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Synthesis, crystal structure and Hirshfeld analysis of [Zn(H2O)4(ampyz)2][Zn(H2O)6](SO4)2(H2O)2
Accepted Manuscript
Synthesis, crystal structure and Hirshfeld analysis of [Zn(H2 O)4 (ampyz)2 ][Zn(H2 O)6 ](SO4 )2 (H2 O)2 Jose´ Antonio do NascimentoNeto , Ana K. Valdo , ˆ Patricia da Cruz Souza , Felipe T. Martins PII: DOI: Reference:
S2405-8300(18)30115-0 10.1016/j.cdc.2018.07.003 CDC 124
To appear in:
Chemical Data Collections
Received date: Revised date: Accepted date:
4 June 2018 11 July 2018 13 July 2018
Please cite this article as: Jose´ Antonio do NascimentoNeto , Ana K. Valdo , ˆ Patricia da Cruz Souza , Felipe T. Martins , Synthesis, crystal structure and Hirshfeld analysis of [Zn(H2 O)4 (ampyz)2 ][Zn(H2 O)6 ](SO4 )2 (H2 O)2 , Chemical Data Collections (2018), doi: 10.1016/j.cdc.2018.07.003
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ACCEPTED MANUSCRIPT Title: Synthesis, crystal structure and Hirshfeld analysis of
[Zn(H2O)4(ampyz)2][Zn(H2O)6](SO4)2(H2O)2 Authors: José Antônio do Nascimento Neto, Ana K. Valdo*, Patricia da Cruz Souza and Felipe T. Martins
Goiânia, GO, PO Box 131, 74690-900, Brazil Contact emails:[email protected]
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Affiliation: Instituto de Química, Universidade Federal de Goiás, Campus Samambaia,
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Graphical abstract
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Abstract The wide range of ligands and metals led to an extensive development of coordination chemistry. These compounds have been studied due to possible applications in several fields, as catalysis and nonlinear optics. The crystal structure of a coordination compound allows to establish a direct relation between structure and properties. Among the ligands, nitrogen aromatic compounds have been used largely in synthesis, since they enable strong coordination bond and stable intermolecular interactions, increasing also the possibility to study them in the crystalline state. This work reports the synthesis, crystal structure, infrared and UV-Vis spectroscopy of a Zn(II) complex with 2-aminopyrazine (ampyz) and water as ligands, resulting in the formula [Zn(H2O)4(ampyz)2][Zn(H2O)6](SO4)2(H2O)2. Moreover, to illustrate the intermolecular interactions, we also report the analysis of the Hirshfeld surface and its fingerprint for the main complex [Zn(H2O)4(ampyz)2]2+.
Keywords: single crystal structure; X-Ray diffraction; 2-aminopyrazine; coordination compound; intermolecular interactions.
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Specifications Table
Crystallography
Compounds
bis(2-Aminopyrazine)-tetra-aqua-zinc(ii) hexa-aqua-zinc(ii) disulfatedihydrate
Data category
Crystallographic and spectral (IR and UV-Vis)
Data acquisition format
Single crystal X-Ray diffraction method and IR and UV-Vis spectra
Data type
Analyzed
Procedure
Collect, indexing, integration and scaling of single crystal X-ray diffraction intensities from suitably sized single crystals of [Zn(H2O)4(ampyz)2][Zn(H2O)6](SO4)2(H2O)2 ; Hirshfeld surface analysis of [Zn(H2O)4(ampyz)2]2+; IR and UV-Vis spectral data acquisition for the complex.
Data accessibility
CCDC 1522493. Free of charge, copies of this file may be solicited from The Director, CCDC, 12 Union Road, Cambridge, CB2 1EZ, UK, fax: +44123-336-033; e-mail: [email protected] or http:www.ccdc.cam.ac.uk
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Subject área
ACCEPTED MANUSCRIPT 1. Rationale
The coordination chemistry is a vast area that increased rapidly in these last decades [1]. These compounds have been used in many applied fields, including nonlinear optics, heterogeneous catalysis and biomedical properties [2]. These coordination compounds show a wide range of possible architectures such chains, dimers and clusters. This is caused by the large variety of ligands and how they
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establish coordination bonds to metals, changing the geometry and consequently the possible interactions. On the other side, maintaining the ligand is an interesting possibility to evaluate the influence of the metal in the desirable properties. Among the classes of ligands able to coordinate metal sites, the N-donor heterocyclic ligands are extensively used [3]. Allied to their supramolecular features such as hydrogen bonds
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and π–π stacking, very distinct three-dimensional frameworks can be obtained. In this work, we report the synthesis and crystal structure of a coordination compound with a N-donor heterocyclic ligand, namely, [Zn(H2O)4(ampyz)2][Zn(H2O)6](SO4)2(H2O)2, and the Hirshfeld surface analyses for the main complex [Zn(H2O)4(ampyz)2]2+. This
2. Procedure
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Mn(II), Fe(II) and Co(II) [4,5].
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complex fills the gap for a series of isostructural compounds described with the metals
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2.1. Materials and methods
All reagents were obtained from commercial sources and used without further
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purification. The reaction was performed at room temperature by a direct mixture of the solutions. Glass crystallizer containing the mixture was then allowed to evaporate at
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room temperature, and, after four weeks, colorless needles single crystals were isolated out from mother solution.
2.2. Synthesis
The complex was prepared using an ethanolic solution (5 mL) of 2aminopyrazine (ampyz) (0.11 mmol; 13.9 mg) that was carefully mixed together with an aqueous solution (5 mL) of ZnSO4·7H2O (0.11 mmol, 28.7 mg.
