4-(2-Pyridyl)-1H,2H-pyrido­[1,2-c]­pyrimidine-1,3-dione

The maximum deviation from the mean plane of the pyrido­pyrimidine skeleton of the title compound, C₁₃H₉N₃O₂, indicates a reasonably planar system. The planar pyridyl ring is twisted with respect to the pyrido­[1,2-c]­pyrimidine-1,3-dione fragment. The mol­ecules form centrosymmetric dimers via intermolecular N—H...O hydrogen bonds. Short intra- and intermolecular C—H...O and C—H...N contacts are observed.

Key indicators

• Single-crystal X-ray study
• T = 293 K
• Mean [sigma](C-C) = 0.002 Å
• R factor = 0.044
• wR factor = 0.127
• Data-to-parameter ratio = 14.8

checkCIF results

No syntax errors found

ADDSYM reports no extra symmetry

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S1. Comment

In continuation of our research on the synthesis of condensed heterobicyclic compounds, we focused our interest on the derivatives of 4-(aryl/heteroaryl)pyrido[1,2-c]pyrimidine (Herold et al., 1999; Herold, Kleps, Anulewicz-Ostrowska & Szczęsna, 2002; Herold, Kleps, Wolska & Nowak, 2002). The obtained compounds will be further applied as starting materials in the synthesis of new ligands of the 5-HT_{1 A} receptor. Due to the increased lipophilicity, the presence of imide group in their structure, and the elements providing a possibility of interaction with the 5-HT_{1 A} receptor, higher affinity and selectivity for this receptor can be expected for 4-(2-pyridyl)-1H,2H-pyrido[1,2-c]pyrimidine-1,3-dione derivatives (Orjales et al., 1995; López-Rodriquez et al., 1999; Herold, Kleps, Wolska & Nowak, 2002).

The molecular structure of the title compound,(I), showing the labelling scheme, is presented in Fig. 1. The pyridopyrimidine fragment is essentially planar, with no atomic deviation greater than 0.071 (1) Å (for C6) from its least-squares plane. Atoms O10 and O11 are found to be insignificantly out of this plane [−0.120 (2) and −0.105 (2) Å for O10 and O11, respectively]. The pyridyl ring is planar with deviations from the best plane ranging from −0.001 (1) Å for N6' to 0.009 (1) Å for C2', and makes an angle of 56.64 (6)° with the best plane of the pyridopyrimidine system. The twisting of the heteroaryl substituent at C4 with respect to the pyrido[1,2-c]pyrimidine-1,3-dione skeleton can be described by the torsion angle C3—C4—C1'—N6' of 126.9 (1)°. This twisting is likely due to steric reasons and is stabilized by short intramolecular C5—H5···N6' contact (Table 2). A similar arrangement of substituent at C4 has been affirmed in the 4-arylhexahydropyridopyrimidine derivatives (Herold et al., 1999, 2000; Maciejewska et al., 2000; Wolska & Herold, 1999, 2000, 2002) and for these compounds the most interesting feature is the formation of centrosymmetric dimers by means of intermolecular hydrogen bonds. In (I), the molecules are also connected into centrosymmetric dimers and they are held together by an N—H···O hydrogen bond (Fig. 2). As a result, the C3═O11 bond length is slightly longer than C1═O10 (Table 1). Atoms O10, O11 and N6' are also involved in weak intermolecular C—H···O and C—H···N hydrogen bonds (Desiraju, 1996), which are an effect of the crystal packing of the molecules. The geometric parameters of all hydrogen bonds are listed in Table 2. The bond lengths and angles pattern is quite typical, only the C4—C4a bond length is insignificantly longer than the same distance in the pyridopyrimidine derivatives presented until now (Herold et al., 1999, 2000; Maciejewska et al., 2000; Wolska & Herold, 1999, 2000, 2002) and typical Csp²—Csp² bond length (Allen et al., 1987), may be as a result of delocalization of π-electrons in this fragment of the molecule.

S2. Experimental

The title compound was prepared in accordance with (Herold, 2003). Crystals were grown from ethanol solution by slow evaporation.

S3. Refinement

Only positional and displacement parameters for H2 atom, which is involved in an N—H···O hydrogen bond, were refined isotropically. The other H atoms were refined with a riding model and their U_iso values were set at 1.2U_eq of their carrier atoms.

Computing details

Data collection: CrysAlis CCD (Kuma, 2001); cell refinement: CrysAlis RED (Kuma, 2001); data reduction: CrysAlis RED; program(s) used to solve structure: SHELXS97 (Sheldrick, 1990); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: Stereochemical Workstation (Siemens, 1989); software used to prepare material for publication: SHELXL97.

