organic compounds
2,4-Dimethylpyrido[1,2-a]pyrimidin-5-ium perchlorate
aInstitute of Chemistry, University of Neuchâtel, Av. de Bellevaux 51, CH-2000 Neuchâtel, Switzerland, and bInstitute of Physics, University of Neuchâtel, rue Emile-Argand 11, CH-2000 Neuchâtel, Switzerland
*Correspondence e-mail: helen.stoeckli-evans@unine.ch
In the title molecular salt, C10H11N2+·ClO4−, the pyrido[1,2-a]pyrimidin-5-ium cation is planar, with an r.m.s. deviation of 0.027 Å for all 12 non-H atoms. The perchlorate anions are distributed over two twofold rotation axes; for one, three of the O atoms are disordered over two sites (occupancies of 1/2). In the crystal, the cations are linked via C—H⋯N hydrogen bonds, forming chains propagating along [001]. The chains are linked by a C—H⋯O hydrogen bond involving the non-disordered perchlorate anion, forming double layers parallel to the bc plane. These layers are linked by a number of weak C—H⋯O hydrogen bonds involving the disordered perchlorate anion, forming a three-dimensional framework.
Keywords: crystal structure; pyrido[1,2-a]pyrimidin-5-ium; pyrimidinium; perchlorate; hydrogen bonding; framework.
CCDC reference: 1507737
Structure description
Reports on the crystal structures of pyrido[1,2-a]pyrimidin-5-ium cations are rare (Koval'chukova et al., 2000, 2003). The title compound was obtained when studying the reaction of the ligand 5,7-bis(2-aminopyridine)-5H,-6,7-dihydropyrrolo[3.4-b]pyrazine (L1) with Mn(ClO4)2·6H2O in methanol in the presence of triethylamine (Posel, 1998). The solid obtained from this reaction was recrystallized from a mixture of solvents (methanol/acetonitrile/water) also containing acetylacetone, and dark-brown crystals of the title molecular salt were obtained.
The molecular structure of the title molecular salt is illustrated in Fig. 1. The perchlorate anions are distributed over two twofold rotation axes and for one, involving atom Cl1, three O atoms are disordered over two sites (occupancies of 1/2). The pyrido[1,2-a]pyrimidin-5-ium cation is planar (r.m.s. deviation of 0.027 Å for all twelve non-H atoms). The bond distances and angles in the cation are very similar to those observed for 2,4-dimethyl-9-hydroxypyrido[1,2-a]pyrimidinium perchlorate (Koval'chukova et al., 2000).
In the crystal, the cations are linked via C—H⋯N hydrogen bonds, forming chains propagating along the c-axis direction (Table 1 and Fig. 2). The chains are linked by a C—H⋯O interaction involving the Cl2 perchlorate anion, forming double layers parallel to the bc plane. The layers are linked by weak C—H⋯O hydrogen bonds (H⋯A > 2.6 Å), involving the Cl1 disordered perchlorate anion, forming a three-dimensional framework (Table 1 and Fig. 2).
Synthesis and crystallization
To a mixture of 5,7-bis(2-aminopyridine)-5H,-6,7-dihydropyrrolo[3.4 − b]pyrazine [L1] (0.0646 g, 0.0001 mol) in 7 ml of dry methanol and 0.1 ml of triethylamine was added Mn(ClO4)2·6H2O (0.0362 g, 0.0001 mol) in 3 ml of dry methanol, and the mixture stirred at room temperature under nitrogen for four days. The mixture was then filtered and the filtrate left to evaporate, but no crystals were obtained. The solid left after evaporation of the solvent was recrystallized several times from different solvents (containing acetylacetone). Finally a mixture of solvents, methanol/acetonitrile/water (1/4/3) was used and it gave a small amount of brown block-like crystals that were examined by X-ray and shown to be the title molecular salt (yield 0.0036 g, m.p. > 623 K). The IR spectrum (KBr pellet, cm−1) is shown in Fig. 3. Compound L1 was synthesized by reacting 2,3-dicyanopyrazine with 2-aminopyridine (Posel, 1998). It is possible that during the reaction of L1 with Mn(ClO4)2, it decomposed reforming 2-aminopyridine which then reacted with the acetylacetone to form the title compound.
