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ISSN: 2414-3146

2-(4-Hy­dr­oxy­phen­yl)-4,6-di­methyl-2,3-di­hydro­pyrimidin-1-ium acetate

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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

Edited by L. Van Meervelt, Katholieke Universiteit Leuven, Belgium (Received 9 July 2018; accepted 20 July 2018; online 24 July 2018)

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.

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

Structure description

Pyrimidine and its derivatives are bioactive mol­ecules and play an important role in several biological processes (Selvam et al., 2012[Selvam, T. P., James, C. R., Dniandev, P. V. & Valzita, S. K. (2012). Res. Pharm. 2, 1-9.]). These derivatives have also been used in coordination chemistry and in corrosion inhibitors (Ansari et al., 2015[Ansari, K. R., Sudheer, Singh, A. & Quraishi, M. A. (2015). J. Dispersion Sci. Technol. 36, 908-917.]). Several methods have been proposed for the synthesis of pyrimidine derivatives (Gore & Rajput, 2013[Gore, R. P. & Rajput, A. P. (2013). Drug Invention Today, 5, 148-152.]). The crystal structures of several pyrimidine derivatives have been reported (Fun et al., 2012[Fun, H.-K., Chia, T. S., Samshuddin, S., Narayana, B. & Sarojini, B. K. (2012). Acta Cryst. E68, o807-o808.]). In view of the importance of pyrimidine derivatives, a new pyrimidine derivative is synthesized and the crystal structure has been determined (Fig. 1[link]).

[Figure 1]
Figure 1
The title mol­ecule with labeling scheme and 30% probability ellipsoids.

The di­hydro­pyrimidinium ring adopts an envelope conformation with puckering parameters 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]) 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[link] and 3[link]).

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA 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+{\script{1\over 2}}, y+{\script{1\over 2}}, z+{\script{1\over 2}}]; (ii) [-x+{\script{1\over 2}}, y+{\script{1\over 2}}, z-{\script{1\over 2}}]; (iii) [-x+1, -y+1, z-{\script{1\over 2}}]; (iv) x, y, z-1.
[Figure 2]
Figure 2
A portion of one corrugated layer viewed along the b-axis direction. O—H⋯O and N—H⋯O hydrogen bonds are shown, respectively, by red and blue dashed lines. The C—H⋯O hydrogen bonds are omitted for clarity.
[Figure 3]
Figure 3
Elevation view of two layers seen along the a-axis direction. Hydrogen bonds are depicted as in Fig. 2[link].

Synthesis 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 refinement details are summarized in Table 2[link].

Table 2
Experimental details

Crystal data
Chemical formula C12H15N2O+·C2H3O2
Mr 262.30
Crystal system, space group Orthorhombic, Pna21
Temperature (K) 296
a, b, c (Å) 12.2836 (4), 14.5343 (5), 7.8596 (3)
V3) 1403.20 (9)
Z 4
Radiation type Cu Kα
μ (mm−1) 0.72
Crystal size (mm) 0.35 × 0.24 × 0.06
 
Data collection
Diffractometer Bruker D8 VENTURE PHOTON 100 CMOS
Absorption correction Multi-scan (SADABS; Krause et al., 2015[Krause, L., Herbst-Irmer, R., Sheldrick, G. M. & Stalke, D. (2015). J. Appl. Cryst. 48, 3-10.])
Tmin, Tmax 0.79, 0.95
No. of measured, independent and observed [I > 2σ(I)] reflections 9762, 2702, 2611
Rint 0.042
(sin θ/λ)max−1) 0.618
 
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.035, 0.093, 1.08
No. of reflections 2702
No. of parameters 176
No. of restraints 1
H-atom treatment H-atom parameters constrained
Δρmax, Δρmin (e Å−3) 0.16, −0.15
Absolute structure Flack x determined using 1136 quotients [(I+)−(I)]/[(I+)+(I)] (Parsons et al., 2013[Parsons, S., Flack, H. D. & Wagner, T. (2013). Acta Cryst. B69, 249-259.])
Absolute structure parameter 0.03 (8)
Computer programs: APEX3 and SAINT (Bruker, 2016[Bruker (2016). APEX3, SADABS and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]), SHELXT (Sheldrick, 2015a[Sheldrick, G. M. (2015a). Acta Cryst. A71, 3-8.]), SHELXL2018 (Sheldrick, 2015b[Sheldrick, G. M. (2015b). Acta Cryst. C71, 3-8.]), Mercury (Macrae et al., 2008[Macrae, C. F., Bruno, I. J., Chisholm, J. A., Edgington, P. R., McCabe, P., Pidcock, E., Rodriguez-Monge, L., Taylor, R., van de Streek, J. & Wood, P. A. (2008). J. Appl. Cryst. 41, 466-470.]) and SHELXTL (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]).

