L-Cysteinium semioxalate: a new monoclinic polymorph or a hydrate?

The title compound, C₃H₈NO₂S⁺·C₂HO₄^-, (I), crystallizes in the monoclinic C2 space group and is a new form (possibly a hydrate) of L-cysteinium semioxalate with a stoichiometric cation-anion ratio of 1:1. In contrast to the previously known ortho­rhom­bic form of L-cysteinium semioxalate, (I) has a layered structure resembling those of monoclinic L-cysteine, as well as of DL-cysteine and its oxalates. The conformations of the cysteinium cation and the oxalate anion in (I) differ substanti­ally from those in the ortho­rhom­bic form. The structure of (I) has voids with a size sufficient to incorporate water mol­ecules. The residual density, however, suggests that if water is in fact present in the voids, it is strongly disordered and its amount does not exceed 0.3 mol­ecules per void. The difference in conformation of the cysteinium cations in (I) and in the ortho­rhom­bic form is similar to that in DL-cysteine under ambient conditions and in DL-cysteine under high pressure or at low temperature.

S1. Comment

The sulfhydryl group plays an important role in biology (Jocelyn, 1972). In proteins, sulfhydryl-containing amino acids are involved in the formation of additional hydrogen bonds. In addition, the side chain of such an amino acid can be easily oxidized, giving rise to cystine with a disulfide bond. These interactions contribute to the stabilization of a protein active form. Therefore, investigation of the conformation of sulfhydryl-containing fragments and of their specific interactions is important. Cysteine is the simplest and widespread sulfhydryl-containing amino acid and may be considered therefore as a model object. Notwithstanding its seeming simplicity, cysteine has already demonstrated a variety of different zwitterion conformations and hydrogen-bonding patterns even in the crystalline state. Under ambient conditions, there are two polymorphic modifications of L-cysteine, namely the monoclinic (Harding & Long, 1968; Görbitz & Dalhus, 1996) and the orthorhombic (Kerr & Ashmore, 1973) forms, and one polymorph of DL-cysteine (Luger & Weber, 1999). On cooling, both DL-cysteine (Minkov, Tumanov et al., 2009) and the orthorhombic polymorph of L-cysteine (Kolesov et al., 2008) undergo polymorphic transformations, whereas only a subtle structural change has been reported for monoclinic L-cysteine (Bordallo et al., 2010). With increasing pressure, a series of phase transitions occurs in DL-cysteine, as well as in the two polymorphs of L-cysteine (Moggach et al., 2006; Minkov et al., 2008; Minkov, Tumanov et al., 2010; Minkov, Goryainov et al., 2010). It is worth noting that all the polymorphs of L- and DL-cysteine, including those obtained and existing under non-ambient conditions only, differ substantially in their molecular conformation and intermolecular hydrogen bonds, especially in the hydrogen bonds formed by the side chain of the amino acid.

Another way to study the conformational lability of cysteine at ambient temperature and pressure is to investigate its salts and cocrystals. Several cysteinium salts described previously show the diversity of zwitterion conformations easily provoked by changing the crystalline environment (Shan & Huang, 1999; Fujii et al., 2005; Drebushchak et al., 2008; Minkov & Boldyreva, 2008; Minkov & Boldyreva, 2009). The present paper provides a new example of a cysteinium salt with interesting features in the crystal structure.

The title compound, (I), consisting of L-cysteinium cations with protonated carboxylate groups and partially deprotonated semioxalate anions may be classified as a salt. As in the case of the orthorhombic form of L-cysteinium semioxalate, (II), the carboxylate group in (I) is protonated in a trans position with respect to amino group (Fig. 1). Depending on the orientation of the –CH₂—SH side chain, cysteine cations are prone to adopt gauche+ or gauche- conformations with positive or negative values of the S—C—C—N torsion angle of ca +60 and -60°, respectively. There is only one exception, namely the monoclinic polymorph of L-cysteine (Harding & Long, 1968), in which one of the two molecules in the asymmetric unit has the orientation of the side chain corresponding to a trans conformation (with S—C—C—N torsion angles of ca 180°), the other one to a gauche+ conformation. In (I), the conformation of the cysteinium cation is gauche+ (Table 1), similar to that in the orthorhombic polymorph of L-cysteine (Kerr & Ashmore, 1973) and DL-cysteinium semioxalate (Minkov & Boldyreva, 2009). In all the L-cysteinium salts known up to now the orientation of the –CH₂—SH residue corresponds to gauche- conformation (Shan & Huang, 1999; Fujii et al., 2005; Minkov & Boldyreva, 2008). The same holds for the high-pressure polymorphs of L-cysteine (Moggach et al., 2006). Such a large dispersion in the amino acid side chain orientations in cysteinium salts (the difference in the torsion angles N—C—C—S is about 120°) is comparable with the difference in the values of the torsion angle N—C—C—S in the ambient-temperature (gauche+ conformation) and the low-temperature or high-pressure (gauche- conformation) polymorphs of racemic DL-cysteine (Minkov, Tumanov et al., 2009). The semioxalate anion is somewhat twisted, the value of an angle between the two COO^- planes being 13.9 (3)°, what is significantly smaller than in (II) [38.6 (3)°] and larger than in DL-cysteinium oxalates [0 and 7.1 (3)°].