ACCEPTED MANUSCRIPT 2.3. Crystallographic characterization
The reflection data were collected on a Bruker-AXS Kappa Duo diffractometer with an APEX II CCD detector with a graphite-monochromated X-ray beam (Mo-Kα radiation = 0.71073 Å). The diffraction frames were recorded by ϕ and ω scans using APEX2 and raw dataset treatment was performed using the programs SAINT and SADABS [6]. Multi-scan absorption correction has been employed to all datasets [7].
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The structure was solved by direct methods of phase retrieval with SHELXS-2014 [8]. All full-matrix refinements were performed on F2 using SHELXL-2014 [8], accessed by WinGX [9] platform software. All non-hydrogen atoms were refined with free anisotropic displacement parameters, while the hydrogens had their displacement parameter fixed and set to isotropic. Their isotropic thermal parameters were fixed
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[Uiso(H) = 1.2Ueq(Csp2 and N) or 1.5Ueq(O)] using a riding model with fixed bond lengths of 0.93 Å for C—H (aromatic), 0.86 Å for N—H (amine) and 0.84 Å for O— H. The hydrogen positions were calculated according both intramolecular and intermolecular requirements. The ORTEP-3 [9] and Mercury [10] programs were used
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to prepare artwork representations. Zn1 and Zn2 are located over a crystallographic inversion center at (0.5, 1, 0.5) and (0.5, 0.5, 1) positions, respectively, with 50% of site occupancy factor. Crystallographic data and refinement parameters for the coordination
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compound are summarized in Table 1. The geometry of coordination (bond length and angles) is presented in Table 2, while the hydrogen bonds are grouped in Table 3. The
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crystallographic data is available in the CIF file. CCDC number is 1522493.
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2.4. Calculation of Hirshfeld surfaces
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To illustrate the intermolecular interactions found in the reported structure,
Hirshfeld surfaces were calculated for the main complex [Zn(H2O)4(ampyz)2]2+. The analysis of this surface was also done by the fingerprint plot of external distance (de) versus internal distance (di), meaning the distance between an atom to either external or internal Hirshfeld surfaces, respectively [11]. This graphical tool enables prompt investigation about the supramolecular structure through analysis of intermolecular interactions, using graphic colored as the frequency of contacts to specify properties of the surface. All graphical representations were done using Crystal Explorer 2.1 software [12].
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2.5. Infrared (IR) and UV-Vis spectroscopy
Infrared spectrum was collected on a 400FT-IR/FT-FIR spectrometer (PerkinElmer) upon the transmission mode, being averaged on 16 acquisition at resolution spectral of 4 cm-1. The sample was analyzed in the form of KBr pellets. The UV-Vis spectrum complex was collected in water solution using a Lambda 45 – UV-
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VIS spectrophotometer (PerkinElmer). The wavelength ranged from 220 to 800 nm with a fixed resolution slit of 2.0 nm.
3.1. Single crystal X-ray diffraction
The
coordination
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3. Results and Discussion
compound
has
formula
[Zn(H2O)4(ampyz)2][Zn(H2O)6](SO4)2(H2O)2 and was solved in the space group P-1. Its
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asymmetric unit contains half of two independent crystallographic Zn(II) complexes, one water molecule and a sulfate ion (Fig. 1). The mentioned complexes have formula
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[Zn(H2O)4(ampyz)2]2+ and [Zn(H2O)6]2+. Both Zn2+ ions (Zn1 and Zn2) occupy coordinates of inversion centers. The same molecular motif was already reported, however, for Co(II), Fe(II) and Mn(II) [4,5]. Therefore, this structure belongs to an
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isostructural series of complexes with transition metals containing ampyz as ligand, sulfate and an acquacomplex as counterions. The Zn:ampyz stoichiometry 1:1 was the
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same used in the preparation of the precedent isostructures [4]. The crystallographic
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data and refinement parameters are shown in Table 1.
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Figure 1. ORTEP view for asymmetric unit with 50% probability level ellipsoids for all non-hydrogen atoms. Hydrogen atoms were not labelled for clarity. Symmetry
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operation i: 1-x, 2-y, 1-z; and ii: -1-x, 1-y, 2-z.
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Table 1. Crystal data and refinement parameters for coordination compound reported here. Chemical formula
C8H34N6O20S2Zn2
Fw (g.mol-1)
729.31
1.604 -
(°)
25.358
index ranges
Triclinic
Space group
P-1
Z
1
T (K)
296(2)
Unit cell dimensions
-10 to 10
l
-15 to 15
Data collected
5921
Unique reflections
2423
0.0219
b (Å)
8.347(6)
Completeness to θmax (%)
97.4
c (Å)
13.273(9)
F(000)
376
α (°)
75.73(2)
Refined parameters
175
β (°)
78.439(18)
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6.579(4)
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78.660(18) 683.7(8)
1.771
Goodness-of-fit on F2(S)a
1.055
Final R1bfactor[ I> 2σ(I)]
0.0461
wR2c factor (all data)
0.1380
Largest diff. peak / hole (e
1.78/-0.349
Å-3)
Absorption coefficient μ (mm-1)
1.999
absorption correc. (multi-scan)
0.724/0.819
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k
a (Å)
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ρcalc (g.cm-3)
-7 to 7
Symmetry factor (Rint)
γ (°) V (Å3)
h
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Cryst syst
θ range for data collection
CCDC deposit no.
1522493
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Tmin/Tmax
Those two metal centers are six-coordinated with octahedral geometry. The
coordination set for Zn1 is defined by two nitrogens from distinct ampyz ligands and four oxygens from water molecules, while for Zn2 is defined by six oxygens from water molecules. Polyhedral representations of coordination sphere can be seen in Fig. 2.
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b) Zn2 present in the reported structure.
