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Al-Wahaibi L, El-Emam AA, S. M. Abdelbaky M, Garcia-Granda S, Maurya A, Pal M, Siddiqui Z, Shukla R, Pathak SK, Srivastava R, Shukla VK, Prasad O, Sinha L. Structural Characterization, Spectroscopic Profile, Molecular Docking, ADMET Properties, Molecular Dynamics Simulation Studies, and Molecular Mechanics Generalized Born Surface Area Analysis of 5-(Adamantan-1-yl)-4-butyl-2,4-dihydro-3 H-1,2,4-triazole-3-thione as a Potential COX Inhibitor. ACS OMEGA 2024; 9:26651-26672. [PMID: 38911725 PMCID: PMC11191079 DOI: 10.1021/acsomega.4c03512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 05/22/2024] [Accepted: 05/24/2024] [Indexed: 06/25/2024]
Abstract
Employing a synergistic combination of theoretical density functional theory (DFT) and experimental techniques, we conducted a comprehensive analysis elucidating the structural and pharmacological attributes of 5-(adamantan-1-yl)-4-butyl-2,4-dihydro-3H-1,2,4-triazole-3-thione (5A4BT) as a potent COX inhibitor. The X-ray crystallographic data of 5A4BT showed the pivotal role played by weak interactions, notably π-π and C-H-π interactions, alongside hydrogen bonding, in orchestrating the intricate supramolecular architectures within the crystalline lattice. A quantitative analysis of the arrangement of the crystal structure, as well as both inter- and intramolecular interactions, was conducted using Hirshfeld surfaces and 2D fingerprint plots. Additionally, a comprehensive examination of the IR spectra was undertaken, employing both experimental methods and theoretical DFT techniques, to elucidate the vibrational characteristics of the compound. The strength of intermolecular N-H···S hydrogen bonding and charge transfer within the system was assessed through natural bonding orbital analysis. Moreover, Bader's atoms in molecules theory was employed to estimate the strength of intermolecular hydrogen bonds, revealing strong interactions within the 5A4BT dimer. The title compound exhibited binding affinities of -6.4 and -6.5 kcal/mol for COX1 (PDB 3KK6) and COX2 (1CX2) target proteins, respectively. For the first time, predictions regarding ADMET properties, drug-likeness, and toxicity, including favorable bioavailability, along with 100 ns molecular dynamics simulations, binding free energy, and energy decomposition per residue in the binding cavity of the protein from molecular mechanics generalized born surface area approach, collectively indicate the potential of 5A4BT as a nonselective COX inhibitor.
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Affiliation(s)
- Lamya
H. Al-Wahaibi
- Department
of Chemistry, College of Sciences, Princess
Nourah bint Abdulrahman University, Riyadh 11671, Saudi Arabia
| | - Ali A. El-Emam
- Department
of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Mohammed S. M. Abdelbaky
- Department
of Physical and Analytical Chemistry, Faculty of Chemistry, Oviedo University-CINN, Oviedo 33006, Spain
| | - Santiago Garcia-Granda
- Department
of Physical and Analytical Chemistry, Faculty of Chemistry, Oviedo University-CINN, Oviedo 33006, Spain
| | - Anushree Maurya
- Department
of Physics, University of Lucknow, Lucknow 226007, Uttar Pradesh, India
| | - Mamta Pal
- Department
of Physics, University of Lucknow, Lucknow 226007, Uttar Pradesh, India
| | - Zohra Siddiqui
- Department
of Physics, University of Lucknow, Lucknow 226007, Uttar Pradesh, India
| | - Raj Shukla
- Department
of Physics, University of Lucknow, Lucknow 226007, Uttar Pradesh, India
| | - Shilendra K. Pathak
- Department
of Physics, M. M. M. P. G. College, Deoria 274502, Uttar Pradesh, India
| | - Ruchi Srivastava
- Department
of Physics, University of Lucknow, Lucknow 226007, Uttar Pradesh, India
| | - Vikas K. Shukla
- Department
of Physics, Maharishi University of Information
Technology, Lucknow 226013, Uttar Pradesh, India
| | - Onkar Prasad
- Department
of Physics, University of Lucknow, Lucknow 226007, Uttar Pradesh, India
| | - Leena Sinha
- Department
of Physics, University of Lucknow, Lucknow 226007, Uttar Pradesh, India
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2
