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Molecules of the title compound, C15H21N3O3S, have a markedly polarized electronic structure; the carbocyclic ring adopts an envelope conformation and the overall molecular conformation appears to be controlled by two intramolecular hydrogen bonds, one each of the O-H...O and N-H...O types. The mol­ecules are linked into C(6) chains by an intermol­ecular N-H...O hydrogen bond, and pairs of these hydrogen-bonded chains are linked by a [pi]-[pi] stacking interaction.

Supporting information

cif

Crystallographic Information File (CIF) https://doi.org/10.1107/S0108270104001118/sk1697sup1.cif
Contains datablocks global, I

hkl

Structure factor file (CIF format) https://doi.org/10.1107/S0108270104001118/sk1697Isup2.hkl
Contains datablock I

CCDC reference: 235341

Comment top

As part of a program for the synthesis of fused pyrimido derivatives, we have investigated the three-component cyclocondensation between 4-amino-1-methyl-2-(methylsulfanyl)pyrimidin-6(1H)-one, formaldehyde and 5,5-dimethylcyclohexane-1,3-dione (dimedone), but instead of the desired pyrimido[3,4-b]quinoline, the intermediate title compound, (I), was obtained. We report here its molecular and supramolecular structure. Three-component reactions of this general type can also provide, as a by-product, the twofold symmetrical compound 2,2'-methylenebis(5,5-dimethyl-3-hydroxy-2-cyclohexen-1-one), (II), whose structure we have reported recently (Low et al., 2003).

Within the heterocyclic ring of (I), the C4—C5 and C5—C6 distances (Table 1) are similar, and they cannot be associated readily with double and single bonds, respectively. In addition, the C4—N4 distance is very much shorter than the mean value (1.355 Å; Allen et al., 1987) for bonds of type C(aryl)—NH2, where N is planar. In contrast to the C—C bonds, the C2—N3 and N3—C4 bonds have distances typical of those for localized double and single bonds of these types. While the C6—O6 distance is typical of those in unstrained amides, the C6—N1 distance is very long for its type (mean value 1.346 Å; Allen et al., 1987). These values, taken together, point to the significance of the polar form (Ia) as an important contributor to the overall molecular electronic structure, but effectively eliminate as contributors other forms such as (Ib) and (Ic).

There is clear evidence for bond fixation in the atom-sequence between O52 and O56. Within the carbocyclic ring, the total puckering amplitude Q is 0.455 (2) Å, markedly less than the value of 0.63 Å for an ideal cyclohexane chair of −3 m (D3 d) molecular symmetry with a C—C distances of 1.54 Å (Cremer & Pople, 1975). For the atom sequence C51 to C56, the angular parameters, θ 53.9 (3)° and ϕ 195.8 (4), are clearly indicative of the sofa or envelope conformation as the best single qualitative descriptor, with a local pseudo-mirror plane passing through atoms C5, C54, C541 and C542 (Fig. 1); this conformation is confirmed by the leading torsional angles involving this ring (Table 1). However, the envelope conformation can itself be represented as a linear combination of the three primitive forms chair, boat and twist-boat (Evans & Boeyens, 1989), with the chair form dominant here.

There are three hydrogen bonds (Table 2), two of which are intramolecular, and these doubtless control the overall molecular conformation, in particular the twist angles about the C5—C57 and C51—C57 bonds (Table 1). The short O···O distance in the intramolecular O—H···O hydrogen bond is consistent with the development of a significant negative charge on atom O6 [cf. form (Ia)]. Each of the intramolecular hydrogen bonds gives rise to an independent S(8) motif (Bernstein et al., 1995). The molecules are linked into chains by a single intermolecular N—H···O hydrogen bond; amine atom N4 in the molecule at (x, y, z) acts as a hydrogen-bond donor, via atom H4B, to amide atom O6 in the molecule at (x, 1 + y, z), so generating by translation a C(6) chain running parallel to the [010] direction (Fig. 2).

