Ph.D. Theses

Permanent URI for this collection

https://digitalarchive.library.bogazici.edu.tr/handle/123456789/11657

Browse

Now showing 1 - 20 of 57

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.
Conformational analysis of 2-substituted cyclohexanone ketal derivatives by molecular mechanics and nuclear magnetic resonance
(Thesis (Ph.D.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 1986., 1986.) Varnalı, Tereza.; Özbal, Hadi.
The present study is concerned with the application of the Molecular Mechanics Method to 2-substituted cyclohexanoneketals. The object is to find the conformational free energy difference between the equilibrating conformers and to compare the theoretical results to those found experimentally. For the application of molecular mechanics, models of the compounds underinvestigation were described, the inter-atomic distances and angles were computed, the most important interactions were determined and the parameters needed for calculations of the interactions and functions relating parameter to energy were chosen. First, molecular mechanics was applied to spiro- [5,4]-1-halo-6,9-dioxodecane (1 in Fig. 1.1.1) and spiro-[5,5]-1-halo-6, 10-dioxoundecane(2 in Fig.1.1.1) where the halogen was chlorine or bromine. The results obtained theoretically showed preference for the conformer bearing the axialhalogen in (2) system and the conformer bearing the equational halogenin (1) system, being in accordance to experimental results reported by Zefirovet et. al. Secondly, molecular mechanics was applied to spiro- [5,4]-1-halo-6,9-dioxodecane and spiro-[5,5]-1-nitro-6,10 undecane and the results obtained theoretically in contrast to halogens, showed preference for the conformation in which the nitro group is equatorial in both cases ( 1 ) and ( 2 ). Finally, the 4-t-butyl derivatives of the nitro-(1) and (2) systems, and the (1) and (2) systems were synthesized and the free energy difference between the equilibrating conformers were obtained experimentally using NMR parameters. Experimental results were in parallel to those found theoretically. In previous studies the nitro group has been shown to behave differently than halogens and similar groups due to its electronic distribution, size, structure and formal change. The unique behavior of the nitro group has been shown once more both theoretically and experimentally.
Molecular dynamics study of macromolecular motions and polypeptide helical stabilities in solution
(Thesis (Ph.D.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 1995., 1995.) Doruker, Pemra.; Bahar, Ivet.
Molecular dynamics simulations have been performed to investigate the relative importance of solvent effect and intramolecular conformational potentials on the properties of polymers in dilute solition. Bead-spring, free-rotating and polyethylene model chains, each composed of 30 beads, have been simulated in 738 solvent molecules. Results indicate that chain statistics are equally sensitive to solvent effect and intramolecular constraints, whereas local chain dynamics are predominantly described by intramolecular potentials. Translational diffusivities of all chains exhibit a linear decrease with increasing polymer-solvent interactions. A power law relation of the form t na is observed betveen the orientational correlation times t and the size n of chains segments for n = 8. a values increase with solvent quality. Stability of short helical polypeptides have been studied by molecular dynamics simulations. 13-residue polypeptides, composed of alanine, valine, serine or glycine, have been simulated in water and in vacuum. Water destabilizes the helical structure of alanine and valine, whereas glycine and serine exhibit intrinsic helix-breaking propensities in vacuum. Local solvation patterns around alanine Cb, valine Cg and serine Og atom are similar in helical state. Backbone hydrogen bonds are well protected by valine side chains, compared to alanine and serine.
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.
TiO2 semiconductor photodegradation of substituted resorcinols: |kinetic and mechanistic studies
(Thesis (Ph.D.)- Bogazici University. Institute for Graduate Studies in Science and Engineering, 1999., 1999.) Ökte, Ayşe Neren.; İnel, Yüksel.
