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Acta Crystallographica Section E: Crystallographic Communications logoLink to Acta Crystallographica Section E: Crystallographic Communications
. 2020 Oct 23;76(Pt 11):1771–1774. doi: 10.1107/S2056989020014036

Crystal structure and Hirshfeld surface analysis of di­chlorido­(methanol-κO)bis­(2-methyl­pyridine-κN)copper(II)

J Prakasha Reddy a,*
PMCID: PMC7643234  PMID: 33209351

In the title complex, the CuII is in a tetra­gonal–pyramidal environment. The crystal structure features O—H⋯Cl and C—H⋯Cl inter­actions.

Keywords: crystal structure, hydrogen bonding, α-picoline, coordination chemistry

Abstract

In the title complex, [CuCl2(C6H7N)2(CH3OH)], the copper atom is five-coordinated by two nitro­gen atoms of 2-methyl­pyridine ligands, two chloro ligands and an oxygen atom of the methanol mol­ecule, being in a tetra­gonal–pyramidal environment with N and Cl atoms forming the basal plane. In the crystal, complex mol­ecules related by the twofold rotation axis are joined into dimeric units by pairs of O—H⋯Cl hydrogen bonds. These dimeric units are assembled through C—H⋯Cl inter­actions into layers parallel to (001).

Chemical context  

Both organic (from simple mol­ecules to peptides and proteins) and inorganic complexes have been known for more than a century and are central to modern chemistry because of their fascinating, aesthetic architectures and multiple applications (Gan et al., 2011; Gellman, 1998; Thorat et al., 2013; Vijayadas et al., 2013; Ziach et al., 2018). Recently, coordination compounds have been reported that find applications in fields such as catalysis, gas storage, separation technology and mol­ecular sensing (Mueller et al., 2006; Wan et al., 2006; Férey et al., 2003; James, 2003; Eddaoudi et al., 2002; Ruben et al., 2005, Kitagawa et al., 2004). There are many reports of coordination complexes where solvent mol­ecules are located in the voids of the crystal structure. However, reports describing the replacement of coordinated solvent mol­ecules with other mol­ecules are relatively scarce. As part of ongoing work in our laboratory, employing pyridine ligands in the preparation of various coordination networks (PrakashaReddy & Pedireddi, 2007), we have extended our work to the synthesis of other coordination networks. A literature survey revealed that coordination complex aqua­dichloro­bis­(2-methyl­pyridine)­copper(II) had been reported (Marsh et al., 1982). Our inter­est was to see whether we could replace the coordinated water mol­ecule in the complex with other solvent mol­ecules such as methanol or ethanol via single-crystal-to-single-crystal transition (SCSCT) to investigate the structural changes. Although we could not succeed in SCSCT of the complex, we were successful in synthesizing the methanol-coordinated copper complex incorporating 2-methyl­pyridine as reported herein.graphic file with name e-76-01771-scheme1.jpg

Structural commentary  

The title complex crystallizes in the monoclinic space group C2/c with one complex mol­ecule per asymmetric unit. Two nitro­gen atoms of 2-methyl­pyridine and two chloride ligands, which are trans to each other, form a rectangle around the copper atom, and its coordination is accomplished by the methanol oxygen atom, thus giving a tetra­gonal pyramid with the oxygen atom in the apical position (Fig. 1). The copper atom deviates by 0.161 (1) Å from the basal plane, and the angles around the copper atom are close to 90 and 180°. A plausible reason why the formation of a dimeric unit, as observed in [Cu(2-pic)2Cl2] (Marsh et al., 1982), was precluded might be the presence of the coordinated methanol mol­ecule on one side of the coordination rectangle and the methyl groups on the other side. The methyl­pyridine rings form angles of 83.96 (8) and 85.70 (8)° with respect to the basal plane of the coordination polyhedron, thereby plausibly blocking the sixth coordination position at the copper atom. The Cu—O bond distance of 2.353 (2) Å is relatively short for an apical atom in typical copper(II) tetra­gonal–pyramidal structure, whereas the Cu—N bond lengths [Cu1—N1= 2.031 (2) Å, Cu1—N2 = 2.017 (2) Å] agree well with those reported for related structures (Wang et al., 2006; Gong et al., 2009; Hu & Zhang, 2010; Li, 2011; Sun et al., 2013; Sanram et al., 2016).