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Figure 2. Coordination polyhedral for crystallographic independent Zn(II), a) Zn1 and
Table 2. Bond lengths (Å) and angles (°) of Zn(II) in coordination complexes. Angle (°)
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Length (Å) 2.219(4)
O2W-Zn1-O3Wi
92.72(11)
Zn1-O2W
2.056(3)
O2Wi-Zn1-O3W
92.72(11)
Zn1-O3W
2.102 (3)
O2Wi-Zn1-O3Wi
87.28(11)
Zn2-O4W
2.081(3)
O3W-Zn1-O3Wi
180
Zn2-O5W
2.132(4)
O4W-Zn2-O4Wi
180
O4W-Zn2-O5W
93.11(14)
O4W-Zn2-O5Wi
86.89(14)
180
O4W-Zn2-O6W
89.23(12)
N1-Zn1-O2W
88.41(14)
O4W-Zn2-O6Wi
90.77(12)
N1-Zn1-O2Wi
91.44(11)
O5W-Zn-O5Wi
180
N1-Zn1-O3W
90.51(11)
O5W-Zn2-O6W
89.95(12)
N1-Zn1-O3Wi
89.49(11)
O5W-Zn2-O6Wi
90.05(12)
O2W-Zn1-O2Wi
180
O6W-Zn-O6Wi
180
O2W-Zn1-O3W
87.28(11)
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Zn1-N1
Angle (°)
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N1-Zn1-N1i
2.077(3)
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Zn2-O6W
ACCEPTED MANUSCRIPT The packing is built-up by alternated layers parallel to bc plane. One of these layers is constituted by [Zn(H2O)4(ampyz)2]2+, while the another one is assembled with [Zn(H2O)6]2+, sulfate anions and the free water molecule (O1W), as can be seen in Fig. 3a. In addition, the connection between the different layers occurs through hydrogen bonds. The geometry of hydrogen bonds found in this structure is shown in Table 3. In one layer, only classical hydrogen bonds (O—H•••O) are observed, which are connecting sulfate ions, water molecules and [Zn(H2O)6]2+ units (Fig. 3b). On the other
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hand, in the alternated layer, [Zn(H2O)4(ampyz)2]2+ units are cross linked through hydrogen bonds (O2W—H12W•••N2) and π•••π contacts (Cg1ii•••Cg1iii; Cg1 is the ampyz centroid calculated through cyclic atoms) between adjacent ampyz rings (Fig. 3c). In addition, the oxygen atom (O2) from sulfate anion acts like a bridge, connecting two units of [Zn(H2O)4(ampyz)2]2+ by means of N3-H3A•••O2, O2W-H22W•••O2 and
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O3W-H23W•••O2 interactions along the a axis (Fig. 3d). Yet, another π•••π interaction (Cg1•••Cg1i) is responsible for connecting neighboring layers of same composition (Fig. 3d). The π•••π interactions represented as Cg1•••Cg1i and Cg1ii•••Cg1iii show
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different geometric parameters, as can be seen in Table 4.
Figure 3. (a) Packing view showing the two alternated layers onto the bc plane. Intermolecular interactions onto the layers comprised by (b) sulfate anion, the acquacomplex and water molecule, involving only classical hydrogen bonds (O— H•••O), (c) [Zn(H2O)4(ampyz)2]2+ units, involving hydrogen bond (O—H•••N) and π•••π contacts. Besides, the two π•••π interactions present in this structure and the
ACCEPTED MANUSCRIPT important role of sulfate anion interlinking two units of the main complex are shown in (d). Dashed black lines represent hydrogen bonds and dashed cyan lines are π•••π interactions. Symmetry operation i: 2-x,1-y,1-z; ii: 1-x,2-y,1-z; iii: x,1+y,z.
Table 3. Hydrogen-bond geometry found in [Zn(H2O)4(ampyz)2][Zn(H2O)6](SO4)2(H2O)2 . H∙∙∙A (Å)
0.84
1.96
O1W-H21W...O4
0.99
1.73
O4W-H14W...O1W
0.85
1.92
O4W-H24W...O3
0.86
O6W-H16W...O4
0.83
O6W-H26W...O1
0.85
O5W-H15W...O3
0.83
O5W-H25W...O1W
O1W—
D—H∙∙∙A(°)
2.791(4)
169
2.714(4)
171
2.736(4)
159
1.91
2.734(4)
159
1.95
2.725(4)
154
2.00
2.813(4)
159
1.93
2.757(4)
175
0.80
2.00
2.795(4)
173
0.85
1.95
2.798(5)
175
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H11W∙∙∙O1
O2W-H12W...N2
D∙∙∙A (Å)
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D—H (Å)
D—H∙∙∙A
0.84
1.96
2.767(4)
160
O3W-H13W...O1
0.86
1.92
2.781(4)
176
O3W-H23W...O2
0.90
1.88
2.777(4)
177
N3-H3A...O2
0.86
2.18
3.031(5)
169
N3-H3B...O4W
0.86
2.62
3.357(6)
144
N3-H3B...O5W
0.86
2.52
3.279(5)
147
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O2W-H22W...O2
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Table 4. Geometrical parameters for π•••π interactions, involving Cg1•••Cg1i and Cg1ii•••Cg1iii. Distance between centroids (dcg-cg), perpendicular distance between Cg and the plane from another ring (dπ•••π), slippage (ds), dihedral angle between planes calculated through atom of Cg (??), slipping angle (?? and ??) between dcg-cg and normal (from centroid to other plane). Parameters
dπ•••π (Å)
ds (Å)
Cg1•••Cg1i
3.557(3)
3.1952(16)
1.563
Cg1ii•••Cg1iii
3.422(3)
3.3281(16)
?? (°) = ?? (°)
0.02(19)
26.1
0.795
0.02(19)
13.4
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3.2. Hirshfeld surfaces analysis
?? (°)
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dcg-cg (Å)
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Interaction
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Hirshfeld surfaces analysis provides a graphical way to interpret intermolecular interactions in crystal structures. In Fig. 4, dnorm Hirshfeld surface for the main complex
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[Zn(H2O)4(ampyz)2]2+ is shown. The color of the surface indicates closer (red) to longer (blue) contacts. Closer and longer contacts refer to interactions with distances lower and
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higher than the sum of vdW radius of the involved atoms, respectively. In our complex, closer contact areas are nearby coordinated water molecules, whose interactions were
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represented in Fig. 3c,d. Analyzing the Hirshfeld surface (Fig. 4), it is possible to observe closer contacts near O2W (region a), related to interaction with oxygen from sulfate anion (O2) and the non-coordinated nitrogen (N2) from ampyz ligand (region b). Moreover, it is also observed the interaction involving O3W (region d and e), which are related to contacts with the same oxygen from sulfate anion (O2). The primary amine (N3) also is involved in hydrogen bonds with sulfate anion (region f). Yet, the slight formation of red regions (region g) can also be noted above the center of aromatic rings. This indicates the presence of π•••π contacts discussed before. Therefore, many regions committed to strong interactions are observed in this Hirshfeld surface, which
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crystal structure packing.
