Crystal structure, hydrogen bonding and Hirshfeld surface analysis of 2-amino-4-meth­oxy-6-methyl­pyrimidinium 4-chloro­benzoate

Jeevaraj, M.; Sivajeyanthi, P.; Edison, B.; Thanigaimani, K.; Balasubramani, K.

doi:10.1107/S2056989018005583

Crystal structure, hydrogen bonding and Hirshfeld surface analysis of 2-amino-4-methoxy-6-methylpyrimidinium 4-chlorobenzoate

M. Jeevaraj, P. Sivajeyanthi, B. Edison, K. Thanigaimani and K. Balasubramani

In the crystal structure of the title compound, C₆H₁₀N₃O⁺·C₇H₄Cl_O2⁻, the pyrimidine N atom of the cation is hydrogen-bonded to the 4-chlorobenzoate anion through a pair of N—H

O_carboxyl hydrogen bonds, forming an $R_{2}^{2}$ (8) ring motif which is linked through centrosymmetric $R_{4}^{2}$ (8) ring motifs, forming a pseudotetrameric DDAA array.

Keywords: crystal structure; pseudotetrameric; pyrimidine.

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Supporting information

	Crystallographic Information File (CIF) https://doi.org/10.1107/S2056989018005583/zs2399sup1.cif Contains datablocks global, I, 81R
	Structure factor file (CIF format) https://doi.org/10.1107/S2056989018005583/zs2399Isup2.hkl Contains datablock I
	Chemical Markup Language (CML) file https://doi.org/10.1107/S2056989018005583/zs2399Isup3.cml Supplementary material

CCDC reference: 1835970

checkCIF report

Key indicators

Single-crystal X-ray study
T = 296 K
Mean (C-C) = 0.003 Å
R factor = 0.047
wR factor = 0.152
Data-to-parameter ratio = 18.2

checkCIF/PLATON results

No syntax errors found



Alert level C
PLAT353_ALERT_3_C Long   N-H (N0.87,N1.01A)  N1       - H1N1     .       1.04 Ang.
PLAT905_ALERT_3_C Negative K value in the Analysis of Variance ...     -0.484 Report
PLAT911_ALERT_3_C Missing FCF Refl Between Thmin & STh/L=    0.600         12 Report

Alert level G
PLAT007_ALERT_5_G Number of Unrefined Donor-H Atoms ..............          2 Report
PLAT012_ALERT_1_G N.O.K.   _shelx_res_checksum Found in CIF ......     Please Check
PLAT042_ALERT_1_G Calc. and Reported MoietyFormula Strings  Differ     Please Check
PLAT066_ALERT_1_G Predicted and Reported Tmin&Tmax Range Identical          ? Check
PLAT128_ALERT_4_G Alternate Setting for Input Space Group  P21/c        P21/n Note
PLAT720_ALERT_4_G Number of Unusual/Non-Standard Labels ..........          1 Note
PLAT910_ALERT_3_G Missing # of FCF Reflection(s) Below Theta(Min).          2 Note
PLAT912_ALERT_4_G Missing # of FCF Reflections Above STh/L=  0.600        104 Note
PLAT933_ALERT_2_G Number of OMIT Records in Embedded .res File ...          2 Note
PLAT978_ALERT_2_G Number C-C Bonds with Positive Residual Density.          2 Info

   0 ALERT level A = Most likely a serious problem - resolve or explain
   0 ALERT level B = A potentially serious problem, consider carefully
   3 ALERT level C = Check. Ensure it is not caused by an omission or oversight
  10 ALERT level G = General information/check it is not something unexpected

   3 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
   2 ALERT type 2 Indicator that the structure model may be wrong or deficient
   4 ALERT type 3 Indicator that the structure quality may be low
   3 ALERT type 4 Improvement, methodology, query or suggestion
   1 ALERT type 5 Informative message, check

Computing details top

Data collection: APEX2 (Bruker, 2004); cell refinement: APEX2 and SAINT (Bruker, 2004); data reduction: SAINT and XPREP (Bruker, 2004); program(s) used to solve structure: SIR92 (Altomare et al., 1999); program(s) used to refine structure: SHELXL2017 (Sheldrick, 2015); molecular graphics: ORTEP-3 (Farrugia, 2012) and Mercury (Macrae et al., 2008); software used to prepare material for publication: SHELXL2017 (Sheldrick, 2015).

