Co-existence of water-mediated and normal base pairs in a supramolecular ribbon in 2-amino-4,6-di­methyl­pyrimidinium bromide 2-amino-4,6-di­methyl­pyrimidine monohydrate

Panneerselvam, P.; Muthiah, P.T.; Francis, S.

doi:10.1107/S1600536804007597

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Co-existence of water-mediated and normal base pairs in a supramolecular ribbon in 2-amino-4,6-dimethylpyrimidinium bromide 2-amino-4,6-dimethylpyrimidine monohydrate

P. Panneerselvam, P. T. Muthiah and S. Francis

In the crystal structure of the title compound, C₆H₁₀N₃⁺·Br⁻·C₆H₉N₃·H₂O, the asymmetric unit contains a 2-amino-4,6-dimethylpyrimidinium cation, a Br⁻ anion, a neutral 2-amino-4,6-dimethylpyrimidine molecule and a water molecule. Each neutral base molecule is paired with another inversion-related molecule through N—H

N hydrogen bonds to form dimers, and these are linked to one another through water-mediated hydrogen bonds, generating a supramolecular ribbon. The cations also pair with one another through N—H

N hydrogen bonds. The cation pairs are stacked on top of the neutral pairs. The Br⁻ anion also takes part in hydrogen bonding (N/O—H

Br).

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Supporting information

	Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536804007597/ci6355sup1.cif Contains datablocks global, I
	Structure factor file (CIF format) https://doi.org/10.1107/S1600536804007597/ci6355Isup2.hkl Contains datablock I

CCDC reference: 239135

checkCIF report

Key indicators

Single-crystal X-ray study
T = 293 K
Mean (C-C) = 0.007 Å
R factor = 0.045
wR factor = 0.136
Data-to-parameter ratio = 15.2

checkCIF/PLATON results

No syntax errors found



Alert level A
PLAT052_ALERT_1_A (Proper) Absorption Correction Method Missing ..          ?

Alert level B
PLAT027_ALERT_3_B _diffrn_reflns_theta_full (too) Low ............      24.98 Deg.
PLAT057_ALERT_3_B Correction for Absorption Required   RT(exp) ...       1.24

Alert level C
PLAT042_ALERT_1_C Calc. and Rep. MoietyFormula Strings Differ ....          ?
PLAT341_ALERT_3_C Low Bond Precision on C-C bonds (x 1000) Ang ...          7

   1 ALERT level A = In general: serious problem
   2 ALERT level B = Potentially serious problem
   2 ALERT level C = Check and explain
   0 ALERT level G = General alerts; check

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

Computing details top

Data collection: MolEN (Fair, 1990); cell refinement: MolEN; data reduction: MolEN; program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: ORTEP-3 (Farrugia, 1997); software used to prepare material for publication: PLATON97 (Spek, 1997).

2-amino-4,6-dimethylpyrimidinium bromide 2-amino-4,6-dimethylpyrimidine monohydrate top

Crystal data top

C₆H₁₀N₃⁺·Br⁻·C₆H₉N₃·H₂O	Z = 2
M_r = 345.25	F(000) = 356
Triclinic, P1	D_x = 1.410 Mg m⁻³
Hall symbol: -P 1	Mo Kα radiation, λ = 0.71073 Å
a = 7.002 (4) Å	Cell parameters from 25 reflections
b = 9.438 (8) Å	θ = 3–25°
c = 12.658 (6) Å	µ = 2.53 mm⁻¹
α = 79.56 (5)°	T = 293 K
β = 83.85 (4)°	Plate, colourless
γ = 82.98 (6)°	0.35 × 0.35 × 0.25 mm
V = 813.4 (9) Å³

Data collection top

Enraf-Nonius CAD-4 diffractometer	2095 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tube	R_int = 0.030
Graphite monochromator	θ_max = 25.0°, θ_min = 2.2°
ω/2θ scans	h = 0→8
Absorption correction: ψ scan (North et al., 1968)	k = −11→11
T_min = 0.439, T_max = 0.531	l = −14→15
3101 measured reflections	2 standard reflections every 60 min
2843 independent reflections	intensity decay: none