Figure 4. Hirshfeld surface (dnorm mapped) for main complex [Zn(H2O)4(ampyz)2]2+.
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The regions of closer contacts were labeled as a-f.
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Two dimensional plot grids were calculated using the internal and external distance (di and de) for each point on the Hirshfeld surface, as can be seen in Fig. 5. The
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plots were obtained to the total contribution of interactions (Fig. 5a) and for individuals (Fig. 5b-f). The ligands present in the main complex (ampyz and water) enable many strong intermolecular contacts, as hydrogen bonds. As result, in the fingerprints, we see
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two long sharp spikes pointing to the bottom left (minor distances) of the plot, mainly due to the contacts O•••H and N•••H (contribution sum of 39.9%). The most abundant interactions (H•••H) are located on the center of the graphical plot with a wide range of distances (1.0 to 2.3 Å), which are known to have large contribution in many compounds [12]. As mentioned, C•••C can be seen in this structure through π•••π involving the parallel offset ampyz rings, whose distance (~ 1.8 Å) is close to vdW radius of carbon atom. Moreover, C•••H interaction has a small contribution in the
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top (di < de) and bottom (de < di), indicating the presence of C-H•••π interactions.
Figure 5. Fingerprint of Hirshfeld surface (0.4 to 2.6 Å) and the contribution of each
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type of interaction (in %) for [Zn(H2O)4(ampyz)2]2+, showing (a) total interactions, (b) H•••H, (c) O•••H, (d) N•••H, (e) C•••C and (f) C•••H. The gradient color from blue
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(few) to red (many) indicates to contribution of the point to the global Hirshfeld surface. The gray shadow (b-f) is the outline of full fingerprint. di and de are the internal and
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external distance from a point to the surface, respectively.
Besides, the Hirshfeld surfaces mapped over shape index (Fig. 6a) and
curvedness (Fig. 6b) were performed. Both surfaces revealed π•••π contacts. In the shape index surface, blue and red triangles over the ampyz aromatic rings indicated the presence of π•••π interactions. Likewise, in the curvedness surface, the π•••π contacts are notable due to the presence of flat regions on aromatic rings.
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Figure 6. Hirshfeld surface mapped over (a) shape index and (b) curvedness for the
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main complex [Zn(H2O)4(ampyz)2]2+.
3.3. Infrared (IR) and UV-Vis spectroscopy
The IR spectrum of the Zn(II) complex (Fig. 7) shows the presence of ampyz
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ligand due to five peaks. The two high intensity sharp peaks at 3465 and 3311 cm-1 refer to the primary amine [ʋ(N−H)]. The broad signal of water (ʋ(O−H)) at approximately
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3500 cm-1 was slightly suppressed by the peaks of primary amine. Meanwhile, the heterocyclic aromatic ring can be also characterized by the presence of two high intense sharp peaks at 1630 [ʋ(C=N)Ar] and 1530 cm−1 [ʋ(C=C)Ar]. The presence of sulfate
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[ʋ(S−O)].
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anion can be attributed to the high intensity peaks at 1112 cm−1 [ʋ(S=O)] and 622 cm−1
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Figure 7. IR spectrum of the Zn complex.
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The UV-vis spectrum of Zn complex was prepared in water and no absorption bands were observed in the visible region, since Zn(II) doesn't show any d-d transitions.
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The spectrum (Fig. 8) presents only two broad absorption bands, centered at 315 and 285 nm. The strongest bands for this complex can be attributed to metal to ligand
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charge transfer (MLCT) and ligand to metal charge transfer (LMCT).
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Figure 8. UV-Vis spectrum of Zn complex in water.
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4. Conclusion
and
UV-Vis
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In this study, we report the synthesis, single crystal X-Ray diffraction and IR spectral
data
of
the
coordination
compound
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[Zn(H2O)4(ampyz)2][Zn(H2O)6](SO4)2(H2O)2 and the Hirshfeld surface analysis of the main complex [Zn(H2O)4(ampyz)2]2+. The crystal structure revealed a packing made
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with alternate layers, which are constituted with only one type of the two Zn(II) complexes. The formation of these layers was possible due to π•••π and many hydrogen
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bonding interactions. The analysis of intermolecular interactions through Hirshfeld surfaces and their fingerprints illustrate the contribution of such contacts. The presence of strong hydrogen bond is seen in the formation of sharp spikes at left side of 2D plot grid of de versus di. Also, in this graphic, it is noted the common π•••π interactions between parallel ampyz rings. This complex contributes to increase a series of isostructural coordination compounds containing ampyz and water as ligands and the acquacomplex of same metal, sulfate anion as counterion and one lattice water molecule. This expands our structural knowledge related to physicochemical properties of the isostructural series.
