Supporting information
Crystallographic Information File (CIF) https://doi.org/10.1107/S0108270109013493/sk3315sup1.cif | |
Structure factor file (CIF format) https://doi.org/10.1107/S0108270109013493/sk3315Isup2.hkl |
CCDC reference: 742179
To a suspension of 6-amino-3-methyl-2-(methylsulfanyl)pyrimidin-4(3H)-one (10 mmol) in dimethylformamide (30 ml) cooled in an ice–water bath, phosphoryl chloride (12 mmol) was added dropwise: the mixture was then stirred at room temperature for 1 h. The reaction mixture was poured onto crushed ice (400 ml), after which the whole was permitted to warm to ambient temperature; the mixture was then heated to boiling and sodium hydroxide pellets were added until the solution was basic. The resulting mixture was allowed to cool to ambient temperature, and the white solid thus formed was collected by filtration, washed with ethanol, dried and recrystallized from ethanol [yield 50%; decomposed without melting at 573 K; literature m.p. > 573 K (Cherdantseva et al., 1983]. Crystals suitable for single-crystal X-ray diffraction were grown from by slow evaporation of a solution in dimethylsulfoxide.
All H atoms were located from difference maps and then treated as riding atoms with C—H distances of 0.95 or 0.98 Å and N—H distances of 0.88 Å, and with Uiso(H) = kUeq(carrier) (k = 1.2 or 1.5). Conventional refinement then converged to R of 0.165 for 1513 reflections (1284 labelled observed) with Rint = 0.057, but analysis with PLATON/TwinRotMat (Spek, 2009) of this solution indicated non-merohedral twinning about a twofold rotation axis (201) (which makes an angle of 0.26° with [100]). The TwinRotMat routine was used to prepare a modified hkl file for use with the HKLF5 option in SHELXL97 (Sheldrick, 2008). The resulting twin fractions were 0.2076 (10) and 0.7924 (10).
Data collection: COLLECT (Hooft, 1999); cell refinement: DIRAX/LSQ (Duisenberg et al., 2000); data reduction: EVALCCD (Duisenberg et al., 2003); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: PLATON (Spek, 2009); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008) and PLATON (Spek, 2009).
C6H7N3O3 | F(000) = 352 |
Mr = 169.14 | Dx = 1.707 Mg m−3 |
Monoclinic, P21/c | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: -P 2ybc | Cell parameters from 1513 reflections |
a = 6.6749 (4) Å | θ = 3.4–27.5° |
b = 5.0712 (5) Å | µ = 0.14 mm−1 |
c = 19.7422 (4) Å | T = 120 K |
β = 99.996 (2)° | Block, colourless |
V = 658.12 (8) Å3 | 0.29 × 0.23 × 0.12 mm |
Z = 4 |
Bruker–Nonius KappaCCD diffractometer | 9103 independent reflections |
Radiation source: Bruker-Nonius FR591 rotating anode | 7474 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.000 |
