metal-organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

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ISSN: 2414-3146

trans-Bis(di­methyl sulfoxide-κO)bis­­(3-nitro­benzo­hydroxamato-κ2O,O′)zinc(II)

aLaboratório de Físico-Química Aplicada e Tecnológica, Escola de Química e Alimentos, Universidade Federal do Rio Grande, Av. Itália km 08, Campus Carreiros, 96203-900, Rio Grande-RS, Brazil, and bLaboratório de Materiais Inorgânicos, Departamento de Química, Universidade Federal de Santa Maria, Av. Roraima, 97105-900, Santa Maria-RS, Brazil
*Correspondence e-mail: julianovicenti@gmail.com

Edited by M. Weil, Vienna University of Technology, Austria (Received 10 July 2019; accepted 13 July 2019; online 19 July 2019)

Single crystals of the title complex, [Zn(C7H5N2O4)2(C2H6OS)2] or [Zn(NBZH)2(DMSO)2], were isolated from a dimethyl sulfoxide (DMSO) solution containing [Zn(NBZH)2]·2H2O (NBZH = 3-nitro­benzo­hydroxamate anion). The asymmetric unit comprises of one O,O′-chelating NBZH anion, one O-bound DMSO ligand and one zinc(II) cation localized on an inversion centre. The three-dimensional crystal packing includes N—H⋯O and C—H⋯O hydrogen bonding, as well as O⋯H and H⋯H contacts identified by Hirshfeld isosurface analysis.

3D view (loading...)
[Scheme 3D1]
Chemical scheme
[Scheme 1]

Structure description

Hydroxamic acids, RC(=O)–NH–OH (where R = alkyl, ar­yl), play important roles in biology and medicine and have been a source of great inter­est because they present a wide variety of biological activities (Codd, 2008[Codd, R. (2008). Coord. Chem. Rev. 252, 1387-1408.]; Marmion et al., 2004[Marmion, C. J., Griffith, D. & Nolan, K. B. (2004). Eur. J. Inorg. Chem. 2004, 3003-3016.]). These are related to the ability to form stable complexes with metal ions, especially iron(III) (Ugwu et al., 2014[Ugwu, D. I., Ezema, B. E., Eze, F. U., Ayogu, J. I., Ezema, C. G. & Ugwuja, D. I. (2014). Am. J. Org. Chem. 4, 26-51.]; Griffith et al., 2008[Griffith, D., Krot, K., Comiskey, J., Nolan, K. B. & Marmion, C. J. (2008). Dalton Trans. pp. 137-147.]). In addition, this class of compounds provides several sites for hydrogen-bonding inter­actions with enzyme structures, thus becoming potent and selective inhibitors of a number of enzymes such as matrix metalloproteinase (Muri et al., 2002[Muri, E. M. F., Nieto, M. J., Sindelar, R. D. & Williamson, J. S. (2002). Curr. Med. Chem. 9, 1631-1653.]; Sani et al., 2004[Sani, M., Belotti, D., Giavazzi, R., Panzeri, W., Volonterio, A. & Zanda, M. (2004). Tetrahedron Lett. 45, 1611-1615.]), peroxidases (O'Brien et al., 2000[O'Brien, E. C., Farkas, E., Gil, M. J., Fitzgerald, D., Castineras, A. & Nolan, K. B. (2000). J. Inorg. Biochem. 79, 47-51.]; Indiani et al., 2003[Indiani, C., Santoni, E., Becucci, B., Boffi, A., Fukuyama, K. & Smulevich, G. (2003). Biochemistry, 42, 14066-14074.]), histone de­acetyl­ases (Richon, 2006[Richon, V. M. (2006). Br. J. Cancer, 95, S2-S6.]; Krennhrubec et al., 2007[Krennhrubec, K., Marshall, B. L., Hedglin, M., Verdin, E. & Ulrich, S. M. (2007). Bioorg. Med. Chem. Lett. 17, 2874-2878.]), or ureases (Xiao et al., 2013[Xiao, Z.-P., Peng, Z.-P., Dong, J.-J., Deng, R.-C., Wang, X.-D., Ouyang, H., Yang, P., He, J., Wang, W.-F., Zhu, M., Peng, X.-C., Peng, W.-X. & Zhu, H.-L. (2013). Eur. J. Med. Chem. 68, 212-221.]; Krajewska, 2009[Krajewska, B. (2009). J. Mol. Catal. B Enzym. 59, 9-21.]; Shi et al., 2016[Shi, W.-K., Deng, R.-C., Wang, P.-F., Yue, Q.-Q., Liu, Q., Ding, K.-L., Yang, M.-H., Zhang, H.-Y., Gong, S.-H., Deng, M., Liu, W.-R., Feng, Q.-J., Xiao, Z.-P. & Zhu, -L. (2016). Bioorg. Med. Chem. 24, 4519-4527.]). In our previous work, we have synthesized, characterized and investigated some physical-chemical properties of zinc(II) aromatic hydroxamates (Gonçalves et al., 2019[Gonçalves, B. L., Ramos, D. F., Halicki, P. C. B., da Silva, P. E. A. & Vicenti, J. R. M. (2019). Chemical Data Collections, 22, 100240-100248.]) and report here the crystal structure of [Zn(C7H5N2O4)2(C2H6OS)2] or [Zn(NBZH)2(DMSO)2].

