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  • 1.
    Erdtman, Edvin
    et al.
    Örebro University, Department of Natural Sciences.
    dos Santos, Daniel J. V. A.
    Löfgren, Lennart
    Eriksson, Leif A.
    Örebro University, Department of Natural Sciences.
    Modelling the behavior of 5-aminolevulinic acid and its alkyl esters in a lipid bilayer2008In: Chemical Physics Letters, ISSN 0009-2614, E-ISSN 1873-4448, Vol. 463, no 1-3, p. 178-182Article in journal (Refereed)
    Abstract [en]

    5-Aminolevulinic acid (5ALA) and ester derivates thereof are used as prodrugs in photodynamic therapy (PDT). The behavior of 5ALA and three esters of 5ALA in a DPPC lipid bilayer is investigated. In particular, the methyl ester displays a very different free energy profile, where the highest barrier is located in the region with highest lipid density, while the others have their peak in the middle of the membrane, and also displays a considerably lower permeability coefficient than neutral 5ALA and the ethyl ester. The zwitterion of 5ALA has the highest permeability constant, but a significant free energy minimum in the polar head-group region renders an accumulation in this region.

  • 2.
    Erdtman, Edvin
    et al.
    Örebro University, School of Science and Technology.
    dos Santos, Daniel J. V. A.
    Örebro University, School of Science and Technology.
    Löfgren, Lennart
    Orebro Univ Hosp, Head & Neck Oncol Ctr, S-70185 Orebro, Sweden.
    Eriksson, Leif A.
    Örebro University, Department of Natural Sciences.
    Modelling the behavior of 5-aminolevulinic acid and its alkyl esters in a lipid bilayer (vol 463, pg 178, 2008)2009In: Chemical Physics Letters, ISSN 0009-2614, E-ISSN 1873-4448, Vol. 470, no 4-6, p. 369-369Article in journal (Refereed)
  • 3.
    Erdtman, Edvin
    et al.
    Örebro University, Department of Natural Sciences.
    Eriksson, Leif A.
    Örebro University, Department of Natural Sciences.
    Theoretical study of 5-aminolevulinic acid (5ALA) and some pharmaceutically important derivatives2007In: Chemical Physics Letters, ISSN 0009-2614, E-ISSN 1873-4448, Vol. 434, no 1-3, p. 101-106Article in journal (Refereed)
    Abstract [en]

    5-Aminolevulinic acid (5ALA) is the key synthetic building block in protoporphyrin IX (PpIX), the heme chromophore in mitochondria. The addition of extracorporeal 5ALA and its alkyl ester derivatives are in current clinical use in photodynamical diagnostics and photodynamic therapy of tumors and skin disorders. In the current study density functional theory calculations are performed on 5ALA and its methyl, ethyl, and hexyl esters, in order to explore the basic chemical properties of these species. It is concluded that even in aqueous media the zwitterionic form of 5ALA is less stable than the non-zwitterionic one, that the local environment (lipid vs water) affects the energetics of reaction considerably, and that the hexyl species is most prone to hydrolysis of the three alkyl ester derivatives.

  • 4. Omar, Salama
    et al.
    Eriksson, Leif A.
    Örebro University, School of Science and Technology.
    Interaction and photobinding between 8-methoxypsoralen and thymine2009In: Chemical Physics Letters, ISSN 0009-2614, E-ISSN 1873-4448, Vol. 471, no 1-3, p. 128-132Article in journal (Refereed)
    Abstract [en]

    The intercalation and photobinding of 8-methoxypsoralen with thymine in DNA is studied by computational chemistry techniques. Photochemical [2+2] cycloadditions at the S-1 surface display barriers of approximately 20 kcal/mol. The lowest lying excited surface has a defined potential well at the ground state TS, enabling for efficient decay. Avoided crossings between the S-1 and S-2 surfaces are also observed, which may influence the photochemical reactivity. The further reactions leading to crosslink formation from furan monoadducts but not from pyrone ones are fully explained by the excitation energies of the monoadducts, whereas the predominance of furan over pyrone monoadduct formation is not explained looking at the excitation energy surfaces alone. (C) 2009 Elsevier B.V. All rights reserved.

  • 5.
    Saenz-Mendez, Patricia
    et al.
    Örebro University, Department of Natural Sciences.
    Guedes, Rita C.
    dos Santos, Daniel J.V.A.
    Eriksson, Leif A.
    Örebro University, Department of Natural Sciences.
    Theoretical prediction of binding modes and hot sequences for allopsoralen-DNA interaction2007In: Chemical Physics Letters, ISSN 0009-2614, E-ISSN 1873-4448, Vol. 450, no 1-3, p. 127-131Article in journal (Refereed)
    Abstract [en]

    Molecular docking studies of two duplex DNA sequences as target fragments and allopsoralen as ligand were performed. The calculated interaction energies showed that the ligand can be docked into the minor groove as well as become intercalated. However, unlike psoralen, allopsoralen preferred binding mode for non-poly-TA sequences is minor groove binding. Calculated energies for intercalation between different base pairs suggest that the predicted sequence selectivity for allopsoralen is analogous to that observed for psoralen. Intercalation is favored in 5'-TpA sites in poly-TA sequences.