(I) top

Crystal data top

C₆H₁₀N₃O⁺·C₇H₄ClO₂⁻	F(000) = 616
M_r = 295.72	D_x = 1.384 Mg m⁻³
Monoclinic, P2₁/c	Mo Kα radiation, λ = 0.71073 Å
a = 10.1148 (8) Å	Cell parameters from 3319 reflections
b = 11.2236 (8) Å	θ = 4.7–53.1°
c = 14.579 (1) Å	µ = 0.28 mm⁻¹
β = 120.940 (5)°	T = 296 K
V = 1419.57 (19) Å³	Block, colorless
Z = 4	0.35 × 0.30 × 0.20 mm

Data collection top

Bruker Kappa APEXII CCD diffractometer	2125 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tube	R_int = 0.024
ω and φ scan	θ_max = 28.4°, θ_min = 2.7°
Absorption correction: multi-scan (SADABS; Bruker, 2004)	h = −13→12
T_min = 0.909, T_max = 0.946	k = −14→14
10962 measured reflections	l = −15→18
3423 independent reflections

Refinement top

Refinement on F²	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: mixed
R[F² > 2σ(F²)] = 0.047	H atoms treated by a mixture of independent and constrained refinement
wR(F²) = 0.152	w = 1/[σ²(F_o²) + (0.0728P)² + 0.324P] where P = (F_o² + 2F_c²)/3
S = 0.99	(Δ/σ)_max = 0.003
3423 reflections	Δρ_max = 0.26 e Å⁻³
188 parameters	Δρ_min = −0.34 e Å⁻³
0 restraints	Extinction correction: SHELXL2017 (Sheldrick, 2015), Fc^*=kFc[1+0.001xFc²λ³/sin(2θ)]^-1/4
Primary atom site location: structure-invariant direct methods	Extinction coefficient: 0.020 (3)

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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å²) top

