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In the title compound, C7H9N3O3, the primary packing motif, viz. an infinite tape, is formed via inter­molecular hydrogen bonds of different strengths. In the formation of the tapes, only inversion centres are used; the other symmetry elements of P21/c connect the tapes into a three-dimensional structure through only weak hydrogen bonds.

Supporting information

cif

Crystallographic Information File (CIF) https://doi.org/10.1107/S0108270106015460/gd3012sup1.cif
Contains datablocks global, I

hkl

Structure factor file (CIF format) https://doi.org/10.1107/S0108270106015460/gd3012Isup2.hkl
Contains datablock I

CCDC reference: 612461

Comment top

In the course of studies of weak interactions in molecular crystals (Kubicki et al., 2001, 2002), the crystal structure of (1-thyminyl)acetamide, (I) (Fig. 1), has been determined. In this simple molecule the three carbonyl groups can potentially be involved in intermolecular carbonyl–carbonyl interactions that are able to compete successfully with hydrogen bonds (Allen et al., 1998). On the other hand, the primary acetamide group and the secondary amine group, as well as the carbonyl groups, can form intermolecular hydrogen bonds of different energies; moreover weak C—H···O and C—H···N hydrogen bonds can also be formed and influence the supramolecular packing motif.

The molecule of (I) contains planar thyminyl and acetamide moieties, which make a dihedral angle of 87.05 (3)°. Of the several possible tautomeric forms for the flat uracyl ring, the diketo tautomer has been found in the solid state. Appreciable differences have been observed in the values of the CO bond lengths, 1.2436 (11) Å and 1.2304 (10) Å for C2O2 and C4O4, respectively, however, the differences in their lengths are less pronounced than in thymine itself (Portalone et al., 1999). The existence of C O groups of different lengths can be easily explained by observing the respective crystal structures. In thymine (Portalone et al., 1999), as well as in the crystals of (I), centrosymmetric dimers are formed via N3—H3···O2C2 hydrogen bonds. The second carbonyl group, C4O4, is in (I) involved in a weak C—H···O hydrogen bond only (Table 1), and for this reason the C4O4 bond is shorter. This geometrical perturbation is mainly due to self-association and confirms the fundamental role of conjugative stabilization of the intermolecular hydrogen bonding.

Intermolecular hydrogen bonds, the main driving force for crystal packing, connect the molecules of (I) into infinite tapes. Only inversion centres participate in the formation of the tape and no other symmetry operations are used in creating this principal packing motif. This mimics the packing of thymine molecules in the solid state (Portalone et al., 1999). In (I), one type of centrosymmetric dimers is formed via almost linear and quite strong N3—H3···O2i hydrogen bonds (symmetry codes as in Table 1 and Fig. 2), which form eight-membered rings. The same O2 atoms participate in bifurcated hydrogen bonds to the amide groups, O2ii···H12B—N12, thus forming the second kind of centrosymmetric dimer, featuring 14 (13?)-membered rings. The molecular tapes also contain weak C—H···O hydrogen bonds (Fig. 2 and Table 1), but these are secondary interactions only. The molecular tapes in the crystal of (I) are further connected into a three-dimensional structure by weak bifurcated hydrogen bonds to O12; N12—H12A···O12iii and C6—H6···O12iv (Table 1 and Fig. 2). No carbonyl–carbonyl interactions have been found.

There are also some similarities in the crystal-packing modes of (I) and two imidazole derivatives, namely 2-methyl-4-nitro-1-phenyl-1H-imidazole-5-carbonitrile, (II), and 1-(4-chlorophenyl)-2-methyl-4-nitro-1H-imidazole-5-carbonitrile, (III) (Kubicki, 2004). These two imidazole derivatives likewise form infinite tapes in their crystal structures using two consecutive inversion centres in space group P21/n, and the molecular conformations in the crystals are similar to that in (I), with dihedral angles between the two planar fragments of 76.29 (4) and 87.64 (6)° in (II) and (III), respectively. On the other hand, the differences between the crystal structures of (I), (II) and (III) are determined by the intermolecular interactions. There are intermolecular hydrogen bonds in (I); in (II) dipole–dipole interactions between antiparallel cyano groups connect molecules into centrosymmetric dimers; while in (III), the dimers are connected by CN···Cl—C interactions together with weak C—H···O(N) hydrogen bonds. All this diversity of interactions can be understood on the basis of a simple electrostatic model; moreover, the halogen bond is an analogue of the hydrogen bond (Legon, 1999).

