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

Dai, J.; Wen, X.-C.

doi:10.1107/S160053680802922X

organic compounds

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Volume 64| Part 10| October 2008| Page o1960

doi:10.1107/S160053680802922X

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

Jing Dai ^a and Xiao-Chun Wen ^a ^*

^aOrdered Matter Science Research Center, College of Chemistry and Chemical Engineering, Southeast University, Nanjing 210096, People's Republic of China
^*Correspondence e-mail: fudavid88@yahoo.com.cn

(Received 5 September 2008; accepted 11 September 2008; online 17 September 2008)

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.

Related literature

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

Experimental

Crystal data

C₁₁H₁₆N₂O₂²⁺·2Cl⁻·0.5H₂O
M_r = 288.17
Monoclinic, C 2
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 ) 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[F² > 2σ(F²)] = 0.033
wR(F²) = 0.085
S = 1.07
3154 reflections
172 parameters
4 restraints
H-atom parameters constrained
Δρ_max = 0.16 e Å⁻³
Δρ_min = −0.20 e Å⁻³
Absolute structure: Flack (1983 ), 1420 Friedel pairs
Flack parameter: 0.02 (5)

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
O1—H1B⋯Cl2	0.82	2.22	2.9869 (19)	155
N1—H1A⋯Cl1	0.86	2.19	2.9980 (19)	157
N2—H2⋯Cl2ⁱ	0.91	2.27	3.1405 (18)	159
O1W—H1W⋯Cl2ⁱⁱ	0.90	2.46	3.342 (15)	166
Symmetry codes: (i) $[x+{\script{1\over 2}}, y-{\script{1\over 2}}, z]$ ; (ii) $[-x+{\script{1\over 2}}, y-{\script{3\over 2}}, -z+1]$ .

Data collection: CrystalClear (Rigaku, 2005); cell refinement: CrystalClear; data reduction: CrystalClear; 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.

Supporting information

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

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

checkCIF report

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.

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

	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.

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

Crystal data top

C₁₁H₁₆N₂O₂²⁺·2Cl⁻·0.5H₂O	F(000) = 604
M_r = 288.17	D_x = 1.416 Mg m⁻³
Monoclinic, C2	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: C 2y	Cell parameters from 3101 reflections
a = 13.070 (5) Å	θ = 3.2–27.5°
b = 6.9215 (15) Å	µ = 0.48 mm⁻¹
c = 15.027 (5) Å	T = 298 K
β = 97.90 (2)°	Block, colorless
V = 1346.5 (7) Å³	0.24 × 0.20 × 0.18 mm
Z = 4

Data collection top

Rigaku Mercury2 diffractometer	3154 independent reflections
Radiation source: fine-focus sealed tube	2893 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.020
Detector resolution: 13.6612 pixels mm^-1	θ_max = 27.9°, θ_min = 2.7°
ω scans	h = −17→17
Absorption correction: multi-scan (CrystalClea; Rigaku, 2005)	k = −9→9
T_min = 0.892, T_max = 0.918	l = −19→19
6833 measured reflections

Refinement top

Refinement on F²	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F² > 2σ(F²)] = 0.033	H-atom parameters constrained
wR(F²) = 0.085	w = 1/[σ²(F_o²) + (0.0472P)² + 0.0829P] where P = (F_o² + 2F_c²)/3
S = 1.07	(Δ/σ)_max = 0.001
3154 reflections	Δρ_max = 0.16 e Å⁻³
172 parameters	Δρ_min = −0.21 e Å⁻³
4 restraints	Absolute structure: Flack (1983), 1420 Friedel pairs
Primary atom site location: structure-invariant direct methods	Absolute structure parameter: 0.02 (5)

