Supporting information
Crystallographic Information File (CIF) https://doi.org/10.1107/S0108270104001118/sk1697sup1.cif | |
Structure factor file (CIF format) https://doi.org/10.1107/S0108270104001118/sk1697Isup2.hkl |
CCDC reference: 235341
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%.
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.
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).
C15H21N3O3S | F(000) = 664 |
Mr = 323.41 | Dx = 1.394 Mg m−3 |
Monoclinic, P21/n | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: -P 2yn | Cell parameters from 3586 reflections |
a = 7.5524 (2) Å | θ = 3.4–28.2° |
b = 7.1370 (3) Å | µ = 0.23 mm−1 |
c = 28.6208 (11) Å | T = 120 K |
β = 93.128 (2)° | Block, colourless |
V = 1540.40 (10) Å3 | 0.50 × 0.30 × 0.20 mm |
Z = 4 |
Nonius KappaCCD diffractometer | 3586 independent reflections |
Radiation source: rotating anode | 2600 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.071 |
ϕ scans, and ω scans with κ offsets | θmax = 28.2°, θmin = 3.4° |
Absorption correction: multi-scan (SORTAV; Blessing 1995, 1997) | h = −9→9 |
Tmin = 0.868, Tmax = 0.956 | k = −8→9 |
18675 measured reflections | l = −37→37 |
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)] = 0.042 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.109 | H-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 parameters | Δρmax = 0.28 e Å−3 |
0 restraints | Δρmin = −0.29 e Å−3 |
C15H21N3O3S | V = 1540.40 (10) Å3 |
Mr = 323.41 | Z = 4 |
Monoclinic, P21/n | Mo Kα radiation |
a = 7.5524 (2) Å | µ = 0.23 mm−1 |
b = 7.1370 (3) Å | T = 120 K |
c = 28.6208 (11) Å | 0.50 × 0.30 × 0.20 mm |
β = 93.128 (2)° |
Nonius KappaCCD diffractometer | 3586 independent reflections |
Absorption correction: multi-scan (SORTAV; Blessing 1995, 1997) | 2600 reflections with I > 2σ(I) |
Tmin = 0.868, Tmax = 0.956 | Rint = 0.071 |
18675 measured reflections |
R[F2 > 2σ(F2)] = 0.042 | 0 restraints |
wR(F2) = 0.109 | H-atom parameters constrained |
S = 1.01 | Δρmax = 0.28 e Å−3 |
3586 reflections | Δρmin = −0.29 e Å−3 |
204 parameters |
x | y | z | Uiso*/Ueq | ||
N1 | 0.7539 (2) | 0.3798 (2) | 0.49141 (5) | 0.0198 (3) | |
C2 | 0.7498 (2) | 0.5505 (3) | 0.51029 (6) | 0.0194 (4) | |
N3 | 0.6955 (2) | 0.6963 (2) | 0.48764 (5) | 0.0213 (3) | |
C4 | 0.6362 (2) | 0.6744 (2) | 0.44168 (6) | 0.0200 (4) | |
N4 | 0.5820 (2) | 0.8288 (2) | 0.41993 (5) | 0.0255 (4) | |
C5 | 0.6339 (2) | 0.5062 (2) | 0.41944 (6) | 0.0194 (4) | |
C6 | 0.7005 (2) | 0.3536 (3) | 0.44411 (6) | 0.0208 (4) | |
