 (13) |
N1 | 0.0250 (15) | 0.0172 (13) | 0.0228 (14) | 0.0019 (12) | 0.0100 (12) | 0.0017 (11) |
C19 | 0.049 (3) | 0.038 (2) | 0.031 (2) | 0.015 (2) | 0.0146 (19) | 0.0116 (17) |
C13 | 0.0305 (18) | 0.0193 (16) | 0.0223 (17) | 0.0013 (15) | 0.0141 (15) | 0.0024 (13) |
C14 | 0.037 (2) | 0.029 (2) | 0.030 (2) | 0.0012 (17) | 0.0115 (17) | −0.0021 (15) |
C15 | 0.059 (3) | 0.024 (2) | 0.038 (2) | −0.0064 (18) | 0.018 (2) | −0.0088 (16) |
C16 | 0.061 (3) | 0.0201 (18) | 0.040 (2) | 0.0108 (19) | 0.027 (2) | 0.0032 (17) |
C17 | 0.042 (2) | 0.032 (2) | 0.031 (2) | 0.0106 (17) | 0.0145 (18) | 0.0001 (16) |
C18 | 0.033 (2) | 0.0270 (18) | 0.0256 (18) | 0.0038 (16) | 0.0121 (16) | 0.0002 (15) |
C7 | 0.0339 (19) | 0.0197 (15) | 0.0226 (16) | 0.0091 (16) | 0.0143 (14) | 0.0018 (14) |
C8 | 0.0280 (19) | 0.0244 (18) | 0.0255 (18) | 0.0017 (15) | 0.0118 (15) | −0.0034 (14) |
C9 | 0.040 (2) | 0.0215 (17) | 0.0269 (19) | 0.0028 (16) | 0.0189 (17) | 0.0001 (14) |
C10 | 0.043 (2) | 0.0215 (18) | 0.032 (2) | 0.0043 (16) | 0.0185 (18) | 0.0010 (15) |
C11 | 0.034 (2) | 0.0286 (19) | 0.0239 (18) | 0.0047 (16) | 0.0071 (16) | −0.0010 (14) |
C12 | 0.0326 (19) | 0.0203 (17) | 0.0251 (18) | −0.0003 (14) | 0.0125 (15) | −0.0023 (13) |
O1 | 0.0471 (17) | 0.0246 (13) | 0.0347 (15) | −0.0018 (13) | 0.0130 (13) | 0.0054 (11) |
C20 | 0.050 (3) | 0.0221 (19) | 0.043 (2) | −0.0059 (18) | 0.014 (2) | −0.0023 (17) |
Se1 | 0.0422 (2) | 0.02427 (19) | 0.02738 (19) | 0.00485 (18) | 0.01730 (15) | −0.00053 (16) |
Geometric parameters (Å, º) top
C2—N3 | 1.353 (4) | C16—C17 | 1.382 (6) |
C2—N1 | 1.399 (4) | C16—H16 | 0.93 |
C2—Se1 | 1.829 (3) | C17—C18 | 1.382 (5) |
N3—C4 | 1.332 (4) | C17—H17 | 0.93 |
C4—C5 | 1.398 (5) | C18—H18 | 0.93 |
C4—C19 | 1.491 (5) | C7—C8 | 1.372 (5) |
C5—C6 | 1.361 (5) | C7—C12 | 1.385 (5) |
C5—H5 | 0.93 | C8—C9 | 1.405 (5) |
C6—N1 | 1.379 (4) | C8—H8 | 0.93 |
C6—C13 | 1.492 (5) | C9—O1 | 1.371 (4) |
N1—C7 | 1.462 (4) | C9—C10 | 1.386 (5) |
C19—H19A | 0.96 | C10—C11 | 1.377 (5) |
C19—H19B | 0.96 | C10—H10 | 0.93 |
C19—H19C | 0.96 | C11—C12 | 1.396 (5) |
C13—C14 | 1.384 (5) | C11—H11 | 0.93 |
C13—C18 | 1.395 (5) | C12—H12 | 0.93 |
C14—C15 | 1.382 (5) | O1—C20 | 1.434 (5) |
C14—H14 | 0.93 | C20—H20A | 0.96 |
C15—C16 | 1.392 (6) | C20—H20B | 0.96 |
C15—H15 | 0.93 | C20—H20C | 0.96 |
