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Qin W, Guo K, Chen C, Fang J. Differences in the Reaction Mechanisms of Chlorine Atom and Hydroxyl Radical with Organic Compounds: From Thermodynamics to Kinetics. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:17886-17897. [PMID: 39344971 DOI: 10.1021/acs.est.4c03872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/01/2024]
Abstract
Hydroxyl radical (HO•) and chlorine atom (Cl•) are common reactive species in aqueous environments. However, the intrinsic difference in their reactions with organic compounds has not been revealed. This study compared the reaction mechanisms of HO• and Cl• with 13 aromatic and 11 aliphatic compounds by quantum chemical calculation and laser flash photolysis. Both HO• and Cl• can spontaneously react with aromatic compounds via radical adduct formation (RAF), hydrogen atom transfer (HAT), and single electron transfer (SET) pathways. The SET reactions of Cl• were more thermodynamically favorable than HO•, but contrary results were obtained for HAT reactions. According to the free energy of activation (ΔGaq‡), the dominant oxidation mechanisms of aromatic compounds were RAF and SET by HO• and SET by Cl•. The important role of SET in the HO• reactions with aromatic compounds was further verified by accurately calculating the solvation free energy of HO•/HO- and experimentally tracking the radical cations, which were generally neglected in previous studies. Meanwhile, the ΔGaq‡ value of each reaction pathway of Cl• was lower than that of HO•, resulting in higher rate constants of Cl• with aromatic compounds than HO•. For saturated aliphatic compounds, HAT was found to be the only mechanism accounting for their transformation by HO• and Cl•. This study proposed general rules for the reaction mechanisms of HO• and Cl• and unraveled their differences in the aspects of thermodynamics and kinetics, providing fundamental information for understanding contaminant transformation in processes involving HO• and Cl•.
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Affiliation(s)
- Wenlei Qin
- Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou 510275, China
| | - Kaiheng Guo
- Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou 510275, China
| | - Chunyan Chen
- Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou 510275, China
| | - Jingyun Fang
- Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou 510275, China
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Li H, Fan M, Liu Q. Unveiling the Unique Reactivity of Anionic Mn(I) Complexes via Metal-Ligand Cooperation: Nucleophilic Attack on C(sp 3)-X Bonds. J Am Chem Soc 2024; 146:26649-26656. [PMID: 39295280 DOI: 10.1021/jacs.4c01683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/21/2024]
Abstract
Metal-ligand cooperation (MLC) has emerged as a pivotal strategy for the catalytic activation of small molecules within both synthetic and biological arenas. Leveraging this approach, a suite of potent catalytic reactions─encompassing hydrogenation, hydroelementation, and dehydrogenative processes─have been realized, with notable advances in manganese catalysis in recent years. However, the activation of alkyl halides by Mn complexes, which typically requires strong reductants to form Mn(-I) complexes that are incompatible with standard cross-coupling conditions, remains a significant challenge. This limitation underscores the urgent need to investigate alternative methods for activating C(sp3)-X bonds using higher valence state Mn complexes. In response to this challenge, we present the synthesis, characterization, and reactivity of a new anionic Mn(I) complex featuring a redox-active dianionic ligand that induces multiple MLC functionalities. We have discovered an innovative mechanism of MLC, characterized by a single ligand transferring two electrons to the metal center. This novel process facilitates an orbital-symmetry-allowed nucleophilic attack on C(sp3)-X bonds, preserving manganese's oxidative state at +1. To the best of our knowledge, this is the first instance where the MLC strategy via a two-electron transfer process has been utilized to execute an SN2 nucleophilic attack at a C(sp3)-X bond by a relatively electron-deficient metal center like Mn(I). Additionally, the dianionic ligand of the anionic Mn(I) complex exhibits ambident nucleophilicity by reacting with different electrophiles, further highlighting its versatile reactivity.
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Affiliation(s)
- Hengxu Li
- Center of Basic Molecular Science, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Mingjie Fan
- Center of Basic Molecular Science, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Qiang Liu
- Center of Basic Molecular Science, Department of Chemistry, Tsinghua University, Beijing 100084, China
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Chagaleti BK, B SK, G V A, Rajagopal R, Alfarhan A, Arockiaraj J, Muthu Kumaradoss K, Karthick Raja Namasivayam S. Targeting cyclin-dependent kinase 2 CDK2: Insights from molecular docking and dynamics simulation - A systematic computational approach to discover novel cancer therapeutics. Comput Biol Chem 2024; 112:108134. [PMID: 38964206 DOI: 10.1016/j.compbiolchem.2024.108134] [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: 04/18/2024] [Accepted: 06/20/2024] [Indexed: 07/06/2024]
Abstract
Global public health is confronted with significant challenges due to the prevalence of cancer and the emergence of treatment resistance. This work focuses on the identification of cyclin-dependent kinase 2 (CDK2) through a systematic computational approach to discover novel cancer therapeutics. A ligand-based pharmacophore model was initially developed using a training set of seven potent CDK2 inhibitors. The obtained most robust model was characterized by three features: one donor (|Don|) and two acceptors (|Acc|). Screening this model against the ZINC database resulted in identifying 108 hits, which underwent further molecular docking studies. The docking results indicated binding affinity, with energy values ranging from -6.59 kcal mol⁻¹ to -7.40 kcal mol⁻¹ compared to the standard Roscovitine. The top 10 compounds (Z1-Z10) selected from the docking data were further screened for ADMET profiling, ensuring their compliance with pharmacokinetic and toxicological criteria. The top 3 compounds (Z1-Z3) chosen from the docking were subjected to Density Functional Theory (DFT) studies. They revealed significant variations in electronic properties, providing insights into the reactivity, stability, and polarity of these compounds. Molecular dynamics simulations confirmed the stability of the ligand-protein complexes, with acceptable RMSD and RMSF values. Specifically, compound Z1 demonstrated stability, around 2.4 Å, and maintained throughout the 100 ns simulation period with minimal conformational changes, stable RMSD, and consistent protein-ligand interactions.
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Affiliation(s)
- Bharath Kumar Chagaleti
- Department of Pharmaceutical Chemistry, SRM College of Pharmacy, SRM Institute of Science and Technology, Chengalpattu District, Kattankulathur, Tamil Nadu 603203, India
| | - Shantha Kumar B
- Department of Pharmaceutical Chemistry, SRM College of Pharmacy, SRM Institute of Science and Technology, Chengalpattu District, Kattankulathur, Tamil Nadu 603203, India
| | - Anjana G V
- Department of Pharmaceutical Chemistry, SRM College of Pharmacy, SRM Institute of Science and Technology, Chengalpattu District, Kattankulathur, Tamil Nadu 603203, India
| | - Rajakrishnan Rajagopal
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box No. 2455, Riyadh 11451, Saudi Arabia
| | - Ahmed Alfarhan
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box No. 2455, Riyadh 11451, Saudi Arabia
| | - Jesu Arockiaraj
- Department of Biotechnology, Faculty of Science and Humanities, SRM Institute of Science and Technology, Chengalpattu District, Kattankulathur, Tamil Nadu 603203, India.
| | - Kathiravan Muthu Kumaradoss
- Dr. APJ Kalam Research Lab, Department of Pharmaceutical Chemistry, SRM College of Pharmacy, SRM Institute of Science and Technology, Chengalpattu District, Kattankulathur, Tamil Nadu 603203, India.
| | - S Karthick Raja Namasivayam
- Centre for Applied Research, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences (SIMATS), Chennai, Tamil Nadu 602105, India.
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Chauhan C, Tanuj, Kumar R, Kumar J, Sharma S, Benmansour S, Kumar S. Synthesis, structural characterization, DFT and molecular dynamics simulations of dinuclear (μ-hydroxo)-bridged triethanolamine copper(II) complexes: efficient candidates towards visible light-mediated photo-Fenton degradation of organic dyes. Dalton Trans 2024. [PMID: 39087793 DOI: 10.1039/d4dt01463d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/02/2024]
Abstract
Multinuclear (di/tri) copper(II) complexes bridged through hydroxyl groups are very interesting coordination complexes owing to their potential applications in various fields. In this work, three novel dinuclear (μ-hydroxo)-bridged copper(II) complexes in the crystal form, namely, [Cu2(3,5-DIFLB)2(H2tea)2](H2O) (1), [Cu2(4-ClB)2(H2tea)2](H2O) (2), and [Cu2(4-ETHB)2(H2tea)2](H2O)2 (3) (where DIFLB = difluorobenzoate, CLB = chlorobenzoate, ETHB = ethoxybenzoate, and H3tea = triethanolamine), were isolated at room temperature using methanol and water in a 4 : 1 v/v ratio as a solvent. Furthermore, all three complexes (1-3) were characterised using spectroscopic (UV-vis, DRS, and FT-IR), electrochemical (CV) and single-crystal X-ray diffraction techniques. Structural insights gained by packing analysis revealed the role of steric constraints of substituents and various non-covalent interactions in lattice stabilization, which were indeed supported by theoretical and molecular electrostatic potential illustrations. Hirshfeld surface analysis provided quantitative verification about various non-covalent interactions (interatomic contacts) involved in the packing of molecules. Interestingly, as a potential application, complexes 1-3 all exhibited remarkable visible light-mediated photo-Fenton degradation of approximately 98% for 50 ppm concentration of organic dyes (fuchsin basic (FB) and methyl orange (MO)) in 90 minutes with the optimized conditions of 1 mg mL-1 of dye solution. In all the cases, dye degradation by these materials was ascribed to the symbiotic relations among the molecular structures of complexes 1-3, which were endowed with various electron-withdrawing and electron-releasing substituents and ionic strength, with respect to the structure, shape and interacting patterns of dye molecules. The adsorption mechanism indicates that various weak interactions between the donor and acceptor groups of complexes and dyes, such as electrostatic, hydrogen bonding, and direct coordination to metal sites, play a crucial role, which is confirmed by molecular dynamics (MD) simulations. Theoretical studies by DFT-based descriptors, molecular electrostatic potentials, and band gaps provided deep insights into various electronic and reactivity parameters. For subsequent processes of dye degradation, complexes 1-3 were stable and recoverable. The successful integration of experimental and theoretical approaches sheds light on copper-based dinuclear stable coordination complexes, showcasing a significant step towards the development of novel heterogeneous photo-Fenton catalysts.
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Affiliation(s)
- Chetan Chauhan
- Department of Chemistry, Himachal Pradesh University, Summer Hill, Shimla, India.
| | - Tanuj
- Department of Chemistry, Himachal Pradesh University, Summer Hill, Shimla, India.
| | - Rajesh Kumar
- Department of Chemistry, Himachal Pradesh University, Summer Hill, Shimla, India.
| | - Jitendra Kumar
- Department of Chemistry, MLPK, College, Balrampur, UP, India
| | - Subhash Sharma
- CONAHCyT-Centro de Nanociencias y Nanotecnología. Universidad Nacional Autónoma de México, Km 107 Carretera Tijuana-Ensenada AP14, Ensenada, 22860, B.C, Mexico
| | - Samia Benmansour
- Departamento de Química Inorgánica, Edificio F Grupo M4 (Materiales moleculares Multifuncionales y Modulables) C/Doctor Moliner, 50 46100-Burjassot, Spain.
| | - Santosh Kumar
- Department of Chemistry, Himachal Pradesh University, Summer Hill, Shimla, India.