Detector resolution: 9.091 pixels mm-1 | θmax = 27.5°, θmin = 3.4° |
ϕ & ω scans | h = −8→8 |
Absorption correction: multi-scan (SADABS; Sheldrick, 2003) | k = −6→6 |
Tmin = 0.972, Tmax = 0.983 | l = −25→25 |
9103 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)] = 0.058 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.152 | H-atom parameters constrained |
S = 1.08 | w = 1/[σ2(Fo2) + (0.0619P)2 + 0.3795P] where P = (Fo2 + 2Fc2)/3 |
9103 reflections | (Δ/σ)max = 0.001 |
111 parameters | Δρmax = 0.30 e Å−3 |
0 restraints | Δρmin = −0.32 e Å−3 |
C6H7N3O3 | V = 658.12 (8) Å3 |
Mr = 169.14 | Z = 4 |
Monoclinic, P21/c | Mo Kα radiation |
a = 6.6749 (4) Å | µ = 0.14 mm−1 |
b = 5.0712 (5) Å | T = 120 K |
c = 19.7422 (4) Å | 0.29 × 0.23 × 0.12 mm |
β = 99.996 (2)° |
Bruker–Nonius KappaCCD diffractometer | 9103 independent reflections |
Absorption correction: multi-scan (SADABS; Sheldrick, 2003) | 7474 reflections with I > 2σ(I) |
Tmin = 0.972, Tmax = 0.983 | Rint = 0.000 |
9103 measured reflections |
R[F2 > 2σ(F2)] = 0.058 | 0 restraints |
wR(F2) = 0.152 | H-atom parameters constrained |
S = 1.08 | Δρmax = 0.30 e Å−3 |
9103 reflections | Δρmin = −0.32 e Å−3 |
111 parameters |
x | y | z | Uiso*/Ueq | ||
N1 | 0.57570 (16) | 1.1821 (2) | 0.63728 (5) | 0.0193 (3) | |
H1 | 0.7075 | 1.2076 | 0.6407 | 0.023* | |
C2 | 0.47247 (19) | 1.3483 (3) | 0.67337 (7) | 0.0185 (3) | |
N3 | 0.26579 (15) | 1.3079 (2) | 0.66410 (5) | 0.0178 (2) | |
C4 | 0.16639 (19) | 1.1091 (2) | 0.62456 (7) | 0.0182 (3) | |
C5 | 0.28259 (19) | 0.9429 (3) | 0.58818 (6) | 0.0175 (3) | |
C6 | 0.49261 (18) | 0.9817 (2) | 0.59668 (6) | 0.0177 (3) | |
O2 | 0.56033 (14) | 1.51777 (18) | 0.70932 (5) | 0.0230 (2) | |
C31 | 0.1492 (2) | 1.4724 (3) | 0.70406 (7) | 0.0225 (3) | |
H31A | 0.1210 | 1.3727 | 0.7439 | 0.034* | |
H31B | 0.0206 | 1.5240 | 0.6752 | 0.034* | |
H31C | 0.2278 | 1.6306 | 0.7199 | 0.034* | |
O4 | −0.01878 (13) | 1.08385 (19) | 0.62243 (5) | 0.0231 (2) | |
C51 | 0.1867 (2) | 0.7404 (3) | 0.54487 (7) | 0.0212 (3) | |
H51 | 0.0430 | 0.7265 | 0.5402 | 0.025* | |
O5 | 0.27217 (14) | 0.58170 (18) | 0.51294 (4) | 0.0241 (2) | |
N6 | 0.61547 (16) | 0.8349 (2) | 0.56832 (6) | 0.0214 (3) | |
H61 | 0.7469 | 0.8681 | 0.5759 | 0.026* | |
H62 | 0.5670 | 0.7026 | 0.5416 | 0.026* |
U11 | U22 | U33 | U12 | U13 | U23 | |
N1 | 0.0125 (5) | 0.0261 (6) | 0.0198 (6) | −0.0026 (4) | 0.0047 (4) | −0.0025 (4) |
C2 | 0.0170 (6) | 0.0221 (7) | 0.0170 (7) | 0.0003 (5) | 0.0045 (5) | 0.0019 (5) |
N3 | 0.0162 (5) | 0.0226 (6) | 0.0158 (5) | 0.0000 (4) | 0.0056 (4) | −0.0015 (4) |
C4 | 0.0165 (7) | 0.0216 (7) | 0.0170 (6) | 0.0001 (5) | 0.0042 (5) | 0.0027 (5) |
C5 | 0.0141 (6) | 0.0213 (7) | 0.0172 (6) | −0.0002 (5) | 0.0031 (5) | 0.0006 (5) |