Crystal data top

C₁₁H₁₆N₂O₂²⁺·2Cl⁻·0.5H₂O	V = 1346.5 (7) Å³
M_r = 288.17	Z = 4
Monoclinic, C2	Mo Kα radiation
a = 13.070 (5) Å	µ = 0.48 mm⁻¹
b = 6.9215 (15) Å	T = 298 K
c = 15.027 (5) Å	0.24 × 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)
T_min = 0.892, T_max = 0.918	R_int = 0.020
6833 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.033	H-atom parameters constrained
wR(F²) = 0.085	Δρ_max = 0.16 e Å⁻³
S = 1.07	Δρ_min = −0.21 e Å⁻³
3154 reflections	Absolute structure: Flack (1983), 1420 Friedel pairs
172 parameters	Absolute structure 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

	x	y	z	U_iso*/U_eq	Occ. (<1)
C1	0.49977 (16)	0.5154 (3)	0.12620 (12)	0.0360 (4)
H1	0.4894	0.6481	0.1286	0.043*
C2	0.43049 (14)	0.3904 (3)	0.15703 (11)	0.0314 (4)
C3	0.44775 (16)	0.1940 (3)	0.15117 (15)	0.0438 (5)
H3	0.4014	0.1066	0.1704	0.053*
C4	0.5344 (2)	0.1274 (3)	0.11651 (17)	0.0515 (6)
H4	0.5471	−0.0045	0.1136	0.062*
C5	0.60084 (15)	0.2572 (4)	0.08674 (13)	0.0421 (5)
H5	0.6585	0.2142	0.0626	0.051*
C6	0.33723 (16)	0.4708 (4)	0.19263 (13)	0.0404 (5)
H6A	0.3133	0.5847	0.1583	0.049*
H6B	0.2822	0.3757	0.1849	0.049*
C7	0.40028 (17)	0.3566 (3)	0.35056 (14)	0.0421 (5)	0.50
H71	0.3900	0.2356	0.3180	0.051*	0.50
H72	0.4736	0.3723	0.3707	0.051*	0.50
C8	0.3426 (3)	0.3553 (7)	0.4284 (3)	0.0439 (10)	0.50
H81	0.3887	0.3327	0.4837	0.053*	0.50
H82	0.2899	0.2556	0.4217	0.053*	0.50
C9	0.29262 (18)	0.5601 (4)	0.42867 (14)	0.0474 (5)	0.50
H91	0.2306	0.5587	0.4574	0.057*	0.50
H92	0.3407	0.6544	0.4582	0.057*	0.50
C7'	0.40028 (17)	0.3566 (3)	0.35056 (14)	0.0421 (5)	0.50
H71'	0.4718	0.3271	0.3455	0.051*	0.50
H72'	0.3586	0.2415	0.3376	0.051*	0.50
C8'	0.3884 (4)	0.4405 (8)	0.4435 (3)	0.0474 (11)	0.50
H81'	0.3816	0.3379	0.4862	0.057*	0.50
H82'	0.4477	0.5194	0.4661	0.057*	0.50
C9'	0.29262 (18)	0.5601 (4)	0.42867 (14)	0.0474 (5)	0.50
H91'	0.3031	0.6808	0.4614	0.057*	0.50
H92'	0.2358	0.4916	0.4498	0.057*	0.50
