Supporting information
Crystallographic Information File (CIF) https://doi.org/10.1107/S0108270103009302/sk1637sup1.cif | |
Structure factor file (CIF format) https://doi.org/10.1107/S0108270103009302/sk1637Isup2.hkl |
CCDC reference: 214412
An aqueous solution of potassium 6-amino-3-methyl-5-nitrosopyrimidine-2,4(1H,3H)-dionate was neutralized using excess potassium aluminium sulfate dodecahydrate. The gelatinous precipitate that formed initially was filtered off, and the resulting solution was set aside to crystallize, providing analytically pure crystals of (I), which were washed with cold water and then with ethanol. Analysis found: C 34.9, H 3.6, N 32.4%; C5H6N4O3 requires: C 35.2, H 3.5, N 32.9%.
Crystals of (I) are monoclinic and the space group P21/c was assigned uniquely from the systematic absences. All H atoms were treated as riding atoms, with C—H distances of 0.98 Å and N—H distances of 0.88 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: 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).
C5H6N4O3 | F(000) = 352 |
Mr = 170.14 | Dx = 1.769 Mg m−3 |
Monoclinic, P21/c | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: -P 2ybc | Cell parameters from 1399 reflections |
a = 4.9634 (3) Å | θ = 3.5–27.4° |
b = 11.1829 (9) Å | µ = 0.15 mm−1 |
c = 11.7960 (8) Å | T = 120 K |
β = 102.665 (4)° | Prism, pink |
V = 638.81 (8) Å3 | 0.15 × 0.10 × 0.06 mm |
Z = 4 |
Nonius KappaCCD diffractometer | 1399 independent reflections |
Radiation source: rotating anode | 1106 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.040 |
ϕ scans, and ω scans with κ offsets | θmax = 27.4°, θmin = 3.5° |
Absorption correction: multi-scan (DENZO–SMN; Otwinowski & Minor, 1997) | h = −5→6 |
Tmin = 0.972, Tmax = 0.991 | k = −14→13 |
4417 measured reflections | l = −15→13 |
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)] = 0.045 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.118 | H-atom parameters constrained |
S = 1.03 | w = 1/[σ2(Fo2) + (0.0702P)2 + 0.0762P] where P = (Fo2 + 2Fc2)/3 |
1399 reflections | (Δ/σ)max < 0.001 |
110 parameters | Δρmax = 0.27 e Å−3 |
0 restraints | Δρmin = −0.37 e Å−3 |
C5H6N4O3 | V = 638.81 (8) Å3 |
Mr = 170.14 | Z = 4 |
Monoclinic, P21/c | Mo Kα radiation |
a = 4.9634 (3) Å | µ = 0.15 mm−1 |
b = 11.1829 (9) Å | T = 120 K |
c = 11.7960 (8) Å | 0.15 × 0.10 × 0.06 mm |
β = 102.665 (4)° |
Nonius KappaCCD diffractometer | 1399 independent reflections |
Absorption correction: multi-scan (DENZO–SMN; Otwinowski & Minor, 1997) | 1106 reflections with I > 2σ(I) |
Tmin = 0.972, Tmax = 0.991 | Rint = 0.040 |
4417 measured reflections |