C6 | 0.0172 (7) | 0.0212 (6) | 0.0155 (6) | 0.0007 (5) | 0.0050 (5) | 0.0041 (5) |
O2 | 0.0200 (5) | 0.0254 (5) | 0.0238 (5) | −0.0020 (4) | 0.0041 (4) | −0.0045 (4) |
C31 | 0.0194 (7) | 0.0248 (7) | 0.0245 (7) | 0.0011 (5) | 0.0072 (6) | −0.0056 (6) |
O4 | 0.0136 (5) | 0.0297 (5) | 0.0271 (5) | −0.0006 (4) | 0.0070 (4) | −0.0040 (4) |
C51 | 0.0147 (7) | 0.0276 (8) | 0.0213 (7) | −0.0012 (6) | 0.0034 (5) | 0.0005 (6) |
O5 | 0.0224 (5) | 0.0261 (5) | 0.0249 (5) | 0.0001 (4) | 0.0073 (4) | −0.0066 (4) |
N6 | 0.0143 (6) | 0.0273 (6) | 0.0232 (6) | −0.0002 (4) | 0.0052 (5) | −0.0036 (5) |
N1—C2 | 1.3650 (16) | C51—O5 | 1.2229 (15) |
C2—N3 | 1.3753 (16) | C6—N6 | 1.3037 (16) |
N3—C4 | 1.3733 (17) | N1—H1 | 0.8800 |
C4—C5 | 1.4215 (18) | C31—H31A | 0.9800 |
C5—C6 | 1.3966 (18) | C31—H31B | 0.9800 |
C6—N1 | 1.3522 (16) | C31—H31C | 0.9800 |
C2—O2 | 1.2006 (15) | C51—H51 | 0.9500 |
N3—C31 | 1.4619 (16) | N6—H61 | 0.8800 |
C4—O4 | 1.2360 (15) | N6—H62 | 0.8800 |
C5—C51 | 1.4163 (18) | ||
C6—N1—C2 | 125.53 (11) | N6—C6—N1 | 117.38 (11) |
C6—N1—H1 | 117.2 | N6—C6—C5 | 124.13 (12) |
C2—N1—H1 | 117.2 | N1—C6—C5 | 118.49 (11) |
O2—C2—N1 | 120.76 (12) | N3—C31—H31A | 109.5 |
O2—C2—N3 | 124.14 (12) | N3—C31—H31B | 109.5 |
N1—C2—N3 | 115.09 (11) | H31A—C31—H31B | 109.5 |
C4—N3—C2 | 124.04 (11) | N3—C31—H31C | 109.5 |
C4—N3—C31 | 118.40 (10) | H31A—C31—H31C | 109.5 |
C2—N3—C31 | 117.31 (11) | H31B—C31—H31C | 109.5 |
O4—C4—N3 | 118.48 (12) | O5—C51—C5 | 125.86 (13) |
O4—C4—C5 | 123.48 (12) | O5—C51—H51 | 117.1 |
N3—C4—C5 | 118.04 (11) | C5—C51—H51 | 117.1 |
C6—C5—C51 | 120.93 (12) | C6—N6—H61 | 120.0 |
C6—C5—C4 | 118.69 (11) | C6—N6—H62 | 120.0 |
C51—C5—C4 | 120.38 (12) | H61—N6—H62 | 120.0 |
C6—N1—C2—O2 | 178.42 (12) | N3—C4—C5—C6 | 2.82 (17) |
C6—N1—C2—N3 | −2.61 (18) | O4—C4—C5—C51 | 2.07 (19) |
O2—C2—N3—C4 | −177.99 (12) | N3—C4—C5—C51 | −177.92 (12) |
N1—C2—N3—C4 | 3.08 (18) | C2—N1—C6—N6 | −177.03 (12) |
O2—C2—N3—C31 | −3.87 (19) | C2—N1—C6—C5 | 2.39 (19) |
N1—C2—N3—C31 | 177.19 (11) | C51—C5—C6—N6 | −2.2 (2) |
C2—N3—C4—O4 | 176.70 (12) | C4—C5—C6—N6 | 177.01 (12) |
C31—N3—C4—O4 | 2.65 (18) | C51—C5—C6—N1 | 178.37 (11) |
C2—N3—C4—C5 | −3.31 (18) | C4—C5—C6—N1 | −2.37 (18) |
C31—N3—C4—C5 | −177.36 (12) | C4—C5—C51—O5 | −177.67 (13) |
O4—C4—C5—C6 | −177.19 (12) | C6—C5—C51—O5 | 1.6 (2) |
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1···O4i | 0.88 | 2.02 | 2.8172 (14) | 150 |
N6—H61···O4i | 0.88 | 2.00 | 2.7910 (14) | 149 |
N6—H62···O5 | 0.88 | 2.05 | 2.6880 (14) | 129 |
N6—H62···O5ii | 0.88 | 2.19 | 2.8314 (14) | 130 |
Symmetry codes: (i) x+1, y, z; (ii) −x+1, −y+1, −z+1. |
Experimental details
Crystal data | |
Chemical formula | C6H7N3O3 |
Mr | 169.14 |
Crystal system, space group | Monoclinic, P21/c |
