Rerefinement of poly[[[μ-2,3-di-4-pyridyl­butane-2,3-diol-κ²N:N′]-μ-iodido-copper(I)] dimethyl sulfoxide solvate] as an anhydrous honeycomb structure

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.

Key indicators

• Single-crystal X-ray study
• T = 291 K
• Mean [sigma](C-C) = 0.009 Å
Some non-H atoms missing
• Disorder in solvent or counterion
• R factor = 0.046
• wR factor = 0.184
• Data-to-parameter ratio = 23.2

checkCIF/PLATON results

No syntax errors found



Alert level A
PLAT601_ALERT_2_A Structure Contains Solvent Accessible VOIDS of .     369.00 A   3 

Author Response: The final difference Fourier map had only one peak larger than 1 <i>e</i>A^-3^, at 3.5 \%A from H1, but was otherwise featureless. This peak at (0.482, 0.167, 0.145) is 2.2 \%A from its symmetry-related peak.

 There is no solvent in the solvent-accessible voids other than the disordered
 DMSO. The original paper by Niu <i>et al.</i> (2006) had formulated the
 compound (C~14~H~16~N~2~O~2~)CuI^.^DMSO^.^CH~3~OH^.^H~2~O~0.25~ 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).


Alert level B
PLAT722_ALERT_1_B Angle   Calc      112.00, Rep      109.50 Dev...       2.50 Deg.
              H8B  -C8   -H8C     1.555   1.555   1.555

Alert level C
CHEMW03_ALERT_2_C The ratio of given/expected molecular weight as
            calculated from the _atom_site* data lies outside
            the range 0.99 <> 1.01
           From the CIF: _cell_formula_units_Z                    4
           From the CIF: _chemical_formula_weight           512.86
           TEST: Calculate formula weight from _atom_site_*
           atom     mass    num     sum
           C        12.01   17.00  204.19
           H         1.01   22.00   22.18
           N        14.01    2.00   28.01
           O        16.00    3.00   48.00
           S        32.07    1.00   32.07
           Cu       63.55    1.00   63.55
           I       126.90    1.00  126.90
           Calculated formula weight              524.89
PLAT042_ALERT_1_C Calc. and Rep. MoietyFormula Strings Differ ....          ?
PLAT062_ALERT_4_C Rescale T(min) & T(max) by .....................       0.96
PLAT094_ALERT_2_C Ratio of Maximum / Minimum Residual Density ....       2.44
PLAT180_ALERT_3_C Check Cell Rounding: # of Values Ending with 0 =          3
PLAT241_ALERT_2_C Check High      Ueq as Compared to Neighbors for         C5
PLAT244_ALERT_4_C Low   'Solvent' Ueq as Compared to Neighbors for         S1
PLAT250_ALERT_2_C Large U3/U1 Ratio for Average U(i,j) Tensor ....       2.50
PLAT302_ALERT_4_C Anion/Solvent Disorder .........................      43.00 Perc.
PLAT342_ALERT_3_C Low Bond Precision on C-C Bonds (x 1000) Ang ...          9
PLAT721_ALERT_1_C Bond    Calc     0.98000, Rep     0.96000 Dev...       0.02 Ang.
              C8   -H8A     1.555   1.555
PLAT721_ALERT_1_C Bond    Calc     0.94000, Rep     0.96000 Dev...       0.02 Ang.
              C8   -H8B     1.555   1.555
PLAT722_ALERT_1_C Angle   Calc      108.00, Rep      109.50 Dev...       1.50 Deg.
              S1   -C8   -H8A     1.555   1.555   1.555