  • 6.
    Scherbak, Nikolai
    et al.
    Örebro University, Department of Natural Sciences.
    Strid, Åke
    Örebro University, Department of Natural Sciences.
    Eriksson, Leif A.
    Örebro University, Department of Natural Sciences.
    Non-enzymatic oxidation of NADH by quinones2005In: Chemical Physics Letters, ISSN 0009-2614, E-ISSN 1873-4448, Vol. 414, no 1-3, p. 243-247Article in journal (Refereed)
    Abstract [en]

    Non-enzymatic oxidation of NADH by a large number of different quinones has been explored both theoretically and experimentally. It is concluded that the smaller benzo- and naphtho-quinones are capable of oxidising NADH in aqueous solution, whereas the larger anthraquinone is not. The mechanisms of stepwise electron and proton transfers are explored, and ruled out in favour of direct hydride transfer. For menadione (2-methyl-1,4-naphthoquinone), no reaction is observed experimentally; theoretically we find that there is a very close balance between the energetic cost of hydride removal from NADH and the energy gain of formation of the menadione semiquinone radical anion.

  • 7. Schyman, Patric
    et al.
    Eriksson, Leif A.
    Örebro University, Department of Natural Sciences.
    Zhang, Ru bo
    Laaksonen, Aatto
    Hydroxyl radical - thymine adduct induced DNA damages2008In: Chemical Physics Letters, ISSN 0009-2614, E-ISSN 1873-4448, Vol. 458, no 1-3, p. 186-189Article in journal (Refereed)
    Abstract [en]

    DNA damages caused by a 5-hydroxy-5,6-dihydrothymine-6-yl radical (5-OHT-6yl) abstracting a C20 hydrogen from a neighboring sugar (inter-H abstraction) have been theoretically investigated using hybrid DFT in gas phase and in water solution. The inter-H abstraction was here shown to be comparable in energy (24 kcal mol 1) with the intra-H abstraction in which the 5-OHT-6yl abstracts a C20 hydrogen from its own sugar. The effect of a neutrally or a negatively charged phosphate group was also studied and the results show no significant impact on the activation energy of the hydrogen abstraction whereas base release and strand break reactions are affected.

  • 8. Tu, Guangde
    et al.
    Tu, Yaoquan
    Örebro University, School of Science and Technology.
    Vahtras, Olav
    Ågren, Hans
    Core electron chemical shifts of hydrogen-bonded structures2009In: Chemical Physics Letters, ISSN 0009-2614, E-ISSN 1873-4448, Vol. 468, no 4-6, p. 294-298Article in journal (Refereed)
    Abstract [en]

    We examine the possibility to study hydrogen-bonded structures through core ionization energies. We use a recently derived self-interaction corrected density functional theory method where the core ionization energies for all chemically shifted elements are obtained by a single calculation of the ground state of the structures. A direct dependency between the hydrogen atom to acceptor atom bond length and the chemical shift of the core ionization energy of the acceptor atom is found, something that has ramifications for the possibility of effective predictions of hydrogen bond lengths in hydrogen-bonded systems. This observation is verified by the conventional, much more time-consuming, self-consistent field calculations based on density functional theory.

  • 9.
    Wu, Min
    et al.
    University of Gothenburg, Gothenburg, Sweden.
    Strid, Åke
    Örebro University, School of Science and Technology.
    Eriksson, Leif A.
    University of Gothenburg, Gothenburg, Sweden.
    Development of non-standard arginine residue parameters for use with the AMBER force fields2013In: Chemical Physics Letters, ISSN 0009-2614, E-ISSN 1873-4448, Vol. 584, p. 188-194Article in journal (Refereed)
    Abstract [en]

    Amino acid radicals are often involved as intermediates in biological processes, but are difficult to capture by experiment. Computational modeling can be employed to study the features of the species involved. The neutral arginyl radical has previously been detected experimentally using ECD and ETD spectroscopy. Protonation of the radical can occur on the guanidinium carbon, depending on the peptide structure and protein environment. Accurate force fields are essential for reproducing the conformational and dynamic behavior of these intermediates. New AMBER ff99 parameters for the arginyl radical and hydrogenated arginyl side chains are presented based on ab initio quantum chemical calculations. (c) 2013 Elsevier B.V. All rights reserved.

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