Cadmium(II) dimer complex of type  [Cd2(phen)2Cl4] was made available in a high yield, the structure of the dimer was solved by XRD then optimized via density functional theory (DFT) and  Hirschfield computed methods. The structure parameters like: angles and bonds lengths were compared to their DFT-relatives, Hirschfield surface analysis (HAS), molecular electrostatic potential (MEP) and Mulliken charge populations were also matched to the XRD-packing collected result. The dimer was crystallized in the Triclinic/P-1 system with Z = 4. The two Cd(II) centers in the dimer found to be with a distorted square-pyramidal geometry. Crystallographic data for desired dimer was deposited to the Cambridge Crystallographic Center under CCDC No. 1911235

N. K. Lokanath, I. Warad, S. Amereih, A. Al Ali, A. Zarrouk, A. Chetouni, K. Kumara,

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Revues Scientifiques Marocaines

MoroccanJournal of Chemistry ISSN: 2351-812X http://revues.imist.ma/?journal=morjchem&page=login Amereih & al. / Mor. J. Chem. 7 N°2 (2019) 392-400   Mor. J. Chem. 7 N°2 (2019) 392-400 392   Synthesis, XRD, DFT-optimization, MEP and Hirshfeld surface analysis of di-μ-Chloro-bis[chloro(1,10-phenanthroline)Cd(II)dimer  Sameer Amereih1, Anas Al Ali2, Abdelkader Zarrouk3, Ahmed Chetouni4, Karthik Kumara5, Neartur K. Lokanath5, Ismail Warad2,*   1Department of Chemistry, Science College, Palestine Technical University, P.O. Box 7, Tulkarm, Palestine 2Department of Chemistry, An-Najah National University P.O. Box 7, Nablus, Palestine Laboratory of Materials, 3Nanotechnology and Environment, Mohammed V University, Faculty of Science, 4Av. Ibn Battuta, B.P. 1014 Rabat, Morocco 4Laboratoire de Chimie Analytique Appliquée, Matériaux et Environnement (LC2AME), Faculté des Sciences, Université Mohamed I, 60 000 Oujda, Morocco 5Department of Studies in Physics, University of Mysore, Manasagangotri, Mysuru, 570 006, India      * Corresponding Author: Tel.: +972-9234-5982 E-mail: warad@najah.edu Received 24 Jan  2019, Revised 23 April 2019, Accepted  16 June 2019 Abstract Cadmium(II) dimer complex of type[Cd2(phen)2Cl4]was made available in a high yield, the structure of the dimer was solved by XRD then optimized via density functional theory (DFT) and  Hirschfield computed methods.The structure parameters like: angles and bonds lengths were compared to their DFT-relatives, Hirschfield surface analysis (HAS), molecular electrostatic potential (MEP)and Mulliken charge populations were also matched to the XRD-packing collected result. The dimer wascrystallized in the Triclinic/P-1 system with Z = 4. The two Cd(II) centers in the dimer found to be with a distorted square-pyramidalgeometry. Crystallographic data for desired dimerwas deposited to the Cambridge Crystallographic Center under CCDC No. 1911235.    Keywords: Cd(II) dimer, XRD, DFT, HSA.            Mor. J. Chem. 7 N°2 (2019) 392-400 393 1. Introduction 1,10-Phenanthrolines as bidentate N-ligands are well-known metal ions coordinators [1-6]. Its complexing ability was used to establish metalloenzymes biomimetic for supramolecules self-assembling processes[4]. The M/phenDNA-complex base pairs binding ability were currently develops to be used as chemotherapy agents [7]. Cd(II)  is not common used as in metalloenzymes and metalloproteins ion like Zn(II) for example. For long Cd(II) was thought as a highly toxic ion and was often correlated with lead and mercury and as harmful biological ions [5-11]. Currently, interest in the metal ionscomplexes coordination chemistry was increased due to their biological recognition role [9], and structural rich materials [11-16].The metalscoordination behaviors have played a critical role in developing of inorganic material and enhancing their biologically activities [17, 18]. The presence of nitrogen, sulfur, phosphorus and oxygen donors in such complexes reflects high anticancer and antibacterial activities [19]. 