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Kiruthika M, Raveena R, Yogeswaran R, Elangovan N, Arumugam N, Padmanaban R, Djearamane S, Wong LS, Kayarohanam S. Spectroscopic characterization, DFT, antimicrobial activity and molecular docking studies on 4,5-bis[(E)-2-phenylethenyl]-1H,1'H-2,2'-biimidazole. Heliyon 2024; 10:e29566. [PMID: 38707390 PMCID: PMC11066587 DOI: 10.1016/j.heliyon.2024.e29566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Revised: 04/10/2024] [Accepted: 04/10/2024] [Indexed: 05/07/2024] Open
Abstract
The newly synthesized imidazole derivative namely, 4,5-bis[(E)-2-phenylethenyl]-1H,1'H-2,2'-biimidazole (KA1), was studied for its molecular geometry, docking studies, spectral analysis and density functional theory (DFT) studies. Experimental vibrational frequencies were compared with scaled ones. The reactivity sites were determined using average localized ionization analysis (ALIE), electron localized function (ELF), localized orbital locator (LOL), reduced density gradient (RDG), Fukui functions and frontier molecular orbital (FMO). Due to the solvent effect, a lower gas phase energy gap was observed. Through utilization of the noncovalent interaction (NCI) method, the hydrogen bond interaction, steric effect and Vander Walls interaction were investigated. Molecular docking simulations were employed to determine the specific atom inside the molecules that exhibits a preference for binding with protein. The parameters for the molecular electrostatic potential (MESP) and global reactivity descriptors were also determined. The thermodynamic characteristics were determined through calculations employing the B3LYP/cc-pVDZ basis set. Antimicrobial activity was carried out using the five different microorganisms like Escherichia coli, Streptococcus pneumoniae, Staphylococcus aureus, Klebsiella pneumoniae and Candida albicans.
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Affiliation(s)
- M. Kiruthika
- Department of Chemistry, Arignar Anna Government Arts College, Affiliated to Bharathidasan University, Musiri, 621211, Tiruchirappalli, Tamilnadu, India
| | - R. Raveena
- Department of Chemistry, Arignar Anna Government Arts College, Affiliated to Bharathidasan University, Musiri, 621211, Tiruchirappalli, Tamilnadu, India
| | - R. Yogeswaran
- Department of Chemistry, Arignar Anna Government Arts College, Affiliated to Bharathidasan University, Musiri, 621211, Tiruchirappalli, Tamilnadu, India
| | - N. Elangovan
- Research Centre for Computational and Theoretical Chemistry, Musiri, Anjalam, 621208, Tiruchirappalli, Tamilnadu, India
| | - Natarajan Arumugam
- Department of Chemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh, 11451, Saudi Arabia
| | - R. Padmanaban
- Department of Chemistry, School of Physical, Chemical & Applied Sciences, Pondicherry University, R.V. Nagar, Kalapet, Puducherry, 605 014, India
| | - Sinouvassane Djearamane
- Department of Allied Health Sciences, Faculty of Science, Universiti Tunku Abdul Rahman, Jalan universiti, Bandar Barat, Kampar, 31900, Malaysia
- Biomedical Research Unit and Lab Animal Research Centre, Saveetha Dental College, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, 602105, India
| | - Ling Shing Wong
- Faculty of Health and Life Sciences, INTI International University, Nilai, 71800, Malaysia
| | - Saminathan Kayarohanam
- Faculty of Bioeconomics and Health Sciences, University Geomatika Malaysia, Kuala Lumpur, 54200, Malaysia
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Elangovan N, Arumugam N, Almansour AI, Mathew S, Djearamane S, Wong LS, Kayarohanam S. Synthesis, solvent role, absorption and emission studies of cytosine derivative. Heliyon 2024; 10:e28623. [PMID: 38590870 PMCID: PMC11000011 DOI: 10.1016/j.heliyon.2024.e28623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Revised: 03/19/2024] [Accepted: 03/21/2024] [Indexed: 04/10/2024] Open
Abstract
The (E)-4-((4-hydroxy-3-methoxy-5-nitrobenzylidene) amino) pyrimidin-2(1H)-one (C5NV) was synthesized from cytosine and 5-nitrovanilline by simple straightforward condensation reaction. The structural characteristics of the compound was determined and optimized by WB97XD/cc-pVDZ basis set. The vibrational frequencies were computed and subsequently compared to the experimental frequencies. We investiated the electronic properties of the synthesized compound in gas and solvent phases using the time-dependent density functional theory (TD-DFT) approach, and compared them to experimental values. The fluorescence study showed three different wavelengths indicating the nature of the optical material properties. Frontier molecular orbital (FMO) and molecular electrostatic potential (MEP) analyses were conducted for the title compound, and electron localized functions (ELF) and localized orbital locators (LOL) were used to identify the orbital positions of localized and delocalized atoms. Non-covalent interactions (H-bond interactions) were investigated using reduced density gradients (RDGs). The objective of the study was to determine the physical, chemical, and biological properties of the C5NV. The molecular docking study was conducted between C5NV and 2XNF protein, its lowest binding energy score is -7.92 kcal/mol.