Refinement top

Refinement on F²	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F² > 2σ(F²)] = 0.045	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.136	H atoms treated by a mixture of independent and constrained refinement
S = 1.14	w = 1/[σ²(F_o²) + (0.0646P)² + 0.8382P] where P = (F_o² + 2F_c²)/3
2843 reflections	(Δ/σ)_max = 0.002
187 parameters	Δρ_max = 0.47 e Å⁻³
0 restraints	Δρ_min = −0.57 e Å⁻³

Special details top

Geometry. Bond distances, angles etc. have been calculated using the rounded fractional coordinates. All e.s.d.'s are estimated from the variances of the (full) variance-covariance matrix. The cell e.s.d.'s are taken into account in the estimation of distances, angles and torsion angles

Refinement. Refinement on F^{2 for ALL reflections except those flagged by the user
for potential systematic errors. Weighted} ^R^-factors ^wR ^{and all goodnesses of fit} ^S ^{are based on} ^F2, conventional R-factors R are based on F, with F set to zero for negative F^{2. The observed criterion of} ^F2 > σ(F^{2) is used only for calculating -}^R^-factor-obs ^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
N11	0.6470 (5)	0.0555 (4)	0.7223 (3)	0.0389 (11)
N12	0.5696 (6)	−0.1002 (4)	0.8791 (3)	0.0508 (14)
N13	0.5505 (5)	0.1434 (4)	0.8841 (3)	0.0396 (11)
C12	0.5885 (6)	0.0334 (4)	0.8289 (3)	0.0367 (12)
C14	0.5758 (6)	0.2755 (4)	0.8302 (4)	0.0402 (14)
C15	0.6414 (6)	0.3013 (5)	0.7217 (4)	0.0451 (16)
C16	0.6747 (6)	0.1887 (5)	0.6665 (3)	0.0440 (14)
C17	0.7351 (8)	0.1979 (6)	0.5490 (4)	0.065 (2)
C18	0.5276 (8)	0.3967 (5)	0.8942 (4)	0.0595 (17)
N1	0.0883 (5)	0.3243 (4)	0.8157 (3)	0.0427 (11)
N2	−0.0040 (6)	0.2064 (4)	0.9853 (3)	0.0505 (13)
N3	0.0698 (5)	0.0678 (4)	0.8529 (3)	0.0388 (11)
C2	0.0540 (6)	0.1991 (4)	0.8824 (3)	0.0380 (12)
C4	0.1306 (6)	0.0610 (5)	0.7508 (3)	0.0403 (14)
C5	0.1721 (6)	0.1831 (5)	0.6777 (4)	0.0470 (14)
C6	0.1467 (6)	0.3142 (5)	0.7129 (4)	0.0455 (16)
C7	0.1796 (8)	0.4529 (6)	0.6380 (4)	0.0670 (19)
C8	0.1529 (8)	−0.0857 (5)	0.7183 (4)	0.0566 (17)
O1W	0.0647 (7)	0.4027 (4)	0.1283 (4)	0.0820 (18)
Br1	0.30561 (8)	0.25741 (6)	0.35557 (4)	0.0621 (2)
H5A	0.66230	0.39450	0.68720	0.0540*
H11	0.66730	−0.01740	0.68900	0.0470*
