Supporting information
Crystallographic Information File (CIF) https://doi.org/10.1107/S0108270106015460/gd3012sup1.cif | |
Structure factor file (CIF format) https://doi.org/10.1107/S0108270106015460/gd3012Isup2.hkl |
CCDC reference: 612461
The synthesis of (1-thyminyl)acetonitrile was described by Spychała (1997). Crystals suitable for data collection were grown from hot water by slow cooling.
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.
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 C═O bond lengths, 1.2436 (11) Å and 1.2304 (10) Å for C2═O2 and C4═O4, 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···O2═C2 hydrogen bonds. The second carbonyl group, C4═O4, is in (I) involved in a weak C—H···O hydrogen bond only (Table 1), and for this reason the C4═O4 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 C≡N···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).
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.
C7H9N3O3 | F(000) = 384 |
Mr = 183.17 | Dx = 1.556 Mg m−3 |
Monoclinic, P21/c | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: -P 2ybc | Cell parameters from 35533 reflections |
a = 8.0388 (1) Å | θ = 3.5–30° |
b = 6.1476 (1) Å | µ = 0.12 mm−1 |
c = 15.8390 (1) Å | T = 100 K |
β = 92.923 (1)° | Prism, colourless |
V = 781.74 (2) Å3 | 0.55 × 0.25 × 0.10 mm |
Z = 4 |
Kuma KM-4 CCD four-circle diffractometer | 2262 reflections with I > 2σ(I) |
Radiation source: fine-focus sealed tube | Rint = 0.056 |
Graphite monochromator | θmax = 30.0°, θmin = 3.5° |
ω scans | h = −11→11 |
30900 measured reflections | k = −8→8 |
2287 independent reflections | l = −22→22 |
Refinement on F2 | Secondary atom site location: difference Fourier map |
Least-squares matrix: full | Hydrogen site location: inferred from neighbouring sites |
R[F2 > 2σ(F2)] = 0.036 | All 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 reflections | Δρmax = 0.42 e Å−3 |
155 parameters | Δρmin = −0.27 e Å−3 |
0 restraints | Extinction correction: SHELXL97, Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4 |
Primary atom site location: structure-invariant direct methods | Extinction coefficient: 0.021 (4) |
C7H9N3O3 | V = 781.74 (2) Å3 |
Mr = 183.17 | Z = 4 |
Monoclinic, P21/c | Mo Kα radiation |
a = 8.0388 (1) Å | µ = 0.12 mm−1 |
b = 6.1476 (1) Å | T = 100 K |
c = 15.8390 (1) Å | 0.55 × 0.25 × 0.10 mm |
β = 92.923 (1)° |
Kuma KM-4 CCD four-circle diffractometer | 2262 reflections with I > 2σ(I) |
30900 measured reflections | Rint = 0.056 |
2287 independent reflections |
R[F2 > 2σ(F2)] = 0.036 | 0 restraints |
wR(F2) = 0.094 | All H-atom parameters refined |
S = 1.06 | Δρmax = 0.42 e Å−3 |
2287 reflections | Δρmin = −0.27 e Å−3 |
155 parameters |
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. |
x | y | z | Uiso*/Ueq | ||
N1 | 0.20032 (9) | 0.17468 (12) | 0.40450 (5) | 0.01045 (16) | |
C11 | 0.02801 (10) | 0.25259 (15) | 0.40099 (5) | 0.01133 (17) | |
H11A | −0.0418 (17) | 0.134 (2) | 0.3818 (9) | 0.016 (3)* | |
H11B | −0.0029 (16) | 0.298 (2) | 0.4575 (8) | 0.015 (3)* | |
C12 | 0.00604 (10) | 0.43807 (14) | 0.33698 (5) | 0.01108 (17) | |
O12 | 0.09113 (8) | 0.44495 (11) | 0.27405 (4) | 0.01392 (16) | |
