Master Degree / Yüksek Lisans Tezleri

Permanent URI for this collectionhttps://hdl.handle.net/11147/3008

Browse

Filters

2004 - 200932010 - 20193

Settings

Author: search.filters.author.Elmacı Irmak, NuranCOAR Access Rights: search.filters.coarAccessRights.open access

Search Results

Now showing 1 - 6 of 6
  • Master Thesis
    Molecular Dynamics Simulation Study on the Interactions Between Dna and a Conjugated Polyelectrolyte (cationic Oligothiophene)
    (Izmir Institute of Technology, 2019) Nalıncı Bardak, Nehir; Elmacı Irmak, Nuran
    The absorption spectra of the cationic polythiophenes shift to the red, or the color changes in the solution are visible to the naked eye, when single-strand DNA (ssDNA) is added, so that they can be used as a tool for DNA detection, theranostic applications, and biological sensors. The red shift or color change is explained by the fact that the ssDNA leads to conformational changes in the polythiophene, but the form of structural change remains to be elusive (i.e. flattening, twisting, stacking, etc.). In this study, molecular dynamics (MD) simulations of complexes consisted by ssDNA sequences with different nucleotides and polythiophene containing cationic side group were performed to enlighten the experimental studies. For this purpose, force field parameters of polythiophene which are not present in the current databases, were generated. The interactions between them were analyzed to determine the nature of conformational changes in the polythiophene when ssDNA was added. MD simulations has been carried out with the CHARMM-compatible force field parameters obtained in the content of this work. Radius of gyration of oligomer increases with addition of ssDNA but is more affected by homopurine strand. Planarity index gets larger upon complexation with homopurine and T_rich strand, does not change with others. H-O and electrostatic interactions which are almost doubled in nonplanar complexes can be interpreted as the major sources of conformational changes in oligomer. Considering all types of interactions between atoms in duplexes, it was observed that planarity was high in structures with less interaction of oligomer side groups.
  • Master Thesis
    Detection of Dna Methylation of Multiple Tumor Supressor P16ink4a Gene by Polythiophene Based Optical Sensor
    (Izmir Institute of Technology, 2018) Kaya, Hakan; Yıldız, Ümit Hakan; Elmacı Irmak, Nuran
    DNA methylation is epigenetic events commonly occurs in mammalian genome starting from formation of embryo to the end of life. Especially, hypermethylation in tumor suppressor genes, corresponds the cancer growth and detection of DNA methylation in these genes crucial for the diagnosis of cancer. Water soluble polythiophenes are frequently used for the detection of biomolecules through the optoelectronic properties. In this study, detection of DNA methylation of multiple tumor suppressor p16INK4A gene via polythiophene based optical sensor was achieved. Newly designed, synthesized and characterized poly(1-(3-((4-methylthiophen-3-yl) oxy) propyl)-1,4diazabicyclo [2.2.2] octan-1-ium bromide) was used during characterization of DNA sequences and detection of DNA methylation. The target sequence position is +137 to +156 in p16INK4A gene which have three potential CG dinucleotide to be methylated. Detection of DNA methylation based on sodium bisulfite treatment, complementary sequence of unmethylated ssDNA and the conformational change of water soluble polythiophene. In our fluorometric analysis, unmethylated sequence/complementary successfully hybridized and dsDNA Io/I ratio is under the 1.40 while the methylated sequence/complementary hybridization failed due to different base content and remain as ssDNA and, Io/I ratio is higher than 1,60. The novelty of work is detection mechanism is PCR and FRET free with a range of 300 ng to 700 ng sample requirement. Characterization of homopurines, homopyrimidines, methylated and unmethylated sequence with cationic polythiophenes also accomplished. PolyG (10), polyG (20) and polyA (10) yielded a no signal in UV-VIS region while the polyA (20) yielded a 100 nm red shift. Furthermore, PolyC (10), PolyC (20), PolyT (10), PolyT (20) yielded three vibrionic peaks at 505 nm, 545 nm and 595 nm with different intensities and unique isosbestic points. All 10 bases long homopyrimidine and homopurine have a unique quencher character with cationic polythiophene. Lastly, conformational change of polythiophene investigated with computational methods and heptamer used as a model.
  • Master Thesis
    A Computational Study on the Structures and Proton Affinities of B3+ Ions; Peptide Mass Fragment Product
    (Izmir Institute of Technology, 2015) Boz, Seçkin; Elmacı Irmak, Nuran
    Mass spectrometry is the tool of choice during most of the proteomics studies to get amino acid sequence. However, unambiguously identifying amino acid sequence from mass spectra is not easy and straight forward task. Deeper understanding is needed to support both existing knowledge and develop newer models on dissociation patterns of protonated peptides and it will help to improve efficiency of current algorithms used in peptide identification. In this study, the structures of b3+ ions and their neutral forms were investigated by using computational methods. First, potential energy surface of b ions are scanned using molecular dynamics simulations and conformer samples are collected. Then, in order to reduce number of conformers, principal coordinate analysis was applied to find and select different structures within the sample. Selected conformers were optimized using density functional theory calculations. Proton affinities of b ions are determined by the energy difference between most stable conformers of the positively charged and neutral peptide fragments. Different amino acids were used to understand the role of side chain of amino acids on both structures and proton affinities of b3+ ions; XA2+ where X=N, H, C, Y, D, L and F. The results showed that, b3+ ions prefer to have linear oxazolone structure. However, in their neutral states, cyclic structures are relatively far more stable than linear isomers. Histidine display different behavior than other amino acids. Side chain of histidine holds protons and forms stable structures. The energies of cyclic and linear isomers of Histidine containing b ions are close to each other. Histidine containing peptide fragments have larger proton affinity comparing to others. Difference of proton affinities between linear and cyclic conformers varies based on amino acid used. This difference is lower than 10kcal/mol in histidine, asparagine and aspartic acid containing peptide fragments. There is no dramatic position preference of the X-amino acid for the N- or C- terminals or middle position with the exception of Asn and Asp (unlike the center) and Histidine which likes to be at C-terminal.