In the crystal structure of (I), semioxalate anions are linked with each other via O5—H5O···O3 hydrogen bonds forming infinite C(5) chains expanding along the crystallographic b axis (Fig. 2). The distance between atoms O3 and O5 in this strongest hydrogen bond is slightly shorter than that in (II) [2.5346 (18) Å; Table 2]. At the same time, a little longer O1—H1O···O4 hydrogen bond connecting the carboxyl group of the cysteinium cation with the semioxalate anion is also present in the structure of (I), similar to (II). The carboxyl group of the cysteinium cation forms an R₂²(6) motif with neighboring ammonium and carboxylate groups. Each H atom of the amino group in the cysteinium cation participates in the formation of four different hydrogen bonds with neighboring semioxalate anions, and one with another cation. The N1—H2N···O2 hydrogen bond links cations into infinite chains along a screw axis 2₁ and the crystallographic b axis. The same H atom, H2N, also participates in the formation of the N1—H2N···O4 hydrogen bond with a semioxalate anion. As in all the previously investigated cysteinium oxalates, in (I) there is a common R₁²(5) ring motif formed by the N—H···O bifurcated hydrogen bond between the N1—H1N group and and atoms O3 and O6 of the semioxalate anion as acceptors. Although in (II) this motif includes the protonated O atom from the semioxalate carboxyl group, this is not the case for (I). Interestingly enough, in spite of the significant difference in the electronegativity between the protonated (O5) and nonprotonated (O4) O atoms of the carboxyl group in the structure of (II), the difference in the two N—O distances [2.912 (2) and 3.041 (2) Å] in this bifurcated bond is smaller than that in (I). In addition to the N1—H1N···O6 hydrogen bond, there is a very long N1—H3N···O6 hydrogen bond. Moreover, atom H3N participates in the formation of this long hydrogen bond only.

We could not see any strong directional hydrogen bonds formed by SH groups in the structure of (I). The shortest S···S distance in the structure is 4.201 (1) Å, i.e. much longer than required to form an S—H···S hydrogen bond. For a comparison, the S···S distance in a very weak S—H···S bond in the structure of the monoclinic polymorph of L-cysteine is 4.080 (1) Å. At the same time, there are some short contacts (S···O3, S···O4 and S···O5) of the –SH group with a neighboring semioxalate anion [with S—H distances of 3.649 (3), 3.720 (2) and 3.716 (3) Å, respectively]. This would suggest that a sulfhydryl group interacts simultaneously with several O atoms of the same semioxalate anion. SH groups could also be weakly interacting with potential host water molecules in the crystal voids. Anyhow, if the SH groups are involved in S—H···O attractive interactions, these interactions should be very weak.

Crystal packing in (I) and (II) is significantly different. In (II), as well as in the orthorhombic polymorph of L-cysteine, the crystal structure is built as a three-dimensional framework with infinite channels, in which the –CH₂—SH side chains are locked up. Moreover, these channels are preserved on cooling and with increasing pressure, even after the phase transitions (Moggach et al., 2006). In contrast, the crystal structure of (I) is layered, like in the case of the monoclinic polymorph of L-cysteine or of DL-cysteine (Fig. 3). The layers are parallel to the (201) crystallographic plane and are formed by infinite chains of cations and anions stretched along the crystallographic b axis. The distance between layers in (I) [8.863 (3) Å] is longer, than in DL-cysteinium semioxalate [8.197 (3) Å], but is significantly shorter, than the interlayer distance in the monoclinic polymorph of L-cysteine [10.719 (3) Å; Görbitz & Dalhus, 1996]. The layers are not bound by any hydrogen bonds with each other.