Structural data


Computing details top

Data collection: APEX3 (Bruker, 2016); cell refinement: 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).

2-(4-Hydroxyphenyl)-4,6-dimethyl-2,3-dihydropyrimidin-1-ium acetate top
Crystal data top
C12H15N2O+·C2H3O2Dx = 1.242 Mg m3
Mr = 262.30Cu Kα radiation, λ = 1.54178 Å
Orthorhombic, Pna21Cell parameters from 9919 reflections
a = 12.2836 (4) Åθ = 3.0–72.5°
b = 14.5343 (5) ŵ = 0.72 mm1
c = 7.8596 (3) ÅT = 296 K
V = 1403.20 (9) Å3Plate, amber
Z = 40.35 × 0.24 × 0.06 mm
F(000) = 560
Data collection top
Bruker D8 VENTURE PHOTON 100 CMOS
diffractometer
2702 independent reflections
Radiation source: INCOATEC IµS micro-focus source2611 reflections with I > 2σ(I)
Mirror monochromatorRint = 0.042
ω scansθmax = 72.4°, θmin = 4.7°
Absorption correction: multi-scan
(SADABS; Krause et al., 2015)
h = 1415
Tmin = 0.79, Tmax = 0.95k = 1714
9762 measured reflectionsl = 99
Refinement top
Refinement on F2Hydrogen site location: mixed
Least-squares matrix: fullH-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 = 1.08Δρmax = 0.16 e Å3
2702 reflectionsΔρmin = 0.15 e Å3
176 parametersExtinction correction: SHELXL2018 (Sheldrick, 2015b), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
1 restraintExtinction coefficient: 0.044 (3)
Primary atom site location: structure-invariant direct methodsAbsolute structure: Flack x determined using 1136 quotients [(I+)-(I-)]/[(I+)+(I-)] (Parsons et al., 2013)
Secondary atom site location: difference Fourier mapAbsolute structure parameter: 0.03 (8)
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.

