Literature DB >> 21578492

2-Amino-4,6-dimethyl-pyrimidinium chloro-acetate.

Cui-Hua Lin, Nai-Sheng Liu, Fang-Fang Jian.

Abstract

There are two cations and two anions in the asymmetric unit of the title compound, C(6)H(10)N(3) (+)·C(2)H(2)ClO(2) (-). In the crystal, the components are linked by inter-molecular N-H⋯O and N-H⋯N hydrogen bonds to form a two-dimensional network. Additional stabilization is provided by weak inter-molecular C-H⋯O inter-actions.

Entities: Chemical Disease Species

Year: 2009 PMID： 21578492 PMCID： PMC2971421 DOI： 10.1107/S1600536809044444

Source DB: PubMed Journal: Acta Crystallogr Sect E Struct Rep Online ISSN： 1600-5368

Related literature

For background to pyrimidine derivatives, see: Xue et al. (1993 ▶); Hemamalini et al. (2005 ▶).

Experimental

Crystal data

C6H10N3 +·C2H2ClO2 − M = 217.66 Triclinic, a = 4.4560 (9) Å b = 12.302 (3) Å c = 19.441 (4) Å α = 92.90 (3)° β = 96.53 (3)° γ = 91.15 (3)° V = 1057.1 (4) Å3 Z = 4 Mo Kα radiation μ = 0.34 mm−1 T = 293 K 0.20 × 0.15 × 0.11 mm

Data collection

Bruker SMART CCD diffractometer Absorption correction: none 10303 measured reflections 4761 independent reflections 3452 reflections with I > 2σ(I) R int = 0.028

Refinement

R[F 2 > 2σ(F 2)] = 0.055 wR(F 2) = 0.195 S = 1.08 4761 reflections 253 parameters H-atom parameters constrained Δρmax = 0.42 e Å−3 Δρmin = −0.43 e Å−3 Data collection: SMART (Bruker, 1997 ▶); cell refinement: SAINT (Bruker, 1997 ▶); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ▶); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 ▶); molecular graphics: SHELXTL (Sheldrick, 2008 ▶); software used to prepare material for publication: SHELXTL. Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536809044444/hb5174sup1.cif Structure factors: contains datablocks I. DOI: 10.1107/S1600536809044444/hb5174Isup2.hkl Additional supplementary materials: crystallographic information; 3D view; checkCIF report

C₆H₁₀N₃⁺·C₂H₂ClO₂⁻	Z = 4
M_r = 217.66	F(000) = 456
Triclinic, P1	D_x = 1.368 Mg m⁻³
Hall symbol: -P 1	Mo Kα radiation, λ = 0.71073 Å
a = 4.4560 (9) Å	Cell parameters from 3452 reflections
b = 12.302 (3) Å	θ = 3.2–27.5°
c = 19.441 (4) Å	µ = 0.34 mm⁻¹
α = 92.90 (3)°	T = 293 K
β = 96.53 (3)°	Block, colourless
γ = 91.15 (3)°	0.20 × 0.15 × 0.11 mm
V = 1057.1 (4) Å³

Bruker SMART CCD diffractometer	3452 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tube	R_int = 0.028
graphite	θ_max = 27.5°, θ_min = 3.2°
ω scans	h = −5→5
10303 measured reflections	k = −15→15
4761 independent reflections	l = −25→25

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)] = 0.055	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.195	H-atom parameters constrained
S = 1.08	w = 1/[σ²(F_o²) + (0.1056P)² + 0.3945P] where P = (F_o² + 2F_c²)/3
4761 reflections	(Δ/σ)_max < 0.001
253 parameters	Δρ_max = 0.42 e Å⁻³
0 restraints	Δρ_min = −0.43 e Å⁻³

Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell e.s.d.'s are taken into account individually in the estimation of e.s.d.'s in distances, angles and torsion angles; correlations between e.s.d.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell e.s.d.'s is used for estimating e.s.d.'s 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 > σ(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.