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Zossimova E, Fiedler J, Vollmer F, Walter M. Hybrid quantum-classical polarizability model for single molecule biosensing. NANOSCALE 2024; 16:5820-5828. [PMID: 38436120 DOI: 10.1039/d3nr05396b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/05/2024]
Abstract
Optical whispering gallery mode biosensors are able to detect single molecules through effects of their polarizability. We address the factors that affect the polarizability of amino acids, which are the building blocks of life, via electronic structure theory. Amino acids are detected in aqueous environments, where their polarizability is different compared to the gasphase due to solvent effects. Solvent effects include structural changes, protonation and the local field enhancement through the solvent (water). We analyse the impact of these effects and find that all contribute to an increased effective polarizability in the solvent. We also address the excess polarizability relative to the displaced water cavity and develop a hybrid quantum-classical model that is in good agreement with self-consistent calculations. We apply our model to calculate the excess polarizability of 20 proteinogenic amino acids and determine the minimum resolution required to distinguish the different molecules and their ionised conformers based on their polarizability.
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Affiliation(s)
- Ekaterina Zossimova
- Department of Physics and Astronomy, Living Systems Institute, University of Exeter, EX4 4QD, Exeter, UK.
- Freiburg Center for Interactive Materials and Bioinspired Technologies (FIT), University of Freiburg, D-79110 Freiburg, Germany
| | - Johannes Fiedler
- Department of Physics and Technology, University of Bergen, Allégaten 55, 5007 Bergen, Norway
| | - Frank Vollmer
- Department of Physics and Astronomy, Living Systems Institute, University of Exeter, EX4 4QD, Exeter, UK.
| | - Michael Walter
- Freiburg Center for Interactive Materials and Bioinspired Technologies (FIT), University of Freiburg, D-79110 Freiburg, Germany
- Cluster of Excellence livMatS @ FIT, Freiburg, Germany
- Fraunhofer IWM, MikroTribologie Centrum μTC, Freiburg, Germany
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3
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Góger S, Sandonas LM, Müller C, Tkatchenko A. Data-driven tailoring of molecular dipole polarizability and frontier orbital energies in chemical compound space. Phys Chem Chem Phys 2023; 25:22211-22222. [PMID: 37566426 PMCID: PMC10445328 DOI: 10.1039/d3cp02256k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 07/27/2023] [Indexed: 08/12/2023]
Abstract
Understanding correlations - or lack thereof - between molecular properties is crucial for enabling fast and accurate molecular design strategies. In this contribution, we explore the relation between two key quantities describing the electronic structure and chemical properties of molecular systems: the energy gap between the frontier orbitals and the dipole polarizability. Based on the recently introduced QM7-X dataset, augmented with accurate molecular polarizability calculations as well as analysis of functional group compositions, we show that polarizability and HOMO-LUMO gap are uncorrelated when considering sufficiently extended subsets of the chemical compound space. The relation between these two properties is further analyzed on specific examples of molecules with similar composition as well as homooligomers. Remarkably, the freedom brought by the lack of correlation between molecular polarizability and HOMO-LUMO gap enables the design of novel materials, as we demonstrate on the example of organic photodetector candidates.
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Affiliation(s)
- Szabolcs Góger
- Department of Physics and Materials Science, University of Luxembourg, L-1511 Luxembourg City, Luxembourg.
| | - Leonardo Medrano Sandonas
- Department of Physics and Materials Science, University of Luxembourg, L-1511 Luxembourg City, Luxembourg.
| | - Carolin Müller
- Department of Physics and Materials Science, University of Luxembourg, L-1511 Luxembourg City, Luxembourg.
| | - Alexandre Tkatchenko
- Department of Physics and Materials Science, University of Luxembourg, L-1511 Luxembourg City, Luxembourg.
