organic compounds
2-(4-Hydroxyphenyl)-4,6-dimethyl-2,3-dihydropyrimidin-1-ium acetate
aDepartment of Chemistry, Shree Devi Institute of Technology, Kenjar, Mangalore, Karnataka 574 142, India, bDepartment of Chemistry, Sri Dharmasthala Manjunatheshwara Institute of, Technology, Ujire, Karnataka 574 240, India, cDepartment of Chemistry, Tulane University, New Orleans, LA 70118, USA, and dLaboratory of Medicinal Chemistry, Faculty of Medicine and Pharmacy, Research Center for Medicinal Sciences Mohammed V University, Rabat, Morocco
*Correspondence e-mail: y.ramli@um5s.net.ma
In the title compound, C12H15N2O+·C2H3O2−, the phenoxy group is nearly perpendicular [80.73 (11)°] to the dihydropyrimidinium ring. In the crystal, O—H⋯O, N—H⋯O and C—H⋯O hydrogen bonds form corrugated layers parallel to the ac plane.
Keywords: crystal structure; hydrogen bond; dihydropyrimidinium.
CCDC reference: 1857057
Structure description
Pyrimidine and its derivatives are bioactive molecules and play an important role in several biological processes (Selvam et al., 2012). These derivatives have also been used in coordination chemistry and in corrosion inhibitors (Ansari et al., 2015). Several methods have been proposed for the synthesis of pyrimidine derivatives (Gore & Rajput, 2013). The crystal structures of several pyrimidine derivatives have been reported (Fun et al., 2012). In view of the importance of pyrimidine derivatives, a new pyrimidine derivative is synthesized and the has been determined (Fig. 1).
The dihydropyrimidinium ring adopts an Q = 0.419 (2) Å, θ = 108.3 (3)° and φ = 237.7 (3)°. The phenoxy ring is nearly perpendicular to the dihydropyrimidinium ring, as indicated by the dihedral angle of 80.73 (11)° between the mean planes of the two rings. In the crystal, O1—H1B⋯O3, N1—H1⋯O2, N2—H2⋯O3 and C1—H1A⋯O1 hydrogen bonds (Table 1) link the molecules into corrugated layers parallel to the ac plane with one of the methyl groups on the dihydropyrimidinium ring protruding from each surface of the layer (Figs. 2 and 3).
with puckering parametersSynthesis and crystallization
A mixture of 4-hydroxy benzaldehyde (0.01 mol), acetyl acetone (0.01 mol) and ammonium acetate (5 g) was refluxed for 8 h in 30 ml of acetic acid. The reaction mixture was cooled to room temperature and the solid product obtained was filtered and recrystallized from ethanol. Single crystals were grown from ethanol by the slow evaporation method (yield 67%, m.p. 529 K).
Refinement
Crystal data, data collection and structure .
details are summarized in Table 2Structural data
CCDC reference: 1857057
