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Ahmed M, Gupta MK, Ansari A. DFT and TDDFT exploration on the role of pyridyl ligands with copper toward bonding aspects and light harvesting. J Mol Model 2023; 29:358. [PMID: 37919553 DOI: 10.1007/s00894-023-05765-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 10/24/2023] [Indexed: 11/04/2023]
Abstract
CONTEXT Schiff base-containing metal complexes have been the subject of extensive research. In this work, a coordination polymer-derived complex called [Cu(L)] that is solution-stable (L = 2-(2-hydroxybenzylidene-amino)phenol) has been explored theoretically with five different pyridyl-based ligands using DFT/TDDFT in order to understand the structural-functional and electronic transitions of these five complexes. Frontier molecular orbital (FMO) analysis was carried out to assess the reactivity behavior of all five complexes. For the purpose of studying the charge energy distribution over complexes, electrostatic potential maps were also drawn. Furthermore, in order to identify any stabilizing interactions that may be present in the given complexes, an NBO analysis was studied. To learn more about any potential correlations between the properties of these five complexes, a comparative analysis was explored. Our calculations demonstrate that complex 3 having pyridine-4-carboxamide as a ligand has a lower energy gap and a higher negative electrostatic potential which may indicate its higher reactivity and this may be due to the electron withdrawing group (carboxamide). TDDFT results show that the highest light harvesting efficiency (LHE) of all the studied complexes is found in the range of 440-448 nm. Complexes 1, 2, and 4 show the higher light harvesting efficiency as compared to complexes 3 and 5. Our findings are in good accordance with the available experimental data. METHODS All DFT computations were performed using the Gaussian16 with unrestricted B3LYP-D2 functional with the basis sets 6-31G(d,p) for O, N, C, and H while LanL2DZ for Cu. The polarized continuum model (PCM) was used for the solvation. The software GaussView6.1 was utilized for the modeling of initial geometries and the plotting of MEP maps. The NBO6.0 program which is incorporated in Gaussian16 was utilized to investigate the bonding nature and stabilization energies of the complexes. The ORCA program was used to simulate the absorption spectra.
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Affiliation(s)
- Mukhtar Ahmed
- Department of Chemistry, Central University of Haryana, Mahendergarh, Haryana, 123031, India
| | - Manoj Kumar Gupta
- Department of Chemistry, Central University of Haryana, Mahendergarh, Haryana, 123031, India
| | - Azaj Ansari
- Department of Chemistry, Central University of Haryana, Mahendergarh, Haryana, 123031, India.
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Monika, Kumar M, Somi, Sarkar A, Gupta MK, Ansari A. Theoretical study of the formation of metal-oxo species of the first transition series with the ligand 14-TMC: driving factors of the "Oxo Wall". Dalton Trans 2023; 52:14160-14169. [PMID: 37750348 DOI: 10.1039/d3dt02109b] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/27/2023]
Abstract
Terminal metal-oxo species of the early transition metal series are well known, whereas those for the late transition series are rare, and this is related to the "Oxo Wall". Here, we have undertaken a theoretical study on the formation of metal-oxo species from the metal hydroperoxo species of the 3d series (Cr, Mn, Fe, Co, Ni, and Cu) with the ligand 14-TMC (1,4,8,11-tetramethyl-1,4,8,11-tetraazacyclotetradecane) via O⋯O bond cleavage. DFT calculations reveal that the barrier for O⋯O bond cleavage is higher with the late transition metals (Co, Ni, and Cu) than the early transition metals (Cr, Mn, and Fe), and the formed late metal-oxo species are also thermodynamically less stable. The higher barrier may be due to electronic repulsion because of the pairing of d electrons. In the late transition metal series, the electron goes into an antibonding orbital, which decreases the bond order and hence decreases the possibility of metal-oxo formation. Computed structural parameters and spin densities suggest that valence tautomerism occurs in the late transition metal-oxo species which remain as a metal-oxyl. Our findings support the concept of the "Oxo Wall".
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Affiliation(s)
- Monika
- Department of Chemistry, Central University of Haryana, Mahendergarh-123031, Haryana, India.
| | - Manjeet Kumar
- Department of Chemistry, Central University of Haryana, Mahendergarh-123031, Haryana, India.
| | - Somi
- Department of Chemistry, Central University of Haryana, Mahendergarh-123031, Haryana, India.
| | - Arup Sarkar
- Department of Chemistry, The University of Chicago 5735 South Ellis Avenue, Chicago, IL 60637, USA
| | - Manoj Kumar Gupta
- Department of Chemistry, Central University of Haryana, Mahendergarh-123031, Haryana, India.
| | - Azaj Ansari
- Department of Chemistry, Central University of Haryana, Mahendergarh-123031, Haryana, India.