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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
O10.27724 (14)0.75133 (12)0.7694 (2)0.0546 (4)
H1B0.2177820.7229530.7988670.082*
N10.36392 (14)0.57083 (11)0.0439 (2)0.0420 (4)
H10.2984780.5634930.0086220.050*
N20.51651 (14)0.66729 (12)0.0645 (2)0.0420 (4)
H20.5450840.7211040.0257080.050*
C10.39948 (16)0.66268 (13)0.0918 (3)0.0390 (4)
H1A0.3640860.7073730.0165330.047*
C20.42312 (18)0.49979 (14)0.0923 (3)0.0433 (5)
C30.52904 (18)0.51327 (15)0.1474 (3)0.0462 (5)
H30.5659200.4679610.2079220.055*
C40.57816 (17)0.59665 (16)0.1094 (3)0.0434 (5)
C50.3741 (2)0.40638 (17)0.0759 (4)0.0654 (7)
H5A0.3007850.4118060.0347100.098*
H5B0.3736330.3767780.1851290.098*
H5C0.4162040.3704180.0025390.098*
C60.69929 (19)0.6085 (2)0.1048 (4)0.0627 (7)
H6A0.7233300.6113860.0113100.094*
H6B0.7334010.5572810.1605210.094*
H6C0.7187480.6644250.1622200.094*
C70.36783 (16)0.68454 (13)0.2754 (3)0.0378 (4)
C80.42471 (19)0.74749 (17)0.3707 (3)0.0520 (5)
H80.4853630.7761320.3236590.062*
C90.3937 (2)0.76929 (18)0.5356 (3)0.0594 (7)
H90.4337860.8118620.5978280.071*
C100.30388 (18)0.72830 (14)0.6075 (3)0.0428 (5)
C110.2443 (2)0.66604 (16)0.5124 (3)0.0523 (6)
H110.1826000.6387350.5586440.063*
C120.2766 (2)0.64423 (17)0.3479 (3)0.0519 (6)
H120.2363150.6019120.2852690.062*
O20.33630 (14)0.03653 (13)0.4068 (4)0.0796 (7)
O30.39509 (17)0.17870 (13)0.4094 (3)0.0729 (6)
C130.4095 (2)0.09335 (17)0.4226 (3)0.0529 (5)
C140.5234 (3)0.0608 (3)0.4529 (7)0.0972 (13)
H14A0.5738480.1065190.4132930.146*
H14B0.5352850.0043260.3923590.146*
H14C0.5342620.0507370.5724020.146*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O10.0600 (10)0.0655 (10)0.0384 (8)0.0097 (8)0.0013 (7)0.0062 (7)
N10.0390 (9)0.0462 (9)0.0406 (9)0.0000 (7)0.0013 (7)0.0045 (7)
N20.0417 (9)0.0411 (8)0.0432 (9)0.0018 (7)0.0082 (8)0.0061 (7)
C10.0404 (10)0.0396 (9)0.0370 (9)0.0037 (8)0.0009 (8)0.0027 (8)
C20.0484 (11)0.0427 (10)0.0387 (10)0.0018 (9)0.0100 (9)0.0010 (8)
C30.0478 (12)0.0442 (11)0.0467 (11)0.0080 (9)0.0029 (9)0.0104 (9)
C40.0389 (10)0.0543 (11)0.0371 (9)0.0017 (9)0.0046 (9)0.0048 (8)
C50.0803 (18)0.0455 (12)0.0705 (17)0.0120 (12)0.0148 (15)0.0064 (12)
C60.0378 (11)0.0830 (17)0.0674 (15)0.0003 (11)0.0060 (11)0.0124 (14)
C70.0367 (9)0.0366 (8)0.0401 (10)0.0066 (7)0.0015 (8)0.0008 (8)
C80.0480 (12)0.0565 (12)0.0514 (12)0.0106 (10)0.0064 (10)0.0084 (11)
C90.0567 (14)0.0671 (15)0.0545 (14)0.0102 (12)0.0038 (11)0.0207 (12)
C100.0481 (11)0.0443 (10)0.0362 (10)0.0132 (9)0.0017 (9)0.0005 (8)
C110.0503 (12)0.0588 (12)0.0478 (13)0.0075 (10)0.0104 (10)0.0066 (10)
C120.0515 (13)0.0561 (13)0.0480 (12)0.0117 (11)0.0078 (10)0.0114 (10)
O20.0478 (10)0.0576 (11)0.133 (2)0.0061 (8)0.0135 (12)0.0193 (12)
O30.0754 (12)0.0562 (10)0.0873 (15)0.0097 (9)0.0357 (11)0.0046 (9)
C130.0454 (12)0.0571 (13)0.0562 (13)0.0040 (10)0.0018 (11)0.0058 (11)
C140.0515 (16)0.111 (3)0.129 (4)0.0017 (16)0.0141 (19)0.022 (3)
Geometric parameters (Å, º) top
O1—C101.356 (3)C6—H6B0.9600
O1—H1B0.8700C6—H6C0.9600
N1—C21.319 (3)C7—C81.373 (3)
N1—C11.454 (3)C7—C121.387 (3)
N1—H10.9099C8—C91.388 (3)
N2—C41.324 (3)C8—H80.9300
N2—C11.455 (3)C9—C101.375 (3)
N2—H20.9100C9—H90.9300
C1—C71.528 (3)C10—C111.383 (3)
C1—H1A0.9800C11—C121.389 (3)
C2—C31.385 (3)C11—H110.9300
C2—C51.491 (3)C12—H120.9300
C3—C41.386 (3)O2—C131.227 (3)
C3—H30.9300O3—C131.257 (3)
C4—C61.498 (3)C13—C141.497 (4)
C5—H5A0.9600C14—H14A0.9600
C5—H5B0.9600C14—H14B0.9600
C5—H5C0.9600C14—H14C0.9600
C6—H6A0.9600
C10—O1—H1B109.6C4—C6—H6C109.5
C2—N1—C1118.59 (18)H6A—C6—H6C109.5
C2—N1—H1121.8H6B—C6—H6C109.5
C1—N1—H1119.4C8—C7—C12118.0 (2)
C4—N2—C1119.38 (17)C8—C7—C1121.60 (19)
C4—N2—H2122.4C12—C7—C1120.37 (19)
C1—N2—H2118.0C7—C8—C9121.4 (2)
N1—C1—N2107.52 (16)C7—C8—H8119.3
N1—C1—C7111.02 (16)C9—C8—H8119.3
N2—C1—C7112.37 (17)C10—C9—C8120.4 (2)
N1—C1—H1A108.6C10—C9—H9119.8
N2—C1—H1A108.6C8—C9—H9119.8
C7—C1—H1A108.6O1—C10—C9118.2 (2)
N1—C2—C3119.82 (19)O1—C10—C11122.8 (2)
N1—C2—C5117.7 (2)C9—C10—C11119.0 (2)
C3—C2—C5122.4 (2)C10—C11—C12120.1 (2)
C2—C3—C4117.71 (19)C10—C11—H11119.9
C2—C3—H3121.1C12—C11—H11119.9
C4—C3—H3121.1C7—C12—C11121.1 (2)
N2—C4—C3119.11 (19)C7—C12—H12119.5
N2—C4—C6118.2 (2)C11—C12—H12119.5
C3—C4—C6122.5 (2)O2—C13—O3123.6 (2)
C2—C5—H5A109.5O2—C13—C14119.3 (3)
C2—C5—H5B109.5O3—C13—C14117.1 (2)
H5A—C5—H5B109.5C13—C14—H14A109.5
C2—C5—H5C109.5C13—C14—H14B109.5
H5A—C5—H5C109.5H14A—C14—H14B109.5
H5B—C5—H5C109.5C13—C14—H14C109.5
C4—C6—H6A109.5H14A—C14—H14C109.5
C4—C6—H6B109.5H14B—C14—H14C109.5
H6A—C6—H6B109.5
C2—N1—C1—N243.2 (2)N2—C1—C7—C834.0 (3)
C2—N1—C1—C780.1 (2)N1—C1—C7—C1228.8 (3)
C4—N2—C1—N141.8 (3)N2—C1—C7—C12149.3 (2)
C4—N2—C1—C780.6 (2)C12—C7—C8—C91.2 (4)
C1—N1—C2—C316.4 (3)C1—C7—C8—C9177.9 (2)
C1—N1—C2—C5166.9 (2)C7—C8—C9—C100.4 (4)
N1—C2—C3—C416.2 (3)C8—C9—C10—O1179.5 (2)
C5—C2—C3—C4160.4 (2)C8—C9—C10—C110.8 (4)
C1—N2—C4—C313.4 (3)O1—C10—C11—C12179.1 (2)
C1—N2—C4—C6170.9 (2)C9—C10—C11—C121.3 (4)
C2—C3—C4—N217.7 (3)C8—C7—C12—C110.7 (4)
C2—C3—C4—C6157.9 (2)C1—C7—C12—C11177.5 (2)
N1—C1—C7—C8154.5 (2)C10—C11—C12—C70.5 (4)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O1—H1B···O3i0.871.762.609 (3)165
N1—H1···O2ii0.911.832.731 (3)172
N2—H2···O3iii0.911.872.771 (2)170
C1—H1A···O1iv0.982.313.214 (3)154
Symmetry codes: (i) x+1/2, y+1/2, z+1/2; (ii) x+1/2, y+1/2, z1/2; (iii) x+1, y+1, z1/2; (iv) x, y, z1.
 

