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Wang Y, Li C, Li Z, Moalin M, den Hartog GJM, Zhang M. Computational Chemistry Strategies to Investigate the Antioxidant Activity of Flavonoids-An Overview. Molecules 2024; 29:2627. [PMID: 38893503 PMCID: PMC11173571 DOI: 10.3390/molecules29112627] [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: 05/27/2024] [Accepted: 05/29/2024] [Indexed: 06/21/2024] Open
Abstract
Despite several decades of research, the beneficial effect of flavonoids on health is still enigmatic. Here, we focus on the antioxidant effect of flavonoids, which is elementary to their biological activity. A relatively new strategy for obtaining a more accurate understanding of this effect is to leverage computational chemistry. This review systematically presents various computational chemistry indicators employed over the past five years to investigate the antioxidant activity of flavonoids. We categorize these strategies into five aspects: electronic structure analysis, thermodynamic analysis, kinetic analysis, interaction analysis, and bioavailability analysis. The principles, characteristics, and limitations of these methods are discussed, along with current trends.
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Affiliation(s)
- Yue Wang
- Department of Pharmacology and Personalized Medicine, School of Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University, 6200 MD Maastricht, The Netherlands; (Y.W.); (C.L.); (G.J.M.d.H.)
| | - Chujie Li
- Department of Pharmacology and Personalized Medicine, School of Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University, 6200 MD Maastricht, The Netherlands; (Y.W.); (C.L.); (G.J.M.d.H.)
| | - Zhengwen Li
- School of Pharmacy, Chengdu University, 2025 Chengluo Avenue, Chengdu 610106, China;
| | - Mohamed Moalin
- Research Centre Material Sciences, Zuyd University of Applied Science, 6400 AN Heerlen, The Netherlands;
| | - Gertjan J. M. den Hartog
- Department of Pharmacology and Personalized Medicine, School of Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University, 6200 MD Maastricht, The Netherlands; (Y.W.); (C.L.); (G.J.M.d.H.)
| | - Ming Zhang
- Hainan University-HSF/LWL Collaborative Innovation Laboratory, College of Food Sciences & Engineering, Hainan University, 58 People Road, Haikou 570228, China
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2
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Liu P, Han J, Chen Y, Yu H, Zhou X, Zhang W. Binding Strengths and Orientations in CO 2 Adsorption on Cationic Scandium Oxides: Governing Factor Revealed by a Combined Infrared Spectroscopy and Theoretical Study. J Phys Chem A 2024; 128:3007-3014. [PMID: 38581407 DOI: 10.1021/acs.jpca.4c01562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/08/2024]
Abstract
Carbon dioxide (CO2) adsorption is a critical step to curbing carbon emissions from fossil fuel combustion. Among various options, transition metal oxides have received extensive attention as promising CO2 adsorbents due to their affordability and sustainability for large-scale use. Here, the nature of binding interactions between CO2 molecules and cationic scandium oxides of different sizes, i.e., ScO+, Sc2O2+, and Sc3O4+, is investigated by mass-selective infrared photodissociation spectroscopy combined with quantum chemical calculations. The well-accepted electrostatic considerations failed to provide explanations for the trend in the binding strengths and variations in the binding orientations between CO2 and metal sites of cationic scandium oxides. The importance of orbital interactions in the driving forces for CO2 adsorption on cationic scandium oxides was revealed by energy decomposition analyses. A molecular surface property, known as the local electron attachment energy, is introduced to elucidate the binding affinity and orientation-specific reactivity of cationic scandium oxides upon the CO2 attachment. This study not only reveals the governing factor in the binding behaviors of CO2 adsorption on cationic scandium oxides but also serves as an archetype for predicting and rationalizing favorable binding sites and orientations in extended surface-adsorbate systems.
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Affiliation(s)
- Pengcheng Liu
- Anhui Institute of Optics and Fine Mechanics, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
- Science Island Branch, Graduate School, University of Science and Technology of China, Hefei 230026, China
| | - Jia Han
- Hefei National Research Center for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei 230026, China
| | - Yan Chen
- Department of Chemical Physics, University of Science and Technology of China, Hefei 230026, China
| | - Haili Yu
- Department of Chemical Physics, University of Science and Technology of China, Hefei 230026, China
| | - Xiaoguo Zhou
- Hefei National Research Center for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei 230026, China
- Department of Chemical Physics, University of Science and Technology of China, Hefei 230026, China
| | - Weijun Zhang
- Anhui Institute of Optics and Fine Mechanics, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
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3
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Liu CW, Peng CH, Liu MH. Theoretical investigation on action mechanism and mollifying efficacy of propellant stabilizers. J Mol Model 2024; 30:130. [PMID: 38607447 DOI: 10.1007/s00894-024-05919-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: 02/14/2024] [Accepted: 03/27/2024] [Indexed: 04/13/2024]
Abstract
CONTEXT This project performed quantum chemical computation, through kinetic and thermodynamic analyses to compare relative reactivity, reaction rate, and equilibrium composition from the possible pathways in connection with stabilizer-nitrodioxide reactions to determine the stability of the materials for practical application. Corresponding achievements have promoted the use of N-methyl-p-nitroaniline (MNA) and dinitrophenyl malonamide series (M3, M4, and M5) stabilizers as high priorities for selection. METHODS The Gaussian 09 program (G09) (Frisch et al 2009) and density functional theory (DFT) calculations with the B3LYP/6-31G(d,p) function were performed to obtain related geometric and thermodynamic energy data for the molecular systems in this study. The synchronous transit-guided quasi-Newton method (STQN) (Peng and Schlegel Isr J Chem 33:49, 1993) was applied through the QST3 procedure to identify single imaginary frequency-valued transition-state species. The related reaction rate constant (k) and pre-exponential factor (A) were obtained, based on transition state theory (Su 2008), using Eqs. 11 and 12.
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Affiliation(s)
- Chuan-Wen Liu
- Department of Chemistry, Military Academy, Taiwan, Republic of China
| | - Cheng-Hsiung Peng
- Department of Applied Materials Science and Technology, Minghsin University of Science and Technology, Taiwan, Republic of China
| | - Min-Hsien Liu
- Department of Chemical and Materials Engineering, Chung Cheng Institute of Technology, National Defense University, Taiwan, Republic of China.