https://doi.org/10.1107/S2414314618010465/vm4037sup1.cif
contains datablocks global, I. DOI:Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2414314618010465/vm4037Isup2.hkl
Supporting information file. DOI: https://doi.org/10.1107/S2414314618010465/vm4037Isup3.cml
Data collection: APEX3 (Bruker, 2016); cell
SAINT (Bruker, 2016); data reduction: SAINT (Bruker, 2016); program(s) used to solve structure: SHELXT (Sheldrick, 2015a); program(s) used to refine structure: SHELXL2018 (Sheldrick, 2015b); molecular graphics: Mercury (Macrae et al., 2008); software used to prepare material for publication: SHELXTL (Sheldrick, 2008).C12H15N2O+·C2H3O2− | Dx = 1.242 Mg m−3 |
Mr = 262.30 | Cu Kα radiation, λ = 1.54178 Å |
Orthorhombic, Pna21 | Cell parameters from 9919 reflections |
a = 12.2836 (4) Å | θ = 3.0–72.5° |
b = 14.5343 (5) Å | µ = 0.72 mm−1 |
c = 7.8596 (3) Å | T = 296 K |
V = 1403.20 (9) Å3 | Plate, amber |
Z = 4 | 0.35 × 0.24 × 0.06 mm |
F(000) = 560 |
Bruker D8 VENTURE PHOTON 100 CMOS diffractometer | 2702 independent reflections |
Radiation source: INCOATEC IµS micro-focus source | 2611 reflections with I > 2σ(I) |
Mirror monochromator | Rint = 0.042 |
ω scans | θmax = 72.4°, θmin = 4.7° |
Absorption correction: multi-scan (SADABS; Krause et al., 2015) | h = −14→15 |
Tmin = 0.79, Tmax = 0.95 | k = −17→14 |
9762 measured reflections | l = −9→9 |
Refinement on F2 | Hydrogen site location: mixed |
Least-squares matrix: full | H-atom parameters constrained |
R[F2 > 2σ(F2)] = 0.035 | w = 1/[σ2(Fo2) + (0.0477P)2 + 0.1696P] where P = (Fo2 + 2Fc2)/3 |
wR(F2) = 0.093 | (Δ/σ)max < 0.001 |
S = 1.08 | Δρmax = 0.16 e Å−3 |
2702 reflections | Δρmin = −0.15 e Å−3 |
176 parameters | Extinction correction: SHELXL2018 (Sheldrick, 2015b), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4 |
1 restraint | Extinction coefficient: 0.044 (3) |
Primary atom site location: structure-invariant direct methods | Absolute structure: Flack x determined using 1136 quotients [(I+)-(I-)]/[(I+)+(I-)] (Parsons et al., 2013) |
Secondary atom site location: difference Fourier map | Absolute structure parameter: 0.03 (8) |
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. |
Refinement. Refinement of F2 against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F2, conventional R-factors R are based on F, with F set to zero for negative F2. The threshold expression of F2 > 2sigma(F2) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F2 are statistically about twice as large as those based on F, and R- factors based on ALL data will be even larger. H-atoms attached to carbon were placed in calculated positions (C—H = 0.95 - 1.00 