organic compounds
Hydrogen-bonded sheets in 4-amino-8,8-dimethyl-2-(methylsulfanyl)-8,9-dihydropyrimidino[4,5-b]quinolin-6(7H)-one
aDepartamento de Química, Universidad de Nariño, Ciudad Universitaria, Torobajo, AA 1175, Pasto, Colombia, bDepartamento de Química Inorgánica y Orgánica, Universidad de Jaén, 23071 Jaén, Spain, cDepartment of Chemistry, University of Aberdeen, Meston Walk, Old Aberdeen AB24 3UE, Scotland, and dSchool of Chemistry, University of St Andrews, Fife KY16 9ST, Scotland
*Correspondence e-mail: cg@st-andrews.ac.uk
The title molecule, C14H16N4OS, shows strong bond fixation within the fused heterocyclic rings. In the molecules are linked into sheets by a combination of N—H⋯N and N—H⋯O hydrogen bonds.
Comment
We report here the structure of the title compound, (I) (Fig. 1), which was prepared by microwave irradiation of a two-component mixture of a 6-aminopyrimidine and the condensation product formed from dimedone and formaldehyde. By contrast a similar reaction between 6-aminopyrimidines, 5,5-dimethylcyclohexane-1,3-dione and a large excess of formaldehyde yielded spiranopyridopyrimidines (Quiroga et al., 2006).
The bond distances within the fused heterocyclic system (Table 1) provide evidence for significant bond fixation of the naphthalene type. Thus, for example, the bonds N1—C2, N3—C4 and C9A—N10 are all significantly shorter than the bonds C2—N3, N10—C10A and C10A—N1, while C5—C5A is the shortest of the C—C bonds. The carbocyclic ring adopts a conformation best described as intermediate between an envelope form, with the fold across the vector C7⋯C9, and a half-chair form. The ring-puckering parameters (Cremer & Pople, 1975) for the atom sequence C5A—C6—C7—C8—C9—C9A are θ = 129.2 (2)° and φ = 342.4 (4)°; the idealized values for the envelope and half-chair forms, respectively, are θ = 126.3 and 129.8°, and φ = (60k) and (60k + 30)°, where k is zero or an integer. The two S—C distances are clearly different, and atom C21 lies almost in the plane of the adjacent pyrimidine ring.
The molecules are linked into sheets by two hydrogen bonds (Table 2), and the formation of the sheets is readily analysed in terms of two simple substructures, each formed by just one hydrogen bond. In the first amino atom N4 in the molecule at (x, y, z) acts as a hydrogen-bond donor, via H4A, to the pyrimidine ring atom N3 in the molecule at (1 − x, 1 − y, 2 − z), so generating by inversion an R22(8) (Bernstein et al., 1995) ring centred at (, , 1) (Fig. 2). In the second amino atom N4 at (x, y, z) acts as a hydrogen-bond donor, via H4B, to atom O6 in the molecule at (x, − y, + z), so forming a simple C(8) chain running parallel to the [001] direction and generated by the c-glide plane at y = 0.75 (Fig. 3). The combination of these two substructures generates a sheet parallel to (100) (Fig. 4), but there are no direction-specific interactions between adjacent sheets; in particular C—H⋯π hydrogen bonds and π–π stacking interactions are absent.
Experimental
A mixture of 4,6-diamino-2-methylsulfanylpyrimidine (1.0 mmol), 2,2-methylenebis(3-hydroxy-5,5-dimethylcyclohex-2-en-1-one) (1.0 mmol) and triethylamine (0.5 mmol) was placed in an open Pyrex-glass vessel and irradiated in a domestic microwave oven for 80 s at 600 W. The resulting solid product was collected by filtration, washed with cold ethanol, dried and then recrystallized from ethanol to provide crystals of compound (I) suitable for single-crystal X-ray diffraction; yield 60%, m.p. 580 K.
Crystal data
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Refinement
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All H atoms were located in difference maps and then treated as riding atoms with distances C—H = 0.95 Å (aromatic), 0.98 Å (CH3) or 0.99 Å (CH2) and N—H = 0.90 Å, and with Uiso(H) = kUeq(C,N), where k = 1.5 for methyl H atoms and 1.2 for all other H atoms.
