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Acta Cryst. (2007). E63, m2003    [ doi:10.1107/S1600536807030607 ]

Rerefinement of poly[[[[mu]-2,3-di-4-pyridylbutane-2,3-diol-[kappa]2N:N']-[mu]-iodido-copper(I)] dimethyl sulfoxide solvate] as an anhydrous honeycomb structure

S. W. Ng

Abstract top

The crystal structure of the title compound, {[CuI(C14H16N2O2)]·C2H6OS}n, consists of (2,3-di-4-pyridylbutane-2,3-diol)iodidocopper(I) units that are connected through Cu-N and Cu-I bonds into a flat honeycomb motif. The dimethyl sulfoxide (DMSO) molecules occupy the spaces within the layer and are hydrogen-bonded to it. The iodide ligand lies on a special position of site symmetry m, the Cu atom on a special position of site symmetry 2, and the ligand about a centre of inversion. The DMSO solvent is disordered about a special position of site symmetry m. The structure has been re-refined as an anhydrous structure from the diffraction data of Niu, Song, Wang, Guo, Zhu & Hou [Chem. Lett (2006), pp. 650-651], who described the structure as a methanol and 0.25-water solvate.

Comment top

The crystal structure of (C14H16N2O2)CuI·DMSO was originally refined as a monohydrate; the water molecule is disordered over two positions, and each was refined with quarter site occupacy (Niu et al., 2006). Further, the (C14H16N2O2)CuI·DMSO·H2O formula, as given in the CIF, differs from the (C14H16N2O2)CuI·DMSO·CH3OH·(H2O)0.25 given in the publication. Moreover, the study did not mention the use of methanol in the synthesis (Niu et al., 2006). The discrepancy between the formula given in the cif and that presented in the communication promted the present rerefinement. When the structure was refined without water and methanol, the formula corresponded with the formula expected from the reported CH&N elemental percentages (Niu et al., 2006).

The crystal structure has a void of 29% as calculated by PLATON (Spek, 2003). With the exclusion of the DMSO molecules from the calcuation, the void is increased to 53%, so that the compound can be described as being somewhat porous. The layer itself exhibits a flat honeycomb motif. Figure 2 depicts the motif for which the copper atoms are represented as nodes. The DMSO molecules occupy the spaces inside the layer as they interact through H atoms bonds [O···O 2.77 (1) Å].

Related literature top

[CuI(C14H16N2O2)]·DMSO was originally incorrectly refined as [CuI(C14H16N2O2)]·DMSO·H2O; see the CIF deposited by Niu et al. (2006). Their communication misrepresented the compound as [CuI(C14H16N2O2)]·DMSO·CH3OH·0.25H2O.

Experimental top

The raw diffraction measurements of the original study by Niu et al. (2006) were kindly provided by the senior author. In the rerefinement, the raw data were processed by using a multi-scan absorption correction program (Sheldrick, 1996) in which a model with heavy atoms was assumed.

Refinement top

The DMSO is disordered about a mirror plane; the two S—C distances were restrained to be within 0.01 Å of each other.

All H atoms were generated geometrically (O—H 0.82 and C—H 0.93 to 0.97 Å), and were included in the refinement in the riding model approximation, with U(H) set to 1.2–1.5Ueq(C,O).

The final difference Fourier map had only one peak larger than 1 eA−3, at 3.5 Å from H1, but was otherwise featureless. This peak at (0.482, 0.167, 0.145) is 2.2 Å from its symmetry-related peak.

There is no solvent in the solvent-accessible voids other than the disordered DMSO. The original paper by Niu et al. (2006) had formulated the compound (C14H16N2O2)CuI·DMSO·CH3OH·H2O0.25 although the authors did not mention the use of methanol in the synthesis. The present methanol- and water-free formulation is supported by the calculated CH&N percentages (compared with found percentages given in the study) of C 37.26 (37.47), H 4.44 (4.19) and N 5.5 (5.30).

Furthermore, the authors probably used racemic 2,3-di(4-pyridyl)-2,3-butanediol instead of the meso compound in their synthesis as the ligand lies about a center-of-inversion instead of a mirror plane in the crystal structure.

Computing details top

Data collection: APEX2 (Bruker, 2004); cell refinement: SAINT (Bruker, 2004); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997) and PLATON (Spek, 2003); molecular graphics: X-SEED (Barbour, 2001) and OLEX (Dolomanov et al., 2003); software used to prepare material for publication: publCIF (Westrip, 2007).

