supplementary materials


HTML versionpdf versioncif file3d viewstructure factorssupplementary materialsCIF check reportsimilar papers Open access

Acta Cryst. (2009). E65, m470    [ doi:10.1107/S1600536809011283 ]

Tetraaquabis[3-(2-pyridylsulfanyl)propionato N-oxide]nickel(II)

B. Ravindran Durai Nayagam, S. R. Jebas, J. P. Edward Rajkumar and D. Schollmeyer

Abstract top

In the centrosymmetric title compound, [Ni(C8H8NO3S)2(H2O)4], the NiII ion, which lies on an inversion centre, is six coordinated by four water molecules and two propionate O atoms from two 2-pyridylsulfanylpropionate N-oxide ligands, forming a slightly distorted octahedral geometry. An intramolecular O-H...O hydrogen bond stabilizes the molecular conformation. The crystal packing is consolidated by intermolecular O-H...O and C-H...O hydrogen bonding.

Comment top

N-oxides and their derivatives show a broad spectrum of biological activity such as antifungal, antimicrobial and antibacterial activities (Lobana & Bhatia, 1989; Symons & West, 1985). These compounds are also found to be involved in DNA strand scission under physiological conditions (Katsuyuki et al., 1991; Bovin et al., 1992). Pyridine N–oxides bearing a sulfur group in position two display significant antimicrobial activity (Leonard et al., 1955). In view of the importance of N–oxides, we have previously reported the crystal structures of N–oxide derivatives (Jebas et al., 2005; Ravindran et al., 2008). As an extension of our work on N–oxide derivatives, we report here the crystal structure of the title compound.

The asymmetric unit comprises of half molecule of the title compound, the other half is symmetry generated [symmetry code: -x + 1,-y + 1,-z + 1]. The NiII ion which lies on an inversion centre is six coordinated by four water molecules and two propianoto oxygen atoms from two 2-pyridylsulfanylpropionato N-oxide ligands forming a slightly distorted octahedral geometry. The bond lengths and angles agree well with the N–oxide derivatives reported earlier (Jebas et al., 2005)

Intramolecular O—H···O hydrogen bonding influences the conformation of the molecule. The crystal packing (Fig. 2) is consolidated by intermolecular O—H···O and C—H···O hydrogen bonding together with intramolecular S···O = 2.6968 (10) Å; O···O = 2.6248 (12) Å, intermolecular O···Oi = 2.6469 (12) Å; O···Oii = 2.6570 (12) Å and O···Oiii = 2.9455 (12) Å [symmetry code: (i):1 + x,y,-1 + z; (ii) 2 - x,1 - y,1 - z; (iii) 1 - x,1 - y,1 - z] short contacts. The molecules are stacked along the a axis.

Related literature top

For the biological activities of N-oxide derivatives, see: Bovin et al. (1992); Katsuyuki et al. (1991). Leonard et al. (1955); Lobana & Bhatia (1989); Symons & West (1985). For related literature, see: Jebas et al. (2005); Ravindran et al. (2008).

Experimental top

A mixture of the potassium salt of 3(1-oxo-pyridinine- 2-sulfanyl)propionic acid (0.237 g,1 mmol) and Nickel (II) chloride (0.13 g, 0.5 mmol), in water (20 ml) was heated at 333k with continous stirring for one hour. The solution was kept aside for slow evaporation. After two weeks, green colored crystals were obtained.

Refinement top

After checking their presence in the Fourier map, all the hydrogen atoms were fixed on the calculated positions and allowed to ride on their parent atoms with the C—H = 0.95 Å (aromatic), C—H = 0.99 Å (methylene) and O—H = 0.81–0.82 Å (water) with Uiso(C) in the range of 1.2Ueq(C) and 1.5Ueq(O).

Computing details top

Data collection: APEX2 (Bruker, 2008); cell refinement: APEX2 (Bruker, 2008); data reduction: APEX2 (Bruker, 2008); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL (Sheldrick, 2008) and PLATON (Spek, 2009).