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Acknowledgment The authors acknowledge CNPq and CAPES for financial support and for research fellowships (AKV and FTM).
[1]
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University of Western Australia, 2012.
Synthesis, crystal structure and Hirshfeld analysis of [Zn(H2 O)4 (ampyz)2 ][Zn(H2 O)6 ](SO4 )2 (H2 O)2 Jose´ Antonio do NascimentoNeto , Ana K. Valdo , ˆ Patricia da Cruz Souza , Felipe T. Martins PII: DOI: Reference:
S2405-8300(18)30115-0 10.1016/j.cdc.2018.07.003 CDC 124
To appear in:
Chemical Data Collections
Received date: Revised date: Accepted date:
4 June 2018 11 July 2018 13 July 2018
Please cite this article as: Jose´ Antonio do NascimentoNeto , Ana K. Valdo , ˆ Patricia da Cruz Souza , Felipe T. Martins , Synthesis, crystal structure and Hirshfeld analysis of [Zn(H2 O)4 (ampyz)2 ][Zn(H2 O)6 ](SO4 )2 (H2 O)2 , Chemical Data Collections (2018), doi: 10.1016/j.cdc.2018.07.003
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ACCEPTED MANUSCRIPT Title: Synthesis, crystal structure and Hirshfeld analysis of
[Zn(H2O)4(ampyz)2][Zn(H2O)6](SO4)2(H2O)2 Authors: José Antônio do Nascimento Neto, Ana K. Valdo*, Patricia da Cruz Souza and Felipe T. Martins
Goiânia, GO, PO Box 131, 74690-900, Brazil Contact emails:[email protected]
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Affiliation: Instituto de Química, Universidade Federal de Goiás, Campus Samambaia,
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Graphical abstract
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Abstract The wide range of ligands and metals led to an extensive development of coordination chemistry. These compounds have been studied due to possible applications in several fields, as catalysis and nonlinear optics. The crystal structure of a coordination compound allows to establish a direct relation between structure and properties. Among the ligands, nitrogen aromatic compounds have been used largely in synthesis, since they enable strong coordination bond and stable intermolecular interactions, increasing also the possibility to study them in the crystalline state. This work reports the synthesis, crystal structure, infrared and UV-Vis spectroscopy of a Zn(II) complex with 2-aminopyrazine (ampyz) and water as ligands, resulting in the formula [Zn(H2O)4(ampyz)2][Zn(H2O)6](SO4)2(H2O)2. Moreover, to illustrate the intermolecular interactions, we also report the analysis of the Hirshfeld surface and its fingerprint for the main complex [Zn(H2O)4(ampyz)2]2+.
Keywords: single crystal structure; X-Ray diffraction; 2-aminopyrazine; coordination compound; intermolecular interactions.
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Specifications Table
Crystallography
Compounds
bis(2-Aminopyrazine)-tetra-aqua-zinc(ii) hexa-aqua-zinc(ii) disulfatedihydrate
Data category
Crystallographic and spectral (IR and UV-Vis)
Data acquisition format
Single crystal X-Ray diffraction method and IR and UV-Vis spectra
Data type
Analyzed
Procedure
Collect, indexing, integration and scaling of single crystal X-ray diffraction intensities from suitably sized single crystals of [Zn(H2O)4(ampyz)2][Zn(H2O)6](SO4)2(H2O)2 ; Hirshfeld surface analysis of [Zn(H2O)4(ampyz)2]2+; IR and UV-Vis spectral data acquisition for the complex.
Data accessibility
CCDC 1522493. Free of charge, copies of this file may be solicited from The Director, CCDC, 12 Union Road, Cambridge, CB2 1EZ, UK, fax: +44123-336-033; e-mail: [email protected] or http:www.ccdc.cam.ac.uk
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Subject área
ACCEPTED MANUSCRIPT 1. Rationale
The coordination chemistry is a vast area that increased rapidly in these last decades [1]. These compounds have been used in many applied fields, including nonlinear optics, heterogeneous catalysis and biomedical properties [2]. These coordination compounds show a wide range of possible architectures such chains, dimers and clusters. This is caused by the large variety of ligands and how they
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establish coordination bonds to metals, changing the geometry and consequently the possible interactions. On the other side, maintaining the ligand is an interesting possibility to evaluate the influence of the metal in the desirable properties. Among the classes of ligands able to coordinate metal sites, the N-donor heterocyclic ligands are extensively used [3]. Allied to their supramolecular features such as hydrogen bonds
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and π–π stacking, very distinct three-dimensional frameworks can be obtained. In this work, we report the synthesis and crystal structure of a coordination compound with a N-donor heterocyclic ligand, namely, [Zn(H2O)4(ampyz)2][Zn(H2O)6](SO4)2(H2O)2, and the Hirshfeld surface analyses for the main complex [Zn(H2O)4(ampyz)2]2+. This
2. Procedure
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Mn(II), Fe(II) and Co(II) [4,5].
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complex fills the gap for a series of isostructural compounds described with the metals
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2.1. Materials and methods
All reagents were obtained from commercial sources and used without further
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purification. The reaction was performed at room temperature by a direct mixture of the solutions. Glass crystallizer containing the mixture was then allowed to evaporate at
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room temperature, and, after four weeks, colorless needles single crystals were isolated out from mother solution.
2.2. Synthesis
The complex was prepared using an ethanolic solution (5 mL) of 2aminopyrazine (ampyz) (0.11 mmol; 13.9 mg) that was carefully mixed together with an aqueous solution (5 mL) of ZnSO4·7H2O (0.11 mmol, 28.7 mg.
ACCEPTED MANUSCRIPT 2.3. Crystallographic characterization
The reflection data were collected on a Bruker-AXS Kappa Duo diffractometer with an APEX II CCD detector with a graphite-monochromated X-ray beam (Mo-Kα radiation = 0.71073 Å). The diffraction frames were recorded by ϕ and ω scans using APEX2 and raw dataset treatment was performed using the programs SAINT and SADABS [6]. Multi-scan absorption correction has been employed to all datasets [7].
