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Baliza LRSP, Freitas TR, Gonçalves EKS, Antunes GR, Souza AJF, Yoneda J, Duarte CL, Andrade SN, de Paula Sabino A, Varotti FP, Sangi DP. Synthesis and cytotoxic evaluation of heterocyclic compounds by vinylic substitution of ketene dithioacetals. Chem Biol Drug Des 2024; 104:e14581. [PMID: 38997237 DOI: 10.1111/cbdd.14581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 05/27/2024] [Accepted: 07/01/2024] [Indexed: 07/14/2024]
Abstract
N-heterocyclic compounds are important molecular scaffolds in the search for new drugs, since most drugs contain heterocyclic moieties in their molecular structure, and some of these classes of heterocycles are able to provide ligands for two or more biological targets. Ketene dithioacetals are important building blocks in organic synthesis and are widely used in the synthesis of N-heterocyclic compounds. In this work, we used double vinylic substitution reactions on ketene dithioacetals to synthesize a small library of heterocyclic derivatives and evaluated their cytotoxic activity in breast and ovarian cancer cells, identifying two benzoxazoles with good potency and selectivity. In silico predictions indicate that the two most active derivatives exhibit physicochemical properties within the range of drug-like compounds and showed potential to interact with HDAC8 and ERK1 cancer-related targets.
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Affiliation(s)
- Larissa R S P Baliza
- Departamento de Química, Instituto de Ciências Exatas, Universidade Federal Fluminense, Rio de Janeiro, Brazil
| | - Túlio R Freitas
- Departamento de Análises Clínicas e Toxicológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Edward K S Gonçalves
- Departamento de Química, Instituto de Ciências Exatas, Universidade Federal Fluminense, Rio de Janeiro, Brazil
| | - Gabriel R Antunes
- Departamento de Química, Instituto de Ciências Exatas, Universidade Federal Fluminense, Rio de Janeiro, Brazil
| | - Ana J F Souza
- Departamento de Química, Instituto de Ciências Exatas, Universidade Federal Fluminense, Rio de Janeiro, Brazil
| | - Julliane Yoneda
- Departamento de Química, Instituto de Ciências Exatas, Universidade Federal Fluminense, Rio de Janeiro, Brazil
| | - Caique Lopes Duarte
- Centro de Ciências da Saúde, Universidade Federal de São João Del-Rei, Divinópolis, Minas Gerais, Brazil
| | - Silmara N Andrade
- Centro de Ciências da Saúde, Universidade Federal de São João Del-Rei, Divinópolis, Minas Gerais, Brazil
| | - Adriano de Paula Sabino
- Departamento de Análises Clínicas e Toxicológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Fernando P Varotti
- Centro de Ciências da Saúde, Universidade Federal de São João Del-Rei, Divinópolis, Minas Gerais, Brazil
| | - Diego P Sangi
- Departamento de Química, Instituto de Ciências Exatas, Universidade Federal Fluminense, Rio de Janeiro, Brazil
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2
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Olukunle OF, Olowosoke CB, Khalid A, Oke GA, Omoboyede V, Umar HI, Ibrahim O, Adeboboye CF, Iwaloye O, Olawale F, Adedeji AA, Bello T, Alabere HO, Chukwuemeka PO. Identification of a 1, 8-naphthyridine-containing compound endowed with the inhibition of p53-MDM2/X interaction signaling: a computational perspective. Mol Divers 2024; 28:1109-1127. [PMID: 37029281 DOI: 10.1007/s11030-023-10637-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 03/17/2023] [Indexed: 04/09/2023]
Abstract
Various studies have established that molecules specific for MDMX inhibition or optimized for dual inhibition of p53-MDM2/MDMX interaction signaling are more suitable for activating the Tp53 gene in tumor cells. Nevertheless, there are sparse numbers of approved molecules to treat the health consequences brought by the lost p53 functions in tumor cells. Consequently, this study explored the potential of a small molecule ligand containing 1, 8-naphthyridine scaffold to act as a dual inhibitor of p53-MDM2/X interactions using computational methods. The results obtained from quantum mechanical calculations revealed our studied compound entitled CPO is more stable but less reactive compared to standard dual inhibitor RO2443. Like RO2443, CPO also exhibited good non-linear optical properties. The results of molecular docking studies predicted that CPO has a higher potential to inhibit MDM2/MDMX than RO2443. Furthermore, CPO was stable over 50 ns molecular dynamics (MD) simulation in complex with MDM2 and MDMX respectively. On the whole, CPO also exhibited good drug-likeness and pharmacokinetics properties compared to RO2443 and was found with more anti-cancer activity than RO2443 in bioactivity prediction. CPO is anticipated to elevate effectiveness and alleviate drug resistance in cancer therapy. Ultimately, our results provide an insight into the mechanism that underlay the inhibition of p53-MDM2/X interactions by a molecule containing 1, 8-naphthyridine scaffold in its molecular structure.
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Affiliation(s)
- Oluwatoyin Folake Olukunle
- Department of Biotechnology, School of Life Sciences (SLS), Federal University of Technology Akure, P.M.B 704, Akure, Ondo, Nigeria
| | - Christopher Busayo Olowosoke
- Department of Biotechnology, School of Life Sciences (SLS), Federal University of Technology Akure, P.M.B 704, Akure, Ondo, Nigeria
| | - Aqsa Khalid
- Research Center for Modelling and Simulation (RCMS), National University of Science and Technology (NUST), Islamabad, Pakistan
| | - Grace Ayomide Oke
- Department of Food Science and Technology, School of Agriculture and Agricultural Technology (SAAT), Federal University of Technology Akure, P.M.B 704, Akure, Ondo, Nigeria
| | - Victor Omoboyede
- Department of Biochemistry, School of Life Sciences (SLS), Federal University of Technology Akure, P.M.B 704, Akure, Ondo, Nigeria
- Computer Aided Therapeutics and Drug Design (CATDD) Group, School of Life Sciences (SLS), Federal University of Technology Akure, P.M.B 704, Akure, Ondo, Nigeria
| | - Haruna Isiyaku Umar
- Department of Biochemistry, School of Life Sciences (SLS), Federal University of Technology Akure, P.M.B 704, Akure, Ondo, Nigeria
- Computer Aided Therapeutics and Drug Design (CATDD) Group, School of Life Sciences (SLS), Federal University of Technology Akure, P.M.B 704, Akure, Ondo, Nigeria
| | - Ochapa Ibrahim
- Faculty of Pharmaceutical Sciences, Ahmadu Bello University, Zaria, Kaduna, Nigeria
| | - Covenant Femi Adeboboye
- Department of Microbiology, School of Life Sciences (SLS), Federal University of Technology Akure, P.M.B 704, Akure, Ondo, Nigeria
| | - Opeyemi Iwaloye
- Department of Biochemistry, School of Life Sciences (SLS), Federal University of Technology Akure, P.M.B 704, Akure, Ondo, Nigeria
| | - Femi Olawale
- Nano-Gene and Drug Delivery Group, Department of Biochemistry, School of Life Sciences, University of Kwazulu Natal, Durban, 4000, South Africa
- Department of Biochemistry, University of Lagos, Lagos, Nigeria
| | - Ayodeji Adeola Adedeji
- Department of Biochemistry, School of Life Sciences (SLS), Federal University of Technology Akure, P.M.B 704, Akure, Ondo, Nigeria
| | - Taye Bello
- Department of Medical Rehabilitation, College of Health Sciences, Obafemi Awolowo University, Ile-Ife, Osun, Nigeria
| | - Hafsat Olateju Alabere
- Computer Aided Therapeutics and Drug Design (CATDD) Group, School of Life Sciences (SLS), Federal University of Technology Akure, P.M.B 704, Akure, Ondo, Nigeria
- Department of Microbiology, School of Life Sciences (SLS), Federal University of Technology Akure, P.M.B 704, Akure, Ondo, Nigeria
| | - Prosper Obed Chukwuemeka
- Department of Biotechnology, School of Life Sciences (SLS), Federal University of Technology Akure, P.M.B 704, Akure, Ondo, Nigeria.
- Computer Aided Therapeutics and Drug Design (CATDD) Group, School of Life Sciences (SLS), Federal University of Technology Akure, P.M.B 704, Akure, Ondo, Nigeria.
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3
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Olukunle OF, Omoboyede V, Chukwuemeka PO. Network pharmacology and molecular docking-based identification of drug candidates and key targets of Allium sativum for colorectal cancer treatment. J Biomol Struct Dyn 2024; 42:4442-4455. [PMID: 37325859 DOI: 10.1080/07391102.2023.2220823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 05/28/2023] [Indexed: 06/17/2023]
Abstract
Colorectal cancer (CRC) is a type of cancer with high morbidity and mortality in several developing and developed countries of the world. Its mortality and morbidity are predicted to increase over the next decade, hence, efforts aimed at combating it have remained unabated. In the context of its treatment, the use of chemotherapeutics is often limited by challenges including cost-ineffectiveness, side effects, and drug resistance. Hence, medicinal plants are actively being explored for alternatives. In this study, Allium sativum (A. sativum) was explored for the discovery of key compounds that are worthy of exploration in the context of CRC treatment and the potential mechanism of its anti-CRC effects. The bioactive compounds of A. sativum were retrieved and subjected to drug-likeness and pharmacokinetics properties evaluation, the putative targets of compounds with admirable properties were predicted using PharmMapper while the targets of CRC were retrieved from GeneCards. The interactions between the targets common to both were retrieved from the String database while Cytoscape software was used to visualize and analyze the interactions. Gene set enrichment analysis (GSEA) study revealed the biological processes and pathways A. sativum could potentially restore in CRC. These analyses revealed the key targets via which A. sativum compounds exert their anti-CRC properties, while molecular docking studies of the key compounds against the key targets revealed beta-sitosterol and alpha-bisabolene as the compounds with the highest binding affinity for the key targets. Ultimately, further experimental studies are needed to validate the findings of this study.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Oluwatoyin Folake Olukunle
- Department of Biotechnology, School of Life Sciences (SLS), Federal University of Technology Akure, Akure, Nigeria
| | - Victor Omoboyede
- Department of Biochemistry, School of Life Sciences (SLS), Federal University of Technology Akure, Akure, Nigeria
- Computer-Aided therapeutic laboratory (CATL), School of Life Sciences (SLS), Federal University of Technology, Akure, Nigeria
| | - Prosper Obed Chukwuemeka
- Department of Biotechnology, School of Life Sciences (SLS), Federal University of Technology Akure, Akure, Nigeria
- Computer-Aided therapeutic laboratory (CATL), School of Life Sciences (SLS), Federal University of Technology, Akure, Nigeria
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4
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Tromer RM, Felix IM, Pereira LFC, da Luz MGE, Junior LAR, Galvão DS. Lattice thermal conductivity of 2D nanomaterials: a simple semi-empirical approach. Phys Chem Chem Phys 2023; 25:28703-28715. [PMID: 37849351 DOI: 10.1039/d3cp02896h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2023]
Abstract
Extracting reliable information on certain physical properties of materials, such as thermal transport, can be computationally very demanding. Aiming to overcome such difficulties in the particular case of lattice thermal conductivity (LTC) of 2D nanomaterials, we propose a simple, fast, and accurate semi-empirical approach for LTC calculation. The approach is based on parameterized thermochemical equations and Arrhenius-like fitting procedures, thus avoiding molecular dynamics or ab initio protocols, which frequently require computationally expensive simulations. As a proof of concept, we obtain the LTC of some prototypical physical systems, such as graphene (and other 2D carbon allotropes), hexagonal boron nitride (hBN), silicene, germanene, binary, and ternary BNC lattices and two examples of the fullerene network family. Our obtained values are in good agreement with other theoretical and experimental estimations, nonetheless, being derived in a rather straightforward way, at a fraction of the usual computational cost.