The photocatalytic degradation of 1,3-dihydroxybenzene (1,3-DHB) (resorcinol) and the substituted resorcinols, 3,5-dihydroxytoluene (3,5-DHT), 1,3-dihydroxy-5-methoxybenzene (1,3-DHMB) and 3,5-dihydroxybenzoic acid (3,5-DHBA) in the presence of aqueous suspensions of TiO2 are investigated kinetically and mechanistically. The effects of initial concentrations of the reactants, the pH of the medium, temperature, incident photon flux, and irradiation time are examined in detail. It is found that 1,3-DHB and 3,5-DHT obey pseudo-first order kinetics whereas 1,3-DHMB and 3,5-DHBA obey zero order kinetics. The Langmuir type of plot confirms that reactions take place on the surface of TiO2. 1,3-DHB, 3,5-DHT, and 1,3-DHMB are found to be most efficient at pH 9.0 while 3,5-DHBA had highest efficiency at its natural pH 4.4. The activation energy is found as 11.2 kJ/mol, 17.4 kJ/mol, 17.1 kJ/mol, and 10.3 kJ/mol for 1,3- DHB, 3,5-DHT, 1,3-DHMB, and 3,5-DHBA, respectively. Based on the relative photonic efficiency concept, the quantum yield is found as 0.34, 0.22, 0.35, and 0.38 for 1,3- DHB, 3,5-DHT, 1,3-DHMB, and 3,5-DHBA, respectively. Deposition of Fe3+, Ni2+, Zn2+, Nb5+, Ta5+, Co2+, Mn2+, Al3+, Cr3+ and V4+ on the surface of TiO2 affects the photocatalytic degradation of reactant molecules. Fe3+ showed the highest efficiency.
Barriers to enantiomerization of 1-(o-ARYL) barbituric and -2-thiobarbituric acid derivaties
(Thesis (Ph.D.) - Bogazici University. Institue for Graduate Studies in Science and Engineering, 2002., 2002.) Oğuz, Semin Funda.; Doğan, İlknur.
In this study, 5,5-dimethyl-1-(0-aryl)barbituricI, 1-(0-ary1)barbituric and 1-(0-aryi)- 2-thiobarbituric acids have been synthesized by the reaction of the o-arylureas or the oaryl- 2-thioureas with the diethylmalonate or 1,l-diethyl-2,2-dimethyl malonate in the presence of sodiumethoxide, 5,5-dimethyl-1-(o-ary1)-2-thiobarbituric acids have been synthesized by the reaction of the o-aryl-2-thioureas with the dimethylmalonic acid in the presence of acetylchloride. The studied barbituric and 2-thiobarbituric acids are chiral due to nonplanar ground states. The aim of this study is to separate the enantiomers of the barbituric and 2-thiobarbituric acid derivatives by liquid chromatography on an optically active sorbent and subsequent racemization to obtain the activation energies for the racemization process. The chiralities of the compounds have been proved by 'H and 13c NMR spectroscopy. The enantiomers have been separated by liquid chromatography on chiral sorbents, triacetylcellulose or cellulose tris-(3,s-dimethylphenyl) carbamate. The optical activities of the separated enantiomers have been detected by CD spectrometer or polarimeter. Upon thermal racemization the activation barriers of the 5,5-dimethyl-1-(0- ary1)barbituric and -2-thiobarbituric acids have been determined by using liquid chromatography. The activation barrier of the 1-(0-toly1)barbituric acid has been determined by using dynamic NMR spectroscopy. The racemization mechanisms have been discussed with reference to the determined barriers. In addition, the keto-en01 tautomerization of the 1-(0-ary1)barbituric and 1-(0-ary1)-2-thiobarbituric acids have been investigated in different solvents by using 'H and I3c NhXR spectroscopy.
