1
|
Al-Otaibi JS, Mary YS, Mary YS, Mondal A, Acharjee N, Rajendran Nair DS. Investigation of the interaction of thymine drugs with Be 12O 12 and Ca 12O 12 nanocages: A quantum chemical study. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 308:123728. [PMID: 38056182 DOI: 10.1016/j.saa.2023.123728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 11/28/2023] [Accepted: 12/01/2023] [Indexed: 12/08/2023]
Abstract
Based on the DFT in a Wb97xd/6-311+G* level of theory, the interaction of thymine derivatives with Be12O12 and Ca12O12 nanocages was investigated. It was found that adsorption energies of thymine molecules on the Be12/Ca12-O12 surface was around -43.16, -60.06 and -29.62, -50.71, -45.95, -30.27 kcal/mol, for thymine (TH1), 1-amino thymine (TH2) and thymine glycol (TH3), respectively and this result supported the drug's adsorption. Additionally, according to the FMOs and MEP studies, a charge transfer from TH's to nanocages. Additionally, both molecular orbitals demonstrate that the LUMO and HOMO are primarily found on the BeO's surface.
Collapse
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, FMNC, University of Kerala, Kollam, Kerala, India
| | | | - Asmita Mondal
- Department of Chemistry, Durgapur Government College, J. N. Avenue, Paschim Bardhaman, West Bengal, India
| | - Nivedita Acharjee
- Department of Chemistry, Durgapur Government College, J. N. Avenue, Paschim Bardhaman, West Bengal, India
| | - Deepthi S Rajendran Nair
- Department of Ophthalmology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| |
Collapse
|
2
|
Dhali P, Oishi AA, Das A, Hossain MR, Ahmed F, Roy D, Hasan MM. A DFT and QTAIM insight into ethylene oxide adsorption on the surfaces of pure and metal-decorated inorganic fullerene-like nanoclusters. Heliyon 2023; 9:e19407. [PMID: 37809619 PMCID: PMC10558507 DOI: 10.1016/j.heliyon.2023.e19407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 08/10/2023] [Accepted: 08/22/2023] [Indexed: 10/10/2023] Open
Abstract
In this industrial era, the use of low-dimensional nanomaterials as gas sensors for environmental monitoring has received enormous interest. To develop an effective sensing method for ethylene oxide (EO), DFT computations are conducted using method ωB97X-D and B3LYP with 6-31G(d,p) basis set to evaluate the adsorption behavior of ethylene oxide gas on the surfaces of pristine, as well as Scandium and Titanium decorated B12N12, Al12N12, and Al12P12 nanocages. Several properties like structural, physical, and electronic are studied methodically to better understand the sensing behavior. Scandium-decorated aluminum phosphate and boron nitride nanocages were shown to perform better in terms of adsorption properties. The short recovery time observed in this study is beneficial for the repetitive use of the gas sensor. The Natural Bond Orbital and molecular electrostatic potential analysis demonstrated a substantial quantity of charge transfer from adsorbate to adsorbents. The bandgap alternation after adsorption shows an influence of adsorption on electronic properties. The interactions of adsorbate and adsorbents are further studied using the ultraviolet-visible predicted spectrum, and quantum theory of atoms in molecules all of which yielded promising findings.
Collapse
Affiliation(s)
- Palash Dhali
- Department of Physics, Jashore University of Science and Technology, Jashore, 7408, Bangladesh
| | - Adita Afrin Oishi
- Department of Physics, Jashore University of Science and Technology, Jashore, 7408, Bangladesh
| | - Antu Das
- Department of Physics, Jashore University of Science and Technology, Jashore, 7408, Bangladesh
| | - Md Rakib Hossain
- Department of Physics, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, 8100, Bangladesh
| | - Farid Ahmed
- Department of Physics, Jahangirnagar University, Savar, Dhaka, 1342, Bangladesh
| | - Debashis Roy
- Department of Physics, Jashore University of Science and Technology, Jashore, 7408, Bangladesh
| | - Md Mehade Hasan
- Department of Physics, Jashore University of Science and Technology, Jashore, 7408, Bangladesh
| |
Collapse
|
3
|
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]
|
4
|
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]
|
5
|
Al-Otaibi JS, Mary YS, Mary YS, Acharjee N, Churchill DG. Theoretical study of glycoluril by highly symmetrical magnesium oxide Mg 12O 12 nanostructure: adsorption, detection, SERS enhancement, and electrical conductivity study. J Mol Model 2022; 28:332. [PMID: 36163521 DOI: 10.1007/s00894-022-05332-3] [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: 07/01/2022] [Accepted: 09/21/2022] [Indexed: 12/07/2022]
Abstract
Using metal substrates that are nanoscale in size, surface-enhanced Raman scattering (SERS) is a technique for enhancing the Raman signal of biomolecules. Numerous industries including sensing materials, adsorption and medical devices, use nanomaterials like nanocages and nanoclusters. To discover a possible novel sensor platform involving a small metal cluster and a curved rigid substrate, we used density functional theoretical (DFT) simulations to explore the adsorption of glycoluril (GLC), a prospective drug intermediate, on a pure magnesium oxide cage (Mg12O12). This well defined cage was used as (i) an exact probable structure that could be used as well as (ii) a general model for MgO nanostructures. We also investigated the mono Al-doped Mg12O12 nanocage version Mg11AlO12. All computations were performed at the M06-2X level of theory. The GLC binds to the Mg12O12 nanocage by way of strong donor-acceptor interactions. The adsorption is releasing - 45.80 kcal mol-1 of energy. Due to Al doping, the energy gap of GLC-Mg11AlO12 (1.91 eV) is reduced from that of GLC-Mg12O12 (4.28 eV) and hence there is an increase in electrical conductivity of GLC-Mg11AlO12. The electronic change in the nanocage's conductivity can be transformed into an electrical signal which can be used to detect the presence of the drug analyte. In addition, when a GLC molecule is present, the work function of the nanocage is also reduced. The MgO nanocage, we conclude, is a work function type as well as a possible electronic sensor for GLC drug detection. GLC desorption from the Mg11AlO12 surface recovers more quickly in comparison with Mg12O12 recovery time. The AIM and NCIs assessed in this study were performed to help analyze the electronic structures of the complexes. Our findings pave the possibility for Mg11AlO12 nanostructures to be used in drug recognition.
