Crystal structure of (2S,4S)-5,5-dimethyl-2-(pyridin-2-yl)-1,3-thia­zolidine-4-carb­oxy­lic acid

Laskar, P.; Kuwamura, N.; Yoshinari, N.; Konno, T.

doi:10.1107/S1600536814024854

organic compounds

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doi:10.1107/S1600536814024854

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Crystal structure of (2S,4S)-5,5-dimethyl-2-(pyridin-2-yl)-1,3-thiazolidine-4-carboxylic acid

Payel Laskar,^a Naoto Kuwamura,^a ^* Nobuto Yoshinari ^a and Takumi Konno ^a,^b

^aDepartment of Chemistry, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan, and ^bCREST, Japan Science and Technology Agency, Toyonaka, Osaka 560-0043, Japan
^*Correspondence e-mail: kuwamuran12@chem.sci.osaka-u.ac.jp

Edited by H. Ishida, Okayama University, Japan (Received 18 October 2014; accepted 12 November 2014; online 15 November 2014)

In the title compound, C₁₁H₁₄N₂O₂S, the thiazolidine ring has an envelope conformation with the C atom bonded to the carboxylic acid group at the flap. Two C atoms of the thiazolidine ring adopt S conformations. In the crystal, O—H⋯N hydrogen bonds between the amine and carboxylic acid groups construct a helical chain structure along the a-axis direction. The chains are further connected via weak C—H⋯π contacts, forming a layer parallel to the ac plane.

Keywords: crystal structure; thiazolidine; hydrogen bonding; C—H⋯π contacts.

CCDC reference: 1033831

1. Related literature

For background to compounds containing thiazoline or thiazolidine rings, see: Bolos et al. (2002 ); Pontiki et al. (2006 ); Shih & Ke (2004 ). For related structures, see: Brunner et al. (1984 , 2001 ). For the preparation of D-penicillamine-coordinated metal complexes, see: Igashira-Kamiyama & Konno (2011 ).

2. Experimental

2.1. Crystal data

C₁₁H₁₄N₂O₂S
M_r = 238.30
Orthorhombic, P 2₁ 2₁ 2₁
a = 7.906 (4) Å
b = 11.306 (5) Å
c = 13.504 (7) Å
V = 1207.1 (10) Å³
Z = 4
Mo Kα radiation
μ = 0.26 mm⁻¹
T = 200 K
0.25 × 0.25 × 0.25 mm

2.2. Data collection

Rigaku R-AXIS RAPID diffractometer
Absorption correction: multi-scan (ABSCOR; Higashi, 1995 ) T_min = 0.785, T_max = 0.938
9629 measured reflections
2767 independent reflections
2711 reflections with F² > 2σ(F²)
R_int = 0.020

2.3. Refinement

R[F² > 2σ(F²)] = 0.028
wR(F²) = 0.074
S = 1.10
2767 reflections
152 parameters
H atoms treated by a mixture of independent and constrained refinement
Δρ_max = 0.23 e Å⁻³
Δρ_min = −0.18 e Å⁻³
Absolute structure: Flack x determined using 1118 quotients [(I⁺)−(I⁻)]/[(I⁺)+(I⁻)] (Parsons et al., 2013 )
Absolute structure parameter: 0.01 (9)

Table 1
Hydrogen-bond geometry (Å, °)

Cg is the centroid of the N1/C1–C5 ring.

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
O2—H13⋯N2ⁱ	0.79 (3)	1.87 (3)	2.654 (2)	173 (3)
C3—H3⋯Cgⁱⁱ	0.95	2.81	3.629 (2)	145
Symmetry codes: (i) $[x+{\script{1\over 2}}, -y+{\script{3\over 2}}, -z+1]$ ; (ii) $[x-{\script{1\over 2}}, -y+{\script{3\over 2}}, -z+2]$ .

Data collection: PROCESS-AUTO (Rigaku, 1998 ); cell refinement: PROCESS-AUTO; data reduction: PROCESS-AUTO; program(s) used to solve structure: SIR92 (Altomare et al., 1993 ); program(s) used to refine structure: SHELXL2013 (Sheldrick, 2008 ); molecular graphics: CrystalStructure (Rigaku, 2014 ); software used to prepare material for publication: CrystalStructure.