H12A	0.53320	−0.11610	0.94690	0.0610*
H12B	0.59380	−0.17120	0.84410	0.0610*
H17A	0.79330	0.10490	0.53510	0.0960*
H17B	0.82670	0.26780	0.52760	0.0960*
H17C	0.62400	0.22700	0.50880	0.0960*
H18A	0.41780	0.37700	0.94470	0.0890*
H18B	0.49820	0.48600	0.84620	0.0890*
H18C	0.63610	0.40430	0.93240	0.0890*
H2A	−0.02970	0.12920	1.02960	0.0600*
H2B	−0.01590	0.28830	1.00740	0.0600*
H5	0.21590	0.17690	0.60650	0.0560*
H7A	0.05740	0.50510	0.62060	0.1000*
H7B	0.25300	0.43170	0.57320	0.1000*
H7C	0.24950	0.51060	0.67230	0.1000*
H8A	0.14780	−0.15890	0.78170	0.0850*
H8B	0.27480	−0.09980	0.67700	0.0850*
H8C	0.05020	−0.09220	0.67540	0.0850*
H1A	0.13290	0.37250	0.17610	0.08 (2)*
H1B	0.00840	0.47740	0.14210	0.10 (2)*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
N11	0.042 (2)	0.0415 (19)	0.0333 (18)	0.0032 (15)	−0.0034 (15)	−0.0115 (15)
N12	0.078 (3)	0.038 (2)	0.035 (2)	−0.0023 (19)	0.0029 (18)	−0.0099 (16)
N13	0.044 (2)	0.039 (2)	0.0373 (19)	−0.0059 (15)	−0.0010 (15)	−0.0109 (16)
C12	0.036 (2)	0.039 (2)	0.036 (2)	−0.0006 (17)	−0.0047 (17)	−0.0103 (18)
C14	0.034 (2)	0.039 (2)	0.049 (3)	−0.0035 (17)	−0.0052 (18)	−0.0107 (19)
C15	0.045 (3)	0.043 (2)	0.046 (3)	−0.010 (2)	−0.005 (2)	0.000 (2)
C16	0.039 (2)	0.056 (3)	0.034 (2)	−0.004 (2)	−0.0055 (18)	0.001 (2)
C17	0.079 (4)	0.075 (4)	0.035 (3)	−0.006 (3)	−0.007 (2)	0.003 (2)
C18	0.074 (3)	0.041 (3)	0.069 (3)	−0.015 (2)	0.003 (3)	−0.023 (2)
N1	0.045 (2)	0.0348 (19)	0.046 (2)	−0.0012 (15)	−0.0094 (17)	0.0002 (16)
N2	0.086 (3)	0.0323 (18)	0.034 (2)	−0.0067 (18)	−0.0062 (19)	−0.0066 (15)
N3	0.043 (2)	0.0382 (19)	0.0368 (19)	−0.0050 (15)	−0.0035 (15)	−0.0099 (15)
C2	0.040 (2)	0.037 (2)	0.037 (2)	−0.0016 (18)	−0.0092 (18)	−0.0044 (18)
C4	0.034 (2)	0.051 (3)	0.037 (2)	−0.0018 (19)	−0.0034 (18)	−0.012 (2)
C5	0.040 (2)	0.063 (3)	0.035 (2)	−0.002 (2)	−0.0028 (19)	−0.003 (2)
C6	0.041 (2)	0.050 (3)	0.041 (3)	−0.002 (2)	−0.007 (2)	0.004 (2)
C7	0.073 (4)	0.061 (3)	0.053 (3)	0.004 (3)	0.001 (3)	0.016 (3)
C8	0.070 (3)	0.056 (3)	0.049 (3)	−0.010 (2)	0.005 (2)	−0.026 (2)
O1W	0.132 (4)	0.048 (2)	0.072 (3)	−0.001 (2)	−0.024 (3)	−0.023 (2)
Br1	0.0760 (4)	0.0533 (3)	0.0591 (4)	0.0077 (2)	−0.0149 (3)	−0.0197 (2)

