PMCCPMCCPMCC

Search tips
Search criteria 

Advanced

 
Logo of actaeInternational Union of Crystallographysearchopen accessarticle submissionjournal home pagethis article
 
Acta Crystallogr Sect E Struct Rep Online. 2010 August 1; 66(Pt 8): o2150.
Published online 2010 July 31. doi:  10.1107/S1600536810029624
PMCID: PMC3007299

2-Amino-6-(2,6-difluoro­benzamido)­pyridinium chloride

Abstract

In the cation of the title compound, C12H10F2N3O+·Cl, the dihedral angle between the pyridine and benzene rings is 16.1 (1)°. In the crystal structure, mol­ecules linked into two-dimensional sheets parallel to the bc plane by inter­molecular N—H(...)Cl, C—H(...)Cl and C—H(...)F hydrogen bonds.

Related literature

For general background to 2,6-diflorobenzyl­chloride derivatives, see: Beavo (1995 [triangle]); Beavo & Reifsnyder (1990 [triangle]); Hidaka & Asano (1976 [triangle]); Nicholson et al. (1991 [triangle]). For the stability of the temperature controller used in the data collection, see: Cosier & Glazer (1986 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-66-o2150-scheme1.jpg

Experimental

Crystal data

  • C12H10F2N3O+·Cl
  • M r = 285.68
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-66-o2150-efi1.jpg
  • a = 7.3196 (2) Å
  • b = 13.6314 (3) Å
  • c = 12.2892 (3) Å
  • β = 99.755 (1)°
  • V = 1208.44 (5) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 0.34 mm−1
  • T = 100 K
  • 0.34 × 0.12 × 0.08 mm

Data collection

  • Bruker SMART APEXII CCD area-detector diffractometer
  • Absorption correction: multi-scan (SADABS; Bruker, 2009 [triangle]) T min = 0.895, T max = 0.972
  • 11996 measured reflections
  • 3524 independent reflections
  • 2628 reflections with I > 2σ(I)
  • R int = 0.041

Refinement

  • R[F 2 > 2σ(F 2)] = 0.047
  • wR(F 2) = 0.113
  • S = 1.07
  • 3524 reflections
  • 188 parameters
  • H atoms treated by a mixture of independent and constrained refinement
  • Δρmax = 0.37 e Å−3
  • Δρmin = −0.35 e Å−3

Data collection: APEX2 (Bruker, 2009 [triangle]); cell refinement: SAINT (Bruker, 2009 [triangle]); data reduction: SAINT; program(s) used to solve structure: SHELXTL (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL and PLATON (Spek, 2009 [triangle]).

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536810029624/lh5090sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536810029624/lh5090Isup2.hkl

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

Acknowledgments

NM gratefully acknowledges funding from Universiti Sains Malaysia (USM) under the University Research Grant (No. 1001/PFARMASI/815025). HKF and CSY thank USM for the Research University Golden Goose Grant (No. 1001/PFIZIK/811012). CSY also thanks USM for the award of a USM Fellowship.

supplementary crystallographic information

Comment

Thr derivatives of 2,6-diflorobenzylchloride involved in the inhibition of phosphodiesterases (PDEs) are enzymes which catalyze PDEs. These derivatives are classified into seven families, five of which, PDE1–PDE5, have been characterized (Beavo, 1995). The hydrolysis of cyclic nucleotides was evaluated according to the methods of Beavo & Reifsnyder (1990); Hidaka & Asano, (1976); Nicholson et al. (1991).

The asymmetric unit of the title compound contains one protonated 2-amino-6-(2,6-difluorobenzamido)pyridin-1-ium cation and one chloride anion (Fig. 1). The cation molecule is twisted with the dihedral angle between the pyridine ring and the benzene ring being 16.1 (1)°. In the crystal structure, molecules are linked into infinite chains along c axis by intermolecular C3—H3A···F2 hydrogen bonds. The chloride anions link these chains into two-dimensional sheets parallel to the bc plane by intermolecular N—H···Cl and C—H···Cl hydrogen bonds (Fig. 2, Table 1).

