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Al-Otaibi JS, Mary YS, Jethawa U, Chakraborty B, Gamberini MC. Examining the adsorption and sensing characteristics of cytosine (CTE) on Y9N9 (Y = Al, B, Ga) nanorings using solvent effects, DFT, AIM and SERS analyses. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2025; 337:126148. [PMID: 40184987 DOI: 10.1016/j.saa.2025.126148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Revised: 03/24/2025] [Accepted: 03/30/2025] [Indexed: 04/07/2025]
Abstract
Nucleobases are nitrogenous biological compounds that are more significant in a range of biological and in medical applications. They are constituents of nucleotides in deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). Therefore, we assessed the sensing applicability by studying the cytosine (CTE)-Y9N9 (Y = Al, B, Ga) nanoring interaction using density functional theory. It was evident that CTE interacted strongly with each ring. Due to charge transfer between the nanoring and CTE, a dipole moment (DM) is generated. All complexes have band gaps less than that of CTE. Complexes' band gap energies are lower in aqueous phase and vacuum than they are in pristine rings. All complexes exhibit higher adsorption energies in solvent medium in comparison with that in vacuum. Changes in the frontier molecular orbitals (FMOs) energies of nanorings after interaction have a major impact on their electrical conductivity and work function. In addition to being an electrical sensor, the Y9N9 nanorings for CTE can also be utilized as a work function-based sensor. But Y9N9's CTE recovery time indicates that it can be used to extract or store CTE depending on the environment. The current work can be expanded to examine the impact of Ag/Au/Cu doping using Y9N9 in order to examine the characteristics of drug delivery carriers and the consequence of doping. The interaction between the analyte and substrate was further studied using reduced density gradient (RDG) analysis, comparing the nature and strength of the interaction in both vacuum and aqueous medium. The observations revealed a stronger interaction in the presence of an aqueous medium, which aligns with the higher adsorption energy values.
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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
| | - Unnati Jethawa
- Department of Physics, SIES College of Arts, Science & Commerce, Mumbai 400022, India
| | - Brahmananda Chakraborty
- High Pressure &Synchroton Radiation Physics Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India; Homi J Bhabha National Institute, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, 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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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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Baiju S, Afzal A, Shahin Thayyil M, S.Al-Otaibi J, Kashif Ali S. Computational Studies on Anticancerous Camptothecin and it’s derivative Camp-10 by Density Functional Theory. RESULTS IN CHEMISTRY 2023. [DOI: 10.1016/j.rechem.2023.100837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023] Open
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Al-Otaibi JS, Mary YS, Mary YS, Acharjee N, Churchill DG. Spectroscopic studies of 5-fluoro-1H-pyrimidine-2,4-dione adsorption on nanorings, solvent effects and SERS analysis. COMPUT THEOR CHEM 2022. [DOI: 10.1016/j.comptc.2022.113873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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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: 0.3] [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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DFT and Molecular Simulation Study of Gold Clusters as Effective Drug Delivery Systems for 5-Fluorouracil Anticancer Drug. J CLUST SCI 2022. [DOI: 10.1007/s10876-022-02329-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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Comprehensive Study of the Chemistry behind the Stability of Carboxylic SWCNT Dispersions in the Development of a Transparent Electrode. NANOMATERIALS 2022; 12:nano12111901. [PMID: 35683756 PMCID: PMC9182667 DOI: 10.3390/nano12111901] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 05/27/2022] [Accepted: 05/30/2022] [Indexed: 02/04/2023]
Abstract
Single-walled carbon nanotubes (SWCNTs) are well-known for their excellent electrical conductivity. One promising application for SWCNT-based thin films is as transparent electrodes for uncooled mid-IR detectors (MIR). In this paper, a combination of computational and experimental studies were performed to understand the chemistry behind the stability of carboxylic SWCNTs (SWCNTs-COOH) dispersions in different solvents. A computational study based on the density functional tight-binding (DFTB) method was applied to understand the interactions of COOH-functionalized carbon nanotubes with selected solvents. Attention was focused on understanding how the protonation of COOH groups influences the binding energies between SWCNTs and different solvents. Thin film electrodes were prepared by alternately depositing PEI and SWCNT-COOH on soda lime glass substrates. To prepare a stable SWCNT dispersion, different solvents were tested, such as deionized (DI) water, ethanol and acetone. The SWCNT-COOH dispersion stability was tested in different solvents. Samples were prepared to study the relationship between the number of depositions, transparency in the MIR range (2.5–5 µm) and conductivity, looking for the optimal thickness that would satisfy the application. The MIR transparency of the electrode was reduced by 20% for the thickest SWCNT layers, whereas sheet resistance values were reduced to 150–200 kΩ/sq.
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Armaković S, Vujić Đ, Brkić B. A computational study of polydimethylsiloxane derivatives as a semi-permeable membrane for in-field identification of naphthenic acids in water using portable mass spectrometry. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.118657] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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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: 6] [Impact Index Per Article: 2.0] [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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