Pseudosymmetry in ammonium [(carboxymethyl)sulfanyl]acetate

The structure of the title compound, NH₄⁺·C₄H₅O₄S⁻, is composed of mono­carboxyl­ate anions of [(carboxymethyl)sulfanyl]acetic acid linked into infinite chains via strong O—H...O⁻ hydrogen bonds. The three-dimensional structure is completed by the ammonium cations, which interlink neighbouring chains via N—H...O hydrogen bonds. Solution and refinement in the true space group Pn led to an unambiguous position for the single carboxyl H atom. In the higher symmetry space group P2/n, the carboxylate anion would be located on a twofold axis.

S1. Comment

Sodium borohydride (NaBH₄) is a valuable reducing agent in modern organic synthesis and is the reagent of choice in the many reductions of C—O, C—N and even C—C multiple bonds. The reactivity of NaBH₄ can be readily modified and enhanced through its reaction with various additives and modifying agents (Perisamy & Thirumalaikumar, 2000).

Over the past decade we have been interested in the (stereo)selective synthesis of various natural or medicinally significant products (Ziółkowski et al., 1999; Biała et al., 2002). In some cases, the above-mentioned borohydride reduction was the key step. Recently, we have studied selective reductions of prochiral fragments of intermediates in the stereoselective synthesis of natural protoberberines and mianserin. Thus, the intermediate compounds (I) and (II) were prepared (Sotomayor et al., 1996; Pawłowska et al., 2003) and subjected to reduction with a variety of acyloxyborohydrides. The best results (65–70% d.e.) were obtained with tris(trimethylacetoxyborohydride) (Pawłowska et al., 2004). In the search for even better diastereo control, we focused our attention on [(carboxymethyl)thio]acetic acid, (III) [alternative names: 2,2'-thiobis(acetic acid), mercaptodiacetic acid, thiodiglycolic acid], which has never been used as a substituent for borohydride modifications. We surmise that the molecule of (III) combines steric demands with a remarkable ability to form complexes with transition metals (Efimenko et al., 1991), thus making it a good reagent for borohydride derivatization. Having experienced some problems with the solubility of the protoberberine precursor, (I), in the same solvent as the reducing agent, we decided to make the reagent water-soluble and stable by transforming the acid into its mono-ammonium salt. Thus, the title [(carboxymethyl)thio]acetic acid ammonium salt, (IV), was prepared from 1,4-oxathiane-2,6-dione, (V), by the action of aqueous ammonia. \sch

Initially, the diffraction data for (IV) were collected at room temperature on a conventional four-circle diffractometer. Although the structure could be solved and refined in both centrosymmetric and non-centrosymmetric space groups (P2/n and Pn, respectively), better results (see below) were obtained in the latter, for which there was also a slight preference in terms of the intensity statistics (mean |E² − 1| = 0.801). However, although the structure was qualitatively reasonable, some features were unsatisfactory, for instance discrepancies in N—H distances or relatively high and unequal isotropic displacement parameters for these H atoms. For this reason, a complete sphere of low-temperature data was collected on an area detector. Here, we present and discuss only the low-temperature data, which provide a strong indication that the lower-symmetry space group Pn is correct.

The asymmetric unit of (IV) (Fig. 2) consists of the mono-anion of the acid, (III), and an ammonium cation. Bond distances and angles are summarized in Table 2. There are three types of hydrogen bonds stabilizing the present structure. One type is between carboxyl and carboxylate groups, leading to a zigzag chain of anions with overall direction parallel to [1 0 1]. The second type has three N—H···O linkages involving carboxyl and carboxylate O atoms, and the third type has N—H···S hydrogen bonds (Fig. 3 and Table 3). The ammonium ions thus link the chains into a three-dimensional array.

There are some similarities between the structure of (IV) and that of ammonium hydrogen glutarate (with the S atom replaced by a methylene group; Macdonald & Speakman, 1971). One dissimilarity lies in the overall molecule conformation: the glutarate anion forms a planar zigzag chain that is almost linear, whereas the hydrogen thiobiacetate anion is twisted in all structures, so that the S and C atoms are not in the same plane. Even more important is the difference in overall packing in these structures. Ammonium hydrogen glutarate consists of alternate planes of glutarate dianions and ammonium cations perpendicular to the a direction in the orthorhombic lattice. The anions pass approximately parallel to the a direction (perpendicular to the layers).

