organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

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ISSN: 2056-9890
Volume 64| Part 6| June 2008| Pages o967-o968

4-Ammonio­benzamidinium dichloride

aInstitut Européen des Membranes, UMR 5635, CC 047 Université de Montpellier II, Montpellier, France
*Correspondence e-mail: yves-marie.legrand@iemm.univ-montp2.fr

(Received 8 April 2008; accepted 14 April 2008; online 3 May 2008)

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 π-stacked, with a centroid–centroid distance of 4.178 (1) Å.

Related literature

For related literature, see: Boyd (1991[Boyd, V. (1991). The Chemistry of Amidines and Imidates, Vol. 2, edited by S. Patai, pp. 339-366. New York: John Wiley.]); Nguyen & Loung (1990[Nguyen, A. L. & Loung, J. H. T. (1990). Enzyme Microb. Technol. 12, 663-668.]); Jarak et al. (2005[Jarak, I., Karminski-Zamola, G., Pavlović, G. & Popović, Z. (2005). Acta Cryst. C61, o98-o100.]); Hranjec et al. (2003[Hranjec, M., Grdisa, M., Pavelić, K., Boykin, D. W. & Karminski-Zamola, G. (2003). Farmaco, 58, 1319-1324.]); Danan et al. (1997[Danan, A., Charon, D., Kirkiacharian, S., Bories, K. & Loiseau, P. M. (1997). Farmaco, 52, 227-229.]); Del Poeta, Schell, Dykstra, Jones, Tidwell, Czarny et al. (1998[Del Poeta, M., Schell, W. A., Dykstra, C. C., Jones, S. K., Tidwell, R. R., Czarny, A., Bajić, M., Kumar, A., Boykin, D. W. & Perfect, J. R. (1998). Antimicrob. Agents Chemother. 42, 2495-2502.]); Del Poeta, Schell, Dykstra, Jones, Tidwell, Kumar et al., (1998[Del Poeta, M., Schell, W. A., Dykstra, C. C., Jones, S. K., Tidwell, R. R., Kumar, A., Boykin, D. W. & Perfect, J. R. (1998). Antimicrob. Agents Chemother. 42, 2503-2510.]); Janiak (2000[Janiak, C. (2000). J. Chem. Soc. Dalton Trans. pp. 3885-3896.]); Fujita et al. (1995[Fujita, M., Oguro, D., Miyazawa, M., Oka, H., Yamaguchi, K. & Ogura, K. (1995). Nature (London), 378, 469-471.]); Müller et al. (2006[Müller, A., Zhou, Y. S., Bogge, H., Schmidtmann, M., Mitra, T., Haupt, E. T. K. & Berkle, A. (2006). Angew. Chem. Int. Ed. 45, 460-465.]); Kimata et al. (1990[Kimata, K., Tsuboi, R., Hosoya, K., Tanaka, N. & Araki, T. (1990). J. Chromatogr. A, 515, 73-84.]). For examples of related tubular superstructures, see: Barboiu et al. (2003[Barboiu, M., Vaughan, G. & van der Lee, A. (2003). Org. Lett. 5, 3073-3076.]); Blondeau et al. (2005[Blondeau, P., van der Lee, A. & Barboiu, M. (2005). Inorg. Chem. 44, 5649-5653.]).

[Scheme 1]

Experimental

Crystal data
  • C7H11N32+·2Cl

  • Mr = 208.09

  • Monoclinic, C 2/c

  • a = 4.1779 (2) Å

  • b = 20.9388 (10) Å

  • c = 11.6260 (5) Å

  • β = 94.920 (4)°

  • V = 1013.30 (8) Å3

  • Z = 4

  • Mo Kα radiation

  • μ = 0.59 mm−1

  • T = 175 K

  • 0.49 × 0.09 × 0.05 mm

Data collection
  • Oxford Diffraction XCalibur diffractometer

  • Absorption correction: multi-scan (CrysAlis RED; Oxford Diffraction, 2007[Oxford Diffraction (2007). CrysAlis CCD and CrysAlis RED. Oxford Diffraction Ltd, Abingdon, Oxfordshire, England.]) Tmin = 0.95, Tmax = 0.97

  • 7752 measured reflections

  • 1750 independent reflections

  • 1144 reflections with I > 2σ(I)

  • Rint = 0.018

Refinement
  • R[F2 > 2σ(F2)] = 0.027

  • wR(F2) = 0.034

  • S = 1.00

  • 1144 reflections

  • 59 parameters

  • 2 restraints

  • H-atom parameters constrained

  • Δρmax = 0.34 e Å−3

  • Δρmin = −0.20 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA 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+{\script{1\over 2}}, -y+{\script{1\over 2}}, -z+2]; (ii) [x+{\script{1\over 2}}, y+{\script{1\over 2}}, z]; (iii) [x-{\script{1\over 2}}, y+{\script{1\over 2}}, z]; (iv) [-x-{\script{1\over 2}}, -y+{\script{1\over 2}}, -z+2].

