| 1. |
- Banerjee, Debapriya, et al.
(författare)
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Spectroscopic and DFT studies on 6-Aminophenanthridine and its derivatives provide insights in their activity towards ribosomal RNA
- 2014
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Ingår i: Biochimie. - : Elsevier BV. - 0300-9084 .- 1638-6183. ; 97, s. 194-199
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Tidskriftsartikel (refereegranskat)abstract
- 6-Aminophenanthridine (6AP), a plant alkaloid possessing antiprion activity, inhibits ribosomal RNA dependent protein folding activity of the ribosome (referred as PFAR). We have compared 6AP and its three derivatives 6AP8Cl, 6AP8CF3 and 6APi for their activity in inhibition of PFAR. Since PFAR inhibition requires 6AP and its derivatives to bind to the ribosomal RNA (rRNA), we have measured the binding affinity of these molecules to domain V of 23S rRNA using fluorescence spectroscopy. Our results show that similar to the antiprion activity, both the inhibition of PFAR and the affinity towards rRNA follow the order 6AP8CF3 > 6AP8Cl > 6AP, while 6APi is totally inactive. To have a molecular insight for the difference in activity despite similarities in structure, we have calculated the nucleus independent chemical shift using first principles density functional theory. The result suggests that the deviation of planarity in 6APi and steric hindrance from its bulky side chain are the probable reasons which prevent it from interacting with rRNA. Finally, we suggest a probable mode of action of 6AP, 6AP8CF3 and 6AP8Cl towards rRNA.
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| 2. |
- Vovusha, Hakkim, et al.
(författare)
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Binding Characteristics of Anticancer Drug Doxorubicin with Two-Dimensional Graphene and Graphene Oxide : Insights from Density Functional Theory Calculations and Fluorescence Spectroscopy
- 2018
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Ingår i: The Journal of Physical Chemistry C. - : AMER CHEMICAL SOC. - 1932-7447 .- 1932-7455. ; 122:36, s. 21031-21038
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Tidskriftsartikel (refereegranskat)abstract
- There has been a perpetual interest in identifying suitable nano-carriers for drug delivery. In this regard, graphene-based two-dimensional materials have been proposed and demonstrated as drug carriers. In this paper, we have investigated the adsorption characteristics of a widely used anticancer drug, doxorubicin (DOX), on graphene (G) and graphene oxide (GO) by density functional theory calculations and fluorescence and X-ray photoelectron spectroscopies. From the calculated structural and electronic properties, we have concluded that G is a better binder of DOX compared to GO, which is also supported by our fluorescence measurements. The binding of DOX to G is mainly based on strong pi-pi stacking interactions. Consistent with this result, we also found that the sp(2) regions of GO interact with DOX stronger than the sp(3) regions attached with the functional groups; the binding is characterized by pi-pi and hydrogen-bonding interactions, respectively.
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| 3. |
- Vovusha, Hakkim, et al.
(författare)
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Electronic structure and spectroscopic properties of 6-aminophenanthridine and its derivatives : Insights from density functional theory
- 2015
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Ingår i: International Journal of Quantum Chemistry. - : Wiley. - 0020-7608 .- 1097-461X. ; 115:13, s. 846-852
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Tidskriftsartikel (refereegranskat)abstract
- 6-Aminophenanthridine (6AP) and its derivatives show important biological activities as antiprion compounds and inhibitors of the protein folding activity of the ribosome. Both of these activities depend on the RNA binding property of these compounds, which has been recently characterized by fluorescence spectroscopy. Hence, fundamental insights into the photophysical properties of 6AP compounds are highly important to understand their biological activities. In this work, we have calculated electronic structures and optical properties of 6AP and its three derivatives 6AP8CF(3), 6AP8Cl, and 6APi by density functional theory (DFT) and time-dependent density functional theory (TDDFT). Our calculated spectra show a good agreement with the experimental absorption and fluorescence spectra, and thus, provide deep insights into the optical properties of the compounds. Furthermore, comparing the results obtained with four different hybrid functionals, we demonstrate that the accuracy of the functionals varies in the order B3LYP>PBE0>M062X>M06HF.
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| 4. |
- Vovusha, Hakkim, et al.
