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Acta Crystallogr Sect E Struct Rep Online. 2010 July 1; 66(Pt 7): o1815–o1816.
Published online 2010 June 26. doi:  10.1107/S160053681002427X
PMCID: PMC3007020

2,6-Di(pyrrolidin-1-yl)pyridinium chloride monohydrate

Abstract

In the organic cation of the title compound, C13H20N3 +·Cl·H2O, the two pyrrolidine rings adopt twisted conformations. The pyridine ring makes dihedral angles of 14.57 (6) and 23.96 (6)° with the mean planes of the pyrrolidine rings. In the crystal structure, pairs of bifurcated inter­molecular O—H(...)Cl hydrogen bonds link the water mol­ecules and chloride anions into an R 4 4(8) ring motif. Inter­molecular N—H(...)Cl, C—H(...)Cl and C—H(...)O hydrogen bonds further inter­connect these rings with the organic cations into a two-dimensional network parallel to the bc plane.

Related literature

For general background to and applications of the title compound, see: Cornell et al. (2003 [triangle]); Fetzner (1998 [triangle]); Padoley et al. (2008 [triangle]); Xue & Warshawsky (2005 [triangle]); Zhu et al. (2003 [triangle]). For puckering analysis and ring conformations, see: Cremer & Pople (1975 [triangle]). For graph-set descriptions of hydrogen-bond ring motifs, see: Bernstein et al. (1995 [triangle]). For reference bond-length data, see: Allen et al. (1987 [triangle]). For related structures, see: Al-Dajani et al. (2009 [triangle]); Rubin-Preminger & Englert (2007 [triangle]). For the stability of the temperature controller used for the data collection, see: Cosier & Glazer (1986 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-66-o1815-scheme1.jpg

Experimental

Crystal data

  • C13H20N3 +·Cl·H2O
  • M r = 271.79
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-66-o1815-efi1.jpg
  • a = 11.5728 (15) Å
  • b = 12.2724 (16) Å
  • c = 11.3622 (16) Å
  • β = 119.214 (2)°
  • V = 1408.5 (3) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 0.27 mm−1
  • T = 100 K
  • 0.36 × 0.25 × 0.21 mm

Data collection

  • Bruker APEXII DUO CCD area-detector diffractometer
  • Absorption correction: multi-scan (SADABS; Bruker, 2009 [triangle]) T min = 0.911, T max = 0.947
  • 20960 measured reflections
  • 5073 independent reflections
  • 4506 reflections with I > 2σ(I)
  • R int = 0.028

Refinement

  • R[F 2 > 2σ(F 2)] = 0.033
  • wR(F 2) = 0.129
  • S = 1.26
  • 5073 reflections
  • 163 parameters
  • H-atom parameters constrained
  • Δρmax = 0.85 e Å−3
  • Δρmin = −0.47 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/S160053681002427X/is2565sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S160053681002427X/is2565Isup2.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 JHG thank USM for the Research University Golden Goose grant (No. 1001/PFIZIK/811012). JHG also thanks USM for the award of a USM fellowship.

supplementary crystallographic information

Comment

Nitrogen heterocyclic compounds have received a lot of attention especially by the environment scientists. The main sources of these compounds in the environment are the coal gasification, shale oil extraction and pesticide production (Zhu et al., 2003; Fetzner, 1998). The metabolic activation of the heterocyclic compounds and the DNA damage produced (Xue & Warshawsky, 2005) as well as their roles as a pollutants (Padoley et al., 2008) and their deposition on land and coastal environments (Cornell et al., 2003) have been reported. The title compound can be used for the synthesis of new organometallic complexes and in the field of biological activity and drug design.

The asymmetric unit of the title salt comprises of a protonated 2,6-di(pyrrolidin-1-yl)pyridinium cation, a chloride anion and a water molecule (Fig. 1). In the organic cation, the two pyrrolidine rings adopts twisted conformations (Cremer & Pople, 1975). The puckering parameters are Q = 0.3969 (12) Å, [var phi] = 94.02 (16)° for C1-C4/N1; and Q = 0.3732 (13) Å, [var phi] = 274.73 (17)° for C10-C13/N3. The essentially planar pyridine ring (C5-C9/N2) makes dihedral angles of 23.96 (6) and 14.57 (6)°, respectively, with the mean planes formed through the C1-C4/N1 and C10-C13/N3 pyrrolidine rings. Comparing to the unprotonated structure (Rubin-Preminger & Englert, 2007), protonation at atom N2 has lead to a slight increase in the C5—N2—C9 angle to 122.97 (8)°. The bond lengths (Allen et al., 1987) and angles are within normal ranges and comparable to a related pyridine structure (Al-Dajani et al., 2009).