Data collection: COLLECT (Hooft, 1999); cell DENZO (Otwinowski & Minor, 1997) and COLLECT; data reduction: DENZO and COLLECT; program(s) used to solve structure: OSCAIL (McArdle, 2003) and SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: OSCAIL and SHELXL97 (Sheldrick, 1997); molecular graphics: PLATON (Spek, 2003); software used to prepare material for publication: SHELXL97 and PRPKAPPA (Ferguson, 1999).
Supporting information
https://doi.org/10.1107/S1600536806040633/lh2204sup1.cif
contains datablocks global, I. DOI:Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S1600536806040633/lh2204Isup2.hkl
Data collection: COLLECT (Hooft, 1999); cell
DENZO (Otwinowski & Minor, 1997) and COLLECT; data reduction: DENZO and COLLECT; program(s) used to solve structure: OSCAIL (McArdle, 2003) and SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: OSCAIL and SHELXL97 (Sheldrick, 1997); molecular graphics: PLATON (Spek, 2003); software used to prepare material for publication: SHELXL97 and PRPKAPPA (Ferguson, 1999).C14H16N4OS | F(000) = 608 |
Mr = 288.37 | Dx = 1.351 Mg m−3 |
Monoclinic, P21/c | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: -P 2ybc | Cell parameters from 3245 reflections |
a = 10.7138 (11) Å | θ = 2.4–27.5° |
b = 15.1368 (15) Å | µ = 0.23 mm−1 |
c = 8.9112 (6) Å | T = 120 K |
β = 101.208 (6)° | Block, colourless |
V = 1417.6 (2) Å3 | 0.40 × 0.24 × 0.18 mm |
Z = 4 |
Bruker–Nonius KappaCCD diffractometer | 3245 independent reflections |
Radiation source: Bruker-Nonius FR591 rotating anode | 2115 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.072 |
Detector resolution: 9.091 pixels mm-1 | θmax = 27.5°, θmin = 2.4° |
φ and ω scans | h = −13→13 |
Absorption correction: multi-scan (SADABS; Sheldrick, 2003) | k = −19→19 |
Tmin = 0.926, Tmax = 0.960 | l = −11→11 |
20540 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)] = 0.054 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.143 | H-atom parameters constrained |
S = 1.02 | w = 1/[σ2(Fo2) + (0.0693P)2 + 0.6375P] where P = (Fo2 + 2Fc2)/3 |
3245 reflections | (Δ/σ)max < 0.001 |
184 parameters | Δρmax = 0.35 e Å−3 |
0 restraints | Δρmin = −0.33 e Å−3 |
Experimental. MS (70 eV) m/z (%) 290 (100, M+), 289 (62), 275 (34), 259 (5), 245 (9), 220 (17) |
x | y | z | Uiso*/Ueq | ||
N1 | 0.74462 (19) | 0.39484 (12) | 0.7310 (2) | 0.0288 (5) | |
C2 | 0.6764 (2) | 0.39091 (15) | 0.8384 (3) | 0.0290 (5) | |
S2 | 0.69070 (6) | 0.29872 (4) | 0.95954 (7) | 0.0350 (2) | |
C21 | 0.8107 (3) | 0.23543 (17) | 0.8931 (3) | 0.0355 (6) | |
