organic compounds
2-Amino-4-(4-methoxyphenyl)-6-(4-methylphenyl)pyrimidin-1-ium chloride
aDepartment of Applied Chemistry, Dongduk Women's University, Seoul 136-714, Republic of Korea
*Correspondence e-mail: dskoh@dongduk.ac.kr
In the title salt, C18H18N3O+·Cl−, the aminopyrimidine molecule is protonated at one of the pyrimidine N atoms. The chloride anion interacts with the protonated pyrimidine N—H group and one of the amino N—H groups through two N—H⋯Cl hydrogen bonds, forming a six-membered ring. The chloride anion interacts further with the other amino N—H group to form an additional N—H⋯Cl hydrogen bond, which links the molecules along [001] in a helical manner.
Keywords: crystal structure; pyrimidinium; molecular salt; N—H⋯Cl hydrogen bonds.
CCDC reference: 1862115
Structure description
As a result of their being a natural component of nucleic acid, aminopyrimidine derivatives are biologically important and have shown a broad spectrum of biological activities including anti-platelet (Giridhar et al., 2012), antitumor (Lee et al., 2011), anti-bacterial (Nagarajan et al., 2014) and anti-diabetic properties (Singh et al., 2011). As a continuation of our research program to expand the use of novel synthetic (Lee et al. 2016), the title aminopyrimidine compound was synthesized from chalcone and its was determined. Other examples of aminopyrimidinium salt structures have been published recently (Swinton Darious et al., 2018; Jeevaraj et al., 2016).
The molecular structure of the title compound is shown in Fig. 1. The aminopyrimidine molecule is protonated at one of the pyrimidine nitrogen atoms. As a result, the two C—N—C bond angles in the pyrimidine ring are different: the C1—N2—C4 angle at protonated atom N2 is 121.1 (2)°, while for the unprotonated atom N1, the C1—N1—C2 angle is 117.8 (2)°.
In the crystal, a six-membered ring is formed through N—H⋯Cl hydrogen bonds (aqua coloured dashed lines in Fig. 2, Table 1) involving one of the hydrogen atoms in the amino group (N3—H3B) and a hydrogen atom in the pyrimidium ring (N2—H2A) and the chlorine anion. An additional hydrogen bond is formed by the other hydrogen atom in the amino group (N3—H3A) and the chloride anion (orange dashed line in Fig. 2, Table 1), which links the molecules into a chain along [001]. The three N—H⋯Cl hydrogen bonds connect the molecules in helical manner along [001]. Six molecules are involved in one turn of the helix (Fig. 3).
Synthesis and crystallization
The same synthetic procedures were used as described in our previous report (Koh & Lee, 2018), but starting from 4-methoxy acetophenone and 4-methyl benzaldehyde for the synthesis of the chalcone intermediate, as shown in Fig. 4.
