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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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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.
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Physicochemical investigation of mercury sorption on mesoporous thioacetamide/chitosan from wastewater. CHEMOSPHERE 2023; 341:140062. [PMID: 37689155 DOI: 10.1016/j.chemosphere.2023.140062] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 08/24/2023] [Accepted: 09/02/2023] [Indexed: 09/11/2023]
Abstract
Mercury is a toxic environmental element, so it was necessary to prepare a new, highly efficient, cheap sorbent to remove it. A mesoporous thioacetamide/chitosan (MTA/CS) was manufactured via a simplistic strategy; the chitin deacetylation to gain chitosan (CS) and the addition of thioacetamide. The as-prepared MTA/CS was characterized using X-ray diffraction, EDX, SEM, FTIR, and BET surface analysis. According to the findings, the MTA/CS was effectively synthesized. The removal behaviors of Hg2+ onto MTA/CS composite were inspected, which suggested that the MTA/CS composite exhibited great sorption properties for Hg2+ in liquid solutions. The maximal Hg2+ sorption capacity was 195 mg/g. The effects of temperature, Hg2+ concentration, contacting time, and MTA/CS concentration on sorption were analyzed. The 2nd-order model and Langmuir isotherm were suitable for the physicochemical adsorption processes. Thermodynamic analysis showed that the Hg2+ adsorption process onto the MTA/CS composite is exothermic and occurred spontaneously. The desorption condition of Hg2+ from its loaded MTA/CS was also gained. Likewise, the MTA/CS sorbent was undoubtedly regenerated by 0.8 M NaNO3 80 min contacting and 1:50 S:L ratio. The versatility and durability of MTA/CS sorbent were investigated via nine sorption-extraction cycles. The optimum parameters were applied to wastewater. Based on the result, the as-prepared MTA/CS might be a potential sorbent for removing Hg2+ from liquid solutions.
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DFT, ADME studies and evaluation of the binding with HSA and MAO-B inhibitory potential of protoberberine alkaloids from Guatteria friesiana: theoretical insights of promising candidates for the treatment of Parkinson's disease. J Mol Model 2023; 29:353. [PMID: 37907772 DOI: 10.1007/s00894-023-05756-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 10/13/2023] [Indexed: 11/02/2023]
Abstract
CONTEXT Parkinson's disease is a chronic neurodegenerative condition that has no cure, characterized by the progressive degeneration of specific brain cells responsible for producing dopamine, a crucial neurotransmitter for controlling movement and muscle coordination. Parkinson's disease is estimated to affect around 1% of the world's population over the age of 60, but it can be diagnosed at younger ages. One of the treatment strategies for Parkinson's disease involves the use of drugs that aim to increase dopamine levels or simulate the action of dopamine in the brain. A class of commonly prescribed drugs are the so-called monoamine oxidase B (MAO-B) inhibitors due to the fact that this enzyme is responsible for metabolizing dopamine, thus reducing its levels in the brain. Studies have shown that berberine-derived alkaloids have the ability to selectively inhibit MAO-B activity, resulting in increased dopamine availability in the brain. In this context, berberine derivatives 13-hydroxy-discretinine and 7,8-dihydro-8-hydroxypalmatine, isolated from Guatteria friesiana, were evaluated via density functional theory followed by ADME studies, docking and molecular dynamic simulations with MAO-B, aiming to evaluate their anti-Parkinson potential, which have not been reported yet. Docking simulations with HSA were carried out aiming to evaluate the transport of these molecules through the circulatory system. METHODS The 3D structures of the berberine-derived alkaloids were modeled via the DFT approach at B3LYP-D3(BJ)/6-311 + + G(2df, 2pd) theory level using Gaussian 09 software. Solvation free energies were determined through Truhlar's solvation model. MEP and ALIE maps were generated with Multiwfn software. Autodock Vina software was used for molecular docking simulations and analysis of the interactions in the binding sites. The 3D structure of MAO-B was obtained from the Protein Data Bank website under PDB code 2V5Z. For the interaction of studied alkaloids with human serum albumin (HSA) drug sites, 3D structures with PDB codes 2BXD, 2BXG, and 4L9K were used. Molecular dynamics simulations were carried out using GROMACS 2019.4 software, with the GROMOS 53A6 force field at 100 ns simulation time. The estimation of the ligand's binding free energies was obtained via molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) method.