Supporting information

CCDC reference: 1033831

Crystal structure: contains datablocks New_Global_Publ_Block, I. DOI: 10.1107/S1600536814024854/is5377sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536814024854/is5377Isup2.hkl

Supporting information file. DOI: 10.1107/S1600536814024854/is5377Isup3.cml

checkCIF report

Structural commentary top

The compounds containing thiazoline or thiazolidine rings are of attractive attention for their coordination chemistry and potential antibiotic and antitumoral activities (Pontiki et al., 2006; Shih & Ke, 2004; Bolos et al., 2002). As part of our continuing study to create sulfur coordinated coordination compounds (Igashira-Kamiyama & Konno, 2011), we synthesized a novel thiazolidine compound, which is prepared from the condensation of D-penicillamine and 2-pyridine carboxaldehyde. Herein the structure and synthesis of (2S,4S)-5,5-dimethyl-2-(pyridin-2-yl)thiazolidine-4-carboxylic acid are reported.

The title compound is enantiometrically pure and the absolute structure was determined by the refinement of the Flack parameter [0.01 (9)]. The chiral C-2 and C-4 atoms (atoms C6 and C7, respectively) have S configurations (Fig. 1). In the crystal, the molecules are interacted through O—H···N hydrogen bonds and weak C–H···π contacts (Table 1), forming a layer parallel to the ac plane (Fig. 2).

Synthesis and crystallization top

To a white suspension of D-penicillamine (60 mg, 0.40 mmol) in MeOH (2.5 mL) was added 2-pyridine carboxaldehyde (43 mg, 0.40 mmol). The mixture was stirred at 50 °C for 2 h to give a pale yellow solution. The reaction mixture was allowed to stand at room temperature. Colorless crystals were obtained by slow evaporation of the reaction mixture after 10 days. Yield: 38 mg (40%). Anal Calcd for C₁₁H₁₄N₂O₂S: C 55.44, H 5.92, N 11.71%. Found: C 55.20, H 5.82, N 11.71%. IR: ν_max (cm^-1): 1570, 1591.

Refinement top

C-bound H atoms were placed at calculated positions (C—H = 0.95, 0.98, or 1.00 Å) and refined as riding, with U_iso(H) = 1.2U_eq(C). N and O-bound H atoms were located in a difference Fourier map and their positions were refined with U_iso(H) = 1.5U_eq(N or O).

Related literature top

For background to compounds containing thiazoline or thiazolidine rings, see: Bolos et al. (2002); Pontiki et al. (2006); Shih & Ke (2004). For related structures, see: Brunner et al. (1984, 2001). For the preparation of D-penicillamine-coordinated metal complexes, see: Igashira-Kamiyama & Konno (2011).

Computing details top

Data collection: PROCESS-AUTO (Rigaku, 1998); cell refinement: PROCESS-AUTO (Rigaku, 1998); data reduction: PROCESS-AUTO (Rigaku, 1998); program(s) used to solve structure: SIR92 (Altomare et al., 1993); program(s) used to refine structure: SHELXL2013 (Sheldrick, 2008); molecular graphics: CrystalStructure (Rigaku, 2014); software used to prepare material for publication: CrystalStructure (Rigaku, 2014).

Figures top

Molecular structure of the title compound with the atom numbering scheme. Displacement ellipsoids are at the 70% probability level. H atoms are drawn as spheres of arbitrary radii.

Crystal packing diagram of the title compound, viewed along with the a axis. Orange and blue dotted lines indicate the weak C—H···π contact and the O—H···N hydrogen bond, respectively.