Refinement
Crystal data, data collection and structure . The perchlorate anions are distributed over two twofold rotation axes and for one, involving atom Cl1, the O atoms (O12–O14) are disordered with occupancies of 0.5. Only one equivalent of data were measured, hence Rint = 0.
details are summarized in Table 2Structural data
CCDC reference: 1507737
https://doi.org/10.1107/S2414314616015431/xu4014sup1.cif
contains datablocks I, Global. DOI:Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2414314616015431/xu4014Isup2.hkl
Supporting information file. DOI: https://doi.org/10.1107/S2414314616015431/xu4014Isup3.cml
Data collection: STADI4 (Stoe & Cie, 1997); cell
STADI4 (Stoe & Cie, 1997); data reduction: X-RED (Stoe & Cie, 1997); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL2014 (Sheldrick, 2015); molecular graphics: Mercury (Macrae et al., 2008); software used to prepare material for publication: SHELXL2014 (Sheldrick, 2015), PLATON (Spek, 2009) and publCIF (Westrip, 2010).C10H11N2+·ClO4− | F(000) = 536 |
Mr = 258.66 | Dx = 1.456 Mg m−3 |
Monoclinic, P2/c | Mo Kα radiation, λ = 0.71073 Å |
a = 12.5178 (11) Å | Cell parameters from 25 reflections |
b = 7.8321 (9) Å | θ = 14.1–17.4° |
c = 12.6354 (15) Å | µ = 0.33 mm−1 |
β = 107.763 (8)° | T = 293 K |
V = 1179.7 (2) Å3 | Block, brown |
Z = 4 | 0.30 × 0.27 × 0.27 mm |
Stoe AED2 four-circle diffractometer | Rint = 0.0 |
Radiation source: fine-focus sealed tube | θmax = 25.5°, θmin = 2.6° |
Graphite monochromator | h = −15→14 |
ω/2θ scans | k = 0→9 |
2198 measured reflections | l = 0→15 |
2198 independent reflections | 2 standard reflections every 120 min |
1447 reflections with I > 2σ(I) | intensity decay: 2% |
Refinement on F2 | Secondary atom site location: difference Fourier map |
Least-squares matrix: full | Hydrogen site location: inferred from neighbouring sites |
R[F2 > 2σ(F2)] = 0.072 | H-atom parameters constrained |
wR(F2) = 0.168 | w = 1/[σ2(Fo2) + (0.0364P)2 + 1.9648P] where P = (Fo2 + 2Fc2)/3 |
S = 1.13 | (Δ/σ)max = 0.001 |
2198 reflections | Δρmax = 0.43 e Å−3 |
172 parameters | Δρmin = −0.24 e Å−3 |
0 restraints | Extinction correction: SHELXL2014 (Sheldrick, 2015), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4 |
Primary atom site location: structure-invariant direct methods | Extinction coefficient: 0.0139 (17) |
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. |
x | y | z | Uiso*/Ueq | Occ. (<1) | |
N1 | 0.2789 (3) | 0.1607 (5) | 0.4607 (3) | 0.0569 (10) | |
N2 | 0.2637 (3) | 0.0349 (4) | 0.2851 (3) | 0.0448 (9) | |
C1 | 0.2140 (4) | 0.2878 (6) | 0.4095 (4) | 0.0611 (13) | |
C2 | 0.1683 (4) | 0.2900 (6) | 0.2934 (4) | 0.0579 (12) | |
