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Article

Synthesis, Molecular and Supramolecular Structures of Symmetric Dinuclear Cd(II) Azido Complex with bis-Pyrazolyl s-Triazine Pincer Ligand

by
Kholood A. Dahlous
1,
Saied M. Soliman
2,*,
Ayman El-Faham
2 and
Raghdaa A. Massoud
2
1
Department of Chemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
2
Department of Chemistry, Faculty of Science, Alexandria University, Ibrahimia, P.O. Box 426, Alexandria 21321, Egypt
*
Author to whom correspondence should be addressed.
Symmetry 2022, 14(11), 2409; https://doi.org/10.3390/sym14112409
Submission received: 31 October 2022 / Revised: 9 November 2022 / Accepted: 10 November 2022 / Published: 14 November 2022

Abstract

:
A new dinuclear Cd(II)-azido complex of 2,4-bis(3,5-dimethyl-1H-pyrazol-1-yl)-6-methoxy-1,3,5-triazine (PMT) pincer ligand is synthesized. Its single crystal X-ray structure reveals the dinuclear [Cd(PMT)(Cl)(N3)]2 formula. The triclinic crystal parameters are a = 9.323(4) Å, b = 10.936(5) Å, c = 11.312(6) Å, α = 112.637(10)°, β = 104.547(11)° and γ = 105.133(10)° while V = 944.1(8) Å3. Due to symmetry considerations, the asymmetric unit comprises a half [Cd(PMT)(Cl)(N3)]2 formula. The Cd(II) is hexa-coordinated with one tridentate PMT ligand in a pincer fashion mode in addition to one terminal chloride and two azide ions bridging the two Cd(II) centers in double μ(1,1) bridging mode. Unusually, the Cd-N(s-triazine) bond is not the shortest among the Cd-N interactions with the PMT pincer ligand. The supramolecular structure of the dinuclear [Cd(PMT)(Cl)(N3)]2 formula is controlled by a significant amount of Cl…H (16.4%), N…H (25.3%), H…C (9.8%) and H…H (37.2%) interactions based on Hirshfeld surface analysis. Careful inspection of the shape index map reveals the presence of some weak π-π stacking interactions between the s-triazine and pyrazolyl moieties. The percentage of C…C contacts is 1.9% where the C2…C8 (3.462 Å) is the shortest while the centroid–centroid distance is 3.686 Å. Natural charge analysis describes the charge transferences from the ligand groups to the Cd(II), while and atoms in molecules (AIM) give an indication on the properties of the Cd-N and Cd-Cl bonds.

1. Introduction

The chemistry of coordination compounds has attracted much interest from researchers, who have explored the application of these compounds in different areas [1,2,3,4,5,6]. Coordination compounds have been used for many applications such as drug delivery, gas storage, catalysis, and in separation techniques [7,8]. The structural features of coordination compounds depend on different factors such as metal ion nature, ligand coordination behavior, and the nature of donor atoms [9,10]. In addition, the presence of a linker could help the molecular aggregation of small complex fragments leading to polynuclear complexes that could be used in different applications including device fabrication [11,12], molecular sensing [7,13,14,15,16], and opto-electronic devices [17,18,19,20]. These complexes also have interesting magnetic applications [21].
In light of the importance of a bridging ligand in the construction of polynuclear coordination compounds, researchers have especially been attracted to the azide ion [22,23,24,25,26,27,28]. This simple small-size linear linker could aggregate different metal sites via diverse coordination modes of bonding. A schematic presentation for the azide bonding modes is presented in Scheme 1. The most common bonding modes are the end-on (μ(1,1) or EO) and end-to-end (μ(1,3) or EE) [21,22,23]. With the aid of this fascinating bridging ligand, many fascinating complexes with different nuclearity have been constructed [22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40].
In the last couple of years, our research group has focused on the study of the coordination chemistry of s-triazine-type ligands [41,42,43,44,45,46]. Among these ligands, 2,4-bis(3,5-dimethyl-1H-pyrazol-1-yl)-6-methoxy-1,3,5-triazine (PMT, Figure 1) is the most attractive due to its ease of preparation with high yield, in addition to its diverse coordination behavior with different metal ions as well as the interesting biological activities of the synthesized complexes compared with the free ligand. The most common coordination behavior for this ligand is the tridentate pincer mode of bonding via three interactions with the s-triazine core and the two pyrazolyl arms. The reaction of PMT with different metal(II) salts has afforded the corresponding mononuclear complexes [41,42,43]. Only in the case of CuCl2 and Cu(ClO4)2, hydrolysis of the PMT ligand has occurred and 1D coordination polymers have been isolated [44]. The reaction of PMT with trivalent metal ion (Fe(III)) has also proceeded with hydrolysis affording the mononuclear [45] and µ-oxo binuclear [46] complexes depending on the nature of the anion. In this work, we tested the reaction of the PMT ligand with CdCl2 in the presence of azide as an auxiliary linker ligand. The newly synthesized complex was characterized by elemental analysis and FTIR, and unambiguously determined by single-crystal X-ray diffraction. Its molecular and supramolecular structure aspects are also presented.