Figures

	Fig. 1. A view of the title compound with the atom numbering scheme. Displacement ellipsoids are drawn at the 50% probability level.
	Fig. 2. The centrosymmetric hydrogen-bonded dimer [symmetry code: (i) 2 − x, 1 − y, −z]. Hydrogen bonds are drawn as dashed solid lines.

4-(2-pyridyl)-1H,3H-pyrido[1,2-c]pyrimidine-1,3-dione

Crystal data

C13H9N3O2	F(000) = 496
Mr = 239.23	Dx = 1.467 Mg m^−3
Monoclinic, P21/c	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybc	Cell parameters from 5139 reflections
a = 8.631 (2) Å	θ = 2.0–27.1°
b = 8.041 (2) Å	µ = 0.10 mm^−1
c = 16.054 (3) Å	T = 293 K
β = 103.51 (3)°	Prism, yellow
V = 1083.3 (4) Å^3	0.55 × 0.50 × 0.40 mm
Z = 4

Data collection

Kuma KM-4 CCD diffractometer	2374 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tube	Rint = 0.014
Graphite monochromator	θmax = 28.0°, θmin = 3.6°
ω/2θ scans	h = −11→11
6578 measured reflections	k = −10→10
2608 independent reflections	l = −21→14

Refinement

Refinement on F^2	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F^2 > 2σ(F^2)] = 0.044	H atoms treated by a mixture of independent and constrained refinement
wR(F^2) = 0.127	w = 1/[σ^2(Fo^2) + (0.0711P)^2 + 0.2921P] where P = (Fo^2 + 2Fc^2)/3
S = 1.07	(Δ/σ)max = 0.006
2608 reflections	Δρmax = 0.24 e Å^−3
176 parameters	Δρmin = −0.23 e Å^−3
0 restraints	Extinction correction: SHELXL97, Fc^*=kFc[1+0.001xFc^2λ^3/sin(2θ)]^-1/4
Primary atom site location: structure-invariant direct methods	Extinction coefficient: 0.079 (7)

Special details

Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell e.s.d.'s are taken into account individually in the estimation of e.s.d.'s in distances, angles and torsion angles; correlations between e.s.d.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell e.s.d.'s is used for estimating e.s.d.'s involving l.s. planes.

Refinement. Refinement of F² against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F², conventional R-factors R are based on F, with F set to zero for negative F². The threshold expression of F² > σ(F²) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F² are statistically about twice as large as those based on F, and R- factors based on ALL data will be even larger.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Ų)

	x	y	z	Uiso*/Ueq
C1	0.66728 (14)	0.37519 (16)	0.02778 (7)	0.0300 (3)
N2	0.81401 (12)	0.44383 (14)	0.03738 (6)	0.0319 (3)
H2	0.8434 (18)	0.464 (2)	−0.0114 (11)	0.038 (4)*
C3	0.92808 (14)	0.46936 (17)	0.11354 (7)	0.0310 (3)
C4	0.88079 (13)	0.42448 (15)	0.19022 (7)	0.0270 (3)
C4a	0.73298 (13)	0.35177 (14)	0.18474 (7)	0.0251 (2)
C5	0.68228 (15)	0.28362 (16)	0.25680 (7)	0.0316 (3)
H5	0.7501	0.2907	0.3110	0.041 (4)*
C6	0.53887 (16)	0.20962 (18)	0.24799 (8)	0.0382 (3)
H6	0.5106	0.1641	0.2956	0.049 (5)*
C7	0.43085 (15)	0.20087 (19)	0.16639 (9)	0.0393 (3)
H7	0.3304	0.1540	0.1606	0.056 (5)*
C8	0.47598 (14)	0.26122 (18)	0.09789 (8)	0.0342 (3)
H8	0.4059	0.2555	0.0443	0.045 (4)*
N9	0.62590 (11)	0.33244 (13)	0.10541 (6)	0.0275 (2)
O10	0.57679 (11)	0.34905 (14)	−0.04136 (6)	0.0416 (3)
O11	1.05933 (11)	0.52654 (16)	0.10936 (6)	0.0468 (3)
C1'	0.99499 (13)	0.44937 (15)	0.27416 (7)	0.0267 (3)
C2'	1.14888 (15)	0.38492 (18)	0.29000 (8)	0.0360 (3)
H2'	1.1833	0.3273	0.2474	0.051 (5)*
C3'	1.25007 (16)	0.40770 (19)	0.36993 (9)	0.0414 (3)
H3'	1.3526	0.3638	0.3822	0.058 (5)*
C4'	1.19598 (17)	0.49666 (18)	0.43100 (8)	0.0400 (3)
H4'	1.2610	0.5138	0.4853	0.053 (5)*
C5'	1.04281 (17)	0.55966 (17)	0.40952 (8)	0.0362 (3)
H5'	1.0077	0.6214	0.4505	0.044 (4)*
N6'	0.94195 (12)	0.53711 (13)	0.33324 (6)	0.0310 (3)

