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In the title compound, C10H16N2O4S2·H2O, both the (but-2-yne-1,4-diyl)­bis(L-cysteine) moieties and the water mol­ecule lie on crystallographic twofold axes. As a result of this symmetry, the two cysteine moieties (zwitterions), which are separated by the linear but-2-yne-1,4-diyl moiety, have exactly the same conformation. The conformation is characterized by the S atoms being anti to carboxyl groups and gauche to the protonated amino groups. There are hydrogen bonds which connect the structure in three dimensions.

Supporting information

cif

Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536802021487/lh6006sup1.cif
Contains datablocks global, I

hkl

Structure factor file (CIF format) https://doi.org/10.1107/S1600536802021487/lh6006Isup2.hkl
Contains datablock I

CCDC reference: 202363

Key indicators

  • Single-crystal X-ray study
  • T = 293 K
  • Mean [sigma](C-C) = 0.005 Å
  • R factor = 0.043
  • wR factor = 0.094
  • Data-to-parameter ratio = 6.4

checkCIF results

No syntax errors found

ADDSYM reports no extra symmetry


Yellow Alert Alert Level C:
PLAT_736 Alert C H...A Calc 1.98(4), Rep 1.982(12) .... 3.33 su-Ratio H1B -O2 1.555 1.445 PLAT_736 Alert C H...A Calc 2.05(5), Rep 2.053(13) .... 3.85 su-Ratio H1C -O1 1.555 1.545 PLAT_741 Alert C Bond Calc 0.85(2), Rep 0.85000 .... Missing s.u. N1 -H1A 1.555 1.555 PLAT_741 Alert C Bond Calc 0.85(4), Rep 0.85000 .... Missing s.u. N1 -H1B 1.555 1.555 PLAT_741 Alert C Bond Calc 0.85(6), Rep 0.85000 .... Missing s.u. N1 -H1C 1.555 1.555 PLAT_745 Alert C D-H Calc 0.85(4), Rep 0.85000 .... Missing su N1 -H1B 1.555 1.555 PLAT_745 Alert C D-H Calc 0.85(6), Rep 0.85000 .... Missing su N1 -H1C 1.555 1.555 General Notes
ABSTM_02 When printed, the submitted absorption T values will be replaced by the scaled T values. Since the ratio of scaled T's is identical to the ratio of reported T values, the scaling does not imply a change to the absorption corrections used in the study. Ratio of Tmax expected/reported 0.922 Tmax scaled 0.922 Tmin scaled 0.810 REFLT_03 From the CIF: _diffrn_reflns_theta_max 26.32 From the CIF: _reflns_number_total 1262 Count of symmetry unique reflns 921 Completeness (_total/calc) 137.02% TEST3: Check Friedels for noncentro structure Estimate of Friedel pairs measured 341 Fraction of Friedel pairs measured 0.370 Are heavy atom types Z>Si present yes WARNING: Large fraction of Friedel related reflns may be needed to determine absolute structure
0 Alert Level A = Potentially serious problem
0 Alert Level B = Potential problem
7 Alert Level C = Please check

Comment top

It is widely known that L-cysteine and its derivatives exhibit remarkable bioactivities, which prompts us to synthesize new compounds containing two or more cysteine groups and investigate the relationships between structure and bioactivities. A few compounds containing two cysteine moieties bridged through the S atom with varied carbon hydrogen diyls have been reported (Armstrong & Vigneaud, 1947; Struhar et al., 1975; Hu et al., 1999); however, the crystal structures of these derivatives are rarely studied (Bigoli et al., 1982; Shi et al., 2002). We report herein the crystal structure of a new compound S,S'-(but-2-yne-1,4-diyl)bis(L-cysteine) monohydrate, (I).

The trigonal unit-cell consists of three molecules of (I). The but-2-yne-1,4-diyl group is linear with a C4—C5—C5i angle of 178.8 (4)° [symmetry code: (i) x - 1, y - 1, z]. The dihedral angle between the S1/C4/C5 and S1i/C4i/C5i planes is 30.2 (4)°. The C5—C5i triple-bond length is 1.191 (7) Å, which agrees with the value of 1.204 (2) Å in ethyne (Weast, 1988–1989) and 1.200 (4) Å in but-2-yne-1,4-diol (Steiner, 1996). There is little difference in the C—S bond lengths [C3—S1 = 1.799 (3) Å and C4—S1 = 1.816 (4) Å] from that in S,S'-(but-2-ene-1,4-diyl)bis(L-cysteine) (BEDC; Shi et al., 2002) and L-cysteine (Kerr & Ashmore, 1973). The C3—S1—C4 angle of 101.25 (17)° is slightly larger than that of 99.05° in dimethyl sulfide (Lide, 1992, 1993) and between the values of 102.1 (2) and 100.4 (2)° when compared with BEDC (Shi et al., 2002).