  • Master Thesis
    The Study of Ground State and Excited State Properties of Cyanine Dyes by Using Computational Chemical Methods
    (Izmir Institute of Technology, 2008) Karaca, Sıla; Elmacı Irmak, Nuran
    The 5,5.,6,6.-tetrachloro-1,1.,3,3.-tetraethyl-benzimidazolo carbocyanine (TTBC) iodide, abbreviated CBIC2(3) or JC-1, is used for the molecular probe especially as measuring mitochondrial membrane potential and allows to visualize mitochondria, apoptosis or not.The behaviors of the TTBC at the ground and excited states have been investigated by using quantum chemical methods. DFT/6-31G** levels of theory calculations have been carried out for the optimization and the frequencies with B3LYP and PBEPBE functionals for the ground state structure. TDDFT/6-31G** and CIS/6-31G** methods have been used for the excited state properties. In addition to those, solvation calculations were performed with CPCM and IEFPCM.The effects of the functional groups, length of the conjugated chain, and alkyl groups on TTBC have been analyzed. There is no significant effect of functional groups either as donor or acceptor on the optimum structure. Only the alkyl groups change the planarity of the molecule. TTBC has a very rigid geometry. But it is possible to tune up max with NH2 and butyl/propyl and increasing polymethine chain length.To explain the shoulder on the fluorescence spectrum, the PES section was obtained. The fluorescence property of TTBC was compared with the experimental data. Although perpendicular structure is favorable in the first excited state, there is no significant difference in dipoles. The twisted charge transfer state is absent in this dye based on these calculations. The solvent effect on TTBC in different solvents was investigated. The solvation calculations show that, max values are independent of the polarity of the solvents as seen experimentally.
  • Master Thesis
    A Computational Study on the Structure of Allene Polymers by Using Quantum Chemical Methods
    (Izmir Institute of Technology, 2005) Dağtepe, Pınar; Elmacı Irmak, Nuran
    The conformational analysis of 1,3-dicyanodiethynylallene and 1,3- diethynylallene oligomers have been carried out by using quantum mechanical semiempirical AM1 method implemented in G03 and G98.Although chiral 1,3-diethynylallene unit upon forming intramolecular hydrogen bond is expected to form helical oligomers and polymers that have optically active character, our results indicate that the oligomers of this molecule have lack of helicity.Instead, the conformations observed for 1,3-diethynylallene oligomers are all unfolded zig-zag like chains.1,3-dicyanodiethynylallene oligomer, a derivative of 1,3-diethynylallene, is also expected to have a helical conformation. In oligomer structures, the results of optimizations show that 1,3-dicyanodiethynylallene has a well defined three-dimensional helical conformation. This helicity is attributed to electrostatic interactions between cyano carbon which has a high negative charge and oppositely charged allene carbons along the helical axis. We observe P-helix rather than M-helix, no the conformers which may lead to M character is encountered.
  • Master Thesis
    Quantum Chemical Investigations on Acetylenic Carbon Rich Compounds as Molecular Construction Kit
    (Izmir Institute of Technology, 2004) Aydın, Mustafa; Elmacı Irmak, Nuran
    Ground and excited state behaviors of Radialenes, Expanded Radialenes and TEE monomer and dimer derivatives, which are carbon rich compounds were investigated by using quantum chemical calculations. Most of these advanced materials have non-linear optical properties and they can be used as molecular electronics. AM1 and DFT/B3LYP with 3-21G and 6-31G* basis sets methods were used for the ground state calculations of radialenes, expanded radialenes and TEE monomers and dimers. TDDFT/3-21G, TDDFT/6-31G* level of calculations were carried out for the excited state behaviors on AM1, DFT/3-21G* and DFT/6-31G* ground state structures. All the methods that we have used gave similar results with a very small discrepansies. Radialenes and expanded radialenes have planar ground state structures except the one with size 6; the three dimensional chair like geometry is slightly stable than the planar one. There is no effect of the size of radialenes on the the geometrical parameters. The introduction of ethynyls instead of hydrogens causes a red-shift about 100-150 nm. The maximum absorption wavelength usually increases with the size of radialenes with some exceptions for the planar structures. The effect of various acceptors such that p-NO2-benzene- , p-CH3-benzene-, p-CHO-benzene- and their locations which are mainly CIS, TRANS and GEMINAL with respect to donor positions to the TICT state on push-pull TEE derivatives were investigated by using excited state calculations. The probable donor units on the TEE derivates were considered as dimethyl amine and dimethyl aniline units. TICT property for the rotation of dimethylaniline group is observed for many of isomers. TICT state appeared both for cis and trans conformer of the donor substituted TEE dimer.