(2S,4S)-5,5-Dimethyl-2-(pyridin-2-yl)-1,3-thiazolidine-4-carboxylic acid top

Crystal data top

C₁₁H₁₄N₂O₂S	D_x = 1.311 Mg m⁻³
M_r = 238.30	Mo Kα radiation, λ = 0.71075 Å
Orthorhombic, P2₁2₁2₁	Cell parameters from 606 reflections
a = 7.906 (4) Å	θ = 3.0–21.8°
b = 11.306 (5) Å	µ = 0.26 mm⁻¹
c = 13.504 (7) Å	T = 200 K
V = 1207.1 (10) Å³	Block, colorless
Z = 4	0.25 × 0.25 × 0.25 mm
F(000) = 504.00

Data collection top

Rigaku R-AXIS RAPID diffractometer	2711 reflections with F² > 2σ(F²)
ω scans	R_int = 0.020
Absorption correction: multi-scan (ABSCOR; Higashi, 1995)	θ_max = 27.5°, θ_min = 3.0°
T_min = 0.785, T_max = 0.938	h = −10→10
9629 measured reflections	k = −14→13
2767 independent reflections	l = −17→17

Refinement top

Refinement on F²	Hydrogen site location: inferred from neighbouring sites
R[F² > 2σ(F²)] = 0.028	H atoms treated by a mixture of independent and constrained refinement
wR(F²) = 0.074	w = 1/[σ²(F_o²) + (0.045P)² + 0.1433P] where P = (F_o² + 2F_c²)/3
S = 1.10	(Δ/σ)_max < 0.001
2767 reflections	Δρ_max = 0.23 e Å⁻³
152 parameters	Δρ_min = −0.18 e Å⁻³
0 restraints	Absolute structure: Flack x determined using 1118 quotients [(I⁺)-(I^-)]/[(I⁺)+(I^-)] (Parsons et al., 2013)
Primary atom site location: structure-invariant direct methods	Absolute structure parameter: 0.01 (9)
Secondary atom site location: difference Fourier map

Crystal data top

C₁₁H₁₄N₂O₂S	V = 1207.1 (10) Å³
M_r = 238.30	Z = 4
Orthorhombic, P2₁2₁2₁	Mo Kα radiation
a = 7.906 (4) Å	µ = 0.26 mm⁻¹
b = 11.306 (5) Å	T = 200 K
c = 13.504 (7) Å	0.25 × 0.25 × 0.25 mm

Data collection top

Rigaku R-AXIS RAPID diffractometer	2767 independent reflections
Absorption correction: multi-scan (ABSCOR; Higashi, 1995)	2711 reflections with F² > 2σ(F²)
T_min = 0.785, T_max = 0.938	R_int = 0.020
9629 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.028	H atoms treated by a mixture of independent and constrained refinement
wR(F²) = 0.074	Δρ_max = 0.23 e Å⁻³
S = 1.10	Δρ_min = −0.18 e Å⁻³
2767 reflections	Absolute structure: Flack x determined using 1118 quotients [(I⁺)-(I^-)]/[(I⁺)+(I^-)] (Parsons et al., 2013)
152 parameters	Absolute structure parameter: 0.01 (9)
0 restraints

Special details top

Geometry. ENTER SPECIAL DETAILS OF THE MOLECULAR GEOMETRY

Refinement. Refinement was performed using all reflections. The weighted R-factor (wR) and goodness of fit (S) are based on F². R-factor (gt) are based on F. The threshold expression of F² > 2.0 σ(F²) is used only for calculating R-factor (gt).

