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The structural data for sodium 2-hydroxy-5-nitrobenzylsulfonate monohydrate, Na+·C7H6NO6S-·H2O, which mimics an artificial substrate for human arylsulfatase A, viz. p-nitrocatechol sulfate, reveal that the geometric parameters of the substrate and its analogue are very similar. Two water molecules, the phenolic O atom and three sulfonate O atoms form the coordination sphere of the Na+ ion, which is a distorted octahedron. The Na+ cations and the O atoms join to form a chain polymer.
Supporting information
CCDC reference: 182970
Compound (I) was synthesized according the procedure of Kaiser & Lo (1969),
except 2-hydroxy-5-nitrobenzyl bromide (purchased from Fluka) was used instead
of 2-hydroxy-5-nitrobenzyl chloride. The substrate (5.0 g) was mixed with
anhydrous sodium sulphite (7.9 g) and distilled water (100 ml). The colour of
the mixture changed to yellow. The mixture was then heated under reflux for
1.5 h. Water was removed under reduced pressure and the residual sodium salts
were dissolved in 0.1 M HCl. The solution was filtered and placed in
Petri dishes. After evaporation of the water, two types of crystals were found
in the dishes. A pale yellow crystal, which was expected to be the salt of
NBSA, was taken for X-ray analysis. The crystals of the second type were
colourless, and they were assumed to be crystals of sodium bromide.
Data collection: COLLECT (Nonius, 1997-2000); cell refinement: HKL SCALEPACK (Otwinowski & Minor 1997); data reduction: HKL DENZO (Otwinowski & Minor 1997) and SCALEPACK; program(s) used to solve structure: SHELXS97 (Sheldrick, 1990); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: ORTEPIII (Burnett & Johnson, 1996) and ORTEP-3 (Farrugia, 1997).
sodium 2-hydroxy-5-nitrobenzylsulfonate monohydrate
top
Crystal data top
Na(C7H6NO6S)·H2O | F(000) = 560 |
Mr = 273.19 | Dx = 1.741 Mg m−3 |
Monoclinic, P21/c | Mo Kα radiation, λ = 0.71073 Å |
a = 12.4940 (1) Å | Cell parameters from 2893 reflections |
b = 12.0800 (3) Å | θ = 1.0–30.0° |
c = 7.1600 (3) Å | µ = 0.38 mm−1 |
β = 105.264 (1)° | T = 293 K |
V = 1042.52 (5) Å3 | Prism, pale yellow |
Z = 4 | 0.3 × 0.2 × 0.1 mm |
Data collection top
Nonius KappaCCD area-detector diffractometer | 2606 reflections with I > 2σ(I) |
Radiation source: fine-focus sealed tube | Rint = 0.015 |
Horizonally mounted graphite crystal monochromator | θmax = 30.0°, θmin = 2.4° |
Detector resolution: 9 pixels mm-1 | h = 0→17 |
ϕ scans, and ω scans with κ offsets | k = −16→15 |
5291 measured reflections | l = −10→9 |
3026 independent reflections | |
Refinement top
Refinement on F2 | Primary atom site location: structure-invariant direct methods |
Least-squares matrix: full | Secondary atom site location: difference Fourier map |
R[F2 > 2σ(F2)] = 0.035 | Hydrogen site location: difference Fourier map |
wR(F2) = 0.094 | All H-atom parameters refined |