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Affiliation(s)
- N. Elangovan
- Research Centre for Computational and Theoretical Chemistry, Anjalam, 621208, Musiri, Tiruchirappalli, Tamilnadu, India
| | - Natarajan Arumugam
- Department of Chemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Abdulrahman I. Almansour
- Department of Chemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Shanty Mathew
- Department of Chemistry, St. Joseph's College Research Center, Shanthinagar, 560027, Bangalore, India
| | - Sinouvassane Djearamane
- Department of Allied Health Sciences, Faculty of Science, Universiti Tunku Abdul Rahman, Jalan Universiti, Bandar Barat, Kampar, 31900, Malaysia
- Biomedical Research Unit and Lab Animal Research Centre, Saveetha Dental College, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, 602 105, India
| | - Ling Shing Wong
- Faculty of Health and Life Sciences, INTI International University, Nilai, 71800, Malaysia
| | - Saminathan Kayarohanam
- Faculty of Bioeconomics and Health Sciences, University Geomatika Malaysia, Kuala Lumpur, 54200, Malaysia
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Sankar Ganesan T, Elangovan N, Thirumavalavan M, Seenan S, Sowrirajan S, Chandrasekar S, Arumugam N, Almansour AI, Mahalingam SM, V M DD, Kanchi S, Sivaramakrishnan V. Synthesis, topology, molecular docking and dynamics studies of o-phenylenediamine derivative. J Biomol Struct Dyn 2024:1-20. [PMID: 38577881 DOI: 10.1080/07391102.2024.2317981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 02/07/2024] [Indexed: 04/06/2024]
Abstract
The N, N'-(1,2-phenylene) bis (1- (4- chlorophenyl) methanimine) (CS4) was synthesized and characterized by infrared (IR), absorption (UV-vis) and NMR (1H and 13C) spectral analyses. The structural parameters, vibrational frequencies, potential energy and the distribution analysis (PED) were calculated by using DFT with the basis set of B3LYP/cc-pVDZ and these spectral values were compared to the experimental values. HOMO and LUMO studied were performed in order to understand the stability and biological activity of the compound. The most reactive sites on the compound were investigated by utilizing MEP energy surface and Fukui function descriptor with the natural population analysis (NPA) of the charges. The study of the natural bond orbitals (NBO) reveals the delocalization of the intramolecular interaction of the charges in the compound. Additionally, topological investigations (ELF, LOL), determination of thermodynamic parameters and noncovalent interaction (NCI) study by using topology (RDG) analysis were also carried out. Finally, the molecular docking and molecular dynamics simulations was carried out by examining against glycosylphosphatidylinositol phospholipase D inhibitor receptor for distinct protein targets (3MZG).Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- T Sankar Ganesan
- Department of Chemistry, Arignar Anna Government Arts College, Affiliated to Bharathidasan University, Tiruchirappalli, Tamilnadu, India
| | - N Elangovan
- Research Centre for Computational and Theoretical Chemistry, Tiruchirappalli, Tamilnadu, India
| | | | - Shanthi Seenan
- Department of Chemistry, Saveetha Engineering College, Chennai, Tamil Nadu, India
| | - S Sowrirajan
- Research Centre for Computational and Theoretical Chemistry, Tiruchirappalli, Tamilnadu, India
| | - S Chandrasekar
- Department of Chemistry, Arignar Anna Government Arts College, Affiliated to Bharathidasan University, Tiruchirappalli, Tamilnadu, India
| | - Natarajan Arumugam
- Department of Chemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | | | | | - Datta Darshan V M
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Anantapur, Andhra Pradesh, India
| | - Subbarao Kanchi
- Department of Physics, Sri Sathya Sai Institute of Higher Learning, Puttaparthi, Andhra Pradesh, India
| | - Venketesh Sivaramakrishnan
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Anantapur, Andhra Pradesh, India
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Kunjumol VS, Jeyavijayan S, Sumathi S, Karthik N. Spectroscopic, computational, cytotoxicity, and docking studies of 6-bromobenzimidazole as anti-breast cancer agent. J Mol Recognit 2024; 37:e3074. [PMID: 38168749 DOI: 10.1002/jmr.3074] [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: 08/28/2023] [Revised: 11/25/2023] [Accepted: 12/05/2023] [Indexed: 01/05/2024]