N3 | 0.59209 (19) | 0.45107 (12) | 0.8743 (2) | 0.0283 (5) | |
C4 | 0.5710 (2) | 0.52293 (15) | 0.7856 (2) | 0.0250 (5) | |
N4 | 0.48914 (19) | 0.58258 (13) | 0.8191 (2) | 0.0301 (5) | |
C4A | 0.6340 (2) | 0.53342 (14) | 0.6572 (2) | 0.0250 (5) | |
C5 | 0.6103 (2) | 0.60132 (15) | 0.5486 (2) | 0.0260 (5) | |
C5A | 0.6734 (2) | 0.60094 (14) | 0.4270 (2) | 0.0247 (5) | |
C6 | 0.6463 (2) | 0.66958 (15) | 0.3058 (2) | 0.0274 (5) | |
O6 | 0.58072 (17) | 0.73385 (11) | 0.32040 (18) | 0.0338 (4) | |
C7 | 0.7028 (2) | 0.65422 (16) | 0.1666 (3) | 0.0311 (6) | |
C8 | 0.8376 (2) | 0.61671 (15) | 0.2029 (2) | 0.0274 (5) | |
C81 | 0.8854 (3) | 0.59856 (16) | 0.0546 (3) | 0.0334 (6) | |
C82 | 0.9273 (3) | 0.68183 (16) | 0.3016 (3) | 0.0358 (6) | |
C9 | 0.8344 (2) | 0.52914 (15) | 0.2897 (3) | 0.0312 (6) | |
C9A | 0.7636 (2) | 0.53374 (14) | 0.4198 (2) | 0.0252 (5) | |
N10 | 0.78922 (18) | 0.46986 (12) | 0.5234 (2) | 0.0279 (5) | |
C10A | 0.7220 (2) | 0.46742 (15) | 0.6375 (2) | 0.0263 (5) | |
H21A | 0.7841 | 0.2243 | 0.7832 | 0.053* | |
H21B | 0.8226 | 0.1790 | 0.9479 | 0.053* | |
H21C | 0.8910 | 0.2684 | 0.9119 | 0.053* | |
H4A | 0.4592 | 0.5712 | 0.9047 | 0.036* | |
H4B | 0.4941 | 0.6379 | 0.7837 | 0.036* | |
H5 | 0.5517 | 0.6471 | 0.5583 | 0.031* | |
H7A | 0.7041 | 0.7109 | 0.1115 | 0.037* | |
H7B | 0.6476 | 0.6128 | 0.0975 | 0.037* | |
H81A | 0.8307 | 0.5543 | −0.0060 | 0.050* | |
H81B | 0.9729 | 0.5764 | 0.0793 | 0.050* | |
H81C | 0.8831 | 0.6534 | −0.0044 | 0.050* | |
H82A | 0.9243 | 0.7388 | 0.2489 | 0.054* | |
H82B | 1.0144 | 0.6587 | 0.3190 | 0.054* | |
H82C | 0.9008 | 0.6897 | 0.4000 | 0.054* | |
H9A | 0.7943 | 0.4834 | 0.2165 | 0.037* | |
H9B | 0.9230 | 0.5103 | 0.3305 | 0.037* |
U11 | U22 | U33 | U12 | U13 | U23 | |
N1 | 0.0383 (12) | 0.0191 (10) | 0.0309 (11) | 0.0019 (9) | 0.0112 (9) | 0.0049 (8) |
C2 | 0.0341 (14) | 0.0219 (12) | 0.0303 (12) | −0.0026 (10) | 0.0048 (10) | 0.0034 (9) |
S2 | 0.0459 (4) | 0.0266 (3) | 0.0350 (4) | 0.0031 (3) | 0.0143 (3) | 0.0098 (3) |
C21 | 0.0468 (16) | 0.0229 (12) | 0.0380 (14) | 0.0050 (12) | 0.0111 (12) | 0.0083 (10) |
N3 | 0.0351 (11) | 0.0213 (10) | 0.0298 (11) | 0.0004 (9) | 0.0094 (8) | 0.0029 (8) |
C4 | 0.0286 (12) | 0.0194 (12) | 0.0266 (11) | −0.0033 (10) | 0.0047 (9) | −0.0015 (9) |
N4 | 0.0429 (12) | 0.0191 (10) | 0.0309 (11) | −0.0006 (9) | 0.0137 (9) | 0.0007 (8) |
C4A | 0.0317 (13) | 0.0169 (11) | 0.0267 (12) | −0.0025 (10) | 0.0064 (9) | −0.0022 (9) |
C5 | 0.0308 (13) | 0.0197 (12) | 0.0279 (12) | −0.0015 (10) | 0.0068 (10) | −0.0022 (9) |