C10	0.26803 (14)	0.5995 (3)	0.32803 (12)	0.0313 (4)
H10	0.2075	0.5229	0.3038	0.038*
C11	0.24701 (14)	0.8082 (3)	0.30450 (12)	0.0346 (4)
Cl1	0.67434 (4)	0.78893 (6)	0.01140 (3)	0.04105 (13)
Cl2	0.06792 (4)	1.25793 (8)	0.32514 (4)	0.04764 (15)
N1	0.58244 (13)	0.4454 (3)	0.09258 (11)	0.0382 (4)
H1A	0.6252	0.5256	0.0741	0.046*
N2	0.36060 (11)	0.5234 (2)	0.29028 (9)	0.0285 (3)
H2	0.4098	0.6173	0.2959	0.034*
O1	0.16413 (12)	0.8657 (3)	0.33754 (12)	0.0583 (5)
H1B	0.1530	0.9797	0.3249	0.088*
O2	0.29780 (12)	0.9077 (2)	0.26191 (11)	0.0534 (4)
O1W	0.4711 (9)	−0.0105 (7)	0.4873 (10)	0.123 (5)	0.50
H1W	0.4729	−0.0753	0.5396	0.185*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
C1	0.0464 (12)	0.0296 (10)	0.0320 (9)	−0.0014 (8)	0.0055 (8)	−0.0005 (7)
C2	0.0344 (9)	0.0324 (10)	0.0279 (9)	0.0017 (8)	0.0065 (7)	−0.0020 (7)
C3	0.0482 (13)	0.0338 (11)	0.0545 (13)	−0.0074 (9)	0.0249 (10)	−0.0030 (9)
C4	0.0657 (16)	0.0318 (11)	0.0635 (14)	0.0076 (10)	0.0314 (12)	0.0003 (10)
C5	0.0372 (9)	0.0516 (13)	0.0401 (10)	0.0091 (10)	0.0140 (8)	0.0024 (9)
C6	0.0343 (10)	0.0552 (14)	0.0321 (9)	0.0065 (9)	0.0059 (8)	−0.0093 (8)
C7	0.0484 (12)	0.0362 (11)	0.0434 (11)	0.0035 (9)	0.0125 (9)	0.0089 (9)
C8	0.038 (2)	0.050 (3)	0.044 (2)	−0.004 (2)	0.0081 (19)	0.010 (2)
C9	0.0525 (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)
C10	0.0264 (9)	0.0338 (10)	0.0355 (9)	−0.0026 (7)	0.0110 (7)	−0.0032 (7)
C11	0.0337 (9)	0.0380 (11)	0.0340 (9)	−0.0001 (8)	0.0111 (7)	−0.0036 (8)
Cl1	0.0415 (2)	0.0343 (3)	0.0504 (3)	−0.0046 (2)	0.01712 (19)	−0.0065 (2)
Cl2	0.0374 (2)	0.0372 (3)	0.0681 (3)	−0.0070 (2)	0.0062 (2)	−0.0065 (2)
N1	0.0363 (8)	0.0447 (10)	0.0351 (8)	−0.0105 (7)	0.0098 (7)	0.0028 (7)
N2	0.0252 (7)	0.0299 (8)	0.0315 (7)	−0.0032 (6)	0.0077 (6)	−0.0023 (6)
O1	0.0527 (9)	0.0428 (9)	0.0882 (12)	0.0126 (8)	0.0411 (9)	0.0056 (9)
O2	0.0530 (9)	0.0414 (9)	0.0724 (10)	0.0029 (8)	0.0320 (8)	0.0112 (8)
O1W	0.201 (15)	0.071 (3)	0.112 (8)	0.044 (5)	0.077 (9)	0.033 (5)

