Shigeru Ohba1, Masanobu Tsuchimoto2, Saeko Kurachi3. 1. Research and Education Center for Natural Sciences, Keio University, Hiyoshi 4-1-1, Kohoku-ku, Yokohama 223-8521, Japan. 2. Department of Chemistry, Chiba Institute of Technology, Shibazono 2-1-1, Narashino, Chiba 275-0023, Japan. 3. Department of Chemistry, Faculty of Science and Technology, Keio University, Hiyoshi 3-14-1, Kohoku-ku, Yokohama 223-8522, Japan.
Abstract
The reaction cavities of the nitro groups in the crystals of the title compounds, trans-[Co(NO2)(NCS)(C2H8N2)2]·X, X = SCN- (I), Cl-·H2O (II), and (ClO4 -)0.75(SCN-)0.25 (III), have been investigated, revealing that the geometry of the inter-molecular N-H⋯O hydrogen bonds in (I) is unsuitable for nitro-nitrito photo-isomerization. The common main building block of these crystal structures is a centrosymmetric pair of complex cations connected by pairwise N-H⋯O(nitro) hydrogen bonds forming an R 2 2(4) ring, which is a narrow diamond shape in (I) but is approximately square in (II) and (III). The structure of (I) was reported earlier [Börtin (1976 ▸). Acta Chem. Scand. A, 30, 503-506] but is described here with an improved disorder model for the thio-cyanate anions and to higher precision.
The reaction cavities of the nitro groups in the crystals of the title compounds, trans-[Co(NO2)(NCS)(C2H8N2)2]·X, X = SCN- (I), Cl-·H2O (II), and (ClO4 -)0.75(SCN-)0.25 (III), have been investigated, revealing that the geometry of the inter-molecular N-H⋯O hydrogen bonds in (I) is unsuitable for nitro-nitrito photo-isomerization. The common main building block of these crystal structures is a centrosymmetric pair of complex cations connected by pairwise N-H⋯O(nitro) hydrogen bonds forming an R 2 2(4) ring, which is a narrow diamond shape in (I) but is approximately square in (II) and (III). The structure of (I) was reported earlier [Börtin (1976 ▸). Acta Chem. Scand. A, 30, 503-506] but is described here with an improved disorder model for the thio-cyanate anions and to higher precision.
The nitrite ion is one of the well-known ligands that show linkage isomerism even in the solid state (Hatcher & Raithby, 2013 ▸). Adell (1971 ▸) prepared trans-[Co(en)2(NO2)(NCS)]X (en = ethylenediamine, X = a counter-anion and a solvent molecule if incorporated into the crystal structure) to show that irradiation by sunlight or visible light (λ > 430 nm) alters the color of the crystals from orange to red for perchlorate and nitrate salts, indicating nitro–nitrito photochemical isomerization, but not for thiocyanate. These facts suggest that the photo-isomerization is interrupted by some steric condition in (I) where X = SCN−. Börtin (1976 ▸) determined the crystal structure of (I), but failed to find the steric obstacles to the reaction, and the puzzle has been left unsolved. Kubota & Ohba (1992 ▸) investigated the solid-state nitro–nitrito photochemical reaction of [Co(NH3)5NO2]Cl2 to show that the shape of the reaction cavity in the nitro plane is of crucial importance. It is noted that not only the steric condition around the nitro group, but also the electronic effects of the co-existing ligands are important for the longer lifetime of the much less stable nitrito form (Miyoshi et al., 1983 ▸), the thiocyanate ligand at the trans position being favorable. When the powders were irradiated by a 150 W Xe lamp without filtering, the color changed immediately from yellow to orange for (II) and (III) but not for (I), in agreement with the observations of Adell (1971 ▸). In the present study, the structures of the three title crystals were investigated to reveal the steric conditions that make (I) photo-inactive.