2. Materials and Methods

2.1. Synthesis of [Cd(PMT)(Cl)(N3)]2

The new dinuclear Cd(II) complex was synthesized by mixing a 10 mL methanolic solution of PMT (30.0 mg, 0.01 mmol) with CdCl2 (18.3 mg, 0.01 mmol) in 5 mL distilled water followed by the addition of 1 mL of NaN3 aqueous solution. The Cd(II) azido complex was obtained as pure colorless crystals after 6 days of slow evaporation, and these were harvested by filtration.
Yield; C28H34Cd2Cl2N20O2 (1): (89.3%). Anal. Calc. C, 34.37; H, 3.50; N, 28.63; Cl, 7.25; Cd, 22.98%. Found: C, 34.14; H, 3.42; N, 28.47; Cl, 7.19; Cd, 22.86%. IR (KBr, cm−1): 3115, 3022, 2959, 2047, 1596, 1572, 1538, 1471; Figure S1, (Supplementary data).

2.2. Physicochemical Characterizations

All instrumental and chemicals used as well as the X-ray measurements including data collection and structure solution details are described in Supplementary data [47,48,49].

2.3. Computational Details

All details regarding Hirshfeld [50] and DFT [51,52,53,54,55,56,57] calculations are described in Supplementary data.

3. Results and Discussion

3.1. Chemistry

In our previous studies, the reaction of PMT with different CdX2 salts (X=Cl, NO3 or ClO4) afforded the mononuclear [Cd(PMT)Cl2], [Cd(PMT)(H2O)(NO3)2] and [Cd(PMT)2](ClO4)2 complexes, respectively (Scheme 2) [42,58]. The reaction of the same ligand with CdCl2 in the presence of sodium azide afforded the dinuclear [Cd(PMT)(Cl)(N3)]2 complex in good yields. In the FTIR spectra of the dinuclear [Cd(PMT)(Cl)(N3)]2 complex, a sharp band was detected at 2047 cm−1 corresponding to the stretching mode of the azide ion. The ν(C=N) and ν(C=C) vibrational bands were detected at 1596–1572 cm−1 and 1538 cm−1, respectively, while the free ligands were detected at 1593 cm−1 and 1555 cm−1, respectively. It is clear that the complexation affected both stretching modes compared with the free PMT ligand.

