Supporting information
Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536802021487/lh6006sup1.cif | |
Structure factor file (CIF format) https://doi.org/10.1107/S1600536802021487/lh6006Isup2.hkl |
CCDC reference: 202363
Key indicators
- Single-crystal X-ray study
- T = 293 K
- Mean (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
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
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.
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.
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).
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.
C10H16N2O4S2·H2O | Dx = 1.500 Mg m−3 |
Mr = 310.38 | Mo Kα radiation, λ = 0.71073 Å |
Trigonal, P3221 | Cell parameters from 691 reflections |
Hall symbol: P 32 2" | θ = 4.4–26.3° |
a = 5.3906 (10) Å | µ = 0.41 mm−1 |
c = 40.964 (15) Å | T = 293 K |
V = 1030.9 (5) Å3 | Prism, colourless |
Z = 3 | 0.30 × 0.25 × 0.20 mm |
F(000) = 492 |
Bruker CCD area-detector diffractometer | 1262 independent reflections |
Radiation source: fine-focus sealed tube | 1017 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.048 |
φ and ω scans | θmax = 26.3°, θmin = 4.4° |
Absorption correction: multi-scan (SADABS; Bruker, 1997) | h = −6→6 |
Tmin = 0.878, Tmax = 1.000 | k = −6→6 |
4241 measured reflections | l = −32→51 |
Refinement on F2 | H 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) = 0.094 | Δρmax = 0.89 e Å−3 |
S = 0.99 | Δρmin = −0.21 e Å−3 |
1262 reflections | Absolute structure: Flack (1983), 341 Friedel pairs |
197 parameters | Absolute structure parameter: 0.00 (16) |
0 restraints |
C10H16N2O4S2·H2O | Z = 3 |
Mr = 310.38 | Mo Kα radiation |
Trigonal, P3221 | µ = 0.41 mm−1 |
a = 5.3906 (10) Å | T = 293 K |
c = 40.964 (15) Å | 0.30 × 0.25 × 0.20 mm |
V = 1030.9 (5) Å3 |
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 = 1.000 | Rint = 0.048 |
4241 measured reflections |
R[F2 > 2σ(F2)] = 0.043 | H atoms treated by a mixture of independent and constrained refinement |
wR(F2) = 0.094 | Δρmax = 0.89 e Å−3 |
S = 0.99 | Δρmin = −0.21 e Å−3 |
1262 reflections | Absolute structure: Flack (1983), 341 Friedel pairs |
197 parameters | Absolute structure parameter: 0.00 (16) |
0 restraints |
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. |
x | y | z | Uiso*/Ueq | ||
S1 | 0.4329 (2) | 0.60161 (18) | 0.11571 (2) | 0.0348 (2) | |
N1 | 0.5174 (8) | 0.7537 (6) | 0.04095 (6) | 0.0334 (7) | |
H1A | 0.570 (10) | 0.815 (9) | 0.0216 (4) | 0.067 (15)* | |
H1B | 0.339 (2) | 0.661 (13) | 0.0450 (13) | 0.11 (2)* | |
H1C | 0.550 (13) | 0.615 (8) | 0.0394 (15) | 0.10 (2)* | |
