organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

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ISSN: 2414-3146

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

Edited by J. Simpson, University of Otago, New Zealand (Received 25 May 2018; accepted 30 May 2018; online 5 June 2018)

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].

3D view (loading...)
[Scheme 3D1]
Chemical scheme
[Scheme 1]

Structure description

2-Amino­pyrimidine pharmacophores have shown a broad spectrum of biological activities including use against Parkinson's disease (Robinson et al., 2016[Robinson, S. J., Petzer, J. P., Rousseau, A. L., Terre'Blanche, G., Petzer, A. & Lourens, A. C. U. (2016). Bioorg. Med. Chem. Lett. 26, 734-738.]) and displaying anti-bacterial (Nagarajan et al., 2014[Nagarajan, S., Shanmugavelan, P., Sathishkumar, M., Selvi, R., Ponnuswamy, A., Harikrishnan, H., Shanmugaiah, V. & Murugavel, S. (2014). Bioorg. Med. Chem. Lett. 24, 4999-5007.]), anti-platelet (Giridhar et al., 2012[Giridhar, R., Tamboli, R. S., Ramajayam, R., Prajapati, D. G. & Yadav, M. R. (2012). Eur. J. Med. Chem. 50, 428-432.]), anti­diabetic (Singh et al., 2011[Singh, N., Pandey, S. K., Anand, N., Dwivedi, R., Singh, S., Sinha, S. K., Chaturvedi, V., Jaiswal, N., Srivastava, A. K., Shah, P., Siddiqui, M. I. & Tripathi, R. P. (2011). Bioorg. Med. Chem. Lett. 21, 4404-4408.]) and anti­tumor properties (Lee et al., 2011[Lee, J., Kim, K.-H. & Jeong, S. (2011). Bioorg. Med. Chem. Lett. 21, 4203-4205.]). The title 2-amino­pyrimidine compound was synthesized in a continuation of our research program to expand the use of novel synthetic chalcones (Lee et al. 2016[Lee, Y., Kim, B. S., Ahn, S., Koh, D., Lee, Y. H., Shin, S. Y. & Lim, Y. (2016). Bioorg. Chem. 68, 166-176.]), and its crystal structure was determined and is reported here.

The mol­ecular structure of the title compound is shown in Fig. 1[link]. 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)°].

[Figure 1]
Figure 1
The mol­ecular structure of the title compound, showing the atom-labelling scheme with displacement ellipsoids drawn at the 30% probability level.

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[link], Fig. 2[link]).

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA 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.
[Figure 2]
Figure 2
Part of the crystal structure with inter­molecular hydrogen bonds shown as dashed lines. For clarity only those H atoms involved in hydrogen bonding are shown.

Some examples of other 2-amino­pyrimidine structures have also been published recently (Sangeetha et al., 2016[Sangeetha, R., Edison, B., Thanikasalam, K., Kavitha, S. J. & Balasubramani, K. (2016). IUCrData, 1, x160794.]; Thanigaimani et al., 2012[Thanigaimani, K., Khalib, N. C., Arshad, S. & Razak, I. A. (2012). Acta Cryst. E68, o3318.]).

Synthesis and crystallization

A synthetic scheme is shown in Fig. 3[link]. 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[Koh, D., Jung, Y., Kim, B. S., Ahn, S. & Lim, Y. (2016). Magn. Reson. Chem. 54, 842-851.]). 2-Amino pyrimidine was obtained by a cyclization 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.

[Figure 3]
Figure 3
Synthetic scheme for the preparation of the title compound.

Refinement

Crystal data, data collection and structure refinement details are summarized in Table 2[link].

Table 2
Experimental details

Crystal data
Chemical formula C19H19N3O3
Mr 337.37
Crystal system, space group Triclinic, P[\overline{1}]
Temperature (K) 223
a, b, c (Å) 7.5867 (7), 10.2680 (7), 11.4684 (8)
α, β, γ (°) 95.592 (4), 102.147 (4), 109.987 (3)
V3) 806.71 (11)
Z 2
Radiation type Mo Kα
μ (mm−1) 0.10
Crystal size (mm) 0.18 × 0.10 × 0.06
 
Data collection
Diffractometer Bruker PHOTON 100 CMOS
Absorption correction Multi-scan (SADABS; Bruker, 2012[Bruker (2012). APEX2, SAINT and SADABS, Bruker AXS Inc. Madison, Wisconsin, USA.])
Tmin, Tmax 0.690, 0.746
No. of measured, independent and observed [I > 2σ(I)] reflections 26671, 4065, 2736
Rint 0.063
(sin θ/λ)max−1) 0.671
 
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.046, 0.112, 1.02
No. of reflections 4065
No. of parameters 229
H-atom treatment H-atom parameters constrained
Δρmax, Δρmin (e Å−3) 0.24, −0.21
Computer programs: APEX2 and SAINT (Bruker, 2012[Bruker (2012). APEX2, SAINT and SADABS, Bruker AXS Inc. Madison, Wisconsin, USA.]), SHELXS and SHELXTL (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]), SHELXL2014 (Sheldrick, 2015[Sheldrick, G. M. (2015). Acta Cryst. C71, 3-8.]) and publCIF (Westrip, 2010[Westrip, S. P. (2010). J. Appl. Cryst. 43, 920-925.]).