A slightly distorted octa­hedral environment around the zinc(II) cation (site symmetry [\overline{1}]) is generated by symmetry operation 2 − x, −y, −z, leading to an all-trans configuration of the two ligands (Fig. 1[link]). In the mol­ecular structure, the O-bound DMSO mol­ecule has a distance of 2.3473 (12) Å for Zn1—O5, indicating an elongation along the axial position. The O,O′-chelating NBZH ligand shows shorter distances of 2.0029 (11) Å for Zn1—O1 and 2.0675 (11) Å for Zn1—O2 in the equatorial positions. The nitro group attached to the NBZH ligand is almost planar with the aromatic ring, displaying a dihedral angle of 3.2 (2)°.

[Figure 1]
Figure 1
Mol­ecular structure of [Zn(NBZH)2(DMSO)2]. Ellipsoids are drawn at the 50% probability level [symmetry code: (i) −x + 1, −y + 1, −z + 2].

In the crystal structure, discrete mol­ecular units of [Zn(NBZH)2(DMSO)2] (Fig. 2[link]) are packed along the [010] and [001] directions. The inter­molecular inter­actions collated in Table 1[link] are suggestive of two weak non-classical C—H⋯O hydrogen bonds involving di­methyl­sulfoxide mol­ecules. As shown in Fig. 3[link], the hydroxamate fragment plays a dominant role in the packing through an N—H⋯O5 hydrogen bond of medium strength along [100] (Table 1[link]). These structural features generate a three-dimensional supra­molecular network that was further investigated by Hirshfeld surface analysis (Fig. 4[link]), as determined with CrystalExplorer (Turner et al., 2017[Turner, M. J., McKinnon, J. J., Wolff, S. K., Grimwood, D. J., Spackman, P. R., Jayatilaka, D. & Spackman, M. A. (2017). CrystalExplorer17. University of Western Australia. http://hirshfeldsurface.net]). The results indicate a significant contribution by O⋯H contacts, corresponding to 43.1% of the two-dimensional fingerprint plots. H⋯H and C⋯H contacts are also observed, covering 30.1% and 11.6% of the isosurface, respectively, followed by C⋯C (2.9%), S⋯H (2.6%) and N⋯H (1%) inter­actions.

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
C8—H8C⋯O4i 0.96 2.55 3.381 (3) 145
C8—H8A⋯O1ii 0.96 2.66 3.533 (3) 150
N1—H1⋯O5iii 0.84 (2) 2.08 (2) 2.916 (1) 175 (2)
Symmetry codes: (i) -x+1, -y+1, -z+1; (ii) -x+1, -y+2, -z+2; (iii) x+1, y, z.
[Figure 2]
Figure 2
Hydrogen bonding in [Zn(NBZH)2(DMSO)2] along the [010] and [001] directions.
[Figure 3]
Figure 3
Hydrogen bonding in [Zn(NBZH)2(DMSO)2] along the [100] direction.
[Figure 4]
Figure 4
Results of Hirshfeld analysis for [Zn(NBZH)2(DMSO)2].

Synthesis and crystallization

Suitable single crystals of the title compound were obtained within one week from a di­methyl­sulfoxide solution containing [Zn(NBZH)2]·2H2O, previously reported by us (Gonçalves et al., 2019[Gonçalves, B. L., Ramos, D. F., Halicki, P. C. B., da Silva, P. E. A. & Vicenti, J. R. M. (2019). Chemical Data Collections, 22, 100240-100248.]).

Refinement

Crystal data, data collection and structure refinement details are summarized in Table 2[link].