In the crystal structure (Fig. 2), the chloride anions provide the most extensive part as hydrogen bond acceptors. Pairs of intermolecular O1W—H1W1···Cl1 and O1W—H2W1···Cl1 bifurcated hydrogen bonds (Table 1) link the chloride anions and water molecules into R44(8) ring motifs (Bernstein et al., 1995) in a DAAD manner. These ring motifs are further interconnected with the organic cations into two-dimensional arrays parallel to the bc plane via intermolecular N2—H1N2···Cl1, C1—H1B···Cl1, C7—H7A···O1W and C13—H13A···Cl1 hydrogen bonds (Table 1).

Experimental

In a two-neck round bottom flask, pyridine (0.01 mol, 1.0 g) was dissolved in THF (50 ml). The flask was connected to dropping funnel containing anhydrous aluminum chloride (2.7 g, 0.02 mol) dissolved in THF (25 ml) and ended with anhydrous calcium chloride drying tube. In an ice bath, the aluminum chloride solution was added in small portions and the temperature was maintained between 273–278 K during the addition. The mixture was refluxed for 30 mins at 323–328 K under dry condition. Pyrrolidine (0.02 mol, 1.5 g) was added in small portions to the formed red colour reaction mixture. After stirring for 1 h, the mixture was decanted on ice water and the organic layer was extracted with butanol. The solvent was evaporated by using the rotary evaporator. Deep brown single crystals were formed after one week at room temperature and washed with methanol and dried at room temperature.

Refinement

H atoms bound to N and O atoms were located in a difference Fourier map (N—H = 0.84 and O—H = 0.82–0.91 Å) and constrained to ride with their parent atoms, with Uiso(H) = 1.2Ueq(N) or 1.5Ueq(O). The remaining H atoms were placed in calculated positions (C—H = 0.93 or 0.97 Å), with Uiso(H) = 1.2Ueq(C).

Figures

Fig. 1.
The molecular structure of the title salt, showing the atomic numbering scheme. Displacement ellipsoids are drawn at the 50% probability level.
Fig. 2.
The crystal structure of the title salt, viewed along the a axis, showing a two-dimensional array parallel to the bc plane. H atoms not involved in intermolecular hydrogen bonds (dashed lines) have been omitted for clarity.

Crystal data

C13H20N3+·Cl·H2OF(000) = 584
Mr = 271.79Dx = 1.282 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 9025 reflections
a = 11.5728 (15) Åθ = 3.6–35.1°
b = 12.2724 (16) ŵ = 0.27 mm1
c = 11.3622 (16) ÅT = 100 K
β = 119.214 (2)°Block, brown
V = 1408.5 (3) Å30.36 × 0.25 × 0.21 mm
Z = 4

