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Öğe Adsorption of adipic acid in Al/B-N/P nanocages: DFT investigations(Springer, 2021) Al-Otaibi, Jamelah S.; Mary, Y. Sheena; Mary, Y. Shyma; Serdaroglu, GoncagulDrug 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.Öğe Biological perspective of a triazine derivative with isatin/chalcone/acridone: DFT and docking investigations(Springer/Plenum Publishers, 2021) Mary, Y. Sheena; Mary, Y. Shyma; Ciltas, Arzuhan CetindagThe article highlights insights into biological activity using computational methods in products of 1,3,5-triazine-2,4-diamine with 1H-indole-2,3-dione (isatin)/(2E)-13-diphenylprop-2-en-1-one (chalcone)/10H-acridin-9-one (acridone). Biological activity is carried out using the method of electron density, 6-311++G(d,p) for molecular and electronic characteristics. Frontier molecular orbitals provide quantum mechanical descriptors to determine electronic properties. Studies show reduced energy gap with high kinetic stability and the index of electrophilicity is a consequence of delocalized sites of 1,3,5-triazine-2,4-diamine and nucleophilic sites are responsible for biological activity. Enhancement in electrophilicity index of products confirms electron acceptor between the reactants. The structural and molecular docking with different proteins shows that the product molecules are good drugs for the corresponding activity.Öğe A complete computational and spectroscopic study of 2-bromo-1, 4-dichlorobenzene - A frequently used benzene derivative(ELSEVIER SCIENCE BV, 2018) Vennila, P.; Govindaraju, M.; Venkatesh, G.; Kamal, C.; Mary, Y. Sheena; Panicker, C. Yohannan; Kaya, S.; Armakovic, Stevan; Armakovic, Sanja J.The coupled experimental and theoretical vibrational investigation of 2-bromo-1, 4-dichlorobenzene (BDB) molecule has been carried out and they have been duly compared with standard values in order to produce the reliability of the results. Results of DFT analysis carried out using B3LYP functional with 6-31 + G/6-311++G (d,p) basis set revealed that BDB has higher electronic density. The molecular geometry,C-13 & H-1 Nuclear Magnetic Resonance (NMR), Natural Bond Orbital (NBO) and Natural Atomic Charge analyses have been obtained by OFT calculations. Nonlinear optical (NLO) properties, quantum chemical descriptors and first order hyperpolarizability have been calculated. In addition, Local reactivity properties reflected through average local ionization energies (ALIE), Fukui functions and bond dissociation energies have also been investigated. Besides investigation of docking properties, molecular dynamics simulations were also taken in account with a view to identify atoms that have relatively important interactions with water molecules. The title compound forms a stable complex with isopentenylpyrophosphate transferase with a binding affinity value as -4.6 kCal./Mol. and shows inhibitory activity against isopentenylpyrophosphate transferase. (C) 2017 Published by Elsevier B.V.Öğe Conformational analysis and DFT investigations of two triazole derivatives and its halogenated substitution by using spectroscopy, AIM and Molecular docking(Elsevier B.V., 2021) Kumar, Veena S.; Mary, Y. Sheena; Mary, Y. Shyma; Serdaroğlu, Goncagül; Rad, Ali Shokuhi; Roxy, M.S.; Manjula, P.S.4-[(E)-(4-Hydroxybenzylidene)amino]-3-(4-chlorobenzyl)-1H-1,2,4-triazole-5(4H) -thione (HTH) and 4-[(E)-(4-Hydroxybenzylidene)amino]-3-(2-chlorobenzyl)-1H-1,2,4-triazole-5(4H)-thione (HAC) were synthesized and characterized using spectral analysis. The fundamental structural aspects of these derivatives have been examined based on optimized geometry, spectroscopic behavior, intermolecular interaction, chemical reactivity and molecular docking analysis. The most stable minimum energy conformer of the title molecules was identified by potential energy surface scan along the rotational bonds. QTAIM study has also been performed to investigate the nature and strength of hydrogen bonding interactions. Halogen substitution on the phenyl ring at different position's are studied. Accordingly global and local chemical reactivity descriptors were investigated. Docking predicts inhibitory activity against tuberculosis and prediction of new anti-TB drug possibility. © 2020 Elsevier B.V.