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Öğe Anisotropic Dielectric Screened Range-Separated Hybrid Density Functional Theory Calculations of Charge Transfer States across an Anthracene-TCNQ Donor-Acceptor Interface(Amer Chemical Soc, 2024) Chakravarty, Chandrima; Saller, Maximilian A. C.; Aksu, Hüseyin; Dunietz, Barry D.A density functional theory framework is developed to study electronic excited states affected by an anisotropic dielectric environment. In particular, an anisotropic dielectric screened range-separated hybrid (SRSH[r]) functional is defined and combined with an anisotropic polarizable continuum model (PCM) implemented through a generalized Poisson equation solver. We develop the SRSH-PCM(r) approach and use it to quantify the effect of anisotropy on an excited charge transfer (CT) state energy. In particular, the dielectric interface effect on the CT state within a donor-acceptor molecular complex of antrancene and tetracyanoquinodimethane is studied. The donor-acceptor complex and the dielectric interface are used to represent the interface between thin films consisting of these materials. We report the effect of such a dielectric interface on the energy of a CT and follow its dependence on the donor-acceptor distance. We also benchmark the anisotropy-affected energy by comparing to homogeneous dielectric calculated energies. Due to the planar interface, the anisotropic energies are expected to to match with those obtained based on isotropic calculations of the larger dielectric constant at large enough distances. The approach is applicable, in general, to more complicated dielectric constant distributions as expected to be found in actual interfaces of such thin films or in other systems, for example, for CT processes within photosystems.Öğe Antioxidative Triplet Excitation Energy Transfer in Bacterial Reaction Center Using a Screened Range Separated Hybrid Functional(Amer Chemical Soc, 2024) Begam, Khadiza; Aksu, Hüseyin; Dunietz, Barry D.Excess energy absorbed by photosystems (PSs) can result in photoinduced oxidative damage. Transfer of such energy within the core pigments of the reaction center in the form of triplet excitation is important in regulating and preserving the functionality of PSs. In the bacterial reaction center (BRC), the special pair (P) is understood to act as the electron donor in a photoinduced charge transfer process, triggering the charge separation process through the photoactive branch A pigments that experience a higher polarizing environment. At this work, triplet excitation energy transfer (TEET) in BRC is studied using a computational perspective to gain insights into the roles of the dielectric environment and interpigment orientations. We find in agreement with experimental observations that TEET proceeds through branch B. The TEET process toward branch B pigment is found to be significantly faster than the hypothetical process proceeding through branch A pigments with ps and ms time scales, respectively. Our calculations find that conformational differences play a major role in this branch asymmetry in TEET, where the dielectric environment asymmetry plays only a secondary role in directing the TEET to proceed through branch B. We also address TEET processes asserting the role of carotenoid as the final triplet energy acceptor and in a mutant form, where the branch pigments adjacent to P are replaced by bacteriopheophytins. The necessary electronic excitation energies and electronic state couplings are calculated by the recently developed polarization-consistent framework combining a screened range-separated hybrid functional and a polarizable continuum mode. The polarization-consistent potential energy surfaces are used to parametrize the quantum mechanical approach, implementing Fermi's golden rule expression of the TEET rate calculations.Öğe Calculation of negative ions of B, C, N, O and F using noninteger n Slater type orbitals(Chinese Chemical Soc, 2008) Guseinov, İsrafil İsa; Ertürk, Murat; Şahin, Ercan; Aksu, Hüseyin; Bağcı, AliCombined Hartree-Fock-Roothaan calculations have been performed using noninteger n Slater type orbitals for the ground states of the lowest electron configurations 1s(2)2s(2)2p(n) (2 <= n <= 6) for negative ions of B, C, N, O and F. These results are compared with the corresponding results obtained from the use of integer n Slater type orbitals. All of the nonlinear parameters are fully optimized. The results of calculation of coupling-projection coefficients, orbital and total energies and virial ratios are presented. It is shown that the noninteger n Slater type orbitals, in general, improve the orbital energies.