BOUN Repository :: Browsing by Author "Aviyente, Viktorya."

Browsing by Author "Aviyente, Viktorya."

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A computational analysis of solvent effect :|thiol-ene reactions and CaO bond strength within hydrated calcium clusters
(Thesis (M.S.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 2020., 2020.) Munar, İpek.; Avcı, Duygu.; Aviyente, Viktorya.
In the first part this thesis, the solvent effect on thiol-ene reaction kinetics is elucidated. The effect of polar media on the reaction kinetics is taken into account by using the transition state theory, the reactivities of the carbon and sulfur radicals have also been rationalized by using conceptual DFT. The results have shown that the solvents have more impact on hydrogen atom transfer reactions and the chain transfer rate constant, kCT , can be increased by using non-polar solvents, while propagation reactions are less sensitive to media. Similarly, the kP /kCT ratio can be manipulated by changing the environment in order to obtain tailor-made polymers. Regarding the DFT descriptors, the local and global electrophilicity indices are well correlated with the propagation rate constant kP , whereas global electrophilicty index is associated with the chain transfer rate constant kCT . Overall, electrophilicy indices can be used with confidence to predict the kinetics of thiol-ene reactions. In the second part, the solvent effect on hydrated calcium clusters are investi gated. Calcium ions have significant role on biochemical processes, which makes the enlightenment of hydration of calcium ion crucial. The most stable form of calcium clusters is determined by using vibrational spectroscopy. DFT is used for structural optimizations and local mode analysis (LMA) is utilized in order to obtain the force constants of Ca-O bonds in vacuum and water environment. Bond strength orders are calculated for each bond, and it is concluded that CN of 6 is preferred in aqueous solutions, whereas the bonds get weaker as the cluster size increases in gas phase.
A computational approach the free radical polymerization of acrylates and methacrylates
(Thesis (Ph.D.)-Bogazici University. Institute for Graduate Studies in Science and Engineering, 2010., 2010.) Değirmenci, İsa.; Aviyente, Viktorya.; Van Speybroeck, Veronique.
Free radical polymerization (FRP) is one of the most favorable chemical reactions employed in both industry- and laboratory-scale chemical productions, because it can convert a wide variety of vinyl monomers into high molecular weight polymeric materials without extensive purification of commercially available monomers and solvents. On the other hand, the poor control of some of the key elements of macromolecular structures such as molecular weight (MW), polydispersity, end functionality, chain architecture, and composition are some important limitations for FRP. If the behavior of monomers during the FRP is well identified and understood, these limitations can be adjusted to moderate levels. The mechanism of the free radical polymerization process basically consists of four different types of reaction families involving free radicals: (1) initiation, (2) propagation, (3) chain transfer reactions, (4) termination reactions. Most of the reactions studied in this thesis are propagation reactions. However in some cases, also the termination reactions and chain transfer reactions have been modeled as they also influence the overall rate of polymerization. In the first part of this work the reactivity of a series of acrylates and alkyl - hydroxymethacrylates are modeled in order to understand the effect of the pendant group size, the polarity of a pendant group, and the nature of the pendant group (linear vs cyclic) on their polymerizability. Generally the rate constants for propagation kp mimic the qualitative polymerization trend of the monomers modeled and can be used with confidence in predicting the polymerizability behavior of acrylates. In the second part of this thesis, attention was focused on the polymerization behavior of alpha substituted acrylates. It is well known that the introduction of a heteroatom in the -position of acrylates can influence the reaction kinetics. In addition to investigation of this effect the chain length dependency of the propagation rate constant was examined by modeling monomeric, dimeric, trimeric, and tetrameric radical additions to a monomer. In the third part of this thesis, we focused on the influence of the solvent on the tacticity of free radical polymerization of methyl methacrylate by considering the propagation rate constants for the syndiotactic and isotactic free radical polymerization of MMA in vacuum, in methanol (CH3OH) and in 1,1,1,3,3,3-hexafluoro-2-(trifluoromethyl)propan-2-ol ((CF3)3COH). Solvent effect has been explored by using explicit solvent molecules and a polarizable continuum model (IEF-PCM) with a dielectric constant specific to the solvent. In a forth part of this thesis the effect of solvent on the propagation rate coefficient of acrylic acid (AA) and methacrylic acid (MAA) has been elucidated. Both for MAA and AA it was experimentally found that the propagation rate constant of non-ionized monomers increases by more than one order of magnitude in going from the bulk to a highly dilute system. The reactivity of these two monomers have been explained in the bulk medium by using quantum chemical tools. In addition to the main part of the thesis concerning acrylates and methacrylates, some research was performed in collaboration with other researchers from the Bogaziçi University on chain transfer to poly ethylene. These results are taken up in part five of the thesis. This work brings a new perspective to the modeling of free radical polymerization reactions and provides a deeper insight into the factors that affect the polymerizability of various monomers. However, the scope of exploring the FRP reactions is very large and highly useful examples are not limited to the ones discussed in this study. Lots of DFT methodologies have been tested against the experimental results in order to assess the level of theory for modeling the FRP. In all cases, the MPWB1K/6-311+G(3df,2p)//B3LYP/6- 31+G(d) methodology is found to reproduce the experimental trend the best as a cost effective method. Future work will undoubtedly uncover many other important aspects of the FRP reactions.