(författare)
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Interaction of Nucleobases and Aromatic Amino Acids with Graphene Oxide and Graphene Flakes
- 2013
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Ingår i: The Journal of Physical Chemistry Letters. - : American Chemical Society (ACS). - 1948-7185. ; 4:21, s. 3710-3718
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Tidskriftsartikel (refereegranskat)abstract
- In this work, we have studied interactions of nucleobases and aromatic amino acids with graphene (G) and graphene oxide (GO) flakes by ab initio density functional theory (DFT). It is evident from the results that GO complexes are stabilized by hydrogen bonding interactions whereas G complexes are stabilized by pi-pi interactions, leading to enhanced binding energies for GO complexes compared to G complexes. Moreover, time-dependent DFT (TD-DFT) calculations for the optical properties reveal that the GO nanoflakes and GO-nucleobase composite absorb visible light in the range of 400-700 nm, which may be useful for light-emitting devices. The insights obtained from our study will be useful to understand the role of GO flakes as carriers in targeted drug delivery and biosensors.
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| 5. |
- Akansel, Serkan, et al.
(författare)
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Enhanced Gilbert damping in Re-doped FeCo films : Combined experimental and theoretical study
- 2019
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Ingår i: Physical Review B. - 2469-9950 .- 2469-9969. ; 99:17
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Tidskriftsartikel (refereegranskat)abstract
- The effects of rhenium doping in the range 0-10 at.% on the static and dynamic magnetic properties of Fe65Co35 thin films have been studied experimentally as well as with first-principles electronic structure calculations focusing on the change of the saturation magnetization (M-s) and the Gilbert damping parameter (alpha). Both experimental and theoretical results show that M-s decreases with increasing Re-doping level, while at the same time alpha increases. The experimental low temperature saturation magnetic induction exhibits a 29% decrease, from 2.31 to 1.64 T, in the investigated doping concentration range, which is more than predicted by the theoretical calculations. The room temperature value of the damping parameter obtained from ferromagnetic resonance measurements, correcting for extrinsic contributions to the damping, is for the undoped sample 2.1 x 10(-3), which is close to the theoretically calculated Gilbert damping parameter. With 10 at.% Re doping, the damping parameter increases to 7.8 x 10(-3), which is in good agreement with the theoretical value of 7.3 x 10(-3). The increase in damping parameter with Re doping is explained by the increase in the density of states at the Fermi level, mostly contributed by the spin-up channel of Re. Moreover, both experimental and theoretical values for the damping parameter weakly decrease with decreasing temperature.
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| 6. |
- Akansel, Serkan, et al.
(författare)
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Enhanched Gilbert Damping in Re doped FeCo Films : A combined experimental and theoretical study
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- The effects of rhenium doping in the range 0 – 10 at% on the static and dynamic magnetic properties of Fe65Co35 thin films have been studied experimentally as well as with first principles electronic structure calculations focussing on the change of the saturation magnetization (Ms ) and the Gilbert damping parameter (α ). Both experimental and theoretical results show that Ms decreases with increasing Re doping level, while at the same time α increases. The experimental low temperature saturation magnetic induction exhibits a 29% decrease, from 2.31T to 1.64T, in the investigated doping concentration range, which is more than predicted by the theoretical calculations. The room temperature value of the damping parameter obtained from ferromagnetic resonance measurements, correcting for extrinsic contributions to the damping, is for the undoped sample 2.7X103, which is close to the Gilbert damping parameter extracted from the theoretical calculations. The room temperature experimental value for the damping parameter increases to 9X103 when doping with 10 at% Re; the corresponding increase of the Gilbert damping parameter obtained from theoretical calculations is 7.3X103. Both experimental and theoretical values for the damping parameter weakly decrease with decreasing temperature.
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| 7. |
- Alam, Aftab, et al.
(författare)
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Effect of disorder on the electronic properties of graphene : A theoretical approach
- 2012
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Ingår i: Physical Review B. Condensed Matter and Materials Physics. - 1098-0121 .- 1550-235X. ; 86:8, s. 085454-
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Tidskriftsartikel (refereegranskat)abstract
- In order to manipulate the properties of graphene, it is very important to understand the electronic structure in the presence of disorder. We investigate, within a tight-binding description, the effects of disorder in the on-site (diagonal disorder) term in the Hamiltonian as well as in the hopping integral (off-diagonal disorder) on the electronic dispersion and density of states by the augmented space recursion method. Extrinsic off-diagonal disorder is shown to have dramatic effects on the two-dimensional (2D) Dirac cone, including asymmetries in the band structures as well as the presence of discontinuous bands (because of resonances) in certain limits. Disorder-induced broadening, related to the scattering length (or lifetime) of Bloch electrons, is modified significantly with increasing strength of disorder. We propose that our methodology is suitable for the study of the effects of disorder in other 2D materials, such as a boron nitride monolayer.