Experimental top

The synthesis of (1-thyminyl)acetonitrile was described by Spychała (1997). Crystals suitable for data collection were grown from hot water by slow cooling.

Refinement top

All H atoms were freely refined, giving C—H distances of 0.959 (14)–1.003 (15) Å and N—H distances of 0.887 (17)–0.931 (16) Å.

Structure description top

In the course of studies of weak interactions in molecular crystals (Kubicki et al., 2001, 2002), the crystal structure of (1-thyminyl)acetamide, (I) (Fig. 1), has been determined. In this simple molecule the three carbonyl groups can potentially be involved in intermolecular carbonyl–carbonyl interactions that are able to compete successfully with hydrogen bonds (Allen et al., 1998). On the other hand, the primary acetamide group and the secondary amine group, as well as the carbonyl groups, can form intermolecular hydrogen bonds of different energies; moreover weak C—H···O and C—H···N hydrogen bonds can also be formed and influence the supramolecular packing motif.

The molecule of (I) contains planar thyminyl and acetamide moieties, which make a dihedral angle of 87.05 (3)°. Of the several possible tautomeric forms for the flat uracyl ring, the diketo tautomer has been found in the solid state. Appreciable differences have been observed in the values of the CO bond lengths, 1.2436 (11) Å and 1.2304 (10) Å for C2O2 and C4O4, respectively, however, the differences in their lengths are less pronounced than in thymine itself (Portalone et al., 1999). The existence of C O groups of different lengths can be easily explained by observing the respective crystal structures. In thymine (Portalone et al., 1999), as well as in the crystals of (I), centrosymmetric dimers are formed via N3—H3···O2C2 hydrogen bonds. The second carbonyl group, C4O4, is in (I) involved in a weak C—H···O hydrogen bond only (Table 1), and for this reason the C4O4 bond is shorter. This geometrical perturbation is mainly due to self-association and confirms the fundamental role of conjugative stabilization of the intermolecular hydrogen bonding.

Intermolecular hydrogen bonds, the main driving force for crystal packing, connect the molecules of (I) into infinite tapes. Only inversion centres participate in the formation of the tape and no other symmetry operations are used in creating this principal packing motif. This mimics the packing of thymine molecules in the solid state (Portalone et al., 1999). In (I), one type of centrosymmetric dimers is formed via almost linear and quite strong N3—H3···O2i hydrogen bonds (symmetry codes as in Table 1 and Fig. 2), which form eight-membered rings. The same O2 atoms participate in bifurcated hydrogen bonds to the amide groups, O2ii···H12B—N12, thus forming the second kind of centrosymmetric dimer, featuring 14 (13?)-membered rings. The molecular tapes also contain weak C—H···O hydrogen bonds (Fig. 2 and Table 1), but these are secondary interactions only. The molecular tapes in the crystal of (I) are further connected into a three-dimensional structure by weak bifurcated hydrogen bonds to O12; N12—H12A···O12iii and C6—H6···O12iv (Table 1 and Fig. 2). No carbonyl–carbonyl interactions have been found.

There are also some similarities in the crystal-packing modes of (I) and two imidazole derivatives, namely 2-methyl-4-nitro-1-phenyl-1H-imidazole-5-carbonitrile, (II), and 1-(4-chlorophenyl)-2-methyl-4-nitro-1H-imidazole-5-carbonitrile, (III) (Kubicki, 2004). These two imidazole derivatives likewise form infinite tapes in their crystal structures using two consecutive inversion centres in space group P21/n, and the molecular conformations in the crystals are similar to that in (I), with dihedral angles between the two planar fragments of 76.29 (4) and 87.64 (6)° in (II) and (III), respectively. On the other hand, the differences between the crystal structures of (I), (II) and (III) are determined by the intermolecular interactions. There are intermolecular hydrogen bonds in (I); in (II) dipole–dipole interactions between antiparallel cyano groups connect molecules into centrosymmetric dimers; while in (III), the dimers are connected by CN···Cl—C interactions together with weak C—H···O(N) hydrogen bonds. All this diversity of interactions can be understood on the basis of a simple electrostatic model; moreover, the halogen bond is an analogue of the hydrogen bond (Legon, 1999).

