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S Al-Otaibi J, Mary YS, Mary YS, Cristina Gamberini M. SERS analysis, DFT, and solution effects regarding the structural and optical characteristics of folic acid biomolecule adsorbed on a Cu 3 metal cluster. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 313:124161. [PMID: 38493513 DOI: 10.1016/j.saa.2024.124161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Revised: 03/07/2024] [Accepted: 03/13/2024] [Indexed: 03/19/2024]
Abstract
The optical characteristics of folic acid (ABP) and metal clusters of copper (Cu3) at various locations were investigated by means of density functional theory (DFT) computations. Mulliken charge analysis and molecular electrostatic potential (MEP) surface show how charge moves from Cu3 to ABP through the various groups. The peak in the UV-Vis spectra of ABP-Cu3 is caused by bonding and anti-bonding orbitals. In both vacuum and aqueous conditions, the polarizability values of ABP-Cu3 cluster are significantly higher than those of pure ABP, indicating a possible enhancement of the nonlinear optical (NLO) effect. Our research investigates the possibility of using ABP adsorbed metal clusters for NLO materials. Surface enhanced Raman scattering (SERS) in the ABP adsorbed metal clusters enhances the vibrational modes of ABP. Adsorption energies are found to be in the range -17.08 to -58.52 kcal/mol in vacuum and -53.34 to -93.44 kcal/mol in aqueous medium for the different configurations for ABP-Cu3. It indicates that metal clusters adsorbed by ABP are stable in the aqueous media. Experimental IR and UV-Vis of ABP is in agreement with theoretically predicted ones.
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Affiliation(s)
- Jamelah S Al-Otaibi
- Department of Chemistry, College of Science, Princess Nourah Bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia.
| | - Y Sheena Mary
- Department of Physics, FMN College (Autonomous), Kollam, Kerala, University of Kerala, India
| | | | - Maria Cristina Gamberini
- Department of Life Sciences, University of Modena and Reggio Emilia, via G. Campi 103, 41125 Modena, Italy
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Al-Otaibi JS, Mary YS, Mary YS, Krátký M, Vinsova J, Gawad J, Gamberini MC. SERS spectra of a bioactive carboximidamide derivative at different concentrations: Experimental and DFT investigations. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2022.134754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Al-Otaibi JS, Mary YS, Mary YS, Krátký M, Vinsova J, Gamberini MC. SERS spectroscopy for the therapeutic N-butyl-2-isonicotinoylhydrazine-1-carboxamide in silver nanocolloids at different concentrations: Experimental and DFT investigations. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2023.134905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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Investigation of the adsorption of a DNA based purine derivative on N/B-doped coronene and coronene by means of DFT and NCI interaction analysis. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.120373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Keskin ZS, Mine Şenol Z, Kaya S, Şimşek S. Prunus mahaleb shell as a sustainable bioresource for carminic acid removal from aqueous solution: Experimental and theoretical studies. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.134618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Al-Otaibi JS, Sheena Mary Y, Shyma Mary Y, Kumar Trivedi R, Chakraborty B, Churchill DG. Theoretical SERS study of the strength and suitability of Cu12 nanostar for SERS: Complete theoretical studies, coinage metal SM12 comparisons, benzothiazole (BTH) adsorbent. COMPUT THEOR CHEM 2022. [DOI: 10.1016/j.comptc.2022.113889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Understanding the mechanism of thioguanine's binding to Ag6 and bimetallic (Ag3–Au3 and Ag3–Cu3) clusters. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133415] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Cluster formation between an oxadiazole derivative with metal nanoclusters (Ag/Au/Cu), graphene quantum dot sheets, SERS studies, and solvent effects. Struct Chem 2022. [DOI: 10.1007/s11224-022-02052-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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Al-Otaibi JS, Shabeer M, Mary YS, Mary YS, Thomas R. Adsorption of a thione derivative on carbon, AlN, and BN nanotubes: a detailed DFT and MD investigation. J Mol Model 2022; 28:181. [PMID: 35668144 DOI: 10.1007/s00894-022-05179-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 05/30/2022] [Indexed: 12/30/2022]
Abstract
The performance of nanotubes (NT) of carbon (CC), aluminium-nitrogen (AlN), and boron-nitrogen (BN) as a sensor and nanocarrier for mercaptopurine (MCP) was investigated by means of a theoretical approach. The calculated negative values of adsorption energy showed the interaction and adsorption of MCP. Highest-occupied molecular orbital (HOMO) and lowest-unoccupied molecular orbital (LUMO) distributions were only found on the NT counter portion of the drug-nanotube not on MCP for AlN-NT and BN-NT while HOMO is over MCP and LUMO is over NT for CC-NT. The polarizability of MCP-NTs is greater than that of MCP. Raman wavenumbers of MCP are enhanced in NTs, and hence, NTs can act as a sensor for the detection of MCP. Solvent dependency on adsorption behaviour is also presented in the manuscript, where we found that the AlN nanotube showed exceptionally high free energy of adsorption over other nanotubes in all solvent mediums. Solvation-free energies were also reported. Noncovalent interaction scattered plot also showed significant intermolecular interaction between AlN nanotubes and the mercaptopurine when compared to other nanotubes under study. To find the antiviral activity of MCP and MCP-NTs against antiviral activities, docking and molecular dynamics simulations were performed with 1HMP PDB. Recovery times show that MCP desorption occurs quickly. The MD simulations and docking results show that BN and CC-NTs with MCP show good activity as drug carriers.