O6 | 0.71906 (19) | 0.19762 (17) | 0.42643 (4) | 0.0262 (3) | |
C11 | 0.8209 (3) | 0.2222 (3) | 0.51881 (7) | 0.0260 (4) | |
S2 | 0.82976 (6) | 0.56773 (7) | 0.568820 (15) | 0.02358 (14) | |
C21 | 0.7849 (3) | 0.8037 (3) | 0.57990 (7) | 0.0307 (5) | |
C57 | 0.5750 (2) | 0.4850 (3) | 0.36838 (6) | 0.0206 (4) | |
C51 | 0.7154 (2) | 0.5431 (3) | 0.33565 (6) | 0.0191 (4) | |
C52 | 0.8609 (2) | 0.4398 (2) | 0.32941 (6) | 0.0198 (4) | |
O52 | 0.88973 (18) | 0.27490 (17) | 0.34900 (4) | 0.0238 (3) | |
C53 | 1.0093 (2) | 0.4934 (3) | 0.29979 (6) | 0.0217 (4) | |
C54 | 1.0156 (2) | 0.6982 (3) | 0.28889 (6) | 0.0226 (4) | |
C55 | 0.8268 (2) | 0.7601 (3) | 0.27475 (6) | 0.0229 (4) | |
C56 | 0.6944 (2) | 0.7138 (3) | 0.31032 (6) | 0.0211 (4) | |
O56 | 0.5690 (2) | 0.8186 (2) | 0.31668 (6) | 0.0277 (4) | |
C541 | 1.0852 (3) | 0.8074 (3) | 0.33172 (7) | 0.0297 (4) | |
C542 | 1.1342 (3) | 0.7320 (3) | 0.24834 (8) | 0.0325 (5) | |
H11A | 0.7994 | 0.1061 | 0.5011 | 0.039* | |
H11B | 0.7602 | 0.2160 | 0.5482 | 0.039* | |
H11C | 0.9486 | 0.2376 | 0.5257 | 0.039* | |
H21A | 0.8014 | 0.8281 | 0.6136 | 0.046* | |
H21B | 0.6623 | 0.8323 | 0.5693 | 0.046* | |
H21C | 0.8660 | 0.8829 | 0.5630 | 0.046* | |
H4A | 0.5433 | 0.8241 | 0.3904 | 0.031* | |
H4B | 0.5845 | 0.9364 | 0.4350 | 0.031* | |
H57A | 0.5428 | 0.3525 | 0.3622 | 0.025* | |
H57B | 0.4675 | 0.5620 | 0.3617 | 0.025* | |
H52 | 0.8159 | 0.2569 | 0.3695 | 0.036* | |
H53A | 0.9975 | 0.4225 | 0.2701 | 0.026* | |
H53B | 1.1229 | 0.4564 | 0.3161 | 0.026* | |
H54A | 1.0781 | 0.9420 | 0.3251 | 0.044* | |
H54B | 1.2089 | 0.7725 | 0.3394 | 0.044* | |
H54C | 1.0134 | 0.7780 | 0.3583 | 0.044* | |
H54G | 1.1285 | 0.8644 | 0.2393 | 0.049* | |
H54H | 1.0936 | 0.6543 | 0.2216 | 0.049* | |
H54I | 1.2568 | 0.6989 | 0.2580 | 0.049* | |
H55A | 0.8263 | 0.8972 | 0.2695 | 0.027* | |
H55B | 0.7894 | 0.6992 | 0.2447 | 0.027* |
U11 | U22 | U33 | U12 | U13 | U23 | |
N1 | 0.0252 (8) | 0.0148 (7) | 0.0195 (7) | 0.0005 (6) | 0.0023 (6) | 0.0021 (6) |
C2 | 0.0188 (9) | 0.0199 (9) | 0.0198 (8) | −0.0010 (7) | 0.0037 (7) | 0.0001 (7) |
N3 | 0.0263 (8) | 0.0177 (8) | 0.0197 (7) | 0.0002 (6) | 0.0005 (6) | 0.0009 (6) |
C4 | 0.0209 (9) | 0.0184 (9) | 0.0207 (9) | 0.0000 (7) | 0.0026 (7) | 0.0020 (7) |
N4 | 0.0377 (10) | 0.0171 (8) | 0.0211 (8) | 0.0043 (7) | −0.0038 (7) | −0.0001 (6) |
C5 | 0.0222 (9) | 0.0174 (9) | 0.0188 (8) | −0.0026 (7) | 0.0025 (7) | 0.0003 (7) |
C6 | 0.0243 (10) | 0.0185 (10) | 0.0200 (9) | −0.0034 (7) | 0.0057 (7) | 0.0010 (7) |