A computational approach to evaluate the pKa's of quinazoline derivatives
(Thesis (M.S.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 2022., 2022) Kıran, Melisa.; Akın, Fatma Ahu.; Aviyente, Viktorya.
One of the most important constants in chemistry is the ionization (dissociation) constant (pKa). Estimating the pKa value(s) for a potential drug is critical, especially since computations are considerably less expensive than obtaining pKa values experi mentally. Nearly 68 % of ionized medicines are said to have weak bases [1]. As a first step in developing an efficient estimation methodology for the pKa of quinazoline and derivatives we studied three protocols. First one is based on the linear relationship between computed atomic charges of quinazoline and derivatives and the experimental pKa. Based on our observations, the optimum method for reproducing observed pKa’s is to compute NPA (Natural Population Analysis) atomic charge using the CPCM (Conductor Like Polarizable Continuum Model) at the M06L/6-311++G** level (R2 = 0.93). The experimental pKa of a collection of quinazoline and derivatives were compared to several Conceptual Density Functional Theory descriptors computed. The highest approximations were observed when employing the M06L/6-311++G** with the CPCM solvation model using water as a solvent. In the final part of our study, M06L/6-311++G** have been used, in combination with CPCM continuum solvent model, to calculate the aqueous pKa values of quinazoline derivatives by using an isodesmic reaction. Possible improvements to current methodology are suggested.
A computational approach to optical and charge carrier properties of organic semiconductors
(Thesis (M.S.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 2017., 2016.) Turan, Haydar Taylan.; Aviyente, Viktorya.
In this study, the structural and optical properties of various organic semiconductors have been computationally investigated. In the first part, linear and nonlinear optical properties of a series of bis(E-dimesitylborylethenyl)-substituted arenes have been modeled by high-level computational protocols. The former compounds show a remarkable interest as infrared two-photon absorbers and hence may be used in the field of optical active and smart materials or for energy storage purposes. Excited state topologies, absorption and emission spectra, excited state metrics, natural transition orbitals and two-photon absorption cross-section of a series of chromophores have been computed by means of density functional theory (DFT) and time dependent DFT (TD-DFT). Extended benchmark tests on the performance of different functionals have been used. Dynamic and vibronic effects on absorption and emission spectra have been taken into account by sampling the conformational space by means of the Wigner distribution. Important infrared two photon absorption cross sections involving transitions to the second excited state have been observed. In the second part, aim of the study was to understand the unusual electron mobility loss of a bifuran derivative. A benchmark test was performed to choose the ideal functional/basis set combination. Potential energy scans, reorganization energies and transfer integrals of two bifuran and bithiophene derivatives have been performed to analyze intramolecular and intermolecular charge transfers in the molecules. The study shows that lack of intermolecular charge transportation was the reason behind the electron mobility loss in the bifuran derivative compared to the bithiophene derivative.
A computational approach to the core of eunicellins
(Thesis (M.S.)-Bogazici University. Institute for Graduate Studies in Science and Engineering, 2012., 2012.) Bozkurt, Esra.; Aviyente, Viktorya.
