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Acta Crystallogr Sect E Struct Rep Online. 2008 October 1; 64(Pt 10): o1960.
Published online 2008 September 17. doi:  10.1107/S160053680802922X
PMCID: PMC2959231

(1S,2S)-2-Carboxy-1-(3-pyridiniometh­yl)pyrrolidin-1-ium dichloride hemihydrate

Abstract

In the title mol­ecule, C11H16N2O2 2+·2Cl·0.5H2O, all N atoms are protonated. In the crystal structure, the organic cation and Cl ions are linked by N—H(...)Cl and O—H(...)Cl hydrogen bonds, forming a one-dimensional infinite ribbon extending parallel to the (110) plane.

Related literature

For the chemistry of amino acid derivatives, see: Fu et al. (2007 [triangle]); Dai & Fu (2008 [triangle]); Wen (2008 [triangle]).

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Object name is e-64-o1960-scheme1.jpg

Experimental

Crystal data

  • C11H16N2O2 2+·2Cl·0.5H2O
  • M r = 288.17
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-64-o1960-efi1.jpg
  • a = 13.070 (5) Å
  • b = 6.9215 (15) Å
  • c = 15.027 (5) Å
  • β = 97.90 (2)°
  • V = 1346.5 (7) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 0.48 mm−1
  • T = 298 (2) K
  • 0.24 × 0.20 × 0.18 mm

Data collection

  • Rigaku Mercury2 diffractometer
  • Absorption correction: multi-scan (CrystalClear; Rigaku, 2005 [triangle]) T min = 0.892, T max = 0.918
  • 6833 measured reflections
  • 3154 independent reflections
  • 2893 reflections with I > 2σ(I)
  • R int = 0.020

Refinement

  • R[F 2 > 2σ(F 2)] = 0.033
  • wR(F 2) = 0.085
  • S = 1.07
  • 3154 reflections
  • 172 parameters
  • 4 restraints
  • H-atom parameters constrained
  • Δρmax = 0.16 e Å−3
  • Δρmin = −0.20 e Å−3
  • Absolute structure: Flack (1983 [triangle]), 1420 Friedel pairs
  • Flack parameter: 0.02 (5)

Data collection: CrystalClear (Rigaku, 2005 [triangle]); cell refinement: CrystalClear; data reduction: CrystalClear; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 [triangle]); molecular graphics: PLATON (Spek, 2003 [triangle]), ORTEPIII (Burnett & Johnson, 1996 [triangle]) and ORTEP-3 for Windows (Farrugia, 1997 [triangle]); software used to prepare material for publication: SHELXL97.

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks I, New_Global_Publ_Block. DOI: 10.1107/S160053680802922X/dn2371sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S160053680802922X/dn2371Isup2.hkl

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

Acknowledgments

This work was supported by a start-up grant from Southeast University to Professor Ren-Gen Xiong.

supplementary crystallographic information

Comment

Amino acid derivatives have found wide range of applications in coordination chemistry because of their multiple coordination modes as ligands to metal ions and for the construction of novel metal-organic frameworks (Fu et al. 2007; Dai & Fu 2008; Wen 2008). We report here the crystal structure of the title compound, 1-((pyridin-3-yl)methyl)pyrrolidine-2-carboxylic acid-1, 1'-ium-dichloride.

In the title compound (Fig.1), the N1 and N2 atoms of the pyrrolidine and pyridine ring are protonated. The two rings are linked by methylene bridge. Bond lengths and angles lie within normal ranges.

In the crystal structure, the organic cation and Cl- ions are linked to form a one-dimentional infinite ribbon developping parallel to the (1 1 0) plane through N—H···Cl and O—H···Cl hydrogen bonds (Table 1, Fig.2).

Experimental

1-((pyridin-3-yl)methyl)pyrrolidine-2-carboxylic acid (3 mmol) was dissolved in the solution of ethanol (20 ml) and hydrochloric acid (1 ml). The solution was allowed to evaporate to obtain colourless block-shaped crystals of the title compound for X-ray analysis.