1,10-Phen and its derivative can coordinate Cd(II) to formviabis-phendimer or mono-phensimple complexes [13-16]. Cd(II)/phen complexes were broadly reported as bioactivities hybrid material like, antibacterial, DNA binding and antitumor activities [6], Cd(II) ions complexes enhance their anticancer activities since it possessed via low cytotoxic behaviors [20]. Previously, we reported two newCd(II) neutral dimers of [Cd2(dmdphphen)X4] formula was synthesized and characterized by different spectroscopic methods[1-2].In this work we have prepared the Cd2(dmdphphen)Cl4dimer, the structure of the desired dimer was proved by XRD and optimized viadensity functional theory (DFT) and  Hirschfield surface analysis (HSA) methods.  2. Methodology 2.1. Chemicals  CdCl2.2.5H2O and 2,9-dimethyl-4,7-diphenyl-1,10-phenanthroline ligand, were purchased from Fluka.  2.2. Crystallography  A colorlessblock single suitable crystal of D 0.22×0.25×0.26 mm of the desired dimer wasselected for the XRD-diffraction studies. The X-ray data was performed on a BrukerProteum2 CCD diffractometer equipped with an X-ray generator operating at 10 mA and45 kV, using Cu-Kα radiation source of wavelength 1.54178 Å [21-22].  2.3. Theoretical calculations The theoretical calculations in this work are described in previous publications [23].The structure optimized and other physical calculations of the dimer were performed via DFT/B3LYP/6-31+G(2d,p) using Gaussian 09 [24] andHAS calculations were performed via CRYSTAL EXPLORER 3.1 program[25].  3.Results and discussion 3.1. Synthesis of the desired dimer  Treating of phen with CdCl2 hydrated salt in CH2Cl2/EtOH solvents revealed the formation of [CdCl2(phen)]2 dimer in good yield, as seen in Scheme 1. The dimer was XRD characterized and DFT-optimized. Moreover, the conductivity and the solubility reflected the dimer as non-electrolytic complex in its nature.   Scheme 1. Dimer synthesis.  Mor. J. Chem. 7 N°2 (2019) 392-400 394  3.2. X-Ray Crystal structure The structure of the desired dimer (Fig. 1a) consists with [Cd2Cl4(dmdphphen)2] formation, where 2Cl atoms form bridge to Cd(II) center. The 2Cl atoms and the bidentate chelating phen ligands coordinated neutrally the center. The coordination mode around both Cd(II) centers is slightly distorted square-pyramidal geometry. The dimer was crystallized with triclinic system and P-1 space group and Z= 4 as seen in the packing figure (Fig. 1b).   Fig.1. (a)ORTEP and (b) packing system of the desired dimer.  3.3.Structure optimizations  The structure of the desired dimer was subjected to B3LYP/6-311G (d,p) optimization  (Fig.2a). The structural parameters such as angles and bond lengths were matched to their XRD-experimental relatives. A high degree of matching between theoretical and calculated bond length with 0.985 correlation coefficient was collected as in Fig.2b, and Table 1. Similarly, 0.999 correlation coefficient was recorded by comparing experimental/calculated angles (Fig.2c, and Table 1).  