In the title compound, C
10H
9N
3O
5, which was formed by the reaction of 6-amino-2-methoxy-4(3
H)-pyrimidinone with dimethyl acetylenedicarboxylate, the molecules are linked by N—H
O hydrogen bonds [N
O 2.8974 (15) and 3.0300 (15) Å, and N—H
O 165 and 174°] into planar sheets built from alternating
R22(8) and
R66(42) rings.
Supporting information
CCDC reference: 164662
Dimethyl acetylenedicarboxylate (2.84 g, 20 mmol) was added to a suspension of
6-amino-2-methoxy-4(3H)-pyrimidinone (1.41 g, 10 mmol) in dioxane (40 ml) containing a catalytic amount of trifluoroacetic acid (0.29 g, 2.5 mmol).
The mixture was stirred at 358 K for 12 h. The solvent was evaporated under
reduced pressure and compound (I) was isolated and purified by flash column
chromatography on silica gel using methylene chloride/ethyl ether (7:3
v/v) as eluent (yield: 0.58 g, 23%). Crystals suitable for
single-crystal X-ray diffraction were obtained by slow evaporation of a
solution in methanol [m.p. 529 K (decomposition)]. Analysis: found: C 47.9, H
3.6, N 16.7%; C10H9N3O5 requires: C 47.8, H 3.6, N 16.7%.
H atoms were treated as riding, with C—H 0.98 and N—H 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, 2000); software used to prepare material for publication: SHELXL97 and PRPKAPPA (Ferguson, 1999).
Methyl 4-amino-1,3-dioxo-2,3-dihydro-6-methoxy-1
H-
pyrrolo[3,4-
c]pyridine-7-carboxylate
top
Crystal data top
C10H9N3O5 | F(000) = 520 |
Mr = 251.20 | Dx = 1.602 Mg m−3 |
Monoclinic, P21/n | Mo Kα radiation, λ = 0.71073 Å |
a = 6.8189 (2) Å | Cell parameters from 2309 reflections |
b = 16.1505 (4) Å | θ = 3.3–27.5° |
c = 9.6257 (3) Å | µ = 0.13 mm−1 |
β = 100.7612 (13)° | T = 150 K |
V = 1041.42 (5) Å3 | Block, colourless |
Z = 4 | 0.2 × 0.2 × 0.2 mm |
Data collection top
KappaCCD area-detector diffractometer | 2309 independent reflections |
Radiation source: fine-focus sealed X-ray tube | 1913 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.03 |
ϕ and ω scans with κ offsets | θmax = 27.5°, θmin = 3.3° |
Absorption correction: multi-scan (DENZO-SMN; Otwinowski & Minor, 1997) | h = −8→8 |
Tmin = 0.974, Tmax = 0.974 | k = −20→20 |
8132 measured reflections | l = −12→12 |
Refinement top
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)] = 0.041 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.113 | H-atom parameters constrained |
S = 1.05 | w = 1/[σ2(Fo2) + (0.06P)2 + 0.2574P] where P = (Fo2 + 2Fc2)/3 |
2309 reflections | (Δ/σ)max = 0.001 |
165 parameters | Δρmax = 0.26 e Å−3 |
0 restraints | Δρmin = −0.28 e Å−3 |
Crystal data top