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Affiliation(s)
- R M Tromer
- Applied Physics Department, State University of Campinas, Campinas-SP, 13083-970, Brazil.
- Center for Computing in Engineering & Sciences, Unicamp, Campinas-SP, Brazil
| | - I M Felix
- Departamento de Física, Universidade Federal do Rio Grande do Norte, Natal-RN, 59078-970, Brazil
| | - L F C Pereira
- Departamento de Física, Universidade Federal de Pernambuco, Recife-PE, 50670-901, Brazil
| | - M G E da Luz
- Departamento de Física, Universidade Federal do Paraná, Curitiba-PR, 81531-980, Brazil.
| | - L A Ribeiro Junior
- Institute of Physics, University of Brasília, Brasília-DF, 70910-970, Brazil.
| | - D S Galvão
- Applied Physics Department, State University of Campinas, Campinas-SP, 13083-970, Brazil.
- Center for Computing in Engineering & Sciences, Unicamp, Campinas-SP, Brazil
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5
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Bourhia M, Shahab M, Zheng G, Bin Jardan YA, Sitotaw B, Ouahmane L, Khallouki F. Napthyridine-derived compounds as promising inhibitors for Staphylococcus aureus CrtM: a primer for the discovery of potential anti- Staphylococcus aureus agents. Front Microbiol 2023; 14:1279082. [PMID: 37954245 PMCID: PMC10635275 DOI: 10.3389/fmicb.2023.1279082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 09/25/2023] [Indexed: 11/14/2023] Open
Abstract
The disease-free existence of humans is constantly under attack by a variety of infections caused by a variety of organisms including bacteria. Notable among the bacteria is Staphylococcus aureus which is an etiological organism for infections including impetigo, folliculitis, and furuncles. The response of the human immune system against this disease is often neutralized by the production of a pigment called Staphyloxanthin (STX) via a series of reactions mediated by several enzymes. Among these enzymes, dehydrosqualene synthase, also known as CrtM, has emerged as a viable drug target due to its role in mediating the first step of the pathway. Consequently, this study employs molecular modeling approaches including molecular docking, quantum mechanical calculations, and molecular dynamics (MD) simulations among others to investigate the potential of napthyridine derivatives to serve as inhibitors of the CrtM. The results of the study revealed the high binding affinities of the compounds for the target as demonstrated by their docking scores, while further subjection to screening pipeline aimed at determining their fitness for development into drugs revealed just one compound namely 6-[[1-[(2-fluorophenyl) methyl]triazol-4-yl]methoxy]-4-oxo-1H-1,5-naphthyridine-3-carboxylic acid as the compound with good drug-like, pharmacokinetics, and toxicity properties profiles. A 100 ns-long MD simulation of the complexes formed after molecular docking revealed the stable interaction of the compound with the target. Ultimately, this study can be a promising outlet to discover a weapon to fight against clinically resistant bacteria, however, further experimental studies are suggested to carry out in the wet lab, pre-clinical, and clinical levels.
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Affiliation(s)
- Mohammed Bourhia
- Department of Chemistry and Biochemistry, Faculty of Medicine and Pharmacy, Ibn Zohr University, Laayoune, Morocco
| | - Muhammad Shahab
- State Key Laboratories of Chemical Resources Engineering, Beijing University of Chemical Technology, Beijing, China
| | - Guojun Zheng
- State Key Laboratories of Chemical Resources Engineering, Beijing University of Chemical Technology, Beijing, China
| | - Yousef A. Bin Jardan
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Baye Sitotaw
- Department of Biology, Bahir Dar University, Bahir Dar, Ethiopia
| | - Lahcen Ouahmane
- Laboratory of Microbial Biotechnologies, Agrosciences and Environment (BioMAgE), Labeled Research Unit-CNRSTN°4, Cadi Ayyad University, Marrakesh, Morocco
| | - Farid Khallouki
- Department of Biology, FSTE, University Moulay Ismail, Errachidia, Morocco
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6
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Ali A, Ahmed Z, Rahisuddin, Iftikhar K. Pure red-light emitting europium based complexes as efficient UV light converters: synthesis, crystal structure and photoluminescence properties. Dalton Trans 2023; 52:14075-14087. [PMID: 37743694 DOI: 10.1039/d3dt01536j] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
This paper reports three new crystallographically characterized europium complexes with composition as follows: [Eu(fod)3(L1)] (1), [Eu(fod)3(L2)] (2) and [Eu(fod)3(L3)] (3) {L1 = benzimidazole (bzi), L2 = 4,7-diphenyl-1,10-phenanthroline (bath), L3 = 2-(2-pyridyl) benzimidazole (py-im) and fod = anion of 6,6,7,7,8,8,8-heptafluoro-2,2-dimethyl-3,5-octanedione (Hfod)}. The single crystal (SC) XRD analysis shows that complex 1 is seven-coordinated while complexes 2 and 3 are eight-coordinated with the geometrical structures of a mono-capped octahedron and a trigonal dodecahedron, respectively. The NMR spectra of the complexes validate the SC-XRD results in solution. The complexes are stable in solution as no dissociation of any ligand was observed in the NMR spectra of the complexes. The photophysical properties of the complexes in solution, solid state, and PMMA thin films were studied. The hypersensitive transition 5D0 → 7F2 dominates the emission spectra in all phases, showing the highly asymmetric environment around the Eu(III) ion. The bath ligand is found to be the best sensitizer of the Eu ion and hence complex 2 shows the strongest luminescence properties with the highest absolute quantum yield among the three complexes. The CIE coordinate analysis shows that pure red-luminescence is emitted by the Eu complexes in the solid state since the coordinates found in this phase are closer to the standard NTSC 1987 values. The optical band gaps were determined for the complexes and the observed values suggest that the complexes can have possible applications in the field of semiconductor materials.
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Affiliation(s)
- Asgar Ali
- Lanthanide Research Laboratory, Department of Chemistry, Jamia Millia Islamia, New Delhi 110025, India.
| | - Zubair Ahmed
- Lanthanide Research Laboratory, Department of Chemistry, Jamia Millia Islamia, New Delhi 110025, India.
- Department of Chemistry, School of Basic and Applied Sciences, Galgotias University, Greater Noida, India
| | - Rahisuddin
- Lanthanide Research Laboratory, Department of Chemistry, Jamia Millia Islamia, New Delhi 110025, India.
| | - K Iftikhar
- Lanthanide Research Laboratory, Department of Chemistry, Jamia Millia Islamia, New Delhi 110025, India.
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Pick LM, Wenzlaff J, Yousefi M, Davari MD, Ansorge-Schumacher MB. Lipase-Mediated Conversion of Protecting Group Silyl Ethers: An Unspecific Side Reaction. Chembiochem 2023; 24:e202300384. [PMID: 37224395 DOI: 10.1002/cbic.202300384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 05/24/2023] [Indexed: 05/26/2023]
Abstract
Silyl ether protecting groups are important tools in organic synthesis, ensuring selective reactions of hydroxyl functional groups. Enantiospecific formation or cleavage could simultaneously enable the resolution of racemic mixtures and thus significantly increase the efficiency of complex synthetic pathways. Based on reports that lipases, which today are already particularly important tools in chemical synthesis, can catalyze the enantiospecific turnover of trimethylsilanol (TMS)-protected alcohols, the goal of this study was to determine the conditions under which such a catalysis occurs. Through detailed experimental and mechanistic investigation, we demonstrated that although lipases mediate the turnover of TMS-protected alcohols, this occurs independently of the known catalytic triad, as this is unable to stabilize a tetrahedral intermediate. The reaction is essentially non-specific and therefore most likely completely independent of the active site. This rules out lipases as catalysts for the resolution of racemic mixtures of alcohols through protection or deprotection with silyl groups.