Structural data


Computing details top

Data collection: APEX2 (Bruker, 2012); cell refinement: 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).

4-(3,5-Dimethoxyphenyl)-6-(2-methoxyphenyl)pyrimidin-2-amine top
Crystal data top
C19H19N3O3Z = 2
Mr = 337.37F(000) = 356
Triclinic, P1Dx = 1.389 Mg m3
a = 7.5867 (7) ÅMo Kα radiation, λ = 0.71073 Å
b = 10.2680 (7) ÅCell parameters from 5933 reflections
c = 11.4684 (8) Åθ = 2.6–27.9°
α = 95.592 (4)°µ = 0.10 mm1
β = 102.147 (4)°T = 223 K
γ = 109.987 (3)°Block, yellow
V = 806.71 (11) Å30.18 × 0.10 × 0.06 mm
Data collection top
Bruker PHOTON 100 CMOS
diffractometer
2736 reflections with I > 2σ(I)
φ and ω scansRint = 0.063
Absorption correction: multi-scan
(SADABS; Bruker, 2012)
θmax = 28.5°, θmin = 2.9°
Tmin = 0.690, Tmax = 0.746h = 1010
26671 measured reflectionsk = 1313
4065 independent reflectionsl = 1515
Refinement top
Refinement on F20 restraints
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.046H-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 reflectionsΔρmax = 0.24 e Å3
229 parametersΔρmin = 0.21 e Å3
Special details top

Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
C11.2100 (2)0.51141 (15)0.91277 (13)0.0264 (3)
N11.04986 (18)0.52945 (13)0.85350 (11)0.0277 (3)
C20.9093 (2)0.41773 (15)0.77721 (13)0.0240 (3)
C30.9345 (2)0.29009 (16)0.75753 (14)0.0266 (3)
H30.84090.21280.70010.032*
C41.1029 (2)0.28096 (15)0.82566 (13)0.0251 (3)
N21.24219 (18)0.38985 (13)0.90484 (11)0.0277 (3)
N31.3510 (2)0.62546 (13)0.98728 (12)0.0346 (3)
H3A1.33570.70580.99510.052*
H3B1.45750.61891.02760.052*
C50.7267 (2)0.44012 (15)0.72488 (13)0.0250 (3)
C60.5714 (2)0.34812 (16)0.62920 (14)0.0282 (3)
C70.4022 (2)0.37506 (19)0.59430 (17)0.0387 (4)
H70.29800.31200.53140.046*
C80.3857 (3)0.49308 (19)0.65090 (18)0.0425 (4)
H80.27040.51000.62670.051*
C90.5371 (3)0.58643 (18)0.74266 (17)0.0382 (4)
H90.52690.66810.78030.046*
C100.7041 (2)0.55922 (17)0.77906 (15)0.0311 (4)
H100.80630.62300.84260.037*
O10.59265 (17)0.23350 (12)0.57163 (11)0.0385 (3)
C110.4395 (3)0.14655 (19)0.46928 (17)0.0456 (5)
H11A0.32580.09690.49610.068*
H11B0.48090.07880.42920.068*
H11C0.40790.20490.41300.068*
C121.1292 (2)0.14340 (15)0.81773 (14)0.0253 (3)
C131.0781 (2)0.05546 (16)0.70723 (14)0.0269 (3)
H131.03400.08430.63510.032*
C141.0924 (2)0.07653 (16)0.70354 (14)0.0259 (3)
C151.1509 (2)0.12181 (16)0.80938 (14)0.0268 (3)
H151.15330.21300.80670.032*
C161.2062 (2)0.03059 (15)0.91990 (13)0.0260 (3)
C171.1975 (2)0.10205 (15)0.92550 (14)0.0259 (3)
H171.23680.16351.00040.031*
O21.04676 (17)0.15512 (12)0.59013 (10)0.0349 (3)
C181.0753 (3)0.28546 (17)0.58342 (16)0.0358 (4)
H18A1.20730.26920.62730.054*
H18B1.05340.32590.49910.054*
H18C0.98480.35000.61930.054*
O31.26833 (17)0.08393 (11)1.01866 (10)0.0348 (3)
C191.3421 (2)0.00789 (18)1.13319 (14)0.0347 (4)
H19A1.44540.09321.12870.052*
H19B1.39260.03861.19420.052*
H19C1.23860.03181.15490.052*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
C10.0294 (8)0.0204 (8)0.0277 (8)0.0096 (6)0.0031 (6)0.0041 (6)
N10.0291 (7)0.0207 (7)0.0298 (7)0.0095 (5)0.0008 (5)0.0032 (5)
C20.0261 (8)0.0215 (7)0.0248 (7)0.0094 (6)0.0052 (6)0.0062 (6)
C30.0278 (8)0.0191 (7)0.0279 (8)0.0082 (6)0.0010 (6)0.0012 (6)
C40.0281 (8)0.0193 (7)0.0263 (8)0.0091 (6)0.0031 (6)0.0044 (6)
N20.0287 (7)0.0199 (6)0.0308 (7)0.0098 (5)0.0007 (5)0.0034 (5)
N30.0339 (8)0.0200 (7)0.0398 (8)0.0102 (6)0.0078 (6)0.0023 (6)
C50.0266 (8)0.0226 (8)0.0273 (8)0.0102 (6)0.0069 (6)0.0081 (6)
C60.0277 (8)0.0245 (8)0.0325 (8)0.0116 (6)0.0051 (7)0.0044 (7)
C70.0282 (9)0.0333 (9)0.0487 (11)0.0128 (7)0.0018 (8)0.0019 (8)
C80.0303 (9)0.0382 (10)0.0622 (12)0.0209 (8)0.0055 (8)0.0074 (9)
C90.0394 (10)0.0306 (9)0.0494 (11)0.0201 (8)0.0113 (8)0.0036 (8)
C100.0333 (9)0.0261 (8)0.0336 (9)0.0129 (7)0.0058 (7)0.0043 (7)
O10.0339 (7)0.0347 (7)0.0396 (7)0.0182 (5)0.0071 (5)0.0095 (5)
C110.0466 (11)0.0345 (10)0.0433 (10)0.0166 (9)0.0108 (9)0.0062 (8)
C120.0223 (7)0.0183 (7)0.0320 (8)0.0073 (6)0.0007 (6)0.0039 (6)
C130.0273 (8)0.0232 (8)0.0279 (8)0.0102 (6)0.0001 (6)0.0061 (6)
C140.0236 (8)0.0228 (8)0.0276 (8)0.0089 (6)0.0006 (6)0.0003 (6)
C150.0264 (8)0.0189 (7)0.0334 (8)0.0103 (6)0.0022 (6)0.0032 (6)
C160.0248 (8)0.0226 (8)0.0289 (8)0.0092 (6)0.0021 (6)0.0068 (6)
C170.0242 (7)0.0215 (8)0.0274 (8)0.0078 (6)0.0002 (6)0.0010 (6)
O20.0477 (7)0.0272 (6)0.0286 (6)0.0197 (5)0.0010 (5)0.0009 (5)
C180.0431 (10)0.0292 (9)0.0380 (9)0.0204 (8)0.0075 (8)0.0001 (7)
O30.0471 (7)0.0255 (6)0.0279 (6)0.0162 (5)0.0027 (5)0.0050 (5)
C190.0373 (9)0.0333 (9)0.0275 (8)0.0111 (7)0.0001 (7)0.0047 (7)