N12 | −0.11265 (10) | 0.58350 (14) | 0.35248 (5) | 0.01517 (17) | |
H12A | −0.1341 (19) | 0.690 (3) | 0.3143 (10) | 0.024 (4)* | |
H12B | −0.167 (2) | 0.573 (3) | 0.3995 (11) | 0.034 (4)* | |
C2 | 0.31875 (10) | 0.30289 (14) | 0.44480 (5) | 0.00998 (17) | |
O2 | 0.28183 (8) | 0.47192 (11) | 0.48271 (4) | 0.01277 (15) | |
N3 | 0.48048 (8) | 0.23458 (12) | 0.44053 (5) | 0.01036 (16) | |
H3 | 0.5603 (19) | 0.322 (3) | 0.4685 (9) | 0.025 (4)* | |
C4 | 0.53446 (10) | 0.04796 (14) | 0.39965 (5) | 0.01024 (17) | |
O4 | 0.68339 (8) | 0.00082 (12) | 0.40276 (4) | 0.01429 (16) | |
C5 | 0.40329 (10) | −0.07795 (14) | 0.35600 (5) | 0.01090 (17) | |
C51 | 0.45245 (11) | −0.27430 (15) | 0.30725 (6) | 0.01506 (18) | |
H51A | 0.5310 (19) | −0.232 (3) | 0.2654 (10) | 0.026 (4)* | |
H51B | 0.5117 (18) | −0.382 (3) | 0.3456 (9) | 0.022 (3)* | |
H51C | 0.3525 (19) | −0.345 (3) | 0.2787 (9) | 0.024 (4)* | |
C6 | 0.24417 (10) | −0.00998 (14) | 0.36052 (5) | 0.01097 (17) | |
H6 | 0.1519 (17) | −0.084 (2) | 0.3324 (9) | 0.017 (3)* |
U11 | U22 | U33 | U12 | U13 | U23 | |
N1 | 0.0069 (3) | 0.0115 (3) | 0.0129 (3) | −0.0002 (2) | −0.0003 (2) | −0.0010 (2) |
C11 | 0.0061 (3) | 0.0140 (4) | 0.0139 (4) | 0.0004 (3) | 0.0006 (3) | 0.0007 (3) |
C12 | 0.0077 (3) | 0.0128 (4) | 0.0126 (4) | −0.0008 (3) | −0.0011 (3) | −0.0009 (3) |
O12 | 0.0117 (3) | 0.0171 (3) | 0.0132 (3) | 0.0005 (2) | 0.0025 (2) | 0.0002 (2) |
N12 | 0.0124 (3) | 0.0170 (4) | 0.0164 (4) | 0.0046 (3) | 0.0032 (3) | 0.0018 (3) |
C2 | 0.0082 (3) | 0.0115 (4) | 0.0102 (3) | −0.0006 (3) | 0.0004 (3) | 0.0014 (3) |
O2 | 0.0105 (3) | 0.0125 (3) | 0.0154 (3) | −0.0002 (2) | 0.0013 (2) | −0.0029 (2) |
N3 | 0.0069 (3) | 0.0118 (3) | 0.0123 (3) | −0.0009 (2) | −0.0003 (2) | −0.0014 (2) |
C4 | 0.0094 (4) | 0.0111 (4) | 0.0104 (3) | −0.0002 (3) | 0.0015 (3) | 0.0016 (3) |
O4 | 0.0080 (3) | 0.0168 (3) | 0.0182 (3) | 0.0011 (2) | 0.0017 (2) | −0.0003 (2) |
C5 | 0.0105 (4) | 0.0107 (4) | 0.0115 (3) | −0.0007 (3) | 0.0007 (3) | 0.0001 (3) |
C51 | 0.0139 (4) | 0.0128 (4) | 0.0186 (4) | 0.0000 (3) | 0.0020 (3) | −0.0037 (3) |
C6 | 0.0104 (4) | 0.0110 (4) | 0.0115 (4) | −0.0011 (3) | −0.0007 (3) | −0.0002 (3) |
N1—C2 | 1.3686 (11) | C2—N3 | 1.3711 (10) |
N1—C6 | 1.3869 (11) | N3—C4 | 1.3972 (11) |
N1—C11 | 1.4640 (10) | N3—H3 | 0.931 (16) |
C11—C12 | 1.5301 (12) | C4—O4 | 1.2304 (10) |
C11—H11A | 0.959 (14) | C4—C5 | 1.4542 (12) |
C11—H11B | 0.981 (13) | C5—C6 | 1.3510 (11) |
C12—O12 | 1.2380 (10) | C5—C51 | 1.4968 (12) |
C12—N12 | 1.3394 (11) | C51—H51A | 0.974 (16) |
N12—H12A | 0.901 (16) | C51—H51B | 1.003 (15) |
N12—H12B | 0.887 (17) | C51—H51C | 1.002 (15) |
C2—O2 | 1.2436 (11) | C6—H6 | 0.961 (14) |
C2—N1—C6 | 121.13 (7) | C2—N3—C4 | 126.30 (7) |
C2—N1—C11 | 117.62 (7) | C2—N3—H3 | 115.6 (10) |
C6—N1—C11 | 120.86 (7) | C4—N3—H3 | 118.1 (10) |
N1—C11—C12 | 110.24 (7) | O4—C4—N3 | 119.96 (8) |
N1—C11—H11A | 107.5 (8) | O4—C4—C5 | 125.04 (8) |
C12—C11—H11A | 108.1 (8) | N3—C4—C5 | 115.00 (7) |
N1—C11—H11B | 110.0 (8) | C6—C5—C4 | 118.40 (8) |
C12—C11—H11B | 111.5 (8) | C6—C5—C51 | 123.53 (8) |
H11A—C11—H11B | 109.5 (11) | C4—C5—C51 | 118.06 (7) |