S = 1.10 | Calculated w = 1/[σ2(Fo2) + (0.0318P)2 + 0.6053P] where P = (Fo2 + 2Fc2)/3 |
3026 reflections | (Δ/σ)max = 0.002 |
186 parameters | Δρmax = 0.30 e Å−3 |
0 restraints | Δρmin = −0.44 e Å−3 |
Crystal data top
Na(C7H6NO6S)·H2O | V = 1042.52 (5) Å3 |
Mr = 273.19 | Z = 4 |
Monoclinic, P21/c | Mo Kα radiation |
a = 12.4940 (1) Å | µ = 0.38 mm−1 |
b = 12.0800 (3) Å | T = 293 K |
c = 7.1600 (3) Å | 0.3 × 0.2 × 0.1 mm |
β = 105.264 (1)° | |
Data collection top
Nonius KappaCCD area-detector diffractometer | 2606 reflections with I > 2σ(I) |
5291 measured reflections | Rint = 0.015 |
3026 independent reflections | |
Refinement top
R[F2 > 2σ(F2)] = 0.035 | 0 restraints |
wR(F2) = 0.094 | All H-atom parameters refined |
S = 1.10 | Δρmax = 0.30 e Å−3 |
3026 reflections | Δρmin = −0.44 e Å−3 |
186 parameters | |
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 | x | y | z | Uiso*/Ueq | |
Na | 0.51268 (6) | 0.68316 (5) | −0.25367 (9) | 0.02991 (16) | |
S | 0.63218 (3) | 0.57656 (3) | 0.22544 (5) | 0.02100 (10) | |
O1 | 0.58125 (11) | 0.66148 (10) | 0.08673 (16) | 0.0334 (3) | |
O2 | 0.55192 (10) | 0.50288 (10) | 0.27538 (19) | 0.0344 (3) | |
O3 | 0.70769 (10) | 0.62568 (11) | 0.39595 (15) | 0.0339 (3) | |
C7 | 0.71423 (13) | 0.49101 (13) | 0.1142 (2) | 0.0241 (3) | |
H1 | 0.6606 (17) | 0.4555 (18) | 0.005 (3) | 0.033 (5)* | |
H2 | 0.7453 (19) | 0.4345 (19) | 0.208 (3) | 0.041 (6)* | |
O4 | 0.68967 (9) | 0.58223 (11) | −0.25615 (16) | 0.0295 (3) | |
H5 | 0.698 (2) | 0.601 (2) | −0.369 (4) | 0.049 (7)* | |
C2 | 0.78967 (12) | 0.59583 (13) | −0.1285 (2) | 0.0229 (3) | |
C1 | 0.80549 (12) | 0.55308 (12) | 0.0590 (2) | 0.0227 (3) | |
C6 | 0.90826 (13) | 0.56561 (13) | 0.1910 (2) | 0.0260 (3) | |
H6 | 0.9210 (18) | 0.5351 (18) | 0.315 (3) | 0.036 (5)* | |
C5 | 0.99296 (13) | 0.61849 (13) | 0.1342 (2) | 0.0271 (3) | |
C4 | 0.97869 (14) | 0.65959 (14) | −0.0513 (3) | 0.0311 (3) | |
H4 | 1.0387 (19) | 0.689 (2) | −0.085 (3) | 0.046 (6)* | |
C3 | 0.87651 (13) | 0.64914 (14) | −0.1826 (2) | 0.0293 (3) | |
H3 | 0.8617 (17) | 0.6796 (18) | −0.314 (3) | 0.036 (5)* | |
N1 | 1.10174 (12) | 0.62824 (13) | 0.2711 (2) | 0.0358 (3) | |
O5 | 1.11698 (13) | 0.58883 (14) | 0.4319 (2) | 0.0538 (4) | |
O6 | 1.17458 (12) | 0.67840 (15) | 0.2188 (3) | 0.0583 (4) | |
O7 | 0.41280 (12) | 0.82522 (12) | −0.1144 (2) | 0.0373 (3) | |
H7 | 0.346 (3) | 0.828 (3) | −0.141 (4) | 0.072 (9)* | |
H8 | 0.430 (4) | 0.888 (4) | −0.154 (6) | 0.124 (15)* | |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
Na | 0.0338 (4) | 0.0292 (3) | 0.0269 (3) | 0.0001 (3) | 0.0083 (3) | 0.0027 (2) |
S | 0.02316 (18) | 0.02339 (18) | 0.01724 (16) | −0.00021 (12) | 0.00672 (12) | 0.00101 (12) |
O1 | 0.0422 (7) | 0.0327 (6) | 0.0260 (5) | 0.0126 (5) | 0.0101 (5) | 0.0070 (5) |
O2 | 0.0320 (6) | 0.0336 (6) | 0.0432 (7) | −0.0068 (5) | 0.0200 (5) | 0.0000 (5) |
O3 | 0.0387 (7) | 0.0440 (7) | 0.0190 (5) | −0.0101 (5) | 0.0072 (5) | −0.0069 (5) |