Preparation characterization and drug release behavior of thermo-and pH-responsive hydrogels and microspheres
(Thesis (Ph.D.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 2002., 2002.) Taşdelen, Dinçer Betül.; Haliloğlu, Türkan.; Baysal, Bahattin M.,
In the present work, N-isopropylacrylamide/itaconic acid and N-isopropylacrylamide /maleic acid copolymeric hydrogels were prepared by irradiating the ternary mixtures of Nisopl- opylacrylamide/diprotic acid moieties (itaconic or maleic acid)/water by y-rays at ambient temperature. The influence of external stimuli such as pH and temperature of the swelling media on the equilibrium swelling properties were investigated. The hydrogels showed both temperature and pH responses. The effect of comonomer concentration and irradiation dose on the swelling equilibria and phase transition were studied. For the characterization of network structures of these hydrogels, molecular weight between cross-links and crosslinking densities were also determined. PNIPAAm microspheres (71-500pm) were prepared by using inverse suspension polymerization technique. The selected fraction (1 80- 250pm) was used for preparing NIPAAmIitaconic acid graft copolymer by radiationinduced surface modification technique. Finally, methylene blue, sildenafil citrate and lidocaine were used as model drugs for the investigation of drug adsorption and controlled release behaviour for the hydrogels and micospheres. Specific adsorption capacity of: hydrogels are found to increase with increasing amount of itaconic acid in the gel system. The effect of the initial drug loading amount, temperature and pH of the solution on the controlled release behaviour of the hydrogels were investigated. The release studies show that some of the basic parameters affecting the drug release behaviour of the hydrogels are, pH and temperature of the solution.
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
Synthesis of new dental adhesive monomers and polymers
(Thesis (Ph.D.)-Bogazici University. Institute for Graduate Studies in Science and Engineering, 2006., 2006.) Albayrak, Aylin Ziylan.; Avcı, Duygu.
New phosphonate, phosphonic acid, carboxylic acid, iminodiacetate containing adhesive monomers based on alkyl-hydroxymethyl acrylates and their derivatives were synthesized. A new phosphonate-containing cyclic monomer was obtained from the reaction of 2-(2-chlorocarbonyl-allyloxymethyl)-acryloyl chloride with diethyl hydroxymethyl phosphonate. This monomer showed high cyclization tendency during homopolymerization and copolymerization with 2-(2-tert-butoxycarbonylallyloxymethyl)- acrylic acid tert-butyl ester (TBEED) using initiators 2,2’- azobis(isobutyronitrile) (AIBN) at 75-77 ºC. The Tg of the copolymers decreased with increasing amounts of phosphonate-containing monomer whereas the char residues of the copolymers increased. The selective hydrolysis of the phosphonate monomer with trimethylsilyl bromide gave a water soluble phosphonic acid-containing monomer. This monomer could not be homopolymerized but copolymerized with TBEED and its dicarboxylic acid derivative, 2-(2-carboxy-allyloxymethyl)-acrylic acid. A series of 4,4-disubstituted 1,6-heptadiene monomers were synthesized from the reaction of ethyl- -bromomethyl acrylate and tert-butyl- -bromomethyl acrylate with triethylphosphonoacetate and tetraethylmethylenediphosphonate using sodium hydride followed by selective hydrolysis of the ester groups. Photopolymerizations of the monomers were investigated to understand the effect of the cyclic monomer structure on their polymerization reactivity. A strong effect of the substituents at 2, 4 and 6 positions of the monomers on polymerization rate was observed. The polymerizability of the monomers were successfully correlated with the 13C-NMR chemical shifts of the vinyl carbons. Conversion values were consistent with the Tg being a measure of the flexibility of a monomer. The monomers containing phosphonic acid groups were soluble in water and ethanol. The acidic nature of the aqueous solutions of these monomers is expected to give them etching properties, important for dental applications. The interaction of the acid monomers with hydroxyapatite was investigated using 13C NMR technique. It was found that phosphonic