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Singh S, Choudhary M. Unusual Ni⋯Ni interaction in Ni(ii) complexes as potential inhibitors for the development of new anti-SARS-CoV-2 Omicron drugs. RSC Med Chem 2024; 15:895-915. [PMID: 38516589 PMCID: PMC10953495 DOI: 10.1039/d3md00601h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 01/05/2024] [Indexed: 03/23/2024] Open
Abstract
Two nickel(ii) coordination complexes [Ni(L)]2(1) and [Ni(L)]n(2) of a tetradentate Schiff base ligand (H2L) derived from 2-hydroxy-1-naphthaldehyde with ethylenediamine were synthesized, designed, and characterized via spectroscopic and single crystal XRD analyses. Both nickel(ii) complexes exhibited unusual Ni⋯Ni interactions and were fully characterized via single-crystal X-ray crystallography. Nickel(ii) complexes [Ni(L)]2(1) and [Ni(L)]n(2) crystallize in monoclinic and triclinic crystal systems with P21/c and P1̄ space groups, respectively, and revealed square planar geometry around each Ni(ii) ion. The structure of both the complexes have established the existence of a new kind of metal system containing nickel(ii)-nickel(ii) interactions with a square planar-like geometry about the nickel(ii) atoms. Both square planar Ni(ii) complexes were often stacked with relatively short Ni⋯Ni distances. The non-bonded Ni-Ni distance (Ni⋯Ni separation) seems to be 3.356 Å and 3.214 Å from the nickel atoms of [Ni(L)]2(1) and [Ni(L)]n(2), respectively. These distances are shorter than the sum of their van der Waals radii (4.80 Å) but longer than the sum of their covalent radii (2.50 Å), indicating that there is a Ni⋯Ni interaction but not a Ni-Ni bond. The discrete molecules are π-stacked and connected via weak intermolecular interactions (C-H⋯O and C-H⋯N). Cyclic voltammetry measurements were obtained for both the complexes, and their pharmacokinetic and chemoinformatics properties were also explored. Detailed structural analysis and non-covalent supramolecular interactions were investigated using single-crystal structure analysis and computational approaches. Both the unique structures show good inhibition performance for the Omicron spike proteins of the SARS CoV-2 virus. To gain insights into potential SARS-CoV-2 Omicron drugs and find inhibitors against the Omicron variants of SARS-CoV-2, we examined the molecular docking of the nickel(ii) complexes [Ni(L)]2(1) and [Ni(L)]n(2) with the SARS-CoV-2 Omicron spike protein (PDB ID: 7WK2 and 7WVO). A strong binding was predicted between Ni(ii) coordination complexes [Ni(L)]2(1) and [Ni(L)]n(2) with the SARS-CoV-2 Omicron variant receptor protein through the negative value of binding affinity. Molecular docking of Nil(ii) complexes [Ni(L)]2(1) and [Ni(L)]n(2) with a DNA duplex (PDB ID: 7D3T) and RNA (PDB ID: 7TDC) binding protein was also studied. Overall, this study suggests that Ni(ii) complexes can be considered as drug candidates against the Omicron variants of SARS-CoV-2.
