Ph.D. Theses

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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 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.
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.
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.
Experimental and computational investigation of structure- reactivity relationship of methacrylates
(Thesis (Ph.D.)-Bogazici University. Institute for Graduate Studies in Science and Engineering, 2012., 2012.) Karahan, Özlem.; Avcı, Duygu.; Aviyente, Viktorya.
In the first part of this work, a series of alkyl α-hydroxymethacrylates (RHMA) were synthesized and computationally modeled in order to understand the structure-reactivity relationships in their polymerizations. Several factors including H-bonding, π-π interactions and dipole moment were investigated. Experimentally, among the studied monomers, aromatic carbamates containing π-π stacking and H-bonding were found to have highest rate of polymerization. Computationally, the rate constants for propagation kp mimic the qualitative polymerization trends of the monomers modeled and can be used with confidence in predicting the polymerizability behaviors of alkyl α-hydroxymethacrylates. Finally, these studies are expected to be used for the prediction of RHMA monomers prior to synthesis. In addition, RHMA based polymerizable and polymeric photoinitiators were synthesized and evaluated for UV curable coatings. In the second part of this work, glycidyl methacrylate (GMA) derivatives were synthesized and evaluated with respect to their potential to be used as reactive diluents in dental materials. An explanation was also proposed for the cyclopolymerization of methyl α-[(allyloxy) methyl] acrylate via 5-membered rings, while allyl methacrylate (AMA) and allyl 2-cyanoacrylate (ACA) polymerize without ring formation. It has been pointed out that the presence of carbonyl group at C3 in AMA and ACA inhibits the cyclization because of its incompatibility in hybridization with the other unsaturated carbon next to the oxygen. In the last part of this thesis, the effect of solvent on the propagation rate coefficients of acrylic acid (AA) and methacrylic acid (MAA) have been elucidated. Both for MAA and AA it was experimentally found that the propagation rate constants of the monomers increase by more than one order of magnitude in going from the bulk to a highly dilute system. The reactivities of these two monomers have been explained in the bulk and dilute medium by using quantum chemical methods.
Investigation of the deamidation reaction in the enzyme triosephosphate isomerase by means of computational chemistry tools
(Thesis (Ph.D.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 2014., 2014.) Uğur, İlke.; Aviyente, Viktorya.; Monard, Gérald.
Deamidation is the posttranslational modi cation of asparagine (Asn) and glutamine (Gln) residues, which is observed in several proteins and peptides. It has been shown that deamidation limits the lifetime of these macromolecules. In this work, deamidation of asparagine in small peptides and in the enzyme triosephosphate isomerase has been modeled. Deamidation in mammalian triosephosphate isomerase has been observed at two distinct deamidation sites: Asn15 and Asn71. Asn71 deamidates faster than Asn15 and slower than a small peptide. Deamidation at Asn15 is supposed to occur with the in uence of deamidated Asn71. In order to explain these experimental ndings, microsecond long classical molecular dynamics simulations and free energy calculations using quantum mechanics/molecular mechanics tools combined with umbrella sampling technique have been performed. The sequential deamidation in triosephosphate isomerase has been shown to be related with both global and local e ects. These results bring a new perspective to the impact of the high-order structure on deamidation rate. The most plausible route of this reaction was also determined. The pKa shift of backbone amide of the residue adjacent to asparagine has been found to be one of the most crucial factor determining the rate of deamidation. Considering the importance of pKa shifts in protein environment, a computational protocol was suggested in order to obtain accurate and fast pKa predictions. This protocol was applied to small organic molecules, and it has been shown to be applicable to studies concerning aminoacid pKa predictions.
Modeling the selectivity in pericyclic reactions
(Thesis (Ph.D.)-Bogazici University. Institute for Graduate Studies in Science and Engineering, 2009., 2009.) Ölçüm, Nihan Çelebi.; Aviyente, Viktorya.