Figures top
[Figure 1] Fig. 1. The molecular structure of the title compound, showing 50% probability displacement ellipsoids and the atom numbering scheme. Symmetry code: -x + 1,-y + 1,-z + 1.
[Figure 2] Fig. 2. The crystal packing of the title compound, viewed down the a axis. Molecules are stacked along the a axis.
Tetraaquabis[3-(2-pyridylsulfanyl)propionato N-oxide]nickel(II) top
Crystal data top
[Ni(C8H8NO3S)2(H2O)4]Z = 1
Mr = 527.20F(000) = 274
Triclinic, P1Dx = 1.636 Mg m−3
Hall symbol: -P 1Mo Kα radiation, λ = 0.71069 Å
a = 4.8155 (5) ÅCell parameters from 6946 reflections
b = 8.765 (1) Åθ = 2.3–28.2°
c = 12.9560 (15) ŵ = 1.16 mm−1
α = 86.400 (2)°T = 173 K
β = 79.501 (2)°Plate, green
γ = 84.929 (2)°0.35 × 0.28 × 0.07 mm
V = 534.98 (10) Å3
Data collection top
Bruker SMART APEXII CCD
diffractometer		2615 independent reflections
Radiation source: sealed Tube2501 reflections with I > 2σ(I)
graphiteRint = 0.017
CCD scanθmax = 28.2°, θmin = 1.6°
Absorption correction: multi-scan
(SADABS; Sheldrick, 2008)		h = −6→6
Tmin = 0.405, Tmax = 0.492k = −11→11
9627 measured reflectionsl = −17→17
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.020Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.055H-atom parameters constrained
S = 1.05 w = 1/[σ2(Fo2) + (0.0294P)2 + 0.2035P]
where P = (Fo2 + 2Fc2)/3
2615 reflections(Δ/σ)max < 0.001
142 parametersΔρmax = 0.40 e Å−3
0 restraintsΔρmin = −0.36 e Å−3
Crystal data top
[Ni(C8H8NO3S)2(H2O)4]γ = 84.929 (2)°
Mr = 527.20V = 534.98 (10) Å3
Triclinic, P1Z = 1
a = 4.8155 (5) ÅMo Kα radiation
b = 8.765 (1) ŵ = 1.16 mm−1
c = 12.9560 (15) ÅT = 173 K
α = 86.400 (2)°0.35 × 0.28 × 0.07 mm
β = 79.501 (2)°
Data collection top
Bruker SMART APEXII CCD
diffractometer		2615 independent reflections
Absorption correction: multi-scan
(SADABS; Sheldrick, 2008)		2501 reflections with I > 2σ(I)
Tmin = 0.405, Tmax = 0.492Rint = 0.017
9627 measured reflectionsθmax = 28.2°
Refinement top
R[F2 > 2σ(F2)] = 0.020H-atom parameters constrained
wR(F2) = 0.055Δρmax = 0.40 e Å−3
S = 1.05Δρmin = −0.36 e Å−3
2615 reflectionsAbsolute structure: ?
142 parametersFlack parameter: ?
0 restraintsRogers parameter: ?
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
Ni10.50000.50000.50000.01405 (6)
N11.2267 (2)0.77325 (12)−0.20598 (8)0.0197 (2)
C21.0696 (2)0.79224 (13)−0.10776 (8)0.0167 (2)
C30.8347 (3)0.89789 (14)−0.09608 (9)0.0212 (2)
H30.72290.9119−0.02850.025*
C40.7627 (3)0.98279 (15)−0.18222 (10)0.0254 (3)
H40.60271.0555−0.17410.031*
C50.9266 (3)0.96061 (16)−0.28069 (10)0.0291 (3)
H50.87941.0180−0.34060.035*
C61.1567 (3)0.85564 (16)−0.29110 (10)0.0274 (3)
H61.26850.8403−0.35860.033*
O71.44740 (19)0.67209 (11)−0.21521 (7)0.0264 (2)
S81.19805 (6)0.67388 (3)−0.01121 (2)0.01821 (7)
C90.9142 (2)0.70873 (14)0.09994 (8)0.0176 (2)
H9A0.88800.81940.11360.021*