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The structure was solved by direct methods of phase retrieval with SHELXS-2014 [8]. All full-matrix refinements were performed on F2 using SHELXL-2014 [8], accessed by WinGX [9] platform software. All non-hydrogen atoms were refined with free anisotropic displacement parameters, while the hydrogens had their displacement parameter fixed and set to isotropic. Their isotropic thermal parameters were fixed
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[Uiso(H) = 1.2Ueq(Csp2 and N) or 1.5Ueq(O)] using a riding model with fixed bond lengths of 0.93 Å for C—H (aromatic), 0.86 Å for N—H (amine) and 0.84 Å for O— H. The hydrogen positions were calculated according both intramolecular and intermolecular requirements. The ORTEP-3 [9] and Mercury [10] programs were used
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to prepare artwork representations. Zn1 and Zn2 are located over a crystallographic inversion center at (0.5, 1, 0.5) and (0.5, 0.5, 1) positions, respectively, with 50% of site occupancy factor. Crystallographic data and refinement parameters for the coordination
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compound are summarized in Table 1. The geometry of coordination (bond length and angles) is presented in Table 2, while the hydrogen bonds are grouped in Table 3. The
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crystallographic data is available in the CIF file. CCDC number is 1522493.
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2.4. Calculation of Hirshfeld surfaces
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To illustrate the intermolecular interactions found in the reported structure,
Hirshfeld surfaces were calculated for the main complex [Zn(H2O)4(ampyz)2]2+. The analysis of this surface was also done by the fingerprint plot of external distance (de) versus internal distance (di), meaning the distance between an atom to either external or internal Hirshfeld surfaces, respectively [11]. This graphical tool enables prompt investigation about the supramolecular structure through analysis of intermolecular interactions, using graphic colored as the frequency of contacts to specify properties of the surface. All graphical representations were done using Crystal Explorer 2.1 software [12].
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2.5. Infrared (IR) and UV-Vis spectroscopy
Infrared spectrum was collected on a 400FT-IR/FT-FIR spectrometer (PerkinElmer) upon the transmission mode, being averaged on 16 acquisition at resolution spectral of 4 cm-1. The sample was analyzed in the form of KBr pellets. The UV-Vis spectrum complex was collected in water solution using a Lambda 45 – UV-
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VIS spectrophotometer (PerkinElmer). The wavelength ranged from 220 to 800 nm with a fixed resolution slit of 2.0 nm.
3.1. Single crystal X-ray diffraction
The
coordination
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3. Results and Discussion
compound
has
formula
[Zn(H2O)4(ampyz)2][Zn(H2O)6](SO4)2(H2O)2 and was solved in the space group P-1. Its
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asymmetric unit contains half of two independent crystallographic Zn(II) complexes, one water molecule and a sulfate ion (Fig. 1). The mentioned complexes have formula
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[Zn(H2O)4(ampyz)2]2+ and [Zn(H2O)6]2+. Both Zn2+ ions (Zn1 and Zn2) occupy coordinates of inversion centers. The same molecular motif was already reported, however, for Co(II), Fe(II) and Mn(II) [4,5]. Therefore, this structure belongs to an
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isostructural series of complexes with transition metals containing ampyz as ligand, sulfate and an acquacomplex as counterions. The Zn:ampyz stoichiometry 1:1 was the
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same used in the preparation of the precedent isostructures [4]. The crystallographic
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data and refinement parameters are shown in Table 1.
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Figure 1. ORTEP view for asymmetric unit with 50% probability level ellipsoids for all non-hydrogen atoms. Hydrogen atoms were not labelled for clarity. Symmetry
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operation i: 1-x, 2-y, 1-z; and ii: -1-x, 1-y, 2-z.
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Table 1. Crystal data and refinement parameters for coordination compound reported here. Chemical formula
C8H34N6O20S2Zn2
Fw (g.mol-1)
729.31
1.604 -
(°)
25.358
index ranges
Triclinic
Space group
P-1
Z
1
T (K)
296(2)
Unit cell dimensions
-10 to 10
l
-15 to 15
Data collected
5921
Unique reflections
2423
0.0219
b (Å)
8.347(6)
Completeness to θmax (%)
97.4
c (Å)
13.273(9)
F(000)
376
α (°)
75.73(2)
Refined parameters
175
β (°)
78.439(18)
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6.579(4)
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78.660(18) 683.7(8)
1.771
Goodness-of-fit on F2(S)a
1.055
Final R1bfactor[ I> 2σ(I)]
0.0461
wR2c factor (all data)
0.1380
Largest diff. peak / hole (e
1.78/-0.349
Å-3)
Absorption coefficient μ (mm-1)
1.999
absorption correc. (multi-scan)
0.724/0.819
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k
a (Å)
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ρcalc (g.cm-3)
-7 to 7
Symmetry factor (Rint)
γ (°) V (Å3)
h
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Cryst syst
θ range for data collection
CCDC deposit no.
1522493
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Tmin/Tmax
Those two metal centers are six-coordinated with octahedral geometry. The
coordination set for Zn1 is defined by two nitrogens from distinct ampyz ligands and four oxygens from water molecules, while for Zn2 is defined by six oxygens from water molecules. Polyhedral representations of coordination sphere can be seen in Fig. 2.
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b) Zn2 present in the reported structure.