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4
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Utsu PM, Gber TE, Nwosa DO, Nwagu AD, Benjamin I, Ikot IJ, Eno EA, Offiong OE, Adeyinka A, Louis H. Modeling of Anthranilhydrazide (HL1) Salicylhydrazone and Its Copper Complexes Cu(I) and Cu(II) as a Potential Antimicrobial and Antituberculosis Therapeutic Candidate. Polycycl Aromat Compd 2023. [DOI: 10.1080/10406638.2023.2186444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/22/2023]
Affiliation(s)
- Patrick M. Utsu
- 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
| | - Terkumbur E. Gber
- 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
| | - Deborah O. Nwosa
- Department of Pure and Applied Chemistry, Faculty of Physical Sciences, University of Calabar, Calabar, Nigeria
| | - Adanna D. Nwagu
- 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
| | - Innocent Benjamin
- Computational and Bio-Simulation Research Group, University of Calabar, Calabar, Nigeria
| | - Immaculata J. Ikot
- 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
| | - Ededet A. Eno
- 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
| | - Offiong E. Offiong
- Department of Pure and Applied Chemistry, Faculty of Physical Sciences, University of Calabar, Calabar, Nigeria
| | - Adedabo Adeyinka
- Research Centre for Synthesis and Catalysis, Department of Chemical Sciences, University of Johannesburg, South Africa
| | - 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
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5
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Abdelkader H, Farouk Z, Mohamed M, Abdelghani M, Houdheifa L, Imene K, Ines H, Anis B, Nadjib C, Meriem H, Souad R, Lasnouni T, Omar LB. Efficient one-pot synthesis, characterization and  DFT study of solvents polarity effects on the structural, energetic and thermodynamic proprieties of (a-methylamino-ethyl)-phosphonic acid dimethyl ester. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2022.134165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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6
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Borah HJ, Borah A, Yadav A, Hazarika S. Extraction of malic acid from Dillenia indica in organic solvents and its antimicrobial activity. SEP SCI TECHNOL 2022. [DOI: 10.1080/01496395.2022.2115381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Affiliation(s)
- Hirok Jyoti Borah
- Department of Chemistry, Jorhat Institute of Science and Technology, Jorhat, Assam, India
| | - Alimpia Borah
- Chemical Engineering Group, Engineering Sciences & Technology Division
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Archana Yadav
- Biological Sciences & Technology Division, CSIR-North East Institute of Science and Technology, Jorhat, Assam, India
| | - Swapnali Hazarika
- Chemical Engineering Group, Engineering Sciences & Technology Division
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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7
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Xing Z, An MW, Chen ZC, Hu M, Huang X, Deng LL, Zhang Q, Guo X, Xie SY, Yang S. Surface Re-Engineering of Perovskites with Buckybowls to Boost the Inverted-Type Photovoltaics. J Am Chem Soc 2022; 144:13839-13850. [PMID: 35862295 DOI: 10.1021/jacs.2c05235] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Despite their multifaceted advantages, inverted perovskite solar cells (PSCs) still suffer from lower power conversion efficiencies (PCEs) than their regular counterparts, which is largely due to recombination energy losses (Eloss) that arise from the chemical, physical, and energy level mismatches, especially at the interfaces between perovskites and fullerene electron transport layers (ETLs). To address this problem, we herein introduce an aminium iodide derivative of a buckybowl (aminocorannulene) that is molecularly layered at the perovskite-ETL interface. Strikingly, besides passivating the PbI2-rich perovskite surface, the aminocorannulene enforces a vertical dipole and enhances the surface n-type character that is more compatible with the ETL, thus boosting the electron extraction and transport dynamics and suppressing interfacial Eloss. As a result, the champion PSC achieves an excellent PCE of over 22%, which is superior compared to that of the control device (∼20%). Furthermore, the device stability is significantly enhanced, owing to a lock-and-key-like grip on the mobile iodides by the buckybowls and the resultant increase of the interfacial ion-migration barrier. This work highlights the potential of buckybowls for the multifunctional surface engineering of perovskite toward high-performance and stable PSCs.