The asymmetric Diels-Alder reaction has attracted much interest for decades. Most recently, interest in the use of catalysts in cycloadditions has gained momentum due to their capacity to provide complex stereoselectivity throughout natural product synthesis. In this study, the origin of diastereoselectivity of intramolecular Diels-Alder reaction with chiral imidazolidinones is investigated to construct the skeleton of eunicellin which is a marine metabolite and two of medium ring ethers found in some natural products. The first reaction of interest was the intramolecular Diels-Alder reaction of acyclic precursor, seven, eight and nine membered reactants with and without aldehyde substituent in order to better understand the origin of diastereoselectivity. The exo and endo selectivity of the cycloadditon reactions, and the rate of thermal reactions are discussed in detail. Secondly, an organocatalyst controlled intramolecular Diels-Alder reaction of seven membered ring to synthesize the tricyclic core is investigated. Lastly, the cycloaddition reactions of eight and nine membered model Diels-Alder precursors are further explored to rationalize the effects of medium ring constraints and to elucidate the difference in diastereoselectivity of the intramolecular Diels-Alder reaction with chiral imidazolidinones. In this work, the effect of MacMillan Catalyst on the mechanism and stereoselectivity of the reaction have been studied with DFT and discussed in detail..
A computational insight on self - etchinh and bistyrenic monomers
(Thesis (M.S.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 2019., 2019.) Özaydın, Gül Beste.; Semiz, Duygu Avcı.; Aviyente, Viktorya.
Cyclopolymerization reaction of difunctional styrene monomers and the efficient binding of self-etching monomers to the hydroxyapatite component of the tooth have been widely studied using empirical approaches. However, the literature lacks a relevant computational basis to supplement such findings. Therefore, this thesis aims at bringing a computational insight into the i) cyclopolymerization reaction of difunctional styrenic monomers and ii) self-etching monomers in dental applications. In the first part of this work, the synthesis and the efficient cyclopolymerization of difunctional monomers containing styrene moieties tethered each other by the dichlorodiphenylsilane, the dichloro(methyl)phenylsilane and malonate ester protecting groups are illustrated. The experimental findings are rationalized theoretically by tackling the initial steps of cyclopolymerization reaction such as initiation, cyclization, propagation. In the second part, self-etching monomers and pre-nucleation complexes are modeled by computational protocols. These monomers are of interest in the dental adhesive system applications due to their strong binding to the hydroxyapatite component of the tooth. In order to analyze the strength of the interaction between calcium (HAP) and acid groups (selfetching monomer), pre-nucleation complexes (PNC), have been considered. The interaction between monomers and pre-nucleation complex is examined by the calculation of dissociation energy and the evaluation of NPA charges for PNC-monomer complexes. The computational findings have supported the experimental stability order of the monomers, The computational approach enables the scope of the evaluation of newly designed monomers to be wide in a short period of time without high experimental cost.
A computational study on the design of donor - acceptor copolymers for organic photovoltaic materials
(Thesis (M.S.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 2017., 2017.) Kahraman, Birce.; Doğan, İlknur.; Aviyente, Viktorya.
Organic solar cells are one kind of renewable energy. In this study, 50 different donor-acceptor oligomers, which were used for photovoltaic materials, were investigated by using 5 different acceptors, which are cyclopentadiphenyl (CPDP), benzodithiophene isomer 1 (BDT1), benzodithiophene isomer 2 (BDT2), cyclopentadithiophene (CPTz), dithienopyridine (DTPn), and 5 different donors, which are benzo[c][1,2,5]thiadiazole (BT), benzo[c][1,2,5]oxadiazole (BX), hydrogentriazole (HTAZ), benzo[c][1,2,5]selenadiazole (BSe), quinoxaline (Qx). Density functional theory (DFT) and time-dependent DFT (TD-DFT) at the B3LYP/6-311G* level have been employed for the calculations. The number of donors increased from 5 to10 by using the heteroatom substitution on the donors. Thus, the effect of heteroatom substitution on optical and geometrical properties of molecules was investigated. Benchmark studies on the methodology were performed to determine HOMO, LUMO energies and optical band gaps of the oligomers. Transition dipole moments, HOMO, LUMO energies and band gaps were calculated as a function of the chain length so, tetramers were found as suitable materials to ensure the energy saturation. Tetramers, which were the optimal chain length, have been used to evaluate the optical and geometrical properties like reorganization energies, distortion energies, frontier molecular orbitals, bond length alternations and excited-state vertical transition energies of oligomers. In conclusion, suitable photovoltaic materials were designed from a class of oligomers by taking 4 important factors into consideration. The choice of oligomers was based on the following criteria: low reorganization energy, LUMO energy higher than -3.8 eV, HOMO energy range between -5.27 eV and -5.7 eV and the optical band gap between 1.4 eV to 1.9 eV. Overall,16 out of 50 tetramers were found as suitable materials which can be used in solar cells.
