organic compounds
6-Chloro-N4,N4-dimethylpyrimidine-2,4-diamine
aDepartment of Chemistry, Shandong Normal University, Jinan 250014, People's Republic of China
*Correspondence e-mail: chdsguo@sdnu.edu.cn
The 6H9ClN4, contains four independent molecules (A, B, C and D). Their main difference is the torsion angles, ranging from 1.6 (5) to 5.9 (5)°, between the methyl group and the pyrimidine plane. A pair of intermolecular N—H⋯N hydrogen bonds link molecules A and C into a twisted dimer with a dihedral angle of 32.9 (1)° between the two pyrimidine rings, creating an R22(8) motif. In the packing, each two molecules of B, C and D form centrosymmetric dimers through two intermolecular N—H⋯N hydrogen bonds, locally creating R22(8) motifs. The dimers of C and D are alternately bridged by A into an infinite zigzag strip, locally creating two different R22(8) motifs with dihedral angles of 32.9 (1) and 63.4 (1)° between the pyrimidine rings. Finally, these strips together with the dimers of B associate into a complicated three-dimensional framework.
of the title compound, CRelated literature
For background to pyrimidine derivatives, see: Ligthart et al. (2005); Rabie et al. (2007); Goswami et al.(2008); Sherrington & Taskinen (2001). For similar structures, see: Cetina et al. (2005); Fun et al. (2006); Li et al. (2008); Ebenezer & Muthiah (2010); Cheng et al. (2011). For hydrogen-bond motifs, see: Bernstein et al. (1995).
Experimental
Crystal data
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Refinement
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Data collection: SMART (Bruker, 1999); cell SAINT (Bruker, 1999); 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.
Supporting information
10.1107/S1600536812013517/zq2159sup1.cif
contains datablocks I, global. DOI:Structure factors: contains datablock I. DOI: 10.1107/S1600536812013517/zq2159Isup2.hkl
Supporting information file. DOI: 10.1107/S1600536812013517/zq2159Isup3.cml
2-Amino-4,6-dichloropyrimidine (0.082 g, 0.5 mmol) and K2CO3 (0.276 g, 2 mmol) were dissolved in DMF (2 ml) and H2O (2 ml), the mixture was heated at 343 K for 0.5 h and then cooled to room temperature. The resulting mixture was extracted with ethyl acetate. The organic layer was separated and washed with brine, then dried over anhydrous MgSO4. Removal of the solvent under reduced pressure gave the title compound as a yellow solid (yield 85%). Single crystals suitable for X-ray
were obtained by liquid–liquid diffusion from hexane and CH2Cl2 at 298 K.All non-hydrogen atoms were refined with anisotropic displacement parameters. Hydrogen atoms attached to anisotropically refined atoms were placed in geometrically idealized positions and included as riding atoms with C—H = 0.93 Å and Uiso(H) = 1.2 Ueq(C) (aromatic); C—H = 0.96 Å and Uiso(H) = 1.5 Ueq(C) (methyl); N—H = 0.87–0.88 Å and Uiso(H) = 1.2Ueq(N).
Data collection: SMART (Bruker, 1999); cell
SAINT (Bruker, 1999); data reduction: SAINT (Bruker, 1999); 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 (Sheldrick, 2008).Fig. 1. The molecular structure of the title compound, with displacement ellipsoids drawn at the 30% probability level. Dashed lines indicate hydrogen bonds. | |