Experimental

2,6-Difluorobenzylchloride (0.01 mol, 1.7 g) was added drop-wise into a round bottom flask containing 25 ml mixture of tetrahydrofuran (THF) and 2,6-diamino pyridine (0.01 mol, 1.1 g) with stirring. The mixture was then refluxed for two and a half hours. The oily precipitate formed was filtrated and dissolved in water and then filtrated and evaporated. The green precipitate formed was dissolved in methanol. Green needle-shaped crystals which were formed at room temperature overnight and were filtrated and dried at 333 K.

Refinement

The N-bound hydrogen atoms were located from a difference Fourier map and refined freely. The remaining H atoms were positioned geometrically [C–H = 0.93 Å and refined using a riding model, with Uiso(H) = 1.2Ueq(C)].

Figures

Fig. 1.
The molecular structure of the title compound with atom labels and 50% probability ellipsoids for non-H atoms.
Fig. 2.
The crystal packing of title compound, viewed down the c axis, showing two 2-D planes parallel to bc plane.

Crystal data

C12H10F2N3O+·ClF(000) = 584
Mr = 285.68Dx = 1.570 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 3017 reflections
a = 7.3196 (2) Åθ = 3.4–30.0°
b = 13.6314 (3) ŵ = 0.34 mm1
c = 12.2892 (3) ÅT = 100 K
β = 99.755 (1)°Needle, green
V = 1208.44 (5) Å30.34 × 0.12 × 0.08 mm
Z = 4

Data collection

Bruker SMART APEXII CCD area-detector diffractometer3524 independent reflections
Radiation source: fine-focus sealed tube2628 reflections with I > 2σ(I)
graphiteRint = 0.041
[var phi] and ω scansθmax = 30.0°, θmin = 2.3°
Absorption correction: multi-scan (SADABS; Bruker, 2009)h = −7→10
Tmin = 0.895, Tmax = 0.972k = −15→19
11996 measured reflectionsl = −17→17

Refinement

Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.047Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.113H atoms treated by a mixture of independent and constrained refinement
S = 1.07w = 1/[σ2(Fo2) + (0.0421P)2 + 0.7252P] where P = (Fo2 + 2Fc2)/3
3524 reflections(Δ/σ)max < 0.001
188 parametersΔρmax = 0.37 e Å3
0 restraintsΔρmin = −0.35 e Å3

Special details

Experimental. The crystal was placed in the cold stream of an Oxford Cryosystems Cobra open-flow nitrogen cryostat (Cosier & Glazer, 1986) operating at 100.0 (1) K.
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)

