organic compounds
8-Methyl-5-oxo-5,6-dihydrodipyrido[1,2-a:3′,2′-e]pyrimidin-11-ium chloride trihydrate 120 K
aDepartment of Chemistry, University of Aberdeen, Meston Walk, Aberdeen AB24 3UE, Scotland, bFundaçâo Oswaldo Cruz, Instituto de Tecnologia em Fármacos, Far-Manguinhos, Rua Sizenando Nabuco 100, Manguinhos, CEP 21041-250 Rio de Janeiro, RJ, Brazil, and cDepartamento de Química Inorgânica, Instituto de Química, Universidade Federal do Rio de Janeiro, CP 68563, 21945-970 Rio de Janeiro, RJ, Brazil
*Correspondence e-mail: r.a.howie@abdn.ac.uk
In the structure of the title salt, C12H10N3O+·Cl−·3H2O, the only species which do not coincide with the mirror plane in the P63/m are one complete water molecule, one H atom of another water molecule and two H atoms of the methyl group of the cation. Consequently, apart from the two H atoms of the methyl group, the cation is completely planar. The hydrogen bonding between the water molecules and, through Cl− anions, to the cations, although extensive, can be modelled satisfactorily only by treating one H atom in each of the two types of water molecules as disordered.
Comment
The title compound, (I), is an example of a more elaborate, potentially biologically active, pyridine-containing compound of the type provided by 2-chloronicotinoyl chloride, (II), as precursor, undergoing with a dinucleophilic reagent, in this case 2-amino-4-methylpyridine, (III). The in the structure of (I) is shown in Fig. 1. Bond lengths and bond angles within the cation of (I) are summarized in Table 1. Particularly notable are the C4a—C5 and C10a—N2 distances of 1.468 (2) and 1.429 (2) Å, respectively, and the bond angles N6—C5—C4a [114.00 (14)°] and C6a—N6—C5 [126.04 (14)°]. The somewhat extreme variation in bond lengths and more especially bond angles suggests that the cation is not altogether an aromatic species. This is certainly true of the lactam ring defined by C4a/C5/N6/C6a/N2/C10a. In the of the structure of (I) described here, the only atoms which are not coincident with a mirror plane of the P63/m are two H atoms of the methyl group, one H atom of the water molecule involving O2 and the entire water molecule involving O3. As a consequence the cation, with the exception of the methyl H atoms, is completely flat and the entire structure can be described in terms of well defined layers parallel to (001) at z = and such as that shown in Fig. 2. Adjacent layers are related to one another by the operation of crystallographic centres of symmetry. The layers are also connected to one another by hydrogen bonding as described later. A further consequence of the mirror symmetry is that both water molecules must be present in two distinct orientations which must be present in equal numbers resulting, therefore, in disorder. For the water molecule involving O2, H1W is ordered but H2W is distributed over two mirror-plane-related sites both of occupancy 0.5. The atom H3W is common to both orientations of the water molecule involving O3 and is accompanied by H4W in one orientation and H5W in the other. Thus, while the H3W site is fully occupied, H4W and H5W both have occupancies of 0.5. The disorder of the H atoms has serious implications for the disposition of the hydrogen bonds in which they are involved (Table 2). As shown in Fig. 3, the majority of the hydrogen bonds given in Table 2 interconnect the water molecules to form infinite tube-like columns propagated in the direction of c. These constitute spines of connectivity with branches at z = and to Cl1 atoms which, by means of the N6—H6⋯Cl1 hydrogen bonds, extend the linkage to the cations. The surface of the aqueous `tube' comprises six chains of the form shown in Fig. 4 connected to one another by hydrogen bonds of the form O3—H3W⋯O3i [symmetry code (i) 1 + x − y, x, 1 − z]. Notable here is the polarity, in the example shown in Fig. 4 in the positive direction of z, of the donor to acceptor alignment of the hydrogen bonds involved in the propagation of the chain in the [001] direction. Fig. 4 shows an arbitrary choice of mutually compatible H atoms consistent with only one of the two possible polarities of the chain. This ordered arrangement is clearly incompatible, as far as the H atoms are concerned, with the mirror planes upon which the O2 atoms lie and which relate the O3 atoms to one another. Clearly chains of this and of the opposite polarity must be distributed throughout the structure in equal numbers in order to bring about the observed disorder. Weak C—H⋯O contacts, also given in Table 2, provide, as shown in Fig. 2, inter-cation connectivity within the layers.