A hybrid computational approach to the benzoin synthesis in different media
(Thesis (Ph.D.)-Bogazici University. Institute for Graduate Studies in Science and Engineering, 2008., 2008.) Topal, Kevser Göçmen.; Aviyente, Viktorya.
Benzoin derivatives are widely used in organic chemistry, mainly as starting materials in drug synthesis and photoinitiators in polymer chemistry, due to their bifunctionality, the presence of the asymmetric center, and the photolabile benzoyl group. In this study, the synthesis of benzoin has been modeled in two different media in the presence of two different catalysts. In the first part of the study, the reactions of benzil derivatives (donor aldehydes) with benzaldehyde derivatives (acceptor aldehydes) have been modeled with PM3 and B3LYP/6-31G*. The reaction mechanism and the effect of ortho substitutions on the aromatic phenyl rings have been discussed. The rate determining steps have been rationalized based on the effect of the substituents. Among the substituted benzaldehydes o-fluoro benzaldehyde has been found to decrease the activation barrier of the reaction. In the second part of the reaction, the enantioselective benzoin synthesis in benzoylformate decarboxylase (BFD) environment has been investigated with molecular dynamics. The effect of the surrounding residues in the vicinity of the active center has been elucidated. Ten models with various protonation states of the amino acids and their mutated counterparts near the active center have been devised, modeled and analysed. Our studies indicate that H70, S26 and H281 are the catalytically important amino acids besides E47 cited in the literature. The role of these residues in the catalytic function of the enzyme has been rationalized. Furthermore, the experimentally observed enantioselectivity was explained on the basis of the face selectivity of the enamine/carbanion produced during the reaction.
A theoretical investigation of solvent effect on the conformational equilibria of 2-substituted cyclohexanone ketal derivatives
(Thesis (Ph.D.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 1995., 1995.) Sağ-Erdem, Safiye.; Varnalı, Tereza.; Aviyente, Viktorya.
The conformational equilibria of 6-substituted-1,4-dioxospiro-[4.5]decanes and 7substituted-1,5-dioxospiro [5.5]undecanes, relatively complex polar systems, with substituents X=-CH3, -F, -CI, -CN, -OH, -OCH3, -N02 have been studied. The complete geometry optimizations have been carried out sequentially in the gas phase and in solution to represent the effect of the solvent. The methodology consists of the semiempirical PM3 hamiltonian and the self consistent reaction field computations. The effect of the solvent is implemented by the "cavity model". Ab initio calculations have also been performed on 1 ,1 , 2-trihydroxy ethane as a model for the hydroxy derivatives of the ketals studied.The discussion of the results is focused on the solvent effects arising from structural aspects, steric and electrostatic interactions on the axial/equatorial relative stability. The role played by multipole moments is considered. Good agreement with available experimental data and with previous theoretical studies has been obtained in general. The semiempirical methods and the simple solvent models are useful to predict the main role of solute-solvent interactions in conformational equilibria of complex systems for which ab initio calculations cannot be performed.
Activity of topotecan as topoisomerase IB inhibitor
(Thesis (M.S.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 2018., 2018.) Bali, Semiha Kevser.; Çatak, Şaron.; Aviyente, Viktorya.