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Affiliation(s)
- Zhou Xing
- Guangdong Provincial Key Lab of Nano-Micro Materials Research, School of Chemical Biology and Biotechnology, Shenzhen Graduate School, Peking University, Shenzhen, Guangdong 518055, China
| | - Ming-Wei An
- State Key Lab for Physical Chemistry of Solid Surfaces, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China.,Department of Materials Science and Engineering, Guangdong Provincial Key Laboratory of Functional Oxide Materials and Devices, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Zuo-Chang Chen
- State Key Lab for Physical Chemistry of Solid Surfaces, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| | - Mingyu Hu
- Guangdong Provincial Key Lab of Nano-Micro Materials Research, School of Chemical Biology and Biotechnology, Shenzhen Graduate School, Peking University, Shenzhen, Guangdong 518055, China
| | - Xianzhen Huang
- Guangdong Provincial Key Lab of Nano-Micro Materials Research, School of Chemical Biology and Biotechnology, Shenzhen Graduate School, Peking University, Shenzhen, Guangdong 518055, China
| | - Lin-Long Deng
- Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University, Xiamen, Fujian 361005, China
| | - Qianyan Zhang
- State Key Lab for Physical Chemistry of Solid Surfaces, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| | - Xugang Guo
- Department of Materials Science and Engineering, Guangdong Provincial Key Laboratory of Functional Oxide Materials and Devices, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Su-Yuan Xie
- State Key Lab for Physical Chemistry of Solid Surfaces, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| | - Shihe Yang
- Guangdong Provincial Key Lab of Nano-Micro Materials Research, School of Chemical Biology and Biotechnology, Shenzhen Graduate School, Peking University, Shenzhen, Guangdong 518055, China.,Institute of Biomedical Engineering, Shenzhen Bay Laboratory, Shenzhen, Guangdong 518055, China
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8
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Effect of electrical stimulation on red meat Neu5Gc content reduction: a combined experimental and DFT study. FOOD SCIENCE AND HUMAN WELLNESS 2022. [DOI: 10.1016/j.fshw.2022.03.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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9
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Singh I, Srivastava R, Shukla VK, Pathak SK, Burman T, Al-Mutairi AA, El-Emam AA, Prasad O, Sinha L. Spectroscopic, electronic structure, molecular docking, and molecular dynamics simulation study of 7-Trifluoromethyl-1H-indole-2-carboxylic acid as an aromatase inhibitor. SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 280:121530. [PMID: 35752037 DOI: 10.1016/j.saa.2022.121530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 06/12/2022] [Accepted: 06/16/2022] [Indexed: 10/31/2022]
Abstract
The present work encompasses a combined experimental and theoretical investigation of the molecular structure, vibrational wavenumbers, electronic structure at the ground and electronic excited states, molecular electrostatic potential surface of 7-(Trifluoromethyl)-1H-indole-2-carboxylic acid (TICA) and possibility of the title molecule as an aromatase inhibitor using molecular docking and molecular dynamic simulations. A stable conformer has been obtained using potential energy scans by varying appropriate dihedral angles. The obtained minimum energy conformer was further optimized at the 6-311++G (d, p) basis set by applying the most accepted B3LYP functional. A good agreement between experimental and calculated normal modes of vibration has been observed. The hydrogen-bonded interaction between two monomeric units of TICA has been investigated using NBO,QTAIM, and NCI (noncovalent interactions) analysis. Molecular docking of TICA with human placental aromatase (PDB ID: 3S79) reveals the formation of polar hydrogen bonds as well as hydrophobic interactions between the ligand and the protein, right in the binding cavity. TICA satisfies all pharmacokinetic filters (Lipinski rule of five, the Veber rule, Ghose rule, Egan rule, as well as the Muegge rule) and has a high bioavailability score of 0.85. Dynamic stability of the ligand within the binding pocket of the target protein has been confirmed by 100 ns molecular dynamics simulation results. The present study provides an excellent starting point for additional in vivo research, and TICA may eventually serve as a significant therapeutic candidate for the treatment of breast cancer.