- Department of Materials Science and Engineering, National Chiao Tung University, Taiwan, Republic of China.
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Miranda TG, Ciribelli NN, Bihain MFR, Santos Pereira AKD, Cavallini GS, Pereira DH. Interactions between DNA and the acridine intercalator: A computational study. Comput Biol Chem 2024; 109:108029. [PMID: 38387123 DOI: 10.1016/j.compbiolchem.2024.108029] [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: 12/15/2023] [Revised: 02/08/2024] [Accepted: 02/08/2024] [Indexed: 02/24/2024]
Abstract
Cancer is a global public health problem characterized by deviations in the mechanisms that control cell proliferation, resulting in mutations and variations in the structure of DNA. The mechanisms of action of chemotherapeutic drugs are related to their interactions and binding with DNA; consequently, the development of antineoplastic agents that target DNA has extensively focused on use of acridine, a heterocyclic molecule that binds to deoxyribonucleic acid via intercalation, a process that modifies DNA and makes replication impossible. In this context, this study aimed to computationally investigate how acridine intercalators interact with DNA by evaluating the mechanism of interactions, binding, and interaction energies using quantum mechanics calculations. Molecular electrostatic potential (MEP) analysis revealed that acridine has well- distributed negative charges in the center of the molecule, indicative of a dominant electron-rich region. Acridine exhibits well-defined π orbitals (HOMO and LUMO) on the aromatic rings, suggesting that charge transfer occurs within the molecule and may be responsible for the pharmacological activity of the compound. Structural analysis revealed that acridine interacts with DNA mainly through hydrogen bonds between HAcridine… ODNA with bond lengths ranging from 2.370 Å to 3.472 Å. The Binding energy (ΔEBind) showed that acridine interacts with DNA effectively for all complexes and the electronic energy results (E+ZPE) for complexes revealed that the complexes are more stable when the DNA-centered acridine molecule. The Laplacian-analysis topological QTAIM parameter (∇2ρ(r)) and total energy (H(r)) categorized the interactions as being non-covalent in nature. The RGD peak distribution in the NCI analysis reveals the presence of van der Waals interactions, predominantly between the intercalator and DNA. Accordingly, we confirm that acridine/DNA interactions are relevant for understanding how the intercalator acts within nucleic acids.
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Affiliation(s)
- Thaynara Guimarães Miranda
- Programa de Pós Graduação em Biotecnologia, Universidade Federal do Tocantins (UFT), Gurupi, Tocantins CEP 77.402-970, Brazil
| | - Nicolas Nascimento Ciribelli
- Programa de Pós Graduação em Biotecnologia, Universidade Federal do Tocantins (UFT), Gurupi, Tocantins CEP 77.402-970, Brazil
| | | | - Anna Karla Dos Santos Pereira
- Programa de Pós Graduação em Química, Universidade Federal do Tocantins (UFT), Gurupi, Tocantins CEP 77.402-970, Brazil
| | - Grasiele Soares Cavallini
- Programa de Pós Graduação em Química, Universidade Federal do Tocantins (UFT), Gurupi, Tocantins CEP 77.402-970, Brazil
| | - Douglas Henrique Pereira
- Programa de Pós Graduação em Biotecnologia, Universidade Federal do Tocantins (UFT), Gurupi, Tocantins CEP 77.402-970, Brazil; Departamento de Química, Instituto Tecnológico de Aeronáutica (ITA), Praça Marechal Eduardo Gomes, 50, Vila das Acácias, São José dos Campos SP CEP 12228-900, Brazil.
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Hesamzadeh P, Seif A, Mahmoudzadeh K, Ganjali Koli M, Mostafazadeh A, Nayeri K, Mirjafary Z, Saeidian H. De novo antioxidant peptide design via machine learning and DFT studies. Sci Rep 2024; 14:6473. [PMID: 38499731 PMCID: PMC10948870 DOI: 10.1038/s41598-024-57247-z] [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: 12/29/2023] [Accepted: 03/15/2024] [Indexed: 03/20/2024] Open
Abstract
Antioxidant peptides (AOPs) are highly valued in food and pharmaceutical industries due to their significant role in human function. This study introduces a novel approach to identifying robust AOPs using a deep generative model based on sequence representation. Through filtration with a deep-learning classification model and subsequent clustering via the Butina cluster algorithm, twelve peptides (GP1-GP12) with potential antioxidant capacity were predicted. Density functional theory (DFT) calculations guided the selection of six peptides for synthesis and biological experiments. Molecular orbital representations revealed that the HOMO for these peptides is primarily localized on the indole segment, underscoring its pivotal role in antioxidant activity. All six synthesized peptides exhibited antioxidant activity in the DPPH assay, while the hydroxyl radical test showed suboptimal results. A hemolysis assay confirmed the non-hemolytic nature of the generated peptides. Additionally, an in silico investigation explored the potential inhibitory interaction between the peptides and the Keap1 protein. Analysis revealed that ligands GP3, GP4, and GP12 induced significant structural changes in proteins, affecting their stability and flexibility. These findings highlight the capability of machine learning approaches in generating novel antioxidant peptides.
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Affiliation(s)
- Parsa Hesamzadeh
- Department of Chemistry, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Abdolvahab Seif
- Dipartimento di Fisica, Universita' di Padova, Via Marzolo 8, 35131, Padua, Italy
- Department of Chemistry, University of Turin, Via Pietro Giuria 7, 10125, Turin, Italy
| | - Kazem Mahmoudzadeh
- Department of Organic Chemistry and Oil, Faculty of Chemistry, Shahid Beheshti University, Tehran, Iran
| | | | - Amrollah Mostafazadeh
- Cellular and Molecular Biology Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran
| | - Kosar Nayeri
- Student Research Committee, Babol University of Medical Sciences, Babol, Iran
| | - Zohreh Mirjafary
- Department of Chemistry, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Hamid Saeidian
- Department of Science, Payame Noor University (PNU), PO Box: 19395-4697, Tehran, Iran.