Geometric parameters (Å, º) top

O1W—H1B	0.80	C16—C17	1.492 (6)
O1W—H1A	0.80	C15—H5A	0.93
N11—C16	1.351 (6)	C17—H17C	0.96
N11—C12	1.354 (5)	C17—H17A	0.96
N12—C12	1.320 (5)	C17—H17B	0.96
N13—C12	1.339 (5)	C18—H18C	0.96
N13—C14	1.331 (6)	C18—H18B	0.96
N11—H11	0.86	C18—H18A	0.96
N12—H12B	0.86	C4—C8	1.500 (7)
N12—H12A	0.86	C4—C5	1.381 (7)
N1—C6	1.338 (6)	C5—C6	1.375 (7)
N1—C2	1.353 (5)	C6—C7	1.498 (7)
N2—C2	1.334 (5)	C5—H5	0.93
N3—C4	1.327 (5)	C7—H7B	0.96
N3—C2	1.346 (5)	C7—H7C	0.96
N2—H2A	0.86	C7—H7A	0.96
N2—H2B	0.86	C8—H8C	0.96
C14—C18	1.504 (7)	C8—H8A	0.96
C14—C15	1.388 (7)	C8—H8B	0.96
C15—C16	1.359 (7)

Br1···N12ⁱ	3.537 (5)	C17···C5^x	3.594 (8)
Br1···O1W	3.471 (6)	C18···C18^xi	3.551 (8)
Br1···N11ⁱ	3.248 (5)	C2···H1Bⁱⁱⁱ	2.9948
Br1···H8Cⁱⁱ	3.1894	C4···H2A^vii	3.0869
Br1···H17C	3.0631	C6···H1Bⁱⁱⁱ	2.9624
Br1···H12Bⁱ	2.7874	C7···H1Bⁱⁱⁱ	3.0952
Br1···H5	3.1425	C7···H17B^v	3.0551
Br1···H7Aⁱⁱⁱ	3.2037	C12···H12A^viii	3.0840
Br1···H11ⁱ	2.4126	C14···H12A^viii	3.0145
Br1···H1A	2.6789	C18···H12A^viii	3.0663
Br1···H8Bⁱ	3.1478	H1A···H12Bⁱ	2.5533
O1W···N2^iv	2.926 (6)	H1A···Br1	2.6789
O1W···N1ⁱⁱⁱ	2.848 (6)	H1B···C2ⁱⁱⁱ	2.9948
O1W···Br1	3.471 (6)	H1B···N1ⁱⁱⁱ	2.0546
O1W···H2B^iv	2.1815	H1B···C6ⁱⁱⁱ	2.9624
O1W···H8Aⁱⁱ	2.8862	H1B···C7ⁱⁱⁱ	3.0952
O1W···H18C^v	2.8945	H2A···N3^vii	2.1872
N1···C14	3.408 (6)	H2A···C4^vii	3.0869
N1···O1Wⁱⁱⁱ	2.848 (6)	H2A···H8A^vii	2.4961
N2···O1W^vi	2.926 (6)	H2B···O1W^vi	2.1815
N2···N3^vii	3.045 (6)	H5···H8B	2.5995
N3···N2^vii	3.045 (6)	H5···Br1	3.1425
N11···Br1ⁱ	3.248 (5)	H5···H7B	2.4063
N12···N13^viii	2.993 (6)	H5A···H18B	2.4512
N12···Br1ⁱ	3.537 (5)	H7A···Br1ⁱⁱⁱ	3.2037
N13···N12^viii	2.993 (6)	H7B···H5	2.4063
N1···H1Bⁱⁱⁱ	2.0546	H8A···O1Wⁱⁱ	2.8862
N3···H2A^vii	2.1872	H8A···H2A^vii	2.4961
N13···H12A^viii	2.1341	H8B···Br1ⁱ	3.1478
C2···C14^ix	3.447 (7)	H8B···H5	2.5995
C4···C16^ix	3.479 (7)	H8C···Br1ⁱⁱ	3.1894
C4···C12	3.421 (7)	H11···Br1ⁱ	2.4126
C5···C16^ix	3.494 (7)	H11···H12B	2.2715
C5···C17^ix	3.594 (8)	H11···H17A	2.2297
C5···C16	3.513 (7)	H12A···N13^viii	2.1341
C6···C14	3.443 (7)	H12A···C12^viii	3.0840
C6···C15^ix	3.544 (7)	H12A···C14^viii	3.0145
C6···C15	3.464 (7)	H12A···C18^viii	3.0663
C7···C15	3.561 (8)	H12A···H18A^viii	2.5949
C12···C4	3.421 (7)	H12B···H1Aⁱ	2.5533
C14···C2^x	3.447 (7)	H12B···H11	2.2715
C14···N1	3.408 (6)	H12B···Br1ⁱ	2.7874
C14···C6	3.443 (7)	H17A···H11	2.2297
C15···C6^x	3.544 (7)	H17B···C7^v	3.0551
C15···C7	3.561 (8)	H17C···Br1	3.0631
C15···C6	3.464 (7)	H18A···H12A^viii	2.5949
C16···C5	3.513 (7)	H18B···H5A	2.4512
C16···C5^x	3.494 (7)	H18C···O1W^v	2.8945
C16···C4^x	3.479 (7)