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Affiliation(s)
- Jamelah S Al-Otaibi
- Department of Chemistry, College of Science, Princess Nourah Bint Abdulrahman University, P.O. Box 84428, Riyadh, 11671, Saudi Arabia.
| | - Muhammad Shabeer
- School of Science, Westlake University, Hangzhou, People's Republic of China
| | | | | | - Renjith Thomas
- Deparment of Chemistry, St Berchmans College (Autonomous), Mahatma Gandhi University, Changanassery, Kerala, India
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Venkatesh G, Sixto-López Y, Vennila P, Mary YS, Correa-Basurto J, Mary YS, Manikandan A. An investigation on the molecular structure, interaction with metal clusters, anti-Covid-19 ability of 2-deoxy-D-glucose: DFT calculations, MD and docking simulations. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.132678] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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Al-Otaibi JS, Mary YS, Mary YS. DFT analysis of valproic acid adsorption onto Al 12/B 12-N 12/P 12 nanocages with solvent effects. J Mol Model 2022; 28:98. [PMID: 35322870 DOI: 10.1007/s00894-022-05088-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 03/11/2022] [Indexed: 01/30/2023]
Abstract
Using density functional theory, the adsorption of valproic acid onto the surface of fullerene-like nanocages was investigated. Valproic acid interacts with the nanocages through the carboxylic group with energies of - 144.14, - 109.71, - 105.22, and - 84.96 kcal/mol. The frontier molecular orbital (FMO) energy levels were considerably altered upon adsorption, resulting in a reduction in energy gap and increase in electrical conductivity. This suggests that nanocages could be used as sensors as well as options for drug administration in biological systems. Solvation effects in water are also reported.
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Affiliation(s)
- Jamelah S Al-Otaibi
- Department of Chemistry, College of Science, Princess Nourah Bint Abdulrahman University, P.O. Box 84428, Riyadh, 11671, Saudi Arabia.
| | - Y Sheena Mary
- Thushara, Neethinagar-64, Pattathanam, Kollam, Kerala, India
| | - Y Shyma Mary
- Thushara, Neethinagar-64, Pattathanam, Kollam, Kerala, India
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Evidence of cluster formation of pyrrole with mixed silver metal clusters, Agx-My (x = 4,5, y = 2/1 and M = Au/Ni/Cu) using DFT/SERS analysis. COMPUT THEOR CHEM 2022. [DOI: 10.1016/j.comptc.2021.113569] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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S.Al-Otaibi J, Mary Y, Mary Y. Adsorption of a thione bioactive derivative over different silver/gold clusters – DFT investigations. COMPUT THEOR CHEM 2022. [DOI: 10.1016/j.comptc.2021.113497] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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Zhao C, Yu H, Liu Z, Chen H, Ma X, Chen Y, Liu A, Zhong H, Guo ZY. Facile synthesis of Au@palladium oxide nano-sunflowers for ultrasensitive surface-enhanced Raman scattering analysis. NEW J CHEM 2022. [DOI: 10.1039/d2nj01578a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Metal-semiconductor nanocomposites have gain more and more attention as novel surface-enhanced Raman scattering (SERS) substrates due to the coupling Raman enhancement mechanism between the nanocomponents. Herein, Au@palladium oxide (Au@PdOx) nanohybrids...
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