organic compounds
4-(3,5-Dimethoxyphenyl)-6-(2-methoxyphenyl)pyrimidin-2-amine
aDepartment of Applied Chemistry, Dongduk Women's University, Seoul 136-714, Republic of Korea
*Correspondence e-mail: dskoh@dongduk.ac.kr
In the title molecule, C19H19N3O3, the 2-methoxyphenyl and 3,5-dimethoxyphenyl rings are attached at the 4- and 6-positions, respectively, of the central 2-aminopyrimidine ring. The dihedral angles between the planes of the benzene rings and that of the 2-aminopyrimidine ring are 17.31 (9) and 44.39 (6)°, respectively. In the crystal, pairs of N—H⋯N hydrogen bonds form inversion dimers enclosing R22(8) rings. Pairs of N—H⋯O hydrogen bonds link the dimers into chains along [010].
CCDC reference: 1846182
Structure description
2-Aminopyrimidine pharmacophores have shown a broad spectrum of biological activities including use against Parkinson's disease (Robinson et al., 2016) and displaying anti-bacterial (Nagarajan et al., 2014), anti-platelet (Giridhar et al., 2012), antidiabetic (Singh et al., 2011) and antitumor properties (Lee et al., 2011). The title 2-aminopyrimidine compound was synthesized in a continuation of our research program to expand the use of novel synthetic (Lee et al. 2016), and its was determined and is reported here.
The molecular structure of the title compound is shown in Fig. 1. The central 2-aminopyrimidine ring contains two benzene rings at the C4 and C6 positions respectively. The dihedral angles between central 2-aminopyrimidine ring and the C5–C10 and C12–C17 benzene rings are 17.31 (9) and 44.39 (6)°, respectively. All three methoxy groups on the benzene rings are slightly twisted from the ring plane [C17—C16—O3—C19 = −4.9 (2), C15—C14—O2—C18 = −4.5 (2) and C7—C6—O1—C11 = 3.7 (2)°].
In the crystal, pairs of N3—H3B⋯N2 hydrogen bonds form inversion dimers that enclose R22(8) rings. These dimers are linked into chains along the b-axis direction by pairs of N3—H3A⋯O3 hydrogen bonds (Table 1, Fig. 2).
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Some examples of other 2-aminopyrimidine structures have also been published recently (Sangeetha et al., 2016; Thanigaimani et al., 2012).
Synthesis and crystallization
A synthetic scheme is shown in Fig. 3. The chalcone (E)-1-(3,5-dimethoxyphenyl)-3-(2-methoxyphenyl)prop-2-en-1-one was prepared as a starting material by a previously reported method (Koh et al. 2016). 2-Amino pyrimidine was obtained by a reaction of this chalcone with guanidine hydrogen chloride in basic solution. To an ethanol solution of 3,5-dimethoxyacetophenone (I) and 2-methoxybenzaldehyde (II) an excess amount of 50% aqueous KOH was added and the mixture was stirred at room temperature for 20 h. After completion of reaction, the reaction mixture was poured into 6M HCl in an ice-bath to give a precipitate of the chalcone (III). The solid was filtered and washed with ethanol and was used for the next reaction without further purification. The chalcone (III, 1 eq.) and the guanidine HCl salt (1.5 eq.) were dissolved in a DMF solution to which was added solid K2CO3 (3 eq.). The reaction mixture was refluxed for 2 h and cooled to room temperature. The reaction mixture was then poured into 3M HCl in an ice bath to give a precipitate of the title 2-aminopyrimidine compound, which was purified by recrystallization from ethanol.
Refinement
Crystal data, data collection and structure .