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Kenari F, Pintér Z, Molnár S, Borges ID, Camargo AJ, Napolitano HB, Perjési P. ( E)-2-Benzylidenecyclanones: Part XIX. Reaction of ( E)-2-(4'-X-Benzylidene)-1-tetralones with Cellular Thiols: Comparison of Thiol Reactivities of Open-Chain Chalcones and Their Six- and Seven-Membered Cyclic Analogs. Int J Mol Sci 2024; 25:7773. [PMID: 39063017 PMCID: PMC11277078 DOI: 10.3390/ijms25147773] [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: 04/28/2024] [Revised: 06/27/2024] [Accepted: 07/12/2024] [Indexed: 07/28/2024] Open
Abstract
Non-enzyme-catalyzed thiol addition onto the α,β-unsaturated carbonyl system is associated with several biological effects. Kinetics and diastereoselectivity of non-enzyme catalyzed nucleophilic addition of reduced glutathione (GSH) and N-acetylcysteine (NAC) to the six-membered cyclic chalcone analogs 2a and 2b were investigated at different pH values (pH 3.2, 7.4 and 8.0). The selected compounds displayed in vitro cancer cell cytotoxicity (IC50) of different orders of magnitude. The chalcones intrinsically reacted with both thiols under all incubation conditions. The initial rates and compositions of the final mixtures depended both on the substitution and the pH. The stereochemical outcome of the reactions was evaluated using high-pressure liquid chromatography with UV detection (HPLC-UV). The structures of the formed thiol-conjugates and the retro-Michael products (Z)-2a and (Z)-2b were confirmed by high-pressure liquid chromatography-mass spectrometry (HPLC-MS). Frontier molecular orbitals and the Fukui function calculations were carried out to investigate their effects on the six-membered cyclic analogs. Data were compared with those obtained with the open-chain (1) and the seven-membered (3) analogs. The observed reactivities do not directly relate to the difference in in vitro cancer cell cytotoxicity of the compounds.
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Affiliation(s)
- Fatemeh Kenari
- Institute of Pharmaceutical Chemistry, University of Pécs, H-7624 Pécs, Hungary; (F.K.); (Z.P.); (S.M.)
| | - Zoltán Pintér
- Institute of Pharmaceutical Chemistry, University of Pécs, H-7624 Pécs, Hungary; (F.K.); (Z.P.); (S.M.)
| | - Szilárd Molnár
- Institute of Pharmaceutical Chemistry, University of Pécs, H-7624 Pécs, Hungary; (F.K.); (Z.P.); (S.M.)
- Research Institute for Viticulture and Oenology, University of Pécs, H-7634 Pécs, Hungary
| | - Igor D. Borges
- Grupo de Química Teórica e Estrutural de Anápolis, Universidade Estadual de Goiás, Anápolis 75132-903, GO, Brazil; (I.D.B.); (A.J.C.); (H.B.N.)
| | - Ademir J. Camargo
- Grupo de Química Teórica e Estrutural de Anápolis, Universidade Estadual de Goiás, Anápolis 75132-903, GO, Brazil; (I.D.B.); (A.J.C.); (H.B.N.)
| | - Hamilton B. Napolitano
- Grupo de Química Teórica e Estrutural de Anápolis, Universidade Estadual de Goiás, Anápolis 75132-903, GO, Brazil; (I.D.B.); (A.J.C.); (H.B.N.)
| | - Pál Perjési
- Institute of Pharmaceutical Chemistry, University of Pécs, H-7624 Pécs, Hungary; (F.K.); (Z.P.); (S.M.)
- Grupo de Química Teórica e Estrutural de Anápolis, Universidade Estadual de Goiás, Anápolis 75132-903, GO, Brazil; (I.D.B.); (A.J.C.); (H.B.N.)
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Roua A, Hassani AAE, Fitri A, Benjelloun AT, Benzakour M, Mcharfi M, Tanji K. Adsorption studies of isoxazole derivatives as corrosion inhibitors for mild steel in 1M HCl solution: DFT studies and molecular dynamics simulation. J Mol Model 2024; 30:193. [PMID: 38819596 DOI: 10.1007/s00894-024-05982-5] [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: 02/28/2024] [Accepted: 05/16/2024] [Indexed: 06/01/2024]
Abstract
CONTEXT The corrosion of mild steel is a significant issue in various industries, prompting the need for effective corrosion inhibitors. This study focuses on understanding the corrosion inhibition properties of organic compounds derived from isoxazole, namely series Iso(a), Iso(b), Iso(c), Iso(d), Iso(e), Iso(f), Iso(g), and Iso(h), which could have implications for materials science and industrial applications. By investigating the influence of different substitutions on these compounds, valuable insights can be gained into designing better corrosion inhibitors for practical use. METHODS Theoretical studies were conducted using density functional theory (DFT) with the B3LYP functional and the 6-31G (d,p) basis set. These calculations enabled the evaluation of various parameters including frontier orbital energies (EHOMO, ELUMO), energy gap (∆E), electronegativity (χ), absolute hardness (η), softness (σ), fraction of transferred electrons (∆N), as well as local properties such as natural atomic populations and Fukui indices. Additionally, molecular dynamics simulations were performed to study the adsorption behavior of the inhibitors on the surface of Fe (110). The simulations were conducted using Materials Studio version 8.0 software package using COMPASS force field to understand the impact of different functional groups on the inhibitors before and after adsorption on the iron surface.
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Affiliation(s)
- Amal Roua
- Laboratoire d'Ingénierie, Modélisation Et Analyse Des Systèmes, LIMAS, Faculté Des Sciences Dhar El Mahraz, Université Sidi Mohammed Ben Abdellah, BP 1796, 30000, Fès, Morocco.
| | - Anouar Ameziane El Hassani
- Laboratoire d'Ingénierie, Modélisation Et Analyse Des Systèmes, LIMAS, Faculté Des Sciences Dhar El Mahraz, Université Sidi Mohammed Ben Abdellah, BP 1796, 30000, Fès, Morocco
| | - Asmae Fitri
- Laboratoire d'Ingénierie, Modélisation Et Analyse Des Systèmes, LIMAS, Faculté Des Sciences Dhar El Mahraz, Université Sidi Mohammed Ben Abdellah, BP 1796, 30000, Fès, Morocco
| | - Adil Touimi Benjelloun
- Laboratoire d'Ingénierie, Modélisation Et Analyse Des Systèmes, LIMAS, Faculté Des Sciences Dhar El Mahraz, Université Sidi Mohammed Ben Abdellah, BP 1796, 30000, Fès, Morocco
| | - Mohammed Benzakour
- Laboratoire d'Ingénierie, Modélisation Et Analyse Des Systèmes, LIMAS, Faculté Des Sciences Dhar El Mahraz, Université Sidi Mohammed Ben Abdellah, BP 1796, 30000, Fès, Morocco
| | - Mohammed Mcharfi
- Laboratoire d'Ingénierie, Modélisation Et Analyse Des Systèmes, LIMAS, Faculté Des Sciences Dhar El Mahraz, Université Sidi Mohammed Ben Abdellah, BP 1796, 30000, Fès, Morocco
| | - Karim Tanji
- Laboratory of Advanced Materials and Process Engineering, Department of Chemistry, Faculty of Sciences, Ibn Tofaïl University, B.P. 133, 14000, Kenitra, Morocco.
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Sun CS, Yuan SW, Hou R, Zhang SQ, Huang QY, Lin L, Li HX, Liu S, Cheng YY, Li ZH, Xu XR. First insights into the bioaccumulation, biotransformation and trophic transfer of typical tetrabromobisphenol A (TBBPA) analogues along a simulated aquatic food chain. JOURNAL OF HAZARDOUS MATERIALS 2024; 465:133390. [PMID: 38163409 DOI: 10.1016/j.jhazmat.2023.133390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 11/28/2023] [Accepted: 12/26/2023] [Indexed: 01/03/2024]
Abstract
Tetrabromobisphenol A (TBBPA) analogues have been investigated for their prevalent occurrence in environments and potential hazardous effects to humans and wildlife; however, there is still limited knowledge regarding their toxicokinetics and trophic transfer in aquatic food chains. Using a developed toxicokinetic model framework, we quantified the bioaccumulation, biotransformation and trophic transfer of tetrabromobisphenol S (TBBPS) and tetrabromobisphenol A di(allyl ether) (TBBPA-DAE) during trophic transfer from brine shrimp (Artemia salina) to zebrafish (Danio rerio). The results showed that the two TBBPA analogues could be readily accumulated by brine shrimp, and the estimated bioconcentration factor (BCF) value of TBBPS (5.68 L kg-1 ww) was higher than that of TBBPA-DAE (1.04 L kg-1 ww). The assimilation efficiency (AE) of TBBPA-DAE in zebrafish fed brine shrimp was calculated to be 16.3%, resulting in a low whole-body biomagnification factor (BMF) in fish (0.684 g g-1 ww). Based on the transformation products screened using ultra-high-performance liquid chromatograph-high resolution mass spectrometry (UPLC-HRMS), oxidative debromination and hydrolysis were identified as the major transformation pathways of TBBPS, while the biotransformation of TBBPA-DAE mainly took place through ether bond breaking and phase-II metabolism. Lower accumulation of TBBPA as a metabolite than its parent chemical was observed in both brine shrimp and zebrafish, with metabolite parent concentration factors (MPCFs) < 1. The investigated BCFs for shrimp of the two TBBPA analogues were only 3.77 × 10-10 - 5.59 × 10-3 times of the theoretical Kshrimp-water based on the polyparameter linear free energy relationships (pp-LFERs) model, and the BMF of TBBPA-DAE for fish was 0.299 times of the predicted Kshrimp-fish. Overall, these results indicated the potential of the trophic transfer in bioaccumulation of specific TBBPA analogues in higher trophic-level aquatic organisms and pointed out biotransformation as an important mechanism in regulating their bioaccumulation processes. ENVIRONMENTAL IMPLICATION: The internal concentration of a pollutant in the body determines its toxicity to organisms, while bioaccumulation and trophic transfer play important roles in elucidating its risks to ecosystems. Tetrabromobisphenol A (TBBPA) analogues have been extensively investigated for their adverse effects on humans and wildlife; however, there is still limited knowledge regarding their toxicokinetics and trophic transfer in aquatic food chains. This study investigated the bioaccumulation, biotransformation and trophic transfer of TBBPS and TBBPA-DAE in a simulated di-trophic food chain. This state-of-art study will provide a reference for further research on this kind of emerging pollutant in aquatic environments.
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Affiliation(s)
| | - Sheng-Wu Yuan
- National Engineering Laboratory for Lake Pollution Control and Ecological Restoration, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Rui Hou
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China.
| | - Si-Qi Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Qian-Yi Huang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Lang Lin
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Heng-Xiang Li
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China
| | - Shan Liu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China
| | - Yuan-Yue Cheng
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Zhi-Hua Li
- Marine College, Shandong University, Weihai 264209, China.