Computing details top

Data collection: CrysAlis CCD (Oxford Diffraction, 2004); cell refinement: CrysAlis CCD; data reduction: CrysAlis RED (Oxford Diffraction, 2004); program(s) used to solve structure: SHELXS97 (Sheldrick, 1990); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: Stereochemical Workstation Operation Manual (Siemens, 1989); software used to prepare material for publication: SHELXL97.

Figures top
[Figure 1] Fig. 1. A view of the molecule of (1-thyminyl)acetamide. Displacement ellipsoids are drawn at the %????? probability level and H atoms are depicted as spheres of arbitrary radii.
[Figure 2] Fig. 2. The molecular tape connected by hydrogen bonds (dashed lines), viewed approximately along the [100] direction. [Symmetry codes: (i) x - 1, y, z; (ii) x + 1, y, z; (iii) -x, -y + 1, -z + 1; (iv) -x + 1, -y + 1, -z + 1; (v) -x, y + 1/2, -z + 1/2.]
(1-thyminyl)acetamide(5-methyl-2,4-dioxo-1,2,3,4- tetrahydropyrimidin-1-yl)acetamide top
Crystal data top
C7H9N3O3F(000) = 384
Mr = 183.17Dx = 1.556 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 35533 reflections
a = 8.0388 (1) Åθ = 3.5–30°
b = 6.1476 (1) ŵ = 0.12 mm1
c = 15.8390 (1) ÅT = 100 K
β = 92.923 (1)°Prism, colourless
V = 781.74 (2) Å30.55 × 0.25 × 0.10 mm
Z = 4
Data collection top
Kuma KM-4 CCD four-circle
diffractometer
2262 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tubeRint = 0.056
Graphite monochromatorθmax = 30.0°, θmin = 3.5°
ω scansh = 1111
30900 measured reflectionsk = 88
2287 independent reflectionsl = 2222
Refinement top
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.036All H-atom parameters refined
wR(F2) = 0.094 w = 1/[σ2(Fo2) + (0.0479P)2 + 0.3534P]
where P = (Fo2 + 2Fc2)/3
S = 1.06(Δ/σ)max < 0.001
2287 reflectionsΔρmax = 0.42 e Å3
155 parametersΔρmin = 0.27 e Å3
0 restraintsExtinction correction: SHELXL97, Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
Primary atom site location: structure-invariant direct methodsExtinction coefficient: 0.021 (4)
Crystal data top
C7H9N3O3V = 781.74 (2) Å3
Mr = 183.17Z = 4
Monoclinic, P21/cMo Kα radiation
a = 8.0388 (1) ŵ = 0.12 mm1
b = 6.1476 (1) ÅT = 100 K
c = 15.8390 (1) Å0.55 × 0.25 × 0.10 mm
β = 92.923 (1)°
Data collection top
Kuma KM-4 CCD four-circle
diffractometer
2262 reflections with I > 2σ(I)
30900 measured reflectionsRint = 0.056
2287 independent reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0360 restraints
wR(F2) = 0.094All H-atom parameters refined
S = 1.06Δρmax = 0.42 e Å3
2287 reflectionsΔρmin = 0.27 e Å3
155 parameters
Special details top

