Synthesis, physicochemical, XRD/HSA-interactions, Heteromeric [CH⋅⋅⋅Cl/CH⋅⋅⋅πPh] synthon, DFT, thermal and 1BNA-DNA docking of cis-Ni(S,N) 2 complex using hydrazine carbodithioate Schiff base

doi:10.21203/rs.3.rs-3903401/v1

Download PDF

Research Article

Synthesis, physicochemical, XRD/HSA-interactions, Heteromeric [CH⋅⋅⋅Cl/CH⋅⋅⋅πPh] synthon, DFT, thermal and 1BNA-DNA docking of cis-Ni(S,N) 2 complex using hydrazine carbodithioate Schiff base

https://doi.org/10.21203/rs.3.rs-3903401/v1

This work is licensed under a CC BY 4.0 License

You are reading this latest preprint version

The reaction of bidentate-S,N-thione Schiff base ligand, Phenyl (E)-2-(1-phenylethylidene)hydrazine-1-carbodithioate (PPEHCDT) with NiCl₂.3H₂O produced a neutral Ni^II(S,N)₂ complex in high yield. The structural formula of the obtained material was established by, EDX, FAB-MS, UV-Vis, IR, CHN and XRD-crystal analysis. The XRD-results revealed a cis-isomer as anionic S-thiol and bis-bidentate-N-azomethine and as well as a slightly distorted square planar neutral cis-Ni(PPEHCDT)₂ complex. In contrast, the DFT simulation supported a distorted tetrahedral as favor geometry, despite that the XRD/DFT structural parameters results were in agreement. Moreover, the Molecular Electrostatic Potential (MEP) together with the Hirshfeld Surface Analysis (HSA) confirmed the XRD seen in appearing of the Heteromeric sub-synthons via C-H_….πPh and C-H_⸱⸱⸱S interactions. Moreover, the thermal properties of the cis-Ni(PPEHCDT)₂ complex was determined via TG/DTG. Additionally, molecular docking has been evaluated for both, the free ligand and its cis-Ni(PPEHCDT)₂ complex against 1BNA-DNA.

Ni(II) complex

DFT

crystal structure

hydrazonodithioate

HSA

Docking

The transition metal ions nitrogen-sulfur bi-chelated ligands complexes that were accomplished from dithiocarbazic acid and S-alkyl thioesters were recently studied for their structural uniqueness and applications [1–4]. The mode of coordination of such ligands together with their thiol/thione isomerization pronounced their biological activities against cancer cells, viruses, microbes, antifungal, and antibacterial [2–4]. Moreover, the multifaceted industrial chemistry ligands-complexes suit results in the participation of such new materials in non-biological and biological catalysis approaches [5]. Furthermore, the coordination of several types of hydrazones dithioate (as S and N ligands) is an essential piece of research to develop new complexes with industrial molecular magnetism, semiconducting behavior, electrochemical and optoelectronic properties [6].

The transition metal ions [M(S,N)₂]_n complexes using hydrazone dithioate ligands established several metal centers with different oxidation numbers of Fe(II&III), Mn(II, IV & VI), Co(III&II), Cu(I&II) and Ni(II), engage in the electrochemical oxidation of water [7–10]. Ni(S,N)₂ complexes were found to be the best catalysts among the others for oxidation of water process [11–16]. Therefore, the oxidation catalytic properties of such complexes, especially Ni(II) have been developed industrially for oxidation of enantioselective sulfides, alcohols, and alkenes [17–20]. In the natural biological system, Ni(II) with N,S containing bi-, tri-, or multi-chelated ligands complexes were used as a model for the Ni(II)-enzymes like Ni-containing superoxide dismutase and bi-functional acetyl–CoA/carbon monoxide dehydrogenase synthase [21, 22].

Our growing interest in dithiocarbazic acid ligands and their metal complexes [1, 23–25] stimulated our group to investigate the cis-Ni(PPEHCDT)₂ complex. The new structure was well identified by XRD-crystal, and several other spectral tools. The DFT, XRD, thermal behavior, HSA, MEP, MAC/NPA, DOS, HOMO/LUMO, and physicochemical properties together with their 1BNA-DNA docking behaviors were investigated.

2.1. Chemicals and Measurements

Chemicals and solvents fine are available from Fluka. In order to measure the infrared vibrations in the 4000–200 cm^− 1 wavenumber range, the PerkinElmer Spectrum 1000 FT-IR Spectrometer was used. The UV–Vis. data was achieved via TU-1901 double-beam spectrophotometer. Using a 711A (8 kV) Finnigan, FAB-MS data were gathered. An Elementar Analyzer Varrio EL was used to get the CHN analysis.