Abstract
6-Bromobenzimidazole (6BBZ) has been calculated in this study utilizing the 6-311++G(d,p) basis set and the Becke-3-Lee-Yang-Parr density functional approaches. The basic frequencies and geometric optimization are known. FTIR, FT-Raman, and UV-Vis spectra of the substance are compared between its computed and observed values. The energy gap between highest occupied molecular orbital-lowest unoccupied molecular orbital and molecule electrostatic potentials has been represented by charge density distributions that may be associated with the biological response. Time-dependent density functional theory calculations in the gas phase and dimethyl sulfoxide were carried out to ascertain the electronic properties and energy gap values using the same basis set. Molecular orbital contributions are investigated using the overlap population, partial, and total densities of states. Natural bond analysis was found to have strong electron delocalization by means of π(C4-C9) → π*(C5-C6), LP (N1) → π*(C7-C8), and LP(Br12) → π*(C5-C6) interactions. The Fukui function and Mulliken analysis have been explored on the atomic charges of the molecule. The nuclear magnetic resonance chemical shifts for 1 H and 13 C have been computed using the gauge-independent atomic orbital technique. With the highest binding affinity (-6.2 kcal mol-1 ) against estrogen sulfotransferase receptor (PDB ID: 1AQU) and low IC50 value of 17.23 μg/mL, 6BBZ demonstrated potent action against the MCF-7 breast cancer cell line. Studies on the antibacterial activity and ADMET prediction of the molecule have also been carried out.
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Affiliation(s)
- V S Kunjumol
- Department of Engineering, University of Technology and Applied Science, Shinas, Oman
| | - S Jeyavijayan
- Department of Physics, Kalasalingam Academy of Research and Education, Krishnankoil, Tamil Nadu, India
| | - S Sumathi
- Department of Physics, Kalasalingam Academy of Research and Education, Krishnankoil, Tamil Nadu, India
| | - N Karthik
- Department of Physics, Kalasalingam Academy of Research and Education, Krishnankoil, Tamil Nadu, India
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Khajavian M, Kaviani S, Piyanzina I, Tayurskii DA, Nedopekin OV. Chitosan-based adsorptive membrane modified by carboxymethyl cellulose for heavy metal ion adsorption: Experimental and density functional theory investigations. Int J Biol Macromol 2024; 257:128706. [PMID: 38101669 DOI: 10.1016/j.ijbiomac.2023.128706] [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: 07/03/2023] [Revised: 11/16/2023] [Accepted: 12/07/2023] [Indexed: 12/17/2023]
Abstract
Low adsorption capacity and weak mechanical stability are the main drawbacks of chitosan (CS)-based adsorptive membranes for heavy metal ion removal. Polyvinyl alcohol (PVA) has been used to improve the mechanical stability of CS membranes, but adsorption capacity is disregarded. In the current study, the surface of the chitosan/polyvinyl alcohol (CP) membrane was modified using carboxymethyl cellulose (CMC) to increase its heavy metal ion adsorption capacity. Experimental and density functional theory (DFT) calculations were used to evaluate the heavy metal ion (As3+ and Cr3+) adsorption capabilities of CP and carboxymethyl cellulose-functionalized CP (CMC-CP) membranes. The batch adsorption process presented a higher heavy metal adsorption capacity of the CMC-CP membrane (As3+/CMC-CP = 234.78 mg/g and Cr3+/CMC-CP = 230.12 mg/g) compared to the CP membrane (As3+/CP = 89.02 mg/g and Cr3+/CP = 75.61 mg/g). The heavy metal/CMC-CP complexes confirmed higher adsorption energies (As3+/CMC-CP = -23.62 kcal/mol and Cr3+/CMC-CP = -23.21 kcal/mol) than the heavy metal/CP complexes (As3+/CP = -3.47 kcal/mol and Cr3+/CP = -2.92 kcal/mol). The electronic band structure was higher for CMC-CP (5.42 eV) compared to CP (4.43 eV). Experimental and theoretical findings were close, implying that the CMC-CP membrane has superior heavy metal adsorption capability than the CP membrane.
