Elmacı Irmak, Nuran
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Elmaci, Nuran
Elmacı, N
Elmacı, N.
Elmacı, Nuran
Irmak, Nuran Elmaci
Irmak, Nuran Elmacı
Elmaci, N.
Elmaci, N
Elmaci Irmak, Nuran
Elmacı, N
Elmacı, N.
Elmacı, Nuran
Irmak, Nuran Elmaci
Irmak, Nuran Elmacı
Elmaci, N.
Elmaci, N
Elmaci Irmak, Nuran
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nuranelmaci@iyte.edu.tr
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04.01. Department of Chemistry
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15
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245
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23
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10
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16530/11837
Supervised MSc Theses
10
Supervised PhD Theses
3
WoS Citation Count
88
Scopus Citation Count
96
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2
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3.83
Scopus Citations per Publication
4.17
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17
Supervised Theses
13
| Journal | Count |
|---|---|
| Journal of Organic Chemistry | 2 |
| ChemPhysChem | 1 |
| Computational and Theoretical Chemistry | 1 |
| International Journal of Mass Spectrometry | 1 |
| Journal of Molecular Graphics & Modelling | 1 |
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Article Citation - WoS: 18Citation - Scopus: 18A Computational Study on the Excited State Properties of a Cationic Cyanine Dye: Ttbc(Elsevier Ltd., 2011) Karaca, Sıla; Elmacı Irmak, Nuran; Elmacı, NuranThe ground and excited state behaviors of a biologically important mitochondria selective dye, 5,5',6,6'-tetrachloro-1,1',3,3'-tetraethyl-benzimidazolo carbocyanine (TTBC), were investigated in order to give useful information related to the enhancement of its electronic and optical properties. DFT and TDDFT levels of theory with different functionals and basis sets were used. The results obtained by using PBEPBE/6-31+G(d,p)/C-PCM are in good agreement with the experiments. The potential energy surface sections of TTBC were explored and the geometry optimized in the first excited state, S 1, to analyze the fluorescence spectrum of the dye. There are two distinct minima on the S 1 surface, one located near the ground state geometry and an energetically favorable twisted geometry, having a charge transfer character. The observation of similar ground and excited state dipoles as well as solvent-independent fluorescence and absorption wavelengths reveals that there is no competition between the two minima; the emission is dominantly coming from the more planar configuration.Master Thesis Doping Effect on the Anode Material Capability of 2d Bn Nanosheets(01. Izmir Institute of Technology, 2024) Elmacı Irmak, Nuran; Özdemir, Mustafa Coşkun; Irmak, Nuran ElmacıIn this thesis, the potential of BNN surfaces doped with Al, Cl, Co, Fe, Ga, O, P, and S atoms as anode materials in K, Li, Mg, and Na ion batteries was investigated. Semi-empirical tight-binding combined with meta-dynamics methods and density functional theory were utilized to discover these properties. The effects of doping atoms on the electronic structure and geometry of BNN surfaces were also studied. Changes in the electronic structure and conductivity were reported by examining the HOMO-LUMO orbitals and the energy differences between these orbitals. Using previously reported experimental data and examining similar studies from the literature, the atoms to be doped were chosen. While vacancies at the sites of boron atoms in single-layer boron-nitride nanosheets were observed, vacancies formed by nitrogen atoms were not observed, indicating that boron vacancies are much more likely for the doping position. So that doping was performed on the boron atom. The level of quantum calculations used in this work was validated using experimental data. B3LYP/def2-SVP/D4/gCP level