H1A—O1W—H1B	105.97	C14—C18—H18B	109.42
C12—N11—C16	122.0 (4)	C14—C18—H18C	109.42
C12—N13—C14	117.2 (4)	C14—C18—H18A	109.44
C12—N11—H11	119.08	H18A—C18—H18B	109.50
C16—N11—H11	118.90	H18B—C18—H18C	109.51
H12A—N12—H12B	120.02	H18A—C18—H18C	109.55
C12—N12—H12A	119.95	N1—C2—N3	125.3 (4)
C12—N12—H12B	120.03	N2—C2—N3	117.2 (4)
C2—N1—C6	116.4 (4)	N1—C2—N2	117.5 (4)
C2—N3—C4	116.8 (4)	N3—C4—C5	121.7 (4)
H2A—N2—H2B	119.97	N3—C4—C8	117.0 (4)
C2—N2—H2A	119.99	C5—C4—C8	121.4 (4)
C2—N2—H2B	120.05	C4—C5—C6	118.2 (4)
N12—C12—N13	119.6 (4)	N1—C6—C7	116.7 (4)
N11—C12—N13	121.6 (4)	C5—C6—C7	121.8 (5)
N11—C12—N12	118.8 (4)	N1—C6—C5	121.5 (4)
N13—C14—C15	122.7 (4)	C6—C5—H5	120.85
N13—C14—C18	115.7 (4)	C4—C5—H5	120.92
C15—C14—C18	121.6 (4)	C6—C7—H7A	109.43
C14—C15—C16	119.2 (4)	C6—C7—H7B	109.43
C15—C16—C17	126.3 (4)	H7A—C7—H7B	109.53
N11—C16—C17	116.4 (4)	H7A—C7—H7C	109.53
N11—C16—C15	117.3 (4)	C6—C7—H7C	109.43
C14—C15—H5A	120.43	H7B—C7—H7C	109.48
C16—C15—H5A	120.37	C4—C8—H8B	109.49
C16—C17—H17B	109.40	C4—C8—H8C	109.46
C16—C17—H17A	109.49	C4—C8—H8A	109.42
H17A—C17—H17B	109.53	H8A—C8—H8C	109.48
C16—C17—H17C	109.43	H8B—C8—H8C	109.45
H17B—C17—H17C	109.52	H8A—C8—H8B	109.53
H17A—C17—H17C	109.46

C16—N11—C12—N12	−178.1 (4)	C4—N3—C2—N2	−178.9 (4)
C16—N11—C12—N13	1.6 (6)	C4—N3—C2—N1	2.5 (6)
C12—N11—C16—C15	0.0 (6)	C2—N3—C4—C5	−1.2 (6)
C12—N11—C16—C17	−178.7 (4)	C2—N3—C4—C8	178.6 (4)
C14—N13—C12—N11	−1.1 (6)	N13—C14—C15—C16	2.5 (7)
C14—N13—C12—N12	178.6 (4)	C18—C14—C15—C16	−177.1 (4)
C12—N13—C14—C15	−0.9 (6)	C14—C15—C16—N11	−2.0 (6)
C12—N13—C14—C18	178.7 (4)	C14—C15—C16—C17	176.6 (4)
C2—N1—C6—C7	178.4 (4)	C8—C4—C5—C6	179.4 (4)
C6—N1—C2—N2	179.9 (4)	N3—C4—C5—C6	−0.8 (6)
C2—N1—C6—C5	−0.6 (6)	C4—C5—C6—N1	1.7 (7)
C6—N1—C2—N3	−1.6 (6)	C4—C5—C6—C7	−177.2 (4)

Symmetry codes: (i) −x+1, −y, −z+1; (ii) −x, −y, −z+1; (iii) −x, −y+1, −z+1; (iv) x, y, z−1; (v) −x+1, −y+1, −z+1; (vi) x, y, z+1; (vii) −x, −y, −z+2; (viii) −x+1, −y, −z+2; (ix) x−1, y, z; (x) x+1, y, z; (xi) −x+1, −y+1, −z+2.

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
O1W—H1A···Br1	0.80	2.68	3.471 (6)	170
O1W—H1B···N1ⁱⁱⁱ	0.80	2.06	2.848 (6)	169
N2—H2A···N3^vii	0.86	2.19	3.045 (6)	175
N2—H2B···O1W^vi	0.86	2.18	2.926 (6)	145
N11—H11···Br1ⁱ	0.86	2.41	3.248 (5)	164
N12—H12A···N13^viii	0.86	2.13	2.993 (6)	177
N12—H12B···Br1ⁱ	0.86	2.79	3.537 (5)	147

Symmetry codes: (i) −x+1, −y, −z+1; (iii) −x, −y+1, −z+1; (vi) x, y, z+1; (vii) −x, −y, −z+2; (viii) −x+1, −y, −z+2.

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