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.

Abstract

Numerous crystal structures are available for the dimeric amino acid cystine. In proteins it is formed by oxidation of the –SH thiol groups of two closely spaced cysteine residues, resulting in the formation of a familiar di­sulfide bridge. The title compound [systematic name: (R,R)-1,1′-dicarb­oxy-2,2′-(diselanedi­yl)diethanaminium dichloride], C₆H₁₄N₂O₄Se₂ ²⁺·2Cl⁻, is the first example of a small mol­ecule structure of the biologically important analogue with a —CH₂—Se—Se—CH₂— bridging unit. Bond lengths and angles of seleno-l-cystine di­hydro­chloride and its isotypic sulfur analogue l-cystine di­hydro­chloride are compared.

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 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 —CH₂—S—Se—CH₂— bridge). To provide detailed structural information for this biologically important link, an investigation of its structure, in the di­hydro­chloride salt C₆H₁₄N₂O₄Se₂ ²⁺·2Cl⁻, (I), has been undertaken.

Structural commentary  

The mol­ecular structure of (I) is shown in Fig. 1 ▸ a. 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 & Ramamurthi, 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 P2₁2₁2. The di­sulfide/diselenide bridges adopt helical conformations in all three structures, characterized by having gauche —C—C—X—X—, —C—X—X—C— and —X—X—C—C— torsion angles (X = S or Se) of the same sign, in this case between −81 and −89° [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 —CH₂—Se—Se—CH₂— 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, β = 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. 1 ▸ b 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.

Figure 1.

(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 −x + 1, y, −z. 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.

Figure 2.

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

Table 1. Geometric parameters (, ) of diselenide and disulfide bridges.

Compound	CSe/CS	SeSe/SS	CCSe/S	CSe/SSe/S	CCSe/SSe/S	CSe/SSe/SC
(I)	1.9671(18)	2.3213(4)	113.96(12)	100.88(5)	88.72(12)	83.05(10)
Averagea	1.967	2.310	114.17	101.29
(II)b	1.817	2.040	114.48	103.40	89.04	81.04

Notes: (a) average of 16 CH₂SeSeCH₂ bridges in acyclic non-amino acid structures; (b) Leela Ramamurthi (2007 ▸).

Supra­molecular features  

The four strong hydrogen bonds with N—H and O—H donors all have Cl⁻ as the acceptor atom (Fig. 3 ▸ a). 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^α—H donor and two carbonyl oxygen atoms as acceptors, Fig. 3 ▸ b.

Figure 3.

(a) Stereodrawing showing the coordination of hydrogen-bond donors around a Cl⁻ anion (see Table 2 ▸ for symmetry operators). (b) Tape motif along the b axis generated from C^α—H⋯O hydrogen bonds. O1* is at (x, y + 1, z), O1′ at (−x + , y + , −z + 1). Side chains have been truncated beyond C^β.

Table 2. Hydrogen-bond geometry (, ).

DHA	DH	HA	D A	DHA
N1H1Cl1i	0.91	2.25	3.1425(16)	167
N1H2Cl1ii	0.91	2.40	3.2110(18)	149
N1H3Cl1iii	0.91	2.32	3.1794(15)	157
O2H4Cl1	0.79(6)	2.22(6)	3.0080(19)	172(4)
C2H21O1iv	1.00	2.39	3.292(2)	150
C2H21O1iii	1.00	2.55	3.216(2)	124

Symmetry codes: (i) ; (ii) ; (iii) ; (iv) .

Synthesis and crystallization  

Seleno­cystine has very low solubility in water as well as in organic solvents, including tri­fluoro­ethanol and 1,1,1,3,3,3-hexa­fluoro­propan-2-ol, so a saturated solution was prepared in 0.1 M NaOH solution. 100 µl of this solution was pipetted into a small test tube (5 × 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.

Refinement  

Crystal data, data collection and structure refinement details are summarized in Table 3 ▸. The position of the carboxyl H atom was restrained to the plane defined by O1, O2, C1 and C2; other H atoms were positioned with idealized geometry with fixed C/N—H distances for NH₃, CH₂ (methyl­ene) and CH (methine) groups of 0.91, 0.99 and 1.00 Å, respectively. 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.