C7 | 0.0263 (7) | 0.0244 (7) | 0.0231 (6) | 0.0015 (5) | 0.0088 (6) | 0.0009 (5) |
O4 | 0.0235 (5) | 0.0456 (7) | 0.0183 (5) | −0.0036 (5) | 0.0037 (4) | 0.0023 (5) |
C2 | 0.0207 (7) | 0.0263 (7) | 0.0213 (6) | 0.0018 (5) | 0.0048 (5) | −0.0005 (5) |
C1 | 0.0224 (7) | 0.0255 (7) | 0.0212 (6) | 0.0029 (5) | 0.0075 (5) | −0.0001 (5) |
C6 | 0.0257 (7) | 0.0288 (8) | 0.0224 (7) | 0.0047 (6) | 0.0041 (6) | 0.0010 (5) |
C5 | 0.0206 (7) | 0.0262 (7) | 0.0309 (7) | 0.0024 (6) | 0.0007 (6) | −0.0027 (6) |
C4 | 0.0250 (7) | 0.0310 (8) | 0.0378 (8) | −0.0022 (6) | 0.0094 (7) | 0.0031 (6) |
C3 | 0.0279 (8) | 0.0336 (8) | 0.0269 (7) | −0.0023 (6) | 0.0082 (6) | 0.0053 (6) |
N1 | 0.0262 (7) | 0.0327 (8) | 0.0425 (8) | 0.0030 (6) | −0.0015 (6) | −0.0043 (6) |
O5 | 0.0438 (8) | 0.0631 (10) | 0.0414 (8) | −0.0011 (7) | −0.0121 (6) | 0.0073 (7) |
O6 | 0.0259 (7) | 0.0713 (11) | 0.0701 (11) | −0.0125 (7) | −0.0010 (7) | 0.0078 (9) |
O7 | 0.0287 (7) | 0.0392 (7) | 0.0425 (7) | 0.0061 (5) | 0.0066 (5) | 0.0044 (6) |
Geometric parameters (Å, º) top
Na—O1 | 2.3756 (13) | C7—H2 | 0.96 (2) |
Na—O1i | 2.4652 (13) | O4—C2 | 1.3500 (18) |
Na—O2ii | 2.3791 (14) | O4—H5 | 0.87 (3) |
Na—O4 | 2.5293 (14) | C2—C3 | 1.401 (2) |
Na—O7 | 2.4804 (15) | C2—C1 | 1.403 (2) |
Na—O7i | 2.5573 (15) | C1—C6 | 1.388 (2) |
Na—Si | 3.2855 (8) | C6—C5 | 1.386 (2) |
Na—Naiii | 3.9273 (6) | C6—H6 | 0.94 (2) |
Na—Nai | 3.9273 (6) | C5—C4 | 1.385 (2) |
S—C7 | 1.7842 (15) | N1—C5 | 1.456 (2) |
C7—C1 | 1.502 (2) | C4—C3 | 1.378 (2) |
S—O1 | 1.4529 (12) | C4—H4 | 0.92 (2) |
S—O2 | 1.4541 (12) | C3—H3 | 0.98 (2) |
S—O3 | 1.4582 (11) | N1—O5 | 1.213 (2) |
S—Naiii | 3.2855 (8) | N1—O6 | 1.231 (2) |
O1—Naiii | 2.4652 (13) | O7—Naiii | 2.5573 (15) |
O2—Naii | 2.3791 (14) | O7—H7 | 0.81 (3) |
C7—H1 | 0.98 (2) | O7—H8 | 0.86 (5) |
| | | |
O1—Na—O2ii | 89.28 (5) | O3—S—C7 | 106.76 (8) |
O1—Na—O1i | 118.95 (5) | O1—S—Naiii | 44.34 (5) |
O2ii—Na—O1i | 147.37 (5) | O2—S—Naiii | 100.28 (5) |
O1—Na—O7 | 75.37 (5) | O3—S—Naiii | 78.69 (6) |
O2ii—Na—O7 | 118.81 (5) | C7—S—Naiii | 148.59 (5) |
O1i—Na—O7 | 86.15 (5) | S—O1—Na | 138.93 (8) |
O1—Na—O4 | 82.77 (4) | S—O1—Naiii | 111.33 (6) |
O2ii—Na—O4 | 80.00 (5) | S—O2—Naii | 143.72 (8) |
O1i—Na—O4 | 87.28 (5) | C1—C7—S | 113.17 (11) |
O7—Na—O4 | 150.42 (5) | C1—C7—H1 | 114.4 (12) |
O1—Na—O7i | 168.52 (5) | S—C7—H1 | 104.8 (12) |
O2ii—Na—O7i | 80.19 (5) | C1—C7—H2 | 110.0 (14) |
O1i—Na—O7i | 72.47 (4) | S—C7—H2 | 105.9 (14) |
O7—Na—O7i | 105.67 (6) | H1—C7—H2 | 108.1 (18) |
O4—Na—O7i | 99.72 (5) | C2—O4—Na | 126.27 (10) |
O1—Na—Si | 95.66 (4) | C2—O4—H5 | 106.5 (16) |
O2ii—Na—Si | 169.11 (4) | Na—O4—H5 | 101.1 (17) |
O1i—Na—Si | 24.33 (3) | O4—C2—C3 | 120.97 (13) |
O7—Na—Si | 71.93 (4) | O4—C2—C1 | 118.38 (13) |
O4—Na—Si | 90.97 (3) | C3—C2—C1 | 120.63 (14) |
O7i—Na—Si | 95.50 (4) | C6—C1—C2 | 118.93 (14) |
O1—Na—Naiii | 36.55 (3) | C6—C1—C7 | 120.37 (13) |
O2ii—Na—Naiii | 111.50 (4) | C2—C1—C7 | 120.66 (13) |