Four of these chains pass through each unit cell, and they are linked in pairs by a single π···π stacking interaction. The pyrimidine rings of the molecules are (x, y, z) and (1 − x, 1 − y, 1 − z) are parallel with an interplanar spacing of 3.498 (2) Å: the centroid separation is 3.646 (2) Å coresponding to a centroid offset of 1.028 (2) Å. The resulting pair of π-stacked chains (Fig. 3) lies in the domain 0.24 < z < 0.76, and a second double chain, related to the first by the translational symmetry operators, lies in the domain 0.74 < z < 1.26. There are no direction-specific interactions between the double chains.

Experimental top

To a hot solution of 4-amino-1-methyl-2-(methylsulfanyl)pyrimidin-6(1H)-one (2 mmol) in 20 cm3 of ethanol (96%) were added formaldehyde (2 mmol) and dimedone (2 mmol); the reaction mixture was heated under reflux for 4 h. The white powder that formed during the reaction was filtered off and the remaining solution was cooled to 270 K. After 2 d, a white solid was filtered off and recrystallized from ethanol, affording crystalline needles suitable for single-crystal X-ray diffraction. Yield 30%, m.p. 426–428 K. Analysis found: C 55.7, H 6.7, N 12.8, S 9.9%; C15H21N3O3S requires: C 55.7, H 6.6, N 13.0, S 9.9%.

Refinement top

Space group P21/n was assigned uniquely from the systematic absences. All H atoms were located from difference maps and thereafter treated as riding atoms, with C—H distances of 0.98 (CH3) and 0.99 Å (CH2), N—H distances of 0.88 Å and an O—H distance of 0.84 Å.

Computing details top

Data collection: KappaCCD Server Software (Nonius, 1997); cell refinement: DENZO–SMN (Otwinowski & Minor, 1997); data reduction: DENZO–SMN; program(s) used to solve structure: OSCAIL (McArdle, 2003) and SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: PLATON (Spek, 2003); software used to prepare material for publication: SHELXL97 and PRPKAPPA (Ferguson, 1999).