2.2. Synthesis of Ni(II) Complex

The BPEHCDT ligand was synthesized in quantitative yield following the literature procedure [1]. The desired complex was prepared by adding a hot solution of 0.31 g (1.0 mmol) BPEHCDT ligand in 20 mL of ethanol to a solution of 0.24 g (1 mmol) of NiCl₂.3H₂O in ethanol (30 mL). The obtained mixture was stirred for 1h. Thereafter, the volume of the sol. was reduced to half and cooled in a refrigerator for 8 h. The greenish precipitate was filtrated, washed well with methanol and n-hexane, respectively. M.p 223°C, yield in 76%. Anal. Calcd for C₃₀H₂₆N₄NiS₄: C, 57.24; H, 4.16; and N, 8.90. Found C, 57.21; H, 4.27; N, 8.73. FAB-MS: [M⁺] = 629.3m/z. Selected IR data (cm^-1): v(C-H, Ph) 3080 − 3020 m, v(C-H, alkyl) 292–2890 m, v(2C = N) 1570 b, v(N-N) 1118 s, v(CSS) 825 m, v(Ni-N) 622 m, v(Ni-S) 502 m. UV–vis. Ligand bands like π→π* at 238 nm, π →n, at 302, n→π* at 360, 397 nm 238, 290, and d→d (Ni²⁺) band at 420 nm [28].

2.3. Computation and XRD-crystal

HSA was achieved via CrystalExplorer platform, version 17 [26]. Gaussian W09 software was utilized for all the DFT stimulations [27]. The LANL2DZ was served as a basis set for Ni(II) the heavy atoms, meanwhile DFT 6-311G(d,p) was used for the other atoms. The docking studies were performed via Autodock 4.2 software [28] to apprehend the interaction between free ligand and Ni(II)-complexes and 1BNA-DNA [29].

Single-crystal XRD data was collected on a Bruker AXS Smart Apex CCD diffractometer with graphite monochromatic Mo-K_α radiation of λ = 0.071073 Å at a temperature of 130 ± 2 K, using the scanning technique to a maximum of a 137 ± 2 K. The structure was solved by direct method employing SIR-92 and full-matrix least squares refinement [29]. All nonhydrogen atoms were anisotropically refined through SHELXL [30, 31]. Hydrogen atoms were located geometrically and were refined isotropically. Crystal data is reported in Table 1.

Table 1. cis-Ni(PPEHCDT)₂complex structure refinement data.

3.1. Preparation, CHN-EA, MS, EDX and IR of cis-Ni(PPEHDC)₂ Complex

The desired cis-Ni(PPEHDC)₂complex was made available by treating equivalent of PPEHDC ligand with NiCl₂.3H₂O in methanol solution under RT conditions as illustrated in Scheme 1. The cis-Ni(PPEHDC)₂complex was collected as a brownish powder in a good yield of 78%. The complex is slightly soluble in methanol, chlorinated solvent, hot water but never in n-hexane. The molecular formula of the cis-Ni(PPEHDC)₂was analyzed base on several spectral tools: IR, FAB-MS, CHN-EA, UV-vis, EDX, TG/DTG, and XRD-crystal. The XRD result showed the PPEHDC ligand as S (thiol) and N (azomethine) bidentate and not thione form ligand. Moreover, the cis-isomer of the neutral cis-Ni(PPEHDC)₂ complex, there is no evidence of trans-Ni(PPEHDC)₂ complex formation and this fact has been confirmed by XRD-crystal analysis.

Cis-Ni(PPEHDC)₂ complex formula weight was confirmed by FAB-MS, [M+1⁺] = 629.3 m/z (628.2 m/z theoretical). The CHN-elemental analysis is consistent with the molecular formula of the complex C₃₀H₂₆N₄NiS₄. Moreover, EDX-analysis supported the purity and the atomic continent, since only energy peaks belong to C, N, S and Ni were recorded as shown in Fig. 1a.

The solid-state FT-IR of cis-Ni(PPEHDC)₂complex was recorded as seen in Fig.1b. Several IR stretching vibration bands were observed; the main groups C_Ph-H, C_alkyl-H, C=NàNi, C=N, N-N, CS₂, NàNi and SàNi stretching vibrations were sited to 3080-3020, 292-2890, 1575, 1570, 1118, 825, 622, 502 cm^-1, respectively. The same functional groups stretching vibrations were observed by DFT-IR with slight shifts in their wavenumber values as seen in Fig.1c. Moreover, the DFT and experimental IR wavenumber values are in an excellent degree of matching since 0.997 graphical correlation as in Fig.1d.