Data collection: CrysAlis CCD (Oxford Diffraction, 2007[Oxford Diffraction (2007). CrysAlis CCD and CrysAlis RED. Oxford Diffraction Ltd, Abingdon, Oxfordshire, England.]); cell refinement: CrysAlis RED (Oxford Diffraction, 2007[Oxford Diffraction (2007). CrysAlis CCD and CrysAlis RED. Oxford Diffraction Ltd, Abingdon, Oxfordshire, England.]); data reduction: CrysAlis RED; program(s) used to solve structure: SIR2004 (Burla et al., 2003[Burla, M. C., Camalli, M., Carrozzini, B., Cascarano, G. L., Giacovazzo, C., Polidori, G. & Spagna, R. (2003). J. Appl. Cryst. 36, 1103.]); program(s) used to refine structure: CRYSTALS (Betteridge et al., 2003[Betteridge, P. W., Carruthers, J. R., Cooper, R. I., Prout, K. & Watkin, D. J. (2003). J. Appl. Cryst. 36, 1487.]); molecular graphics: CAMERON (Watkin et al., 1996[Watkin, D. J., Prout, C. K. & Pearce, L. J. (1996). CAMERON. Chemical Crystallography Laboratory, Oxford, England.]) and Mercury (Macrae et al., 2006[Macrae, C. F., Edgington, P. R., McCabe, P., Pidcock, E., Shields, G. P., Taylor, R., Towler, M. & van de Streek, J. (2006). J. Appl. Cryst. 39, 453-457.]); software used to prepare material for publication: CRYSTALS.

Supporting information


Comment top

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.

Related literature top

For related literature, see: Boyd (1991); Nguyen & Loung (1990); Jarak et al. (2005); Hranjec et al. (2003); Danan et al. (1997); Del Poeta, Schell, Dykstra, Jones, Tidwell, Czarny et al. (1998); Del Poeta, Schell, Dykstra, Jones, Tidwell, Kumar et al., (1998); Janiak (2000); Fujita et al. (1995); Müller et al. (2006); Kimata et al. (1990). For examples of related tubular superstructures, see: Barboiu et al. (2003); Blondeau et al. (2005).

Experimental top

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.

Refinement top

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.

Computing details top

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).