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DFT analysis on the adsorption of melamine in Ga 12-N 12/P 12 nanocages: solvent effects, SERS analysis, reactivity properties. J Biomol Struct Dyn 2023; 41:8844-8855. [PMID: 36300533 DOI: 10.1080/07391102.2022.2137700] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 10/14/2022] [Indexed: 10/31/2022]
Abstract
Due to its negative effects on people, melamine contamination in food products are detected and filtered. Amongst several sensory schemes for the screening of melamine poisoning, one of the most promising techniques is the use of nanomaterial based sensing for real time applicability in industries. In the current work, we have looked into the way melamine binds to Ga12-N12/P12 nanocages. Surface-enhanced Raman scattering (SERS), a successful spectroscopic technique is used to monitor melamine. Density functional theoretical (DFT) computations were used to study the sensing properties of melamine (Me) with Ga12-N12/P12 nanocages. Reactivity and Mulliken charge analyses show charge transfer from melamine to nanocage. Me-Ga12-N12 and Me-Ga12P12 clusters have adsorption energies of -47.54 and -33.12 kcal/mol, respectively. All nanocage-Me systems have a significant increase in polarizability. The electron densities revealed non-covalent interactions in the adsorbed systems. All adsorption energies in aqueous media are negative, indicating an attractive and exothermic reaction, with maximum value in water for Me-Ga12N12 and in acetone for Me-Ga12P12. Evidence of SERS is observed due to the enhancement of different vibrational modes.Communicated by Ramaswamy H. Sarma.
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TD-DFT, DFT, docking, MD simulations, and concentration-dependent SERS investigations of a bioactive trifluoromethyl derivative having human acetylcholinesterase and butyrylcholinesterase in silver colloids. J Mol Model 2023; 29:271. [PMID: 37535185 DOI: 10.1007/s00894-023-05679-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 07/26/2023] [Indexed: 08/04/2023]
Abstract
CONTEXT Various concentrations of (E)-4-methoxy-N'-(2-(trifluoromethyl)benzylidene) benzohydrazide (EMT) adsorbed on colloidal silver nanoparticles were studied using SERS and results were compared to the normal Raman spectrum. DFT calculations were used to validate experimental findings. Theoretically, the structures of the EMT and EMT-Ag6 systems were optimized. The UV-Vis spectral analysis's red shift and lower intensity behavior show that EMT has chemisorbed onto Ag nanoparticles. Charge transfer (CT) from Ag to EMT is highlighted by FMO analysis. The CT interaction in EMT and EMT-Ag6 was further verified by MEP and Mulliken charge analyses. The EMT was adsorbed on Ag nanoparticles with tilted orientation and orientation changes with colloidal concentration, according to SERS spectrum analysis. Docking EMT with 4PQE and 5DYW binding affinities are found to be -9.7 and -8.1 kcal/mol. MD simulations give the competence of 5DYW-EMT and 4PQE-EMT in their intended binding interactions and their ability to establish enduring associations with the protein of interest. METHODS DFT was used to optimize the molecular structures of EMT and EMT-Ag6 using B3LYP/6-311++G* (LANL2DZ basis set for Ag). A molecular dynamics simulation study was conducted on the 4PQE-EMT and 5DYW-EMT systems using the Desmond software for 100 ns.