C10H9N3O5 | V = 1041.42 (5) Å3 |
Mr = 251.20 | Z = 4 |
Monoclinic, P21/n | Mo Kα radiation |
a = 6.8189 (2) Å | µ = 0.13 mm−1 |
b = 16.1505 (4) Å | T = 150 K |
c = 9.6257 (3) Å | 0.2 × 0.2 × 0.2 mm |
β = 100.7612 (13)° | |
Data collection top
KappaCCD area-detector diffractometer | 2309 independent reflections |
Absorption correction: multi-scan (DENZO-SMN; Otwinowski & Minor, 1997) | 1913 reflections with I > 2σ(I) |
Tmin = 0.974, Tmax = 0.974 | Rint = 0.03 |
8132 measured reflections | |
Refinement top
R[F2 > 2σ(F2)] = 0.041 | 0 restraints |
wR(F2) = 0.113 | H-atom parameters constrained |
S = 1.05 | Δρmax = 0.26 e Å−3 |
2309 reflections | Δρmin = −0.28 e Å−3 |
165 parameters | |
Special details top
Experimental. The program DENZO-SMN (Otwinowski & Minor, 1997) uses a scaling algorithm
[Fox, G·C. & Holmes, K·C. (1966), Acta Cryst. 20, 886–891] which
effectively corrects for absorption effects. High redundancy data were used in
the scaling program hence the 'multi-scan' code word was used. no transmission
coefficients are available from the program (only scale factors for each
frame). The scale factors in the experimental table are calculated from the
'size' command in the SHELXL97 input file. |
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top | x | y | z | Uiso*/Ueq | |
C1 | 0.67449 (19) | −0.08914 (8) | 0.65942 (14) | 0.0176 (3) | |
O1 | 0.66397 (15) | −0.16356 (6) | 0.66857 (11) | 0.0255 (3) | |
N2 | 0.80860 (17) | −0.04508 (7) | 0.59647 (12) | 0.0191 (3) | |
C3 | 0.77914 (19) | 0.03962 (8) | 0.60138 (14) | 0.0167 (3) | |
O3 | 0.87926 (14) | 0.09233 (6) | 0.55494 (10) | 0.0219 (3) | |
C3a | 0.60898 (19) | 0.05205 (8) | 0.67079 (14) | 0.0165 (3) | |
C4 | 0.51154 (19) | 0.12418 (8) | 0.70192 (14) | 0.0163 (3) | |
N4 | 0.56930 (17) | 0.19970 (7) | 0.67062 (13) | 0.0218 (3) | |
N5 | 0.35197 (17) | 0.11809 (7) | 0.76768 (12) | 0.0176 (3) | |
C6 | 0.29409 (19) | 0.04426 (8) | 0.80225 (14) | 0.0168 (3) | |
O61 | 0.14164 (14) | 0.03787 (6) | 0.87169 (10) | 0.0224 (3) | |
C61 | 0.0602 (2) | 0.11365 (9) | 0.91752 (17) | 0.0260 (3) | |
C7 | 0.38358 (19) | −0.03238 (8) | 0.77545 (14) | 0.0168 (3) | |
C71 | 0.3131 (2) | −0.11357 (8) | 0.82132 (14) | 0.0177 (3) | |
O71 | 0.15249 (15) | −0.14415 (6) | 0.77735 (11) | 0.0259 (3) | |
O72 | 0.45425 (14) | −0.14791 (6) | 0.91840 (10) | 0.0221 (3) | |
C72 | 0.4128 (2) | −0.23050 (9) | 0.96374 (16) | 0.0261 (3) | |
C7a | 0.54364 (19) | −0.02467 (8) | 0.70925 (14) | 0.0165 (3) | |
H2 | 0.9020 | −0.0683 | 0.5577 | 0.023* | |
H4A | 0.5047 | 0.2436 | 0.6925 | 0.026* | |