Pericyclic reactions are very powerful and widely utilized transformations to obtain complex molecules. The selective versions have received remarkable interest and have found extensive use in synthetic organic chemistry to access complex biologically active targets. In this work, the mechanistic details of some highly useful pericyclic reactions have been explored and the origins of the selectivity have been investigated. The first reaction of interest was the Diels−Alder reactions of -keto- , -unsaturated phosphonates with cyclopentadiene and 1,3-cyclohexadiene. The reaction constitutes an easy and straightforward method for the synthesis of dihydropyran derivatives, which are efficient substrates in the preparation of chiral building blocks. Second, diastereoselective cycloadditions of different chiral anthracene templates with maleic anhydride were explored. This reaction serves as the key element in determining the final stereochemistry of the product in the preparation of complex biologically active molecules such as butenolides, , -unsaturared lactams and related compounds in their enantiomerically pure forms. Finally, [3,3]- and [1,3]-sigmatropic rearrangements of allylic acetimidates have been studied. These reactions yield -amino acid and allyl amine derivatives that are important building blocks found in many bioactive molecules. In this work, bis-pericyclic, pseudopericyclic and stepwise pathways were shown to play a substantial role in determining the experimental observables such as the product distributions and the selectivity of the reaction, beside the widely accepted concerted pericyclic mechanism. The effect of catalysts on the mechanism and the selectivity have been studied and discussed in detail. The fundamental interactions in the key transition states have been analyzed and the factors affecting the stereoselectivity of the reaction have been elucidated. Comparative studies on highly selective and non selective variants have allowed us to identify the elements responsible for controlling the selectivity of the reactions of interest. This work brings a new perspective to the mechanism of pericyclic reactions and provides a deeper insight into the factors that determine the selectivity. However, the scope of the pericyclic reactions is very large and highly useful examples are not limited to the ones discussed in this dissertation. Future work will undoubtedly uncover many other important aspects of selective pericyclic reactions. Several suggestions for prospective studies have been outlined in the final chapter.
Modeling the selectivity, catalytic and binding effects in organic reactions and protein environment
(Thesis (Ph.D.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 2015., 2015.) Dedeoğlu, Burcu.; Aviyente, Viktorya.; Özen, Alimet Sema.
In this dissertation, quantum chemical tools, in particular density functional methods are used to address problems related with the selectivity, catalytic and binding effects in different fields of chemistry, such as materials science, organic chemistry and biochemistry. The selectivity of photoluminescent polymers towards analytes in the explosive detection field has been investigated by modelling the complexes between the polymers and analytes. The simulated optoelectronic properties of the polymers and their complexes with the analytes highlighted the detection mechanism based on fluorescence quenching. The mechanism and selectivity in the asymmetric desymmetrization of meso-cyclic anhydrides induced by cinchona alkaloids have been investigated and base catalysis mechanism has been shown to operate in these reactions. The origins of stereoselectivity have been attributed to the spatial arrangement of the cinchona alkaloid catalyst in the transition state of asymmetric desymmetrization reaction related with the oxyanion stabilization. The inverse electron demand Diels-Alder reaction of phthalazine and siloxy alkyne activated by Ag(I)-bipyridine catalysis have been modeled and the barriers are compared with the uncatalyzed cycloaddition reaction to highlight the catalytic effect of Ag(I)-bipyridine. It has been shown that the primary role of Ag(I)-bipyridine catalyst in an inverse electron demand Diels-Alder reaction is to facilitate the overlap between HOMO of the dienophile and LUMO of the diene by reducing the energy gap. The iron binding-release mechanisms have been investigated in the cluster models of transferrin, iron binding protein. Possible routes for iron release are evaluated on the basis of the thermodynamic stabilities of the models.
Modeling the solvent effect, kinetics, morphology and catalysis in polymerization reactions
(Thesis (Ph.D.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 2016., 2016.) Özaltın, Tuğba.; Aviyente, Viktorya.
In this dissertation, quantum chemical tools, in particular density functional theory (DFT), molecular dynamics (MD) and coarse-grained (CG) simulations are used to address the solvent e ect, kinetics, morphology and catalysis in polymerization reactions. The free-radical copolymerization kinetics of styrene (ST) and 2-hydroxyethyl methacrylate (HEMA) have been investigated by DFT in three di erent media (bulk, dimethylformamide (DMF), toluene). In DMF, the reactivity of the monomer HEMA, thereby its composition in the copolymer decreases because of the H-bonding tendency of the monomer with DMF. The e ect of Lewis acid coordination on the propagation kinetics and mechanism of N,N -dimethyl acrylamide (DMAM) has also modeled with DFT. It is shown that the terminal-monomer type of propagation is the most probable pathway favoring the isotactic product formation. A multiscale approach has been used to understand the morphological behavior of thermo-responsive polymer poly (2-isopropyl-2-oxazoline) (PIPOX) in aqueous solution. The most probable structure for the PIPOX chain above Tc is obtained by torsional analysis after reversemapping of the CG structure followed by MD simulations. X-ray di raction pattern well-reproduces the experimental one for crystalline PIPOX nanoribbons formed in water above Tc. The results are important in identifying a new helical conformation for PIPOX prior to crystallization. The mechanisms of cationic ring-opening polymerization of benzoxazines are still not well established. Reaction mechanisms giving phenoxy and phenolic type products have been modeled for pC-m monomer which is expected to give phenolic type product; the rearrangement mechanisms to obtain phenolic type products are also evaluated.