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Priyadharsan RR, Timothy RA, Thomas JM, Jeyakumar TC, Rajaram R, Louis H. Investigating the structure, bonding, and energy decomposition analysis of group 10 transition metal carbonyls with substituted terminal germanium chalcogenides [M(CO) 3GeX] (M = Ni, Pd, and Pt; X = O, S, Se, and Te) complexes: insight from first-principles calculations. J Mol Model 2023; 29:344. [PMID: 37847395 DOI: 10.1007/s00894-023-05745-8] [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: 08/28/2023] [Accepted: 10/02/2023] [Indexed: 10/18/2023]
Abstract
CONTEXT This research focused on the theoretical investigation of transition metal carbonyls [M(CO)4] coordinated with terminal germanium chalcogenides complexes [M(CO)3GeX], where M represents Ni, Pd, and Pt and X represents O, S, Se, and Te labeled 1-15. While the notable complexes M(CO)4 (where M = Ni, Pd, Pt) numbered 1, 6, and 11 are of significance, substituting one of the CO ligands in 1, 6, and 11 with a GeX ligand (where X = O, S, Se, or Te) result in substituted complexes (2-5, 7-10, and 11-15). Substituting of the CO ligand slightly alters these bond angles. Specifically, the ∠CMC bond angles for [Ni] complexes range from 111.9° to 112.2°, for [Pd] complexes from 111.4° to 111.7°, and for [Pt] complexes from 112.4° to 112.8°. These findings indicate a minor deviation from the tetrahedral geometry due to the influence of the new GeX ligand. Similarly, there is a slight change in the geometry of the metal complexes, where the ∠GeMC angles for [Ni] complexes are between 106.7° and 106.9°, for [Pd] complexes between 107.2° and 107.5°, and for [Pt] complexes between 105.9° and 106.4°. Comparing among the substituted GeX complexes, those containing GeTe exhibit a higher natural bond orbital (NBO) contribution from the Ge atom compared to the M atom. Consequently, based on the above observations, it can be inferred that GeX acts as an effective sigma donor in contrast to carbonyl compounds. Results of energy decomposition analysis (EDA) for the M-CO bond in 1, 6, and 11 and for the M-GeX bond in the other [M(CO)3(GeX)] complexes where M = Ni, Pd and Pt. The percentage contribution of ΔEelstat and ΔEorb shows a relatively identical behavior for all ligands in case of each metal complexes. METHODS Density functional theory (DFT) calculations were conducted using the B3LYP/gen/6-31G*/LanL2DZ level of theory to examine transition metal carbonyls [M(CO)4] coordinated with terminal germanium chalcogenides complexes [M(CO)3GeX], where M represents Ni, Pd, and Pt, and X represents O, S, Se, and Te labeled 1-15 utilized through the use of Gaussian 09W and GaussView 6.0.16 software packages. Post-processing computational code such as multi-wave function was employed for results analysis and visualization.
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Affiliation(s)
- R Rameshbabu Priyadharsan
- PG & Research Department of Chemistry, The American College (Autonomous), Madurai, Tamil Nadu, India
| | - Rawlings A Timothy
- Computational and Bio-Simulation Research Group, University of Calabar, Calabar, Nigeria
| | - Jisha Mary Thomas
- Department of Chemistry, Pondicherry University, Puducherry, 605014, India
| | | | - Rajendran Rajaram
- Department of Chemistry, Madanapalle Institute of Technology and Science, Angallu (V), Madanapalle, Andhra Pradesh, 517325, India
| | - Hitler Louis
- Computational and Bio-Simulation Research Group, University of Calabar, Calabar, Nigeria.
- Centre for Herbal Pharmacology and Environmental Sustainability, Chettinad Hospital and Research Institute, Chettinad Academy of Research and Education, Kelambakkam, 603103, Tamil Nadu, India.
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7
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Doust Mohammadi M, Louis H, Chukwu UG, Bhowmick S, Rasaki ME, Biskos G. Gas-Phase Interaction of CO, CO 2, H 2S, NH 3, NO, NO 2, and SO 2 with Zn 12O 12 and Zn 24 Atomic Clusters. ACS OMEGA 2023; 8:20621-20633. [PMID: 37323380 PMCID: PMC10268014 DOI: 10.1021/acsomega.3c01177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 05/22/2023] [Indexed: 06/17/2023]
Abstract
Atmospheric pollutants pose a high risk to human health, and therefore it is necessary to capture and preferably remove them from ambient air. In this work, we investigate the intermolecular interaction between the pollutants such as CO, CO2, H2S, NH3, NO, NO2, and SO2 gases with the Zn24 and Zn12O12 atomic clusters, using the density functional theory (DFT) at the meta-hybrid functional TPSSh and LANl2Dz basis set. The adsorption energy of these gas molecules on the outer surfaces of both types of clusters has been calculated and found to have a negative value, indicating a strong molecular-cluster interaction. The largest adsorption energy has been observed between SO2 and the Zn24 cluster. In general, the Zn24 cluster appears to be more effective for adsorbing SO2, NO2, and NO than Zn12O12, whereas the latter is preferable for the adsorption of CO, CO2, H2S, and NH3. Frontier molecular orbital (FMO) analysis showed that Zn24 exhibits higher stability upon adsorption of NH3, NO, NO2, and SO2, with the adsorption energy falling within the chemisorption range. The Zn12O12 cluster shows a characteristic decrease in band gap upon adsorption of CO, H2S, NO, and NO2, suggesting an increase in electrical conductivity. Natural bond orbital (NBO) analysis also suggests the presence of strong intermolecular interactions between atomic clusters and the gases. This interaction was recognized to be strong and noncovalent, as determined by noncovalent interaction (NCI) and quantum theory of atoms in molecules (QTAIM) analyses. Overall, our results suggest that both Zn24 and Zn12O12 clusters are good candidate species for promoting adsorption and, thus, can be employed in different materials and/or systems for enhancing interaction with CO, H2S, NO, or NO2.