details are summarized in Table 2Structural data
CCDC reference: 1846182
https://doi.org/10.1107/S2414314618007964/sj4180sup1.cif
contains datablock I. DOI:Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2414314618007964/sj4180Isup2.hkl
Supporting information file. DOI: https://doi.org/10.1107/S2414314618007964/sj4180Isup3.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: SHELXTL (Sheldrick, 2008) and publCIF (Westrip, 2010).C19H19N3O3 | Z = 2 |
Mr = 337.37 | F(000) = 356 |
Triclinic, P1 | Dx = 1.389 Mg m−3 |
a = 7.5867 (7) Å | Mo Kα radiation, λ = 0.71073 Å |
b = 10.2680 (7) Å | Cell parameters from 5933 reflections |
c = 11.4684 (8) Å | θ = 2.6–27.9° |
α = 95.592 (4)° | µ = 0.10 mm−1 |
β = 102.147 (4)° | T = 223 K |
γ = 109.987 (3)° | Block, yellow |
V = 806.71 (11) Å3 | 0.18 × 0.10 × 0.06 mm |
Bruker PHOTON 100 CMOS diffractometer | 2736 reflections with I > 2σ(I) |
φ and ω scans | Rint = 0.063 |
Absorption correction: multi-scan (SADABS; Bruker, 2012) | θmax = 28.5°, θmin = 2.9° |
Tmin = 0.690, Tmax = 0.746 | h = −10→10 |
26671 measured reflections | k = −13→13 |
4065 independent reflections | l = −15→15 |
Refinement on F2 | 0 restraints |
Least-squares matrix: full | Hydrogen site location: inferred from neighbouring sites |
R[F2 > 2σ(F2)] = 0.046 | H-atom parameters constrained |
wR(F2) = 0.112 | w = 1/[σ2(Fo2) + (0.0434P)2 + 0.2728P] where P = (Fo2 + 2Fc2)/3 |
S = 1.02 | (Δ/σ)max < 0.001 |
4065 reflections | Δρmax = 0.24 e Å−3 |
229 parameters | Δρmin = −0.21 e Å−3 |
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 | 1.2100 (2) | 0.51141 (15) | 0.91277 (13) | 0.0264 (3) | |
N1 | 1.04986 (18) | 0.52945 (13) | 0.85350 (11) | 0.0277 (3) | |
C2 | 0.9093 (2) | 0.41773 (15) | 0.77721 (13) | 0.0240 (3) | |
C3 | 0.9345 (2) | 0.29009 (16) | 0.75753 (14) | 0.0266 (3) | |
H3 | 0.8409 | 0.2128 | 0.7001 | 0.032* | |
C4 | 1.1029 (2) | 0.28096 (15) | 0.82566 (13) | 0.0251 (3) | |
N2 | 1.24219 (18) | 0.38985 (13) | 0.90484 (11) | 0.0277 (3) | |
N3 | 1.3510 (2) | 0.62546 (13) | 0.98728 (12) | 0.0346 (3) | |
H3A | 1.3357 | 0.7058 | 0.9951 | 0.052* | |
H3B | 1.4575 | 0.6189 | 1.0276 | 0.052* | |
C5 | 0.7267 (2) | 0.44012 (15) | 0.72488 (13) | 0.0250 (3) | |
C6 | 0.5714 (2) | 0.34812 (16) | 0.62920 (14) | 0.0282 (3) | |
C7 | 0.4022 (2) | 0.37506 (19) | 0.59430 (17) | 0.0387 (4) | |
H7 | 0.2980 | 0.3120 | 0.5314 | 0.046* | |
C8 | 0.3857 (3) | 0.49308 (19) | 0.65090 (18) | 0.0425 (4) | |
H8 | 0.2704 | 0.5100 | 0.6267 | 0.051* | |
C9 | 0.5371 (3) | 0.58643 (18) | 0.74266 (17) | 0.0382 (4) | |
H9 | 0.5269 | 0.6681 | 0.7803 | 0.046* | |
C10 | 0.7041 (2) | 0.55922 (17) | 0.77906 (15) | 0.0311 (4) | |