H4B | 0.6720 | 0.2057 | 0.6281 | 0.026* | |
H61A | 0.1647 | 0.1434 | 0.9822 | 0.039* | |
H61B | −0.0498 | 0.1004 | 0.9663 | 0.039* | |
H61C | 0.0105 | 0.1485 | 0.8351 | 0.039* | |
H72A | 0.2958 | −0.2290 | 1.0094 | 0.039* | |
H72B | 0.5283 | −0.2511 | 1.0311 | 0.039* | |
H72C | 0.3861 | −0.2674 | 0.8815 | 0.039* | |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
C1 | 0.0167 (6) | 0.0165 (7) | 0.0200 (7) | 0.0010 (5) | 0.0045 (5) | −0.0009 (5) |
O1 | 0.0287 (6) | 0.0149 (5) | 0.0356 (6) | 0.0017 (4) | 0.0125 (5) | −0.0009 (4) |
N2 | 0.0178 (6) | 0.0165 (6) | 0.0251 (6) | 0.0029 (4) | 0.0098 (5) | −0.0012 (5) |
C3 | 0.0157 (6) | 0.0168 (7) | 0.0179 (7) | 0.0005 (5) | 0.0034 (5) | −0.0010 (5) |
O3 | 0.0213 (5) | 0.0195 (6) | 0.0277 (6) | −0.0023 (4) | 0.0119 (4) | 0.0004 (4) |
C3a | 0.0152 (6) | 0.0159 (7) | 0.0189 (7) | 0.0005 (5) | 0.0046 (5) | −0.0007 (5) |
C4 | 0.0164 (6) | 0.0163 (7) | 0.0163 (6) | −0.0011 (5) | 0.0031 (5) | −0.0011 (5) |
N4 | 0.0223 (6) | 0.0149 (6) | 0.0308 (7) | 0.0001 (4) | 0.0122 (5) | 0.0009 (5) |
N5 | 0.0178 (6) | 0.0167 (6) | 0.0191 (6) | 0.0001 (4) | 0.0052 (5) | −0.0010 (5) |
C6 | 0.0148 (6) | 0.0188 (7) | 0.0178 (6) | −0.0009 (5) | 0.0052 (5) | −0.0006 (5) |
O61 | 0.0227 (5) | 0.0192 (5) | 0.0295 (6) | 0.0003 (4) | 0.0156 (4) | −0.0014 (4) |
C61 | 0.0244 (7) | 0.0251 (8) | 0.0321 (8) | 0.0028 (6) | 0.0148 (6) | −0.0057 (6) |
C7 | 0.0175 (6) | 0.0153 (7) | 0.0181 (7) | 0.0004 (5) | 0.0048 (5) | −0.0001 (5) |
C71 | 0.0193 (7) | 0.0160 (7) | 0.0197 (7) | 0.0002 (5) | 0.0084 (5) | −0.0013 (5) |
O71 | 0.0194 (5) | 0.0214 (5) | 0.0361 (6) | −0.0040 (4) | 0.0034 (4) | 0.0053 (4) |
O72 | 0.0236 (5) | 0.0172 (5) | 0.0242 (5) | −0.0028 (4) | 0.0015 (4) | 0.0046 (4) |
C72 | 0.0339 (8) | 0.0162 (7) | 0.0268 (8) | −0.0018 (6) | 0.0022 (6) | 0.0049 (6) |
C7a | 0.0162 (6) | 0.0156 (7) | 0.0177 (6) | 0.0001 (5) | 0.0033 (5) | −0.0014 (5) |
Geometric parameters (Å, º) top
C1—N2 | 1.3844 (17) | N4—H4A | 0.8800 |
N2—C3 | 1.3847 (17) | N4—H4B | 0.8800 |
C1—C7a | 1.5068 (18) | C6—O61 | 1.3407 (16) |
C3—C3a | 1.4569 (18) | O61—C61 | 1.4464 (16) |
C3a—C7a | 1.3901 (18) | C61—H61A | 0.9800 |
C1—O1 | 1.2082 (17) | C61—H61B | 0.9800 |
C3—O3 | 1.2266 (16) | C61—H61C | 0.9800 |
C3a—C4 | 1.4009 (18) | C7—C71 | 1.4914 (18) |
C4—N5 | 1.3607 (18) | C71—O71 | 1.2041 (17) |
N5—C6 | 1.3181 (17) | C71—O72 | 1.3307 (17) |
C6—C7 | 1.4247 (18) | O72—C72 | 1.4475 (16) |
C7—C7a | 1.3684 (19) | C72—H72A | 0.9800 |
C4—N4 | 1.3334 (17) | C72—H72B | 0.9800 |
N2—H2 | 0.8800 | C72—H72C | 0.9800 |
| | | |
O1—C1—N2 | 126.61 (13) | O61—C61—H61A | 109.5 |