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Correction: Evidences of noncovalent interactions between indole and dichloromethane under different solvent conditions. J Mol Model 2023; 29:264. [PMID: 37498377 DOI: 10.1007/s00894-023-05676-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/28/2023]
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Evidences of noncovalent interactions between indole and dichloromethane under different solvent conditions. J Mol Model 2023; 29:246. [PMID: 37442832 DOI: 10.1007/s00894-023-05623-3] [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: 04/22/2023] [Accepted: 06/14/2023] [Indexed: 07/15/2023]
Abstract
CONTEXT Theoretical investigation of indole (IND) and its binary combination with dichloromethane (DC) in various solvents were computed to track the impact of molecular interactions on spectral characteristics. When transitioning from plain drug to complexes, different modes of IND display a substantial shift in peak location. The 3561.26 cm-1 band shows (~15.58 cm-1) red shift upon dilution. The geometry in various solvents was calculated using quantum chemical calculation utilizing density functional theory (DFT). The highest ALIE values are located at the indole skeleton and on complexation with DC, and the ring atoms become more electron rich. The atom-centered density matrix propagation (ADMP) molecular dynamic (MD) calculation shows that the geometries optimized through the DFT calculation match the global minima effectively. MD simulations indicate that indole is more stable in water and methanol. METHODS DFT studies have been employed to study the interaction between indole and dichloromethane. CAM-B3LYP/6-311++G(d)(6D,7F) level of theory was employed using Gaussian 16 W suite. Quantum topological descriptors were discussed using quantum theory of atoms in molecules (QTAIM) with the help of Multiwfn software. Reduced density gradient (RDG) plot describes the nature of the interaction, while average local ionization energy (ALIE) explained the variation in local ionization energy of the molecular surface before and after complexation.
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DFT, TD-DFT and SERS analysis of a bioactive benzohydrazide’s adsorption in silver hydrosols at various concentrations. J Mol Liq 2023. [DOI: 10.1016/j.molliq.2023.121243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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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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Structural, Spectral, Molecular Docking, and Molecular Dynamics Simulations of Phenylthiophene-2-Carboxylate Compounds as Potential Anticancer Agents. Polycycl Aromat Compd 2023. [DOI: 10.1080/10406638.2023.2172052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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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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Modeling the structure and reactivity landscapes of a pyrazole-ammonium ionic derivative using wavefunction-dependent characteristics and screening for potential anti-inflammatory activity. J Biomol Struct Dyn 2022; 40:11190-11202. [PMID: 34328395 DOI: 10.1080/07391102.2021.1957020] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Spectroscopic investigations of 1-phenyl -2,3-dimethyl-5-oxo-1,2-dihydro-1H-pyrazol-4-ammonium 2[(2-carboxyphenyl) disulfanyl]benzoate (PACB) reported experimentally and theoretically. NH-O interaction is observed and there is a very large downshift for NH-O stretching frequency. Reactive sites are identified from the chemical and electronic properties. For PACB the maximum repulsion was around H33, H55 and H57 atom. LOL shows red regions between C-C and blue around C atoms are surrounded by a delocalized electron cloud. The red ring is a hallmark of electron density depletion from the NCI plot due to electrostatic repulsion and its existences suggests that coordination sphere for PACB is minimally strained around the central ion. Atomic contact energy values and high score of the docking results obtained propose that, PACB may have inhibitory properties and have a significant function in pharmacological chemistry. Molecular dynamics simulation was performed to validate the stability of the title compound with the Bovine thrombin-activatable fibrinolysis inhibitor protein.Communicated by Ramaswamy H. Sarma.
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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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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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Synthesis, crystal structure and anti-tumour activity studies of 4- Tertiarybutylcyclohexanonethiosemicarbazone. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Solvation Effects, Reactivity Studies and Molecular Dynamics of Two Phosphonic Acids – Theoretical Investigation. Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2126504] [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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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.