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Affiliation(s)
| | - Sadegh Kaviani
- Institute of Physics, Kazan Federal University, 420008 Kazan, Russia..
| | - Irina Piyanzina
- Institute of Physics, Kazan Federal University, 420008 Kazan, Russia
| | | | - Oleg V Nedopekin
- Institute of Physics, Kazan Federal University, 420008 Kazan, Russia
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Geetha Priya C, Venkatraman BR, Arockiaraj I, Sowrirajan S, Elangovan N, Islam MS, Mahalingam SM. Antimicrobial activity prediction, inter- and intramolecular charge transfer investigation, reactivity analysis and molecular docking studies of adenine derivatives. J Biomol Struct Dyn 2023:1-14. [PMID: 37978905 DOI: 10.1080/07391102.2023.2281636] [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: 08/21/2023] [Accepted: 11/04/2023] [Indexed: 11/19/2023]
Abstract
The utilization of the density functional theory (DFT) methodology has developed as a highly efficient method for investigating molecular structure and vibrational spectra, and it is increasingly being employed in various applications relating to biological systems. This study focuses on conducting investigations, both experimental and computed, to analyze the molecular structure, electronic properties and features of (E)-4-(((9H-purin-6-yl)imino)methyl)-2-methoxyphenol (ANVA). The expression ANVA should be rewritten as follows: the compound is a derivative of adenine (primary amine), specifically a vanillin (aldehyde). The present study reports the synthesis, characterization, DFT, docking and antimicrobial activity of ANVA. The optimization of the molecular structure was conducted, and the determination of its structural features was performed using DFT with the B3LYP/cc-pVDZ method. The vibrational assignments were determined in detail by analyzing the potential energy distribution. A strong correlation was observed between the spectra that were observed and the spectra that were calculated. The calculation of intramolecular charge transfer was performed using natural bond orbital analysis. In addition, several computational methods were employed, including highest occupied molecular orbital-least unoccupied molecular orbital analysis, molecular electrostatic potential calculations, non-linear optical, reduced density gradient, localization orbital locator and electron localization function analysis. This paper examines the present use of adenine derivatives in combatting bacterial and fungal infections, as well as the inclusion of spectral and quantum chemical calculations in the discussion.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- C Geetha Priya
- Department of Chemistry, Thanthai Periyar Government Arts and Science College (Autonomous), Affiliated to Bharathidasan University, Tiruchirappalli, Tamil Nadu, India
| | - B R Venkatraman
- Department of Chemistry, Thanthai Periyar Government Arts and Science College (Autonomous), Affiliated to Bharathidasan University, Tiruchirappalli, Tamil Nadu, India
| | - I Arockiaraj
- Department of Chemistry, St. Joseph's College (Autonomous), Affiliated to Bharathidasan University, Tiruchirappalli, Tamil Nadu, India
| | - S Sowrirajan
- Research Centre for Computational and Theoretical Chemistry, Tiruchirappalli, Tamil Nadu, India
| | - N Elangovan
- Research Centre for Computational and Theoretical Chemistry, Tiruchirappalli, Tamil Nadu, India
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Louis H, Chukwuemeka K, Agwamba EC, Abdullah HY, Pembere AMS. Molecular simulation of Cu, Ag, and Au-decorated Si-doped graphene quantum dots (Si@QD) nanostructured as sensors for SO 2 trapping. J Mol Graph Model 2023; 124:108551. [PMID: 37399776 DOI: 10.1016/j.jmgm.2023.108551] [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: 04/22/2023] [Revised: 06/06/2023] [Accepted: 06/13/2023] [Indexed: 07/05/2023]
Abstract
