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

Rasheeda, K.; Samshuddin, S.; Swathi, P.N.; Alva, V.D.P.; Mague, J.T.; Ramli, Y.

doi:10.1107/S2414314618010465

organic compounds

IUCrDATA

ISSN: 2414-3146

Volume 3| Part 7| July 2018| x181046

https://doi.org/10.1107/S2414314618010465

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

Kedila Rasheeda,^a Seranthimata Samshuddin,^b Phadke N. Swathi,^b Vijaya D. P. Alva,^a Joel T. Mague ^c and Youssef Ramli ^d ^*

^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.

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 crystal structure has been determined (Fig. 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 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).

Table 1
Hydrogen-bond geometry (Å, °)

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⋯O1^iv	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
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
Elevation view of two layers seen along the a-axis direction. Hydrogen bonds are depicted as in Fig. 2

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.

Table 2
Experimental details

Crystal data
Chemical formula	C₁₂H₁₅N₂O⁺·C₂H₃O₂⁻
M_r	262.30
Crystal system, space group	Orthorhombic, Pna2₁
Temperature (K)	296
a, b, c (Å)	12.2836 (4), 14.5343 (5), 7.8596 (3)
V (Å³)	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 )
T_min, T_max	0.79, 0.95
No. of measured, independent and observed [I > 2σ(I)] reflections	9762, 2702, 2611
R_int	0.042
(sin θ/λ)_max (Å⁻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
Δρ_max, Δρ_min (e Å⁻³)	0.16, −0.15
Absolute structure	Flack x determined using 1136 quotients [(I⁺)−(I⁻)]/[(I⁺)+(I⁻)] (Parsons et al., 2013 )
Absolute structure parameter	0.03 (8)
Computer programs: APEX3 and SAINT (Bruker, 2016 ), SHELXT (Sheldrick, 2015a ), SHELXL2018 (Sheldrick, 2015b ), Mercury (Macrae et al., 2008 ) and SHELXTL (Sheldrick, 2008 ).

Structural data

CCDC reference: 1857057

Crystal structure: contains datablocks global, I. DOI: https://doi.org/10.1107/S2414314618010465/vm4037sup1.cif

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

checkCIF report

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⁺·C₂H₃O₂⁻	D_x = 1.242 Mg m⁻³
M_r = 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

Data collection top

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	R_int = 0.042
ω scans	θ_max = 72.4°, θ_min = 4.7°
Absorption correction: multi-scan (SADABS; Krause et al., 2015)	h = −14→15
T_min = 0.79, T_max = 0.95	k = −17→14
9762 measured reflections	l = −9→9

Refinement top

Refinement on F²	Hydrogen site location: mixed
Least-squares matrix: full	H-atom parameters constrained
R[F² > 2σ(F²)] = 0.035	w = 1/[σ²(F_o²) + (0.0477P)² + 0.1696P] where P = (F_o² + 2F_c²)/3
wR(F²) = 0.093	(Δ/σ)_max < 0.001
S = 1.08	Δρ_max = 0.16 e Å⁻³
2702 reflections	Δρ_min = −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)

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

	x	y	z	U_iso*/U_eq
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*

Atomic displacement parameters (Å²) top

	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)

Geometric parameters (Å, º) top

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)

Hydrogen-bond geometry (Å, º) top

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···O1^iv	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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