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ISSN: 2414-3146

2,4-Di­methyl­pyrido[1,2-a]pyrimidin-5-ium perchlorate

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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

Edited by D.-J. Xu, Zhejiang University (Yuquan Campus), China (Received 25 September 2016; accepted 2 October 2016; online 14 October 2016)

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.

3D view (loading...)
[Scheme 3D1]
Chemical scheme
[Scheme 1]

Structure description

Reports on the crystal structures of pyrido[1,2-a]pyrimidin-5-ium cations are rare (Koval'chukova et al., 2000[Koval'chukova, O. V., Strashnova, S. B., Zaitsev, B. E., Belskii, V. K., Stash, A. I., Nikitin, S. V., Goncharov, O. V. & Shchelokov, R. N. (2000). Russ. J. Coord. Chem. 26, 290-294.], 2003[Koval'chukova, O. V., Kuz'mina, N. E., Strashnova, S. B., Palkina, K. K., Mordovina, N. I., Zaitsev, B. E. & Nikitin, S. V. (2003). Russ. J. Coord. Chem. 29, 123-128.]). 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[Posel, M. (1998). PhD thesis, University of Neuchâtel, Switzerland.]). 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[link]. 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[Koval'chukova, O. V., Strashnova, S. B., Zaitsev, B. E., Belskii, V. K., Stash, A. I., Nikitin, S. V., Goncharov, O. V. & Shchelokov, R. N. (2000). Russ. J. Coord. Chem. 26, 290-294.]).

[Figure 1]
Figure 1
A view of the mol­ecular structure of the title mol­ecular salt, showing the atom labelling. Displacement ellipsoids are drawn at the 50% probability level. For clarity, the perchlorate anions have been omitted.

In the crystal, the cations are linked via C—H⋯N hydrogen bonds, forming chains propagating along the c-axis direction (Table 1[link] and Fig. 2[link]). 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[link] and Fig. 2[link]).

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
C4—H4⋯N1i 0.93 2.49 3.349 (6) 154
C2—H2⋯O21 0.93 2.47 3.345 (7) 158
C5—H5⋯O12ii 0.93 2.62 3.541 (14) 170
C5—H5⋯O14iii 0.93 2.61 3.449 (12) 150
C9—H9B⋯O14iv 0.96 2.64 3.493 (13) 149
Symmetry codes: (i) [x, -y, z-{\script{1\over 2}}]; (ii) [-x+1, y-1, -z+{\script{1\over 2}}]; (iii) x, y-1, z; (iv) [x, -y+1, z+{\script{1\over 2}}].
[Figure 2]
Figure 2
A view along the b axis of the crystal packing of the title mol­ecular salt. The hydrogen bonds are shown as dashed lines (see Table 1[link]) and only the H atoms involved in these inter­actions have been included.

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 diffraction analysis, 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[link]. Compound L1 was synthesized by reacting 2,3-di­cyano­pyrazine with 2-amino­pyridine (Posel, 1998[Posel, M. (1998). PhD thesis, University of Neuchâtel, Switzerland.]). 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.

[Figure 3]
Figure 3
The IR spectrum of the title mol­ecular salt.

Refinement

Crystal data, data collection and structure refinement details are summarized in Table 2[link]. 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.

Table 2
Experimental details

Crystal data
Chemical formula C10H11N2+·ClO4
Mr 258.66
Crystal system, space group Monoclinic, P2/c
Temperature (K) 293
a, b, c (Å) 12.5178 (11), 7.8321 (9), 12.6354 (15)
β (°) 107.763 (8)
V3) 1179.7 (2)
Z 4
Radiation type Mo Kα
μ (mm−1) 0.33
Crystal size (mm) 0.30 × 0.27 × 0.27
 
Data collection
Diffractometer Stoe AED2 four-circle
No. of measured, independent and observed [I > 2σ(I)] reflections 2198, 2198, 1447
(sin θ/λ)max−1) 0.606
 
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.072, 0.168, 1.13
No. of reflections 2198
No. of parameters 172
H-atom treatment H-atom parameters constrained
Δρmax, Δρmin (e Å−3) 0.43, −0.24
Computer programs: STADI4 and X-RED (Stoe & Cie, 1997[Stoe & Cie (1997). STADI4 and X-RED. Stoe & Cie GmbH, Damstadt, Germany.]), SHELXS97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]), Mercury (Macrae et al., 2008[Macrae, C. F., Bruno, I. J., Chisholm, J. A., Edgington, P. R., McCabe, P., Pidcock, E., Rodriguez-Monge, L., Taylor, R., van de Streek, J. & Wood, P. A. (2008). J. Appl. Cryst. 41, 466-470.]), SHELXL2014 (Sheldrick, 2015[Sheldrick, G. M. (2015). Acta Cryst. C71, 3-8.]), PLATON (Spek, 2009[Spek, A. L. (2009). Acta Cryst. D65, 148-155.]) and publCIF (Westrip, 2010[Westrip, S. P. (2010). J. Appl. Cryst. 43, 920-925.]).