O1i—Na—Naiii | 101.12 (4) | C5—C6—C1 | 119.43 (14) |
O7—Na—Naiii | 39.49 (4) | C5—C6—H6 | 120.5 (13) |
O4—Na—Naiii | 114.48 (3) | C1—C6—H6 | 119.9 (13) |
O7i—Na—Naiii | 145.06 (4) | C4—C5—C6 | 122.11 (14) |
Si—Na—Naiii | 77.72 (2) | C4—C5—N1 | 118.57 (15) |
O1—Na—Nai | 153.38 (4) | C6—C5—N1 | 119.29 (14) |
O2ii—Na—Nai | 114.22 (4) | C3—C4—C5 | 118.94 (15) |
O1i—Na—Nai | 35.02 (3) | C3—C4—H4 | 121.9 (14) |
O7—Na—Nai | 101.71 (4) | C5—C4—H4 | 119.1 (14) |
O4—Na—Nai | 88.97 (3) | C4—C3—C2 | 119.95 (15) |
O7i—Na—Nai | 38.08 (3) | C4—C3—H3 | 121.8 (12) |
Si—Na—Nai | 59.08 (2) | C2—C3—H3 | 118.2 (12) |
Naiii—Na—Nai | 131.44 (4) | O5—N1—O6 | 122.54 (16) |
Na—O1—Naiii | 108.43 (5) | O5—N1—C5 | 119.50 (16) |
Na—O7—Naiii | 102.43 (5) | O6—N1—C5 | 117.95 (16) |
O1—S—O2 | 113.21 (8) | Na—O7—H7 | 122 (2) |
O1—S—O3 | 110.81 (8) | Naiii—O7—H7 | 116 (2) |
O2—S—O3 | 112.29 (7) | Na—O7—H8 | 106 (3) |
O1—S—C7 | 107.67 (7) | Naiii—O7—H8 | 105 (3) |
O2—S—C7 | 105.65 (7) | H7—O7—H8 | 103 (3) |
Symmetry codes: (i) x, −y+3/2, z−1/2; (ii) −x+1, −y+1, −z; (iii) x, −y+3/2, z+1/2. |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
O4—H5···O3iv | 0.87 (3) | 1.74 (3) | 2.613 (2) | 174 (3) |
O7—H7···O6v | 0.81 (3) | 2.11 (3) | 2.901 (2) | 165 (3) |
O7—H8···O2i | 0.86 (5) | 2.17 (5) | 2.946 (2) | 151 (4) |
Symmetry codes: (i) x, −y+3/2, z−1/2; (iv) x, y, z−1; (v) x−1, −y+3/2, z−1/2. |
Experimental details
Crystal data |
Chemical formula | Na(C7H6NO6S)·H2O |
Mr | 273.19 |
Crystal system, space group | Monoclinic, P21/c |
Temperature (K) | 293 |
a, b, c (Å) | 12.4940 (1), 12.0800 (3), 7.1600 (3) |
β (°) | 105.264 (1) |
V (Å3) | 1042.52 (5) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 0.38 |
Crystal size (mm) | 0.3 × 0.2 × 0.1 |
|
Data collection |
Diffractometer | Nonius KappaCCD area-detector diffractometer |
Absorption correction | – |
No. of measured, independent and observed [I > 2σ(I)] reflections | 5291, 3026, 2606 |
Rint | 0.015 |
(sin θ/λ)max (Å−1) | 0.704 |
|
Refinement |
R[F2 > 2σ(F2)], wR(F2), S | 0.035, 0.094, 1.10 |
No. of reflections | 3026 |
No. of parameters | 186 |
H-atom treatment | All H-atom parameters refined |
Δρmax, Δρmin (e Å−3) | 0.30, −0.44 |
Selected geometric parameters (Å, º) topNa—O1 | 2.3756 (13) | C7—C1 | 1.502 (2) |
Na—O1i | 2.4652 (13) | S—O1 | 1.4529 (12) |
Na—O2ii | 2.3791 (14) | S—O2 | 1.4541 (12) |
Na—O4 | 2.5293 (14) | S—O3 | 1.4582 (11) |
Na—O7 | 2.4804 (15) | N1—C5 | 1.456 (2) |
Na—O7i | 2.5573 (15) | N1—O5 | 1.213 (2) |
S—C7 | 1.7842 (15) | N1—O6 | 1.231 (2) |
| | | |
O1—Na—O2ii | 89.28 (5) | O1—S—C7 | 107.67 (7) |
O1—Na—O1i | 118.95 (5) | O2—S—C7 | 105.65 (7) |
O1—Na—O7 | 75.37 (5) | O3—S—C7 | 106.76 (8) |
O1—Na—O4 | 82.77 (4) | C1—C7—S | 113.17 (11) |
O1—Na—O7i | 168.52 (5) | O5—N1—O6 | 122.54 (16) |
O7—Na—O7i | 105.67 (6) | O5—N1—C5 | 119.50 (16) |
Na—O1—Naiii | 108.43 (5) | O6—N1—C5 | 117.95 (16) |
Na—O7—Naiii | 102.43 (5) | | |