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Insights into solvation effects, spectroscopic, Hirshfeld surface Analysis, reactivity analysis and anti-Covid-19 ability of doxylamine succinate: Experimental, DFT, MD and docking simulations. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119609] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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Spectroscopic analyses on an azatricycloderivative by DFT with different solvents, reactivity analysis and MD simulations. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.132845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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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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Physico-chemical characterizations and biological evaluation of a new semiconducting metal–organic compound based on pyrimidine frameworks. INORG CHEM COMMUN 2022. [DOI: 10.1016/j.inoche.2022.109279] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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DFT and MD investigations of the biomolecules of phenothiazine derivatives: interactions with gold and water molecules and investigations in search of effective drug for SARS-CoV-2. J Biomol Struct Dyn 2022:1-12. [PMID: 35470781 DOI: 10.1080/07391102.2022.2068649] [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] [Indexed: 01/18/2023]
Abstract
Theoretical analyses of two phenothiazine derivatives, 10-[3-(dimethylamino)-2-methylpropyl]phenothiazine-2-carbonitrile (CYM) and 2-[4-[3-(2-chlorophenothiazin-10-yl)propyl]piperazin-1-yl]ethanol (PAZ) are reported using density functional theory (DFT) and molecular dynamics (MD) simulations. Spectroscopic studies, different electronic and chemical parameters are predicted. Red and yellow in electrostatic potential plot is in rings and oxygen atom in PAZ and C≡N and rings in CYM are sensitive to nucleophilic attacks. The blue in hydrogen atoms refer to electrophilic attack in both PAZ and CYM. Stability of the protein-ligand complex formed with these derivatives and angiotensin-converting enzyme 2 (ACE2) was investigated using MD simulation. Radius of gyration of C-alpha atom of 6VW1 displayed the conformational convergence toward a compact structure leading to stable 6VW1-ligand complex which are also in agreement with root mean square fluctuation (RMSF) values. Localized area predicts reactive sites for Au and H2O molecules interaction with these compounds for further practical applications. Charge density is localized on both molecules and also tries to move toward Au-Au dimer and water molecule and such they are expected to contribute to the sensing performance. Communicated by Ramaswamy H. Sarma.
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Insights into solvation, chemical reactivity, structural, vibrational and anti-hypertensive properties of a thiazolopyrimidine derivative by DFT and MD simulations. Struct Chem 2022. [DOI: 10.1007/s11224-022-01931-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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Theoretical and experimental investigation of a pyrazole derivative- solvation effects, reactivity analysis and MD simulations. Chem Phys Lett 2022. [DOI: 10.1016/j.cplett.2022.139469] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Electronic Structure, Solvation Effects and Wave Function Based Properties of a New Triazole Based Symmetric Chromene Derivative of Apigenin. Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2055583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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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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Adsorption properties of dacarbazine with graphene/fullerene/metal nanocages - Reactivity, spectroscopic and SERS analysis. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 268:120677. [PMID: 34872861 DOI: 10.1016/j.saa.2021.120677] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 10/26/2021] [Accepted: 11/26/2021] [Indexed: 06/13/2023]
Abstract
Drug delivery devices are an effective way to minimize anticancer drug toxicity and nanostructures are used in the targeted drug delivery. In the present work, adsorption and interaction behavior of 4-(dimethylaminodiazenyl)-1H-imidazole-5-carboxamide (DAIC) with nano complexes (graphene, fullerene and fullerene like metal cages) are reported theoretically. From the reactivity studies, the electrophilicity index of DAIC-nanoclusters are increasing and this gives the bioactivity of the nanocluster systems. Adsorption energy is highest in the case of AlP and lowest in the case of BP clusters. Mulliken charge distribution of all systems is an evidence for chemical enhancement. DAIC adsorption over nanocages causes changes in electronic properties resulting in chemical enhancement and variation in Raman spectra which suggests that nanocages could be a good candidate for DAIC detection.
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Cetylpyridinium Bromide/Polyvinyl Chloride for Substantially Efficient Capture of Rare Earth Elements from Chloride Solution. Polymers (Basel) 2022; 14:polym14050954. [PMID: 35267777 PMCID: PMC8912479 DOI: 10.3390/polym14050954] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 02/17/2022] [Accepted: 02/24/2022] [Indexed: 12/04/2022] Open
Abstract
A new sorbent cetylpyridinium bromide/polyvinylchloride (CPB/PVC) was prepared and tested to extract rare earth elements (REEs) from their chloride solutions. It was identified by FTIR, TGA, SEM, EDX, and XRD. The impact of various factors such as pH, RE ion initial concentration, contacting time, and dose amount via sorption process was inspected. The optimum pH was 6.0, and the equilibrium contact time was reached at 60 min at 25 °C. The prepared adsorbent (CPB/PVC) uptake capacity was 182.6 mg/g. The adsorption of RE ions onto the CPB/PVC sorbent was found to fit the Langmuir isotherm as well as pseudo-second-order models well. In addition, the thermodynamic parameters of RE ion sorption were found to be exothermic and spontaneous. The desorption of RE ions from the loaded CPB/PVC sorbent was investigated. It was observed that the optimum desorption was achieved at 1.0 M HCl for 60 min contact time at ambient room temperature and a 1:60 solid: liquid phase ratio (S:L). As a result, the prepared CPB/PVC sorbent was recognized as a competitor sorbent for REEs.