xyzUiso*/Ueq
Cl10.00538 (7)0.25071 (3)0.48845 (3)0.02010 (13)
F10.25530 (18)0.41301 (9)0.78112 (10)0.0280 (3)
F20.45736 (17)0.69690 (9)0.61851 (10)0.0250 (3)
O10.3723 (2)0.41722 (10)0.57487 (11)0.0235 (3)
N10.2196 (2)0.55280 (13)0.49862 (13)0.0179 (3)
N20.1692 (2)0.42610 (12)0.36587 (13)0.0174 (3)
N30.1129 (3)0.29372 (13)0.24827 (14)0.0212 (4)
C10.3195 (3)0.50617 (15)0.78901 (16)0.0209 (4)
C20.3485 (3)0.55016 (18)0.89145 (16)0.0267 (5)
H2A0.32190.51700.95300.032*
C30.4181 (3)0.64466 (18)0.90068 (17)0.0284 (5)
H3A0.43960.67500.96950.034*
C40.4564 (3)0.69494 (16)0.80912 (17)0.0245 (4)
H4A0.50630.75780.81560.029*
C50.4181 (3)0.64856 (15)0.70798 (16)0.0193 (4)
C60.3492 (3)0.55372 (14)0.69319 (15)0.0175 (4)
C70.3170 (3)0.50038 (14)0.58476 (15)0.0176 (4)
C80.1933 (3)0.52380 (14)0.38828 (15)0.0164 (4)
C90.1878 (3)0.58888 (15)0.30421 (16)0.0195 (4)
H9A0.20190.65570.31870.023*
C100.1605 (3)0.55403 (15)0.19510 (16)0.0208 (4)
H10A0.15800.59810.13710.025*
C110.1375 (3)0.45590 (15)0.17297 (15)0.0188 (4)
H11A0.12150.43330.10060.023*
C120.1384 (3)0.38928 (14)0.26127 (14)0.0164 (4)
H1N10.181 (3)0.6086 (19)0.512 (2)0.031 (7)*
H1N20.166 (3)0.3855 (18)0.420 (2)0.027 (6)*
H1N30.095 (3)0.2722 (18)0.183 (2)0.030 (7)*
H2N30.105 (3)0.2579 (18)0.303 (2)0.025 (6)*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
Cl10.0327 (3)0.0136 (2)0.01412 (19)0.00100 (19)0.00408 (17)0.00081 (17)
F10.0345 (7)0.0215 (7)0.0282 (6)−0.0066 (5)0.0053 (5)0.0033 (5)
F20.0321 (7)0.0177 (6)0.0235 (6)−0.0045 (5)−0.0004 (5)0.0025 (5)
O10.0313 (8)0.0155 (7)0.0210 (7)0.0069 (6)−0.0038 (6)−0.0023 (6)
N10.0250 (9)0.0120 (8)0.0155 (7)0.0029 (7)0.0005 (6)−0.0011 (6)
N20.0245 (9)0.0145 (8)0.0130 (7)−0.0002 (7)0.0027 (6)0.0010 (6)
N30.0359 (10)0.0154 (9)0.0124 (7)−0.0024 (7)0.0048 (7)−0.0008 (7)
C10.0200 (10)0.0200 (11)0.0222 (9)0.0002 (8)0.0020 (8)0.0003 (8)
C20.0256 (11)0.0372 (13)0.0173 (9)0.0028 (10)0.0037 (8)−0.0016 (9)
C30.0273 (12)0.0364 (13)0.0205 (9)0.0056 (10)0.0009 (8)−0.0120 (9)
C40.0244 (11)0.0202 (11)0.0271 (10)0.0047 (8)−0.0011 (8)−0.0085 (8)
C50.0214 (10)0.0160 (10)0.0193 (9)0.0018 (8)0.0006 (7)−0.0013 (7)
C60.0189 (9)0.0160 (10)0.0166 (8)0.0025 (7)−0.0002 (7)−0.0019 (7)
C70.0181 (9)0.0167 (10)0.0170 (8)−0.0012 (8)0.0003 (7)−0.0007 (7)
C80.0175 (9)0.0148 (10)0.0159 (8)0.0007 (7)0.0001 (7)−0.0025 (7)
C90.0244 (10)0.0127 (10)0.0208 (9)−0.0005 (8)0.0019 (8)0.0008 (7)
C100.0255 (10)0.0183 (10)0.0180 (8)−0.0001 (8)0.0025 (8)0.0046 (8)
C110.0233 (10)0.0199 (10)0.0130 (8)−0.0012 (8)0.0024 (7)−0.0005 (7)
C120.0186 (9)0.0152 (9)0.0150 (8)0.0007 (7)0.0017 (7)−0.0007 (7)

Geometric parameters (Å, °)

