Browsing by Author "KAYI, Hakan"
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Item A computational study on 4,7-di(furan-2-yl)benzo[c][1,2,5] thiadiazole monomer and its oligomers(Journal of Molecular Modeling, 2014-04-23) KAYI, HakanThe energy gap, Eg, between the highest occupied molecular orbital (HOMO) and the lowest unoccupied molec ular orbital (LUMO) energy levels that determines the elec tronic and optical properties of 4,7-di(furan-2- yl)benzo[c][1,2,5]thiadiazole (FSF) polymer is calculated by performing quantum chemical calculations. First, we theoret ically investigated the most stable conformers of FSF mono mer and its corresponding oligomers at the B3LYP/6-31G(d) and B3LYP/LANL2DZ levels of theory. We reveal the theoret ical molecular structure of this very recently synthesized novel monomer and its oligomers for the first time in the literature. Our results from the B3LYP/6-31G(d) calculations indicated that FSF polymer has a low HOMO-LUMO gap of 1.55 eV to be in good agreement with the experiments. Experimental design and synthesis of novel conjugated polymers require time-consuming and expensive procedures. The findings from this study are promising for the use of computational methods in the design of the novel conjugated polymers, and help to narrow the materials to be used in design and synthesis of conjugated polymers with desired properties.Item Conformational behaviors of trans-2,3- and trans-2,5-dihalo 1,4-diselenanes. A complete basis set, hybrid-density functional theory study and natural bond orbital interpretations(Journal of Molecular Modeling, 2014-05-14) NORİ-SHARGH, Davood; MOUSAVI, Seiedeh Negar; KAYI, HakanComplete basis set CBS-4, hybrid-density func tional theory (hybrid-DFT: B3LYP/6-311+G**) based methods and natural bond orbital (NBO) interpretations have been used to examine the contributions of the hyperconjugative, electrostatic, and steric effects on the con formational behaviors of trans-2,3-dihalo-1,4-diselenane [halo=F (1), Cl (2), Br (3)] and trans-2,5-dihalo-1,4- diselenane [halo = F (4), Cl (5), Br (6)]. Both levels of theory showed that the axial conformation stability, compared to its corresponding equatorial conformation, decreases from com pounds 1→3 and 4→6. Based on the results obtained from the NBO analysis, there are significant anomeric effects for compounds 1-6. The anomeric effect associated with the electron delocalization is in favor of the axial conformation and increases from compounds 1→3 and 4→6. On the other hand, dipole moment differences between the axial and equa torial conformations [Δ(μeq - μax)] decrease from compounds 1→3. Although Δ(μeq-μax) parameter decreases from com pound 1 to compound 3, the dipole moment values of the axial conformations are smaller than those of their corresponding equatorial conformations. Therefore, the anomeric effect as sociated with the electron delocalizations (for halogen-C-Se segments) and the electrostatic model associated with the dipole-dipole interactions fail to account for the increase of the equatorial conformations stability on going from com pound 1 to compound 3. Since there is no dipole moment for the axial and equatorial conformations of compounds 4-6, consequently, the conformational preferences in compounds 1-6 is in general dictated by the steric hindrance factor asso ciated with the 1,3-syn-axial repulsions. Importantly, the CBS-4 results show that the entropy difference (ΔS) between the equatorial axial conformations increases from compounds 1→3 and 4→6. This fact can be explained by the anomeric effect associated with the electron delocalization which affects the C2-Se bond orders and increase the rigidity of the corre sponding rings. The Gibbs free energy difference values be tween the axial and equatorial conformations (i.e. ΔGax-ax and ΔGeq-eq) of compounds 1 and 4, 2 and 5 and also 3 and 6 have been calculated. The correlations between the anomeric effect, electrostatic model, ΔGeq-ax, ΔGax-ax, ΔGeq-eq, bond orders, dipole-dipole interactions, structural parameters and confor mational behaviors of compounds 1-6 have been investigated.Item Correlations between hardness, electrostatic interactions, and thermodynamic parameters in the decomposition reactions of 3-buten-1-ol, 3-methoxy-1-propene, and ethoxyethene(Structural Chemistry, 2014-08-11) HASANZADEH, Neda; NORİ-SHARGH, Davood; KAYI, Hakan; JAVID, Nargess RezaiDecomposition of the three isomeric com pounds, 3-buten-1-ol (1), 3-methoxy-1-propene (2), and ethoxyethene (3), at two different (300 and 550 K) tem peratures has been investigated by means of ab initio molecular orbital theory (MP2/6-311?G**//B3LYP/6- 311?G**), hybrid-density functional theory (B3LYP/6- 311?G**), the complete basis set, nuclear magnetic reso nance analysis, and the electrostatic model associated with the dipole–dipole interactions. All three levels of theory showed that the calculated Gibbs free energy differences between the transition and ground state structures (DG=) increase from compound 1 to compound 3. The variations of the calculated DG= values can not be justified by the decrease of the calculated global