Structural commentary
The crystal structure of (I) has been redetermined in the present study with a more sophisticated treatment of the disorder of thiocyanate ions [R(F
2) = 0.048 for 2845 observed reflections] than that reported by Börtin (1976 ▸) [R(F) = 0.077 for 1970 reflections], and the s.u.’s of the bond lengths were reduced to less than half of the previous values. The molecular structures of (I)–(III) are shown in Figs. 1 ▸–3 ▸
▸, respectively. The coordination geometry around the Co atoms is octahedral, and the Co—N(nitro) bond lengths are similar to one another, 1.905 (3) Å in (I), 1.912 (2) Å in (II) and 1.915 (4) and 1.916 (4) Å in (III). The conformations of the ethylenediammine ligands are gauche in (I) and (III), and envelope in (II). The short C17—C18 distance of 1.417 (8) Å in (I) may be an artifact of unresolved disorder over two orientations by the puckering of the chelate ring as mentioned by Börtin (1976 ▸). The combination of the two ethylenediamine chelate rings in each complex is δ and λ, and the Co(en)2 moiety possesses approximate mirror symmetry. In (I), there are two independent thiocyanate counter-ions, which are disordered around twofold axes and are therefore half occupied. In (II), there is a chloride counter-ion and an ordered water molecule of crystallization. In (III), one of the two perchlorate ions (Cl4/O16–O19) lies on a center of symmetry, showing orientational disorder. Furthermore, an unexpected thiocyanate ion (S7/C43/N32) exists on a center of symmetry, possessing two possible orientations. The asymmetric unit of (III) comprises two complex cations, one and half perchlorate ions, and half a thiocyanate ion.
Figure 1
The molecular structure of (I), showing displacement ellipsoids at the 30% probability level. Only one of two possible orientations of the disordered thiocyanate (N13/C20/S3 and N14/C21/S4) ions is indicated for clarity.
Figure 2
The molecular structure of (II), showing displacement ellipsoids at the 30% probability level.
Figure 3
The molecular structure of (III), showing displacement ellipsoids at the 30% probability level. Only one of two possible orientations of the disordered thiocyanate (S7/C43/N32) and perchlorate (Cl4/O16–O19) ions is indicated for clarity.
Supramolecular features
The crystal structures of (I)–(III) are shown in Figs. 4 ▸–6 ▸
▸, respectively. The complex cations and the counter-anions are connected via numerous hydrogen bonds (Tables 1 ▸–3 ▸
▸), forming three-dimensional networks. The circumstances of the nitro groups in (I) and (II) are compared in Fig. 7 ▸, where the surrounding hydrogen-bond donors are projected on the nitro plane. The nitro O atoms act as acceptors of intra- and intermolecular N/O—H⋯O hydrogen bonds. It is expected that the nitro–nitrito photo-isomerization occurs via an N,O-bidentate transition state (Johnson & Pashman, 1975 ▸) by rotating the nitrite ion in its original plane because of the feasible charge density due to the lone pairs of the nitriteN and O atoms (Okuda et al., 1990 ▸). It seems that the N,O-bidentate mode is prevented by the intermolecular N—H⋯O hydrogen bonds in (I), but it may be allowed in (II) because of the vacant space behind the nitro O4 atom. This can be seen from the slices of the cavity around the NO2
− group (Fig. 8 ▸), which is defined as the concave space limited by the envelope surfaces of spheres placed at the positions of neighboring atoms, each sphere having a radius 1.0 Å greater (as selected by Kubota & Ohba, 1992 ▸) than the corresponding van der Waals radius (Bondi, 1964 ▸) except for the Co, its radius being assumed to be 1.90 Å, which is a little shorter than the Co—N(nitro) distance. Asymmetric intermolecular hydrogen-bond contacts are also observed in (III) (Fig. 9 ▸), and the reaction cavities show the vacancy at one of the two O atoms, O8 and O10 (Fig. 10 ▸). The (4) ring formed by the pair of nitro groups is observed not only in (III) but also in (I) and (II) (Fig. 11 ▸). These four-membered rings are essentially planar with the O⋯H distances ranging from 2.33 to 2.49 Å. However, there are apparent differences in the geometry. That in (I) is a narrow rhomb with the interior angles at O6 and H10B being 33.3 and 146.7°, respectively, and inclined to the nitro plane by 79.2 (3)°. The corresponding angles at O4 and H9A in (II) are 98.7 and 81.3°, and the dihedral angle with the nitro plane is 45.5 (2)°. The shape of the ring in (III) is also nearly square with interior angles of 87.3–92.4°, and the dihedral angles with the nitro planes are 53.6 (2) and 53.8 (2)°.
Figure 4
The crystal structure of (I), projected along c. N—H⋯O/N/S hydrogen bonds are shown as blue dashed lines. Both possible orientations of the disordered thiocyanate ions are indicated.
Figure 5
The crystal structure of (II), projected along a. Hydrogen bonds are shown as dashed lines in blue for O—H⋯O/Cl and N—H⋯O, and in red for N—H⋯Cl.