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å²) top

	x	y	z	U_iso*/U_eq
S1	0.73917 (6)	0.55168 (4)	0.77596 (3)	0.03414 (14)
O1	0.8795 (2)	0.83178 (13)	0.53057 (12)	0.0499 (4)
O2	0.9289 (2)	0.65820 (14)	0.45666 (11)	0.0409 (4)
N1	0.63325 (18)	0.85167 (14)	0.83052 (11)	0.0277 (3)
N2	0.65342 (19)	0.73327 (14)	0.65780 (10)	0.0261 (3)
C1	0.5500 (2)	0.74879 (16)	0.82907 (12)	0.0256 (3)
C2	0.4421 (3)	0.71255 (17)	0.90457 (14)	0.0334 (4)
C3	0.4220 (3)	0.78569 (19)	0.98617 (14)	0.0363 (4)
C4	0.5073 (3)	0.89258 (17)	0.98869 (14)	0.0335 (4)
C5	0.6099 (2)	0.92190 (16)	0.90928 (14)	0.0308 (4)
C6	0.5841 (2)	0.66856 (16)	0.74195 (12)	0.0263 (3)
C7	0.7626 (2)	0.65411 (15)	0.60028 (11)	0.0242 (3)
C8	0.8809 (2)	0.58482 (16)	0.67186 (13)	0.0265 (3)
C9	0.8626 (2)	0.72556 (17)	0.52484 (12)	0.0295 (4)
C10	0.9418 (3)	0.46896 (18)	0.62677 (16)	0.0390 (4)
C11	1.0304 (3)	0.6594 (2)	0.70700 (16)	0.0407 (5)
H2	0.38344	0.63938	0.90033	0.0401*
H3	0.35091	0.76278	1.03953	0.0436*
H4	0.49563	0.94457	1.04353	0.0402*
H5	0.66695	0.99584	0.91074	0.0369*
H6	0.47579	0.63008	0.72142	0.0315*
H7	0.68972	0.59616	0.56409	0.0290*
H10A	0.84418	0.42248	0.60474	0.0468*
H10B	1.01526	0.48577	0.57003	0.0468*
H10C	1.00522	0.42406	0.67652	0.0468*
H11A	0.98853	0.73348	0.73572	0.0488*
H11B	1.09424	0.61552	0.75716	0.0488*
H11C	1.10427	0.67722	0.65067	0.0488*
H12	0.711 (3)	0.790 (2)	0.6820 (17)	0.0392*
H13	0.992 (4)	0.696 (3)	0.424 (2)	0.0614*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
S1	0.0440 (3)	0.0322 (2)	0.0262 (2)	0.0066 (2)	0.00704 (19)	0.00796 (16)
O1	0.0704 (11)	0.0304 (8)	0.0487 (9)	−0.0018 (7)	0.0192 (8)	0.0082 (7)
O2	0.0512 (9)	0.0432 (8)	0.0282 (7)	−0.0165 (7)	0.0152 (6)	−0.0046 (6)
N1	0.0281 (7)	0.0288 (8)	0.0263 (7)	−0.0001 (6)	0.0014 (6)	0.0008 (6)
N2	0.0305 (7)	0.0296 (8)	0.0183 (6)	0.0036 (6)	−0.0018 (6)	0.0012 (6)
C1	0.0241 (7)	0.0314 (9)	0.0214 (7)	0.0026 (6)	−0.0028 (6)	0.0014 (6)
C2	0.0336 (9)	0.0336 (10)	0.0331 (9)	−0.0037 (8)	0.0061 (8)	0.0012 (8)
C3	0.0391 (10)	0.0418 (11)	0.0281 (9)	0.0034 (9)	0.0105 (8)	0.0032 (8)
C4	0.0402 (10)	0.0344 (10)	0.0259 (8)	0.0106 (8)	0.0019 (7)	−0.0020 (7)
C5	0.0331 (9)	0.0274 (9)	0.0318 (9)	0.0026 (7)	−0.0001 (7)	−0.0002 (7)
C6	0.0262 (8)	0.0310 (8)	0.0216 (8)	−0.0017 (7)	−0.0010 (6)	0.0010 (7)
C7	0.0269 (7)	0.0273 (7)	0.0184 (6)	−0.0040 (7)	−0.0009 (6)	0.0005 (6)
C8	0.0289 (8)	0.0267 (8)	0.0238 (8)	−0.0004 (6)	0.0015 (7)	0.0013 (6)
C9	0.0331 (8)	0.0333 (9)	0.0222 (8)	−0.0035 (7)	−0.0001 (7)	0.0044 (7)
C10	0.0444 (11)	0.0324 (10)	0.0402 (11)	0.0066 (9)	0.0088 (9)	−0.0016 (8)
C11	0.0365 (10)	0.0435 (11)	0.0421 (11)	−0.0056 (9)	−0.0132 (9)	0.0019 (9)