O1—C1—C7a | 128.13 (13) | O61—C61—H61B | 109.5 |
N2—C1—C7a | 105.24 (11) | H61A—C61—H61B | 109.5 |
C1—N2—C3 | 112.39 (11) | O61—C61—H61C | 109.5 |
C1—N2—H2 | 123.8 | H61A—C61—H61C | 109.5 |
C3—N2—H2 | 123.8 | H61B—C61—H61C | 109.5 |
O3—C3—N2 | 125.38 (13) | C7a—C7—C6 | 114.27 (12) |
O3—C3—C3a | 128.07 (13) | C7a—C7—C71 | 123.16 (12) |
N2—C3—C3a | 106.55 (11) | C6—C7—C71 | 122.53 (12) |
C7a—C3a—C4 | 119.72 (12) | O71—C71—O72 | 124.54 (13) |
C7a—C3a—C3 | 108.76 (11) | O71—C71—C7 | 125.36 (12) |
C4—C3a—C3 | 131.52 (12) | O72—C71—C7 | 110.11 (11) |
N4—C4—N5 | 117.83 (11) | C71—O72—C72 | 116.07 (11) |
N4—C4—C3a | 122.71 (12) | O72—C72—H72A | 109.5 |
N5—C4—C3a | 119.46 (12) | O72—C72—H72B | 109.5 |
C4—N4—H4A | 120.0 | H72A—C72—H72B | 109.5 |
C4—N4—H4B | 120.0 | O72—C72—H72C | 109.5 |
H4A—N4—H4B | 120.0 | H72A—C72—H72C | 109.5 |
C6—N5—C4 | 119.07 (11) | H72B—C72—H72C | 109.5 |
N5—C6—O61 | 119.47 (12) | C7—C7a—C3a | 121.89 (12) |
N5—C6—C7 | 125.57 (12) | C7—C7a—C1 | 131.04 (12) |
O61—C6—C7 | 114.94 (11) | C3a—C7a—C1 | 107.03 (11) |
C6—O61—C61 | 117.68 (11) | | |
| | | |
O1—C1—N2—C3 | 178.90 (13) | O61—C6—C7—C71 | −0.07 (19) |
C7a—C1—N2—C3 | 0.42 (14) | C7a—C7—C71—O71 | −116.96 (16) |
C1—N2—C3—O3 | 178.96 (12) | C6—C7—C71—O71 | 65.65 (19) |
C1—N2—C3—C3a | −1.22 (15) | C7a—C7—C71—O72 | 62.90 (17) |
O3—C3—C3a—C7a | −178.61 (12) | C6—C7—C71—O72 | −114.48 (14) |
N2—C3—C3a—C7a | 1.57 (15) | O71—C71—O72—C72 | 5.0 (2) |
O3—C3—C3a—C4 | 1.1 (2) | C7—C71—O72—C72 | −174.85 (11) |
N2—C3—C3a—C4 | −178.75 (13) | C7—C6—O61—C61 | 172.57 (11) |
C7a—C3a—C4—N4 | 178.55 (12) | C6—C7—C7a—C3a | −0.8 (2) |
C3—C3a—C4—N4 | −1.1 (2) | C71—C7—C7a—C3a | −178.38 (12) |
C7a—C3a—C4—N5 | −0.97 (19) | C6—C7—C7a—C1 | −178.23 (12) |
C3—C3a—C4—N5 | 179.39 (12) | C71—C7—C7a—C1 | 4.2 (2) |
N4—C4—N5—C6 | −178.72 (12) | C4—C3a—C7a—C7 | 1.0 (2) |
C3a—C4—N5—C6 | 0.82 (19) | C3—C3a—C7a—C7 | −179.29 (11) |
C4—N5—C6—O61 | 177.57 (11) | C4—C3a—C7a—C1 | 178.96 (11) |
C4—N5—C6—C7 | −0.7 (2) | C3—C3a—C7a—C1 | −1.32 (14) |
N5—C6—O61—C61 | −5.89 (19) | O1—C1—C7a—C7 | −0.1 (2) |
N5—C6—C7—C7a | 0.7 (2) | N2—C1—C7a—C7 | 178.31 (14) |
O61—C6—C7—C7a | −177.67 (11) | O1—C1—C7a—C3a | −177.87 (13) |
N5—C6—C7—C71 | 178.28 (13) | N2—C1—C7a—C3a | 0.59 (14) |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
N2—H2···O3i | 0.88 | 2.04 | 2.8974 (15) | 165 |
N4—H4A···O71ii | 0.88 | 2.15 | 3.0300 (15) | 174 |
N4—H4B···O3 | 0.88 | 2.49 | 3.0973 (15) | 126 |
Symmetry codes: (i) −x+2, −y, −z+1; (ii) −x+1/2, y+1/2, −z+3/2. |
Experimental details
Crystal data |
Chemical formula | C10H9N3O5 |
