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Electronic Struture of Organic Molecules Containing Transition-Metal Atoms
(Izmir Institute of Technology, 2019) Kandemir, Zafer; Bulut, Nejat
Hemoglobin 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.
Magnetic Effect in the Biological Functioning of Hemoglobin: Dft+qmc Approach Within an Effective Multi-Orbital Anderson Impurity Model
(Izmir Institute of Technology, 2019) Mayda, Selma; Bulut, Nejat; Demir, Mustafa Muammer
Hemoglobin corresponds to O2 transportation from lungs to the tissues and exhibits high-spin to low-spin transition by binding of O2 to Fe. In this thesis, we study the electronic and magnetic properties of the deoxy and the oxy forms of the human adult hemoglobin (HbA) to investigate the mechanism of the spin transition. We use an effective multi-orbital Anderson model and the parameters of this model are determined by the density functional theory (DFT) calculations. Then, this model is solved by using a quantum Monte Carlo (QMC) algorithm. The DFT+QMC results show that new electronic states named as the impurity bound states (IBS) exist in both deoxy-HbA and oxy-HbA.We also observe that as the temperature decreases, a magnetic gap is opened at the Fermi level for oxy-HbA. This gap arises from the Fe-O2 charge transfer. We find that both the IBS and the opening of the magnetic gap are responsible for the spin transition in hemoglobin. In addition, the DFT+QMC calculations show that antiferromagnetic (AF) correlations between the Fe(3d) and the surrounding orbitals exist in both deoxy-HbA and oxy-HbA. For deoxy-HbA, the anomalous magnetic circular dichrosim signal in the UV region is experimental evidence for these AF correlations. In the light of these magnetic measurements, we propose some explanations for the Bohr effect and the cooperativity which are the fundemental functional properties of the hemoglobin. The results presented in this thesis show that the magnetic effects play a crucial role in the funtioning of the hemoglobin.

Phd Degree / Doktora

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