Figures top
[Figure 1] Fig. 1. The molecule of (I), showing the atom-labelling scheme. Displacement ellipsoids are drawn at the 30% probability level.
[Figure 2] Fig. 2. Part of the crystal structure of (I), showing the formation of a C(6) chain along [010]. For clarity, H atoms bonded to C atoms have been omitted. Atoms marked with an asterisk (*) or a hash (#) are at the symmetry positions (x, 1 + y, z) and (x, −1 + y, z), respectively.
[Figure 3] Fig. 3. A stereoview of part of the crystal structure of (I), showing the π-stacked double chain in the domain 0.24 < z < 0.76. For clarity, H atoms bonded to C atoms have been omitted.
4-Amino-1-methyl-5-(2-hydroxy-4,4-dimethyl-2-oxocyclohexenylmethyl)- 2-(methylsulfanyl)pyrimidin-6(1H)-one top
Crystal data top
C15H21N3O3SF(000) = 664
Mr = 323.41Dx = 1.394 Mg m3
Monoclinic, P21/nMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ynCell parameters from 3586 reflections
a = 7.5524 (2) Åθ = 3.4–28.2°
b = 7.1370 (3) ŵ = 0.23 mm1
c = 28.6208 (11) ÅT = 120 K
β = 93.128 (2)°Block, colourless
V = 1540.40 (10) Å30.50 × 0.30 × 0.20 mm
Z = 4
Data collection top
Nonius KappaCCD
diffractometer
3586 independent reflections
Radiation source: rotating anode2600 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.071
ϕ scans, and ω scans with κ offsetsθmax = 28.2°, θmin = 3.4°
Absorption correction: multi-scan
(SORTAV; Blessing 1995, 1997)
h = 99
Tmin = 0.868, Tmax = 0.956k = 89
18675 measured reflectionsl = 3737
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.042Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.109H-atom parameters constrained
S = 1.01 w = 1/[σ2(Fo2) + (0.0505P)2 + 0.5167P]
where P = (Fo2 + 2Fc2)/3
3586 reflections(Δ/σ)max = 0.001
204 parametersΔρmax = 0.28 e Å3
0 restraintsΔρmin = 0.29 e Å3
Crystal data top
C15H21N3O3SV = 1540.40 (10) Å3
Mr = 323.41Z = 4
Monoclinic, P21/nMo Kα radiation
a = 7.5524 (2) ŵ = 0.23 mm1
b = 7.1370 (3) ÅT = 120 K
c = 28.6208 (11) Å0.50 × 0.30 × 0.20 mm
β = 93.128 (2)°
Data collection top
Nonius KappaCCD
diffractometer
3586 independent reflections
Absorption correction: multi-scan
(SORTAV; Blessing 1995, 1997)
2600 reflections with I > 2σ(I)
Tmin = 0.868, Tmax = 0.956Rint = 0.071
18675 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0420 restraints
wR(F2) = 0.109H-atom parameters constrained
S = 1.01Δρmax = 0.28 e Å3
3586 reflectionsΔρmin = 0.29 e Å3
204 parameters
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
N10.7539 (2)0.3798 (2)0.49141 (5)0.0198 (3)
C20.7498 (2)0.5505 (3)0.51029 (6)0.0194 (4)
N30.6955 (2)0.6963 (2)0.48764 (5)0.0213 (3)
C40.6362 (2)0.6744 (2)0.44168 (6)0.0200 (4)
N40.5820 (2)0.8288 (2)0.41993 (5)0.0255 (4)
C50.6339 (2)0.5062 (2)0.41944 (6)0.0194 (4)
C60.7005 (2)0.3536 (3)0.44411 (6)0.0208 (4)
O60.71906 (19)0.19762 (17)0.42643 (4)0.0262 (3)
C110.8209 (3)0.2222 (3)0.51881 (7)0.0260 (4)
S20.82976 (6)0.56773 (7)0.568820 (15)0.02358 (14)
C210.7849 (3)0.8037 (3)0.57990 (7)0.0307 (5)
