Kandemir, Zafer
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Z. Kandemir
Kandemir, Z.
Kandemir, Zafer.
Kandemir, Z.
Kandemir, Zafer.
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01. Izmir Institute of Technology
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Former Staff
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Scholarly Output
6
Articles
3
Views / Downloads
4788/1985
Supervised MSc Theses
1
Supervised PhD Theses
1
WoS Citation Count
16
Scopus Citation Count
19
Patents
0
Projects
1
WoS Citations per Publication
2.67
Scopus Citations per Publication
3.17
Open Access Source
6
Supervised Theses
2
| Journal | Count |
|---|---|
| European Physical Journal B | 1 |
| Handbook of Nanomaterials for Industrial Applications | 1 |
| Journal of Superconductivity and Novel Magnetism | 1 |
| Scientific Reports | 1 |
Current Page: 1 / 1
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6 results
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Now showing 1 - 6 of 6
Book Part Future Applications of Artificially-Synthesized Organic Molecules Containing Transition-Metal Atoms(Elsevier, 2018) Mayda, Selma; Kandemir, Zafer; Bulut, NejatArtificially-synthesized organic molecules which contain transition-metal atoms offer new possibilities for applications in the electronics, pharmaceutical, and chemical industries. Hence, developing an understanding of the electronic properties of this kind of organic molecules is important. With this purpose, here we study the electronic properties of metalloproteins, metalloenzymes, and Ru-based dye molecules as examples for this kind of organic molecules. In particular, we perform combined Hartree-Fock (HF) and quantum Monte Carlo (HF+QMC) calculations, as well as combined density functional theory (DFT) and QMC (DFT+QMC) calculations to study the electronic properties of these molecules. Our results show that new electronic states named as impurity bound states (IBS) form in metalloproteins, metalloenzymes, and Ru-based dye molecules. We show that the electron occupancy of IBS is critically important in determining the low-energy electronic properties of these molecules. In this respect, the IBS may play a central role in developing new applications based on artificially-synthesized organic molecules containing transition-metal atoms. © 2018 Elsevier Inc. All rights reserved.Article Citation - WoS: 2Citation - Scopus: 2Electronic Structure of Cyanocobalamin: Dft+qmc Study(Springer Verlag, 2017) Mayda, Selma; Kandemir, Zafer; Bulut, NejatWe study the electronic structure and the magnetic correlations of cyanocobalamin (C63H88CoN14O14P) by using the framework of the multi-orbital single-impurity Haldane-Anderson model of a transition metal impurity in a semiconductor host. Here, we first determine the parameters of the Anderson Hamiltonian by performing density functional theory (DFT) calculations. Then, we use the quantum Monte Carlo (QMC) technique to obtain the electronic structure and the magnetic correlation functions for this effective model. We find that new electronic states, which correspond to impurity bound states, form above the lowest unoccupied level of the host semiconductor. These new states derive from the atomic orbitals at the cobalt site and the rest of the molecule. We observe that magnetic moments develop at the Co(3dν) orbitals and over the surrounding sites. We also observe that antiferromagnetic correlations exist between the Co (3dν) orbitals and the surrounding atoms. These antiferromagnetic correlations depend on the filling of the impurity bound states.Master Thesis Mapping of the Electronic Structure of Metalloproteins Onto Multi-Orbital Anderson Model Using the Density Functional Theory(Izmir Institute of Technology, 2013) Kandemir, Zafer; Bulut, NejatIn this thesis, an effective Haldane-Anderson model is constructed in order to describe the electronic properties of a system where a the transition-metal impurity atom is added into a semiconductor host material. Metalloenzymes and metalloproteins are proteins which contain a transition metal. Vitamin B12 is a metalloenzyme which contains a cobalt (Co) atom. The vitamin B12 exhibits semiconducting properties due to the presence of a semiconductor gap in the electronic density of states. Thus, we argue that the electronic properties of vitamin B12 can be studied within the framework of the Haldane- Anderson model. In this thesis, firstly, the electronic structure of vitamin B12, which is known as cyanocobalamin, is obtained by using the Density Functional Theory (DFT) via the Gaussian program. By using the DFT results, the energies of the host and the 3d orbitals, and the hybridization terms between them are calculated. The final Haldane- Anderson Hamiltonian is obtained by adding the onsite Coulomb repulsion at the impurity 3d orbitals. The Haldane-Anderson Hamiltonian which has been constructed in this way from the DFT results can be studied by using the