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 (Å2) top
xyzUiso*/Ueq
N10.20032 (9)0.17468 (12)0.40450 (5)0.01045 (16)
C110.02801 (10)0.25259 (15)0.40099 (5)0.01133 (17)
H11A0.0418 (17)0.134 (2)0.3818 (9)0.016 (3)*
H11B0.0029 (16)0.298 (2)0.4575 (8)0.015 (3)*
C120.00604 (10)0.43807 (14)0.33698 (5)0.01108 (17)
O120.09113 (8)0.44495 (11)0.27405 (4)0.01392 (16)
N120.11265 (10)0.58350 (14)0.35248 (5)0.01517 (17)
H12A0.1341 (19)0.690 (3)0.3143 (10)0.024 (4)*
H12B0.167 (2)0.573 (3)0.3995 (11)0.034 (4)*
C20.31875 (10)0.30289 (14)0.44480 (5)0.00998 (17)
O20.28183 (8)0.47192 (11)0.48271 (4)0.01277 (15)
N30.48048 (8)0.23458 (12)0.44053 (5)0.01036 (16)
H30.5603 (19)0.322 (3)0.4685 (9)0.025 (4)*
C40.53446 (10)0.04796 (14)0.39965 (5)0.01024 (17)
O40.68339 (8)0.00082 (12)0.40276 (4)0.01429 (16)
C50.40329 (10)0.07795 (14)0.35600 (5)0.01090 (17)
C510.45245 (11)0.27430 (15)0.30725 (6)0.01506 (18)
H51A0.5310 (19)0.232 (3)0.2654 (10)0.026 (4)*
H51B0.5117 (18)0.382 (3)0.3456 (9)0.022 (3)*
H51C0.3525 (19)0.345 (3)0.2787 (9)0.024 (4)*
C60.24417 (10)0.00998 (14)0.36052 (5)0.01097 (17)
H60.1519 (17)0.084 (2)0.3324 (9)0.017 (3)*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
N10.0069 (3)0.0115 (3)0.0129 (3)0.0002 (2)0.0003 (2)0.0010 (2)
C110.0061 (3)0.0140 (4)0.0139 (4)0.0004 (3)0.0006 (3)0.0007 (3)
C120.0077 (3)0.0128 (4)0.0126 (4)0.0008 (3)0.0011 (3)0.0009 (3)
O120.0117 (3)0.0171 (3)0.0132 (3)0.0005 (2)0.0025 (2)0.0002 (2)
N120.0124 (3)0.0170 (4)0.0164 (4)0.0046 (3)0.0032 (3)0.0018 (3)
C20.0082 (3)0.0115 (4)0.0102 (3)0.0006 (3)0.0004 (3)0.0014 (3)
O20.0105 (3)0.0125 (3)0.0154 (3)0.0002 (2)0.0013 (2)0.0029 (2)
N30.0069 (3)0.0118 (3)0.0123 (3)0.0009 (2)0.0003 (2)0.0014 (2)
C40.0094 (4)0.0111 (4)0.0104 (3)0.0002 (3)0.0015 (3)0.0016 (3)
O40.0080 (3)0.0168 (3)0.0182 (3)0.0011 (2)0.0017 (2)0.0003 (2)
C50.0105 (4)0.0107 (4)0.0115 (3)0.0007 (3)0.0007 (3)0.0001 (3)
C510.0139 (4)0.0128 (4)0.0186 (4)0.0000 (3)0.0020 (3)0.0037 (3)
C60.0104 (4)0.0110 (4)0.0115 (4)0.0011 (3)0.0007 (3)0.0002 (3)
Geometric parameters (Å, º) top
N1—C21.3686 (11)C2—N31.3711 (10)
N1—C61.3869 (11)N3—C41.3972 (11)
N1—C111.4640 (10)N3—H30.931 (16)
C11—C121.5301 (12)C4—O41.2304 (10)
C11—H11A0.959 (14)C4—C51.4542 (12)
C11—H11B0.981 (13)C5—C61.3510 (11)
C12—O121.2380 (10)C5—C511.4968 (12)
C12—N121.3394 (11)C51—H51A0.974 (16)
N12—H12A0.901 (16)C51—H51B1.003 (15)
N12—H12B0.887 (17)C51—H51C1.002 (15)
C2—O21.2436 (11)C6—H60.961 (14)
C2—N1—C6121.13 (7)C2—N3—C4126.30 (7)
C2—N1—C11117.62 (7)C2—N3—H3115.6 (10)
C6—N1—C11120.86 (7)C4—N3—H3118.1 (10)
N1—C11—C12110.24 (7)O4—C4—N3119.96 (8)
N1—C11—H11A107.5 (8)O4—C4—C5125.04 (8)
C12—C11—H11A108.1 (8)N3—C4—C5115.00 (7)
N1—C11—H11B110.0 (8)C6—C5—C4118.40 (8)
C12—C11—H11B111.5 (8)C6—C5—C51123.53 (8)
H11A—C11—H11B109.5 (11)C4—C5—C51118.06 (7)
O12—C12—N12123.56 (8)C5—C51—H51A109.3 (9)
O12—C12—C11120.60 (8)C5—C51—H51B110.5 (9)
N12—C12—C11115.80 (7)H51A—C51—H51B106.7 (12)
C12—N12—H12A118.4 (10)C5—C51—H51C110.9 (9)
C12—N12—H12B119.7 (11)H51A—C51—H51C110.1 (12)
H12A—N12—H12B122.0 (15)H51B—C51—H51C109.4 (12)
O2—C2—N1121.93 (8)C5—C6—N1123.05 (8)
O2—C2—N3122.00 (8)C5—C6—H6122.6 (8)
N1—C2—N3116.07 (7)N1—C6—H6114.3 (8)
C2—N1—C11—C1274.19 (9)C2—N3—C4—O4177.66 (8)
C6—N1—C11—C1298.82 (9)C2—N3—C4—C52.01 (12)
N1—C11—C12—O1230.62 (11)O4—C4—C5—C6177.72 (8)
N1—C11—C12—N12151.50 (8)N3—C4—C5—C61.93 (11)
C6—N1—C2—O2178.17 (8)O4—C4—C5—C513.23 (13)
C11—N1—C2—O25.18 (12)N3—C4—C5—C51177.12 (7)
C6—N1—C2—N31.52 (12)C4—C5—C6—N10.31 (13)
C11—N1—C2—N3174.50 (7)C51—C5—C6—N1178.68 (8)
O2—C2—N3—C4179.99 (8)C2—N1—C6—C51.53 (13)
N1—C2—N3—C40.31 (12)C11—N1—C6—C5174.29 (8)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N3—H3···O2i0.93 (2)1.93 (2)2.855 (1)173 (1)
N12—H12B···O2ii0.89 (2)2.14 (2)3.024 (1)175 (2)
N12—H12A···O12iii0.90 (2)2.14 (2)3.003 (1)160 (1)
C6—H6···O12iv0.96 (1)2.52 (1)3.362 (1)146 (1)
C11—H11A···O4v0.96 (1)2.40 (1)3.175 (1)138 (1)
Symmetry codes: (i) x+1, y+1, z+1; (ii) x, y+1, z+1; (iii) x, y+1/2, z+1/2; (iv) x, y1/2, z+1/2; (v) x1, y, z.