| | - Xiang-Rong Xu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China
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Kumari S, Thakur M, Chauhan C, Kumari M. Synthesis, characterization, biological activity and computation-based efficacy of cobalt(II) complexes of biphenyl-2-ol against SARS-CoV-2 virus. J Biomol Struct Dyn 2023:1-15. [PMID: 37990487 DOI: 10.1080/07391102.2023.2283144] [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: 07/13/2023] [Accepted: 11/06/2023] [Indexed: 11/23/2023]
Abstract
Cobalt(II) complexes of biphenyl-2-ol of composition, CoCl2-n(OC6H4C6H5-2)n(H2O)4 (where n = 1 or 2), were prepared by reacting cobaltous(II) chloride with equi- and bimolar ratios of sodium salt of biphenyl-2-ol. The structural characterization of the synthesized complexes was accomplished by NMR, FTIR, thermogravimetry (TGA), high resolution mass spectroscopy (HRMS), electronic spectroscopic techniques coupled with density functional theory (DFT). The stability of the complexes in different pH media of solvent was studied. Chemical reactivity parameters of the newly synthesized complexes, computed using DFT, indicated greater reactivity of complex 2 over complex 1 and free ligand as indicated by its low HOMO-LUMO energy gap corresponding to 1.71 eV. Molecular docking (MD) studies were carried out in order to study the binding affinities between amino acid residues of DNA duplex (PDB ID: 1BNA) and SARS-CoV-2 (PDB ID: 7T9K) with newly synthesized complexes. Complex 2 has shown promising antivirus behaviour with an inhibition constant value of 0.0423 µmol-1 with amino acid residues of SARS-CoV-2 virus. Toxicity of the complexes was predicted using ProTox-II online server. Antibacterial studies have indicated the complexes to exhibit greater efficacy than the free ligand, while the antioxidant activities have suggested them to display enhanced antioxidant behaviour as compared to reference compounds.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shalima Kumari
- Department of Chemistry, Himachal Pradesh University, Shimla, India
| | - Maridula Thakur
- Department of Chemistry, Himachal Pradesh University, Shimla, India
| | - Chetan Chauhan
- Department of Chemistry, Himachal Pradesh University, Shimla, India
| | - Meena Kumari
- Department of Chemistry, Himachal Pradesh University, Shimla, India
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Yamaguchi K, Miyagawa K, Shoji M, Kawakami T, Isobe H, Yamanaka S, Nakajima T. Theoretical elucidation of the structure, bonding, and reactivity of the CaMn 4O x clusters in the whole Kok cycle for water oxidation embedded in the oxygen evolving center of photosystem II. New molecular and quantum insights into the mechanism of the O-O bond formation. PHOTOSYNTHESIS RESEARCH 2023:10.1007/s11120-023-01053-7. [PMID: 37945776 DOI: 10.1007/s11120-023-01053-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 09/25/2023] [Indexed: 11/12/2023]
Abstract
This paper reviews our historical developments of broken-symmetry (BS) and beyond BS methods that are applicable for theoretical investigations of metalloenzymes such as OEC in PSII. The BS hybrid DFT (HDFT) calculations starting from high-resolution (HR) XRD structure in the most stable S1 state have been performed to elucidate structure and bonding of whole possible intermediates of the CaMn4Ox cluster (1) in the Si (i = 0 ~ 4) states of the Kok cycle. The large-scale HDFT/MM computations starting from HR XRD have been performed to elucidate biomolecular system structures which are crucial for examination of possible water inlet and proton release pathways for water oxidation in OEC of PSII. DLPNO CCSD(T0) computations have been performed for elucidation of scope and reliability of relative energies among the intermediates by HDFT. These computations combined with EXAFS, XRD, XFEL, and EPR experimental results have elucidated the structure, bonding, and reactivity of the key intermediates, which are indispensable for understanding and explanation of the mechanism of water oxidation in OEC of PSII. Interplay between theory and experiments have elucidated important roles of four degrees of freedom, spin, charge, orbital, and nuclear motion for understanding and explanation of the chemical reactivity of 1 embedded in protein matrix, indicating the participations of the Ca(H2O)n ion and tyrosine(Yz)-O radical as a one-electron acceptor for the O-O bond formation. The Ca-assisted Yz-coupled O-O bond formation mechanisms for water oxidation are consistent with recent XES and very recent time-resolved SFX XFEL and FTIR results.
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Affiliation(s)
- Kizashi Yamaguchi
- Center for Quantum Information and Quantum Biology, Osaka University, Toyonaka, Osaka, 560-0043, Japan.
- RIKEN Center for Computational Science, Kobe, Hyogo, 650-0047, Japan.
- SANKEN, Osaka University, Ibaraki, Osaka, 567-0047, Japan.
| | - Koichi Miyagawa
- Center of Computational Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8577, Japan
| | - Mitsuo Shoji
- Center of Computational Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8577, Japan
| | - Takashi Kawakami
- RIKEN Center for Computational Science, Kobe, Hyogo, 650-0047, Japan
- Graduate School of Science, Osaka University, Toyonaka, Osaka, 560-0043, Japan
| | - Hiroshi Isobe
- Research Institute for Interdisciplinary Science, and Graduate School of Natural Science and Technology, Okayama University, Okayama, 700-8530, Japan
| | - Shusuke Yamanaka
- Graduate School of Science, Osaka University, Toyonaka, Osaka, 560-0043, Japan
| | - Takahito Nakajima
- RIKEN Center for Computational Science, Kobe, Hyogo, 650-0047, Japan
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10
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Yamaguchi K, Isobe H, Shoji M, Kawakami T, Miyagawa K. The Nature of the Chemical Bonds of High-Valent Transition-Metal Oxo (M=O) and Peroxo (MOO) Compounds: A Historical Perspective of the Metal Oxyl-Radical Character by the Classical to Quantum Computations. Molecules 2023; 28:7119. [PMID: 37894598 PMCID: PMC10609222 DOI: 10.3390/molecules28207119] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 10/08/2023] [Accepted: 10/10/2023] [Indexed: 10/29/2023] Open
Abstract
This review article describes a historical perspective of elucidation of the nature of the chemical bonds of the high-valent transition metal oxo (M=O) and peroxo (M-O-O) compounds in chemistry and biology. The basic concepts and theoretical backgrounds of the broken-symmetry (BS) method are revisited to explain orbital symmetry conservation and orbital symmetry breaking for the theoretical characterization of four different mechanisms of chemical reactions. Beyond BS methods using the natural orbitals (UNO) of the BS solutions, such as UNO CI (CC), are also revisited for the elucidation of the scope and applicability of the BS methods. Several chemical indices have been derived as the conceptual bridges between the BS and beyond BS methods. The BS molecular orbital models have been employed to explain the metal oxyl-radical character of the M=O and M-O-O bonds, which respond to their radical reactivity. The isolobal and isospin analogy between carbonyl oxide R2C-O-O and metal peroxide LFe-O-O has been applied to understand and explain the chameleonic chemical reactivity of these compounds. The isolobal and isospin analogy among Fe=O, O=O, and O have also provided the triplet atomic oxygen (3O) model for non-heme Fe(IV)=O species with strong radical reactivity. The chameleonic reactivity of the compounds I (Cpd I) and II (Cpd II) is also explained by this analogy. The early proposals obtained by these theoretical models have been examined based on recent computational results by hybrid DFT (UHDFT), DLPNO CCSD(T0), CASPT2, and UNO CI (CC) methods and quantum computing (QC).
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Affiliation(s)
- Kizashi Yamaguchi
- SANKEN, Osaka University, Ibaraki 567-0047, Osaka, Japan
- Center for Quantum Information and Quantum Biology (QIQB), Osaka University, Toyonaka 560-0043, Osaka, Japan
| | - Hiroshi Isobe
- Research Institute for Interdisciplinary Science, Okayama University, Okayama 700-8530, Okayama, Japan;
| | - Mitsuo Shoji
- Center for Computational Sciences, University of Tsukuba, Tsukuba 305-8577, Ibaraki, Japan; (M.S.); (K.M.)
| | - Takashi Kawakami
- Department of Chemistry, Graduate School of Science, Osaka University, Toyonaka 560-0043, Osaka, Japan;
| | - Koichi Miyagawa
- Center for Computational Sciences, University of Tsukuba, Tsukuba 305-8577, Ibaraki, Japan; (M.S.); (K.M.)
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11
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Alves TV, Fernández I. Understanding the reactivity and selectivity of Diels-Alder reactions involving furans. Org Biomol Chem 2023; 21:7767-7775. [PMID: 37698053 DOI: 10.1039/d3ob01343j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/13/2023]
Abstract
The reactivity and endo/exo selectivity of the Diels-Alder cycloaddition reactions involving furan and substituted furans as dienes have been computationally explored. In comparison to cyclopentadiene, it is found that furan is comparatively less reactive and also less endo-selective in the reaction with maleic anhydride as the dienophile. Despite that, both the reactivity and the selectivity can be successfully modified by the presence of substituents at either 2- or 3-positions of the heterocycle. In this sense, it is found that the presence of strong electron-donor groups significantly increases the reactivity of the system while the opposite is found in the presence of electron-withdrawing groups. The observed trends in both the reactivity and selectivity are analyzed quantitatively in detail by means of the activation strain model of reactivity in combination with the energy decomposition analysis methods.
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Affiliation(s)
- Tiago Vinicius Alves
- Departamento de Físico-Química, Instituto de Química - Universidade Federal da Bahia, Salvador, 40170-115, Bahia, Brazil.
| | - Israel Fernández
- Departmento de Química Orgánica and Centro de Innovación en Química Avanzada (ORFEO-CINQA), Facultad de Ciencias Químicas, Universidad Complutense de Madrid, Ciudad Universitaria, 28040 Madrid, Spain.
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12
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Dias LD, Aguiar ASN, de Melo NJ, Inada NM, Borges LL, de Aquino GLB, Camargo AJ, Bagnato VS, Napolitano HB. Structural basis of antibacterial photodynamic action of curcumin against S. aureus. Photodiagnosis Photodyn Ther 2023; 43:103654. [PMID: 37308043 DOI: 10.1016/j.pdpdt.2023.103654] [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: 03/26/2023] [Revised: 05/07/2023] [Accepted: 06/09/2023] [Indexed: 06/14/2023]
Abstract
Antimicrobial photodynamic therapy (aPDT) is an alternative tool to commercial antibiotics for the inactivation of pathogenic bacteria (e.g., S. aureus). However, there is still a lack of understanding of the molecular modeling of the photosensitizers and their mechanism of action through oxidative pathways. Herein, a combined experimental and computational evaluation of curcumin as a photosensitizer against S. aureus was performed. The radical forms of keto-enol tautomers and the energies of curcumin's frontier molecular orbitals were evaluated by density functional theory (DFT) to point out the photodynamic action as well as the photobleaching process. Furthermore, the electronic transitions of curcumin keto-enol tautomers were undertaken to predict the transitions as a photosensitizer during the antibacterial photodynamic process. Moreover, molecular docking was used to evaluate the binding affinity with the S. aureus tyrosyl-tRNA synthetase as the proposed a target for curcumin. In this regard, the molecular orbital energies show that the curcumin enol form has a character of 4.5% more basic than the keto form - the enol form is a more promising electron donor than its tautomer. Curcumin is a strong electrophile, with the enol form being 4.6% more electrophilic than its keto form. In addition, the regions susceptible to nucleophilic attack and photobleaching were evaluated by the Fukui function. Regarding the docking analysis, the model suggested that four hydrogen bonds contribute to the binding energy of curcumin's interaction with the ligand binding site of S. aureus tyrosyl-tRNA synthetase. Finally, residues Tyr36, Asp40, and Asp177 contact curcumin and may contribute to orienting the curcumin in the active area. Moreover, curcumin presented a photoinactivation of 4.5 log unit corroborating the necessity of the combined action of curcumin, light, and O2 to promote the photooxidation damage of S. aureus. These computational and experimental data suggest insights regarding the mechanism of action of curcumin as a photosensitizer to inactivate S. aureus bacteria.
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Affiliation(s)
- Lucas D Dias
- Laboratório de Novos Materiais, Universidade Evangélica de Goiás, Anápolis GO, Brazil; Grupo de Química Teórica e Estrutural de Anápolis, Universidade Estadual de Goiás, Anápolis, GO, Brazil.
| | - Antônio S N Aguiar
- Grupo de Química Teórica e Estrutural de Anápolis, Universidade Estadual de Goiás, Anápolis, GO, Brazil
| | - Nícolas J de Melo
- São Carlos Institute of Physics, University of São Paulo, São Carlos, SP, Brazil
| | - Natalia M Inada
- São Carlos Institute of Physics, University of São Paulo, São Carlos, SP, Brazil
| | - Leonardo L Borges
- Grupo de Química Teórica e Estrutural de Anápolis, Universidade Estadual de Goiás, Anápolis, GO, Brazil; Escola de Ciências Médicas e da Vida, Pontifícia Universidade Católica de Goiás, Goiânia, GO, Brazil
| | - Gilberto L B de Aquino
- Laboratório de Pesquisa em Bioprodutos e Síntese, Universidade Estadual de Goiás, Anápolis, GO, Brazil
| | - Ademir J Camargo
- Grupo de Química Teórica e Estrutural de Anápolis, Universidade Estadual de Goiás, Anápolis, GO, Brazil
| | - Vanderlei S Bagnato
- São Carlos Institute of Physics, University of São Paulo, São Carlos, SP, Brazil; Department of Biomedical Engineering, Texas A&M University, College Station, TX, USA
| | - Hamilton B Napolitano
- Laboratório de Novos Materiais, Universidade Evangélica de Goiás, Anápolis GO, Brazil; Grupo de Química Teórica e Estrutural de Anápolis, Universidade Estadual de Goiás, Anápolis, GO, Brazil.