H2 | 0.1214 | 0.3791 | 0.2591 | 0.069* | |
C3 | 0.1918 (4) | 0.1641 (6) | 0.2309 (4) | 0.0540 (11) | |
C4 | 0.2936 (4) | −0.0962 (6) | 0.2268 (4) | 0.0571 (12) | |
H4 | 0.2671 | −0.0963 | 0.1496 | 0.069* | |
C5 | 0.3607 (4) | −0.2242 (6) | 0.2802 (5) | 0.0681 (14) | |
H5 | 0.3798 | −0.3117 | 0.2396 | 0.082* | |
C6 | 0.4009 (4) | −0.2262 (7) | 0.3946 (5) | 0.0697 (14) | |
H6 | 0.4465 | −0.3153 | 0.4311 | 0.084* | |
C7 | 0.3741 (4) | −0.0984 (6) | 0.4536 (4) | 0.0607 (13) | |
H7 | 0.4024 | −0.0992 | 0.5307 | 0.073* | |
C8 | 0.3036 (3) | 0.0364 (5) | 0.3996 (3) | 0.0481 (10) | |
C9 | 0.1890 (5) | 0.4263 (8) | 0.4800 (5) | 0.0931 (19) | |
H9C | 0.1338 | 0.5022 | 0.4343 | 0.140* | |
H9B | 0.2564 | 0.4888 | 0.5154 | 0.140* | |
H9A | 0.1607 | 0.3766 | 0.5356 | 0.140* | |
C10 | 0.1435 (5) | 0.1578 (7) | 0.1067 (4) | 0.0770 (16) | |
H10C | 0.0931 | 0.2521 | 0.0817 | 0.115* | |
H10B | 0.1033 | 0.0526 | 0.0852 | 0.115* | |
H10A | 0.2030 | 0.1646 | 0.0737 | 0.115* | |
Cl1 | 0.5000 | 0.3239 (2) | 0.2500 | 0.0559 (5) | |
O11 | 0.5000 | 0.1448 (6) | 0.2500 | 0.101 (2) | |
O12 | 0.5458 (15) | 0.4207 (12) | 0.3408 (8) | 0.113 (4) | 0.5 |
O13 | 0.5533 (12) | 0.3630 (13) | 0.1648 (11) | 0.116 (4) | 0.5 |
O14 | 0.3885 (7) | 0.3640 (14) | 0.1956 (14) | 0.125 (5) | 0.5 |
Cl2 | 0.0000 | 0.7762 (2) | 0.2500 | 0.0607 (5) | |
O21 | 0.0652 (5) | 0.6759 (7) | 0.2040 (5) | 0.151 (2) | |
O22 | −0.0649 (5) | 0.8791 (8) | 0.1674 (4) | 0.163 (3) |
U11 | U22 | U33 | U12 | U13 | U23 | |
N1 | 0.068 (2) | 0.057 (2) | 0.044 (2) | 0.005 (2) | 0.0147 (19) | −0.0025 (19) |
N2 | 0.049 (2) | 0.047 (2) | 0.0399 (19) | −0.0041 (17) | 0.0152 (16) | 0.0012 (17) |
C1 | 0.072 (3) | 0.053 (3) | 0.061 (3) | 0.001 (3) | 0.023 (2) | −0.003 (2) |
C2 | 0.062 (3) | 0.051 (3) | 0.056 (3) | 0.004 (2) | 0.011 (2) | 0.011 (2) |
C3 | 0.057 (3) | 0.057 (3) | 0.047 (2) | −0.009 (2) | 0.015 (2) | 0.006 (2) |
C4 | 0.065 (3) | 0.056 (3) | 0.053 (3) | −0.008 (2) | 0.023 (2) | −0.008 (2) |
C5 | 0.073 (3) | 0.054 (3) | 0.080 (4) | 0.007 (3) | 0.028 (3) | −0.006 (3) |
C6 | 0.063 (3) | 0.063 (3) | 0.078 (4) | 0.013 (3) | 0.014 (3) | 0.007 (3) |
C7 | 0.060 (3) | 0.066 (3) | 0.051 (3) | 0.006 (3) | 0.011 (2) | 0.007 (2) |
C8 | 0.051 (3) | 0.047 (2) | 0.047 (3) | −0.001 (2) | 0.015 (2) | 0.002 (2) |
C9 | 0.120 (5) | 0.076 (4) | 0.079 (4) | 0.025 (4) | 0.023 (4) | −0.016 (3) |
C10 | 0.091 (4) | 0.085 (4) | 0.050 (3) | 0.007 (3) | 0.013 (3) | 0.014 (3) |
Cl1 | 0.0524 (10) | 0.0447 (9) | 0.0658 (11) | 0.000 | 0.0110 (8) | 0.000 |
O11 | 0.124 (5) | 0.044 (3) | 0.141 (6) | 0.000 | 0.048 (4) | 0.000 |
O12 | 0.172 (12) | 0.080 (7) | 0.066 (6) | −0.005 (8) | 0.005 (7) | −0.020 (5) |