O1 | 0.5828 (5) | 1.2629 (5) | 0.02738 (6) | 0.0427 (6) | |
O2 | 0.9418 (5) | 1.4985 (5) | 0.06143 (6) | 0.0342 (6) | |
C1 | 0.7454 (7) | 1.2771 (7) | 0.04912 (7) | 0.0252 (6) | |
C2 | 0.6984 (7) | 0.9922 (7) | 0.06362 (6) | 0.0258 (7) | |
H2A | 0.8840 | 1.0027 | 0.0664 | 0.031* | |
C3 | 0.5517 (7) | 0.9436 (7) | 0.09668 (7) | 0.0297 (7) | |
H3A | 0.3870 | 0.9691 | 0.0941 | 0.036* | |
H3B | 0.6833 | 1.0915 | 0.1115 | 0.036* | |
C4 | 0.7612 (9) | 0.6594 (8) | 0.13492 (9) | 0.0429 (10) | |
H4A | 0.7220 | 0.4870 | 0.1466 | 0.052* | |
H4B | 0.9007 | 0.6922 | 0.1181 | 0.052* | |
C5 | 0.8852 (8) | 0.9004 (8) | 0.15759 (8) | 0.0382 (8) | |
O1W | 0.0310 (6) | 1.0310 (6) | 0.0000 | 0.0386 (8) | |
H1D | 0.1962 | 1.0769 | 0.0103 | 0.055 (12)* |
U11 | U22 | U33 | U12 | U13 | U23 | |
S1 | 0.0432 (6) | 0.0290 (5) | 0.0269 (4) | 0.0140 (4) | 0.0035 (4) | 0.0076 (3) |
N1 | 0.046 (2) | 0.0235 (16) | 0.0322 (15) | 0.0185 (16) | 0.0076 (14) | 0.0027 (12) |
O1 | 0.0426 (16) | 0.0269 (13) | 0.0570 (15) | 0.0162 (12) | −0.0189 (11) | 0.0058 (11) |
O2 | 0.0306 (13) | 0.0222 (12) | 0.0446 (14) | 0.0093 (10) | −0.0029 (10) | −0.0044 (10) |
C1 | 0.0283 (17) | 0.0213 (16) | 0.0266 (14) | 0.0129 (14) | 0.0007 (15) | 0.0023 (12) |
C2 | 0.0269 (17) | 0.0216 (17) | 0.0284 (16) | 0.0118 (14) | 0.0007 (12) | 0.0060 (12) |
C3 | 0.040 (2) | 0.0286 (18) | 0.0245 (15) | 0.0199 (16) | 0.0009 (13) | 0.0048 (12) |
C4 | 0.060 (3) | 0.044 (2) | 0.0284 (19) | 0.029 (2) | −0.0044 (16) | −0.0046 (15) |
C5 | 0.051 (2) | 0.038 (2) | 0.0307 (17) | 0.0261 (19) | 0.0026 (14) | 0.0063 (13) |
O1W | 0.0359 (14) | 0.0359 (14) | 0.0355 (16) | 0.0116 (17) | −0.0018 (8) | 0.0018 (8) |
S1—C3 | 1.799 (3) | C2—C3 | 1.524 (4) |
S1—C4 | 1.816 (4) | C2—H2A | 0.9800 |
N1—C2 | 1.488 (4) | C3—H3A | 0.9700 |
N1—H1A | 0.85 | C3—H3B | 0.9700 |
N1—H1B | 0.85 | C4—C5 | 1.459 (5) |
N1—H1C | 0.85 | C4—H4A | 0.9700 |
O1—C1 | 1.225 (4) | C4—H4B | 0.9700 |
O2—C1 | 1.239 (4) | C5—C5i | 1.191 (7) |
C1—C2 | 1.545 (4) | O1W—H1D | 0.90 |
C3—S1—C4 | 101.25 (17) | C1—C2—H2A | 109.4 |
C2—N1—H1A | 107 (3) | C2—C3—S1 | 116.7 (2) |
C2—N1—H1B | 117 (4) | C2—C3—H3A | 108.1 |
H1A—N1—H1B | 118 (5) | S1—C3—H3A | 108.1 |
C2—N1—H1C | 118 (4) | C2—C3—H3B | 108.1 |
H1A—N1—H1C | 95 (5) | S1—C3—H3B | 108.1 |
H1B—N1—H1C | 100 (6) | H3A—C3—H3B | 107.3 |
O1—C1—O2 | 126.6 (3) | C5—C4—S1 | 113.7 (3) |
O1—C1—C2 | 117.4 (3) | C5—C4—H4A | 108.8 |
O2—C1—C2 | 115.9 (3) | S1—C4—H4A | 108.8 |
N1—C2—C3 | 110.3 (3) | C5—C4—H4B | 108.8 |
N1—C2—C1 | 109.2 (2) | S1—C4—H4B | 108.8 |
C3—C2—C1 | 109.0 (2) | H4A—C4—H4B | 107.7 |
N1—C2—H2A | 109.4 | C5i—C5—C4 | 178.9 (4) |
C3—C2—H2A | 109.4 | ||
O1—O1—C1—O2 | 0.0 (7) | O1—C1—C2—C3 | −103.2 (3) |