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13
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Rodríguez HA, Bickelhaupt FM, Fernández I. Origin of the Bürgi-Dunitz Angle. Chemphyschem 2023; 24:e202300379. [PMID: 37306022 DOI: 10.1002/cphc.202300379] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 06/09/2023] [Accepted: 06/12/2023] [Indexed: 06/13/2023]
Abstract
The Bürgi-Dunitz (BD) angle plays a pivotal role in organic chemistry to rationalize the nucleophilic addition to carbonyl groups. Yet, the origin of the obtuse trajectory of the nucleophile remains incompletely understood. Herein, we quantify the importance of the underlying physical factors quantum chemically. The obtuse BD angle appears to originate from the concerted action of a reduced Pauli repulsion between the nucleophile HOMO and carbonyl π bond, a more stabilizing HOMO-π*-LUMO(C=O) interaction, as well as a more favorable electrostatic attraction.
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Affiliation(s)
- Humberto A Rodríguez
- Departamento de Química Orgánica and Centro de Innovación en Química Avanzada (ORFEO-CINQA), Facultad de Ciencias Químicas, Universidad Complutense de Madrid Ciudad Universitaria, 28040-, Madrid, Spain
- Instituto de Productos Naturales y Agrobiología (IPNA), Consejo Superior de Investigaciones Científicas (CSIC), 38206-, La Laguna, Tenerife, Spain
| | - F Matthias Bickelhaupt
- Theoretical Chemistry, Department of Chemistry and Pharmaceutical Sciences, Vrije Universiteit Amsterdam, The Netherlands
- Institute for Molecules and Materials (IMM), Radboud University, Nijmegen, The Netherlands
- Department of Chemical Sciences, University of Johannesburg, South Africa
| | - Israel Fernández
- Departamento de Química Orgánica and Centro de Innovación en Química Avanzada (ORFEO-CINQA), Facultad de Ciencias Químicas, Universidad Complutense de Madrid Ciudad Universitaria, 28040-, Madrid, Spain
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14
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Laconsay CJ, Tantillo DJ. Modulating Escape Channels of Cycloheptatrienyl Rhodium Carbenes To Form Semibullvalene. J Org Chem 2023. [PMID: 37335974 DOI: 10.1021/acs.joc.3c00735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2023]
Abstract
We describe the various escape channels available to dirhodium carbene intermediates from cycloheptatrienyl diazo compounds located with density functional theory. An intramolecular cyclopropanation would, in principle, provide a new route to semibullvalenes (SBVs). A detailed exploration of the potential energy surface reveals that methylating carbon-7 suppresses a competing β-hydride migration pathway to heptafulvene products, giving SBV formation a reasonable chance. During our explorations, we additionally discovered unusual spirononatriene, spironorcaradiene, and metal-stabilized 9-barbaralyl cation structures as local minima.
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Affiliation(s)
- Croix J Laconsay
- Department of Chemistry, University of California─Davis, Davis, California 95616, United States
| | - Dean J Tantillo
- Department of Chemistry, University of California─Davis, Davis, California 95616, United States
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15
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Molteni G, Ponti A. Is DFT Accurate Enough to Calculate Regioselectivity? The Case of 1,3-Dipolar Cycloaddition of Azide to Alkynes and Alkenes. Chemphyschem 2023; 24:e202300114. [PMID: 36896728 DOI: 10.1002/cphc.202300114] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 03/07/2023] [Accepted: 03/09/2023] [Indexed: 03/11/2023]
Abstract
The importance of regioselectivity in 1,3-dipolar cycloadditions (DCs) makes it surprising that no benchmarking study on this problem has appeared. We investigated whether DFT calculations are an accurate tool to predict the regioselectivity of uncatalyzed thermal azide 1,3-DCs. We considered the reaction between HN3 and 12 dipolarophiles, comprising ethynes HC≡C-R and ethenes H2 C=CH-R (R=F, OH, NH2 , Me, CN, CHO), which cover a broad range of electron demand and conjugation ability. We established benchmark data by the W3X protocol [complete-basis-set-extrapolated CCSD(T)-F12 energy with T-(T) and (Q) corrections and MP2-calculated core/valence and relativistic effects] and showed that core/valence effects and high-order excitations are important for accurate regioselectivity. Regioselectivities calculated using an extensive set of density functional approximations (DFAs) were compared with benchmark data. Range-separated and meta-GGA hybrids gave the best results. Good treatment of self-interaction and electron exchange are the key features for accurate regioselectivity. Dispersion correction slightly improves agreement with W3X results. The best DFAs provide the isomeric TS energy difference with an expected error ≈0.7 mh and errors ≈2 mh can occur. The isomer yield provided by the best DFA has an expected error of ±5 %, though errors up to 20 % are not rare. At present, an accuracy of 1-2 % is unfeasible but it seems that we are not far from achieving this goal.
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Affiliation(s)
- Giorgio Molteni
- Dipartimento di Chimica, Università degli Studi di Milano, Via C. Golgi 19, 20133, Milano, Italy
| | - Alessandro Ponti
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta", Consiglio Nazionale delle Ricerche, Via C. Golgi 19, 20133, Milano, Italy
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16
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Tirkasheva SI, Ziyadullaev OE, Eshimbetov AG, Ibragimov BT, Ashurov JM. Synthesis, crystal structure, Hirshfeld surface analysis and DFT study of the 1,1'-(buta-1,3-diyne-1,4-di-yl)bis-(cyclo-hexan-1-ol). Acta Crystallogr E Crystallogr Commun 2023; 79:605-609. [PMID: 37601586 PMCID: PMC10439439 DOI: 10.1107/s2056989023004772] [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: 11/28/2022] [Accepted: 05/31/2023] [Indexed: 08/22/2023]
Abstract
The title compound, C16H22O2, was synthesized in order to obtain its guest-free form because 'wheel-and-axle'-shaped mol-ecules tend to crystallize from solutions as solvates or host-guest mol-ecules. It crystallizes in the monoclinic space group P2/c with two crystallographically non-equivalent mol-ecules, one situated on an inversion center and the other on a twofold axis. The rod-like 1,3-diyne fragments have the usual linear geometry. In the crystal, O-H ⋯ O bonds form eight-membered rings of the R 4 4(8) type, linking mol-ecules into layers. The Hirshfeld surface analysis indicates that the largest con-tributions are from inter-molecular H⋯H (ca 71%) and H⋯C/C⋯H (ca 19%) contacts. The energies of the frontier mol-ecular orbitals were determined by DFT calculations at the B3LYP/def2-TZVP level of theory.
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Affiliation(s)
| | | | - Alisher G. Eshimbetov
- Institute of Bioorganic Chemistry, Academy of Sciences of Uzbekistan, 100125, M. Ulugbek Str 83, Tashkent, Uzbekistan
| | - Bakhtiyar T. Ibragimov
- Institute of Bioorganic Chemistry, Academy of Sciences of Uzbekistan, 100125, M. Ulugbek Str 83, Tashkent, Uzbekistan
| | - Jamshid M. Ashurov
- Institute of Bioorganic Chemistry, Academy of Sciences of Uzbekistan, 100125, M. Ulugbek Str 83, Tashkent, Uzbekistan
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17
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Jeba Reeda V, Bena Jothy V, Asif M, Nasibullah M, Alharbi NS, Abbas G, Muthu S. Synthesis, solvent polarity(polar and nonpolar), structural and electronic properties with diverse solvents and biological studies of (E)-3-((3-chloro-4-fluorophenyl) imino) indolin-2-one. J Mol Liq 2023. [DOI: 10.1016/j.molliq.2023.121709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
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18
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Kenari F, Molnár S, Borges ID, Napolitano HB, Perjési P. ( E)-2-Benzylidenecyclanones: Part XVIII Study the Possible Link between Glutathione Reactivity and Cancer Cell Cytotoxic Effects of Some Cyclic Chalcone Analogs A Comparison of the Reactivity of the Open-Chain and the Seven-Membered Homologs. Int J Mol Sci 2023; 24:ijms24108557. [PMID: 37239911 DOI: 10.3390/ijms24108557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 05/01/2023] [Accepted: 05/05/2023] [Indexed: 05/28/2023] Open
Abstract
Non-enzymatic thiol addition into the α,β-unsaturated carbonyl system is associated with several biological effects. In vivo, the reactions can form small-molecule thiol (e.g., glutathione) or protein thiol adducts. The reaction of two synthetic (4'-methyl- and 4'-methoxy substituted) cyclic chalcone analogs with reduced glutathione (GSH) and N-acetylcysteine (NAC) was studied by (high-pressure liquid chromatography-ultraviolet spectroscopy) HPLC-UV method. The selected compounds displayed in vitro cancer cell cytotoxicity (IC50) of different orders of magnitude. The structure of the formed adducts was confirmed by (high-pressure liquid chromatography-mass spectrometry) HPLC-MS. The incubations were performed under three different pH conditions (pH 3.2/3.7, 6.3/6.8, and 8.0/7.4). The chalcones intrinsically reacted with both thiols under all incubation conditions. The initial rates and compositions of the final mixtures depended on the substitution and the pH. The frontier molecular orbitals and the Fukui function were carried out to investigate the effects on open-chain and seven-membered cyclic analogs. Furthermore, machine learning protocols were used to provide more insights into physicochemical properties and to support the different thiol-reactivity. HPLC analysis indicated diastereoselectivity of the reactions. The observed reactivities do not directly relate to the different in vitro cancer cell cytotoxicity of the compounds.
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Affiliation(s)
- Fatemeh Kenari
- Institute of Pharmaceutical Chemistry, University of Pécs, H-7624 Pécs, Hungary
| | - Szilárd Molnár
- Institute of Pharmaceutical Chemistry, University of Pécs, H-7624 Pécs, Hungary
- Research Institute for Viticulture and Oenology, University of Pécs, H-7634 Pécs, Hungary
| | - Igor D Borges
- Grupo de Química Teórica e Estrutural de Anápolis, Universidade Estadual de Goiás, Anápolis 75070-290, GO, Brazil
| | - Hamilton B Napolitano
- Grupo de Química Teórica e Estrutural de Anápolis, Universidade Estadual de Goiás, Anápolis 75070-290, GO, Brazil
| | - Pál Perjési
- Institute of Pharmaceutical Chemistry, University of Pécs, H-7624 Pécs, Hungary
- Grupo de Química Teórica e Estrutural de Anápolis, Universidade Estadual de Goiás, Anápolis 75070-290, GO, Brazil
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19
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Wang P, Bu L, Zhou S, Wu Y, Deng L, Shi Z. Predictive models for the aqueous phase reactivity of inorganic radicals with organic micropollutants. CHEMOSPHERE 2023; 332:138793. [PMID: 37119929 DOI: 10.1016/j.chemosphere.2023.138793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 04/12/2023] [Accepted: 04/25/2023] [Indexed: 05/10/2023]
Abstract
Single-electron transfer (SET) is one of the most common reaction mechanisms for degrading organic micropollutants (OMPs) in advanced oxidation processes. We collected 300 SET reactions (CO3•-, SO4•-, Cl2•-, and Br2•--mediated) and calculated three key parameters for understanding the SET mechanism: aqueous phase free energies of activation (ΔG‡), free energies of reactions (ΔG), and orbital energy gaps of reactants (EOMPsHOMO-ERadiLUMO). Then, we classified the OMPs according to their structure, developed and evaluated linear energy relationships of the second-order rate constants (k) with ΔG‡, ΔG, or EOMPsHOMO-ERadiLUMO in each class. Considering that a single descriptor cannot capture all the chemical diversity, we combined ΔG‡, ΔG, and EOMPsHOMO-ERadiLUMO as inputs to develop multiple linear regression (MLR) models. Chemical classification is critical to the linear model described above. However, OMPs usually have multiple functional groups, making the classification challenging and uncertain. Therefore, we tried machine learning algorithms to predict k values without chemical classification. We found that decision trees (R2 = 0.88-0.95) and random forest (R2 = 0.90-0.94) algorithms show better performance on the prediction of the k values, whereas boosted tree algorithm cannot make an accurate prediction (R2 = 0.19-0.36). Overall, our study provides a powerful tool to predict the aqueous phase reactivity of OMP to certain radicals without the need for chemical classification.