3.2. X-Ray and DFT computations

The DFT-optimized and the ORTEP diagrams of cis-Ni(PPEHDC)₂complex structures and their parameters have been illustrated in Fig.2 and Table 2. C ₃₂ H₃₀N ₄NiS₄is Monoclinic in crystal system, C 2/c with Z = 4 per cell. The two PPEHDC ligands bonded to Ni(II) center via S, N provided by 2 anionic via S^-and 2 neutral N-groups to form the neutral cis-Ni(PPEHDC)₂complex with two five-hetero-metal-membered center cis-Ni(N,S)₂ rings (Fig.2b). The bond and angles values of the Ni(II)-complex are in high agreement with previously similar structures [1, 23, 30]. The Ni(II) center geometry was solved as a distorted square planar with τ = 30.2^o (Fig.2b). Based on the DFT optimization result of the cis-Ni(PPEHDC)₂ complex the tetrahedron geometry found to favor the square planar geometry. This observation was not surprising since the DFT theory neglected any internal interactions (gaseous state) [32, 33]. Therefore, it is possible through DFT to observe that the tetrahedral structure around Metal centers as favored isomer over the square planar geometry it is with lower steric hindrance that minimizes the internal repulsion. As the distorted square planar around the Ni(II) center has been confirmed experimentally by XRD-crystal, then it can be said in this manuscript that the DFT-theory contradicted the results of XRD in judging the final geometry around the metal central atom, but it agreed in judging the other structural parameters.

Table 2. Designated DFT/XRD bonds and angles lengths.

			Bond length [Å]						Angle value (^o)
Bond No.	Bond type		XRD	DFT	Angle No.	Angle type			XRD	DFT
1	Ni1	S2	2.1759	2.2912	1	S2	Ni1	N2	86.02	89.35
2	Ni1	N2	1.906	1.7947	2	S2	Ni1	S2	98.44	97.78
3	Ni1	S2	2.1759	2.2911	3	S2	Ni1	N2	159.84	151.42
4	Ni1	N2	1.906	1.7947	4	N2	Ni1	S2	159.84	151.43
5	S1	C1	1.830(2)	1.9333	5	N2	Ni1	N2	96.56	97.52
6	S1	C8	1.747(2)	1.8185	6	S2	Ni1	N2	86.02	89.35
7	S2	C8	1.756(2)	1.7961	7	C1	S1	C8	100.7(9)	99.66
8	N1	N2	1.408(2)	1.4633	8	Ni1	S2	C8	92.33	88.7
9	N1	C8	1.292(2)	1.2988	9	N2	N1	C8	110.5(1)	111.7
10	N2	C9	1.300(2)	1.313	10	Ni1	N2	N1	118.2	119.34
11	C1	C2	1.502(2)	1.5018	11	Ni1	N2	C9	127.2	128.37
12	C2	C3	1.389(3)	1.402	12	N1	N2	C9	114.6(1)	112.27
13	C2	C7	1.390(3)	1.4019	13	S1	C1	C2	110.3(1)	108
14	C3	C4	1.381(3)	1.3949	14	C1	C2	C3	120.7(2)	120.45
15	C4	C5	1.379(4)	1.3973	15	C1	C2	C7	120.3(2)	120.6
16	C5	C6	1.377(4)	1.397	16	C3	C2	C7	119.0(2)	118.95
17	C6	C7	1.391(3)	1.3953	17	C2	C3	C4	120.6(2)	120.59
18	C9	C10	1.497(3)	1.5078	18	C3	C4	C5	120.0(2)	120.06
19	C9	C11	1.483(2)	1.4743	19	C4	C5	C6	120.3(2)	119.77
20	C11	C12	1.393(2)	1.4055	20	C5	C6	C7	120.0(2)	120.1
21	C11	C16	1.394(2)	1.4076	21	C2	C7	C6	120.2(2)	120.54
22	C12	C13	1.388(2)	1.394	22	S1	C8	S2	116.1(1)	116.04
23	C13	C14	1.387(3)	1.3961	23	S1	C8	N1	119.0(1)	118.08
24	C14	C15	1.382(3)	1.3998	24	S2	C8	N1	124.8(1)	125.89
25	C15	C16	1.385(3)	1.393	25	N2	C9	C10	122.3(2)	120.73
26	S1	C1	1.830(2)	1.9333	26	N2	C9	C11	118.8(2)	119.94
27	S1	C8	1.747(2)	1.8186	27	C10	C9	C11	118.9(2)	119.2
28	S2	C8	1.756(2)	1.7961	28	C9	C11	C12	119.9(2)	119.83
29	N1	N2	1.408(2)	1.4633	29	C9	C11	C16	120.6(2)	121.09
30	N1	C8	1.292(2)	1.2987	30	C12	C11	C16	119.4(2)	119
31	N2	C9	1.300(2)	1.313	31	C11	C12	C13	120.1(2)	120.51
32	C1	C2	1.502(2)	1.5019	32	C12	C13	C14	120.1(2)	120.1
33	C2	C3	1.389(3)	1.402	33	C13	C14	C15	120.0(2)	119.87
34	C2	C7	1.390(3)	1.4019	34	C14	C15	C16	120.4(2)	120.2
35	C3	C4	1.381(3)	1.3949	35	C11	C16	C15	120.1(2)	120.31
36	C4	C5	1.379(4)	1.3972	36	C1	S1	C8	100.7(9)	99.66
37	C5	C6	1.377(4)	1.397	37	N2	N1	C8	110.5(1)	111.7
38	C6	C7	1.391(3)	1.3954	38	N1	N2	C9	114.6(1)	112.27
39	C9	C10	1.497(3)	1.5079	39	S1	C1	C2	110.3(1)	108
40	C9	C11	1.483(2)	1.4743	40	C1	C2	C3	120.7(2)	120.45
41	C11	C12	1.393(2)	1.4055	41	C1	C2	C7	120.3(2)	120.6
42	C11	C16	1.394(2)	1.4076	42	C3	C2	C7	119.0(2)	118.95
43	C12	C13	1.388(2)	1.394	43	C2	C3	C4	120.6(2)	120.58
44	C13	C14	1.387(3)	1.3961	44	C3	C4	C5	120.0(2)	120.06
45	C14	C15	1.382(3)	1.3998	45	C4	C5	C6	120.3(2)	119.77
46	C15	C16	1.385(3)	1.393	46	C5	C6	C7	120.0(2)	120.1