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Affiliation(s)
- Isha Singh
- Department of Physics, University of Lucknow, 226007 Lucknow, India
| | - Ruchi Srivastava
- Department of Physics, University of Lucknow, 226007 Lucknow, India
| | - Vikas K Shukla
- Department of Physics, Maharishi University of Information Technology Lucknow, Uttar Pradesh, India
| | - Shilendra K Pathak
- Department of Physics, M. M. M. P. G. College, Bhatpar Rani, Deoria, India
| | | | - Aamal A Al-Mutairi
- Department of Chemistry, College of Sciences, Imam Mohammad lbn Saud Islamic University (IMSIU), Riyadh 11623, Saudi Arabia
| | - Ali A El-Emam
- Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Onkar Prasad
- Department of Physics, University of Lucknow, 226007 Lucknow, India
| | - Leena Sinha
- Department of Physics, University of Lucknow, 226007 Lucknow, India.
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10
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Synthesis, crystal structure, quantum calculation and Hirshfeld surface analysis of 4-bromoanilinium oxalate hemihydrate single crystal. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.132087] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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11
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Obaleye JA, Lawal M, Jadeja RN, Gupta VK, Nnabuike GG, Bamigboye MO, Roy H, Yusuff OK, Raji AT. Cu(II) complex based on lemofloxacin and N,N-donor ligand: Synthesis, crystal structure, DFT calculations, and in vitro antimicrobial evaluation. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.131542] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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12
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Kanagathara N, MaryAnjalin F, Ragavendran V, Dhanasekaran D, Usha R, Rao RGS, Marchewka MK. Experimental and theoretical (DFT) investigation of crystallographic, spectroscopic and Hirshfeld surface analysis of anilinium arsenate. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2020.128965] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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13
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Electronic and nonlinear optical properties of 3-(((2-substituted-4-nitrophenyl)imino)methyl)phenol. COMPUT THEOR CHEM 2020. [DOI: 10.1016/j.comptc.2020.113050] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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14
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Hrivnák T, Reis H, Neogrády P, Zaleśny R, Medved’ M. Accurate Nonlinear Optical Properties of Solvated para-Nitroaniline Predicted by an Electrostatic Discrete Local Field Approach. J Phys Chem B 2020; 124:10195-10209. [DOI: 10.1021/acs.jpcb.0c06046] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Tomáš Hrivnák
- Department of Physical and Theoretical Chemistry, Faculty of Natural Sciences, Comenius University, Mlynská dolina, Ilkovičova 6, SK-842 15 Bratislava, Slovakia
| | - Heribert Reis
- Institute of Chemical Biology, National Hellenic Research Foundation, Vasileos Constantinou 48, GR-11635 Athens, Greece
| | - Pavel Neogrády
- Department of Physical and Theoretical Chemistry, Faculty of Natural Sciences, Comenius University, Mlynská dolina, Ilkovičova 6, SK-842 15 Bratislava, Slovakia
| | - Robert Zaleśny
- Department of Physical and Quantum Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspiańskiego 27, PL-50370 Wrocław, Poland
| | - Miroslav Medved’
- Department of Chemistry, Faculty of Natural Sciences, Matej Bel University, Tajovského 40, SK-97400 Banská Bystrica, Slovakia
- Regional Centre of Advanced Technologies and Materials, Faculty of Science, Palacký University Olomouc, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
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15
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Islam SM, Ibnat Z. New Insights into the Structure and Reactivity of Uracil Derivatives in Different Solvents-A Computational Study. ACS OMEGA 2020; 5:22449-22458. [PMID: 32923803 PMCID: PMC7482307 DOI: 10.1021/acsomega.0c02943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 08/10/2020] [Indexed: 06/11/2023]