	x	y	z	U_iso*/U_eq
O3	1.08061 (18)	0.73298 (18)	0.57812 (14)	0.0840 (5)
N1	0.62562 (18)	0.71035 (13)	0.45066 (13)	0.0513 (4)
N2	0.61625 (18)	0.91121 (14)	0.47011 (15)	0.0649 (5)
H1N	0.659761	0.979882	0.489408	0.078*
H2N	0.518251	0.904882	0.442578	0.078*
N3	0.85256 (18)	0.82711 (15)	0.52563 (13)	0.0555 (4)
C8	1.1555 (3)	0.8473 (3)	0.6048 (2)	0.0926 (9)
H8A	1.258389	0.838988	0.618161	0.139*
H8B	1.159254	0.877851	0.667577	0.139*
H8C	1.098704	0.901435	0.546305	0.139*
C9	0.9288 (2)	0.7287 (2)	0.53678 (16)	0.0616 (6)
C10	0.8601 (3)	0.6168 (2)	0.50699 (19)	0.0703 (6)
H10	0.919348	0.548952	0.518504	0.084*
C11	0.7049 (3)	0.60891 (17)	0.46085 (17)	0.0595 (5)
C12	0.6128 (3)	0.49752 (19)	0.4188 (2)	0.0872 (8)
H12A	0.531726	0.509732	0.346014	0.131*
H12B	0.568913	0.477063	0.461457	0.131*
H12C	0.678410	0.433995	0.421663	0.131*
C13	0.6995 (2)	0.81598 (16)	0.48261 (15)	0.0489 (4)
Cl1	−0.42873 (6)	0.70123 (7)	0.18780 (6)	0.0859 (3)
O1	0.30336 (15)	0.87707 (12)	0.40502 (13)	0.0710 (5)
O2	0.32766 (15)	0.68727 (12)	0.37489 (12)	0.0648 (4)
C1	0.2501 (2)	0.77506 (16)	0.37387 (15)	0.0506 (5)
C2	0.0808 (2)	0.75559 (16)	0.33048 (14)	0.0455 (4)
C3	0.0178 (2)	0.64290 (17)	0.30515 (16)	0.0532 (5)
H3	0.081505	0.577740	0.317181	0.064*
C4	−0.1384 (2)	0.62496 (19)	0.26221 (16)	0.0591 (5)
H4	−0.179743	0.548535	0.245653	0.071*
C5	−0.2314 (2)	0.72173 (19)	0.24443 (16)	0.0552 (5)
C6	−0.1725 (2)	0.83473 (19)	0.26959 (17)	0.0615 (5)
H6	−0.237007	0.899426	0.257249	0.074*
C7	−0.0160 (2)	0.85154 (17)	0.31355 (16)	0.0559 (5)
H7	0.025012	0.927932	0.332014	0.067*
H1N1	0.508 (3)	0.700 (2)	0.418 (2)	0.089 (8)*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
O3	0.0495 (9)	0.1165 (14)	0.0927 (12)	0.0275 (9)	0.0414 (9)	0.0152 (11)
N1	0.0479 (9)	0.0476 (9)	0.0551 (9)	0.0080 (7)	0.0242 (8)	−0.0032 (7)
N2	0.0389 (8)	0.0483 (9)	0.0946 (13)	0.0010 (7)	0.0251 (8)	−0.0125 (8)
N3	0.0411 (9)	0.0722 (11)	0.0533 (10)	0.0081 (7)	0.0243 (7)	−0.0019 (8)
C8	0.0457 (13)	0.140 (3)	0.0899 (19)	0.0033 (14)	0.0337 (13)	0.0031 (17)
C9	0.0507 (12)	0.0858 (15)	0.0564 (13)	0.0194 (10)	0.0333 (10)	0.0100 (11)
C10	0.0728 (15)	0.0697 (14)	0.0839 (16)	0.0340 (12)	0.0514 (13)	0.0182 (12)
C11	0.0738 (14)	0.0508 (11)	0.0653 (13)	0.0173 (9)	0.0439 (11)	0.0081 (9)
C12	0.112 (2)	0.0478 (12)	0.121 (2)	0.0116 (12)	0.0732 (18)	0.0017 (13)
C13	0.0406 (9)	0.0533 (10)	0.0497 (11)	0.0050 (8)	0.0210 (8)	−0.0029 (8)
Cl1	0.0454 (3)	0.1120 (6)	0.0929 (5)	−0.0142 (3)	0.0302 (3)	−0.0069 (4)
O1	0.0424 (7)	0.0458 (8)	0.1021 (12)	−0.0028 (6)	0.0210 (7)	−0.0149 (7)
O2	0.0454 (8)	0.0481 (7)	0.0872 (11)	0.0023 (6)	0.0242 (7)	−0.0098 (7)
C1	0.0404 (9)	0.0449 (10)	0.0527 (11)	0.0003 (7)	0.0141 (8)	−0.0010 (8)
C2	0.0406 (9)	0.0447 (9)	0.0424 (10)	0.0005 (7)	0.0149 (8)	0.0012 (7)
C3	0.0495 (11)	0.0465 (10)	0.0573 (11)	−0.0031 (8)	0.0230 (9)	−0.0053 (8)
C4	0.0549 (12)	0.0578 (12)	0.0623 (13)	−0.0144 (9)	0.0285 (10)	−0.0095 (10)
C5	0.0416 (10)	0.0722 (13)	0.0468 (11)	−0.0074 (9)	0.0191 (8)	−0.0020 (9)
C6	0.0429 (10)	0.0607 (12)	0.0702 (14)	0.0087 (9)	0.0215 (10)	0.0076 (10)
C7	0.0442 (10)	0.0459 (10)	0.0643 (12)	0.0007 (8)	0.0184 (9)	0.0034 (9)

Geometric parameters (Å, º) top

O3—C9	1.331 (2)	C12—H12A	0.9600
O3—C8	1.438 (4)	C12—H12B	0.9600
N1—C13	1.350 (2)	C12—H12C	0.9600
N1—C11	1.356 (2)	Cl1—C5	1.7385 (19)
N1—H1N1	1.03 (3)	O1—C1	1.247 (2)
N2—C13	1.314 (2)	O2—C1	1.255 (2)
N2—H1N	0.8600	C1—C2	1.506 (2)
N2—H2N	0.8600	C2—C3	1.379 (3)
N3—C9	1.308 (3)	C2—C7	1.389 (3)
N3—C13	1.344 (2)	C3—C4	1.383 (3)
C8—H8A	0.9600	C3—H3	0.9300
C8—H8B	0.9600	C4—C5	1.372 (3)
C8—H8C	0.9600	C4—H4	0.9300
C9—C10	1.392 (3)	C5—C6	1.369 (3)
C10—C11	1.356 (3)	C6—C7	1.381 (3)
C10—H10	0.9300	C6—H6	0.9300
C11—C12	1.490 (3)	C7—H7	0.9300