| | | |
N3—C2—N1 | 118.9 (3) | C15—C16—H16 | 120.1 |
N3—C2—Se1 | 120.2 (2) | C16—C17—C18 | 120.5 (4) |
N1—C2—Se1 | 120.9 (2) | C16—C17—H17 | 119.7 |
C4—N3—C2 | 119.9 (3) | C18—C17—H17 | 119.7 |
N3—C4—C5 | 122.5 (3) | C17—C18—C13 | 119.7 (4) |
N3—C4—C19 | 116.8 (3) | C17—C18—H18 | 120.1 |
C5—C4—C19 | 120.8 (3) | C13—C18—H18 | 120.1 |
C6—C5—C4 | 118.7 (3) | C8—C7—C12 | 123.5 (3) |
C6—C5—H5 | 120.6 | C8—C7—N1 | 118.4 (3) |
C4—C5—H5 | 120.6 | C12—C7—N1 | 118.0 (3) |
C5—C6—N1 | 118.7 (3) | C7—C8—C9 | 117.6 (3) |
C5—C6—C13 | 121.1 (3) | C7—C8—H8 | 121.2 |
N1—C6—C13 | 120.3 (3) | C9—C8—H8 | 121.2 |
C6—N1—C2 | 121.2 (3) | O1—C9—C10 | 116.5 (3) |
C6—N1—C7 | 118.9 (3) | O1—C9—C8 | 123.5 (3) |
C2—N1—C7 | 119.9 (3) | C10—C9—C8 | 120.0 (3) |
C4—C19—H19A | 109.5 | C11—C10—C9 | 121.0 (3) |
C4—C19—H19B | 109.5 | C11—C10—H10 | 119.5 |
H19A—C19—H19B | 109.5 | C9—C10—H10 | 119.5 |
C4—C19—H19C | 109.5 | C10—C11—C12 | 120.0 (4) |
H19A—C19—H19C | 109.5 | C10—C11—H11 | 120 |
H19B—C19—H19C | 109.5 | C12—C11—H11 | 120 |
C14—C13—C18 | 119.6 (3) | C7—C12—C11 | 117.9 (3) |
C14—C13—C6 | 118.5 (3) | C7—C12—H12 | 121 |
C18—C13—C6 | 121.8 (3) | C11—C12—H12 | 121 |
C15—C14—C13 | 120.5 (4) | C9—O1—C20 | 116.1 (3) |
C15—C14—H14 | 119.7 | O1—C20—H20A | 109.5 |
C13—C14—H14 | 119.7 | O1—C20—H20B | 109.5 |
C14—C15—C16 | 119.8 (4) | H20A—C20—H20B | 109.5 |
C14—C15—H15 | 120.1 | O1—C20—H20C | 109.5 |
C16—C15—H15 | 120.1 | H20A—C20—H20C | 109.5 |
C17—C16—C15 | 119.8 (4) | H20B—C20—H20C | 109.5 |
C17—C16—H16 | 120.1 | | |
| | | |
N1—C2—N3—C4 | 5.1 (5) | C13—C14—C15—C16 | 0.0 (6) |
Se1—C2—N3—C4 | −174.8 (3) | C14—C15—C16—C17 | −0.6 (6) |
C2—N3—C4—C5 | −1.0 (5) | C15—C16—C17—C18 | 0.9 (6) |
C2—N3—C4—C19 | 179.9 (3) | C16—C17—C18—C13 | −0.7 (5) |
N3—C4—C5—C6 | −2.6 (5) | C14—C13—C18—C17 | 0.1 (5) |
C19—C4—C5—C6 | 176.5 (4) | C6—C13—C18—C17 | −175.2 (3) |
C4—C5—C6—N1 | 1.8 (5) | C6—N1—C7—C8 | −72.6 (4) |
C4—C5—C6—C13 | −177.8 (3) | C2—N1—C7—C8 | 106.7 (4) |
C5—C6—N1—C2 | 2.3 (5) | C6—N1—C7—C12 | 103.6 (4) |
C13—C6—N1—C2 | −178.1 (3) | C2—N1—C7—C12 | −77.2 (4) |
C5—C6—N1—C7 | −178.4 (3) | C12—C7—C8—C9 | −0.5 (5) |
C13—C6—N1—C7 | 1.1 (5) | N1—C7—C8—C9 | 175.4 (3) |
N3—C2—N1—C6 | −5.8 (5) | C7—C8—C9—O1 | −178.9 (3) |
Se1—C2—N1—C6 | 174.1 (2) | C7—C8—C9—C10 | 0.7 (5) |
N3—C2—N1—C7 | 174.9 (3) | O1—C9—C10—C11 | 179.3 (3) |