R[F2 > 2σ(F2)] = 0.045 | 0 restraints |
wR(F2) = 0.118 | H-atom parameters constrained |
S = 1.03 | Δρmax = 0.27 e Å−3 |
1399 reflections | Δρmin = −0.37 e Å−3 |
110 parameters |
x | y | z | Uiso*/Ueq | ||
N1 | 0.6958 (3) | 0.40093 (12) | 0.41374 (12) | 0.0169 (3) | |
C2 | 0.4930 (3) | 0.45663 (15) | 0.33287 (14) | 0.0156 (4) | |
O2 | 0.3284 (2) | 0.52409 (11) | 0.36355 (10) | 0.0208 (3) | |
N3 | 0.4814 (3) | 0.43161 (12) | 0.21777 (11) | 0.0148 (3) | |
C31 | 0.2701 (3) | 0.49157 (15) | 0.12970 (14) | 0.0182 (4) | |
C4 | 0.6580 (3) | 0.35010 (14) | 0.17997 (14) | 0.0151 (4) | |
O4 | 0.6195 (2) | 0.32622 (11) | 0.07656 (10) | 0.0194 (3) | |
C5 | 0.8787 (3) | 0.29996 (14) | 0.26872 (14) | 0.0154 (4) | |
N5 | 1.0602 (3) | 0.23116 (12) | 0.22777 (12) | 0.0169 (3) | |
O5 | 1.2584 (2) | 0.18399 (11) | 0.30075 (11) | 0.0218 (3) | |
C6 | 0.8911 (3) | 0.32605 (14) | 0.38832 (14) | 0.0148 (4) | |
N6 | 1.0775 (3) | 0.28214 (13) | 0.47405 (12) | 0.0189 (3) | |
H1 | 0.6999 | 0.4147 | 0.4876 | 0.020* | |
H31A | 0.1662 | 0.5475 | 0.1678 | 0.027* | |
H31B | 0.1439 | 0.4318 | 0.0864 | 0.027* | |
H31C | 0.3592 | 0.5355 | 0.0760 | 0.027* | |
H6A | 1.0750 | 0.3011 | 0.5462 | 0.023* | |
H6B | 1.2055 | 0.2336 | 0.4596 | 0.023* |
U11 | U22 | U33 | U12 | U13 | U23 | |
N1 | 0.0193 (8) | 0.0202 (7) | 0.0113 (7) | 0.0027 (6) | 0.0032 (6) | −0.0008 (5) |
C2 | 0.0172 (8) | 0.0147 (8) | 0.0152 (8) | −0.0024 (6) | 0.0042 (7) | 0.0005 (6) |
O2 | 0.0229 (7) | 0.0220 (7) | 0.0176 (6) | 0.0059 (5) | 0.0045 (5) | −0.0002 (5) |
N3 | 0.0168 (7) | 0.0145 (7) | 0.0125 (7) | 0.0002 (5) | 0.0019 (6) | 0.0009 (5) |
C31 | 0.0215 (9) | 0.0176 (9) | 0.0146 (8) | 0.0031 (6) | 0.0018 (7) | 0.0018 (6) |
C4 | 0.0158 (8) | 0.0150 (8) | 0.0150 (8) | −0.0041 (6) | 0.0047 (7) | −0.0004 (6) |
O4 | 0.0211 (7) | 0.0237 (7) | 0.0132 (6) | −0.0011 (5) | 0.0032 (5) | −0.0024 (5) |
C5 | 0.0174 (9) | 0.0142 (8) | 0.0148 (8) | −0.0024 (6) | 0.0036 (7) | 0.0008 (6) |
N5 | 0.0173 (7) | 0.0153 (7) | 0.0181 (7) | −0.0008 (5) | 0.0041 (6) | 0.0022 (5) |
O5 | 0.0196 (7) | 0.0231 (7) | 0.0218 (6) | 0.0032 (5) | 0.0029 (5) | 0.0029 (5) |
C6 | 0.0144 (8) | 0.0138 (8) | 0.0163 (8) | −0.0024 (6) | 0.0034 (6) | 0.0016 (6) |
N6 | 0.0198 (8) | 0.0222 (8) | 0.0144 (7) | 0.0024 (6) | 0.0031 (6) | 0.0015 (6) |
N1—C2 | 1.375 (2) | C5—N5 | 1.352 (2) |
C2—N3 | 1.375 (2) | N5—O5 | 1.271 (2) |
N3—C4 | 1.403 (2) | C6—N6 | 1.308 (2) |
C4—C5 | 1.452 (2) | N1—H1 | 0.88 |
C5—C6 | 1.429 (2) | C31—H31A | 0.98 |
C6—N1 | 1.363 (2) | C31—H31B | 0.98 |
C2—O2 | 1.224 (2) | C31—H31C | 0.98 |
N3—C31 | 1.466 (2) | N6—H6A | 0.88 |
C4—O4 | 1.222 (2) | N6—H6B | 0.88 |
C6—N1—C2 | 124.99 (14) | H31B—C31—H31C | 109.5 |