Refinement

All H atoms attached to C, N and O atoms were fixed geometrically and treated as riding with C–H = 0.93 Å (aromatic), 0.97 Å (methylene), N–H = 0.86 Å (N1), 0.91 Å (N2) and O–H = 0.85 Å with Uiso(H) = 1.2Ueq(C or N) and Uiso(H) = 1.5Ueq(O).

One of the pyrrolidine rings is disordered with the C8 atom statistically distributed over two positions. The solvate water molecule is also disordered around an inversion center. These disorders were treated using the tools (SAME, PART) available in SHELXL-97 (Sheldrick, 2008).

Figures

Fig. 1.
A view of the title compound with the atom labelling scheme. Displacement ellipsoids are drawn at the 30% probability level. Solvent water molecule is omitted for clarity. H atoms are represented as small sphere of arbitrary radii.
Fig. 2.
Part of the crystal packing of the title compound viewed along the b axis. H atoms not involved in hydrogen bonding (dashed lines) have been omitted for clarity.

Crystal data

C11H16N2O22+·2Cl·0.5H2OF(000) = 604
Mr = 288.17Dx = 1.416 Mg m3
Monoclinic, C2Mo Kα radiation, λ = 0.71073 Å
Hall symbol: C 2yCell parameters from 3101 reflections
a = 13.070 (5) Åθ = 3.2–27.5°
b = 6.9215 (15) ŵ = 0.48 mm1
c = 15.027 (5) ÅT = 298 K
β = 97.90 (2)°Block, colorless
V = 1346.5 (7) Å30.24 × 0.20 × 0.18 mm
Z = 4

Data collection

Rigaku Mercury2 diffractometer3154 independent reflections
Radiation source: fine-focus sealed tube2893 reflections with I > 2σ(I)
graphiteRint = 0.020
Detector resolution: 13.6612 pixels mm-1θmax = 27.9°, θmin = 2.7°
ω scansh = −17→17
Absorption correction: multi-scan (CrystalClea; Rigaku, 2005)k = −9→9
Tmin = 0.892, Tmax = 0.918l = −19→19
6833 measured reflections

Refinement

Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.033H-atom parameters constrained
wR(F2) = 0.085w = 1/[σ2(Fo2) + (0.0472P)2 + 0.0829P] where P = (Fo2 + 2Fc2)/3
S = 1.07(Δ/σ)max = 0.001
3154 reflectionsΔρmax = 0.16 e Å3
172 parametersΔρmin = −0.21 e Å3
4 restraintsAbsolute structure: Flack (1983), 1420 Friedel pairs
Primary atom site location: structure-invariant direct methodsFlack parameter: 0.02 (5)