Role of ionic liquids on the reactivity and selectivity of diels- alder reactions and single site catalysts
(Thesis (Ph.D.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 2022., 2022) Akgül, Deniz.; Doğan, İlknur.; Aviyente, Viktorya.
Ionic liquids (ILs) have gained interest because of their features such as high thermal stability, high chemical inertness, conductivity, their ability to dissolve organic and inorganic substances. It is possible to tune these properties offering advantages for a wide range of applications namely solutions, synthesis and catalysis. In this thesis, the solvent and ligand effects of ILs are investigated in the case of organic reactions and single-site catalysts (SACs) by using Density Functional Theory (DFT). Then, the influence of electron-donor/acceptor properties of the SACs on the catalytic activities and stabilities of Ir/Rh including complexes are examined by means of computational tools. Firstly, the role of ILs as solvents in the Diels-Alder reactions is modeled. The fact that ILs can have hydrogen bonding interac tions with the dienophiles, and thus significantly affect the endo selectivity and the rate of the Diels-Alder reactions has been assessed. The atomically dispersed catalysts in the pres ence of SiO2-, γ-Al2O3- and MgO supported-Ir(CO)2 complexes are analyzed in order to understand the support effects on the electronic properties of the active sites and stabilities of the catalysts. Chapter 5 deals with the electron-donor/acceptor properties of ILs by us ing IL coated/uncoated MgO supported Ir(CO)2 complexes in the presence of [Bmim][OAc] and [Bmim][PF6]. In order to understand the ligand effects on the catalytic properties of the SACs, ligand modification reactions between carbonyl and acetylene groups in the case of zeolite- supported Rh(CO)2 complexes are modeled by considering the proton mobility. Finally, the hydrogenation reaction mechanisms for 1,3-butadiene over γ-Al4O6 supported Ir(CO)2 complex is studied and the reasons behind the 1-butene selectivity have been clari fied. Overall, this study contributes to a better understanding of the solvent and ligand effects of ILs on the chemical reactions and the catalytic systems.
Synthesis, evlatuation of functional methacrylates and a computational approach to the reactions of molecules with biological potential
(Thesis (Ph.D.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 2017., 2017.) Agopcan, Sesil.; Avcı, Duygu.; Aviyente, Viktorya.
In this dissertation, experimental and computational methods are used to in vestigate the molecules which are biologically active and have potential in pharma ceutical ﬁeld. This study sheds light on the synthesis procedures of methacrylate based monomers, characterization of the synthesized materials, and also detection of reaction mechanisms, calculations of thermodynamic properties in several reactions. In the ﬁrst three chapters, several methacrylate monomers were investigated which have various biomedical applications. The synthesis and photoinitiating abilities of six novel methacrylate-based monomeric photoinitiators (MPIs) has been carried out. In order to make useful predictions on the reactivities of methacrylates, a relationship between reactivities of 21 methacrylates in free radical polymerization and their chem ical structures were built by a non-linear expression. Finally, methacrylates were used to prepare PEG-based carboxylic-acid functionalized monomers which were incorpo rated into hydrogel scaﬀolds for biomedical applications. In the last three chapters, the reactions of biologically active molecules were analyzed by computational tools. The exo-stereoselectivity of norbornene in the synthesis of thiazolidine derivatives which have diverse biological potential, are clariﬁed by means of Density Functional Theory (DFT). Another biologically active molecule, diclofenac that is used as a drug, was examined to enlighten the degradation mechanism and byproduct formations. Finally, the reactions of cyclohexanone with 3-methyl indole and N-methyl indole, which are the basis of many biologically active compounds, are modeled to determine the origins of regioselectivities.

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