O13 | 0.143 (9) | 0.099 (7) | 0.141 (11) | −0.010 (7) | 0.098 (9) | 0.011 (7) |
O14 | 0.051 (5) | 0.095 (8) | 0.204 (15) | 0.026 (5) | 0.003 (7) | 0.019 (8) |
Cl2 | 0.0508 (9) | 0.0570 (10) | 0.0725 (12) | 0.000 | 0.0161 (8) | 0.000 |
O21 | 0.148 (5) | 0.124 (4) | 0.214 (6) | 0.063 (4) | 0.103 (5) | 0.008 (4) |
O22 | 0.174 (5) | 0.210 (6) | 0.104 (4) | 0.122 (5) | 0.041 (3) | 0.056 (4) |
N1—C1 | 1.322 (6) | C10—H10C | 0.9600 |
N1—C8 | 1.337 (5) | C10—H10B | 0.9600 |
N2—C8 | 1.378 (5) | C10—H10A | 0.9600 |
N2—C4 | 1.381 (5) | Cl1—O12i | 1.349 (9) |
N2—C3 | 1.388 (5) | Cl1—O12 | 1.349 (9) |
C1—C2 | 1.402 (6) | Cl1—O14 | 1.390 (8) |
C1—C9 | 1.497 (7) | Cl1—O14i | 1.391 (8) |
C2—C3 | 1.351 (6) | Cl1—O11 | 1.402 (5) |
C2—H2 | 0.9300 | Cl1—O13 | 1.461 (8) |
C3—C10 | 1.501 (6) | Cl1—O13i | 1.461 (8) |
C4—C5 | 1.349 (7) | O12—O14i | 1.147 (13) |
C4—H4 | 0.9300 | O12—O13i | 1.301 (14) |
C5—C6 | 1.378 (7) | O13—O12i | 1.301 (14) |
C5—H5 | 0.9300 | O13—O14i | 1.690 (15) |
C6—C7 | 1.350 (7) | O14—O12i | 1.147 (13) |
C6—H6 | 0.9300 | O14—O13i | 1.690 (15) |
C7—C8 | 1.411 (6) | Cl2—O22ii | 1.371 (5) |
C7—H7 | 0.9300 | Cl2—O22 | 1.371 (5) |
C9—H9C | 0.9600 | Cl2—O21ii | 1.382 (5) |
C9—H9B | 0.9600 | Cl2—O21 | 1.382 (5) |
C9—H9A | 0.9600 | ||
C1—N1—C8 | 118.8 (4) | H10C—C10—H10A | 109.5 |
C8—N2—C4 | 119.7 (4) | H10B—C10—H10A | 109.5 |
C8—N2—C3 | 119.0 (4) | O12i—Cl1—O12 | 111.5 (9) |
C4—N2—C3 | 121.2 (4) | O12i—Cl1—O14 | 49.5 (6) |
N1—C1—C2 | 121.0 (4) | O12—Cl1—O14 | 113.3 (7) |
N1—C1—C9 | 117.6 (4) | O12i—Cl1—O14i | 113.3 (7) |
C2—C1—C9 | 121.4 (5) | O12—Cl1—O14i | 49.5 (6) |
C3—C2—C1 | 120.7 (4) | O14—Cl1—O14i | 153.9 (9) |
C3—C2—H2 | 119.6 | O12i—Cl1—O11 | 124.2 (4) |
C1—C2—H2 | 119.6 | O12—Cl1—O11 | 124.2 (4) |
C2—C3—N2 | 117.8 (4) | O14—Cl1—O11 | 103.1 (5) |
C2—C3—C10 | 123.1 (5) | O14i—Cl1—O11 | 103.1 (5) |
N2—C3—C10 | 119.1 (4) | O12i—Cl1—O13 | 55.0 (6) |
C5—C4—N2 | 121.0 (4) | O12—Cl1—O13 | 109.7 (7) |
C5—C4—H4 | 119.5 | O14—Cl1—O13 | 101.7 (7) |
N2—C4—H4 | 119.5 | O14i—Cl1—O13 | 72.7 (7) |
C4—C5—C6 | 120.4 (5) | O11—Cl1—O13 | 102.1 (4) |
C4—C5—H5 | 119.8 | O12i—Cl1—O13i | 109.7 (7) |
C6—C5—H5 | 119.8 | O12—Cl1—O13i | 55.0 (6) |
C7—C6—C5 | 119.9 (5) | O14—Cl1—O13i | 72.7 (6) |
C7—C6—H6 | 120.1 | O14i—Cl1—O13i | 101.7 (7) |
C5—C6—H6 | 120.1 | O11—Cl1—O13i | 102.1 (4) |
C6—C7—C8 | 120.8 (5) | O13—Cl1—O13i | 155.8 (9) |
C6—C7—H7 | 119.6 | O14i—O12—O13i | 129.2 (11) |
C8—C7—H7 | 119.6 | O14i—O12—Cl1 | 67.2 (7) |
N1—C8—N2 | 122.6 (4) | O13i—O12—Cl1 | 66.9 (7) |
N1—C8—C7 | 119.1 (4) | O12i—O13—Cl1 | 58.1 (5) |
N2—C8—C7 | 118.3 (4) | O12i—O13—O14i | 98.9 (8) |