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Affiliation(s)
- Pin Wang
- Hunan Engineering Research Center of Water Security Technology and Application, College of Civil Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Building Safety and Energy Efficiency, Ministry of Education, Hunan University, Changsha, 410082, PR China
| | - Lingjun Bu
- Hunan Engineering Research Center of Water Security Technology and Application, College of Civil Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Building Safety and Energy Efficiency, Ministry of Education, Hunan University, Changsha, 410082, PR China.
| | - Shiqing Zhou
- Hunan Engineering Research Center of Water Security Technology and Application, College of Civil Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Building Safety and Energy Efficiency, Ministry of Education, Hunan University, Changsha, 410082, PR China
| | - Yangtao Wu
- Department of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, PR China
| | - Lin Deng
- Hunan Engineering Research Center of Water Security Technology and Application, College of Civil Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Building Safety and Energy Efficiency, Ministry of Education, Hunan University, Changsha, 410082, PR China
| | - Zhou Shi
- Hunan Engineering Research Center of Water Security Technology and Application, College of Civil Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Building Safety and Energy Efficiency, Ministry of Education, Hunan University, Changsha, 410082, PR China
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20
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Lgaz H, Lee HS, Kaya S, Salghi R, Ibrahim SM, Chafiq M, Bazzi L, Ko YG. Unraveling Bonding Mechanisms and Electronic Structure of Pyridine Oximes on Fe(110) Surface: Deeper Insights from DFT, Molecular Dynamics and SCC-DFT Tight Binding Simulations. Molecules 2023; 28:molecules28083545. [PMID: 37110779 PMCID: PMC10141362 DOI: 10.3390/molecules28083545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 04/07/2023] [Accepted: 04/13/2023] [Indexed: 04/29/2023] Open
Abstract
The development of corrosion inhibitors with outstanding performance is a never-ending and complex process engaged in by researchers, engineers and practitioners. The computational assessment of organic corrosion inhibitors' performance is a crucial step towards the design of new task-specific materials. Herein, the electronic features, adsorption characteristics and bonding mechanisms of two pyridine oximes, namely 2-pyridylaldoxime (2POH) and 3-pyridylaldoxime (3POH), with the iron surface were investigated using molecular dynamics (MD), and self-consistent-charge density-functional tight-binding (SCC-DFTB) simulations. SCC-DFTB simulations revealed that the 3POH molecule can form covalent bonds with iron atoms in its neutral and protonated states, while the 2POH molecule can only bond with iron through its protonated form, resulting in interaction energies of -2.534, -2.007, -1.897, and -0.007 eV for 3POH, 3POH+, 2POH+, and 2POH, respectively. Projected density of states (PDOSs) analysis of pyridines-Fe(110) interactions indicated that pyridine molecules were chemically adsorbed on the iron surface. Quantum chemical calculations (QCCs) revealed that the energy gap and Hard and Soft Acids and Bases (HSAB) principles were efficient in predicting the bonding trend of the molecules investigated with an iron surface. 3POH had the lowest energy gap of 1.706 eV, followed by 3POH+ (2.806 eV), 2POH+ (3.121 eV), and 2POH (3.431 eV). In the presence of a simulated solution, MD simulation showed that the neutral and protonated forms of molecules exhibited a parallel adsorption mode on an iron surface. The excellent adsorption properties and corrosion inhibition performance of 3POH may be attributed to its low stability compared to 2POH molecules.
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Affiliation(s)
- Hassane Lgaz
- Innovative Durable Building and Infrastructure Research Center, Center for Creative Convergence Education, Hanyang University ERICA, 55 Hanyangdaehak-ro, Sangrok-gu, Ansan-si 15588, Gyeonggi-do, Republic of Korea
| | - Han-Seung Lee
- Department of Architectural Engineering, Hanyang University-ERICA, 55 Hanyangdaehak-ro, San-grok-gu, Ansan-si 15588, Gyeonggi-do, Republic of Korea
| | - Savaş Kaya
- Department of Pharmacy, Health Services Vocational School, Sivas Cumhuriyet University, Sivas 58140, Turkey
| | - Rachid Salghi
- Laboratory of Applied Chemistry and Environment, Applied Science National School (ENSA), University Ibn Zohr, P.O. Box 1136, Agadir 80000, Morocco
- Laboratoire de Génie Industriel, de l'Énergétique et de l'Environnement (LGI2E), SupMTI, Rabat 10000, Morocco
| | - Sobhy M Ibrahim
- Department of Biochemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Maryam Chafiq
- Materials Electrochemistry Group, School of Materials Science and Engineering, Yeungnam University, Gyeongsan 38541, Gyeongsangbuk-do, Republic of Korea
| | - Lahcen Bazzi
- Laboratoire de Génie Industriel, de l'Énergétique et de l'Environnement (LGI2E), SupMTI, Rabat 10000, Morocco
| | - Young Gun Ko
- Materials Electrochemistry Group, School of Materials Science and Engineering, Yeungnam University, Gyeongsan 38541, Gyeongsangbuk-do, Republic of Korea
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Computational insights into the adsorption mechanisms of anionic dyes on the rutile TiO2 (110) surface: Combining SCC-DFT tight binding with quantum chemical and molecular dynamics simulations. J Mol Liq 2023. [DOI: 10.1016/j.molliq.2023.121554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
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22
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El-Asri A, Rguiti MM, Jmiai A, Oukhrib R, Bourzi H, Lin Y, Issami SE. Carissa macrocarpa extract (ECM) as a new efficient and ecologically friendly corrosion inhibitor for copper in nitric acid: Experimental and theoretical approach. J Taiwan Inst Chem Eng 2023. [DOI: 10.1016/j.jtice.2022.104633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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23
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Vieira DF, Borges ID, Aguiar AS, Duarte VS, d'Oliveira GD, Vaz WF, Costa RF, Perez CN, Napolitano HB. A comparative structural analysis of arylsulfonamide chalcones with potential as a biofuel additive. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.134736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
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24
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Aguiar ASN, Borges ID, Borges LL, Dias LD, Camargo AJ, Perjesi P, Napolitano HB. New Insights on Glutathione's Supramolecular Arrangement and Its In Silico Analysis as an Angiotensin-Converting Enzyme Inhibitor. Molecules 2022; 27:7958. [PMID: 36432059 PMCID: PMC9695799 DOI: 10.3390/molecules27227958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 11/03/2022] [Accepted: 11/10/2022] [Indexed: 11/19/2022] Open
Abstract
Angiotensin-converting enzyme (ACE) inhibitors are one of the most active classes for cardiovascular diseases and hypertension treatment. In this regard, developing active and non-toxic ACE inhibitors is still a continuous challenge. Furthermore, the literature survey shows that oxidative stress plays a significant role in the development of hypertension. Herein, glutathione's molecular structure and supramolecular arrangements are evaluated as a potential ACE inhibitor. The tripeptide molecular modeling by density functional theory, the electronic structure by the frontier molecular orbitals, and the molecular electrostatic potential map to understand the biochemical processes inside the cell were analyzed. The supramolecular arrangements were studied by Hirshfeld surfaces, quantum theory of atoms in molecules, and natural bond orbital analyses. They showed distinct patterns of intermolecular interactions in each polymorph, as well as distinct stabilizations of these. Additionally, the molecular docking study presented the interactions between the active site residues of the ACE and glutathione via seven hydrogen bonds. The pharmacophore design indicated that the hydrogen bond acceptors are necessary for the interaction of this ligand with the binding site. The results provide useful information for the development of GSH analogs with higher ACE inhibitor activity.
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Affiliation(s)
- Antônio S. N. Aguiar
- Grupo de Química Teórica e Estrutural de Anápolis, Universidade Estadual de Goiás, Anapolis 75132-903, GO, Brazil
| | - Igor D. Borges
- Grupo de Química Teórica e Estrutural de Anápolis, Universidade Estadual de Goiás, Anapolis 75132-903, GO, Brazil
- Centro de Pesquisa e Eficiência Energética, CAOA Montadora de Veículos LTDA, Anapolis 75184-000, GO, Brazil
| | - Leonardo L. Borges
- Grupo de Química Teórica e Estrutural de Anápolis, Universidade Estadual de Goiás, Anapolis 75132-903, GO, Brazil
- Escola de Ciências Médicas e da Vida, Pontifícia Universidade Católica de Goiás, Goiania 74605-010, GO, Brazil
| | - Lucas D. Dias
- Grupo de Química Teórica e Estrutural de Anápolis, Universidade Estadual de Goiás, Anapolis 75132-903, GO, Brazil
- Laboratório de Novos Materiais, Universidade Evangélica de Goiás, Anapolis 75083-515, GO, Brazil
| | - Ademir J. Camargo
- Grupo de Química Teórica e Estrutural de Anápolis, Universidade Estadual de Goiás, Anapolis 75132-903, GO, Brazil
| | - Pál Perjesi
- Laboratório de Novos Materiais, Universidade Evangélica de Goiás, Anapolis 75083-515, GO, Brazil
| | - Hamilton B. Napolitano
- Grupo de Química Teórica e Estrutural de Anápolis, Universidade Estadual de Goiás, Anapolis 75132-903, GO, Brazil
- Laboratório de Novos Materiais, Universidade Evangélica de Goiás, Anapolis 75083-515, GO, Brazil
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25
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Synthesis, experimental and theoretical characterization of a new copolymer bearing pyrrole and anthracene units. J Photochem Photobiol A Chem 2022. [DOI: 10.1016/j.jphotochem.2022.114056] [Citation(s) in RCA: 1] [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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26
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Acar ET. An experimental and theoretical investigation of cationic azine dye adsorption on natural sepiolite in single and multi-component systems. Chem Eng Res Des 2022. [DOI: 10.1016/j.cherd.2022.09.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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27
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Aguiar ASN, dos Santos VD, Borges ID, Navarrete A, Aguirre G, Valverde C, Camargo AJ, Oliveira SS, Osório FAP, Fonseca TL, Napolitano HB. Bromine Substitution Effect on Structure, Reactivity, and Linear and Third-Order Nonlinear Optical Properties of 2,3-Dimethoxybenzaldehyde. J Phys Chem A 2022; 126:7852-7863. [DOI: 10.1021/acs.jpca.2c04658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Antônio Sérgio Nakao Aguiar
- Grupo de Química Teórica e Estrutural de Anápolis, Universidade Estadual de Goiás, Anápolis75143-190, GO, Brazil
| | - Viviane Dias dos Santos
- Grupo de Química Teórica e Estrutural de Anápolis, Universidade Estadual de Goiás, Anápolis75143-190, GO, Brazil
| | - Igor Dalarmelino Borges
- Grupo de Química Teórica e Estrutural de Anápolis, Universidade Estadual de Goiás, Anápolis75143-190, GO, Brazil
| | - Angélica Navarrete
- Tecnológico Nacional de México/Instituto Tecnológico de Tijuana, Centro de Graduados e Investigación en Química, 22444Tijuana, BC, Mexico
| | - Gerardo Aguirre
- Tecnológico Nacional de México/Instituto Tecnológico de Tijuana, Centro de Graduados e Investigación en Química, 22444Tijuana, BC, Mexico
| | - Clodoaldo Valverde
- Grupo de Química Teórica e Estrutural de Anápolis, Universidade Estadual de Goiás, Anápolis75143-190, GO, Brazil
- Laboratório de Modelagem Molecular Aplicada e Simulação, Universidade Paulista, Goiânia54741-501, GO, Brazil
| | - Ademir João Camargo
- Grupo de Química Teórica e Estrutural de Anápolis, Universidade Estadual de Goiás, Anápolis75143-190, GO, Brazil
| | - Solemar Silva Oliveira
- Grupo de Química Teórica e Estrutural de Anápolis, Universidade Estadual de Goiás, Anápolis75143-190, GO, Brazil
| | - Francisco Aparecido Pinto Osório
- Instituto de Física, Universidade Federal de Goiás, Goiânia54741-501, GO, Brazil
- Escola Politécnica, Pontifícia Universidade Católica de Goiás, Goiânia54741-501, GO, Brazil
| | - Tertius Lima Fonseca
- Instituto de Física, Universidade Federal de Goiás, Goiânia54741-501, GO, Brazil
| | - Hamilton Barbosa Napolitano
- Grupo de Química Teórica e Estrutural de Anápolis, Universidade Estadual de Goiás, Anápolis75143-190, GO, Brazil
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DFT study of therapeutic potential of graphitic carbon nitride as a carrier for controlled release of melphalan: an anticancer drug. J Mol Model 2022; 28:359. [PMID: 36227378 DOI: 10.1007/s00894-022-05337-y] [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: 04/23/2022] [Accepted: 09/28/2022] [Indexed: 10/17/2022]
Abstract
In the present research, the drug-delivery efficiency of graphitic carbon nitride (g-CN) for melphalan (an anti-cancer drug) was evaluated. To investigate the efficacy of g-CN as a drug-delivery system, the electronic properties of melphalan drug, g-CN, and g-CN-melphalan were calculated at the ground and excited states. The adsorption energy calculated for g-CN-melphalan complex in the water phase is - 1.51 eV. The interactions between g-CN and melphalan were investigated by a non-covalent interactions (NCl) analysis, which showed that there were weak interactions between g-CN and melphalan drug. These low intermolecular forces will allow for easy off-loading of the melphalan at the targeted site. Frontier molecular-orbitals (FMOs) analysis showed that the charge was transferred from melphalan to g-CN during the excitation process. Charge transfer was studied by charge decomposition analysis. Calculations at the excited state revealed that the g-CN-melphalan complex's λmax showed a redshift of 15 nm and 39 nm in the gas and water phase, respectively. The photoinduced electron transfer (PET) process was studied for 1-2 excited state by using electron hole theory. PET process suggests that fluorescence quenching may take place. The findings demonstrated that g-CN can be used as a drug-delivery system for melphalan drug to treat cancer. This investigation may also encourage more consideration of different 2D substances for drug delivery.