C9—O3—C8	118.61 (18)	H12A—C12—H12C	109.5
C13—N1—C11	120.53 (17)	H12B—C12—H12C	109.5
C13—N1—H1N1	124.1 (13)	N2—C13—N3	119.43 (17)
C11—N1—H1N1	115.4 (13)	N2—C13—N1	117.68 (16)
C13—N2—H1N	120.0	N3—C13—N1	122.89 (16)
C13—N2—H2N	120.0	O1—C1—O2	124.51 (17)
H1N—N2—H2N	120.0	O1—C1—C2	118.10 (16)
C9—N3—C13	116.32 (18)	O2—C1—C2	117.39 (16)
O3—C8—H8A	109.5	C3—C2—C7	118.48 (17)
O3—C8—H8B	109.5	C3—C2—C1	121.00 (16)
H8A—C8—H8B	109.5	C7—C2—C1	120.51 (16)
O3—C8—H8C	109.5	C2—C3—C4	121.22 (18)
H8A—C8—H8C	109.5	C2—C3—H3	119.4
H8B—C8—H8C	109.5	C4—C3—H3	119.4
N3—C9—O3	119.7 (2)	C5—C4—C3	118.90 (18)
N3—C9—C10	123.68 (19)	C5—C4—H4	120.5
O3—C9—C10	116.64 (19)	C3—C4—H4	120.5
C11—C10—C9	118.62 (18)	C6—C5—C4	121.40 (18)
C11—C10—H10	120.7	C6—C5—Cl1	119.04 (16)
C9—C10—H10	120.7	C4—C5—Cl1	119.55 (16)
C10—C11—N1	117.9 (2)	C5—C6—C7	119.23 (18)
C10—C11—C12	125.36 (19)	C5—C6—H6	120.4
N1—C11—C12	116.74 (19)	C7—C6—H6	120.4
C11—C12—H12A	109.5	C6—C7—C2	120.74 (18)
C11—C12—H12B	109.5	C6—C7—H7	119.6
H12A—C12—H12B	109.5	C2—C7—H7	119.6
C11—C12—H12C	109.5

O1—C1—C2—C3	−173.20 (19)	C4—C5—C6—C7	0.2 (3)
O1—C1—C2—C7	7.8 (3)	C5—C6—C7—C2	1.2 (3)
O2—C1—C2—C3	7.7 (3)	C13—N1—C11—C10	2.1 (3)
O2—C1—C2—C7	−171.35 (18)	C13—N1—C11—C12	−177.2 (2)
C1—C2—C3—C4	−177.99 (18)	C11—N1—C13—N2	179.63 (19)
C7—C2—C3—C4	1.0 (3)	C11—N1—C13—N3	−0.1 (3)
C1—C2—C7—C6	177.29 (19)	C13—N3—C9—O3	179.53 (18)
C3—C2—C7—C6	−1.8 (3)	C13—N3—C9—C10	−0.1 (3)
C2—C3—C4—C5	0.3 (3)	C9—N3—C13—N1	−0.9 (3)
C8—O3—C9—C10	176.7 (2)	C9—N3—C13—N2	179.37 (19)
C8—O3—C9—N3	−2.9 (3)	O3—C9—C10—C11	−177.6 (2)
C3—C4—C5—C6	−0.9 (3)	N3—C9—C10—C11	2.0 (4)
C3—C4—C5—Cl1	178.62 (16)	C9—C10—C11—N1	−2.9 (3)
Cl1—C5—C6—C7	−179.32 (16)	C9—C10—C11—C12	176.3 (2)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1N1···O2	1.04 (3)	1.60 (3)	2.636 (3)	176 (2)
N2—H1N···O1ⁱ	0.86	2.12	2.846 (2)	142
N2—H2N···O1	0.86	1.97	2.824 (3)	169
C8—H8A···Cl1ⁱⁱ	0.96	2.82	3.770 (3)	171

Symmetry codes: (i) −x+1, −y+2, −z+1; (ii) x+2, −y+3/2, z+1/2.

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Crystal structure, hydrogen bonding and Hirshfeld surface analysis of 2-amino-4-meth­oxy-6-methyl­pyrimidinium 4-chloro­benzoate

Supporting information

Key indicators

checkCIF/PLATON results

Crystal structure, hydrogen bonding and Hirshfeld surface analysis of 2-amino-4-methoxy-6-methylpyrimidinium 4-chlorobenzoate