Browsing by Author "Mirzaei, M."
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Item Open Access Chemically uracil-functionalized carbon and silicon carbide nanotubes: computational studies(Elsevier, 2018) Harismah, K.; Mirzaei, M.; Sahebi, H.; Gülseren, Oğuz; Rad, A. S.Chemical additions of uracil (U) nucleobase to sidewall of each of representative (4,4) armchair carbon and silicon carbide nanotubes (CNT and SiCNT) were investigated based on density functional theory (DFT) calculations. All singular and hybrid models were optimized to obtain the minimum-energy structures. The evaluated molecular properties indicated the effects of U-attachment on properties of both of U and NT counterparts, in which additional evaluated atomic-scale chemical shifts indicated the role of atomic sites in the U-attachment processes. Both of U-CNT and U-SiCNT hybrids could be considered as achievable compounds; however, the aim of application could organize the achievement of which hybrid. There was one possibility of U-attachment for the homo-atomic system of CNT whereas there were two possibilities of U-attachment for the hetero-atomic system of SiCNT. Interestingly, the evaluated atomic and molecular properties indicated differences between the characteristics of U-SiCNT-1 and U-SiCNT-2 as an advantage of computational chemistry methodologies, in which the results were very much interesting for the water-solvated systems.Item Open Access A computational molecular approach on chitosan vehicle for metformin(ICC, 2019) Mirzaei, M.; Gülseren, Oğuz; Jafari, E.; Aramideh, M.Density functional theory (DFT) calculations have been performed to study properties of chitosan (Chit) as a possible vehicle for carrying metformin (Met) drug. To this aim, the singular molecules of Met and Chit have been first optimized and, then, sixteen possible bimolecular complexes have been subsequently constructed and optimized to obtaine the stabilized interacting structures. Two bimolecular complexs have been seen as the most powerful interacting systems among all complexes. N5 and N8 atoms of Met are very important atoms for interacting with Chit counterpart. Molecular parameters such as molecular orbital energies and dipole moments approved the effects of interations on both Chit and Met counterparts. Atomic scale quadrupole coupling constants demonstrated the effects of interactions on the electronic atomic sites. As a final remark, although the Chit could be used as a vehicle for Met; further investigations are still required to see what’s happening inside the molecular systems.Item Open Access Cubane cluster surface for pyrimidine nucleobases relaxation: DFT approach(Danishgah-i Azad-i Islami, 2020-12-27) Mirzaei, M.; Hadipour, N.; Gülseren, OğuzDensity functional theory (DFT) approach was employed to investigate relaxation processes of each of pyrimidine nucleobases (NBs); cytosine (C), thymine (T) and uracil (U), at the Cubane Cluster Surface (CCS). The main idea was about providing a material for recognition of NBs, in which a nanostructure form of cubane (CCS) was first generated by optimization process. In the next step, relaxation processes of each of NBs at the surface were investigated to examine the function of such system for NBs recognition. The results indicated that the electronic based molecular properties could work as proper parameters for recognizing such molecular system, in which energy gap (EG) could be referred for the purpose. Measuring EG could help to recognize the complexes of CCS-C, CCS-T and CCS-U from each other. Strength of such complex formations was investigated using values of binding energy (BE); CCS-U > CCS-C > CCS-T. Total results of EG, BE and additional atomic scale properties indicated that the investigated CCS could work very well to recognize U as the characteristic NB of RNA.Item Open Access DFT explorations of quadrupole coupling constants for planar 5-fluorouracil pairs(Elsevier, 2016-08) Mirzaei, M.; Gülseren, O.; Hadipour, N.Atomic scale properties of quadrupole coupling constants (CQ) have been evaluated for singular and paired 5-fluorouracil (FU) models. Structural possibilities and properties for various types of hydrogen bonded (HB) homo pairs of FU have been investigated based on density functional theory (DFT) calculations. The models have been optimized to obtain the minimum energy level structures and only the planar molecular pairs have been considered. Various types of HB interactions have also managed the molecular shapes for the FU pairs. Different types of energies and also electron transferring properties have been investigated by the evaluated optimized properties. The atomic scale results indicated different strengths of HB interactions for FU pairs according to the changes of CQ properties