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Silva BR, Queiroz PA, Amaral PHRD, Freitas BCD, Stocco AF, Sampiron EG, Vandresen F, Tognim MCB, Caleffi-Ferracioli KR, Scodro RBDL, Cardoso RF, La Porta FDA, Siqueira VLD. Polymyxin B Activity Rescue by (−)-Camphene-Based Thiosemicarbazide Against Carbapenem-Resistant Enterobacterales. Microb Drug Resist 2022; 28:962-971. [PMID: 36256860 DOI: 10.1089/mdr.2021.0334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Due to the significant shortage of therapeutic options for carbapenem-resistant Enterobacterales (CRE) infections, new drugs or therapeutic combinations are urgently required. We show in this study that (-)-camphene-based thiosemicarbazide (TSC) may act synergistically with polymyxin B (PMB) against CRE, rescuing the activity of this antimicrobial. With the specific aim of a better molecular understanding of this effect caused by the presence of TSC, theoretical calculations were also performed in this study. Based on these findings, it is concluded that the presence of TSC moieties contributes to significant changes in the hydrogen atom charge of PMB structure, which trend more positives for the PMB/TSC system studied. This could lead to the formation of stronger hydrogen bonds in the Enterobacterales active site and, thus contribute to a molecular understanding of the PMB rescue of activity promoted by the presence of TSC moiety. As such, the clinical potential of these drug combinations requires further evaluation.
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Affiliation(s)
- Bruna Renata Silva
- Postgraduate Program in Bioscience and Physiopathology, State University of Maringa, Maringa, Parana, Brazil
| | - Paula Assis Queiroz
- Postgraduate Program in Bioscience and Physiopathology, State University of Maringa, Maringa, Parana, Brazil
| | - Pedro Henrique Rodrigues do Amaral
- Laboratory of Medical Bacteriology, Department of Clinical Analysis and Biomedicine, State University of Maringa, Maringa, Parana, Brazil
| | - Beatriz Cardoso de Freitas
- Postgraduate Program in Bioscience and Physiopathology, State University of Maringa, Maringa, Parana, Brazil
| | - Alison Fernando Stocco
- Department of Chemistry, Federal Technological University of Parana, Londrina, Parana, Brazil
| | - Eloisa Gibin Sampiron
- Postgraduate Program in Health Sciences, State University of Maringa, Maringa, Parana, Brazil
| | - Fábio Vandresen
- Department of Chemistry, Federal Technological University of Parana, Londrina, Parana, Brazil
| | | | - Katiany Rizzieri Caleffi-Ferracioli
- Postgraduate Program in Bioscience and Physiopathology, State University of Maringa, Maringa, Parana, Brazil
- Laboratory of Medical Bacteriology, Department of Clinical Analysis and Biomedicine, State University of Maringa, Maringa, Parana, Brazil
| | - Regiane Bertin de Lima Scodro
- Laboratory of Medical Bacteriology, Department of Clinical Analysis and Biomedicine, State University of Maringa, Maringa, Parana, Brazil
- Postgraduate Program in Health Sciences, State University of Maringa, Maringa, Parana, Brazil
| | - Rosilene Fressatti Cardoso
- Postgraduate Program in Bioscience and Physiopathology, State University of Maringa, Maringa, Parana, Brazil
- Laboratory of Medical Bacteriology, Department of Clinical Analysis and Biomedicine, State University of Maringa, Maringa, Parana, Brazil
| | | | - Vera Lucia Dias Siqueira
- Postgraduate Program in Bioscience and Physiopathology, State University of Maringa, Maringa, Parana, Brazil
- Laboratory of Medical Bacteriology, Department of Clinical Analysis and Biomedicine, State University of Maringa, Maringa, Parana, Brazil
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30
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Insight into the adsorption of dyes onto chitin in aqueous solution: An experimental and computational study. ARAB J CHEM 2022. [DOI: 10.1016/j.arabjc.2022.104293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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31
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Abuelizz HA, Bakheit AH, Marzouk M, Abdellatif MM, Al-Salahi R. Reactivity of 4,5-Dichlorophthalic Anhydride towards Thiosemicarbazide and Amines: Synthesis, Spectroscopic Analysis, and DFT Study. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27113550. [PMID: 35684489 PMCID: PMC9182083 DOI: 10.3390/molecules27113550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 05/27/2022] [Accepted: 05/28/2022] [Indexed: 12/05/2022]
Abstract
The cyclic anhydrides are broadly employed in several fields, such as the chemical, plastic, agrochemical, and pharmaceutical industries. This study describes the chemical reactivity of 4,5-dichlorophthalic anhydride towards several nucleophiles, including thiosemicarbazide and different amines, to produce the carboxylic acid derivatives resulting from anhydride’s opening, namely, phthalimide and dicarboxylic acid (1–12) products. Their chemical structures are confirmed by NMR, IR and MS spectra analyses. Density–functional theory (DFT) studies are performed using (DFT/B3LYP) with the 6-311G(d, p) basis sets to recognize different chemical and physical features of the target compounds.
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Affiliation(s)
- Hatem A. Abuelizz
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia;
- Correspondence: (H.A.A.); (R.A.-S.); Tel.: +96-61-1467-7194 (H.A.A. & R.A.-S.)
| | - Ahmed H. Bakheit
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia;
| | - Mohamed Marzouk
- Chemistry of Tanning Materials and Leather Technology Department, Chemical Industries Research Institute, National Research Centre, 33 El-Bohouth St. (Former El-Tahrir St.), Dokki, Cairo 12622, Egypt;
| | - Mohamed M. Abdellatif
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, 1-1 Minami Osawa, Tokyo 192-0397, Japan;
| | - Rashad Al-Salahi
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia;
- Correspondence: (H.A.A.); (R.A.-S.); Tel.: +96-61-1467-7194 (H.A.A. & R.A.-S.)
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Verlinden B, Van Hecke K, Wilden A, Hupert M, Santiago-Schübel B, Egberink RJM, Verboom W, Kowalski PM, Modolo G, Verwerft M, Binnemans K, Cardinaels T. Gamma radiolytic stability of the novel modified diglycolamide 2,2'-oxybis( N, N-didecylpropanamide) (mTDDGA) for grouped actinide extraction. RSC Adv 2022; 12:12416-12426. [PMID: 35480374 PMCID: PMC9036757 DOI: 10.1039/d1ra08761d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 04/08/2022] [Indexed: 11/29/2022] Open
Abstract
Reprocessing of spent nuclear fuel aims at improving resource efficiency and reducing its radiotoxicity and heat production in the long term. The necessary separation of certain metal ions from the spent fuel solutions can be achieved using different solvent extraction processes. For the scenario of the EURO-GANEX process, the use of the new, modified diglycolamide 2,2′-oxybis(N,N-didecylpropanamide) (mTDDGA) was recently proposed to simplify the current solvent composition and reduce extraction of fission products. Before further developing the process based on this new ligand, its stability under ionizing radiation conditions needs to be studied. For this reason, gamma irradiation experiments were conducted followed by analyses with high performance liquid chromatography coupled to a mass spectrometer (HPLC-MS). The determined degradation rate of mTDDGA was found to be lower than that of the reference molecule N,N,N′,N′-tetra-n-octyl-diglycolamide (TODGA). Many identified degradation compounds of both molecules are analogues showing the same bond breaking, although also unreported de-methylation, double/triple de-alkylation and n-dodecane addition products were observed. The radiolysis behavior of a new diglycolamide for solvent extraction of actinides and lanthanides was studied. The observed degradation rate was lower than for the reference molecule and 22 degradation compounds were identified.![]()
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Affiliation(s)
- Bart Verlinden
- Belgian Nuclear Research Centre (SCK CEN), Institute for Nuclear Materials Science Boeretang 200 2400 Mol Belgium .,Department of Chemistry, KU Leuven Celestijnenlaan 200F, P.O. Box 2404 3001 Leuven Belgium.,JARA Energy, Center for Simulation and Data Science (CSD) Jülich Germany
| | - Karen Van Hecke
- Belgian Nuclear Research Centre (SCK CEN), Institute for Nuclear Materials Science Boeretang 200 2400 Mol Belgium
| | - Andreas Wilden
- Forschungszentrum Jülich GmbH, Institut für Energie- und Klimaforschung - Nukleare Entsorgung und Reaktorsicherheit (IEK-6) 52428 Jülich Germany
| | - Michelle Hupert
- Forschungszentrum Jülich GmbH, Zentralinstitut für Engineering, Elektronik und Analytik (ZEA-3) 52428 Jülich Germany
| | - Beatrix Santiago-Schübel
- Forschungszentrum Jülich GmbH, Zentralinstitut für Engineering, Elektronik und Analytik (ZEA-3) 52428 Jülich Germany
| | - Richard J M Egberink
- Department of Molecules & Materials, Mesa+ Institute for Nanotechnology, University of Twente P.O. Box 217 7500 AE Enschede The Netherlands
| | - Willem Verboom
- Department of Molecules & Materials, Mesa+ Institute for Nanotechnology, University of Twente P.O. Box 217 7500 AE Enschede The Netherlands
| | - Piotr M Kowalski
- JARA Energy, Center for Simulation and Data Science (CSD) Jülich Germany.,Forschungszentrum Jülich GmbH, Institute of Energy and Climate Research: Theory and Computation of Energy Materials (IEK-13) 52428 Jülich Germany
| | - Giuseppe Modolo
- Forschungszentrum Jülich GmbH, Institut für Energie- und Klimaforschung - Nukleare Entsorgung und Reaktorsicherheit (IEK-6) 52428 Jülich Germany
| | - Marc Verwerft
- Belgian Nuclear Research Centre (SCK CEN), Institute for Nuclear Materials Science Boeretang 200 2400 Mol Belgium
| | - Koen Binnemans
- Department of Chemistry, KU Leuven Celestijnenlaan 200F, P.O. Box 2404 3001 Leuven Belgium
| | - Thomas Cardinaels
- Belgian Nuclear Research Centre (SCK CEN), Institute for Nuclear Materials Science Boeretang 200 2400 Mol Belgium .,Department of Chemistry, KU Leuven Celestijnenlaan 200F, P.O. Box 2404 3001 Leuven Belgium
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Morales-Bayuelo A, Sánchez-Márquez J. Exploring the maximum Fukui function sites with the frontier-controlled soft-soft reactions using 1,3-dipolar cycloaddition reactions of nitrilium betaines. J Mol Model 2022; 28:116. [PMID: 35397020 DOI: 10.1007/s00894-022-05077-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 02/26/2022] [Indexed: 11/25/2022]
Abstract
According to P.K. Chattaraj. J Phys Chem A 2001, 105, 511-513 "the maximum Fukui function site is the best for the frontier-controlled soft-soft reactions whereas for the charge-controlled hard-hard interactions the preferred site is associated with the maximum net charge and not necessarily the minimum Fukui function". Taking into account these outcomes in this research is explored this reactivity scheme using in first case the reaction between fulminic acid with ethylene (reference reaction), after is varying the dipolarophile in the reaction between fulminic acid with acetylene, and finally is varying the dipole in the reaction between formonitrile imine with ethylene. These results allow study parameter such as charge transfer, polarizability, covalent character on bonding, among other; also shown the preference by the sf- / sf+ interactions in the transition state on the sf- / sf- interactions. On the other hand, these results also were justified using net electrophilicity which is defined as the electrophilic power of a system relative to its own nucleophilic power.