C5A | 0.0306 (13) | 0.0156 (11) | 0.0280 (12) | −0.0026 (9) | 0.0058 (10) | −0.0012 (9) |
C6 | 0.0338 (13) | 0.0219 (12) | 0.0258 (12) | −0.0026 (11) | 0.0042 (10) | 0.0007 (9) |
O6 | 0.0452 (11) | 0.0210 (9) | 0.0362 (9) | 0.0063 (8) | 0.0104 (8) | 0.0039 (7) |
C7 | 0.0376 (14) | 0.0277 (13) | 0.0284 (12) | 0.0010 (11) | 0.0078 (10) | 0.0048 (10) |
C8 | 0.0372 (14) | 0.0200 (12) | 0.0265 (12) | −0.0008 (10) | 0.0102 (10) | −0.0008 (9) |
C81 | 0.0450 (16) | 0.0258 (14) | 0.0321 (13) | −0.0013 (11) | 0.0138 (11) | 0.0000 (10) |
C82 | 0.0400 (15) | 0.0307 (14) | 0.0391 (14) | −0.0059 (12) | 0.0137 (11) | −0.0054 (11) |
C9 | 0.0448 (15) | 0.0218 (12) | 0.0300 (13) | 0.0031 (11) | 0.0152 (11) | 0.0018 (10) |
C9A | 0.0329 (13) | 0.0171 (11) | 0.0264 (12) | −0.0009 (10) | 0.0081 (10) | 0.0001 (9) |
N10 | 0.0381 (12) | 0.0182 (10) | 0.0294 (10) | 0.0025 (9) | 0.0117 (9) | 0.0028 (8) |
C10A | 0.0336 (13) | 0.0198 (12) | 0.0257 (11) | −0.0018 (10) | 0.0062 (9) | 0.0001 (9) |
N1—C2 | 1.314 (3) | C5—H5 | 0.95 |
C2—N3 | 1.364 (3) | C5A—C6 | 1.486 (3) |
N3—C4 | 1.338 (3) | C6—O6 | 1.221 (3) |
C4—C4A | 1.445 (3) | C6—C7 | 1.501 (3) |
C4A—C5 | 1.401 (3) | C7—C8 | 1.526 (3) |
C5—C5A | 1.384 (3) | C7—H7A | 0.99 |
C5A—C9A | 1.413 (3) | C7—H7B | 0.99 |
C9A—N10 | 1.328 (3) | C8—C82 | 1.530 (3) |
N10—C10A | 1.356 (3) | C8—C81 | 1.532 (3) |
C10A—N1 | 1.371 (3) | C8—C9 | 1.538 (3) |
C4A—C10A | 1.408 (3) | C81—H81A | 0.98 |
C2—S2 | 1.753 (2) | C81—H81B | 0.98 |
S2—C21 | 1.794 (3) | C81—H81C | 0.98 |
C21—H21A | 0.98 | C82—H82A | 0.98 |
C21—H21B | 0.98 | C82—H82B | 0.98 |
C21—H21C | 0.98 | C82—H82C | 0.98 |
C4—N4 | 1.332 (3) | C9—C9A | 1.506 (3) |
N4—H4A | 0.90 | C9—H9A | 0.99 |
N4—H4B | 0.90 | C9—H9B | 0.99 |
C2—N1—C10A | 114.9 (2) | C8—C7—H7B | 108.8 |
N1—C2—N3 | 128.9 (2) | H7A—C7—H7B | 107.7 |
N1—C2—S2 | 119.38 (18) | C7—C8—C82 | 110.2 (2) |
N3—C2—S2 | 111.68 (17) | C7—C8—C81 | 110.20 (19) |
C2—S2—C21 | 101.78 (12) | C82—C8—C81 | 109.5 (2) |
S2—C21—H21A | 109.5 | C7—C8—C9 | 108.33 (19) |
S2—C21—H21B | 109.5 | C82—C8—C9 | 109.8 (2) |
H21A—C21—H21B | 109.5 | C81—C8—C9 | 108.84 (18) |
S2—C21—H21C | 109.5 | C8—C81—H81A | 109.5 |
H21A—C21—H21C | 109.5 | C8—C81—H81B | 109.5 |
H21B—C21—H21C | 109.5 | H81A—C81—H81B | 109.5 |
C4—N3—C2 | 116.59 (19) | C8—C81—H81C | 109.5 |
N4—C4—N3 | 117.5 (2) | H81A—C81—H81C | 109.5 |
N4—C4—C4A | 122.1 (2) | H81B—C81—H81C | 109.5 |
N3—C4—C4A | 120.4 (2) | C8—C82—H82A | 109.5 |
C4—N4—H4A | 114.8 | C8—C82—H82B | 109.5 |
C4—N4—H4B | 117.8 | H82A—C82—H82B | 109.5 |
H4A—N4—H4B | 122.0 | C8—C82—H82C | 109.5 |