In view of the numerous environmental hazards and health challenges linked to sulfur (iv) oxide (SO2), an indirect greenhouse gas, and the resultant need to develop efficient gas nanosensor devices, this research had as its principal focus on the theoretical evaluation of the gas sensing potential of metals: Ag, Au and Cu functionalized silicon-doped quantum dots (Si@QD) for the detection and adsorption of SO2 gas investigated using the first-principles density functional theory (DFT) computation at the B3LYP-D3(BJ)/def2-SVP level of theory. Eight (8) possible adsorption modes: SO2_O_Si@QD, SO2_O_Ag_Si@QD, SO2_O_Au_Si@QD, SO2_O_Cu_Si@QD, SO2_S_Si@QD, SO2_S_Ag_Si@QD, SO2_S_Au_Si@QD, and SO2_S_Cu_Si@QD were considered based on SO2 interactions with the studied materials at the -S and -O sites of the SO2 molecule. The counterpoise correction (BSSE) showed that five of the eight interactions had favorable Ead + BSSE values ranging from -0.31 to -1.98 eV. All the eight interactions were observed to be thermodynamically favorable with ΔG and ΔH ranging from -129.01 to -200.24 kcal/mol and -158.26 to -229.73 kcal/mol respectively. Results from the topology analysis reveal that van der Waals forces occurred the greatest at the gas-sensor interphase while SO2_S_ Cu_Si@QD is predicted to have the highest sensing potency based on the conductivity and recovery time estimations. These results confirm the potential efficient feasibility of real-world device application of the metals (Ag, Au, Cu) functionalized Si-doped QDs.
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Affiliation(s)
- Hitler Louis
- Computational and Bio-Simulation Research Group, University of Calabar, Calabar, Nigeria; Department of Pure and Applied Chemistry, University of Calabar, Calabar, Nigeria; Faculty of Allied Health Sciences, Chettinad Hospital and Research Institute, Chettinad Academy of Research and Education, Kelambakkam, 603103, Tamil Nadu, India.
| | - Kelechi Chukwuemeka
- Computational and Bio-Simulation Research Group, University of Calabar, Calabar, Nigeria; Department of Chemical Sciences, Clifford University, Owerrinta, Nigeria
| | - Ernest C Agwamba
- Computational and Bio-Simulation Research Group, University of Calabar, Calabar, Nigeria; Department of Chemistry, Covenant University, Ota, Nigeria
| | - Hewa Y Abdullah
- Physics Education Department, Tishk International University, Erbil, Iraq
| | - Anthony M S Pembere
- Department of Chemical Sciences, Jaramogi Odinga University of Science and Technology, Bondo, Kenya
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Cruz ÁB, de Brito LG, Leal PVB, Dos Santos Ramos WT, Pereira DH. Intramolecular hydrogen bonds interactions in the isomers of the bilirubin molecule: DFT and QTAIM analysis. J Mol Model 2023; 29:318. [PMID: 37718354 DOI: 10.1007/s00894-023-05720-3] [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: 07/25/2023] [Accepted: 09/02/2023] [Indexed: 09/19/2023]
Abstract
CONTEXT Bilirubin is an important molecule, used as a marker of some liver diseases, and it can also be toxic and cause jaundice, especially in newborns. The main treatment for neonatal jaundice is phototherapy with blue light, which is still widely studied because the photophysical processes involved are not fully understood. METHODS Calculations based on the density functional theory (DFT) at M062X/6-31G(d,p) level were performed in order to evaluate the structural, electronic, and topological properties of bilirubin isomers. It was found that the ZZ conformation can form a greater number of hydrogen bonds, which gives the isomer greater energy stabilization compared to the other ZE, EZ, and EE isomers, and that the EE isomer is the conformer with the lowest energy of stabilization. The hydrogen bonds were characterized by the quantum theory of atoms in molecules (QTAIM) and for the ZZ isomer four hydrogen bonds (HBs) were found classified as intermediate, ∇2ρ(r) > 0, H(r) > 0. The ZE, EZ, and EE isomers show weak HBs, ∇2ρ(r) > 0, H(r) > 0.
