Acta Cryst. (2008). E64, o967-o968 [ doi:10.1107/S1600536808010179 ]
The crystal structure of the title compound, C7H11N32+·2Cl-, has been determined as part of a project focusing on the ability of the benzamidine system to form strong hydrogen bonds in aqueous media. It is commonly used as a ligand in affinity chromatography for purification and immobilization of enzymes. A twofold rotation axis runs along the axis of the cation. The orientation of the amidinium group with respect to the benzene ring is indicated by the N-C-C-C torsion angle of 40.2 (1)°. In the crystal structure, cations and anions are linked via hydrogen bonds. The chloride anion is surrounded by four ammonium cations in a tetrahedral environment. The aromatic rings of the amidinium cations are ![[pi]](/logos/entities/pi_rmgif.gif)
-stacked, with a centroid-centroid distance of 4.178 (1) Å.
The title compound is commercially available. To purify it, it has been crystallized from a mixture of water and methanol (10:2). The crystals formed over a period of one week.
The H atoms, including those attached to nitrogen atoms, were all located in a difference map, and then repositioned geometrically. The H atoms were initially refined with soft restraints on the bond lengths and angles to regularize their geometry (C—H in the range 0.99-1.00, N—H = 0.85-0.94 Å) and Uiso(H) (in the range 1.3-1.8 times Ueq of the parent atom), after which the positions were refined with riding constraints.
Data collection: CrysAlis CCD (Oxford Diffraction, 2007); cell refinement: CrysAlis RED (Oxford Diffraction, 2007); data reduction: CrysAlis RED (Oxford Diffraction, 2007); program(s) used to solve structure: SIR2004 (Burla et al., 2003); program(s) used to refine structure: CRYSTALS (Betteridge et al., 2003); molecular graphics: CAMERON (Watkin et al., 1996) and Mercury (Macrae et al., 2006); software used to prepare material for publication: CRYSTALS (Betteridge et al., 2003).
![[Figure 1]](./wn2252fig1thm.gif)
| Fig. 1. Representation of the structure of the title compound, with the numbering scheme adopted. The Cl atoms is light-green, the C atom green, the N atoms blue and the H atoms in grey. Displacement ellipsoids are drawn at the 50% probability level [symmetry code: (i) -x, y, -z + 3/2]. |
![[Figure 2]](./wn2252fig2thm.gif)
| Fig. 2. The two-dimensional framework of the title compound, viewed down the a cell direction. |
![[Figure 3]](./wn2252fig3thm.gif)
| Fig. 3. Representation of the hydrogen bonding network between the cations and the chloride anions, giving rise to a pyramidal scaffold architecture. Hydrogen bonds are denoted by dotted lines. |
| C7H11N32+·2Cl– | F000 = 432 |
| Mr = 208.09 | Dx = 1.364 Mg m−3 |
| Monoclinic, C2/c | Mo Kα radiation λ = 0.71073 Å |
| Hall symbol: -C 2yc | Cell parameters from 4424 reflections |
| a = 4.1779 (2) Å | θ = 4–32º |
| b = 20.9388 (10) Å | µ = 0.59 mm−1 |
| c = 11.6260 (5) Å | T = 175 K |
| β = 94.920 (4)º | Stick, colourless |
| V = 1013.30 (8) Å3 | 0.49 × 0.09 × 0.05 mm |
| Z = 4 |
| Oxford Diffraction XCALIBUR diffractometer | 1750 independent reflections |
| Radiation source: Enhance (Mo) X-ray Source | 1144 reflections with I > 2σ(I) |
| Monochromator: graphite | Rint = 0.018 |
| Detector resolution: 16.0143 pixels mm-1 | θmax = 32.7º |
| T = 175 K | θmin = 3.9º |
| ω scans | h = −5→6 |
| Absorption correction: multi-scan (CrysAlis RED; Oxford Diffraction, 2007); empirical (using intensity measurements) absorption correction using spherical harmonics, implemented in SCALE3 ABSPACK scaling algorithm | k = −31→29 |
| Tmin = 0.95, Tmax = 0.97 | l = −17→15 |
| 7752 measured reflections |
| Refinement on F | Primary atom site location: structure-invariant direct methods |
| Least-squares matrix: full | Hydrogen site location: inferred from neighbouring sites |
| R[F2 > 2σ(F2)] = 0.027 | H-atom parameters constrained |
| wR(F2) = 0.034 | Method, part 1, Chebychev polynomial [Watkin, D. J. (1994). Acta Cryst. A50,
411-437. Prince, E. (1982). Mathematical Techniques in Crystallography and
Materials Science. New York: Springer-Verlag.]