H10 | 0.8063 | 0.6230 | 0.8426 | 0.037* | |
O1 | 0.59265 (17) | 0.23350 (12) | 0.57163 (11) | 0.0385 (3) | |
C11 | 0.4395 (3) | 0.14655 (19) | 0.46928 (17) | 0.0456 (5) | |
H11A | 0.3258 | 0.0969 | 0.4961 | 0.068* | |
H11B | 0.4809 | 0.0788 | 0.4292 | 0.068* | |
H11C | 0.4079 | 0.2049 | 0.4130 | 0.068* | |
C12 | 1.1292 (2) | 0.14340 (15) | 0.81773 (14) | 0.0253 (3) | |
C13 | 1.0781 (2) | 0.05546 (16) | 0.70723 (14) | 0.0269 (3) | |
H13 | 1.0340 | 0.0843 | 0.6351 | 0.032* | |
C14 | 1.0924 (2) | −0.07653 (16) | 0.70354 (14) | 0.0259 (3) | |
C15 | 1.1509 (2) | −0.12181 (16) | 0.80938 (14) | 0.0268 (3) | |
H15 | 1.1533 | −0.2130 | 0.8067 | 0.032* | |
C16 | 1.2062 (2) | −0.03059 (15) | 0.91990 (13) | 0.0260 (3) | |
C17 | 1.1975 (2) | 0.10205 (15) | 0.92550 (14) | 0.0259 (3) | |
H17 | 1.2368 | 0.1635 | 1.0004 | 0.031* | |
O2 | 1.04676 (17) | −0.15512 (12) | 0.59013 (10) | 0.0349 (3) | |
C18 | 1.0753 (3) | −0.28546 (17) | 0.58342 (16) | 0.0358 (4) | |
H18A | 1.2073 | −0.2692 | 0.6273 | 0.054* | |
H18B | 1.0534 | −0.3259 | 0.4991 | 0.054* | |
H18C | 0.9848 | −0.3500 | 0.6193 | 0.054* | |
O3 | 1.26833 (17) | −0.08393 (11) | 1.01866 (10) | 0.0348 (3) | |
C19 | 1.3421 (2) | 0.00789 (18) | 1.13319 (14) | 0.0347 (4) | |
H19A | 1.4454 | 0.0932 | 1.1287 | 0.052* | |
H19B | 1.3926 | −0.0386 | 1.1942 | 0.052* | |
H19C | 1.2386 | 0.0318 | 1.1549 | 0.052* |
U11 | U22 | U33 | U12 | U13 | U23 | |
C1 | 0.0294 (8) | 0.0204 (8) | 0.0277 (8) | 0.0096 (6) | 0.0031 (6) | 0.0041 (6) |
N1 | 0.0291 (7) | 0.0207 (7) | 0.0298 (7) | 0.0095 (5) | 0.0008 (5) | 0.0032 (5) |
C2 | 0.0261 (8) | 0.0215 (7) | 0.0248 (7) | 0.0094 (6) | 0.0052 (6) | 0.0062 (6) |
C3 | 0.0278 (8) | 0.0191 (7) | 0.0279 (8) | 0.0082 (6) | −0.0010 (6) | 0.0012 (6) |
C4 | 0.0281 (8) | 0.0193 (7) | 0.0263 (8) | 0.0091 (6) | 0.0031 (6) | 0.0044 (6) |
N2 | 0.0287 (7) | 0.0199 (6) | 0.0308 (7) | 0.0098 (5) | −0.0007 (5) | 0.0034 (5) |
N3 | 0.0339 (8) | 0.0200 (7) | 0.0398 (8) | 0.0102 (6) | −0.0078 (6) | −0.0023 (6) |
C5 | 0.0266 (8) | 0.0226 (8) | 0.0273 (8) | 0.0102 (6) | 0.0069 (6) | 0.0081 (6) |
C6 | 0.0277 (8) | 0.0245 (8) | 0.0325 (8) | 0.0116 (6) | 0.0051 (7) | 0.0044 (7) |
C7 | 0.0282 (9) | 0.0333 (9) | 0.0487 (11) | 0.0128 (7) | −0.0018 (8) | 0.0019 (8) |
C8 | 0.0303 (9) | 0.0382 (10) | 0.0622 (12) | 0.0209 (8) | 0.0055 (8) | 0.0074 (9) |
C9 | 0.0394 (10) | 0.0306 (9) | 0.0494 (11) | 0.0201 (8) | 0.0113 (8) | 0.0036 (8) |
C10 | 0.0333 (9) | 0.0261 (8) | 0.0336 (9) | 0.0129 (7) | 0.0058 (7) | 0.0043 (7) |
O1 | 0.0339 (7) | 0.0347 (7) | 0.0396 (7) | 0.0182 (5) | −0.0071 (5) | −0.0095 (5) |
C11 | 0.0466 (11) | 0.0345 (10) | 0.0433 (10) | 0.0166 (9) | −0.0108 (9) | −0.0062 (8) |