O6 | 0.0401 (8) | 0.0141 (7) | 0.0243 (7) | −0.0012 (6) | 0.0027 (6) | 0.0004 (5) |
C11 | 0.0349 (11) | 0.0189 (10) | 0.0241 (9) | 0.0032 (8) | 0.0019 (8) | 0.0045 (7) |
S2 | 0.0294 (3) | 0.0223 (3) | 0.0187 (2) | 0.0011 (2) | −0.00129 (17) | 0.00093 (18) |
C21 | 0.0402 (12) | 0.0274 (11) | 0.0236 (10) | 0.0053 (9) | −0.0058 (8) | −0.0036 (8) |
C57 | 0.0234 (9) | 0.0186 (9) | 0.0198 (9) | −0.0014 (7) | 0.0009 (7) | 0.0002 (7) |
C51 | 0.0209 (9) | 0.0201 (9) | 0.0160 (8) | −0.0010 (7) | −0.0015 (7) | −0.0001 (7) |
C52 | 0.0276 (10) | 0.0156 (9) | 0.0157 (8) | −0.0016 (7) | −0.0023 (7) | −0.0016 (7) |
O52 | 0.0325 (8) | 0.0161 (7) | 0.0231 (7) | 0.0029 (6) | 0.0045 (5) | 0.0023 (5) |
C53 | 0.0254 (10) | 0.0204 (9) | 0.0194 (9) | 0.0014 (8) | 0.0014 (7) | −0.0003 (7) |
C54 | 0.0236 (10) | 0.0205 (10) | 0.0238 (9) | −0.0012 (8) | 0.0014 (7) | 0.0011 (7) |
C55 | 0.0272 (10) | 0.0198 (9) | 0.0215 (9) | −0.0010 (8) | 0.0000 (7) | 0.0036 (7) |
C56 | 0.0233 (10) | 0.0218 (10) | 0.0178 (8) | 0.0002 (8) | −0.0032 (7) | −0.0007 (7) |
O56 | 0.0291 (7) | 0.0261 (7) | 0.0273 (7) | 0.0080 (6) | 0.0029 (6) | 0.0057 (6) |
C541 | 0.0291 (11) | 0.0234 (10) | 0.0359 (11) | −0.0024 (8) | −0.0041 (8) | −0.0036 (9) |
C542 | 0.0311 (11) | 0.0297 (11) | 0.0376 (11) | −0.0017 (9) | 0.0095 (9) | 0.0061 (9) |
N1—C2 | 1.334 (2) | N4—H4B | 0.88 |
C2—N3 | 1.282 (2) | C5—C57 | 1.512 (2) |
N3—C4 | 1.375 (2) | C57—C51 | 1.511 (2) |
C4—C5 | 1.359 (3) | C57—H57A | 0.99 |
C5—C6 | 1.378 (3) | C57—H57B | 0.99 |
C6—N1 | 1.404 (2) | C52—C53 | 1.491 (3) |
C2—S2 | 1.7536 (18) | O52—H52 | 0.84 |
S2—C21 | 1.750 (2) | C53—C54 | 1.496 (3) |
N1—C11 | 1.447 (2) | C53—H53A | 0.99 |
C4—N4 | 1.319 (2) | C53—H53B | 0.99 |
C6—O6 | 1.234 (2) | C54—C541 | 1.522 (3) |
C51—C52 | 1.343 (3) | C54—C542 | 1.523 (3) |
C52—O52 | 1.317 (2) | C54—C55 | 1.526 (3) |
C51—C56 | 1.423 (3) | C541—H54A | 0.98 |
C56—O56 | 1.227 (2) | C541—H54B | 0.98 |
C11—H11A | 0.98 | C541—H54C | 0.98 |
C11—H11B | 0.98 | C542—H54G | 0.98 |
C11—H11C | 0.98 | C542—H54H | 0.98 |
C21—H21A | 0.98 | C542—H54I | 0.98 |
C21—H21B | 0.98 | C55—C56 | 1.503 (3) |
C21—H21C | 0.98 | C55—H55A | 0.99 |
N4—H4A | 0.88 | C55—H55B | 0.99 |
C2—N1—C6 | 120.05 (15) | O52—C52—C53 | 111.08 (15) |
C2—N1—C11 | 120.37 (15) | C51—C52—C53 | 125.47 (16) |
C6—N1—C11 | 119.52 (15) | C52—O52—H52 | 109.5 |
N1—C11—H11A | 109.5 | C52—C53—C54 | 113.76 (15) |
N1—C11—H11B | 109.5 | C52—C53—H53A | 108.8 |
H11A—C11—H11B | 109.5 | C54—C53—H53A | 108.8 |
