
![[triple bond]](/logos/entities/z-tbnd_rmgif.gif)


Supporting information
![]() | Crystallographic Information File (CIF) https://doi.org/10.1107/S0108270104003294/gd1304sup1.cif |
![]() | Structure factor file (CIF format) https://doi.org/10.1107/S0108270104003294/gd1304Isup2.hkl |
![]() | Structure factor file (CIF format) https://doi.org/10.1107/S0108270104003294/gd1304IIsup3.hkl |
CCDC references: 237936; 237937
The method of synthesis of (I) and (II) was described by Salwińska & Suwiński (1990) and Suwiński et al. (1994). Crystals suitable for data collection were grown from a methanol solution.
The positional parameters of H atoms in aryl groups were refined isotropically, giving C—H distances in the range 0.89 (2)–0.97 (3) Å; methyl H atoms were treated as riding, with C—H distances of 0.96 Å.
Weak intermolecular interactions play decisive role in the determination of three-dimensional structure of molecular crystals. By far the most important – and best known – are hydrogen bonds, but in the absence of strong hydrogen-bond donors or acceptors (or sometimes in spite of their presence) other weak interactions stabilize certain structures. The list of these interactions is long and still growing.
Among these, the attractive interaction between a carbon-bound halogen and atoms having electron lone pairs has been known for a long time (Hassel & Rømming, 1962; Hassel, 1970). This interaction has been termed `halogen bonding' (Dumas et al., 1983; Legon, 1998) in order to stress the analogy with hydrogen bonding [for recent reviews see, for example, Legon (1999), Metrangolo & Resnati (2001) and Metrangolo et al. (2003)]. The reorganization of electron-density distribution connected with this interaction is directed from a Lewis base electron-donor site to the halogen atom, which acts as a Lewis acid. The acidity scale I>Br>Cl (for fluorine there is no detectable tendency to form this type of interaction) was established on the basis of Cambridge Structural Database (CSD; Allen, 2002) studies (Lommerse et al., 1996) and quantum-chemical calculations (Valerio et al., 2000). A special case of this interaction involves the cyano group as an electron donor. The existence of short C≡ N···X—C contacts was postulated over 40 years ago (Hassel & Rømming, 1962) and confirmed by the structures of some simple cyano–halogen compounds (Witt et al., 1972). The role of the cyano–halogen interactions in the crystal structures of 4-halobenzonitriles was described by Desiraju & Harlow (1989), and C≡N···Cl—C halogen bonds were used as the supramolecular synthon [as defined by Desiraju (1995)] to create linear zigzag arrays of flat molecules (molecular tapes; Reddy et al., 1993a). These contacts were also identified in the series of tetrachlorodicyanobenzenes (Britton, 2002, and references therein).
In addition, the cyano group can accept hydrogen bonds (Ziao et al., 2001) and it can be involved in dipole–dipole interactions, analogous to the carbonyl···carbonyl interactions that were found to be able to compete successfully with hydrogen bonds (Allen et al., 1998).
In the course of studies of weak interactions in nitroimidazoles (Kubicki et al., 2001, 2002), the crystal structures of two closely related 5-cyano derivatives have been determined, namely 1-phenyl-2-methyl-4-nitro-5-cyanoimidazole, (I), and 1-(4'-chlorophenyl)-2-methyl-4-nitro-5-cyanoimidazole, (II). Because of the lack of strong hydrogen-bond donors, these compounds offer the opportunity of comparing the weak interactions described above.
Figs. 1 and 2 show the anisotropic displacement-ellipsoid representations of the molecules of (I) and (II), respectively. The bond lengths and angles are almost identical; the only – and obvious – differences are connected to the presence of the Cl substituent in (II). This substituent causes modest changes in the intra-annular bond angles of the benzene ring, in general agreement with those described by Domenicano & Murray-Rust (1979) for monosubstituted benzene derivatives; in the chloro-derivative (II), the angle at the site of substitution (C13—C14—C15) is larger and the two adjacent angles (C12—C13—C14 and C14—C15—C16) are smaller than the equivalent angles in (I).
The conformations of (I) and (II) are slightly different. The dihedral angles involving the three effectively planar fragments, viz. the imidazole ring (A), the benzene ring (B) and the nitro group (C), are larger in (II); the angle between planes A and B is 87.64 (6)° in (II) and 76.29 (4)° in (I), and the angle between planes A and C is 7.65 (2) in (II) and 0.59 (13) in (I).
In the crystal structure of (I), relatively short contacts exist between antiparallel C≡N groups from molecules connected (related?) by a center of inversion. The distance between the mid-points of these bonds is 3.271 (2) Å and the C5—C51···N51 angle is 82.9 (1)°. These dipole···dipole interactions lead to the formation of centrosymmetric dimers in (I). The only other intermolecular interaction that plays role in the crystal packing is the weak C12—H12···O41 hydrogen bond, which also closes the dimers related by another center of inversion (Fig. 1).