Refinement
Crystal data, data collection and structure .
details are summarized in Table 2Structural data
CCDC reference: 1862115
https://doi.org/10.1107/S2414314618011525/lh4038sup1.cif
contains datablock I. DOI:Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2414314618011525/lh4038Isup2.hkl
Supporting information file. DOI: https://doi.org/10.1107/S2414314618011525/lh4038Isup3.cml
Data collection: APEX2 (Bruker, 2012); cell
SAINT (Bruker, 2012); data reduction: SAINT (Bruker, 2012); program(s) used to solve structure: SHELXS (Sheldrick, 2008); program(s) used to refine structure: SHELXL2014 (Sheldrick, 2015); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: publCIF (Westrip, 2010).C18H18N3O+·Cl− | Dx = 1.327 Mg m−3 |
Mr = 327.80 | Mo Kα radiation, λ = 0.71073 Å |
Hexagonal, P65 | Cell parameters from 9935 reflections |
a = 9.9013 (9) Å | θ = 2.4–26.1° |
c = 28.981 (2) Å | µ = 0.24 mm−1 |
V = 2460.6 (5) Å3 | T = 223 K |
Z = 6 | Block, colourless |
F(000) = 1032 | 0.18 × 0.10 × 0.07 mm |
Bruker PHOTON 100 CMOS diffractometer | 3401 reflections with I > 2σ(I) |
φ and ω scans | Rint = 0.081 |
Absorption correction: multi-scan (SADABS; Bruker, 2012) | θmax = 28.3°, θmin = 2.4° |
Tmin = 0.721, Tmax = 0.746 | h = −13→13 |
135729 measured reflections | k = −13→13 |
4073 independent reflections | l = −38→38 |
Refinement on F2 | Hydrogen site location: inferred from neighbouring sites |
Least-squares matrix: full | Only H-atom displacement parameters refined |
R[F2 > 2σ(F2)] = 0.040 | w = 1/[σ2(Fo2) + (0.0281P)2 + 0.7437P] where P = (Fo2 + 2Fc2)/3 |
wR(F2) = 0.083 | (Δ/σ)max = 0.005 |
S = 1.10 | Δρmax = 0.19 e Å−3 |
4073 reflections | Δρmin = −0.15 e Å−3 |
228 parameters | Absolute structure: Flack x determined using 1416 quotients [(I+)-(I-)]/[(I+)+(I-)] (Parsons et al., 2013) |
1 restraint | Absolute structure parameter: 0.016 (15) |
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. |
x | y | z | Uiso*/Ueq | ||
C1 | 1.1580 (3) | 0.9339 (3) | 0.12113 (9) | 0.0327 (6) | |
N1 | 1.0866 (3) | 0.9519 (3) | 0.08454 (8) | 0.0324 (5) | |
C2 | 0.9390 (3) | 0.8427 (3) | 0.07668 (9) | 0.0317 (6) | |
C3 | 0.8602 (3) | 0.7103 (3) | 0.10505 (10) | 0.0363 (6) | |
H3 | 0.7569 | 0.6335 | 0.0984 | 0.041 (9)* | |
C4 | 0.9356 (3) | 0.6949 (3) | 0.14220 (9) | 0.0327 (6) | |
N2 | 1.0862 (3) | 0.8080 (3) | 0.14949 (8) | 0.0335 (5) | |
H2A | 1.1373 | 0.7995 | 0.1727 | 0.056 (11)* | |
N3 | 1.3025 (3) | 1.0421 (3) | 0.13150 (9) | 0.0402 (6) | |
H3A | 1.3512 | 1.1252 | 0.1145 | 0.050 (10)* | |