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Affiliation(s)
| | - Hitler Louis
- Computational
and Bio-Simulation Research Group, University
of Calabar, Calabar 540221, Nigeria
| | - Udochukwu G. Chukwu
- Computational
and Bio-Simulation Research Group, University
of Calabar, Calabar 540221, Nigeria
| | - Somnath Bhowmick
- Climate
and Atmosphere Research Centre, The Cyprus
Institute, Nicosia 2121, Cyprus
| | - Michael E. Rasaki
- Computational
and Bio-Simulation Research Group, University
of Calabar, Calabar 540221, Nigeria
| | - George Biskos
- Climate
and Atmosphere Research Centre, The Cyprus
Institute, Nicosia 2121, Cyprus
- Faculty
of Civil Engineering and Geosciences, Delft
University of Technology, Delft 2628CN, The Netherlands
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8
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Hussein AM, Abbas ZS, Kadhim MM, Rheima AM, Barzan M, Al-Attia LH, Elameer AS, Hachim SK, Hadi MA. Inhibitory behavior and adsorption of asparagine dipeptide amino acid on the Fe(111) surface. J Mol Model 2023; 29:162. [PMID: 37118157 DOI: 10.1007/s00894-023-05555-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: 02/10/2023] [Accepted: 04/12/2023] [Indexed: 04/30/2023]
Abstract
CONTEXT The inhibitory effect of asparagine (Asn) and its derivatives on iron (Fe) corrosion was studied by performing density functional theory (DFT) calculations. In this paper, the global and local reactivity descriptors of Asn in the protonated and neutral forms were evaluated. Also, the changes in reactivity were investigated when dipeptides were combined with Asn. Due to the increase in the reaction centers within their molecular structure, there was an enhancement in the inhibitory effect of these dipeptides. Moreover, the adsorption energies (Eads) and the adsorption configurations of Asn and small peptides (SPs) with most stability were determined on the surface of Fe(111). It was found that dipeptides had a chemical adsorption on these substrates. In the protonated forms, there was an enhancement in the absolute values of Eads between the inhibitors and the Fe(111) surfaces. Peptides were more likely to be adsorbed on the Fe surfaces, showing the great inhibitory effect of these moieties. The results of the current research demonstrate the possibility of utilizing SPs as efficient "green" corrosion inhibitors. METHODS DFT computations were undertaken by employing the BIOVIA Material Studio with B3LYP-D3 functional and 6-31 + G* basis set. The theoretical evaluation of the inhibitory effect of asparagine (Asn) dipeptides, and the potential analysis of small peptides to protect against the corrosion of Fe, was done.
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Affiliation(s)
- Alaa Mohammed Hussein
- Biomedical Engineering Department, Al-Mustaqbal University College, 51001, Hilla, Iraq
| | - Zainab S Abbas
- Department of Chemistry, The University of Mashreq, Research Center, Baghdad, Iraq
| | - Mustafa M Kadhim
- Department of Dentistry, Kut University College, Kut, Wasit, 52001, Iraq.
| | - Ahmed Mahdi Rheima
- Department of Chemistry, College of Science, Mustansiriyah University, Baghdad, Iraq
| | - Maysm Barzan
- Department of Pharmacy, Mazaya University College, Thi-Qar, Iraq
| | | | - Amer S Elameer
- Department of Chemistry, Alshaab University, Baghdad, Iraq
| | - Safa K Hachim
- College of Technical Engineering, The Islamic University, Najaf, Iraq
- Medical Laboratory Techniques Department, Al-Turath University College, Baghdad, Iraq
| | - Mohammed Abdul Hadi
- Medical Laboratory Techniques Department, Al-Farahidi University, Baghdad, 10022, Iraq
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Gannouni A, Louis H, Roisnel T, Isang BB, Benjamin I, Kefi R. X-Ray Crystallography, Spectral Analysis, DFT Studies, and Molecular Docking of (C 9H 15N 3)[CdCl 4] Hybrid Material against Methicillin-Resistant Staphylococcus aureus (MRSA). Polycycl Aromat Compd 2023. [DOI: 10.1080/10406638.2023.2169721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Affiliation(s)
- Afef Gannouni
- Faculté Des Sciences De Bizerte, Laboratoire de Chimie Des Matériaux, Zarzouna, Tunisie
| | - Hitler Louis
- Computational and Bio-Simulation Research Group, University of Calabar, Calabar, Nigeria
- Department of Pure and Applied Chemistry, Faculty of Physical Sciences, University of Calabar, Calabar, Nigeria
| | - Thierry Roisnel
- Centre de Diffractométrie X, UMR 6226 CNRS, Institut Sciences Chimiques De Rennes, Université De Rennes I, Rennes, France
| | - Bartholomew B. Isang
- Computational and Bio-Simulation Research Group, University of Calabar, Calabar, Nigeria
- Department of Mathematics, Faculty of Physical Sciences, University of Calabar, Calabar, Nigeria
| | - Innocent Benjamin
- Computational and Bio-Simulation Research Group, University of Calabar, Calabar, Nigeria
- Department of Microbiology, Faculty of Biological Sciences, University of Calabar, Calabar, Nigeria
| | - Riadh Kefi
- Faculté Des Sciences De Bizerte, Laboratoire de Chimie Des Matériaux, Zarzouna, Tunisie
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10
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Salih RHH, Hasan AH, Hussen NH, Hawaiz FE, Hadda TB, Jamalis J, Almalki FA, Adeyinka AS, Coetzee LCC, Oyebamiji AK. Thiazole-Pyrazoline Hybrids as Potential Antimicrobial Agent: Synthesis, Biological Evaluation, Molecular Docking, DFT Studies and POM analysis. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2023.135191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
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11
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Cao TT, Cui H, Zhou DD, Ren X, Cui CW. Degradation mechanism of BPA under VUV irradiation: efficiency contribution and DFT calculations. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:12813-12824. [PMID: 36114959 DOI: 10.1007/s11356-022-22893-1] [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: 05/22/2022] [Accepted: 09/01/2022] [Indexed: 06/15/2023]
Abstract
Bisphenol A (BPA) is regarded as a hazardous pollutant that exists widely in aquatic environments, posing a severe threat to human health. In this study, a vacuum ultraviolet (VUV) lamp emitting a hybrid of 254 nm and 185 nm light was used to degrade BPA. Results indicated that photolysis via 254 nm wavelength accounted for 24.93% for BPA decay, while indirect oxidation was responsible for 52.27% of decay. Results confirmed that the degradation of BPA under VUV illumination mainly occurred via photo-excited degradation and ·OH electrophilic addition reactions based on average local ionization energy (ALIE) calculation and density functional theory (DFT) calculations. Therefore, only light with a wavelength of 254 nm was able to induce the first three excited states of BPA, forming the electron transition type of n → π* from O atom to a single benzene ring and π → π* in the single benzene ring. Indirect oxidation by ·OH occurred as it preferentially attacked the C6 atom in BPA ring A. Moreover, the energy required for photo-excited degradation was about twofold than that of ·OH electrophilic addition reactions.