Fig. 2. A centrosymmetric dimer of the D molecule, viewed along the crystallographic b axis, showing the R22(8) motif. For the sake of clarity, H atoms not involved in the motif have been omitted [symmetry code: (i) -x + 1, -y + 1, -z]. | |
Fig. 3. An infinite zigzag strip formed by a combination of A, C and D through hydrogen bonds, showing different R22(8) motifs. For the sake of clarity, H atoms not involved in the motifs have been omitted [symmetry codes: (ii) -x + 1, -y + 1, -z + 1; (iii) -x, -y, -z + 1]. |
C6H9ClN4 | Z = 8 |
Mr = 172.62 | F(000) = 720 |
Triclinic, P1 | Dx = 1.417 Mg m−3 |
Hall symbol: -P 1 | Mo Kα radiation, λ = 0.71073 Å |
a = 7.9438 (19) Å | Cell parameters from 2311 reflections |
b = 14.225 (3) Å | θ = 2.6–27.7° |
c = 14.895 (3) Å | µ = 0.41 mm−1 |
α = 100.114 (3)° | T = 298 K |
β = 94.421 (4)° | Block, colourless |
γ = 100.524 (4)° | 0.21 × 0.18 × 0.16 mm |
V = 1618.7 (7) Å3 |
Bruker SMART CCD area-detector diffractometer | 5619 independent reflections |
Radiation source: fine-focus sealed tube | 3769 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.029 |
phi and ω scans | θmax = 25.0°, θmin = 1.5° |
Absorption correction: multi-scan (SADABS; Bruker, 1999) | h = −9→8 |
Tmin = 0.919, Tmax = 0.937 | k = −16→16 |
8239 measured reflections | l = −17→15 |
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)] = 0.058 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.136 | H-atom parameters constrained |
S = 0.97 | w = 1/[σ2(Fo2) + (0.0681P)2] where P = (Fo2 + 2Fc2)/3 |
5619 reflections | (Δ/σ)max = 0.001 |
405 parameters | Δρmax = 0.27 e Å−3 |
0 restraints | Δρmin = −0.32 e Å−3 |
C6H9ClN4 | γ = 100.524 (4)° |
Mr = 172.62 | V = 1618.7 (7) Å3 |
Triclinic, P1 | Z = 8 |
a = 7.9438 (19) Å | Mo Kα radiation |
b = 14.225 (3) Å | µ = 0.41 mm−1 |
c = 14.895 (3) Å | T = 298 K |
α = 100.114 (3)° | 0.21 × 0.18 × 0.16 mm |
β = 94.421 (4)° |
Bruker SMART CCD area-detector diffractometer | 5619 independent reflections |
Absorption correction: multi-scan (SADABS; Bruker, 1999) | 3769 reflections with I > 2σ(I) |
Tmin = 0.919, Tmax = 0.937 | Rint = 0.029 |
8239 measured reflections |
R[F2 > 2σ(F2)] = 0.058 | 0 restraints |
wR(F2) = 0.136 | H-atom parameters constrained |
S = 0.97 | Δρmax = 0.27 e Å−3 |
5619 reflections | Δρmin = −0.32 e Å−3 |
405 parameters |
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 | Uiso*/Ueq | ||
N1 | 0.3407 (3) | 0.34115 (18) | 0.54662 (16) | 0.0383 (6) | |
N2 | 0.4648 (3) | 0.47960 (18) | 0.66542 (16) | 0.0369 (6) | |
N3 | 0.5150 (4) | 0.32771 (19) | 0.67110 (18) | 0.0534 (8) | |
N4 | 0.1803 (4) | 0.3573 (2) | 0.41724 (17) | 0.0498 (8) | |
N5 | 0.3131 (3) | 0.56029 (17) | 0.00737 (15) | 0.0377 (6) | |
N6 | 0.2031 (3) | 0.57494 (17) | 0.15383 (16) | 0.0356 (6) | |
N7 | 0.4281 (4) | 0.49791 (19) | 0.12364 (16) | 0.0469 (8) | |
N8 | −0.0361 (4) | 0.64285 (19) | 0.18002 (18) | 0.0451 (7) | |
N9 | 0.4193 (3) | 0.08990 (18) | 0.62696 (16) | 0.0379 (6) | |