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Figure 2. Coordination polyhedral for crystallographic independent Zn(II), a) Zn1 and
Table 2. Bond lengths (Å) and angles (°) of Zn(II) in coordination complexes. Angle (°)
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Length (Å) 2.219(4)
O2W-Zn1-O3Wi
92.72(11)
Zn1-O2W
2.056(3)
O2Wi-Zn1-O3W
92.72(11)
Zn1-O3W
2.102 (3)
O2Wi-Zn1-O3Wi
87.28(11)
Zn2-O4W
2.081(3)
O3W-Zn1-O3Wi
180
Zn2-O5W
2.132(4)
O4W-Zn2-O4Wi
180
O4W-Zn2-O5W
93.11(14)
O4W-Zn2-O5Wi
86.89(14)
180
O4W-Zn2-O6W
89.23(12)
N1-Zn1-O2W
88.41(14)
O4W-Zn2-O6Wi
90.77(12)
N1-Zn1-O2Wi
91.44(11)
O5W-Zn-O5Wi
180
N1-Zn1-O3W
90.51(11)
O5W-Zn2-O6W
89.95(12)
N1-Zn1-O3Wi
89.49(11)
O5W-Zn2-O6Wi
90.05(12)
O2W-Zn1-O2Wi
180
O6W-Zn-O6Wi
180
O2W-Zn1-O3W
87.28(11)
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Zn1-N1
Angle (°)
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N1-Zn1-N1i
2.077(3)
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Zn2-O6W
ACCEPTED MANUSCRIPT The packing is built-up by alternated layers parallel to bc plane. One of these layers is constituted by [Zn(H2O)4(ampyz)2]2+, while the another one is assembled with [Zn(H2O)6]2+, sulfate anions and the free water molecule (O1W), as can be seen in Fig. 3a. In addition, the connection between the different layers occurs through hydrogen bonds. The geometry of hydrogen bonds found in this structure is shown in Table 3. In one layer, only classical hydrogen bonds (O—H•••O) are observed, which are connecting sulfate ions, water molecules and [Zn(H2O)6]2+ units (Fig. 3b). On the other
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hand, in the alternated layer, [Zn(H2O)4(ampyz)2]2+ units are cross linked through hydrogen bonds (O2W—H12W•••N2) and π•••π contacts (Cg1ii•••Cg1iii; Cg1 is the ampyz centroid calculated through cyclic atoms) between adjacent ampyz rings (Fig. 3c). In addition, the oxygen atom (O2) from sulfate anion acts like a bridge, connecting two units of [Zn(H2O)4(ampyz)2]2+ by means of N3-H3A•••O2, O2W-H22W•••O2 and
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O3W-H23W•••O2 interactions along the a axis (Fig. 3d). Yet, another π•••π interaction (Cg1•••Cg1i) is responsible for connecting neighboring layers of same composition (Fig. 3d). The π•••π interactions represented as Cg1•••Cg1i and Cg1ii•••Cg1iii show
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different geometric parameters, as can be seen in Table 4.
Figure 3. (a) Packing view showing the two alternated layers onto the bc plane. Intermolecular interactions onto the layers comprised by (b) sulfate anion, the acquacomplex and water molecule, involving only classical hydrogen bonds (O— H•••O), (c) [Zn(H2O)4(ampyz)2]2+ units, involving hydrogen bond (O—H•••N) and π•••π contacts. Besides, the two π•••π interactions present in this structure and the
ACCEPTED MANUSCRIPT important role of sulfate anion interlinking two units of the main complex are shown in (d). Dashed black lines represent hydrogen bonds and dashed cyan lines are π•••π interactions. Symmetry operation i: 2-x,1-y,1-z; ii: 1-x,2-y,1-z; iii: x,1+y,z.
Table 3. Hydrogen-bond geometry found in [Zn(H2O)4(ampyz)2][Zn(H2O)6](SO4)2(H2O)2 . H∙∙∙A (Å)
0.84
1.96
O1W-H21W...O4
0.99
1.73
O4W-H14W...O1W
0.85
1.92
O4W-H24W...O3
0.86
O6W-H16W...O4
0.83
O6W-H26W...O1
0.85
O5W-H15W...O3
0.83
O5W-H25W...O1W
O1W—
D—H∙∙∙A(°)
2.791(4)
169
2.714(4)
171
2.736(4)
159
1.91
2.734(4)
159
1.95
2.725(4)
154
2.00
2.813(4)
159
1.93
2.757(4)
175
0.80
2.00
2.795(4)
173
0.85
1.95
2.798(5)
175
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H11W∙∙∙O1
O2W-H12W...N2
D∙∙∙A (Å)
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D—H (Å)
D—H∙∙∙A
0.84
1.96
2.767(4)
160
O3W-H13W...O1
0.86
1.92
2.781(4)
176
O3W-H23W...O2
0.90
1.88
2.777(4)
177
N3-H3A...O2
0.86
2.18
3.031(5)
169
N3-H3B...O4W
0.86
2.62
3.357(6)
144
N3-H3B...O5W
0.86
2.52
3.279(5)
147
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O2W-H22W...O2
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Table 4. Geometrical parameters for π•••π interactions, involving Cg1•••Cg1i and Cg1ii•••Cg1iii. Distance between centroids (dcg-cg), perpendicular distance between Cg and the plane from another ring (dπ•••π), slippage (ds), dihedral angle between planes calculated through atom of Cg (??), slipping angle (?? and ??) between dcg-cg and normal (from centroid to other plane). Parameters
dπ•••π (Å)
ds (Å)
Cg1•••Cg1i
3.557(3)
3.1952(16)
1.563
Cg1ii•••Cg1iii
3.422(3)
3.3281(16)
?? (°) = ?? (°)
0.02(19)
26.1
0.795
0.02(19)
13.4
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3.2. Hirshfeld surfaces analysis
?? (°)
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dcg-cg (Å)
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Interaction
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Hirshfeld surfaces analysis provides a graphical way to interpret intermolecular interactions in crystal structures. In Fig. 4, dnorm Hirshfeld surface for the main complex
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[Zn(H2O)4(ampyz)2]2+ is shown. The color of the surface indicates closer (red) to longer (blue) contacts. Closer and longer contacts refer to interactions with distances lower and
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higher than the sum of vdW radius of the involved atoms, respectively. In our complex, closer contact areas are nearby coordinated water molecules, whose interactions were
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represented in Fig. 3c,d. Analyzing the Hirshfeld surface (Fig. 4), it is possible to observe closer contacts near O2W (region a), related to interaction with oxygen from sulfate anion (O2) and the non-coordinated nitrogen (N2) from ampyz ligand (region b). Moreover, it is also observed the interaction involving O3W (region d and e), which are related to contacts with the same oxygen from sulfate anion (O2). The primary amine (N3) also is involved in hydrogen bonds with sulfate anion (region f). Yet, the slight formation of red regions (region g) can also be noted above the center of aromatic rings. This indicates the presence of π•••π contacts discussed before. Therefore, many regions committed to strong interactions are observed in this Hirshfeld surface, which
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crystal structure packing.