Table 3. Experimental details.

Crystal data
Chemical formula	C6H14N2O4Se2 2+2(Cl)
M r	407.02
Crystal system, space group	Monoclinic, C2
Temperature (K)	100
a, b, c ()	18.8045(16), 5.2529(4), 7.2719(6)
()	102.219(1)
V (3)	702.03(10)
Z	2
Radiation type	Mo K
(mm1)	5.65
Crystal size (mm)	0.85 0.08 0.07
Data collection
Diffractometer	Bruker D8 Advance single-crystal CCD
Absorption correction	Multi-scan (SADABS; Bruker, 2014 ▸)
T min, T max	0.514, 1.000
No. of measured, independent and observed [I > 2(I)] reflections	11089, 4209, 4080
R int	0.024
(sin /)max (1)	0.908
Refinement
R[F 2 > 2(F 2)], wR(F 2), S	0.023, 0.062, 1.10
No. of reflections	4209
No. of parameters	78
No. of restraints	3
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
max, min (e 3)	4.55, 0.87
Absolute structure	Flack x determined using 1708 quotients (Parsons et al., 2013 ▸)
Absolute structure parameter	0.044(4)

Computer programs: APEX2 and SAINT (Bruker, 2014 ▸), SHELXT (Sheldrick, 2015a ▸), SHELXL2014 (Sheldrick, 2015b ▸) and Mercury (Macrae et al., 2008 ▸).

A rather large residual peak in the electron density map, with Δρ_max = 4.55 e Å⁻³, 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.

Supplementary Material

CCDC reference: 1403356

Additional supporting information: crystallographic information; 3D view; checkCIF report

supplementary crystallographic information

Crystal data

C6H14N2O4Se22+·2(Cl−)	F(000) = 396
Mr = 407.02	Dx = 1.925 Mg m−3
Monoclinic, C2	Mo Kα radiation, λ = 0.71073 Å
a = 18.8045 (16) Å	Cell parameters from 9938 reflections
b = 5.2529 (4) Å	θ = 2.2–40.2°
c = 7.2719 (6) Å	µ = 5.65 mm−1
β = 102.219 (1)°	T = 100 K
V = 702.03 (10) Å3	Needle, colourless
Z = 2	0.85 × 0.08 × 0.07 mm

Data collection

Bruker D8 Advance single-crystal CCD diffractometer	4209 independent reflections
Radiation source: fine-focus sealed tube	4080 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.024
Detector resolution: 8.3 pixels mm-1	θmax = 40.2°, θmin = 2.2°
Sets of exposures each taken over 0.5° ω rotation scans	h = −34→34
Absorption correction: multi-scan (SADABS; Bruker, 2014)	k = −9→9
Tmin = 0.514, Tmax = 1.000	l = −13→13
11089 measured reflections

Refinement

Refinement on F2	Hydrogen site location: inferred from neighbouring sites
Least-squares matrix: full	H atoms treated by a mixture of independent and constrained refinement
R[F2 > 2σ(F2)] = 0.023	w = 1/[σ2(Fo2) + (0.0169P)2 + 0.004P] where P = (Fo2 + 2Fc2)/3
wR(F2) = 0.062	(Δ/σ)max < 0.001
S = 1.10	Δρmax = 4.55 e Å−3
4209 reflections	Δρmin = −0.87 e Å−3
78 parameters	Absolute structure: Flack x determined using 1708 quotients (Parsons et al., 2013)
3 restraints	Absolute structure parameter: 0.044 (4)

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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Ų)

	x	y	z	Uiso*/Ueq
Se1	0.50147 (2)	0.56610 (5)	0.16037 (2)	0.01306 (4)
Cl1	0.65288 (2)	0.16979 (8)	0.87546 (6)	0.01345 (7)
O1	0.69775 (8)	0.3451 (3)	0.4104 (2)	0.0158 (2)
O2	0.62968 (9)	0.5697 (5)	0.57259 (19)	0.0225 (3)
H4	0.6356 (18)	0.454 (12)	0.644 (6)	0.058 (15)*
N1	0.67823 (8)	0.6777 (3)	0.1266 (2)	0.0125 (2)
H1	0.6681	0.8028	0.0384	0.019*
H2	0.6563	0.5305	0.0787	0.019*
H3	0.7272	0.6536	0.1591	0.019*
C1	0.66257 (8)	0.5306 (3)	0.4320 (2)	0.0125 (3)
C2	0.65058 (9)	0.7531 (3)	0.2961 (2)	0.0114 (2)
H21	0.6808	0.8988	0.3574	0.014*
C3	0.57160 (9)	0.8414 (3)	0.2457 (3)	0.0123 (2)
H31	0.5667	0.9713	0.1451	0.015*
H32	0.5592	0.9238	0.3573	0.015*