Several structures with no hydrogen bonds between the layers have been described earlier for `cysteine-family' [DL-cysteine-II (Minkov et al., 2009), monoclinic L-cysteine (Görbitz & Dalhus, 1996) and DL-cysteinium oxalate (Drebushchak et al., 2008] and semioxalate (Minkov & Boldyreva, 2009)). In most of these structures, the SH groups were involved in hydrogen bonds within the layers. At the same time, in DL-cysteinium semioxalate the SH groups form no significant hydrogen bonds, although they are involved in many short contacts with O atoms, and this is confirmed also by Raman spectra (Minkov & Boldyreva, 2009), which are very sensitive to the interactions of SH groups with the environment. Unfortunately, we could not study the interactions of the SH group in the crystal structure of (I) by Raman spectroscopy, since the few crystals available were used for the single-crystal diffraction study and a new attempt of crystallization was not successful (see Experimental).

The major difference between the crystal packing in the two salts of L-cysteine is that in (I) the infinite chains formed by the semioxalate anions and those formed by the cysteinium cations are both extended along the same crystallographic b axis, whereas in (II) these chains extend along orthogonal directions. Interestingly, the crystal packing in (I) is similar to that in DL-cysteinium semioxalate. In the latter, cations form dimers, not infinite chains as in (I), but these dimers are further stacked into piles and linked also with each other via oxalate anions. These piles and infinite chains of semioxalate anions are directed along the same crystallographic axis.

Related literature

For related literature, see: Bordallo et al. (2010); Drebushchak et al. (2008); Fujii et al. (2005); Görbitz & Dalhus (1996); Harding & Long (1968); Jocelyn (1972); Kerr & Ashmore (1973); Kolesov et al. (2008); Luger & Weber (1999); Minkov & Boldyreva (2008, 2009); Minkov, Goryainov, Boldyreva & Görbitz (2010); Minkov, Krylov, Boldyreva, Goryainov, Bizyaev & Vtyurin (2008); Minkov, Tumanov, Boldyreva & Cabrera (2010); Minkov, Tumanov, Kolesov, Boldyreva & Bizyaev (2009); Moggach et al. (2006); Shan & Huang (1999).

S2. Experimental

Colorless prismatic crystals of (I) were obtained by slow diffusion of acetonitrile into a saturated aqueous solution of L-cysteine and oxalic acid in an equimolar ratio. The crystals were not stable on storage. After being taken out of the mother solution and kept in air for a few days they were found to be cracked, which may indicate that the new form is a solvate (a hydrate?) and loses crystal water. Unfortunately, we could not analyze the phase after cracking due to the small amount of sample. Additional tests using complementary techniques (TG, DSC, IR spectroscopy) would be necessary to distinguish between a true new polymorph and a new `crystal form' which is actually a hydrate. However, we could not grow any more crystals of (I) to carry out these tests.

S3. Refinement

Methine, methylene and hydroxy H atoms were placed in geometrically calculated positions and constrained to ride on their parent atoms, with X—H distances of 0.98, 0.97 and 0.82 Å, respectively, and refined using a riding model. The H atoms of the ammonium group were also constrained to an ideal geometry, with N—H distances of 0.89 Å, but were allowed to rotate freely about the N—C bond. The position of sulfhydryl H atom was found from a difference Fourier map and refined with a restraint on the S—H distance of 1.20 Å. In order to check the localization of the sulfhydryl H atom, a dummy SH₃ group was introduced. The occupancies of several possible H-atom positions were refined and eventually estimated as 0.54 for the relevant H atom and less than 0.15 for the other two H atoms. The positions for both H atoms found from the difference Fourier map and from the introduced dummy SH₃ group are coincided [?]. For all H atoms, U_iso(H) values were set at 1.2U_eq(parent atom). In the present structural model, a residual electron-density peak still remained with a value of 0.45 e. Searching for solvent-accessible voids in the structure shows the presence of two voids with a size of 34 ų (grid = 0.2 Å and probe radius = 1.2 Å) and an electron count of 3 (cutoff level = 0.5 e Å^-3). Both voids are located between layers exactly in (0.000, 0.405, 1/2) and (0.500, -0.095, 0.500). The total positive electron count in the voids per unit cell is 6. Although the volume of a void is somewhat smaller than is typically required to host a water molecule (40 ų), one can suppose that the new structure can be in fact a hydrate, with highly disordered guest molecules and average void occupancy not exceeding 0.3 molecules per void. Crystal cracking on storage in air can be a consequence of dehydration. However, the potential water guest molecules, if present, could not be refined in a structural model of a hydrate, probably because of low occupancy and strong disorder.

Computing details

Data collection: X-AREA (Stoe & Cie, 2007); cell refinement: X-AREA (Stoe & Cie, 2007); data reduction: X-RED (Stoe & Cie, 2007); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: Mercury (Version 1.4.2; Macrae et al., 2008); software used to prepare material for publication: publCIF (Westrip, 2010).