[weight] = 1.0/[A0*T0(x) + A1*T1(x) ··· + An-1]*Tn-1(x)]
where Ai are the Chebychev coefficients listed below and x = F /Fmax Method = Robust Weighting (Prince, 1982) W = [weight] * [1-(deltaF/6*sigmaF)2]2 Ai are 20.0 -14.7 15.4 |
| S = 1.01 | (Δ/σ)max = 0.001 |
| 1144 reflections | Δρmax = 0.34 e Å−3 |
| 59 parameters | Δρmin = −0.20 e Å−3 |
| 2 restraints | Extinction correction: None |
| C7H11N32+·2Cl– | V = 1013.30 (8) Å3 |
| Mr = 208.09 | Z = 4 |
| Monoclinic, C2/c | Mo Kα |
| a = 4.1779 (2) Å | µ = 0.59 mm−1 |
| b = 20.9388 (10) Å | T = 175 K |
| c = 11.6260 (5) Å | 0.49 × 0.09 × 0.05 mm |
| β = 94.920 (4)º |
| Oxford Diffraction XCALIBUR diffractometer | 1750 independent reflections |
| Absorption correction: multi-scan (CrysAlis RED; Oxford Diffraction, 2007); empirical (using intensity measurements) absorption correction using spherical harmonics, implemented in SCALE3 ABSPACK scaling algorithm | 1144 reflections with I > 2σ(I) |
| Tmin = 0.95, Tmax = 0.97 | Rint = 0.018 |
| 7752 measured reflections |
| R[F2 > 2σ(F2)] = 0.027 | 2 restraints |
| wR(F2) = 0.034 | H-atom parameters constrained |
| S = 1.01 | Δρmax = 0.34 e Å−3 |
| 1144 reflections | Δρmin = −0.20 e Å−3 |
| 59 parameters |
| x | y | z | Uiso*/Ueq | Occ. (<1) | |
| Cl1 | 0.03602 (8) | 0.146532 (14) | 0.92627 (3) | 0.0297 | |
| N2 | 0.0839 (4) | 0.29292 (6) | 0.84632 (10) | 0.0380 | |
| C3 | 0.0000 | 0.32303 (8) | 0.7500 | 0.0271 | |
| C4 | 0.0000 | 0.39368 (8) | 0.7500 | 0.0236 | |
| C5 | −0.1109 (3) | 0.42664 (6) | 0.84251 (11) | 0.0282 | |
| C6 | −0.1138 (3) | 0.49282 (6) | 0.84200 (11) | 0.0296 | |
| C7 | 0.0000 | 0.52485 (8) | 0.7500 | 0.0264 | |
| N8 | 0.000000 (10) | 0.59418 (7) | 0.750000 (10) | 0.0381 | |
| H9 | 0.1600 | 0.3149 | 0.9089 | 0.0500* | |
| H10 | 0.0659 | 0.2491 | 0.8520 | 0.0500* | |
| H11 | −0.1867 | 0.4022 | 0.9091 | 0.0500* | |
| H12 | −0.1892 | 0.5181 | 0.9058 | 0.0500* | |
| H13 | 0.1342 | 0.6109 | 0.8006 | 0.0500* | 0.7500 |
| H14 | −0.1333 | 0.6116 | 0.8033 | 0.0500* | 0.7500 |
| U11 | U22 | U33 | U12 | U13 | U23 | |
| Cl1 | 0.04130 (17) | 0.02485 (14) | 0.02214 (13) | −0.00435 (13) | −0.00233 (9) | −0.00073 (11) |
| N2 | 0.0652 (9) | 0.0209 (5) | 0.0252 (5) | −0.0030 (5) | −0.0122 (5) | 0.0038 (4) |
| C3 | 0.0386 (9) | 0.0198 (7) | 0.0218 (7) | 0.0000 | −0.0043 (6) | 0.0000 |
| C4 | 0.0324 (9) | 0.0184 (6) | 0.0191 (6) | 0.0000 | −0.0030 (6) | 0.0000 |
| C5 | 0.0403 (7) | 0.0236 (5) | 0.0208 (5) | 0.0006 (5) | 0.0021 (4) | 0.0000 (4) |
| C6 | 0.0379 (7) | 0.0238 (6) | 0.0265 (5) | 0.0036 (5) | −0.0011 (4) | −0.0043 (4) |