Human Topoisomerase I (TopoI) is an enzyme that relaxes the supercoils on the DNA. First, it creates a nick only on one strand of DNA by covalently binding to it, and relaxes DNA by rotating the nicked strand around the intact one and re-ligating it back. Camptothecin (CPT) and its derivatives are known to target only Topoiso merase enzymes. When CPT or its analog Topotecan (TPT) is added to DNA-TopoI complex, the drug intercalates where the nick occurs and prevents relaxation by turn ing TopoI into a DNA-damaging agent. TPT has two forms: lactone and carboxylate forms, which are in equilibrium at neutral pH. It was shown that the lactone form is the “active” form of the drug, however, in the crystal structure of ternary complex (TPT DNA-TopoI) both forms were intercalating at the same site. This ﬁnding raises the question regarding the cause of activity diﬀerence between two forms despite binding to the same site. In this study, using Molecular Dynamics (MD) and hybrid Quantum Mechanics/Molecular Mechanics (QM/MM) approaches the diﬀerence in activity is in vestigated. 450 ns long MD simulation of both forms was performed and interaction energies were calculated using QM/MM method. Decomposition of the interaction energies showed that the interaction with TopoI is the reason for their activity diﬀer ence. When the contribution of residues on the interaction energy was investigated, it was found that the most striking eﬀect was due to K532 residue, and the topological analysis has further supported this ﬁnding. In addition, when the hydrogen bond net works around the drug were investigated, it was observed that in lactone form K532 was interacting with the drug, which was lost in carboxylate form. In conclusion, lac tone form of TPT is held by K532 residue strongly and N722 forms a hydrogen bond network around the binding pocket in the lactone form only.
An investigation of the carbon-carbon bond rupture in fluoroethanes by RRKM theory
(Thesis (Ph.D.)- Bogazici University. Institute for Graduate Studies in Social Sciences, 1983., 1983.) Aviyente, Viktorya.; İnel, Yüksel.
In this dissertation, the thermal decompositions of ethane, 1,1,2,2-tetrafl uoroethane, pentafl uoroethane and hexafl uoroethane have been subjected to a theoretical treatment i n terms of the quantum statistical RRKM theory. The RRKM theory assumes that the activated molecule has a certain amount of vibrational energy spread among the various vibrational degrees of freedom of the molecule. Then the probability of one particular mode of vibration acquiring so much of this energy that the vibration leads to dissociation into fragments is calculated. The experimental results have shown that the first order rate constant for unimolecular reactions is not a true constant but declines at low pressures. The decline or "fall-off" in the first order rate constant with pressure is an important criterion of unimolecular reactions. The rate constants in this fall-off region as well as the rate constants at the experimental pressures and temperatures for the carboncarbon bond rupture for the above molecules have been evaluated. As already known, the major difficulty in this field is the determination of the configuration of the transition state . This is done in two different ways where two different models are suggested in the first one, the complex is considered as a decomposing diatomic molecule in which the atoms have the masses of the actual fragments. From this assumption follows the derivation of the length of the critical bond (Gorin Model ). In the second one, the critical configuration has a value o f the reaction coordinate such that the number of accessible internal states o f the molecule is minimized. The R+ value given by the criterion of minimum state density is less than the value given by the Gorin Model at the rotational barrier. Choosing the critical configuration at the rotational barrier gives an overestimate of the animolecular rate. In fact, the kuni values calculated for the first model are higher than those obtained for the second one. I n the evaluation of the rate constants, the centrifugal effects which reduce the activation energy for the reaction and the anharmonicity, resulting in a decreasing spacing between successive vibrational levels , are considered. As a result , the pressure at which the rate constant reaches one half it slimiting high pressure value increases with the number of fluorine atoms. This behaviour is in harmony with activation energies for the carbon-carbon bond scission, increasing with the number of fluorine atoms in the hydrocarbon.
Analysis of the radical polymerizability of diallyl monomers
(Thesis (Ph.D.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 2002., 2002.) Tüzün, Nurcan Şenyurt.; Aviyente, Viktorya.