C570.5750 (2)0.4850 (3)0.36838 (6)0.0206 (4)
C510.7154 (2)0.5431 (3)0.33565 (6)0.0191 (4)
C520.8609 (2)0.4398 (2)0.32941 (6)0.0198 (4)
O520.88973 (18)0.27490 (17)0.34900 (4)0.0238 (3)
C531.0093 (2)0.4934 (3)0.29979 (6)0.0217 (4)
C541.0156 (2)0.6982 (3)0.28889 (6)0.0226 (4)
C550.8268 (2)0.7601 (3)0.27475 (6)0.0229 (4)
C560.6944 (2)0.7138 (3)0.31032 (6)0.0211 (4)
O560.5690 (2)0.8186 (2)0.31668 (6)0.0277 (4)
C5411.0852 (3)0.8074 (3)0.33172 (7)0.0297 (4)
C5421.1342 (3)0.7320 (3)0.24834 (8)0.0325 (5)
H11A0.79940.10610.50110.039*
H11B0.76020.21600.54820.039*
H11C0.94860.23760.52570.039*
H21A0.80140.82810.61360.046*
H21B0.66230.83230.56930.046*
H21C0.86600.88290.56300.046*
H4A0.54330.82410.39040.031*
H4B0.58450.93640.43500.031*
H57A0.54280.35250.36220.025*
H57B0.46750.56200.36170.025*
H520.81590.25690.36950.036*
H53A0.99750.42250.27010.026*
H53B1.12290.45640.31610.026*
H54A1.07810.94200.32510.044*
H54B1.20890.77250.33940.044*
H54C1.01340.77800.35830.044*
H54G1.12850.86440.23930.049*
H54H1.09360.65430.22160.049*
H54I1.25680.69890.25800.049*
H55A0.82630.89720.26950.027*
H55B0.78940.69920.24470.027*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
N10.0252 (8)0.0148 (7)0.0195 (7)0.0005 (6)0.0023 (6)0.0021 (6)
C20.0188 (9)0.0199 (9)0.0198 (8)0.0010 (7)0.0037 (7)0.0001 (7)
N30.0263 (8)0.0177 (8)0.0197 (7)0.0002 (6)0.0005 (6)0.0009 (6)
C40.0209 (9)0.0184 (9)0.0207 (9)0.0000 (7)0.0026 (7)0.0020 (7)
N40.0377 (10)0.0171 (8)0.0211 (8)0.0043 (7)0.0038 (7)0.0001 (6)
C50.0222 (9)0.0174 (9)0.0188 (8)0.0026 (7)0.0025 (7)0.0003 (7)
C60.0243 (10)0.0185 (10)0.0200 (9)0.0034 (7)0.0057 (7)0.0010 (7)
O60.0401 (8)0.0141 (7)0.0243 (7)0.0012 (6)0.0027 (6)0.0004 (5)
C110.0349 (11)0.0189 (10)0.0241 (9)0.0032 (8)0.0019 (8)0.0045 (7)
S20.0294 (3)0.0223 (3)0.0187 (2)0.0011 (2)0.00129 (17)0.00093 (18)
C210.0402 (12)0.0274 (11)0.0236 (10)0.0053 (9)0.0058 (8)0.0036 (8)
C570.0234 (9)0.0186 (9)0.0198 (9)0.0014 (7)0.0009 (7)0.0002 (7)
C510.0209 (9)0.0201 (9)0.0160 (8)0.0010 (7)0.0015 (7)0.0001 (7)
C520.0276 (10)0.0156 (9)0.0157 (8)0.0016 (7)0.0023 (7)0.0016 (7)
O520.0325 (8)0.0161 (7)0.0231 (7)0.0029 (6)0.0045 (5)0.0023 (5)
C530.0254 (10)0.0204 (9)0.0194 (9)0.0014 (8)0.0014 (7)0.0003 (7)
C540.0236 (10)0.0205 (10)0.0238 (9)0.0012 (8)0.0014 (7)0.0011 (7)
C550.0272 (10)0.0198 (9)0.0215 (9)0.0010 (8)0.0000 (7)0.0036 (7)
C560.0233 (10)0.0218 (10)0.0178 (8)0.0002 (8)0.0032 (7)0.0007 (7)
O560.0291 (7)0.0261 (7)0.0273 (7)0.0080 (6)0.0029 (6)0.0057 (6)
C5410.0291 (11)0.0234 (10)0.0359 (11)0.0024 (8)0.0041 (8)0.0036 (9)
C5420.0311 (11)0.0297 (11)0.0376 (11)0.0017 (9)0.0095 (9)0.0061 (9)
Geometric parameters (Å, º) top
N1—C21.334 (2)N4—H4B0.88
C2—N31.282 (2)C5—C571.512 (2)
N3—C41.375 (2)C57—C511.511 (2)
C4—C51.359 (3)C57—H57A0.99
C5—C61.378 (3)C57—H57B0.99
C6—N11.404 (2)C52—C531.491 (3)
C2—S21.7536 (18)O52—H520.84
S2—C211.750 (2)C53—C541.496 (3)
N1—C111.447 (2)C53—H53A0.99
C4—N41.319 (2)C53—H53B0.99
C6—O61.234 (2)C54—C5411.522 (3)
C51—C521.343 (3)C54—C5421.523 (3)