Experimental
To a solution of 2-chloronicotinoyl chloride, (II) (1.0 g, 5.68 mmol), in anhydrous tetrahydrofuran (30 ml) were successively added, with stirring, 2-amino-4-methylpyridine, (III) (1.1 ml, 5.68 mmol), and triethylamine (1.63 ml, 11.36 mmol) at room temperature. The reaction mixture was stirred for 8 h at room temperature, quenched with water (20 ml), and ethyl acetate (15 ml) was added. The organic layer was collected, washed with saturated sodium bicarbonate solution (2 × 20 ml), dried over sodium sulfate and rotary evaporated. The residue was purified by 1H NMR [400.00 MHz (FIDRES ±0.15 Hz), DMSO-d6]: δ 9.80 (1H, d, J = 7.3 Hz, H10), 9.15 (1H, dd, J = 2.0 and 4.8 Hz, H2), 8.80 (1H, dd, J = 2.0 and 8.0 Hz, H4), 8.03 (1H, dd, J = 4.8 and 8.0 Hz, H3), 7.71 (1H, s, H7), 7.64 (1H, dd, J = 2.0 and 7.2 Hz, H9), 2.65 (3H, s, CH3). 13C NMR (100.0 MHz, DMSO-d6): δ 159.4 (C5), 157.9 (C10), 154.3 (C2), 147.0 (C6a), 146.1 (C10a), 137.9 (C4), 129.9 (C9), 126.7 (C3), 120.7 (C4a), 116.7 (C8), 114.8 (C7), 21.8 (CH3). IR (cm−1, KBr disk): νmax 3080 (NH), 1712 (C=O).
with hexane–ethyl acetate (7:3) as eluant. The sample used in the crystallographic study was recrystallized from ethanol (m.p. 535–536 K).Crystal data
|
Refinement
|
|
Initial positions for the H atoms of the water molecules were obtained from difference maps, revised to provide a realistic hydrogen-bonding scheme and the geometry of the water molecules idealized to provide O—H distances and H—O—H angles in the ranges 0.81–0.86 Å and 105–111°, respectively. All other H atoms were placed in calculated positions, with C—H distances set at 0.95 and 0.98 Å for aryl and methyl H atoms, respectively, and the N—H distance set to 0.88 Å for the H atom of the NH group, placed as for an aryl H atom. The H atoms of the methyl group, H11A and H11B, were placed in positions appropriate to the mirror plane of the group whose orientation was therefore fixed accordingly. In all cases, the H atoms were then refined using a riding model, with Uiso(H) = 1.3Ueq(C,N,O).
Data collection: COLLECT (Hooft, 1998); cell DENZO (Otwinowski & Minor, 1997) and COLLECT; data reduction: DENZO and COLLECT; program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: ORTEP-3 for Windows (Farrugia, 1997); software used to prepare material for publication: SHELXL97 and PLATON (Spek, 2003).
Supporting information
https://doi.org/10.1107/S1600536805031521/wk6062sup1.cif
contains datablocks global, I. DOI:Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S1600536805031521/wk6062Isup2.hkl
Data collection: COLLECT (Hooft, 1998); cell
DENZO (Otwinowski & Minor, 1997) and COLLECT; data reduction: DENZO and COLLECT; program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: ORTEP-3 for Windows (Farrugia, 1997); software used to prepare material for publication: SHELXL97 and PLATON (Spek, 2003).C12H10N3O+·Cl−·3H2O | Melting point = 535–536 K |
