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Üstün E, Düşünceli SD, Coşkun F, Özdemir İ. Molybdenum Carbonyl Complexes with Benzimidazole Derivatives Against SARS-CoV-2 by Molecular Docking and DFT/TDDFT Methods. JOURNAL OF COMPUTATIONAL BIOPHYSICS AND CHEMISTRY 2021. [DOI: 10.1142/s2737416521500502] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Abstract
Benzimidazole derivative molecules attract attention of scientists due to their bioactivities. The dramatic changes in recorded activities according to the type and position of the substituents motivate synthesis and analysis of new molecules. Commercial benzimidazole-based molecules have been used in therapeutic procedures. It is known that the activities of metal complexes with benzimidazole derivative ligands have different activities when compared to the benzimidazole main structure. Nowadays, one of the most important health problems is COVID-19, which caused the pandemic that we are still experiencing. Although vaccine studies are important to overcome acute problems, regarding the possible post-vaccination adverse effects, the need for new drugs against the virus is obvious. Considering the urgency and the limited facilities during the pandemic, preliminary in silico studies of candidate molecules are essential. In this study, {[bis-(N-benzylbenzimidazole)] tetracarbonylmolybdenum}, {[bis-(N-4-chlorobenzylbenzimidazole)] tetracarbonylmolybdenum} and {[bis-(N-4-methoxybenzylbenzimidazole)] tetracarbonylmolybdenum} were synthesized and characterized. The optimization and the structural analysis of these molecules were performed by DFT/TDDFT methods. The molecules were docked into SARS coronavirus main peptidase (PDB ID: 2gtb), COVID-19 main protease in complex with Z219104216 (PDB ID: 5r82), COVID-19 main protease in complex with an inhibitor N3 (PDB ID: 6lu7) and Papain-like protease of SARS-CoV-2 (PDB ID: 6w9c) crystal structures for evaluation of their anti-viral activity.
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Affiliation(s)
- Elvan Üstün
- Department of Chemistry, Faculty of Art and Science, Ordu University, 52200 Ordu, Turkey
| | - Serpil Demir Düşünceli
- Department of Chemistry Faculty of Art and Science, İnönü University, 44280 Malatya, Turkey
- Catalysis Research and Application Center, İnönü University, 44280 Malatya, Turkey
| | - Feyzullah Coşkun
- Department of Chemistry Faculty of Art and Science, İnönü University, 44280 Malatya, Turkey
- Catalysis Research and Application Center, İnönü University, 44280 Malatya, Turkey
| | - İsmail Özdemir
- Department of Chemistry Faculty of Art and Science, İnönü University, 44280 Malatya, Turkey
- Catalysis Research and Application Center, İnönü University, 44280 Malatya, Turkey
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2
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Gloriozov IP, Dem'yanov PI, Zhulyaev NS, Nechaev MS, Oprunenko YF, Gam F, Saillard JY, Kuznetsov AE. DFT Investigation of the η 6 ⇌ η 6-Inter-ring Haptotropic Rearrangement of the Group 8 Metals Complexes [(graphene)MCp] + (M = Fe, Ru, Os). J Phys Chem A 2021; 125:366-375. [PMID: 33356252 DOI: 10.1021/acs.jpca.0c08251] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Metalcyclopentadienyl complexes (MCp)+ (M = Fe, Ru, Os) bound to the large polyaromatic hydrogenated hydrocarbon (PAH) C96H24 used as a model for pristine graphene have been studied using a density functional theory (DFT) generalized gradient approximation (PBE functional) to reveal their structural features and dynamic behavior. The inter-ring haptotropic rearrangements (IRHRs) for these complexes were shown to occur via two transition states and one intermediate. The energy barriers of the η6 ⇌ η6 IRHRs of the (MCp)+ unit were found to be 30, 27, and 29 kcal/mol for M = Fe, Ru, and Os, respectively. These values are significantly lower than the values found previously for smaller PAHs. Both polar and nonpolar solvents were found not to affect significantly the energy barrier heights. Investigated transition metal complexes could be used in general as catalysts in the design of novel derivatives or materials with promising properties. Metalcyclopentadienyl complexes (MCp)+ of PAHs show catalytic properties mainly due to their structural details as well as their important characteristic of inter-ring haptotropic rearrangement. IRHRs take place usually by intramolecular mechanisms. During IRHRs, the MLn organometallic groups (OMGs) undergo shifting along the PAH plane and could coordinate additional reagents, which is important for catalysis. Large PAHs such as graphene, fullerenes, and nanotubes possess intrinsic anticancer activity, and numerous arene complexes of Ru and Os have been proven to have anticancer properties as well. We suppose that coordinating Ru or Os to very large PAHs could synergistically increase the anticancer activity of resulting complexes.