| C7 | 0.0275 (8) | 0.0180 (6) | 0.0319 (8) | 0.0000 | −0.0074 (6) | 0.0000 |
| N8 | 0.0296 (8) | 0.0177 (7) | 0.0651 (12) | 0.0000 | −0.0072 (8) | 0.0000 |
| N2—C3 | 1.3064 (13) | C6—C7 | 1.3810 (16) |
| N2—H9 | 0.896 | C6—H12 | 0.985 |
| N2—H10 | 0.923 | C7—N8 | 1.452 (2) |
| C3—C4 | 1.479 (2) | N8—H14i | 0.942 |
| C4—C5 | 1.3904 (15) | N8—H13i | 0.852 |
| C5—C6 | 1.3859 (18) | N8—H13 | 0.852 |
| C5—H11 | 1.002 | N8—H14 | 0.942 |
| C3—N2—H9 | 120.0 | C6—C7—N8 | 119.05 (8) |
| C3—N2—H10 | 121.5 | C6i—C7—N8 | 119.05 (8) |
| H9—N2—H10 | 118.5 | C7—N8—H14i | 112.8 |
| N2—C3—N2i | 122.30 (16) | C7—N8—H13i | 114.3 |
| N2—C3—C4 | 118.85 (8) | H14i—N8—H13i | 77.2 |
| C3—C4—C5 | 119.75 (8) | C7—N8—H13 | 114.3 |
| C5i—C4—C5 | 120.49 (16) | H14i—N8—H13 | 84.5 |
| C4—C5—C6 | 119.76 (13) | H13i—N8—H13 | 131.5 |
| C4—C5—H11 | 119.5 | C7—N8—H14 | 112.8 |
| C6—C5—H11 | 120.7 | H14i—N8—H14 | 134.3 |
| C5—C6—C7 | 119.04 (13) | H13i—N8—H14 | 84.5 |
| C5—C6—H12 | 122.5 | H13—N8—H14 | 77.2 |
| C7—C6—H12 | 118.5 | ||
| C(4)—C(5)—C(6)—C(7) | −1.2 (1) | C(5)—C(6)—C(7)—N(8) | −179.4 (1) |
| C(5)—C(4)—C(3)—N(2) | −40.2 (1) |
| Symmetry codes: (i) −x, y, −z+3/2. |
| D—H···A | D—H | H···A | D···A | D—H···A |
| N2—H9···Cl1ii | 0.90 | 2.35 | 3.2247 (13) | 166 |
| N2—H10···Cl1 | 0.92 | 2.32 | 3.2142 (13) | 162 |
| N8—H13···Cl1iii | 0.85 | 2.26 | 3.1031 (6) | 173 |
| N8—H14···Cl1iv | 0.94 | 2.20 | 3.1369 (6) | 176 |
| C5—H11···Cl1v | 1.00 | 2.70 | 3.6806 (13) | 165 |
| Symmetry codes: (ii) −x+1/2, −y+1/2, −z+2; (iii) x+1/2, y+1/2, z; (iv) x−1/2, y+1/2, z; (v) −x−1/2, −y+1/2, −z+2. |
| D—H···A | D—H | H···A | D···A | D—H···A |
| N2—H9···Cl1i | 0.90 | 2.35 | 3.2247 (13) | 166 |
| N2—H10···Cl1 | 0.92 | 2.32 | 3.2142 (13) | 162 |
| N8—H13···Cl1ii | 0.85 | 2.26 | 3.1031 (6) | 173 |
| N8—H14···Cl1iii | 0.94 | 2.20 | 3.1369 (6) | 176 |
| C5—H11···Cl1iv | 1.00 | 2.70 | 3.6806 (13) | 165 |
| Symmetry codes: (i) −x+1/2, −y+1/2, −z+2; (ii) x+1/2, y+1/2, z; (iii) x−1/2, y+1/2, z; (iv) −x−1/2, −y+1/2, −z+2. |
This work, conducted as part of the award `Dynamic Adaptive Materials for Separation and Sensing Microsystems' (to MB) made under the European Heads of Research Councils and European Science Foundation EURYI (European Young Investigator) Awards Scheme in 2004, was supported by funds from the Participating Organizations of EURYI and the EC Sixth Framework Program (see http://www.esf.org/euryi). This research was also supported in part by the CNRS and the University of Montpellier II.
