Spectroscopic (FT-IR and FT-Raman) and quantum chemical study on monomer and dimer of benznidazole from DFT and molecular docking approaches
This work presents the quantum chemical calculations of the monomer and dimer of benznidazole using density functional theory (DFT) at the B3LYP/6−311++G(d,2p) level of theory. A one-dimensional potential energy surface scan was carried out across flexible bonds to find the minimum energy structure....
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Elsevier
2025-02-01
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| Series: | Heliyon |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2405844025004840 |
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| author | Tirth Raj Paneru Manoj Kumar Chaudhary Poonam Tandon Bhawani Datt Joshi Beatriz Pinheiro Bezerra Alejandro Pedro Ayala |
| author_facet | Tirth Raj Paneru Manoj Kumar Chaudhary Poonam Tandon Bhawani Datt Joshi Beatriz Pinheiro Bezerra Alejandro Pedro Ayala |
| author_sort | Tirth Raj Paneru |
| collection | DOAJ |
| description | This work presents the quantum chemical calculations of the monomer and dimer of benznidazole using density functional theory (DFT) at the B3LYP/6−311++G(d,2p) level of theory. A one-dimensional potential energy surface scan was carried out across flexible bonds to find the minimum energy structure. The structure with minimum energy was taken as a monomer and dimer is constructed based on intermolecular hydrogen bonding N−H…O. The vibrational analysis was conducted by comparing the calculated FT-IR and FT-Raman spectra of the monomer and dimer with the experimental ones. The red shift in the spectra of amide and carbonyl functional groups indicates their involvement in intermolecular hydrogen bonding in crystal packing, while the other peaks showed good agreement with the experimental result. The intra- and intermolecular interactions in the monomer and dimer were analyzed using various tools. The steric effects and van der Waals forces in the dimer were found to be more effective than the monomer. The dimer in the gaseous medium was found to have a lower Frontier molecular orbital energy (ΔEL-H) value than the monomer, suggesting that it is more reactive in a gaseous medium. The ELF value for hydrogen in monomer and dimer around the ring was found to be more which confirms that the electrons in these regions are more localized. The negative value of the overlap population density of states (OPDOS) both in monomer and dimer indicate that there are anti-bonding orbitals between the acetamide and the benzyl groups of the compound. The drug potential of benznidazole was evaluated by molecular docking with carbonic anhydrase XII, which shows the highest binding affinity of (−8.3 kcal/mol) with 6YH8, indicating that benznidazole is its potent inhibitor. |
| format | Article |
| id | doaj-art-01a37c6387544714a9edb99817560203 |
| institution | Kabale University |
| issn | 2405-8440 |
| language | English |
| publishDate | 2025-02-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Heliyon |
| spelling | doaj-art-01a37c6387544714a9edb998175602032025-01-26T05:04:16ZengElsevierHeliyon2405-84402025-02-01113e42104Spectroscopic (FT-IR and FT-Raman) and quantum chemical study on monomer and dimer of benznidazole from DFT and molecular docking approachesTirth Raj Paneru0Manoj Kumar Chaudhary1Poonam Tandon2Bhawani Datt Joshi3Beatriz Pinheiro Bezerra4Alejandro Pedro Ayala5Central Department of General Science, Far Western University, Mahendranagar, 10400, Nepal; Central Department of Physics, Tribhuvan University, Kirtipur, Kathmandu, NepalDepartment of Physics, Tribhuvan University, Amrit Campus, Institute of Science and Technology, Kathmandu, 44600, NepalDeen Dayal Upadhyaya Gorakhpur University and University of Lucknow, Lucknow, 226007, India; Corresponding author.Department of Physics, Tribhuvan University, Siddhanath Science Campus, Mahendranagar, 10400, Nepal; Corresponding author.Department of Physics, Federal University of Ceará, Fortaleza, CE, 60440-900, BrazilDepartment of Physics, Federal University of Ceará, Fortaleza, CE, 60440-900, BrazilThis work presents the quantum chemical calculations of the monomer and dimer of benznidazole using density functional theory (DFT) at the B3LYP/6−311++G(d,2p) level of theory. A one-dimensional potential energy surface scan was carried out across flexible bonds to find the minimum energy structure. The structure with minimum energy was taken as a monomer and dimer is constructed based on intermolecular hydrogen bonding N−H…O. The vibrational analysis was conducted by comparing the calculated FT-IR and FT-Raman spectra of the monomer and dimer with the experimental ones. The red shift in the spectra of amide and carbonyl functional groups indicates their involvement in intermolecular hydrogen bonding in crystal packing, while the other peaks showed good agreement with the experimental result. The intra- and intermolecular interactions in the monomer and dimer were analyzed using various tools. The steric effects and van der Waals forces in the dimer were found to be more effective than the monomer. The dimer in the gaseous medium was found to have a lower Frontier molecular orbital energy (ΔEL-H) value than the monomer, suggesting that it is more reactive in a gaseous medium. The ELF value for hydrogen in monomer and dimer around the ring was found to be more which confirms that the electrons in these regions are more localized. The negative value of the overlap population density of states (OPDOS) both in monomer and dimer indicate that there are anti-bonding orbitals between the acetamide and the benzyl groups of the compound. The drug potential of benznidazole was evaluated by molecular docking with carbonic anhydrase XII, which shows the highest binding affinity of (−8.3 kcal/mol) with 6YH8, indicating that benznidazole is its potent inhibitor.http://www.sciencedirect.com/science/article/pii/S2405844025004840Molecular dockingBenznidazoleNatural bond orbitalReduced density gradientPDOSVibrational spectra |
| spellingShingle | Tirth Raj Paneru Manoj Kumar Chaudhary Poonam Tandon Bhawani Datt Joshi Beatriz Pinheiro Bezerra Alejandro Pedro Ayala Spectroscopic (FT-IR and FT-Raman) and quantum chemical study on monomer and dimer of benznidazole from DFT and molecular docking approaches Heliyon Molecular docking Benznidazole Natural bond orbital Reduced density gradient PDOS Vibrational spectra |
| title | Spectroscopic (FT-IR and FT-Raman) and quantum chemical study on monomer and dimer of benznidazole from DFT and molecular docking approaches |
| title_full | Spectroscopic (FT-IR and FT-Raman) and quantum chemical study on monomer and dimer of benznidazole from DFT and molecular docking approaches |
| title_fullStr | Spectroscopic (FT-IR and FT-Raman) and quantum chemical study on monomer and dimer of benznidazole from DFT and molecular docking approaches |
| title_full_unstemmed | Spectroscopic (FT-IR and FT-Raman) and quantum chemical study on monomer and dimer of benznidazole from DFT and molecular docking approaches |
| title_short | Spectroscopic (FT-IR and FT-Raman) and quantum chemical study on monomer and dimer of benznidazole from DFT and molecular docking approaches |
| title_sort | spectroscopic ft ir and ft raman and quantum chemical study on monomer and dimer of benznidazole from dft and molecular docking approaches |
| topic | Molecular docking Benznidazole Natural bond orbital Reduced density gradient PDOS Vibrational spectra |
| url | http://www.sciencedirect.com/science/article/pii/S2405844025004840 |
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