for atoms in the singular and paired systems depending on the strength of interactions.Item Open Access DFT studies of CNT-functionalized uracil-acetate hybrids(Elsevier, 2015) Mirzaei, M.; Gulseren, O.Calculations based on density functional theory (DFT) have been performed to investigate the stabilities and properties of hybrid structures consisting of a molecular carbon nanotube (CNT) and uracil acetate (UA) counterparts. The investigated models have been relaxed to minimum energy structures and then various physical properties and nuclear magnetic resonance (NMR) properties have been evaluated. The results indicated the effects of functionalized CNT on the properties of hybrids through comparing the results of hybrids and individual structures. The oxygen atoms of uracil counterparts have been seen as the detection points of properties for the CNT-UA hybrids.Item Open Access DFT studies of graphene-functionalised derivatives of capecitabine(Walter de Gruyter GmbH, 2017-10) Aramideh, M.; Mirzaei, M.; Khodarahmi, G.; Gülseren, O.Cancer is one of the major problems for so many people around the world; therefore, dedicating efforts to explore efficient therapeutic methodologies is very important for researchers of life sciences. In this case, nanostructures are expected to be carriers of medicinal compounds for targeted drug design and delivery purposes. Within this work, the graphene (Gr)-functionalised derivatives of capecitabine (CAP), as a representative anticancer, have been studied based on density functional theory calculations. Two different sizes of Gr molecular models have been used for the functionalisation of CAP counterparts, CAP-Gr3 and CAP-Gr5, to explore the effects of Gr-functionalisation on the original properties of CAP. All singular and functionalised molecular models have been optimised and the molecular and atomic scale properties have been evaluated for the optimised structures. Higher formation favourability has been obtained for CAP-Gr5 in comparison with CAP-Gr3 and better structural stability has been obtained in the water-solvated system than the isolated gas-phase system for all models. The CAP-Gr5 model could play a better role of electron transferring in comparison with the CAP-Gr3 model. As a concluding remark, the molecular properties of CAP changed from singular to functionalised models whereas the atomic properties remained almost unchanged, which is expected for a carrier not to use significant perturbations to the original properties of the carried counterpart.Item Open Access DNA codon recognition by a cubane wire: In silico approach(DergiPark, 2021) Mirzaei, M.; Hadipour, N.; Gülseren, OğuzDNA codons, consisting of triplet nucleotides (NTs), could play important roles for RNA transcription and protein translation in living systems. Therefore, their recognition could be seen important for diagnosis and therapy purposes. Based on triplet sequence formations of Adenine (A), Guanine (G), Cytosine (C) and Thymine (T) NTs, 64 codons were investigated in this work regarding their complexation with a molecular cubane (CUB) wire. To achieve this aim, each of singular 64 codons and CUB were optimized to be prepared for docking processes of complex formations. Hence, 64 complexes of codon-CUB were docked to see the recognition potency of CUB wire versus each of DNA codons. Interestingly, the obtained docking scores indicated that the CUB could work specifically versus the DNA codons, in which G-rich and A-rich triples were seen to be more favorable for complexation with CUB in comparison with other C-rich and T-rich triplet codons. Moreover, the results indicated that not pure G triplet but GAG codon was the most favorable one to be recognized by the CUB wire. However, pure T triplet was the worst one for such complex formations. The results of this work remarkably indicated that the CUB wire could work for recognition process of DNA codons from each other and such recognition could be very much specified for each of G-rich and A-rich codons, in which GAG codon was the best one among all the 64 investigated codons.Item Open Access Functionalization of (n,0) CNTs (n=3-16) by uracil: DFT studies(Springer Heidelberg, 2018) Mirzaei, M.; Harismah, K.; Jafari, E.; Gülseren, Oğuz; Rad, A. S.Density functional theory (DFT) calculations were performed to investigate stabilities and properties for uracil (U)-functionalized carbon nanotubes (CNTs). To this aim, the optimized molecular properties were evaluated for (n, 0) models of CNTs (n = 3-16) in the original and U-functionalized forms. The results indicated that the dipole moments and energy gaps were independent of tubular diameters whereas the binding energies showed that the U-functionalization could be better achieved for n = 8-11 curvatures