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Affiliation(s)
- Simranjeet Singh
- Department of Chemistry, National Institute of Technology Patna Patna-800005 Bihar India
| | - Mukesh Choudhary
- Department of Chemistry, National Institute of Technology Patna Patna-800005 Bihar India
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Korusenko PM, Petrova OV, Vereshchagin AA, Katin KP, Levin OV, Nekipelov SV, Sivkov DV, Sivkov VN, Vinogradov AS. A Comparative XPS, UV PES, NEXAFS, and DFT Study of the Electronic Structure of the Salen Ligand in the H 2(Salen) Molecule and the [Ni(Salen)] Complex. Int J Mol Sci 2023; 24:9868. [PMID: 37373016 DOI: 10.3390/ijms24129868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 06/03/2023] [Accepted: 06/06/2023] [Indexed: 06/29/2023] Open
Abstract
A comparative study of the electronic structure of the salen ligand in the H2(Salen) molecule and the [Ni(Salen)] complex was performed using the experimental methods of XPS, UV PES, and NEXAFS spectroscopy along with DFT calculations. Significant chemical shifts of +1.0 eV (carbon), +1.9 eV (nitrogen), and -0.4 eV (oxygen) were observed in the 1s PE spectra of the salen ligand atoms when passing from a molecule to a complex, unambiguously indicating a substantial redistribution of the valence electron density between these atoms. It is proposed that the electron density transfer to the O atoms in [Ni(Salen)] occurred not only from the Ni atom, but also from the N and C atoms. This process seemed to be realized through the delocalized conjugated π-system of the phenol C 2p electronic states of the ligand molecule. The DFT calculations (total and partial DOS) for the valence band H2(Salen) and [Ni(Salen)] described well the spectral shape of the UV PE spectra of both compounds and confirmed their experimental identification. An analysis of the N and O 1s NEXAFS spectra clearly indicated that the atomic structure of the ethylenediamine and phenol fragments was retained upon passing from the free salen ligand to the nickel complex.
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Affiliation(s)
- Petr M Korusenko
- Department of Solid State Electronics, V.A. Fock Institute of Physics, St. Petersburg State University, 7/9 Universitetskaya nab., 199034 Saint Petersburg, Russia
| | - Olga V Petrova
- Department of Solid State Electronics, V.A. Fock Institute of Physics, St. Petersburg State University, 7/9 Universitetskaya nab., 199034 Saint Petersburg, Russia
- Institute of Physics and Mathematics, Komi Science Centre, Ural Branch of the Russian Academy of Sciences, 167982 Syktyvkar, Russia
| | - Anatoliy A Vereshchagin
- Department of Electrochemistry, Institute of Chemistry, St. Petersburg State University, 7/9 Universitetskaya nab., 199034 Saint Petersburg, Russia
| | - Konstantin P Katin
- Department of Condensed Matter Physics, National Research Nuclear University "MEPhI", Kashirskoe Sh. 31, 115409 Moscow, Russia
| | - Oleg V Levin
- Department of Electrochemistry, Institute of Chemistry, St. Petersburg State University, 7/9 Universitetskaya nab., 199034 Saint Petersburg, Russia
| | - Sergey V Nekipelov
- Institute of Physics and Mathematics, Komi Science Centre, Ural Branch of the Russian Academy of Sciences, 167982 Syktyvkar, Russia
| | - Danil V Sivkov
- Department of Solid State Electronics, V.A. Fock Institute of Physics, St. Petersburg State University, 7/9 Universitetskaya nab., 199034 Saint Petersburg, Russia
- Institute of Physics and Mathematics, Komi Science Centre, Ural Branch of the Russian Academy of Sciences, 167982 Syktyvkar, Russia
| | - Victor N Sivkov
- Institute of Physics and Mathematics, Komi Science Centre, Ural Branch of the Russian Academy of Sciences, 167982 Syktyvkar, Russia
| | - Alexander S Vinogradov
- Department of Solid State Electronics, V.A. Fock Institute of Physics, St. Petersburg State University, 7/9 Universitetskaya nab., 199034 Saint Petersburg, Russia
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Man LL, La YT, Feng LC, Zhang Y, Dong WK. Investigation of syntheses, structures, theoretical calculations, and fluorescence properties of two N 3O-donor half-salamo-type Cu(II) complexes. J COORD CHEM 2022. [DOI: 10.1080/00958972.2022.2147000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Li-Li Man
