| 1. |
- Schyman, Patric, et al.
(författare)
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Hydrogen Abstraction from Deoxyribose by a Neighbouring Uracil-5-yl Radical
- 2007
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Ingår i: Physical Chemistry, Chemical Physics - PCCP. - : Royal Society of Chemistry. - 1463-9076 .- 1463-9084. ; 9, s. 5975-5979
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Tidskriftsartikel (refereegranskat)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. |
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| 3. |
- Schyman, Patric, et al.
(författare)
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Hydroxyl radical - thymine adduct induced DNA damages
- 2008
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Ingår i: Chemical Physics Letters. - Amsterdam : Elsevier. - 0009-2614 .- 1873-4448. ; 458:1-3, s. 186-189
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Tidskriftsartikel (refereegranskat)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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| 4. |
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| 5. |
- Maurina Morais, Eduardo, 1989, et al.
(författare)
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Solvent-free synthesis of protic ionic liquids. Synthesis, characterization and computational studies of triazolium based ionic liquids
- 2022
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Ingår i: Journal of Molecular Liquids. - : Elsevier BV. - 0167-7322. ; 360
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Tidskriftsartikel (refereegranskat)abstract
- A series of triazolium and imidazolium based protic ionic liquids were synthesized using a solvent-free method designed to address several limitations encountered with other commonly used methods. Using this method, pure (98–99% m/m) and dry (128–553 ppm of water) protic ionic liquids were synthesized (in a laboratory scale) without the need for purification methods that require heating the ionic liquid, hence avoiding the common issue of thermal decomposition. This method was also designed to allow for the accurate measurement of acid and base, and for the controlled mixing of both compounds, which is essential to avoid producing impure protic ionic liquids with excess of either acid or base. The system is constructed of only glass and chemically resistant polymer (PTFE and PVDF) parts, which avoid other contaminants that can result from unwanted reactions involving the reagents with common laboratory tools (metallic objects, paper, plastic, etc.). This process is described in detail in the paper as well as in a video. The resulting ionic liquids were carefully analyzed by spectroscopic and thermal methods designed to avoid water absorption, which is known to affect their properties. To complement this experimental characterization, computational chemistry tools were used to assess the ionic liquids’ properties, as well as to assign vibrational modes.
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| 6. |
- Zhang, Ru Bo, et al.
(författare)
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Theoretical studies of damage to 3'-uridine monophosphate induced by electron attachment
- 2008
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Ingår i: Chemistry - A European Journal. - Weinheim : Wiley-VCH-Verl.. - 0947-6539 .- 1521-3765. ; 14:9, s. 2850-2856
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Tidskriftsartikel (refereegranskat)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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| 7. |
- Laarz, Eric, et al.
(författare)
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Colloidal processing of Al2O3-based composites reinforced with TiN and TiC particulates, whiskers and nanoparticles
- 2001
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Ingår i: Journal of the European Ceramic Society. - 0955-2219 .- 1873-619X. ; 21:8, s. 1027-1035
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Tidskriftsartikel (refereegranskat)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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| 8. |
- Bushnell, Eric A. C., et al.
(författare)
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The first branching point in porphyrin biosynthesis : a systematic docking, molecular dynamics and quantum mechanical/molecular mechanical study of substrate binding and mechanism of uroporphyrinogen-III decarboxylase
- 2011
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Ingår i: Journal of Computational Chemistry. - New York : John Wiley & Sons. - 0192-8651 .- 1096-987X. ; 32:5, s. 822-834
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Tidskriftsartikel (refereegranskat)abstract
- In humans, uroporphyrinogen decarboxylase is intimately involved in the synthesis of heme, where the decarboxylation of the uroporphyrinogen-III occurs in a single catalytic site. Several variants of the mechanistic proposal exist; however, the exact mechanism is still debated. Thus, using an ONIOM quantum mechanical/molecular mechanical approach, the mechanism by which uroporphyrinogen decarboxylase decarboxylates ring D of uroporphyrinogen-III has been investigated. From the study performed, it was found that both Arg37 and Arg50 are essential in the decarboxylation of ring D, where experimentally both have been shown to be critical to the catalytic behavior of the enzyme. Overall, the reaction was found to have a barrier of 10.3 kcal mol−1 at 298.15 K. The rate-limiting step was found to be the initial protontransfer from Arg37 to the substrate before the decarboxylation. In addition, it has been found that several key interactions exist between the substrate carboxylate groups and backbone amides of various activesite residues as well as several other functional groups.
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| 9. |
- Erdtman, Edvin, et al.
(författare)
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Computational studies on Schiff-base formation : Implications for the catalytic mechanism of porphobilinogen synthase
- 2011
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Ingår i: Computational and Theoretical Chemistry. - Amsterdam : Elsevier. - 2210-271X .- 2210-2728. ; 963:2-3, s. 479-489
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Tidskriftsartikel (refereegranskat)abstract
- Schiff bases are common and important intermediates in many bioenzymatic systems. The mechanism by which they are formed, however,is dependent on the solvent, pH and other factors. In the present study we have used density functional theory methods in combination with appropriate chemical models to get a better understanding of the inherent chemistry of the formation of two Schiff bases that have been proposed to be involved in the catalytic mechanism of porphobilinogensynthase (PBGS), a key enzyme in the biosynthesis of porphyrins. More specifically, we have investigated the uncatalysed reaction of its substrate 5-aminolevulinic acid (5-ALA) with a lysine residue for theformation of the P-site Schiff base, and as possibly catalysed by the second active site lysine, water or the 5-ALA itself. It is found that cooperatively both the second lysine and the amino group of the initial 5-ALA itself are capable of reducing the rate-limiting energy barrier to14.0 kcal mol-1. We therefore propose these to be likely routes involved in the P-site Schiff-base formation in PBGS.
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| 10. |
- Halldin Stenlid, Joakim, 1987-
(författare)
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Computational Studies of Chemical Interactions: Molecules, Surfaces and Copper Corrosion
- 2017
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The chemical bond – a corner stone in science and a prerequisite for life – is the focus of this thesis. Fundamental and applied aspects of chemical bonding are covered including the development of new computational methods for the characterization and rationalization of chemical interactions. The thesis also covers the study of corrosion of copper-based materials. The latter is motivated by the proposed use of copper as encapsulating material for spent nuclear fuel in Sweden.In close collaboration with experimental groups, state-of-the-art computational methods were employed for the study of chemistry at the atomic scale. First, oxidation of nanoparticulate copper was examined in anoxic aqueous media in order to better understand the copper-water thermodynamics in relation to the corrosion of copper material under oxygen free conditions. With a similar ambition, the water-cuprite interface was investigated with regards to its chemical composition and reactivity. This was compared to the behavior of methanol and hydrogen sulfide at the cuprite surface.An overall ambition during the development of computational methods for the analysis of chemical bonding was to bridge the gap between molecular and materials chemistry. Theory and results are thus presented and applied in both a molecular and a solid-state framework. A new property, the local electron attachment energy, for the characterization of a compound’s local electrophilicity was introduced. Together with the surface electrostatic potential, the new property predicts and rationalizes regioselectivity and trends of molecular reactions, and interactions on metal and oxide nanoparticles and extended surfaces.Detailed atomistic understanding of chemical processes is a prerequisite for the efficient development of chemistry. We therefore envisage that the results of this thesis will find widespread use in areas such as heterogeneous catalysis, drug discovery, and nanotechnology.
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