C6—N1—H1 | 117.5 | O4—C4—N3 | 119.16 (15) |
C2—N1—H1 | 117.5 | O4—C4—C5 | 124.29 (15) |
O2—C2—N1 | 120.59 (15) | N3—C4—C5 | 116.55 (14) |
O2—C2—N3 | 122.10 (15) | N5—C5—C6 | 125.56 (15) |
N1—C2—N3 | 117.30 (14) | N5—C5—C4 | 114.75 (14) |
C2—N3—C4 | 123.51 (14) | C6—C5—C4 | 119.69 (15) |
C2—N3—C31 | 118.37 (14) | O5—N5—C5 | 118.13 (13) |
C4—N3—C31 | 118.12 (13) | N6—C6—N1 | 118.51 (15) |
N3—C31—H31A | 109.5 | N6—C6—C5 | 123.84 (15) |
N3—C31—H31B | 109.5 | N1—C6—C5 | 117.65 (15) |
H31A—C31—H31B | 109.5 | C6—N6—H6A | 120.0 |
N3—C31—H31C | 109.5 | C6—N6—H6B | 120.0 |
H31A—C31—H31C | 109.5 | H6A—N6—H6B | 120.0 |
C6—N1—C2—O2 | −178.84 (15) | N3—C4—C5—N5 | −173.81 (13) |
C6—N1—C2—N3 | 2.2 (2) | O4—C4—C5—C6 | −174.67 (15) |
O2—C2—N3—C4 | −176.66 (14) | N3—C4—C5—C6 | 5.7 (2) |
N1—C2—N3—C4 | 2.2 (2) | C6—C5—N5—O5 | 0.7 (2) |
O2—C2—N3—C31 | 2.2 (2) | C4—C5—N5—O5 | −179.76 (13) |
N1—C2—N3—C31 | −178.89 (13) | C2—N1—C6—N6 | 177.85 (14) |
C2—N3—C4—O4 | 174.33 (14) | C2—N1—C6—C5 | −2.3 (2) |
C31—N3—C4—O4 | −4.5 (2) | N5—C5—C6—N6 | −2.5 (3) |
C2—N3—C4—C5 | −6.0 (2) | C4—C5—C6—N6 | 177.97 (15) |
C31—N3—C4—C5 | 175.08 (13) | N5—C5—C6—N1 | 177.64 (14) |
O4—C4—C5—N5 | 5.8 (2) | C4—C5—C6—N1 | −1.8 (2) |
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1···O2i | 0.88 | 1.92 | 2.785 (2) | 168 |
N6—H6A···N5ii | 0.88 | 2.19 | 3.017 (2) | 157 |
N6—H6B···O5 | 0.88 | 2.03 | 2.645 (2) | 126 |
N6—H6B···O4iii | 0.88 | 2.31 | 2.957 (2) | 130 |
Symmetry codes: (i) −x+1, −y+1, −z+1; (ii) x, −y+1/2, z+1/2; (iii) x+1, −y+1/2, z+1/2. |
Experimental details
Crystal data | |
Chemical formula | C5H6N4O3 |
Mr | 170.14 |
Crystal system, space group | Monoclinic, P21/c |
Temperature (K) | 120 |
a, b, c (Å) | 4.9634 (3), 11.1829 (9), 11.7960 (8) |
β (°) | 102.665 (4) |
V (Å3) | 638.81 (8) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 0.15 |
Crystal size (mm) | 0.15 × 0.10 × 0.06 |
Data collection | |
Diffractometer | Nonius KappaCCD diffractometer |
Absorption correction | Multi-scan (DENZO–SMN; Otwinowski & Minor, 1997) |
Tmin, Tmax | 0.972, 0.991 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 4417, 1399, 1106 |
Rint | 0.040 |
(sin θ/λ)max (Å−1) | 0.648 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.045, 0.118, 1.03 |
No. of reflections | 1399 |
No. of parameters | 110 |
H-atom treatment | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 0.27, −0.37 |
Computer programs: KappaCCD Server Software (Nonius, 1997), DENZO–SMN (Otwinowski & Minor, 1997), DENZO–SMN, SHELXS97 (Sheldrick, 1997), SHELXL97 (Sheldrick, 1997), PLATON (Spek, 2003), SHELXL97 and PRPKAPPA (Ferguson, 1999).