Geometric parameters (Å, º) top

C1—N1	1.344 (3)	C8—C9	1.561 (5)
C1—C2	1.378 (3)	C8—H81	0.9700
C1—H1	0.9300	C8—H82	0.9700
C2—C3	1.383 (3)	C9—C10	1.527 (3)
C2—C6	1.504 (3)	C9—H91	0.9700
C3—C4	1.389 (3)	C9—H92	0.9700
C3—H3	0.9300	C8'—H81'	0.9700
C4—C5	1.366 (3)	C8'—H82'	0.9700
C4—H4	0.9300	C10—N2	1.501 (2)
C5—N1	1.330 (3)	C10—C11	1.503 (3)
C5—H5	0.9300	C10—H10	0.9800
C6—N2	1.502 (2)	C11—O2	1.201 (2)
C6—H6A	0.9700	C11—O1	1.314 (2)
C6—H6B	0.9700	N1—H1A	0.8600
C7—C8	1.476 (5)	N2—H2	0.9100
C7—N2	1.514 (3)	O1—H1B	0.8200
C7—H71	0.9700	O1W—H1W	0.9015
C7—H72	0.9700

N1—C1—C2	119.96 (19)	C7—C8—H82	110.8
N1—C1—H1	120.0	C9—C8—H82	110.8
C2—C1—H1	120.0	H81—C8—H82	108.9
C1—C2—C3	118.38 (18)	C10—C9—C8	101.0 (2)
C1—C2—C6	119.32 (19)	C10—C9—H91	111.6
C3—C2—C6	122.27 (18)	C8—C9—H91	111.6
C2—C3—C4	119.93 (19)	C10—C9—H92	111.6
C2—C3—H3	120.0	C8—C9—H92	111.6
C4—C3—H3	120.0	H91—C9—H92	109.4
C5—C4—C3	119.5 (2)	H81'—C8'—H82'	108.8
C5—C4—H4	120.3	N2—C10—C11	112.30 (15)
C3—C4—H4	120.3	N2—C10—C9	103.93 (16)
N1—C5—C4	119.58 (19)	C11—C10—C9	114.30 (16)
N1—C5—H5	120.2	N2—C10—H10	108.7
C4—C5—H5	120.2	C11—C10—H10	108.7
N2—C6—C2	111.79 (16)	C9—C10—H10	108.7
N2—C6—H6A	109.3	O2—C11—O1	124.9 (2)
C2—C6—H6A	109.3	O2—C11—C10	125.44 (18)
N2—C6—H6B	109.3	O1—C11—C10	109.62 (16)
C2—C6—H6B	109.3	C5—N1—C1	122.67 (18)
H6A—C6—H6B	107.9	C5—N1—H1A	118.7
C8—C7—N2	108.0 (2)	C1—N1—H1A	118.7
C8—C7—H71	110.1	C10—N2—C6	112.84 (14)
N2—C7—H71	110.1	C10—N2—C7	105.62 (14)
C8—C7—H72	110.1	C6—N2—C7	114.01 (16)
N2—C7—H72	110.1	C10—N2—H2	108.0
H71—C7—H72	108.4	C6—N2—H2	108.0
C7—C8—C9	104.8 (3)	C7—N2—H2	108.0
C7—C8—H81	110.8	C11—O1—H1B	109.5
C9—C8—H81	110.8

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
O1—H1B···Cl2	0.82	2.22	2.9869 (19)	155
N1—H1A···Cl1	0.86	2.19	2.9980 (19)	157
N2—H2···Cl2ⁱ	0.91	2.27	3.1405 (18)	159
O1W—H1W···Cl2ⁱⁱ	0.90	2.46	3.342 (15)	166

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

Experimental details

Crystal data
Chemical formula	C₁₁H₁₆N₂O₂²⁺·2Cl⁻·0.5H₂O
M_r	288.17
Crystal system, space group	Monoclinic, C2
Temperature (K)	298
a, b, c (Å)	13.070 (5), 6.9215 (15), 15.027 (5)
β (°)	97.90 (2)
V (Å³)	1346.5 (7)
Z	4
Radiation type	Mo Kα
µ (mm⁻¹)	0.48
Crystal size (mm)	0.24 × 0.20 × 0.18

Data collection
Diffractometer	Rigaku Mercury2 diffractometer
Absorption correction	Multi-scan (CrystalClea; Rigaku, 2005)
T_min, T_max	0.892, 0.918
No. of measured, independent and observed [I > 2σ(I)] reflections	6833, 3154, 2893
R_int	0.020
(sin θ/λ)_max (Å⁻¹)	0.658

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.033, 0.085, 1.07
No. of reflections	3154
No. of parameters	172
No. of restraints	4
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.16, −0.21
Absolute structure	Flack (1983), 1420 Friedel pairs
Absolute structure parameter	0.02 (5)

Computer programs: CrystalClear (Rigaku, 2005), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), PLATON (Spek, 2003); ORTEPIII (Burnett & Johnson, 1996) and ORTEP-3 for Windows (Farrugia, 1997).

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
O1—H1B···Cl2	0.82	2.22	2.9869 (19)	154.9
N1—H1A···Cl1	0.86	2.19	2.9980 (19)	156.7
N2—H2···Cl2ⁱ	0.91	2.27	3.1405 (18)	159.4
O1W—H1W···Cl2ⁱⁱ	0.90	2.46	3.342 (15)	166.1

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

Acknowledgements

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

References

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ISSN: 2056-9890

Volume 64| Part 10| October 2008| Page o1960

doi:10.1107/S160053680802922X

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

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

Related literature

Experimental

Crystal data

Data collection

Refinement

Supporting information

Acknowledgements

References

organic compounds

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