Nipecotic acid hydro­chloride

The title compound (3-carboxy­piperidinium chloride), C₆H₁₂NO₂⁺·Cl⁻, is the hydro­chloride of nipecotic acid and is used as a drug inter­mediate and in the synthesis of γ-amino­butyric acid (GABA) uptake inhibitors. The geometric parameters are in the normal ranges. The crystal packing is stabilized by O—H...Cl and N—H...Cl hydrogen bonds.

Key indicators

• Single-crystal X-ray study
• T = 173 K
• Mean [sigma](C-C) = 0.002 Å
• R factor = 0.022
• wR factor = 0.057
• Data-to-parameter ratio = 14.2

checkCIF/PLATON results

No syntax errors found



Alert level B
PLAT111_ALERT_2_B ADDSYM Detects (Pseudo) Centre of Symmetry .....         80 PerFit

Alert level C
PLAT213_ALERT_2_C Atom O2      has ADP max/min Ratio .............       3.80 prolat
PLAT222_ALERT_3_C Large Non-Solvent    H     Ueq(max)/Ueq(min) ...       3.14 Ratio
PLAT242_ALERT_2_C Check Low       Ueq as Compared to Neighbors for         C7
PLAT250_ALERT_2_C Large U3/U1 Ratio for Average U(i,j) Tensor ....       3.17
PLAT790_ALERT_4_C Centre of Gravity not Within Unit Cell: Resd.  #          2
              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           25.48
           From the CIF: _reflns_number_total               1477
           Count of symmetry unique reflns          816
           Completeness (_total/calc)            181.00%
           TEST3: Check Friedels for noncentro structure
           Estimate of Friedel pairs measured       661
           Fraction of Friedel pairs measured     0.810
           Are heavy atom types Z>Si present        yes

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

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

---

Computing details

Data collection: X-AREA (Stoe & Cie, 2001); cell refinement: X-AREA; data reduction: X-AREA; program(s) used to solve structure: SHELXS97 (Sheldrick, 1990); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: PLATON (Spek, 2003); software used to prepare material for publication: SHELXL97 and PLATON.

3-carboxypiperidinium chloride

Crystal data

C6H12NO2^+·Cl^−	F(000) = 176
Mr = 165.62	Dx = 1.364 Mg m^−3
Monoclinic, P21	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2yb	Cell parameters from 8363 reflections
a = 7.2545 (10) Å	θ = 3.8–25.7°
b = 7.2018 (9) Å	µ = 0.42 mm^−1
c = 7.7886 (13) Å	T = 173 K
β = 97.819 (12)°	Block, colourless
V = 403.14 (10) Å^3	0.37 × 0.23 × 0.19 mm
Z = 2

Data collection

Stoe IPDS-II two-circle diffractometer	1477 independent reflections
Radiation source: fine-focus sealed tube	1460 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.020
ω scans	θmax = 25.5°, θmin = 3.9°
Absorption correction: multi-scan (MULABS; Spek, 2003; Blessing, 1995)	h = −8→8
Tmin = 0.861, Tmax = 0.925	k = −8→8
3354 measured reflections	l = −9→9

Refinement

Refinement on F^2	Hydrogen site location: inferred from neighbouring sites
Least-squares matrix: full	H atoms treated by a mixture of independent and constrained refinement
R[F^2 > 2σ(F^2)] = 0.022	w = 1/[σ^2(Fo^2) + (0.0315P)^2 + 0.0946P] where P = (Fo^2 + 2Fc^2)/3
wR(F^2) = 0.057	(Δ/σ)max < 0.001
S = 1.10	Δρmax = 0.20 e Å^−3
1477 reflections	Δρmin = −0.17 e Å^−3
104 parameters	Extinction correction: SHELXL97, Fc^*=kFc[1+0.001xFc^2λ^3/sin(2θ)]^-1/4
1 restraint	Extinction coefficient: 0.075 (10)
Primary atom site location: structure-invariant direct methods	Absolute structure: Flack (1983), 671 Friedel pairs
Secondary atom site location: difference Fourier map	Absolute structure parameter: 0.10 (6)

Special details

Experimental. ;

Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell e.s.d.'s are taken into account individually in the estimation of e.s.d.'s in distances, angles and torsion angles; correlations between e.s.d.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell e.s.d.'s is used for estimating e.s.d.'s 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 > σ(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
Cl1	−0.19824 (4)	0.89548 (5)	0.87208 (4)	0.01996 (13)
C1	0.2393 (2)	0.8196 (2)	0.41007 (19)	0.0182 (3)
H1	0.2663	0.6838	0.4037	0.022*
C2	0.11341 (19)	0.8717 (3)	0.24271 (17)	0.0193 (3)
H2A	−0.0040	0.8002	0.2340	0.023*
H2B	0.0825	1.0055	0.2441	0.023*
N3	0.21165 (19)	0.82958 (19)	0.09018 (17)	0.0187 (3)
H3A	0.225 (3)	0.696 (3)	0.091 (3)	0.034 (6)*
H3B	0.131 (3)	0.863 (3)	−0.002 (3)	0.030 (5)*
C4	0.3972 (2)	0.9239 (2)	0.0966 (2)	0.0236 (4)
H4A	0.3790	1.0600	0.0888	0.028*
H4B	0.4578	0.8838	−0.0037	0.028*
C5	0.5219 (2)	0.8764 (3)	0.26385 (19)	0.0246 (3)
H5A	0.6395	0.9473	0.2696	0.029*
H5B	0.5528	0.7425	0.2645	0.029*
C6	0.4268 (2)	0.9222 (2)	0.42292 (19)	0.0216 (4)
H6A	0.4061	1.0578	0.4289	0.026*
H6B	0.5077	0.8838	0.5297	0.026*
C7	0.1465 (2)	0.8503 (2)	0.5709 (2)	0.0246 (4)
O1	−0.03690 (16)	0.8621 (2)	0.53883 (15)	0.0353 (4)
H1O	−0.074 (4)	0.872 (5)	0.642 (3)	0.069 (8)*
O2	0.2290 (2)	0.8526 (5)	0.71339 (17)	0.0714 (8)