C1—C9—H9C | 109.5 | Cl1—O13—O14i | 51.7 (4) |
C1—C9—H9B | 109.5 | O12i—O14—Cl1 | 63.3 (6) |
H9C—C9—H9B | 109.5 | O12i—O14—O13i | 106.6 (10) |
C1—C9—H9A | 109.5 | Cl1—O14—O13i | 55.6 (5) |
H9C—C9—H9A | 109.5 | O22ii—Cl2—O22 | 108.0 (6) |
H9B—C9—H9A | 109.5 | O22ii—Cl2—O21ii | 107.6 (3) |
C3—C10—H10C | 109.5 | O22—Cl2—O21ii | 111.4 (4) |
C3—C10—H10B | 109.5 | O22ii—Cl2—O21 | 111.4 (4) |
H10C—C10—H10B | 109.5 | O22—Cl2—O21 | 107.6 (3) |
C3—C10—H10A | 109.5 | O21ii—Cl2—O21 | 110.7 (5) |
C8—N1—C1—C2 | 2.2 (7) | O13i—Cl1—O12—O14i | 157.6 (11) |
C8—N1—C1—C9 | −179.3 (5) | O12i—Cl1—O12—O13i | 99.6 (8) |
N1—C1—C2—C3 | −1.6 (7) | O14i—Cl1—O12—O13i | −157.6 (11) |
C9—C1—C2—C3 | 179.9 (5) | O14—Cl1—O12—O13i | 45.8 (9) |
C1—C2—C3—N2 | −1.0 (7) | O11—Cl1—O12—O13i | −80.4 (8) |
C1—C2—C3—C10 | 178.6 (5) | O13—Cl1—O12—O13i | 158.7 (8) |
C8—N2—C3—C2 | 2.8 (6) | O12—Cl1—O13—O12i | −103.0 (11) |
C4—N2—C3—C2 | −178.6 (4) | O14i—Cl1—O13—O12i | −136.4 (9) |
C8—N2—C3—C10 | −176.8 (4) | O14—Cl1—O13—O12i | 17.2 (9) |
C4—N2—C3—C10 | 1.8 (6) | O11—Cl1—O13—O12i | 123.5 (6) |
C8—N2—C4—C5 | 0.6 (6) | O13i—Cl1—O13—O12i | −56.5 (6) |
C3—N2—C4—C5 | −177.9 (4) | O12i—Cl1—O13—O14i | 136.4 (9) |
N2—C4—C5—C6 | −0.1 (7) | O12—Cl1—O13—O14i | 33.4 (7) |
C4—C5—C6—C7 | −0.7 (8) | O14—Cl1—O13—O14i | 153.6 (9) |
C5—C6—C7—C8 | 1.0 (8) | O11—Cl1—O13—O14i | −100.1 (5) |
C1—N1—C8—N2 | −0.3 (7) | O13i—Cl1—O13—O14i | 79.9 (5) |
C1—N1—C8—C7 | 179.1 (4) | O12—Cl1—O14—O12i | 99.1 (12) |
C4—N2—C8—N1 | 179.1 (4) | O14i—Cl1—O14—O12i | 55.9 (7) |
C3—N2—C8—N1 | −2.3 (6) | O11—Cl1—O14—O12i | −124.1 (7) |
C4—N2—C8—C7 | −0.3 (6) | O13—Cl1—O14—O12i | −18.6 (9) |
C3—N2—C8—C7 | 178.3 (4) | O13i—Cl1—O14—O12i | 137.1 (10) |
C6—C7—C8—N1 | −179.9 (4) | O12i—Cl1—O14—O13i | −137.1 (10) |
C6—C7—C8—N2 | −0.5 (7) | O12—Cl1—O14—O13i | −37.9 (7) |
O12i—Cl1—O12—O14i | −102.8 (10) | O14i—Cl1—O14—O13i | −81.2 (5) |
O14—Cl1—O12—O14i | −156.6 (9) | O11—Cl1—O14—O13i | 98.8 (5) |
O11—Cl1—O12—O14i | 77.2 (10) | O13—Cl1—O14—O13i | −155.6 (9) |
O13—Cl1—O12—O14i | −43.7 (10) |
Symmetry codes: (i) −x+1, y, −z+1/2; (ii) −x, y, −z+1/2. |
D—H···A | D—H | H···A | D···A | D—H···A |
C4—H4···N1iii | 0.93 | 2.49 | 3.349 (6) | 154 |
C2—H2···O21 | 0.93 | 2.47 | 3.345 (7) | 158 |
C5—H5···O12iv | 0.93 | 2.62 | 3.541 (14) | 170 |
C5—H5···O14v | 0.93 | 2.61 | 3.449 (12) | 150 |
C9—H9B···O14vi | 0.96 | 2.64 | 3.493 (13) | 149 |
Symmetry codes: (iii) x, −y, z−1/2; (iv) −x+1, y−1, −z+1/2; (v) x, y−1, z; (vi) x, −y+1, z+1/2. |
Acknowledgements
We are grateful to the Swiss National Science Foundation and the University of Neuchâtel for financial support.
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