Figures

	Fig. 1. The asymmetric unit of (I), showing the atom-labelling scheme. Displacement ellipsoids are drawn at the 50% probability level and H atoms are shown as spheres of arbitrary radii.
	Fig. 2. Hydrogen bonding (dashed lines) between semioxalate anions and L-cysteinium cations in (I). [Symmetry codes: (i) x-1/2, y+1/2, z-1; (ii) x-1/2, y-1/2, z-1; (iii) x-1/2, y-3/2, z-1; (iv) -x+1/2, y+1/2, -z+1; (v) -x+1/2, y-1/2, -z+1; (vi) x, y-1, z; (vii) -x+1/2, y-3/2, -z+1.]
	Fig. 3. A fragment of a crystal structure of (I), projected on the ac plane. Hydrogen bonds are shown as dashed lines.

L-cysteinium semioxalate

Crystal data

C3H8NO2S^+·C2HO4^−	F(000) = 440
Mr = 211.20	Dx = 1.451 Mg m^−3
Monoclinic, C2	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: C 2y	Cell parameters from 3468 reflections
a = 18.604 (4) Å	θ = 2.2–29.1°
b = 5.5723 (6) Å	µ = 0.34 mm^−1
c = 11.270 (2) Å	T = 293 K
β = 124.192 (13)°	Prism, colourless
V = 966.4 (3) Å^3	0.41 × 0.34 × 0.14 mm
Z = 4

Data collection

Stoe IPDS 2 diffractometer	2112 independent reflections
Radiation source: sealed X-ray tube, 12 x 0.4 mm long-fine focus	1500 reflections with I > 2σ(I)
Plane graphite monochromator	Rint = 0.045
Detector resolution: 6.67 pixels mm^-1	θmax = 28.3°, θmin = 2.2°
rotation method scans	h = −24→24
Absorption correction: numerical (X-SHAPE; Stoe & Cie, 2003)	k = −7→6
Tmin = 0.657, Tmax = 0.885	l = −15→15
4404 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)] = 0.036	H atoms treated by a mixture of independent and constrained refinement
wR(F^2) = 0.093	w = 1/[σ^2(Fo^2) + (0.0491P)^2] where P = (Fo^2 + 2Fc^2)/3
S = 0.99	(Δ/σ)max < 0.001
2112 reflections	Δρmax = 0.45 e Å^−3
122 parameters	Δρmin = −0.19 e Å^−3
2 restraints	Absolute structure: Flack (1983), ???? Friedel pairs
Primary atom site location: structure-invariant direct methods	Absolute structure parameter: −0.08 (11)

Special details

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
C1	0.31814 (15)	0.4543 (5)	0.4617 (2)	0.0375 (6)
C2	0.26302 (15)	0.2977 (5)	0.3293 (2)	0.0353 (5)
H2	0.2651	0.1323	0.3607	0.042*
C3	0.29583 (18)	0.2999 (5)	0.2320 (2)	0.0453 (6)
H31	0.2584	0.1977	0.1500	0.054*
H32	0.3537	0.2307	0.2841	0.054*
C4	0.53610 (14)	0.6612 (4)	0.8787 (2)	0.0306 (5)
C5	0.56486 (14)	0.4117 (4)	0.9464 (2)	0.0321 (5)
O1	0.39574 (13)	0.3608 (4)	0.54721 (19)	0.0639 (7)
H1O	0.4283	0.4610	0.6068	0.077*
O2	0.29193 (10)	0.6377 (4)	0.47965 (17)	0.0481 (5)
O3	0.57480 (12)	0.8321 (3)	0.96393 (17)	0.0486 (5)
O4	0.47809 (10)	0.6816 (3)	0.74970 (16)	0.0418 (4)
O5	0.53635 (12)	0.2436 (3)	0.85100 (18)	0.0490 (5)
H5O	0.5450	0.1127	0.8900	0.059*
O6	0.60818 (11)	0.3855 (3)	1.07557 (16)	0.0411 (4)
N1	0.17177 (13)	0.3854 (4)	0.25345 (19)	0.0412 (5)
H1N	0.1400	0.3196	0.1665	0.049*
H3N	0.1710	0.5444	0.2453	0.049*
H2N	0.1498	0.3445	0.3033	0.049*
S1	0.30008 (6)	0.59190 (18)	0.16806 (9)	0.0674 (3)
H1S	0.347 (2)	0.705 (6)	0.274 (3)	0.081*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
C1	0.0366 (12)	0.0436 (15)	0.0245 (10)	−0.0030 (11)	0.0124 (9)	−0.0051 (9)
C2	0.0394 (12)	0.0342 (13)	0.0218 (9)	−0.0064 (10)	0.0109 (9)	−0.0038 (9)
C3	0.0482 (14)	0.0509 (17)	0.0338 (11)	0.0003 (13)	0.0213 (11)	−0.0061 (11)
C4	0.0289 (10)	0.0267 (12)	0.0272 (9)	0.0017 (9)	0.0103 (8)	−0.0036 (9)
C5	0.0284 (11)	0.0285 (12)	0.0288 (10)	−0.0027 (9)	0.0096 (9)	−0.0053 (9)
O1	0.0461 (10)	0.0632 (14)	0.0387 (9)	0.0134 (10)	−0.0028 (8)	−0.0162 (9)
O2	0.0406 (9)	0.0539 (13)	0.0360 (8)	0.0010 (9)	0.0130 (7)	−0.0167 (8)
O3	0.0573 (11)	0.0254 (9)	0.0313 (7)	0.0009 (8)	0.0056 (7)	−0.0040 (7)
O4	0.0393 (9)	0.0351 (9)	0.0269 (7)	0.0026 (7)	0.0039 (6)	−0.0015 (6)
O5	0.0657 (12)	0.0252 (9)	0.0328 (8)	0.0025 (8)	0.0136 (8)	−0.0037 (7)
O6	0.0426 (9)	0.0362 (10)	0.0288 (7)	0.0009 (7)	0.0104 (7)	0.0014 (7)
N1	0.0362 (10)	0.0555 (14)	0.0286 (9)	−0.0154 (9)	0.0163 (8)	−0.0111 (9)
S1	0.0731 (5)	0.0769 (6)	0.0739 (5)	0.0102 (5)	0.0545 (4)	0.0241 (5)

