Crystal structure of seleno-l-cystine dihydrochloride

The crystal structure of seleno-l-cystine, in its hydrochloric acid salt, is isotypic with the common analogue with Se atoms replaced by sulfur, i.e. L-cystine hydrochloride.


Chemical context
In addition to the 20 amino acids directly encoded by the genetic code, three more are incorporated into proteins during translation. These three, selenocystine, pyrrolysine and N-formylmethionine, are considered to belong to a group of 23 proteinogenic amino acids. The UGA codon, normally a stop codon, is made to encode selenocysteine by the presence of a selenocysteine insertion sequence (SECIS) in the mRNA (Kryukov et al., 2003).
Analogous to the common sulfur analogue cysteine, selenocysteine dimerizes through the formation of an Se-Se bridge to selenocystin, a substance that has received considerable attention recently for its anticancer efficacy (Yu et al., 2015) as well as its potential in the prevention of cardiovascular and neurodegenerative diseases (Weekley & Harris, 2013).
In the Cambridge Structural Database (CSD, version 5.36; Groom & Allen, 2014) there are about 80 distinct structures of cystine deposited, either as an amino acid, a modified amino ISSN 2056-9890 acid or as an integrate part of a peptide or another large organic molecule. In contrast, there are no entries for selenocystine (and also none for sulfur-selenium hybrids with a -CH 2 -S-Se-CH 2 -bridge). To provide detailed structural information for this biologically important link, an investigation of its structure, in the dihydrochloride salt C 6 H 14 N 2 O 4 Se 2 2+ Á2Cl À , (I), has been undertaken.

Structural commentary
The molecular structure of (I) is shown in Fig. 1a. A twofold rotation axis relates the two parts of the molecule. The crystal packing is depicted in Fig. 2, with molecules stacked on top of each other along the 5.2529 (4) Å monoclinic axis. Compound (I) is isotypic with the structure of l-cystine dihydrochloride, (II) (Gupta et al., 1974;Jones et al., 1974;Leela & Rama-murthi, 2007), but not with the structure of l-cystine dihydrobromide (Anbuchezhiyan et al., 2010), which forms a related packing arrangement but crystallizes in the orthorhombic space group P2 1 2 1 2. The disulfide/diselenide bridges adopt helical conformations in all three structures, characterized by having gauche -C-C-X-X-, -C-X-X-Cand -X-X-C-C-torsion angles (X = S or Se) of the same sign, in this case between À81 and À89 [ Table 1; -C-C-X-X-= -X-X-C-C-by symmetry]. Geometric parameters for (I) and (II) are furthermore compared in Table 1 with average values from 16 acyclic -CH 2 -Se-Se-CH 2 -links in non-amino acid structures retrieved from the CSD (Groom & Allen, 2014). The bond lengths and bond angles of (I) are similar to those in the previous seleno structures. The most important differences with respect to (II) [X-ray data at 173 K: a = 18.4405 (15), b = 5.2116 (6), c = 7.2191 (6) Å , = 103.856 (6) ; Leela & Ramamurthi, 2007] are (obviously) the two Se-Se and S-S bond lengths, with modest changes for bond angles and torsion angles. Concerning the dimensions of the unit cell, there is above all an increase in the length of the cell edge a (+ 0.364 Å , 2%) due to longer C-Se than C-S bonds. An equivalent, anticipated effect on c as a result of the increased length of the Se-Se bond, which runs parallel to the z axis, is effectively counteracted by a 2.52 decrease for the two C-Se-Se angles along the bridge compared to the C-S-S angles, see: Fig. 1b and Table 1. The length of the short monoclinic axis b is determined by direct stacking of amino acid molecules, for which the S-to-Se substitution has less impact since neither is involved in any close intermolecular contacts. (a) The molecular structure of seleno-l-cystine dihydrochloride. The right-hand part, coloured in a light tone, is generated by application of twofold rotation symmetry in space group C2; Se1*, C3* etc are generated by the symmetry code Àx + 1, y, Àz. Displacement ellipsoids are shown at the 50% probability level. (b) Best overlap between the structures of (I) (dark grey O, N and C atoms) and (II) (light grey; Leela & Ramamurthi, 2007) with a root-mean-square deviation of 0.133 Å . The view is along the twofold rotation axis (lens-shaped symbol), the dashed line gives the direction of the z axis. Table 1 Geometric parameters (Å , ) of diselenide and disulfide bridges.  (2007).

Figure 2
The crystal packing of seleno-l-cystine dihydrochloride viewed approximately along the b axis.

Supramolecular features
The four strong hydrogen bonds with N-H and O-H donors all have Cl À as the acceptor atom (Fig. 3a). The geometric parameters of the hydrogen bonds listed in Table 2 are almost identical to those of (II). There is also a three-centre interaction with a C -H donor and two carbonyl oxygen atoms as acceptors, Fig. 3b.

Synthesis and crystallization
Selenocystine has very low solubility in water as well as in organic solvents, including trifluoroethanol and 1,1,1,3,3,3hexafluoropropan-2-ol, so a saturated solution was prepared in 0.1 M NaOH solution. 100 ml of this solution was pipetted into a small test tube (5 Â 50 mm) to which a small amount of BTB pH indicator was added. The tube was sealed with parafilm punctured with a needle (one small hole) and placed inside a larger tube with concentrated hydrochloric acid. After 15 h the colour had shifted from blue to green, and small crystals of the hydrochloride could be harvested.
Free rotation was permitted for the ammonium group. U iso (H) values were set to 1.2U eq of the carrier atom, or 1.5U eq for the ammonium group. A rather large residual peak in the electron density map, with Á max = 4.55 e Å À3 , remained after completion of the refinement. This peak is located on the twofold rotation axis at the center of the Se-Se bond, and evidently reflects bonding electrons. As a test, an extra isotropic C atom was introduced close to the axis. Its occupancy was subsequently refined to 0.17 (equivalent to one electron), and the R-factor fell from 0.0233 to 0.0180.