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
Cl1	0.01918 (18)	0.02398 (19)	0.01762 (17)	0.00124 (17)	0.00571 (11)	0.00071 (17)
C1	0.0171 (7)	0.0238 (7)	0.0137 (7)	0.0006 (6)	0.0019 (6)	−0.0003 (6)
C2	0.0170 (6)	0.0289 (10)	0.0124 (6)	0.0022 (7)	0.0034 (5)	−0.0001 (7)
N3	0.0199 (6)	0.0248 (7)	0.0116 (6)	0.0021 (5)	0.0028 (5)	0.0003 (5)
C4	0.0230 (7)	0.0296 (11)	0.0197 (7)	−0.0015 (7)	0.0083 (6)	0.0038 (7)
C5	0.0167 (6)	0.0341 (9)	0.0235 (7)	−0.0028 (8)	0.0048 (5)	−0.0018 (8)
C6	0.0208 (7)	0.0258 (10)	0.0175 (6)	−0.0033 (7)	−0.0001 (5)	−0.0034 (6)
C7	0.0229 (8)	0.0354 (12)	0.0159 (7)	−0.0005 (6)	0.0035 (6)	0.0001 (6)
O1	0.0221 (6)	0.0668 (11)	0.0179 (5)	0.0079 (6)	0.0064 (4)	−0.0031 (7)
O2	0.0276 (6)	0.174 (3)	0.0125 (5)	0.0070 (11)	0.0020 (5)	−0.0038 (10)

Geometric parameters (Å, º)

C1—C7	1.516 (2)	C4—H4A	0.9900
C1—C2	1.5329 (19)	C4—H4B	0.9900
C1—C6	1.539 (2)	C5—C6	1.534 (2)
C1—H1	1.0000	C5—H5A	0.9900
C2—N3	1.4972 (18)	C5—H5B	0.9900
C2—H2A	0.9900	C6—H6A	0.9900
C2—H2B	0.9900	C6—H6B	0.9900
N3—C4	1.502 (2)	C7—O2	1.187 (2)
N3—H3A	0.96 (2)	C7—O1	1.323 (2)
N3—H3B	0.90 (2)	O1—H1O	0.89 (3)
C4—C5	1.521 (2)
C7—C1—C2	112.75 (13)	C5—C4—H4A	109.5
C7—C1—C6	111.35 (12)	N3—C4—H4B	109.5
C2—C1—C6	110.91 (13)	C5—C4—H4B	109.5
C7—C1—H1	107.2	H4A—C4—H4B	108.1
C2—C1—H1	107.2	C4—C5—C6	111.29 (13)
C6—C1—H1	107.2	C4—C5—H5A	109.4
N3—C2—C1	109.41 (12)	C6—C5—H5A	109.4
N3—C2—H2A	109.8	C4—C5—H5B	109.4
C1—C2—H2A	109.8	C6—C5—H5B	109.4
N3—C2—H2B	109.8	H5A—C5—H5B	108.0
C1—C2—H2B	109.8	C5—C6—C1	109.56 (12)
H2A—C2—H2B	108.2	C5—C6—H6A	109.8
C2—N3—C4	113.78 (12)	C1—C6—H6A	109.8
C2—N3—H3A	104.8 (14)	C5—C6—H6B	109.8
C4—N3—H3A	111.3 (14)	C1—C6—H6B	109.8
C2—N3—H3B	104.6 (12)	H6A—C6—H6B	108.2
C4—N3—H3B	113.1 (13)	O2—C7—O1	122.79 (15)
H3A—N3—H3B	108.7 (19)	O2—C7—C1	123.39 (16)
N3—C4—C5	110.65 (13)	O1—C7—C1	113.68 (14)
N3—C4—H4A	109.5	C7—O1—H1O	104.9 (18)
C7—C1—C2—N3	−177.50 (13)	C7—C1—C6—C5	176.03 (15)
C6—C1—C2—N3	56.85 (18)	C2—C1—C6—C5	−57.54 (18)
C1—C2—N3—C4	−56.29 (19)	C2—C1—C7—O2	−165.3 (2)
C2—N3—C4—C5	55.54 (19)	C6—C1—C7—O2	−39.9 (3)
N3—C4—C5—C6	−54.7 (2)	C2—C1—C7—O1	18.9 (2)
C4—C5—C6—C1	56.3 (2)	C6—C1—C7—O1	144.29 (16)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
O1—H1O···Cl1	0.89 (3)	2.11 (3)	2.9985 (13)	173 (2)
N3—H3A···Cl1^i	0.96 (2)	2.20 (2)	3.1428 (15)	166 (2)
N3—H3B···Cl1^ii	0.90 (2)	2.47 (2)	3.2525 (15)	146.8 (16)
N3—H3B···O2^ii	0.90 (2)	2.419 (19)	2.9590 (19)	119.0 (15)

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