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Affiliation(s)
- Lisa M Pick
- Professur für Molekulare Biotechnologie, Technische Universität Dresden, 01062, Dresden, Germany
| | - Jessica Wenzlaff
- Professur für Molekulare Biotechnologie, Technische Universität Dresden, 01062, Dresden, Germany
| | - Mohammad Yousefi
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle, Germany
| | - Mehdi D Davari
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle, Germany
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8
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Ganaie AB, Iftikhar K. Structure, optical absorption and NIR-Photoluminescence of ternary Neodymium (III) complexes with fluorinated β-diketone and heterocyclic Lewis bases. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2022.134352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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9
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Alves FDM, Bellei JCB, Barbosa CDS, Duarte CL, da Fonseca AL, Pinto ACDS, Raimundo FO, Carpinter BA, Lemos ASDO, Coimbra ES, Taranto AG, Rocha VN, de Pilla Varotti F, Ribeiro Viana GH, Scopel KKG. Rational-Based Discovery of Novel β-Carboline Derivatives as Potential Antimalarials: From In Silico Identification of Novel Targets to Inhibition of Experimental Cerebral Malaria. Pathogens 2022; 11:pathogens11121529. [PMID: 36558863 PMCID: PMC9781199 DOI: 10.3390/pathogens11121529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 12/08/2022] [Accepted: 12/11/2022] [Indexed: 12/15/2022] Open
Abstract
Malaria is an infectious disease widespread in underdeveloped tropical regions. The most severe form of infection is caused by Plasmodium falciparum, which can lead to development of cerebral malaria (CM) and is responsible for deaths and significant neurocognitive sequelae throughout life. In this context and considering the emergence and spread of drug-resistant P. falciparum isolates, the search for new antimalarial candidates becomes urgent. β-carbolines alkaloids are good candidates since a wide range of biological activity for these compounds has been reported. Herein, we designed 20 chemical entities and performed an in silico virtual screening against a pool of P. falciparum molecular targets, the Brazilian Malaria Molecular Targets (BRAMMT). Seven structures showed potential to interact with PfFNR, PfPK7, PfGrx1, and PfATP6, being synthesized and evaluated for in vitro antiplasmodial activity. Among them, compounds 3−6 and 10 inhibited the growth of the W2 strain at µM concentrations, with low cytotoxicity against the human cell line. In silico physicochemical and pharmacokinetic properties were found to be favorable for oral administration. The compound 10 provided the best results against CM, with important values of parasite growth inhibition on the 5th day post-infection for both curative (67.9%) and suppressive (82%) assays. Furthermore, this compound was able to elongate mice survival and protect them against the development of the experimental model of CM (>65%). Compound 10 also induced reduction of the NO level, possibly by interaction with iNOS. Therefore, this alkaloid showed promising activity for the treatment of malaria and was able to prevent the development of experimental cerebral malaria (ECM), probably by reducing NO synthesis.
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Affiliation(s)
- Fernanda de Moura Alves
- Research Center on Biological Chemistry (NQBio), Federal University of São João Del Rei, Divinópolis 35501-296, Brazil
| | - Jessica Correa Bezerra Bellei
- Research Center Parasitology, Departament of Parasitology, Microbiology and Immunology, Federal University of Juiz de Fora, Juiz de Fora 36036-900, Brazil
| | - Camila de Souza Barbosa
- Research Center on Biological Chemistry (NQBio), Federal University of São João Del Rei, Divinópolis 35501-296, Brazil
| | - Caíque Lopes Duarte
- Research Center on Biological Chemistry (NQBio), Federal University of São João Del Rei, Divinópolis 35501-296, Brazil
| | - Amanda Luisa da Fonseca
- Research Center on Biological Chemistry (NQBio), Federal University of São João Del Rei, Divinópolis 35501-296, Brazil
| | - Ana Claudia de Souza Pinto
- Research Center on Biological Chemistry (NQBio), Federal University of São João Del Rei, Divinópolis 35501-296, Brazil
| | - Felipe Oliveira Raimundo
- Research Center Parasitology, Departament of Parasitology, Microbiology and Immunology, Federal University of Juiz de Fora, Juiz de Fora 36036-900, Brazil
| | - Bárbara Albuquerque Carpinter
- Research Center Parasitology, Departament of Parasitology, Microbiology and Immunology, Federal University of Juiz de Fora, Juiz de Fora 36036-900, Brazil
| | - Ari Sérgio de Oliveira Lemos
- Research Center Parasitology, Departament of Parasitology, Microbiology and Immunology, Federal University of Juiz de Fora, Juiz de Fora 36036-900, Brazil
| | - Elaine Soares Coimbra
- Research Center Parasitology, Departament of Parasitology, Microbiology and Immunology, Federal University of Juiz de Fora, Juiz de Fora 36036-900, Brazil
| | - Alex Gutterres Taranto
- Research Center on Biological Chemistry (NQBio), Federal University of São João Del Rei, Divinópolis 35501-296, Brazil
| | - Vinícius Novaes Rocha
- Research Center of Pathology and Veterinary Histology, Departament of Veterinary Medicine, Federal University of Juiz de Fora, Juiz de Fora 36036-900, Brazil
| | - Fernando de Pilla Varotti
- Research Center on Biological Chemistry (NQBio), Federal University of São João Del Rei, Divinópolis 35501-296, Brazil
- Correspondence: (F.d.P.V.); (K.K.G.S.)
| | | | - Kézia K. G. Scopel
- Research Center Parasitology, Departament of Parasitology, Microbiology and Immunology, Federal University of Juiz de Fora, Juiz de Fora 36036-900, Brazil
- Correspondence: (F.d.P.V.); (K.K.G.S.)
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10
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Balogun TA, Chukwudozie OS, Ogbodo UC, Junaid IO, Sunday OA, Ige OM, Aborode AT, Akintayo AD, Oluwarotimi EA, Oluwafemi IO, Saibu OA, Chuckwuemaka P, Omoboyowa DA, Alausa AO, Atasie NH, Ilesanmi A, Dairo G, Tiamiyu ZA, Batiha GE, Alkhuriji AF, Al-Megrin WAI, De Waard M, Sabatier JM. Discovery of putative inhibitors against main drivers of SARS-CoV-2 infection: Insight from quantum mechanical evaluation and molecular modeling. Front Chem 2022; 10:964446. [PMID: 36304744 PMCID: PMC9593047 DOI: 10.3389/fchem.2022.964446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 08/10/2022] [Indexed: 11/13/2022] Open
Abstract
SARS-CoV-2 triggered a worldwide medical crisis, affecting the world’s social, emotional, physical, and economic equilibrium. However, treatment choices and targets for finding a solution to COVID-19’s threat are becoming limited. A viable approach to combating the threat of COVID-19 is by unraveling newer pharmacological and therapeutic targets pertinent in the viral survival and adaptive mechanisms within the host biological milieu which in turn provides the opportunity to discover promising inhibitors against COVID-19. Therefore, using high-throughput virtual screening, manually curated compounds library from some medicinal plants were screened against four main drivers of SARS-CoV-2 (spike glycoprotein, PLpro, 3CLpro, and RdRp). In addition, molecular docking, Prime MM/GBSA (molecular mechanics/generalized Born surface area) analysis, molecular dynamics (MD) simulation, and drug-likeness screening were performed to identify potential phytodrugs candidates for COVID-19 treatment. In support of these approaches, we used a series of computational modeling approaches to develop therapeutic agents against COVID-19. Out of the screened compounds against the selected SARS-CoV-2 therapeutic targets, only compounds with no violations of Lipinski’s rule of five and high binding affinity were considered as potential anti-COVID-19 drugs. However, lonchocarpol A, diplacol, and broussonol E (lead compounds) were recorded as the best compounds that satisfied this requirement, and they demonstrated their highest binding affinity against 3CLpro. Therefore, the 3CLpro target and the three lead compounds were selected for further analysis. Through protein–ligand mapping and interaction profiling, the three lead compounds formed essential interactions such as hydrogen bonds and hydrophobic interactions with amino acid residues at the binding pocket of 3CLpro. The key amino acid residues at the 3CLpro active site participating in the hydrophobic and polar inter/intra molecular interaction were TYR54, PRO52, CYS44, MET49, MET165, CYS145, HIS41, THR26, THR25, GLN189, and THR190. The compounds demonstrated stable protein–ligand complexes in the active site of the target (3CLpro) over a 100 ns simulation period with stable protein–ligand trajectories. Drug-likeness screening shows that the compounds are druggable molecules, and the toxicity descriptors established that the compounds demonstrated a good biosafety profile. Furthermore, the compounds were chemically reactive with promising molecular electron potential properties. Collectively, we propose that the discovered lead compounds may open the way for establishing phytodrugs to manage COVID-19 pandemics and new chemical libraries to prevent COVID-19 entry into the host based on the findings of this computational investigation.
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Affiliation(s)
- Toheeb A. Balogun
- Department of Biochemistry, Adekunle Ajasin University, Akungba-Akoko, Nigeria
- *Correspondence: Toheeb A. Balogun, ; Gaber E. Batiha,
| | - Onyeka S. Chukwudozie
- Department of Biological Sciences, University of California, San Diego, San Diego, CA, United States
| | | | - Idris O. Junaid
- Department of Chemistry and Chemical Biology, Stevens Institute of Technology, Hoboken, NJ, United States
| | - Olugbodi A. Sunday
- Department of Environmental Toxicology, Universitat Duisburg-Essen, Essen, Germany
| | - Oluwasegun M. Ige
- Department of Marine Biological Resources, Ghent University, Ghent, Belgium
| | - Abdullahi T. Aborode
- Department of Chemistry, Mississippi State University, Starkville, MS, United States
| | - Abiola D. Akintayo
- Department of Chemistry, University of Texas at Dallas, Richardson, TX, United States
| | - Emmanuel A. Oluwarotimi
- Department of Chemistry, Missouri University of Science and Technology, Rolla, MO, United States
| | - Isaac O. Oluwafemi
- Department of Chemistry, Adekunle Ajasin University, Akungba-Akoko, Nigeria
| | - Oluwatosin A. Saibu
- Department of Environmental Toxicology, Universitat Duisburg-Essen, Essen, Germany
| | - Prosper Chuckwuemaka
- Department of Biotechnology, Federal University of Technology Akure, Akure, Nigeria
| | | | | | - Nkechi H. Atasie
- Clinical Pharmacy Department, Nigeria Correctional Service, Enugu Custodial Centre, Enugu, Nigeria
| | - Ayooluwa Ilesanmi
- Department of Chemistry, Mississipi University for Women Columbus, Columbus, United States
| | - Gbenga Dairo
- Department of Biological Sciences, Western Illinois University, Macomb, IL, United States
| | - Zainab A. Tiamiyu
- Department of Biochemistry and Molecular Biology, Federal University Dutsin-ma, Dutsin-Ma, Nigeria
| | - Gaber E. Batiha
- Department of Pharmacology and Therapeutics, Faculty of Veterinary Medicine, Damanhour University, Damanhour, Egypt
- *Correspondence: Toheeb A. Balogun, ; Gaber E. Batiha,
| | - Afrah Fahad Alkhuriji
- Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Wafa Abdullah I. Al-Megrin
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Michel De Waard
- Smartox Biotechnology, Saint-Egréve, France
- L‘institut du Thorax, INSERM, CNRS, Université de Nantes, Nantes, France
- LabEx Ion Channels, Science and Therapeutics, Université de Nice Sophia-Antipolis, Valbonne, France
| | - Jean-Marc Sabatier
- Institut de Neurophysiopathologie (INP), Faculté des Sciences Médicales et Paramédicales, Aix-Marseille Université, CNRS UMR 7051, Marseille, France
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11
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Sun Q, Gieseking RLM. Parametrization of the PM7 Semiempirical Quantum Mechanical Method for Silver Nanoclusters. J Phys Chem A 2022; 126:6558-6569. [PMID: 36082665 DOI: 10.1021/acs.jpca.2c05782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Semiempirical quantum mechanical methods (SEQMs) are widely used in computational chemistry because of their low computational cost, but their accuracy depends on the quality of the parameters. The neglect of diatomic differential overlap method PM7 is among the few SEQMs that contain parameters for Ag, but the experimental reference data was insufficient to obtain reliable parameters in the original parametrization. In this work, we reparametrize the PM7 parameters for Ag to accurately reproduce the ground-state potential energy surfaces of Ag clusters. Since little experimental data is available, we use reference data obtained from the ab initio method CCSD(T). The resulting parameters significantly reduce the errors in binding energies, energies required to displace clusters along their normal modes, and relative energies of isomers compared to the default PM7 Ag parameters.