In (II), the presence of the Cl atom changes the hierarchy of intermolecular interactions. In this case, the main driving force of crystal packing is the C—Cl···N≡C interactions, which also close the centrosymmetric dimers (Fig. 2). The Cl···N distance is short but typical for this kind of interaction [3.250 (2) Å], and the linearity of the C—Cl···N contact [168.30 (8)°] testifies to the proposed mechanism of the charge donation (the donation of the lone pair into the σ antibonding orbital of C—X). The C—H···N hydrogen bonds between neighboring molecules (connected by another center of inversion) also take part in the crystal packing (Fig. 2).
There are some similarities in the crystal-packing modes of (I) and (II). In both cases, the structure consists of tapes of molecules connected by alternating pairs of weak interactions [~dipole···dipole ~ C—H···O ~in (I) and ~C≡N···Cl—C ~C—H···N ~in (II)], and these tapes utilize the consecutive centers of inversion. No other symmetry elements are used in creating the principal packing motifs, even though the space group (P21/n) contains such elements.
Data collection: CrysAlis CCD (Oxford Diffraction, 2002) for (I). For both compounds, cell refinement: CrysAlis CCD; data reduction: CrysAlis RED (Oxford Diffraction, 2002); program(s) used to solve structure: SHELXS97 (Sheldrick, 1990); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997).
C11H8N4O2 | F(000) = 472 |
Mr = 228.21 | Dx = 1.402 Mg m−3 |
Monoclinic, P21/n | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: -P 2yn | Cell parameters from 2418 reflections |
a = 9.8976 (9) Å | θ = 3–21° |
b = 9.6168 (9) Å | µ = 0.10 mm−1 |
c = 11.670 (1) Å | T = 293 K |
β = 103.313 (7)° | Prism, colourless |
V = 1080.94 (17) Å3 | 0.3 × 0.25 × 0.15 mm |
Z = 4 |
KUMA KM-4 CCD four-circle diffractometer | 1380 reflections with I > 2σ(I) |
Radiation source: fine-focus sealed tube | Rint = 0.027 |
Graphite monochromator | θmax = 29.3°, θmin = 4.7° |
ω scan | h = −13→11 |
6917 measured reflections | k = −11→13 |
2708 independent reflections | l = −14→15 |
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)] = 0.039 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.093 | H atoms treated by a mixture of independent and constrained refinement |
S = 0.91 | w = 1/[σ2(Fo2) + (0.04P)2] where P = (Fo2 + 2Fc2)/3 |
2708 reflections | (Δ/σ)max = 0.003 |
176 parameters | Δρmax = 0.11 e Å−3 |
0 restraints | Δρmin = −0.18 e Å−3 |
C11H8N4O2 | V = 1080.94 (17) Å3 |
Mr = 228.21 | Z = 4 |
Monoclinic, P21/n | Mo Kα radiation |
a = 9.8976 (9) Å | µ = 0.10 mm−1 |
b = 9.6168 (9) Å | T = 293 K |
c = 11.670 (1) Å | 0.3 × 0.25 × 0.15 mm |
β = 103.313 (7)° |
KUMA KM-4 CCD four-circle diffractometer | 1380 reflections with I > 2σ(I) |
6917 measured reflections | Rint = 0.027 |
2708 independent reflections |
R[F2 > 2σ(F2)] = 0.039 | 0 restraints |
wR(F2) = 0.093 | H atoms treated by a mixture of independent and constrained refinement |
S = 0.91 | Δρmax = 0.11 e Å−3 |
2708 reflections | Δρmin = −0.18 e Å−3 |
176 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 | 0.68836 (11) | 0.07163 (12) | 0.35541 (10) | 0.0422 (3) | |