The DFT-optimized angles and bond distances matched well with experimental XRD results as displayed in Fig.3. Accepted levels of DFT and XRD in terms of angles and bond lengths are observed as seen in Fig.3a. Bond lengths were in excellent agreement as seen in Fig.3a with graphical correlation R² = 0.972 (Fig.3b). Even two different geometries were suggested, the tetrahedral structure was observed by DFT and the square planar was confirmed by XRD, their angles also showed an excellent agreement as seen in Fig.3c, with graphical correlation R² = 0.9798 (Fig.3d).

3.3. Heteromeric [CH⋅⋅⋅Cl/CH⋅⋅⋅πPh] synthon and HSA investigation

The presence of two main huge synthons of 2D-S24 type cyclic bonding is usually rare (Fig. 4a), since each synthon consists of a triple-side sub-synthon as 2S11 and 1S10 binding via two short contacts C_alkyl-H⸱⸱⸱S with 2.902 Å and C_ph-H⸱⸱⸱πPh with 2.974 Å (Fig.4b). The non-classical shorter H-bonds of the type H⸱⸱⸱S and H⸱⸱⸱πPh reflecting a two-dimensional chain formation (Fig.4b). Moreover, presence of eight of such interactions per two synthons recorded in the cis-Ni(PPEHDC)₂lattice raised the crystalline matrix stability as well as its optical and electronic properties [34].

To confirm the packing result, the HSA of cis-Ni(PPEHDC)₂was performed in between -0.632-1.876 a.u. using the CIF crystallographic data [35-43]. The HSA and 2D-FP collected results are illustrated in Fig. 5. The existence of S and N heteroatoms together with π of the aromatic rings in addition to several polar hydrogens enhanced the formation of eight red-dots were detected including the presence of short interactions like H….S and H⸱⸱⸱πPh as seen in d_orm(Fig.5a). Moreover, 2D-FP intermolecular H-to-atom ratios are displayed in Fig.5b. It was found that the H⸱⸱⸱H (51.5%) interaction has the highest ratio among all interactions, while the H⸱⸱⸱Ni reflected is 0.1% ratio (Fig.5c). The 2D-FP ratios analysis are illustrated as in the following order H….H>C….H>S…H>(N….H, Ni….H, 0%)