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| 8. |
- Ali, Ehesan, et al.
(författare)
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Tuning the Magnetic Interaction between Manganese Porphyrins and Ferromagnetic Co Substrate through Dedicated Control of the Adsorption
- 2009
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Ingår i: The Journal of Physical Chemistry C. - : American Chemical Society (ACS). - 1932-7447 .- 1932-7455. ; 113:32, s. 14381-14383
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Tidskriftsartikel (refereegranskat)abstract
- We report, on the basis of density-functional theory+U (DFT+U) calculations that metalloporphyrins can adsorb on ferromagnetic metal surfaces in two distinct configurations. Two separate adsorption minima are obtained for manganese porphyrin (MnP) on Co from our DFT+U total energy calculations, which correspond to strong and weak adsorption strengths, respectively. By steering the nature of adsorption, we find that distinct chemical interactions as well as magnetic exchange interactions between the metalloporphyrin and the metal surface can be realized. We furthermore show that a switching of the MnP molecule's spin state can occur even for the weakly adsorbed case. This new discovery opens up prospects for engineering the chemical and magnetic exchange interaction in new functionalized spintronic materials.
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| 9. |
- Ali, Md. Ehesan, et al.
(författare)
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Electronic Structure, Spin-States, and Spin-Crossover Reaction of Heme-Related Fe-Porphyrins : A Theoretical Perspective
- 2012
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Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 116:20, s. 5849-5859
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Tidskriftsartikel (refereegranskat)abstract
- The electronic structures, spin-states, and geometrical parameters of tetra-, penta-, and hexa-coordinated iron-porphyrins are investigated applying density functional theory (DFT) based calculations, utilizing the plane-wave pseudopotential as well as localized basis set approaches. The splitting of the spin multiplet energies are investigated applying various functionals including recently developed hybrid meta-GGA (M06 family) functionals. Almost all of the hybrid functionals accurately reproduce the experimental ground state spins of the investigated Fe-porphyrins. However, the energetic ordering of the spin-states and the energies between them are still an issue. The widely used B3LYP provides consistent results for all chosen systems. The GGA+U functionals are found to be equally competent. After assessing the performance of various functionals in spin-state calculations, the potential energy surfaces of the oxygen binding process by heme is investigated. This reveals a "double spin-crossover" feature for the lowest energy reaction path that is consistent with previous CASPT2 calculations but predicting a lowest energy singlet state. The calculations have hence captured the spin-crossover as well as spin-flip processes. These are driven by the intra-atomic orbital polarization on the central metal atom due to the atomic and orbitals rearrangements. The nature of the chemical bonding and a molecular orbital analysis are also performed for the geometrically simple but electronic structurally complicated system tetra-coordinated planar Fe porphyrin in comparison to the penta-coordinated systems. This analysis explains the observed paradoxical appearance of certain peaks in the local density of states (DOS).
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| 10. |
- Amft, Martin, et al.
(författare)
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First-principles calculations of optical and magneto-optical properties of Ga1-xMnxAs and MnAs
- 2009
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Ingår i: Physica. B, Condensed matter. - : Elsevier BV. - 0921-4526 .- 1873-2135. ; 404:20, s. 3782-3788
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Tidskriftsartikel (refereegranskat)abstract
- We present a first-principles density-functional investigation of the optical and magneto-optical properties of MnGa1-xAs (with x = 0,0.0625, and 1) systems. Our calculated dielectric function, magneto-optical Kerr effect, and magnetic circular dichroism spectra agree reasonably well with existing experimental results. A comparison of the optical and magneto-optical spectra of MnAs in the naturally occurring hexagonal phase and in the cubic zinc-blende structure is made. The differences in the spectral properties of these two phases could aid detection of MnAs in the zinc-blende structure. (C) 2009 Elsevier B.V. All rights reserved.
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