Kimya

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A comparative study on selective biosorption in aqueous mixtures of dyes with different ionic characters by chlorella sp. biomass
(Thesis (M.S.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 2022., 2022) Yılmaz, Beyza.; İlker, Mehmet Fırat.
In this study, the adsorption percentages of Chlorella Sp. biomass towards five ionic dyes and their relevant combinations in aqueous media were studied as a model system for wastewater remediation compared to a proper type of activated carbon. Since wastewater effluents often contain a large variety of ionic micropollutants, there are an ongoing need to determine biosorption potential against various structures of single chemical contaminants. To have a more realistic model and understanding of biosorption to remove aqueous chemical contamination, combinations of aqueous contaminants are herein proposed to be monitored. Five molecules with distinct ionic and structural characteristics, namely a cationic dye Methylene Blue, anionic dyes Isolan Dark Blue and Eriochrome Black T, a zwitterionic dye Methyl Orange, and a larger molecular weight zwitterionic dye Congo Red constituted the targeted set of model adsorbates. Cationic molecules demonstrate a higher tendency to be adsorbed onto Chlorella Sp. than anionic and zwitterionic dyes. Therefore, the cationic dye was selected to investigate its potential to facilitate better biosorption of the selected anionic and zwitterionic dyes, through the possible generation of additional positive charges on the adsorbent surface of microalgae biomass. Single dyes and selected mixtures of them were employed to determine the removal percentages of Chlorella Sp., by monitoring dye removal through observation of decreasing concentrations using UV absorption spectroscopy, under different aqueous conditions. Reliable measurements of concentration changes in the case of dye mixtures based on light absorption from multiple wavelengths were established.
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 DFT study of the four-center HF eliminations from fluoroethylenes: transition state and charge analysis along the IRC
(Thesis (M.S.)-Bogazici University. Institute for Graduate Studies in Science and Engineering, 2008., 2008.) Önlü, Serli.; İnel, Yüksel.
The unimolecular, ground-state, four-center hydrogen fluoride elimination from vinyl fluoride, 1,1-difluoroethylene, trans-1,2-difluoroethylene, and trifluoroethylene reactions were investigated in this thesis. Hartree-Fock and Density Functional Theoretical calculations were performed to identify the stationary points in terms of their geometrical parameters and energies on the potential energy surface for each reaction under consideration. The entire study is composed of two parts: In the first part, the equilibrium geometries, infrared vibrational frequencies, and the energies of the reactants, four-center transition states, and the products were obtained at the Hartree-Fock Theory and Density Functional Theory by using Becke-style three-parameter functional. Five types of basis sets, composing of 6-31G*, 6-31G**, 6-31+G*, 6-311G*, and 6-311+G**, were used together with each method in the calculations, in order to search the possible effects of the basis sets on the results. In the second part, an alternative Density Functional Theory approach was used. All the geometries of the involved species were obtained at LDA/DZ, LDA/TZP, and LDA/TZ2P levels. Intrinsic Reaction Coordinate (IRC) analyses, in terms of geometry, energy, and gross atomic charge changes during the course of the reactions were applied at LDA/TZ2P level in order to follow the mechanism of eliminations. In all cases the obtained results were compared with the available corresponding theoretical and, if possible, experimantal literature values. Generally, the results were found to be quite reasonable and in alignment with literature.
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 parametric study of laboratory scale manifacture of sodiumallysulfonate
(Thesis (M.S.)- Bogazici University. Institute for Graduate Studies in Scieence and Engineering, 1986., 1986.) Börekcioğlu, Pınar.; Arıcan, Haluk.
The main aim of this work involyes the manufacture of sodium allylsulfonate from allylbromide and sodium sulfite by using laboratory scale testing of the commonly used industrial batch method(1). Yield of sodium allylsulfonate by processing conditions were examined. Sodium allylsulfonate (SAS), is mainly used in nickel electroplating bath as a brightening and levelling agent . It improves the throwing power of thebath, thus; yielding deposits of high brightness and good adherence. At the same time, it possesses the other properties of brightening agents by being a rapid adsorber on the cathode withit subsequent incorporation into the electrodeposit. It has strong inhibition action on the discharge of nickel ions without significantly affecting the discharge of hydronium ion . SAS also possesses the ability to considerably decrease the Nickel current efficiency within crease in SAS concentration in the electrolyte. Sodiumallylsulfonate, besides the other unsaturated sulfonates, is an important copolymerizable emulsifying agent in copolymerization with larger proportions of acrylonitrile for the preparation of dyeable acrylic fibers with improved whiteness. Because of the molecular structure; having a double bond; a sulfonate group and low molecular weight, Sodiumallylsulfonate is the preferred copolymer among the other unsaturated sulfonates. The compound was synthesized by using a new reagent other than recommended in literature. Allylbromide was used instead of allylchloride and methanol was used as the solvent in the reaction mixture. The analysis of the samples obtained from experiments, showed the identical properties with the commerciallyl used sample synthesized by allylchloride as the primary reagent. A number of experiments were carried out based on the same procedure but with different experimental reaction parameters . Physical and chemical tests were carried out on the products obtained . A process was then chosen to optimize the cost and ease of manufacture with the optimum results. The repetition of the experiments at the selected reaction conditions were examined, and it was found that at 44 and 180 minutes of reaction time the best yield and quality of SAS samples were obtained.