C5—C4A—C10A | 118.0 (2) | H82A—C82—H82C | 109.5 |
C5—C4A—C4 | 125.3 (2) | H82B—C82—H82C | 109.5 |
C10A—C4A—C4 | 116.6 (2) | C9A—C9—C8 | 114.27 (19) |
C5A—C5—C4A | 119.2 (2) | C9A—C9—H9A | 108.7 |
C5A—C5—H5 | 120.4 | C8—C9—H9A | 108.7 |
C4A—C5—H5 | 120.4 | C9A—C9—H9B | 108.7 |
C5—C5A—C9A | 118.7 (2) | C8—C9—H9B | 108.7 |
C5—C5A—C6 | 120.7 (2) | H9A—C9—H9B | 107.6 |
C9A—C5A—C6 | 120.6 (2) | N10—C9A—C5A | 122.9 (2) |
O6—C6—C5A | 121.0 (2) | N10—C9A—C9 | 115.76 (19) |
O6—C6—C7 | 123.0 (2) | C5A—C9A—C9 | 121.32 (19) |
C5A—C6—C7 | 116.0 (2) | C9A—N10—C10A | 118.2 (2) |
C6—C7—C8 | 113.59 (19) | N10—C10A—N1 | 114.8 (2) |
C6—C7—H7A | 108.8 | N10—C10A—C4A | 122.7 (2) |
C8—C7—H7A | 108.8 | N1—C10A—C4A | 122.4 (2) |
C6—C7—H7B | 108.8 | ||
C10A—N1—C2—N3 | −3.9 (4) | C6—C7—C8—C82 | −62.0 (3) |
C10A—N1—C2—S2 | 176.91 (17) | C6—C7—C8—C81 | 177.1 (2) |
N1—C2—S2—C21 | 2.1 (2) | C6—C7—C8—C9 | 58.1 (3) |
N3—C2—S2—C21 | −177.21 (17) | C7—C8—C9—C9A | −47.8 (3) |
N1—C2—N3—C4 | 2.8 (4) | C82—C8—C9—C9A | 72.6 (3) |
S2—C2—N3—C4 | −177.99 (16) | C81—C8—C9—C9A | −167.7 (2) |
C2—N3—C4—N4 | −179.9 (2) | C5—C5A—C9A—N10 | 1.1 (3) |
C2—N3—C4—C4A | 1.2 (3) | C6—C5A—C9A—N10 | −178.5 (2) |
N4—C4—C4A—C5 | −5.2 (4) | C5—C5A—C9A—C9 | 179.4 (2) |
N3—C4—C4A—C5 | 173.6 (2) | C6—C5A—C9A—C9 | −0.3 (3) |
N4—C4—C4A—C10A | 177.7 (2) | C8—C9—C9A—N10 | −161.0 (2) |
N3—C4—C4A—C10A | −3.5 (3) | C8—C9—C9A—C5A | 20.6 (3) |
C10A—C4A—C5—C5A | 0.2 (3) | C5A—C9A—N10—C10A | 2.6 (3) |
C4—C4A—C5—C5A | −176.9 (2) | C9—C9A—N10—C10A | −175.7 (2) |
C4A—C5—C5A—C9A | −2.5 (3) | C9A—N10—C10A—N1 | 173.8 (2) |
C4A—C5—C5A—C6 | 177.2 (2) | C9A—N10—C10A—C4A | −5.2 (3) |
C5—C5A—C6—O6 | 9.5 (3) | C2—N1—C10A—N10 | −177.8 (2) |
C9A—C5A—C6—O6 | −170.8 (2) | C2—N1—C10A—C4A | 1.1 (3) |
C5—C5A—C6—C7 | −169.9 (2) | C5—C4A—C10A—N10 | 3.8 (3) |
C9A—C5A—C6—C7 | 9.7 (3) | C4—C4A—C10A—N10 | −178.9 (2) |
O6—C6—C7—C8 | 140.8 (2) | C5—C4A—C10A—N1 | −175.0 (2) |
C5A—C6—C7—C8 | −39.8 (3) | C4—C4A—C10A—N1 | 2.3 (3) |
D—H···A | D—H | H···A | D···A | D—H···A |
N4—H4A···N3i | 0.90 | 2.17 | 3.067 (3) | 173 |
N4—H4B···O6ii | 0.90 | 2.15 | 2.946 (3) | 147 |
Symmetry codes: (i) −x+1, −y+1, −z+2; (ii) x, −y+3/2, z+1/2. |
Acknowledgements
X-ray data were collected at the EPSRC X-ray Crystallographic Service, University of Southampton, England. JC and JT thank the Consejería de Innovación, Ciencia y Empresa (Junta de Andalucía, Spain) and the Universidad de Jaén for financial support. SC thanks COLCIENCIAS and UDENAR (Universidad de Nariño, Colombia) for financial support.
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