Å) while those attached to nitrogen and oxygen were placed in locations derived from a difference map and their coordinates adjusted to give N—H = 0.91 and O—H = 0.87 %A. All were included as riding contributions with isotropic displacement parameters 1.2 - 1.5 times those of the attached atoms. H-atoms attached to carbon were placed in calculated positions while those attached to nitrogen and oxygen were placed in locations derived from a difference map and their coordinates adjusted to give N—H = 0.91 and O—H = 0.87 Å. All were included as riding contributions. |
x | y | z | Uiso*/Ueq | ||
O1 | 0.27724 (14) | 0.75133 (12) | 0.7694 (2) | 0.0546 (4) | |
H1B | 0.217782 | 0.722953 | 0.798867 | 0.082* | |
N1 | 0.36392 (14) | 0.57083 (11) | 0.0439 (2) | 0.0420 (4) | |
H1 | 0.298478 | 0.563493 | −0.008622 | 0.050* | |
N2 | 0.51651 (14) | 0.66729 (12) | 0.0645 (2) | 0.0420 (4) | |
H2 | 0.545084 | 0.721104 | 0.025708 | 0.050* | |
C1 | 0.39948 (16) | 0.66268 (13) | 0.0918 (3) | 0.0390 (4) | |
H1A | 0.364086 | 0.707373 | 0.016533 | 0.047* | |
C2 | 0.42312 (18) | 0.49979 (14) | 0.0923 (3) | 0.0433 (5) | |
C3 | 0.52904 (18) | 0.51327 (15) | 0.1474 (3) | 0.0462 (5) | |
H3 | 0.565920 | 0.467961 | 0.207922 | 0.055* | |
C4 | 0.57816 (17) | 0.59665 (16) | 0.1094 (3) | 0.0434 (5) | |
C5 | 0.3741 (2) | 0.40638 (17) | 0.0759 (4) | 0.0654 (7) | |
H5A | 0.300785 | 0.411806 | 0.034710 | 0.098* | |
H5B | 0.373633 | 0.376778 | 0.185129 | 0.098* | |
H5C | 0.416204 | 0.370418 | −0.002539 | 0.098* | |
C6 | 0.69929 (19) | 0.6085 (2) | 0.1048 (4) | 0.0627 (7) | |
H6A | 0.723330 | 0.611386 | −0.011310 | 0.094* | |
H6B | 0.733401 | 0.557281 | 0.160521 | 0.094* | |
H6C | 0.718748 | 0.664425 | 0.162220 | 0.094* | |
C7 | 0.36783 (16) | 0.68454 (13) | 0.2754 (3) | 0.0378 (4) | |
C8 | 0.42471 (19) | 0.74749 (17) | 0.3707 (3) | 0.0520 (5) | |
H8 | 0.485363 | 0.776132 | 0.323659 | 0.062* | |
C9 | 0.3937 (2) | 0.76929 (18) | 0.5356 (3) | 0.0594 (7) | |
H9 | 0.433786 | 0.811862 | 0.597828 | 0.071* | |
C10 | 0.30388 (18) | 0.72830 (14) | 0.6075 (3) | 0.0428 (5) | |
C11 | 0.2443 (2) | 0.66604 (16) | 0.5124 (3) | 0.0523 (6) | |
H11 | 0.182600 | 0.638735 | 0.558644 | 0.063* | |
C12 | 0.2766 (2) | 0.64423 (17) | 0.3479 (3) | 0.0519 (6) | |
H12 | 0.236315 | 0.601912 | 0.285269 | 0.062* | |
O2 | 0.33630 (14) | 0.03653 (13) | 0.4068 (4) | 0.0796 (7) | |
O3 | 0.39509 (17) | 0.17870 (13) | 0.4094 (3) | 0.0729 (6) | |
C13 | 0.4095 (2) | 0.09335 (17) | 0.4226 (3) | 0.0529 (5) | |
C14 | 0.5234 (3) | 0.0608 (3) | 0.4529 (7) | 0.0972 (13) | |
H14A | 0.573848 | 0.106519 | 0.413293 | 0.146* | |
H14B | 0.535285 | 0.004326 | 0.392359 | 0.146* | |