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Affiliation(s)
- Ting-Ting Cao
- Northeast Normal University, Changchun, 130117, People's Republic of China
- State Key Laboratory of Urban Water Resources Centre, School of Environment, Harbin Institute of Technology, Harbin, 150090, People's Republic of China
| | - Han Cui
- State Key Laboratory of Urban Water Resources Centre, School of Environment, Harbin Institute of Technology, Harbin, 150090, People's Republic of China
| | - Dan-Dan Zhou
- Northeast Normal University, Changchun, 130117, People's Republic of China
| | - Xin Ren
- College of Environmental Science and Engineering, Jilin Normal University, Siping, 136000, China
| | - Chong-Wei Cui
- State Key Laboratory of Urban Water Resources Centre, School of Environment, Harbin Institute of Technology, Harbin, 150090, People's Republic of China.
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12
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Kaur S, Kaur J, Islam N, Anand A. Organocatalytic Synthesis and DFT Study of Versatile Biologically Active Scaffold of Isatylidene Malononitrile Derivatives. ChemistrySelect 2022. [DOI: 10.1002/slct.202203894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Sukhmeet Kaur
- Department of Chemistry Khalsa College Amritsar 143001 India
| | - Jasneet Kaur
- Department of Chemistry Khalsa College Amritsar 143001 India
| | - Nasarul Islam
- Department of Chemistry Govt. Degree College Bandipora- 193502 Kashmir India
| | - Amit Anand
- Department of Chemistry Khalsa College Amritsar 143001 India
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13
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Zhu X, Chen Z, Ai H. Mechanistic insight into the tautomerization of histidine initiated by water-catalyzed N-H and C-H cleavages. J Mol Model 2022; 28:325. [PMID: 36136156 DOI: 10.1007/s00894-022-05222-8] [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: 05/24/2022] [Accepted: 07/12/2022] [Indexed: 10/14/2022]
Abstract
The N-H and C-H activation is of great significance in organic chemistry and chemical industry fields, especially, in the utilization of petroleum raw materials. High NδH (tautomer of natural histidine) content would increase Alzheimer's disease risk. To inhibit this and improve the activation of N-H and C-H bonds, the isomerization mechanism from NδH to NεH of histidine-containing dipeptide catalyzed by water cluster was explored. The results discovered that water cluster assists this reaction by reducing the activation energies from 68.20 to 9.60 kcal mol-1, and its size not only affects the reaction rate but also determines the reaction pathway in a degree. Moreover, water cluster, taken as a potential green catalyst, is more effective on the reactions involving N-H and C-H bond cleavages than reported common toxic organometallic compounds and has different catalytic mechanisms. This work also provides some theoretical guidance for the modulation of Alzheimer's disease induced by histidine isomerization.
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Affiliation(s)
- Xueying Zhu
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan, 250022, People's Republic of China.
| | - Zijiao Chen
- Institute of Science and Technology, Xinjiang University, Aksu, 843100, People's Republic of China
| | - Hongqi Ai
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan, 250022, People's Republic of China.
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14
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Han J, Wang L, Cao W, Yuan Q, Zhou X, Liu S, Wang XB. Manifesting Direction-Specific Complexation in [HFIP -H·H 2O 2] -: Exclusive Formation of a High-Lying Conformation. J Phys Chem Lett 2022; 13:8607-8612. [PMID: 36073972 DOI: 10.1021/acs.jpclett.2c02237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Size-selective, negative ion photoelectron spectroscopy in conjunction with quantum chemical calculations is employed to investigate the geometric and electronic structures of a protype system in catalytic olefin epoxidation research, that is, deprotonated hexafluoroisopropanol ([HFIP-H]-) complexed with hydrogen peroxide (H2O2). Spectral assignments and molecular electrostatic surface analyses unveil a surprising prevalent existence of a high-lying isomer with asymmetric dual hydrogen-bonding configuration that is preferably formed driven by influential direction-specific electrostatic interactions upon H2O2 approaching [HFIP-H]- anion. Subsequent inspections of molecular orbitals, charge, and spin density distributions indicate the occurrence of partial charge transfer from [HFIP-H]- to H2O2 upon hydrogen-bonding interactions. Accompanied with electron detachment, a proton transfer occurs to form the neutral complex of [HFIP·HOO•] structure. This work conspicuously illustrates the importance of directionality encoded in intermolecular interactions involving asymmetric and complex molecules, while the produced hydroperoxyl radical HOO• offers a possible new pathway in olefin epoxidation chemistry.
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Affiliation(s)
- Jia Han
- Hefei National Laboratory for Physical Sciences at the Microscale, Department of Chemical Physics, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Lei Wang
- Hefei National Laboratory for Physical Sciences at the Microscale, Department of Chemical Physics, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Wenjin Cao
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Qinqin Yuan
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
- Department of Chemistry, Anhui University, Hefei, Anhui 230601, P. R. China
| | - Xiaoguo Zhou
- Hefei National Laboratory for Physical Sciences at the Microscale, Department of Chemical Physics, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Shilin Liu
- Hefei National Laboratory for Physical Sciences at the Microscale, Department of Chemical Physics, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Xue-Bin Wang
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
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15
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Mahmood EA, Poor Heravi MR, Khanmohammadi A, Mohammadi-Aghdam S, Ebadi AG, Habibzadeh S. DFT calculations, structural analysis, solvent effects, and non-covalent interaction study on the para-aminosalicylic acid complex as a tuberculosis drug: AIM, NBO, and NMR analyses. J Mol Model 2022; 28:297. [PMID: 36066691 DOI: 10.1007/s00894-022-05279-5] [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: 06/23/2022] [Accepted: 08/19/2022] [Indexed: 11/28/2022]
Abstract
In this study, the effect of non-covalent interactions on the para-aminosalicylic acid complex is explored using density functional theory (DFT) in the gas phase and the solution. Our findings exhibit that the achieved binding energies considerably change on going from the gas phase to the solution. Based on the obtained results, the absolute value of the binding energy of the complex in the polar solvents is lower than the non-polar ones while in the gas phase it is higher than the solution. The atoms in molecules (AIM) and the natural bond orbital (NBO) analyses are applied to estimate the topological properties and the charge transfer during complexation, respectively. The results indicate that the presence of the cation-π interaction increases the strength of the intramolecular hydrogen bond in the studied complex. Finally, the various electronic descriptors such as energy gap, hardness, softness, and electronic chemical potential are investigated to gain further insight into these interactions. According to the achieved results, the high energy gap of the complex in the water solvent indicates high chemical stability and low reactivity compared to the others. On the other hand, the most reactive as well as the softest complex belongs to the gas phase.