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Affiliation(s)
- Qiwei Sun
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, Massachusetts 02453, United States
| | - Rebecca L M Gieseking
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, Massachusetts 02453, United States
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12
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Mixtures of Diethyl Sulfoxide and Methanol: Structure and Thermodynamics. J SOLUTION CHEM 2022. [DOI: 10.1007/s10953-022-01167-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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13
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Canisares FS, Mutti AM, Cavalcante DG, Job AE, Pires AM, Lima SA. Luminescence and cytotoxic study of red emissive europium(III) complex as a cell dye. J Photochem Photobiol A Chem 2022. [DOI: 10.1016/j.jphotochem.2021.113552] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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14
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Borges AS, Dutra JDL, Santos GS, Diniz R, Kai J, Araujo MH. Theoretical and experimental spectroscopic investigation of new Eu(III)-FOD complex containing 2-pyrrolidone ligand. J Mol Model 2021; 27:293. [PMID: 34549346 DOI: 10.1007/s00894-021-04883-1] [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: 03/31/2021] [Accepted: 08/18/2021] [Indexed: 10/20/2022]
Abstract
The preparation and photoluminescent properties of the new [Eu(FOD)3(2-Pyr)2] complex (FOD = 6,6,7,7,8,8,8-heptafluoro-2,2-dimethyl-3,5-octadionate; 2-Pyr = 2-pyrrolidone) are reported. The obtained complex was characterized by elemental analysis, complexometric titration using EDTA, infrared spectroscopy, and single-crystal X-ray diffraction studies. The coordination polyhedron of the complex is described as a distorted square antiprismatic with both 2-Pyr monodentate ligands coordinated to Eu(III) via the oxygen atoms, in neutral form, while the three FOD molecules are coordinated in the anionic form. Structural modeling at the PBE1PBE/SVP/MWB52 level of theory provided a geometry in excellent agreement with the one obtained experimentally. Spectroscopy properties such as intensity parameters (Ω2 and Ω4), radiative emission rate (Arad), and chemical partition of Arad for [Eu(FOD)3(2-Pyr)2] and [Eu(FOD)3(H2O)2] were calculated by using the QDC model with help of the semiempirical wavefunctions. The modeling of the ligand-to-metal energy transfer for both complexes was performed, allowing to obtain the theoretical emission quantum yield and to characterize the most relevant molecular orbitals involved.
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Affiliation(s)
- Alex Santos Borges
- Coordenadoria de Química E Biologia, IFES, Vitória, ES, 29040-780, Brazil.
| | - José Diogo L Dutra
- Pople Computational Chemistry Laboratory, Departamento de Química, UFS, São Cristóvão, SE, 49100-000, Brazil.
| | - Gabriel Silva Santos
- Pople Computational Chemistry Laboratory, Departamento de Química, UFS, São Cristóvão, SE, 49100-000, Brazil
| | - Renata Diniz
- Departamento de Química, UFMG, Belo Horizonte, MG, 31270-901, Brazil
| | - Jiang Kai
- Departamento de Química, PUC-Rio, Rio de Janeiro, RJ, 22451-900, Brazil.,Nutriplant, Barueri, SP, 06415-110, Brazil
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15
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Ganaie A, Iftikhar K. Theoretical Modeling (Sparkle RM1 and PM7) and Crystal Structures of the Luminescent Dinuclear Sm(III) and Eu(III) Complexes of 6,6,7,7,8,8,8- Heptafluoro-2,2-dimethyl-3,5-octanedione and 2,3-Bis(2-pyridyl)pyrazine: Determination of Individual Spectroscopic Parameters for Two Unique Eu 3+ Sites. ACS OMEGA 2021; 6:21207-21226. [PMID: 34471726 PMCID: PMC8387994 DOI: 10.1021/acsomega.0c05976] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 06/14/2021] [Indexed: 06/13/2023]
Abstract
Heteroleptic homo dinuclear complexes [Sm(fod)3(μ-bpp)Sm(fod)3] and [Eu(fod)3(μ-bpp)Eu(fod)3] and their diamagnetic analogue [Lu(fod)3(μ-bpp)Lu(fod)3] (fod is the anion of 6,6,7,7,8,8,8- heptafluoro-2,2-dimethyl-3,5-octanedione (Hfod) and bpp is 2,3-bis(2-pyridyl)pyrazine) are synthesized and thoroughly characterized. The lanthanum gave a 1:1 adduct of La(fod)3 and bpp with the molecular formula of [La(fod)3bpp]. The 1H NMR and 1H-1H COSY spectra of the complexes were used to assign the proton resonances. In the case of paramagnetic Sm3+ and Eu3+ complexes, the methine (of the fod moiety) and the bpp resonances are shifted in the opposite direction and the paramagnetic shifts are dipolar in nature, which decrease with increasing distance of the proton from the metal ion. The single-crystal X-ray analyses reveal that the complexes (Sm3+ and Eu3+) are dinuclear and crystallize in the triclinic P1 space group. Each metal in a given complex is eight coordinate by coordinating with six oxygen atoms of three fod moieties and two nitrogen atoms of the bpp. Of the two metal centers, in a given complex, one has a distorted square antiprism arrangement and the other acquires a distorted dodecahedron geometry. The Sparkle RM1 and PM7 optimized structures of the complexes are also presented and compared with the crystal structure. Theoretically observed bond distances are in excellent agreement with the experimental values, and the RMS deviations for the optimized structures are 2.878, 2.217, 2.564, and 2.675 Å. The photophysical properties of Sm3+ and Eu3+ complexes are investigated in different solvents, solid, and PMMA-doped thin hybrid films. The spectroscopic parameters (the Judd-Ofelt intensity parameters, radiative parameters, and intrinsic quantum yield) of each Eu3+ sites are calculated using the overlap polyhedra method. The theoretically obtained parameters are close to the experimental results. The lifetime of the excited state is 38.74 μs for Sm3+ and 713.62 μs for the Eu3+ complex in the solid state.
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16
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Filho EV, Pina JWS, Antoniazi MK, Loureiro LB, Ribeiro MA, Pinheiro CB, Guimarães CJ, de Oliveira FCE, Pessoa C, Taranto AG, Greco SJ. Synthesis, docking, machine learning and antiproliferative activity of the 6-ferrocene/heterocycle-2-aminopyrimidine and 5-ferrocene-1H-Pyrazole derivatives obtained by microwave-assisted Atwal reaction as potential anticancer agents. Bioorg Med Chem Lett 2021; 48:128240. [PMID: 34217828 DOI: 10.1016/j.bmcl.2021.128240] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 06/02/2021] [Accepted: 06/28/2021] [Indexed: 11/16/2022]
Abstract
A simple and fast methodology under microwave irradiation for the synthesis of 2-aminopyrimidine and pyrazole derivatives using Atwal reaction is reported. After the optimization of the reaction conditions, eight 2-aminolpyrimidines containing ferrocene and heterocycles and three ferrocene pyrazoles were synthesized from the respective chalcones in good yields. Eight compounds had their structure determined by X-ray diffraction. The molecular hybrid 6a-h and 9a-c were tested on four cancer cell lines - HCT116, PC3, HL60 and SNB19 - where four pyrimidine 6a, 6f-h and one pyrazole 9c derivatives show promising antiproliferative activity. In addition, docking simulation and machine learning methods were carried out to explain the biological activity achieved by the synthetized compounds.
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Affiliation(s)
- Eclair Venturini Filho
- Chemistry Department, Federal University of Espírito Santo, Vitória, Espírito Santo CEP.:29075-910, Brazil
| | - Jorge W S Pina
- Chemistry Department, Federal University of Espírito Santo, Vitória, Espírito Santo CEP.:29075-910, Brazil
| | - Mariana K Antoniazi
- Chemistry Department, Federal University of Espírito Santo, Vitória, Espírito Santo CEP.:29075-910, Brazil
| | - Laiza B Loureiro
- Chemistry Department, Federal University of Espírito Santo, Vitória, Espírito Santo CEP.:29075-910, Brazil
| | - Marcos A Ribeiro
- Chemistry Department, Federal University of Espírito Santo, Vitória, Espírito Santo CEP.:29075-910, Brazil
| | - Carlos B Pinheiro
- Physical Department, Minas Gerais Federal University, Av. Antônio Carlos 6627, Pampulha, Belo Horizonte, Minas Gerais CEP.: 30161-970 Brazil
| | - Celina J Guimarães
- Department of Physiology and Pharmacology, Faculty of Medicine, Federal University of Ceará., Fortaleza, Ceará CEP 60430-275, Brazil; Pharmacy Sector, Foundation of Oncology Control of the State of Amazonas, Manaus, Amazonas, CEP 69040-010, Brazil
| | - Fátima C E de Oliveira
- Department of Physiology and Pharmacology, Faculty of Medicine, Federal University of Ceará., Fortaleza, Ceará CEP 60430-275, Brazil
| | - Claudia Pessoa
- Department of Physiology and Pharmacology, Faculty of Medicine, Federal University of Ceará., Fortaleza, Ceará CEP 60430-275, Brazil
| | - Alex G Taranto
- Laboratory of Drug Design and Bioinformatics, Federal University of São João del-Rei, São João del-Rei, Minas Gerais CEP: 36307-352, Brazil
| | - Sandro J Greco
- Chemistry Department, Federal University of Espírito Santo, Vitória, Espírito Santo CEP.:29075-910, Brazil.