Mr = 301.73 | Mo Kα radiation, λ = 0.71073 Å |
Hexagonal, P63/m | Cell parameters from 3270 reflections |
a = 19.4419 (3) Å | θ = 2.9–27.5° |
c = 6.5498 (1) Å | µ = 0.28 mm−1 |
V = 2144.05 (6) Å3 | T = 120 K |
Z = 6 | Block, colourless |
F(000) = 948 | 0.24 × 0.12 × 0.10 mm |
Dx = 1.402 Mg m−3 |
Bruker–Nonius KappaCCD diffractometer | 1783 independent reflections |
Radiation source: Bruker-Nonius FR591 rotating anode | 1600 reflections with I > 2σ(I) |
10 cm confocal mirrors monochromator | Rint = 0.036 |
Detector resolution: 9.091 pixels mm-1 | θmax = 27.5°, θmin = 3.2° |
φ and ω scans | h = −22→25 |
Absorption correction: multi-scan (SADABS; Sheldrick, 2003) | k = −25→25 |
Tmin = 0.649, Tmax = 1.000 | l = −8→8 |
16137 measured reflections |
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)] = 0.032 | Hydrogen site location: geom and difmap |
wR(F2) = 0.090 | H-atom parameters constrained |
S = 1.15 | w = 1/[σ2(Fo2) + (0.0426P)2 + 0.6158P] where P = (Fo2 + 2Fc2)/3 |
1783 reflections | (Δ/σ)max = 0.001 |
118 parameters | Δρmax = 0.25 e Å−3 |
0 restraints | Δρmin = −0.23 e Å−3 |
Experimental. Unit cell determined with DIRAX (Duisenberg, 1992; Duisenberg et al. 2000) but refined with the DENZO/COLLECT HKL package. Refs as: Duisenberg, A. J. M. (1992). J. Appl. Cryst. 25, 92–96. Duisenberg, A. J. M., Hooft, R. W. W., Schreurs, A. M. M. & Kroon, J. (2000). J. Appl. Cryst. 33, 893–898. |
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 | Occ. (<1) | |
Cl1 | 0.59489 (2) | 0.63371 (2) | 0.2500 | 0.02589 (14) | |
N1 | 0.31683 (9) | 0.21861 (8) | 0.2500 | 0.0233 (3) | |
N2 | 0.35594 (8) | 0.35325 (8) | 0.2500 | 0.0183 (3) | |
N6 | 0.49140 (8) | 0.45024 (8) | 0.2500 | 0.0222 (3) | |
H6 | 0.5271 | 0.5011 | 0.2500 | 0.029* | |
O1 | 0.58999 (7) | 0.42027 (8) | 0.2500 | 0.0368 (4) | |
O2 | 0.74225 (8) | 0.80351 (8) | 0.2500 | 0.0312 (3) | |
H1W | 0.7048 | 0.7548 | 0.2500 | 0.041* | |
H2W | 0.7687 | 0.8119 | 0.3541 | 0.041* | 0.50 |
O3 | 0.85472 (5) | 0.87284 (5) | 0.54356 (15) | 0.0294 (2) | |
H3W | 0.8927 | 0.8697 | 0.5071 | 0.038* | |
H4W | 0.8471 | 0.8648 | 0.6729 | 0.038* | 0.50 |
H5W | 0.8202 | 0.8503 | 0.4499 | 0.038* | 0.50 |
C2 | 0.33541 (11) | 0.16126 (10) | 0.2500 | 0.0272 (4) | |
H2 | 0.2932 | 0.1077 | 0.2500 | 0.035* | |
C3 | 0.41286 (11) | 0.17494 (11) | 0.2500 | 0.0268 (4) | |
H3 | 0.4231 | 0.1320 | 0.2500 | 0.035* | |
C4 | 0.47436 (11) | 0.25274 (11) | 0.2500 | 0.0242 (4) | |
H4 | 0.5280 | 0.2644 | 0.2500 | 0.032* | |
C4A | 0.45646 (10) | 0.31379 (10) | 0.2500 | 0.0212 (4) | |
C5 | 0.51927 (10) | 0.39755 (10) | 0.2500 | 0.0242 (4) | |
C6A | 0.41393 (9) | 0.43090 (9) | 0.2500 | 0.0189 (3) | |
C7 | 0.39353 (10) | 0.49036 (10) | 0.2500 | 0.0225 (4) | |
H7 | 0.4342 | 0.5445 | 0.2500 | 0.029* | |
C8 | 0.31520 (11) | 0.47143 (10) | 0.2500 | 0.0234 (4) | |