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Affiliation(s)
- Evan Abdulkareem Mahmood
- Medical Laboratory Sciences Department, College of Health Sciences, University of Human Development, Sulaymaniyah, Iraq
| | | | - Azadeh Khanmohammadi
- Department of Chemistry, Payame Noor University (PNU), P.O.Box 19395-4697, Tehran, Iran
| | | | - Abdol Ghaffar Ebadi
- Department of Agriculture, Jouybar Branch, Islamic Azad University, Jouybar, Iran
| | - Sepideh Habibzadeh
- Department of Chemistry, Payame Noor University (PNU), P.O.Box 19395-4697, Tehran, Iran
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16
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A Theoretical Evaluation of the Efficiencies of Metal-Free 1,3,4-Oxadiazole Dye-Sensitized Solar Cells: Insights from Electron–Hole Separation Distance Analysis. ENERGIES 2022. [DOI: 10.3390/en15134913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Herein, some novel metal-free 1,3,4-oxadiazole compounds O1–O7 were evaluated for their photovoltaic properties using density functional theory (DFT) and time-dependent density functional theory (TD-DFT) calculations to determine if they can serve as metal-free organic dyes in the use of dye-sensitized solar cells (DSSCs). To understand the trends in the relative efficiencies of the investigated compounds as dyes in DSSCs, their electron contributions, hole contributions, and electron–hole overlaps for each respective atom and fragment within the molecule were analyzed with a particular focus on the electron densities on the anchoring segments. As transition density matrices (TDM) provide details about the departure of each electron from its corresponding hole during excitations, which results in charge transfer (CT), the charge separation distance (Δr) between the electron and its corresponding hole was studied, in addition to the degree of electron–hole overlap (Λ). The latter, single-point excitation energy of each electron, the percentage electron contribution to the anchoring segments of each compound, the incident-photon-conversion-efficiency (IPCE), charge recombination, light harvesting efficiency (LHE), electron injection (Φinj), and charge collection efficiency (ncollect) were then compared to Δr to determine whether the expected relationships hold. Moreover, parameters such as diffusion constant (Dπ) and electron lifetime (t), amongst others, were also used to describe electron excitation processes. Since IPCE is the key parameter in determining the efficiency, O3 was found to be the best dye due to its highest value.
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17
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HeLian Y, Cui S, Ma X, Wang Y. The effect of tourmaline on the denitration performance of MnOx/TiO2 catalysts and DFT calculation. MOLECULAR CATALYSIS 2022. [DOI: 10.1016/j.mcat.2022.112289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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18
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Magnesium oxide nanotube as a promising material for detection of methamphetamine drug: theoretical study. J Mol Model 2022; 28:150. [PMID: 35562620 DOI: 10.1007/s00894-022-05151-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 05/06/2022] [Indexed: 10/18/2022]
Abstract
Owing to the negative impacts of abusing illegal drugs like methamphetamine (MAF), their detection and control are of paramount importance. Therefore, it is very critical to determine MAF in biological samples. The current research study investigated the sensing interaction of inherent and MgO nanotubes (MgONT) toward MAF via density functional theory computations. We determined that the MgONT has a sensing response of 283.31, and it remarkably improves the reactivity toward MAF. The levels of energy for the highest occupied and the lowest unoccupied molecular orbitals have changed to a great extent, thereby reducing bandgap (Eg) values which increased electrical conductivity. Furthermore, a short recovery time (~ 28.65 ms) has been anticipated for MAF desorption from the MgONT exterior. This piece of research showed that MgONT might be a possible electronic sensor and an appropriate choice to deliver MAF in biological samples.
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19
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Shen T, Han T, Zhao Q, Ding F, Mao S, Gao M. Efficient removal of mefenamic acid and ibuprofen on organo-Vts with a quinoline-containing gemini surfactant: Adsorption studies and model calculations. CHEMOSPHERE 2022; 295:133846. [PMID: 35120953 DOI: 10.1016/j.chemosphere.2022.133846] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 01/24/2022] [Accepted: 01/31/2022] [Indexed: 06/14/2023]
Abstract
To pursue the adsorptivity of versatile vermiculite (Na-Vt)-based adsorbent targeted at emerging pharmaceuticals (mefenamic acid and ibuprofen, corresponding to MEA and IBP, respectively), a quinoline-based gemini surfactant (DHQU) with multi-functional groups is applied as modifier on Na-Vt. Enhanced hydrophobicity, enlarged interlayer space and decreased surface area of DHQU-Vt are obtained, whose modifier availability (the mole ratio of modifier intercalated to added) reaches up to 84.18% as characterized by FT-IR, XRD, TG-DTG, EA and BET analysis. Efficient adsorption of MEA/IBP (123.71/240.69 mg/g) is achieved under an extremely low DHQU dosage (0.2 CEC lower than the usual saturated dosage of organo-Vts), with all the processes fitting satisfactorily with pseudo-second order and Freundlich isotherm models accompanied by an exothermic nature. Acid pickling testifies a stable and reliable reusability process of DHQU-Vt even after 3 cycles. Multiple interactions (i.e., partition process, XH-π interaction, π-π interaction, π-π stacking and electrostatic interaction) are revealed and compared from not only characterization results, but also simulation of frontier orbital analysis, the adsorption configuration and bonding analysis: (i) The greater molecular flexibility of the adsorbate, the greater intra particle diffusion effect. (ii) π-π stacking between isolated aromatic rings is stronger than that between parallelly connected aromatic rings. (iii) The strength of multiple active sites provided by quinoline (CH-π, NH-π and π-π interactions) are comparable but weaker than electrostatic interaction/intra particle diffusion.