Mr | 251.20 |
Crystal system, space group | Monoclinic, P21/n |
Temperature (K) | 150 |
a, b, c (Å) | 6.8189 (2), 16.1505 (4), 9.6257 (3) |
β (°) | 100.7612 (13) |
V (Å3) | 1041.42 (5) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 0.13 |
Crystal size (mm) | 0.2 × 0.2 × 0.2 |
|
Data collection |
Diffractometer | KappaCCD area-detector diffractometer |
Absorption correction | Multi-scan (DENZO-SMN; Otwinowski & Minor, 1997) |
Tmin, Tmax | 0.974, 0.974 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 8132, 2309, 1913 |
Rint | 0.03 |
(sin θ/λ)max (Å−1) | 0.649 |
|
Refinement |
R[F2 > 2σ(F2)], wR(F2), S | 0.041, 0.113, 1.05 |
No. of reflections | 2309 |
No. of parameters | 165 |
H-atom treatment | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 0.26, −0.28 |
Selected geometric parameters (Å, º) topC1—N2 | 1.3844 (17) | C3a—C4 | 1.4009 (18) |
N2—C3 | 1.3847 (17) | C4—N5 | 1.3607 (18) |
C1—C7a | 1.5068 (18) | N5—C6 | 1.3181 (17) |
C3—C3a | 1.4569 (18) | C6—C7 | 1.4247 (18) |
C3a—C7a | 1.3901 (18) | C7—C7a | 1.3684 (19) |
C1—O1 | 1.2082 (17) | C4—N4 | 1.3334 (17) |
C3—O3 | 1.2266 (16) | | |
| | | |
C6—C7—C71—O71 | 65.65 (19) | C7—C71—O72—C72 | −174.85 (11) |
C6—C7—C71—O72 | −114.48 (14) | C7—C6—O61—C61 | 172.57 (11) |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
N2—H2···O3i | 0.88 | 2.04 | 2.8974 (15) | 165 |
N4—H4A···O71ii | 0.88 | 2.15 | 3.0300 (15) | 174 |
N4—H4B···O3 | 0.88 | 2.49 | 3.0973 (15) | 126 |
Symmetry codes: (i) −x+2, −y, −z+1; (ii) −x+1/2, y+1/2, −z+3/2. |
The title compound, (I), was obtained from the reaction between 6-amino-2-methoxy-4(3H)-pyrimidine and dimethyl acetylenedicarboxylate (Scheme 2), and the structure determination reported here provides definitive proof of the constitution of (I), not readily obtained from spectroscopic data alone. It also allows comparison between (I) and the substituted analogue, (II) (Low et al., 2001). Thirdly, it reveals an almost planar hydrogen-bonded network made up of alternating large and small rings. \sch
The bicyclic molecules of (I) (Fig. 1) are essentially planar, except for the methyl carboxylate group, which is significantly twisted out of the ring plane (Table 1). A similar twist of this substituent was observed in compound (II), where the C—C—C—O torsion angles involving the carbonyl O are -58.1 (7)° and 120.0 (7)°. The formation of (I) is most simply rationalized (Scheme 2) in terms of a hetero Diels-Alder reaction to give the bicyclic intermediate, (III), followed by acid-catalysed rearrangement with loss of methanol to give (I).