Öğe Conformational analysis and quantum descriptors of two bifonazole derivatives of immense anti-tuber potential by using vibrational spectroscopy and molecular docking studies(Springer/Plenum Publishers, 2021) Mary, Y. Sheena; Mary, Y. Shyma; Serdaroglu, Goncagul; Sarojini, B. K.1-[([1,1(I)-Biphenyl]-4-yl](phenyl)methyl]-1H-imidazolium-2,5-dichloro-3,6-dihydroxy-cyclohexa-2,5-diene-1,4-dione (BCAA) and 1-[([1,1(I)-Biphenyl]-4-yl](phenyl)methyl]-1H-imidazolium-4,5-dichloro-3,6-dioxocyclohexa-1,4-diene-1,2-dicarbonitrile (BDDQ) were synthesized and characterized using spectral analysis. The fundamental structural aspects of these derivatives have been examined based on optimized geometry, spectroscopic behavior, intermolecular interaction, chemical reactivity, and molecular docking analysis. The most stable minimum energy conformer of the title molecules was identified by potential energy surface scan along the rotational bonds. Accordingly, global and local chemical reactivity descriptors were investigated. The wavenumber downshift of different modes is noted. Title molecules exhibit inhibitory activity against different receptors.Öğe Conformational analysis and quantum descriptors of two new imidazole derivatives by experimental, DFT, AIM, molecular docking studies and adsorption activity on graphene(Cell Press, 2020) Kumar, Veena S.; Mary, Y. Sheena; Pradhan, Kiran; Brahman, Dhiraj; Mary, Y. Shyma; Serdaroglu, Goncagul; Rad, Ali Shokuhi1-[2-(2-hydroxy-3-methoxy-5-(4-methoxyphenylazo)benzaldeneamino)ethyl]-3-methyl-3H-imidazole (HMY) and 1-[2-(2-hydroxy-3-methoxy-5-(4-methylphenylazo)benzaldene amino)ethyl]-3-methyl-3H-imidazole (HMM) were synthesized and characterized using spectral analysis. Conformational analysis has been achieved using potential energy scan for different rotable bonds for obtaining the lowest energy conformer. Conformer with minimum energy is obtained along the dihedral angle N30-C31-C34-N37. QTAIM analysis gives nature and strength of hydrogen bonding interactions. UV-Vis, electrostatic potential and chemical descriptors are analyzed. Interaction of HMY and HMM with graphene is analyzed in terms of SERS activity. Chemical reactivity descriptors were investigated for graphene-drug systems. NLO activity of parent drugs and its graphene complexes show good activity. The wavenumber downshift of different modes is noted. Title molecules exhibit inhibitory activity against cytochrome C peroxidase. Interactions with graphene sheets are theoretically predicted for the title compounds.Öğe Conformational Analysis, Spectroscopic Insights, Chemical Descriptors, ELF, LOL and Molecular Docking Studies of Potential Pyrimidine Derivative with Biological Activities(Taylor & Francis Ltd, 2022) Mary, Y. Sheena; Mary, Y. Shyma; Serdaroglu, Goncagul; Kaya, Savas; Sarojini, B. K.; Umamahesvari, H.; Mohan, B. J.The geometry, frontier molecular orbitals, chemical reactivity, vibrational, NBO analysis and molecular docking simulations of Ethyl -2-(4-propoxybenzylidene)-7-methyl-3-oxo-5-(4-benzyloxy phenyl)-2,3-dihydro-5H-[1, 3]thiazolo[3,2-a]pyrimidine-6-carboxylate (EBPC) have been extensively studied and discussed on DFT calculations. The stable structural conformational analysis has been achieved using potential energy scan for different rotable bonds. The lowest energy of the conformer was obtained from rotation along C2-C3-C26-O27. Electrostatic potential map, UV-Vis and chemical descriptors and drug-likeness properties are analyzed. Localization function and local orbital locator functions are also discussed. Charge delocalization patterns and second order perturbation energies of the most interacting natural bond orbitals have also been computed and predicted. Most of covalent region is in between blue circles around sulfur and few carbon, nitrogen atoms show that the electron depletion region. Docking binding affinities and the formation of a good number of hydrogen bonds suggests that the title compound appears to be a promising drug for the selected inhibitors.