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Affiliation(s)
- Tao Shen
- State Key Laboratory of Heavy Oil Processing, College of Science, China University of Petroleum, Beijing, 102249, PR China.
| | - Tong Han
- Unconventional Natural Gas Institute, China University of Petroleum, Beijing, 102249, PR China.
| | - Qing Zhao
- State Key Laboratory of Heavy Oil Processing, College of Science, China University of Petroleum, Beijing, 102249, PR China.
| | - Fan Ding
- State Key Laboratory of Heavy Oil Processing, College of Science, China University of Petroleum, Beijing, 102249, PR China.
| | - Shanshan Mao
- State Key Laboratory of Heavy Oil Processing, College of Science, China University of Petroleum, Beijing, 102249, PR China.
| | - Manglai Gao
- State Key Laboratory of Heavy Oil Processing, College of Science, China University of Petroleum, Beijing, 102249, PR China.
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20
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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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21
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Gomes OP, Rheinheimer JPC, Dias LFG, Batagin-Neto A, Lisboa-Filho PN. Revisiting the hydroxylation phenomenon of SiO 2: a study through "hard-hard" and "soft-soft" interactions. J Mol Model 2022; 28:115. [PMID: 35391628 DOI: 10.1007/s00894-022-05107-w] [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: 02/14/2022] [Accepted: 03/31/2022] [Indexed: 11/29/2022]
Abstract
Surface hydroxylation has been extensively studied over the years for a variety of applications, and studies involving hydroxylation of different silica surfaces are still carried out due to the interesting properties obtained from those modified surfaces. Although a number of theoretical studies have been employed to evaluate details on the hydroxylation phenomenon on silica (SiO2) surfaces, most of these studies are based on computationally expensive models commonly based on extended systems. In order to circumvent such an aspect, here we present a low-cost theoretical study on the SiO2 hydroxylation process aiming to evaluate aspects associated with water-SiO2 interaction. Details about local reactivity, chemical softness, and electrostatic potential were evaluated for SiO2 model substrates in the framework of the density functional theory (DFT) using a molecular approach. The obtained results from this new and promising approach were validated and complemented by fully atomistic reactive molecular dynamics (FARMD) simulations. Furthermore, the implemented approach proves to be a powerful tool that is not restricted to the study of hydroxylation, opening a promising route for low computational cost to analyze passivation and anchoring processes on a variety of oxide surfaces.
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Affiliation(s)
- Orisson P Gomes
- School of Sciences, São Paulo State University (UNESP), POSMAT, Bauru, SP, 17033-360, Brazil.
| | - João P C Rheinheimer
- Department of Physics, School of Sciences, São Paulo State University (UNESP), Bauru, SP, 17033-360, Brazil
| | - Leonardo F G Dias
- School of Sciences, São Paulo State University (UNESP), POSMAT, Bauru, SP, 17033-360, Brazil
| | - Augusto Batagin-Neto
- School of Sciences, São Paulo State University (UNESP), POSMAT, Bauru, SP, 17033-360, Brazil.,São Paulo State University (UNESP), Campus of Itapeva, Itapeva, SP, 18409-010, Brazil
| | - Paulo N Lisboa-Filho
- School of Sciences, São Paulo State University (UNESP), POSMAT, Bauru, SP, 17033-360, Brazil.,Department of Physics, School of Sciences, São Paulo State University (UNESP), Bauru, SP, 17033-360, Brazil
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22
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Polythiophene as a sensor model for chlorofluorocarbon, fluorine, and oxygen gas using DFT calculations. J Mol Model 2022; 28:59. [DOI: 10.1007/s00894-022-05048-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 02/04/2022] [Indexed: 10/19/2022]
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23
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Rajhi AA, Alamri S. Density functional theory investigation to surface modification of boron nitride nanotubes. J Mol Model 2022; 28:50. [PMID: 35102455 DOI: 10.1007/s00894-022-05039-5] [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: 12/16/2021] [Accepted: 01/21/2022] [Indexed: 12/07/2022]
Abstract
We studied the boron nitride nanotube (BNNT) modification through pyrrole molecule properties by implementing B3LYP and M06-2X methods. The results of DFT show that the pyrrole molecule has a strong interaction with BNNT, showing that its adsorption onto the nanotube surface is corresponding to chemical functionalization. Also, after the chemical modification, density of states shows that there is a slight modification in the BNNT electronic properties. Furthermore, electrical conductivity of functionalized BNNT (f-BNNT) was increased compared to BNNT, which shows that an increase in the electron-donating nature of functional groups increases the functionalization energy. Maintaining the BNNT electronic properties along with the improved solubility gives us an idea that BNNT chemical modification through pyrrole can affect the way BNNTs are purified.
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Affiliation(s)
- Ali A Rajhi
- Department of Mechanical Engineering, College of Engineering, King Khalid University, PO Box 394, Abha, 61421, Saudi Arabia
| | - Sagr Alamri
- Department of Mechanical Engineering, College of Engineering, King Khalid University, PO Box 394, Abha, 61421, Saudi Arabia.
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24
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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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25
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Yergaliyeva EM, Kayukova LA, Bazhykova KB, Gubenko MA, Langer P. COMPUTATIONAL STUDIES OF THE PRODUCTS OF TOSYLATION AND para-NITROBENZENESULFOCHLORINATION OF β-AMINOPROPIOAMIDOXIMES. J STRUCT CHEM+ 2021. [DOI: 10.1134/s0022476621120167] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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26
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DFT calculation, molecular docking, and molecular dynamics simulation study on substituted phenylacetamide and benzohydrazide derivatives. J Mol Model 2021; 27:359. [PMID: 34816313 DOI: 10.1007/s00894-021-04987-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 11/15/2021] [Indexed: 10/19/2022]
Abstract
The atomic and molecular properties of the title compounds were calculated by Jaguar using a basis set B3LYP/6-31G**++ with hybrid DFT in the gas phase, to determine the chemical reactivity. Analysis of quantum chemical features such as HOMO and LUMO explained that the electronic charge transfer occurred within the system through conjugated paths of the selected compounds. The nucleophilic and electrophilic reactive sites are recognized from the molecular electrostatic potential plot. Electrophilic and nucleophilic attack-prone molecular sites were predicted by mapping ALIE value to the molecular surface. The bond dissociation energy of the high active compound 15 (2-chloro-N-(2-(2-(2-(2-chlorobenzoyl)hydrazineyl)-2-oxoethoxy)phenyl)acetamide) was calculated to assess the probability of compound autoxidation or degradation. Further, molecular docking, binding free energy calculations, and ADMET profile of the degradation products (DPs) of compound 15 was carried out to determine the binding affinity and toxicity profile of the formed DPs compared with the parent compound. A 150-ns molecular dynamics (MD) simulation was performed to evaluate the binding stability of the compound 15/4URL complex using Desmond. Binding free energy and binding affinity of the complex were computed for 100 trajectory frames using the MM-GBSA approach.
