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

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.

Key indicators

• Single-crystal X-ray study
• T = 298 K
• Mean [sigma](C-C) = 0.003 Å
• Disorder in main residue
• R factor = 0.034
• wR factor = 0.086
• Data-to-parameter ratio = 18.3

checkCIF/PLATON results

No syntax errors found



Alert level C
PLAT301_ALERT_3_C Main Residue  Disorder .........................      17.00 Perc.
PLAT041_ALERT_1_C Calc. and Rep. SumFormula Strings    Differ ....          ?
PLAT042_ALERT_1_C Calc. and Rep. MoietyFormula Strings Differ ....          ?
PLAT045_ALERT_1_C Calculated and Reported Z Differ by ............       0.50 Ratio
PLAT066_ALERT_1_C Predicted and Reported Transmissions Identical .          ?
PLAT790_ALERT_4_C Centre of Gravity not Within Unit Cell: Resd.  #          4
              Cl

Alert level G
REFLT03_ALERT_4_G Please check that the estimate of the number of Friedel pairs is
            correct. If it is not, please give the correct count in the
            _publ_section_exptl_refinement section of the submitted CIF.
           From the CIF: _diffrn_reflns_theta_max           27.88
           From the CIF: _reflns_number_total               3154
           Count of symmetry unique reflns         1734
           Completeness (_total/calc)            181.89%
           TEST3: Check Friedels for noncentro structure
           Estimate of Friedel pairs measured      1420
           Fraction of Friedel pairs measured     0.819
           Are heavy atom types Z>Si present        yes
PLAT860_ALERT_3_G Note: Number of Least-Squares Restraints .......          4
PLAT302_ALERT_4_G Anion/Solvent Disorder .........................      25.00 Perc.

   0 ALERT level A = In general: serious problem
   0 ALERT level B = Potentially serious problem
   6 ALERT level C = Check and explain
   3 ALERT level G = General alerts; check

   4 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
   0 ALERT type 2 Indicator that the structure model may be wrong or deficient
   2 ALERT type 3 Indicator that the structure quality may be low
   3 ALERT type 4 Improvement, methodology, query or suggestion
   0 ALERT type 5 Informative message, check

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S1. 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).

Related literature

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

S2. 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.

S3. 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).

Computing details

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

	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

Crystal data

C11H16N2O2^2+·2Cl^−·0.5H2O	F(000) = 604
Mr = 288.17	Dx = 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) Å^3	0.24 × 0.20 × 0.18 mm
Z = 4

Data collection

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

Refinement

Refinement on F^2	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F^2 > 2σ(F^2)] = 0.033	H-atom parameters constrained
wR(F^2) = 0.085	w = 1/[σ^2(Fo^2) + (0.0472P)^2 + 0.0829P] where P = (Fo^2 + 2Fc^2)/3
S = 1.07	(Δ/σ)max = 0.001
3154 reflections	Δρmax = 0.16 e Å^−3
172 parameters	Δρmin = −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)

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 (Ų)

	x	y	z	Uiso*/Ueq	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 (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
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)

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)

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···Cl2^i	0.91	2.27	3.1405 (18)	159
O1W—H1W···Cl2^ii	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.