Atomic displacement parameters (Ų)

	U11	U22	U33	U12	U13	U23
Se1	0.00843 (6)	0.01357 (7)	0.01686 (7)	−0.00112 (6)	0.00199 (4)	0.00422 (7)
Cl1	0.01334 (15)	0.01271 (15)	0.01538 (15)	0.00216 (12)	0.00550 (12)	0.00565 (12)
O1	0.0175 (6)	0.0106 (5)	0.0193 (6)	0.0028 (4)	0.0037 (5)	0.0040 (4)
O2	0.0349 (7)	0.0201 (6)	0.0146 (5)	0.0104 (8)	0.0100 (5)	0.0067 (7)
N1	0.0104 (5)	0.0118 (5)	0.0159 (5)	0.0005 (4)	0.0045 (4)	0.0045 (5)
C1	0.0125 (5)	0.0113 (7)	0.0126 (6)	0.0005 (4)	0.0000 (4)	0.0034 (4)
C2	0.0114 (6)	0.0083 (5)	0.0138 (6)	0.0003 (5)	0.0011 (5)	0.0021 (5)
C3	0.0125 (6)	0.0096 (5)	0.0147 (6)	0.0022 (5)	0.0029 (5)	0.0019 (5)

Geometric parameters (Å, º)

Se1—C3	1.9671 (18)	N1—H2	0.9100
Se1—Se1i	2.3213 (4)	N1—H3	0.9100
O1—C1	1.206 (2)	C1—C2	1.516 (2)
O2—C1	1.319 (2)	C2—C3	1.525 (2)
O2—H4	0.79 (6)	C2—H21	1.0000
N1—C2	1.490 (2)	C3—H31	0.9900
N1—H1	0.9100	C3—H32	0.9900
C3—Se1—Se1i	100.88 (5)	N1—C2—C3	112.00 (14)
C1—O2—H4	112 (4)	C1—C2—C3	113.22 (14)
C2—N1—H1	109.5	N1—C2—H21	107.9
C2—N1—H2	109.5	C1—C2—H21	107.9
H1—N1—H2	109.5	C3—C2—H21	107.9
C2—N1—H3	109.5	C2—C3—Se1	113.96 (12)
H1—N1—H3	109.5	C2—C3—H31	108.8
H2—N1—H3	109.5	Se1—C3—H31	108.8
O1—C1—O2	125.92 (18)	C2—C3—H32	108.8
O1—C1—C2	123.24 (17)	Se1—C3—H32	108.8
O2—C1—C2	110.84 (16)	H31—C3—H32	107.7
N1—C2—C1	107.72 (14)
O1—C1—C2—N1	9.3 (2)	N1—C2—C3—Se1	70.66 (16)
O2—C1—C2—N1	−170.64 (15)	C1—C2—C3—Se1	−51.39 (17)
O1—C1—C2—C3	133.72 (17)	C2—C3—Se1—Se1i	−88.72 (12)
O2—C1—C2—C3	−46.24 (19)	C3—Se1—Se1i—C3i	−83.05 (10)

Symmetry code: (i) −x+1, y, −z.

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1···Cl1ii	0.91	2.25	3.1425 (16)	167
N1—H2···Cl1iii	0.91	2.40	3.2110 (18)	149
N1—H3···Cl1iv	0.91	2.32	3.1794 (15)	157
O2—H4···Cl1	0.79 (6)	2.22 (6)	3.0080 (19)	172 (4)
C2—H21···O1v	1.00	2.39	3.292 (2)	150
C2—H21···O1iv	1.00	2.55	3.216 (2)	124

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