Data collection

Bruker APEXII DUO CCD area-detector diffractometer5073 independent reflections
Radiation source: fine-focus sealed tube4506 reflections with I > 2σ(I)
graphiteRint = 0.028
[var phi] and ω scansθmax = 32.5°, θmin = 3.6°
Absorption correction: multi-scan (SADABS; Bruker, 2009)h = −17→17
Tmin = 0.911, Tmax = 0.947k = −18→18
20960 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)] = 0.033Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.129H-atom parameters constrained
S = 1.26w = 1/[σ2(Fo2) + (0.0709P)2 + 0.155P] where P = (Fo2 + 2Fc2)/3
5073 reflections(Δ/σ)max = 0.001
163 parametersΔρmax = 0.85 e Å3
0 restraintsΔρmin = −0.47 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 esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds 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 > 2sigma(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
Cl10.19322 (2)0.62909 (2)0.66837 (2)0.01949 (8)
N10.36262 (7)0.57142 (7)1.04747 (8)0.01531 (15)
N20.14198 (7)0.52984 (6)0.90169 (8)0.01275 (14)
H1N20.14090.57340.84460.015*
N3−0.08202 (7)0.50501 (7)0.75519 (8)0.01540 (15)
C10.34608 (9)0.68840 (8)1.01429 (10)0.01729 (17)
H1A0.26530.71631.00900.021*
H1B0.34460.70220.92950.021*
C20.46810 (9)0.73903 (9)1.13225 (11)0.0226 (2)
H2A0.45140.75681.20580.027*
H2B0.49540.80451.10450.027*
C30.57226 (10)0.64951 (9)1.17295 (12)0.0231 (2)
H3A0.60870.64681.11210.028*
H3B0.64370.66011.26440.028*
C40.49368 (9)0.54686 (9)1.16178 (10)0.02016 (19)
H4A0.53250.48351.14350.024*
H4B0.48880.53441.24360.024*
C50.26136 (9)0.50134 (7)1.01015 (9)0.01296 (16)
C60.27123 (9)0.40293 (8)1.07522 (10)0.01685 (17)
H6A0.35160.38021.14670.020*
C70.15781 (10)0.33922 (8)1.03070 (10)0.01769 (18)
H7A0.16370.27351.07400.021*
C80.03737 (10)0.36996 (7)0.92503 (10)0.01668 (18)
H8A−0.03720.32660.89840.020*
C90.02951 (8)0.46816 (7)0.85822 (9)0.01324 (16)
C10−0.20146 (9)0.43731 (9)0.69091 (11)0.02049 (19)
H10A−0.23890.42690.75010.025*
H10B−0.18270.36670.66570.025*
C11−0.29411 (10)0.50344 (10)0.56689 (11)0.0251 (2)
H11A−0.38570.49260.54400.030*
H11B−0.28360.48360.49000.030*
C12−0.25148 (10)0.62099 (9)0.60917 (11)0.0217 (2)
H12A−0.27770.66750.53120.026*
H12B−0.28930.64920.66270.026*
C13−0.10123 (9)0.61292 (8)0.69258 (10)0.01769 (18)
H13A−0.06030.61710.63590.021*
H13B−0.06540.67000.76010.021*
O1W0.07681 (10)0.38244 (7)0.62242 (9)0.02792 (19)
H1W10.09860.45420.62610.042*
H2W10.00480.38280.55360.042*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
Cl10.01614 (12)0.02374 (14)0.01981 (13)0.00041 (7)0.00973 (10)0.00133 (8)
N10.0105 (3)0.0137 (3)0.0163 (3)−0.0004 (2)0.0023 (3)0.0012 (3)
N20.0111 (3)0.0121 (3)0.0131 (3)−0.0003 (2)0.0044 (3)0.0008 (2)
N30.0101 (3)0.0150 (3)0.0172 (3)−0.0008 (2)0.0036 (3)−0.0021 (3)
C10.0140 (4)0.0132 (4)0.0203 (4)−0.0011 (3)0.0050 (3)−0.0005 (3)
C20.0140 (4)0.0192 (4)0.0281 (5)−0.0034 (3)0.0054 (4)−0.0073 (4)
C30.0116 (4)0.0236 (5)0.0275 (5)−0.0019 (3)0.0045 (4)−0.0028 (4)
C40.0111 (4)0.0231 (5)0.0189 (4)0.0012 (3)0.0016 (3)0.0022 (3)
C50.0115 (3)0.0134 (4)0.0129 (4)0.0006 (3)0.0051 (3)−0.0003 (3)
C60.0167 (4)0.0154 (4)0.0165 (4)0.0017 (3)0.0066 (3)0.0032 (3)
C70.0207 (4)0.0133 (4)0.0207 (4)0.0007 (3)0.0114 (3)0.0023 (3)
C80.0171 (4)0.0133 (4)0.0208 (4)−0.0020 (3)0.0101 (3)−0.0009 (3)
C90.0116 (3)0.0128 (4)0.0150 (4)−0.0011 (3)0.0063 (3)−0.0031 (3)
C100.0126 (4)0.0214 (4)0.0242 (5)−0.0043 (3)0.0063 (3)−0.0079 (4)
C110.0119 (4)0.0369 (6)0.0209 (5)−0.0010 (4)0.0037 (3)−0.0053 (4)
C120.0125 (4)0.0310 (5)0.0200 (5)0.0052 (3)0.0066 (3)0.0054 (4)
C130.0124 (4)0.0204 (4)0.0189 (4)0.0022 (3)0.0066 (3)0.0034 (3)
O1W0.0333 (4)0.0220 (4)0.0218 (4)0.0079 (3)0.0082 (3)−0.0016 (3)

Geometric parameters (Å, °)