Se1—C2—N1—C7 | −5.2 (4) | C8—C9—C10—C11 | −0.2 (5) |
C5—C6—C13—C14 | −61.2 (4) | C9—C10—C11—C12 | −0.4 (5) |
N1—C6—C13—C14 | 119.2 (4) | C8—C7—C12—C11 | −0.1 (5) |
C5—C6—C13—C18 | 114.2 (4) | N1—C7—C12—C11 | −176.0 (3) |
N1—C6—C13—C18 | −65.4 (4) | C10—C11—C12—C7 | 0.5 (5) |
C18—C13—C14—C15 | 0.2 (5) | C10—C9—O1—C20 | −161.7 (3) |
C6—C13—C14—C15 | 175.7 (3) | C8—C9—O1—C20 | 17.8 (5) |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
C5—H5···O1i | 0.93 | 2.63 | 3.557 (4) | 175 |
C8—H8···N3ii | 0.93 | 2.72 | 3.415 (5) | 133 |
C19—H19B···Se1iii | 0.96 | 3.06 | 3.674 (4) | 123 |
Symmetry codes: (i) x, −y+1/2, z−1/2; (ii) −x, −y+1, −z+1; (iii) x, −y+3/2, z−1/2. |
4-Methyl-1-(4-methoxyphenyl)-6-phenylpyrimidine-2(1
H)-selenone (3)
top
Crystal data top
C18H16N2OSe | F(000) = 720 |
Mr = 355.29 | Dx = 1.496 Mg m−3 |
Monoclinic, P21/n | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: -P 2yn | Cell parameters from 18676 reflections |
a = 12.7330 (3) Å | θ = 1.0–27.5° |
b = 8.9500 (2) Å | µ = 2.38 mm−1 |
c = 14.1399 (5) Å | T = 100 K |
β = 101.862 (2)° | Needle, orange |
V = 1576.98 (7) Å3 | 0.99 × 0.43 × 0.08 mm |
Z = 4 | |
Data collection top
Bruker KappaCCD diffractometer | 3626 independent reflections |
Horizonally mounted graphite crystal monochromator | 3229 reflections with I > 2σ(I) |
Detector resolution: 9 pixels mm-1 | Rint = 0.104 |
CCD scans | θmax = 27.7°, θmin = 3.0° |
Absorption correction: multi-scan (DENZO-SMN; Otwinowski & Minor, 1997) | h = −15→16 |
Tmin = 0.868, Tmax = 1.187 | k = −11→11 |
17877 measured reflections | l = −22→21 |
Refinement top
Refinement on F2 | Hydrogen site location: inferred from neighbouring sites |
Least-squares matrix: full | H-atom parameters constrained |
R[F2 > 2σ(F2)] = 0.039 | w = 1/[σ2(Fo2) + (0.0604P)2 + 1.1117P] where P = (Fo2 + 2Fc2)/3 |
wR(F2) = 0.107 | (Δ/σ)max = 0.001 |
S = 1.03 | Δρmax = 0.94 e Å−3 |
3626 reflections | Δρmin = −0.82 e Å−3 |
202 parameters | Extinction correction: SHELXL2014 (Sheldrick, 2015), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4 |
0 restraints | Extinction coefficient: 0.0249 (17) |
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 | |
N1 | 0.52843 (15) | 0.7407 (2) | 0.43405 (13) | 0.0123 (4) | |
C2 | 0.46185 (19) | 0.6927 (2) | 0.49498 (17) | 0.0117 (4) | |