Öğe Detailed Electronic Structure, Physico-Chemical Properties, Excited State Properties, Virtual Bioactivity Screening and SERS Analysis of Three Guanine Based Antiviral Drugs Valacyclovir HCl Hydrate, Acyclovir and Ganciclovir(Taylor & Francis Ltd, 2022) Al-Otaibi, Jamelah S.; Mary, Y. Sheena; Thomas, Renjith; Kaya, SavasValacyclovir HCl hydrate, acyclovir and ganciclovir are three commonly used anti viral drugs which are guanidine derivatives with ether side chain and all of them act by interfering with the viral DNA production. This manuscript tries to examine the structure and properties of these three purine based compounds using electronic structure methods and molecular mechanics. Density functional theory was used to optimize the ground state geometry of the molecules from frontier molecular orbitals are analyzed using B3LYP functional. They give wealth of information about the electronic properties and descriptors, which will enable to predict the bioactivity of the molecules. As the electrons interact with electromagnetic radiations, electronic excitations between different energy levels are analyzed in detail using TD-DFT with CAM-B3LYP orbital. Calculations shows that they are with excellent light-harvesting efficiency hence be used as photo sensitizers. Molecular docking studies predict the biological activity of the molecules against ADP-thymidine kinase, hence inhibits its action, subsequently affecting the viral DNA production. It is interesting to see that on adsorption with a graphene quantum dot surface, all adsorbed complex show enhancement in the Raman activity giving Surface Enhanced Raman Spectra (SERS) when studied using dispersion force corrected omega-B97XD functional. This can be used for the detection of these drugs in a pharmacological or biological sample. Interestingly the graphene drug molecular assembly shows enhanced biological activity when compared to individual drug molecules.Öğe DFT computational study of trihalogenated aniline derivative's adsorption onto graphene/fullerene/fullerene-like nanocages, X12Y12 (X = Al, B, and Y = N, P)(Taylor & Francis Inc, 2022) Al-Otaibi, Jamelah S.; Mary, Y. Sheena; Mary, Y. Shyma; Kaya, Savas; Serdaroglu, GoncagulAdsorption 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).Öğe Modeling the DFT structural and reactivity studies of a pyrimidine-6-carboxylate derivative with reference to its wavefunction-dependent, MD simulations and evaluation for potential antimicrobial activity(Elsevier, 2021) Smitha, M.; Mary, Y. Sheena; Mary, Y. Shyma; Serdaroglu, Goncagul; Chowdhury, Papia; Rana, Meenakshi; Umamahesvari, H.Spectroscopic, electronic and chemical properties and molecular docking simulations of ethyl2-(4-ethoxybenzylidene)-7-methyl-3-oxo-5-(4-benzyloxyphenyl)-2,3-dihydro-5H-[1,3] thiazolo [3,2a]pyrimidine-6-carboxylate (EMTP) have been extensively studied and discussed on DFT calculations. Using potential energy scans for various rotable bonds to obtain the lowest energy conformer, conformational analysis was achieved. Electronic, chemical, and drug-likeness properties are analyzed. Charge delocalization patterns and second-order perturbation energies of the most interacting natural bond orbitals have also been computed and predicted from wavefunction analysis. To understand the interaction between receptor and inhibitor EMTP ligand drug, we have performed molecular docking and molecular dynamics (MD) simulations. Docking binding affinities and the formation of a good number of hydrogen bonds suggest that EMTP appears to be a promising drug for the selected inhibitors. ? 2021 Elsevier B.V. All rights reserved.Öğe Molecular dynamic simulations, ALIE surface, Fukui functions geometrical, molecular docking and vibrational spectra studies of tetra chloro p and m-xylene(ELSEVIER SCIENCE BV, 2018) Venkatesh, G.; Kamal, C.; Vennila, P.; Govindaraju, M.; Mary, Y. Sheena; Armakovic, Stevan; Armakovic, Sanja J.; Kaya, S.; Panicker, C. YohannanThe optimized molecular geometry, vibrational assessments, natural bond orbital (NBO) analyses for Tetra chloro p-xylene (TCPX) and Tetra chloro m-xylene (TCMX) were performed by B3LYP/6-311++G (d,p) functional. The experimental vibrational frequencies were compared with scaled vibrational wave numbers. Average local ionization energy (ALIE), Fukui functions and bond dissociation energies (BDE) were used to determine reactivity sites of TCPX and TCMX. BDE for hydrogen abstraction helped us to investigate the possibility for autoxidation mechanism of the investigated molecules. Molecular dynamics (MD) simulations were utilized to find out the exact atom of both TCPX and TCMX molecules have the tendency to bind preferably with water molecules. The molecular electrostatic potential (MEP) and global reactivity descriptor parameters were also established. Molecular docking studies were performed on Auto Dock-Vina software. The thermodynamical properties of title compounds have been calculated using B3LYP/6-311++G (d,p) functional. (C) 2018 Elsevier B.V. All rights reserved.