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Quantum Mechanical Investigation into the Adsorption Pattern of Clomipramine and Methotrimeprazine HCl with Graphene and Fullerene. Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2041678] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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Chitosan Functionalized with Carboxyl Groups as a Recyclable Biomaterial for the Adsorption of Cu (II) and Zn (II) Ions in Aqueous Media. Int J Mol Sci 2022; 23:ijms23042396. [PMID: 35216511 PMCID: PMC8875004 DOI: 10.3390/ijms23042396] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Revised: 02/13/2022] [Accepted: 02/14/2022] [Indexed: 12/20/2022] Open
Abstract
The modification of chitosan represents a challenging task in obtaining biopolymeric materials with enhanced removal capacity for heavy metals. In the present work, the adsorption characteristics of chitosan modified with carboxyl groups (CTS-CAA) towards copper (II) and zinc (II) ions have been tested. The efficacy of the synthesis of CTS-CAA has been evaluated by studying various properties of the modified chitosan. Specifically, the functionalized chitosan has been characterized by using several techniques, including thermal analyses (differential scanning calorimetry and thermogravimetry), spectroscopies (FT-IR, XRD), elemental analysis, and scanning electron microscopy. The kinetics and the adsorption isotherms of CTS-CAA towards both Cu (II) and Zn (II) have been determined in the aqueous solvent under variable pH. The obtained results have been analyzed by using different adsorption models. In addition, the experiments have been conducted at variable temperatures to explore the thermodynamics of the adsorption process. The regeneration of CTS-CAA has been investigated by studying the desorption process using different eluents. This paper reports an efficient protocol to synthesize chitosan-based material perspective as regenerative adsorbents for heavy metals.
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Computational Studies, GERS, Photovoltaic Modelling and Molecular Docking Studies of Diethylstilbestrol and Its Methyl Ether. Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2038219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Conformational, Reactivity Analysis, Wavefunction-Based Properties, Molecular Docking and Simulations of a Benzamide Derivative with Potential Antitumor Activity-DFT and MD Simulations. Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2039229] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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DFT Conformational, Wavefunction Based Reactivity Analysis, Docking and MD Simulations of a Carboxamide Derivative with Potential Anticancer Activity. Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2032765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Theoretical Insights into the Solvation, Electronic, Chemical Properties and Molecular Docking of Some Thiazole Derivatives. Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2030767] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Evidence of cluster formation of croconic acid with Ag, Au and Cu cages, enhancement of electronic properties and Raman activity. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 264:120233. [PMID: 34358780 DOI: 10.1016/j.saa.2021.120233] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 07/21/2021] [Accepted: 07/25/2021] [Indexed: 06/13/2023]
Abstract
Investigation of the adsorption properties croconic acid (CCA) with metal clusters (mC: Ag, Au and Cu) are reported using DFT method. CCA is found to form stable cluster with transition metal clusters of copper, silver and gold. The drug-cluster complexaton energy is slightly more for the copper nanocluster-drug complex. Non-covalent interaction analysis indicated that strong interactions and weak van der Waal interaction is present between drug and metal clusters. Dipole moment of the drug-gold cluster is found to be higher than that of the other systems. SERS studies demonstrates improved Raman signals for multiple wavenumbers of all CCA-metal cluster complexes. Mulliken charge analysis show that all CCA oxygen atom's charge changes due to the interactions with the mCs. Clustering of CCA with metal cages enhances the medicinal properties and the metal nanoclusters will act as a drug carrier of CCA.