Figure 6
The crystal structure of (III), projected along a. N—H⋯O/N and C—H⋯O hydrogen bonds are shown as blue dashed lines. Both possible orientations of the disordered thiocyanate (S7/C43/N32) and perchlorate (Cl4/O16–O19) ions are indicated.
Comparison of the steric circumstances of the nitro group in (I) and (II). Dashed lines in blue indicate O(nitro)⋯H short contacts shorter than 2.5 Å. Only part of the diamine ligands are shown for clarity. Symmetry codes for (I): (v) −x + , −y + , −z; (ix) x, −y, z − . For (II): (ii) −x + 1, −y + 1, −z + 1; (v) x − , −y + , z + .
Figure 8
Comparison of the slices of the cavity around the nitro group within 0.1 Å from the plane in (I) and (II).
Figure 9
The steric circumstances of the nitro groups in (III). Dashed lines in blue show the O(nitro)⋯H short contacts shorter than 2.5 Å. Only parts of the diamine ligands are shown for clarity. Symmetry codes: (ix) −x + , y + , −z + ; (x) −x + , y − , −z + .
Figure 10
The slices of the cavity in (III) around the nitro groups within 0.1 Å from the planes.
Figure 11
Comparison of the short contact pair of the nitro group in (I) and (II). Dashed lines in blue show the O(nitro)⋯H short contacts shorter than 2.5 Å. Only parts of the diamine ligands are shown for clarity. Symmetry codes for (I): (ii) −x + , y − , −z + ; (v) −x + , −y + , −z; (ix) x, −y, z − . For (II): (ii) −x + 1, −y + 1, −z + 1, (v) x − , −y + , z + ; (vii) −x + , y + , −z + .
Database survey
Grenthe & Nordin (1979 ▸) reported the structures of trans-{Co(en)2(NO2)(NCS)]·X (X = ClO4
− and I−) obtained after solid-state thermal isomerization of the nitrito complexes (monoclinic P21, Z = 2). The lattice constants did not correspond to the crystals grown from aqueous solutions of the nitro complexes. Except for Börtin (1976 ▸) (X = SCN−) there is no other entry of the title nitrocobalt complex in the Cambridge Structural Database (CSD Version 5.39; Groom et al., 2016 ▸).
Synthesis and crystallization
The title thiocyanate salt (I) was prepared by a literature method (Adell, 1971 ▸; Nakahara & Shibata, 1977 ▸) from cobalt(II) nitrate hexahydrate via trans-[Co(en)2(NO2)2]NO3 and then trans-[Co(en)2Cl(NO2)]NO3. The crystals of (I) were grown from a hot aqueous solution. Crystals of (I) were pulverized and dissolved in conc. HCl over a moderate heat, and impurities were removed by filtration. To the filtrate, some amount of ethanol was added. The solution was concentrated to precipitate the chloride (II), which was recrystallized with a small amount of water as solvent. To the saturated aqueous solution of (II), NaClO4 powder was added to precipitate the perchlorate (III). Crystals of (III) were grown from an aqueous solution. The possibility of contamination of (III) by chloride ions was eliminated because no precipitation of AgCl occurred when AgNO3 was added to an aqueous solution.
Refinement
Crystal data, data collection and structure refinement details are summarized in Table 4 ▸. The H atoms bound to C and N were positioned geometrically. They were refined as riding, with N—H = 0.89 Å, C—H = 0.97 Å, and U
iso(H) = 1.2U
eq(C/N).