3.2. Crystal Structure Description

The crystal structure of the [Cd(PMT)(Cl)(N3)]2 complex is shown in Figure 2 while the crystallographic data are depicted in Table 1. The structure of the dinuclear [Cd(PMT)(Cl)(N3)]2 complex is crystallized in the triclinic space group P-1. The unit cell parameters are a = 9.323(4) Å, b = 10.936(5) Å, c = 11.312(6) Å, α = 112.637(10)°, β = 104.547(11)° and γ = 105.133(10)° while the unit cell volume is 944.1(8) Å3. The asymmetric unit consists of a half molecule of the previously mentioned formula.
In this complex, both Cd(II) ions are hexa-coordinated with the same coordination environment due to symmetry considerations. Each of the Cd(II) is coordinated with one tridentate PMT ligand in a pincer mode. The three Cd-N distances are not equidistant (Table 2). The metal-to-nitrogen distances in the mononuclear complexes of the same ligand follow the order M-N(s-triazine) < M-N(pyrazole) [42,58]. In the current case, this habit is violated. The Cd1-N1 bond with the s-triazine core is not the shortest (2.412(2) Å). The Cd1-N4 bond (2.408(2) Å) is also shorter, while the Cd1-N6 bond (2.452(2) Å) is longer than the Cd1-N1 bond. The bite angles of the PMT tridentate chelate are 64.57(7)° and 65.67(7)° for the N1-Cd1-N6 and N4-Cd1-N1, respectively. The coordination environment of the Cd(II) is completed by two interactions with one terminally coordinated chloride ion and two μ(1,1) bridged azides. The Cd1-Cl1, Cd1-N8 and Cd1-N8i distances are 2.4704(13), 2.317(2) and 2.416(3) Å, respectively. The N4-Cd1-N6 (130.17(7)°), N8-Cd1-Cl1 (168.57(6)°) and N8-Cd1-N1i (154.37(8)°) deviate significantly from the ideal value of 180°. Similarly, the cis bond angles are far from 90°. Hence, the CdN5Cl coordination environment has a distorted octahedral geometry.
In the studied crystal, classical hydrogen-bonding interactions are not detected. The molecular packing is controlled by C-H…N interactions between the C12-H12C as a hydrogen bond donor and the freely un-coordinated nitrogen atom (N10) of the azide as a hydrogen bond acceptor (Figure 3). The hydrogen-acceptor and donor-acceptor distances are 2.61 Å and 3.549(5) Å, respectively, while the C12-H12C…N10 angle is 167°. A view of the packing for the complex units along the crystallographic a-direction is shown in Figure 4.
In addition, the [Cd(PMT)(Cl)(N3)]2 complex units are stacked together via some π-π stacking interactions between the aromatic s-triazine and pyrazole rings, respectively. The shortest C…C contact is C2…C8, where the interaction distance is 3.462(6) Å and the distance between the two ring centroids is 3.686 Å. A presentation of the π-π contacts and the π-π stacking scheme is shown in Figure 5.

3.3. Analysis of Molecular Packing

The supramolecular structure in crystalline materials depends on a number of interactions such as hydrogen bonding, π-π stacking, C-H…π, etc., which hold the molecules in a specific arrangement and keep the crystal’s stability. In this regard, the possible atom…atom contacts in the crystal structure of the dinuclear Cd(II) complex are analyzed based on Hirshfeld calculations (Figure 6).
As clearly seen from Figure 6, there are many red spots appearing in the dnorm map related to regions at which there are short contacts between the atoms inside the surface and the neighboring complex molecules outside the surface. The short contacts detected in the studied system are the Cl…H, N…H, H…C and H…H interactions. Their percentages are calculated, based on the decomposition of the fingerprint plots, to be 16.4, 25.3, 9.8 and 37.2%, respectively (Figure 7). These contacts represent the most dominant interactions in the studied system. There are many other contacts shown in Figure 7, which not only have low percentages but also appear as blue regions in the dnorm map, indicating longer interaction distances than the vdWs radii sum of the atoms included in such interactions.
Analysis of the close contact distances is performed, and the shortest interaction distances of the Cl…H, N…H, H…C and H…H contacts are depicted in Table 3. The Cl1…H14A (2.769 Å), N9…H12C (2.604 Å), N10…H12C (2.487 Å), C5…H11B (2.656 Å), and H13A…H13C (2.515 Å) are the shortest contacts observed in the studied system. In the corresponding decomposed fingerprint plots of the Cl…H, N…H and H…C contacts, the pattern of the fingerprint plot of these interactions appeared as sharp spikes, which further reveal short-distance interaction (Figure 8).
Additionally, careful inspection of the shape index map indicates the presence of red and blue triangles. A flat green surface is also found close to the same region at the curvedness map. For better clarity, the regions at which the C…C contacts occur are manifested by the black arrow in the shape index map in Figure 6. All these features leave no doubt about the presence of some π-π stacking interactions, which agree with the X-ray structure analysis. The relatively short C2…C8 (3.462 Å) contact between the s-triazine moiety and the pyrazolyl moiety is clearly evident. The percentage of the C…C contacts detected in the dinuclear Cd(II) complex is only 1.9% of the whole contacts.