N1—C11—H11C | 109.5 | C52—C53—H53B | 108.8 |
H11A—C11—H11C | 109.5 | C54—C53—H53B | 108.8 |
H11B—C11—H11C | 109.5 | H53A—C53—H53B | 107.7 |
N3—C2—N1 | 123.40 (16) | C53—C54—C541 | 110.23 (15) |
N3—C2—S2 | 120.69 (14) | C53—C54—C542 | 109.89 (16) |
N1—C2—S2 | 115.90 (13) | C541—C54—C542 | 109.97 (16) |
C21—S2—C2 | 100.40 (9) | C53—C54—C55 | 107.32 (15) |
S2—C21—H21A | 109.5 | C541—C54—C55 | 110.01 (16) |
S2—C21—H21B | 109.5 | C542—C54—C55 | 109.37 (15) |
H21A—C21—H21B | 109.5 | C54—C541—H54A | 109.5 |
S2—C21—H21C | 109.5 | C54—C541—H54B | 109.5 |
H21A—C21—H21C | 109.5 | H54A—C541—H54B | 109.5 |
H21B—C21—H21C | 109.5 | C54—C541—H54C | 109.5 |
C2—N3—C4 | 118.04 (15) | H54A—C541—H54C | 109.5 |
N4—C4—C5 | 121.40 (16) | H54B—C541—H54C | 109.5 |
N4—C4—N3 | 115.66 (16) | C54—C542—H54G | 109.5 |
C5—C4—N3 | 122.95 (16) | C54—C542—H54H | 109.5 |
C4—N4—H4A | 120.0 | H54G—C542—H54H | 109.5 |
C4—N4—H4B | 120.0 | C54—C542—H54I | 109.5 |
H4A—N4—H4B | 120.0 | H54G—C542—H54I | 109.5 |
C4—C5—C6 | 117.60 (16) | H54H—C542—H54I | 109.5 |
C4—C5—C57 | 122.47 (16) | C56—C55—C54 | 113.82 (15) |
C6—C5—C57 | 119.76 (16) | C56—C55—H55A | 108.8 |
C51—C57—C5 | 113.09 (15) | C54—C55—H55A | 108.8 |
C51—C57—H57A | 109.0 | C56—C55—H55B | 108.8 |
C5—C57—H57A | 109.0 | C54—C55—H55B | 108.8 |
C51—C57—H57B | 109.0 | H55A—C55—H55B | 107.7 |
C5—C57—H57B | 109.0 | O56—C56—C51 | 120.84 (17) |
H57A—C57—H57B | 107.8 | O56—C56—C55 | 120.90 (16) |
C52—C51—C56 | 118.16 (16) | C51—C56—C55 | 118.24 (16) |
C52—C51—C57 | 122.62 (16) | O6—C6—C5 | 123.32 (17) |
C56—C51—C57 | 119.21 (16) | O6—C6—N1 | 118.86 (16) |
O52—C52—C51 | 123.45 (16) | C5—C6—N1 | 117.80 (16) |
C6—N1—C2—N3 | 1.5 (3) | C51—C52—C53—C54 | 18.6 (3) |
C11—N1—C2—N3 | 178.55 (17) | C52—C53—C54—C55 | −45.3 (2) |
C6—N1—C2—S2 | −176.98 (13) | C52—C53—C54—C541 | 74.5 (2) |
C11—N1—C2—S2 | 0.1 (2) | C52—C53—C54—C542 | −164.09 (15) |
N3—C2—S2—C21 | 5.73 (17) | C5—C57—C51—C52 | 72.9 (2) |
N1—C2—S2—C21 | −175.76 (15) | C52—C51—C56—O56 | −175.95 (17) |
N1—C2—N3—C4 | 0.9 (3) | C57—C51—C56—O56 | 3.9 (3) |
S2—C2—N3—C4 | 179.25 (13) | C52—C51—C56—C55 | 5.7 (2) |
C2—N3—C4—N4 | −179.89 (16) | C57—C51—C56—C55 | −174.49 (15) |
C2—N3—C4—C5 | −0.4 (3) | C54—C55—C56—O56 | 145.49 (17) |
N4—C4—C5—C6 | 177.06 (17) | C54—C55—C56—C51 | −36.1 (2) |
N3—C4—C5—C6 | −2.4 (3) | C53—C54—C55—C56 | 54.6 (2) |
N4—C4—C5—C57 | 1.8 (3) | C56—C55—C54—C541 | −65.4 (2) |
N3—C4—C5—C57 | −177.65 (16) | C56—C56—C54—C542 | 173.75 (16) |
C4—C5—C57—C51 | 78.6 (2) | C4—C5—C6—O6 | −173.71 (18) |