C12 | 0.0223 (7) | 0.0183 (7) | 0.0320 (8) | 0.0073 (6) | 0.0007 (6) | 0.0039 (6) |
C13 | 0.0273 (8) | 0.0232 (8) | 0.0279 (8) | 0.0102 (6) | 0.0001 (6) | 0.0061 (6) |
C14 | 0.0236 (8) | 0.0228 (8) | 0.0276 (8) | 0.0089 (6) | 0.0006 (6) | 0.0003 (6) |
C15 | 0.0264 (8) | 0.0189 (7) | 0.0334 (8) | 0.0103 (6) | 0.0022 (6) | 0.0032 (6) |
C16 | 0.0248 (8) | 0.0226 (8) | 0.0289 (8) | 0.0092 (6) | 0.0021 (6) | 0.0068 (6) |
C17 | 0.0242 (7) | 0.0215 (8) | 0.0274 (8) | 0.0078 (6) | −0.0002 (6) | 0.0010 (6) |
O2 | 0.0477 (7) | 0.0272 (6) | 0.0286 (6) | 0.0197 (5) | 0.0010 (5) | −0.0009 (5) |
C18 | 0.0431 (10) | 0.0292 (9) | 0.0380 (9) | 0.0204 (8) | 0.0075 (8) | −0.0001 (7) |
O3 | 0.0471 (7) | 0.0255 (6) | 0.0279 (6) | 0.0162 (5) | −0.0027 (5) | 0.0050 (5) |
C19 | 0.0373 (9) | 0.0333 (9) | 0.0275 (8) | 0.0111 (7) | 0.0001 (7) | 0.0047 (7) |
C1—N1 | 1.3428 (19) | O1—C11 | 1.427 (2) |
C1—N3 | 1.3453 (19) | C11—H11A | 0.9700 |
C1—N2 | 1.3497 (19) | C11—H11B | 0.9700 |
N1—C2 | 1.3395 (19) | C11—H11C | 0.9700 |
C2—C3 | 1.392 (2) | C12—C13 | 1.379 (2) |
C2—C5 | 1.492 (2) | C12—C17 | 1.400 (2) |
C3—C4 | 1.388 (2) | C13—C14 | 1.394 (2) |
C3—H3 | 0.9400 | C13—H13 | 0.9400 |
C4—N2 | 1.3349 (19) | C14—O2 | 1.3702 (18) |
C4—C12 | 1.489 (2) | C14—C15 | 1.382 (2) |
N3—H3A | 0.8700 | C15—C16 | 1.391 (2) |
N3—H3B | 0.8700 | C15—H15 | 0.9400 |
C5—C10 | 1.397 (2) | C16—O3 | 1.3704 (17) |
C5—C6 | 1.406 (2) | C16—C17 | 1.382 (2) |
C6—O1 | 1.3675 (19) | C17—H17 | 0.9400 |
C6—C7 | 1.390 (2) | O2—C18 | 1.4246 (18) |
C7—C8 | 1.375 (2) | C18—H18A | 0.9700 |
C7—H7 | 0.9400 | C18—H18B | 0.9700 |
C8—C9 | 1.374 (3) | C18—H18C | 0.9700 |
C8—H8 | 0.9400 | O3—C19 | 1.4199 (19) |
C9—C10 | 1.378 (2) | C19—H19A | 0.9700 |
C9—H9 | 0.9400 | C19—H19B | 0.9700 |
C10—H10 | 0.9400 | C19—H19C | 0.9700 |
N1—C1—N3 | 116.69 (13) | O1—C11—H11B | 109.5 |
N1—C1—N2 | 126.16 (14) | H11A—C11—H11B | 109.5 |
N3—C1—N2 | 117.15 (13) | O1—C11—H11C | 109.5 |
C2—N1—C1 | 117.58 (13) | H11A—C11—H11C | 109.5 |
N1—C2—C3 | 120.33 (13) | H11B—C11—H11C | 109.5 |
N1—C2—C5 | 114.92 (13) | C13—C12—C17 | 120.67 (14) |
C3—C2—C5 | 124.63 (14) | C13—C12—C4 | 120.77 (13) |
C4—C3—C2 | 117.65 (14) | C17—C12—C4 | 118.48 (14) |
C4—C3—H3 | 121.2 | C12—C13—C14 | 119.40 (14) |
C2—C3—H3 | 121.2 | C12—C13—H13 | 120.3 |
N2—C4—C3 | 122.85 (14) | C14—C13—H13 | 120.3 |
N2—C4—C12 | 116.92 (13) | O2—C14—C15 | 123.43 (13) |
C3—C4—C12 | 120.12 (13) | O2—C14—C13 | 115.83 (13) |
C4—N2—C1 | 115.26 (13) | C15—C14—C13 | 120.73 (14) |
C1—N3—H3A | 120.0 | C14—C15—C16 | 119.08 (14) |
C1—N3—H3B | 120.0 | C14—C15—H15 | 120.5 |
H3A—N3—H3B | 120.0 | C16—C15—H15 | 120.5 |
C10—C5—C6 | 117.11 (14) | O3—C16—C17 | 124.54 (14) |
