| 1. |
- Schyman, Patric, et al.
(author)
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Hydrogen Abstraction from Deoxyribose by a Neighbouring Uracil-5-yl Radical
- 2007
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In: Physical Chemistry, Chemical Physics - PCCP. - : Royal Society of Chemistry. - 1463-9076 .- 1463-9084. ; 9, s. 5975-5979
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Journal article (peer-reviewed)abstract
- Hydrogen abstraction from the C1 and C2 positions of deoxyadenosine by a neighbouring uracil-5-yl radical in the 5-AU-3 DNA sequence is explored using DFT. This hydrogen abstraction is the first step in a sequence leading to single or double strand break in DNA. The uracil-5-yl radical can be the result of photolysis or low-energy electron (LEE) attachment. If the radical is produced by photolysis the neighbouring adenine will become a cation radical and if it is produced by LEE the adenine will remain neutral. The hydrogen abstraction reactions for both cases were investigated. It is concluded that it is possible for the uracil-5-yl to abstract hydrogen from C1 and C2. When adenine is neutral there is a preference for the C1 site and when the adenine is a radical cation the C2 site is the preferred. If adenine is positively charged, the rate-limiting step when abstracting hydrogen from C1 is the formation of an intermediate crosslink between uracil and adenine. This crosslink might be avoided in dsDNA, making C1 the preferred site for abstraction.
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| 2. |
- Schyman, Patric, et al.
(author)
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Hydroxyl radical - thymine adduct induced DNA damages
- 2008
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In: Chemical Physics Letters. - Amsterdam : Elsevier. - 0009-2614 .- 1873-4448. ; 458:1-3, s. 186-189
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Journal article (peer-reviewed)abstract
- 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.
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| 3. |
- Zhang, Ru Bo, et al.
(author)
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Theoretical studies of damage to 3'-uridine monophosphate induced by electron attachment
- 2008
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In: Chemistry - A European Journal. - Weinheim : Wiley-VCH-Verl.. - 0947-6539 .- 1521-3765. ; 14:9, s. 2850-2856
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Journal article (peer-reviewed)abstract
- Low-energy electrons (LEE) are well known to induce nucleic acid damage. However, the damage mechanisms related to charge state and structural features remain to be explored in detail. In the present work, we have investigated the N1-glycosidic and C3'-O(P) bond ruptures of 3'-UMP (UMP=uridine monophosphate) and the protonated form 3'-UMPH with -1 and zero charge, respectively, based on hybrid density functional theory (DFT) B3 LYP together with the 6-31+G(d,p) basis set. The glycosidic bond breakage reactions of the 3'UMP and 3'UMPH electron adducts are exothermic in both cases, with barrier heights of 19-20 kcal mol(-1) upon inclusion of bulk solvation. The effects of the charge state on the phosphate group are marginal, but the C2'-OH group destabilizes the transition structure of glycosidic bond rupture of 3'-UMPH in the gas phase by approximately 5.0 kcal mol(-1). This is in contrast with the C3'-O(P) bond ruptures induced by LEE in which the charge state on the phosphate influences the barrier heights and reaction energies considerably. The barrier towards C3'-O(P) bond dissociation in the 3'UMP electron adduct is higher in the gas phase than the one corresponding to glycosidic bond rupture and is dramatically influenced by the C2'-OH group and bulk salvation, which decreases the barrier to 14.7 kcal mol(-1). For the C3'-O(P) bond rupture of the 3'UMPH electron adduct, the reaction is exothermic and the barrier is even lower, 8.2 kcal mol(-1), which is in agreement with recent results for 3'-dTMPH and 5'-dTMPH (dTMPH=deoxythymidine monophosphate). Both the Mulliken atomic charges and unpaired-spin distribution play significant roles in the reactions
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| 4. |
- Laarz, Eric, et al.