Figures top
[Figure 1] Fig. 1. Thermal ellipsoid plot of a portion of the layer structure of (C14H16N2O2)CuI·DMSO; displacement ellipsoids are drawn at the 50% probability level. [Symmetry codes are given in Table 1.]
[Figure 2] Fig. 2. OLEX (Dolomanov et al., 2003) depiction of the (6,3) honeycomb topology, shown projected against the unit cell.
poly[[[µ-2,3-di-4-pyridylbutane-2,3-diol-κ2N:N']-µ-\ iodido-copper(I)] dimethyl sulfoxide solvate] top
Crystal data top
[CuI(C14H16N2O2)]·C2H6OSF000 = 1016
Mr = 512.86Dx = 1.328 Mg m−3
Monoclinic, C2/mMo Kα radiation
λ = 0.71073 Å
Hall symbol: -C 2yCell parameters from 4414 reflections
a = 19.122 (1) Åθ = 2.6–28.4º
b = 18.499 (1) ŵ = 2.15 mm−1
c = 7.2538 (4) ÅT = 291 (2) K
β = 91.424 (1)ºBlock, light yellow
V = 2565.1 (2) Å30.37 × 0.25 × 0.22 mm
Z = 4
Data collection top
Bruker APEX2
diffractometer		3012 independent reflections
Radiation source: fine-focus sealed tube2601 reflections with I > 2σ(I)
Monochromator: graphiteRint = 0.014
T = 291(2) Kθmax = 27.5º
φ and ω scansθmin = 2.8º
Absorption correction: multi-scan
(SADABS; Sheldrick, 1996)		h = −24→22
Tmin = 0.501, Tmax = 0.649k = −23→16
7562 measured reflectionsl = −9→8
Refinement top
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.046H-atom parameters constrained
wR(F2) = 0.184  w = 1/[σ2(Fo2) + (0.1259P)2 + 4.989P]
where P = (Fo2 + 2Fc2)/3
S = 1.10(Δ/σ)max = 0.001
3012 reflectionsΔρmax = 1.27 e Å−3
130 parametersΔρmin = −0.52 e Å−3
1 restraintExtinction correction: none
Primary atom site location: structure-invariant direct methods
Crystal data top
[CuI(C14H16N2O2)]·C2H6OSV = 2565.1 (2) Å3
Mr = 512.86Z = 4
Monoclinic, C2/mMo Kα
a = 19.122 (1) ŵ = 2.15 mm−1
b = 18.499 (1) ÅT = 291 (2) K
c = 7.2538 (4) Å0.37 × 0.25 × 0.22 mm
β = 91.424 (1)º
Data collection top
Bruker APEX2
diffractometer		3012 independent reflections
Absorption correction: multi-scan
(SADABS; Sheldrick, 1996)		2601 reflections with I > 2σ(I)
Tmin = 0.501, Tmax = 0.649Rint = 0.014
7562 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0461 restraint
wR(F2) = 0.184H-atom parameters constrained
S = 1.10Δρmax = 1.27 e Å−3
3012 reflectionsΔρmin = −0.52 e Å−3
130 parameters
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/UeqOcc. (<1)
I10.42163 (2)0.50001.23186 (6)0.0491 (2)
Cu10.50000.42451 (5)1.00000.0501 (3)
S10.2536 (3)0.0590 (2)0.0681 (8)0.104 (1)0.50
O10.3145 (3)0.2268 (3)0.3303 (6)0.079 (1)
O20.3108 (7)0.0914 (8)0.167 (2)0.132 (5)0.50
N10.4296 (2)0.3634 (2)0.8486 (5)0.051 (1)