N1—C51.3444 (11)C5—C61.3914 (13)
N1—C41.4681 (12)C6—C71.3935 (14)
N1—C11.4729 (13)C6—H6A0.9300
N2—C91.3724 (11)C7—C81.3759 (14)
N2—C51.3740 (11)C7—H7A0.9300
N2—H1N20.8360C8—C91.4034 (13)
N3—C91.3289 (11)C8—H8A0.9300
N3—C101.4659 (12)C10—C111.5229 (16)
N3—C131.4680 (13)C10—H10A0.9700
C1—C21.5261 (13)C10—H10B0.9700
C1—H1A0.9700C11—C121.5244 (17)
C1—H1B0.9700C11—H11A0.9700
C2—C31.5263 (15)C11—H11B0.9700
C2—H2A0.9700C12—C131.5241 (14)
C2—H2B0.9700C12—H12A0.9700
C3—C41.5223 (15)C12—H12B0.9700
C3—H3A0.9700C13—H13A0.9700
C3—H3B0.9700C13—H13B0.9700
C4—H4A0.9700O1W—H1W10.9117
C4—H4B0.9700O1W—H2W10.8189
C5—N1—C4120.85 (8)C5—C6—H6A120.8
C5—N1—C1123.94 (7)C7—C6—H6A120.8
C4—N1—C1112.06 (7)C8—C7—C6122.44 (9)
C9—N2—C5122.97 (8)C8—C7—H7A118.8
C9—N2—H1N2114.9C6—C7—H7A118.8
C5—N2—H1N2119.1C7—C8—C9118.56 (9)
C9—N3—C10121.35 (8)C7—C8—H8A120.7
C9—N3—C13125.88 (8)C9—C8—H8A120.7
C10—N3—C13112.77 (8)N3—C9—N2118.17 (8)
N1—C1—C2102.89 (8)N3—C9—C8123.19 (8)
N1—C1—H1A111.2N2—C9—C8118.64 (8)
C2—C1—H1A111.2N3—C10—C11103.05 (9)
N1—C1—H1B111.2N3—C10—H10A111.2
C2—C1—H1B111.2C11—C10—H10A111.2
H1A—C1—H1B109.1N3—C10—H10B111.2
C1—C2—C3103.21 (8)C11—C10—H10B111.2
C1—C2—H2A111.1H10A—C10—H10B109.1
C3—C2—H2A111.1C10—C11—C12103.85 (8)
C1—C2—H2B111.1C10—C11—H11A111.0
C3—C2—H2B111.1C12—C11—H11A111.0
H2A—C2—H2B109.1C10—C11—H11B111.0
C4—C3—C2102.66 (8)C12—C11—H11B111.0
C4—C3—H3A111.2H11A—C11—H11B109.0
C2—C3—H3A111.2C13—C12—C11103.30 (8)
C4—C3—H3B111.2C13—C12—H12A111.1
C2—C3—H3B111.2C11—C12—H12A111.1
H3A—C3—H3B109.1C13—C12—H12B111.1
N1—C4—C3102.77 (8)C11—C12—H12B111.1
N1—C4—H4A111.2H12A—C12—H12B109.1
C3—C4—H4A111.2N3—C13—C12102.53 (8)
N1—C4—H4B111.2N3—C13—H13A111.3
C3—C4—H4B111.2C12—C13—H13A111.3
H4A—C4—H4B109.1N3—C13—H13B111.3
N1—C5—N2117.40 (8)C12—C13—H13B111.3
N1—C5—C6123.70 (8)H13A—C13—H13B109.2
N2—C5—C6118.90 (8)H1W1—O1W—H2W199.6
C5—C6—C7118.41 (9)
C5—N1—C1—C2150.43 (9)C6—C7—C8—C91.27 (15)
C4—N1—C1—C2−9.59 (11)C10—N3—C9—N2171.36 (8)
N1—C1—C2—C330.83 (11)C13—N3—C9—N2−8.05 (14)
C1—C2—C3—C4−40.78 (11)C10—N3—C9—C8−9.15 (14)
C5—N1—C4—C3−176.31 (9)C13—N3—C9—C8171.44 (9)
C1—N1—C4—C3−15.59 (11)C5—N2—C9—N3177.66 (8)
C2—C3—C4—N134.27 (11)C5—N2—C9—C8−1.85 (13)
C4—N1—C5—N2−179.62 (8)C7—C8—C9—N3−179.98 (9)
C1—N1—C5—N222.02 (13)C7—C8—C9—N2−0.49 (14)
C4—N1—C5—C60.56 (14)C9—N3—C10—C11−170.91 (9)
C1—N1—C5—C6−157.79 (9)C13—N3—C10—C118.57 (11)
C9—N2—C5—N1−176.46 (8)N3—C10—C11—C12−28.80 (10)
C9—N2—C5—C63.37 (13)C10—C11—C12—C1338.50 (11)
N1—C5—C6—C7177.33 (9)C9—N3—C13—C12−165.45 (9)
N2—C5—C6—C7−2.48 (14)C10—N3—C13—C1215.10 (11)
C5—C6—C7—C80.23 (15)C11—C12—C13—N3−32.44 (10)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
N2—H1N2···Cl10.842.453.2246 (10)153
O1W—H1W1···Cl10.912.353.2502 (11)169
O1W—H2W1···Cl1i0.822.453.2594 (11)171
C1—H1B···Cl10.972.763.5100 (11)135
C7—H7A···O1Wii0.932.353.2122 (15)154
C13—H13A···Cl10.972.783.5555 (13)138

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

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: IS2565).

References

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