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17
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Wankar S, Khan I, Pandit UJ. Exploration of photophysical behavior of lanthanide complex and its hybrids. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 254:119629. [PMID: 33721749 DOI: 10.1016/j.saa.2021.119629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 02/06/2021] [Accepted: 02/09/2021] [Indexed: 06/12/2023]
Abstract
The present work envisioned to synthesize europium complexes [Eu-(L)3-phen] (where, L is 4,4,4-Trifluoro-1-(2-furyl)-1,3-butanedione (TFB), phen-1,10 -phenanthroline) and its hybrids via embedding pure complex into silica and PMMA. The sol-gel method was adopted for incorporating europium complex into silica matrix as [Eu-(L)3-phen]-silica and this method was proved to be highly effective and excellent approach for obtaining such lanthanide hybrid material. Another hybrid was prepared by incorporating complex into PMMA (polymethyl methyl acrylate), an organic polymer, transformed into flexible thin film. The structure of the [Eu-(L)3-phen] was elucidated using various spectroscopic techniques, moreover Sparkle model calculation were utilized for prediction of ground state geometry. The photophysical properties of pure complex [Eu-(L)3-phen] and its hybrids were studied in detail and compared. The incorporation of pure complex into PMMA is highly supportive to enhance the stability of complex as evident from enhanced luminescent intensity, intensity ratio value 6.52, longer lifetime value 842μs and higher quantum efficiency 77% over pure complex. The organic polymer PMMA is expected to interact well with europium complex via antenna effect. The use of such inorganic and organic entities for hybrid preparation purposefully overcomes the flaws of lanthanide complexes in terms of thermal stability and mechanical strength. The promising and fascinating properties of synthesized lanthanide hybrids are fruitful in material research.
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Affiliation(s)
- Sneha Wankar
- Department of Chemistry, Visvesvaraya National Institute Of Technology, Nagpur, Maharashtra 440010, India
| | - Imran Khan
- Department of Chemistry, Dr. Harisingh Gour Vishwavidyalaya (A Central University), Sagar, M.P. 470003, India
| | - Umar Jan Pandit
- Department of Chemistry, Dr. Harisingh Gour Vishwavidyalaya (A Central University), Sagar, M.P. 470003, India
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18
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Akbar R, Baral M, Kanungo BK. Spectroscopic, photophysical, solution thermodynamics and computational study of europium and terbium complexes with a flexible quinolinol-based symmetric tripodal chelator. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 247:119124. [PMID: 33161269 DOI: 10.1016/j.saa.2020.119124] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 10/14/2020] [Accepted: 10/16/2020] [Indexed: 06/11/2023]
Abstract
Coordination behaviour and photonic properties of a flexible tripodal multidentate ligand, 5,5',5''-(Cyclohexane-1,3,5-triyltris(oxy))tris(methylene)triquinolin-8-ol (CYTOM5OX), with Eu and Tb ions were explored through potentiometric, UV-visible and fluorescence spectrophotometric methods. The interaction of tripod towards the lanthanides has been examined for thermodynamic equilibrium, photophysical behavior, and time-resolved luminescence measurements. Besides, a theoretically empirical method followed by quantum mechanical treatment of these chelates has also been summarized. A noticeable change in the electronic spectra of these complexes disclose CYTOM5OX as a pH-sensitive optical sensor for lanthanides detection; also, a strong green fluorescence allows simultaneous sensing in the visible region in a competitive medium. The intense fluorescence intermittently gets quenched under acidic and basic conditions due to photoinduced intramolecular electron transfer from the excited 8-hydroxyquinoline (8-HQ) moiety to the metal ion. The thermodynamically stable Ln3+ complexes in aqueous solution show stability constants in the range log β110 = 33-35 and pLn3+ in the range of 21-22. The hydration number that was predicted by the coordination scan was substantiated by lifetime measurements reveal presence of coordinated water molecules in Eu(CYTOM5OX) and Tb(CYTOM5OX) complexes. Theoretical spectra were also calculated by ZINDO/s methodology at single excitations (CIS) level on PM7 as sparkle energy-minimized geometries.
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Affiliation(s)
- Rifat Akbar
- Department of Chemistry, Sant Longowal Institute of Engineering & Technology, Longowal, Punjab 148106, India
| | - Minati Baral
- Department of Chemistry, National Institute of Technology Kurukshetra, Haryana 136119, India
| | - B K Kanungo
- Department of Chemistry, Sant Longowal Institute of Engineering & Technology, Longowal, Punjab 148106, India.
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19
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Silva GS, Dutra JDL, da Costa NB, Alves S, Freire RO. Lanthanide Contraction in Lanthanide Organic Frameworks: A Theoretical and Experimental Study. J Phys Chem A 2020; 124:7678-7684. [PMID: 32693596 DOI: 10.1021/acs.jpca.0c05065] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
In this work, the lanthanide (Ln) contraction phenomenon has been analyzed for three-dimensional structures in the solid state. We chose to study an isostructural series of lanthanide organic frameworks (LOFs) of formula [Ln2(C4H4O4)3(H2O)2]n·H2O and 14 crystallographic structures (except promethium complex). The analysis of Ln contraction was made by analyzing the sum of all Ln-O bond lengths and the sum of all O-O distances, for the oxygen atoms of the coordination polyhedra, calculated with different semiempirical quantum mechanical models. The ∑Ln-O and ∑O-O for this LOF can be fit to a second-order polynomial. Based on the crystallographic structures, it is concluded that the phenomenon of Ln contraction is observed. Our results also suggest that the semiempirical Sparkle/PM3 and Sparkle/RM1 models reproduce the Ln contraction phenomenon well, and similar fits were obtained for ∑Ln-O and ∑O-O bond lengths.
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Affiliation(s)
- Gustavo S Silva
- Pople Computational Chemistry Laboratory, Department of Chemistry, Federal University of Sergipe-UFS, 49100-000 São Cristóvão, SE, Brazil
| | - José Diogo L Dutra
- Pople Computational Chemistry Laboratory, Department of Chemistry, Federal University of Sergipe-UFS, 49100-000 São Cristóvão, SE, Brazil
| | - Nivan B da Costa
- Pople Computational Chemistry Laboratory, Department of Chemistry, Federal University of Sergipe-UFS, 49100-000 São Cristóvão, SE, Brazil
| | - Severino Alves
- Department of Elemental Chemistry, Federal University of Pernambuco-UFPE, 50590-470 Recife, PE, Brazil
| | - Ricardo O Freire
- Pople Computational Chemistry Laboratory, Department of Chemistry, Federal University of Sergipe-UFS, 49100-000 São Cristóvão, SE, Brazil
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20
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Mladentsev DY, Zakirova GG, Zakirova ZK. A semiempirical approach toward the origin of f-element binding selectivity of pyridine-2,6-diylbis(diphenylphosphine oxide). MENDELEEV COMMUNICATIONS 2020. [DOI: 10.1016/j.mencom.2020.09.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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21
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Neugebauer H, Bohle F, Bursch M, Hansen A, Grimme S. Benchmark Study of Electrochemical Redox Potentials Calculated with Semiempirical and DFT Methods. J Phys Chem A 2020; 124:7166-7176. [DOI: 10.1021/acs.jpca.0c05052] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Hagen Neugebauer
- Mulliken Center for Theoretical Chemistry, Institute for Physical and Theoretical Chemistry, University of Bonn, Beringstr. 4, 53115 Bonn, Germany
| | - Fabian Bohle
- Mulliken Center for Theoretical Chemistry, Institute for Physical and Theoretical Chemistry, University of Bonn, Beringstr. 4, 53115 Bonn, Germany
| | - Markus Bursch
- Mulliken Center for Theoretical Chemistry, Institute for Physical and Theoretical Chemistry, University of Bonn, Beringstr. 4, 53115 Bonn, Germany
| | - Andreas Hansen
- Mulliken Center for Theoretical Chemistry, Institute for Physical and Theoretical Chemistry, University of Bonn, Beringstr. 4, 53115 Bonn, Germany
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Institute for Physical and Theoretical Chemistry, University of Bonn, Beringstr. 4, 53115 Bonn, Germany
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22
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Sarkar R, Kumari S, Kundu TK. Density functional theory based studies on the adsorption of rare-earth ions from hydrated nitrate salt solutions on g-C 3N 4 monolayer surface. J Mol Graph Model 2020; 97:107577. [PMID: 32179421 DOI: 10.1016/j.jmgm.2020.107577] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Revised: 02/28/2020] [Accepted: 03/03/2020] [Indexed: 12/14/2022]
Abstract
This article represents density functional theory (DFT) based comparative analysis on six trivalent rare-earth ions (RE3+; RE: Y, La, Ce, Sm, Eu and Gd) absorption, from the respective nitrate-hexahydrate salts, on graphitic carbon nitride (g-C3N4) 2D monolayer, and the photocatalytic properties of the RE3+ adsorbed g-C3N4 systems (g-C3N4/RE3+) based on the ground-state electronic structure calculations. Structure, stability and coordination chemistry of two configurations of each hydrated RE-salt system are discussed in detail. Both DFT (B3LYP/SDD) and semi-empirical (Sparkle/PM7) calculations identify the central N6 vacancy of pristine g-C3N4 as the most suitable site for RE3+ adsorption. Bader's QTAIM, Mayer bond order and charge population analyses (ADCH, CHELPG and DDEC) are performed to describe the bond characteristics within the systems under study. Thermochemical calculations suggest that the adsorption process is thermodynamically more feasible for higher atomic number (Z) RE3+ [Sm3+, Eu3+ and Gd3+], compared to lower-Z RE3+ [Y3+, La3+ and Ce3+] ions. Besides, the better photocatalytic properties of higher-Z RE3+ adsorbed g-C3N4 systems are revealed from better HOMO-LUMO delocalization, decreased HOMO-LUMO gap, increased softness, higher electrophilicity and electron transfer parameter, compared to pristine or lower-Z RE3+ adsorbed g-C3N4 systems, as obtained from Hirshfeld orbital compositions, density of states and condensed Fukui function analyses.