Temperature (K) | 120 |
a, b, c (Å) | 6.6749 (4), 5.0712 (5), 19.7422 (4) |
β (°) | 99.996 (2) |
V (Å3) | 658.12 (8) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 0.14 |
Crystal size (mm) | 0.29 × 0.23 × 0.12 |
Data collection | |
Diffractometer | Bruker–Nonius KappaCCD diffractometer |
Absorption correction | Multi-scan (SADABS; Sheldrick, 2003) |
Tmin, Tmax | 0.972, 0.983 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 9103, 9103, 7474 |
Rint | 0.000 |
(sin θ/λ)max (Å−1) | 0.649 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.058, 0.152, 1.08 |
No. of reflections | 9103 |
No. of parameters | 111 |
H-atom treatment | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 0.30, −0.32 |
Computer programs: COLLECT (Hooft, 1999), DIRAX/LSQ (Duisenberg et al., 2000), EVALCCD (Duisenberg et al., 2003), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008) and PLATON (Spek, 2009).
N1—C2 | 1.3650 (16) | C2—O2 | 1.2006 (15) |
C2—N3 | 1.3753 (16) | N3—C31 | 1.4619 (16) |
N3—C4 | 1.3733 (17) | C4—O4 | 1.2360 (15) |
C4—C5 | 1.4215 (18) | C5—C51 | 1.4163 (18) |
C5—C6 | 1.3966 (18) | C51—O5 | 1.2229 (15) |
C6—N1 | 1.3522 (16) | C6—N6 | 1.3037 (16) |
C4—C5—C51—O5 | −177.67 (13) | C6—C5—C51—O5 | 1.6 (2) |
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1···O4i | 0.88 | 2.02 | 2.8172 (14) | 150 |
N6—H61···O4i | 0.88 | 2.00 | 2.7910 (14) | 149 |
N6—H62···O5 | 0.88 | 2.05 | 2.6880 (14) | 129 |
N6—H62···O5ii | 0.88 | 2.19 | 2.8314 (14) | 130 |
Symmetry codes: (i) x+1, y, z; (ii) −x+1, −y+1, −z+1. |
The title compound, (I), has been prepared as an intermediate for the preparation of fused pyrimidine derivatives. Its synthesis utilized the Vilsmeier–Haack formylation procedure applied to 6-amino-3-methyl-2-(methylsulfanyl)pyrimidin-4(3H)-one in which the work-up using aqueous sodium hydroxide effected the hydrolysis of the methylsulfanyl group at C2, so providing the title compound in a single process. Compound (I) is closely related to the 1,3-dimethyl analogue (II), which, unlike (I), crystallizes as a monohydrate. The structure of (II) was first determined some years ago, using diffraction data collected at ambient temperature (Low et al., 1992); more recently, the structure of (II) was re-examined using data collected at 120 K (de la Torre et al., 2007), and the improved precision afforded by the low-temperature data enabled a detailed examination of the intramolecular dimensions, which were interpreted in terms of a polarized electronic structure. A combination of three N—H···O hydrogen bonds and two O—H···O hydrogen bonds links the molecular components of the monohydrate of (II) into two linked and interwoven three-dimensional frameworks.