Table 4
Experimental details
(I)
(II)
(III)
Crystal data
Chemical formula
[Co(NCS)(NO2)(C2H8N2)2](CNS)
[Co(NCS)(NO2)(C2H8N2)2]Cl·H2O
[Co(NCS)(NO2)(C2H8N2)2](ClO4)0.75(CNS)0.25
Mr
341.31
336.69
372.33
Crystal system, space group
Monoclinic, C2/c
Monoclinic, P21/n
Monoclinic, P21/n
Temperature (K)
299
301
301
a, b, c (Å)
16.3222 (7), 16.0137 (6), 11.1284 (4)
8.9059 (4), 12.3302 (5), 12.2915 (5)
11.3141 (6), 16.2969 (7), 16.1298 (7)
β (°)
110.2599 (13)
92.295 (2)
109.023 (2)
V (Å3)
2728.77 (19)
1348.67 (10)
2811.7 (2)
Z
8
4
8
Radiation type
Mo Kα
Mo Kα
Mo Kα
μ (mm−1)
1.57
1.63
1.58
Crystal size (mm)
0.25 × 0.25 × 0.20
0.25 × 0.20 × 0.20
0.35 × 0.30 × 0.27
Data collection
Diffractometer
Bruker D8 VENTURE
Bruker D8 VENTURE
Bruker D8 VENTURE
Absorption correction
Integration (SADABS; Bruker, 2016 ▸)
Integration (SADABS; Bruker, 2016 ▸)
Integration (SADABS; Bruker, 2016 ▸)
Tmin, Tmax
0.667, 0.743
0.697, 0.762
0.544, 0.774
No. of measured, independent and observed [I > 2σ(I)] reflections
14627, 3166, 2845
14312, 3153, 2830
30435, 6595, 5411
Rint
0.023
0.024
0.034
(sin θ/λ)max (Å−1)
0.659
0.659
0.659
Refinement
R[F2 > 2σ(F2)], wR(F2), S
0.048, 0.173, 1.06
0.032, 0.131, 0.98
0.063, 0.221, 1.10
No. of reflections
3166
3153
6595
No. of parameters
179
161
379
No. of restraints
18
3
13
H-atom treatment
H-atom parameters constrained
H atoms treated by a mixture of independent and constrained refinement
H-atom parameters constrained
Δρmax, Δρmin (e Å−3)
0.99, −0.92
0.74, −0.54
1.40, −1.15
Computer programs: APEX3 and SAINT (Bruker, 2016 ▸), SHELXT (Sheldrick, 2015a
▸), SHELXL2014 (Sheldrick, 2015b
▸), Mercury (Macrae et al., 2008 ▸), CAVITY (Ohashi et al., 1981 ▸) and publCIF (Westrip, 2010 ▸).
In (I), the non-coordinating thiocyanate ions S3/C20/N13 and S4/C21/N14 lie around the twofold axis with the molecular axes perpendicular and slightly inclined, respectively, showing orientational disorder. Their geometries were restrained with EADP or SIMU commands. Three reflections showing very poor agreement with I
obs much smaller than I
calc were omitted from the final refinement.In (II), the H atoms of the water molecule were located from difference-density maps, and their coordinates were refined with the geometry restrained, and with U
iso(H) = 1.5U
eq(O). Eight reflections showing poor agreement were omitted from the final refinement, since their I
obs were much smaller than I
calc.In (III), atom Cl4 of one of the two independent perchlorate ions lies on a center of symmetry, showing orientational disorder. Another independent and indistinct anion lies over the center of symmetry, but is not a perchlorate ion since the electron-density peaks of the O atoms are missing. It is not a chloride ion either, judging from the lack of precipitation of AgCl with silver nitrate. The most probable and suitable assumption is that the thiocyanate ion has two possible orientations as seen in (I), and the expected composition is supported by the measured density of the crystals, 1.76 (2) Mg m−3, which agrees well with the calculated value, 1.759 Mg m−3. The geometry of the disordered thiocyanate ion was restrained with an EADP instruction for the terminal S7/N32 atoms and DELU and ISOR instructions for the central C43 atom to avoid the abnormally large residual peak near the C43 atom. One reflection with I
obs much smaller than I
calc was omitted from the final refinement.Crystal structure: contains datablock(s) I, II, III, general. DOI: 10.1107/S2056989018013634/hb7774sup1.cifStructure factors: contains datablock(s) I. DOI: 10.1107/S2056989018013634/hb7774Isup2.hklClick here for additional data file.Supporting information file. DOI: 10.1107/S2056989018013634/hb7774Isup5.cdxStructure factors: contains datablock(s) II. DOI: 10.1107/S2056989018013634/hb7774IIsup3.hklClick here for additional data file.Supporting information file. DOI: 10.1107/S2056989018013634/hb7774IIsup6.cdxStructure factors: contains datablock(s) III. DOI: 10.1107/S2056989018013634/hb7774IIIsup4.hklClick here for additional data file.Supporting information file. DOI: 10.1107/S2056989018013634/hb7774IIIsup7.cdxCCDC references: 1869545, 1869544, 1869543Additional supporting information: crystallographic information; 3D view; checkCIF report
Primary atom site location: structure-invariant direct methods
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.
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.
Hydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.063
H-atom parameters constrained
wR(F2) = 0.221
w = 1/[σ2(Fo2) + (0.1199P)2 + 7.1456P] where P = (Fo2 + 2Fc2)/3
S = 1.10
(Δ/σ)max = 0.001
6595 reflections
Δρmax = 1.40 e Å−3
379 parameters
Δρmin = −1.15 e Å−3
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.