Alert level G
FORMU01_ALERT_2_G  There is a discrepancy between the atom counts in the
            _chemical_formula_sum and the formula from the _atom_site* data.
            Atom count from _chemical_formula_sum:C16 H22 Cu1 I1 N2 O3 S1
            Atom count from the _atom_site data:  C17 H22 Cu1 I1 N2 O3 S1
CELLZ01_ALERT_1_G Difference between formula and atom_site contents detected.
CELLZ01_ALERT_1_G ALERT: Large difference may be due to a
            symmetry error - see SYMMG tests
           From the CIF: _cell_formula_units_Z    4
           From the CIF: _chemical_formula_sum  C16 H22 Cu I N2 O3 S
           TEST: Compare cell contents of formula and atom_site data

           atom    Z*formula  cif sites diff
           C         64.00     68.00   -4.00
           H         88.00     88.00    0.00
           Cu         4.00      4.00    0.00
           I          4.00      4.00    0.00
           N          8.00      8.00    0.00
           O         12.00     12.00    0.00
           S          4.00      4.00    0.00
PLAT793_ALERT_1_G Check the Absolute Configuration of C6     = ...          S
PLAT860_ALERT_3_G Note: Number of Least-Squares Restraints .......          1

   1 ALERT level A = In general: serious problem
   1 ALERT level B = Potentially serious problem
  13 ALERT level C = Check and explain
   5 ALERT level G = General alerts; check

   8 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
   6 ALERT type 2 Indicator that the structure model may be wrong or deficient
   3 ALERT type 3 Indicator that the structure quality may be low
   3 ALERT type 4 Improvement, methodology, query or suggestion
   0 ALERT type 5 Informative message, check

---

S1. Comment

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

[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.

S2. Experimental

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.

S3. Refinement

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 1.2–1.5U_eq(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.H₂O_0.25 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

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

	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.]
	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-ιodido-copper(I)] dimethyl sulfoxide solvate]

Crystal data

[CuI(C14H16N2O2)]·C2H6OS	F(000) = 1016
Mr = 512.86	Dx = 1.328 Mg m^−3
Monoclinic, C2/m	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -C 2y	Cell parameters from 4414 reflections
a = 19.122 (1) Å	θ = 2.6–28.4°
b = 18.499 (1) Å	µ = 2.15 mm^−1
c = 7.2538 (4) Å	T = 291 K
β = 91.424 (1)°	Block, light yellow
V = 2565.1 (2) Å^3	0.37 × 0.25 × 0.22 mm
Z = 4

Data collection

Bruker APEX2 diffractometer	3012 independent reflections
Radiation source: fine-focus sealed tube	2601 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.014
φ and ω scans	θmax = 27.5°, θmin = 2.8°
Absorption correction: multi-scan (SADABS; Sheldrick, 1996)	h = −24→22
Tmin = 0.501, Tmax = 0.649	k = −23→16
7562 measured reflections	l = −9→8

Refinement

Refinement on F^2	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F^2 > 2σ(F^2)] = 0.046	Hydrogen site location: inferred from neighbouring sites
wR(F^2) = 0.184	H-atom parameters constrained
S = 1.10	w = 1/[σ^2(Fo^2) + (0.1259P)^2 + 4.989P] where P = (Fo^2 + 2Fc^2)/3
3012 reflections	(Δ/σ)max = 0.001
130 parameters	Δρmax = 1.27 e Å^−3
1 restraint	Δρmin = −0.52 e Å^−3

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Ų)

	x	y	z	Uiso*/Ueq	Occ. (<1)
I1	0.42163 (2)	0.5000	1.23186 (6)	0.0491 (2)
Cu1	0.5000	0.42451 (5)	1.0000	0.0501 (3)
S1	0.2536 (3)	0.0590 (2)	0.0681 (8)	0.104 (1)	0.50
O1	0.3145 (3)	0.2268 (3)	0.3303 (6)	0.079 (1)
O2	0.3108 (7)	0.0914 (8)	0.167 (2)	0.132 (5)	0.50
N1	0.4296 (2)	0.3634 (2)	0.8486 (5)	0.051 (1)
C1	0.3357 (3)	0.2772 (4)	0.6314 (8)	0.064 (1)
C2	0.3343 (4)	0.2783 (4)	0.8263 (8)	0.075 (2)
C3	0.3819 (3)	0.3202 (4)	0.9252 (7)	0.064 (2)
C4	0.4282 (3)	0.3658 (4)	0.6656 (8)	0.067 (2)
C5	0.3825 (4)	0.3243 (5)	0.5539 (8)	0.082 (2)
C6	0.2850 (3)	0.2308 (4)	0.5105 (8)	0.066 (2)
C7	0.2775 (4)	0.1568 (4)	0.5977 (11)	0.079 (2)
C8	0.2060 (8)	0.001 (2)	0.218 (2)	0.110 (6)
C9	0.290 (1)	−0.011 (2)	−0.071 (4)	0.16 (1)	0.50
H1	0.3021	0.1890	0.2800	0.119*
H2	0.3014	0.2509	0.8878	0.091*
H3	0.3807	0.3185	1.0532	0.077*
H4	0.4592	0.3967	0.6082	0.080*
H5	0.3839	0.3287	0.4263	0.098*
H7a	0.3226	0.1341	0.6081	0.119*
H7b	0.2469	0.1275	0.5220	0.119*
H7c	0.2583	0.1618	0.7180	0.119*
H8a	0.1824	0.0302	0.3075	0.165*	0.50
H8b	0.2378	−0.0312	0.2802	0.165*	0.50
H8c	0.1721	−0.0259	0.1471	0.165*	0.50
H9a	0.3228	0.0105	−0.1542	0.243*	0.50
H9b	0.2535	−0.0343	−0.1406	0.243*	0.50
H9c	0.3140	−0.0451	0.0067	0.243*	0.50