Figures top
[Figure 1] 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] Fig. 2. The two-dimensional framework of the title compound, viewed down the a cell direction.
[Figure 3] 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.
4-Ammoniobenzamidinium dichloride top
Crystal data top
C7H11N32+·2ClF(000) = 432
Mr = 208.09Dx = 1.364 Mg m3
Monoclinic, C2/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -C 2ycCell parameters from 4424 reflections
a = 4.1779 (2) Åθ = 4–32°
b = 20.9388 (10) ŵ = 0.59 mm1
c = 11.6260 (5) ÅT = 175 K
β = 94.920 (4)°Stick, colourless
V = 1013.30 (8) Å30.49 × 0.09 × 0.05 mm
Z = 4
Data collection top
Oxford Diffraction XCALIBUR
diffractometer
1750 independent reflections
Radiation source: Enhance (Mo) X-ray Source1144 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.018
Detector resolution: 16.0143 pixels mm-1θmax = 32.7°, θmin = 3.9°
ω scansh = 56
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 = 3129
Tmin = 0.95, Tmax = 0.97l = 1715
7752 measured reflections
Refinement top
Refinement on FPrimary atom site location: structure-invariant direct methods
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.027H-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 reflectionsΔρmax = 0.34 e Å3
59 parametersΔρmin = 0.20 e Å3
2 restraints
Crystal data top
C7H11N32+·2ClV = 1013.30 (8) Å3
Mr = 208.09Z = 4
Monoclinic, C2/cMo Kα radiation
a = 4.1779 (2) ŵ = 0.59 mm1
b = 20.9388 (10) ÅT = 175 K
c = 11.6260 (5) Å0.49 × 0.09 × 0.05 mm
β = 94.920 (4)°
Data collection top
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 = 0.97Rint = 0.018
7752 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0272 restraints
wR(F2) = 0.034H-atom parameters constrained
S = 1.01Δρmax = 0.34 e Å3
1144 reflectionsΔρmin = 0.20 e Å3
59 parameters
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/UeqOcc. (<1)
Cl10.03602 (8)0.146532 (14)0.92627 (3)0.0297
N20.0839 (4)0.29292 (6)0.84632 (10)0.0380
C30.00000.32303 (8)0.75000.0271
C40.00000.39368 (8)0.75000.0236
C50.1109 (3)0.42664 (6)0.84251 (11)0.0282
C60.1138 (3)0.49282 (6)0.84200 (11)0.0296
C70.00000.52485 (8)0.75000.0264
N80.000000 (10)0.59418 (7)0.750000 (10)0.0381
H90.16000.31490.90890.0500*
H100.06590.24910.85200.0500*
H110.18670.40220.90910.0500*
H120.18920.51810.90580.0500*
H130.13420.61090.80060.0500*0.7500
H140.13330.61160.80330.0500*0.7500
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Cl10.04130 (17)0.02485 (14)0.02214 (13)0.00435 (13)0.00233 (9)0.00073 (11)
N20.0652 (9)0.0209 (5)0.0252 (5)0.0030 (5)0.0122 (5)0.0038 (4)
C30.0386 (9)0.0198 (7)0.0218 (7)0.00000.0043 (6)0.0000
C40.0324 (9)0.0184 (6)0.0191 (6)0.00000.0030 (6)0.0000
C50.0403 (7)0.0236 (5)0.0208 (5)0.0006 (5)0.0021 (4)0.0000 (4)
C60.0379 (7)0.0238 (6)0.0265 (5)0.0036 (5)0.0011 (4)0.0043 (4)
C70.0275 (8)0.0180 (6)0.0319 (8)0.00000.0074 (6)0.0000
N80.0296 (8)0.0177 (7)0.0651 (12)0.00000.0072 (8)0.0000
Geometric parameters (Å, º) top
N2—C31.3064 (13)C6—C71.3810 (16)
N2—H90.896C6—H120.985
N2—H100.923C7—N81.452 (2)
C3—C41.479 (2)N8—H14i0.942
C4—C51.3904 (15)N8—H13i0.852
C5—C61.3859 (18)N8—H130.852
C5—H111.002N8—H140.942
C3—N2—H9120.0C6—C7—N8119.05 (8)
C3—N2—H10121.5C6i—C7—N8119.05 (8)
H9—N2—H10118.5C7—N8—H14i112.8
N2—C3—N2i122.30 (16)C7—N8—H13i114.3
N2—C3—C4118.85 (8)H14i—N8—H13i77.2
C3—C4—C5119.75 (8)C7—N8—H13114.3
C5i—C4—C5120.49 (16)H14i—N8—H1384.5
C4—C5—C6119.76 (13)H13i—N8—H13131.5
C4—C5—H11119.5C7—N8—H14112.8
C6—C5—H11120.7H14i—N8—H14134.3
C5—C6—C7119.04 (13)H13i—N8—H1484.5
C5—C6—H12122.5H13—N8—H1477.2
C7—C6—H12118.5
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 code: (i) x, y, z+3/2.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N2—H9···Cl1ii0.902.353.2247 (13)166
N2—H10···Cl10.922.323.2142 (13)162
N8—H13···Cl1iii0.852.263.1031 (6)173
N8—H14···Cl1iv0.942.203.1369 (6)176
C5—H11···Cl1v1.002.703.6806 (13)165
Symmetry codes: (ii) x+1/2, y+1/2, z+2; (iii) x+1/2, y+1/2, z; (iv) x1/2, y+1/2, z; (v) x1/2, y+1/2, z+2.

Experimental details

Crystal data
Chemical formulaC7H11N32+·2Cl
Mr208.09
Crystal system, space groupMonoclinic, C2/c
Temperature (K)175
a, b, c (Å)4.1779 (2), 20.9388 (10), 11.6260 (5)
β (°) 94.920 (4)
V3)1013.30 (8)
Z4
Radiation typeMo Kα
µ (mm1)0.59
Crystal size (mm)0.49 × 0.09 × 0.05
Data collection
DiffractometerOxford Diffraction XCALIBUR
diffractometer
Absorption correctionMulti-scan
(CrysAlis RED; Oxford Diffraction, 2007); empirical (using intensity measurements) absorption correction using spherical harmonics, implemented in SCALE3 ABSPACK scaling algorithm
Tmin, Tmax0.95, 0.97
No. of measured, independent and
observed [I > 2σ(I)] reflections
7752, 1750, 1144
Rint0.018
(sin θ/λ)max1)0.759
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.027, 0.034, 1.01
No. of reflections1144
No. of parameters59
No. of restraints2
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)0.34, 0.20

Computer programs: CrysAlis CCD (Oxford Diffraction, 2007), CrysAlis RED (Oxford Diffraction, 2007), SIR2004 (Burla et al., 2003), CRYSTALS (Betteridge et al., 2003), CAMERON (Watkin et al., 1996) and Mercury (Macrae et al., 2006).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N2—H9···Cl1i0.902.353.2247 (13)166
N2—H10···Cl10.922.323.2142 (13)162
N8—H13···Cl1ii0.852.263.1031 (6)173
N8—H14···Cl1iii0.942.203.1369 (6)176
C5—H11···Cl1iv1.002.703.6806 (13)165
Symmetry codes: (i) x+1/2, y+1/2, z+2; (ii) x+1/2, y+1/2, z; (iii) x1/2, y+1/2, z; (iv) x1/2, y+1/2, z+2.
 

Acknowledgements

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.

References

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ISSN: 2056-9890
Volume 64| Part 6| June 2008| Pages o967-o968
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