Figure 4. Hirshfeld surface (dnorm mapped) for main complex [Zn(H2O)4(ampyz)2]2+.
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The regions of closer contacts were labeled as a-f.
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Two dimensional plot grids were calculated using the internal and external distance (di and de) for each point on the Hirshfeld surface, as can be seen in Fig. 5. The
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plots were obtained to the total contribution of interactions (Fig. 5a) and for individuals (Fig. 5b-f). The ligands present in the main complex (ampyz and water) enable many strong intermolecular contacts, as hydrogen bonds. As result, in the fingerprints, we see
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two long sharp spikes pointing to the bottom left (minor distances) of the plot, mainly due to the contacts O•••H and N•••H (contribution sum of 39.9%). The most abundant interactions (H•••H) are located on the center of the graphical plot with a wide range of distances (1.0 to 2.3 Å), which are known to have large contribution in many compounds [12]. As mentioned, C•••C can be seen in this structure through π•••π involving the parallel offset ampyz rings, whose distance (~ 1.8 Å) is close to vdW radius of carbon atom. Moreover, C•••H interaction has a small contribution in the
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top (di < de) and bottom (de < di), indicating the presence of C-H•••π interactions.
Figure 5. Fingerprint of Hirshfeld surface (0.4 to 2.6 Å) and the contribution of each
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type of interaction (in %) for [Zn(H2O)4(ampyz)2]2+, showing (a) total interactions, (b) H•••H, (c) O•••H, (d) N•••H, (e) C•••C and (f) C•••H. The gradient color from blue
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(few) to red (many) indicates to contribution of the point to the global Hirshfeld surface. The gray shadow (b-f) is the outline of full fingerprint. di and de are the internal and
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external distance from a point to the surface, respectively.
Besides, the Hirshfeld surfaces mapped over shape index (Fig. 6a) and
curvedness (Fig. 6b) were performed. Both surfaces revealed π•••π contacts. In the shape index surface, blue and red triangles over the ampyz aromatic rings indicated the presence of π•••π interactions. Likewise, in the curvedness surface, the π•••π contacts are notable due to the presence of flat regions on aromatic rings.
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Figure 6. Hirshfeld surface mapped over (a) shape index and (b) curvedness for the
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main complex [Zn(H2O)4(ampyz)2]2+.
3.3. Infrared (IR) and UV-Vis spectroscopy
The IR spectrum of the Zn(II) complex (Fig. 7) shows the presence of ampyz
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ligand due to five peaks. The two high intensity sharp peaks at 3465 and 3311 cm-1 refer to the primary amine [ʋ(N−H)]. The broad signal of water (ʋ(O−H)) at approximately
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3500 cm-1 was slightly suppressed by the peaks of primary amine. Meanwhile, the heterocyclic aromatic ring can be also characterized by the presence of two high intense sharp peaks at 1630 [ʋ(C=N)Ar] and 1530 cm−1 [ʋ(C=C)Ar]. The presence of sulfate
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[ʋ(S−O)].
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anion can be attributed to the high intensity peaks at 1112 cm−1 [ʋ(S=O)] and 622 cm−1
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Figure 7. IR spectrum of the Zn complex.
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The UV-vis spectrum of Zn complex was prepared in water and no absorption bands were observed in the visible region, since Zn(II) doesn't show any d-d transitions.
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The spectrum (Fig. 8) presents only two broad absorption bands, centered at 315 and 285 nm. The strongest bands for this complex can be attributed to metal to ligand
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charge transfer (MLCT) and ligand to metal charge transfer (LMCT).
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Figure 8. UV-Vis spectrum of Zn complex in water.
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4. Conclusion
and
UV-Vis
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In this study, we report the synthesis, single crystal X-Ray diffraction and IR spectral
data
of
the
coordination
compound
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[Zn(H2O)4(ampyz)2][Zn(H2O)6](SO4)2(H2O)2 and the Hirshfeld surface analysis of the main complex [Zn(H2O)4(ampyz)2]2+. The crystal structure revealed a packing made
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with alternate layers, which are constituted with only one type of the two Zn(II) complexes. The formation of these layers was possible due to π•••π and many hydrogen
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bonding interactions. The analysis of intermolecular interactions through Hirshfeld surfaces and their fingerprints illustrate the contribution of such contacts. The presence of strong hydrogen bond is seen in the formation of sharp spikes at left side of 2D plot grid of de versus di. Also, in this graphic, it is noted the common π•••π interactions between parallel ampyz rings. This complex contributes to increase a series of isostructural coordination compounds containing ampyz and water as ligands and the acquacomplex of same metal, sulfate anion as counterion and one lattice water molecule. This expands our structural knowledge related to physicochemical properties of the isostructural series.
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Acknowledgment The authors acknowledge CNPq and CAPES for financial support and for research fellowships (AKV and FTM).
[1]
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