H9B0.73440.67650.08480.021*
C100.9942 (2)0.61698 (13)0.19529 (8)0.0177 (2)
H10A1.02680.50710.17960.021*
H10B1.17300.65110.21000.021*
C110.7643 (2)0.63642 (13)0.29187 (8)0.0159 (2)
O120.55540 (18)0.72858 (11)0.28796 (7)0.02341 (18)
O130.80467 (17)0.55410 (10)0.37393 (6)0.01937 (17)
O140.26378 (17)0.70791 (10)0.47964 (6)0.01973 (17)
H14A0.32640.72710.41790.030*
H14B0.09520.70070.48490.030*
O150.71999 (16)0.60521 (10)0.59458 (6)0.01836 (17)
H15A0.62070.62520.65140.028*
H15B0.85960.55220.60920.028*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Ni10.01095 (10)0.01935 (11)0.01075 (10)0.00213 (7)−0.00158 (7)0.00208 (7)
N10.0229 (5)0.0205 (5)0.0145 (4)−0.0001 (4)−0.0011 (4)−0.0011 (4)
C20.0191 (5)0.0181 (5)0.0127 (5)−0.0037 (4)−0.0019 (4)−0.0001 (4)
C30.0223 (5)0.0220 (6)0.0178 (5)0.0001 (4)−0.0012 (4)0.0002 (4)
C40.0277 (6)0.0222 (6)0.0259 (6)0.0029 (5)−0.0068 (5)0.0018 (5)
C50.0399 (7)0.0273 (6)0.0199 (6)0.0009 (5)−0.0090 (5)0.0055 (5)
C60.0377 (7)0.0291 (6)0.0135 (5)0.0006 (5)−0.0017 (5)0.0019 (5)
O70.0259 (4)0.0308 (5)0.0188 (4)0.0075 (4)0.0012 (3)−0.0025 (3)
S80.01735 (13)0.02289 (15)0.01281 (13)0.00103 (10)−0.00070 (10)0.00202 (10)
C90.0165 (5)0.0228 (5)0.0121 (5)−0.0006 (4)−0.0004 (4)0.0017 (4)
C100.0159 (5)0.0229 (5)0.0131 (5)−0.0003 (4)−0.0016 (4)0.0021 (4)
C110.0147 (5)0.0205 (5)0.0127 (5)−0.0024 (4)−0.0027 (4)0.0011 (4)
O120.0214 (4)0.0286 (5)0.0168 (4)0.0067 (3)−0.0004 (3)0.0053 (3)
O130.0137 (4)0.0298 (4)0.0129 (4)0.0020 (3)−0.0015 (3)0.0052 (3)
O140.0164 (4)0.0241 (4)0.0169 (4)0.0030 (3)−0.0013 (3)0.0019 (3)
O150.0147 (4)0.0256 (4)0.0139 (4)0.0030 (3)−0.0024 (3)−0.0009 (3)
Geometric parameters (Å, °) top
Ni1—O13i2.0488 (8)C5—H50.9500
Ni1—O132.0488 (8)C6—H60.9500
Ni1—O15i2.0644 (8)S8—C91.8165 (11)
Ni1—O152.0644 (8)C9—C101.5216 (15)
Ni1—O142.0898 (8)C9—H9A0.9900
Ni1—O14i2.0898 (8)C9—H9B0.9900
N1—O71.3154 (13)C10—C111.5195 (15)
N1—C61.3579 (16)C10—H10A0.9900
N1—C21.3687 (14)C10—H10B0.9900
C2—C31.3889 (16)C11—O121.2395 (14)
C2—S81.7405 (11)C11—O131.2818 (13)
C3—C41.3823 (17)O14—H14A0.8142
C3—H30.9500O14—H14B0.8100
C4—C51.3877 (19)O15—H15A0.8216
C4—H40.9500O15—H15B0.8268
C5—C61.3685 (19)
O13i—Ni1—O13180.0C6—C5—H5120.2
O13i—Ni1—O15i88.53 (3)C4—C5—H5120.2
O13—Ni1—O15i91.47 (3)N1—C6—C5120.67 (11)
O13i—Ni1—O1591.47 (3)N1—C6—H6119.7
O13—Ni1—O1588.53 (3)C5—C6—H6119.7
O15i—Ni1—O15180.0C2—S8—C9100.23 (5)
O13i—Ni1—O1488.50 (3)C10—C9—S8108.10 (8)
O13—Ni1—O1491.50 (3)C10—C9—H9A110.1
O15i—Ni1—O1490.66 (3)S8—C9—H9A110.1
O15—Ni1—O1489.34 (3)C10—C9—H9B110.1
O13i—Ni1—O14i91.50 (3)S8—C9—H9B110.1
O13—Ni1—O14i88.50 (3)H9A—C9—H9B108.4
O15i—Ni1—O14i89.34 (3)C11—C10—C9111.71 (9)
O15—Ni1—O14i90.66 (3)C11—C10—H10A109.3
O14—Ni1—O14i180.0C9—C10—H10A109.3
O7—N1—C6121.11 (10)C11—C10—H10B109.3
O7—N1—C2117.75 (10)C9—C10—H10B109.3
C6—N1—C2121.15 (10)H10A—C10—H10B107.9
N1—C2—C3118.82 (10)O12—C11—O13124.27 (10)