The difference in the two C—O bond lengths [O1—C1 = 1.225 (4) Å and O2—C1 = 1.239 (4)°] is seemingly caused by diverse hydrogen environment in which atom O1 is involved in two hydrogen bonds (O1W—H1D···O1 and N1—H1C···O1), while O2 participates in just one (N1—H1B···O2) (see Table 2). The same situation is also found in BEDC (Shi et al., 2002) and orthorhombic cysteine (Kerr & Ashmore, 1973).

The molecular conformation can be described by the position of the S atom which is gauche to the protonated amino group [S1—C3—C2—N1 = 52.1 (3)°] and anti to the carboxyl group [S1—C3—C2—C1 = 172.0 (2)°], while in BEDC, one S atom is anti to carboxyl group and the other is gauche to it (Shi et al., 2002). A Newman projection can clearly show the conformation of (I) (see Fig. 3).

The packing diagram (Fig. 4) shows the existence of some hydrogen bonds. Two distinct N—H···O hydrogen bonds formed from two N—H bonds of the protonated amino group and two carboxyl O atoms from two different neighboring molecules, which leads to the formation of a eight-membered ring with a water molecule situated inside. The water molecule also produces an hydrogen-bond interaction with the O atom from one of the four neighboring molecules of (I) (Table 2).

Experimental top

The title compound was synthesized by a modified literature method (Kalopissis, 1975). Under the protection of nitrogen gas and cooled by an ice bath, a solution of 0.53 g (0.0025 mol) of 1,4-dibromo-2-butyne in 5 ml of ethanol was added dropwise to a mixture of 0.88 g (0.005 mol) of L-cysteine hydrochloride monohydrate, 0.001 mol (1 ml, 10 mol l-1) of sodium hydroxide, 5 ml of water and 7.5 ml of ethanol. After that, the reaction mixture was stirred for another 24 h at room temperature. The precipitate is filtered and recrystallized with water. Pale yellow flakes were obtained with a yield of 37%; m.p. 513–515 K (decomposition); IR (KBr) of (I): 3446 (s), 3226 (b), 2910 (s), 1599 (versus, b), 1501 (s), 1391 (versus), 1333 (s), 1300 (w), 1240 (w), 1169 (w), 1069 (s), 902 (s) cm-1; 1H NMR (D2O): δ 3.43 (4H, s), 4.30 (2H, q), 3.20 (2H, m), 3.37 (2H, dd) p.p.m. 10 mg of (I) was dissolved in 15 ml of hot distilled water, after cooling and filtration, the solution was kept at room temperature for 60 d to yield single-crystal of (I) suitable for X-ray analysis.

Refinement top

The water H atoms were located in a difference Fourier map and refined using constraints. All other H atoms were located in difference Fourier maps, positioned geometrically and refined as riding on their parent atoms.

Structure description top

It is widely known that L-cysteine and its derivatives exhibit remarkable bioactivities, which prompts us to synthesize new compounds containing two or more cysteine groups and investigate the relationships between structure and bioactivities. A few compounds containing two cysteine moieties bridged through the S atom with varied carbon hydrogen diyls have been reported (Armstrong & Vigneaud, 1947; Struhar et al., 1975; Hu et al., 1999); however, the crystal structures of these derivatives are rarely studied (Bigoli et al., 1982; Shi et al., 2002). We report herein the crystal structure of a new compound S,S'-(but-2-yne-1,4-diyl)bis(L-cysteine) monohydrate, (I).