Geometric parameters (Å, º) top

S1—C6	1.8599 (19)	C8—C11	1.528 (3)
S1—C8	1.8362 (19)	O2—H13	0.79 (3)
O1—C9	1.211 (2)	N2—H12	0.85 (2)
O2—C9	1.305 (2)	C2—H2	0.950
N1—C1	1.337 (2)	C3—H3	0.950
N1—C5	1.340 (2)	C4—H4	0.950
N2—C6	1.458 (2)	C5—H5	0.950
N2—C7	1.466 (2)	C6—H6	1.000
C1—C2	1.391 (3)	C7—H7	1.000
C1—C6	1.510 (2)	C10—H10A	0.980
C2—C3	1.387 (3)	C10—H10B	0.980
C3—C4	1.384 (3)	C10—H10C	0.980
C4—C5	1.385 (3)	C11—H11A	0.980
C7—C8	1.556 (2)	C11—H11B	0.980
C7—C9	1.522 (2)	C11—H11C	0.980
C8—C10	1.523 (3)

C6—S1—C8	93.90 (8)	C7—N2—H12	110.5 (16)
C1—N1—C5	117.35 (15)	C1—C2—H2	120.764
C6—N2—C7	109.13 (14)	C3—C2—H2	120.760
N1—C1—C2	123.21 (16)	C2—C3—H3	120.513
N1—C1—C6	116.48 (15)	C4—C3—H3	120.502
C2—C1—C6	120.26 (16)	C3—C4—H4	120.818
C1—C2—C3	118.48 (18)	C5—C4—H4	120.808
C2—C3—C4	118.98 (18)	N1—C5—H5	118.207
C3—C4—C5	118.37 (18)	C4—C5—H5	118.203
N1—C5—C4	123.59 (17)	S1—C6—H6	108.899
S1—C6—N2	107.54 (12)	N2—C6—H6	108.902
S1—C6—C1	110.63 (12)	C1—C6—H6	108.903
N2—C6—C1	111.90 (15)	N2—C7—H7	108.652
N2—C7—C8	109.38 (13)	C8—C7—H7	108.655
N2—C7—C9	109.66 (14)	C9—C7—H7	108.656
C8—C7—C9	111.77 (14)	C8—C10—H10A	109.475
S1—C8—C7	102.22 (12)	C8—C10—H10B	109.471
S1—C8—C10	108.89 (13)	C8—C10—H10C	109.472
S1—C8—C11	110.30 (13)	H10A—C10—H10B	109.472
C7—C8—C10	112.01 (15)	H10A—C10—H10C	109.467
C7—C8—C11	112.32 (15)	H10B—C10—H10C	109.470
C10—C8—C11	110.76 (16)	C8—C11—H11A	109.470
O1—C9—O2	125.42 (18)	C8—C11—H11B	109.475
O1—C9—C7	122.76 (16)	C8—C11—H11C	109.473
O2—C9—C7	111.80 (16)	H11A—C11—H11B	109.465
C9—O2—H13	109 (2)	H11A—C11—H11C	109.474
C6—N2—H12	106.1 (15)	H11B—C11—H11C	109.470

Hydrogen-bond geometry (Å, º) top

Cg is the centroid of the N1/C1–C5 ring.

D—H···A	D—H	H···A	D···A	D—H···A
O2—H13···N2ⁱ	0.79 (3)	1.87 (3)	2.654 (2)	173 (3)
C3—H3···Cgⁱⁱ	0.95	2.81	3.629 (2)	145

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

Hydrogen-bond geometry (Å, º) top

Cg is the centroid of the N1/C1–C5 ring.

D—H···A	D—H	H···A	D···A	D—H···A
O2—H13···N2ⁱ	0.79 (3)	1.87 (3)	2.654 (2)	173 (3)
C3—H3···Cgⁱⁱ	0.95	2.81	3.629 (2)	145

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

Acknowledgements

This work was supported by a Grant-in-Aid for Science Research (grant No. 23350026) from the Ministry of Education, Culture, Sports, Science and Technology of Japan.

References

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Crystal structure of (2S,4S)-5,5-di­methyl-2-(pyridin-2-yl)-1,3-thia­zolidine-4-carb­­oxy­lic acid

1. Related literature

2. Experimental

2.1. Crystal data

2.2. Data collection

2.3. Refinement

Supporting information

Acknowledgements

References

organic compounds

Crystal structure of (2S,4S)-5,5-dimethyl-2-(pyridin-2-yl)-1,3-thiazolidine-4-carboxylic acid