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Affiliation(s)
- Ranjini Sarkar
- Department of Metallurgical and Materials Engineering, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, 721302, India.
| | - Sweta Kumari
- Department of Metallurgical and Materials Engineering, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, 721302, India
| | - Tarun Kumar Kundu
- Department of Metallurgical and Materials Engineering, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, 721302, India
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Peters JA, Djanashvili K, Geraldes CF, Platas-Iglesias C. The chemical consequences of the gradual decrease of the ionic radius along the Ln-series. Coord Chem Rev 2020. [DOI: 10.1016/j.ccr.2019.213146] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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24
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Endo K, Ida T, Yamazaki A, Akitsu T, Hasegawa Y. Luminescence spectral analysis for Eu(III), and the dinuclear (Zn(II), Cu(II)) complexes with organic ligands by quantum chemical methods. Chem Phys 2020. [DOI: 10.1016/j.chemphys.2019.110552] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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25
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Vaz RCA, Esteves IO, Oliveira WXC, Honorato J, Martins FT, Marques LF, dos Santos GL, Freire RO, Jesus LT, Pedroso EF, Nunes WC, Julve M, Pereira CLM. Mononuclear lanthanide(iii)-oxamate complexes as new photoluminescent field-induced single-molecule magnets: solid-state photophysical and magnetic properties. Dalton Trans 2020; 49:16106-16124. [DOI: 10.1039/d0dt02497j] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Lanthanide(iii)-oxamate complexes can switch into Light Conversion Molecular Devices (LCMDs) or field-induced Single-Molecule Magnets (SMMs) depending on the external stimulus.
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26
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Ansari AA, Ganaie AB, Iftikhar K. Synthesis and 4f 4f absorption studies of tris(acetylacetonato)praseodymium(III) and holmium(III) complexes with imidazole and pyrazole in non-aqueous solvents. Structure elucidation by Sparkle / PM7. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2019.07.073] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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27
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Ilmi R, Anjum S, Haque A, Khan MS. A new brilliant red emitting Eu(III) ternary complex and its transparent flexible and photostable poly(urethane) hybrid thin film for optoelectronic applications. J Photochem Photobiol A Chem 2019. [DOI: 10.1016/j.jphotochem.2019.111968] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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28
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de Souza KM, de Carvalho LP, da Silva JA, Longo RL. On the structures of dinuclear symmetric lanthanide complexes and the selectivity towards heterodinuclear complexes based on molecular modeling. Inorganica Chim Acta 2019. [DOI: 10.1016/j.ica.2019.05.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Kruck C, Nazari P, Dee C, Richards BS, Turshatov A, Seitz M. Efficient Ytterbium Near-Infrared Luminophore Based on a Nondeuterated Ligand. Inorg Chem 2019; 58:6959-6965. [PMID: 31050288 DOI: 10.1021/acs.inorgchem.9b00548] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A novel molecular ytterbium complex is reported with a new tetradentate ligand based on the 2,2'-bipyridine-6,6'-dicarboxylic acid scaffold. The photophysical properties are investigated, especially with respect to near-infrared luminescence. The ytterbium complex shows a rather high absolute luminescence quantum yield of Φ = 3.0% and a luminescence lifetime of τobs = 72 μs at room temperature in CD3OD solution.
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Affiliation(s)
- Christian Kruck
- Institute of Inorganic Chemistry , University of Tübingen , Auf der Morgenstelle 18 , 72076 Tübingen , Germany
| | - Pariya Nazari
- Institute of Microstructure Technology , Karlsruhe Institute of Technology , Hermann-von-Helmholtz-Platz 1 , 76344 Eggenstein-Leopoldshafen , Germany
| | - Carolin Dee
- Institute of Inorganic Chemistry , University of Tübingen , Auf der Morgenstelle 18 , 72076 Tübingen , Germany
| | - Bryce S Richards
- Institute of Microstructure Technology , Karlsruhe Institute of Technology , Hermann-von-Helmholtz-Platz 1 , 76344 Eggenstein-Leopoldshafen , Germany
| | - Andrey Turshatov
- Institute of Microstructure Technology , Karlsruhe Institute of Technology , Hermann-von-Helmholtz-Platz 1 , 76344 Eggenstein-Leopoldshafen , Germany
| | - Michael Seitz
- Institute of Inorganic Chemistry , University of Tübingen , Auf der Morgenstelle 18 , 72076 Tübingen , Germany
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31
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de P. Santos AM, Bertoli AC, Duarte HA, Garcia JS, Trevisan MG. The stability and mechanism of cerium complexation with humic substances from poultry manure – A combined experimental/theoretical approach. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2018.10.045] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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32
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Modeling intramolecular energy transfer in lanthanide chelates: A critical review and recent advances. INCLUDING ACTINIDES 2019. [DOI: 10.1016/bs.hpcre.2019.08.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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33
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Chong BSK, Moore EG. Quantitative Sensitization Efficiencies in NIR-Emissive Homoleptic Ln(III) Complexes Using 2-(5-Methylpyridin-2-yl)-8-hydroxyquinoline. Inorg Chem 2018; 57:14062-14072. [PMID: 30403139 DOI: 10.1021/acs.inorgchem.8b01438] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A series of isostructural lanthanide complexes [Ln(MPQ)3] (Ln = Nd, Gd, Er, Yb, Lu) using a monoanionic tridentate methylpyridyl-substituted 8-hydroxyquinoline ligand (MPHQ = 2-(5-methylpyridin-2-yl)-8-hydroxyquinoline) have been prepared and characterized using elemental analysis (CHN), single-crystal X-ray diffraction (XRD), and 1H NMR spectroscopy. This ligand forms homoleptic charge-neutral lanthanide complexes with three coordinated ligands arranged in an "up-up-down" fashion around the metal center. The photophysical properties of the Nd, Er, and Yb complexes were investigated using absorption and emission spectroscopy, with the latter species displaying efficient sensitization in the Near Infra-Red (NIR) region and a photoluminescence quantum yield (PLQY) as high as 1.0% in CH2Cl2 solution. The intersystem crossing and energy-transfer processes involved in the antenna effect were further investigated using transient absorption techniques, which revealed essentially quantitative sensitization efficiencies for the NIR-emitting cations.
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Affiliation(s)
- Bowie S K Chong
- School of Chemistry and Molecular Biosciences , The University of Queensland , Brisbane , Queensland 4072 , Australia
| | - Evan G Moore
- School of Chemistry and Molecular Biosciences , The University of Queensland , Brisbane , Queensland 4072 , Australia
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Saito T, Takano Y. Transition State Search Using rPM6: Iron- and Manganese-Catalyzed Oxidation Reactions as a Test Case. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2018. [DOI: 10.1246/bcsj.20180119] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Toru Saito
- Graduate School of Information Sciences, Hiroshima City University, 3-4-1 Ozuka-Higashi, Asa-Minami-ku, Hiroshima 731-3194, Japan
| | - Yu Takano
- Graduate School of Information Sciences, Hiroshima City University, 3-4-1 Ozuka-Higashi, Asa-Minami-ku, Hiroshima 731-3194, Japan
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Beltrán-Leiva MJ, Páez-Hernández D, Arratia-Pérez R. Theoretical Determination of Energy Transfer Processes and Influence of Symmetry in Lanthanide(III) Complexes: Methodological Considerations. Inorg Chem 2018; 57:5120-5132. [DOI: 10.1021/acs.inorgchem.8b00159] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- María J. Beltrán-Leiva
- Relativistic Molecular Physics (ReMoPh) Group, Ph.D. Program in Molecular Physical Chemistry, Universidad Andrés Bello, Av. República 275, Santiago 8370146, Chile
| | - Dayán Páez-Hernández
- Relativistic Molecular Physics (ReMoPh) Group, Ph.D. Program in Molecular Physical Chemistry, Universidad Andrés Bello, Av. República 275, Santiago 8370146, Chile
- Center of Applied Nanosciences (CANS), Facultad de Ciencias Exactas, Universidad Andrés Bello, Av. República 275, Santiago 8370146, Chile
| | - Ramiro Arratia-Pérez
- Relativistic Molecular Physics (ReMoPh) Group, Ph.D. Program in Molecular Physical Chemistry, Universidad Andrés Bello, Av. República 275, Santiago 8370146, Chile
- Center of Applied Nanosciences (CANS), Facultad de Ciencias Exactas, Universidad Andrés Bello, Av. República 275, Santiago 8370146, Chile
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36
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Bursch M, Hansen A, Grimme S. Fast and Reasonable Geometry Optimization of Lanthanoid Complexes with an Extended Tight Binding Quantum Chemical Method. Inorg Chem 2017; 56:12485-12491. [DOI: 10.1021/acs.inorgchem.7b01950] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Markus Bursch
- Mulliken Center for Theoretical
Chemistry, Institut für Physikalische und Theoretische Chemie, Universität Bonn, 53115 Bonn, Beringstraße
4, Germany
| | - Andreas Hansen
- Mulliken Center for Theoretical
Chemistry, Institut für Physikalische und Theoretische Chemie, Universität Bonn, 53115 Bonn, Beringstraße
4, Germany
| | - Stefan Grimme
- Mulliken Center for Theoretical
Chemistry, Institut für Physikalische und Theoretische Chemie, Universität Bonn, 53115 Bonn, Beringstraße
4, Germany
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37
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Influence of upper rim dibromo-substitution in bis-1,3-diketone calix[4]arenes on spectral properties of ligands and their lanthanide complexes. Tetrahedron 2017. [DOI: 10.1016/j.tet.2017.07.043] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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38
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Wang L, Fu W, Shen Y, Tan H, Xu H. Molecularly Imprinted Polymers for Selective Extraction of Oblongifolin C from Garcinia yunnanensis Hu. Molecules 2017; 22:molecules22040508. [PMID: 28333096 PMCID: PMC6153995 DOI: 10.3390/molecules22040508] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 03/19/2017] [Accepted: 03/21/2017] [Indexed: 11/28/2022] Open
Abstract
Molecularly imprinted polymers (MIPs) were synthesized and applied for the selective extraction of oblongifolin C (OC) from fruit extracts of Garcinia yunnanensis Hu. A series of experiments and computational approaches were employed to improve the efficiency of screening for optimal MIP systems in the study. The molar ratio (1:4) was eventually chosen based on the comparison of the binding energy of the complexes between the template (OC) and the functional monomers using density functional theory (DFT) at the RI-PBE-D3-gCP/def2-TZVP level of theory. The binding characterization and the molecular recognition mechanism of MIPs were further explained using the molecular modeling method along with NMR and IR spectra data. The reusability of this approach was demonstrated in over 20 batch rebinding experiments. A mass of 140.5 mg of OC (>95% purity) was obtained from the 5 g extracts, with 2 g of MIPs with the best binding properties, through a gradient elution program from 35% to 70% methanol-water solution. At the same time, another structural analog, 46.5 mg of guttiferone K (GK) (>88% purity), was also obtained by the gradient elution procedure. Our results showed that the structural analogs could be separated from the crude extracts by the molecularly imprinted solid-phase extraction (MISPE) using a gradient elution procedure for the first time.