	x	y	z	U_iso*/U_eq
Cl1	0.92264 (17)	0.01264 (6)	0.17209 (4)	0.0623 (2)
O4	0.7689 (5)	0.14297 (17)	−0.00572 (10)	0.0681 (6)
C16	0.8811 (6)	0.13347 (19)	0.05672 (13)	0.0463 (5)
O3	1.0794 (5)	0.19170 (18)	0.08873 (11)	0.0742 (7)
C15	0.7353 (7)	0.0407 (2)	0.09016 (14)	0.0616 (7)
H15A	0.7320	−0.0243	0.0596	0.074*
H15B	0.5276	0.0584	0.0954	0.074*
Cl2	0.8148 (2)	0.60659 (7)	0.34169 (5)	0.0862 (3)
O2	0.9854 (5)	0.38470 (15)	0.37047 (10)	0.0594 (5)
C14	0.8160 (6)	0.4192 (2)	0.41493 (13)	0.0497 (6)
O1	0.7445 (6)	0.36870 (18)	0.46320 (12)	0.0798 (7)
C13	0.6862 (8)	0.5308 (2)	0.40795 (16)	0.0632 (7)
H13A	0.7342	0.5722	0.4518	0.076*
H13B	0.4680	0.5230	0.3993	0.076*
N5	0.1724 (4)	0.18552 (15)	0.37450 (10)	0.0418 (4)
H5A	0.1093	0.2511	0.3762	0.050*
N6	0.1954 (5)	0.01175 (16)	0.42234 (10)	0.0467 (5)
C10	0.1065 (6)	0.11536 (19)	0.42261 (12)	0.0436 (5)
C9	0.4323 (6)	0.0461 (2)	0.32177 (13)	0.0502 (6)
H9A	0.5446	0.0210	0.2870	0.060*
C12	0.3572 (6)	−0.02223 (19)	0.37232 (13)	0.0477 (5)
C8	0.3363 (5)	0.15178 (19)	0.32440 (12)	0.0430 (5)
N4	−0.0552 (6)	0.15065 (18)	0.47176 (12)	0.0610 (6)
H4A	−0.1012	0.1075	0.5026	0.073*
H4B	−0.1145	0.2167	0.4729	0.073*
C7	0.4002 (7)	0.2310 (2)	0.27171 (13)	0.0554 (6)
H7A	0.3149	0.2998	0.2829	0.083*
H7B	0.3119	0.2038	0.2266	0.083*
H7C	0.6146	0.2402	0.2718	0.083*
C11	0.4550 (8)	−0.1383 (2)	0.37303 (18)	0.0689 (8)
H11A	0.3841	−0.1721	0.4118	0.103*
H11B	0.6715	−0.1400	0.3770	0.103*
H11C	0.3719	−0.1768	0.3308	0.103*
N2	0.0615 (5)	0.69331 (16)	0.07225 (10)	0.0457 (5)
H2A	0.1088	0.7470	0.0486	0.055*
N3	−0.2359 (5)	0.53279 (17)	0.07940 (11)	0.0489 (5)
C6	−0.0956 (6)	0.5215 (2)	0.14272 (13)	0.0493 (6)
N1	−0.2951 (5)	0.63311 (18)	−0.01745 (11)	0.0566 (6)
H1A	−0.4349	0.5876	−0.0354	0.068*
H1B	−0.2464	0.6878	−0.0401	0.068*
C4	−0.1547 (5)	0.61899 (19)	0.04524 (12)	0.0443 (5)
C2	0.2013 (5)	0.6821 (2)	0.13654 (13)	0.0472 (5)
C3	0.1249 (6)	0.5956 (2)	0.17351 (14)	0.0520 (6)
H3B	0.2183	0.5868	0.2181	0.062*
C1	0.4302 (6)	0.7682 (2)	0.16441 (15)	0.0594 (7)
H1C	0.4485	0.8204	0.1300	0.089*
H1D	0.6220	0.7355	0.1759	0.089*
H1E	0.3673	0.8039	0.2052	0.089*
C5	−0.1883 (8)	0.4234 (2)	0.17923 (16)	0.0657 (8)
H5B	−0.3422	0.3821	0.1499	0.099*
H5C	−0.2654	0.4466	0.2216	0.099*
H5D	−0.0162	0.3788	0.1896	0.099*