C52—O521.317 (2)C54—C551.526 (3)
C51—C561.423 (3)C541—H54A0.98
C56—O561.227 (2)C541—H54B0.98
C11—H11A0.98C541—H54C0.98
C11—H11B0.98C542—H54G0.98
C11—H11C0.98C542—H54H0.98
C21—H21A0.98C542—H54I0.98
C21—H21B0.98C55—C561.503 (3)
C21—H21C0.98C55—H55A0.99
N4—H4A0.88C55—H55B0.99
C2—N1—C6120.05 (15)O52—C52—C53111.08 (15)
C2—N1—C11120.37 (15)C51—C52—C53125.47 (16)
C6—N1—C11119.52 (15)C52—O52—H52109.5
N1—C11—H11A109.5C52—C53—C54113.76 (15)
N1—C11—H11B109.5C52—C53—H53A108.8
H11A—C11—H11B109.5C54—C53—H53A108.8
N1—C11—H11C109.5C52—C53—H53B108.8
H11A—C11—H11C109.5C54—C53—H53B108.8
H11B—C11—H11C109.5H53A—C53—H53B107.7
N3—C2—N1123.40 (16)C53—C54—C541110.23 (15)
N3—C2—S2120.69 (14)C53—C54—C542109.89 (16)
N1—C2—S2115.90 (13)C541—C54—C542109.97 (16)
C21—S2—C2100.40 (9)C53—C54—C55107.32 (15)
S2—C21—H21A109.5C541—C54—C55110.01 (16)
S2—C21—H21B109.5C542—C54—C55109.37 (15)
H21A—C21—H21B109.5C54—C541—H54A109.5
S2—C21—H21C109.5C54—C541—H54B109.5
H21A—C21—H21C109.5H54A—C541—H54B109.5
H21B—C21—H21C109.5C54—C541—H54C109.5
C2—N3—C4118.04 (15)H54A—C541—H54C109.5
N4—C4—C5121.40 (16)H54B—C541—H54C109.5
N4—C4—N3115.66 (16)C54—C542—H54G109.5
C5—C4—N3122.95 (16)C54—C542—H54H109.5
C4—N4—H4A120.0H54G—C542—H54H109.5
C4—N4—H4B120.0C54—C542—H54I109.5
H4A—N4—H4B120.0H54G—C542—H54I109.5
C4—C5—C6117.60 (16)H54H—C542—H54I109.5
C4—C5—C57122.47 (16)C56—C55—C54113.82 (15)
C6—C5—C57119.76 (16)C56—C55—H55A108.8
C51—C57—C5113.09 (15)C54—C55—H55A108.8
C51—C57—H57A109.0C56—C55—H55B108.8
C5—C57—H57A109.0C54—C55—H55B108.8
C51—C57—H57B109.0H55A—C55—H55B107.7
C5—C57—H57B109.0O56—C56—C51120.84 (17)
H57A—C57—H57B107.8O56—C56—C55120.90 (16)
C52—C51—C56118.16 (16)C51—C56—C55118.24 (16)
C52—C51—C57122.62 (16)O6—C6—C5123.32 (17)
C56—C51—C57119.21 (16)O6—C6—N1118.86 (16)
O52—C52—C51123.45 (16)C5—C6—N1117.80 (16)
C6—N1—C2—N31.5 (3)C51—C52—C53—C5418.6 (3)
C11—N1—C2—N3178.55 (17)C52—C53—C54—C5545.3 (2)
C6—N1—C2—S2176.98 (13)C52—C53—C54—C54174.5 (2)
C11—N1—C2—S20.1 (2)C52—C53—C54—C542164.09 (15)
N3—C2—S2—C215.73 (17)C5—C57—C51—C5272.9 (2)
N1—C2—S2—C21175.76 (15)C52—C51—C56—O56175.95 (17)
N1—C2—N3—C40.9 (3)C57—C51—C56—O563.9 (3)
S2—C2—N3—C4179.25 (13)C52—C51—C56—C555.7 (2)
C2—N3—C4—N4179.89 (16)C57—C51—C56—C55174.49 (15)
C2—N3—C4—C50.4 (3)C54—C55—C56—O56145.49 (17)
N4—C4—C5—C6177.06 (17)C54—C55—C56—C5136.1 (2)
N3—C4—C5—C62.4 (3)C53—C54—C55—C5654.6 (2)
N4—C4—C5—C571.8 (3)C56—C55—C54—C54165.4 (2)
N3—C4—C5—C57177.65 (16)C56—C56—C54—C542173.75 (16)
C4—C5—C57—C5178.6 (2)C4—C5—C6—O6173.71 (18)
C6—C5—C57—C5196.5 (2)C57—C5—C6—O61.6 (3)
C5—C57—C51—C56106.97 (18)C4—C5—C6—N14.6 (3)
C56—C51—C52—O52176.21 (15)C57—C5—C6—N1179.92 (15)
C57—C51—C52—O523.9 (3)C2—N1—C6—O6174.12 (17)
C56—C51—C52—C533.4 (3)C11—N1—C6—O63.0 (3)
C57—C51—C52—C53176.43 (16)C2—N1—C6—C54.2 (2)
O52—C52—C53—C54161.73 (15)C11—N1—C6—C5178.66 (16)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O52—H52···O60.841.872.681 (2)161
N4—H4A···O560.882.132.952 (2)155
N4—H4B···O6i0.882.142.831 (3)134
Symmetry code: (i) x, y+1, z.