N3 | 0.36047 (15) | 0.6493 (2) | 0.45589 (14) | 0.0136 (4) | |
C4 | 0.32605 (18) | 0.6505 (2) | 0.36117 (17) | 0.0149 (4) | |
C5 | 0.39026 (19) | 0.6995 (2) | 0.29741 (17) | 0.0149 (5) | |
H5 | 0.362934 | 0.702177 | 0.229651 | 0.018* | |
C6 | 0.49275 (18) | 0.7429 (2) | 0.33549 (16) | 0.0136 (4) | |
C7 | 0.63567 (19) | 0.7957 (2) | 0.47412 (16) | 0.0125 (4) | |
C8 | 0.72006 (19) | 0.6957 (2) | 0.49859 (16) | 0.0132 (4) | |
H8 | 0.707767 | 0.59125 | 0.491031 | 0.016* | |
C9 | 0.82185 (18) | 0.7494 (3) | 0.53396 (16) | 0.0154 (4) | |
H9 | 0.880382 | 0.681985 | 0.55034 | 0.018* | |
C10 | 0.83927 (18) | 0.9039 (2) | 0.54585 (16) | 0.0148 (4) | |
C11 | 0.75435 (19) | 1.0028 (2) | 0.52104 (17) | 0.0166 (4) | |
H11 | 0.765976 | 1.107268 | 0.52918 | 0.02* | |
C12 | 0.65183 (18) | 0.9478 (2) | 0.48407 (16) | 0.0155 (4) | |
H12 | 0.593266 | 1.014712 | 0.465773 | 0.019* | |
C13 | 0.56766 (19) | 0.7855 (3) | 0.27191 (16) | 0.0142 (4) | |
C14 | 0.6437 (2) | 0.6833 (3) | 0.25498 (19) | 0.0202 (5) | |
H14 | 0.651673 | 0.590285 | 0.288079 | 0.024* | |
C15 | 0.7082 (2) | 0.7171 (3) | 0.1895 (2) | 0.0233 (5) | |
H15 | 0.760413 | 0.647327 | 0.178138 | 0.028* | |
C16 | 0.6964 (2) | 0.8524 (3) | 0.14084 (18) | 0.0227 (5) | |
H16 | 0.740188 | 0.875011 | 0.095883 | 0.027* | |
C17 | 0.6205 (2) | 0.9548 (3) | 0.15775 (19) | 0.0237 (5) | |
H17 | 0.612471 | 1.047513 | 0.124347 | 0.028* | |
C18 | 0.55606 (19) | 0.9218 (3) | 0.22372 (18) | 0.0190 (5) | |
H18 | 0.504449 | 0.992138 | 0.235664 | 0.023* | |
C19 | 0.21606 (19) | 0.5904 (3) | 0.32206 (18) | 0.0204 (5) | |
H19A | 0.221102 | 0.484575 | 0.3057 | 0.031* | |
H19B | 0.183076 | 0.646321 | 0.26395 | 0.031* | |
H19C | 0.171978 | 0.600824 | 0.370911 | 0.031* | |
C20 | 0.9634 (2) | 1.0987 (3) | 0.60663 (19) | 0.0243 (5) | |
H20A | 0.943755 | 1.158416 | 0.54755 | 0.036* | |
H20B | 1.039785 | 1.112586 | 0.63465 | 0.036* | |
H20C | 0.920634 | 1.130813 | 0.65322 | 0.036* | |
O1 | 0.94287 (13) | 0.94392 (19) | 0.58392 (12) | 0.0197 (4) | |
Se1 | 0.50781 (2) | 0.68872 (2) | 0.62690 (2) | 0.01518 (12) | |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
N1 | 0.0136 (9) | 0.0105 (8) | 0.0131 (9) | 0.0011 (7) | 0.0030 (7) | 0.0012 (7) |
C2 | 0.0151 (11) | 0.0084 (9) | 0.0124 (10) | 0.0022 (7) | 0.0046 (8) | 0.0013 (7) |