The trigonal unit-cell consists of three molecules of (I). The but-2-yne-1,4-diyl group is linear with a C4—C5—C5i angle of 178.8 (4)° [symmetry code: (i) x - 1, y - 1, z]. The dihedral angle between the S1/C4/C5 and S1i/C4i/C5i planes is 30.2 (4)°. The C5—C5i triple-bond length is 1.191 (7) Å, which agrees with the value of 1.204 (2) Å in ethyne (Weast, 1988–1989) and 1.200 (4) Å in but-2-yne-1,4-diol (Steiner, 1996). There is little difference in the C—S bond lengths [C3—S1 = 1.799 (3) Å and C4—S1 = 1.816 (4) Å] from that in S,S'-(but-2-ene-1,4-diyl)bis(L-cysteine) (BEDC; Shi et al., 2002) and L-cysteine (Kerr & Ashmore, 1973). The C3—S1—C4 angle of 101.25 (17)° is slightly larger than that of 99.05° in dimethyl sulfide (Lide, 1992, 1993) and between the values of 102.1 (2) and 100.4 (2)° when compared with BEDC (Shi et al., 2002).

The difference in the two C—O bond lengths [O1—C1 = 1.225 (4) Å and O2—C1 = 1.239 (4)°] is seemingly caused by diverse hydrogen environment in which atom O1 is involved in two hydrogen bonds (O1W—H1D···O1 and N1—H1C···O1), while O2 participates in just one (N1—H1B···O2) (see Table 2). The same situation is also found in BEDC (Shi et al., 2002) and orthorhombic cysteine (Kerr & Ashmore, 1973).

The molecular conformation can be described by the position of the S atom which is gauche to the protonated amino group [S1—C3—C2—N1 = 52.1 (3)°] and anti to the carboxyl group [S1—C3—C2—C1 = 172.0 (2)°], while in BEDC, one S atom is anti to carboxyl group and the other is gauche to it (Shi et al., 2002). A Newman projection can clearly show the conformation of (I) (see Fig. 3).

The packing diagram (Fig. 4) shows the existence of some hydrogen bonds. Two distinct N—H···O hydrogen bonds formed from two N—H bonds of the protonated amino group and two carboxyl O atoms from two different neighboring molecules, which leads to the formation of a eight-membered ring with a water molecule situated inside. The water molecule also produces an hydrogen-bond interaction with the O atom from one of the four neighboring molecules of (I) (Table 2).

Computing details top

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

Figures top
[Figure 1] Fig. 1. View of the molecular structure of (I), with 30% probability ellipsoids [symmetry code: (i) 1 + x-y, 2 - y, 1/3 - z].
[Figure 2] Fig. 2. The trigonal unit-cell contents of (I) viewed along c axis.
[Figure 3] Fig. 3. Newman projection of (I)
[Figure 4] Fig. 4. Packing diagram of (I), viewed along a axis.
S,S'-(But-2-yne-1,4-diyl)bis(L-cysteine) monohydrate top
Crystal data top
C10H16N2O4S2·H2ODx = 1.500 Mg m3
Mr = 310.38Mo Kα radiation, λ = 0.71073 Å
Trigonal, P3221Cell parameters from 691 reflections
Hall symbol: P 32 2"θ = 4.4–26.3°
a = 5.3906 (10) ŵ = 0.41 mm1
c = 40.964 (15) ÅT = 293 K
V = 1030.9 (5) Å3Prism, colourless
Z = 30.30 × 0.25 × 0.20 mm
F(000) = 492
Data collection top
Bruker CCD area-detector
diffractometer
1262 independent reflections
Radiation source: fine-focus sealed tube1017 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.048
φ and ω scansθmax = 26.3°, θmin = 4.4°
Absorption correction: multi-scan
(SADABS; Bruker, 1997)
h = 66
Tmin = 0.878, Tmax = 1.000k = 66
4241 measured reflectionsl = 3251
Refinement top
Refinement on F2H atoms treated by a mixture of independent and constrained refinement
Least-squares matrix: full w = 1/[σ2(Fo2) + (0.0519P)2]
where P = (Fo2 + 2Fc2)/3
R[F2 > 2σ(F2)] = 0.043(Δ/σ)max < 0.001
wR(F2) = 0.094Δρmax = 0.89 e Å3
S = 0.99Δρmin = 0.21 e Å3
1262 reflectionsAbsolute structure: Flack (1983), 341 Friedel pairs
197 parametersAbsolute structure parameter: 0.00 (16)
0 restraints
Crystal data top
C10H16N2O4S2·H2OZ = 3
Mr = 310.38Mo Kα radiation
Trigonal, P3221µ = 0.41 mm1
a = 5.3906 (10) ÅT = 293 K
c = 40.964 (15) Å0.30 × 0.25 × 0.20 mm
V = 1030.9 (5) Å3
Data collection top
Bruker CCD area-detector
diffractometer
1262 independent reflections
Absorption correction: multi-scan
(SADABS; Bruker, 1997)
1017 reflections with I > 2σ(I)
Tmin = 0.878, Tmax = 1.000Rint = 0.048
4241 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.043H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.094Δρmax = 0.89 e Å3
S = 0.99Δρmin = 0.21 e Å3
1262 reflectionsAbsolute structure: Flack (1983), 341 Friedel pairs
197 parametersAbsolute structure parameter: 0.00 (16)
0 restraints
Special details top