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Yadav O, Ansari M, Ansari A. Electronic structures, bonding aspects and spectroscopic parameters of homo/hetero valent bridged dinuclear transition metal complexes. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 278:121331. [PMID: 35597159 DOI: 10.1016/j.saa.2022.121331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 04/25/2022] [Accepted: 04/27/2022] [Indexed: 06/15/2023]
Abstract
Bridged dinuclear metal complexes have fascinated scientists worldwide, and remarkable success has been achieved to unravel the electronic structures, structure-function relationship, coordination environments, and fine mechanistic details of the enzymes owing to the repercussion of biomimetic studies carried out on dinuclear model systems. Molecular level study of these systems integrated with spectroscopic study helps in gaining deep insights about structural and electronic aspects of natural enzymatic systems. Considering the same, here first time we report DFT study on bridged non-heme metal complexes based on N-Et-HPTB ligand system containing homovalent (MIIMII); {[(MnII)2(O2CCH3)(N-Et-HPTB)]2+; Species I), [(FeII)2(O2CCH3)(N-Et-HPTB)]2+; Species II), [(CoII)2(O2CCH3)(N-Et-HPTB)]2+; Species III)} and heterovalent (MIIIMII): {[(MnIII)(MnII)(O2)(N-Et-HPTB)]2+; Species Ia) [(FeIII)(FeII)(O2)(N-Et-HPTB)]2+; Species IIa) and [(CoIII)(CoII)(O2)(N-Et-HPTB)]2+; Species IIIa)} dinuclear metal centres. Bridging oxygen bears a significant spin density which may prompt important chemical reactions involving activation of bonds like C-H/O-H/N-H etc. TD-DFT calculations for UV-Visible absorption have been carried out to further shed light on structural-functional and electronic structures of these dinuclear species. Studying these dinuclear species may be a good starting point for the study of active sites of the bimetallic centre of dinuclear enzymes and thus may serve as fascinating spectroscopic models. Further, FMO analysis, MEP mapping, and NBO calculations were employed to analyze bonding aspects predict theoretical reactivity behaviour and any kind of stabilizing interactions present in the reported species.
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Affiliation(s)
- Oval Yadav
- Department of Chemistry, Central University of Haryana, Mahendergarh 123031, India
| | - Mursaleem Ansari
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai, Pawai 400076, India
| | - Azaj Ansari
- Department of Chemistry, Central University of Haryana, Mahendergarh 123031, India.
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Yadav O, Kumar M, Mittal H, Yadav K, Seidel V, Ansari A. Theoretical exploration on structures, bonding aspects and molecular docking of α-aminophosphonate ligated copper complexes against SARS-CoV-2 proteases. Front Pharmacol 2022; 13:982484. [PMID: 36263127 PMCID: PMC9575937 DOI: 10.3389/fphar.2022.982484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 08/24/2022] [Indexed: 11/13/2022] Open
Abstract
Recent years have witnessed a growing interest in the biological activity of metal complexes of α-aminophosphonates. Here for the first time, a detailed DFT study on five α-aminophosphonate ligated mononuclear/dinuclear CuII complexes is reported using the dispersion corrected density functional (B3LYP-D2) method. The electronic structures spin densities, FMO analysis, energetic description of spin states, and theoretical reactivity behaviour using molecular electrostatic potential (MEP) maps of all five species are reported. All possible spin states of the dinuclear species were computed and their ground state S values were determined along with the computation of their magnetic coupling constants. NBO analysis was also performed to provide details on stabilization energies. A molecular docking study was performed for the five complexes against two SARS-CoV-2 coronavirus protein targets (PDB ID: 6LU7 and 7T9K). The docking results indicated that the mononuclear species had a higher binding affinity for the targets compared to the dinuclear species. Among the species investigated, species I showed the highest binding affinity with the SARS-CoV-2 Omicron protease. NPA charge analysis showed that the heteroatoms of model species III had a more nucleophilic nature. A comparative study was performed to observe any variations and/or correlations in properties among all species.