C11 | 0.72914 (14) | 0.05299 (14) | 0.24477 (12) | 0.0401 (3) | |
C12 | 0.64864 (17) | −0.02692 (16) | 0.15774 (13) | 0.0498 (4) | |
H12 | 0.5670 (16) | −0.0706 (15) | 0.1701 (12) | 0.054 (4)* | |
C13 | 0.68759 (18) | −0.0407 (2) | 0.05250 (15) | 0.0607 (5) | |
H13 | 0.6374 (17) | −0.0988 (17) | −0.0065 (15) | 0.069 (5)* | |
C14 | 0.80361 (18) | 0.02539 (19) | 0.03470 (16) | 0.0618 (5) | |
H14 | 0.8225 (16) | 0.0164 (18) | −0.0381 (17) | 0.080 (6)* | |
C15 | 0.88281 (19) | 0.10485 (19) | 0.12165 (15) | 0.0588 (5) | |
H15 | 0.9612 (18) | 0.1520 (16) | 0.1141 (14) | 0.068 (5)* | |
C16 | 0.84701 (16) | 0.11851 (17) | 0.22847 (15) | 0.0494 (4) | |
H16 | 0.9023 (16) | 0.1678 (14) | 0.2905 (14) | 0.054 (4)* | |
C2 | 0.58798 (14) | 0.15987 (15) | 0.37605 (13) | 0.0464 (4) | |
C21 | 0.50057 (17) | 0.24700 (17) | 0.28327 (15) | 0.0623 (5) | |
H21A | 0.4376 | 0.3009 | 0.3167 | 0.146 (5)* | |
H21B | 0.4488 | 0.1884 | 0.2221 | 0.146 (5)* | |
H21C | 0.5587 | 0.3083 | 0.2508 | 0.146 (5)* | |
N3 | 0.58068 (12) | 0.15680 (13) | 0.48740 (11) | 0.0504 (3) | |
C4 | 0.67827 (15) | 0.06517 (16) | 0.53828 (12) | 0.0467 (4) | |
N4 | 0.70230 (15) | 0.03338 (16) | 0.66203 (12) | 0.0599 (4) | |
O41 | 0.63201 (15) | 0.09102 (14) | 0.72030 (11) | 0.0862 (4) | |
O42 | 0.79373 (14) | −0.05070 (16) | 0.70153 (10) | 0.0839 (4) | |
C5 | 0.74742 (14) | 0.00858 (15) | 0.46121 (12) | 0.0429 (4) | |
C51 | 0.85333 (16) | −0.09359 (17) | 0.47370 (12) | 0.0485 (4) | |
N51 | 0.93848 (15) | −0.17517 (16) | 0.48416 (12) | 0.0680 (4) |
U11 | U22 | U33 | U12 | U13 | U23 | |
N1 | 0.0431 (7) | 0.0448 (7) | 0.0402 (7) | −0.0005 (6) | 0.0128 (5) | −0.0010 (6) |
C11 | 0.0421 (8) | 0.0412 (8) | 0.0380 (8) | 0.0021 (6) | 0.0115 (6) | 0.0018 (6) |
C12 | 0.0445 (9) | 0.0534 (10) | 0.0511 (10) | −0.0031 (8) | 0.0100 (7) | −0.0046 (7) |
C13 | 0.0588 (11) | 0.0735 (13) | 0.0461 (10) | 0.0050 (9) | 0.0042 (8) | −0.0127 (9) |
C14 | 0.0638 (12) | 0.0829 (13) | 0.0420 (10) | 0.0137 (10) | 0.0188 (9) | 0.0035 (9) |
C15 | 0.0542 (10) | 0.0687 (12) | 0.0597 (11) | −0.0004 (9) | 0.0257 (9) | 0.0107 (9) |
C16 | 0.0470 (9) | 0.0531 (10) | 0.0483 (9) | −0.0032 (8) | 0.0114 (8) | −0.0018 (8) |
C2 | 0.0470 (9) | 0.0434 (9) | 0.0519 (10) | −0.0005 (7) | 0.0179 (7) | −0.0020 (7) |
C21 | 0.0643 (11) | 0.0568 (10) | 0.0669 (11) | 0.0157 (9) | 0.0173 (9) | 0.0089 (8) |
N3 | 0.0499 (7) | 0.0541 (8) | 0.0508 (8) | −0.0019 (6) | 0.0192 (6) | −0.0040 (6) |
C4 | 0.0477 (9) | 0.0550 (10) | 0.0392 (8) | −0.0109 (7) | 0.0140 (7) | −0.0018 (7) |
N4 | 0.0580 (10) | 0.0777 (11) | 0.0462 (8) | −0.0130 (8) | 0.0168 (7) | −0.0014 (8) |
O41 | 0.0985 (10) | 0.1148 (11) | 0.0573 (8) | −0.0010 (8) | 0.0428 (7) | −0.0084 (8) |
O42 | 0.0812 (9) | 0.1163 (12) | 0.0531 (8) | 0.0112 (9) | 0.0132 (7) | 0.0181 (7) |
C5 | 0.0412 (8) | 0.0468 (9) | 0.0409 (8) | −0.0050 (7) | 0.0096 (6) | 0.0002 (7) |
C51 | 0.0479 (9) | 0.0529 (10) | 0.0426 (9) | −0.0036 (8) | 0.0063 (7) | 0.0002 (7) |
N51 | 0.0661 (9) | 0.0689 (10) | 0.0644 (10) | 0.0127 (8) | 0.0056 (7) | −0.0014 (8) |
N1—C2 | 1.3695 (17) | C16—H16 | 0.930 (15) |
N1—C5 | 1.3790 (17) | C2—N3 | 1.3183 (17) |