N10 | 0.1931 (3) | −0.03793 (18) | 0.54295 (16) | 0.0390 (7) | |
N11 | 0.1596 (4) | 0.12009 (19) | 0.5723 (2) | 0.0542 (8) | |
N12 | 0.6743 (4) | 0.0572 (2) | 0.68555 (18) | 0.0478 (7) | |
N13 | 0.3235 (4) | 0.9764 (2) | 0.83692 (19) | 0.0511 (8) | |
N14 | 0.5994 (4) | 1.03959 (18) | 0.90517 (17) | 0.0405 (7) | |
N15 | 0.8008 (3) | 0.93718 (19) | 0.93227 (17) | 0.0412 (7) | |
N16 | 0.8765 (4) | 1.10315 (19) | 0.9711 (2) | 0.0567 (8) | |
C1 | 0.2689 (4) | 0.3996 (2) | 0.4992 (2) | 0.0387 (8) | |
C2 | 0.2883 (4) | 0.4998 (2) | 0.5353 (2) | 0.0405 (8) | |
H2 | 0.2382 | 0.5412 | 0.5047 | 0.049* | |
C3 | 0.3852 (4) | 0.5320 (2) | 0.6179 (2) | 0.0370 (8) | |
C4 | 0.4379 (4) | 0.3849 (2) | 0.6250 (2) | 0.0399 (8) | |
C5 | 0.1705 (5) | 0.2558 (3) | 0.3791 (2) | 0.0619 (11) | |
H5A | 0.2531 | 0.2309 | 0.4139 | 0.093* | |
H5B | 0.1951 | 0.2490 | 0.3164 | 0.093* | |
H5C | 0.0568 | 0.2198 | 0.3815 | 0.093* | |
C6 | 0.1034 (5) | 0.4146 (3) | 0.3586 (2) | 0.0667 (11) | |
H6A | 0.0397 | 0.4559 | 0.3942 | 0.100* | |
H6B | 0.0272 | 0.3715 | 0.3092 | 0.100* | |
H6C | 0.1929 | 0.4541 | 0.3340 | 0.100* | |
C7 | 0.0773 (4) | 0.6171 (2) | 0.1222 (2) | 0.0362 (8) | |
C8 | −0.1760 (5) | 0.6879 (3) | 0.1505 (3) | 0.0643 (11) | |
H8A | −0.1297 | 0.7441 | 0.1262 | 0.096* | |
H8B | −0.2361 | 0.7072 | 0.2020 | 0.096* | |
H8C | −0.2544 | 0.6420 | 0.1039 | 0.096* | |
C9 | −0.0343 (5) | 0.6179 (3) | 0.2706 (2) | 0.0570 (10) | |
H9A | −0.1284 | 0.5649 | 0.2705 | 0.086* | |
H9B | −0.0458 | 0.6735 | 0.3150 | 0.086* | |
H9C | 0.0725 | 0.5990 | 0.2861 | 0.086* | |
C10 | 0.0687 (4) | 0.6347 (2) | 0.0317 (2) | 0.0376 (8) | |
H10 | −0.0150 | 0.6648 | 0.0084 | 0.045* | |
C11 | 0.1901 (4) | 0.6050 (2) | −0.01859 (19) | 0.0363 (8) | |
C12 | 0.3096 (4) | 0.5455 (2) | 0.09442 (19) | 0.0348 (7) | |
C13 | 0.7969 (5) | −0.0067 (3) | 0.6925 (2) | 0.0623 (11) | |
H13A | 0.7474 | −0.0597 | 0.7204 | 0.093* | |
H13B | 0.9006 | 0.0295 | 0.7293 | 0.093* | |
H13C | 0.8232 | −0.0321 | 0.6322 | 0.093* | |
C14 | 0.7279 (5) | 0.1570 (2) | 0.7337 (3) | 0.0610 (11) | |
H14A | 0.7736 | 0.1970 | 0.6921 | 0.092* | |
H14B | 0.8149 | 0.1607 | 0.7833 | 0.092* | |
H14C | 0.6306 | 0.1797 | 0.7577 | 0.092* | |
C15 | 0.5186 (4) | 0.0239 (2) | 0.63617 (19) | 0.0375 (8) | |
C16 | 0.4614 (4) | −0.0744 (2) | 0.5956 (2) | 0.0418 (8) | |
H16 | 0.5303 | −0.1203 | 0.5987 | 0.050* | |
C17 | 0.2997 (4) | −0.0987 (2) | 0.55161 (19) | 0.0367 (8) | |
C18 | 0.2619 (4) | 0.0556 (2) | 0.5810 (2) | 0.0380 (8) | |
C19 | 0.1863 (5) | 0.8969 (3) | 0.7904 (3) | 0.0694 (12) | |
H19A | 0.2290 | 0.8584 | 0.7410 | 0.104* | |
H19B | 0.0928 | 0.9228 | 0.7663 | 0.104* | |
H19C | 0.1462 | 0.8569 | 0.8330 | 0.104* | |
C20 | 0.2873 (5) | 1.0738 (3) | 0.8461 (2) | 0.0594 (11) | |
H20A | 0.3797 | 1.1194 | 0.8848 | 0.089* | |
H20B | 0.1816 | 1.0755 | 0.8730 | 0.089* | |
H20C | 0.2765 | 1.0909 | 0.7867 | 0.089* | |
C21 | 0.4788 (4) | 0.9608 (2) | 0.8677 (2) | 0.0394 (8) | |
C22 | 0.5135 (4) | 0.8663 (2) | 0.8614 (2) | 0.0447 (9) | |
H22 | 0.4315 | 0.8106 | 0.8359 | 0.054* | |
C23 | 0.6750 (5) | 0.8624 (2) | 0.8952 (2) | 0.0419 (8) | |