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Affiliation(s)
- Igor P Gloriozov
- Department of Chemistry, M. V. Lomonosov Moscow State University, Leninskie Gory 1, Building 3, 119991 Moscow, Russia
| | - Piotr I Dem'yanov
- Department of Chemistry, M. V. Lomonosov Moscow State University, Leninskie Gory 1, Building 3, 119991 Moscow, Russia
| | - Nikolay S Zhulyaev
- Department of Chemistry, M. V. Lomonosov Moscow State University, Leninskie Gory 1, Building 3, 119991 Moscow, Russia
| | - Mikhail S Nechaev
- Department of Chemistry, M. V. Lomonosov Moscow State University, Leninskie Gory 1, Building 3, 119991 Moscow, Russia.,A. V. Topchiev Institute of Petrochemical Synthesis, Russian Academy of Sciences, Leninsky Prospect 29, 119991 Moscow, Russia
| | - Yuri F Oprunenko
- Department of Chemistry, M. V. Lomonosov Moscow State University, Leninskie Gory 1, Building 3, 119991 Moscow, Russia
| | - Franck Gam
- ISCR-UMR 6226, Université Rennes, CNRS, F-35000 Rennes, France
| | | | - Aleksey E Kuznetsov
- Department of Chemistry, Universidad Técnica Federico Santa Maria, Av. Santa Maria 6400, Vitacura, 7660251 Santiago, Chile
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1,6-Methano[10]annulene as prospective organometallic ligand from the annulene family: A DFT study of transition metal π-complexes and their inter-ring haptotropic rearrangements. J Organomet Chem 2018. [DOI: 10.1016/j.jorganchem.2017.11.023] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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4
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Quantum chemical study of the structures and dynamic behavior of tricarbonyl complexes of Group 6 metals (Cr, Mo, W) with polyaromatic hydrocarbons using the density functional theory. Russ Chem Bull 2017. [DOI: 10.1007/s11172-017-1868-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Oloba-Whenu OA, Albright TA, Soubra-Ghaoui C. Ring-whizzing in polyene-PtL2 complexes revisited. Beilstein J Org Chem 2016; 12:1410-20. [PMID: 27559391 PMCID: PMC4979650 DOI: 10.3762/bjoc.12.135] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 06/23/2016] [Indexed: 01/21/2023] Open
Abstract
Ring-whizzing was investigated by hybrid DFT methods in a number of polyene-Pt(diphosphinylethane) complexes. The polyenes included cyclopropenium(+), cyclobutadiene, cyclopentadienyl(+), hexafluorobenzene, cycloheptatrienyl(+), cyclooctatetraene, octafluorooctatetraene, 6-radialene, pentalene, phenalenium(+), naphthalene and octafluoronaphthalene. The HOMO of a d(10) ML2 group (with b2 symmetry) interacting with the LUMO of the polyene was used as a model to explain the occurrence of minima and maxima on the potential energy surface.
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Affiliation(s)
| | - Thomas A Albright
- Department of Chemistry, University of Houston, Houston, Texas 77204-5003, USA
| | - Chirine Soubra-Ghaoui
- Department of Chemistry and Physics, University of St. Thomas, Houston, Texas 77006, USA
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Rioja M, Hamon P, Roisnel T, Sinbandhit S, Fuentealba M, Letelier K, Saillard JY, Vega A, Hamon JR. [(η5-C5Me5)Ru]+ fragments ligated to polyaromatic hydrocarbons: an experimental and computational approach to pathways for haptotropic migration. Dalton Trans 2015; 44:316-29. [DOI: 10.1039/c4dt02736a] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
DFT calculations indicated rather high activation energies for the thermally induced intramolecular inter-ring haptotropic migration of the [(η5-C5Me5)Ru+] moiety.
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Affiliation(s)
- Matias Rioja
- Universidad Andres Bello
- Facultad de Ciencias Exactas
- Santiago
- Chile
| | - Paul Hamon
- UMR 6226 “Institut des Sciences Chimiques de Rennes”
- CNRS-Université de Rennes 1
- France
| | - Thierry Roisnel
- UMR 6226 “Institut des Sciences Chimiques de Rennes”
- CNRS-Université de Rennes 1
- France
| | | | | | - Karina Letelier
- Universidad Andres Bello
- Facultad de Ciencias Exactas
- Santiago
- Chile
| | - Jean-Yves Saillard
- UMR 6226 “Institut des Sciences Chimiques de Rennes”
- CNRS-Université de Rennes 1
- France
| | - Andrés Vega
- Universidad Andres Bello
- Facultad de Ciencias Exactas
- Santiago
- Chile
- Centro para el Desarrollo de la Nanociencia y la Nanotecnología
| | - Jean-René Hamon
- UMR 6226 “Institut des Sciences Chimiques de Rennes”
- CNRS-Université de Rennes 1
- France
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Fetisov EO, Gloriozov IP, Kissounko DA, Nechaev MS, Kahlal S, Saillard JY, Oprunenko YF. DFT study of dihydrogen addition to molybdenum π-heteroaromatic complexes: a prerequisite step for the catalytic hydrodenitrogenation process. NEW J CHEM 2015. [DOI: 10.1039/c5nj01585e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The mechanism proceeds via consecutive steps of oxidative H2 addition, hydrogen metal-to-ligand transfer, accompanied by a change of metal–ligand hapticity.