In this study, the radical cyclopolymerization mechanism of diallylamine and diallyl ether monomers and their derivatives has been investigated by computational modeling. The calculations were performed by the Density Functional Theory using the B3LYP/6-31G* basis set. In the first part of the study, a correlation has been built between the stucture of the monomer and the polymerizability. The experimentally measured 13C NMR chemical shifts of the diallylamine monomers, which were in line with their polymerizabilities, could be successfully correlated to the descriptors derived from calculations. The charges, bond orders, reaction barriers have successfully reproduced the polymerizability trend. In the second and third parts of this study, the regioselectivities and stereoselectivities of ring closure reactions of diallylamine and derivatives have been explained by considering steric and electronic factors. Diallylamine monomers formed 5-membered rings even though the thermodynamically more stable 6-membered rings would be expected to form. It has been shown that the 5-membered rings have lower barriers for cyclization. The fourth part of the study includes the modeling of diallylether monomers and their derivatives. The fast and efficient polymerizability of diallylether monomer has been investigated by considering the similarities and differences between this compound and its amine analogue. In the last part of the study, the competing reactions, homopolymerization and H-transfer reactions, as well as standard cyclopolymerization reactions have been considered. The efficiencies of the competing reactions have been investigated in their relation to the standard cyclopolymerization reactions. Comparison of free energies of activation for cyclopolymerization and competing reactions has shown that competing reactions are less efficient in the case of cationic monomers
Assessing protein - ligand binding modes, novel drug skeleton candidates for PDE4B and conformational rearrangements of EF-TU in GTP hydrolysis with computational tools
(Thesis (Ph.D.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 2017., 2017.) Çifci, Gülşah.; Çatak, Şaron.; Aviyente, Viktorya.
In the first part of this dissertation, computer-aided drug design approaches, structurebased methodologies such as docking, molecular dynamics simulations and Gibbs free energy calculations with Molecular Mechanics-Generalized Born/Surface Area (MMGB/SA) and ligand-based drug design methodologies like pharmacophore modeling are used to propose novel inhibitors for Phosphodiesterase4B (PDE4B) inhibitors. Virtual screening based on structure-based pharmacophore models has been performed for PDE4B inhibitors. The free energy of binding (ΔGbinding) as the total average of 40 independent simulations of each PDE4B inhibitors has been calculated with the MM-GB/SA method. The linear correlation between half maximal inhibitory concentration (IC50) and MM-GB/SA results have been analyzed with the linear dependency between binding affinity (Ki) and IC50, assuming that Michaelis-Menten constant (Km), substrate concentrations [S], and experimental conditions are similar. In the second part of this dissertation, the role of important amino acids in GTPase activity of EF-Tu-GTP for different organisms (Thermos-Aquaticus (T.aquaticus) and Escheria Coli (E.coli) complex have been determined by the aid of molecular dynamics (MD) simulations. The study has been carried out by comparing the experimental results with the results of the MD simulations. The conformational changes during the GTP hydrolysis in the Elongation factor-thermo unstable (EF-Tu) is explained with MD simulations.
Computational approaches to assess the binding properties of ligands :|the case of the NMDA receptor
(Thesis (Ph.D.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 2019., 2019.) Haşlak, Zeynep Pınar.; Doğan, İlknur.; Aviyente, Viktorya.
One of the important issues in drug design is the identification of the biological activity of receptor ligands. Development, synthesis and activity measurements of ligands have a major importance in drug design. However, there are certain limits in experimental studies; synthesis of a large number of compounds to cover all the potentially active molecules is unrealistic. Computational studies could therefore provide a valuable aid to experimental studies on ligand design for glutamate receptors. By combining the strengths of Molecular Dynamics and Quantum Chemical approaches, a more focused inspection, characterisation and rationalization of the drug design studies is allowed to be established. In this dissertation, computational methods have been used to investigate the intrinsic properties of the biologically active molecules that cause the selectivity. The results of this study will be introduced in 4 chapters. In Chapters 4 and 5, we aimed to differentiate between agonists, antagonists and partial agonists based on Quantum Chemical descriptors and binding Gibbs free energies. Several molecular properties that could play a role in ligand binding to the glycine GluN1 subunit of NMDA and calculated binding Gibbs free energies were further used to provide a link between the efficacies and binding affinities of the ligands. Prediction of the acid dissociation constants of amino acids in proteins and ligands allows us to have information about the binding affinity and efficacy of the ligand to its target protein. Considering the significance of pKa’s, how atomic charges of carboxylic acids can be related to the prediction of pKa of the ligands have been explored in Chapter 6. In order to shed light on the origins of the stereoselectivity of biologically active ligands, several mechanistic pathways have been evaluated for 2-thiohydantoins which are potent androgen receptor antagonists and the results are given in Chapter 7.