3.4. MEP, and MAC/NPA

MEP map of cis-Ni(PPEHDC)₂complex is computed to explore the binding properties of the complex. The potential increased ranging from blue, green, yellow, orange, and red reflecting the degree of the electronic density of each atom. The MEP results indicated that the etheric S and coordinated S atoms display the highest e-rich/nucleophilic sites (red color). Meanwhile, the e-poor/electrophilic spots (blue) are highly seated on the phenyl and methyl protons. Usually, aromatic rings are rich with electrons, they were distinguished as yellow areas, Fig 6. Non-classical C-H⸱⸱⸱πPh and C-H^….S H-bond interactions can be computed using MEP theory that is consistent with the HSA and XRD outcome. The atomic charge of our molecule surface behavior MAC and NPA charge distribution in cis-Ni(PPEHDC)₂complex were calculated and displayed as seen in Fig.6. In general, the NPA reflected the Ph charges with higher values compared to MAC results. All atomic charges of each atom in the surface of the core of the molecule were collected in Table 3. The comparative study of both the models, MAC and NPA are accepted since a high graphical correlation is detected as 0.8921, as seen in Fig.6d.

Table 3. NPA/MAC charge population.

No.	Atom	MAC	NPA	No.	Atom	MAC	NPA
1	Ni	0.773991	0.47953	37	S	0.428473	1.09673
2	S	0.428479	1.09846	38	S	0.029384	0.01851
3	S	0.029393	0.02495	39	N	-0.30618	-0.39583
4	N	-0.30617	-0.39799	40	N	-0.58893	-0.32677
5	N	-0.58894	-0.32517	41	C	-0.6439	-0.68963
6	C	-0.6439	-0.69496	42	H	0.245213	0.2827
7	H	0.245211	0.27978	43	H	0.257552	0.28873
8	H	0.257556	0.28763	44	C	0.009012	-0.06272
9	C	0.009016	-0.05458	45	C	-0.17697	-0.24844
10	C	-0.17697	-0.24863	46	H	0.183214	0.23135
11	H	0.183216	0.22624	47	C	-0.18242	-0.21721
12	C	-0.18242	-0.22399	48	H	0.188746	0.24536
13	H	0.188747	0.24454	49	C	-0.18403	-0.23838
14	C	-0.18403	-0.23783	50	H	0.190087	0.24446
15	H	0.190088	0.24366	51	C	-0.18176	-0.226
16	C	-0.18176	-0.22341	52	H	0.191285	0.24465
17	H	0.191285	0.24384	53	C	-0.17602	-0.22458
18	C	-0.17602	-0.2277	54	H	0.192236	0.24129
19	H	0.192234	0.24245	55	C	-0.36979	-0.3656
20	C	-0.36981	-0.35085	56	C	0.37293	0.22568
21	C	0.372934	0.2238	57	C	-0.59781	-0.70643
22	C	-0.59782	-0.70653	58	H	0.242664	0.24544
23	H	0.242663	0.2453	59	H	0.197974	0.227
24	H	0.197976	0.22637	60	H	0.246672	0.26099
25	H	0.246675	0.26247	61	C	-0.03467	-0.06863
26	C	-0.03467	-0.06978	62	C	-0.21812	-0.10338
27	C	-0.21812	-0.09712	63	H	0.243342	0.12813
28	H	0.243337	0.12819	64	C	-0.17587	-0.21638
29	C	-0.17587	-0.19096	65	H	0.218091	-0.184
30	H	0.21809	-0.18743	66	C	-0.19307	-0.23435
31	C	-0.19307	-0.23478	67	H	0.197867	0.22665
32	H	0.19787	0.22787	68	C	-0.18269	-0.24134
33	C	-0.18268	-0.24223	69	H	0.195581	0.24506
34	H	0.195581	0.24623	70	C	-0.19438	-0.20181
35	C	-0.19438	-0.19899	71	H	0.189295	0.23989
36	H	0.189295	0.24049

3.5. HOMO/LUMO and DOS

The HOMO and LUMO shapes and energy levels provide input about stability, the relationship orbitals, and general chemical and structural properties of the prepared new compounds. In the HOMO, the main electron density focused around the Ni(II) and the core atoms of cis-Ni(PPEHDC)₂; meanwhile, in LUMO focused only around the core atoms and not on Ni(II) center. Both HOMO and LUMO defocused the terminal phenyls. Moreover, the E_LUMO,E_HOMO, and ΔE were calculated to be -0.0833, -0.1921, and 0.1088 a.u (2.9598 eV), respectively, as shown in Fig. 7a. In order to verify the HOMO and LUMO energy values, it was calculated using another model like the Density of State (DOS). The net energy resulted in by DOS ΔE_DOSwas found to be consistent with ΔE_HOMO/LUMOwith very closed 2.988 eV as seen in Fig. 7b.