H14C | 0.534262 | 0.050737 | 0.572402 | 0.146* |
U11 | U22 | U33 | U12 | U13 | U23 | |
O1 | 0.0600 (10) | 0.0655 (10) | 0.0384 (8) | 0.0097 (8) | 0.0013 (7) | −0.0062 (7) |
N1 | 0.0390 (9) | 0.0462 (9) | 0.0406 (9) | 0.0000 (7) | 0.0013 (7) | −0.0045 (7) |
N2 | 0.0417 (9) | 0.0411 (8) | 0.0432 (9) | −0.0018 (7) | 0.0082 (8) | 0.0061 (7) |
C1 | 0.0404 (10) | 0.0396 (9) | 0.0370 (9) | 0.0037 (8) | 0.0009 (8) | 0.0027 (8) |
C2 | 0.0484 (11) | 0.0427 (10) | 0.0387 (10) | −0.0018 (9) | 0.0100 (9) | −0.0010 (8) |
C3 | 0.0478 (12) | 0.0442 (11) | 0.0467 (11) | 0.0080 (9) | 0.0029 (9) | 0.0104 (9) |
C4 | 0.0389 (10) | 0.0543 (11) | 0.0371 (9) | 0.0017 (9) | 0.0046 (9) | 0.0048 (8) |
C5 | 0.0803 (18) | 0.0455 (12) | 0.0705 (17) | −0.0120 (12) | 0.0148 (15) | −0.0064 (12) |
C6 | 0.0378 (11) | 0.0830 (17) | 0.0674 (15) | 0.0003 (11) | 0.0060 (11) | 0.0124 (14) |
C7 | 0.0367 (9) | 0.0366 (8) | 0.0401 (10) | 0.0066 (7) | 0.0015 (8) | 0.0008 (8) |
C8 | 0.0480 (12) | 0.0565 (12) | 0.0514 (12) | −0.0106 (10) | 0.0064 (10) | −0.0084 (11) |
C9 | 0.0567 (14) | 0.0671 (15) | 0.0545 (14) | −0.0102 (12) | 0.0038 (11) | −0.0207 (12) |
C10 | 0.0481 (11) | 0.0443 (10) | 0.0362 (10) | 0.0132 (9) | −0.0017 (9) | −0.0005 (8) |
C11 | 0.0503 (12) | 0.0588 (12) | 0.0478 (13) | −0.0075 (10) | 0.0104 (10) | −0.0066 (10) |
C12 | 0.0515 (13) | 0.0561 (13) | 0.0480 (12) | −0.0117 (11) | 0.0078 (10) | −0.0114 (10) |
O2 | 0.0478 (10) | 0.0576 (11) | 0.133 (2) | −0.0061 (8) | 0.0135 (12) | −0.0193 (12) |
O3 | 0.0754 (12) | 0.0562 (10) | 0.0873 (15) | −0.0097 (9) | −0.0357 (11) | −0.0046 (9) |
C13 | 0.0454 (12) | 0.0571 (13) | 0.0562 (13) | −0.0040 (10) | −0.0018 (11) | −0.0058 (11) |
C14 | 0.0515 (16) | 0.111 (3) | 0.129 (4) | 0.0017 (16) | −0.0141 (19) | 0.022 (3) |
O1—C10 | 1.356 (3) | C6—H6B | 0.9600 |
O1—H1B | 0.8700 | C6—H6C | 0.9600 |
N1—C2 | 1.319 (3) | C7—C8 | 1.373 (3) |
N1—C1 | 1.454 (3) | C7—C12 | 1.387 (3) |
N1—H1 | 0.9099 | C8—C9 | 1.388 (3) |
N2—C4 | 1.324 (3) | C8—H8 | 0.9300 |
N2—C1 | 1.455 (3) | C9—C10 | 1.375 (3) |
N2—H2 | 0.9100 | C9—H9 | 0.9300 |
C1—C7 | 1.528 (3) | C10—C11 | 1.383 (3) |
C1—H1A | 0.9800 | C11—C12 | 1.389 (3) |
C2—C3 | 1.385 (3) | C11—H11 | 0.9300 |
C2—C5 | 1.491 (3) | C12—H12 | 0.9300 |
C3—C4 | 1.386 (3) | O2—C13 | 1.227 (3) |
C3—H3 | 0.9300 | O3—C13 | 1.257 (3) |
C4—C6 | 1.498 (3) | C13—C14 | 1.497 (4) |
C5—H5A | 0.9600 | C14—H14A | 0.9600 |
C5—H5B | 0.9600 | C14—H14B | 0.9600 |
C5—H5C | 0.9600 | C14—H14C | 0.9600 |
C6—H6A | 0.9600 | ||
C10—O1—H1B | 109.6 | C4—C6—H6C | 109.5 |
C2—N1—C1 | 118.59 (18) | H6A—C6—H6C | 109.5 |
C2—N1—H1 | 121.8 | H6B—C6—H6C | 109.5 |