Fig.2. (a) Dimer optimized structure B3LYP/6-311G(d), (b) DFT/XRD bond lengths graphical correlation, and (e) DFT/XRD angles graphical correlation.  Mor. J. Chem. 7 N°2 (2019) 392-400 395  Table 1.Selected XRD/DFT angles (o) and bond lengths (Å). Bond No. Bonds Exp. XRD DFT Angles No. Angles (o) Exp. XRD DFT 1 Cd1 Cl31 2.578 2.4187 1 Cl31 Cd1 N2 144.1 144.1 2 Cd1 N2 2.354 2.354 2 Cl31 Cd1 N3 86.74 86.74 3 Cd1 N3 2.354 2.3541 3 Cl31 Cd1 Cl30 118.33 118.33 4 Cd1 Cl30 2.419 2.578 4 Cl31 Cd1 Cl31 81.12 81.12 5 Cd1 Cl31 2.573 2.5728 5 N2 Cd1 N3 70.1 70.13 6 Cl31 Cd1 2.573 2.5728 6 N2 Cd1 Cl30 109.83 109.83 7 C15 C14 1.5 1.4995 7 N2 Cd1 Cl31 92.72 92.72 8 N2 C16 1.359 1.3594 8 N3 Cd1 Cl30 105.4 105.4 9 N2 C14 1.333 1.3332 9 N3 Cd1 Cl31 130.61 130.61 10 C6 C7 1.37 1.3705 10 Cl30 Cd1 Cl31 110.12 110.12   3.4. Crystal interactions, HAS and 2D Fingerprint (FP) Many shorter interactions (<3 Å) were recorded in the crystal lattice of solved XRD experimental structure, since three heteroatoms 2Cd, 6Cl, 4N and several polar H atoms detected in the dimer formula, therefore, 4 shorter H-bonds as H…..Cl = 2.871 Å connected molecule with its neighbors strongly as illustrated inFig.3a. Moreover, 4 H….ph stacked bonds with 2.898 Å (Fig.3b) and 2 longer H….π-bonds were detected with C=C….H = 2.879 Å (Fig.3c).  Fig.3.Molecular interactions bonds types and lengths.  Mor. J. Chem. 7 N°2 (2019) 392-400 396 In HAS (Fig.4),10 big red spots were recorded close to the Cl and N atoms as seen in the dnorm surface (Fig.4a), such sport reflected the formation of many short interaction in the crystal lattice of the dimer as see in the packing result.  Fig.4. (a) dnorm, (b) curvedness and (c) shape index mapped structures.   Fig.5.Inside…outside atoms 2D-FP ratios.  Mor. J. Chem. 7 N°2 (2019) 392-400 397  By subjecting the dimer to 2D-Fingerprint analysis as see in Fig.5, the plot reflected the H…H as the highest interactions, meanwhile the H…Cd as the lowest interactions presence ratios, moreover, the presence ratios for the whole interactions ratios were illustrated as the following.H…H (42.8%) >H…C (7.8%) > H…S (6.9%) > H…C (3.9%) > H…N (1.7%) with H…overall connections (65.8%), as depicted in Fig. 5.    3.5.B3LYP/6311G(d,P) MEP and Mulliken charge distribution investigations The MEP analysis and Mulliken indicates that the intermoleculars bonding are reasonable, since all the corresponding H-donor atoms are with positive charge and nearby negatively charged nitrogen and chloride atoms. The MEP diagram was served to evaluate the nucleophilic reactive sites for electrophilic one, and for figures out the molecular interactions [26]. The MEP/B3LYP map analysis of the desired dimer revealed an electrophilic/nucleophilic functional groups reflected by their color as the following [red (highest)>orange>yellow>green>blue (lowest)]as seen in Fig.6a. The MEP proved the presence of both e-poor/e-rich positions in the complex, for example, intensity red color reflected the Cl atomsas good nucleophile sites, the yellow color around the N and most of C atoms also reflected as nucleophile sites, on the other hand, the Cd and most of the H atoms were reflected with blue color showing a electrophilic sites [27]. Since MEP reflected the presence of both blue and red colors sites in the dimer structure it is, thereforeconsistent strongly with Mulliken charges result illustrated in Fig.6b. Fig.6b. and Table 2 showMulliken population analysis of each atom. As predicted, the N and Cl-atoms are the highest electronegative atom, respectively, all the H-atoms are electropositive which enhanced for example the H….Cl hydrogen bonds formation, Onthe other hand, most of the C-atoms arewith negativecharges, while the minors are with positive charged, see Table 2.   