acid-containing monomers demineralized the calcium phosphate in the HAP in preference to the carboxylic acid. Four new methacrylate monomers containing phosphonic and/or carboxylic acids were synthesized from the reaction of tert-butyl a-bromomethyl acrylate with triethyl phosphite followed by selective hydrolysis of the phosphonate or tert-butyl ester groups using trimethylsilyl bromide and trifluoroacetic acid. The copolymerization of these monomers with 2-hydroxyethyl methacrylate (HEMA) was investigated by photodifferential scanning calorimetry. The reactivities of the monomers increased by decreasing steric hindrance and increasing hydrogen bonding capacity due to hydrolysis of phosphonate or tert-butyl ester groups. Furthermore, new adhesive monomers with diethyliminodiacetate as a potential chelating group were synthesized from the reaction of ethyl-bromomethyl acrylate, 2-chloromethyl-acryloyl chloride and 2-(2-carboxy-allyloxymethyl)-acrylic acid with diethyl iminodiacetate. The monomers were homopolymerized and copolymerized with TBEED and HEMA. Rate of copolymerizations and conversions decreased with an increase in the monomer concentrations. Low polymerizability of these monomers were explained with the steric effect of the N,N-disubstituted methacrylamides and the presence of allyl amine group leading to degradative chain transfer. The monomers were hydrolyzed by potassium hydroxide solution and the salt derivatives were copolymerized with acrylamide in water using 2,2’-azobis(N,N’-amidinopropane) dihydrochloride (V- 50). Polymer yields after dialysis were low and decreased with increasing monomer concentrations. The Ni+2 chelating ability of the monomers were shown using UV-visible spectroscopy. Thermal stability of the copolymer increased on complexation with Ni+2 ions.
Axialy chiral n-(o-aryl)-2-thioxo-oxazolidine-4-one and rhodanine derivatives: enantiomeric separation and determination of racemization barriers
(Thesis (Ph.D.)-Bogazici University. Institute for Graduate Studies in Science and Engineering, 2008., 2008.) Yılmaz, Esra Müjde.; Doğan, İlknur.
In this study, sterically hindered 5,5-dimethyl-3-(o-aryl)-2-thioxo-4-oxazolidinones, 5,5-dimethyl-3-(o-aryl)-2-thioxo-4-thiazolidinones and 3-(o-aryl)-2-thioxo-4- thiazolidinones(rhodanines) have been synthesized as racemates by either the reaction of oaryl isothiocyanates with α-hydroxyisobutyrate or by treatment of o-arylisothiocyanates with the correponding thioglycolic acid ethyl ester. The 5,5-dimethylrhodanines have been synthesized according to Modified Kaluza synthesis. Chirality of the compounds has been proven by the presence of diastereotopic methylene protons or methyl groups on C-5 of the heterocyclic ring detected by 1H NMR or 13C NMR spectroscopy. The enantiomers of the synthesized compounds have been resolved or enriched micropreparetively on chiralpak AD-H column, packed with amylose tris-(3,5-dimethyl phenyl)carbamate. The activation barriers for interconversion between the enantiomers have been determined by either temperature dependent NMR or by thermal racemization followed by enantioresolution on a chiral sorbent via HPLC. The activation barriers to rotation around C-N bond showed a linear increase with the van der Waals radii of the ortho-halogen substitutents. Absolute conformations have been determined by analysis of NMR spectra of Nnaphthyl substituted derivatives of the series in the presence of the chiral auxiliary (S)-(+)- 1-(9-antryl)-2,2,2-trifluoro ethanol ((S)-TFAE). Plausible diastereomeric association models between the enantiomers of the compounds 3-(α-naphthyl)-2-thioxo-4- ii thiazolidinone and 3-(α-naphthyl)-2,4-thiazolidinedione and the chiral auxiliary (S)-TFAE have been proposed. Enantiodifferentiation of 3-aryl-2-thioxo-4-oxazolidinones by NMR was also studied by using a dirhodium tetracarboxylate complex as the chiral auxiliary. Determination of relative conformations of the series have also been attempted by applying the dirhodium method to the enantiomerically enriched samples, however this could not be achieved.
Functionalization and polymerization of plant oil triglycerides
(Thesis (Ph.D.)-Bogazici University. Institute for Graduate Studies in Science and Engineering, 2008., 2008.) Çaylı, Gökhan.; Küsefoğlu, Selim.