Öğe Spectral analysis and detailed quantum mechanical investigation of some acetanilide analogues and their self-assemblies with graphene and fullerene(Springer, 2020) Almuqrin, Aljawhara H.; Al-Otaibi, Jamelah S.; Mary, Y. Sheena; Thomas, Renjith; Kaya, Savas; Isin, Dilara OzbakirSpectroscopic 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.Öğe Spectral analysis and DFT investigation of some benzopyran analogues and their self-assemblies with graphene(Elsevier, 2020) Al-Otaibi, Jamelah S.; Mary, Y. Sheena; Mary, Y. Shyma; Kaya, Savas; Erkan, SultanSpectroscopic analysis and different quantum mechanical studies of four phramaceutically active flavanoid compounds, 5,7-dihydroxy-3-(4-hydroxyphenyl)-4H-chromen-4-one (genistein) (F1), 5,7-dihydroxy-2-(4-hydroxyphenyl)-4H-chromen-4-one (apigenin) (F2), 5,6,7-trihydroxy-2-phenyl-4H-chromen-4-one (baicalein) (F3) and 2-(3,4-dihydroxyphenyl)-3,7-dihydroxy-4H-chromen-4-one (fisetin) (F4) are reported in this manuscript using DFT/B3LYP/6-311++G(d,p) level of theory. Simulated IR spectrum of these compounds was compared with experimentally available data, and essential functional group assignments were made. NBO studies helped to study the various intramolecular electron delocalisation possible in the molecule. We also report the frontier orbital properties and other derived local energy descriptors which talks about the relative stability and reactivity of the compounds. The photovoltaic efficiency of the compounds was studied from the simulated electronic spectra. The compound was found to interact with graphene, to form molecular self-assembly. These self-assemblies showed tremendous enhancement in various physicochemical properties when compared with its constituents. Biological activity of the compounds were predicted using molecular docking studies. (C) 2020 Elsevier B.V. All rights reserved.Öğe Synthesis, photophysical, electrochemical, and DFT examinations of two new organic dye molecules based on phenothiazine and dibenzofuran(Springer, 2022) Periyasamy, K.; Sakthivel, P.; Venkatesh, G.; Anbarasan, P. M.; Vennila, P.; Mary, Y. Sheena; Kaya, S.New dyes were developed and produced utilizing distinct electron donors (phenothiazine and dibenzofuran), a pi-spacer, and an electron acceptor of cyanoacetohydrazide, and their structures were studied using FT-IR and NMR spectroscopy. Following the synthesis of dye molecules, the photophysical and photovoltaic characteristics were investigated using experimental and theoretical methods. The photosensitizers have been exposed to electrochemical and optical property experiments in order to study their absorption performance and also molecular orbital energies. The monochromatic optical conversion efficiency of (Z)-N-((5-(10H-phenothiazin-2-yl)furan-2-yl)methylene)-2-cyanoacetohydrazide (PFCH) was found higher than that of (Z)-2-cyano-N'-((5-(dibenzo[b,d]furan-4-yl)furan-2-yl)methylene)acetohydrazide (BFCH), with IPCEs of 58 and 64% for BFCH and PFCH, respectively. According to the photosensitizer molecular energy level diagram, the studied dye molecules have strong thermodynamically advantageous ground and excited-state oxidation potentials for electron injection into the conduction band of titanium oxide. It was observed that the ability to attract electrons correlated favorably with molecular orbital energy. While density functional theory calculations were used to examine molecule geometries, vertical electronic excitations, and frontier molecular orbitals, experimental and computed results were consistent. Natural bond orbital and nonlinear optical properties were also calculated and discussed.