An additional distinction in the structure of (IV) is the presence of very strong O—H···O⁻ hydrogen bonds between carboxyl and carboxylate groups. The significant difference between the two C—O distances [1.244 (2) and 1.279 (2) Å for C4—O3 and C4—O4, respectively] may indicate a partial localization of negative charge at O4, consistent with the very short O—H···O4 contact. On the other hand, the C—O distances involving atom C1 [1.320 (2) and 1.212 (2) Å for C1—O1 and C1—O2, respectively] correspond to those expected for carboxylic acids [1.308 (19) and 1.214 (19) Å, respectively (Allen et al., 1987; Maurin, 1998)]. Comparison with thiobiacetic acid (Kepert et al., 1999) is also instructive. In that compound, the usual centrosymmetric carboxylic acid dimers are observed, with O···O and H···O distances of 2.675 and 1.894 Å, respectively, leading to infinite chains of molecules. The C—O bond distances of 1.299 and 1.221 Å, respectively, are normal for carboxylic acids. The molecule of thiobiacetic acid is approximately planar.

We now present our reasons for rejecting the centrosymmetric space group P2/n. The corresponding refinement presented serious problems, the most important of which involved the carboxyl H atom. The special position of the S atom on the twofold axis would, in an ordered structure, imply either the presence of the dicarboxylic acid itself or of its dianion, both inconsistent with the single ammonium cation. The localization of an H atom in the vicinity of one carboxyl O atom resulted, however, in a close H···H contact between molecules related by the inversion centre, and its position could not be refined. The only possible solutions were a localization of this H atom on the inversion centre, or a description of the structure as partially disordered. Nevertheless, such a procedure led to much worse overall results for the initial room-temperature data than refinement in the space group Pn (wR2 = 0.1349 and 0.0775, respectively). These findings were then confirmed by the low-temperature structure solution and refinement (wR2 = 0.0738 in Pn).

The previously solved structures of potassium and rubidium hydrogen thiobiacetates (Herbertsson, 1976) were presented as an isomorphous pair in space group P2/c, but were not entirely satisfactory (OH H atom not located, high R values). The cells can be transformed with the matrix (1 0 0, 0 1 0, 1 0 1) to a cell analogous to that of (IV). We assume, therefore, that these structures are isomorphous with (IV) and should have been refined in the same non-centrosymmetric space group. There is, however, one obvious qualitative distinction between the potassium/rubidium and ammonium salts, namely that the ammonium cation can act as a hydrogen-bond donor.

The problem of pseudosymmetry as presented above is quite common for structures with short carboxyl (–COOH) to carboxylate (–COO⁻) interactions. From a total of 7022 organic and metal-organic structures containing carboxylic groups (Cambridge Structural Database, Version 5.24; Allen, 2002), 49 involve carboxylic H atoms with intermolecular distances closer than the sum of the van der Waals radii, and in 24 structures this distance is even shorter than 1 Å. In 26 cases, the molecules in question are symmetry-related by a centre of symmetry, a twofold axis or a mirror plane. It is interesting that, in all cases, the O···O distance is relatively short [mean value 2.35 Å (2.57 Å for the whole group of 49)], much less then the mean value for O—H···O D···A distances in carboxylic acids (2.64 Å; Maurin, 1998). 18 of 49 structures were described as disordered in the carboxylic acid region. Such an explanation is acceptable for hydrogen bonds between carboxyl and carboxylate groups, but an alternative might be description in a lower-symmetry space group, as in the structure of (IV). The only supporting argument for disorder would be a small difference in the C—O distances of the carboxylic acid group even in the lower-symmetry space group. We believe that careful and precise measurements might resolve many dubious pseudosymmetry cases, which are fairly common not only for carboxyl-carboxylate interactions, but also for many other structures with very strong hydrogen bonds to anionic acceptor sites.

S2. Experimental

Compound (IV) was prepared by the slow addition of 25% ammonia solution (5 ml) to compound (III) (1 g) dissolved in dioxane (20 ml). After the addition, the solvents were removed by evaporation under vacuum and the residue was heated at 503 K for 2 h. The product was recrystallized from ethanol to afford compound (IV) in 93% yield (m. p. 432–433 K). NMR spectra were in accordance with the structure.