In this study, new polymers and were synthesized from different plant oil triglycerides by using allylic groups of the triglycerides. Moreover, allylic positions and double bonds of soybean oil were used for preparation of different type of reactive monomers and their polymers. Soybean, cod liver, and linseed oils were polymerized by oil soluble phenolformaldehyde resins in one step. Phenols which were used to prepare oil soluble resoles were p. ethyl, p. tertiary butyl, p. tertiary octyl, and p. phenyl phenols. Among the triglycerides the best polymerization results were obtained from linseed oil. A series of rubbery polymers were synthesized with linseed oil with 40 per cent phenol formaldehyde resins. For other less unsaturated oils, similar results could be obtained with at least 60 per cent phenolic resin use. Among the oil soluble resoles, the best mechanical and thermal properties were obtained with p. ethyl phenol resole. The mechanical properties of p. phenyl phenol resole were better than p. tertiary butyl and octyl resoles. In the second part of the study, soybean oil was first converted to allylic brominated soybean oil by NBS (N-bromo succinimide) and then reacted with acrylate and methacrylate salts, -OCN, -SCN anions and triethyl amine to give allylic acrylate and methacrylate esters of soybean oil, polyisocyanate and polyisothiocyanates of soybean oil and quaternary ammonium salts of soybean oil respectively. Soybean oil was also reacted with iodine isocyanate to give iodo isocyanate addition products of soybean oil. This poly isocyanate was then polymerized with different type of alcohols and amines to give corresponding polyurethanes and polyureas. Also, similar reactions were performed on methyl oleate as a model compound. Allylic acrylate and methacrylate esters of methyl oleate were obtained by the reaction between allylic brominated methyl oleate and acrylic and methacrylic acid potassium salts. Moreover allylic amine of methyl oleate was prepared by the reaction between allylic brominated methyl oleate and NH3 and this monomer was polymerized to give AB type unsaturated fatty based polyamides by amide-ester interchange. In the third, part of this study, acrylated epoxidized soybean oil was polymerized with p. tertiary butyl phenol furfural resin via Diels-Alder reaction to give cross linked polymers. When the polymer was heated above 140 oC, retro Diels-Alder reaction took place with a 60 per cent yields. After cooling of the materials, cross linking was established again. After each heating and cooling cycle the hardness of the polymer increased due to the increasing the cross linking density which was caused from imperfect retro Diels-Alder reaction of furan and acrylate moieties. The chemical, physical and thermal behaviors of the product polymers were characterized.
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.
Asymmetric syntheses, ring opening and stereoselective reactions, absolute conformation and activation barrier determinations on axially chiral oxazolidine derivatives
(Thesis (Ph.D.)-Bogazici University. Institute for Graduate Studies in Science and Engineering, 2008., 2008.) Ordu, Öznur Demir.; Doğan, İlknur.
In this study, sterically hindered 5-methyl-3-(o-aryl)-2,4-oxazolidinediones, 5-methyl- 3-(o-iodophenyl)-2-thioxo-4-oxazolidinedione and 5,5-dimethyl-3-(o-aryl)-2,4- oxazolidinediones have been synthesized. Diastereomeric isomers of the 5-methyl-3-(oaryl)- 2,4-oxazolidinediones and 5-methyl-3-(o-iodophenyl)-2-thioxo-4-oxazolidinedione and enantiomeric isomers of the 5,5-dimethyl-3-(o-aryl)-2,4-oxazolidinediones have been identified by 1H NMR and 13C NMR. Activation barriers to hindered rotation around C-N single bond have been determined by using temperature dependent NMR or by thermal racemization on chiral sorbents by HPLC. The conformational preferences of the diastereomers have been investigated by one and two dimensional NMR spectroscopy and by HPLC on an optically active sorbent. It was found that when the bulky group on C-5 and the ortho substituent on the aromatic ring are on opposite sites the conformation becomes more