of (n, 0) CNTs. Further studies based on the evaluated atomic-scale properties, including quadrupole coupling constants (CQ), indicated that the electronic properties of atoms could detect the effects of diameters variations of (n, 0) CNTs, in which the effects were very much significant for the atoms around the U-functionalization regions. Finally, the achieved results of singular U, original CNTs, and CNT-U hybrids were compared to each other to demonstrate the stabilities and properties for the U-functionalized (n, 0) CNTs.Item Open Access In silico activity of AS1411 aptamer against nucleolin of cancer cells(Iranian Pediatric Hematology and Oncology Society, 2020) Farahbakhsh, Z.; Zamani, M. R.; Rafienia, M.; Gülseren, Oğuz; Mirzaei, M.Background: It has been expected that AS1411 aptamer could work against the cancer cells. Although the general information is available, there is still lack of details for the purpose. Therefore, activity of AS1411 aptamer against the nucleolin (NCL) target of cancer cells has been investigated in current work at the molecular scale. In addition, the same features have been also investigated for examining the activity of AT11, one of AS1411 derivatives. Methods: This work has been done employing in silico Molecular Docking simulations. Ten starting 3D configurations have been considered for each aptamer to be docked against the NCL target. Conformational search processes of ligands against the target indicated that the starting configuration of ligand could play an important role in determining the final complex formation in both of quantitative and qualitative aspects. Results: A04 and B01 are those starting configurations of AS1411 and AT11 making the strongest complexes with the NCL target among other ligands. The analyses indicated that the complexes of AT11 are slightly stronger than those of AS1411, in which the NCL target structure is more involved in the chelated complexes with the AT11 in comparison with the AS1411. Conclusion: AS1411 and AT11 are specified for targeting the NCL of cancer cells for the diagnosis and therapeutic purposes. They have reasonable binding affinity and could work as possible inhibitors of NCL.Item Open Access Nanocarbon-assisted biosensor for diagnosis of exhaled biomarkers of lung cancer: DFT approach(Sami Publishing Company, 2021-03) Mirzaei, M.; Gülseren, Oğuz; Rafienia, M.; Zare, A.Density functional theory (DFT) calculations were performed to investigate a nanocarbon-assisted biosensor for diagnosis of exhaled biomarkers of lung cancer. To this aim, an oxidized model of C20 fullerene (OC) was chosen as the surface for adsorbing each of five remarkable volatile organic compounds (VOC) biomarkers including hydrogen cyanide, methanol, methyl cyanide, isoprene, and 1-propanol designated by B1-B5. Geometries of the models were first optimized to achieve the minimum energy structures to be involved in further optimization of B@OC bi-molecular complexes. The relaxation of B counterparts at the surface of OC provided insightful information for capability of the investigated system for possible diagnosis of such biomarkers. In this case, B1 was placed at the highest rank of adsorption to make the strongest B1@OC complex among others whereas the weakest complex was seen for B4@OC complex. The achievement was very much important for differential detection of each of VOC biomarkers by the investigated OC nanocarbon. Moreover, the recorded infrared spectra indicated that the complexes could be very well recognized in complex forms and also among other complexes. As a final remark, such proposed nanocarbon-assisted biosensor could work for diagnosis of remarkable VOC biomarkers of lung cancer.Item Open Access Plasmon-phonon coupling in a valley-spin-polarized two-dimensional electron system: a theoretical study on monolayer silicene(American Physical Society, 2018) Mirzaei, M.; Vazifehshenas, T.; Salavati-Fard, T.; Farmanbar, M.; Tanatar, BilalWe study the hybrid excitations due to the coupling between surface optical phonons of a polar insulator substrate and plasmons in the valley-spin-polarized metal phase of silicene under an exchange field. We perform the calculations within the generalized random-phase approximation where the plasmon-phonon coupling is taken into account by the long-range Fröhlich interaction. Our investigation on two hybridized plasmon branches in different spin and valley subbands shows distinct behavior compared to the uncoupled case. Interestingly, in one valley, it is found that while the high-energy hybrid branch is totally damped in the spin-up state, it can be well defined in the spin-down state. Moreover, we show that the electron-phonon coupling is stronger in both spin-down subbands, regardless of valley index, due to their