N3 | 0.0138 (9) | 0.0113 (8) | 0.0162 (9) | 0.0009 (7) | 0.0044 (7) | 0.0013 (7) |
C4 | 0.0139 (11) | 0.0123 (9) | 0.0182 (11) | 0.0018 (8) | 0.0026 (8) | 0.0010 (8) |
C5 | 0.0163 (12) | 0.0170 (11) | 0.0112 (11) | 0.0007 (8) | 0.0023 (8) | 0.0010 (8) |
C6 | 0.0179 (11) | 0.0104 (9) | 0.0130 (11) | 0.0030 (8) | 0.0043 (8) | 0.0019 (8) |
C7 | 0.0144 (11) | 0.0132 (10) | 0.0104 (10) | −0.0005 (8) | 0.0034 (8) | 0.0001 (7) |
C8 | 0.0165 (11) | 0.0109 (10) | 0.0126 (11) | 0.0018 (8) | 0.0041 (8) | 0.0002 (7) |
C9 | 0.0164 (11) | 0.0146 (11) | 0.0156 (11) | 0.0027 (9) | 0.0042 (8) | 0.0019 (9) |
C10 | 0.0151 (11) | 0.0177 (11) | 0.0117 (10) | −0.0018 (8) | 0.0033 (8) | −0.0005 (8) |
C11 | 0.0204 (12) | 0.0121 (10) | 0.0173 (11) | −0.0013 (8) | 0.0041 (8) | −0.0004 (8) |
C12 | 0.0165 (11) | 0.0130 (10) | 0.0175 (11) | 0.0024 (8) | 0.0046 (8) | 0.0009 (8) |
C13 | 0.0145 (11) | 0.0171 (10) | 0.0110 (10) | −0.0039 (8) | 0.0025 (8) | 0.0005 (8) |
C14 | 0.0240 (13) | 0.0209 (12) | 0.0173 (12) | 0.0040 (9) | 0.0078 (10) | 0.0040 (9) |
C15 | 0.0226 (13) | 0.0277 (12) | 0.0223 (13) | 0.0027 (10) | 0.0108 (10) | −0.0014 (10) |
C16 | 0.0225 (12) | 0.0299 (13) | 0.0178 (12) | −0.0072 (10) | 0.0089 (9) | −0.0010 (10) |
C17 | 0.0252 (13) | 0.0237 (12) | 0.0235 (13) | −0.0045 (10) | 0.0082 (10) | 0.0073 (10) |
C18 | 0.0178 (11) | 0.0194 (11) | 0.0203 (12) | −0.0004 (9) | 0.0053 (9) | 0.0036 (9) |
C19 | 0.0151 (11) | 0.0241 (12) | 0.0209 (12) | −0.0029 (9) | 0.0011 (9) | 0.0036 (9) |
C20 | 0.0220 (13) | 0.0259 (13) | 0.0241 (13) | −0.0077 (10) | 0.0027 (10) | −0.0066 (10) |
O1 | 0.0159 (8) | 0.0218 (8) | 0.0205 (9) | −0.0039 (7) | 0.0016 (6) | −0.0031 (7) |
Se1 | 0.01769 (17) | 0.01759 (16) | 0.01080 (16) | 0.00157 (8) | 0.00421 (10) | 0.00130 (7) |
Geometric parameters (Å, º) top
N1—C6 | 1.374 (3) | C11—H11 | 0.95 |
N1—C2 | 1.395 (3) | C12—H12 | 0.95 |
N1—C7 | 1.452 (3) | C13—C14 | 1.388 (3) |
C2—N3 | 1.353 (3) | C13—C18 | 1.390 (3) |
C2—Se1 | 1.837 (2) | C14—C15 | 1.391 (3) |
N3—C4 | 1.321 (3) | C14—H14 | 0.95 |
C4—C5 | 1.406 (3) | C15—C16 | 1.385 (4) |
C4—C19 | 1.496 (3) | C15—H15 | 0.95 |
C5—C6 | 1.362 (3) | C16—C17 | 1.387 (4) |
C5—H5 | 0.95 | C16—H16 | 0.95 |
C6—C13 | 1.489 (3) | C17—C18 | 1.395 (3) |
C7—C12 | 1.380 (3) | C17—H17 | 0.95 |
C7—C8 | 1.387 (3) | C18—H18 | 0.95 |
C8—C9 | 1.377 (3) | C19—H19A | 0.98 |