N1—C11 | 1.4499 (17) | C2—C21 | 1.480 (2) |
C11—C12 | 1.3726 (19) | C21—H21A | 0.9600 |
C11—C16 | 1.377 (2) | C21—H21B | 0.9600 |
C12—C13 | 1.376 (2) | C21—H21C | 0.9600 |
C12—H12 | 0.951 (15) | N3—C4 | 1.3408 (18) |
C13—C14 | 1.370 (2) | C4—C5 | 1.3628 (19) |
C13—H13 | 0.935 (17) | C4—N4 | 1.4413 (19) |
C14—C15 | 1.365 (2) | N4—O41 | 1.2131 (16) |
C14—H14 | 0.914 (19) | N4—O42 | 1.2220 (17) |
C15—C16 | 1.379 (2) | C5—C51 | 1.419 (2) |
C15—H15 | 0.920 (17) | C51—N51 | 1.1372 (18) |
C2—N1—C5 | 106.86 (11) | N3—C2—N1 | 111.48 (13) |
C2—N1—C11 | 126.53 (12) | N3—C2—C21 | 125.32 (13) |
C5—N1—C11 | 126.55 (11) | N1—C2—C21 | 123.20 (13) |
C12—C11—C16 | 121.32 (14) | C2—C21—H21A | 109.5 |
C12—C11—N1 | 119.66 (12) | C2—C21—H21B | 109.5 |
C16—C11—N1 | 119.00 (13) | H21A—C21—H21B | 109.5 |
C11—C12—C13 | 118.71 (16) | C2—C21—H21C | 109.5 |
C11—C12—H12 | 120.2 (9) | H21A—C21—H21C | 109.5 |
C13—C12—H12 | 121.1 (9) | H21B—C21—H21C | 109.5 |
C14—C13—C12 | 120.5 (2) | C2—N3—C4 | 104.70 (12) |
C14—C13—H13 | 119.1 (10) | N3—C4—C5 | 112.97 (13) |
C12—C13—H13 | 120.3 (10) | N3—C4—N4 | 121.26 (13) |
C15—C14—C13 | 120.4 (2) | C5—C4—N4 | 125.77 (15) |
C15—C14—H14 | 122.6 (11) | O41—N4—O42 | 124.15 (15) |
C13—C14—H14 | 117.0 (11) | O41—N4—C4 | 118.76 (16) |
C14—C15—C16 | 120.2 (2) | O42—N4—C4 | 117.09 (14) |
C14—C15—H15 | 123.9 (11) | C4—C5—N1 | 103.98 (12) |
C16—C15—H15 | 115.9 (11) | C4—C5—C51 | 132.83 (14) |
C11—C16—C15 | 118.92 (16) | N1—C5—C51 | 123.17 (12) |
C11—C16—H16 | 119.4 (9) | N51—C51—C5 | 179.70 (19) |
C15—C16—H16 | 121.7 (9) | ||
C2—N1—C11—C12 | −78.56 (17) | N1—C2—N3—C4 | 0.09 (16) |
C5—N1—C11—C12 | 104.58 (16) | C21—C2—N3—C4 | −179.67 (14) |
C2—N1—C11—C16 | 100.17 (17) | C2—N3—C4—C5 | −0.46 (16) |
C5—N1—C11—C16 | −76.69 (18) | C2—N3—C4—N4 | 179.88 (12) |
C16—C11—C12—C13 | −0.1 (2) | N3—C4—N4—O41 | 0.2 (2) |
N1—C11—C12—C13 | 178.59 (13) | C5—C4—N4—O41 | −179.43 (14) |
C11—C12—C13—C14 | −0.7 (2) | N3—C4—N4—O42 | −179.59 (14) |
C12—C13—C14—C15 | 0.6 (3) | C5—C4—N4—O42 | 0.8 (2) |
C13—C14—C15—C16 | 0.4 (3) | N3—C4—C5—N1 | 0.63 (16) |
C12—C11—C16—C15 | 1.1 (2) | N4—C4—C5—N1 | −179.73 (12) |
N1—C11—C16—C15 | −177.63 (13) | N3—C4—C5—C51 | −177.70 (14) |
C14—C15—C16—C11 | −1.2 (2) | N4—C4—C5—C51 | 1.9 (3) |
C5—N1—C2—N3 | 0.29 (15) | C2—N1—C5—C4 | −0.53 (14) |
C11—N1—C2—N3 | −177.07 (12) | C11—N1—C5—C4 | 176.83 (12) |
C5—N1—C2—C21 | −179.95 (13) | C2—N1—C5—C51 | 178.01 (13) |
C11—N1—C2—C21 | 2.7 (2) | C11—N1—C5—C51 | −4.6 (2) |
D—H···A | D—H | H···A | D···A | D—H···A |
C12—H12···O41i | 0.95 (2) | 2.59 (2) | 3.456 (2) | 151 (1) |
Symmetry code: (i) −x+1, −y, −z+1. |
C11H7ClN4O2 | F(000) = 536 |
Mr = 262.66 | Dx = 1.464 Mg m−3 |
Monoclinic, P21/n | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: -P 2yn | Cell parameters from 2798 reflections |
a = 12.6819 (16) Å | θ = 3–18° |
b = 6.8018 (11) Å | µ = 0.32 mm−1 |
c = 15.1799 (16) Å | T = 293 K |
β = 114.497 (11)° | Plate, colourless |
V = 1191.5 (3) Å3 | 0.6 × 0.5 × 0.1 mm |
Z = 4 |
KUMA KM-4 CCD four-circle diffractometer | 2968 independent reflections |
Radiation source: fine-focus sealed tube | 1647 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.038 |