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 (Å2) top
xyzUiso*/Ueq
S10.4329 (2)0.60161 (18)0.11571 (2)0.0348 (2)
N10.5174 (8)0.7537 (6)0.04095 (6)0.0334 (7)
H1A0.570 (10)0.815 (9)0.0216 (4)0.067 (15)*
H1B0.339 (2)0.661 (13)0.0450 (13)0.11 (2)*
H1C0.550 (13)0.615 (8)0.0394 (15)0.10 (2)*
O10.5828 (5)1.2629 (5)0.02738 (6)0.0427 (6)
O20.9418 (5)1.4985 (5)0.06143 (6)0.0342 (6)
C10.7454 (7)1.2771 (7)0.04912 (7)0.0252 (6)
C20.6984 (7)0.9922 (7)0.06362 (6)0.0258 (7)
H2A0.88401.00270.06640.031*
C30.5517 (7)0.9436 (7)0.09668 (7)0.0297 (7)
H3A0.38700.96910.09410.036*
H3B0.68331.09150.11150.036*
C40.7612 (9)0.6594 (8)0.13492 (9)0.0429 (10)
H4A0.72200.48700.14660.052*
H4B0.90070.69220.11810.052*
C50.8852 (8)0.9004 (8)0.15759 (8)0.0382 (8)
O1W0.0310 (6)1.0310 (6)0.00000.0386 (8)
H1D0.19621.07690.01030.055 (12)*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
S10.0432 (6)0.0290 (5)0.0269 (4)0.0140 (4)0.0035 (4)0.0076 (3)
N10.046 (2)0.0235 (16)0.0322 (15)0.0185 (16)0.0076 (14)0.0027 (12)
O10.0426 (16)0.0269 (13)0.0570 (15)0.0162 (12)0.0189 (11)0.0058 (11)
O20.0306 (13)0.0222 (12)0.0446 (14)0.0093 (10)0.0029 (10)0.0044 (10)
C10.0283 (17)0.0213 (16)0.0266 (14)0.0129 (14)0.0007 (15)0.0023 (12)
C20.0269 (17)0.0216 (17)0.0284 (16)0.0118 (14)0.0007 (12)0.0060 (12)
C30.040 (2)0.0286 (18)0.0245 (15)0.0199 (16)0.0009 (13)0.0048 (12)
C40.060 (3)0.044 (2)0.0284 (19)0.029 (2)0.0044 (16)0.0046 (15)
C50.051 (2)0.038 (2)0.0307 (17)0.0261 (19)0.0026 (14)0.0063 (13)
O1W0.0359 (14)0.0359 (14)0.0355 (16)0.0116 (17)0.0018 (8)0.0018 (8)
Geometric parameters (Å, º) top
S1—C31.799 (3)C2—C31.524 (4)
S1—C41.816 (4)C2—H2A0.9800
N1—C21.488 (4)C3—H3A0.9700
N1—H1A0.85C3—H3B0.9700
N1—H1B0.85C4—C51.459 (5)
N1—H1C0.85C4—H4A0.9700
O1—C11.225 (4)C4—H4B0.9700
O2—C11.239 (4)C5—C5i1.191 (7)
C1—C21.545 (4)O1W—H1D0.90
C3—S1—C4101.25 (17)C1—C2—H2A109.4
C2—N1—H1A107 (3)C2—C3—S1116.7 (2)
C2—N1—H1B117 (4)C2—C3—H3A108.1
H1A—N1—H1B118 (5)S1—C3—H3A108.1
C2—N1—H1C118 (4)C2—C3—H3B108.1
H1A—N1—H1C95 (5)S1—C3—H3B108.1
H1B—N1—H1C100 (6)H3A—C3—H3B107.3
O1—C1—O2126.6 (3)C5—C4—S1113.7 (3)
O1—C1—C2117.4 (3)C5—C4—H4A108.8
O2—C1—C2115.9 (3)S1—C4—H4A108.8
N1—C2—C3110.3 (3)C5—C4—H4B108.8
N1—C2—C1109.2 (2)S1—C4—H4B108.8
C3—C2—C1109.0 (2)H4A—C4—H4B107.7
N1—C2—H2A109.4C5i—C5—C4178.9 (4)
C3—C2—H2A109.4
O1—O1—C1—O20.0 (7)O1—C1—C2—C3103.2 (3)
O1—O1—C1—C20.0 (6)O2—C1—C2—C375.1 (3)
O1—C1—C2—N117.3 (4)N1—C2—C3—S152.1 (3)
O1—C1—C2—N117.3 (4)C1—C2—C3—S1172.0 (2)
O2—C1—C2—N1164.3 (3)C4—S1—C3—C282.8 (3)
O1—C1—C2—C3103.2 (3)C3—S1—C4—C557.3 (3)
Symmetry code: (i) xy+1, y+2, z+1/3.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1B···O2ii0.85 (11)1.98 (1)2.821 (4)169 (6)
N1—H1C···O1iii0.85 (11)2.05 (1)2.892 (4)169 (6)
O1W—H1D···O10.901.942.820 (3)166
Symmetry codes: (ii) x1, y1, z; (iii) x, y1, z.