of theory is used for all calculations for BNN-nanosheets studied in this thesis. The bond lengths and the HOMO-LUMO energy difference were found to be nearly the same as the experimental data. The conductivity of the BNN surface was increased with the doping process. However, significant improvements are followed by doping of cobalt, iron, and sulfur atoms with 35%, 34%, and 26% alteration, respectively. For a suitable battery manufacture, the potential anode material should offer structures with high theoretical specific capacity, low anode electrode voltage, and minimal volume change between charged/discharged states. It was observed that none of the doped-BNN surfaces involved in this study were suitable for the use of anode material in magnesium ion batteries. On the other hand, they can be used as a negative electrode for potassium, lithium, and sodium batteries. Their capacity in lithium is better than Na and K batteries. Our results suggest that most of the doped BNN surface with ions studied in this thesis could be used as anode materials. However, none of them owns a better battery capacity than classic lithium batteries.Master Thesis Molecular Dynamics Simulations of a Cationic Thiophene Oligomer and a Nucleotide Complex(Izmir Institute of Technology, 2022) Demirci, Fethi Can; Elmacı Irmak, Nuran; Elmacı Irmak, NuranIn this thesis, parametrization of cationic polythiophene (CPT) and molecular dynamics (MD) simulations of CPT with DNA complexes were performed to understand the behaviors of the CPT with DNA complex and CPT DNA complexes in different salt solutions (NaCl, KCl, MgCl2, CaCl2). The results of MD simulations show that the end-to-end distance of CPT is affected by both the type sequences and length of the DNA, and the addition of 20T elongates the backbone of the oligomer while 20A and MIX ssDNAs almost have no significant effect. When the complementary DNA chain is added to the duplex solutions, the backbone structure of the oligomer becomes very similar to its structure without ssDNAs since Ree values in both cases are almost the same. It was observed that the CPT-20A complex has a more random coil form than the CPT-20T complex. According to the interaction analysis of MD simulations, all the CPT-DNA duplexes except CPT-20A prefer electrostatic interaction rather than π-cation interaction. DNAs like to interact with the oligomer's side chain rather than its backbone in all systems. Thus, electrostatic interactions and the side chain of oligomer play an important role in the structure of duplexes with thymine which gets the highest response from the oligomer. The addition of 20T makes backbone of F0 more elongated and less compact. 20T has higher electrostatic and π-cation interactions. Thus, F0 is more sensitive to 20T than 20A and MIX.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, NuranThe 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.Article Citation - WoS: 10Citation - Scopus: 11A Theoretical Study on the Ground and Excited State Behaviors of Ttbc Related Carbocyanine Dyes(Elsevier Ltd., 2009) Karaca, Sıla; Elmacı, NuranThe effects of functional groups on the benzimidazole rings, length of the conjugated chain and alkyl groups bonded to the nitrogen atoms on the ground and excited state behaviors of the 1,1′,3,3′-tetraethyl-5,5′,6,6′-tetrachlorobenzimidazolocarbocyanine (TTBC or JC-1) have been analyzed via quantum chemical methods. DFT and TDDFT with B3LYP/6-31G(d,p) level of theory were used for the ground and excited state calculations, respectively. It has been found that TTBC has a very rigid geometry; no significant effect of functional groups has been predicted either as donor or acceptor on its optimum structure. However, the length of alkyl groups changes the structure of the molecule. It is possible to increase λmax of TTBC based carbocyanine dye with NH2, butyl/propyl and increasing polymethine chain length.Article Citation - WoS: 