ω scan | θmax = 29.3°, θmin = 4.9° |
Absorption correction: multi-scan (SORTAV; Blessing, 1989) | h = −17→15 |
Tmin = 0.889, Tmax = 0.971 | k = −9→6 |
7375 measured reflections | l = −20→20 |
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)] = 0.042 | H atoms treated by a mixture of independent and constrained refinement |
wR(F2) = 0.102 | w = 1/[σ2(Fo2) + (0.045P)2] where P = (Fo2 + 2Fc2)/3 |
S = 0.97 | (Δ/σ)max = 0.001 |
2968 reflections | Δρmax = 0.17 e Å−3 |
182 parameters | Δρmin = −0.21 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: 0.011 (2) |
C11H7ClN4O2 | V = 1191.5 (3) Å3 |
Mr = 262.66 | Z = 4 |
Monoclinic, P21/n | Mo Kα radiation |
a = 12.6819 (16) Å | µ = 0.32 mm−1 |
b = 6.8018 (11) Å | T = 293 K |
c = 15.1799 (16) Å | 0.6 × 0.5 × 0.1 mm |
β = 114.497 (11)° |
KUMA KM-4 CCD four-circle diffractometer | 2968 independent reflections |
Absorption correction: multi-scan (SORTAV; Blessing, 1989) | 1647 reflections with I > 2σ(I) |
Tmin = 0.889, Tmax = 0.971 | Rint = 0.038 |
7375 measured reflections |
R[F2 > 2σ(F2)] = 0.042 | 0 restraints |
wR(F2) = 0.102 | H atoms treated by a mixture of independent and constrained refinement |
S = 0.97 | Δρmax = 0.17 e Å−3 |
2968 reflections | Δρmin = −0.21 e Å−3 |
182 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 | 0.46832 (11) | 0.6630 (2) | 0.67776 (9) | 0.0434 (3) | |
C11 | 0.50749 (14) | 0.6680 (2) | 0.78171 (11) | 0.0412 (4) | |
C12 | 0.60610 (17) | 0.5694 (3) | 0.83926 (13) | 0.0568 (5) | |
H12 | 0.6452 (19) | 0.502 (3) | 0.8121 (15) | 0.069 (6)* | |
C13 | 0.64644 (18) | 0.5812 (3) | 0.93858 (13) | 0.0585 (5) | |
H13 | 0.717 (2) | 0.515 (3) | 0.9801 (18) | 0.086 (7)* | |
C14 | 0.58618 (15) | 0.6907 (2) | 0.97752 (11) | 0.0455 (4) | |
Cl14 | 0.63698 (5) | 0.71140 (8) | 1.10216 (3) | 0.0664 (2) | |
C15 | 0.48501 (17) | 0.7841 (3) | 0.91997 (13) | 0.0553 (5) | |
H15 | 0.4392 (18) | 0.857 (3) | 0.9473 (15) | 0.074 (6)* | |
C16 | 0.44623 (17) | 0.7743 (3) | 0.82106 (13) | 0.0518 (4) | |
H16 | 0.3826 (19) | 0.841 (3) | 0.7848 (16) | 0.070 (6)* | |
C2 | 0.49558 (15) | 0.7966 (3) | 0.62366 (12) | 0.0498 (4) | |
C21 | 0.5734 (2) | 0.9650 (3) | 0.66616 (15) | 0.0724 (6) | |
H21A | 0.6519 | 0.9192 | 0.6975 | 0.121 (6)* | |
H21B | 0.5521 | 1.0291 | 0.7128 | 0.121 (6)* | |
H21C | 0.5668 | 1.0563 | 0.6159 | 0.121 (6)* | |
N3 | 0.44591 (13) | 0.7517 (2) | 0.53080 (10) | 0.0554 (4) | |
C4 | 0.38577 (14) | 0.5863 (3) | 0.52677 (12) | 0.0488 (4) | |
N4 | 0.32041 (14) | 0.4909 (3) | 0.43596 (11) | 0.0599 (4) | |
O41 | 0.32955 (13) | 0.5505 (2) | 0.36420 (9) | 0.0753 (4) | |
O42 | 0.25971 (16) | 0.3541 (3) | 0.43678 (11) | 0.0949 (6) | |
C5 | 0.39676 (14) | 0.5250 (2) | 0.61538 (11) | 0.0449 (4) | |
C51 | 0.35382 (16) | 0.3609 (3) | 0.64710 (13) | 0.0539 (5) | |
N51 | 0.32224 (18) | 0.2276 (3) | 0.67366 (13) | 0.0802 (6) |
U11 | U22 | U33 | U12 | U13 | U23 | |
N1 | 0.0430 (8) | 0.0511 (8) | 0.0326 (7) | −0.0039 (6) | 0.0120 (6) | 0.0026 (6) |
C11 | 0.0416 (9) | 0.0457 (9) | 0.0326 (8) | −0.0030 (7) | 0.0116 (7) | 0.0034 (7) |
C12 | 0.0513 (11) | 0.0714 (13) | 0.0456 (10) | 0.0165 (10) | 0.0180 (9) | 0.0046 (9) |