N1—C2—S8112.99 (8)O12—C11—C10119.85 (10)
C3—C2—S8128.19 (9)O13—C11—C10115.87 (9)
C4—C3—C2120.43 (11)C11—O13—Ni1126.08 (7)
C4—C3—H3119.8Ni1—O14—H14A98.9
C2—C3—H3119.8Ni1—O14—H14B114.4
C3—C4—C5119.25 (12)H14A—O14—H14B107.5
C3—C4—H4120.4Ni1—O15—H15A111.7
C5—C4—H4120.4Ni1—O15—H15B113.8
C6—C5—C4119.69 (12)H15A—O15—H15B105.3
O7—N1—C2—C3−179.71 (10)N1—C2—S8—C9−171.71 (9)
C6—N1—C2—C30.08 (17)C3—C2—S8—C97.83 (12)
O7—N1—C2—S8−0.12 (14)C2—S8—C9—C10−178.14 (8)
C6—N1—C2—S8179.66 (10)S8—C9—C10—C11−178.64 (8)
N1—C2—C3—C4−0.39 (18)C9—C10—C11—O12−5.56 (15)
S8—C2—C3—C4−179.90 (10)C9—C10—C11—O13175.00 (10)
C2—C3—C4—C50.4 (2)O12—C11—O13—Ni120.56 (17)
C3—C4—C5—C6−0.1 (2)C10—C11—O13—Ni1−160.03 (7)
O7—N1—C6—C5179.99 (12)O15—Ni1—O13—C11−120.55 (9)
C2—N1—C6—C50.2 (2)O14—Ni1—O13—C11−31.25 (10)
C4—C5—C6—N1−0.2 (2)
Symmetry codes: (i) −x+1, −y+1, −z+1.
Hydrogen-bond geometry (Å, °) top
D—H···AD—HH···AD···AD—H···A
O14—H14A···O120.811.842.6248 (12)162
O14—H14B···O15ii0.812.272.9517 (12)142
O14—H14B···O13ii0.812.643.2316 (12)131
O15—H15A···O7iii0.821.832.6469 (12)172
O15—H15B···O13iv0.831.832.6570 (11)172
C4—H4···O12v0.952.483.2044 (17)133
C6—H6···O14vi0.952.463.2515 (16)140
C10—H10B···O12vii0.992.423.3910 (14)167
Symmetry codes: (ii) x−1, y, z; (iii) x−1, y, z+1; (iv) −x+2, −y+1, −z+1; (v) −x+1, −y+2, −z; (vi) x+1, y, z−1; (vii) x+1, y, z.
Table 1
Selected geometric parameters (Å) top
Ni1—O132.0488 (8)Ni1—O142.0898 (8)
Ni1—O152.0644 (8)N1—O71.3154 (13)
Table 2
Hydrogen-bond geometry (Å, °) top
D—H···AD—HH···AD···AD—H···A
O14—H14A···O120.811.842.6248 (12)162
O14—H14B···O15i0.812.272.9517 (12)142
O14—H14B···O13i0.812.643.2316 (12)131
O15—H15A···O7ii0.821.832.6469 (12)172
O15—H15B···O13iii0.831.832.6570 (11)172
C4—H4···O12iv0.952.483.2044 (17)133
C6—H6···O14v0.952.463.2515 (16)140
C10—H10B···O12vi0.992.423.3910 (14)167
Symmetry codes: (i) x−1, y, z; (ii) x−1, y, z+1; (iii) −x+2, −y+1, −z+1; (iv) −x+1, −y+2, −z; (v) x+1, y, z−1; (vi) x+1, y, z.
references
References top

Bovin, D. H. R., Crepon, E. & Zard, S. Z. (1992). Bull. Soc. Chim. Fr. 129, 145–150.

Bruker (2008). APEX2. Bruker AXS Inc., Madison, Wisconsin, USA.

Jebas, S. R., Balasubramanian, T., Ravidurai, B. & Kumaresan, S. (2005). Acta Cryst. E61, o2677–o2678.

Katsuyuki, N., Carter, B. J., Xu, J. & Hetch, S. M. (1991). J. Am. Chem. Soc. 113, 5099–5100.

Leonard, F., Barklay, F. A., Brown, E. V., Anderson, F. E. & Green, D. M. (1955). Antibiot. Chemother. pp. 261–264.

Lobana, T. S. & Bhatia, P. K. (1989). J. Sci. Ind. Res. 48, 394–401.

Ravindran Durai Nayagam, B., Jebas, S. R., Grace, S. & Schollmeyer, D. (2008). Acta Cryst. E64, o409.

Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122.

Spek, A. L. (2009). Acta Cryst. D65, 148–155.

Symons, M. C. R. & West, D.-X. (1985). J. Chem. Soc. Dalton Trans. pp. 379–381.