hardness (g) differences between the ground and transition states structures (i.e., D[g(GS)-g(TS)]). Based on the synchronicity indices, the transition state structures of compounds 1–3 involve syn chronous aromatic transition structures, but there is no significant difference between their calculated synchronicity indices. The optimized geometries for the transition state structures of the decomposition reactions of compounds 1–3 consist in chair-like six-membered rings. The variation of the calculated activation entropy (DS=) values can not be justified by the decrease of D[g(GS)- g(TS)] parameter from compound 1 to compound 3. On the other hand, dipole moment differences between the ground and transition state structures [D(lTS-lGS)] decrease from compound 1 to compound 3. Therefore, the electrostatic model associated with the dipole–dipole interactions jus tifies the increase of the calculated DG= values from compound 1 to compound 3. The correlations between DG=, D[g(GS)-g(TS)], (DS=), k(T), electrostatic model, and structural parameters have been investigated.Item DESIGN OF NOVEL PLATINUM AND PALLADIUM COMPLEXES CONTAINING PYRIDYL TYPE LIGANDS FOR CANCER TUMOR TREATMENT USING MOLECULAR MODELING APPROACH(2022-02-21) EL-HA, RABIA; KAYI, Hakan; ÖZALP YAMAN, ŞenizIn the middle of the last century, after the discovery of a compound of cisplatin, this compound became one of the most important chemical compounds used in the treatment of several different types of cancer. But despite the ability of this compound to kill and destroy cancer cells, it is still unable to treat several types of cancer in addition to side effects caused by this compound, which led scientists to search for another compound is more effective and without side effects. Many of the drugs that have been discovered have shown little of their efficacy against cancer. Despite the techniques and progress we have achieved, and the countless number of doctors devoted to fight it, cancer remains a real threat, an incurable disease, but nevertheless, there is still hope. Scientists have come up with treatments that seemed impossible 50 years ago, and they managed to get rid of some cancers that were called incurable. We started using treatment tools in different ways to achieve great results. Although the cancer may still be terrifying and may always remain so the steps we have taken against it have made treatment not only possible, but within reach. Previous studies can conclude that platinum and palladium compounds are among the most effective compounds against cancer cells if we take in account many parameters such as suitable ligand, good geometry and active leaving group. From here, the research began to design and develop some platinum and palladium compounds as alternative cancer treatment compounds. In this research sixteen platinum and palladium compounds were designed with two different types of ligands. New compounds were designed and tested theoretically by using density functional theory, DFT. The geometry optimizations and spectroscopic properties of these complexes such as FTIR, NMR and UV-vis were calculated using the Gaussian program by using B3LYP/LANL2DZ level of theory. The process of interaction of these compounds with two types of DNA was then simulated using the Docking program which revealed that our complexes interacts with DNA through different mechanisms than that of cisplatin (covalent, electrostatic, groove and intercalation) which may lead to overcome the side effects of cisplatin. The theoretical results of the compounds are very encouraging. Some of these compounds have been experimentally tested on live cells and have proven effective against several types of cancer. The good agreement between the experimental and theoretical results was observed. The new complexes in question have promising results for further future studies on these complexes.Item Natural bond orbital, nuclear magnetic resonance analysis and hybrid-density functional theory study of σ-aromaticity in Al2F6, Al2Cl6, Al2Br6 and Al2I6(Journal of Molecular Modeling, 2013-02-11) NORI-SHARGH, Davood; YAHYAEI, Hooriye; MOUSEVI, Seiedeh Negar; MAASOOMI, Akram; KAYI, HakanNatural bond orbital (NBO), nuclear magnetic res onance (NMR) analysis and hybrid-density functional theory based method (B3LYP/Def2-TZVPP) were used to investigate the correlation between the nucleus-independent chemical shifts [NICS, as an aromaticity criterion], σAl(1)-X2(b) → σ*Al(3)-X4(b) electron delocalizations and the dissociation ener gies of Al2F6, Al2Cl6, Al2Br6 and Al2I6 to 2AlX3 (X=F, Cl, Br, I). The results obtained showed that the dissociation energies of Al2F6, Al2Cl6, Al2Br6 and Al2I6 decrease from Al2F6 to Al2I6. Like aromatic molecules, these compounds have relatively significant negative NICSiso(0) values. Clearly, based on mag netic criteria, they exhibit aromatic character and make it possible to consider them as σ-delocalized aromatic species, such as Möbius σ-aromatic species. The σ-aromatic character which is demonstrated by their NICSiso(0) values decreases from Al2F6 to Al2I6. The NICSiso values are dominated by the in-plane σ22 (i.e., σyy, the plane containing halogen atoms bridged) chemical shift components. The increase of the NICSiso values explains significantly the decrease of the corre sponding dissociation energies of Al2F6, Al2Cl6, Al2Br6 and Al2I6. Importantly, the NBO results suggest that in these compounds the dissociation energies are controlled by the stabilization energies associated with σAl(1)-X2(b) →σ*Al(3)- X4(b) electron delocalizations. The decrease of the stabilization energies associated with σAl(1)-X2(b) →σ*Al(3)-X4(b) electron delocalizations is in accordance with the variation of the calculated NICSiso values. The correlations between the dis sociation energies of Al2F6, Al2Cl6, Al2Br6 and Al2I6, σAl(1)- X2(b) →σ*Al(3)-X4(b) electron delocalizations, natural atomic orbitals (NAOs) and NICSiso values have been investigated.thesis.listelement.badge PREDICTION OF KINEMATIC VISCOSITY AND DENSITY OF DIESEL FUEL FROM PHYSICAL PROPERTIES BY ARTIFICAL NEURAL NETWORKS(2022-01-20) Al Obaidi, Aymen Abdulqader Abbas; KAYI, Hakan; E. MACHIN, NesrinIn this study, the first purpose is to predict the kinematic viscosity and density of diesel fuel from the physical properties of it by employing artificial neural network modeling approach to be able to save time and money spent on experimental studies, and the next one is to ascertain a simple formula to kinematic viscosity and density. The experimental data for diesel fuel utilized throughout this study is taken directly from the North Oil Company in Iraq, hence the original and unique source of data has been used. In daily routine, every truck holding diesel needs to be monitored, and density and viscosity measurements need to be performed. Nonlinear autoregressive neural networks with external input (NARX) and a typical feedforward neural network with backpropagation algorithm (NN) are used in the prediction of kinematic viscosity and density. Evaluation of the obtained results indicated promising performance for these networks. In the prediction of the density values, NARX type neural network performed better than NN, and for the prediction of kinematic viscosity values NN performed superior to NARX. In addition, multiple linear regression (MLR) methodology is employed and the coefficients of the five independent variables for the first order linear equations are obtained for kinematic viscosity and density.thesis.listelement.badge PREDICTION OF THE KINEMATIC VISCOSITY OF PETROLEUM FRACTIONS(2022-02-25) AHMED, Hawa Ahmed Ali; KAYI, Hakan; ALPER, ErdoğanPetroleum fractions are very complex mixtures. In engineering design, it is important to identify the viscosity of fluids, as it is used in calculations. Furthermore, the physical properties of the liquid, as well as its composition, are factors that help to form an understanding of the fluid’s behavior. There are two main methodologies that are used to get the viscosity of the fluid; an experimental approach, which requires measurements, and using a mathematical model for estimation using the physical properties. Because experimental viscosity measurements are expensive and time consuming, it is not always practical to perform these measurements in the lack of experimental data. Hence, reliable and accurate mathematical models are required. This study is concerned with the prediction of the viscosities of some Libyan petroleum products by evaluating the performance of various mathematical models available in the literature. Initially an experimental database was established for this purpose. The database consists of kinematic viscosity and density data for several Libyan petroleum products in kerosene and gas oil ranges. Among all the models evaluated, the modified group-contribution viscosity-thermodynamics model (GC-UNIMOD) was proposed for kinematic viscosities’ prediction at investigated temperature levels (30, 35, 40, 50 °C) using various Libyan petroleum fractions. The model proposed was tested using the collected data and compared with the existing models. It was concluded that utilizing the GC-UNIMOD model to predict results is more accurate and precise than other methods’ predictions, which are used in literature like the investigated empirical models in this work.Item Spectroelectrochemical Investigation of Nuclease Active Pt(II) Complexes Containing Pyrrole Oxime(Electrochimica Acta, 2015-01-28) ALTUNÖZ ERDOĞAN, Deniz; KAYI, Hakan; ÖZALP YAMAN, ŞenizIn this paper, the electrochemical oxidation of three Pt(II) complexes containing pyrrole oxime (HL) having a general formula of [Pt(NH3)Cl(L)] (1), [Pt(L)2] (2), and K[PtCl2(L)] (3) has been investigated by in-situ spectroelectrochemistry in dimethylformamide (DMF). An irreversible metal-based oxidation process occurs during the anodic scan for each of the three complexes. The electronic absorption spectral changes indicate that all the three complexes generate similar Pt(IV) compounds and free ligand. Our experimental data is supported by quantum chemistry calculations utilizing density functional theory. In addition, the frontier orbital energy distributions indicate that electron densities are localized on mainly platinum atom.