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Affiliation(s)
- Liping Wang
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China.
- Engineering Research Center of Shanghai Colleges for TCM New Drug Discovery, Shanghai 201203, China.
| | - Wenwei Fu
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China.
- Engineering Research Center of Shanghai Colleges for TCM New Drug Discovery, Shanghai 201203, China.
| | - Yunhui Shen
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China.
| | - Hongsheng Tan
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China.
- Engineering Research Center of Shanghai Colleges for TCM New Drug Discovery, Shanghai 201203, China.
| | - Hongxi Xu
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China.
- Engineering Research Center of Shanghai Colleges for TCM New Drug Discovery, Shanghai 201203, China.
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39
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New photo/electroluminescent europium(III) β-diketonate complex containing a p,p′-disubstituted bipyridine ligand: Synthesis, solid state characterization, theoretical and experimental spectroscopic studies. Inorganica Chim Acta 2017. [DOI: 10.1016/j.ica.2016.12.022] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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40
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Maia EHB, Campos VA, Dos Reis Santos B, Costa MS, Lima IG, Greco SJ, Ribeiro RIMA, Munayer FM, da Silva AM, Taranto AG. Octopus: a platform for the virtual high-throughput screening of a pool of compounds against a set of molecular targets. J Mol Model 2017; 23:26. [PMID: 28064377 DOI: 10.1007/s00894-016-3184-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2016] [Accepted: 12/06/2016] [Indexed: 01/28/2023]
Abstract
Octopus is an automated workflow management tool that is scalable for virtual high-throughput screening (vHTS). It integrates MOPAC2016, MGLTools, PyMOL, and AutoDock Vina. In contrast to other platforms, Octopus can perform docking simulations of an unlimited number of compounds into a set of molecular targets. After generating the ligands in a drawing package in the Protein Data Bank (PDB) format, Octopus can carry out geometry refinement using the semi-empirical method PM7 implemented in MOPAC2016. Docking simulations can be performed using AutoDock Vina and can utilize the Our Own Molecular Targets (OOMT) databank. Finally, the proposed software compiles the best binding energies into a standard table. Here, we describe two successful case studies that were verified by biological assay. In the first case study, the vHTS process was carried out for 22 (phenylamino)urea derivatives. The vHTS process identified a metalloprotease with the PDB code 1GKC as a molecular target for derivative LE&007. In a biological assay, compound LE&007 was found to inhibit 80% of the activity of this enzyme. In the second case study, compound Tx001 was submitted to the Octopus routine, and the results suggested that Plasmodium falciparum ATP6 (PfATP6) as a molecular target for this compound. Following an antimalarial assay, Tx001 was found to have an inhibitory concentration (IC50) of 8.2 μM against PfATP6. These successful examples illustrate the utility of this software for finding appropriate molecular targets for compounds. Hits can then be identified and optimized as new antineoplastic and antimalarial drugs. Finally, Octopus has a friendly Linux-based user interface, and is available at www.drugdiscovery.com.br . Graphical Abstract Octopus: A platform for inverse virtual screening (IVS) to search new molecular targets for drugs.
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Affiliation(s)
- Eduardo Habib Bechelane Maia
- Universidade Federal de São João del Rei-Campus Centro-Oeste, Divinópolis, MG, Brazil
- Centro Federal de Educação Tecnológica de Minas Gerais-Campus Divinópolis, Divinópolis, MG, Brazil
| | - Vinícius Alves Campos
- Universidade Federal de São João del Rei-Campus Centro-Oeste, Divinópolis, MG, Brazil
- Centro Federal de Educação Tecnológica de Minas Gerais-Campus Divinópolis, Divinópolis, MG, Brazil
| | - Bianca Dos Reis Santos
- Universidade Federal de São João del Rei-Campus Centro-Oeste, Divinópolis, MG, Brazil
- Centro Federal de Educação Tecnológica de Minas Gerais-Campus Divinópolis, Divinópolis, MG, Brazil
| | - Marina Santos Costa
- Universidade Federal de São João del Rei-Campus Centro-Oeste, Divinópolis, MG, Brazil
- Centro Federal de Educação Tecnológica de Minas Gerais-Campus Divinópolis, Divinópolis, MG, Brazil
| | - Iann Gabriel Lima
- Universidade Federal de São João del Rei-Campus Centro-Oeste, Divinópolis, MG, Brazil
- Centro Federal de Educação Tecnológica de Minas Gerais-Campus Divinópolis, Divinópolis, MG, Brazil
| | - Sandro J Greco
- Universidade Federal do Espírito Santo-UFES, Vitória, ES, Brazil
| | - Rosy I M A Ribeiro
- Universidade Federal de São João del Rei-Campus Centro-Oeste, Divinópolis, MG, Brazil
| | - Felipe M Munayer
- Universidade Federal do Espírito Santo-UFES, Vitória, ES, Brazil
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41
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Peraza A, Hernández R, Ruette F. Fundamental relationships between elementary functionals in quantum chemistry. An application for H2 and H2+. COMPUT THEOR CHEM 2017. [DOI: 10.1016/j.comptc.2016.12.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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42
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Biju S, Xu LJ, Hora Alves MA, Freire RO, Chen ZN. Bright orange and red light-emitting diodes of new visible light excitable tetrakis-Ln-β-diketonate (Ln = Sm3+, Eu3+) complexes. NEW J CHEM 2017. [DOI: 10.1039/c6nj03450k] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
A new β-diketonate ligand and its visible light excitable Sm3+, Eu3+-complexes were designed and synthesized; these complexes showed highly efficient photoluminescence and electroluminescence properties.
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Affiliation(s)
- Silvanose Biju
- State Key Laboratory of Structural Chemistry
- Fujian Institute of Research on the Structure of Matter
- Chinese Academy of Science
- Fuzhou
- China
| | - Liang-Jin Xu
- State Key Laboratory of Structural Chemistry
- Fujian Institute of Research on the Structure of Matter
- Chinese Academy of Science
- Fuzhou
- China
| | - Marcelo Augusto Hora Alves
- Pople Computational Chemistry Laboratory
- Departamento de Quımica
- UniversidadeFederal de Sergipe
- São Cristóvão
- Brazil
| | - Ricardo Oliveira Freire
- Pople Computational Chemistry Laboratory
- Departamento de Quımica
- UniversidadeFederal de Sergipe
- São Cristóvão
- Brazil
| | - Zhong-Ning Chen
- State Key Laboratory of Structural Chemistry
- Fujian Institute of Research on the Structure of Matter
- Chinese Academy of Science
- Fuzhou
- China
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43
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Podyachev SN, Sudakova SN, Gimazetdinova GS, Shamsutdinova NA, Syakaev VV, Barsukova TA, Iki N, Lapaev DV, Mustafina AR. Synthesis, metal binding and spectral properties of novel bis-1,3-diketone calix[4]arenes. NEW J CHEM 2017. [DOI: 10.1039/c6nj03381d] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Novel bis-1,3-diketone calix[4]arenes provide good antenna effects on Tb3+- and Yb3+-centered luminescence.