Geometric parameters (Å, º)

C1—O2	1.197 (3)	C4—O3	1.253 (3)
C1—O1	1.312 (3)	C4—C5	1.530 (3)
C1—C2	1.524 (3)	C5—O6	1.213 (3)
C2—N1	1.490 (3)	C5—O5	1.294 (3)
C2—C3	1.525 (3)	O1—H1O	0.8200
C2—H2	0.9800	O5—H5O	0.8200
C3—S1	1.800 (3)	N1—H1N	0.8900
C3—H31	0.9700	N1—H3N	0.8900
C3—H32	0.9700	N1—H2N	0.8900
C4—O4	1.236 (2)	S1—H1S	1.189 (18)
O2—C1—O1	126.8 (2)	O4—C4—O3	125.3 (2)
O2—C1—C2	122.7 (2)	O4—C4—C5	119.94 (18)
O1—C1—C2	110.4 (2)	O3—C4—C5	114.77 (17)
N1—C2—C1	107.3 (2)	O6—C5—O5	126.6 (2)
N1—C2—C3	111.86 (18)	O6—C5—C4	121.20 (18)
C1—C2—C3	112.3 (2)	O5—C5—C4	112.23 (17)
N1—C2—H2	108.5	C1—O1—H1O	109.5
C1—C2—H2	108.5	C5—O5—H5O	109.5
C3—C2—H2	108.5	C2—N1—H1N	109.5
C2—C3—S1	114.9 (2)	C2—N1—H3N	109.5
C2—C3—H31	108.5	H1N—N1—H3N	109.5
S1—C3—H31	108.5	C2—N1—H2N	109.5
C2—C3—H32	108.5	H1N—N1—H2N	109.5
S1—C3—H32	108.5	H3N—N1—H2N	109.5
H31—C3—H32	107.5	C3—S1—H1S	104.6 (19)
O2—C1—C2—N1	−12.6 (3)	C1—C2—C3—S1	−58.3 (3)
O1—C1—C2—N1	168.5 (2)	O4—C4—C5—O6	−165.1 (2)
O2—C1—C2—C3	110.7 (3)	O3—C4—C5—O6	14.1 (3)
O1—C1—C2—C3	−68.3 (3)	O4—C4—C5—O5	13.7 (3)
N1—C2—C3—S1	62.4 (2)	O3—C4—C5—O5	−167.1 (2)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1N···O3^i	0.89	1.89	2.715 (2)	153
N1—H1N···O6^i	0.89	2.56	3.242 (3)	134
O1—H1O···O4	0.82	1.81	2.611 (3)	164
N1—H2N···O4^ii	0.89	2.29	2.992 (3)	136
N1—H2N···O2^ii	0.89	2.35	3.021 (3)	133
N1—H3N···O6^iii	0.89	2.47	3.243 (3)	145
O5—H5O···O3^iv	0.82	1.71	2.523 (3)	171
C2—H2···O2^ii	0.98	2.55	2.992 (3)	107

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