Experimental details

Crystal data
Chemical formulaC7H9N3O3
Mr183.17
Crystal system, space groupMonoclinic, P21/c
Temperature (K)100
a, b, c (Å)8.0388 (1), 6.1476 (1), 15.8390 (1)
β (°) 92.923 (1)
V3)781.74 (2)
Z4
Radiation typeMo Kα
µ (mm1)0.12
Crystal size (mm)0.55 × 0.25 × 0.10
Data collection
DiffractometerKuma KM-4 CCD four-circle
Absorption correction
No. of measured, independent and
observed [I > 2σ(I)] reflections
30900, 2287, 2262
Rint0.056
(sin θ/λ)max1)0.703
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.036, 0.094, 1.06
No. of reflections2287
No. of parameters155
H-atom treatmentAll H-atom parameters refined
Δρmax, Δρmin (e Å3)0.42, 0.27

Computer programs: CrysAlis CCD (Oxford Diffraction, 2004), CrysAlis CCD, CrysAlis RED (Oxford Diffraction, 2004), SHELXS97 (Sheldrick, 1990), SHELXL97 (Sheldrick, 1997), Stereochemical Workstation Operation Manual (Siemens, 1989), SHELXL97.

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N3—H3···O2i0.93 (2)1.93 (2)2.855 (1)173 (1)
N12—H12B···O2ii0.89 (2)2.14 (2)3.024 (1)175 (2)
N12—H12A···O12iii0.90 (2)2.14 (2)3.003 (1)160 (1)
C6—H6···O12iv0.96 (1)2.52 (1)3.362 (1)146 (1)
C11—H11A···O4v0.96 (1)2.40 (1)3.175 (1)138 (1)
Symmetry codes: (i) x+1, y+1, z+1; (ii) x, y+1, z+1; (iii) x, y+1/2, z+1/2; (iv) x, y1/2, z+1/2; (v) x1, y, z.
 

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