Symmetry codes: (i) x, −y+3/2, z−1/2; (ii) −x+1, −y+1, −z; (iii) x, −y+3/2, z+1/2. |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
O4—H5···O3iv | 0.87 (3) | 1.74 (3) | 2.613 (2) | 174 (3) |
O7—H7···O6v | 0.81 (3) | 2.11 (3) | 2.901 (2) | 165 (3) |
O7—H8···O2i | 0.86 (5) | 2.17 (5) | 2.946 (2) | 151 (4) |
Symmetry codes: (i) x, −y+3/2, z−1/2; (iv) x, y, z−1; (v) x−1, −y+3/2, z−1/2. |
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The enzyme human arylsulfatase A (ASA) catalyses the in vivo desulfatation of cerebroside 3-sulfate, and a lack of ASA activity causes the rare disease metachromatic leukodystrophy. In this inherited disorder of myelin metabolism, cerebroside sulfate accumulates in the white matter of the central nervous system and in peripheral nerves (Kolodny & Fluharty, 1995). p-Nitrocatechol sulfate (NCS; Baum et al., 1959) is used in the assay of ASA activity in vitro. Because of the structural similarity between NCS (Bülow & Usón, 2000) and 2-hydroxy-5-nitrobenzylsulfonic acid (NBSA), and the fact that ASA is not able to cleave the C—S bond, NBSA very strongly inhibits sulfatase activity (Zucker-Franklin & Nabi, 1985). The structure of sodium 2-hydroxy-5-nitrobenzylsulfonate monohydrate, (I), the sodium salt of NBSA, is reported here. \sch
The molecular structure of (I) is shown in Fig. 1. The geometric parameters of NBSA and NCS are very similar. Only the geometry of the –CH2SO3- and –OSO3- groups is slightly different, due to the replacement of carbon by oxygen (Table 1). A difference is also observed in the length of the bond between the phenolic O atom and the C atom belonging to the aromatic ring. In (I), the C2—O4 bond is longer than in NCS [1.350 (2) versus 1.285 (2) Å], indicating the different protonation state of the O atom, i.e. it is protonated in (I) and deprotonated in NCS.
Two water molecules, the phenolic O atom and three O atoms from the sulfonate groups form the coordination sphere of the Na+ ion. These six O atoms create a distorted octahedron, with Na—O distances in the range 2.376 (1)–2.557 (2) Å. The Na+ cations and the O atoms form a chain polymer, in which the Na+···Na+ distance is 3.927 (1) Å and atoms O1 and O7 belong to the coordination spheres of two neighbouring metal atoms.
There are no intramolecular hydrogen bonds, but contacts consistent with intermolecular hydrogen bonding (Table 2) are observed. The water molecule present in the structure bridges the Na+ ions and also forms hydrogen bonds to the nitro and sulfonate groups. These connections enrich a network of possible interactions and stabilize the structure.
In the crystal structure of (I), molecules of NBSA form layers parallel to the (100) plane (Fig. 2). The hydrophobic interior of the layer is filled by aromatic rings arranged in antiparallel pairs and linked by face-to-face π stacking, while sulfonate and carboxyl groups give the layer a polar surface. Contacts between the layers are stabilized by Na+ ions and water molecules.