C9 | 0.25658 (10) | 0.39012 (11) | 0.2500 | 0.0238 (4) | |
H9 | 0.2020 | 0.3753 | 0.2500 | 0.031* | |
C10 | 0.27715 (10) | 0.33322 (10) | 0.2500 | 0.0217 (4) | |
H10 | 0.2369 | 0.2788 | 0.2500 | 0.028* | |
C10A | 0.37690 (10) | 0.29249 (9) | 0.2500 | 0.0193 (3) | |
C11 | 0.29336 (11) | 0.53520 (11) | 0.2500 | 0.0299 (4) | |
H11A | 0.2354 | 0.5108 | 0.2500 | 0.039* | |
H11B | 0.3152 | 0.5682 | 0.1278 | 0.039* |
U11 | U22 | U33 | U12 | U13 | U23 | |
Cl1 | 0.0230 (2) | 0.0188 (2) | 0.0271 (2) | 0.00393 (16) | 0.000 | 0.000 |
N1 | 0.0208 (7) | 0.0186 (7) | 0.0260 (8) | 0.0065 (6) | 0.000 | 0.000 |
N2 | 0.0153 (6) | 0.0180 (6) | 0.0201 (7) | 0.0071 (5) | 0.000 | 0.000 |
N6 | 0.0151 (6) | 0.0168 (7) | 0.0301 (8) | 0.0044 (5) | 0.000 | 0.000 |
O1 | 0.0155 (6) | 0.0294 (7) | 0.0634 (10) | 0.0097 (5) | 0.000 | 0.000 |
O2 | 0.0219 (6) | 0.0267 (7) | 0.0346 (7) | 0.0044 (5) | 0.000 | 0.000 |
O3 | 0.0230 (4) | 0.0340 (5) | 0.0285 (5) | 0.0123 (4) | 0.0006 (4) | −0.0004 (4) |
C2 | 0.0300 (9) | 0.0173 (8) | 0.0299 (10) | 0.0086 (7) | 0.000 | 0.000 |
C3 | 0.0356 (10) | 0.0232 (8) | 0.0251 (9) | 0.0173 (8) | 0.000 | 0.000 |
C4 | 0.0260 (9) | 0.0268 (9) | 0.0231 (8) | 0.0156 (7) | 0.000 | 0.000 |
C4A | 0.0203 (8) | 0.0224 (8) | 0.0208 (8) | 0.0107 (7) | 0.000 | 0.000 |
C5 | 0.0196 (8) | 0.0234 (8) | 0.0291 (9) | 0.0103 (7) | 0.000 | 0.000 |
C6A | 0.0168 (7) | 0.0182 (8) | 0.0186 (8) | 0.0064 (6) | 0.000 | 0.000 |
C7 | 0.0212 (8) | 0.0185 (8) | 0.0253 (9) | 0.0082 (7) | 0.000 | 0.000 |
C8 | 0.0260 (9) | 0.0245 (8) | 0.0218 (8) | 0.0143 (7) | 0.000 | 0.000 |
C9 | 0.0169 (8) | 0.0266 (9) | 0.0270 (9) | 0.0101 (7) | 0.000 | 0.000 |
C10 | 0.0157 (7) | 0.0207 (8) | 0.0231 (8) | 0.0049 (6) | 0.000 | 0.000 |
C10A | 0.0208 (8) | 0.0182 (8) | 0.0177 (8) | 0.0089 (6) | 0.000 | 0.000 |
C11 | 0.0294 (9) | 0.0284 (9) | 0.0367 (10) | 0.0179 (8) | 0.000 | 0.000 |
N1—C10A | 1.323 (2) | C3—C4 | 1.382 (3) |
N1—C2 | 1.333 (2) | C3—H3 | 0.9500 |
N2—C6A | 1.359 (2) | C4—C4A | 1.394 (2) |
N2—C10 | 1.379 (2) | C4—H4 | 0.9500 |
N2—C10A | 1.429 (2) | C4A—C10A | 1.387 (2) |
N6—C6A | 1.358 (2) | C4A—C5 | 1.468 (2) |
N6—C5 | 1.378 (2) | C6A—C7 | 1.397 (2) |
N6—H6 | 0.8800 | C7—C8 | 1.376 (2) |
O1—C5 | 1.216 (2) | C7—H7 | 0.9500 |
O2—H1W | 0.8587 | C8—C9 | 1.413 (2) |
O2—H2W | 0.8196 | C8—C11 | 1.498 (2) |
O3—H3W | 0.8060 | C9—C10 | 1.351 (2) |
O3—H4W | 0.8605 | C9—H9 | 0.9500 |
O3—H5W | 0.8516 | C10—H10 | 0.9500 |
C2—C3 | 1.392 (3) | C11—H11A | 0.9800 |
C2—H2 | 0.9500 | C11—H11B | 0.9800 |
C10A—N1—C2 | 116.55 (15) | O1—C5—C4A | 124.43 (16) |
C6A—N2—C10 | 120.06 (14) | N6—C5—C4A | 114.00 (14) |
C6A—N2—C10A | 119.81 (13) | N6—C6A—N2 | 119.78 (14) |
C10—N2—C10A | 120.13 (13) | N6—C6A—C7 | 120.36 (14) |
C6A—N6—C5 | 126.04 (14) | N2—C6A—C7 | 119.86 (14) |
C6A—N6—H6 | 117.0 | C8—C7—C6A | 120.84 (15) |
C5—N6—H6 | 117.0 | C8—C7—H7 | 119.6 |
H1W—O2—H2W | 108.7 | C6A—C7—H7 | 119.6 |