F1—C11.352 (2)C2—H2A0.9300
F2—C51.354 (2)C3—C41.386 (3)
O1—C71.217 (2)C3—H3A0.9300
N1—C71.373 (2)C4—C51.380 (3)
N1—C81.394 (2)C4—H4A0.9300
N1—H1N10.84 (3)C5—C61.388 (3)
N2—C121.363 (2)C6—C71.501 (3)
N2—C81.365 (2)C8—C91.357 (3)
N2—H1N20.87 (2)C9—C101.405 (3)
N3—C121.322 (3)C9—H9A0.9300
N3—H1N30.84 (3)C10—C111.370 (3)
N3—H2N30.84 (2)C10—H10A0.9300
C1—C21.378 (3)C11—C121.414 (3)
C1—C61.393 (3)C11—H11A0.9300
C2—C31.383 (3)
C7—N1—C8124.78 (17)C4—C5—C6123.94 (19)
C7—N1—H1N1117.9 (17)C5—C6—C1115.33 (17)
C8—N1—H1N1117.0 (17)C5—C6—C7124.48 (17)
C12—N2—C8123.00 (16)C1—C6—C7120.10 (18)
C12—N2—H1N2117.7 (16)O1—C7—N1123.10 (18)
C8—N2—H1N2119.2 (16)O1—C7—C6122.36 (17)
C12—N3—H1N3117.0 (17)N1—C7—C6114.54 (17)
C12—N3—H2N3120.1 (16)C9—C8—N2119.86 (17)
H1N3—N3—H2N3123 (2)C9—C8—N1122.45 (18)
F1—C1—C2118.17 (18)N2—C8—N1117.68 (16)
F1—C1—C6118.59 (17)C8—C9—C10119.13 (18)
C2—C1—C6123.2 (2)C8—C9—H9A120.4
C1—C2—C3118.5 (2)C10—C9—H9A120.4
C1—C2—H2A120.7C11—C10—C9120.84 (18)
C3—C2—H2A120.7C11—C10—H10A119.6
C2—C3—C4121.09 (19)C9—C10—H10A119.6
C2—C3—H3A119.5C10—C11—C12119.36 (17)
C4—C3—H3A119.5C10—C11—H11A120.3
C5—C4—C3117.8 (2)C12—C11—H11A120.3
C5—C4—H4A121.1N3—C12—N2118.32 (17)
C3—C4—H4A121.1N3—C12—C11123.91 (17)
F2—C5—C4118.02 (18)N2—C12—C11117.77 (17)
F2—C5—C6117.99 (16)
F1—C1—C2—C3178.58 (19)C5—C6—C7—O1131.1 (2)
C6—C1—C2—C3−2.9 (3)C1—C6—C7—O1−45.2 (3)
C1—C2—C3—C40.7 (3)C5—C6—C7—N1−49.3 (3)
C2—C3—C4—C51.7 (3)C1—C6—C7—N1134.4 (2)
C3—C4—C5—F2−179.22 (18)C12—N2—C8—C9−0.2 (3)
C3—C4—C5—C6−2.1 (3)C12—N2—C8—N1178.56 (18)
F2—C5—C6—C1177.18 (17)C7—N1—C8—C9−144.7 (2)
C4—C5—C6—C10.1 (3)C7—N1—C8—N236.5 (3)
F2—C5—C6—C70.7 (3)N2—C8—C9—C10−1.2 (3)
C4—C5—C6—C7−176.40 (19)N1—C8—C9—C10−179.89 (18)
F1—C1—C6—C5−178.98 (17)C8—C9—C10—C110.8 (3)
C2—C1—C6—C52.5 (3)C9—C10—C11—C121.0 (3)
F1—C1—C6—C7−2.4 (3)C8—N2—C12—N3−178.62 (18)
C2—C1—C6—C7179.1 (2)C8—N2—C12—C112.0 (3)
C8—N1—C7—O1−9.0 (3)C10—C11—C12—N3178.30 (19)
C8—N1—C7—C6171.45 (18)C10—C11—C12—N2−2.3 (3)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
N1—H1N1···Cl1i0.84 (3)2.35 (2)3.1622 (18)163 (2)
N2—H1N2···Cl10.87 (2)2.41 (2)3.1678 (17)146 (2)
N3—H1N3···Cl1ii0.84 (2)2.39 (2)3.2140 (17)166 (2)
N3—H2N3···Cl10.84 (2)2.51 (2)3.2346 (18)145 (2)
C3—H3A···F2iii0.932.523.414 (3)162
C10—H10A···Cl1iv0.932.743.581 (2)151

Symmetry codes: (i) −x, −y+1, −z+1; (ii) x, −y+1/2, z−1/2; (iii) x, −y+3/2, z+1/2; (iv) −x, y+1/2, −z+1/2.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: LH5090).

References

  • Beavo, J. A. (1995). Physiol. Rev.75, 725–748. [PubMed]
  • Beavo, J. A. & Reifsnyder, D. H. (1990). Trends Pharmacol. Sci.11, 150–155. [PubMed]
  • Bruker (2009). APEX2, SAINT and SADABS Bruker AXS Inc., Madison, Wisconsin, USA.
  • Cosier, J. & Glazer, A. M. (1986). J. Appl. Cryst.19, 105–107.
  • Hidaka, H. & Asano, T. (1976). Biochim. Biophys. Acta, 429, 485–497. [PubMed]
  • Nicholson, C. D., Chaliss, R. A. & Shalid, M. (1991). Trends Pharmacol. Sci.12, 19–27. [PubMed]
  • Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. [PubMed]
  • Spek, A. L. (2009). Acta Cryst. D65, 148–155. [PMC free article] [PubMed]

Articles from Acta Crystallographica Section E: Structure Reports Online are provided here courtesy of International Union of Crystallography