C13 | 0.0538 (11) | 0.0682 (12) | 0.0422 (10) | 0.0157 (10) | 0.0087 (8) | 0.0078 (9) |
C14 | 0.0528 (10) | 0.0429 (9) | 0.0345 (8) | −0.0070 (8) | 0.0119 (7) | 0.0023 (7) |
Cl14 | 0.0829 (4) | 0.0685 (3) | 0.0350 (2) | −0.0038 (3) | 0.0118 (2) | 0.0012 (2) |
C15 | 0.0573 (11) | 0.0619 (11) | 0.0428 (10) | 0.0092 (9) | 0.0169 (9) | −0.0037 (9) |
C16 | 0.0482 (10) | 0.0581 (11) | 0.0400 (9) | 0.0118 (9) | 0.0091 (8) | 0.0012 (8) |
C2 | 0.0496 (10) | 0.0570 (10) | 0.0373 (9) | −0.0077 (8) | 0.0125 (7) | 0.0072 (7) |
C21 | 0.0798 (14) | 0.0720 (13) | 0.0528 (11) | −0.0289 (11) | 0.0150 (10) | 0.0049 (10) |
N3 | 0.0544 (9) | 0.0680 (10) | 0.0349 (8) | −0.0095 (8) | 0.0097 (6) | 0.0071 (7) |
C4 | 0.0431 (9) | 0.0605 (11) | 0.0361 (9) | −0.0036 (8) | 0.0097 (7) | −0.0007 (8) |
N4 | 0.0548 (9) | 0.0760 (11) | 0.0392 (9) | −0.0057 (9) | 0.0098 (7) | −0.0029 (8) |
O41 | 0.0754 (10) | 0.1053 (12) | 0.0353 (7) | −0.0050 (8) | 0.0132 (6) | −0.0005 (7) |
O42 | 0.1028 (12) | 0.1071 (13) | 0.0618 (10) | −0.0528 (11) | 0.0211 (9) | −0.0194 (8) |
C5 | 0.0406 (9) | 0.0529 (10) | 0.0384 (9) | −0.0058 (8) | 0.0135 (7) | −0.0012 (7) |
C51 | 0.0537 (11) | 0.0610 (12) | 0.0423 (9) | −0.0105 (9) | 0.0153 (8) | −0.0021 (9) |
N51 | 0.0887 (14) | 0.0836 (13) | 0.0651 (11) | −0.0305 (11) | 0.0285 (10) | 0.0002 (10) |
N1—C2 | 1.362 (2) | C16—H16 | 0.89 (2) |
N1—C5 | 1.374 (2) | C2—N3 | 1.319 (2) |
N1—C11 | 1.445 (2) | C2—C21 | 1.475 (3) |
C11—C16 | 1.367 (3) | C21—H21A | 0.9600 |
C11—C12 | 1.368 (2) | C21—H21B | 0.9600 |
C12—C13 | 1.379 (3) | C21—H21C | 0.9600 |
C12—H12 | 0.89 (2) | N3—C4 | 1.346 (2) |
C13—C14 | 1.365 (3) | C4—C5 | 1.359 (2) |
C13—H13 | 0.97 (3) | C4—N4 | 1.435 (2) |
C14—C15 | 1.372 (3) | N4—O42 | 1.211 (2) |
C14—Cl14 | 1.7333 (17) | N4—O41 | 1.212 (2) |
C15—C16 | 1.374 (3) | C5—C51 | 1.411 (3) |
C15—H15 | 0.98 (2) | C51—N51 | 1.131 (2) |
C2—N1—C5 | 107.49 (13) | N3—C2—N1 | 111.21 (15) |
C2—N1—C11 | 125.77 (13) | N3—C2—C21 | 125.70 (16) |
C5—N1—C11 | 126.74 (13) | N1—C2—C21 | 123.07 (15) |
C16—C11—C12 | 121.00 (16) | C2—C21—H21A | 109.5 |
C16—C11—N1 | 119.30 (15) | C2—C21—H21B | 109.5 |
C12—C11—N1 | 119.68 (16) | H21A—C21—H21B | 109.5 |
C11—C12—C13 | 119.75 (19) | C2—C21—H21C | 109.5 |
C11—C12—H12 | 119.5 (14) | H21A—C21—H21C | 109.5 |
C13—C12—H12 | 120.7 (14) | H21B—C21—H21C | 109.5 |
C14—C13—C12 | 119.00 (18) | C2—N3—C4 | 104.62 (14) |
C14—C13—H13 | 120.4 (14) | N3—C4—C5 | 112.82 (15) |
C12—C13—H13 | 120.6 (14) | N3—C4—N4 | 120.79 (15) |
C13—C14—C15 | 121.36 (16) | C5—C4—N4 | 126.38 (17) |
C13—C14—Cl14 | 119.72 (14) | O42—N4—O41 | 124.35 (16) |
C15—C14—Cl14 | 118.91 (14) | O42—N4—C4 | 116.99 (16) |
C14—C15—C16 | 119.32 (19) | O41—N4—C4 | 118.66 (17) |
C14—C15—H15 | 121.9 (12) | C4—C5—N1 | 103.86 (14) |
C16—C15—H15 | 118.8 (12) | C4—C5—C51 | 133.21 (16) |
C11—C16—C15 | 119.50 (18) | N1—C5—C51 | 122.90 (14) |
C11—C16—H16 | 122.3 (13) | N51—C51—C5 | 178.2 (2) |
C15—C16—H16 | 118.1 (13) | ||
C2—N1—C11—C16 | 86.5 (2) | C11—N1—C2—C21 | 1.8 (3) |
C5—N1—C11—C16 | −93.0 (2) | N1—C2—N3—C4 | 0.2 (2) |
C2—N1—C11—C12 | −92.4 (2) | C21—C2—N3—C4 | 178.7 (2) |
C5—N1—C11—C12 | 88.1 (2) | C2—N3—C4—C5 | −0.3 (2) |