S3. Refinement

Crystals were enantiomeric twins and the structure was refined accordingly. A total of 994 Friedel pairs were used to establish the Flack parameter (Flack, 1983). H atoms attached to C atoms were included at calculated positions and refined using a riding model; other H atoms were refined freely.

Computing details

Data collection: SMART (Bruker, 2000); cell refinement: SAINT (Bruker, 2000); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 1990); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: XP (Bruker, 2000); software used to prepare material for publication: SHELXL97.

Figures

	Fig. 1. The independent part of the unit cell of (IV). Displacement ellipsoids are drawn at the 50% probability level and H atoms are shown as small spheres of arbitrary radii.
	Fig. 2. The crystal packing diagram for (IV) viewed along the b direction. Hydrogen bonds are shown as dashed lines.

Ammonium [(carboxymethyl)thio]acetate

Crystal data

NH4^+·C4H5O4S^−	F(000) = 176
Mr = 167.18	Dx = 1.513 Mg m^−3
Monoclinic, Pn	Melting point = 432–433 K
Hall symbol: P -2yac	Mo Kα radiation, λ = 0.71073 Å
a = 7.0429 (8) Å	Cell parameters from 3980 reflections
b = 4.8135 (6) Å	θ = 3.3–30.0°
c = 10.9047 (12) Å	µ = 0.40 mm^−1
β = 96.885 (3)°	T = 133 K
V = 367.01 (7) Å^3	Tablet, colourless
Z = 2	0.35 × 0.24 × 0.12 mm

Data collection

Bruker SMART CCD area-detector diffractometer	2032 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tube	Rint = 0.023
Graphite monochromator	θmax = 30.0°, θmin = 3.3°
Detector resolution: 8.192 pixels mm^-1	h = −9→9
ω scans	k = −6→6
3980 measured reflections	l = −15→15
2066 independent reflections

Refinement

Refinement on F^2	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: difference Fourier map
R[F^2 > 2σ(F^2)] = 0.026	H atoms treated by a mixture of independent and constrained refinement
wR(F^2) = 0.074	w = 1/[σ^2(Fo^2) + (0.0581P)^2 + 0.0053P] where P = (Fo^2 + 2Fc^2)/3
S = 1.07	(Δ/σ)max < 0.001
2066 reflections	Δρmax = 0.35 e Å^−3
124 parameters	Δρmin = −0.30 e Å^−3
2 restraints	Absolute structure: Flack (1983)
Primary atom site location: structure-invariant direct methods	Absolute structure parameter: 0.46 (5)

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	0.89309 (18)	0.3291 (4)	0.48055 (11)	0.0144 (2)
C2	0.72177 (19)	0.5096 (3)	0.49916 (11)	0.0161 (3)
H2A	0.620 (2)	0.390 (5)	0.5078 (18)	0.019*
H2B	0.694 (3)	0.640 (4)	0.4240 (18)	0.019*
S	0.75499 (6)	0.74416 (4)	0.62873 (4)	0.01471 (9)
C3	0.78028 (18)	0.5062 (3)	0.75725 (11)	0.0156 (3)
H3A	0.900 (2)	0.399 (5)	0.7563 (17)	0.019*
H3B	0.805 (3)	0.604 (4)	0.8284 (16)	0.019*
C4	0.60970 (19)	0.3189 (4)	0.77248 (11)	0.0139 (2)
O1	0.84841 (15)	0.1455 (3)	0.39192 (9)	0.0193 (2)
O2	1.05004 (13)	0.3528 (2)	0.53869 (9)	0.0212 (2)
O3	0.45338 (12)	0.3496 (2)	0.70757 (8)	0.0179 (2)
O4	0.64364 (14)	0.1319 (2)	0.85555 (8)	0.0180 (2)
N	0.2600 (2)	0.84417 (19)	0.61656 (11)	0.01509 (19)
H1N	0.139 (3)	0.807 (5)	0.637 (2)	0.040 (6)*
H2N	0.323 (3)	0.699 (5)	0.647 (2)	0.033 (5)*
H3N	0.245 (3)	0.849 (4)	0.5313 (17)	0.022 (4)*
H4N	0.313 (2)	1.016 (4)	0.6431 (18)	0.027 (4)*
H1O	0.968 (3)	0.067 (4)	0.384 (2)	0.036 (5)*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
C1	0.0182 (6)	0.0110 (6)	0.0142 (5)	−0.0027 (5)	0.0021 (4)	0.0013 (5)
C2	0.0149 (6)	0.0177 (6)	0.0152 (5)	0.0010 (5)	0.0005 (4)	0.0000 (5)
S	0.01703 (13)	0.01111 (13)	0.01620 (13)	−0.00043 (13)	0.00293 (8)	0.00020 (11)
C3	0.0167 (7)	0.0141 (6)	0.0156 (5)	−0.0019 (5)	0.0001 (4)	0.0024 (4)
C4	0.0180 (6)	0.0114 (6)	0.0127 (5)	−0.0013 (5)	0.0033 (4)	−0.0022 (6)
O1	0.0236 (5)	0.0166 (6)	0.0172 (4)	0.0018 (4)	0.0002 (4)	−0.0044 (4)
O2	0.0180 (5)	0.0166 (6)	0.0283 (5)	0.0008 (5)	−0.0007 (4)	−0.0050 (5)
O3	0.0157 (5)	0.0147 (6)	0.0223 (4)	−0.0009 (4)	−0.0011 (3)	0.0020 (4)
O4	0.0231 (5)	0.0171 (5)	0.0134 (4)	−0.0019 (4)	0.0004 (4)	0.0024 (4)
N	0.0154 (4)	0.0137 (4)	0.0156 (4)	0.0003 (5)	−0.0006 (3)	0.0007 (4)