A study on halloysite reinforced chitosan hydrogel nanocomposites: synthesis, characterization & DYE adsorption properties
(Thesis (M.S.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 2015., 2015.) Palantöken, Sinem.; Nugay, Nihan.
In this project, synthesis and characterization of a series of natural silica nanotube reinforced chitosan nanocomposite hydrogels are done. Nanocomposite hydrogels were prepared through physical crosslinking of chitosan and within different percentages of Halloysite nanotube (HNTs) reinforcement. To increase the surface activity of halloysite nanotubes without disturbing the tubular structure, a special modification based on cryoscopic expansion was conducted and modification success was confirmed by X-Ray Diffraction, Brunauer-Emmett-Teller and Scanning Electron Microscope analysis methods. It has been found that both inner and outer diameters as well as surface area of nanotubes can be increased efficiently without disturbing the inherent tubular structure. Hydrogel nanocomposites were then prepared with different percentages of original and modified halloysite nanotubes and their water absorption, mechanical and dye adsorption properties as well as morphologies were investigated with a special focus on lumen modification and loading degree. Compared to neat hydrogels, swelling and mechanical properties of the composite hydrogels were found to be enhanced because of special morphology devolopment depending on composition. This effect was observed in a distinct way when cryo-expanded halloysite nanotubes were considered. Besides that neat chitosan turns out to be a good adsorbent for anionic dye; if small amount of cryo-expanded halloysite is added into the composition, the resultant composite hydrogel displays not only high adsorption capacity for both anionic and cationic type of dyes but also better mechanical properties.
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.
Active and passive tumor targeting via micellar dendritic constructs
(Thesis (Ph.D.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 2017., 2017.) Sümer, Burcu.; Sanyal, Rana.; Sanyal, Amitav.
Among many other nanotherapeutics, polymeric micellar systems are emerging as a very important class of nano-pharmaceuticals due to their ability to improve pharmacokinetics and bio-distribution of chemotherapy drugs as well as to reduce related systemic toxicities. In this thesis three such systems are presented in terms of synthesis, characterization and in vitro activity. In the first one, drug conjugated micellar constructs are fabricated using triblock dendron-polymer conjugates where a hydrophilic linear polyethylene glycol (PEG) chain is flanked by well-defined hydrophobic biodegradable polyester dendrons bearing an anti-angiogenic drug, combretastatin-A4 (CA4). Variation in dendron generation is utilized to obtain a library of micellar constructs with varying sizes and drug loadings. For the second project a cRGDfK targeting group was introduced to micelle shell to achieve active targeting cancer cells over-expressing αυβ3/αυβ5 integrins. Non-toxic, biodegradable, and modularly tunable micellar delivery systems were generated using two dendron-polymer based components. Either an AB type dendronpolymer construct or an ABA type dendron-polymer-dendron conjugate was used as primary construct; along with an AB type dendron-polymer containing a cRGDfK targeting group. In the final section another micellar delivery system was generated with conjugated Trastuzumab antibody which is used as treatment against tumor cells expressing HER2 receptors. Incorporation of this therapeutic antibody to nano drug delivery systems can improve its target specificity further. As a result three systems were generated with different drug release profiles ranging between days to hours depending on loading strategy. Polyester dendron cores rendered them acid labile as well as stable in terms of CMC. Their sizes were in the range of EPR controllable by core components as needed. Furthermore complex targeting groups were introduced to improve the cell uptake profiles further. In conclusion generated micellar platforms exhibited suitable physical and biological characteristic indicating their potential as drug delivery systems.
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.