Conformational analysis of 2-[(4-substituted-phenyl)seleno]-1,3-dithianes: |a theoretical approach
(Thesis (M.S.) - Bogazici University. Institute for Graduate Studies in Sciences and Engineering, 1997., 1997.) Şenyurt, Nurcan.; Aviyente, Viktorya.
In this study the conformational analysis of 2-(4-substituted-phenyl)seleno-1,3-dithiane with H, Cl, F, CH3, CF3, NO2, OCH3 and N(CH3)2 substituents have been studied computationally both in gas phase and in solvent with the semi-emprical PM3 method and ab initio HF/6-31G* basis sets. The optimized geometries have been discussed in terms of endo and exo anomeric effects and their presence in the axial conformers have been confirmed. The conformational free energies have been calculated in gaseous phase in solvent. Comparison between experimental and calculated values has shown that PM3 as well as HF/6-31G* can be used confidentially to treat conformational equilibrium for cyclohexane derivatives with S and Se.
Conformational equilibria of alpha-substituted cyclohexanones with different chalcogens (O, S, Se)
(Thesis (M.S.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 1999., 1999.) Duran, Emine Sevim Dilek.; Aviyente, Viktorya.
The conformational analysis of alpha-substituted cyclohexanones with different chalcogens (OH, SH, SeH, OC6H5, SC6H5, SeC6H5) has been studied in gas phase with semi-empirical PM3 and ab initio HF/6-31G*. The para F, Cl, Br, NO2, NH2, OCH3, alpha-phenoxy, alpha-phenylthio and alpha-phennylseleno substituted cyclohexanones have been investigated in gas phase. The optimized structures (alpha-OH, SH, SeH, OCH3, SCH3, SeCH3, OC6H5, SC6H5, SeC6H5) have been analyzed in polar medium using a continuum Self Consistent Reaction Field (SCRF) model. Computations have provided data on the structure, the dipole moments and the thermodynamic properties of the compounds of interest. Justification of the experimental results has been followed by predictions on similar substituents and overall generalization.
Design of donor-acceptor conjugated polymers for high-performance organic solar cells :|a quantum mechanical approach
(Thesis (M.S.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 2019., 2019.) Ersoy, Deniz.; Kurnaz, M. Levent.; Aviyente, Viktorya.
In this study, the design of donor-acceptor conjugated polymers for high-performance organic solar cells is intended by investigating electronic, geometrical and optical prop erties of a speciﬁc set of donors that are used in polymer solar cells. 4 diﬀerent donors including benzo [1,2-b:4,5-b’] dithiophene (BDT), 3,3’-diﬂuoro-2,2’-bithiophene (diF2T), naphtho [1,2-b:5,6-b’] dithiophene (NDT), thieno[3,2-b] thiophene (TT) and 1 acceptor named 2-propyl-5,6-diﬂuorobenzo[d][1,2,3]triazole(ﬀTAZ) are studied in order to set a benchmark. The 4 diﬀerent donors studied for benchmarking and 7 diﬀerent acceptors including benzo [c] [1,2,5] thiadiazole(cop1), [1,2,5] thiadiazolo [3,4-g] quinox aline (cop2), [1,2,5] thiadiazolo [3,4-d] pyri-dazine (cop3), [1,2,5] thiadiazolo [3,4-c] pyridine (cop4), [1,2,5] oxadiazolo [3,4-d] pyri-dazine (cop5), ﬂuorinated naphtho [1,2 c:5,6-c’] bis [1,2,5] thiadiazole (FNTz), ﬂuori-nated [2,1,3] benzobisthiadiazole (FBTz) are combined and investigated for 28 diﬀerent predictions. Geometrical and optical characteristics were calculated using Density Functional Theory (DFT). Distortion en ergies and reorganizational energies for electron and hole transfer were calculated using B3LYP/6-311G*. In conclusion, 2 out of 28 molecules were chosen as the most eﬀective molecules to be used in high-performance organic solar cells. The molecules chosen contain NDT and TT as donors and FBTz as acceptor.
Design of new thermally activated delayed fluorescence materials for oled applications using computational chemistry
(Thesis (M.S.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 2019., 2019.) Özbek, Rengin Büşra.; Çatak, Şaron.; Aviyente, Viktorya.