C24 | 0.7528 (4) | 1.0241 (2) | 0.9355 (2) | 0.0396 (8) | |
Cl1 | 0.41068 (13) | 0.65460 (6) | 0.66924 (6) | 0.0559 (3) | |
Cl2 | 0.72990 (15) | 0.74846 (7) | 0.89197 (7) | 0.0725 (3) | |
Cl3 | 0.21621 (13) | −0.21962 (6) | 0.49962 (6) | 0.0594 (3) | |
Cl4 | 0.19291 (13) | 0.62621 (7) | −0.13080 (5) | 0.0581 (3) | |
H7A | 0.4312 | 0.4882 | 0.1794 | 0.070* | |
H11B | 0.2061 | 0.1818 | 0.5803 | 0.070* | |
H16A | 0.8516 | 1.1614 | 0.9822 | 0.070* | |
H3A | 0.4991 | 0.2653 | 0.6522 | 0.070* | |
H7B | 0.5017 | 0.4822 | 0.0852 | 0.070* | |
H16B | 0.9661 | 1.0935 | 1.0027 | 0.070* | |
H3B | 0.5805 | 0.3546 | 0.7235 | 0.070* | |
H11A | 0.0579 | 0.1009 | 0.5408 | 0.070* |
U11 | U22 | U33 | U12 | U13 | U23 | |
N1 | 0.0343 (17) | 0.0405 (16) | 0.0382 (14) | 0.0061 (13) | −0.0005 (12) | 0.0055 (12) |
N2 | 0.0337 (17) | 0.0400 (16) | 0.0369 (14) | 0.0079 (13) | 0.0031 (12) | 0.0067 (12) |
N3 | 0.066 (2) | 0.0450 (17) | 0.0496 (17) | 0.0224 (16) | −0.0095 (15) | 0.0045 (13) |
N4 | 0.047 (2) | 0.060 (2) | 0.0405 (16) | 0.0082 (15) | −0.0063 (14) | 0.0101 (14) |
N5 | 0.0362 (17) | 0.0406 (16) | 0.0368 (15) | 0.0086 (13) | 0.0070 (12) | 0.0070 (11) |
N6 | 0.0336 (17) | 0.0365 (15) | 0.0388 (14) | 0.0103 (13) | 0.0078 (12) | 0.0078 (11) |
N7 | 0.050 (2) | 0.0593 (19) | 0.0398 (15) | 0.0284 (16) | 0.0106 (13) | 0.0122 (13) |
N8 | 0.0385 (18) | 0.0476 (17) | 0.0540 (17) | 0.0158 (14) | 0.0164 (14) | 0.0101 (13) |
N9 | 0.0298 (16) | 0.0432 (16) | 0.0411 (15) | 0.0069 (13) | −0.0009 (12) | 0.0115 (12) |
N10 | 0.0314 (17) | 0.0422 (17) | 0.0415 (15) | 0.0040 (14) | −0.0016 (12) | 0.0093 (12) |
N11 | 0.0368 (19) | 0.0418 (17) | 0.081 (2) | 0.0086 (14) | −0.0111 (16) | 0.0110 (14) |
N12 | 0.0370 (18) | 0.0517 (19) | 0.0523 (17) | 0.0066 (15) | −0.0087 (14) | 0.0122 (14) |
N13 | 0.0315 (18) | 0.059 (2) | 0.0599 (18) | 0.0097 (15) | −0.0050 (14) | 0.0063 (14) |
N14 | 0.0359 (18) | 0.0409 (16) | 0.0439 (15) | 0.0071 (14) | 0.0011 (13) | 0.0086 (12) |
N15 | 0.0354 (17) | 0.0395 (17) | 0.0452 (15) | 0.0040 (14) | −0.0049 (13) | 0.0062 (12) |
N16 | 0.048 (2) | 0.0376 (17) | 0.077 (2) | 0.0010 (15) | −0.0156 (16) | 0.0083 (14) |
C1 | 0.0256 (19) | 0.049 (2) | 0.0412 (18) | 0.0038 (16) | 0.0070 (15) | 0.0107 (15) |
C2 | 0.033 (2) | 0.050 (2) | 0.0437 (19) | 0.0134 (16) | 0.0066 (15) | 0.0154 (15) |
C3 | 0.032 (2) | 0.0403 (19) | 0.0410 (18) | 0.0072 (16) | 0.0159 (15) | 0.0094 (14) |
C4 | 0.033 (2) | 0.046 (2) | 0.0418 (18) | 0.0081 (16) | 0.0063 (15) | 0.0116 (16) |
C5 | 0.061 (3) | 0.060 (3) | 0.050 (2) | −0.008 (2) | −0.0051 (19) | −0.0023 (17) |
C6 | 0.054 (3) | 0.095 (3) | 0.051 (2) | 0.019 (2) | −0.0105 (19) | 0.017 (2) |
C7 | 0.034 (2) | 0.0230 (17) | 0.0479 (18) | 0.0003 (15) | 0.0042 (15) | 0.0028 (13) |
C8 | 0.047 (3) | 0.069 (3) | 0.086 (3) | 0.029 (2) | 0.020 (2) | 0.015 (2) |
C9 | 0.057 (3) | 0.059 (2) | 0.058 (2) | 0.010 (2) | 0.0266 (19) | 0.0089 (17) |
C10 | 0.035 (2) | 0.0297 (18) | 0.0488 (19) | 0.0062 (15) | 0.0008 (16) | 0.0107 (14) |
C11 | 0.039 (2) | 0.0290 (17) | 0.0374 (17) | −0.0008 (15) | 0.0005 (15) | 0.0074 (13) |