Special details

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*/UeqOcc. (<1)
C10.49977 (16)0.5154 (3)0.12620 (12)0.0360 (4)
H10.48940.64810.12860.043*
C20.43049 (14)0.3904 (3)0.15703 (11)0.0314 (4)
C30.44775 (16)0.1940 (3)0.15117 (15)0.0438 (5)
H30.40140.10660.17040.053*
C40.5344 (2)0.1274 (3)0.11651 (17)0.0515 (6)
H40.5471−0.00450.11360.062*
C50.60084 (15)0.2572 (4)0.08674 (13)0.0421 (5)
H50.65850.21420.06260.051*
C60.33723 (16)0.4708 (4)0.19263 (13)0.0404 (5)
H6A0.31330.58470.15830.049*
H6B0.28220.37570.18490.049*
C70.40028 (17)0.3566 (3)0.35056 (14)0.0421 (5)0.50
H710.39000.23560.31800.051*0.50
H720.47360.37230.37070.051*0.50
C80.3426 (3)0.3553 (7)0.4284 (3)0.0439 (10)0.50
H810.38870.33270.48370.053*0.50
H820.28990.25560.42170.053*0.50
C90.29262 (18)0.5601 (4)0.42867 (14)0.0474 (5)0.50
H910.23060.55870.45740.057*0.50
H920.34070.65440.45820.057*0.50
C7'0.40028 (17)0.3566 (3)0.35056 (14)0.0421 (5)0.50
H71'0.47180.32710.34550.051*0.50
H72'0.35860.24150.33760.051*0.50
C8'0.3884 (4)0.4405 (8)0.4435 (3)0.0474 (11)0.50
H81'0.38160.33790.48620.057*0.50
H82'0.44770.51940.46610.057*0.50
C9'0.29262 (18)0.5601 (4)0.42867 (14)0.0474 (5)0.50
H91'0.30310.68080.46140.057*0.50
H92'0.23580.49160.44980.057*0.50
C100.26803 (14)0.5995 (3)0.32803 (12)0.0313 (4)
H100.20750.52290.30380.038*
C110.24701 (14)0.8082 (3)0.30450 (12)0.0346 (4)
Cl10.67434 (4)0.78893 (6)0.01140 (3)0.04105 (13)
Cl20.06792 (4)1.25793 (8)0.32514 (4)0.04764 (15)
N10.58244 (13)0.4454 (3)0.09258 (11)0.0382 (4)
H1A0.62520.52560.07410.046*
N20.36060 (11)0.5234 (2)0.29028 (9)0.0285 (3)
H20.40980.61730.29590.034*
O10.16413 (12)0.8657 (3)0.33754 (12)0.0583 (5)
H1B0.15300.97970.32490.088*
O20.29780 (12)0.9077 (2)0.26191 (11)0.0534 (4)
O1W0.4711 (9)−0.0105 (7)0.4873 (10)0.123 (5)0.50
H1W0.4729−0.07530.53960.185*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
C10.0464 (12)0.0296 (10)0.0320 (9)−0.0014 (8)0.0055 (8)−0.0005 (7)
C20.0344 (9)0.0324 (10)0.0279 (9)0.0017 (8)0.0065 (7)−0.0020 (7)
C30.0482 (13)0.0338 (11)0.0545 (13)−0.0074 (9)0.0249 (10)−0.0030 (9)
C40.0657 (16)0.0318 (11)0.0635 (14)0.0076 (10)0.0314 (12)0.0003 (10)
C50.0372 (9)0.0516 (13)0.0401 (10)0.0091 (10)0.0140 (8)0.0024 (9)
C60.0343 (10)0.0552 (14)0.0321 (9)0.0065 (9)0.0059 (8)−0.0093 (8)
C70.0484 (12)0.0362 (11)0.0434 (11)0.0035 (9)0.0125 (9)0.0089 (9)
C80.038 (2)0.050 (3)0.044 (2)−0.004 (2)0.0081 (19)0.010 (2)
C90.0525 (13)0.0551 (15)0.0377 (11)0.0030 (11)0.0174 (9)0.0035 (10)
C7'0.0484 (12)0.0362 (11)0.0434 (11)0.0035 (9)0.0125 (9)0.0089 (9)
C8'0.057 (3)0.050 (3)0.037 (2)0.002 (2)0.013 (2)0.007 (2)
C9'0.0525 (13)0.0551 (15)0.0377 (11)0.0030 (11)0.0174 (9)0.0035 (10)
C100.0264 (9)0.0338 (10)0.0355 (9)−0.0026 (7)0.0110 (7)−0.0032 (7)
C110.0337 (9)0.0380 (11)0.0340 (9)−0.0001 (8)0.0111 (7)−0.0036 (8)
Cl10.0415 (2)0.0343 (3)0.0504 (3)−0.0046 (2)0.01712 (19)−0.0065 (2)
Cl20.0374 (2)0.0372 (3)0.0681 (3)−0.0070 (2)0.0062 (2)−0.0065 (2)
N10.0363 (8)0.0447 (10)0.0351 (8)−0.0105 (7)0.0098 (7)0.0028 (7)
N20.0252 (7)0.0299 (8)0.0315 (7)−0.0032 (6)0.0077 (6)−0.0023 (6)
O10.0527 (9)0.0428 (9)0.0882 (12)0.0126 (8)0.0411 (9)0.0056 (9)
O20.0530 (9)0.0414 (9)0.0724 (10)0.0029 (8)0.0320 (8)0.0112 (8)
O1W0.201 (15)0.071 (3)0.112 (8)0.044 (5)0.077 (9)0.033 (5)

Geometric parameters (Å, °)