3.4. Natural Charge Distribution

In this highly symmetric dinuclear complex, there are two identical [Cd(PMT)(Cl)(N3)] units, which are related by an inversion center located at the center of the (Cd1N8)2 four-membered ring. Hence, the natural charge populations are identical for the two halves. The charge at the Cd(II) ion is decreased to 1.018 e instead of +2.000 e. The decrease in the charge of Cd(II) is a consequence of the electron density transfer from the ligand group to the divalent ion. As clearly seen, the chloride and azide ions have natural charges of −0.651 and −0.668 e, respectively, instead of −1.000 e for both anions. However, the net charge of the pincer ligand is 0.305 e instead of 0.000 e for this neutral ligand. In this regard, the amounts of electrons transferred from these ligand’s groups to the Cd(II) are 0.349, 0.332 and 0.301 e, respectively. Hence, the net electron density transferred from the ligand groups is 0.982 e, which compensates the charge of the divalent cadmium ion to be 1.018 e instead of +2.000.

3.5. The Atoms in Molecules (AIM) Study

The concept of AIM [59,60,61,62,63,64] and their corresponding parameters provide good information about the nature and strength of interactions based on the electron-density analysis at the bond critical point. In this regard, the AIM parameters are employed to describe the nature and strength of the Cd-N and Cd-Cl interactions. The different AIM parameters are listed in Table 4. Based on the electron density function (ρ) depicted in this table, it is clear that the high ρ values are related to shorter bonds, which are found to be in good agreement with the order of the bond strength. Hence, there is an inverse relation between the bond distances and ρ (Figure 9). The straight line relation shows a high correlation coefficient between the two parameters (R2 = 0.9805). Based on AIM theory, the covalent bond has ∇2ρ < 0 while other closed-shell interactions have ∇2ρ > 0 [56]. In addition, negative H(r) and |V(r)|/G(r) > 1 indicate covalent bonding, while positive H(r) and |V(r)|/G(r) < 1 indicate predominantly closed-shell interactions. Typical covalent bonds have |V(r)|/G(r) > 2 [65,66]. The small electron density (ρ < 0.1 a.u) and the positive laplacian (∇2ρ) also indicate that the Cd-Cl and Cd-N bonds have a predominant closed-shell character. Additionally, the total energy density (H(r)) has marginally negative values and the V(r)/G(r) ratios are also marginally higher than 1, indicating low covalent characters for the Cd-N and Cd-Cl bonds.

4. Conclusions

A new dinuclear [Cd(PMT)(Cl)(N3)]2 complex of a bis-pyrazolyl-s-triazine-type ligand was synthesized and characterized with the aid of elemental analysis, FTIR, and single-crystal X-ray diffraction. The X-ray structure analysis revealed that the PMT ligand is acting as a pincer tridentate N-chelate. However, the chloride ion is a terminal monodentate ligand while the azide ion has a μ(1,1) bridging mode connecting the two Cd(II) ions. The Cd(II) is hexa-coordinated with CdN5Cl coordination environment. The crystal stability depends on a number of non-covalent interactions that connect the molecules together in the solid state in a specific pattern. Analysis of the crystal structure with the aid of Hirshfeld calculations revealed the importance of the Cl…H, N…H, H…C, H…H and C…C contacts in the molecular packing. Fingerprint plot decomposition predicted the percentages of these contacts to be 16.4, 25.3, 9.8, 37.2 and 1.9%, respectively. The presence of a flat green area in curvedness and red/blue triangles in shape index confirmed the importance of π-π stacking interactions in the molecular packing. Based on charge calculations, the net electron density transferred from the ligand groups to Cd(II) is 0.982 e. In addition, the Cd-Cl and Cd-N bonds have predominant closed-shell characters.

Supplementary Materials

The following supporting information can be downloaded at: https://www.mdpi.com/article/10.3390/sym14112409/s1, Figure S1. FTIR spectra of the dinuclear [Cd(PMT)(Cl)(N3)]2 complex; Physicochemical characterizations; Synthesis of PMT; X-ray measurements and Computational details.