Figure 1.

Figure 1

The mol­ecular structure of the title compound, showing the atom labelling and displacement ellipsoids drawn at the 50% probability level.

Supra­molecular features and Hirshfeld surface analysis  

Complex mol­ecules related by the twofold rotation axis are connected by pairs of O—H⋯Cl inter­actions (Table 1) involving the apical methanol ligand of one complex and a chloride ligand of the other, thus forming dimers (Fig. 2). The O⋯Cl and H⋯Cl distances and associated O—H⋯Cl angle lie within the ranges observed for other O—H⋯Cl inter­actions reported in the literature (Veal et al., 1972; Taylor, 2016; Ristić et al., 2020; Estes et al., 1976). These dimers are further connected through C—H⋯Cl inter­actions, generating layers parallel to (001) (Fig. 3, Table 1).

Table 1. Hydrogen-bond geometry (Å, °).

D—H⋯A D—H H⋯A DA D—H⋯A
O1—H1⋯Cl2i 0.75 (3) 2.37 (3) 3.1033 (16) 169 (3)
C7—H7⋯O1 0.93 2.46 3.148 (3) 130
C8—H8⋯O1 0.93 2.34 3.036 (3) 131
C11—H11⋯Cl2ii 0.93 2.83 3.624 (2) 143

Symmetry codes: (i) Inline graphic; (ii) Inline graphic.

Figure 2.

Figure 2

The O—H⋯Cl inter­actions between two mol­ecules in the crystal of the title compound. The mol­ecules are related by the symmetry operation −x + 1, y, −z + Inline graphic.

Figure 3.

Figure 3

A general view of the crystal packing of the title compound along the b-axis direction with inter­molecular contacts shown as dashed lines.

A Hirshfeld surface analysis was performed and two-dimensional fingerprint plots were prepared using Crystal Explorer17 (Turner et al., 2017) to further investigate the inter­molecular inter­actions in the title structure. The Hirshfeld surface mapped over d norm with corresponding colours representing inter­molecular inter­actions is shown in Fig. 4. The red spots on the surface correspond to the O—H⋯Cl, C—H⋯Cl and C—H⋯O inter­actions (Table 1). The two-dimensional fingerprint plots (McKinnon et al., 2007) are shown in Fig. 5. Weak van der Waals H⋯H contacts make the largest contribution (53.1%) to the Hirshfeld surface. The two-dimensional fingerprint plot shows two spikes that correspond to H⋯Cl/Cl⋯H (25.2%) inter­actions, which highlight the hydrogen bonds between adjacent mol­ecules. The C⋯H/H⋯C (15.5%) inter­actions also appear as two spikes. These inter­actions play a crucial role in the overall cohesion of the crystal packing.

Figure 4.

Figure 4

Hirshfeld surface mapped over d norm highlighting the regions of O—H⋯Cl and C—H⋯Cl inter­molecular contacts.

Figure 5.

Figure 5

The full two-dimensional fingerprint plot for the title compound and those delineated into H⋯H (53.1%), Cl⋯H/H⋯Cl (25.2%) and C⋯H/H⋯C (15.5%) contacts.

Database survey  

A search of the Cambridge Structural Database (CSD, Version 5.40, update of August 2019; Groom et al., 2016) revealed three closely related complexes: di­chloro­bis­(2-methyl­pyridine)­copper(II) (refcode CMPYCU01; Marsh et al., 1982), aqua­dichloro­bis­(2-methyl­pyridine)­copper(II) (BIJWUM; Marsh et al., 1982) and bis­(iso­thio­cyanato)­methanolbis­(2-methyl­pyridine)­copper(II) (ABOSIW; Handy et al., 2017). Structures CMPYCU01 and BIJWUM display dimeric arrangements of the complex mol­ecules arising from C—H⋯Cl and O—H⋯Cl inter­actions, respectively, while in the copper(II) thio­cyanate complex ABOSIW, the three-dimensional network is formed as a result of O—H⋯S, C—H⋯S and C—H⋯C inter­actions.