C12 | 0.033 (2) | 0.0321 (18) | 0.0383 (17) | 0.0067 (15) | 0.0053 (15) | 0.0040 (13) |
C13 | 0.041 (2) | 0.076 (3) | 0.071 (3) | 0.018 (2) | −0.009 (2) | 0.017 (2) |
C14 | 0.050 (3) | 0.053 (2) | 0.073 (3) | −0.0062 (19) | −0.019 (2) | 0.0236 (19) |
C15 | 0.031 (2) | 0.047 (2) | 0.0357 (17) | 0.0060 (16) | 0.0044 (15) | 0.0143 (14) |
C16 | 0.033 (2) | 0.048 (2) | 0.0485 (19) | 0.0157 (17) | 0.0056 (16) | 0.0128 (16) |
C17 | 0.034 (2) | 0.0422 (19) | 0.0354 (17) | 0.0076 (16) | 0.0033 (15) | 0.0108 (14) |
C18 | 0.030 (2) | 0.046 (2) | 0.0405 (17) | 0.0097 (17) | 0.0055 (15) | 0.0134 (15) |
C19 | 0.038 (2) | 0.088 (3) | 0.076 (3) | 0.006 (2) | −0.010 (2) | 0.014 (2) |
C20 | 0.052 (3) | 0.074 (3) | 0.061 (2) | 0.032 (2) | 0.0055 (19) | 0.0148 (19) |
C21 | 0.035 (2) | 0.043 (2) | 0.0380 (17) | 0.0033 (17) | 0.0050 (15) | 0.0064 (14) |
C22 | 0.039 (2) | 0.042 (2) | 0.0471 (19) | −0.0002 (17) | −0.0058 (16) | 0.0035 (15) |
C23 | 0.046 (2) | 0.037 (2) | 0.0430 (18) | 0.0104 (17) | −0.0022 (17) | 0.0085 (14) |
C24 | 0.038 (2) | 0.039 (2) | 0.0386 (17) | 0.0002 (17) | 0.0019 (15) | 0.0080 (14) |
Cl1 | 0.0686 (7) | 0.0406 (5) | 0.0582 (5) | 0.0122 (5) | 0.0097 (5) | 0.0062 (4) |
Cl2 | 0.0785 (8) | 0.0406 (6) | 0.0913 (7) | 0.0163 (5) | −0.0270 (6) | 0.0051 (5) |
Cl3 | 0.0610 (7) | 0.0407 (5) | 0.0700 (6) | 0.0063 (5) | −0.0074 (5) | 0.0037 (4) |
Cl4 | 0.0674 (7) | 0.0670 (6) | 0.0436 (5) | 0.0108 (5) | 0.0059 (4) | 0.0233 (4) |
N1—C4 | 1.333 (4) | C1—C2 | 1.409 (4) |
N1—C1 | 1.353 (4) | C2—C3 | 1.357 (4) |
N2—C3 | 1.321 (4) | C2—H2 | 0.9300 |
N2—C4 | 1.347 (4) | C3—Cl1 | 1.746 (3) |
N3—C4 | 1.350 (4) | C5—H5A | 0.9600 |
N3—H3A | 0.8649 | C5—H5B | 0.9600 |
N3—H3B | 0.8870 | C5—H5C | 0.9600 |
N4—C1 | 1.343 (4) | C6—H6A | 0.9600 |
N4—C5 | 1.441 (4) | C6—H6B | 0.9600 |
N4—C6 | 1.467 (4) | C6—H6C | 0.9600 |
N5—C11 | 1.329 (4) | C7—C10 | 1.411 (4) |
N5—C12 | 1.351 (3) | C8—H8A | 0.9600 |
N6—C12 | 1.338 (4) | C8—H8B | 0.9600 |
N6—C7 | 1.351 (4) | C8—H8C | 0.9600 |
N7—C12 | 1.344 (4) | C9—H9A | 0.9600 |
N7—H7A | 0.8654 | C9—H9B | 0.9600 |
N7—H7B | 0.8789 | C9—H9C | 0.9600 |
N8—C7 | 1.348 (4) | C10—C11 | 1.349 (4) |
N8—C9 | 1.453 (4) | C10—H10 | 0.9300 |
N8—C8 | 1.456 (4) | C11—Cl4 | 1.751 (3) |
N9—C18 | 1.341 (4) | C13—H13A | 0.9600 |
N9—C15 | 1.350 (4) | C13—H13B | 0.9600 |
N10—C17 | 1.330 (4) | C13—H13C | 0.9600 |
N10—C18 | 1.346 (4) | C14—H14A | 0.9600 |
N11—C18 | 1.348 (4) | C14—H14B | 0.9600 |
N11—H11B | 0.8716 | C14—H14C | 0.9600 |
N11—H11A | 0.8741 | C15—C16 | 1.399 (4) |
N12—C15 | 1.349 (4) | C16—C17 | 1.352 (4) |
N12—C14 | 1.444 (4) | C16—H16 | 0.9300 |
N12—C13 | 1.458 (4) | C17—Cl3 | 1.742 (3) |
N13—C21 | 1.353 (4) | C19—H19A | 0.9600 |
N13—C20 | 1.450 (4) | C19—H19B | 0.9600 |
N13—C19 | 1.452 (5) | C19—H19C | 0.9600 |
N14—C24 | 1.337 (4) | C20—H20A | 0.9600 |
N14—C21 | 1.338 (4) | C20—H20B | 0.9600 |
N15—C23 | 1.325 (4) | C20—H20C | 0.9600 |
N15—C24 | 1.353 (4) | C21—C22 | 1.409 (4) |
N16—C24 | 1.348 (4) | C22—C23 | 1.356 (4) |
N16—H16A | 0.8773 | C22—H22 | 0.9300 |
N16—H16B | 0.8682 | C23—Cl2 | 1.747 (3) |
C4—N1—C1 | 116.3 (3) | H8B—C8—H8C | 109.5 |