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Affiliation(s)
- Evgenii O. Fetisov
- Department of Chemistry
- M.V. Lomonosov Moscow State University
- 119899 Moscow
- Russia
- Department of Chemistry and Chemical Theory Center
| | - Igor P. Gloriozov
- Department of Chemistry
- M.V. Lomonosov Moscow State University
- 119899 Moscow
- Russia
| | | | - Mikhail S. Nechaev
- Department of Chemistry
- M.V. Lomonosov Moscow State University
- 119899 Moscow
- Russia
- A.V. Topchiev Institute of Petrochemical Synthesis
| | - Samia Kahlal
- Institut des Sciences Chimiques de Rennes
- UMR 6226 CNRS-Universite de Rennes 1
- 35042 Rennes cedex
- France
| | - Jean-Yves Saillard
- Institut des Sciences Chimiques de Rennes
- UMR 6226 CNRS-Universite de Rennes 1
- 35042 Rennes cedex
- France
| | - Yuri F. Oprunenko
- Department of Chemistry
- M.V. Lomonosov Moscow State University
- 119899 Moscow
- Russia
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Gloriozov IP, Marchal R, Saillard J, Oprunenko YF. Chromium Tricarbonyl and Chromium Benzene Complexes of Graphene, Their Properties, Stabilities, and Inter‐Ring Haptotropic Rearrangements – A DFT Investigation. Eur J Inorg Chem 2014. [DOI: 10.1002/ejic.201402879] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Igor P. Gloriozov
- Department of Chemistry, M.V. Lomonosov Moscow State University, Vorob'evy Gory, 119899 Moscow, Russia, http://fhmas.ru/ru/personal_oprunenko.htm
| | - Rémi Marchal
- Institut des Sciences Chimiques de Rennes, UMR 6226 CNRS‐Universite de Rennes 1, 35042 Rennes cedex, France E‐mail: jean‐yves.saillard@univ‐rennes1.fr http://www.scienceschimiques.univ‐rennes1.fr/equipes/cti/
| | - Jean‐Yves Saillard
- Institut des Sciences Chimiques de Rennes, UMR 6226 CNRS‐Universite de Rennes 1, 35042 Rennes cedex, France E‐mail: jean‐yves.saillard@univ‐rennes1.fr http://www.scienceschimiques.univ‐rennes1.fr/equipes/cti/
| | - Yuri F. Oprunenko
- Department of Chemistry, M.V. Lomonosov Moscow State University, Vorob'evy Gory, 119899 Moscow, Russia, http://fhmas.ru/ru/personal_oprunenko.htm
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Fetisov EO, Gloriozov IP, Oprunenko YF, Saillard JY, Kahlal S. Influence of Ion Pairing in Inter-Ring Haptotropic Rearrangements in Cationic Cyclopentadienyl Complexes of Ruthenium with Naphthalene: A DFT Investigation. Organometallics 2013. [DOI: 10.1021/om4003335] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- E. O. Fetisov
- Chemistry Department, M. V. Lomonosov Moscow State University, Vorob’evy Gory, 119899 Moscow,
Russia
| | - I. P. Gloriozov
- Chemistry Department, M. V. Lomonosov Moscow State University, Vorob’evy Gory, 119899 Moscow,
Russia
| | - Yu. F. Oprunenko
- Chemistry Department, M. V. Lomonosov Moscow State University, Vorob’evy Gory, 119899 Moscow,
Russia
| | - J.-Y. Saillard
- Institut des Sciences Chimiques de Rennes, UMR 6226 CNRS-Université de Rennes 1, F-35042
Rennes cedex, France
| | - S. Kahlal
- Institut des Sciences Chimiques de Rennes, UMR 6226 CNRS-Université de Rennes 1, F-35042
Rennes cedex, France
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Oprunenko YF, Gloriozov IP. A study of dynamic behavior of transition metal complexes with fullerene C60 using density function theory. J Organomet Chem 2013. [DOI: 10.1016/j.jorganchem.2013.02.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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11
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Czerwinski CJ, Fetisov EO, Gloriozov IP, Oprunenko YF. DFT study of intramolecular interring η6,η6-haptotropic rearrangements in tricarbonylchromium complexes of 2-aminobiphenyl and 4-aminobiphenyl. Dalton Trans 2013; 42:10487-94. [DOI: 10.1039/c3dt50655j] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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12
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On the structure and fluxionality of mononuclear complexes of naphthalene: A DFT investigation of (naphthalene)MCp (M=Sc, V, Mn, Fe, Ni) and related complexes. Inorganica Chim Acta 2012. [DOI: 10.1016/j.ica.2012.05.016] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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13
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Oprunenko YF, Gloriozov IP. A density functional study of intra- and interring haptotropic η2,η2 rearrangements in rhodium, ruthenium, and osmium naphthalene complexes. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2012. [DOI: 10.1134/s0036024412060209] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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