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Affiliation(s)
- Oval Yadav
- Department of Chemistry, Central University of Haryana, Mahendergarh, India
| | - Manjeet Kumar
- Department of Chemistry, Central University of Haryana, Mahendergarh, India
| | - Himanshi Mittal
- Department of Chemistry, Central University of Haryana, Mahendergarh, India
| | - Kiran Yadav
- Department of Chemistry, Central University of Haryana, Mahendergarh, India
| | - Veronique Seidel
- Natural Products Research Laboratory, Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
| | - Azaj Ansari
- Department of Chemistry, Central University of Haryana, Mahendergarh, India
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Monika, Ansari A. Electronic structures and energetic of metal(II)-superoxo species: a DFT exploration. Struct Chem 2022. [DOI: 10.1007/s11224-022-02030-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Mohapatra RK, Azam M, Mohapatra PK, Sarangi AK, Abdalla M, Perekhoda L, Yadav O, Al-Resayes SI, Jong-Doo K, Dhama K, Ansari A, Seidel V, Verma S, Raval MK. Computational studies on potential new anti-Covid-19 agents with a multi-target mode of action. JOURNAL OF KING SAUD UNIVERSITY. SCIENCE 2022; 34:102086. [PMID: 35582633 PMCID: PMC9101701 DOI: 10.1016/j.jksus.2022.102086] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 04/25/2022] [Accepted: 05/09/2022] [Indexed: 05/28/2023]
Abstract
A compound that could inhibit multiple targets associated with SARS-CoV-2 infection would prove to be a drug of choice against the virus. Human receptor-ACE2, receptor binding domain (RBD) of SARS-CoV-2 S-protein, Papain-like protein of SARS-CoV-2 (PLpro), reverse transcriptase of SARS-CoV-2 (RdRp) were chosen for in silico study. A set of previously synthesized compounds (1-5) were docked into the active sites of the targets. Based on the docking score, ligand efficiency, binding free energy, and dissociation constants for a definite conformational position of the ligand, inhibitory potentials of the compounds were measured. The stability of the protein-ligand (P-L) complex was validated in silico by using molecular dynamics simulations using the YASARA suit. Moreover, the pharmacokinetic properties, FMO and NBO analysis were performed for ranking the potentiality of the compounds as drug. The geometry optimizations and electronic structures were investigated using DFT. As per the study, compound-5 has the best binding affinity against all four targets. Moreover, compounds 1, 3 and 5 are less toxic and can be considered for oral consumption.
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Affiliation(s)
- Ranjan K Mohapatra
- Department of Chemistry, Government College of Engineering, Keonjhar, Odisha 758002, India
| | - Mohammad Azam
- Department of Chemistry, College of Science, King Saud University, PO BOX 2455, Riyadh 11451, Saudi Arabia
| | - Pranab K Mohapatra
- Department of Chemistry, C. V. Raman Global University, Bidyanagar, Mahura, Janla, Bhubaneswar, Odisha 752054, India
| | - Ashish K Sarangi
- Department of Chemistry, School of Applied Sciences, Centurion University of Technology and Management, Odisha, India
| | - Mohnad Abdalla
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Pharmaceutics, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 Cultural West Road, Shandong Province 250012, PR China
| | - Lina Perekhoda
- Department of Medicinal Chemistry, National University of Pharmacy, Pushkinska Str. 53, Kharkiv 61002, Ukraine
| | - Oval Yadav
- Department of Chemistry, Central University of Haryana, Mahendergarh, Haryana 123031, India
| | - Saud I Al-Resayes
- Department of Chemistry, College of Science, King Saud University, PO BOX 2455, Riyadh 11451, Saudi Arabia
| | - Kim Jong-Doo
- Buddhist Culture College, Dongguk University, Gyeongju-si, Gyeongsangbuk-do 780-714, South Korea
| | - Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly-243122, Uttar Pradesh, India
| | - Azaj Ansari
- Department of Chemistry, Central University of Haryana, Mahendergarh, Haryana 123031, India
| | - Veronique Seidel
- Natural Products Research Laboratory, Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow G4 0RE, United Kingdom
| | - Sarika Verma
- Council of Scientific and Industrial Research-Advanced Materials and Processes Research Institute, Bhopal, MP 462026, India
- Academy of Council Scientific and Industrial Research - Advanced Materials and Processes Research Institute (AMPRI), Hoshangabad Road, Bhopal, M.P 462026, India
| | - Mukesh K Raval
- Department of Chemistry, G. M. University, Sambalpur, Odisha, India
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Yadav O, Ansari M, Ansari A. Electronic structures, bonding and energetics of non-heme mono and dinuclear iron-TPA complexes: a computational exploration. Struct Chem 2021. [DOI: 10.1007/s11224-021-01775-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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