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
I1	0.0485 (3)	0.0563 (3)	0.0423 (3)	0.000	−0.00370 (19)	0.000
Cu1	0.0469 (5)	0.0587 (5)	0.0439 (5)	0.000	−0.0162 (3)	0.000
S1	0.110 (3)	0.076 (2)	0.125 (4)	0.003 (2)	−0.011 (3)	−0.032 (3)
O1	0.078 (3)	0.099 (3)	0.060 (2)	−0.027 (3)	0.002 (2)	−0.027 (2)
O2	0.11 (1)	0.12 (1)	0.17 (1)	−0.025 (8)	0.005 (9)	−0.07 (1)
N1	0.050 (2)	0.062 (2)	0.041 (2)	−0.009 (2)	−0.012 (2)	−0.003 (2)
C1	0.068 (3)	0.076 (4)	0.048 (3)	−0.021 (3)	−0.013 (2)	−0.001 (3)
C2	0.079 (4)	0.103 (5)	0.044 (3)	−0.046 (4)	−0.015 (3)	0.015 (3)
C3	0.070 (3)	0.084 (4)	0.037 (2)	−0.021 (3)	−0.012 (2)	0.006 (2)
C4	0.069 (3)	0.088 (4)	0.043 (3)	−0.033 (3)	−0.005 (2)	−0.001 (3)
C5	0.089 (4)	0.118 (6)	0.037 (2)	−0.056 (4)	−0.010 (3)	0.001 (3)
C6	0.072 (4)	0.069 (3)	0.057 (3)	−0.020 (3)	−0.007 (3)	−0.001 (3)
C7	0.085 (4)	0.061 (3)	0.090 (5)	−0.018 (3)	−0.031 (4)	0.001 (3)
C8	0.12 (1)	0.11 (1)	0.10 (1)	0.01 (5)	−0.037 (9)	−0.02 (5)
C9	0.11 (1)	0.17 (3)	0.21 (2)	−0.02 (2)	0.02 (1)	−0.13 (3)

Geometric parameters (Å, º)