This study is a theoretical assessment of thermally activated delayed ﬂuorescence (TADF) features of fourteen molecules. The analysis based on three diﬀerent descriptors; the twisting angle (α), Φs index and ∆ES−T. The emitters are modelled by Density Functional Theory (DFT) at diﬀerent levels of theories in vacuum. Conformational analyses that have been conducted at the most convenient level of theory revealed the most stable ground states geometries to be used in excited state investigations. The twisting angle (α) as a deﬁning element of the rigidity, between donor (D) and acceptor (A) frameworks of molecules has been reported. Subsequently, the solvent eﬀects have been taken into consideration at single point calculations in which excited state topolo gies have been analyzed by Time Dependent Density Functional Theory (TD-DFT) and Tamm-Dancoﬀ Approximation (TDA) to show the charge transfer (CT) characters together with the alignment of frontier orbitals (FMOs) and ∆ES−T of compounds have been introduced. Population analysis of Natural Transition Orbitals (NTOs) have been performed by TDA and Φs indices were reported by two diﬀerent charge distributions; Lo¨wdin and Mulliken. Lastly, the substitution eﬀect of a conjugated moiety used for aggregation induced emission (AIE), namely AIEgens on non-TADF emitter was in vestigated. The descriptor analyses show that, (α) indicates the bulkiness of structures which gives rise to a highly twisted molecule with a suitable angle that directly eﬀects the alignment of FMOs. The reported Φs values as indices reﬂecting the diﬀerence be tween the detachment and attachment densities, highly twisted structures have smaller values with a reduced orbital overlap which results in small ∆ES−T. Note that compounds with low twisting angles have high molecular overlap densities together with large singlet-triplet band gaps.
Elucidation of phosphate hydrolysis mechanism in water and in the elongation factor Tu (EF-Tu)
(Thesis (M.S.)-Bogazici University. Institute for Graduate Studies in Science and Engineering, 2007., 2007.) Ertem, Mehmed Zahid.; Aviyente, Viktorya.
The nature of phosphate hydrolysis reactions in solutions and in proteins is a topic that draws significant amount of interest due to the critical role of the phosphate hydrolysis reactions in the cellular activities. Studies on the phosphate hydrolysis reactions, directed towards the elucidation of the mechanism, created the main mechanistic debate on the phosphate hydrolysis reaction; whether it follows an associative or a dissociative pathway. This thesis is focused on two topics; the first one is the detailed investigation of the hydrolysis of methyl pyrophosphate trianion (CH3P2O7-3) and the second one is the analysis of the guanosine triphosphate (GTP) form of EF-Tu, a GTP hydrolyzing protein. Density Functional Theory (DFT) calculations were done for the investigation of the mechanism of the hydrolysis of methyl pyrophosphate trianion (CH3P2O7-3) and dissociative pathway was found to be favored over associative pathway for the hydrolysis reaction in aqueous medium. Moreover, the effect of the presence of the magnesium (Mg+2) ion on the hydrolysis of methyl pyrophosphate trianion was studied. In addition to these, the structural and dynamical properties of EFTu:GTP complex were analyzed by means of molecular dynamics (MD) simulations.
Elucidation of the deamidation mechanism of asparaginyl residues in peptides and proteins
(Thesis (Ph.D.)-Bogazici University. Institute for Graduate Studies in Science and Engineering, 2008., 2008.) Çatak, Şaron.; Aviyente, Viktorya.; Ruiz-Lopez, Manuel F.; Monard, Gérald.
Demidation of proteins is a topic of wide interest that has been subject to experimental and theoretical studies. Deamidation is a nonenzymatic and spontaneous process that converta asparagine conformational changes in proteins and has been associated with protein degradation and ageing. In this study, certain mechanistic aspects of this process have been investigated and many insights have been attained on potential mechanisms leading to deamidation. These mechanisms and their energetics have been presented in detail. Another potential fate of aparagine residues, backbone cleavage, has been introduced and compared with the deamidation mechanism. Finally, attempts to understand the effect of neighboring residues on Asn deamidation have been elaborated and several ideas for future work n-have benn outlined.

Browsing by Author "Aviyente, Viktorya."

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