Experimental details

Crystal data
Chemical formulaC10H16N2O4S2·H2O
Mr310.38
Crystal system, space groupTrigonal, P3221
Temperature (K)293
a, c (Å)5.3906 (10), 40.964 (15)
V3)1030.9 (5)
Z3
Radiation typeMo Kα
µ (mm1)0.41
Crystal size (mm)0.30 × 0.25 × 0.20
Data collection
DiffractometerBruker CCD area-detector
Absorption correctionMulti-scan
(SADABS; Bruker, 1997)
Tmin, Tmax0.878, 1.000
No. of measured, independent and
observed [I > 2σ(I)] reflections
4241, 1262, 1017
Rint0.048
(sin θ/λ)max1)0.624
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.043, 0.094, 0.99
No. of reflections1262
No. of parameters197
H-atom treatmentH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å3)0.89, 0.21
Absolute structureFlack (1983), 341 Friedel pairs
Absolute structure parameter0.00 (16)

Computer programs: SMART (Bruker, 1997), SMART, SAINT (Bruker, 1997) and SHELXTL (Bruker, 1997), SHELXS97 (Sheldrick, 1997), SHELXL97 (Sheldrick, 1997), SHELXTL.

Selected geometric parameters (Å, º) top
S1—C31.799 (3)C1—C21.545 (4)
S1—C41.816 (4)C2—C31.524 (4)
N1—C21.488 (4)C4—C51.459 (5)
O1—C11.225 (4)C5—C5i1.191 (7)
O2—C11.239 (4)
C3—S1—C4101.25 (17)N1—C2—C1109.2 (2)
O1—C1—O2126.6 (3)C3—C2—C1109.0 (2)
O1—C1—C2117.4 (3)C2—C3—S1116.7 (2)
O2—C1—C2115.9 (3)C5—C4—S1113.7 (3)
N1—C2—C3110.3 (3)C5i—C5—C4178.9 (4)
O1—C1—C2—N117.3 (4)N1—C2—C3—S152.1 (3)
O2—C1—C2—N1164.3 (3)C1—C2—C3—S1172.0 (2)
O1—C1—C2—C3103.2 (3)C4—S1—C3—C282.8 (3)
O2—C1—C2—C375.1 (3)C3—S1—C4—C557.3 (3)
Symmetry code: (i) xy+1, y+2, z+1/3.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1B···O2ii0.85 (11)1.982 (12)2.821 (4)169 (6)
N1—H1C···O1iii0.85 (11)2.053 (13)2.892 (4)169 (6)
O1W—H1D···O10.901.942.820 (3)166
Symmetry codes: (ii) x1, y1, z; (iii) x, y1, z.
 

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