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Adsorption behavior and solvent effects of an adamantane-triazole derivative on metal clusters – DFT simulation studies. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2021.118242] [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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Exploring the Detailed Spectroscopic Characteristics, Chemical and Biological Activity of Three Pyrone Derivatives Using Experimental and Theoretical Tools. Polycycl Aromat Compd 2021. [DOI: 10.1080/10406638.2021.2020136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Structural and reactivity studies of pravadoline –An ionic liquid, with reference to its wavefunction-relative properties using DFT and MD simulation. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.131074] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Computational Evaluation of Molecular Structures and Spectroscopic Properties of Tryptamine Derivatives on Its Binding With Novel Corona Virus Proteins. Polycycl Aromat Compd 2021. [DOI: 10.1080/10406638.2021.2006248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Concentration-dependent SERS profile of olanzapine on silver and silver-gold metallic substrates. CHEMICAL PAPERS 2021. [DOI: 10.1007/s11696-021-01783-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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DFT computational study of trihalogenated aniline derivative's adsorption onto graphene/fullerene/fullerene-like nanocages, X 12Y 12 (X = Al, B, and Y = N, P). J Biomol Struct Dyn 2021; 40:8630-8643. [PMID: 33876711 DOI: 10.1080/07391102.2021.1914172] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Adsorption of 2,4,6-tribromoaniline (BA), 2,4,6-trifluoroaniline (FA) and 2,4,6-trichloroaniline (CA) onto the surface of coronene/fullerene/fullerene-like nanocages was investigated by theoretical calculations. Due to the adsorption of BA/FA/CA, there are significant changes in chemical descriptors and nonlinear optical properties. Energy gap values of all nanoclusters are lowered, giving an increase in conductivity of complexes except for fullerene. All complex's ultraviolet visible wavenumber is blue-shifted and especially for fullerene complex, the values are very high. The enhancement of Raman intensities shows that it is possible to design a nanocage sensor for detecting these compounds by surface-enhanced Raman scattering (SERS).Communicated by Ramaswamy H. Sarma.
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Adsorption of adipic acid in Al/B-N/P nanocages: DFT investigations. J Mol Model 2021; 27:113. [PMID: 33765215 DOI: 10.1007/s00894-021-04742-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 03/15/2021] [Indexed: 02/07/2023]
Abstract
Drug delivery clusters based on nanocages recently have been the most capable to study. Adipic acid (ADPA) interaction mechanism over nanocages of X(Al/B)12Y(N/P)12 was investigated. We analyzed various electronic, chemical, and spectroscopic properties with nanocages of the adsorbed ADPA molecule. Adsorption energies were calculated to study the adsorption of ADPA with nanocages. Raman enhanced surface scattering is used to track the drug as an effective approach to vibrational spectroscopy. Detection of the drug has been investigated using the SERS properties of nanocages. Title drug acts as a donor of electrons and adsorbs at the electrophilic site of nanocages. Variations in chemical descriptors to recognize the sensing property of ADPA-nanocages are also noted. Analysis of various properties explains enhancement which makes it possible to detect the drug in other products. • Interaction of adipic acid with fullerene-like metal nanocages • Enhancement of spectral properties • Changes in charge transfer values in nanocage-drug system • Docking studies identify the drug delivery property.
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Ab initio-based kinetics of hydrogen atom abstraction from methyl propionate by H and CH3 radicals: a biodiesel model. Struct Chem 2021. [DOI: 10.1007/s11224-021-01746-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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DFT computational study towards investigating psychotropic drugs, promazine and trifluoperazine adsorption on graphene, fullerene and carbon cyclic ring nanoclusters. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 246:119012. [PMID: 33039847 DOI: 10.1016/j.saa.2020.119012] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 09/05/2020] [Accepted: 09/23/2020] [Indexed: 06/11/2023]
Abstract
Detection and qualification process related to impurities assume importance in pharmacological drug development programmes and the present article gives the structural and spectral characterisation of phenothiazine derivatives, promazine (PME) and trifluoperazine (TPE) and their self-assembly with graphene/fullerene/carbon ring (CG/CF/CR) systems theoretically. The investigation of adsorption behaviour of these compounds can provide valuable information about its reactivity, electronic and structural properties. Three-dimensional electrostatic potential diagrams were mapped. The frontier orbital energies and energy band gaps of the molecules were computed. Delocalization of charge density between the bonding or lone pair and antibonding orbitals is calculated by NBO analysis. Docking was executed to investigate binding areas of chemical compounds. Bioactivity scores show that the pharmacokinetic and pharmacological properties of the ligands are appropriate leading to be considered potential drug agents. The obtained theoretical wavenumber results of the present study were fully compatible with the experimental results.