Table 2
Experimental details

Crystal data
Chemical formula [Zn(C7H5N2O4)2(C2H6OS)2]
Mr 583.91
Crystal system, space group Triclinic, P[\overline{1}]
Temperature (K) 294
a, b, c (Å) 6.4899 (2), 7.8961 (3), 11.4224 (4)
α, β, γ (°) 83.496 (1), 84.591 (1), 89.567 (1)
V3) 578.98 (3)
Z 1
Radiation type Mo Kα
μ (mm−1) 1.30
Crystal size (mm) 0.20 × 0.15 × 0.10
 
Data collection
Diffractometer Bruker APEXII CCD
Absorption correction Multi-scan (SADABS; Bruker, 2014[Bruker (2014). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.])
Tmin, Tmax 0.786, 0.880
No. of measured, independent and observed [I > 2σ(I)] reflections 30874, 3558, 2961
Rint 0.032
(sin θ/λ)max−1) 0.715
 
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.032, 0.097, 0.92
No. of reflections 3558
No. of parameters 166
H-atom treatment H atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å−3) 0.65, −0.53
Computer programs: APEX2 and SAINT (Bruker, 2014[Bruker (2014). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]), SHELXT2014 (Sheldrick, 2015a[Sheldrick, G. M. (2015a). Acta Cryst. A71, 3-8.]), SHELXL2018 (Sheldrick, 2015b[Sheldrick, G. M. (2015b). Acta Cryst. C71, 3-8.]), DIAMOND (Brandenburg, 2006[Brandenburg, K. (2006). DIAMOND. Crystal Impact GbR, Bonn, Germany.]), Mercury (Macrae et al., 2006[Macrae, C. F., Edgington, P. R., McCabe, P., Pidcock, E., Shields, G. P., Taylor, R., Towler, M. & van de Streek, J. (2006). J. Appl. Cryst. 39, 453-457.]), CrystalExplorer17 (Turner et al., 2017[Turner, M. J., McKinnon, J. J., Wolff, S. K., Grimwood, D. J., Spackman, P. R., Jayatilaka, D. & Spackman, M. A. (2017). CrystalExplorer17. University of Western Australia. http://hirshfeldsurface.net]) and publCIF (Westrip, 2010[Westrip, S. P. (2010). J. Appl. Cryst. 43, 920-925.]).

Structural data


Computing details top

Data collection: APEX2 (Bruker, 2014); cell refinement: SAINT (Bruker, 2014); data reduction: SAINT (Bruker, 2014); program(s) used to solve structure: SHELXT2014 (Sheldrick, 2015a); program(s) used to refine structure: SHELXL2018 (Sheldrick, 2015b); molecular graphics: DIAMOND (Brandenburg, 2006), Mercury (Macrae et al., 2006) and CrystalExplorer17 (Turner et al., 2017); software used to prepare material for publication: publCIF (Westrip, 2010).

trans-Bis(dimethyl sulfoxide-κO)bis(3-nitrobenzohydroxamato-κ2O,O')zinc(II) top
Crystal data top
[Zn(C7H5N2O4)2(C2H6OS)2]Z = 1
Mr = 583.91F(000) = 298
Triclinic, P1Dx = 1.663 Mg m3
a = 6.4899 (2) ÅMo Kα radiation, λ = 0.71073 Å
b = 7.8961 (3) ÅCell parameters from 9996 reflections
c = 11.4224 (4) Åθ = 3.0–30.3°
α = 83.496 (1)°µ = 1.30 mm1
β = 84.591 (1)°T = 294 K
γ = 89.567 (1)°Block, yellow
V = 578.98 (3) Å30.20 × 0.15 × 0.10 mm
Data collection top
Bruker APEXII CCD
diffractometer
2961 reflections with I > 2σ(I)
φ and ω scansRint = 0.032
Absorption correction: multi-scan
(SADABS; Bruker, 2014)
θmax = 30.6°, θmin = 3.0°
Tmin = 0.786, Tmax = 0.880h = 99
30874 measured reflectionsk = 1111
3558 independent reflectionsl = 1616
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)] = 0.032Hydrogen site location: mixed
wR(F2) = 0.097H atoms treated by a mixture of independent and constrained refinement
S = 0.92 w = 1/[σ2(Fo2) + (0.0663P)2 + 0.1979P]
where P = (Fo2 + 2Fc2)/3
3558 reflections(Δ/σ)max = 0.001
166 parametersΔρmax = 0.65 e Å3
0 restraintsΔρmin = 0.53 e Å3
Special details top

Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
Zn10.5000000.5000001.0000000.03291 (10)
S10.35743 (8)0.88919 (6)0.91043 (4)0.04435 (13)
C10.8166 (2)0.47473 (18)0.82661 (13)0.0259 (3)
O10.75668 (17)0.64360 (15)0.98049 (10)0.0319 (2)
N10.88330 (19)0.58558 (17)0.89218 (12)0.0281 (3)
H11.006 (3)0.618 (3)0.8898 (19)0.037 (5)*
C30.8709 (2)0.32583 (19)0.64935 (13)0.0288 (3)
H30.7305900.2991270.6597470.035*
O20.63195 (17)0.41942 (16)0.84399 (10)0.0350 (3)
O50.30496 (19)0.70808 (15)0.89650 (12)0.0388 (3)
C61.2902 (3)0.3979 (3)0.61715 (16)0.0396 (4)
H61.4312000.4219720.6070330.048*
O41.0035 (3)0.1408 (2)0.38495 (13)0.0596 (4)
C51.2036 (3)0.3072 (2)0.53664 (15)0.0386 (4)
H51.2838930.2697540.4728400.046*
O30.7091 (3)0.1606 (2)0.48421 (16)0.0629 (4)
C40.9935 (3)0.2746 (2)0.55502 (14)0.0317 (3)
C20.9584 (2)0.41788 (18)0.72915 (12)0.0259 (3)
C80.1489 (5)1.0145 (3)0.8571 (3)0.0721 (8)
H8A0.1658881.1304990.8723060.108*
H8B0.0202590.9704100.8968700.108*
H8C0.1482801.0102100.7735050.108*
N20.8946 (3)0.18484 (19)0.46896 (13)0.0413 (3)
C71.1708 (2)0.4532 (2)0.71197 (15)0.0331 (3)
H71.2318840.5142530.7646630.040*
C90.5491 (5)0.9574 (4)0.7945 (3)0.0868 (10)
H9A0.5075200.9277370.7209480.130*
H9B0.6779780.9027580.8098730.130*
H9C0.5658801.0787670.7897090.130*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Zn10.02448 (13)0.04346 (16)0.03212 (15)0.01039 (10)0.00407 (9)0.01494 (11)
S10.0614 (3)0.0350 (2)0.0395 (2)0.01645 (19)0.0177 (2)0.00475 (17)
C10.0233 (6)0.0292 (7)0.0254 (6)0.0030 (5)0.0023 (5)0.0036 (5)
O10.0265 (5)0.0382 (6)0.0324 (5)0.0062 (4)0.0034 (4)0.0145 (4)
N10.0212 (5)0.0331 (6)0.0303 (6)0.0053 (5)0.0014 (4)0.0082 (5)
C30.0265 (6)0.0305 (7)0.0298 (7)0.0011 (5)0.0033 (5)0.0046 (5)
O20.0234 (5)0.0491 (7)0.0346 (6)0.0105 (4)0.0028 (4)0.0179 (5)
O50.0351 (6)0.0337 (6)0.0491 (7)0.0088 (5)0.0093 (5)0.0071 (5)
C60.0250 (7)0.0538 (10)0.0398 (9)0.0008 (7)0.0016 (6)0.0084 (7)
O40.0774 (11)0.0651 (10)0.0399 (8)0.0042 (8)0.0002 (7)0.0262 (7)
C50.0355 (8)0.0470 (9)0.0328 (8)0.0067 (7)0.0037 (6)0.0090 (7)
O30.0543 (9)0.0770 (11)0.0651 (10)0.0103 (8)0.0140 (7)0.0338 (8)
C40.0375 (8)0.0303 (7)0.0284 (7)0.0026 (6)0.0055 (6)0.0057 (6)
C20.0244 (6)0.0275 (6)0.0258 (6)0.0001 (5)0.0019 (5)0.0032 (5)
C80.102 (2)0.0500 (13)0.0705 (16)0.0217 (13)0.0284 (15)0.0171 (12)
N20.0558 (9)0.0359 (7)0.0350 (7)0.0027 (6)0.0089 (6)0.0124 (6)
C70.0250 (7)0.0431 (8)0.0323 (7)0.0027 (6)0.0028 (5)0.0092 (6)
C90.0757 (18)0.090 (2)0.086 (2)0.0402 (16)0.0005 (15)0.0262 (17)