Abstract
Ab initio calculations were carried out to understand the reactivity and stability of some uracil derivatives, cytosine, 1-methyl cytosine, and cytidine in solvents, water, dimethyl sulfoxide (DMSO), n-octanol, and chloroform. Geometries were fully optimized at MP2 and B3LYP using the 6-31+G(d,p) basis set by applying the Solvation Model on Density (SMD) in solvent systems. The syn conformer of cytidine (cytidine II) is the most stable conformer in the gas phase, while the anticonformer (cytidine IV) is most stable in all of the solvents. Solvation free energy and polarizability values in different solvents decrease in the order water > DMSO > n-octanol > chloroform, while dipole moment, first-order hyperpolarizability, and HOMO-LUMO energy gap values follow the order of polar protic solvent (water and n-octanol) > polar aprotic solvent (DMSO) > nonpolar solvent (chloroform). The solvation free energy, dipole moment, polarizability, and first-order hyperpolarizability values also follow the order of cytosine > 1-methyl cytosine > cytidine. To illustrate that the molecular properties correlate well with the reactivity of the molecules, ab initio calculations were carried out for the reaction of uracil derivatives with Br2 in the gas phase, water, DMSO, n-octanol, and chloroform. All ground and transition state geometries were fully optimized at B3LYP/6-31+G(d,p), and energies were also calculated at G3MP2 for cytosine and 1-methyl cytosine. For cytosine and 1-methyl cytosine, Gibbs energies of activation decrease with the polarity of the solvent that is chloroform > n-octanol > DMSO > water, while the Gibbs energies of activation for the reaction with cytidine decrease in the order of water > DMSO > n-octanol > chloroform. These results suggest that solvent polarity is very important for the stability and reactivity of uracil derivatives. Hydrogen bonding may also play an important role mainly for cytidine. Free energies of activation decrease with the size of the molecule, i.e., cytosine > 1-methyl cytosine > cytidine.
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16
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Molecular modeling and density functional theory calculation of the coordination behavior of 4,5-Dichloroimidazole with Cu(II) ion. SCIENTIFIC AFRICAN 2020. [DOI: 10.1016/j.sciaf.2020.e00533] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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17
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Structural transition of C6−nSinNH7 at n = 0–6 clusters upon substitution of carbon by silicon. Inorganica Chim Acta 2019. [DOI: 10.1016/j.ica.2019.06.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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18
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Bayat M, Taherpour AA, Elahi SM. Molecular interactions between PAMAM dendrimer and some medicines that suppress the growth of hepatitis virus (Adefovir, Entecavir, Telbivudine, Lamivudine, Tenofovir): a theoretical study. INTERNATIONAL NANO LETTERS 2019. [DOI: 10.1007/s40089-019-0277-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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19
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Hrivnák T, Budzák Š, Reis H, Zaleśny R, Carbonnière P, Medveď M. Electric properties of hydrated uracil: From micro- to macrohydration. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2018.11.044] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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20
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Konovalova IS, Shishkina SV, Bani-Khaled G, Muzyka EN, Boyko AN. Intermolecular interactions in crystals of benzene and its mono- and dinitro derivatives: study from the energetic viewpoint. CrystEngComm 2019. [DOI: 10.1039/c8ce02099j] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The weak intermolecular interactions and their role in mono- and dinitrobenzene crystal structure formation have been studied using quantum-chemical calculations.