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
C1	0.0294 (6)	0.0366 (6)	0.0234 (5)	−0.0010 (5)	0.0047 (4)	0.0030 (4)
N2	0.0307 (5)	0.0438 (6)	0.0217 (5)	−0.0063 (4)	0.0072 (4)	0.0042 (4)
C3	0.0283 (6)	0.0406 (6)	0.0245 (6)	−0.0054 (5)	0.0070 (4)	0.0007 (5)
C4	0.0245 (5)	0.0341 (6)	0.0225 (5)	0.0001 (4)	0.0060 (4)	0.0016 (4)
C4a	0.0243 (5)	0.0292 (5)	0.0223 (5)	0.0019 (4)	0.0064 (4)	0.0017 (4)
C5	0.0326 (6)	0.0387 (7)	0.0250 (5)	−0.0022 (5)	0.0094 (4)	0.0024 (5)
C6	0.0395 (7)	0.0463 (7)	0.0334 (6)	−0.0068 (6)	0.0179 (5)	0.0029 (5)
C7	0.0288 (6)	0.0488 (8)	0.0429 (7)	−0.0102 (5)	0.0134 (5)	−0.0013 (6)
C8	0.0243 (6)	0.0440 (7)	0.0335 (6)	−0.0050 (5)	0.0049 (5)	−0.0003 (5)
N9	0.0227 (5)	0.0354 (5)	0.0243 (5)	−0.0017 (4)	0.0054 (4)	0.0029 (4)
O10	0.0366 (5)	0.0610 (7)	0.0241 (4)	−0.0093 (4)	0.0009 (4)	0.0012 (4)
O11	0.0356 (5)	0.0771 (8)	0.0291 (5)	−0.0220 (5)	0.0105 (4)	−0.0005 (5)
C1'	0.0258 (5)	0.0311 (6)	0.0235 (5)	−0.0016 (4)	0.0064 (4)	0.0019 (4)
C2'	0.0292 (6)	0.0446 (7)	0.0338 (6)	0.0035 (5)	0.0065 (5)	−0.0036 (5)
C3'	0.0294 (6)	0.0496 (8)	0.0407 (7)	0.0029 (6)	−0.0009 (5)	0.0025 (6)
C4'	0.0436 (7)	0.0443 (7)	0.0264 (6)	−0.0054 (6)	−0.0031 (5)	0.0036 (5)
C5'	0.0471 (7)	0.0372 (6)	0.0257 (6)	−0.0033 (5)	0.0114 (5)	−0.0012 (5)
N6'	0.0323 (5)	0.0358 (5)	0.0261 (5)	0.0016 (4)	0.0093 (4)	0.0010 (4)

Geometric parameters (Å, º)