O1—O1—C1—C2 | 0.0 (6) | O2—C1—C2—C3 | 75.1 (3) |
O1—C1—C2—N1 | 17.3 (4) | N1—C2—C3—S1 | 52.1 (3) |
O1—C1—C2—N1 | 17.3 (4) | C1—C2—C3—S1 | 172.0 (2) |
O2—C1—C2—N1 | −164.3 (3) | C4—S1—C3—C2 | 82.8 (3) |
O1—C1—C2—C3 | −103.2 (3) | C3—S1—C4—C5 | 57.3 (3) |
Symmetry code: (i) x−y+1, −y+2, −z+1/3. |
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1B···O2ii | 0.85 (11) | 1.98 (1) | 2.821 (4) | 169 (6) |
N1—H1C···O1iii | 0.85 (11) | 2.05 (1) | 2.892 (4) | 169 (6) |
O1W—H1D···O1 | 0.90 | 1.94 | 2.820 (3) | 166 |
Symmetry codes: (ii) x−1, y−1, z; (iii) x, y−1, z. |
Experimental details
Crystal data | |
Chemical formula | C10H16N2O4S2·H2O |
Mr | 310.38 |
Crystal system, space group | Trigonal, P3221 |
Temperature (K) | 293 |
a, c (Å) | 5.3906 (10), 40.964 (15) |
V (Å3) | 1030.9 (5) |
Z | 3 |
Radiation type | Mo Kα |
µ (mm−1) | 0.41 |
Crystal size (mm) | 0.30 × 0.25 × 0.20 |
Data collection | |
Diffractometer | Bruker CCD area-detector |
Absorption correction | Multi-scan (SADABS; Bruker, 1997) |
Tmin, Tmax | 0.878, 1.000 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 4241, 1262, 1017 |
Rint | 0.048 |
(sin θ/λ)max (Å−1) | 0.624 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.043, 0.094, 0.99 |
No. of reflections | 1262 |
No. of parameters | 197 |
H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
Δρmax, Δρmin (e Å−3) | 0.89, −0.21 |
Absolute structure | Flack (1983), 341 Friedel pairs |
Absolute structure parameter | 0.00 (16) |
Computer programs: SMART (Bruker, 1997), SMART, SAINT (Bruker, 1997) and SHELXTL (Bruker, 1997), SHELXS97 (Sheldrick, 1997), SHELXL97 (Sheldrick, 1997), SHELXTL.
S1—C3 | 1.799 (3) | C1—C2 | 1.545 (4) |
S1—C4 | 1.816 (4) | C2—C3 | 1.524 (4) |
N1—C2 | 1.488 (4) | C4—C5 | 1.459 (5) |
O1—C1 | 1.225 (4) | C5—C5i | 1.191 (7) |
O2—C1 | 1.239 (4) | ||
C3—S1—C4 | 101.25 (17) | N1—C2—C1 | 109.2 (2) |
O1—C1—O2 | 126.6 (3) | C3—C2—C1 | 109.0 (2) |
O1—C1—C2 | 117.4 (3) | C2—C3—S1 | 116.7 (2) |
O2—C1—C2 | 115.9 (3) | C5—C4—S1 | 113.7 (3) |
N1—C2—C3 | 110.3 (3) | C5i—C5—C4 | 178.9 (4) |
O1—C1—C2—N1 | 17.3 (4) | N1—C2—C3—S1 | 52.1 (3) |
O2—C1—C2—N1 | −164.3 (3) | C1—C2—C3—S1 | 172.0 (2) |
O1—C1—C2—C3 | −103.2 (3) | C4—S1—C3—C2 | 82.8 (3) |
O2—C1—C2—C3 | 75.1 (3) | C3—S1—C4—C5 | 57.3 (3) |
Symmetry code: (i) x−y+1, −y+2, −z+1/3. |
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1B···O2ii | 0.85 (11) | 1.982 (12) | 2.821 (4) | 169 (6) |
N1—H1C···O1iii | 0.85 (11) | 2.053 (13) | 2.892 (4) | 169 (6) |
O1W—H1D···O1 | 0.90 | 1.94 | 2.820 (3) | 166 |
Symmetry codes: (ii) x−1, y−1, z; (iii) x, y−1, z. |
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).