N1—C2 | 1.375 (2) | C2—O2 | 1.224 (2) |
C2—N3 | 1.375 (2) | N3—C31 | 1.466 (2) |
N3—C4 | 1.403 (2) | C4—O4 | 1.222 (2) |
C4—C5 | 1.452 (2) | C5—N5 | 1.352 (2) |
C5—C6 | 1.429 (2) | N5—O5 | 1.271 (2) |
C6—N1 | 1.363 (2) | C6—N6 | 1.308 (2) |
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1···O2i | 0.88 | 1.92 | 2.785 (2) | 168 |
N6—H6A···N5ii | 0.88 | 2.19 | 3.017 (2) | 157 |
N6—H6B···O5 | 0.88 | 2.03 | 2.645 (2) | 126 |
N6—H6B···O4iii | 0.88 | 2.31 | 2.957 (2) | 130 |
Symmetry codes: (i) −x+1, −y+1, −z+1; (ii) x, −y+1/2, z+1/2; (iii) x+1, −y+1/2, z+1/2. |
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We have recently reported (Cuesta et al., 2001; Low et al., 2003; López Garzón et al., 2003) on the structures of the hydrated sodium, strontium and barium complexes of the 6-amino-3-methyl-5-nitrosopyrimidine-2,4(1H,3H)-dionate anion, derived from the neutral pyrimidine (I), and here we report the molecular and supramolecular structures of neutral (I) itself.
Within the molecule of (I) (Fig. 1), the C5–C6 bond distance (Table 1) is much longer than the mean value (1.330 Å; Allen et al., 1987) for a double bond between two three-connected C atoms, whereas the C4—C5 distance does not differ significantly from the mean value (1.455 Å) for a single bond between a pair of three connected C atoms in a conjugated system. At the same time the C6—N6 distance is significantly smaller than the mean value (1.355 Å) for a Caryl—NH2 distance involving a planar N atom, while the C5—N5 and N5—O5 distances differ by only ca 0.08 Å. The remaining distances show no unexpected values. Hence, it can be concluded that the polarized form, (Ia), is a significant contributor to the overall molecular–electronic structure, alongside the classically localized form, (I).
The molecules exhibit the usual intramolecular N—H···O hydrogen bonding, with nitroso atom O5 as the acceptor (Table 2) and, in addition, there are three intermolecular hydrogen bonds, of both N—H···O and N—H···N types, which link the molecules into layers. Amino atom N6 in the molecule at (x, y, z) acts as hydrogen-bond donor, via H6A, to nitroso atom N5 in the molecule at (x, 0.5 − y, 0.5 + z), while amino atom N6 at (x, 0.5 − y, 0.5 + z) in turn acts as donor to atom N5 at (x, y, 1 + z), so forming a zigzag C(5) chain (Bernstein et al., 1995) running parallel to the [001] direction and generated by the c-glide plane at y = 0.25. Atom N6 also utilizes atom H6B to form an effectively planar three-centre N—H···(O)2 hydrogen bond, in which the two acceptors are nitroso atom O5 at (x, y, z), so forming an S(6) motif, and amide atom O4 in the molecule at (1 + x, 0.5 − y, 0.5 + z). This latter interaction gives rise to a zigzag C(6) chain running parallel to the [201] direction and generated by the same c-glide plane at y = 0.25. The combination of the [001] and [201] chains generates a sheet parallel to (010) in the form of a (4,4) net (Batten & Robson, 1998) containing equal numbers of S(6) and R54(16) rings (Fig. 2). Two sheets of this type pass through each unit cell, in the domains −0.03 < y < 0.53 and 0.47 < y < 1.03, and one further hydrogen bond serves to link the (010) sheets.
Atom N1 in the molecule at (x, y, z) acts as hydrogen-bond donor to atom O4 in the molecule at (1 − x, 1 − y, 1 − z), so forming an R22(8) ring centred at (1/2, 1/2, 1/2) (Fig. 3). The molecules at (x, y, z) and (1 − x, 1 − y, 1 − z) are components of sheets lying in the −0.03 < y < 0.53 and 0.47 < y < 1.03 domains, respectively, and propagation of this R22(8) motif by the space group links all the (010) sheets into a single three-dimensional framework. In this manner, all potential donors and all potential acceptors of hard hydrogen bonds are involved in the overall molecular aggregation.
The supramolecular aggregation of (I) can be contrasted with that of the dimethyl analogue, (II), which crystallizes as a monohydrate (Low et al., 1992). In this hydrate, the atoms all lie on mirror planes in space group Pnam (Pnma; No. 62), and the molecules are linked into sheets by a combination of O—H···O, O—H···N and N—H···O hydrogen bonds (Fig. 4).