The bond lengths in (I) (Table 1) provide clear evidence of electron delocalization between certain of the substituents: C3—O3 is significantly longer than C1—O1, C3—C3a is significantly shorter than C1—C7a, and C4—N4 is not only significantly shorter than C4—N5 but its distance is less than the lower quartile value, 1.340 Å (Allen et al., 1987) for aryl-NH2 bonds. In addition, C3a—C4 is significantly longer than C7—C7a. These features taken together, all of which are closely reproduced in (II), point to the important contribution of the canonical form (Ia) to the overall electronic structure of this bicyclic system. The development of form (Ia) is accompanied by the formation of a weak intramolecular hydrogen bond (Table 2): although the N···O distance is necessarily rather long, as it is constrained by the geometry of the covalently bonded molecular framework, this hydrogen bond is charge-enhanced, since both the donor and the acceptor are charged in form (Ia). The metrical similarities between (I) and (II), despite their different N-substituents, suggest that delocalization of this kind may be typical for compounds of this type.
The molecules of (I) are linked by two N—H···O hydrogen bonds (Table 2) into two-dimensional sheets. Amino N4 acts as donor, via H4A, to carboxyl O71ii [symmetry code: (ii) 1/2 - x, 1/2 + y, 3/2 - z], while N4ii in turn acts as donor to O71iii [symmmetry code: (iii) x, 1 + y, z]. In this manner a C(8) spiral chain is produced, running parallel to the [010] direction and generated by the 21 screw axis along (1/2, y, 3/4) (Fig. 2). The other N—H···O hydrogen bond generates centrosymmetric R22(8) rings: imino N2 acts as donor to carbonyl O3i [symmetry code: (i) 2 - x, -y, 1 - z], while N2i is donor to O3, so generating a ring centred at (1, 0, 1/2) (Fig. 2). The combination of these two motifs, each built from a single hydrogen bond, generates a continuous sheet (Fig. 2) in which the R22(8) rings alternate with centrosymmetric R66(42) rings. Each molecule is hydrogen bonded to three others. If single molecules are regarded as the nodes of the resulting net, then this is of the (6,3) type (Batten & Robson, 1998), while if the centrosymmetric R22(8) dimers are regarded as the nodes, then the net is of the (4,4) type. Although each molecule contains three N—H bonds and three carbonyl groups, carbonyl O1 does not participate in hydrogen bonds. In terms of the canonical forms (I) and (Ia), it is notable that of the chemically similar atoms O1 and O3, only the charged atom O3 acts as a hydrogen-bond acceptor.
The sheets are nearly planar and lie parallel to (103). The formation of each sheet utilizes 4/3 molecules per unit cell, so that with Z = 4, three such sheets are required to define the structure fully. Adjacent sheets are not interwoven, despite the presence of the R66(42) rings, but there are aromatic π···π stacking interactions between molecules in adjacent sheets. The molecule at (x, y, z) forms a π···π stacking interaction with the molecule at (1 - x, -y, 1 - z), which forms part of an adjacent sheet. The perpendicular distance between these molecular planes is 3.335 (3) Å, and the centroid offset between the five-membered rings in the two molecules is ca 0.84 Å, while the centroid offset between the five-membered ring in one molecule and the six-membered ring in the other, which carry opposite net charges (Scheme 1) is ca 1.60 Å (Fig. 3). Propagation of this π···π interaction by the space group serves to link all the sheets into a single three-dimensional framework.