C3—N2—C4 | 113.1 (3) | N8—C9—H9A | 109.5 |
C4—N3—H3A | 122.0 | N8—C9—H9B | 109.5 |
C4—N3—H3B | 118.9 | H9A—C9—H9B | 109.5 |
H3A—N3—H3B | 119.1 | N8—C9—H9C | 109.5 |
C1—N4—C5 | 121.6 (3) | H9A—C9—H9C | 109.5 |
C1—N4—C6 | 121.2 (3) | H9B—C9—H9C | 109.5 |
C5—N4—C6 | 116.9 (3) | C11—C10—C7 | 115.4 (3) |
C11—N5—C12 | 113.1 (3) | C11—C10—H10 | 122.3 |
C12—N6—C7 | 117.2 (2) | C7—C10—H10 | 122.3 |
C12—N7—H7A | 118.4 | N5—C11—C10 | 127.1 (3) |
C12—N7—H7B | 116.9 | N5—C11—Cl4 | 114.1 (2) |
H7A—N7—H7B | 124.6 | C10—C11—Cl4 | 118.8 (2) |
C7—N8—C9 | 121.4 (3) | N6—C12—N7 | 117.7 (3) |
C7—N8—C8 | 121.0 (3) | N6—C12—N5 | 126.5 (3) |
C9—N8—C8 | 117.3 (3) | N7—C12—N5 | 115.8 (3) |
C18—N9—C15 | 116.7 (3) | N12—C13—H13A | 109.5 |
C17—N10—C18 | 113.7 (3) | N12—C13—H13B | 109.5 |
C18—N11—H11B | 119.1 | H13A—C13—H13B | 109.5 |
C18—N11—H11A | 120.3 | N12—C13—H13C | 109.5 |
H11B—N11—H11A | 117.1 | H13A—C13—H13C | 109.5 |
C15—N12—C14 | 122.1 (3) | H13B—C13—H13C | 109.5 |
C15—N12—C13 | 121.0 (3) | N12—C14—H14A | 109.5 |
C14—N12—C13 | 116.9 (3) | N12—C14—H14B | 109.5 |
C21—N13—C20 | 121.8 (3) | H14A—C14—H14B | 109.5 |
C21—N13—C19 | 121.7 (3) | N12—C14—H14C | 109.5 |
C20—N13—C19 | 116.5 (3) | H14A—C14—H14C | 109.5 |
C24—N14—C21 | 116.9 (3) | H14B—C14—H14C | 109.5 |
C23—N15—C24 | 112.7 (3) | N12—C15—N9 | 117.0 (3) |
C24—N16—H16A | 120.6 | N12—C15—C16 | 122.0 (3) |
C24—N16—H16B | 116.8 | N9—C15—C16 | 120.9 (3) |
H16A—N16—H16B | 117.8 | C17—C16—C15 | 115.9 (3) |
N4—C1—N1 | 116.8 (3) | C17—C16—H16 | 122.1 |
N4—C1—C2 | 122.5 (3) | C15—C16—H16 | 122.1 |
N1—C1—C2 | 120.7 (3) | N10—C17—C16 | 126.1 (3) |
C3—C2—C1 | 115.4 (3) | N10—C17—Cl3 | 114.6 (2) |
C3—C2—H2 | 122.3 | C16—C17—Cl3 | 119.3 (2) |
C1—C2—H2 | 122.3 | N9—C18—N10 | 126.6 (3) |
N2—C3—C2 | 126.7 (3) | N9—C18—N11 | 117.6 (3) |
N2—C3—Cl1 | 114.8 (2) | N10—C18—N11 | 115.8 (3) |
C2—C3—Cl1 | 118.5 (2) | N13—C19—H19A | 109.5 |
N1—C4—N2 | 127.6 (3) | N13—C19—H19B | 109.5 |
N1—C4—N3 | 116.7 (3) | H19A—C19—H19B | 109.5 |
N2—C4—N3 | 115.7 (3) | N13—C19—H19C | 109.5 |
N4—C5—H5A | 109.5 | H19A—C19—H19C | 109.5 |
N4—C5—H5B | 109.5 | H19B—C19—H19C | 109.5 |
H5A—C5—H5B | 109.5 | N13—C20—H20A | 109.5 |
N4—C5—H5C | 109.5 | N13—C20—H20B | 109.5 |
H5A—C5—H5C | 109.5 | H20A—C20—H20B | 109.5 |
H5B—C5—H5C | 109.5 | N13—C20—H20C | 109.5 |
N4—C6—H6A | 109.5 | H20A—C20—H20C | 109.5 |
N4—C6—H6B | 109.5 | H20B—C20—H20C | 109.5 |
H6A—C6—H6B | 109.5 | N14—C21—N13 | 116.9 (3) |
N4—C6—H6C | 109.5 | N14—C21—C22 | 121.0 (3) |
H6A—C6—H6C | 109.5 | N13—C21—C22 | 122.1 (3) |
H6B—C6—H6C | 109.5 | C23—C22—C21 | 115.3 (3) |
N8—C7—N6 | 117.9 (3) | C23—C22—H22 | 122.4 |
N8—C7—C10 | 121.8 (3) | C21—C22—H22 | 122.4 |
N6—C7—C10 | 120.4 (3) | N15—C23—C22 | 126.9 (3) |
N8—C8—H8A | 109.5 | N15—C23—Cl2 | 114.3 (2) |
N8—C8—H8B | 109.5 | C22—C23—Cl2 | 118.8 (3) |
H8A—C8—H8B | 109.5 | N14—C24—N16 | 117.3 (3) |
N8—C8—H8C | 109.5 | N14—C24—N15 | 127.2 (3) |
H8A—C8—H8C | 109.5 | N16—C24—N15 | 115.5 (3) |
C5—N4—C1—N1 | −3.6 (5) | C14—N12—C15—N9 | 5.5 (5) |
C6—N4—C1—N1 | −177.5 (3) | C13—N12—C15—N9 | −174.5 (3) |
C5—N4—C1—C2 | 176.3 (3) | C14—N12—C15—C16 | −174.8 (3) |