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Affiliation(s)
- Állefe Barbosa Cruz
- Collegiate of Exact Sciences and Biotechnology, Federal University of Tocantins, 77.402-970, Gurupi, Tocantins, Brazil
- Graduate Program in Chemistry, Federal University of Tocantins, 77.402-970, Gurupi, Tocantins, Brazil
| | - Lívia Gabriela de Brito
- Institute of Engineering, Science and Technology, Universidade Federal Dos Vales Do Jequitinhonha E Mucuri, Janaúba, MG, 39440-000, Brazil
| | - Paulo Vitor Brandão Leal
- Institute of Engineering, Science and Technology, Universidade Federal Dos Vales Do Jequitinhonha E Mucuri, Janaúba, MG, 39440-000, Brazil
| | - Welyson Tiano Dos Santos Ramos
- Institute of Engineering, Science and Technology, Universidade Federal Dos Vales Do Jequitinhonha E Mucuri, Janaúba, MG, 39440-000, Brazil
- Graduate Program On Computacional Modeling and Systems, Universidade Estadual de Montes Claros, Montes Claros, MG, 39401-089, Brazil
| | - Douglas Henrique Pereira
- Collegiate of Exact Sciences and Biotechnology, Federal University of Tocantins, 77.402-970, Gurupi, Tocantins, Brazil.
- Graduate Program in Chemistry, Federal University of Tocantins, 77.402-970, Gurupi, Tocantins, Brazil.
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Zhao X, Li Y, Lin S, Liu C, Guo X, Li X, He L, Chen X, Ye G. DFT studies of solvent effect in hydrogen abstraction reactions from different allyl-type monomers with benzoyl radical. BMC Chem 2023; 17:111. [PMID: 37700296 PMCID: PMC10496217 DOI: 10.1186/s13065-023-01027-9] [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: 04/04/2023] [Accepted: 08/29/2023] [Indexed: 09/14/2023] Open
Abstract
Inert allyl-type monomers have been widely documented due to reduce degradation chain transfer. Recently, we and others discovered that the [3 + 2] cyclization reaction process by a photo-driven radical reaction, which can accelerate the polymerization. It was discovered that allyl ether monomers had much higher reactivity than other allyl monomers in the suspension photopolymerization initiated by Type I photoinitiator. Since the hydrogen abstraction reaction (HAR) is the initial step of cyclization, and in order to clarify the influence of solvents effect, three allyl-type monomers were employed, containing "O", "N" and "S" atom as hydrogen donors. The benzoyl radical obtained from cleavage of photoinitiator was chosen as hydrogen acceptors. We explored the hydrogen abstraction reaction in different solvents (methanol, water and DMSO) by quantum chemistry for geometry and energy. An investigation was undertaken regarding the structural orbital by electrostatic potential (ESP) and topological analysis (ELF and LOL). The findings were also combined with the distortion model and transition state theory. We obtained the molecular interactions used independent gradient method in the Hirshfeld molecular density partition (IGMH). The Eckart's correction allowed to examine the driving factors of the hydrogen abstraction reaction tunnels and these reactions constant rates are determined in the range of 500-2500 K depending on the modified Arrhenius form in different solvents effect. Our results can provide an answer for the different reactivities.
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Affiliation(s)
- Xiaotian Zhao
- Department of Pharmacy, Chengdu Second Peoples Hospital, Chengdu, 610017, People's Republic of China
| | - YaMing Li
- Department of Stomatology, Chengdu Second Peoples Hospital, Chengdu, 610017, People's Republic of China
| | - Shibo Lin
- Department of Pharmacy, Chengdu Second Peoples Hospital, Chengdu, 610017, People's Republic of China
| | - Chun Liu
- Department of Pharmacy, Chengdu Second Peoples Hospital, Chengdu, 610017, People's Republic of China
| | - Xirui Guo
- Department of Pharmacy, Chengdu Second Peoples Hospital, Chengdu, 610017, People's Republic of China
| | - Xuanhao Li
- Department of Pharmacy, Chengdu Second Peoples Hospital, Chengdu, 610017, People's Republic of China
| | - Lihui He
- Department of Pharmacy, Chengdu Second Peoples Hospital, Chengdu, 610017, People's Republic of China
| | - Xi Chen
- Department of Pharmacy, Chengdu Second Peoples Hospital, Chengdu, 610017, People's Republic of China
| | - Guodong Ye
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Molecular Target and Clinical Pharmacology, the NMPA and State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences and the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, 511436, China.