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Affiliation(s)
- Sergey N. Podyachev
- A. E. Arbuzov Institute of Organic and Physical Chemistry
- Kazan Scientific Center of Russian Academy of Sciences
- Kazan
- Russia
| | - Svetlana N. Sudakova
- A. E. Arbuzov Institute of Organic and Physical Chemistry
- Kazan Scientific Center of Russian Academy of Sciences
- Kazan
- Russia
| | | | - Nataliya A. Shamsutdinova
- A. E. Arbuzov Institute of Organic and Physical Chemistry
- Kazan Scientific Center of Russian Academy of Sciences
- Kazan
- Russia
| | - Victor V. Syakaev
- A. E. Arbuzov Institute of Organic and Physical Chemistry
- Kazan Scientific Center of Russian Academy of Sciences
- Kazan
- Russia
| | - Tatjiana A. Barsukova
- A. E. Arbuzov Institute of Organic and Physical Chemistry
- Kazan Scientific Center of Russian Academy of Sciences
- Kazan
- Russia
| | - Nobuhiko Iki
- Graduate School of Environmental Studies
- Tohoku University
- Sendai 980-8579
- Japan
| | - Dmitry V. Lapaev
- Zavoisky Physical-Technical Institute of Kazan Scientific Center of Russian Academy of Sciences
- 420029 Kazan
- Russia
| | - Asiya R. Mustafina
- A. E. Arbuzov Institute of Organic and Physical Chemistry
- Kazan Scientific Center of Russian Academy of Sciences
- Kazan
- Russia
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44
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Akbar R, Baral M, Kanungo BK. Photoluminescence and Coordination Behaviour of Lanthanide Complexes of Tris (Aminomethyl)Ethane-5-Oxine in Aqueous Solution. J Fluoresc 2016; 27:89-103. [PMID: 27704235 DOI: 10.1007/s10895-016-1937-6] [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: 07/17/2016] [Accepted: 09/12/2016] [Indexed: 10/20/2022]
Abstract
Photophysical properties of a multidentate tripodal ligand, 5,5'-(2-(((8-hydroxyquinolin-5-yl) methylamino)methyl)-2-methylpropane-1,3-diyl) bis (azanediyl)bis (methylene)diquinolin-8-ol, (TAME5OX), with La3+ and Er3+ ions have been examined for photonics applications. The change in behavior in electronic spectra of these complexes reveals the use of TAME5OX as a sensitive optical pH based sensor to detect Ln3+ ions whereas indication of strong green fluorescence allows simultaneous sensing within the visible region in competitive medium. The intense fluorescence intermittently gets quenched under acidic and basic conditions due to photoinduced intramolecular electron transfer from the excited 8-hydroxyquinoline (8-HQ) moiety to the metal ion. This renders these compounds the OFF-ON-OFF type of pH-dependent fluorescent sensor. The thermodynamic stability and coordination behaviour of the chelator with the said lanthanide ions have also been probed by potentiometric, UV - visible and fluorescence spectrophotometric method. TAME5OX forms protonated complex [Ln (H4L)]4+ below pH ~4.0 which sequentially deprotonates through one proton process with increase of pH. The stability constants of neutral complexes have been determined to be in the range log β110 = 32-34 and pLn in the range of 14-20, indicating TAME5OX is a good synthetic lanthanide chelator. Theoretical spectra were also calculated by ZINDO/s methodology at single excitations (CIS) level on PM7 as sparkle energy-minimized geometries.
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Affiliation(s)
- Rifat Akbar
- Department of Chemistry, Sant Longowal Institute of Engineering & Technology, Longowal, Punjab, 148106, India
| | - Minati Baral
- Department of Chemistry, National Institute of Technology Kurukshetra, Haryana, 136119, India
| | - B K Kanungo
- Department of Chemistry, Sant Longowal Institute of Engineering & Technology, Longowal, Punjab, 148106, India.
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45
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Urquiza-Carvalho GA, Fragoso WD, Rocha GB. Assessment of semiempirical enthalpy of formation in solution as an effective energy function to discriminate native-like structures in protein decoy sets. J Comput Chem 2016; 37:1962-72. [DOI: 10.1002/jcc.24415] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Revised: 04/29/2016] [Accepted: 05/11/2016] [Indexed: 11/09/2022]
Affiliation(s)
- Gabriel Aires Urquiza-Carvalho
- Departamento De QúImica; CCEN, Universidade Federal Da ParáIba; Jõao, Pessoa/PB, Caixa Postal: 5093 CEP: 58051-970 Brazil
| | - Wallace Duarte Fragoso
- Departamento De QúImica; CCEN, Universidade Federal Da ParáIba; Jõao, Pessoa/PB, Caixa Postal: 5093 CEP: 58051-970 Brazil
| | - Gerd Bruno Rocha
- Departamento De QúImica; CCEN, Universidade Federal Da ParáIba; Jõao, Pessoa/PB, Caixa Postal: 5093 CEP: 58051-970 Brazil
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46
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Filho MAM, Dutra JDL, Rocha GB, Simas AM, Freire RO. Parameters for the RM1 Quantum Chemical Calculation of Complexes of the Trications of Thulium, Ytterbium and Lutetium. PLoS One 2016; 11:e0154500. [PMID: 27223475 PMCID: PMC4880313 DOI: 10.1371/journal.pone.0154500] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 04/14/2016] [Indexed: 11/19/2022] Open
Abstract
The RM1 quantum chemical model for the calculation of complexes of Tm(III), Yb(III) and Lu(III) is advanced. Subsequently, we tested the models by fully optimizing the geometries of 126 complexes. We then compared the optimized structures with known crystallographic ones from the Cambridge Structural Database. Results indicate that, for thulium complexes, the accuracy in terms of the distances between the lanthanide ion and its directly coordinated atoms is about 2%. Corresponding results for ytterbium and lutetium are both 3%, levels of accuracy useful for the design of lanthanide complexes, targeting their countless applications.
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Affiliation(s)
- Manoel A. M. Filho
- Pople Computational Chemistry Laboratory, Departamento de Química, Universidade Federal de Sergipe, São Cristóvão, SE, Brazil
| | - José Diogo L. Dutra
- Pople Computational Chemistry Laboratory, Departamento de Química, Universidade Federal de Sergipe, São Cristóvão, SE, Brazil
- Departamento de Química Fundamental, Universidade Federal de Pernambuco, Recife, PE, Brazil
| | - Gerd B. Rocha
- Departamento de Química, CCEN, Universidade Federal da Paraíba, João Pessoa, PB, Brazil
| | - Alfredo M. Simas
- Departamento de Química Fundamental, Universidade Federal de Pernambuco, Recife, PE, Brazil
- * E-mail: (ROF); (AMS)
| | - Ricardo O. Freire
- Pople Computational Chemistry Laboratory, Departamento de Química, Universidade Federal de Sergipe, São Cristóvão, SE, Brazil
- * E-mail: (ROF); (AMS)
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Zairov R, Shamsutdinova N, Podyachev S, Sudakova S, Gimazetdinova G, Rizvanov I, Syakaev V, Babaev V, Amirov R, Mustafina A. Structure impact in antenna effect of novel upper rim substituted tetra-1,3-diketone calix[4]arenes on Tb(III) green and Yb(III) NIR-luminescence. Tetrahedron 2016. [DOI: 10.1016/j.tet.2016.03.068] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Chemical Partition of the Radiative Decay Rate of Luminescence of Europium Complexes. Sci Rep 2016; 6:21204. [PMID: 26892900 PMCID: PMC4759827 DOI: 10.1038/srep21204] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 01/15/2016] [Indexed: 11/08/2022] Open
Abstract
The spontaneous emission coefficient, Arad, a global molecular property, is one of the most important quantities related to the luminescence of complexes of lanthanide ions. In this work, by suitable algebraic transformations of the matrices involved, we introduce a partition that allows us to compute, for the first time, the individual effects of each ligand on Arad, a property of the molecule as a whole. Such a chemical partition thus opens possibilities for the comprehension of the role of each of the ligands and their interactions on the luminescence of europium coordination compounds. As an example, we applied the chemical partition to the case of repeating non-ionic ligand ternary complexes of europium(III) with DBM, TTA, and BTFA, showing that it allowed us to correctly order, in an a priori manner, the non-obvious pair combinations of non-ionic ligands that led to mixed-ligand compounds with larger values of Arad.
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Greco C, Moro G, Bertini L, Biczysko M, Barone V, Cosentino U. Computational Investigation on the Spectroscopic Properties of Thiophene Based Europium β-Diketonate Complexes. J Chem Theory Comput 2015; 10:767-77. [PMID: 26580051 DOI: 10.1021/ct400865b] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The adiabatic transition energies from the lowest triplet states of four Europium tris β-diketonate/phenantroline complexes have been determined in vacuo and in dicholomethane solution by the ΔSCF approach at the density functional theory level, using the PBE1PBE and the CAM-B3LYP hybrid functionals. The calculated adiabatic transition energies have been compared with the experimental 0-0 transitions of each complex determined from phosphorescence spectra of the corresponding Gd(3+) complexes and followed by direct comparison between simulated and experimental spectra line shapes. For compound 1, the Eu(TTA)3Phen system, triplet states other than the lowest one and conformational isomers other than the one present in the crystallographic structure have been considered. In the crystallographic structure, this compound presents three quasi-degenerate low energy triplet states, differing for the TTA ligand where the two unpaired electrons are localized and showing close adiabatic transition energies. For compound 1, the lowest triplet states of the four investigated conformational isomers show similar characteristics and close adiabatic transition energies. On the basis of these results, an investigation of compounds 2-4 (Eu(Br-TTA)3Phen, Eu(DTDK)3Phen, and Eu(MeT-TTA)3) has been performed by considering only the isomer present in the crystallographic structure and only the lowest triplet state of each compound. For compounds 1-3, the energies of the lowest triplet states calculated by both functionals in solution including zero-point energy corrections well reproduce the experimental trends as well as the values of the adiabatic transition energies: CAM-B3LYP, the best performing functional, provides energies of the lowest triplet state with deviations from experiments lower than 1200 cm(-1). Also, the calculated vibrationally resolved phosphorescence spectra and UV-vis absorptions well reproduce the main features of their experimental counterparts. Significant differences between calculated and experimental results are observed for compound 4, for which difficulties in the experimental determination of the triplet state energy were encountered: our results show that the negligible photoluminescence quantum yield of this compound is due to the fact that the energy of the most stable triplet state is significantly lower than that of the resonance level of the Europium ion, and thus the energy transfer process is prevented. These results confirm the reliability of the adopted computational approach in calculating the energy of the lowest triplet state energy of these systems, a key parameter in the design of new ligands for lanthanide complexes presenting large photoluminescence quantum yields.
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Affiliation(s)
- Claudio Greco
- Dipartimento di Scienze dell'Ambiente e del Territorio e di Scienze della Terra, Università degli Studi di Milano-Bicocca ; Piazza della Scienza 1, 20126 Milano, Italy
| | - Giorgio Moro
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano-Bicocca ; Piazza della Scienza 2, 20126 Milano, Italy
| | - Luca Bertini
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano-Bicocca ; Piazza della Scienza 2, 20126 Milano, Italy
| | | | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Ugo Cosentino
- Dipartimento di Scienze dell'Ambiente e del Territorio e di Scienze della Terra, Università degli Studi di Milano-Bicocca ; Piazza della Scienza 1, 20126 Milano, Italy
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Yang TH, Fu L, Ferreira RAS, Nolasco MM, Rocha J, Carlos LD, Shi FN. Influence of the Crystal Structure on the Luminescence Properties of Mixed Eu,La-(1,10-Phenanthroline) Complexes. Eur J Inorg Chem 2015. [DOI: 10.1002/ejic.201500611] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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