Adsorption of branched polymer chains onto solid substrates
(Thesis (M.S.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 2019., 2019.) Özer, Sümeyye.; Akgün, Bülent.
Polymer thin films have a wide range of applications in photovoltaic materials, biomedical coatings, and nanolithography. Thin films are prepared using either solution or melt deposition techniques in which residual stresses are formed during the deposition. Annealing process above glass transition temperature (Tg) of polymers to remove the residual solvent whereas some of the polymer chains to adsorb onto the surface. Presence of adsorbed polymer layer in thin films cause deviations from bulk behavior in physical properties. In earlier studies, segment-substrate interactions are varied to manipulate the enthalpic effect which in general favors adsorption. When each segment pins to the substrate, polymer chains lose conformational entropy which works against adsorption. In this study, we have elucidated the role of entropic effect by varying the polymer architecture on the structure and growth kinetics of adsorbed layer by ellipsometry, X-ray reflectivity, and atomic force microscopy. Linear polystyrene (PS), 4-arm star PS, comb PS, and centipede PS of similar total molecular weight are used on hydrophilic SiOx and hydrophobic SiH to determine the effect of architecture on adsorption. Quality of the leaching solvent is also investigated for short and long leaching times. Our results demonstrate that the normalized layer thickness increases as the branching increases. Centipede PS always adsorb to give the thickest layers, whereas linear PS forms the thinnest adsorbed layers. For all the polymers since the enthalpic interactions are the same, the difference is the result of a reduction in the entropic loss for more branched architectures. All polymers yield thicker adsorbed layers on SiH surfaces than on SiOx surfaces due to stronger segment-substrate interactions. Toluene is found to be a better solvent for leaching than chloroform despite the opposite claims in the literature. For the first time, we have shown that just modifying the entropic contribution through polymer architecture opens up a new path to control the formation of adsorbed polymer layers.
Aldol reactions of conformationally stable o-CF3 phenyl bearing axially chiral thiohydantoins
(Thesis (M.S.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 2021., 2021.) Bacak Erdik, Melis.; Doğan, İlknur.
Novel axially chiral thiohydantoin derivatives bearing an o-CF3 phenyl ring have been synthesized atroposelectively from the reaction of R and S alanine, phenyl alanine and valine methyl ester HCl salts with ortho-trifluoromethylphenyl isothiocyanate in the presence of triethyl amine (TEA). It was found that after purification of the crude product by simple recrystallization, starting with R amino acids, the products were obtained possessing only M axial chirality whereas starting with S amino acids, only the P isomers were obtained. When the size of the substituent at C5 increased, the RM/SM and the SP/RP ratios increased significantly. The nonaxially chiral thiohydantoins have been shown to have a racemic form. The axially chiral stereoisomers of the products have been identified by comparing their 1H NMR spectra with their HPLC chromatograms. The axially chiral isomers were found to be conformationally and configurationally stable at room temperature. Sterically controlled aldol reactions on M and P thiohydantoins with benzaldehyde and furaldehyde have been carried out and the isomeric products were identified. It was found that during the aldol reaction of alanine and valine derivatives, the o-trifluoromethyl group of the M isomers shielded the Si face of the intermediate enolate and in this way enabled the selective formation of only the R configured aldol products at C5 of the heterocyclic ring. The otrifluoromethyl group of the P thiohydantoins on the other hand shielded the Re face of intermediate enolate and caused the formation of only the S configured aldol products at C5. However, this steric control has not been observed during the aldolization of the phenyl alanine derivatives. A face selectivity of the benzaldehyde and furaldehyde molecules for compound 5 and compound 2 have been observed as 91:9 and 78:22 respectively.
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.
An investigation of the effect of CD, HG and ZN on the growth of two species of blue green algae
(Thesis (M.S.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 1983., 1983.) Ağlarca, Zeynep.; Çalgan, Dilek.
In this research, effects of three metals, cadmium, mercury and zinc were investigated on two species of blue green algae, Anabaena flos aquae and Gloeocapsa. Cells were grown in sterile medium free of combined nitrogen and under continuous illumination. Metal ions were introduced as chloride salts and different concentrations of the metal ion solutions were used. Absorbance and cell counts were determined for each concentration of the metal ion solution and results were evaluated in terms of these two criteria. Zinc was found to be the most toxic metal for both Anabaena flos aquae and Gloeocapsa whereas the other metals showed inhibitory and stimulatory effects depending on the concentration of the metal ion solution. This showed that effect of the metal whether inhibitory or stimulatory is dependent on the species used and the metal ion itself.
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

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