- Key Laboratory of Yellow River Water Environment in Gansu Province, Lanzhou Jiaotong University, Lanzhou, Gansu, China
- School of Chemistry and Chemical Engineering, Lanzhou Jiaotong University, Lanzhou, Gansu, China
| | - Ya-Ting La
- School of Chemistry and Chemical Engineering, Lanzhou Jiaotong University, Lanzhou, Gansu, China
| | - Le-Chuan Feng
- School of Chemistry and Chemical Engineering, Lanzhou Jiaotong University, Lanzhou, Gansu, China
| | - Yang Zhang
- School of Chemistry and Chemical Engineering, Lanzhou Jiaotong University, Lanzhou, Gansu, China
| | - Wen-Kui Dong
- Key Laboratory of Yellow River Water Environment in Gansu Province, Lanzhou Jiaotong University, Lanzhou, Gansu, China
- School of Chemistry and Chemical Engineering, Lanzhou Jiaotong University, Lanzhou, Gansu, China
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Korusenko PM, Koroleva AV, Vereshchagin AA, Sivkov DV, Petrova OV, Levin OV, Vinogradov AS. The Valence Band Structure of the [Ni(Salen)] Complex: An Ultraviolet, Soft X-ray and Resonant Photoemission Spectroscopy Study. Int J Mol Sci 2022; 23:ijms23116207. [PMID: 35682886 PMCID: PMC9181502 DOI: 10.3390/ijms23116207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 05/29/2022] [Accepted: 05/30/2022] [Indexed: 11/16/2022] Open
Abstract
The valence band photoemission (VB PE) spectra of the [Ni(Salen)] molecular complex were measured by ultraviolet, soft X-ray and resonant photoemission (ResPE) using photons with energies ranging from 21.2 eV to 860 eV. It was found that the Ni 3d atomic orbitals' (AOs) contributions are most significant for molecular orbitals (MOs), which are responsible for the low-energy PE band at a binding energy of 3.8 eV in the VB PE spectra. In turn, the PE bands in the binding energies range of 8-16 eV are due to the photoionization of the MOs of the [Ni(Salen)] complex with dominant contributions from C 2p AOs. A detailed consideration was made for the ResPE spectra obtained using photons with absorption resonance energies in the Ni 2p3/2, N 1s, and O 1s Near-Edge X-ray Absorption Fine Structure (NEXAFS) spectra. A strong increase in the intensity of the PE band ab was found when using photons with an energy 854.4 eV in the Ni 2p3/2 NEXAFS spectrum. This finding is due to the high probability of the participator-Auger decay of the Ni 2p3/2-13d9 excitation and confirms the relationship between the PE band ab with the Ni 3d-derived MOs.
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Affiliation(s)
- Petr M. Korusenko
- Department of Solid State Electronics, St. Petersburg State University, 7/9 Universitetskaya nab., 199034 Saint Petersburg, Russia; (D.V.S.); (O.V.P.); (A.S.V.)
- Department of Physics, Omsk State Technical University, 11 Mira prosp., 644050 Omsk, Russia
- Correspondence:
| | - Alexandra V. Koroleva
- Resource Center “Physical Methods of Surface Investigation”, St. Petersburg State University, 7/9 Universitetskaya nab., 199034 Saint Petersburg, Russia;
| | - Anatoliy A. Vereshchagin
- Department of Electrochemistry, Institute of Chemistry, St. Petersburg State University, 7/9 Universitetskaya nab., 199034 Saint Petersburg, Russia; (A.A.V.); (O.V.L.)
| | - Danil V. Sivkov
- Department of Solid State Electronics, St. Petersburg State University, 7/9 Universitetskaya nab., 199034 Saint Petersburg, Russia; (D.V.S.); (O.V.P.); (A.S.V.)
- Institute of Physics and Mathematics, Komi Science Centre, Ural Branch of the Russian Academy of Sciences, 167982 Syktyvkar, Russia
| | - Olga V. Petrova
- Department of Solid State Electronics, St. Petersburg State University, 7/9 Universitetskaya nab., 199034 Saint Petersburg, Russia; (D.V.S.); (O.V.P.); (A.S.V.)
- Institute of Physics and Mathematics, Komi Science Centre, Ural Branch of the Russian Academy of Sciences, 167982 Syktyvkar, Russia
| | - Oleg V. Levin
- Department of Electrochemistry, Institute of Chemistry, St. Petersburg State University, 7/9 Universitetskaya nab., 199034 Saint Petersburg, Russia; (A.A.V.); (O.V.L.)
| | - Alexander S. Vinogradov
- Department of Solid State Electronics, St. Petersburg State University, 7/9 Universitetskaya nab., 199034 Saint Petersburg, Russia; (D.V.S.); (O.V.P.); (A.S.V.)
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