Structural data


Computing details top

Data collection: STADI4 (Stoe & Cie, 1997); cell refinement: 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).

2,4-Dimethylpyrido[1,2-a]pyrimidin-5-ium perchlorate top
Crystal data top
C10H11N2+·ClO4F(000) = 536
Mr = 258.66Dx = 1.456 Mg m3
Monoclinic, P2/cMo Kα radiation, λ = 0.71073 Å
a = 12.5178 (11) ÅCell parameters from 25 reflections
b = 7.8321 (9) Åθ = 14.1–17.4°
c = 12.6354 (15) ŵ = 0.33 mm1
β = 107.763 (8)°T = 293 K
V = 1179.7 (2) Å3Block, brown
Z = 40.30 × 0.27 × 0.27 mm
Data collection top
Stoe AED2 four-circle
diffractometer
Rint = 0.0
Radiation source: fine-focus sealed tubeθmax = 25.5°, θmin = 2.6°
Graphite monochromatorh = 1514
ω/2θ scansk = 09
2198 measured reflectionsl = 015
2198 independent reflections2 standard reflections every 120 min
1447 reflections with I > 2σ(I) intensity decay: 2%
Refinement top
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.072H-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 reflectionsΔρmax = 0.43 e Å3
172 parametersΔρmin = 0.24 e Å3
0 restraintsExtinction correction: SHELXL2014 (Sheldrick, 2015), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
Primary atom site location: structure-invariant direct methodsExtinction coefficient: 0.0139 (17)
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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/UeqOcc. (<1)
N10.2789 (3)0.1607 (5)0.4607 (3)0.0569 (10)
N20.2637 (3)0.0349 (4)0.2851 (3)0.0448 (9)
C10.2140 (4)0.2878 (6)0.4095 (4)0.0611 (13)
C20.1683 (4)0.2900 (6)0.2934 (4)0.0579 (12)
H20.12140.37910.25910.069*
C30.1918 (4)0.1641 (6)0.2309 (4)0.0540 (11)
C40.2936 (4)0.0962 (6)0.2268 (4)0.0571 (12)
H40.26710.09630.14960.069*
C50.3607 (4)0.2242 (6)0.2802 (5)0.0681 (14)
H50.37980.31170.23960.082*
C60.4009 (4)0.2262 (7)0.3946 (5)0.0697 (14)
H60.44650.31530.43110.084*
C70.3741 (4)0.0984 (6)0.4536 (4)0.0607 (13)
H70.40240.09920.53070.073*
C80.3036 (3)0.0364 (5)0.3996 (3)0.0481 (10)
C90.1890 (5)0.4263 (8)0.4800 (5)0.0931 (19)
H9C0.13380.50220.43430.140*
H9B0.25640.48880.51540.140*
H9A0.16070.37660.53560.140*
C100.1435 (5)0.1578 (7)0.1067 (4)0.0770 (16)
H10C0.09310.25210.08170.115*
H10B0.10330.05260.08520.115*
H10A0.20300.16460.07370.115*
Cl10.50000.3239 (2)0.25000.0559 (5)
O110.50000.1448 (6)0.25000.101 (2)
O120.5458 (15)0.4207 (12)0.3408 (8)0.113 (4)0.5
O130.5533 (12)0.3630 (13)0.1648 (11)0.116 (4)0.5
O140.3885 (7)0.3640 (14)0.1956 (14)0.125 (5)0.5
Cl20.00000.7762 (2)0.25000.0607 (5)
O210.0652 (5)0.6759 (7)0.2040 (5)0.151 (2)
O220.0649 (5)0.8791 (8)0.1674 (4)0.163 (3)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