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Affiliation(s)
| | - Jesús Sánchez-Márquez
- Departamento de Química-Física, Facultad de Ciencias, Universidad de Cádiz, Campus Universitario Río San Pedro, Cádiz, Spain
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Tajammal A, Siddiqa A, Irfan A, Azam M, Hafeez H, Munawar MA, Basra MAR. Antioxidant, molecular docking and computational investigation of new flavonoids. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.132189] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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Seeman JI. Kenichi Fukui, Frontier Molecular Orbital Theory, and the Woodward-Hoffmann Rules. Part I. The Person †. CHEM REC 2022; 22:e202100297. [PMID: 35315979 DOI: 10.1002/tcr.202100297] [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: 11/14/2021] [Revised: 02/09/2022] [Accepted: 02/10/2022] [Indexed: 11/07/2022]
Abstract
Kenichi Fukui shared the 1981 Nobel Prize in Chemistry with Roald Hoffmann for "their theories, developed independently, concerning the course of chemical reactions." This is Paper 4 - Part I, of a three-part trilogy within a 27-paper series on the history of the development of the Woodward-Hoffmann rules. The personality and professional style of Fukui is discussed as well as his style of teaching and his mottos and sayings. A brief chronological history of his academic and professional life is presented along with a listing of Fukui's great flexibility in behaviors and in science. Lastly, a short list of Fukui's key awards is provided.
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Affiliation(s)
- Jeffrey I Seeman
- Department of Chemistry, University of Richmond, Richmond, VA, 23173, USA
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36
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Dastan D, Ebadi A. Effect of substitution on the binding affinity of 5-bezylidenebarbituric acid derivatives to ctDNA: in silico and in vitro studies. J CHEM SCI 2022. [DOI: 10.1007/s12039-021-02007-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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37
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Aslam R, Serdaroglu G, Zehra S, Kumar Verma D, Aslam J, Guo L, Verma C, Ebenso EE, Quraishi M. Corrosion inhibition of steel using different families of organic compounds: Past and present progress. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2021.118373] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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38
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Du H, Tian G. First-principles studies of imidazolium chloroaluminate ionic liquids with different substitutions on the Pt(111) surface. Colloids Surf A Physicochem Eng Asp 2022. [DOI: 10.1016/j.colsurfa.2021.128079] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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39
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A facile synthesis and structural elucidation for furfural based chromophores: Prediction of linear and nonlinear optical properties. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.131543] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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40
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Mian SA, Khan SU, Hussain A, Rauf A, Ahmed E, Jang J. Molecular Modelling of Optical Biosensor Phosphorene-Thioguanine for Optimal Drug Delivery in Leukemia Treatment. Cancers (Basel) 2022; 14:545. [PMID: 35158813 PMCID: PMC8833433 DOI: 10.3390/cancers14030545] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 01/14/2022] [Accepted: 01/19/2022] [Indexed: 02/04/2023] Open
Abstract
Thioguanine is an anti-cancer drug used for the treatment of leukemia. However, thioguanine has weak aqueous solubility and low biocompatibility, which limits its performance in the treatment of cancer. In the present work, these inadequacies were targeted using density functional theory-based simulations. Three stable configurations were obtained for the adsorption of thioguanine molecules on the phosphorene surface, with adsorption energies in the range of -76.99 to -38.69 kJ/mol, indicating physisorption of the drug on the phosphorene surface. The calculated bandgap energies of the individual and combined geometries of phosphorene and thioguanine were 0.97 eV, 2.81 eV and 0.91 eV, respectively. Owing to the physisorption of the drug molecule on the phosphorene surface, the bandgap energy of the material had a direct impact on optical conductivity, which was significantly altered. All parameters that determine the potential ability for drug delivery were calculated, such as the dipole moment, chemical hardness, chemical softness, chemical potential, and electrophilicity index. The higher dipole moment (1.74 D) of the phosphorene-thioguanine complex reflects its higher biodegradability, with no adverse physiological effects.
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Affiliation(s)
- Shabeer Ahmad Mian
- Department of Physics, University of Peshawar, Peshawar 25120, Pakistan; (S.U.K.); (A.H.); (A.R.)
| | - Shafqat Ullah Khan
- Department of Physics, University of Peshawar, Peshawar 25120, Pakistan; (S.U.K.); (A.H.); (A.R.)
| | - Akbar Hussain
- Department of Physics, University of Peshawar, Peshawar 25120, Pakistan; (S.U.K.); (A.H.); (A.R.)
| | - Abdur Rauf
- Department of Physics, University of Peshawar, Peshawar 25120, Pakistan; (S.U.K.); (A.H.); (A.R.)
| | - Ejaz Ahmed
- Department of Physics, Abdul Wali Khan University Mardan, Mardan 23200, Pakistan;
| | - Joonkyung Jang
- Department of Nano Energy Engineering, Pusan National University, Pusan 46241, Korea
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41
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Seymour J, Gousseva E, Large A, Held G, Hein D, Wartner G, Quevedo W, Seidel R, Kolbeck C, Clarke CJ, Fogarty R, Bourne R, Bennett R, Palgrave R, Hunt PA, Lovelock KRJ. Resonant Electron Spectroscopy: Identification of Atomic Contributions to Valence States. Faraday Discuss 2022; 236:389-411. [DOI: 10.1039/d1fd00117e] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Valence electronic structure is crucial for understanding and predicting reactivity. Valence non-resonant X-ray photoelectron spectroscopy (NRXPS) provides a direct method for probing the overall valence electronic structure. However, it is...
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42
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Kimberlin A, Saint-Louis G, Guillaumont D, Camès B, Guilbaud P, Berthon L. Effect of Metal Complexation on Diglycolamides Radiolysis: A Comparison between Ex-Situ Gamma and In-Situ Alpha Irradiation. Phys Chem Chem Phys 2022; 24:9213-9228. [DOI: 10.1039/d1cp05731f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Radiolytic degradation is an important aspect to consider when developping a ligand or a complexant for radionucleides. Diglycolamide extractants (DGAs) have been playing an important role in many partition processes...
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43
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Synthesis, crystal structure, computational study and anti-virus effect of mixed ligand copper (II) complex with ONS donor Schiff base and 1, 10-phenanthroline. J Mol Struct 2021; 1246:131246. [PMID: 34658419 PMCID: PMC8510892 DOI: 10.1016/j.molstruc.2021.131246] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Revised: 07/31/2021] [Accepted: 08/03/2021] [Indexed: 12/16/2022]
Abstract
This work deals with the synthesis, crystal structure, computational study and antiviral potential of mixed ligand copper(II) complex [Cu(L)(phen)](1), (where, H2L = (Z)-N'-((E)-2-hydroxy-3,5-diiodobenzylidene)-N,N-dimethylcarbamohydrazonothioic acid, phen = 1,10-phenanthroline). The Schiff base ligand (H2L) is coordinated with Cu(II) ion in O, N, S-tridentate mode. The copper complex (1) crystallized in the monoclinic system of the space group P21/c with eight molecules in the unit cell and reveals a square pyramidal geometry. Furthermore, we also perform quantum chemical calculations to get insights into the structure-property relationship and functional properties of ligand (H2L) and its copper (II) complex [Cu(L)(phen)](1). Complex [Cu(L)(phen)](1) was also virtually designed in-silico evaluation by Swiss-ADME. Additionally, inspiring by recent developments to find a potential inhibitor for the COVID-19 virus, we have also performed molecular docking study of ligand and its copper complex (1) to see if our compounds shows an affinity for the main protease (Mpro) of COVID-19 spike protein (PDB ID: 7C8U). Interestingly, the results are found quite encouraging where the binding affinity and inhibition constant were found to be -7.14 kcal/mol and 5.82 μM for ligand (H2L) and -6.18 kcal/mol and 0.76 μM for complex [Cu(L)(phen)](1) with Mpro protein. This binding affinity is reasonably well as compared to recently known antiviral drugs. For instance, the binding affinity of ligand and complex was found to be better than docking results of chloroquine (-6.293 kcal/mol), hydroxychloroquine (-5.573 kcal/mol) and remdesivir (-6.352 kcal/mol) with Mpro protein. The present study may offer the technological solutions and potential inhibition to the COVID-19 virus in the ongoing and future challenges of the global community. In the framework of synthesis and characterization of mixed ligand copper (II) complex; the major conclusions can be drawn as follow.
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Boudhar K, Debieche M, Serhane A, Zeghdaoui A. Crystal structure, Raman spectroscopy study and quantum chemical DFT calculations of N-phenyl -3-para nitro phenyl isoxazolidine-5-carbonitrile. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.131029] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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45
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Pomogaev V, Lee S, Shaik S, Filatov M, Choi CH. Exploring Dyson's Orbitals and Their Electron Binding Energies for Conceptualizing Excited States from Response Methodology. J Phys Chem Lett 2021; 12:9963-9972. [PMID: 34617764 DOI: 10.1021/acs.jpclett.1c02494] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The molecular orbital (MO) concept is a useful tool, which relates the molecular ground-state energy with the energies (and occupations) of the individual orbitals. However, analysis of the excited states from linear response computations is performed in terms of the initial state MOs or some other forms of orbitals, e.g., natural or natural transition orbitals. Because these orbitals lack the respective energies, they do not allow developing a consistent orbital picture of the excited states. Herein, we argue that Dyson's orbitals enable description of the response states compatible with the concepts of molecular orbital theory. The Dyson orbitals and their energies obtained by mixed-reference spin-flip time-dependent density functional theory (MRSF-TDDFT) for the response ground state are remarkably similar to the canonical MOs obtained by the usual DFT calculation. For excited states, the Dyson orbitals provide a chemically sensible picture of the electronic transitions, thus bridging the chasm between orbital theory and response computations.