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Utilization of O/S-doped graphene nanoclusters for ultrasensitive detection of flurane derivatives-DFT investigations. J Biomol Struct Dyn 2021; 40:5320-5327. [PMID: 33410367 DOI: 10.1080/07391102.2020.1870155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Nanocluster based drug delivery systems are very useful in modern medical treatment and interaction mechanism of desflurane (DES), isoflurane ISO), sevoflurane (SEV) over carboxyl substituted graphene-doped with O and S atoms were investigated in the present study. Different electronic and chemical properties of adsorbed desflurane, isoflurane and sevoflurane with nanoclusters are analyzed. To track the drugs, SERS is used as an efficient method and drug's detection was analyzed using SERS. DES's energy over GQD-S is greater than that over GQD-O nanocluster and for ISO and SEV, adsorption energies over the O/S nanoclusters are same. The title drugs work on the reactives sites and got adsorbed. For ISO, there is an increase in fluorine atom charges and for DES and SEV, the fluorine atom charge decreases due to adsorption in both O/S nanoclusters. Changes in chemical descriptors are identified for the sensing property of drug-nanoclusters.Communicated by Ramaswamy H. Sarma.
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Modeling the Conformational Preference, Spectral Analysis and Other Quantum Mechanical Studies on Three Bioactive Aminobenzoate Derivatives and Their SERS Active Graphene Complexes. Polycycl Aromat Compd 2020. [DOI: 10.1080/10406638.2020.1827270] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Comprehensive quantum mechanical studies on three bioactive anastrozole based triazole analogues and their SERS active graphene complex. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2020.128388] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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Spectral analysis and detailed quantum mechanical investigation of some acetanilide analogues and their self-assemblies with graphene and fullerene. J Mol Model 2020; 26:254. [PMID: 32876867 DOI: 10.1007/s00894-020-04485-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 07/21/2020] [Indexed: 01/21/2023]
Abstract
Spectroscopic analysis and different quantum mechanical studies of four pharmaceutically active compounds phenacetin, p-acetanisidide, 4'-butoxyacetanilide, and 4'-(3-chloropropoxy)acetanilide are reported in this manuscript. Simulated IR spectrum of these compounds was compared with experimentally available data, and essential functional group assignments were made. We also report the frontier orbital properties and other derived local energy descriptors which talks about the relative stability and reactivity. Photovoltaic efficiency of the compounds was studied from the simulated electronic spectra. The compound was found to interact with graphene and fullerene, to form molecular self-assembly. These self-assemblies showed tremendous enhancement in various physicochemical properties when compared with its constituents. The nature of the interactions between studied chemical species was discussed with the help of chemical reactivity principles. Biological activity of the compounds was predicted using molecular docking studies. It is interesting to see that on adsorption with a graphene/fullerene surface, all adsorbed complex shows enhancement in the Raman activity giving surface enhanced Raman spectra (SERS). This can be used for the detection of these drugs in a pharmacological or biological sample. Interestingly the graphene/fullerene drug molecular assembly shows enhanced biological activity when compared with individual drug molecules. Graphical abstract.
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Structural study of letrozole and metronidazole and formation of self-assembly with graphene and fullerene with the enhancement of physical, chemical and biological activities. J Biomol Struct Dyn 2020; 39:5509-5515. [PMID: 32657232 DOI: 10.1080/07391102.2020.1790420] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Letrozole and metronidazole are two commonly used drugs for the management of breast cancer and parasitic infections, respectively. This manuscript attempts to study their structure, geometry, search for stable conformers using relaxed potential energy scan, spectral properties, quantum mechanical properties like energy and reactivity descriptors, intra molecular electron transfer properties, non-linear properties etc using various computational tools. It is found that these compounds will form a self-assembly with graphene sheets and fullerenes and exhibit a surface-enhanced Raman spectra and enhancement in non-linear optical properties when compared to the single molecule. The electronic absorption behavior of the compounds was studied using TD-DFT method. Global chemical reactivity descriptors and activity sites toward electrophilic and nucleophilic attack have been discussed. Studies of intra molecular electron transfer gave information about the relative stability of the compounds. Molecular docking studies indicate that the pure compounds and their self-assemblies with graphene have excellent biological activities.Communicated by Ramaswamy H. Sarma.
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