(author)
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Colloidal processing of Al2O3-based composites reinforced with TiN and TiC particulates, whiskers and nanoparticles
- 2001
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In: Journal of the European Ceramic Society. - 0955-2219 .- 1873-619X. ; 21:8, s. 1027-1035
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Journal article (peer-reviewed)abstract
- A colloidal processing route has been developed for the preparation of dense and homogeneous Al2O3–TiN/TiC composites. The dispersion and rheological properties of mixtures of TiN or TiC particulates and Al2O3 particles were investigated using electrokinetics and steady-shear rheology. We found that well-dispersed aqueous suspensions with low viscosity could be prepared by adding a poly(acrylic acid) dispersant and controlling pH in the alkaline range. This processing scheme was also suitable for preparation of whisker and nanoparticle composite suspensions. The alumina-based composite suspensions with a secondary-phase concentration of 25 vol.% were freeze-granulated and hot-pressed, and the resulting bodies were fully densified with well-dispersed secondary phases. Homogeneous Al2O3–TiN nanoparticle composites could only be prepared with additions of up to 5 vol.% nanoparticles; higher additions resulted in agglomeration and subsequent grain growth of the nanoparticles.
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| 5. |
- Tejero, Ismael, et al.
(author)
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Theoretical modeling of hydroxyl-radical-induced lipid peroxidation reactions
- 2007
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In: Journal of Physical Chemistry B. - : American Chemical Society. - 1520-6106 .- 1520-5207. ; 111:20, s. 5684-5693
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Journal article (peer-reviewed)abstract
- The OH-radical-induced mechanism of lipid peroxidation, involving hydrogen abstraction followed by O2 addition, is explored using the kinetically corrected hybrid density functional MPWB1K in conjunction with the MG3S basis set and a polarized continuum model to mimic the membrane interior. Using a small nonadiene model of linoleic acid, it is found that hydrogen abstraction preferentially occurs at the mono-allylic methylene groups at the ends of the conjugated segment rather than at the central bis-allylic carbon, in disagreement with experimental data. Using a full linoleic acid, however, abstraction is correctly predicted to occur at the central carbon, giving a pentadienyl radical. The Gibbs free energy for abstraction at the central C11 is 8 kcal/mol, compared to 9 kcal/mol at the end points (giving an allyl radical). Subsequent oxygen addition will occur at one of the terminal atoms of the pentadienyl radical fragment, giving a localized peroxy radical and a conjugated butadiene fragment, but is associated with rather high free energy barriers and low exergonicity at the CPCM-MPWB1K/MG3S level. The ZPE-corrected potential energy surfaces obtained without solvent effects, on the other hand, display considerably lower barriers and more exergonic reactions.
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| 6. |
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| 7. |
- Erdtman, Edvin, et al.
(author)
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Modelling the behavior of 5-aminolevulinic acid and its alkyl esters in a lipid bilayer
- 2008
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In: Chemical Physics Letters. - Amsterdam : North-Holland Publishing Co. - 0009-2614 .- 1873-4448. ; 463:1-3, s. 178-182
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Journal article (peer-reviewed)abstract
- 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.
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| 8. |
- Erdtman, Edvin, et al.
(author)
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Theoretical study of 5-aminolevulinic acid tautomerization : a novel self-catalyzed mechanism
- 2008
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In: Journal of Physical Chemistry A. - Washington DC : American Chemical Society. - 1089-5639 .- 1520-5215. ; 112:18, s. 4367-4374
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Journal article (peer-reviewed)abstract
- 5-Aminolevulinic acid (5ALA) is the key synthetic building block in protoporphyrin IX (PpIX), the heme chromophore in mitochondria. In this study density functional theory calculations were performed on the tautomers of 5ALA and the tautomerization reaction mechanism from its enolic forms (5-amino-4-hydroxypent-3-enoic acid and 5-amino-4-hydroxypent-4-enoic acid) to the more stable 5ALA. The hydrated form 5-amino-4,4-dihydroxypentanoic acid was also studied. The lowest energy pathway of 5ALA tautomerization is by means of autocatalysis, in that an oxygen of the carboxylic group transfers the hydrogen atom as a "crane", with an activation energy of similar to 15 kcal/mol. This should be compared to the barriers of about 35 kcal/mol for water assisted tautomerization, and 60 kcal/mol for direct hydrogen transfer. For hydration of 5ALA, the water catalyzed activation barrier is found to be similar to 35 kcal/mol, approximately 5 kcal/mol lower than direct hydration.