C10.3357 (3)0.2772 (4)0.6314 (8)0.064 (1)
C20.3343 (4)0.2783 (4)0.8263 (8)0.075 (2)
C30.3819 (3)0.3202 (4)0.9252 (7)0.064 (2)
C40.4282 (3)0.3658 (4)0.6656 (8)0.067 (2)
C50.3825 (4)0.3243 (5)0.5539 (8)0.082 (2)
C60.2850 (3)0.2308 (4)0.5105 (8)0.066 (2)
C70.2775 (4)0.1568 (4)0.5977 (11)0.079 (2)
C80.2060 (8)0.001 (2)0.218 (2)0.110 (6)
C90.290 (1)−0.011 (2)−0.071 (4)0.16 (1)0.50
H10.30210.18900.28000.119*
H20.30140.25090.88780.091*
H30.38070.31851.05320.077*
H40.45920.39670.60820.080*
H50.38390.32870.42630.098*
H7a0.32260.13410.60810.119*
H7b0.24690.12750.52200.119*
H7c0.25830.16180.71800.119*
H8a0.18240.03020.30750.165*0.50
H8b0.2378−0.03120.28020.165*0.50
H8c0.1721−0.02590.14710.165*0.50
H9a0.32280.0105−0.15420.243*0.50
H9b0.2535−0.0343−0.14060.243*0.50
H9c0.3140−0.04510.00670.243*0.50
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
I10.0485 (3)0.0563 (3)0.0423 (3)0.000−0.00370 (19)0.000
Cu10.0469 (5)0.0587 (5)0.0439 (5)0.000−0.0162 (3)0.000
S10.110 (3)0.076 (2)0.125 (4)0.003 (2)−0.011 (3)−0.032 (3)
O10.078 (3)0.099 (3)0.060 (2)−0.027 (3)0.002 (2)−0.027 (2)
O20.11 (1)0.12 (1)0.17 (1)−0.025 (8)0.005 (9)−0.07 (1)
N10.050 (2)0.062 (2)0.041 (2)−0.009 (2)−0.012 (2)−0.003 (2)
C10.068 (3)0.076 (4)0.048 (3)−0.021 (3)−0.013 (2)−0.001 (3)
C20.079 (4)0.103 (5)0.044 (3)−0.046 (4)−0.015 (3)0.015 (3)
C30.070 (3)0.084 (4)0.037 (2)−0.021 (3)−0.012 (2)0.006 (2)
C40.069 (3)0.088 (4)0.043 (3)−0.033 (3)−0.005 (2)−0.001 (3)
C50.089 (4)0.118 (6)0.037 (2)−0.056 (4)−0.010 (3)0.001 (3)
C60.072 (4)0.069 (3)0.057 (3)−0.020 (3)−0.007 (3)−0.001 (3)
C70.085 (4)0.061 (3)0.090 (5)−0.018 (3)−0.031 (4)0.001 (3)
C80.12 (1)0.11 (1)0.10 (1)0.01 (5)−0.037 (9)−0.02 (5)
C90.11 (1)0.17 (3)0.21 (2)−0.02 (2)0.02 (1)−0.13 (3)
Geometric parameters (Å, °) top
Cu1—N12.055 (4)S1—C81.79 (2)
Cu1—I12.6739 (6)S1—C91.79 (2)
Cu1—N1i2.055 (4)O1—H10.82
Cu1—I1ii2.6738 (6)C2—H20.93
Cu1—Cu1ii2.793 (2)C3—H30.93
O1—C61.438 (8)C4—H40.93
N1—C41.328 (7)C5—H50.93
N1—C31.343 (7)C7—H7a0.96
C1—C51.378 (8)C7—H7b0.96
C1—C21.415 (8)C7—H7c0.96
C1—C61.551 (7)C8—H8a0.96
C2—C31.382 (8)C8—H8b0.96
C4—C51.404 (7)C8—H8c0.96
C6—C71.517 (9)C9—H9a0.96
C6—C6iii1.52 (1)C9—H9b0.96
S1—O21.43 (1)C9—H9c0.96
Cu1—I1—Cu1ii62.97 (3)C6—O1—H1109.5
N1—Cu1—N1i113.2 (3)C3—C2—H2120.1
N1—Cu1—I1104.7 (1)C1—C2—H2120.1
N1—Cu1—I1ii108.7 (1)N1—C3—H3117.8
N1i—Cu1—I1ii104.7 (1)C2—C3—H3117.8
N1i—Cu1—I1108.7 (1)N1—C4—H4118.1
I1—Cu1—I1ii117.03 (3)C5—C4—H4118.1
N1—Cu1—Cu1ii123.4 (1)C1—C5—H5119.7
I1—Cu1—Cu1ii58.52 (2)C4—C5—H5119.7