C10—C5—C2 | 117.29 (14) | O3—C16—C15 | 114.35 (13) |
C6—C5—C2 | 125.53 (14) | C17—C16—C15 | 121.11 (13) |
O1—C6—C7 | 121.48 (14) | C16—C17—C12 | 118.91 (14) |
O1—C6—C5 | 118.28 (13) | C16—C17—H17 | 120.5 |
C7—C6—C5 | 120.23 (15) | C12—C17—H17 | 120.5 |
C8—C7—C6 | 120.64 (16) | C14—O2—C18 | 116.94 (12) |
C8—C7—H7 | 119.7 | O2—C18—H18A | 109.5 |
C6—C7—H7 | 119.7 | O2—C18—H18B | 109.5 |
C9—C8—C7 | 120.26 (16) | H18A—C18—H18B | 109.5 |
C9—C8—H8 | 119.9 | O2—C18—H18C | 109.5 |
C7—C8—H8 | 119.9 | H18A—C18—H18C | 109.5 |
C8—C9—C10 | 119.40 (16) | H18B—C18—H18C | 109.5 |
C8—C9—H9 | 120.3 | C16—O3—C19 | 117.23 (12) |
C10—C9—H9 | 120.3 | O3—C19—H19A | 109.5 |
C9—C10—C5 | 122.32 (16) | O3—C19—H19B | 109.5 |
C9—C10—H10 | 118.8 | H19A—C19—H19B | 109.5 |
C5—C10—H10 | 118.8 | O3—C19—H19C | 109.5 |
C6—O1—C11 | 117.68 (13) | H19A—C19—H19C | 109.5 |
O1—C11—H11A | 109.5 | H19B—C19—H19C | 109.5 |
N3—C1—N1—C2 | 178.82 (14) | C6—C5—C10—C9 | 0.8 (2) |
N2—C1—N1—C2 | −1.4 (2) | C2—C5—C10—C9 | −176.38 (15) |
C1—N1—C2—C3 | −2.6 (2) | C7—C6—O1—C11 | 3.7 (2) |
C1—N1—C2—C5 | 173.46 (13) | C5—C6—O1—C11 | −175.69 (15) |
N1—C2—C3—C4 | 4.4 (2) | N2—C4—C12—C13 | −140.95 (15) |
C5—C2—C3—C4 | −171.27 (14) | C3—C4—C12—C13 | 42.5 (2) |
C2—C3—C4—N2 | −2.4 (2) | N2—C4—C12—C17 | 42.3 (2) |
C2—C3—C4—C12 | 173.89 (14) | C3—C4—C12—C17 | −134.23 (16) |
C3—C4—N2—C1 | −1.2 (2) | C17—C12—C13—C14 | 0.9 (2) |
C12—C4—N2—C1 | −177.64 (13) | C4—C12—C13—C14 | −175.80 (14) |
N1—C1—N2—C4 | 3.3 (2) | C12—C13—C14—O2 | −177.38 (13) |
N3—C1—N2—C4 | −176.92 (14) | C12—C13—C14—C15 | 2.2 (2) |
N1—C2—C5—C10 | −13.77 (19) | O2—C14—C15—C16 | 175.90 (14) |
C3—C2—C5—C10 | 162.12 (14) | C13—C14—C15—C16 | −3.6 (2) |
N1—C2—C5—C6 | 169.36 (14) | C14—C15—C16—O3 | −177.70 (14) |
C3—C2—C5—C6 | −14.8 (2) | C14—C15—C16—C17 | 2.1 (2) |
C10—C5—C6—O1 | 177.62 (14) | O3—C16—C17—C12 | −179.36 (14) |
C2—C5—C6—O1 | −5.5 (2) | C15—C16—C17—C12 | 0.9 (2) |
C10—C5—C6—C7 | −1.8 (2) | C13—C12—C17—C16 | −2.4 (2) |
C2—C5—C6—C7 | 175.08 (15) | C4—C12—C17—C16 | 174.36 (14) |
O1—C6—C7—C8 | −178.07 (16) | C15—C14—O2—C18 | −4.5 (2) |
C5—C6—C7—C8 | 1.3 (3) | C13—C14—O2—C18 | 175.04 (14) |
C6—C7—C8—C9 | 0.3 (3) | C17—C16—O3—C19 | −4.9 (2) |
C7—C8—C9—C10 | −1.3 (3) | C15—C16—O3—C19 | 174.89 (13) |
C8—C9—C10—C5 | 0.8 (3) |
D—H···A | D—H | H···A | D···A | D—H···A |
N3—H3B···N2i | 0.87 | 2.28 | 3.1374 (19) | 167 |
N3—H3A···O3ii | 0.87 | 2.39 | 3.2545 (17) | 175 |
Symmetry codes: (i) −x+3, −y+1, −z+2; (ii) x, y+1, z. |
Funding information
The authors acknowledge financial support from the Basic Science Research Program (award No. NRF– 2016R1D1A1B03931623).
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