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
Cl1	0.0689 (4)	0.0673 (4)	0.0516 (4)	−0.0052 (3)	0.0041 (3)	0.0202 (3)
O4	0.0883 (15)	0.0633 (12)	0.0497 (11)	−0.0230 (11)	−0.0076 (10)	0.0170 (9)
C16	0.0500 (13)	0.0415 (12)	0.0478 (13)	−0.0017 (10)	0.0065 (10)	0.0057 (10)
O3	0.0887 (15)	0.0727 (14)	0.0573 (12)	−0.0334 (12)	−0.0100 (11)	0.0213 (10)
C15	0.0666 (17)	0.0649 (17)	0.0515 (15)	−0.0184 (14)	−0.0035 (12)	0.0182 (13)
Cl2	0.1195 (7)	0.0527 (4)	0.0972 (7)	0.0286 (4)	0.0432 (5)	0.0302 (4)
O2	0.0773 (13)	0.0450 (10)	0.0609 (11)	0.0132 (9)	0.0229 (10)	0.0130 (8)
C14	0.0569 (14)	0.0407 (12)	0.0512 (14)	0.0017 (11)	0.0031 (11)	0.0057 (10)
O1	0.1139 (19)	0.0612 (13)	0.0750 (14)	0.0228 (12)	0.0437 (13)	0.0261 (11)
C13	0.0779 (19)	0.0520 (15)	0.0638 (17)	0.0163 (14)	0.0193 (14)	0.0105 (13)
N5	0.0532 (11)	0.0323 (9)	0.0405 (10)	0.0009 (8)	0.0054 (8)	0.0097 (7)
N6	0.0617 (12)	0.0356 (10)	0.0449 (10)	0.0052 (9)	0.0101 (9)	0.0118 (8)
C10	0.0554 (13)	0.0375 (11)	0.0387 (11)	0.0014 (10)	0.0054 (9)	0.0096 (9)
C9	0.0628 (15)	0.0461 (13)	0.0436 (12)	0.0069 (11)	0.0116 (11)	0.0071 (10)
C12	0.0581 (14)	0.0393 (12)	0.0463 (13)	0.0068 (10)	0.0044 (10)	0.0076 (9)
C8	0.0476 (12)	0.0429 (12)	0.0383 (11)	−0.0006 (9)	0.0008 (9)	0.0096 (9)
N4	0.0932 (17)	0.0420 (11)	0.0545 (13)	0.0128 (11)	0.0300 (12)	0.0158 (9)
C7	0.0702 (16)	0.0512 (14)	0.0475 (13)	−0.0013 (12)	0.0140 (12)	0.0159 (11)
C11	0.094 (2)	0.0426 (14)	0.074 (2)	0.0197 (14)	0.0196 (17)	0.0118 (13)
N2	0.0515 (11)	0.0420 (10)	0.0458 (11)	−0.0001 (9)	0.0120 (8)	0.0094 (8)
N3	0.0563 (12)	0.0423 (10)	0.0505 (12)	0.0016 (9)	0.0129 (9)	0.0112 (9)
C6	0.0574 (14)	0.0451 (12)	0.0490 (13)	0.0119 (11)	0.0147 (11)	0.0138 (10)
N1	0.0679 (14)	0.0504 (12)	0.0507 (12)	−0.0145 (11)	0.0014 (10)	0.0147 (9)
C4	0.0480 (12)	0.0426 (12)	0.0443 (12)	0.0013 (10)	0.0116 (10)	0.0070 (9)
C2	0.0444 (12)	0.0497 (13)	0.0494 (13)	0.0098 (10)	0.0111 (10)	0.0051 (10)
C3	0.0547 (14)	0.0561 (14)	0.0472 (13)	0.0110 (12)	0.0089 (11)	0.0118 (11)
C1	0.0571 (15)	0.0599 (16)	0.0599 (16)	0.0006 (13)	0.0025 (12)	0.0015 (13)
C5	0.085 (2)	0.0530 (15)	0.0628 (17)	0.0037 (14)	0.0126 (15)	0.0231 (13)

Cl1—C15	1.766 (3)	C7—H7A	0.9600
O4—C16	1.271 (3)	C7—H7B	0.9600
C16—O3	1.219 (3)	C7—H7C	0.9600
C16—C15	1.512 (3)	C11—H11A	0.9600
C15—H15A	0.9700	C11—H11B	0.9600
C15—H15B	0.9700	C11—H11C	0.9600
Cl2—C13	1.767 (3)	N2—C2	1.347 (3)
O2—C14	1.273 (3)	N2—C4	1.357 (3)
C14—O1	1.220 (3)	N2—H2A	0.8600
C14—C13	1.507 (4)	N3—C6	1.331 (3)
C13—H13A	0.9700	N3—C4	1.344 (3)
C13—H13B	0.9700	C6—C3	1.389 (4)
N5—C8	1.337 (3)	C6—C5	1.505 (3)
N5—C10	1.356 (3)	N1—C4	1.326 (3)
N5—H5A	0.8600	N1—H1A	0.8600
N6—C12	1.331 (3)	N1—H1B	0.8600
N6—C10	1.342 (3)	C2—C3	1.372 (4)
C10—N4	1.322 (3)	C2—C1	1.493 (4)
C9—C8	1.378 (4)	C3—H3B	0.9300
C9—C12	1.389 (3)	C1—H1C	0.9600
C9—H9A	0.9300	C1—H1D	0.9600
C12—C11	1.501 (4)	C1—H1E	0.9600
C8—C7	1.495 (3)	C5—H5B	0.9600
N4—H4A	0.8600	C5—H5C	0.9600
N4—H4B	0.8600	C5—H5D	0.9600