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Several types of heteroditopic receptors, including the title compound, are being used in our group as bricks for supramolecular construction (Barboiu et al., 2003, Blondeau et al., 2005). Among other functions, amidine compounds have shown antiparasitic (Danan et al., 1997) and antifungal activity (Del Poeta, Schell, Dykstra, Jones, Tidwell, Czarny et al., 1998; Del Poeta, Schell, Dykstra, Jones, Tidwell, Kumar et al., 1998). Indeed, this class of compounds has been widely studied for its biological activities. Surprisingly, only one crystal structure of an aminobenzamidine derivative has been published so far (Jarak et al., 2005). Our project deals with the construction of supramolecular architectures based on hydrogen bonding in aqueous media. This is possible due to the strength of the bonds formed between the very electrophilic amidinium unit and the nucleophilic character of acids, for example. Superstructures made of co-crystals have been designed and surprising results have been achieved by Fujita et al. (1995) and Müller et al. (2006). The amidine group also forms a well recognized class of anticancer compounds (Boyd, 1991, Hranjec et al., 2003) and, based on the same properties, can also be used as ligands in affinity chromatography to immobilize enzymes (Nguyen & Loung, 1990 and Kimata et al., 1990).
The molecule of the title compound (Fig. 1) is not planar. The amidinium group has a synclinal disposition with respect to the benzene ring (N2—C3—C4—C5 = -40.2 (1)°). A twofold rotation axis runs along the axis of the cation. The observed deviation from coplanarity might serve to accommodate the formation of intermolecular hydrogen bonds with chloride ions. The three ammonium protons are free to rotate about the C7—N8 bond. These protons were found by Fourier difference maps at four positions (2 + 2 by symmetry) which appears to be in line with the four chloride anions surrounding the ammonium group (N···Cl = 3.103 Å). The site occupation factors of the four ammonium protons was set at 0.75, as there are, in fact, only three protons attached to this ammonium nitrogen. As Fig. 2 shows, rows of head-to-tail benzamidine are stacked alternately. Interestingly, three of four nitrogen atoms form a plane on which the chloride atom sits, almost perfectly. Each chloride anion is bound to four nitrogen cations by weak hydrogen bonds (N···Cl = 3.103 (1)–3.225 (1) Å), while each amidinium unit is bound to eight chloride anions (four times through the ammonium site, twice through each amidinium nitrogen). This produces a singular pyramidal architecture, as depicted in Fig. 3. The packing is determined by these hydrogen bonds, but also by π-stacking. The aromatic rings of the amidinium cations adopt a parallel offset conformation. The distance Cg···Cg between the centroids of two adjacent rings is 4.178 (1) Å, whereas the angle between the ring-centroid vector and the ring normal of one of the amidine rings is 27.7 (1)° (with a perpendicular interplanar distance of 3.7 Å). The angle between the two benzene rings is 0.02°. These values can be considered to be normal for π-π interactions (Janiak, 2000). Fig. 3 also shows both the hydrogen bonding pattern and the interactions between the aromatic groups held together by π-π non-covalent intermolecular interactions.