O12—C12—N12 | 123.56 (8) | C5—C51—H51A | 109.3 (9) |
O12—C12—C11 | 120.60 (8) | C5—C51—H51B | 110.5 (9) |
N12—C12—C11 | 115.80 (7) | H51A—C51—H51B | 106.7 (12) |
C12—N12—H12A | 118.4 (10) | C5—C51—H51C | 110.9 (9) |
C12—N12—H12B | 119.7 (11) | H51A—C51—H51C | 110.1 (12) |
H12A—N12—H12B | 122.0 (15) | H51B—C51—H51C | 109.4 (12) |
O2—C2—N1 | 121.93 (8) | C5—C6—N1 | 123.05 (8) |
O2—C2—N3 | 122.00 (8) | C5—C6—H6 | 122.6 (8) |
N1—C2—N3 | 116.07 (7) | N1—C6—H6 | 114.3 (8) |
C2—N1—C11—C12 | 74.19 (9) | C2—N3—C4—O4 | −177.66 (8) |
C6—N1—C11—C12 | −98.82 (9) | C2—N3—C4—C5 | 2.01 (12) |
N1—C11—C12—O12 | 30.62 (11) | O4—C4—C5—C6 | 177.72 (8) |
N1—C11—C12—N12 | −151.50 (8) | N3—C4—C5—C6 | −1.93 (11) |
C6—N1—C2—O2 | 178.17 (8) | O4—C4—C5—C51 | −3.23 (13) |
C11—N1—C2—O2 | 5.18 (12) | N3—C4—C5—C51 | 177.12 (7) |
C6—N1—C2—N3 | −1.52 (12) | C4—C5—C6—N1 | 0.31 (13) |
C11—N1—C2—N3 | −174.50 (7) | C51—C5—C6—N1 | −178.68 (8) |
O2—C2—N3—C4 | −179.99 (8) | C2—N1—C6—C5 | 1.53 (13) |
N1—C2—N3—C4 | −0.31 (12) | C11—N1—C6—C5 | 174.29 (8) |
D—H···A | D—H | H···A | D···A | D—H···A |
N3—H3···O2i | 0.93 (2) | 1.93 (2) | 2.855 (1) | 173 (1) |
N12—H12B···O2ii | 0.89 (2) | 2.14 (2) | 3.024 (1) | 175 (2) |
N12—H12A···O12iii | 0.90 (2) | 2.14 (2) | 3.003 (1) | 160 (1) |
C6—H6···O12iv | 0.96 (1) | 2.52 (1) | 3.362 (1) | 146 (1) |
C11—H11A···O4v | 0.96 (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, y−1/2, −z+1/2; (v) x−1, y, z. |
Experimental details
Crystal data | |
Chemical formula | C7H9N3O3 |
Mr | 183.17 |
Crystal system, space group | Monoclinic, P21/c |
Temperature (K) | 100 |
a, b, c (Å) | 8.0388 (1), 6.1476 (1), 15.8390 (1) |
β (°) | 92.923 (1) |
V (Å3) | 781.74 (2) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 0.12 |
Crystal size (mm) | 0.55 × 0.25 × 0.10 |
Data collection | |
Diffractometer | Kuma KM-4 CCD four-circle |
Absorption correction | – |
No. of measured, independent and observed [I > 2σ(I)] reflections | 30900, 2287, 2262 |
Rint | 0.056 |
(sin θ/λ)max (Å−1) | 0.703 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.036, 0.094, 1.06 |
No. of reflections | 2287 |
No. of parameters | 155 |
H-atom treatment | All H-atom parameters refined |
Δρmax, Δρmin (e Å−3) | 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.
D—H···A | D—H | H···A | D···A | D—H···A |
N3—H3···O2i | 0.93 (2) | 1.93 (2) | 2.855 (1) | 173 (1) |
N12—H12B···O2ii | 0.89 (2) | 2.14 (2) | 3.024 (1) | 175 (2) |
N12—H12A···O12iii | 0.90 (2) | 2.14 (2) | 3.003 (1) | 160 (1) |
C6—H6···O12iv | 0.96 (1) | 2.52 (1) | 3.362 (1) | 146 (1) |
C11—H11A···O4v | 0.96 (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, y−1/2, −z+1/2; (v) x−1, y, z. |
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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 C═O bond lengths, 1.2436 (11) Å and 1.2304 (10) Å for C2═O2 and C4═O4, 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···O2═C2 hydrogen bonds. The second carbonyl group, C4═O4, is in (I) involved in a weak C—H···O hydrogen bond only (Table 1), and for this reason the C4═O4 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 C≡N···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).