Synthesis and crystallization  

2-Methyl­pyridine and anhydrous copper(II) chloride were obtained from Aldrich, and HPLC grade methanol was used for reaction. Anhydrous copper(II) chloride (0.675 g, 0.005 mol) was dissolved in 15 ml of methanol. To this solution, 2-methyl­pyridine (0.93 g, 0.01 mol) dissolved in 15 mL of methanol was added. The resulting mixture was stirred for ca 40 min. at room temperature and filtered to remove the greenish precipitate. The blue filtrate was then allowed to stand at room temperature for a few hours, before being filtered and left at room temperature for crystallization. A mixture of dark-blue crystals of different sizes was obtained after 24 h.

Refinement  

Crystal data, data collection and structure refinement details are summarized in Table 2. All H atoms were located in a difference map. The C-bound H atoms were placed in calculated positions with C—H = 0.93-0.96 Å and refined as riding, whereas the coordinates of O-bound H atom were freely refined. All hydrogen atoms were refined with fixed isotropic displacement parameters [U iso(H) = 1.2–1.5U eq(C,O)]

Table 2. Experimental details.

Crystal data
Chemical formula [CuCl2(C6H7N)2(CH4O)]
M r 352.73
Crystal system, space group Monoclinic, C2/c
Temperature (K) 120
a, b, c (Å) 14.4554 (4), 8.5865 (2), 24.8055 (8)
β (°) 99.209 (3)
V3) 3039.22 (16)
Z 8
Radiation type Mo Kα
μ (mm−1) 1.78
Crystal size (mm) 0.21 × 0.16 × 0.11
 
Data collection
Diffractometer Agilent XCalibur diffractometer
Absorption correction Multi-scan (CrysAlis PRO; Rigaku OD, 2018)
T min, T max 0.549, 1.000
No. of measured, independent and observed [I > 2σ(I)] reflections 15974, 5137, 4251
R int 0.040
(sin θ/λ)max−1) 0.758
 
Refinement
R[F 2 > 2σ(F 2)], wR(F 2), S 0.038, 0.081, 1.13
No. of reflections 5137
No. of parameters 178
H-atom treatment H atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å−3) 0.54, −0.51

Computer programs: CrysAlis CCD and CrysAlis RED (Oxford Diffraction, 2009), SHELXT (Sheldrick, 2015a ), SHELXL (Sheldrick, 2015b ) and OLEX2 (Dolomanov et al., 2009).

Supplementary Material

Crystal structure: contains datablock(s) I. DOI: 10.1107/S2056989020014036/yk2140sup1.cif

e-76-01771-sup1.cif (556.4KB, cif)

Structure factors: contains datablock(s) I. DOI: 10.1107/S2056989020014036/yk2140Isup2.hkl

e-76-01771-Isup2.hkl (409.2KB, hkl)

CCDC reference: 1997065

Additional supporting information: crystallographic information; 3D view; checkCIF report

Acknowledgments

The author thanks Professor G. C. Diaz de Delgado for her help and discussions on the crystallographic aspect of this work.

supplementary crystallographic information

Crystal data

[CuCl2(C6H7N)2(CH4O)] F(000) = 1448
Mr = 352.73 Dx = 1.542 Mg m3
Monoclinic, C2/c Mo Kα radiation, λ = 0.71073 Å
a = 14.4554 (4) Å Cell parameters from 4621 reflections
b = 8.5865 (2) Å θ = 3.1–32.0°
c = 24.8055 (8) Å µ = 1.78 mm1
β = 99.209 (3)° T = 120 K
V = 3039.22 (16) Å3 Block, blue
Z = 8 0.21 × 0.16 × 0.11 mm

Data collection

Agilent XCalibur diffractometer 4251 reflections with I > 2σ(I)
Detector resolution: 16.1511 pixels mm-1 Rint = 0.040
ω scans θmax = 32.6°, θmin = 2.8°
Absorption correction: multi-scan (CrysAlisPro; Rigaku OD, 2018) h = −20→21
Tmin = 0.549, Tmax = 1.000 k = −12→11
15974 measured reflections l = −37→37
5137 independent reflections