C8—H8 | 0.95 | C19—H19B | 0.98 |
C9—C10 | 1.405 (3) | C19—H19C | 0.98 |
C9—H9 | 0.95 | C20—O1 | 1.434 (3) |
C10—O1 | 1.366 (3) | C20—H20A | 0.98 |
C10—C11 | 1.386 (3) | C20—H20B | 0.98 |
C11—C12 | 1.393 (3) | C20—H20C | 0.98 |
| | | |
C6—N1—C2 | 120.96 (19) | C11—C12—H12 | 120.1 |
C6—N1—C7 | 118.63 (18) | C14—C13—C18 | 120.1 (2) |
C2—N1—C7 | 120.35 (19) | C14—C13—C6 | 119.4 (2) |
N3—C2—N1 | 119.1 (2) | C18—C13—C6 | 120.3 (2) |
N3—C2—Se1 | 119.17 (16) | C13—C14—C15 | 119.9 (2) |
N1—C2—Se1 | 121.73 (17) | C13—C14—H14 | 120 |
C4—N3—C2 | 120.12 (19) | C15—C14—H14 | 120 |
N3—C4—C5 | 122.5 (2) | C16—C15—C14 | 120.1 (2) |
N3—C4—C19 | 117.5 (2) | C16—C15—H15 | 119.9 |
C5—C4—C19 | 119.9 (2) | C14—C15—H15 | 119.9 |
C6—C5—C4 | 118.1 (2) | C15—C16—C17 | 120.0 (2) |
C6—C5—H5 | 120.9 | C15—C16—H16 | 120 |
C4—C5—H5 | 120.9 | C17—C16—H16 | 120 |
C5—C6—N1 | 119.1 (2) | C16—C17—C18 | 120.1 (2) |
C5—C6—C13 | 121.0 (2) | C16—C17—H17 | 120 |
N1—C6—C13 | 119.8 (2) | C18—C17—H17 | 120 |
C12—C7—C8 | 121.3 (2) | C13—C18—C17 | 119.7 (2) |
C12—C7—N1 | 118.9 (2) | C13—C18—H18 | 120.1 |
C8—C7—N1 | 119.78 (19) | C17—C18—H18 | 120.1 |
C9—C8—C7 | 119.2 (2) | C4—C19—H19A | 109.5 |
C9—C8—H8 | 120.4 | C4—C19—H19B | 109.5 |
C7—C8—H8 | 120.4 | H19A—C19—H19B | 109.5 |
C8—C9—C10 | 120.1 (2) | C4—C19—H19C | 109.5 |
C8—C9—H9 | 120 | H19A—C19—H19C | 109.5 |
C10—C9—H9 | 120 | H19B—C19—H19C | 109.5 |
O1—C10—C11 | 124.9 (2) | O1—C20—H20A | 109.5 |
O1—C10—C9 | 114.91 (19) | O1—C20—H20B | 109.5 |
C11—C10—C9 | 120.2 (2) | H20A—C20—H20B | 109.5 |
C10—C11—C12 | 119.5 (2) | O1—C20—H20C | 109.5 |
C10—C11—H11 | 120.3 | H20A—C20—H20C | 109.5 |
C12—C11—H11 | 120.3 | H20B—C20—H20C | 109.5 |
C7—C12—C11 | 119.7 (2) | C10—O1—C20 | 117.29 (18) |
C7—C12—H12 | 120.1 | | |
| | | |
C6—N1—C2—N3 | −0.7 (3) | C7—C8—C9—C10 | 0.6 (3) |
C7—N1—C2—N3 | 176.62 (18) | C8—C9—C10—O1 | 178.3 (2) |
C6—N1—C2—Se1 | 179.97 (15) | C8—C9—C10—C11 | −0.7 (3) |
C7—N1—C2—Se1 | −2.7 (3) | O1—C10—C11—C12 | −179.0 (2) |
N1—C2—N3—C4 | 1.0 (3) | C9—C10—C11—C12 | −0.2 (3) |
Se1—C2—N3—C4 | −179.63 (16) | C8—C7—C12—C11 | −1.2 (3) |
C2—N3—C4—C5 | −1.7 (3) | N1—C7—C12—C11 | −179.07 (19) |
C2—N3—C4—C19 | 175.46 (19) | C10—C11—C12—C7 | 1.1 (3) |
N3—C4—C5—C6 | 1.9 (3) | C5—C6—C13—C14 | −100.5 (3) |
C19—C4—C5—C6 | −175.1 (2) | N1—C6—C13—C14 | 76.6 (3) |