Cu1—N1	2.055 (4)	S1—C8	1.79 (2)
Cu1—I1	2.6739 (6)	S1—C9	1.79 (2)
Cu1—N1^i	2.055 (4)	O1—H1	0.82
Cu1—I1^ii	2.6738 (6)	C2—H2	0.93
Cu1—Cu1^ii	2.793 (2)	C3—H3	0.93
O1—C6	1.438 (8)	C4—H4	0.93
N1—C4	1.328 (7)	C5—H5	0.93
N1—C3	1.343 (7)	C7—H7a	0.96
C1—C5	1.378 (8)	C7—H7b	0.96
C1—C2	1.415 (8)	C7—H7c	0.96
C1—C6	1.551 (7)	C8—H8a	0.96
C2—C3	1.382 (8)	C8—H8b	0.96
C4—C5	1.404 (7)	C8—H8c	0.96
C6—C7	1.517 (9)	C9—H9a	0.96
C6—C6^iii	1.52 (1)	C9—H9b	0.96
S1—O2	1.43 (1)	C9—H9c	0.96
Cu1—I1—Cu1^ii	62.97 (3)	C6—O1—H1	109.5
N1—Cu1—N1^i	113.2 (3)	C3—C2—H2	120.1
N1—Cu1—I1	104.7 (1)	C1—C2—H2	120.1
N1—Cu1—I1^ii	108.7 (1)	N1—C3—H3	117.8
N1^i—Cu1—I1^ii	104.7 (1)	C2—C3—H3	117.8
N1^i—Cu1—I1	108.7 (1)	N1—C4—H4	118.1
I1—Cu1—I1^ii	117.03 (3)	C5—C4—H4	118.1
N1—Cu1—Cu1^ii	123.4 (1)	C1—C5—H5	119.7
I1—Cu1—Cu1^ii	58.52 (2)	C4—C5—H5	119.7
C4—N1—C3	115.9 (4)	C6—C7—H7a	109.5
C4—N1—Cu1	120.8 (4)	C6—C7—H7b	109.5
C3—N1—Cu1	123.3 (3)	H7a—C7—H7b	109.5
C5—C1—C2	115.3 (5)	C6—C7—H7c	109.5
C5—C1—C6	121.5 (5)	H7a—C7—H7c	109.5
C2—C1—C6	123.0 (5)	H7b—C7—H7c	109.5
C3—C2—C1	119.8 (5)	S1—C8—H8a	109.5
N1—C3—C2	124.3 (5)	S1—C8—H8b	109.5
N1—C4—C5	123.7 (5)	H8a—C8—H8b	109.5
C1—C5—C4	120.7 (5)	S1—C8—H8c	109.5
O1—C6—C7	112.0 (6)	H8a—C8—H8c	109.5
O1—C6—C6^iii	107.3 (6)	H8b—C8—H8c	109.5
C7—C6—C6^iii	111.8 (6)	S1—C9—H9a	109.5
O1—C6—C1	106.8 (5)	S1—C9—H9b	109.5
C7—C6—C1	109.2 (5)	H9a—C9—H9b	109.5
C6^iii—C6—C1	109.6 (7)	S1—C9—H9c	109.5
O2—S1—C8	110 (1)	H9a—C9—H9c	109.5
O2—S1—C9	106.3 (8)	H9b—C9—H9c	109.5
C8—S1—C9	97 (2)
Cu1^ii—I1—Cu1—N1	−120.5 (1)	Cu1—N1—C3—C2	−179.6 (6)
Cu1^ii—I1—Cu1—N1^i	118.3 (1)	C1—C2—C3—N1	2 (1)
Cu1^ii—I1—Cu1—I1^ii	0.0	C3—N1—C4—C5	−3 (1)
N1^i—Cu1—N1—C4	−116.2 (5)	Cu1—N1—C4—C5	178.6 (6)
I1^ii—Cu1—N1—C4	−0.3 (5)	C2—C1—C5—C4	4 (1)
I1—Cu1—N1—C4	125.5 (5)	C6—C1—C5—C4	−179.8 (7)
Cu1^ii—Cu1—N1—C4	63.8 (5)	N1—C4—C5—C1	−0.4 (13)
N1^i—Cu1—N1—C3	65.3 (5)	C5—C1—C6—O1	21.1 (9)
I1^ii—Cu1—N1—C3	−178.8 (5)	C2—C1—C6—O1	−163.4 (7)
I1—Cu1—N1—C3	−53.0 (5)	C5—C1—C6—C7	142.4 (8)
Cu1^ii—Cu1—N1—C3	−114.7 (5)	C2—C1—C6—C7	−42.1 (9)
C5—C1—C2—C3	−5 (1)	C5—C1—C6—C6^iii	−94.8 (9)
C6—C1—C2—C3	179.0 (7)	C2—C1—C6—C6^iii	80.7 (9)
C4—N1—C3—C2	1.8 (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, º)

D—H···A	D—H	H···A	D···A	D—H···A
O1—H1···O2	0.82	1.99	2.77 (1)	158