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Seijas LE, Zambrano CH, Almeida R, Alí-Torres J, Rincón L, Torres FJ. Exploring the Non-Covalent Bonding in Water Clusters. Int J Mol Sci 2023; 24:ijms24065271. [PMID: 36982342 PMCID: PMC10049637 DOI: 10.3390/ijms24065271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 02/13/2023] [Accepted: 02/16/2023] [Indexed: 03/12/2023] Open
Abstract
QTAIM and source function analysis were used to explore the non-covalent bonding in twelve different water clusters (H2O)n obtained by considering n = 2–7 and various geometrical arrangements. A total of seventy-seven O−H⋯O hydrogen bonds (HBs) were identified in the systems under consideration, and the examination of the electron density at the bond critical point (BCP) of these HBs revealed the existence of a great diversity of O−H⋯O interactions. Furthermore, the analysis of quantities, such as |V(r)|/G(r) and H(r), allowed a further description of the nature of analogous O−H⋯O interactions within each cluster. In the case of 2-D cyclic clusters, the HBs are nearly equivalent between them. However, significant differences among the O−H⋯O interactions were observed in 3-D clusters. The assessment of the source function (SF) confirmed these findings. Finally, the ability of SF to decompose the electron density (ρ) into atomic contributions allowed the evaluation of the localized or delocalized character of these contributions to ρ at the BCP associated to the different HBs, revealing that weak O−H⋯O interactions have a significant spread of the atomic contributions, whereas strong interactions have more localized atomic contributions. These observations suggest that the nature of the O−H⋯O hydrogen bond in water clusters is determined by the inductive effects originated by the different spatial arrangements of the water molecules in the studied clusters.
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Affiliation(s)
- Luis E. Seijas
- Grupo de Química Computacional y Teórica (QCT-UR), Escuela de Ingeniería Ciencia y Tecnología (EICT), Universidad del Rosario, Bogotá 111221, Colombia
| | - Cesar H. Zambrano
- Grupo de Química Computacional y Teórica (QCT-USFQ), Departamento de Ingeniería Química, Universidad San Francisco de Quito, Diego de Robles y Vía Interoceánica, Quito 17-1200-841, Ecuador
| | - Rafael Almeida
- Laboratorio de Procesos Dinámicos en Química, Departamento de Química, Facultad de Ciencias, Universidad de Los Andes, Mérida 5101, Venezuela
| | - Jorge Alí-Torres
- Departamento de Química, Universidad Nacional de Colombia, Av. Cra. 30 #45-03, Bogotá 111321, Colombia
| | - Luis Rincón
- Grupo de Química Computacional y Teórica (QCT-USFQ), Departamento de Ingeniería Química, Universidad San Francisco de Quito, Diego de Robles y Vía Interoceánica, Quito 17-1200-841, Ecuador
| | - Fernando Javier Torres
- Grupo de Química Computacional y Teórica (QCT-UR), Escuela de Ingeniería Ciencia y Tecnología (EICT), Universidad del Rosario, Bogotá 111221, Colombia
- Grupo de Química Computacional y Teórica (QCT-USFQ), Departamento de Ingeniería Química, Universidad San Francisco de Quito, Diego de Robles y Vía Interoceánica, Quito 17-1200-841, Ecuador
- Correspondence:
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Geethapriya J, Rexalin Devaraj A, Gayathri K, Swadhi R, Elangovan N, S.Manivel, Sowrirajan S, Thomas R. Solid state synthesis of a fluorescent Schiff base (E)-1-(perfluorophenyl)-N-(o-toly)methanimine followed by computational, quantum mechanical and molecular docking studies. RESULTS IN CHEMISTRY 2023. [DOI: 10.1016/j.rechem.2023.100819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
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Kanagavalli A, Jayachitra R, Thilagavathi G, Elangovan N, Sowrirajan S, Thomas R. Synthesis, characterization, computational, excited state properties, wave function, and molecular docking studies of (E)-4-((2-hydroxybenzylidene)amino)N-(thiazol-2-yl) benzenesulfonamide. J INDIAN CHEM SOC 2023. [DOI: 10.1016/j.jics.2023.100885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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Adalikwu SA, Louis H, Iloanya AC, Edet HO, Akem MU, Eno EA, Manicum ALE. B- and Al-Doped Porous 2D Covalent Organic Frameworks as Nanocarriers for Biguanides and Metformin Drugs. ACS APPLIED BIO MATERIALS 2022; 5:5887-5900. [PMID: 36413624 DOI: 10.1021/acsabm.2c00855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Nanostructures such as nanosheets, nanotubes, nanocages, and fullerenes have been extensively studied as potential candidates in various fields since the advancement of nanoscience. Herein, the interaction between biguanides (BGN) and metformin (MET) on the modified covalent organic framework (COF), COF-B, and COF-Al was investigated using density functional theory at the ωB97XD/6-311+G (d, p) level of computation to explore a new drug delivery system. The electronic properties evaluation reveals that the studied surfaces are suited for the delivery of both drug molecules. The calculated adsorption energies and basis set superposition errors (BSSE) ranged between -21.20 and -65.86 kJ/mol. The negative values obtained are an indication of excellent interaction between the drug molecules and the COF surfaces. Moreover, BGN is better adsorbed on COF-B with Eads of -65.86 kJ/mol, while MET is better adsorbed on COF-Al with Eads = -47.30 kJ/mol. The analysis of the quantum theory of atom in molecules (QTAIM) explained the nature and strength of intermolecular interaction existing between the drug molecules BGN and MET with the adsorbing surfaces. The analysis of noncovalent interaction (NCI) shows a weak hydrogen-bond interaction. Other properties such as quantum chemical descriptors and natural bond orbital (NBO) analysis also agree with the potential of COF surfaces as drug delivery systems. The electron localization function (ELF) is discussed, and it confirms the transitions occurring in the NBO analysis of the complexes. In conclusion, COF-B and COF-Al are suitable candidates for the effective delivery of BGN and MET.
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Affiliation(s)
- Stephen A Adalikwu
- Computational and Bio-Simulation Research Group, University of Calabar, Calabar, P.M.B1115, Nigeria
| | - Hitler Louis
- Computational and Bio-Simulation Research Group, University of Calabar, Calabar, P.M.B1115, Nigeria.,Department of Pure and Applied Chemistry, University of Calabar, Calabar, P.M.B1115, Nigeria
| | - Anthony C Iloanya
- Department of Physics, Lehigh University, Bethlehem, Pennsylvania18015, United States
| | - Henry O Edet
- Computational and Bio-Simulation Research Group, University of Calabar, Calabar, P.M.B1115, Nigeria
| | - Martilda U Akem
- Computational and Bio-Simulation Research Group, University of Calabar, Calabar, P.M.B1115, Nigeria.,Department of Pure and Applied Chemistry, University of Calabar, Calabar, P.M.B1115, Nigeria
| | - Ededet A Eno
- Computational and Bio-Simulation Research Group, University of Calabar, Calabar, P.M.B1115, Nigeria.,Department of Pure and Applied Chemistry, University of Calabar, Calabar, P.M.B1115, Nigeria
| | - Amanda-Lee E Manicum
- Department of Chemistry, Tshwane University of Technology, Pretoria0183, South Africa
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An Accurate Approach for Computational pKa Determination of Phenolic Compounds. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27238590. [PMID: 36500683 PMCID: PMC9736058 DOI: 10.3390/molecules27238590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 11/30/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022]
Abstract
Computational chemistry is a valuable tool, as it allows for in silico prediction of key parameters of novel compounds, such as pKa. In the framework of computational pKa determination, the literature offers several approaches based on different level of theories, functionals and continuum solvation models. However, correction factors are often used to provide reliable models that adequately predict pKa. In this work, an accurate protocol based on a direct approach is proposed for computing phenols pKa. Importantly, this methodology does not require the use of correction factors or mathematical fitting, making it highly practical, easy to use and fast. Above all, DFT calculations performed in the presence two explicit water molecules using CAM-B3LYP functional with 6-311G+dp basis set and a solvation model based on density (SMD) led to accurate pKa values. In particular, calculations performed on a series of 13 differently substituted phenols provided reliable results, with a mean absolute error of 0.3. Furthermore, the model achieves accurate results with -CN and -NO2 substituents, which are usually excluded from computational pKa studies, enabling easy and reliable pKa determination in a wide range of phenols.
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Khodiev M, Holikulov U, ISSAOUI N, Al-Dossary OM, Bousiakoug LG, Lavrik N. Estimation of electrostatic and covalent contributions to the enthalpy of H-bond formation in H-complexes of 1,2,3-benzotriazole with proton-acceptor molecules by IR spectroscopy and DFT calculations. JOURNAL OF KING SAUD UNIVERSITY - SCIENCE 2022. [DOI: 10.1016/j.jksus.2022.102530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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