C16—C11—C12—C13 | −1.8 (3) | C2—N3—C4—N4 | −179.28 (17) |
N1—C11—C12—C13 | 177.10 (17) | N3—C4—N4—O42 | −173.07 (19) |
C11—C12—C13—C14 | 0.5 (3) | C5—C4—N4—O42 | 8.0 (3) |
C12—C13—C14—C15 | 1.9 (3) | N3—C4—N4—O41 | 7.3 (3) |
C12—C13—C14—Cl14 | −178.72 (15) | C5—C4—N4—O41 | −171.58 (18) |
C13—C14—C15—C16 | −2.9 (3) | N3—C4—C5—N1 | 0.2 (2) |
Cl14—C14—C15—C16 | 177.70 (15) | N4—C4—C5—N1 | 179.15 (16) |
C12—C11—C16—C15 | 0.7 (3) | N3—C4—C5—C51 | −177.94 (19) |
N1—C11—C16—C15 | −178.13 (17) | N4—C4—C5—C51 | 1.0 (3) |
C14—C15—C16—C11 | 1.6 (3) | C2—N1—C5—C4 | −0.05 (18) |
C5—N1—C2—N3 | −0.1 (2) | C11—N1—C5—C4 | 179.57 (15) |
C11—N1—C2—N3 | −179.73 (15) | C2—N1—C5—C51 | 178.32 (17) |
C5—N1—C2—C21 | −178.61 (19) | C11—N1—C5—C51 | −2.1 (3) |
D—H···A | D—H | H···A | D···A | D—H···A |
C21—H21A···O41i | 0.96 | 2.61 | 3.392 (3) | 139 |
C21—H21C···N3ii | 0.96 | 2.53 | 3.479 (3) | 171 |
Symmetry codes: (i) x+1/2, −y+3/2, z+1/2; (ii) −x+1, −y+2, −z+1. |
Experimental details
(I) | (II) | |
Crystal data | ||
Chemical formula | C11H8N4O2 | C11H7ClN4O2 |
Mr | 228.21 | 262.66 |
Crystal system, space group | Monoclinic, P21/n | Monoclinic, P21/n |
Temperature (K) | 293 | 293 |
a, b, c (Å) | 9.8976 (9), 9.6168 (9), 11.670 (1) | 12.6819 (16), 6.8018 (11), 15.1799 (16) |
β (°) | 103.313 (7) | 114.497 (11) |
V (Å3) | 1080.94 (17) | 1191.5 (3) |
Z | 4 | 4 |
Radiation type | Mo Kα | Mo Kα |
µ (mm−1) | 0.10 | 0.32 |
Crystal size (mm) | 0.3 × 0.25 × 0.15 | 0.6 × 0.5 × 0.1 |
Data collection | ||
Diffractometer | KUMA KM-4 CCD four-circle diffractometer | KUMA KM-4 CCD four-circle diffractometer |
Absorption correction | – | Multi-scan (SORTAV; Blessing, 1989) |
Tmin, Tmax | – | 0.889, 0.971 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 6917, 2708, 1380 | 7375, 2968, 1647 |
Rint | 0.027 | 0.038 |
(sin θ/λ)max (Å−1) | 0.688 | 0.689 |
Refinement | ||
R[F2 > 2σ(F2)], wR(F2), S | 0.039, 0.093, 0.91 | 0.042, 0.102, 0.97 |
No. of reflections | 2708 | 2968 |
No. of parameters | 176 | 182 |
H-atom treatment | H atoms treated by a mixture of independent and constrained refinement | H atoms treated by a mixture of independent and constrained refinement |
Δρmax, Δρmin (e Å−3) | 0.11, −0.18 | 0.17, −0.21 |
Computer programs: CrysAlis CCD (Oxford Diffraction, 2002), CrysAlis CCD, CrysAlis RED (Oxford Diffraction, 2002), SHELXS97 (Sheldrick, 1990), SHELXL97 (Sheldrick, 1997).
D—H···A | D—H | H···A | D···A | D—H···A |
C12—H12···O41i | 0.95 (2) | 2.59 (2) | 3.456 (2) | 151 (1) |
Symmetry code: (i) −x+1, −y, −z+1. |
D—H···A | D—H | H···A | D···A | D—H···A |
C21—H21A···O41i | 0.96 | 2.61 | 3.392 (3) | 139 |
C21—H21C···N3ii | 0.96 | 2.53 | 3.479 (3) | 171 |
Symmetry codes: (i) x+1/2, −y+3/2, z+1/2; (ii) −x+1, −y+2, −z+1. |
Weak intermolecular interactions play decisive role in the determination of three-dimensional structure of molecular crystals. By far the most important – and best known – are hydrogen bonds, but in the absence of strong hydrogen-bond donors or acceptors (or sometimes in spite of their presence) other weak interactions stabilize certain structures. The list of these interactions is long and still growing.