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.

References

First citationAnsari, K. R., Sudheer, Singh, A. & Quraishi, M. A. (2015). J. Dispersion Sci. Technol. 36, 908–917.  CrossRef Google Scholar
First citationBruker (2016). APEX3, SADABS and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.  Google Scholar
First citationFun, H.-K., Chia, T. S., Samshuddin, S., Narayana, B. & Sarojini, B. K. (2012). Acta Cryst. E68, o807–o808.  CSD CrossRef IUCr Journals Google Scholar
First citationGore, R. P. & Rajput, A. P. (2013). Drug Invention Today, 5, 148–152.  CrossRef Google Scholar
First citationKrause, L., Herbst-Irmer, R., Sheldrick, G. M. & Stalke, D. (2015). J. Appl. Cryst. 48, 3–10.  Web of Science CSD CrossRef CAS IUCr Journals Google Scholar
First citationMacrae, C. F., Bruno, I. J., Chisholm, J. A., Edgington, P. R., McCabe, P., Pidcock, E., Rodriguez-Monge, L., Taylor, R., van de Streek, J. & Wood, P. A. (2008). J. Appl. Cryst. 41, 466–470.  Web of Science CSD CrossRef CAS IUCr Journals Google Scholar
First citationParsons, S., Flack, H. D. & Wagner, T. (2013). Acta Cryst. B69, 249–259.  Web of Science CrossRef CAS IUCr Journals Google Scholar
First citationSelvam, T. P., James, C. R., Dniandev, P. V. & Valzita, S. K. (2012). Res. Pharm. 2, 1–9.  Google Scholar
First citationSheldrick, G. M. (2008). Acta Cryst. A64, 112–122.  Web of Science CrossRef CAS IUCr Journals Google Scholar
First citationSheldrick, G. M. (2015a). Acta Cryst. A71, 3–8.  Web of Science CrossRef IUCr Journals Google Scholar
First citationSheldrick, G. M. (2015b). Acta Cryst. C71, 3–8.  Web of Science CrossRef IUCr Journals Google Scholar

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