Geometric parameters (Å, º) top
Zn1—O1i2.0029 (11)C6—C71.381 (2)
Zn1—O12.0029 (11)C6—C51.389 (3)
Zn1—O2i2.0675 (11)C6—H60.9300
Zn1—O22.0675 (11)O4—N21.219 (2)
Zn1—O52.3473 (12)C5—C41.381 (3)
Zn1—O5i2.3474 (12)C5—H50.9300
S1—O51.5019 (13)O3—N21.214 (2)
S1—C91.769 (3)C4—N21.471 (2)
S1—C81.783 (3)C2—C71.400 (2)
C1—O21.2686 (17)C8—H8A0.9600
C1—N11.3153 (19)C8—H8B0.9600
C1—C21.484 (2)C8—H8C0.9600
O1—N11.3584 (16)C7—H70.9300
N1—H10.84 (2)C9—H9A0.9600
C3—C41.375 (2)C9—H9B0.9600
C3—C21.391 (2)C9—H9C0.9600
C3—H30.9300
O1i—Zn1—O1180.0C7—C6—C5121.26 (15)
O1i—Zn1—O2i81.79 (4)C7—C6—H6119.4
O1—Zn1—O2i98.20 (4)C5—C6—H6119.4
O1i—Zn1—O298.21 (4)C4—C5—C6117.40 (15)
O1—Zn1—O281.80 (4)C4—C5—H5121.3
O2i—Zn1—O2180.0C6—C5—H5121.3
O1i—Zn1—O586.04 (4)C3—C4—C5122.78 (16)
O1—Zn1—O593.96 (4)C3—C4—N2118.22 (15)
O2i—Zn1—O588.40 (5)C5—C4—N2118.98 (15)
O2—Zn1—O591.60 (5)C3—C2—C7118.73 (14)
O1i—Zn1—O5i93.96 (4)C3—C2—C1116.91 (13)
O1—Zn1—O5i86.04 (4)C7—C2—C1124.35 (13)
O2i—Zn1—O5i91.60 (5)S1—C8—H8A109.5
O2—Zn1—O5i88.40 (5)S1—C8—H8B109.5
O5—Zn1—O5i180.00 (5)H8A—C8—H8B109.5
O5—S1—C9106.83 (13)S1—C8—H8C109.5
O5—S1—C8105.71 (11)H8A—C8—H8C109.5
C9—S1—C897.80 (16)H8B—C8—H8C109.5
O2—C1—N1120.85 (13)O3—N2—O4123.43 (17)
O2—C1—C2119.91 (13)O3—N2—C4118.52 (15)
N1—C1—C2119.22 (12)O4—N2—C4118.04 (17)
N1—O1—Zn1106.70 (8)C6—C7—C2120.31 (15)
C1—N1—O1120.95 (12)C6—C7—H7119.8
C1—N1—H1124.8 (15)C2—C7—H7119.8
O1—N1—H1113.9 (15)S1—C9—H9A109.5
C4—C3—C2119.51 (14)S1—C9—H9B109.5
C4—C3—H3120.2H9A—C9—H9B109.5
C2—C3—H3120.2S1—C9—H9C109.5
C1—O2—Zn1107.94 (9)H9A—C9—H9C109.5
S1—O5—Zn1115.22 (7)H9B—C9—H9C109.5
O2—C1—N1—O10.2 (2)C4—C3—C2—C1177.88 (13)
C2—C1—N1—O1178.50 (12)O2—C1—C2—C39.7 (2)
Zn1—O1—N1—C19.65 (16)N1—C1—C2—C3168.60 (14)
N1—C1—O2—Zn19.65 (17)O2—C1—C2—C7171.33 (15)
C2—C1—O2—Zn1172.04 (10)N1—C1—C2—C710.3 (2)
C9—S1—O5—Zn191.19 (13)C3—C4—N2—O30.5 (2)
C8—S1—O5—Zn1165.37 (12)C5—C4—N2—O3178.16 (18)
C7—C6—C5—C40.1 (3)C3—C4—N2—O4179.45 (16)
C2—C3—C4—C51.5 (2)C5—C4—N2—O40.8 (2)
C2—C3—C4—N2177.04 (13)C5—C6—C7—C20.3 (3)
C6—C5—C4—C31.0 (3)C3—C2—C7—C60.3 (2)
C6—C5—C4—N2177.56 (15)C1—C2—C7—C6178.66 (15)
C4—C3—C2—C71.1 (2)
Symmetry code: (i) x+1, y+1, z+2.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C8—H8C···O4ii0.962.553.381 (3)145
C8—H8A···O1iii0.962.663.533 (3)150
N1—H1···O5iv0.84 (2)2.08 (2)2.916 (1)175 (2)
Symmetry codes: (ii) x+1, y+1, z+1; (iii) x+1, y+2, z+2; (iv) x+1, y, z.
 

Acknowledgements

The authors acknowledge CT–Infra (FINEP).

References

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