Prompted by the interesting molecular and supramolecular structures found in (II), we have now taken the opportunity to make a detailed comparison with the monomethyl analogue (I) (Fig. 1). Compound (I) crystallizes in solvent-free form in a unit cell whose dimensions bear no resemblance to those of the unit cell of (II). However, a similar pattern of bond distances is found (Table 1). In particular, the C5—C51 and C6—N6 bonds are both short for their types (Allen et al., 1987), while C51—O5 is long for its type; in addition, the C4—O4 bond is significantly longer than C2—O2. These dimensions (Table 1) provide evidence for the importance of polarized forms (Ia) and (Ib) as contributors to the overall electronic structure. Despite the high degree of substitution of the rings in both (I) and (II), these rings are planar, although puckered pyrimidine rings are quite frequently observed in the presence of contiguous substituents (Melguizo et al., 2003; Quesada et al., 2003, 2004; Low et al., 2007; Trilleras et al., 2007; Cobo et al., 2008). In (I), the maximum deviation of any ring atom from the mean plane is that of atom N3, 0.013 (2) Å. In these respects, therefore, (I) and (II) show considerable similarity. They differ, however, in their patterns of hydrogen bonding, dominated firstly by the presence of a water molecule in (II), which acts as a single acceptor and as a double donor of hydrogen bonds, and secondly by the presence in (I) of an additional N—H bond at N1.
Within the molecule of (I), the N—H···O hydrogen bond (Table 2) generates an S(6) (Bernstein et al., 1995) motif; such an intramolecular motif is highly characteristic of both 6-amino-5-formyl pyrimidines and 6-amino-5-nitrosopyrimidines (Low et al., 1997, 1999, 2000; Quesada et al., 2002, 2004; Melguizo et al., 2003; Cobo et al., 2008), and it may well be a controlling factor in determining in (I) the near coplanarity of the formyl group with the uracil ring (Table 1): the formyl atom O5 deviates from the mean plane of the ring by only 0.008 (2) Å. This intramolecular interaction is, in fact, the shorter component of the three-centre N—H···(O)2 system, the longer component of which links pairs of molecules into a centrosymmetric dimer, characterized by an R22(12) motif; this motif is itself partitioned into a central R22(4) ring flanked by two symmetry-related S(6) rings. Between the dimers related by translation along [100], atoms N1 and N6 both act as hydrogen-bond donors to the amidic carbonyl atom O4 in the adjacent dimer, so forming an R21(6) ring. These interactions thus serve to link the centrosymmetric dimers into a ribbon along [100], in which R22(4) rings centred at (n + 1/2, 1/2, 1/2), where n represents an integer, alternate with R44(16) rings centred at (n, 1/2, 1/2) (Fig. 2). Although the centrosymmetric dimer motif containing an R22(4) ring flanked by two S(6) rings can also be identified within the three-dimensional structure of (II), the subsequent linking of these dimers is entirely different in (I) and (II), leading to hydrogen-bonded structures which are, respectively one-dimensional and three-dimensional. It is of interest to note that, in (I), the hydrogen-bond formation involves the acceptor atoms O4 and O5, which carry enhanced negative changes owing to the charge polarization, but it does not involve atom O2, which is not involved in the polarization. The hydrogen bonds may thus all be regarded as charge-assisted hydrogen bonds (Gilli et al., 1993).
With the exception of the H atoms in the methyl group, the ribbon is almost completely planar, providing a very compact structure. There are two hydrogen-bonded ribbons running through each unit cell in (I); although there are no hydrogen bonds between adjacent chains, the chains are weakly linked into sheets by a dipolar carbonyl–carbonyl interaction. The carbonyl atom O2 in the molecule at (x, y, z) makes a short contact with the carbonyl atom C2 in the molecule at (1 - x, 1/2 + y, 3/2 - z), with dimensions O2···C2iii = 2.8978 (17) Å, C2···C2iii = 3.1791 (13) Å and C2—O2···C2iii = 142.14 (9)° [symmetry code: (iii) -x + 1, y + 1/2, -z + 3/2], so conforming rather closely to the perpendicular, type I carbonyl–carbonyl interaction (Allen et al., 1998). The two molecules concerned are components of the hydrogen-bonded chains along (x, 1/2, 1/2) and (x, 1, 1), respectively; hence propagation by the space-group symmetry of the carbonyl–carbonyl interaction links hydrogen-bonded ribbons into a sheet parallel to (011).