3.6. TG/DTG analysis

The thermal behavior of the desired cis-Ni(PPEHDC)₂complex has been performed in an open room condition with a heat rate of 10 °C/min via TG/DTG as in Fig.8. Fig.8 shows the complex with high thermal stability. It is stable up to ~250 °C resulted from the absence of uncoordinated or coordinated water molecule to the Nickel atom since no loss in the weight of the complex in between 50-160 °C was shown in Fig.8a. This result is consistent with the IR as well as the XRD results. The desired complex was decayed in two main steps, the first one was the sharpest detected mass decay in 250-300 °C with T_DTG = 280 °C (Fig.8b) and 39.6% mass. This loss can be mainly attributed to the de-structured of one piece of the PPEHDC ligand to form cis-Ni(PPEHDC)₂complex. Meanwhile, the second step was a broad step in 420-510 °C with T_DTG = 480 °C and 40.5% mass; such loss can be attributed to the de-structured of the second piece of the ligand parallel to reaction with atmospheric O₂ to prepare the nickel oxide as a final product with ~ 19.3% yield [43].

3.7. Molecular docking studies

The greatest theoretical calculation to understand how chemicals bind to DNA or enzymes is molecular docking; this stimulation approach is a wonderful structural drug design (SDD) technique. In this study [39-41], the 1BNA-DNA was used as a comparative structure for the docking of the free ligand and its cis-Ni(PPEHCDT)₂. Table 4 and Fig. 9 show the final docked pictures and the binding energy estimates for the ligand and its complexes. The PPEHCDT docked with 1BNA resulted like the cisplatin binding mode, mimic a good docking by cross-linking of the 1BNA both double helix [44] with a minor grove site interaction (Fig. 9a), via two short hydrogen bonds, the first on was via NH of hydrazine carbodithioate and cytosine (DC23:O4) bases of DNA with 1.985 A˚ length, and the second hydrogen bond was through Sulfur of dithioate and guanine (DG4:H22) bases of DNA with 2.323 A˚ length (Fig. 9a). This two H-bond resulting the binding energy with a very good value of -8.84 kcal/mol. Other weak binding interactions as Ph π: π, S-π and VdW were also recorded as seen in Fig. 9c. A dramatical change in the bonding mode was obtained when the cis-Ni(PPEHCDT)₂was introduced instead of the free ligand, the complex binds the 1BNA to major grove instead of minor grove position (Fig.9d), only one hydrogen bond via Sulfur of dithioate and adenine (DA18:H62) with 2.234 A˚ length has been detected (Fig.9e), moreover, lower binding energy -6.34 kcal/mol has been recorded as seen in Table 4.

Table 4. Docking data of both the PPEHCDT and its cis-Ni(PPEHCDT)₂

No.

B.E

(kcal/mol)

Ligand Efficiency

I. C, µM
T= 298. 15 K

Hb of residues and
ligands with bond length (Å)

PPEHDC

-8.84

-0.47

9.78

DNA:B:DC23:O4….H (1.985)

DNA:A:DG4:H22….S (2.323)

cis-Ni(PPEHDC)₂

-6.34

-0.11

1.35

DNA:B:DA18:H62….S (2.234)

A novel neutral Nickel(II) complex with two Ni(PPEHDC)₂ bidentate N, S-type ligands has been made in a good yield. The structural formula of cis-Ni(PPEHDC)₂isomer was evidenced by XRD and further supported via EDX, IR, UV-Vis, CHN-EA, and FAB-MS analysis. X-ray diffraction reflected the cis-Ni(PPEHDC)₂ complex with distorted square planar as oppose to the tetrahedral geometry revealed by the DFT theoretical analysis. The cis-Ni(PPEHDC)₂ was chelated to the Ni(II) center via S-thiol and N-azomethine atoms to form a unique cis-conformation square planar. Additionally, the DFT/XRD angles and bond lengths values were in good consistency. The MEP, MAC/NPA, and HSA calculation results proved the XRD-experimental result in the 2D-S24 synthons formation via C-H⸱⸱⸱πPh and C-H⸱⸱⸱S interactions. The cis-Ni(PPEHDC)₂ is thermally stable up to 250 ^oC, it decomposed to Nickel oxide final product in two steps decomposition mechanism. Moreover, investigations of 1BNA docking with the free ligand and its Ni-complex showed a dramatical shift in binding locations, H-bond quantity/type, and binding energy values.

Author Contributions: Study concept and design (A.B., I.W.); data acquisition (N.A.Z., A.F.A., I.M.); methodology (R.A., I.K., N.G.), software (I.W., A.Z.); analysis and interpretation of data (I.W., A.B., N.A.M.); drafting of the manuscript (A.B., I.W., K.S.); critical revision of the manuscript (I.W., N.A.M., H.Q.), supervision (A.B., I.W.).