C4—C5—C6—N1 | −1.5 (3) | C5—C6—C13—C18 | 74.3 (3) |
C4—C5—C6—C13 | 175.6 (2) | N1—C6—C13—C18 | −108.6 (3) |
C2—N1—C6—C5 | 1.0 (3) | C18—C13—C14—C15 | −0.2 (4) |
C7—N1—C6—C5 | −176.35 (19) | C6—C13—C14—C15 | 174.7 (2) |
C2—N1—C6—C13 | −176.16 (19) | C13—C14—C15—C16 | −0.3 (4) |
C7—N1—C6—C13 | 6.5 (3) | C14—C15—C16—C17 | 0.4 (4) |
C6—N1—C7—C12 | 80.2 (3) | C15—C16—C17—C18 | 0.0 (4) |
C2—N1—C7—C12 | −97.1 (2) | C14—C13—C18—C17 | 0.5 (4) |
C6—N1—C7—C8 | −97.7 (2) | C6—C13—C18—C17 | −174.3 (2) |
C2—N1—C7—C8 | 85.0 (3) | C16—C17—C18—C13 | −0.4 (4) |
C12—C7—C8—C9 | 0.3 (3) | C11—C10—O1—C20 | 5.0 (3) |
N1—C7—C8—C9 | 178.2 (2) | C9—C10—O1—C20 | −173.93 (19) |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
C8—H8···N3i | 0.95 | 2.49 | 3.357 (3) | 151 |
C11—H11···N3ii | 0.95 | 2.74 | 3.484 (3) | 135 |
C12—H12···Se1ii | 0.95 | 3.12 | 3.983 (2) | 152 |
C16—H16···N3iii | 0.95 | 2.75 | 3.668 (3) | 163 |
C19—H19B···Se1iv | 0.98 | 3.02 | 3.943 (2) | 157 |
C20—H20C···Se1v | 0.98 | 3.1 | 3.796 (3) | 129 |
Symmetry codes: (i) −x+1, −y+1, −z+1; (ii) −x+1, −y+2, −z+1; (iii) x+1, −y+3/2, z−1/2; (iv) x, −y+3/2, z−1/2; (v) −x+1, y+1/2, −z+3/2. |
The comparison of selected torsion angles (°) for 1, 2, 3
and LS topTorsion angle | 1 A/B | 2 | 3 | LS |
C2—N1—C7—C8 | 87.1 (2)/90.2 (2) | 77.2 (4) | 85.0 (3) | 78.9 (2) |
C2—N1—C7—C12 | -97.7 (2)/-90.8 (2) | -106.7 (4) | -97.1 (3) | -102.6 (2) |
C5—C6—C13—C14 | -120.5 (2)/-97.5 (2) | -114.2 (4) | -100.5 (3) | -112.1 (2) |
C5—C6—C13—C18 | 60.2 (2)/82.1 (2) | 61.2 (5) | 74.3 (3) | 66.5 (2) |
The antimicrobial activity (mg l-1) of reference compounds vancomycin and
fluconazole against reference bacterial and fungal strains topMicroorganism | MIC | MBC | MBC/MIC |
Against vancomycin | | | |
S. aureus ATCC6538 | 0.49 | 1.95 | 4 |
S. aureus ATCC25923 | 0.98 | 7.81 | 8 |
S. aureus ATCC43300 | 0.49 | 1.95 | 4 |
S. epidermidis ATCC12228 | 0.98 | 0.98 | 1 |
M. luteus ATCC10240 | 0.12 | 0.12 | 1 |
B. subtilis ATCC6633 | 0.24 | 0.49 | 2 |
B. cereus ATCC10876 | 0.98 | 15.6 | 16 |
S. pyogenes ATCC19615 | 0.24 | 0.49 | 2 |
S. pneumoniae ATCC49619 | 0.24 | 0.49 | 2 |
S. mutans ATCC25175 | 0.98 | 0.98 | 1 |
| | | |
Against fluconazole | | | |
C. albicans ATCC102231 | 0.98 | 1.95 | 2 |
C. albicans ATCC2091 | 0.25 | 0.25 | 1 |
C. parapsilosis ATCC22019 | 1.95 | 1.95 | 1 |