higher electron densities. In addition, we study the effects of electron-phonon coupling on the quasiparticle scattering rate of four distinct spin-valley locked subbands. The results of our calculations predict a general enhancement in the scattering rate for all subbands and a jump in the case of spin-down states. This sharp increase associated with the damping of hybrid plasmon modes is almost absent in the uncoupled case. The results suggest an effective way for manipulating collective modes of valley-spin-polarized silicene which may become useful in future valleytronic and spintronic applications.Item Open Access Relaxations of fluorouracil tautomers by decorations of fullerene-like SiCs: DFT studies(Elsevier, 2016-06) Kouchaki, A.; Gülseren, O.; Hadipour, N.; Mirzaei, M.Decorations of silicon carbide (SiC) fullerene-like nanoparticles by fluorouracil (FU) and its tautomers are investigated through density functional theory (DFT) calculations. Two models of fullerene-like particles including Si12C8 and Si8C12 are constructed to be counterparts of decorated hybrid structures, FU@Si12C8 and FU@Si8C12, respectively. The initial models including original FU and tautomeric structures and SiC nanoparticles are individually optimized and then combined for further optimizations in the hybrid forms. Covalent bonds are observed for FU@Si12C8 hybrids, whereas non-covalent interactions are seen for FU@Si8C12 ones. The obtained properties indicated that Si12C8 model could be considered as a better counterpart for interactions with FU structures than Si8C12 model. The results also showed significant effects of interactions on the properties of atoms close to the interacting regions in nanoparticles. Finally, the tautomeric structures show different behaviors in interactions with SiC nanoparticles, in which the SiC nanoparticles could be employed to detect the situations of tautomeric processes for FU structures.Item Open Access Relaxations of methylpyridinone tautomers at the C60 surfaces: DFT studies(Islamic Azad University, 2017) Naderi, E.; Mirzaei, M.; Saghaie, L.; Khodarahmi, G.; Gülseren, O.Density functional theory (DFT) based calculations have been performed to examine the relaxations of tautomers of 4–hydroxy–6–methylpyridin–2(1H)–one (MPO), as a representative of pyridinone derivatives, at the fullerene (C60) surfaces. Optimized molecular properties including energies, dipole moments and atomic scale quadrupole coupling constants (CQ) have been evaluated to investigate the structural and electronic properties of the models. The structural configurations of tautomers show different relaxations at the C60 surface yielding different magnitudes of total and binding energies. Moreover, deformation of each tautomer due to relaxation at the C60 surface with respect to the initial singular structure has been examined. Complimentary parameters of energy gaps and dipole moments exhibit the effects of relaxations at the C60 surface for the MPO counterparts. Atomic scale CQ properties also indicate that the electronic properties of atoms show significant changes for tautomers and hybrid systems. As a final note, the tautomeric structures in singular and hybrid forms exhibit different electronic properties because of effects of interactions with C60, especially for the interaction regions.Item Open Access Silicene dynamic optical response in the presence of external electric and exchange fields(Institute of Physics Publishing Ltd., 2022-01-04) Mirzaei, M.; Vazifehshenas, T.; Salavati-fard, T.; Tanatar, BilalWe investigate the dynamic optical transition of monolayer silicene in the presence of external electric and exchange fields within the low-energy tight-binding model. Applying external electric and exchange fields breaks the silicene band structure spin and valley degeneracies. Three phases of silicene corresponding to different strengths of perpendicular electric field with respect to the spin–orbit coupling (Δz < Δso, Δz = Δso and Δz > Δso) are considered. We obtain the spin-valley-dependent optical responses to the incoming circularly polarized light using the Kubo formula. We show and discuss how the magnitude and direction of the transverse and longitudinal optical responses of such a system change with the electric and exchange fields. Our calculations suggest that the intraband part of the longitudinal optical response as well as the initial point of the interband part have strong dependencies on the exchange field. Furthermore, we show that one of the spin subbands plays a dominant role in the response to polarized light. Depending on the type of incident light polarization, the dominant subband may change. Our results shed light on the relation between silicene dynamic optical responses and externally applied fields.