Öğe Charge-Transfer Processes within the Isolated Tetramer Models of the Reaction Center Rhodobacter sphaeroides(Amer Chemical Soc, 2025) Geçit, Fehime Hayal; Aksu, HüseyinOver the last two decades, advancements in structural resolution and spectral characterization have significantly enhanced our understanding of photosynthesis. However, the complexity of photosystem (PS) supercomplexes still presents challenges. In the Rhodobacter sphaeroides reaction center (RSRC), the charge separation process begins with a charge-transfer (CT) step at the special pair (P), a dimer of bacteriochlorophyll a (BChl), which acts as the donor, and continues with electron transport through the active pigments. Our computational study explores CT rectification in RSRC. We find that the CT rate is faster in the A branch compared with the B branch, which can be attributed to the orientation of the pigments near P and the influence of the surrounding protein complex on the dielectric constant. The calculated rate constants are derived using Fermi's golden rule, with a first-principles approach that employs an optimally tuned screened range-separated hybrid functional within a polarizable continuum model (SRSH-PCM).Öğe Electronic Spectra of C60Films Using Screened Range Separated Hybrid Functionals(American Chemical Society, 2021) Chakravarty, Chandrima; Aksu, Hüseyin; Maiti, Buddhadev; Dunietz, Barry D.We study computationally the electronic spectra of C60thin films using the recently developed density functional theory (DFT) framework combining a screened range separated hybrid (SRSH) functional with a polarizable continuum model (PCM). The SRSH-PCM approach achieves excellent correspondence between the frontier orbital’s energy levels and the ionization potential and electron affinity of the molecular systemat the condensed phaseand consequently leads to high quality electronic excitation energies when used in time-dependent DFT calculations. Our calculated excited states reproduce the experimentally main reported spectral peaks at the 3.6-4.6 eV energy range and when addressing excitonic effects also reproduce the red-shifted spectral feature. Notably, we analyze the low-lying peak at 2.7 eV and associate it to an excitonic state.Öğe Hartree-Fock-Roothaan yaklaşımında kesir indisli Coulomb potansiyeli kullanılarak atom özelliklerinin hesaplanması(Çanakkale Onsekiz Mart Üniversitesi, 2009) Aksu, Hüseyin; Hüseyin, İsrafilAtom ve moleküllerin temel durum enerjileri ve diğer fiziksel özelliklerinin hesaplanmasında genellikle Hartree-Fock-Roothaan yöntemi kullanılır. Bu sistemler için Hartree-Fock-Roothaan denklemleri çözülürken dalga fonksiyonlarının seçimi büyük önem taşımaktadır. Bu tez çalışmasında yeni önerilen tam birim boylu fonksiyonlar sistemi kullanılarak elde edilen kesir indisli tek ve iki elektronlu potansiyel etkileşmeleri için matris elemanları oluşturularak bazı açık (C, N) ve kapalı (He ve izo-elektronik serisi, Be ve izo-elektronik serisi Ne, Li-, B+, F-) kabuklu atomlar için temel durum enerjileri, yörüngesel enerjiler, viryal katsayısı hesaplanmıştır. Ayrıca genişletilmiş baz fonksiyonları da kullanılarak uyarılmış seviyelerinin enerjileri ve elektron bağlaşım hesabı yeni potansiyel dikkate alınarak yapılmıştır.Öğe Heat flow enhancement in a nanoscale plasmonic junction induced by Kondo resonances and electron-phonon coupling(Elsevier, 2021) Göker, Ali; Aksu, Hüseyin; Dunietz, Barry D.Recently, we showed that plasmon-exciton coupling can increase entropy current through a bridge coupled to plasmonic metal nanoparticles. Here we show that electron-phonon coupling can also be used to control the entropy current in similar systems. Entropy current tends to decrease due to electron-phonon coupling and to exhibit a monotonous decrease upon temperature ramping. However, an anomaly affecting the current where it is enhanced by electron-phonon coupling is indicated at around 42 times the system’s Kondo temperature. We therefore report means to control heat flow by tuning the Kondo resonance through the electron-phonon coupling. We analyze the conditions that bring about these trends due to electron-phonon coupling by employing non-equilibrium Green’s function formulation addressing the entropy current and the derived heat flow.