H3W—O3—H4W | 111.0 | C7—C8—C9 | 117.70 (15) |
H3W—O3—H5W | 105.4 | C7—C8—C11 | 120.82 (16) |
H4W—O3—H5W | 126.6 | C9—C8—C11 | 121.47 (16) |
N1—C2—C3 | 124.05 (16) | C10—C9—C8 | 120.84 (15) |
N1—C2—H2 | 118.0 | C10—C9—H9 | 119.6 |
C3—C2—H2 | 118.0 | C8—C9—H9 | 119.6 |
C4—C3—C2 | 118.06 (16) | C9—C10—N2 | 120.70 (15) |
C4—C3—H3 | 121.0 | C9—C10—H10 | 119.7 |
C2—C3—H3 | 121.0 | N2—C10—H10 | 119.7 |
C3—C4—C4A | 118.98 (16) | N1—C10A—C4A | 124.85 (15) |
C3—C4—H4 | 120.5 | N1—C10A—N2 | 115.84 (14) |
C4A—C4—H4 | 120.5 | C4A—C10A—N2 | 119.31 (14) |
C10A—C4A—C4 | 117.50 (15) | C8—C11—H11A | 109.5 |
C10A—C4A—C5 | 121.07 (15) | H11Bi—C11—H11B | 109.5 |
C4—C4A—C5 | 121.43 (15) | C8—C11—H11B | 109.5 |
O1—C5—N6 | 121.57 (16) | H11A—C11—H11B | 109.5 |
Symmetry code: (i) x, y, −z+1/2. |
D—H···A | D—H | H···A | D···A | D—H···A |
N6—H6···Cl1 | 0.88 | 2.23 | 3.0976 (15) | 168 |
O2—H1W···Cl1 | 0.86 | 2.25 | 3.1061 (13) | 172 |
O2—H2W···O3 | 0.82 | 1.94 | 2.7108 (13) | 157 |
O3—H3W···O3ii | 0.81 | 1.93 | 2.7263 (9) | 172 |
O3—H4W···O3iii | 0.86 | 1.86 | 2.7042 (19) | 165 |
O3—H5W···O2 | 0.85 | 1.86 | 2.7108 (13) | 177 |
C4—H4···O1iv | 0.95 | 2.50 | 3.179 (2) | 128 |
C7—H7···Cl1 | 0.95 | 2.71 | 3.4904 (17) | 140 |
C9—H9···O2v | 0.95 | 2.54 | 3.357 (2) | 144 |
Symmetry codes: (ii) x−y+1, x, −z+1; (iii) x, y, −z+3/2; (iv) −y+1, x−y, z; (v) −x+y, −x+1, z. |
Parametera | Min. | Max.b |
C4—C3c | 1.498 (2) | |
C3—C3 | 1.351 (2) | 1.468 (2) |
C3—N3 | 1.358 (2) | 1.429 (2) |
C3—N2 | 1.323 (2) | 1.333 (2) |
C3—O1d | 1.216 (2) | |
X—Y—Ze | 114.00 (14) | 126.04 (14) |
Notes: (a) bond type indicated by atoms with subscripts corresponding to the atom connectivities; (b) only present for multiple occurrences; (c) C11—C8; (d) C5—O1; (e) internal angles of the ring system. |
Acknowledgements
The use of the EPSRC X-ray crystallographic service at Southampton and the valuable assistance of the staff there is gratefully acknowledged.
References
Farrugia, L. J. (1997). J. Appl. Cryst. 30, 565. CrossRef IUCr Journals Google Scholar
Hooft, R. W. W. (1998). COLLECT. Nonius BV, Delft, The Netherlands. Google Scholar
Otwinowski, Z. & Minor, W. (1997). Methods in Enzymology, Vol. 276, Macromolecular Crystallography, Part A, edited by C. W. Carter Jr & R. M. Sweet, pp. 307–326. New York: Academic Press. Google Scholar
Sheldrick, G. M. (1997). SHELXS97 and SHELXL97. University of Göttingen, Germany. Google Scholar
Sheldrick, G. M. (2003). SADABS. Version 2.10. Bruker AXS Inc., Madison, Wisconsin, USA. Google Scholar
Spek, A. L. (2003). J. Appl. Cryst. 36, 7–13. Web of Science CrossRef CAS IUCr Journals Google Scholar
© International Union of Crystallography. Prior permission is not required to reproduce short quotations, tables and figures from this article, provided the original authors and source are cited. For more information, click here.