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Affiliation(s)
- Irina S. Konovalova
- SSI “Institute for Single Crystals” National Academy of Science of Ukraine
- Kharkiv
- Ukraine
- National University of Radio Electronics
- Kharkiv
| | - Svitlana V. Shishkina
- SSI “Institute for Single Crystals” National Academy of Science of Ukraine
- Kharkiv
- Ukraine
- National University of Radio Electronics
- Kharkiv
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Oyeneyin OE, Adejoro IA, Ogunyemi BT, Esan OT. Structural and solvent dependence on the molecular and nonlinear optical properties of 10-octyl thiophene-based phenothiazine and substituted derivatives – a theoretical approach. JOURNAL OF TAIBAH UNIVERSITY FOR SCIENCE 2018. [DOI: 10.1080/16583655.2018.1485274] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Oluwatoba Emmanuel Oyeneyin
- Department of Chemical Sciences, Adekunle Ajasin University, Akungba-Akoko, Ondo State, Nigeria
- Department of Chemistry, University of Ibadan, Nigeria
| | - Isaiah Ajibade Adejoro
- Department of Chemistry, University of Ibadan, Nigeria
- Department of Chemistry, University of Medical Science, Ondo, Nigeria
| | - Babatunde Temitope Ogunyemi
- Department of Chemistry, University of Ibadan, Nigeria
- Department of Chemistry, Federal University, Otuoke, Nigeria
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22
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Rezazadeh M, Ghiasi R, Jamehbozorgi S. Solvent Effects on the Structure And Spectroscopic Properties of the Second-Generation Anticancer Drug Carboplatin: A Theoretical Insight. J STRUCT CHEM+ 2018. [DOI: 10.1134/s0022476618010390] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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23
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A first-principle DFT study of solvent effects on metiamide tautomers and imaginary interactions with H2-receptors. JOURNAL OF THE IRANIAN CHEMICAL SOCIETY 2017. [DOI: 10.1007/s13738-017-1102-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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24
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Qi YJ, Lu HN, Zhao YM, Jin NZ. Probing the influence of carboxyalkyl groups on the molecular flexibility and the charge density of apigenin derivatives. J Mol Model 2017; 23:70. [PMID: 28197841 DOI: 10.1007/s00894-017-3221-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2016] [Accepted: 01/11/2017] [Indexed: 12/11/2022]
Abstract
Apigenin is an important flavonoids due to its antidiabetic bioactivity. It was reported experimentally that the 7-substituent derivative of apigenin has higher biological activity than 4'- and 5-substituted derivatives while introducing sole carboxyalkyl group -(CH2)7COOH into the parent structure. Molecular docking studies indicated that the other two derivatives have lower binding affinities than the 7-substituent derivative (-7.52 kcal mol-1), which is considered to be a better inhibitor than the parent molecule. Almost all of the carbon atoms and oxygen atoms are coplaner for all three molecules in solution phase, however, all carboxyalkyl groups bend inside into the parent molecules in the active site, and the jagged geometries of the carbon chains are destroyed correspondingly. In addition, most of the electron densities of the chemical bonds for all molecules are decreased, especially the 7-substituent derivative. In contrast, most of the Laplacian values for three molecules are increased in the active site, which suggests that the charge densities at the bond critical point (bcp) are much more depleted than the solution phase. Dipole moments of derivatives are all increased in the active site, suggesting strong intermolecular interactions. After interacting with the S. cerevisiae α-glucosidase, only the 7-substituent derivative has the lowest energy gap ΔE HOMO-LUMO, which indicates the lowest stability and the highest inhibition activity. Graphical abstract Probing the influence of carboxyalkyl groups on the molecular flexibility and the charge density of apigenin derivatives.
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Affiliation(s)
- Y J Qi
- Department of Chemical Engineering, Northwest University for Nationalities, Lanzhou, 730124, People's Republic of China.
| | - H N Lu
- Department of Life Sciences and Biological Engineering, Northwest University for Nationalities, Lanzhou, 730124, People's Republic of China
| | - Y M Zhao
- Department of Chemical Engineering, Northwest University for Nationalities, Lanzhou, 730124, People's Republic of China
| | - N Z Jin
- Gansu Province Computing Center, Lanzhou, 730000, People's Republic of China
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25
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Shishkina SV, Konovalova IS, Shishkin OV, Boyko AN. Influence of substituents on the acceptor properties of the amino groups in the diaminobenzene analogues. CrystEngComm 2017. [DOI: 10.1039/c7ce01732d] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The influence of substituents on the geometric parameters and acceptor properties of the amino group in the diaminobenzene analogues has been studied using quantum-chemical calculations and the study of crystal packing from the energetic viewpoint.