C6—C5—C57—C51 | −96.5 (2) | C57—C5—C6—O6 | 1.6 (3) |
C5—C57—C51—C56 | −106.97 (18) | C4—C5—C6—N1 | 4.6 (3) |
C56—C51—C52—O52 | −176.21 (15) | C57—C5—C6—N1 | 179.92 (15) |
C57—C51—C52—O52 | 3.9 (3) | C2—N1—C6—O6 | 174.12 (17) |
C56—C51—C52—C53 | 3.4 (3) | C11—N1—C6—O6 | −3.0 (3) |
C57—C51—C52—C53 | −176.43 (16) | C2—N1—C6—C5 | −4.2 (2) |
O52—C52—C53—C54 | −161.73 (15) | C11—N1—C6—C5 | 178.66 (16) |
D—H···A | D—H | H···A | D···A | D—H···A |
O52—H52···O6 | 0.84 | 1.87 | 2.681 (2) | 161 |
N4—H4A···O56 | 0.88 | 2.13 | 2.952 (2) | 155 |
N4—H4B···O6i | 0.88 | 2.14 | 2.831 (3) | 134 |
Symmetry code: (i) x, y+1, z. |
Experimental details
Crystal data | |
Chemical formula | C15H21N3O3S |
Mr | 323.41 |
Crystal system, space group | Monoclinic, P21/n |
Temperature (K) | 120 |
a, b, c (Å) | 7.5524 (2), 7.1370 (3), 28.6208 (11) |
β (°) | 93.128 (2) |
V (Å3) | 1540.40 (10) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 0.23 |
Crystal size (mm) | 0.50 × 0.30 × 0.20 |
Data collection | |
Diffractometer | Nonius KappaCCD diffractometer |
Absorption correction | Multi-scan (SORTAV; Blessing 1995, 1997) |
Tmin, Tmax | 0.868, 0.956 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 18675, 3586, 2600 |
Rint | 0.071 |
(sin θ/λ)max (Å−1) | 0.664 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.042, 0.109, 1.01 |
No. of reflections | 3586 |
No. of parameters | 204 |
H-atom treatment | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 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).
N1—C2 | 1.334 (2) | N1—C11 | 1.447 (2) |
C2—N3 | 1.282 (2) | C4—N4 | 1.319 (2) |
N3—C4 | 1.375 (2) | C6—O6 | 1.234 (2) |
C4—C5 | 1.359 (3) | C51—C52 | 1.343 (3) |
C5—C6 | 1.378 (3) | C52—O52 | 1.317 (2) |
C6—N1 | 1.404 (2) | C51—C56 | 1.423 (3) |
C2—S2 | 1.7536 (18) | C56—O56 | 1.227 (2) |
S2—C21 | 1.750 (2) | ||
C4—C5—C57—C51 | 78.6 (2) | C5—C57—C51—C52 | 72.9 (2) |
C56—C51—C52—C53 | 3.4 (3) | C52—C51—C56—C55 | 5.7 (2) |
C51—C52—C53—C54 | 18.6 (3) | C54—C55—C56—C51 | −36.1 (2) |
C52—C53—C54—C55 | −45.3 (2) | C53—C54—C55—C56 | 54.6 (2) |
C52—C53—C54—C541 | 74.5 (2) | C56—C55—C54—C541 | −65.4 (2) |
C52—C53—C54—C542 | −164.09 (15) | C56—C56—C54—C542 | 173.75 (16) |
D—H···A | D—H | H···A | D···A | D—H···A |
O52—H52···O6 | 0.84 | 1.87 | 2.681 (2) | 161 |
N4—H4A···O56 | 0.88 | 2.13 | 2.952 (2) | 155 |
N4—H4B···O6i | 0.88 | 2.14 | 2.831 (3) | 134 |
Symmetry code: (i) x, y+1, z. |
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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.