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Acta Cryst. (2008). E64, o1960    [ doi:10.1107/S160053680802922X ]

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

J. Dai and X.-C. Wen

Abstract top

In the title molecule, C11H16N2O22+·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.

Comment top

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).

Related literature top

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

Experimental top

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 top

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).

Computing details top

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

Figures top
[Figure 1] 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.
[Figure 2] 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.
(1S,2S)-2-Carboxy-1-(3-pyridiniomethyl)pyrrolidin-1-ium dichloride hemihydrate top
Crystal data top
C11H16N2O22+·2Cl−·0.5H2OF(000) = 604
Mr = 288.17Dx = 1.416 Mg m−3
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 mm−1
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 top
Rigaku Mercury2
diffractometer		3154 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 top
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) = 0.085 w = 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 Å−3
172 parametersΔρmin = −0.21 e Å−3
4 restraintsAbsolute structure: Flack (1983), 1420 Friedel pairs
Primary atom site location: structure-invariant direct methodsFlack parameter: 0.02 (5)
Crystal data top
C11H16N2O22+·2Cl−·0.5H2OV = 1346.5 (7) Å3
Mr = 288.17Z = 4
Monoclinic, C2Mo Kα radiation
a = 13.070 (5) ŵ = 0.48 mm−1
b = 6.9215 (15) ÅT = 298 K
c = 15.027 (5) Å0.24 × 0.20 × 0.18 mm
β = 97.90 (2)°
Data collection top
Rigaku Mercury2
diffractometer		3154 independent reflections
Absorption correction: multi-scan
(CrystalClea; Rigaku, 2005)		2893 reflections with I > 2σ(I)
Tmin = 0.892, Tmax = 0.918Rint = 0.020
6833 measured reflectionsθmax = 27.9°
Refinement top
R[F2 > 2σ(F2)] = 0.033H-atom parameters constrained
wR(F2) = 0.085Δρmax = 0.16 e Å−3
S = 1.07Δρmin = −0.21 e Å−3
3154 reflectionsAbsolute structure: Flack (1983), 1420 Friedel pairs
172 parametersFlack parameter: 0.02 (5)
4 restraints
Special details top

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) top
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) top
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, °) top
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, °) top
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.
Table 1
Hydrogen-bond geometry (Å, °) top
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.
Acknowledgements top

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

references
References top

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.

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.

Rigaku (2005). CrystalClear. Rigaku Corporation, Tokyo, Japan.

Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122.

Spek, A. L. (2003). J. Appl. Cryst. 36, 7–13.

Wen, X.-C. (2008). Acta Cryst. E64, o1460.