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Affiliation(s)
- Svitlana V. Shishkina
- SSI “Institute for Single Crystals” National Academy of Science of Ukraine
- Kharkiv
- Ukraine
- Department of Inorganic Chemistry
- V. N. Karazin Kharkiv National University
| | - Irina S. Konovalova
- SSI “Institute for Single Crystals” National Academy of Science of Ukraine
- Kharkiv
- Ukraine
| | - Oleg. V. Shishkin
- SSI “Institute for Single Crystals” National Academy of Science of Ukraine
- Kharkiv
- Ukraine
- Department of Inorganic Chemistry
- V. N. Karazin Kharkiv National University
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26
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Exploring molecular flexibility and the interactions of Quercetin derivatives in the active site of α-glucosidase using molecular docking and charge density analysis. COMPUT THEOR CHEM 2016. [DOI: 10.1016/j.comptc.2016.09.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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27
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Study of solvent effects on structural and conformational properties of cimetidine tautomers. Med Chem Res 2016. [DOI: 10.1007/s00044-016-1612-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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28
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Sobola A, Watkins G, Van Brecht B, Adejoro I. Synthesis, structure, and theoretical studies of bis(five-coordinate) μ–O–[CuL 2] 2: predicting distortion toward trigonality. J COORD CHEM 2016. [DOI: 10.1080/00958972.2015.1110853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- A.O. Sobola
- Department of Chemistry, Rhodes University, Grahamstown, South Africa
| | - G.M. Watkins
- Department of Chemistry, Rhodes University, Grahamstown, South Africa
| | - B. Van Brecht
- Department of Chemistry, Nelson Mandela Metropolitan University, Port Elizabeth, South Africa
| | - I.A. Adejoro
- Department of Chemistry, University of Ibadan, Ibadan, Nigeria
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30
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Pandith A, Kumar A, Kim HS. 9-N-Alkylaminomethylanthracene probes for selective fluorescence sensing of pentafluorophenol. RSC Adv 2015. [DOI: 10.1039/c5ra15900h] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
9-N-Alkylaminomethylanthracenes (1 and 2) were synthesised for halophenol sensing, and their selectivity and sensitivity towards pentafluorophenol (PFP) in ethanol were investigated.
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Affiliation(s)
- Anup Pandith
- Department of Applied Chemistry
- School of Applied Chemical Engineering
- Kyungpook National University
- Daegu 702-701
- Republic of Korea
| | - Ashwani Kumar
- Department of Applied Chemistry
- School of Applied Chemical Engineering
- Kyungpook National University
- Daegu 702-701
- Republic of Korea
| | - Hong-Seok Kim
- Department of Applied Chemistry
- School of Applied Chemical Engineering
- Kyungpook National University
- Daegu 702-701
- Republic of Korea
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31
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A study of the effects of solvent on structural and conformational properties of ranitidine tautomer forms by DFT method. Struct Chem 2014. [DOI: 10.1007/s11224-014-0510-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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32
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Li HP, Shen XP, Han K, Tang G. Solvent effects on polarizability and hyperpolarizability of spirobifluorene derivative. J Mol Model 2014; 20:2126. [PMID: 24522381 DOI: 10.1007/s00894-014-2126-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Accepted: 12/20/2013] [Indexed: 11/24/2022]
Abstract
We studied the solvent effect on the geometric structure and (hyper)polarizability of spirobifluorene derivative by using quantum chemistry calculations. We found that the geometric structure is slightly affected by the solvent polarity. However, solvent polarity significantly influences first hyperpolarizability and second hyperpolarizability respectively. In addition, the linear polarizability is less affected by the solvent than the hyperpolarizabilities. We also first studied the solvent effect on frontier molecular orbitals and found that the frontier molecular orbitals energy gap is strongly influenced by the surrounding solvent. Our results demonstrate frontier molecular orbitals energy gap and molecular hyperpolarizabilities can be tuned by a suitable choice of the solvent respectively. Such findings have crucial implications for organic nonlinear optical materials applications.
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Affiliation(s)
- Hai-Peng Li
- Department of Physics, College of Science, China University of Mining and Technology, Xuzhou, Jiangsu Province, 221116, People's Republic of China,
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