Refinement

Refinement on F2 Primary atom site location: dual
Least-squares matrix: full Hydrogen site location: mixed
R[F2 > 2σ(F2)] = 0.038 H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.081 w = 1/[σ2(Fo2) + (0.0199P)2 + 4.4488P] where P = (Fo2 + 2Fc2)/3
S = 1.13 (Δ/σ)max = 0.001
5137 reflections Δρmax = 0.54 e Å3
178 parameters Δρmin = −0.51 e Å3
0 restraints

Special details

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)

x y z Uiso*/Ueq
Cu1 0.50986 (2) 0.75598 (3) 0.37062 (2) 0.01272 (6)
Cl1 0.41953 (3) 0.66088 (6) 0.43059 (2) 0.01703 (10)
Cl2 0.61677 (3) 0.86629 (5) 0.32152 (2) 0.01706 (10)
O1 0.40656 (10) 0.69534 (18) 0.29006 (6) 0.0192 (3)
H1 0.408 (2) 0.738 (3) 0.2640 (12) 0.029*
N2 0.45788 (11) 0.97058 (19) 0.38001 (7) 0.0145 (3)
N1 0.57721 (11) 0.54847 (19) 0.37032 (7) 0.0149 (3)
C1 0.49779 (13) 1.0690 (2) 0.41912 (8) 0.0141 (3)
C2 0.45939 (14) 1.2154 (2) 0.42581 (8) 0.0168 (4)
H2 0.488544 1.282802 0.452631 0.020*
C3 0.64638 (14) 0.5067 (2) 0.41102 (9) 0.0175 (4)
C4 0.58446 (14) 1.0157 (2) 0.45567 (8) 0.0188 (4)
H4A 0.571444 0.921107 0.473669 0.028*
H4B 0.604355 1.094501 0.482496 0.028*
H4C 0.633209 0.997353 0.434317 0.028*
C5 0.66783 (15) 0.2646 (2) 0.36638 (9) 0.0220 (4)
H5 0.698699 0.170012 0.364995 0.026*
C6 0.69292 (14) 0.3650 (2) 0.40943 (9) 0.0216 (4)
H6 0.740983 0.338329 0.437494 0.026*
C7 0.37914 (14) 1.0160 (2) 0.34693 (9) 0.0201 (4)
H7 0.351990 0.948582 0.319564 0.024*
C8 0.55316 (15) 0.4492 (2) 0.32849 (8) 0.0190 (4)
H8 0.505512 0.477838 0.300461 0.023*
C9 0.37781 (15) 1.2600 (2) 0.39241 (9) 0.0192 (4)
H9 0.350701 1.356328 0.396982 0.023*
C10 0.59622 (16) 0.3063 (2) 0.32532 (9) 0.0220 (4)
H10 0.577215 0.239722 0.296070 0.026*
C11 0.33724 (15) 1.1589 (3) 0.35209 (9) 0.0223 (4)
H11 0.282686 1.186387 0.328834 0.027*
C12 0.32370 (15) 0.6023 (3) 0.28385 (9) 0.0231 (4)
H12A 0.326320 0.525448 0.256034 0.035*
H12B 0.269827 0.667541 0.273541 0.035*
H12C 0.319211 0.551434 0.317792 0.035*
C13 0.67215 (16) 0.6175 (3) 0.45740 (10) 0.0271 (5)
H13A 0.691508 0.714806 0.443729 0.041*
H13B 0.722622 0.574607 0.482943 0.041*
H13C 0.618872 0.634370 0.475334 0.041*

Atomic displacement parameters (Å2)