stable. Absolute confomations of 5,5-dimethyl-3-(o-aryl)-2,4-oxazolidinediones have been determined by one and two dimensional 1H NMR in the presence of a chiral auxiliary (S)- (+)-1-(9-anthryl)-2,2,2-trifluoro ethanol ((S)-TFAE). A solvation model has been proposed for the determination absolute stereochemistry on the basis of interactions between the enantiomers and (S)-TFAE. vi Asymmetric alkylation and aldol reactions have been carried out on 5-methyl-3-(otolyl)- 2,4-oxazolidinedione, 5-methyl-3-(o-iodophenyl)-2,4-oxazolidinedione and 5- methyl-3-(o-iodophenyl)-2-thioxo-4-oxazolidinedione over the lithium enolate forms. The enolate formation could be achieved by lithium diisopropylamide at -78 0C under nitrogen. It was found that the o-aryl substituents had a stereodirecting effect on the reactions taking place at C-5 of the ring. The stereoselectivity of the reactions was determined by using chiral HPLC. Basic and reductive ring opening reactions of diastereomeric 5S-methyl-N-(o-aryl)- 2,4-oxazolidinediones and enantiomeric 5,5-dimethyl-N-(o-aryl)-2,4-oxazolidinediones have been done to examine the stability of the ring and to synthesize various organic compounds such as chiral –hydroxyamides, carbamoyloxyacids and carbamate derivatives via ring opening. It was observed that 5-methyl-2,4-oxazolidinedione ring cleaved more easily than 5,5-dimethyl-2,4-oxazolidinedione ring. 5-Methyl-2,4- oxazolidinedione ring was reduced to a primary alcohol after ring opening, whereas the reduction of 5,5-dimethyl-2,4-oxazolidinedione ring yielded a secondary alcohol asymmetrically without ring cleavage.
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.
Chemical characterization of lipid residues in neolithic and chalcolithic pottery from Anatolia
(Thesis (Ph.D.)-Bogazici University. Institute for Graduate Studies in Science and Engineering, 2009., 2009.) Bıyık, Ayla Türkekul.; Özbal, Hadi.
.
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.
Polymerization reactions of functionalized vegetable oils with petroleum-based macromonomers
(Thesis (Ph.D.)-Bogazici University. Institute for Graduate Studies in Science and Engineering, 2010., 2010.) Öztürk, Cem.; Küsefoğlu, Selim.
The aim of this work is to synthesize new polymers from plant oils. Polymerization of plant oil triglycerides is possible by attaching a polymerizable group to the triglyceride. This strategy has been used by us and by others in many examples. Polymers derived from such monomers have low connectivity and low mechanical properties due to the bulky structure of the monomer. This manifests itself in low fracture toughness of the polymers obtained. In this work we changed our strategy by starting first with a suitably substituted polymer having a high molecular weight and attaching the triglyceride derivative to it. This strategy provides molecular weights that are higher and provides the entanglement lengths needed for higher fracture toughness. In this work styrene maleic anhydride copolymer (SMA), maleic modified polypropylene (MMPP), poly(4-vinylpyridine) (P4VP), maleic modified polybutadiene (MMPBD) is grafted and/or cross-linked with epoxidized methyl oleate (EMO), epoxidized soybean oil (ESO), methyl ricinoleate (MR), soybean oil maleic anhydride (SOMA), castor oil (CO) and soybean oil diglyceride (DG). Also a new radically polymerizable triglyceride based monomer, 1-(4-vinylbenzene sulfonyl)oxy-2-alkonols of epoxidized soybean oil (SESO), was synthesized by the reaction of epoxidized soybean oil (ESO) with 4-vinylbenzene sulfonic acid (4VBSA). The adduct was homopolymerized into a soft and insoluble polymer in the presence of a free-radical initiator and also copolymerized with a reactive diluents such as styrene. Physical, chemical and mechanical properties of these new polymers are characterized by FTIR, 1H NMR, DSC, DMA and TGA.
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.
Chain extension reactions of unsaturated polyesters using difunctional molecules
(Thesis (Ph.D.)-Bogazici University. Institute for Graduate Studies in Science and Engineering, 2011., 2011.) Taylan, Ediz.; Küsefoğlu, Selim.