Fig.6.B3LYP/6311G(d,P) (a) MEP and (b) Mulliken atomic charges.  Mor. J. Chem. 7 N°2 (2019) 392-400 398  Table 2. Mulliken atomic charges of all atoms belong to the desired dimer. Atom No. Atoms Charge (e) Atom No. Atoms Charge (e) 1 Cd 0.706853 52 Cd 0.70683 2 Cl -0.53431 53 Cl -0.53431 3 C -0.69953 54 C -0.69951 4 H 0.31285 55 H 0.312848 5 H 0.224428 56 H 0.224419 6 H 0.305304 57 H 0.3053 7 N -0.75051 58 N -0.75049 8 C -0.20704 59 C -0.20704 9 H 0.188571 60 H 0.188566 10 C -0.17841 61 C -0.17841 11 H 0.187559 62 H 0.187568 12 N -0.74478 63 N -0.74479 13 C -0.03121 64 C -0.03119 14 C -0.01547 65 C -0.01546 15 C 0.044306 66 C 0.044308 16 C -0.17629 67 C -0.17629 17 H 0.188242 68 H 0.188223 18 C -0.18509 69 C -0.1851 19 H 0.189977 70 H 0.189985 20 C -0.20323 71 C -0.20325 21 H 0.190286 72 H 0.190285 22 C 0.329812 73 C 0.329837 23 C -0.16785 74 C -0.16782 24 H 0.191195 75 H 0.19119 25 C 0.326212 76 C 0.326194 26 C 0.34734 77 C 0.347326 27 C -0.16356 78 C -0.16358 28 H 0.189974 79 H 0.189992 29 C -0.17047 80 C -0.17046 30 H 0.183728 81 H 0.183717 31 C 0.003029 82 C 0.003028 32 C 0.009406 83 C 0.009389 33 C 0.35842 84 C 0.358426 34 C -0.17875 85 C -0.17875 35 H 0.183366 86 H 0.183357 36 C 0.041591 87 C 0.04159 37 C -0.70054 88 C -0.70054 38 H 0.304554 89 H 0.304554 39 H 0.30987 90 H 0.309865 40 H 0.222164 91 H 0.222174 41 C -0.16477 92 C -0.16477 42 H 0.191811 93 H 0.191815 43 C -0.16375 94 C -0.16374 44 H 0.188993 95 H 0.188992 45 C -0.18518 96 C -0.18519 46 H 0.189911 97 H 0.189913 47 Cl -0.53547 98 Cl -0.53546 48 C -0.17942 99 C -0.17944 49 H 0.202061 100 H 0.202053 50 C -0.17879 101 C -0.17876 51 H 0.202599 102 H 0.202599   Mor. J. Chem. 7 N°2 (2019) 392-400 399 4.CONCLUSION In this work, novel Cd2(phen)2Cl4 dimer was prepared in a very good yield via efficient and simple synthetic way. The dimer was characterized by XRD and structurally computed via HAS and DFT. The XRD reflected the Cd(II) ions dimer as triclinic/P-1 system with slightly-distorted square-pyramidal centered. The computed angles and bonds lengths reflected an excellent matching with the experimental XRD one. The HAS and 2D-FP calculations supported the experimental-packing result, where three difference short contacts were discovered in the crystal lattice of the desired dimer, MEP and Mulliken charge population reflected the presence of both nucleophilic and electrophilic positions in the backbone of the dimer which strongly supported the formation of intermolecular bonds detected by XRD result.  REFERENCES [1] I. Warad, A. A. Khan, M. Azam, S. I. Al-Resayes, and S. F. Haddad. J. Mol. Struct., 1062 (2014): 167-173. [2] I.  Warad, M. 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Synthesis, XRD, DFT-optimization, MEP and Hirshfeld surface analysis of di-μ-Chloro-bis[chloro(1,10-phenanthroline)Cd(II) dimer

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Synthesis, XRD, DFT-optimization, MEP and Hirshfeld surface analysis of di-μ-Chloro-bis[chloro(1,10-phenanthroline)Cd(II) dimer

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