U11 U22 U33 U12 U13 U23
Cu1 0.01378 (11) 0.01059 (11) 0.01375 (11) 0.00289 (8) 0.00206 (8) −0.00104 (8)
Cl1 0.0200 (2) 0.0157 (2) 0.0161 (2) 0.00216 (17) 0.00497 (17) 0.00003 (17)
Cl2 0.0182 (2) 0.0149 (2) 0.0192 (2) −0.00028 (16) 0.00627 (17) −0.00322 (17)
O1 0.0226 (7) 0.0190 (7) 0.0152 (7) −0.0020 (6) 0.0008 (6) 0.0024 (6)
N2 0.0145 (7) 0.0122 (7) 0.0175 (8) 0.0024 (6) 0.0047 (6) 0.0004 (6)
N1 0.0152 (7) 0.0133 (7) 0.0168 (8) 0.0020 (6) 0.0045 (6) −0.0011 (6)
C1 0.0168 (8) 0.0135 (8) 0.0128 (8) 0.0014 (7) 0.0049 (7) 0.0018 (7)
C2 0.0226 (9) 0.0128 (9) 0.0165 (9) 0.0015 (7) 0.0075 (8) −0.0011 (7)
C3 0.0157 (9) 0.0155 (9) 0.0217 (10) 0.0024 (7) 0.0041 (7) 0.0004 (8)
C4 0.0216 (9) 0.0175 (9) 0.0164 (9) 0.0042 (8) 0.0005 (8) −0.0029 (8)
C5 0.0252 (10) 0.0135 (9) 0.0304 (11) 0.0057 (8) 0.0138 (9) 0.0027 (8)
C6 0.0186 (9) 0.0196 (10) 0.0264 (11) 0.0077 (8) 0.0030 (8) 0.0034 (8)
C7 0.0178 (9) 0.0175 (9) 0.0237 (10) 0.0031 (7) −0.0009 (8) −0.0033 (8)
C8 0.0235 (10) 0.0190 (10) 0.0154 (9) 0.0031 (8) 0.0055 (8) −0.0020 (8)
C9 0.0233 (10) 0.0138 (9) 0.0225 (10) 0.0058 (7) 0.0094 (8) 0.0022 (8)
C10 0.0293 (11) 0.0163 (9) 0.0222 (10) 0.0021 (8) 0.0101 (9) −0.0044 (8)
C11 0.0198 (9) 0.0205 (10) 0.0252 (11) 0.0076 (8) −0.0007 (8) −0.0007 (8)
C12 0.0202 (10) 0.0289 (11) 0.0202 (10) 0.0001 (8) 0.0033 (8) −0.0023 (9)
C13 0.0236 (10) 0.0235 (11) 0.0303 (12) 0.0082 (9) −0.0081 (9) −0.0069 (9)

Geometric parameters (Å, º)