H3B | 1.3488 | 1.0301 | 0.1554 | 0.052 (11)* | |
C5 | 0.8595 (3) | 0.8685 (3) | 0.03772 (9) | 0.0314 (6) | |
C6 | 0.9184 (3) | 1.0184 (3) | 0.01960 (10) | 0.0353 (6) | |
H6 | 1.0093 | 1.1017 | 0.0323 | 0.038 (8)* | |
C7 | 0.8450 (4) | 1.0454 (3) | −0.01649 (10) | 0.0385 (7) | |
H7 | 0.8863 | 1.1466 | −0.0286 | 0.041 (9)* | |
C8 | 0.7090 (3) | 0.9226 (4) | −0.03525 (10) | 0.0355 (6) | |
C9 | 0.6482 (4) | 0.7740 (3) | −0.01741 (10) | 0.0373 (6) | |
H9 | 0.5561 | 0.6912 | −0.0298 | 0.047 (9)* | |
C10 | 0.7234 (4) | 0.7477 (3) | 0.01875 (10) | 0.0358 (6) | |
H10 | 0.6819 | 0.6464 | 0.0307 | 0.039 (8)* | |
O1 | 0.6439 (3) | 0.9614 (3) | −0.07036 (8) | 0.0485 (6) | |
C11 | 0.5094 (4) | 0.8394 (4) | −0.09247 (12) | 0.0523 (9) | |
H11A | 0.5351 | 0.7651 | −0.1058 | 0.076 (13)* | |
H11B | 0.4752 | 0.8831 | −0.1167 | 0.073 (12)* | |
H11C | 0.4266 | 0.7869 | −0.0700 | 0.066 (12)* | |
C12 | 0.8636 (3) | 0.5676 (3) | 0.17621 (9) | 0.0337 (6) | |
C13 | 0.7053 (4) | 0.4976 (5) | 0.18546 (15) | 0.0597 (10) | |
H13 | 0.6432 | 0.5276 | 0.1687 | 0.084 (14)* | |
C14 | 0.6380 (4) | 0.3837 (5) | 0.21918 (15) | 0.0617 (11) | |
H14 | 0.5307 | 0.3381 | 0.2252 | 0.079 (13)* | |
C15 | 0.7247 (4) | 0.3361 (4) | 0.24390 (10) | 0.0417 (7) | |
C16 | 0.8803 (4) | 0.3997 (4) | 0.23269 (11) | 0.0474 (8) | |
H16 | 0.9402 | 0.3638 | 0.2479 | 0.059 (11)* | |
C17 | 0.9500 (4) | 0.5155 (3) | 0.19954 (11) | 0.0406 (7) | |
H17 | 1.0567 | 0.5586 | 0.1930 | 0.062 (11)* | |
C18 | 0.6526 (5) | 0.2185 (4) | 0.28224 (12) | 0.0597 (10) | |
H18A | 0.7155 | 0.1703 | 0.2880 | 0.088 (16)* | |
H18B | 0.5481 | 0.1391 | 0.2734 | 0.082 (14)* | |
H18C | 0.6477 | 0.2704 | 0.3101 | 0.12 (2)* | |
Cl1 | 0.47413 (9) | 0.33310 (8) | 0.05723 (3) | 0.0449 (2) |
U11 | U22 | U33 | U12 | U13 | U23 | |
C1 | 0.0317 (15) | 0.0354 (15) | 0.0304 (13) | 0.0165 (13) | 0.0060 (11) | 0.0016 (11) |
N1 | 0.0319 (12) | 0.0331 (13) | 0.0304 (12) | 0.0149 (10) | 0.0030 (10) | 0.0038 (10) |
C2 | 0.0343 (15) | 0.0355 (15) | 0.0288 (13) | 0.0201 (12) | 0.0038 (11) | 0.0026 (11) |
C3 | 0.0316 (16) | 0.0355 (15) | 0.0392 (15) | 0.0148 (13) | 0.0015 (12) | 0.0062 (12) |
C4 | 0.0334 (15) | 0.0339 (15) | 0.0319 (15) | 0.0177 (12) | 0.0053 (11) | 0.0033 (11) |
N2 | 0.0328 (13) | 0.0387 (13) | 0.0294 (12) | 0.0182 (11) | 0.0019 (10) | 0.0042 (10) |
N3 | 0.0298 (13) | 0.0434 (15) | 0.0385 (14) | 0.0117 (11) | 0.0008 (11) | 0.0092 (11) |
C5 | 0.0338 (15) | 0.0329 (14) | 0.0293 (13) | 0.0181 (12) | 0.0038 (11) | 0.0019 (11) |
C6 | 0.0349 (15) | 0.0331 (15) | 0.0346 (15) | 0.0145 (13) | −0.0005 (12) | 0.0010 (12) |