Funding: This study did not receive any external support.

Acknowledgments: The Authors would like to thank An Najah National University-Palestine.

Ethics approval and consent to participate: Not applicable.

Consent for publication: Not applicable.

Competing interests: The authors declare that they have no competing interests

Availability of data and materials: The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request.

A. Boshaala, K. S.M.Salih, N. Bader, A. A. Almughery, A. Zarrouk, I. Warad, J. Mol. Liq. 330 (2021) 115551.
N.K. Singh, M.K. Bharty, S.K. Kushawaha, U.P. Singh, Pooja Tyagi, Polyhedron 29 (2010) 1902.
L. Otero, M. Vieites, L. Boiani, A. Denicola, C. Rigol, L. Opazo, C. Olea-Azar, J.D. Maya, A. Morello, R.L. Krauth-Siegel, O.E. Piro, E. Castellano, M. Gonzalez, D. Gambino, H. Cerecetto, J. Med. Chem. 49 (2006) 3322.
M.T.H. Tarafder, M.A. Ali, D.J. Wee, K. Azahari, S. Silong, D.A. Crouse, Trans. Met. Chem. 25 (2000) 456.
R. Beckett, B.F. Hoskins, J. Chem. Soc., Dalton Trans. (1974) 622.
V. Singh, R. Chauhan, A. Kumar, L. Bahadur, N. Singh, Dalton Trans. 39 (2010) 9779.
H. Feizi, F. Shiri, R. Bagheri, J. Singh, K.H. Chae, Z. Song, M.M. Najafpour, Catal. Sci. Technol. 8 (2018) 3954.
M.M. Najafpour, G. Renger, M. Hołyn´ ska, A.N. Moghaddam, E.-M. Aro, R. Carpentier, H. Nishihara, J.J. Eaton-Rye, J.-R. Shen, S.I. Allakhverdiev, Chem. Rev. 116 (2016) 2886.
W. Rüttinger, G.C. Dismukes, Chem. Rev. 97 (1997) 1.
J.P. McEvoy, G.W. Brudvig, Chem. Rev. 106 (2006) 4455.
S. Sarkar, S.K. Nag, A.P. Chattopadhyay, K. Dey, S.M. Islam, A. Sarkar, S. Sarkar, J. Mol. Struct. 1160 (2018) 9.
Y. Cao, M. Lu, J. Fang, L. Shi, D. Zhang, Chem. Commun. 53 (2017) 7549.
Y. Han, Y. Wu, W. Lai, R. Cao, Inorg. Chem. 54 (2015) 5604.
M.M. Najafpour, H. Feizi, Dalton Trans. 41 (2012) 10292.
N.D. Schley, J.D. Blakemore, N.K. Subbaiyan, C.D. Incarvito, F. D’Souza, R. H. Crabtree, G.W. Brudvig, J. Am. Chem. Soc. 133 (2011) 10473.
M. Zhang, M.T. Zhang, C. Hou, Z.F. Ke, T.B. Lu, Angew. Chem., Int. Ed. 53 (2014)13042.
G. Grivani, A.D. Khalaji, V. Tahmasebi, K. Gotoh, H. Ishida, Polyhedron 31 (2012) 265.
S.J. Lippard, J.M. Berg, Principles of Bioinorganic Chemistry, University Science Books, California, 1994.
M. Amini, A. Arab, R. Soleyman, A. Ellern, L.K. Woo, J. Coord. Chem. 66 (2013) 3770.
N. Khadir, M. Amini, A. Assoud, M. Bagherzadeh, D.M. Boghaei, J. Coord. Chem. 69 (2016) 103.
T.I. Doukov, T.M. Iverson, J. Seravalli, S.W. Ragsdale, C.L. Drennan, Science 298 (2002) 567.
J. Wuerges, J.W. Lee, Y.I. Yim, H.S. Yim, S.O. Kang, K.D. Carugo, Proc. Natl. Acad. Sci. USA 101 (2004) 8569.
A. Boshaala, U. Flörke, B. M Yamin, Y. O. Ben Amer, G. S. H. Ghaith,A. A. Almughery, A. Zarrouk, I. Warad, J. Mol. Struct. 1224 (2021) 129207.
A. M. Boshaala, K. A. AlFarha, H. Sheppaek, W. O. Algezzeri, A. Zarrouk, I. Warad, Mor. J. Chem. 8 (2020) 1048.
E. Lindner, S. Al-Gharabli, I. Warad, H. A. Mayera, S. Steinbrecher, E. Plies, M. Seiler, H. Bertagnolli, Z. Anorg. Allg. Chem. 629 (2003) 161.