O3—C16—O4	126.0 (2)	C8—C7—H7C	109.5
O3—C16—C15	121.5 (2)	H7A—C7—H7C	109.5
O4—C16—C15	112.5 (2)	H7B—C7—H7C	109.5
C16—C15—Cl1	113.42 (19)	C12—C11—H11A	109.5
C16—C15—H15A	108.9	C12—C11—H11B	109.5
Cl1—C15—H15A	108.9	H11A—C11—H11B	109.5
C16—C15—H15B	108.9	C12—C11—H11C	109.5
Cl1—C15—H15B	108.9	H11A—C11—H11C	109.5
H15A—C15—H15B	107.7	H11B—C11—H11C	109.5
O1—C14—O2	125.4 (2)	C2—N2—C4	119.3 (2)
O1—C14—C13	116.1 (2)	C2—N2—H2A	120.4
O2—C14—C13	118.5 (2)	C4—N2—H2A	120.4
C14—C13—Cl2	115.3 (2)	C6—N3—C4	117.5 (2)
C14—C13—H13A	108.5	N3—C6—C3	122.1 (2)
Cl2—C13—H13A	108.5	N3—C6—C5	116.2 (2)
C14—C13—H13B	108.5	C3—C6—C5	121.7 (2)
Cl2—C13—H13B	108.5	C4—N1—H1A	120.0
H13A—C13—H13B	107.5	C4—N1—H1B	120.0
C8—N5—C10	119.4 (2)	H1A—N1—H1B	120.0
C8—N5—H5A	120.3	N1—C4—N3	118.6 (2)
C10—N5—H5A	120.3	N1—C4—N2	118.3 (2)
C12—N6—C10	117.6 (2)	N3—C4—N2	123.1 (2)
N4—C10—N6	118.5 (2)	N2—C2—C3	119.7 (2)
N4—C10—N5	118.3 (2)	N2—C2—C1	116.9 (2)
N6—C10—N5	123.2 (2)	C3—C2—C1	123.4 (2)
C8—C9—C12	118.4 (2)	C2—C3—C6	118.4 (2)
C8—C9—H9A	120.8	C2—C3—H3B	120.8
C12—C9—H9A	120.8	C6—C3—H3B	120.8
N6—C12—C9	121.8 (2)	C2—C1—H1C	109.5
N6—C12—C11	116.7 (2)	C2—C1—H1D	109.5
C9—C12—C11	121.5 (2)	H1C—C1—H1D	109.5
N5—C8—C9	119.7 (2)	C2—C1—H1E	109.5
N5—C8—C7	117.8 (2)	H1C—C1—H1E	109.5
C9—C8—C7	122.5 (2)	H1D—C1—H1E	109.5
C10—N4—H4A	120.0	C6—C5—H5B	109.5
C10—N4—H4B	120.0	C6—C5—H5C	109.5
H4A—N4—H4B	120.0	H5B—C5—H5C	109.5
C8—C7—H7A	109.5	C6—C5—H5D	109.5
C8—C7—H7B	109.5	H5B—C5—H5D	109.5
H7A—C7—H7B	109.5	H5C—C5—H5D	109.5

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1A···N3ⁱ	0.86	2.14	2.999 (3)	177
N1—H1B···O3ⁱⁱ	0.86	1.98	2.830 (3)	173
N2—H2A···O4ⁱⁱ	0.86	1.74	2.593 (3)	175
N4—H4A···N6ⁱⁱⁱ	0.86	2.19	3.046 (3)	175
N4—H4B···O1^iv	0.86	2.00	2.851 (3)	173
N5—H5A···O2^iv	0.86	1.75	2.606 (3)	174
C1—H1C···O4ⁱⁱ	0.96	2.56	3.355 (4)	140
C7—H7A···O2^iv	0.96	2.57	3.355 (4)	139

Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N1—H1A⋯N3ⁱ	0.86	2.14	2.999 (3)	177
N1—H1B⋯O3ⁱⁱ	0.86	1.98	2.830 (3)	173
N2—H2A⋯O4ⁱⁱ	0.86	1.74	2.593 (3)	175
N4—H4A⋯N6ⁱⁱⁱ	0.86	2.19	3.046 (3)	175
N4—H4B⋯O1^iv	0.86	2.00	2.851 (3)	173
N5—H5A⋯O2^iv	0.86	1.75	2.606 (3)	174
C1—H1C⋯O4ⁱⁱ	0.96	2.56	3.355 (4)	140
C7—H7A⋯O2^iv	0.96	2.57	3.355 (4)	139

Symmetry codes: (i) ; (ii) ; (iii) ; (iv) .

2 in total

1. A short history of SHELX.

Authors: George M Sheldrick
Journal: Acta Crystallogr A Date: 2007-12-21 Impact factor: 2.290

2. Hydrogen-bonding patterns in 2-amino-4,6-dimethylpyrimidinium hydrogen sulfate.

Authors: Madhukar Hemamalini; Packianathan Thomas Muthiah; Urszula Rychlewska; Agnieszka Plutecka
Journal: Acta Crystallogr C Date: 2005-01-22 Impact factor: 1.172

2 in total