| 1. |
- Alavi, Fatemeh Sadat, et al.
(författare)
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QM/MM study of the conversion of biliverdin into verdoheme by heme oxygenase
- 2019
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Ingår i: Theoretical Chemistry Accounts. - : Springer Science and Business Media LLC. - 1432-881X .- 1432-2234. ; 138:5
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Tidskriftsartikel (refereegranskat)abstract
- It has been shown that after production of oxophlorin, the first step of intermediate, both production of biliverdin and production of verdoheme occur simultaneously (Alavi et al. in Dalton Trans 47:8283–8291, 2018). So the mechanism that converts biliverdin into verdoheme is the subject of some controversy. The detailed conversion of verdoheme to biliverdin was demonstrated before by the Jerusalem group, using combined quantum mechanical and molecular mechanical (QM/MM) calculations. Conversion of iron biliverdin to iron verdoheme in the presence of H + was investigated using the B3LYP method and the def2-QZVP basis set, considering dispersion effects with the DFT-D3 approach, obtaining accurate energies with large QM regions of almost 1000 atoms. Two spin states, singlet and triplet, were considered for the conversion of biliverdin to verdoheme. The reactant and product are triplet and singlet in their ground states, respectively. The potential energy surface suggests that a spin inversion takes place during the course of reaction after TS2. The ring closing process is exothermic by 5.8 kcal/mol with a kinetic barrier of 16.5 kcal/mol. The activation barrier for removing OH from the ring to produce iron verdoheme is estimated to be 23.2 kcal/mol.
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| 2. |
- Eriksson, Emma S. E., et al.
(författare)
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Permeability of 5-aminolevulinic acid oxime derivatives in lipid membranes
- 2016
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Ingår i: Theoretical Chemistry accounts. - : Springer Science and Business Media LLC. - 1432-881X .- 1432-2234. ; 135:1, s. 1-9
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Tidskriftsartikel (refereegranskat)abstract
- The endogenous molecule 5-aminolevulinic acid (5ALA) and its methyl ester (Me-5ALA) have been used as prodrugs in photodynamic treatment of actinic keratosis and superficial non-melanoma skin cancers for over a decade. Recently, a novel set of 5ALA derivatives based on introducing a hydrolyzable oxime functionality was proposed and shown to generate considerably stronger onset of the photoactive molecule protoporphyrin IX (PpIX) in the cells. In the current work, we employ molecular dynamics simulation techniques to explore whether the higher intercellular concentration of PpIX caused by the oxime derivatives is related to enhanced membrane permeability, or whether other factors contribute to this. It is concluded that the oximes show overall similar accumulation at the membrane headgroup regions as the conventional derivatives and that the transmembrane permeabilities are in general close to that of 5ALA. The highest permeability of all compounds explored is found for Me-5ALA, which correlates with a considerably lower fee energy barrier at the hydrophobic bilayer center. The high PpIX concentration must hence be sought in other factors, where slow hydrolysis of the oxime functionality is a plausible reason, enabling stronger buildup of PpIX over time.
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| 3. |
- Finzel, Kati
(författare)
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About the atomic shell structure in real space and the Pauli exclusion principle
- 2016
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Ingår i: Theoretical Chemistry accounts. - : SPRINGER. - 1432-881X .- 1432-2234. ; 135:6, s. 148-
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Tidskriftsartikel (refereegranskat)abstract
- It is shown that any set of eigenfunctions (1s, 2s) of a bare Coulomb Hamiltonian exhibit the same atomic shell structure pattern for the real-space indicator a(1), which is defined as the ratio between the positive kinetic energy density and the electron density. Since this model Hamiltonian excludes all effects due to the electron-electron repulsion, the appearance of the atomic shell structure is attributed to the Pauli exclusion principle that arises from the requirements for a fermionic wavefunction. Since the derivation is independent of the nuclear charge and the energy of the system, reversely imposing proper atomic shell structure behavior in the design of kinetic energy functionals mimics the Pauli exclusion principle during a variational process.
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| 4. |
- Finzel, Kati, et al.
(författare)
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Functional constructions with specified functional derivatives
- 2016
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Ingår i: Theoretical Chemistry accounts. - : SPRINGER. - 1432-881X .- 1432-2234. ; 135:12
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Tidskriftsartikel (refereegranskat)abstract
- A bifunctional construction depending on a specified density-potential pair and an approximate guiding electron density functional is presented. The proposed bifunctional construction properly transforms under homogeneous coordinate scaling and yields the specified functional derivative, which determines the electron density. Whereas the method is general and applicable to all functional types, it will prove especially helpful in the context of orbital-free density functional theory, where most existing approximate density functionals predict inaccurate potentials.