4Citation - Scopus: 4Gas-Phase Structures and Proton Affinities of N-Terminal Proline Containing B2 + Ions From Protonated Model Peptides(Elsevier Ltd., 2015) Karaca, Sıla; Atik, Ahmet Emin; Elmacı, Nuran; Yalçın, TalatIn this study, we investigated the effect of the second amino acid identity of hexapeptides on gas-phase structures and the proton affinities of N-terminal proline containing b2 + ions produced from the fragmentation of b6 + ions under low-energy collision-induced dissociation (CID) tandem mass spectrometry (MS/MS). It should be noted that, among all other fragments, the b2 + and nominally b4 + (AAAA) ions ([M+H]+ → b6 + → b2 + (PX+) + b4 + (AAAA+) were mainly considered in this study. This is a unique example of consecutive cleavage of b6 + ions which fragments to b2 + and nominal b4 + ions. All structural and proton affinity calculations for b2 + ions were carried out with the B3LYP/6-31+G(d,p) level of theory. The study utilized C-terminal amidated model peptides consisting of PAAAAA-NH2 and PXAAAA-NH2 where X is phenylalanine (F), glutamic acid (E), tryptophan (W), and histidine (H) residue. Two main structural isomers of b2 + ions, namely oxazolone and diketopiperazine, have been considered for the computations. The results demonstrated that the proton affinities of oxazolone isomers of PX are greater than its diketopiperazine isomers. Higher correlation coefficient is calculated if the structure of PX is considered as oxazolone rather than diketopiperazine isomer. Additionally, a linear fit is observed between intensity ratio (PX/AAAA) and calculated proton affinities of PX ions. Additionally, MS/MS results revealed that the relative intensities of b2 +-PA, PF, and PE- ions are lower compared to the relative intensity of AAAA fragment ion. In contrast, b2 +-PW and PH- ions have higher relative intensities compared to the AAAA ion. This behavior is explained by the proton affinities of fragment ions computationally.Master Thesis Fenalenon Bazlı Organik Boyaların Kuantum Kimyasal İncelenmesi(2025) Agin, Zelal; Irmak, Nuran ElmacıFenalenon, keton kısmıyla kaynaşmış üç fenil halkasından oluşan bir bileşiktir ve yüksek singlet oksijen kuantum verimi nedeniyle yaygın bir şekilde fotosensitizör olarak kullanılmaktadır. Bu çalışmada, kuantum kimyasal hesaplamalar kullanılarak fotofiziksel ve sensörle ilgili özelliklerini keşfetmek için 3-, 4-, 5- ve 6-pozisyonlarına elektron verici sübstitüentler eklenerek yeni fenalenon türevleri tasarlandı. Yöntem doğrulamasından sonra, konformasyon analizi ile en kararlı yapılar belirlendi, ardından temel hal optimizasyonları DFT/ B3LYP/def2-SVP seviyesinde hesaplama ile yapıldı. TD-DFT hesaplamaları ile (D4 dispersiyon düzeltmesi ile B3LYP/def2-SVP teori seviyesinde ve su içinde) doğal geçiş orbital analizleri yoluyla uyarılma enerjileri, absorpsiyon/emisyon dalga boyları, baskın geçişler ve yük transfer özellikleri elde edildi. Sonuçlar, 3- ve 5- pozisyonundaki türevlerin genellikle büyük konformasyonel değişiklikler, yük transferi karakteri ve Foto-indüklenmiş elektron transferi/bükülmüş molekül içi yük transferi davranışı sergilediğini ve bunun da sönümlenmiş veya düşük floresansa yol açtığını göstermektedir. Tersine, 4 ve 6 konumunda olan türevler daha kararlı geometrilere ve baskın H→L geçişlerine sahiptirler, sınırlı yük transferi ile daha güçlü emisyona neden olmaktadırlar. Özellikle, 3'te ve 5'te yer alan türevlerdeki daha büyük Stokes kaymaları, çevreye karşı duyarlılıklarını vurgulamaktadır. Ayrıca, bazı bükülmüş molekül içi yük transferi içeren bazı yapılarda yakın-IR bölgesinde emisyon gözlendi. Genel olarak, 4 ve 6 ikameli fenalenon türevleri kararlı floresan sensörler olarak daha büyük potansiyel gösterirken, 3 ve 5 ikameli olanların çevresel değişikliklere daha duyarlı olduğu belirlendi. Bu çalışma fenalenon bazlı moleküler sensörlerin tasarımı için ön çalışma olarak deneysel çalışmalara rehberlik edecektir.