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Hamedian A, Vakili M, Brandán SA, Akbari M, Kanaani A, Darugar V. Theoretical study on the structure, spectroscopic, and current-voltage behavior of 11-Cis and Trans retinal isomers in rhodopsin. Sci Rep 2024; 14:12452. [PMID: 38816529 PMCID: PMC11140004 DOI: 10.1038/s41598-024-63249-8] [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: 03/15/2024] [Accepted: 05/27/2024] [Indexed: 06/01/2024] Open
Abstract
In this study, the electronic transport properties of 11-Cis and Trans retinal, components of rhodopsin, were investigated as optical molecular switches using the nonequilibrium Green's function (NEGF) formalism combined with first-principles density functional theory (DFT). These isomers, which can be reversibly converted into each other, were examined in detail. The structural and spectroscopic properties, including infrared (IR), Raman, nuclear magnetic resonance (NMR), and ultraviolet (UV) spectra, were analyzed using the hybrid B3LYP/6-311 + + G** level of theory. Complete vibrational assignments were performed for both forms utilizing the scaled quantum mechanical force field (SQMFF) methodology. To evaluate the conductivity of these molecules, we utilized current-voltage (I-V) characteristics, transmission spectra, molecular projected self-consistent Hamiltonian (MPSH), HOMO-LUMO gap, and second-order interaction energies (E2). The trendline extrapolation of the current-voltage plots confirmed our findings. We investigated the effect of different electrodes (Ag, Au, Pt) and various connection sites (hollow, top, bridge) on conductivity. The Ag electrode with the hollow site exhibited the highest efficiency. Our results indicate that the Cis form has higher conductivity than the Trans form.
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Affiliation(s)
- Amin Hamedian
- Department of Chemistry, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, 91775-1436, Iran
| | - Mohammad Vakili
- Department of Chemistry, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, 91775-1436, Iran.
| | - Silvia A Brandán
- Cátedra de Química General, Instituto de Química, Inorgánica Facultad de Bioquímica, Química y Farmacia, Universidad Nacional de Tucumán, Ayacucho 471, 4000, Tucumán, Argentina
| | - Mahmood Akbari
- UNESCO‑UNISA-ITL Africa Chair in Nanoscience and Nanotechnology (U2ACN2), College of Graduate Studies, University of South Africa (UNISA), Pretoria, South Africa
| | - Ayoub Kanaani
- School of Chemistry, Damghan University, Damghan, 36716-41167, Iran
| | - Vahidreza Darugar
- Department of Chemistry, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, 91775-1436, Iran
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Khalid Z, Shafqat SS, Ahmad HA, Munawar MA, Mutahir S, Elkholi SM, Shafqat SR, Huma R, Asiri AM. A Combined Experimental and Computational Study of Novel Benzotriazinone Carboxamides as Alpha-Glucosidase Inhibitors. Molecules 2023; 28:6623. [PMID: 37764399 PMCID: PMC10535199 DOI: 10.3390/molecules28186623] [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: 05/29/2023] [Revised: 06/26/2023] [Accepted: 07/03/2023] [Indexed: 09/29/2023] Open
Abstract
Diabetes is a chronic metabolic disorder of the endocrine system characterized by persistent hyperglycemia appears due to the deficiency or ineffective use of insulin. The glucose level of diabetic patients increases after every meal and medically recommended drugs are used to control hyperglycemia. Alpha-glucosidase inhibitors are used as antidiabetic medicine to delay the hydrolysis of complex carbohydrates. Acarbose, miglitol, and voglibose are commercial drugs but patients suffer side effects of flatulence, bloating, diarrhea, and loss of hunger. To explore a new antidiabetic drug, a series of benzotriazinone carboxamides was synthesized and their alpha-glucosidase inhibition potentials were measured using in vitro experiments. The compounds 14k and 14l were found to be strong inhibitors compared to the standard drug acarbose with IC50 values of 27.13 ± 0.12 and 32.14 ± 0.11 μM, respectively. In silico study of 14k and 14l was carried out using molecular docking to identify the type of interactions developed between these compounds and enzyme sites. Both potent compounds 14k and 14l exhibited effective docking scores by making their interactions with selected amino acid residues. Chemical hardness and orbital energy gap values were investigated using DFT studies and results depicted affinity of 14k and 14l towards biological molecules. All computational findings were found to be in good agreement with in vitro results.
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Affiliation(s)
- Zunera Khalid
- Department of Chemistry, Kinnaird College for Women, Lahore 54000, Pakistan; (Z.K.); (R.H.)
- School of Chemistry, University of the Punjab, Lahore 54590, Pakistan;
| | - Syed Salman Shafqat
- Department of Chemistry, Division of Science and Technology, University of Education, Lahore 54770, Pakistan
| | - Hafiz Adnan Ahmad
- School of Chemistry, University of the Punjab, Lahore 54590, Pakistan;
| | - Munawar Ali Munawar
- School of Chemistry, University of the Punjab, Lahore 54590, Pakistan;
- Department of Basic and Applied Chemistry, Faculty of Science and Technology, University of Central Punjab, Lahore 54000, Pakistan
| | - Sadaf Mutahir
- School of Chemistry and Chemical Engineering, Linyi University, Linyi 276000, China;
| | - Safaa M. Elkholi
- Department of Rehabilitation Sciences, College of Health and Rehabilitation Sciences, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia;
| | | | - Rahila Huma
- Department of Chemistry, Kinnaird College for Women, Lahore 54000, Pakistan; (Z.K.); (R.H.)