Geometric parameters (Å, º) top
C1—N11.3428 (19)O1—C111.427 (2)
C1—N31.3453 (19)C11—H11A0.9700
C1—N21.3497 (19)C11—H11B0.9700
N1—C21.3395 (19)C11—H11C0.9700
C2—C31.392 (2)C12—C131.379 (2)
C2—C51.492 (2)C12—C171.400 (2)
C3—C41.388 (2)C13—C141.394 (2)
C3—H30.9400C13—H130.9400
C4—N21.3349 (19)C14—O21.3702 (18)
C4—C121.489 (2)C14—C151.382 (2)
N3—H3A0.8700C15—C161.391 (2)
N3—H3B0.8700C15—H150.9400
C5—C101.397 (2)C16—O31.3704 (17)
C5—C61.406 (2)C16—C171.382 (2)
C6—O11.3675 (19)C17—H170.9400
C6—C71.390 (2)O2—C181.4246 (18)
C7—C81.375 (2)C18—H18A0.9700
C7—H70.9400C18—H18B0.9700
C8—C91.374 (3)C18—H18C0.9700
C8—H80.9400O3—C191.4199 (19)
C9—C101.378 (2)C19—H19A0.9700
C9—H90.9400C19—H19B0.9700
C10—H100.9400C19—H19C0.9700
N1—C1—N3116.69 (13)O1—C11—H11B109.5
N1—C1—N2126.16 (14)H11A—C11—H11B109.5
N3—C1—N2117.15 (13)O1—C11—H11C109.5
C2—N1—C1117.58 (13)H11A—C11—H11C109.5
N1—C2—C3120.33 (13)H11B—C11—H11C109.5
N1—C2—C5114.92 (13)C13—C12—C17120.67 (14)
C3—C2—C5124.63 (14)C13—C12—C4120.77 (13)
C4—C3—C2117.65 (14)C17—C12—C4118.48 (14)
C4—C3—H3121.2C12—C13—C14119.40 (14)
C2—C3—H3121.2C12—C13—H13120.3
N2—C4—C3122.85 (14)C14—C13—H13120.3
N2—C4—C12116.92 (13)O2—C14—C15123.43 (13)
C3—C4—C12120.12 (13)O2—C14—C13115.83 (13)
C4—N2—C1115.26 (13)C15—C14—C13120.73 (14)
C1—N3—H3A120.0C14—C15—C16119.08 (14)
C1—N3—H3B120.0C14—C15—H15120.5
H3A—N3—H3B120.0C16—C15—H15120.5
C10—C5—C6117.11 (14)O3—C16—C17124.54 (14)
C10—C5—C2117.29 (14)O3—C16—C15114.35 (13)
C6—C5—C2125.53 (14)C17—C16—C15121.11 (13)
O1—C6—C7121.48 (14)C16—C17—C12118.91 (14)
O1—C6—C5118.28 (13)C16—C17—H17120.5
C7—C6—C5120.23 (15)C12—C17—H17120.5
C8—C7—C6120.64 (16)C14—O2—C18116.94 (12)
C8—C7—H7119.7O2—C18—H18A109.5
C6—C7—H7119.7O2—C18—H18B109.5
C9—C8—C7120.26 (16)H18A—C18—H18B109.5
C9—C8—H8119.9O2—C18—H18C109.5
C7—C8—H8119.9H18A—C18—H18C109.5
C8—C9—C10119.40 (16)H18B—C18—H18C109.5
C8—C9—H9120.3C16—O3—C19117.23 (12)
C10—C9—H9120.3O3—C19—H19A109.5
C9—C10—C5122.32 (16)O3—C19—H19B109.5
C9—C10—H10118.8H19A—C19—H19B109.5
C5—C10—H10118.8O3—C19—H19C109.5
C6—O1—C11117.68 (13)H19A—C19—H19C109.5
O1—C11—H11A109.5H19B—C19—H19C109.5
N3—C1—N1—C2178.82 (14)C6—C5—C10—C90.8 (2)
N2—C1—N1—C21.4 (2)C2—C5—C10—C9176.38 (15)
C1—N1—C2—C32.6 (2)C7—C6—O1—C113.7 (2)
C1—N1—C2—C5173.46 (13)C5—C6—O1—C11175.69 (15)
N1—C2—C3—C44.4 (2)N2—C4—C12—C13140.95 (15)
C5—C2—C3—C4171.27 (14)C3—C4—C12—C1342.5 (2)
C2—C3—C4—N22.4 (2)N2—C4—C12—C1742.3 (2)
C2—C3—C4—C12173.89 (14)C3—C4—C12—C17134.23 (16)
C3—C4—N2—C11.2 (2)C17—C12—C13—C140.9 (2)
C12—C4—N2—C1177.64 (13)C4—C12—C13—C14175.80 (14)
N1—C1—N2—C43.3 (2)C12—C13—C14—O2177.38 (13)
N3—C1—N2—C4176.92 (14)C12—C13—C14—C152.2 (2)
N1—C2—C5—C1013.77 (19)O2—C14—C15—C16175.90 (14)
C3—C2—C5—C10162.12 (14)C13—C14—C15—C163.6 (2)
N1—C2—C5—C6169.36 (14)C14—C15—C16—O3177.70 (14)
C3—C2—C5—C614.8 (2)C14—C15—C16—C172.1 (2)
C10—C5—C6—O1177.62 (14)O3—C16—C17—C12179.36 (14)
C2—C5—C6—O15.5 (2)C15—C16—C17—C120.9 (2)
C10—C5—C6—C71.8 (2)C13—C12—C17—C162.4 (2)
C2—C5—C6—C7175.08 (15)C4—C12—C17—C16174.36 (14)
O1—C6—C7—C8178.07 (16)C15—C14—O2—C184.5 (2)
C5—C6—C7—C81.3 (3)C13—C14—O2—C18175.04 (14)
C6—C7—C8—C90.3 (3)C17—C16—O3—C194.9 (2)
C7—C8—C9—C101.3 (3)C15—C16—O3—C19174.89 (13)
C8—C9—C10—C50.8 (3)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N3—H3B···N2i0.872.283.1374 (19)167
N3—H3A···O3ii0.872.393.2545 (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).

References

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