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| 9. |
- Lyubartsev, Alexander, 1962-, et al.
(author)
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Hierarchical multiscale modelling scheme from first principles to mesoscale
- 2009
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In: Journal of Computational and Theoretical Nanoscience. - : American Scientific Publishers. - 1546-1955 .- 1546-1963. ; 6:5, s. 951-959
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Journal article (peer-reviewed)abstract
- We present a straight-forward implementation of a practical hierarchical multiscale modelling scheme which enables us to start from first-principles atomistic computer simulation and successively coarse-grain the model by leaving out uninteresting degrees of freedom. Using the Car-Parrinello method or our recently developed highly efficient tight-binding-like approximate density-functional quantum mechanical method,w e first perform first-principles simulations we obtain a set of atomistic pair-wise effective interaction potentials to be used as a force field with scaling up the system size 2–3 orders of magnitude. The atomistic simulations similarly provide a new set of effective potentials but at a chosen coarse-grain level suitable for large-scale mesoscopic or soft-matter simulations beyond the atomic resolution. Show several examples are shown of how this scheme is done based on effective interaction potentials to tie together the various scales of modelling.
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| 10. |
- Wallqvist, Viveca, 1977-
(author)
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Interactions between non-polar surfaces in water: Fokus on talc, pitch and surface roughness effects
- 2009
-
Doctoral thesis (other academic/artistic)abstract
- The aim of this thesis work was to gain understanding of the interactions between talc mineral and surfaces, liquids and chemicals relevant for industrial applications, such as pulp and paper. Talc is used in the pulp and paper industry as a filler pigment, in control of pitch (lipophilic extractives) deposits and as a coating pigment. A deeper understanding of talc interactions will be beneficial in optimizing its use. Long-range attractive interactions between talc and hydrophobic model probes, as well as pitch probes, have been measured using the atomic force microscope (AFM) colloidal probe method. Two procedures for preparation of pitch colloidal probes were developed to allow these studies. Model hydrophobic, nanorough surfaces with surface energy characteristics similar to talc have also been prepared and their interactions with hydrophobic model probes compared to interactions between hydrophobic model probes and talc. It is demonstrated that talc mineral interacts with model hydrophobic particles, as well as with pitch, by long-range attractive forces, considerably stronger than the expected van der Waals force. The possible origin of the measured interaction forces is discussed, and the conclusion is that the main cause is an attractive capillary force due to formation of a gas/vapor capillary between the surfaces. Force measurements using model hydrophobic, nanorough surfaces show that a large-scale waviness does not significantly influence the range and magnitude of the capillary attraction, but large local variations in these quantities are found. It is demonstrated that a large variation in adhesion force corresponds to a small variation in local contact angle of the capillaries at the surfaces. The nature of the surface topographical features influences the capillary attraction by affecting the local contact angle and by pinning of the three-phase contact line. The effect is clearly dependent on the size of the surface features and whether they exist in the form of crevices or as extending ridges. Entrapment of air also affects the imbibition of water in pressed talc tablets. The effects of wetting and dispersion agents on the interactions between talc and hydrophobic probes have also been investigated. It is demonstrated that a common dispersing agent used for talc, poly(acrylic acid), does not affect the capillary attraction between talc and non-polar probes. In fact, the results strongly suggest that poly(acrylic acid) does not adsorb on the basal plane of talc. From this finding it is inferred that the stabilizing effect of this additive most likely is due to adsorption to the edges of talc. In contrast, a wetting agent (the non-ionic triblock copolymer Pluronic PE6400) removes the long-range capillary attraction. It is suggested that such an ability to replace air at the talc surface is of great importance for an efficient wetting agent. The Hamaker constant for talc has also been estimated by using optical data obtained from spectroscopic ellipsometry. It is demonstrated that a nanocrystalline talc mineral, cut in different directions displays very small differences in Hamaker constant between the different crystallographic orientations, whereas a microcrystalline sample displays a significantly higher value. The estimated Hamaker constants are discussed for different material combinations of relevance for the pulp- and paper industry, such as cellulose and calcium carbonate.
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