Geometric parameters (Å, º)

C1—O2	1.2119 (17)	C3—H3B	0.907 (18)
C1—O1	1.3196 (19)	C4—O3	1.2443 (17)
C1—C2	1.520 (2)	C4—O4	1.2792 (19)
C2—S	1.8019 (14)	O1—H1O	0.938 (19)
C2—H2A	0.933 (19)	N—H1N	0.92 (2)
C2—H2B	1.03 (2)	N—H2N	0.87 (2)
S—C3	1.8021 (14)	N—H3N	0.923 (18)
C3—C4	1.527 (2)	N—H4N	0.94 (2)
C3—H3A	0.991 (19)
O2—C1—O1	124.65 (14)	C4—C3—H3B	106.7 (11)
O2—C1—C2	124.43 (15)	S—C3—H3B	109.1 (11)
O1—C1—C2	110.92 (12)	H3A—C3—H3B	101.6 (16)
C1—C2—S	115.61 (10)	O3—C4—O4	124.32 (14)
C1—C2—H2A	106.9 (12)	O3—C4—C3	121.47 (14)
S—C2—H2A	109.8 (12)	O4—C4—C3	114.21 (12)
C1—C2—H2B	108.6 (10)	C1—O1—H1O	101.4 (14)
S—C2—H2B	103.6 (12)	H1N—N—H2N	101 (2)
H2A—C2—H2B	112.5 (16)	H1N—N—H3N	104.6 (18)
C2—S—C3	101.71 (4)	H2N—N—H3N	113 (2)
C4—C3—S	117.01 (9)	H1N—N—H4N	115.8 (18)
C4—C3—H3A	112.0 (12)	H2N—N—H4N	115.1 (16)
S—C3—H3A	109.2 (11)	H3N—N—H4N	106.4 (17)
O2—C1—C2—S	−7.2 (2)	C2—S—C3—C4	−62.20 (13)
O1—C1—C2—S	173.45 (9)	S—C3—C4—O3	−7.62 (19)
C1—C2—S—C3	−66.43 (13)	S—C3—C4—O4	171.87 (10)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N—H1N···S^i	0.92 (2)	2.71 (2)	3.6075 (15)	163.5 (19)
N—H4N···O3^ii	0.94 (2)	1.971 (19)	2.9040 (16)	172.4 (16)
N—H3N···O4^iii	0.923 (18)	1.966 (18)	2.8683 (16)	165.1 (17)
N—H2N···O3	0.87 (2)	1.99 (2)	2.8607 (16)	175 (2)
O1—H1O···O4^iv	0.938 (19)	1.622 (19)	2.5418 (11)	166 (2)

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