N10.068 (2)0.057 (2)0.044 (2)0.005 (2)0.0147 (19)0.0025 (19)
N20.049 (2)0.047 (2)0.0399 (19)0.0041 (17)0.0152 (16)0.0012 (17)
C10.072 (3)0.053 (3)0.061 (3)0.001 (3)0.023 (2)0.003 (2)
C20.062 (3)0.051 (3)0.056 (3)0.004 (2)0.011 (2)0.011 (2)
C30.057 (3)0.057 (3)0.047 (2)0.009 (2)0.015 (2)0.006 (2)
C40.065 (3)0.056 (3)0.053 (3)0.008 (2)0.023 (2)0.008 (2)
C50.073 (3)0.054 (3)0.080 (4)0.007 (3)0.028 (3)0.006 (3)
C60.063 (3)0.063 (3)0.078 (4)0.013 (3)0.014 (3)0.007 (3)
C70.060 (3)0.066 (3)0.051 (3)0.006 (3)0.011 (2)0.007 (2)
C80.051 (3)0.047 (2)0.047 (3)0.001 (2)0.015 (2)0.002 (2)
C90.120 (5)0.076 (4)0.079 (4)0.025 (4)0.023 (4)0.016 (3)
C100.091 (4)0.085 (4)0.050 (3)0.007 (3)0.013 (3)0.014 (3)
Cl10.0524 (10)0.0447 (9)0.0658 (11)0.0000.0110 (8)0.000
O110.124 (5)0.044 (3)0.141 (6)0.0000.048 (4)0.000
O120.172 (12)0.080 (7)0.066 (6)0.005 (8)0.005 (7)0.020 (5)
O130.143 (9)0.099 (7)0.141 (11)0.010 (7)0.098 (9)0.011 (7)
O140.051 (5)0.095 (8)0.204 (15)0.026 (5)0.003 (7)0.019 (8)
Cl20.0508 (9)0.0570 (10)0.0725 (12)0.0000.0161 (8)0.000
O210.148 (5)0.124 (4)0.214 (6)0.063 (4)0.103 (5)0.008 (4)
O220.174 (5)0.210 (6)0.104 (4)0.122 (5)0.041 (3)0.056 (4)
Geometric parameters (Å, º) top
N1—C11.322 (6)C10—H10C0.9600
N1—C81.337 (5)C10—H10B0.9600
N2—C81.378 (5)C10—H10A0.9600
N2—C41.381 (5)Cl1—O12i1.349 (9)
N2—C31.388 (5)Cl1—O121.349 (9)
C1—C21.402 (6)Cl1—O141.390 (8)
C1—C91.497 (7)Cl1—O14i1.391 (8)
C2—C31.351 (6)Cl1—O111.402 (5)
C2—H20.9300Cl1—O131.461 (8)
C3—C101.501 (6)Cl1—O13i1.461 (8)
C4—C51.349 (7)O12—O14i1.147 (13)
C4—H40.9300O12—O13i1.301 (14)
C5—C61.378 (7)O13—O12i1.301 (14)
C5—H50.9300O13—O14i1.690 (15)
C6—C71.350 (7)O14—O12i1.147 (13)
C6—H60.9300O14—O13i1.690 (15)
C7—C81.411 (6)Cl2—O22ii1.371 (5)
C7—H70.9300Cl2—O221.371 (5)
C9—H9C0.9600Cl2—O21ii1.382 (5)
C9—H9B0.9600Cl2—O211.382 (5)
C9—H9A0.9600
C1—N1—C8118.8 (4)H10C—C10—H10A109.5
C8—N2—C4119.7 (4)H10B—C10—H10A109.5
C8—N2—C3119.0 (4)O12i—Cl1—O12111.5 (9)
C4—N2—C3121.2 (4)O12i—Cl1—O1449.5 (6)
N1—C1—C2121.0 (4)O12—Cl1—O14113.3 (7)
N1—C1—C9117.6 (4)O12i—Cl1—O14i113.3 (7)
C2—C1—C9121.4 (5)O12—Cl1—O14i49.5 (6)
C3—C2—C1120.7 (4)O14—Cl1—O14i153.9 (9)
C3—C2—H2119.6O12i—Cl1—O11124.2 (4)
C1—C2—H2119.6O12—Cl1—O11124.2 (4)
C2—C3—N2117.8 (4)O14—Cl1—O11103.1 (5)
C2—C3—C10123.1 (5)O14i—Cl1—O11103.1 (5)
N2—C3—C10119.1 (4)O12i—Cl1—O1355.0 (6)
C5—C4—N2121.0 (4)O12—Cl1—O13109.7 (7)
C5—C4—H4119.5O14—Cl1—O13101.7 (7)
N2—C4—H4119.5O14i—Cl1—O1372.7 (7)
C4—C5—C6120.4 (5)O11—Cl1—O13102.1 (4)
C4—C5—H5119.8O12i—Cl1—O13i109.7 (7)
C6—C5—H5119.8O12—Cl1—O13i55.0 (6)
C7—C6—C5119.9 (5)O14—Cl1—O13i72.7 (6)