Experimental details

Crystal data
Chemical formulaC15H21N3O3S
Mr323.41
Crystal system, space groupMonoclinic, P21/n
Temperature (K)120
a, b, c (Å)7.5524 (2), 7.1370 (3), 28.6208 (11)
β (°) 93.128 (2)
V3)1540.40 (10)
Z4
Radiation typeMo Kα
µ (mm1)0.23
Crystal size (mm)0.50 × 0.30 × 0.20
Data collection
DiffractometerNonius KappaCCD
diffractometer
Absorption correctionMulti-scan
(SORTAV; Blessing 1995, 1997)
Tmin, Tmax0.868, 0.956
No. of measured, independent and
observed [I > 2σ(I)] reflections
18675, 3586, 2600
Rint0.071
(sin θ/λ)max1)0.664
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.042, 0.109, 1.01
No. of reflections3586
No. of parameters204
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)0.28, 0.29

Computer programs: KappaCCD Server Software (Nonius, 1997), DENZO–SMN (Otwinowski & Minor, 1997), DENZO–SMN, OSCAIL (McArdle, 2003) and SHELXS97 (Sheldrick, 1997), SHELXL97 (Sheldrick, 1997), PLATON (Spek, 2003), SHELXL97 and PRPKAPPA (Ferguson, 1999).

Selected geometric parameters (Å, º) top
N1—C21.334 (2)N1—C111.447 (2)
C2—N31.282 (2)C4—N41.319 (2)
N3—C41.375 (2)C6—O61.234 (2)
C4—C51.359 (3)C51—C521.343 (3)
C5—C61.378 (3)C52—O521.317 (2)
C6—N11.404 (2)C51—C561.423 (3)
C2—S21.7536 (18)C56—O561.227 (2)
S2—C211.750 (2)
C4—C5—C57—C5178.6 (2)C5—C57—C51—C5272.9 (2)
C56—C51—C52—C533.4 (3)C52—C51—C56—C555.7 (2)
C51—C52—C53—C5418.6 (3)C54—C55—C56—C5136.1 (2)
C52—C53—C54—C5545.3 (2)C53—C54—C55—C5654.6 (2)
C52—C53—C54—C54174.5 (2)C56—C55—C54—C54165.4 (2)
C52—C53—C54—C542164.09 (15)C56—C56—C54—C542173.75 (16)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O52—H52···O60.841.872.681 (2)161
N4—H4A···O560.882.132.952 (2)155
N4—H4B···O6i0.882.142.831 (3)134
Symmetry code: (i) x, y+1, z.
 

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