C4—N1—C3115.9 (4)C6—C7—H7a109.5
C4—N1—Cu1120.8 (4)C6—C7—H7b109.5
C3—N1—Cu1123.3 (3)H7a—C7—H7b109.5
C5—C1—C2115.3 (5)C6—C7—H7c109.5
C5—C1—C6121.5 (5)H7a—C7—H7c109.5
C2—C1—C6123.0 (5)H7b—C7—H7c109.5
C3—C2—C1119.8 (5)S1—C8—H8a109.5
N1—C3—C2124.3 (5)S1—C8—H8b109.5
N1—C4—C5123.7 (5)H8a—C8—H8b109.5
C1—C5—C4120.7 (5)S1—C8—H8c109.5
O1—C6—C7112.0 (6)H8a—C8—H8c109.5
O1—C6—C6iii107.3 (6)H8b—C8—H8c109.5
C7—C6—C6iii111.8 (6)S1—C9—H9a109.5
O1—C6—C1106.8 (5)S1—C9—H9b109.5
C7—C6—C1109.2 (5)H9a—C9—H9b109.5
C6iii—C6—C1109.6 (7)S1—C9—H9c109.5
O2—S1—C8110 (1)H9a—C9—H9c109.5
O2—S1—C9106.3 (8)H9b—C9—H9c109.5
C8—S1—C997 (2)
Cu1ii—I1—Cu1—N1−120.5 (1)Cu1—N1—C3—C2−179.6 (6)
Cu1ii—I1—Cu1—N1i118.3 (1)C1—C2—C3—N12(1)
Cu1ii—I1—Cu1—I1ii0.0C3—N1—C4—C5−3(1)
N1i—Cu1—N1—C4−116.2 (5)Cu1—N1—C4—C5178.6 (6)
I1ii—Cu1—N1—C4−0.3 (5)C2—C1—C5—C44(1)
I1—Cu1—N1—C4125.5 (5)C6—C1—C5—C4−179.8 (7)
Cu1ii—Cu1—N1—C463.8 (5)N1—C4—C5—C1−0.4 (13)
N1i—Cu1—N1—C365.3 (5)C5—C1—C6—O121.1 (9)
I1ii—Cu1—N1—C3−178.8 (5)C2—C1—C6—O1−163.4 (7)
I1—Cu1—N1—C3−53.0 (5)C5—C1—C6—C7142.4 (8)
Cu1ii—Cu1—N1—C3−114.7 (5)C2—C1—C6—C7−42.1 (9)
C5—C1—C2—C3−5(1)C5—C1—C6—C6iii−94.8 (9)
C6—C1—C2—C3179.0 (7)C2—C1—C6—C6iii80.7 (9)
C4—N1—C3—C21.8 (10)
Symmetry codes: (i) −x+1, y, −z+2; (ii) −x+1, −y+1, −z+2; (iii) −x+1/2, −y+1/2, −z+1.
Hydrogen-bond geometry (Å, °) top
D—H···AD—HH···AD···AD—H···A
O1—H1···O20.821.992.77 (1)158
Table 1
Selected geometric parameters (Å, °) top
Cu1—N12.055 (4)Cu1—I12.6739 (6)
Cu1—I1—Cu1i62.97 (3)N1—Cu1—I1i108.7 (1)
N1—Cu1—N1ii113.2 (3)N1ii—Cu1—I1108.7 (1)
N1—Cu1—I1104.7 (1)
Symmetry codes: (i) −x+1, −y+1, −z+2; (ii) −x+1, y, −z+2.
Acknowledgements top

The author thanks Dr Yun-Yin Niu of Zhengzhou University for the diffraction measurements, and the University of Malaya for supporting this study.

references
References top

Barbour, L. J. (2001). J. Supramol. Chem. 1, 189–191.

Bruker (2004). APEX2 software (Version 7.12a [Not concurrent with SAINT. Please give correct version number]) and SAINT (Version 7.12a). Bruker AXS Inc., Madison, Winconsin, USA.

Dolomanov, O. V., Blake, A. J., Champness, N. R. & Schröder, M. (2003). J. Appl. Cryst. 36, 1283–1284.

Niu, Y.-Y., Song, Y.-L., Wang, Q.-L., Guo, X.-L., Zhu, Y. & Hou, H.-W. (2006). Chem. Lett. pp. 650–651.

Sheldrick, G. M. (1996). SADABS. University of Göttingen, Germany.

Sheldrick, G. M. (1997). SHELXS97 and SHELXL97. University of Göttingen, Germany.

Spek, A. L. (2003). J. Appl. Cryst. 36, 7–13.

Westrip, S. P. (2007). publCIF. In preparation.