C6—N4—C1—C2 | 2.4 (5) | C13—N12—C15—C16 | 5.3 (5) |
C4—N1—C1—N4 | 175.7 (3) | C18—N9—C15—N12 | −177.3 (3) |
C4—N1—C1—C2 | −4.2 (4) | C18—N9—C15—C16 | 2.9 (4) |
N4—C1—C2—C3 | −178.4 (3) | N12—C15—C16—C17 | 177.1 (3) |
N1—C1—C2—C3 | 1.4 (5) | N9—C15—C16—C17 | −3.2 (5) |
C4—N2—C3—C2 | −1.8 (5) | C18—N10—C17—C16 | 1.8 (5) |
C4—N2—C3—Cl1 | 178.1 (2) | C18—N10—C17—Cl3 | −178.0 (2) |
C1—C2—C3—N2 | 1.8 (5) | C15—C16—C17—N10 | 0.8 (5) |
C1—C2—C3—Cl1 | −178.2 (2) | C15—C16—C17—Cl3 | −179.5 (2) |
C1—N1—C4—N2 | 4.4 (5) | C15—N9—C18—N10 | −0.2 (5) |
C1—N1—C4—N3 | −177.7 (3) | C15—N9—C18—N11 | 179.0 (3) |
C3—N2—C4—N1 | −1.5 (5) | C17—N10—C18—N9 | −2.1 (5) |
C3—N2—C4—N3 | −179.4 (3) | C17—N10—C18—N11 | 178.7 (3) |
C9—N8—C7—N6 | −5.8 (5) | C24—N14—C21—N13 | −180.0 (3) |
C8—N8—C7—N6 | −179.5 (3) | C24—N14—C21—C22 | 0.4 (4) |
C9—N8—C7—C10 | 175.3 (3) | C20—N13—C21—N14 | −1.5 (5) |
C8—N8—C7—C10 | 1.6 (5) | C19—N13—C21—N14 | 176.5 (3) |
C12—N6—C7—N8 | 176.8 (3) | C20—N13—C21—C22 | 178.1 (3) |
C12—N6—C7—C10 | −4.3 (4) | C19—N13—C21—C22 | −3.9 (5) |
N8—C7—C10—C11 | −179.9 (3) | N14—C21—C22—C23 | −0.3 (4) |
N6—C7—C10—C11 | 1.2 (4) | N13—C21—C22—C23 | −179.9 (3) |
C12—N5—C11—C10 | −0.3 (5) | C24—N15—C23—C22 | 1.0 (5) |
C12—N5—C11—Cl4 | 179.4 (2) | C24—N15—C23—Cl2 | −178.6 (2) |
C7—C10—C11—N5 | 1.2 (5) | C21—C22—C23—N15 | −0.4 (5) |
C7—C10—C11—Cl4 | −178.6 (2) | C21—C22—C23—Cl2 | 179.2 (2) |
C7—N6—C12—N7 | −175.9 (3) | C21—N14—C24—N16 | 178.2 (3) |
C7—N6—C12—N5 | 5.5 (5) | C21—N14—C24—N15 | 0.3 (5) |
C11—N5—C12—N6 | −3.2 (5) | C23—N15—C24—N14 | −1.0 (5) |
C11—N5—C12—N7 | 178.2 (3) | C23—N15—C24—N16 | −178.8 (3) |
D—H···A | D—H | H···A | D···A | D—H···A |
N11—H11B···N1 | 0.87 | 2.48 | 3.310 (4) | 161 |
N3—H3A···N9 | 0.86 | 2.41 | 3.264 (4) | 168 |
N16—H16B···N15i | 0.87 | 2.17 | 3.038 (4) | 174 |
N11—H11A···N10ii | 0.87 | 2.21 | 3.086 (4) | 174 |
N7—H7B···N5iii | 0.88 | 2.19 | 3.064 (3) | 178 |
N3—H3B···N6iv | 0.89 | 2.35 | 3.230 (4) | 169 |
N7—H7A···N2iv | 0.87 | 2.33 | 3.136 (3) | 155 |
Symmetry codes: (i) −x+2, −y+2, −z+2; (ii) −x, −y, −z+1; (iii) −x+1, −y+1, −z; (iv) −x+1, −y+1, −z+1. |
Experimental details
Crystal data | |
Chemical formula | C6H9ClN4 |
Mr | 172.62 |
Crystal system, space group | Triclinic, P1 |
Temperature (K) | 298 |
a, b, c (Å) | 7.9438 (19), 14.225 (3), 14.895 (3) |
α, β, γ (°) | 100.114 (3), 94.421 (4), 100.524 (4) |
V (Å3) | 1618.7 (7) |
Z | 8 |
Radiation type | Mo Kα |
µ (mm−1) | 0.41 |
Crystal size (mm) | 0.21 × 0.18 × 0.16 |
Data collection | |
Diffractometer | Bruker SMART CCD area-detector diffractometer |
Absorption correction | Multi-scan (SADABS; Bruker, 1999) |
Tmin, Tmax | 0.919, 0.937 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 8239, 5619, 3769 |
Rint | 0.029 |
(sin θ/λ)max (Å−1) | 0.595 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.058, 0.136, 0.97 |
No. of reflections | 5619 |
No. of parameters | 405 |
H-atom treatment | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 0.27, −0.32 |
Computer programs: SMART (Bruker, 1999), SAINT (Bruker, 1999), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), SHELXTL (Sheldrick, 2008).