C7 | 0.0411 (17) | 0.0331 (15) | 0.0398 (16) | 0.0174 (14) | 0.0005 (13) | 0.0050 (13) |
C8 | 0.0410 (16) | 0.0439 (17) | 0.0281 (14) | 0.0261 (14) | −0.0010 (12) | 0.0004 (12) |
C9 | 0.0387 (16) | 0.0364 (16) | 0.0334 (15) | 0.0162 (13) | −0.0032 (12) | −0.0035 (12) |
C10 | 0.0427 (16) | 0.0297 (14) | 0.0327 (14) | 0.0163 (13) | 0.0032 (12) | 0.0022 (12) |
O1 | 0.0548 (14) | 0.0477 (13) | 0.0455 (13) | 0.0277 (12) | −0.0140 (10) | 0.0018 (10) |
C11 | 0.061 (2) | 0.058 (2) | 0.047 (2) | 0.0364 (19) | −0.0178 (17) | −0.0105 (16) |
C12 | 0.0370 (15) | 0.0343 (15) | 0.0317 (15) | 0.0194 (13) | 0.0047 (11) | 0.0044 (11) |
C13 | 0.0438 (19) | 0.075 (3) | 0.072 (2) | 0.038 (2) | 0.0222 (17) | 0.041 (2) |
C14 | 0.047 (2) | 0.068 (3) | 0.076 (3) | 0.0336 (19) | 0.0296 (19) | 0.038 (2) |
C15 | 0.0532 (19) | 0.0341 (16) | 0.0328 (15) | 0.0181 (14) | 0.0045 (13) | 0.0022 (13) |
C16 | 0.0474 (18) | 0.0349 (16) | 0.0466 (19) | 0.0106 (14) | −0.0143 (15) | 0.0093 (14) |
C17 | 0.0335 (16) | 0.0342 (15) | 0.0455 (17) | 0.0105 (13) | −0.0069 (13) | 0.0048 (13) |
C18 | 0.080 (3) | 0.043 (2) | 0.0413 (19) | 0.019 (2) | 0.0055 (18) | 0.0100 (16) |
Cl1 | 0.0498 (5) | 0.0295 (3) | 0.0452 (4) | 0.0122 (3) | −0.0071 (3) | −0.0003 (3) |
C1—N3 | 1.324 (4) | C9—C10 | 1.384 (4) |
C1—N1 | 1.335 (4) | C9—H9 | 0.9400 |
C1—N2 | 1.360 (4) | C10—H10 | 0.9400 |
N1—C2 | 1.333 (4) | O1—C11 | 1.426 (4) |
C2—C3 | 1.407 (4) | C11—H11A | 0.9700 |
C2—C5 | 1.470 (4) | C11—H11B | 0.9700 |
C3—C4 | 1.361 (4) | C11—H11C | 0.9700 |
C3—H3 | 0.9400 | C12—C17 | 1.377 (4) |
C4—N2 | 1.361 (4) | C12—C13 | 1.387 (4) |
C4—C12 | 1.473 (4) | C13—C14 | 1.385 (5) |
N2—H2A | 0.8700 | C13—H13 | 0.9400 |
N3—H3A | 0.8700 | C14—C15 | 1.369 (5) |
N3—H3B | 0.8700 | C14—H14 | 0.9400 |
C5—C10 | 1.391 (4) | C15—C16 | 1.380 (5) |
C5—C6 | 1.397 (4) | C15—C18 | 1.506 (4) |
C6—C7 | 1.374 (4) | C16—C17 | 1.386 (4) |
C6—H6 | 0.9400 | C16—H16 | 0.9400 |
C7—C8 | 1.396 (4) | C17—H17 | 0.9400 |
C7—H7 | 0.9400 | C18—H18A | 0.9700 |
C8—O1 | 1.359 (4) | C18—H18B | 0.9700 |
C8—C9 | 1.381 (4) | C18—H18C | 0.9700 |
N3—C1—N1 | 120.2 (3) | C9—C10—C5 | 121.2 (3) |
N3—C1—N2 | 117.6 (3) | C9—C10—H10 | 119.4 |
N1—C1—N2 | 122.2 (3) | C5—C10—H10 | 119.4 |
C2—N1—C1 | 117.8 (2) | C8—O1—C11 | 118.1 (3) |
N1—C2—C3 | 121.9 (3) | O1—C11—H11A | 109.5 |
N1—C2—C5 | 117.1 (2) | O1—C11—H11B | 109.5 |
C3—C2—C5 | 121.0 (3) | H11A—C11—H11B | 109.5 |
C4—C3—C2 | 119.1 (3) | O1—C11—H11C | 109.5 |
C4—C3—H3 | 120.4 | H11A—C11—H11C | 109.5 |
C2—C3—H3 | 120.4 | H11B—C11—H11C | 109.5 |
N2—C4—C3 | 117.9 (3) | C17—C12—C13 | 118.5 (3) |
N2—C4—C12 | 117.5 (2) | C17—C12—C4 | 121.6 (3) |
C3—C4—C12 | 124.6 (3) | C13—C12—C4 | 119.9 (3) |