C1—O10	1.2171 (15)	C7—C8	1.3403 (19)
C1—N2	1.3568 (16)	C7—H7	0.9300
C1—N9	1.4166 (15)	C8—N9	1.3942 (15)
N2—C3	1.3943 (16)	C8—H8	0.9300
N2—H2	0.892 (17)	C1'—N6'	1.3452 (15)
C3—O11	1.2388 (15)	C1'—C2'	1.3928 (17)
C3—C4	1.4307 (16)	C2'—C3'	1.3854 (18)
C4—C4a	1.3873 (15)	C2'—H2'	0.9300
C4—C1'	1.4856 (16)	C3'—C4'	1.380 (2)
C4a—N9	1.3966 (14)	C3'—H3'	0.9300
C4a—C5	1.4377 (15)	C4'—C5'	1.382 (2)
C5—C6	1.3506 (18)	C4'—H4'	0.9300
C5—H5	0.9300	C5'—N6'	1.3388 (16)
C6—C7	1.421 (2)	C5'—H5'	0.9300
C6—H6	0.9300
O10—C1—N2	123.84 (11)	C6—C7—H7	120.5
O10—C1—N9	121.36 (11)	C7—C8—N9	121.30 (12)
N2—C1—N9	114.79 (10)	C7—C8—H8	119.4
C1—N2—C3	127.49 (10)	N9—C8—H8	119.4
C1—N2—H2	114.9 (10)	C8—N9—C4a	121.85 (10)
C3—N2—H2	117.2 (10)	C8—N9—C1	116.31 (10)
O11—C3—N2	118.32 (10)	C4a—N9—C1	121.74 (9)
O11—C3—C4	126.06 (11)	N6'—C1'—C2'	122.24 (11)
N2—C3—C4	115.62 (10)	N6'—C1'—C4	116.57 (10)
C4a—C4—C3	119.65 (10)	C2'—C1'—C4	121.19 (10)
C4a—C4—C1'	121.32 (10)	C3'—C2'—C1'	119.20 (12)
C3—C4—C1'	118.97 (10)	C3'—C2'—H2'	120.4
C4—C4a—N9	120.50 (10)	C1'—C2'—H2'	120.4
C4—C4a—C5	123.91 (10)	C4'—C3'—C2'	118.81 (12)
N9—C4a—C5	115.49 (10)	C4'—C3'—H3'	120.6
C6—C5—C4a	121.83 (11)	C2'—C3'—H3'	120.6
C6—C5—H5	119.1	C3'—C4'—C5'	118.38 (12)
C4a—C5—H5	119.1	C3'—C4'—H4'	120.8
C5—C6—C7	120.41 (11)	C5'—C4'—H4'	120.8
C5—C6—H6	119.8	N6'—C5'—C4'	123.93 (12)
C7—C6—H6	119.8	N6'—C5'—H5'	118.0
C8—C7—C6	118.98 (11)	C4'—C5'—H5'	118.0
C8—C7—H7	120.5	C5'—N6'—C1'	117.41 (10)
O10—C1—N2—C3	−176.11 (13)	C5—C4a—N9—C8	3.94 (16)
N9—C1—N2—C3	2.97 (19)	C4—C4a—N9—C1	4.34 (17)
C1—N2—C3—O11	176.41 (13)	C5—C4a—N9—C1	−172.30 (11)
C1—N2—C3—C4	−3.10 (19)	O10—C1—N9—C8	−0.75 (18)
O11—C3—C4—C4a	−175.89 (13)	N2—C1—N9—C8	−179.86 (11)
N2—C3—C4—C4a	3.57 (18)	O10—C1—N9—C4a	175.68 (11)
O11—C3—C4—C1'	1.1 (2)	N2—C1—N9—C4a	−3.43 (17)
N2—C3—C4—C1'	−179.42 (11)	C4a—C4—C1'—N6'	−56.11 (16)
C3—C4—C4a—N9	−4.36 (17)	C3—C4—C1'—N6'	126.93 (12)
C1'—C4—C4a—N9	178.70 (10)	C4a—C4—C1'—C2'	124.05 (13)
C3—C4—C4a—C5	171.99 (11)	C3—C4—C1'—C2'	−52.91 (17)
C1'—C4—C4a—C5	−4.95 (18)	N6'—C1'—C2'—C3'	1.7 (2)
C4—C4a—C5—C6	−178.03 (12)	C4—C1'—C2'—C3'	−178.43 (12)
N9—C4a—C5—C6	−1.52 (18)	C1'—C2'—C3'—C4'	−1.3 (2)
C4a—C5—C6—C7	−1.7 (2)	C2'—C3'—C4'—C5'	−0.2 (2)
C5—C6—C7—C8	2.6 (2)	C3'—C4'—C5'—N6'	1.3 (2)
C6—C7—C8—N9	−0.2 (2)	C4'—C5'—N6'—C1'	−0.84 (19)
C7—C8—N9—C4a	−3.2 (2)	C2'—C1'—N6'—C5'	−0.69 (18)
C7—C8—N9—C1	173.25 (13)	C4—C1'—N6'—C5'	179.47 (10)
C4—C4a—N9—C8	−179.42 (11)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
C5—H5···N6′	0.93	2.55	3.0658 (18)	115
N2—H2···O11^i	0.892 (17)	1.950 (17)	2.8293 (15)	168.4 (15)
C5—H5···O11^ii	0.93	2.81	3.4095 (18)	124
C2′—H2′···N6′^ii	0.93	2.76	3.4097 (18)	127
C6—H6···O10^iii	0.93	2.55	3.3539 (17)	145
C7—H7···N6′^iv	0.93	2.55	3.4780 (18)	172
C3′—H3′···O10^v	0.93	2.66	3.5165 (19)	154

Symmetry codes: (i) −x+2, −y+1, −z; (ii) −x+2, y−1/2, −z+1/2; (iii) x, −y+1/2, z+1/2; (iv) −x+1, y−1/2, −z+1/2; (v) x+1, −y+1/2, z+1/2.