D—H···A | D—H | H···A | D···A | D—H···A |
N11—H11B···N1 | 0.87 | 2.48 | 3.310 (4) | 160.6 |
N3—H3A···N9 | 0.86 | 2.41 | 3.264 (4) | 167.8 |
N16—H16B···N15i | 0.87 | 2.17 | 3.038 (4) | 173.7 |
N11—H11A···N10ii | 0.87 | 2.21 | 3.086 (4) | 174.3 |
N7—H7B···N5iii | 0.88 | 2.19 | 3.064 (3) | 178.1 |
N3—H3B···N6iv | 0.89 | 2.35 | 3.230 (4) | 169.4 |
N7—H7A···N2iv | 0.87 | 2.33 | 3.136 (3) | 155.1 |
Symmetry codes: (i) −x+2, −y+2, −z+2; (ii) −x, −y, −z+1; (iii) −x+1, −y+1, −z; (iv) −x+1, −y+1, −z+1. |
Acknowledgements
Financial support from the National Natural Science Foundation of China (grant No. 20572064) and the Natural Science Foundation of Shandong Province (grant No. ZR2010BM022) is gratefully acknowledged.
References
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This is an open-access article distributed under the terms of the Creative Commons Attribution (CC-BY) Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.
Functionalized pyrimidines play a major role in molecular recognition and supramolecular chemistry because of their potential ability to form stable hydrogen-bonded chains via their stereochemically associated amino groups and annular N atoms (Sherrington et al., 2001; Ligthart et al., 2005; Rabie et al., 2007; Goswami et al., 2008; Cheng et al., 2011). Lots of substituted 2-aminopyrimidine compounds have been elucidated (Fun et al., 2006; Li et al., 2008; Ebenezer et al., 2010; Cheng et al., 2011). We report here the crystal structure of a related organic compound, 6-chloro-N4,N4-dimethylpyrimidine-2,4-diamine.
The title compound, C6H9ClN4, contains four crystallographically independent molecules (Fig. 1), A, B, C and D, in the asymmetric unit, among which A and C are connected into a twisted dimer by two intermolecular N3—H3A···N9 and N11—H11B···N1 hydrogen bonds (Table 1), with a dihedral angle of 32.9 (1)° between the two pyrimidine rings. The bond lengths and angles of all molecules are similar except for the torsion angles between the methyl groups and the pyrimidine rings, ranging from 1.6 (5) to 5.9 (5)°.
In the packing of the title compound, each inversion-related two molecules of B, C and D form a centrosymmetric dimer through two intermolecular N—H···N hydrogen bonds (Table 1), locally creating an R22(8) motif (Bernstein et al., 1995). For example, in the dimer of D (Fig. 2), hydrogen bonds arise from atoms N7—H7B at (x, y, z) and (-x + 1, -y + 1, -z), which act as hydrogen-bond donors, respectively, to atoms N5 at (-x + 1, -y + 1, -z) and (x, y, z). The dimers of C and D are alternately arranged and bridged by the molecule A, creating an infinite zigzag strip (Cetina et al., 2005) (Fig. 3). In such a strip, the amino group of each molecule acts as a dual donor in N—H···N hydrogen bonds, while the pyrimidine ring serves as a dual acceptor. Interestingly, two different R22(8) motifs are formed with dihedral angles of 32.9 (1) and 63.4 (1)° between two adjacent pyrimidine rings. Finally, these strips together with the dimers of B are packed into a complicated three dimensional framework.