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| 5. |
- Finzel, Kati
(författare)
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Reinvestigation of the ideal atomic shell structure and its application in orbital-free density functional theory
- 2016
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Ingår i: Theoretical Chemistry accounts. - : SPRINGER. - 1432-881X .- 1432-2234. ; 135:4, s. 87-
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Tidskriftsartikel (refereegranskat)abstract
- It is shown how to determine the ideal shell radii solely as a function of the nuclear charge. With the help of those ideal shell radii, an approximation to the Pauli potential for atoms in their groundstate can be constructed. The so-called SSB-ideal potential (shell structure-based) yields self-consistent orbital-free electron densities with proper atomic shell structure from Hohenberg-Kohn variational principle.
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| 6. |
- Francés-Monerris, Antonio, et al.
(författare)
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Triplet versus singlet chemiexcitation mechanism in dioxetanone : a CASSCF/CASPT2 study
- 2017
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Ingår i: Theoretical Chemistry accounts. - : Springer Science and Business Media LLC. - 1432-881X .- 1432-2234. ; 136:6
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Tidskriftsartikel (refereegranskat)abstract
- Chemiluminescence is a fundamental process of chemistry consisting in the conversion of chemical energy stored in chemical bonds into light. It is used by nature and by man-made technology, being especially relevant in chemical analysis. The understanding of the phenomenon strongly relies in the study of peroxide models such as 1,2-dioxetanones. In the present contribution, the singlet S2 and the triplet T2 potential energy surfaces of the unimolecular decomposition of 1,2-dioxetanone have been mapped along the O-O and C-C bond coordinates on the grounds of the multiconfigurational CASPT2//CASSCF approach. Results confirm the energy degeneracy between T2, T1, S1, and S0 at the TS region, whereas S2 is unambiguously predicted at higher energies. Triplet-state population is also supported by the spin-orbit couplings between the singlet and triplet states partaking in the process. In particular, the first-principle calculations show that decomposition along the T2 state is a competitive process, having a small (similar to 3 kcal/mol) energy barrier from the ground-state TS structure. The present findings can explain the higher quantum yield of triplet-state population with respect to the excited singlet states recorded experimentally for the uni-molecular decomposition of 1,2-dioxetanone models.
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| 7. |
- Lindgren, Ingvar, 1931, et al.
(författare)
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Combination of many-body perturbation theory and quantum electrodynamics
- 2015
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Ingår i: Theoretical Chemistry accounts. - : Springer Science and Business Media LLC. - 1432-881X .- 1432-2234. ; 134:11
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Tidskriftsartikel (refereegranskat)abstract
- A procedure for energy-dependent perturbation expansion has been developed, based upon the covariant evolution operator method. This makes it possible to treat energy-dependent perturbations very much like the energy-independent ones in standard many-body perturbation theory. This has been applied to the non-radiative QED perturbations (retardation and virtual electron-positron pairs) as well as the radiative ones (electron self-energy, vacuum polarization and vertex correction). The combination of QED and electron correlation, beyond two-photon exchange, has been evaluated, using the Coulomb gauge. It turned out that in that gauge the extremely time-consuming model-space contributions of the self-energy and vertex corrections do not have to be evaluated in full. In the Feynman gauge no sensible results could be obtained in this way, as is demonstrated by the numerical results.
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| 8. |
- Merced Montero-Campillo, M., et al.
(författare)
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Gas-phase reactivity tuned through the interaction with alkaline-earth derivatives
- 2019
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Ingår i: Theoretical Chemistry accounts. - : Springer Science and Business Media LLC. - 1432-881X .- 1432-2234. ; 138:5
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Tidskriftsartikel (refereegranskat)abstract
- The cooperativity between MX2:XH alkaline-earth bonds and XH:NH3 hydrogen bonds (M=Mg, Ca; X=F, Cl) was investigated at the G4 level of theory. The cooperativity between these two non-covalent linkages is extremely large, to the point that the increase in their bond dissociation enthalpies may be as large as 240%. More importantly, the weaker the interaction, the larger the increase, so in some cases the linkage that stabilizes the most is the alkaline-earth bond, whereas in others is the hydrogen bond. In all cases, the formation of the MX2:XH:NH3 ternary complex is followed by a spontaneous proton transfer, very much as previously found for the Be-containing analogues. Similarly, MX2:FCl:NH3 complexes evolve from a chlorine-shared ternary complex (MX2FClNH3) or from an ion pair (MX2F-NH3Cl+) if M=Ca. Although F is the only halogen without sigma-hole, MgCl2 derivatives induce the appearance of a sigma-hole on it, though less deep than those induced by BeCl2. We have also studied whether Mg and Ca bond-containing complexes MR2:FY (R=H, F, Cl; Y=NH2, OH, F, Cl) may react to form radicals, as it has been found for the Be-containing analogues. These interactions provoke a drastic decrease in the F-Y bond dissociation enthalpy, very much as the one reported for the corresponding Be-analogues, to the point that in some cases the formation of the corresponding MR2F center dot+Y radicals becomes exothermic. Hence, the general conclusion of this study is that Mg or Ca derivatives give place to similar or even larger perturbations on the electron density than those induced by Be, a result not easily predictable.
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