exact techniques many-body physics such as quantum Monte Carlo. Perturbative mean-field treats can also be used to study this Hamiltonian. Hence, the DFT calculations presented in this thesis represent the first step of thorough investigation of metalloproteins using these techniques of many-body physics.Doctoral Thesis Electronic Struture of Organic Molecules Containing Transition-Metal Atoms(Izmir Institute of Technology, 2019) Kandemir, Zafer; Bulut, NejatHemoglobin including iron atom, vitamin B12 containing cobalt atom and ruthenium- based dye molecules are examples of organic molecules. We explore whether electron correlations arising from transition-metal atoms have any special role in the functioning of organic molecules using the effective multi-orbital Anderson model. We choose deoxy and oxy-heme molecules which are examples of hemoglobin derivatives because they have many experimental and theoretical studies. The experimental magnetic susceptibility measurements find that deoxy and oxy-heme molecules exhibit a high-spin to low-spin transition. We use four different computational methods: density functional theory (DFT), DFT+U, DFT+mean-field approximation (DFT+MFA) and DFT+quantum Monte Carlo (DFT+QMC) to study this transition. In this thesis, we compare the results of these methods with each other and the experimental results. DFT and DFT+U methods do not yield the high-spin state for deoxy-heme. DFT method correctly does not find the location of impurity bound state (IBS) known as correlated new electronic states. These methods obtain low-spin for oxy-heme, but they find that magnetic correlations are very small. DFT+MFA works well for high-spin, but this technique does not obtain low-spin because it does not find the location of IBS correctly. DFT+QMC gives the high(low)- spin state for deoxy-heme (oxy-heme) and finds IBS and magnetic correlations. We obtain that DFT+QMC works better among these methods for deoxy and oxy-heme molecules. Moreover, we investigate whether we can observe the IBS and magnetic correlations for vitamin B12, dye molecules and single-atom catalysts by using these computational approaches.Article Citation - WoS: 2Citation - Scopus: 2Electronic Structure and Correlations of Vitamin B12 Studied Within the Haldane-Anderson Impurity Model(Springer Verlag, 2016) Kandemir, Zafer; Mayda, Selma; Bulut, NejatWe study the electronic structure and correlations of vitamin B12 (cyanocobalamine) by using theframework of the multi-orbital single-impurity Haldane-Anderson model of atransition-metal impurity in a semiconductor host. The parameters of the effectiveHaldane-Anderson model are obtained within the Hartree-Fock (HF) approximation. Thequantum Monte Carlo (QMC) technique is then used to calculate the one-electron andmagnetic correlation functions of this effective model. We observe that new states forminside the semiconductor gap found by HF due to the intra-orbital Coulomb interaction atthe impurity 3d orbitals. In particular, the lowest unoccupiedstates correspond to an impurity bound state, which consists of states from mainly the CNaxial ligand and the corrin ring as well as the Co eg-like orbitals. We alsoobserve that the Co (3d) orbitals can develop antiferromagneticcorrelations with the surrounding atoms depending on the filling of the impurity boundstates. In addition, we make comparisons of the HF+QMC data with the density functionaltheory calculations. We also discuss the photoabsorption spectrum of cyanocobalamine.Article Citation - WoS: 12Citation - Scopus: 15Magnetic Mechanism for the Biological Functioning of Hemoglobin(Nature Publishing Group, 2020) Mayda, Selma; Kandemir, Zafer; Bulut, Nejat; Maekawa, SadamichiThe role of magnetism in the biological functioning of hemoglobin has been debated since its discovery by Pauling and Coryell in 1936. The hemoglobin molecule contains four heme groups each having a porphyrin layer with a Fe ion at the center. Here, we present combined density-functional theory and quantum Monte Carlo calculations for an effective model of Fe in a heme cluster. In comparison with these calculations, we analyze the experimental data on human adult hemoglobin (HbA) from the magnetic susceptibility, Mossbauer and magnetic circular dichroism (MCD) measurements. In both the deoxygenated (deoxy) and the oxygenated (oxy) cases, we show that local magnetic moments develop in the porphyrin layer with antiferromagnetic coupling to the Fe moment. Our calculations reproduce the magnetic susceptibility measurements on deoxy and oxy-HbA. For deoxy-HbA, we show that the anomalous MCD signal in the UV region is an experimental evidence for the presence of antiferromagnetic Fe-porphyrin correlations. The functional properties of hemoglobin such as the binding of O-2, the Bohr effect and the cooperativity are explained based on the magnetic correlations. This analysis suggests that magnetism could be involved in the functioning of hemoglobin.