C7—C6—H6120.1O14i—Cl1—O13i101.7 (7)
C5—C6—H6120.1O11—Cl1—O13i102.1 (4)
C6—C7—C8120.8 (5)O13—Cl1—O13i155.8 (9)
C6—C7—H7119.6O14i—O12—O13i129.2 (11)
C8—C7—H7119.6O14i—O12—Cl167.2 (7)
N1—C8—N2122.6 (4)O13i—O12—Cl166.9 (7)
N1—C8—C7119.1 (4)O12i—O13—Cl158.1 (5)
N2—C8—C7118.3 (4)O12i—O13—O14i98.9 (8)
C1—C9—H9C109.5Cl1—O13—O14i51.7 (4)
C1—C9—H9B109.5O12i—O14—Cl163.3 (6)
H9C—C9—H9B109.5O12i—O14—O13i106.6 (10)
C1—C9—H9A109.5Cl1—O14—O13i55.6 (5)
H9C—C9—H9A109.5O22ii—Cl2—O22108.0 (6)
H9B—C9—H9A109.5O22ii—Cl2—O21ii107.6 (3)
C3—C10—H10C109.5O22—Cl2—O21ii111.4 (4)
C3—C10—H10B109.5O22ii—Cl2—O21111.4 (4)
H10C—C10—H10B109.5O22—Cl2—O21107.6 (3)
C3—C10—H10A109.5O21ii—Cl2—O21110.7 (5)
C8—N1—C1—C22.2 (7)O13i—Cl1—O12—O14i157.6 (11)
C8—N1—C1—C9179.3 (5)O12i—Cl1—O12—O13i99.6 (8)
N1—C1—C2—C31.6 (7)O14i—Cl1—O12—O13i157.6 (11)
C9—C1—C2—C3179.9 (5)O14—Cl1—O12—O13i45.8 (9)
C1—C2—C3—N21.0 (7)O11—Cl1—O12—O13i80.4 (8)
C1—C2—C3—C10178.6 (5)O13—Cl1—O12—O13i158.7 (8)
C8—N2—C3—C22.8 (6)O12—Cl1—O13—O12i103.0 (11)
C4—N2—C3—C2178.6 (4)O14i—Cl1—O13—O12i136.4 (9)
C8—N2—C3—C10176.8 (4)O14—Cl1—O13—O12i17.2 (9)
C4—N2—C3—C101.8 (6)O11—Cl1—O13—O12i123.5 (6)
C8—N2—C4—C50.6 (6)O13i—Cl1—O13—O12i56.5 (6)
C3—N2—C4—C5177.9 (4)O12i—Cl1—O13—O14i136.4 (9)
N2—C4—C5—C60.1 (7)O12—Cl1—O13—O14i33.4 (7)
C4—C5—C6—C70.7 (8)O14—Cl1—O13—O14i153.6 (9)
C5—C6—C7—C81.0 (8)O11—Cl1—O13—O14i100.1 (5)
C1—N1—C8—N20.3 (7)O13i—Cl1—O13—O14i79.9 (5)
C1—N1—C8—C7179.1 (4)O12—Cl1—O14—O12i99.1 (12)
C4—N2—C8—N1179.1 (4)O14i—Cl1—O14—O12i55.9 (7)
C3—N2—C8—N12.3 (6)O11—Cl1—O14—O12i124.1 (7)
C4—N2—C8—C70.3 (6)O13—Cl1—O14—O12i18.6 (9)
C3—N2—C8—C7178.3 (4)O13i—Cl1—O14—O12i137.1 (10)
C6—C7—C8—N1179.9 (4)O12i—Cl1—O14—O13i137.1 (10)
C6—C7—C8—N20.5 (7)O12—Cl1—O14—O13i37.9 (7)
O12i—Cl1—O12—O14i102.8 (10)O14i—Cl1—O14—O13i81.2 (5)
O14—Cl1—O12—O14i156.6 (9)O11—Cl1—O14—O13i98.8 (5)
O11—Cl1—O12—O14i77.2 (10)O13—Cl1—O14—O13i155.6 (9)
O13—Cl1—O12—O14i43.7 (10)
Symmetry codes: (i) x+1, y, z+1/2; (ii) x, y, z+1/2.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C4—H4···N1iii0.932.493.349 (6)154
C2—H2···O210.932.473.345 (7)158
C5—H5···O12iv0.932.623.541 (14)170
C5—H5···O14v0.932.613.449 (12)150
C9—H9B···O14vi0.962.643.493 (13)149
Symmetry codes: (iii) x, y, z1/2; (iv) x+1, y1, z+1/2; (v) x, y1, 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.

References

First citationKoval'chukova, O. V., Kuz'mina, N. E., Strashnova, S. B., Palkina, K. K., Mordovina, N. I., Zaitsev, B. E. & Nikitin, S. V. (2003). Russ. J. Coord. Chem. 29, 123–128.  CAS Google Scholar
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