C1—N1—H1 | 119.4 | C8—C7—C12 | 118.0 (2) |
C4—N2—C1 | 119.38 (17) | C8—C7—C1 | 121.60 (19) |
C4—N2—H2 | 122.4 | C12—C7—C1 | 120.37 (19) |
C1—N2—H2 | 118.0 | C7—C8—C9 | 121.4 (2) |
N1—C1—N2 | 107.52 (16) | C7—C8—H8 | 119.3 |
N1—C1—C7 | 111.02 (16) | C9—C8—H8 | 119.3 |
N2—C1—C7 | 112.37 (17) | C10—C9—C8 | 120.4 (2) |
N1—C1—H1A | 108.6 | C10—C9—H9 | 119.8 |
N2—C1—H1A | 108.6 | C8—C9—H9 | 119.8 |
C7—C1—H1A | 108.6 | O1—C10—C9 | 118.2 (2) |
N1—C2—C3 | 119.82 (19) | O1—C10—C11 | 122.8 (2) |
N1—C2—C5 | 117.7 (2) | C9—C10—C11 | 119.0 (2) |
C3—C2—C5 | 122.4 (2) | C10—C11—C12 | 120.1 (2) |
C2—C3—C4 | 117.71 (19) | C10—C11—H11 | 119.9 |
C2—C3—H3 | 121.1 | C12—C11—H11 | 119.9 |
C4—C3—H3 | 121.1 | C7—C12—C11 | 121.1 (2) |
N2—C4—C3 | 119.11 (19) | C7—C12—H12 | 119.5 |
N2—C4—C6 | 118.2 (2) | C11—C12—H12 | 119.5 |
C3—C4—C6 | 122.5 (2) | O2—C13—O3 | 123.6 (2) |
C2—C5—H5A | 109.5 | O2—C13—C14 | 119.3 (3) |
C2—C5—H5B | 109.5 | O3—C13—C14 | 117.1 (2) |
H5A—C5—H5B | 109.5 | C13—C14—H14A | 109.5 |
C2—C5—H5C | 109.5 | C13—C14—H14B | 109.5 |
H5A—C5—H5C | 109.5 | H14A—C14—H14B | 109.5 |
H5B—C5—H5C | 109.5 | C13—C14—H14C | 109.5 |
C4—C6—H6A | 109.5 | H14A—C14—H14C | 109.5 |
C4—C6—H6B | 109.5 | H14B—C14—H14C | 109.5 |
H6A—C6—H6B | 109.5 | ||
C2—N1—C1—N2 | 43.2 (2) | N2—C1—C7—C8 | 34.0 (3) |
C2—N1—C1—C7 | −80.1 (2) | N1—C1—C7—C12 | −28.8 (3) |
C4—N2—C1—N1 | −41.8 (3) | N2—C1—C7—C12 | −149.3 (2) |
C4—N2—C1—C7 | 80.6 (2) | C12—C7—C8—C9 | 1.2 (4) |
C1—N1—C2—C3 | −16.4 (3) | C1—C7—C8—C9 | 177.9 (2) |
C1—N1—C2—C5 | 166.9 (2) | C7—C8—C9—C10 | −0.4 (4) |
N1—C2—C3—C4 | −16.2 (3) | C8—C9—C10—O1 | 179.5 (2) |
C5—C2—C3—C4 | 160.4 (2) | C8—C9—C10—C11 | −0.8 (4) |
C1—N2—C4—C3 | 13.4 (3) | O1—C10—C11—C12 | −179.1 (2) |
C1—N2—C4—C6 | −170.9 (2) | C9—C10—C11—C12 | 1.3 (4) |
C2—C3—C4—N2 | 17.7 (3) | C8—C7—C12—C11 | −0.7 (4) |
C2—C3—C4—C6 | −157.9 (2) | C1—C7—C12—C11 | −177.5 (2) |
N1—C1—C7—C8 | 154.5 (2) | C10—C11—C12—C7 | −0.5 (4) |
D—H···A | D—H | H···A | D···A | D—H···A |
O1—H1B···O3i | 0.87 | 1.76 | 2.609 (3) | 165 |
N1—H1···O2ii | 0.91 | 1.83 | 2.731 (3) | 172 |
N2—H2···O3iii | 0.91 | 1.87 | 2.771 (2) | 170 |
C1—H1A···O1iv | 0.98 | 2.31 | 3.214 (3) | 154 |
Symmetry codes: (i) −x+1/2, y+1/2, z+1/2; (ii) −x+1/2, y+1/2, z−1/2; (iii) −x+1, −y+1, z−1/2; (iv) x, y, z−1. |
Funding information
The support of NSF–MRI grant No. 1228232 for the purchase of the diffractometer and Tulane University for support of the Tulane Crystallography Laboratory are gratefully acknowledged. KR is grateful to the Directorate of Minorities, Government of Karnataka, for providing a research fellowship.
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