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Affiliation(s)
- Vladimir Pomogaev
- Department of Chemistry, Kyungpook National University, Daegu 702-701, South Korea
| | - Seunghoon Lee
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Sason Shaik
- The Lise Meitner-Minerva Center for Computational Quantum Chemistry, Institute of Chemistry, The Hebrew University of Jerusalem, Givat Ram Campus, Jerusalem 91904, Israel
| | - Michael Filatov
- Department of Chemistry, Kyungpook National University, Daegu 702-701, South Korea
| | - Cheol Ho Choi
- Department of Chemistry, Kyungpook National University, Daegu 702-701, South Korea
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46
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Seymour JM, Gousseva E, Large AI, Clarke CJ, Licence P, Fogarty RM, Duncan DA, Ferrer P, Venturini F, Bennett RA, Palgrave RG, Lovelock KRJ. Experimental measurement and prediction of ionic liquid ionisation energies. Phys Chem Chem Phys 2021; 23:20957-20973. [PMID: 34545382 DOI: 10.1039/d1cp02441h] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Ionic liquid (IL) valence electronic structure provides key descriptors for understanding and predicting IL properties. The ionisation energies of 60 ILs are measured and the most readily ionised valence state of each IL (the highest occupied molecular orbital, HOMO) is identified using a combination of X-ray photoelectron spectroscopy (XPS) and synchrotron resonant XPS. A structurally diverse range of cations and anions were studied. The cation gave rise to the HOMO for nine of the 60 ILs presented here, meaning it is energetically more favourable to remove an electron from the cation than the anion. The influence of the cation on the anion electronic structure (and vice versa) were established; the electrostatic effects are well understood and demonstrated to be consistently predictable. We used this knowledge to make predictions of both ionisation energy and HOMO identity for a further 516 ILs, providing a very valuable dataset for benchmarking electronic structure calculations and enabling the development of models linking experimental valence electronic structure descriptors to other IL properties, e.g. electrochemical stability. Furthermore, we provide design rules for the prediction of the electronic structure of ILs.
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Affiliation(s)
- Jake M Seymour
- Department of Chemistry, University of Reading, Reading, RG6 6AD, UK.
| | | | - Alexander I Large
- Department of Chemistry, University of Reading, Reading, RG6 6AD, UK. .,Diamond Light Source, Didcot, Oxfordshire, OX11 0DE, UK
| | - Coby J Clarke
- School of Chemistry, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Peter Licence
- School of Chemistry, University of Nottingham, Nottingham, NG7 2RD, UK
| | | | | | - Pilar Ferrer
- Diamond Light Source, Didcot, Oxfordshire, OX11 0DE, UK
| | | | - Roger A Bennett
- Department of Chemistry, University of Reading, Reading, RG6 6AD, UK.
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47
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Kulkarni SA, Krishnan SBB, Chandrasekhar B, Banerjee K, Sohn H, Madhavan T. Characterization of Phytochemicals in Ulva intestinalis L. and Their Action Against SARS-CoV-2 Spike Glycoprotein Receptor-Binding Domain. Front Chem 2021; 9:735768. [PMID: 34650958 PMCID: PMC8506597 DOI: 10.3389/fchem.2021.735768] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Accepted: 09/10/2021] [Indexed: 12/24/2022] Open
Abstract
Coronavirus disease-2019 (COVID-19) has caused a severe impact on almost all aspects of human life and economic development. Numerous studies are being conducted to find novel therapeutic strategies to overcome COVID-19 pandemic in a much effective way. Ulva intestinalis L. (Ui), a marine microalga, known for its antiviral property, was considered for this study to determine the antiviral efficacy against severe acute respiratory syndrome-associated Coronavirus-2 (SARS-CoV-2). The algal sample was dried and subjected to ethanolic extraction, followed by purification and analysis using gas chromatography-coupled mass spectrometry (GC-MS). Forty-three known compounds were identified and docked against the S1 receptor binding domain (RBD) of the spike (S) glycoprotein. The compounds that exhibited high binding affinity to the RBD of S1 protein were further analyzed for their chemical behaviour using conceptual density-functional theory (C-DFT). Finally, pharmacokinetic properties and drug-likeliness studies were carried out to test if the compounds qualified as potential leads. The results indicated that mainly phenols, polyenes, phytosteroids, and aliphatic compounds from the extract, such as 2,4-di-tert-butylphenol (2,4-DtBP), doconexent, 4,8,13-duvatriene-1,3-diol (DTD), retinoyl-β-glucuronide 6',3'-lactone (RBGUL), and retinal, showed better binding affinity to the target. Pharmacokinetic validation narrowed the list to 2,4-DtBP, retinal and RBGUL as the possible antiviral candidates that could inhibit the viral spike protein effectively.
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Affiliation(s)
- Seema A Kulkarni
- Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Chengalpattu, India
| | - Sabari B B Krishnan
- Computational Biology Laboratory, Department of Genetic Engineering, School of Bioengineering, SRM Institute of Science and Technology, Chengalpattu, India
| | - Bavya Chandrasekhar
- Computational Biology Laboratory, Department of Genetic Engineering, School of Bioengineering, SRM Institute of Science and Technology, Chengalpattu, India
| | - Kaushani Banerjee
- Computational Biology Laboratory, Department of Genetic Engineering, School of Bioengineering, SRM Institute of Science and Technology, Chengalpattu, India
| | - Honglae Sohn
- Department of Chemistry and Department of Carbon Materials, Chosun University, Gwangju, South Korea
| | - Thirumurthy Madhavan
- Computational Biology Laboratory, Department of Genetic Engineering, School of Bioengineering, SRM Institute of Science and Technology, Chengalpattu, India
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48
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Moulandou-Koumba RD, Doggui MY, N'Sikabaka S, Ouamba JM, Arfaoui Y, Frapper G, Guégan F. Proposal of a Fermi-Dirac-Derived Reactivity Descriptor: Beyond the Frontier MO Model. J Phys Chem A 2021; 125:8090-8097. [PMID: 34473520 DOI: 10.1021/acs.jpca.1c04415] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
In this paper, we derive a reactivity descriptor stemming from the Fermi-Dirac population scheme, applied to density functional calculations on molecular systems. Assuming that molecular orbitals only marginally change when temperature is slightly increased from 0 K, we study the response of electron density to a change in temperature. Connection with usual conceptual density functional theory descriptors is made, and the T-variation of electron density for some representative examples is given and discussed.
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Affiliation(s)
- R D Moulandou-Koumba
- IC2MP UMR 7285, Université de Poitiers-CNRS, 4, rue Michel Brunet, TSA 51106, 86073 Cedex 9 Poitiers, France.,Université Marien NGOUABI, Faculté des Sciences et Techniques, Unité de Chimie du Végétal et de la Vie, BP 69 Brazzaville, Congo
| | - M Y Doggui
- IC2MP UMR 7285, Université de Poitiers-CNRS, 4, rue Michel Brunet, TSA 51106, 86073 Cedex 9 Poitiers, France.,Laboratory of Characterizations, Applications & Modeling of Materials (LR18ES08), Department of Chemistry, Faculty of Sciences, University of Tunis El Manar, 2092 Tunis, Tunisia
| | - S N'Sikabaka
- Université Marien NGOUABI, Faculté des Sciences et Techniques, Unité de Chimie du Végétal et de la Vie, BP 69 Brazzaville, Congo
| | - J-M Ouamba
- Université Marien NGOUABI, Faculté des Sciences et Techniques, Unité de Chimie du Végétal et de la Vie, BP 69 Brazzaville, Congo
| | - Y Arfaoui
- Laboratory of Characterizations, Applications & Modeling of Materials (LR18ES08), Department of Chemistry, Faculty of Sciences, University of Tunis El Manar, 2092 Tunis, Tunisia
| | - G Frapper
- IC2MP UMR 7285, Université de Poitiers-CNRS, 4, rue Michel Brunet, TSA 51106, 86073 Cedex 9 Poitiers, France
| | - F Guégan
- IC2MP UMR 7285, Université de Poitiers-CNRS, 4, rue Michel Brunet, TSA 51106, 86073 Cedex 9 Poitiers, France
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Munir I, Perveen M, Nazir S, Khera RA, Ayub AR, Ayub K, Iqbal J. Therapeutic potential of graphyne as a new drug-delivery system for daunorubicin to treat cancer: A DFT study. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.116327] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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50
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Ebenso EE, Verma C, Olasunkanmi LO, Akpan ED, Verma DK, Lgaz H, Guo L, Kaya S, Quraishi MA. Molecular modelling of compounds used for corrosion inhibition studies: a review. Phys Chem Chem Phys 2021; 23:19987-20027. [PMID: 34254097 DOI: 10.1039/d1cp00244a] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Molecular modelling of organic compounds using computational software has emerged as a powerful approach for theoretical determination of the corrosion inhibition potential of organic compounds. Some of the common techniques involved in the theoretical studies of corrosion inhibition potential and mechanisms include density functional theory (DFT), molecular dynamics (MD) and Monte Carlo (MC) simulations, and artificial neural network (ANN) and quantitative structure-activity relationship (QSAR) modeling. Using computational modelling, the chemical reactivity and corrosion inhibition activities of organic compounds can be explained. The modelling can be regarded as a time-saving and eco-friendly approach for screening organic compounds for corrosion inhibition potential before their wet laboratory synthesis would be carried out. Another advantage of computational modelling is that molecular sites responsible for interactions with metallic surfaces (active sites or adsorption sites) and the orientation of organic compounds can be easily predicted. Using different theoretical descriptors/parameters, the inhibition effectiveness and nature of the metal-inhibitor interactions can also be predicted. The present review article is a collection of major advancements in the field of computational modelling for the design and testing of the corrosion inhibition effectiveness of organic corrosion inhibitors.
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Affiliation(s)
- Eno E Ebenso
- Institute for Nanotechnology and Water Sustainability, College of Science, Engineering and Technology, University of South Africa, Johannesburg, South Africa.
| | - Chandrabhan Verma
- Interdisciplinary Research Center for Advanced Materials, King Fahd University of Petroleum and Minerals, Dhahran, 31261, Saudi Arabia
| | - Lukman O Olasunkanmi
- Department of Chemistry, Faculty of Science, Obafemi Awolowo University, Ile-Ife 220005, Nigeria
| | - Ekemini D Akpan
- Material Science Innovation and Modelling Research Focus Area, Faculty of Natural and Agricultural Sciences, North-West University (Mafikeng Campus) Private Bag X2046, Mmabatho 2735, South Africa
| | - Dakeshwar Kumar Verma
- Department of Chemistry, Govt. Digvijay Autonomous Postgraduate College, Rajnandgaon, Chhattisgarh 491441, India
| | - Hassane Lgaz
- Department of Crop Science, College of Sanghur Life Science, Konkuk University, Seoul 05029, South Korea
| | - Lei Guo
- School of Materials and Chemical Engineering, Tongren University, Tongren, 554300, China
| | - Savas Kaya
- Faculty of Science, Department of Chemistry, Cumhuriyet University, 58140, Sivas, Turkey
| | - M A Quraishi
- Interdisciplinary Research Center for Advanced Materials, King Fahd University of Petroleum and Minerals, Dhahran, 31261, Saudi Arabia
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