C1—N2—C4 | 121.1 (2) | C14—C13—C12 | 120.4 (3) |
C1—N2—H2A | 119.5 | C14—C13—H13 | 119.8 |
C4—N2—H2A | 119.5 | C12—C13—H13 | 119.8 |
C1—N3—H3A | 120.0 | C15—C14—C13 | 121.4 (3) |
C1—N3—H3B | 120.0 | C15—C14—H14 | 119.3 |
H3A—N3—H3B | 120.0 | C13—C14—H14 | 119.3 |
C10—C5—C6 | 118.3 (3) | C14—C15—C16 | 117.9 (3) |
C10—C5—C2 | 121.8 (3) | C14—C15—C18 | 121.0 (3) |
C6—C5—C2 | 119.9 (3) | C16—C15—C18 | 121.0 (3) |
C7—C6—C5 | 120.8 (3) | C15—C16—C17 | 121.4 (3) |
C7—C6—H6 | 119.6 | C15—C16—H16 | 119.3 |
C5—C6—H6 | 119.6 | C17—C16—H16 | 119.3 |
C6—C7—C8 | 120.0 (3) | C12—C17—C16 | 120.2 (3) |
C6—C7—H7 | 120.0 | C12—C17—H17 | 119.9 |
C8—C7—H7 | 120.0 | C16—C17—H17 | 119.9 |
O1—C8—C9 | 124.4 (3) | C15—C18—H18A | 109.5 |
O1—C8—C7 | 115.6 (3) | C15—C18—H18B | 109.5 |
C9—C8—C7 | 120.0 (3) | H18A—C18—H18B | 109.5 |
C8—C9—C10 | 119.6 (3) | C15—C18—H18C | 109.5 |
C8—C9—H9 | 120.2 | H18A—C18—H18C | 109.5 |
C10—C9—H9 | 120.2 | H18B—C18—H18C | 109.5 |
N3—C1—N1—C2 | −177.3 (3) | O1—C8—C9—C10 | −179.4 (3) |
N2—C1—N1—C2 | 1.2 (4) | C7—C8—C9—C10 | −0.6 (4) |
C1—N1—C2—C3 | −1.4 (4) | C8—C9—C10—C5 | 0.2 (4) |
C1—N1—C2—C5 | 176.8 (2) | C6—C5—C10—C9 | 0.5 (4) |
N1—C2—C3—C4 | 1.6 (4) | C2—C5—C10—C9 | 178.9 (3) |
C5—C2—C3—C4 | −176.6 (3) | C9—C8—O1—C11 | −4.4 (4) |
C2—C3—C4—N2 | −1.5 (4) | C7—C8—O1—C11 | 176.8 (3) |
C2—C3—C4—C12 | 175.9 (3) | N2—C4—C12—C17 | −32.0 (4) |
N3—C1—N2—C4 | 177.3 (3) | C3—C4—C12—C17 | 150.6 (3) |
N1—C1—N2—C4 | −1.2 (4) | N2—C4—C12—C13 | 147.8 (3) |
C3—C4—N2—C1 | 1.3 (4) | C3—C4—C12—C13 | −29.6 (5) |
C12—C4—N2—C1 | −176.3 (2) | C17—C12—C13—C14 | 3.4 (6) |
N1—C2—C5—C10 | 162.7 (3) | C4—C12—C13—C14 | −176.4 (4) |
C3—C2—C5—C10 | −19.1 (4) | C12—C13—C14—C15 | −0.6 (7) |
N1—C2—C5—C6 | −19.0 (4) | C13—C14—C15—C16 | −3.1 (6) |
C3—C2—C5—C6 | 159.2 (3) | C13—C14—C15—C18 | 176.7 (4) |
C10—C5—C6—C7 | −0.9 (4) | C14—C15—C16—C17 | 4.1 (5) |
C2—C5—C6—C7 | −179.3 (3) | C18—C15—C16—C17 | −175.7 (3) |
C5—C6—C7—C8 | 0.6 (5) | C13—C12—C17—C16 | −2.4 (5) |
C6—C7—C8—O1 | 179.1 (3) | C4—C12—C17—C16 | 177.4 (3) |
C6—C7—C8—C9 | 0.2 (4) | C15—C16—C17—C12 | −1.4 (5) |
D—H···A | D—H | H···A | D···A | D—H···A |
N2—H2A···Cl1i | 0.87 | 2.27 | 3.106 (3) | 160 |
N3—H3A···Cl1ii | 0.87 | 2.44 | 3.305 (3) | 172 |
N3—H3B···Cl1i | 0.87 | 2.56 | 3.332 (3) | 148 |
C14—H14···O1iii | 0.94 | 2.46 | 3.300 (4) | 148 |
Symmetry codes: (i) y+1, −x+y+1, z+1/6; (ii) x+1, y+1, z; (iii) −x+y, −x+1, z+1/3. |
Funding information
The authors acknowledge financial support from the Basic Science Research Program (award No. NRF– 2016R1D1A1B03931623).
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