Author Contributions

Conceptualization, S.M.S., A.E.-F. and R.A.M.; methodology, R.A.M. and S.M.S.; software, R.A.M. and S.M.S.; validation, R.A.M., A.E.-F., K.A.D. and S.M.S.; formal analysis, R.A.M., A.E.-F., K.A.D. and S.M.S.; investigation, R.A.M. and S.M.S.; resources, R.A.M., A.E.-F., K.A.D. and S.M.S.; data curation, R.A.M., A.E.-F. and S.M.S.; writing—original draft preparation, R.A.M., A.E.-F. and S.M.S.; writing—review and editing, R.A.M., A.E.-F., K.A.D. and S.M.S.; visualization, R.A.M. and S.M.S.; supervision, R.A.M. and S.M.S.; project administration, R.A.M., A.E.-F., K.A.D. and S.M.S.; funding acquisition, A.E.-F., K.A.D. and S.M.S. All authors have read and agreed to the published version of the manuscript.

Funding

This project was funded by the Researchers Supporting Project number [RSP-2021/388], King Saud University, Riyadh, Saudi Arabia.

Data Availability Statement

Not applicable.

Acknowledgments

This project was funded by the Researchers Supporting Project number [RSP-2021/388], King Saud University, Riyadh, Saudi Arabia.

Conflicts of Interest

The authors declare no conflict of interest.