Cu1—Cl1 2.2818 (5) C4—H4C 0.9600
Cu1—Cl2 2.3175 (5) C5—H5 0.9300
Cu1—O1 2.3534 (15) C5—C6 1.375 (3)
Cu1—N2 2.0174 (16) C5—C10 1.378 (3)
Cu1—N1 2.0310 (16) C6—H6 0.9300
O1—H1 0.75 (3) C7—H7 0.9300
O1—C12 1.427 (3) C7—C11 1.383 (3)
N2—C1 1.345 (2) C8—H8 0.9300
N2—C7 1.350 (3) C8—C10 1.384 (3)
N1—C3 1.351 (3) C9—H9 0.9300
N1—C8 1.345 (3) C9—C11 1.382 (3)
C1—C2 1.395 (3) C10—H10 0.9300
C1—C4 1.496 (3) C11—H11 0.9300
C2—H2 0.9300 C12—H12A 0.9600
C2—C9 1.382 (3) C12—H12B 0.9600
C3—C6 1.394 (3) C12—H12C 0.9600
C3—C13 1.494 (3) C13—H13A 0.9600
C4—H4A 0.9600 C13—H13B 0.9600
C4—H4B 0.9600 C13—H13C 0.9600
Cl1—Cu1—Cl2 171.17 (2) C6—C5—H5 120.5
Cl1—Cu1—O1 97.06 (4) C6—C5—C10 118.99 (19)
Cl2—Cu1—O1 91.73 (4) C10—C5—H5 120.5
N2—Cu1—Cl1 89.37 (5) C3—C6—H6 120.0
N2—Cu1—Cl2 88.82 (5) C5—C6—C3 120.0 (2)
N2—Cu1—O1 95.90 (6) C5—C6—H6 120.0
N2—Cu1—N1 171.61 (7) N2—C7—H7 118.7
N1—Cu1—Cl1 90.74 (5) N2—C7—C11 122.6 (2)
N1—Cu1—Cl2 89.79 (5) C11—C7—H7 118.7
N1—Cu1—O1 92.42 (6) N1—C8—H8 118.6
Cu1—O1—H1 121 (2) N1—C8—C10 122.9 (2)
C12—O1—Cu1 128.53 (13) C10—C8—H8 118.6
C12—O1—H1 109 (2) C2—C9—H9 120.6
C1—N2—Cu1 122.19 (13) C2—C9—C11 118.84 (19)
C1—N2—C7 118.63 (17) C11—C9—H9 120.6
C7—N2—Cu1 119.16 (14) C5—C10—C8 118.7 (2)
C3—N1—Cu1 121.89 (13) C5—C10—H10 120.7
C8—N1—Cu1 119.60 (13) C8—C10—H10 120.7
C8—N1—C3 118.50 (17) C7—C11—H11 120.6
N2—C1—C2 121.29 (18) C9—C11—C7 118.87 (19)
N2—C1—C4 117.75 (17) C9—C11—H11 120.6
C2—C1—C4 120.96 (18) O1—C12—H12A 109.5
C1—C2—H2 120.1 O1—C12—H12B 109.5
C9—C2—C1 119.71 (19) O1—C12—H12C 109.5
C9—C2—H2 120.1 H12A—C12—H12B 109.5
N1—C3—C6 120.91 (19) H12A—C12—H12C 109.5
N1—C3—C13 118.02 (17) H12B—C12—H12C 109.5
C6—C3—C13 121.06 (19) C3—C13—H13A 109.5
C1—C4—H4A 109.5 C3—C13—H13B 109.5
C1—C4—H4B 109.5 C3—C13—H13C 109.5
C1—C4—H4C 109.5 H13A—C13—H13B 109.5
H4A—C4—H4B 109.5 H13A—C13—H13C 109.5
H4A—C4—H4C 109.5 H13B—C13—H13C 109.5
H4B—C4—H4C 109.5
Cu1—N2—C1—C2 −178.36 (14) C1—C2—C9—C11 −1.5 (3)
Cu1—N2—C1—C4 1.1 (2) C2—C9—C11—C7 0.6 (3)
Cu1—N2—C7—C11 177.53 (17) C3—N1—C8—C10 −0.1 (3)
Cu1—N1—C3—C6 −178.70 (15) C4—C1—C2—C9 −178.23 (18)
Cu1—N1—C3—C13 0.6 (3) C6—C5—C10—C8 1.1 (3)
Cu1—N1—C8—C10 179.63 (16) C7—N2—C1—C2 0.0 (3)
N2—C1—C2—C9 1.2 (3) C7—N2—C1—C4 179.42 (18)
N2—C7—C11—C9 0.5 (3) C8—N1—C3—C6 1.0 (3)
N1—C3—C6—C5 −0.9 (3) C8—N1—C3—C13 −179.70 (19)
N1—C8—C10—C5 −1.0 (3) C10—C5—C6—C3 −0.2 (3)
C1—N2—C7—C11 −0.9 (3) C13—C3—C6—C5 179.8 (2)

Hydrogen-bond geometry (Å, º)

D—H···A D—H H···A D···A D—H···A
O1—H1···Cl2i 0.75 (3) 2.37 (3) 3.1033 (16) 169 (3)
C7—H7···O1 0.93 2.46 3.148 (3) 130
C8—H8···O1 0.93 2.34 3.036 (3) 131
C11—H11···Cl2ii 0.93 2.83 3.624 (2) 143

Symmetry codes: (i) −x+1, y, −z+1/2; (ii) x−1/2, y+1/2, z.

Funding Statement

This work was funded by Indrashil University grant .

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Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Supplementary Materials

Crystal structure: contains datablock(s) I. DOI: 10.1107/S2056989020014036/yk2140sup1.cif

e-76-01771-sup1.cif (556.4KB, cif)

Structure factors: contains datablock(s) I. DOI: 10.1107/S2056989020014036/yk2140Isup2.hkl

e-76-01771-Isup2.hkl (409.2KB, hkl)

CCDC reference: 1997065

Additional supporting information: crystallographic information; 3D view; checkCIF report


Articles from Acta Crystallographica Section E: Crystallographic Communications are provided here courtesy of International Union of Crystallography

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