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Quantum Computational, Spectroscopic (FT-IR, FT-Raman, NMR, and UV–Vis) Hirshfeld Surface and Molecular Docking-Dynamics Studies on 5-Hydroxymethyluracil (Monomer and Trimer)

For many decades, uracil has been an antineoplastic agent used in combination with tegafur to treat various human cancers, including breast, prostate, and liver cancer. Therefore, it is necessary to explore the molecular features of uracil and its derivatives. Herein, the molecule’s 5-hydroxymethylu...

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Autores principales: Kumar, Mohit, Jaiswar, Gautam, Afzal, Mohd., Muddassir, Mohd., Alarifi, Abdullah, Fatima, Aysha, Siddiqui, Nazia, Ayub, Rashid, Abduh, Naaser A. Y., Saeed, Waseem Sharaf, Javed, Saleem
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10004125/
https://www.ncbi.nlm.nih.gov/pubmed/36903362
http://dx.doi.org/10.3390/molecules28052116
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author Kumar, Mohit
Jaiswar, Gautam
Afzal, Mohd.
Muddassir, Mohd.
Alarifi, Abdullah
Fatima, Aysha
Siddiqui, Nazia
Ayub, Rashid
Abduh, Naaser A. Y.
Saeed, Waseem Sharaf
Javed, Saleem
author_facet Kumar, Mohit
Jaiswar, Gautam
Afzal, Mohd.
Muddassir, Mohd.
Alarifi, Abdullah
Fatima, Aysha
Siddiqui, Nazia
Ayub, Rashid
Abduh, Naaser A. Y.
Saeed, Waseem Sharaf
Javed, Saleem
author_sort Kumar, Mohit
collection PubMed
description For many decades, uracil has been an antineoplastic agent used in combination with tegafur to treat various human cancers, including breast, prostate, and liver cancer. Therefore, it is necessary to explore the molecular features of uracil and its derivatives. Herein, the molecule’s 5-hydroxymethyluracil has been thoroughly characterized by NMR, UV–Vis, and FT-IR spectroscopy by means of experimental and theoretical analysis. Density functional theory (DFT) using the B3LYP method at 6-311++G(d,p) was computed to achieve the optimized geometric parameters of the molecule in the ground state. For further investigation and computation of the NLO, NBO, NHO analysis, and FMO, the improved geometrical parameters were utilized. The potential energy distribution was used to allocate the vibrational frequencies using the VEDA 4 program. The NBO study determined the relationship between the donor and acceptor. The molecule’s charge distribution and reactive regions were highlighted using the MEP and Fukui functions. Maps of the hole and electron density distribution in the excited state were generated using the TD-DFT method and PCM solvent model in order to reveal electronic characteristics. The energies and diagrams for the lowest unoccupied molecular orbital (LUMO) and the highest occupied molecular orbital (HOMO) were also provided. The HOMO–LUMO band gap estimated the charge transport within the molecule. When examining the intermolecular interactions in 5-HMU, Hirshfeld surface analysis was used, and fingerprint plots were also produced. The molecular docking investigation involved docking 5-HMU with six different protein receptors. Molecular dynamic simulation has given a better idea of the binding of the ligand with protein.
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spelling pubmed-100041252023-03-11 Quantum Computational, Spectroscopic (FT-IR, FT-Raman, NMR, and UV–Vis) Hirshfeld Surface and Molecular Docking-Dynamics Studies on 5-Hydroxymethyluracil (Monomer and Trimer) Kumar, Mohit Jaiswar, Gautam Afzal, Mohd. Muddassir, Mohd. Alarifi, Abdullah Fatima, Aysha Siddiqui, Nazia Ayub, Rashid Abduh, Naaser A. Y. Saeed, Waseem Sharaf Javed, Saleem Molecules Article For many decades, uracil has been an antineoplastic agent used in combination with tegafur to treat various human cancers, including breast, prostate, and liver cancer. Therefore, it is necessary to explore the molecular features of uracil and its derivatives. Herein, the molecule’s 5-hydroxymethyluracil has been thoroughly characterized by NMR, UV–Vis, and FT-IR spectroscopy by means of experimental and theoretical analysis. Density functional theory (DFT) using the B3LYP method at 6-311++G(d,p) was computed to achieve the optimized geometric parameters of the molecule in the ground state. For further investigation and computation of the NLO, NBO, NHO analysis, and FMO, the improved geometrical parameters were utilized. The potential energy distribution was used to allocate the vibrational frequencies using the VEDA 4 program. The NBO study determined the relationship between the donor and acceptor. The molecule’s charge distribution and reactive regions were highlighted using the MEP and Fukui functions. Maps of the hole and electron density distribution in the excited state were generated using the TD-DFT method and PCM solvent model in order to reveal electronic characteristics. The energies and diagrams for the lowest unoccupied molecular orbital (LUMO) and the highest occupied molecular orbital (HOMO) were also provided. The HOMO–LUMO band gap estimated the charge transport within the molecule. When examining the intermolecular interactions in 5-HMU, Hirshfeld surface analysis was used, and fingerprint plots were also produced. The molecular docking investigation involved docking 5-HMU with six different protein receptors. Molecular dynamic simulation has given a better idea of the binding of the ligand with protein. MDPI 2023-02-24 /pmc/articles/PMC10004125/ /pubmed/36903362 http://dx.doi.org/10.3390/molecules28052116 Text en © 2023 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Kumar, Mohit
Jaiswar, Gautam
Afzal, Mohd.
Muddassir, Mohd.
Alarifi, Abdullah
Fatima, Aysha
Siddiqui, Nazia
Ayub, Rashid
Abduh, Naaser A. Y.
Saeed, Waseem Sharaf
Javed, Saleem
Quantum Computational, Spectroscopic (FT-IR, FT-Raman, NMR, and UV–Vis) Hirshfeld Surface and Molecular Docking-Dynamics Studies on 5-Hydroxymethyluracil (Monomer and Trimer)
title Quantum Computational, Spectroscopic (FT-IR, FT-Raman, NMR, and UV–Vis) Hirshfeld Surface and Molecular Docking-Dynamics Studies on 5-Hydroxymethyluracil (Monomer and Trimer)
title_full Quantum Computational, Spectroscopic (FT-IR, FT-Raman, NMR, and UV–Vis) Hirshfeld Surface and Molecular Docking-Dynamics Studies on 5-Hydroxymethyluracil (Monomer and Trimer)
title_fullStr Quantum Computational, Spectroscopic (FT-IR, FT-Raman, NMR, and UV–Vis) Hirshfeld Surface and Molecular Docking-Dynamics Studies on 5-Hydroxymethyluracil (Monomer and Trimer)
title_full_unstemmed Quantum Computational, Spectroscopic (FT-IR, FT-Raman, NMR, and UV–Vis) Hirshfeld Surface and Molecular Docking-Dynamics Studies on 5-Hydroxymethyluracil (Monomer and Trimer)
title_short Quantum Computational, Spectroscopic (FT-IR, FT-Raman, NMR, and UV–Vis) Hirshfeld Surface and Molecular Docking-Dynamics Studies on 5-Hydroxymethyluracil (Monomer and Trimer)
title_sort quantum computational, spectroscopic (ft-ir, ft-raman, nmr, and uv–vis) hirshfeld surface and molecular docking-dynamics studies on 5-hydroxymethyluracil (monomer and trimer)
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10004125/
https://www.ncbi.nlm.nih.gov/pubmed/36903362
http://dx.doi.org/10.3390/molecules28052116
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