C1—N11.344 (3)C8—C91.561 (5)
C1—C21.378 (3)C8—H810.9700
C1—H10.9300C8—H820.9700
C2—C31.383 (3)C9—C101.527 (3)
C2—C61.504 (3)C9—H910.9700
C3—C41.389 (3)C9—H920.9700
C3—H30.9300C8'—H81'0.9700
C4—C51.366 (3)C8'—H82'0.9700
C4—H40.9300C10—N21.501 (2)
C5—N11.330 (3)C10—C111.503 (3)
C5—H50.9300C10—H100.9800
C6—N21.502 (2)C11—O21.201 (2)
C6—H6A0.9700C11—O11.314 (2)
C6—H6B0.9700N1—H1A0.8600
C7—C81.476 (5)N2—H20.9100
C7—N21.514 (3)O1—H1B0.8200
C7—H710.9700O1W—H1W0.9015
C7—H720.9700
N1—C1—C2119.96 (19)C7—C8—H82110.8
N1—C1—H1120.0C9—C8—H82110.8
C2—C1—H1120.0H81—C8—H82108.9
C1—C2—C3118.38 (18)C10—C9—C8101.0 (2)
C1—C2—C6119.32 (19)C10—C9—H91111.6
C3—C2—C6122.27 (18)C8—C9—H91111.6
C2—C3—C4119.93 (19)C10—C9—H92111.6
C2—C3—H3120.0C8—C9—H92111.6
C4—C3—H3120.0H91—C9—H92109.4
C5—C4—C3119.5 (2)H81'—C8'—H82'108.8
C5—C4—H4120.3N2—C10—C11112.30 (15)
C3—C4—H4120.3N2—C10—C9103.93 (16)
N1—C5—C4119.58 (19)C11—C10—C9114.30 (16)
N1—C5—H5120.2N2—C10—H10108.7
C4—C5—H5120.2C11—C10—H10108.7
N2—C6—C2111.79 (16)C9—C10—H10108.7
N2—C6—H6A109.3O2—C11—O1124.9 (2)
C2—C6—H6A109.3O2—C11—C10125.44 (18)
N2—C6—H6B109.3O1—C11—C10109.62 (16)
C2—C6—H6B109.3C5—N1—C1122.67 (18)
H6A—C6—H6B107.9C5—N1—H1A118.7
C8—C7—N2108.0 (2)C1—N1—H1A118.7
C8—C7—H71110.1C10—N2—C6112.84 (14)
N2—C7—H71110.1C10—N2—C7105.62 (14)
C8—C7—H72110.1C6—N2—C7114.01 (16)
N2—C7—H72110.1C10—N2—H2108.0
H71—C7—H72108.4C6—N2—H2108.0
C7—C8—C9104.8 (3)C7—N2—H2108.0
C7—C8—H81110.8C11—O1—H1B109.5
C9—C8—H81110.8

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
O1—H1B···Cl20.822.222.9869 (19)155.
N1—H1A···Cl10.862.192.9980 (19)157.
N2—H2···Cl2i0.912.273.1405 (18)159.
O1W—H1W···Cl2ii0.902.463.342 (15)166.

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

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: DN2371).

References

  • Burnett, M. N. & Johnson, C. K. (1996). ORTEPIII Report ORNL-6895. Oak Ridge National Laboratory, Tennessee, USA.
  • Dai, W. & Fu, D.-W. (2008). Acta Cryst. E64, o974. [PMC free article] [PubMed]
  • Farrugia, L. J. (1997). J. Appl. Cryst.30, 565.
  • Flack, H. D. (1983). Acta Cryst. A39, 876–881.
  • Fu, D.-W., Song, Y.-M., Wang, G.-X., Ye, Q., Xiong, R.-G., Akutagawa, T., Nakamura, T., Chan, P. W. H. & Huang, S. D. (2007). J. Am. Chem. Soc.129, 5346–5347. [PubMed]
  • Rigaku (2005). CrystalClear Rigaku Corporation, Tokyo, Japan.
  • Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. [PubMed]
  • Spek, A. L. (2003). J. Appl. Cryst.36, 7–13.
  • Wen, X.-C. (2008). Acta Cryst. E64, o1460. [PMC free article] [PubMed]

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