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Scheme 1. Different bonding modes of the azide ion.
Scheme 1. Different bonding modes of the azide ion.
Symmetry 14 02409 sch001
Figure 1. Structure of the PMT ligand.
Figure 1. Structure of the PMT ligand.
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Scheme 2. Synthesis of different Cd(II) complexes with different anions.
Scheme 2. Synthesis of different Cd(II) complexes with different anions.
Symmetry 14 02409 sch002
Figure 2. The X-ray structure of [Cd(PMT)(Cl)(N3)]2 complex. Symmetry code: i -x,-y,-z.
Figure 2. The X-ray structure of [Cd(PMT)(Cl)(N3)]2 complex. Symmetry code: i -x,-y,-z.
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Figure 3. The hydrogen bond contacts in [Cd(PMT)(Cl)(N3)]2 complex.
Figure 3. The hydrogen bond contacts in [Cd(PMT)(Cl)(N3)]2 complex.
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Figure 4. The packing scheme of the [Cd(PMT)(Cl)(N3)]2 complex units via non classical C-H…N interactions along bc plane.
Figure 4. The packing scheme of the [Cd(PMT)(Cl)(N3)]2 complex units via non classical C-H…N interactions along bc plane.
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Figure 5. The possible π-π interactions in the [Cd(PMT)(Cl)(N3)]2 complex.
Figure 5. The possible π-π interactions in the [Cd(PMT)(Cl)(N3)]2 complex.
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Figure 6. Hirshfeld surfaces for the Cd(II) complex. A, B, C and D refer to the Cl…H, C…H, N…H and H…H contacts, respectively.
Figure 6. Hirshfeld surfaces for the Cd(II) complex. A, B, C and D refer to the Cl…H, C…H, N…H and H…H contacts, respectively.
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Figure 7. Summary of the intermolecular interactions and their percentages.
Figure 7. Summary of the intermolecular interactions and their percentages.
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Figure 8. Decomposed fingerprint plots for the important interactions in the Cd(II) complex.
Figure 8. Decomposed fingerprint plots for the important interactions in the Cd(II) complex.
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Figure 9. Correlation between the ρ and Cd-N bond distances.
Figure 9. Correlation between the ρ and Cd-N bond distances.
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Table 1. Crystallographic data for [Cd(PMT)(Cl)(N3)]2 complex.
Table 1. Crystallographic data for [Cd(PMT)(Cl)(N3)]2 complex.
CCDC2212588
FormulaC28H34Cd2Cl2N20O2
F.Wt978.45 g/mol
T293(2) K
Λ0.71073 Å
Crystal systemTriclinic
Space groupP-1
Unit cell dimensionsa = 9.323(4) Åα = 112.637(10)°
b = 10.936(5) Åβ = 104.547(11)°
c = 11.312(6) Åγ = 105.133(10)°
V944.1(8) Å3
Z1
D(calc.)1.721 g/cm3
Absorption coefficient1.326 mm−1
F(000)488
θ-range2.20 to 30.57°
Index ranges−13 ≤ h ≤ 13, −15 ≤ k ≤ 15, −16 ≤ l ≤ 16
Reflections collected40,395
Independent reflections5760 [R(int) = 0.0345]
Completeness to θ = 25.35°99.10%
Refinement methodFull-matrix least-squares on F2
Data/restraints/parameters5760/0/249
Goodness-of-fit on F21.175
Final R indices [I > 2sigma(I)]R1 = 0.0321, wR2 = 0.0685
R indices (all data)R1 = 0.0405, wR2 = 0.0752
Largest diff. peak and hole1.169 and −0.911
Table 2. The most important bond distances and angles in [Cd(PMT)(Cl)(N3)]2 complex.
Table 2. The most important bond distances and angles in [Cd(PMT)(Cl)(N3)]2 complex.
BondDistanceBondDistance
Cd1-N82.317(2)Cd1-N8i2.416(3)
Cd1-N42.408(2)Cd1-N62.452(2)
Cd1-N12.412(2)Cd1-Cl12.4704(13)
BondsAngleBondsAngle
N8-Cd1-N4i109.04(9)N1-Cd1-N664.57(7)
N8-Cd1-N1i154.37(8)N8-Cd1-N684.57(9)
N4-Cd1-N165.67(7)N8i -Cd1-Cl195.60(8)
N8-Cd1-N8i73.38(11)N4-Cd1-Cl195.93(6)
N4-Cd1-N890.66(9)N1-Cd1-Cl1109.74(5)
N1-Cd1-N881.49(8)N8-Cd1-Cl1168.57(6)
N8i -Cd1-N6116.73(9)N6-Cd1-Cl198.14(6)
N4-Cd1-N6130.17(7)
i -x,-y,-z.
Table 3. The short intermolecular contacts in the dinuclear [Cd(PMT)(Cl)(N3)]2 formula.
Table 3. The short intermolecular contacts in the dinuclear [Cd(PMT)(Cl)(N3)]2 formula.
ContactDistance
Cl1…H14A2.769
N9…H12C2.604
N10…H12C2.487
C5…H11B2.656
H13A…H13C2.515
C2…C83.462
Table 4. AIM topology parameters (a.u.) at bond critical points (BCPs) as well as the bond distances (BD) of the coordinated bonds in [Cd(PMT)(Cl)(N3)]2 complex.
Table 4. AIM topology parameters (a.u.) at bond critical points (BCPs) as well as the bond distances (BD) of the coordinated bonds in [Cd(PMT)(Cl)(N3)]2 complex.
Atoms BDρG(r) aV(r) bH(r)2ρ|V(r)|/G(r)
Cd1-N82.3170.05340.0700−0.0763−0.00630.25501.090
Cd1-N12.4120.03690.0579−0.0584−0.00050.23001.009
Cd1-N42.4080.03820.0579−0.0594−0.00150.22501.026
Cd1-N62.4520.03350.0505−0.0507−0.00020.20101.004
Cd1-N8i2.4160.03830.0567−0.0587−0.00200.21901.035
Cd1-Cl12.4700.04790.0707−0.0773−0.00660.25701.093
a V(r) is the potential energy densities and b G(r) is the kinetic energy densities.
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Dahlous, K.A.; Soliman, S.M.; El-Faham, A.; Massoud, R.A. Synthesis, Molecular and Supramolecular Structures of Symmetric Dinuclear Cd(II) Azido Complex with bis-Pyrazolyl s-Triazine Pincer Ligand. Symmetry 2022, 14, 2409. https://doi.org/10.3390/sym14112409

AMA Style

Dahlous KA, Soliman SM, El-Faham A, Massoud RA. Synthesis, Molecular and Supramolecular Structures of Symmetric Dinuclear Cd(II) Azido Complex with bis-Pyrazolyl s-Triazine Pincer Ligand. Symmetry. 2022; 14(11):2409. https://doi.org/10.3390/sym14112409

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Dahlous, Kholood A., Saied M. Soliman, Ayman El-Faham, and Raghdaa A. Massoud. 2022. "Synthesis, Molecular and Supramolecular Structures of Symmetric Dinuclear Cd(II) Azido Complex with bis-Pyrazolyl s-Triazine Pincer Ligand" Symmetry 14, no. 11: 2409. https://doi.org/10.3390/sym14112409

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