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, NuranThe 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.Doctoral Thesis Hidrojel Oluşumunda Hidrojen Bağlarının Rolünün Anlaşılması: Deneysel ve Moleküler Dinamik Simülasyonlarının Birleşik Bir Çalışması(2025) Barbak, Nehir Nalıncı; Irmak, Nuran Elmacı; Yıldız, Ümit HakanJelatin bazlı hidrojeller, ayarlanabilir fizikokimyasal özellikleri ve biyouyumlulukları nedeniyle büyük ilgi görmekte ve biyomedikal, endüstriyel uygulamalar için elverişlidirler. Jelleşme kabiliyetleri ve mekanik özellikleri, jelatinin amino asit içeriğine, konsantrasyonuna ve sıcaklık gibi çevresel koşullara bağlıdır. Bu çalışma, konsantrasyon ve sıcaklığın etkisi altında çapraz bağlayıcı içermeyen jelatinin jelleşme davranışını incelemek için deneysel ve moleküler dinamik (MD) simülasyon yaklaşımlarını kapsamaktadır. Hazırlanan jelatin çözeltilerinin karakterizasyonunda, dinamik ışık saçılması, Fourier dönüşümlü kızılötesi spektroskopisi, kütle spektrometrisi ve şişme oranı testleri kullanılmıştır. Literatürden alınan peptit sekansı ve domuz derisinden elde edilen gelatinin kütle spektrometre analiziyle belirlenen en yüksek olasılıklı iki peptit dizisi kullanılarak MD simülasyonları gerçekleştirilmiştir. Konformasyonel parametreler, hidrojen bağı, çözücüye erişilebilir yüzey alanı ve çeşitli derişimler altında şişme davranışı MD analizi ile irdelenmiştir. Bulgular, sıcaklık ve konsantrasyondaki değişikliklerin konformasyonel parametrelerini anlamlı olarak etkilemediğini ortaya koymuştur. Jelatin zincirleri arasındaki hidrojen bağları sayısı sıcaklıkla artarken, suyla olanların azaldığı, ancak her ikisinin de konsantrasyonla arttığı gözlenmiştir. Simülasyon sonuçları düşük sıcaklıkta (jel), yüksek sıcaklıklara (sol) kıyasla daha fazla sayıda hidrojen bağı göstererek jelatinin sıcaklığa duyarlı davranışını ve jelleşme sırasında suyla artan etkileşiminin önemini göstermiştir. Konsantrasyon artışı daha yüksek çözücü yüzeyine erişebilerek, jelatin-su etkileşimlerini artırmıştır. Simülasyon sonuçları deneysel gözlemlerle uyumlu olup, şişme oranlarının jelleşme sıcaklığında, düşük derişimlerde daha yüksek olduğu gösterilmiştir. Deneysel ve hesaplamalı yaklaşımların birleşimi, çapraz bağlayıcı içermeyen jelatin bazlı hidrojellerin hazırlanmasındaki en iyi koşulların ve MS/MS analizi ile amino asit dizilerinin tanımlanmasının yanı sıra, jelleşme davranışına ilişkin değerli bilgiler sağlamıştır.Article Citation - WoS: 6Citation - Scopus: 5Charmm Force Field Generation for a Cationic Thiophene Oligomer With Fftk(Springer, 2021) Kıbrıs, Erman; Nalıncı Barbak, Nehir; Elmacı Irmak, NuranIn the present work, CHARMM force field parameters are generated for a cationic oligomer of N, N, N-trimethyl-3-(4-methylthiophen-3-yl) oxy) propan-1-aminium) which has the potential for sensing biological molecules such as nucleic acids, nucleobases. We have used ffTK (force field tool kit) to obtain potential parameters. MD simulations are performed for 20-mer and its complexes with AMP and ATP. The simulation results are analyzed to see the number of phosphates in adenosine nucleotides effects on the structure of the backbone of oligomer. The UV-VIS calculations for the conformers which possess the most probable radius of gyration are carried out and compared to the experimental ones to validate the generated force field. Recent studies have shown that, biologically important anions (ATP, AMP, vb.) change the spectroscopic properties of cationic polythiophenes (CPT) in the solutions. This work aims to generate CHARMM compatible force field parameters for a CPT to explain experimental studies. The type of interactions will be investigated deeply to lead new biosensor studies by examining the formation and the structure of complexes that consist of a oligothiophene and biological molecules, ATP, AMP by molecular dynamic simulations.
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