In this study the effectiveness of various chain extenders in increasing the molecular weight of unsaturated polyesters was investigated. For this purpose eight different chain extenders (with di or multi-functionalities) such as epoxides, isocyanates and bisoxazolines were added to short chain oligomeric polyesters with molecular weights of 500-700 and the desired molecular weight of 1500-2000 was reached within very short times. Diglycidyl ether of bisphenol A, 1,2;7,8-diepoxyoctane and epoxidized soybean oil reacted with carboxylic end groups of unsaturated polyesters within 30-60 minutes; two blocked isocyanates, namely diphenylmethane-bis-4,4’-N,N’-ethyleneurea and diphenylmethane-bis-4,4’-carbamoyl-Є-caprolactam reacted with both carboxylic and hydroxylic end groups of the unsaturated polyesters to reach the desired molecular weight within less than one hour. Isocyanated soybean oil reacted with hydroxyl end groups of the polyester chains. 1,3-phenylene-bis-oxazoline and 2,2’-bis-2-oxazoline gave a fast reaction with the carboxylic end groups of the oligomeric polyesters within a reaction time as short as 5 minutes. With the help of these extenders the conventional polyesterification reaction time can be reduced from 20 hours to 6-7 hours, diol loss can be eliminated and product yields can be increased by about 5 per cent. After dilution with styrene to give a styrene concentration of 35 per cent, the resins were cured in the usual manner and the mechanical and thermal properties of the cured resins were found to be comparable to that of the commercial reference product. Thus, the industrial use of the chain extended polyesters was verified. Gel times remained close to that of the commercial reference product (10-15 minutes). Tg values were found about 80-90 oC and the TGA data showed that the 5 per cent weight loss temperature in many cases was about 230-275 oC, very comparable to that of the commercial reference product.
Synthesis of novel potent drug molecules active against prostate cancer and investigation of bioactive properties of cyclopolymers obtained by raft polymerization
(Thesis (Ph.D.)-Bogazici University. Institute for Graduate Studies in Science and Engineering, 2011., 2011.) Erkoç, Selda.; Acar, Ali Ersin.
The first part of the thesis includes synthesis of novel potent drug molecules active against prostate cancer. Structure-based drug design (SBDD) approach was used to discover novel lead compounds active against CYP17 by the researchers Prof. Metin Türkay and Assoc. Prof. İ. Halil Kavaklı from the Koç University. They found a non-steroidal lead compound with the IC50 value of 35.65M. In this study, in order to increase the activity of the lead compound against the CYP17, lead optimization studies were done. Lead compound derivatives were evaluated on the computer generated model of CYP17. The compounds that have favorable energy values in docking studies were synthesized to be effective in nanomolar concentrations. Some of the synthesized compounds were subjected to biological tests in order to measure inhibitory effects of them on CYP17. IC50 value of the compounds that displayed favorable inhibitory activity on human CYP17 were calculated. As a result, a new compound with the IC50 value of 2.3 M was discovered. The activity of this compound is about fifteen times higher than the activity of the lead compound. The second part of the thesis includes the investigation of bioactive properties of cyclopolymers obtained by Reversible Addition Fragmentation Chain Transfer (RAFT) Polymerization. In this study, RAFT polymerization was applied to symmetrical difunctional monomers, alkyl -(hydroxymethyl)acrylate (RHMA) ether dimers (R=alkyl (ethyl, n-butyl, tert-butyl, cyclohexyl, isobornyl)). The livingness of the obtained cyclopolymers with tert-butyl and isobornyl ester groups was shown through successful block copolymerization studies with n-butyl acrylate where the former was used as the macro-chain transfer agent (macroCTA). Finally, the antibacterial activities of the obtained cyclopolymers were investigated using Staphylococcus aureus and Escherichia coli as test organisms.

Browse

Browsing Ph.D. Theses by Issue Date

Results Per Page

Sort Options