Öğe The Role of Polar Functional Groups of the Special Pair on the Excites States in Terms of the Dielectric Environment: Screened Range Separated Time-Dependent Density Functional Theory(Çanakkale Onsekiz Mart Üniversitesi, 2025) Geçit, Fehime Hayal; Güneş, Zühra; Ertürk, Murat; Aksu, HüseyinWe study the role of polar functional groups (PFGs) on the excited states and the changes of net charges on the charge transfer (CT) states in terms of dielectric constant using ab initio theory. It is found that the PFGs play a dielectric medium in which the side PFGs interact strongly with the incoming light, and this interaction contributes to the wave function of excited states. Results reveal that conformer structure due to side groups has more influence on transition dipole moment (TDM) and thus on the electronic excitations. We have also discussed the well-known J- and H- aggregation physical phenomenon for the special pair and shown the excitonic splitting energies of the special pair compared to the monomer's first excited state energies. Excitation energies, oscillator strength, and CT states are obtained by using time-dependent density functional theory (TDDFT) and accompanying screened range-separated hybrid functionals (SRSH) in which comparisons are made with $\omega$B97X-D functional.Öğe Understanding Primary Charge Separation and Revealing Fermi's Golden Rule in the Heliobacterium Modesticaldum Reaction Center(Amer Chemical Soc, 2025) Ertürk, Murat; Güneş, Zühra; Aksu, HüseyinWe investigate the spectroscopic properties and charge transfer (CT) processes in the homodimeric reaction center of Heliobacterium modesticaldum (HbRC), for which we report the first-principles calculation of Fermi's golden rule (FGR) for the first time in the literature. HbRC is the simplest known analogue to other photosystems and consists of the SPP molecule, the adjacent Acc, and key amino acid residues (His537 and Gln458), along with two water molecules. We identify intrapair CT processes within the SPP molecule, which acts as the donor for the simplified model used in this study. We also examine the SPP+Acc- CT processes, where we demonstrate, in agreement with experimental findings, symmetric hole-electron delocalization across both Acc monomers. The calculated forward CT states are lower in energy than the bright states, facilitating electron transfer through a downhill CT reaction pathway. To explore the influence of surrounding molecular pigments on the electronic structure and FGR rate, we use augmented models incorporating nonsymmetrized molecular orientations. Most FGR rates are found to be on the order of picoseconds (ps). All electronic parameters are derived using an optimally tuned screened range-separated hybrid functional within a polarizable continuum model (SRSH-PCM), considering different dielectric constants.Öğe Yükten bağımsız atom çekirdekleri modeli ve uygulamaları(Çanakkale Onsekiz Mart Üniversitesi, 2004) Aksu, Hüseyin; Özel, Mehmet Eminöz Bilindiği gibi, spini V2 olan parçacıklar sisteminin dalga fonksiyonları ortonormallik özelliğine sahip olan Slater determinantlarından oluşur. Determinant dalga fonksiyonları uzay, spin ve izotopik spin koordinatlarını içeren üç tane fonksiyon olarak belirlenen tek parçacıklı dalga fonksiyonlarından oluşur. Bu çalışmada, çekirdekte elektrik yükünden bağımsızlık modelini kullanarak özdeş parçacıklar (nükleonlar) sisteminin oluşturulması ve kabuk modelinin uygulanması amaç edinilmiştir. Kabuk modeline göre, nükleonların bağımsız olduğunu ve bir nükleonun diğer nükleonların oluşturduğu potansiyel alanında hareket ettiğini varsayıyoruz. Kuantum mekaniği yönünden, merkezi bir potansiyel alanda hareket eden parçacığın durumu ile diğer nükleonların meydana getirdiği bir potansiyel alanda hareket eden nükleonun hareketi tamamen özdeştir. Çekirdeğin kabuk modeline göre uzay koordinatlara» içeren dalga fonksiyonları Haartree-Fock (HF) denklemlerinin çözümünden bulunur. HF denklemleri çiftlenim-izdüşüm katsayıları içermektedir. Bu katsayılar çekirdeğin toplam enerji formülünden bulunur. Denklemlerden bulunan bu dalga fonksiyonlardan yararlanarak hafif çekirdeklerin multiplet enerji terimleri ve başka özelliklerinin hesaplanması mümkün olacaktır. Anahtar kelimeler: İzotopik Spin, Yükten Bağımsızlık Modeli, Slater Teoremi, Determinant Dalga Fonksiyonu, Çok Nükleonlu Operatör, Matris Elemanı, Çiftlenim-İzdüşüm Katsayısı, Multiplet Terim