Collapse
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.
| | | | | | - Nivedita Acharjee
- Department of Chemistry, Durgapur Government College, District-Paschim Bardhaman, Durgapur, West Bengal, India
| | - David G Churchill
- Department of Chemistry, Molecular Logic Gate Laboratory, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea. .,Therapeutic Bioengineering Section, KAIST Institute for Health Science and Technology (KIHST), Daejeon, Republic of Korea.
| |
Collapse
|
6
|
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]
|
7
|
Ullah Z, Mustafa B, Kim HJ, Sheena Mary Y, Shyma Mary Y, Kwon HW. DFT of 5-Fluoro-2-Oxo-1H-Pyrazine-3-Carboxamide (OPC) Adsorption, Spectroscopic, Solvent Effect, and SERS Analysis. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119076] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
|
8
|
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.
Collapse
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
| |
Collapse
|
9
|
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.
Collapse
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
| |
Collapse
|
10
|
Theoretical investigation on the adsorption of melamine in Al12/B12-N12/P12 fullerene-like nanocages: a platform for ultrasensitive detection of melamine. CHEMICAL PAPERS 2021. [DOI: 10.1007/s11696-021-01849-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
|
11
|
Jodeh S, Erman I, Hamed O, Massad Y, Hanbali G, Samhan S, Dagdag O, Kaya S, Serdaroğlu G. Zeolite/Cellulose Acetate (ZCA) in Blend Fiber for Adsorption of Erythromycin Residue From Pharmaceutical Wastewater: Experimental and Theoretical Study. Front Chem 2021; 9:709600. [PMID: 34336793 PMCID: PMC8316859 DOI: 10.3389/fchem.2021.709600] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 06/18/2021] [Indexed: 01/21/2023] Open
Abstract
The expanding amount of remaining drug substances in wastewater adversely affects both the climate and human well-being. In the current investigation, we developed new cellulose acetic acid derivation/zeolite fiber as an effective technique to eliminate erythromycin (ERY) from wastewater. The number of interchangeable sites in the adsorbent structures and the ratio of ERY to the three adsorbents were identified as the main reasons for the reduction in adsorption as the initial ERY concentrations increased. Additionally, for all adsorbents, the pseudo–second-order modeling showed better fitting for the adsorption than the pseudo–first-order modeling. However, the findings obtained in the pseudo–first-order model were still enough for explaining the sorption kinetics of ERY, showing that the surface displayed all chemisorption and physi-sorption adsorption processes by both adsorbents. The R2 for the second order was very close to 1 for the three adsorbents in the case of pseudo–second-order. The adsorption capacity reached 17.76 mg/g. The three adsorbents showed negative values of ΔH, and these values were −6,200, −8,500, and −9600 kJ/mol for zeolite, CA, and ZCA, respectively, and this shows that the adsorption is exothermic. The desorption analysis shows no substantial loss of adsorption site after three trials, indicating higher stability and resilience of the three adsorbents, indicating a strong repeatability of their possible use in adsorption without contaminating the environment. In addition, the chemical attitude and possible donor–acceptor interactions of ERY were assessed by the quantum chemical parameters (QCPs) and NBO analysis performed, at the HF/6-311G** calculations.
Collapse
Affiliation(s)
- Shehdeh Jodeh
- Department of Chemistry, Faculty of Science, An-Najah National University, Nablus, Palestine
| | - Israa Erman
- Department of Chemistry, Faculty of Science, An-Najah National University, Nablus, Palestine
| | - Othman Hamed
- Department of Chemistry, Faculty of Science, An-Najah National University, Nablus, Palestine
| | - Younes Massad
- Department of Chemistry, Faculty of Science, An-Najah National University, Nablus, Palestine
| | - Ghadir Hanbali
- Department of Chemistry, Faculty of Science, An-Najah National University, Nablus, Palestine
| | - Subhi Samhan
- Palestinian Water Authority, Ramallah, Palestine
| | - Omar Dagdag
- Laboratory of Agroresources, Polymers and Process Engineering (LAPPE), Department of Chemistry, Faculty of Science, Ibn Tofail University, Kenitra, Morocco
| | - Savaş Kaya
- Department of Pharmacy, Health Services Vocational School, Sivas Cumhuriyet University, Sivas, Turkey
| | - Goncagül Serdaroğlu
- Mathematics and Science Education, Sivas Cumhuriyet University, Sivas, Turkey
| |
Collapse
|