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27
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A theoretical investigation of decorated novel triazoles as DSSCs in PV devices. J Mol Model 2021; 27:353. [PMID: 34779931 DOI: 10.1007/s00894-021-04975-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: 07/28/2021] [Accepted: 11/03/2021] [Indexed: 10/19/2022]
Abstract
Some novel metal-free 1,2,4-triazole compounds A1-A8, based on the 3,5-bis(2-hydroxyphenyl)-1,2,4-triazole derivatives were examined for photovoltaic properties using density functional theory (DFT) and time-dependent density functional theory (TD-DFT) calculations to test their suitability as metal-free organic dyes for use in dye-sensitized solar cells (DSSCs). Through deductive logic, the fluorescence emission (Φf) and charge collection (ηc) efficiencies of these compounds as dyes were obtained and used to determine each dye's incident conversion efficiency (IPCE). From the analyses, A2 displayed the highest IPCE value, followed by A6 and A1. This technique is restricted to evaluating compounds for potential metal-free organic dyes only.
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28
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Politzer P, Murray JS. Are HOMO-LUMO gaps reliable indicators of explosive impact sensitivity? J Mol Model 2021; 27:327. [PMID: 34687370 DOI: 10.1007/s00894-021-04956-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 10/15/2021] [Indexed: 11/27/2022]
Abstract
A high priority in designing and evaluating proposed explosives is to minimize sensitivity, i.e., vulnerability to unintended detonation due to an accidental stimulus, such as impact. In order to establish a capability for predicting impact sensitivity, there have been numerous attempts to correlate it with some molecular or crystal property or properties. One common approach has been to relate impact sensitivity to the difference between the energies of the highest-occupied and lowest-unoccupied molecular orbitals of the explosive molecule, the "HOMO-LUMO gap." In the present study, we tested this approach for a series of twelve explosive nitroaromatics, using four different computational methods. We found that the HOMO-LUMO gap does not appear to be a reliable indicator of relative impact sensitivity. Since detonation initiation involves a series of steps, all of which influence sensitivity; it seems more realistic to try to identify fundamental factors and general trends related to sensitivity ‒ an approach that has already had some success ‒ rather than to seek correlations with one or two specific properties.
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Affiliation(s)
- Peter Politzer
- Department of Chemistry, University of New Orleans, New Orleans, LA, 70148, USA.
| | - Jane S Murray
- Department of Chemistry, University of New Orleans, New Orleans, LA, 70148, USA
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29
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Electronic and physical studies for Teflon FEP as a thermal control in low earth orbit reinforced with ZnO and SiO 2 nanoparticles. J Mol Model 2021; 27:295. [PMID: 34554328 DOI: 10.1007/s00894-021-04912-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 09/08/2021] [Indexed: 10/20/2022]
Abstract
Fluorinated ethylene propylene (Teflon FEP) was used as external layer thermal insulator for Hubble Space Telescope (HST) and on the outside surfaces of space crafts in the low earth orbit (LEO). Teflon FEP was eroding as a result of exposure to atomic oxygen (AO) and different electromagnetic waves such as ultraviolet radiation and X-ray. Model molecules were used to simulate Teflon FEP and its interaction with other nanoparticles such as ZnO and SiO2. Density functional theory (DFT) was used to calculate model structures using B3LYP/LAN2DZ model. Molecular electrostatic potential as contour, band gap energy, and total dipole moment were computed for all models. Thermal stability properties were also studied for Teflon FEP both individually and interacted with ZnO and SiO2. Results showed that a layer of OZn and SiO2 on Teflon FEP, especially Teflon FEP + OZn + OSiO structure, improves the physical, chemical, thermal, and electrical stability of Teflon FEP, potentially acting as a corrosion-inhibiting layer.
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30
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Density functional theory studies of the antioxidants-a review. J Mol Model 2021; 27:271. [PMID: 34463834 DOI: 10.1007/s00894-021-04891-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 08/23/2021] [Indexed: 10/20/2022]
Abstract
The following review article attempts to compare the antioxidant activity of the compounds. For this purpose, density functional theory/Becke three-parameter Lee-Yang-Parr (DFT/B3LYP) methodology was carried out instead of using pharmacological methodologies because of economic benefits and high accuracy. This methodology filtrates the compounds with the lowest antioxidant activity. At first, the Koopmans' theorem was carried out to calculate some descriptors to compare antioxidants. The energy of the highest occupied molecular orbitals (HOMO) was accepted as the best indicator, and then some studies confirmed that the highest occupied molecular orbital/lowest unoccupied molecular orbital (HOMO-LUMO) energy gap is the more precise descriptor. Although it would be better to compare spin density distribution (SDD) on the oxygen of the corresponding radical in the polarizable continuum model (PCM) to evaluate their capability to chain reaction inhibition. Next, it was mentioned that in the multi-target directed ligands (MTDLs), the antioxidant is connected to other moieties in para positions to create better antioxidants or novel hybrid compounds. Indeed, SDD was introduced as a descriptor for MTDL antioxidant effectiveness. Then, the relation between antioxidants and aromaticity was investigated. The more the aromaticity of an antioxidant, the more stable the corresponding radical is. Subsequently, in preferred antioxidant activity, it was defined that the hydrogen atom transfer (HAT) mechanism is more favored in metabolism phase I. It has been seen that the solvent model can change the antioxidant mechanism. Therefore, the solvent model is more important than the chemical structure of antioxidants, and an ideal antioxidant should be evaluated in PCM for pharmacological evaluations.
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