Among these, the attractive interaction between a carbon-bound halogen and atoms having electron lone pairs has been known for a long time (Hassel & Rømming, 1962; Hassel, 1970). This interaction has been termed `halogen bonding' (Dumas et al., 1983; Legon, 1998) in order to stress the analogy with hydrogen bonding [for recent reviews see, for example, Legon (1999), Metrangolo & Resnati (2001) and Metrangolo et al. (2003)]. The reorganization of electron-density distribution connected with this interaction is directed from a Lewis base electron-donor site to the halogen atom, which acts as a Lewis acid. The acidity scale I>Br>Cl (for fluorine there is no detectable tendency to form this type of interaction) was established on the basis of Cambridge Structural Database (CSD; Allen, 2002) studies (Lommerse et al., 1996) and quantum-chemical calculations (Valerio et al., 2000). A special case of this interaction involves the cyano group as an electron donor. The existence of short C≡ N···X—C contacts was postulated over 40 years ago (Hassel & Rømming, 1962) and confirmed by the structures of some simple cyano–halogen compounds (Witt et al., 1972). The role of the cyano–halogen interactions in the crystal structures of 4-halobenzonitriles was described by Desiraju & Harlow (1989), and C≡N···Cl—C halogen bonds were used as the supramolecular synthon [as defined by Desiraju (1995)] to create linear zigzag arrays of flat molecules (molecular tapes; Reddy et al., 1993a). These contacts were also identified in the series of tetrachlorodicyanobenzenes (Britton, 2002, and references therein).
In addition, the cyano group can accept hydrogen bonds (Ziao et al., 2001) and it can be involved in dipole–dipole interactions, analogous to the carbonyl···carbonyl interactions that were found to be able to compete successfully with hydrogen bonds (Allen et al., 1998).
In the course of studies of weak interactions in nitroimidazoles (Kubicki et al., 2001, 2002), the crystal structures of two closely related 5-cyano derivatives have been determined, namely 1-phenyl-2-methyl-4-nitro-5-cyanoimidazole, (I), and 1-(4'-chlorophenyl)-2-methyl-4-nitro-5-cyanoimidazole, (II). Because of the lack of strong hydrogen-bond donors, these compounds offer the opportunity of comparing the weak interactions described above.
Figs. 1 and 2 show the anisotropic displacement-ellipsoid representations of the molecules of (I) and (II), respectively. The bond lengths and angles are almost identical; the only – and obvious – differences are connected to the presence of the Cl substituent in (II). This substituent causes modest changes in the intra-annular bond angles of the benzene ring, in general agreement with those described by Domenicano & Murray-Rust (1979) for monosubstituted benzene derivatives; in the chloro-derivative (II), the angle at the site of substitution (C13—C14—C15) is larger and the two adjacent angles (C12—C13—C14 and C14—C15—C16) are smaller than the equivalent angles in (I).
The conformations of (I) and (II) are slightly different. The dihedral angles involving the three effectively planar fragments, viz. the imidazole ring (A), the benzene ring (B) and the nitro group (C), are larger in (II); the angle between planes A and B is 87.64 (6)° in (II) and 76.29 (4)° in (I), and the angle between planes A and C is 7.65 (2) in (II) and 0.59 (13) in (I).
In the crystal structure of (I), relatively short contacts exist between antiparallel C≡N groups from molecules connected (related?) by a center of inversion. The distance between the mid-points of these bonds is 3.271 (2) Å and the C5—C51···N51 angle is 82.9 (1)°. These dipole···dipole interactions lead to the formation of centrosymmetric dimers in (I). The only other intermolecular interaction that plays role in the crystal packing is the weak C12—H12···O41 hydrogen bond, which also closes the dimers related by another center of inversion (Fig. 1).
In (II), the presence of the Cl atom changes the hierarchy of intermolecular interactions. In this case, the main driving force of crystal packing is the C—Cl···N≡C interactions, which also close the centrosymmetric dimers (Fig. 2). The Cl···N distance is short but typical for this kind of interaction [3.250 (2) Å], and the linearity of the C—Cl···N contact [168.30 (8)°] testifies to the proposed mechanism of the charge donation (the donation of the lone pair into the σ antibonding orbital of C—X). The C—H···N hydrogen bonds between neighboring molecules (connected by another center of inversion) also take part in the crystal packing (Fig. 2).
There are some similarities in the crystal-packing modes of (I) and (II). In both cases, the structure consists of tapes of molecules connected by alternating pairs of weak interactions [~dipole···dipole ~ C—H···O ~in (I) and ~C≡N···Cl—C ~C—H···N ~in (II)], and these tapes utilize the consecutive centers of inversion. No other symmetry elements are used in creating the principal packing motifs, even though the space group (P21/n) contains such elements.