| | - Abdullah Mohammed Asiri
- Chemistry Department, Faculty of Science, King Abdulaziz University, Jeddah 64274, Saudi Arabia;
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Electronic transport on the two state "ON-OFF" of 1,3,3-trimethylindolino-6'-nitrobenzopyrylospiran as a light-driven molecular optical switch: A first-principle study. J Mol Graph Model 2023; 120:108420. [PMID: 36706573 DOI: 10.1016/j.jmgm.2023.108420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 01/10/2023] [Accepted: 01/18/2023] [Indexed: 01/23/2023]
Abstract
Here, the electronic transport characteristics of the 1,3,3-trimethylindolino-6'-nitrobenzopyrylospiran were studied by using NEGF and DFT methods. By being exposed to UV or visible light, this molecule can change from its MC to SP states. The titled structure was optimized at B3LYP/6-311++G(d,p) level of theory. To obtain conductivity results, the electrons of metal and organic atoms were approached by the single-plus polarization (SZP) for single-zeta and double-plus polarization (DZP) for double zeta basis sets, respectively. We examined some factors in this study, including various molecule geometries, the type of surface materials (Platinum, gold, and silver), the switching ratio, the gap between HOMO and LUMO levels, and the transmission spectra, at different bias voltages. The outcomes show that conductivity transforms from an off-state (high resistance) to an on-state as the molecule switches from MC to SP form (low resistance).
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First-principle study of the current–voltage on the β-diketones with alkyl and methoxy groups at the beta position as molecular switches. Chem Phys Lett 2022. [DOI: 10.1016/j.cplett.2022.140152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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First-principle study on the electronic transport properties of 1,2-bis(2,4-dimethyl-5-phenyl-3-thienyl)perfluorocyclopentene (a diarylethene) as an optical molecular switch. JOURNAL OF THE IRANIAN CHEMICAL SOCIETY 2022. [DOI: 10.1007/s13738-022-02670-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Darugar V, Vakili M, Antonia Brandán S. Electrical transport and NDR property on the cis-trans photo-isomerization of (1R,3S)-2,2-dimethyl-3-(2-methylprop-1-en-1-yl)cyclopropanecarboxylate as an optical molecular switch; A DFT-NEGF study. Chem Phys Lett 2022. [DOI: 10.1016/j.cplett.2022.139818] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Sayyar Z, Vakili M, Kanaani A, Vakili SS, Eshghi H. Molecular structure, hydrogen bond strength, and infrared Fourier transform vibrational assignment of 2,6-dimethylheptane-3,5-dione. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130803] [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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Electronic transport behavior of 2-amino-4,5-bis(2,5-dimethylthiophen-3-yl)furan-3-carbonitrile (a diarylethene) as optical molecular switch: a first-principles approach. Theor Chem Acc 2021. [DOI: 10.1007/s00214-021-02837-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Darugar V, Vakili M, Tayyari SF. Voltage–current behavior of 4-phenylamino-3-penten-2-one and its derivatives molecular switch: a first-principles study. MOLECULAR SIMULATION 2021. [DOI: 10.1080/08927022.2021.1917767] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Vahidreza Darugar
- Department of Chemistry, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Mohammad Vakili
- Department of Chemistry, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
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Madanhire T, Pereira MC, Davids H, Hosten EC, Abrahams A. Lanthanide(III) complexes with N-(2,6-dimethylphenyl)oxamate and 1,10-phenanthroline: Synthesis, characterisation and cytotoxicity against MCF-7, HEC-1A and THP-1 cell lines. Polyhedron 2020. [DOI: 10.1016/j.poly.2020.114713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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Conformations, molecular structure, and N–H⋯O hydrogen bond strength in 4-Alkylamino-3-penten-2-ones. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2019.127440] [Citation(s) in RCA: 4] [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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Molecular structure, spectroscopic studies, and copper oxygen bond strength of α-methyl and α-ethyl derivatives of copper (II) acetylacetonate; Experimental and theoretical approach. J Mol Struct 2018. [DOI: 10.1016/j.molstruc.2018.01.075] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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Darugar V, Vakili M, Nekoei A, Tayyari S, Afzali R. Tautomerism, molecular structure, intramolecular hydrogen bond, and enol-enol equilibrium of para halo substituted 4,4,4-trifluoro-1-phenyl-1,3-butanedione; Experimental and theoretical studies. J Mol Struct 2017. [DOI: 10.1016/j.molstruc.2017.09.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Fahid F, Kanaani A, Pourmousavi SA, Ajloo D. Synthesis, tautomeric stability, spectroscopy and computational study of a potential molecular switch of (Z)-4-(phenylamino)pent-3-en-2-one. Mol Phys 2017. [DOI: 10.1080/00268976.2017.1287439] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Farzaneh Fahid
- School of Chemistry, Damghan University, Damghan, 3671641167, Iran
| | - Ayoub Kanaani
- School of Chemistry, Damghan University, Damghan, 3671641167, Iran
| | - Seied Ali Pourmousavi
- School of Chemistry, Damghan University, Damghan, 3671641167, Iran
- Institute of Biological Sciences, Damghan University, Damghan, 3671641167, Iran
| | - Davood Ajloo
- School of Chemistry, Damghan University, Damghan, 3671641167, Iran
- Institute of Biological Sciences, Damghan University, Damghan, 3671641167, Iran
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