S.K. Wolff, D.J. Grimwood, J.J. McKinnon, M.J. Turner, D. Jayatilaka, M.A. Spackman, Crystal Explorer 3.0. University of Western, Perth, Australia, 2012.
G.W.T. M. J. Frisch, H. B. Schlegel, G. E. Scuseria, M. A. Robb, J. R. Cheeseman, et. al, Gaussian 09, Revision E.01, Gaussian, Inc., Wallingford CT, 2009.
S. Forli, R. Huey, M.E. Pique, M.F. Sanner, D.S. Goodsell, A.J. Olson, Nat. Protoc. 11 (2016) 905.
https://www.rcsb.org/structure/1BNA
M.Burla, R. Caliandro, M. Camalli, B. Carrozzini, G.L. Cascarano, L. DeCaro, C. Giacovazzo, G. Polidori, R. Spagna J. Appl. Crystallogr., 38 (2005) 381.
G.M. Sheldrich, SHELX‐97, release 97‐2, University of Goettingen, Germany, 1998.
I. Badran, A. Rauk, Y. Shi, J. Phys. Chem. A 116 (2012) 11806.
I. Badran, A. Rauk, Y. Shi, J. Phys. Chem. A 123 (2019) 1749.
P. J. Srijana, B. Narayana, B. K. Sarojini, Q. Ai Wong, C. K.Quah, U. Likhitha, J. Mol. Struct. 1274 (2023) 134426.
A. Guerraoui, A. Djedouani, E. Jeanneau, A. Boumaza, A. Alsalme, A. Zarrouk, K.S.M. Salih, I. Warad, J. Mol. Struct. 1220 (2020) 1890.
S. Tabti, A. Djedouani, D. Aggoun, I. Warad, S. Rahmouni, S. Romdhane, H. Fouzi, J. Mol. Struct. 1155 (2018) 11.
M.K. Hema, C.S. Karthik, I. Warad, N.K. Lokanath, A. Zarrouk, K. Kumara, K.J. Pampa, P. Mallu, J. Mol. Struct. 1157 (2018) 69.
M.A. Spackman, D. Jayatilaka, CrystEngComm 11 (2009) 19.
I. Warad, F. F. Awwadi, B. Abd Al-Ghani, A. Sawafta, N. Shivalingegowda, N.K. Lokanath, M.S. Mubarak, T. Ben Hadda, A. Zarrouk, F. Al-Rimawi, A.B. Odeh, S.A. Barghouthi, Ultrason. Sonochem. 48 (2018) 1.
M.K. Hema, C.S. Karthik, N.K. Lokanath, P. Mallu, A. Zarrouk, K.S.M. Salih, I. Warad, J. Mol. Liq. 315 (2020) 113756.
M. R. Aouad, M. Messali, N. Rezki, M.A. Said, D. Lentz, L. Zubaydi, I. Warad, J. Mol. Struct. 1180 (2019) 455.
M. R. Aouad, M. Messali, N. Rezki, N. Al-Zaqri, I. Warad, J. Mol. Liq. 264 (2018) 621.
I. Warad, S. Musameh, I. Badran, N. Nassar, P. Brandao, J. Tavares, A. Barakat, J. Mol. Struct. 1148 (2017) 328.
B. Ray, R. Mehrotra, J. Photochem. Photobiol. B: Biol. 211 (2020) 111990

Scheme 1 is available in the Supplementary Files section.

No competing interests reported.

Scheme1.png
Scheme 1. Cis-Ni(PPEHDC)₂complex synthesis.

Download PDF

Editorial decision: Revision requested
22 Feb, 2024
Reviews received at journal
18 Feb, 2024
Reviewers agreed at journal
08 Feb, 2024
Reviewers invited by journal
07 Feb, 2024
Editor assigned by journal
30 Jan, 2024
Submission checks completed at journal
29 Jan, 2024
First submitted to journal
27 Jan, 2024

You are reading this latest preprint version

Synthesis, physicochemical, XRD/HSA-interactions, Heteromeric [CH⋅⋅⋅Cl/CH⋅⋅⋅πPh] synthon, DFT, thermal and 1BNA-DNA docking of cis-Ni(S,N) 2 complex using hydrazine carbodithioate Schiff base

Status:

Version 1

Abstract

Figures

1. Introduction

2. Experimental

2.1. Chemicals and Measurements

2.2. Synthesis of Ni(II) Complex

2.3. Computation and XRD-crystal

3. Results and Discussion

Conclusion

Declarations

References

Scheme

Additional Declarations

Supplementary Files

Status:

Version 1