| 1. |
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| 2. |
- 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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| 3. |
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| 4. |
- 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
-
Ingår i: Journal of Molecular Liquids. - : Elsevier BV. - 0167-7322. ; 360
-
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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| 5. |
- Bunta, Juraj, et al.
(författare)
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Solvating, manipulating, damaging, and repairing DNA in a computer
- 2007
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Ingår i: International Journal of Quantum Chemistry. - New York : Wiley. - 0020-7608 .- 1097-461X. ; 107:2, s. 279-291
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Tidskriftsartikel (refereegranskat)abstract
- This work highlights four different topics in modeling of DNA: (i) the importance of water and ions together with the structure and function of DNA; the hydration structure around the ions appears to be the determining factor in the ion coordination to DNA, as demonstrated in the results of our MD simulations; (ii) how MD simulations can be used to simulate single molecule manipulation experiments as a complement to reveal the structural dynamics of the studied biomolecules; (iii) how damaged DNA can be studied in computer simulations; and (iv) how repair of damaged DNA can be studied theoretically.
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| 6. |
- Grand, André, et al.
(författare)
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*H and *OH radical reactions with 5-methylcytosine
- 2007
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Ingår i: Journal of Physical Chemistry A. - Washington, D.C. : American Chemical Society. - 1089-5639 .- 1520-5215. ; 111:37, s. 8968-8972
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Tidskriftsartikel (refereegranskat)
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| 7. |
- Labet, Vanessa, et al.
(författare)
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Proton catalyzed hydrolytic deamination of cytosine : a computational study
- 2008
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Ingår i: Theoretical Chemistry accounts. - Berlin Heidelberg : Springer. - 1432-881X .- 1432-2234. ; 120:4-6, s. 429-435
-
Tidskriftsartikel (refereegranskat)abstract
- Two pathways involving proton catalyzed hydrolytic deamination of cytosine (to uracil) are investigated at the PCM-corrected B3LYP/6-311G(d,p) level of theory, in the presence of an additional catalyzing water molecule. It is concluded that the pathway involving initial protonation at nitrogen in position 3 of the ring, followed by water addition at C4 and proton transfer to the amino group, is a likely route to hydrolytic deamination. The rate determining step is the addition of water to the cytosine, with a calculated free energy barrier in aqueous solution of G==140 kJ/mol. The current mechanism provides a lower barrier to deamination than previous work based on OH− catalyzed reactions, and lies closer to the experimental barrier derived from rate constants (Ea = 117 ± 4kJ/mol).
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| 8. |
- Matxain, Jon M, et al.
(författare)
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New solids based on B12N12 fullerenes
- 2007
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Ingår i: The Journal of Physical Chemistry C. - Washington, DC : American Chemical Society. - 1932-7447 .- 1932-7455. ; 111:36, s. 13354-60
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Tidskriftsartikel (refereegranskat)abstract
- In recent years, BN fullerenes have been synthesized experimentally. As their carbon counterparts, these BN fullerenes could be assembled in molecular solids, but this possibility has been studied little in the literature. In this work, we focus on the smallest synthesized BN fullerene, B12N12, which is built by squares and hexagons. First, the interaction between two of these fullerenes has been analyzed, using the hybrid B3LYP and MPW1PW91 density functional methods. Two different interactions have been studied in the dimer, a square facing a square (S−S) and a hexagon facing a hexagon (H−H). In both cases, a B is facing a N. The most stable dimer was found to be S−S facing, with covalent interactions between the monomers, but other dimers with weak interactions have been found as well, which opens possibilities of new systems, as in the case of fullerene dimers and solids. The solids resulting from the infinite repetition of the characterized dimers were optimized, finding two different solids, with covalent and weak interactions between monomers, respectively. The solid with covalent interactions is a nanoporous material that is more stable by around 12 eV. Because of the nanoporous character of this solid, it could be used for heterogeneous catalysis, molecular transport, and so forth. The SIESTA code with the GGA-PBE density functional method has been used for the solid-state calculations.
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| 9. |
- Musa, Klefah A K, et al.
(författare)
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Mechanism of Photoinduced Decomposition of Ketoprofen
- 2007
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Ingår i: Journal of Medicinal Chemistry. - Washington, DC : American Chemical Society. - 0022-2623 .- 1520-4804. ; 50:8, s. 1735-1743
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Tidskriftsartikel (refereegranskat)abstract
- UV-induced decarboxylation of the NSAID ketoprofen, followed by activation of molecular oxygen or formation of a decarboxylated peroxide adduct, is explored using computational quantum chemistry. The excited energy surfaces reveal that the neutral species will not decarboxylate, whereas the deprotonated acid decarboxylates spontaneously in the triplet state, and with an associated 3-5 kcal/mol barrier from several low-lying excited singlet states. The observed long lifetimes of the decarboxylated anion is explained in terms of the high stability of the triplet benzoyl ethyl species with protonated carbonylic oxygen, from which there is no obvious decay channel. Mechanisms for the generation of singlet oxygen and superoxide are discussed in detail. Addition of molecular oxygen to give the corresponding peroxyl radical capable of initiating propagating lipid peroxidation reactions is also explored. The computed data explains all features of the observed experimental observations made to date on the photodegradation of ketoprofen.
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| 10. |
- 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
-
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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| 11. |
- Lindström, Anton, 1976-, et al.
(författare)
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Postprocessing of docked protein-ligand complexes using implicit solvation models
- 2011
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Ingår i: Journal of chemical information and modeling. - : American Chemical Society (ACS). - 1549-960X .- 1549-9596. ; 51:2, s. 267-282
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Tidskriftsartikel (refereegranskat)abstract
- Molecular docking plays an important role in drug discovery as a tool for the structure-based design of small organic ligands for macromolecules. Possible applications of docking are identification of the bioactive conformation of a protein−ligand complex and the ranking of different ligands with respect to their strength of binding to a particular target. We have investigated the effect of implicit water on the postprocessing of binding poses generated by molecular docking using MM-PB/GB-SA (molecular mechanics Poisson−Boltzmann and generalized Born surface area) methodology. The investigation was divided into three parts: geometry optimization, pose selection, and estimation of the relative binding energies of docked protein−ligand complexes. Appropriate geometry optimization afforded more accurate binding poses for 20% of the complexes investigated. The time required for this step was greatly reduced by minimizing the energy of the binding site using GB solvation models rather than minimizing the entire complex using the PB model. By optimizing the geometries of docking poses using the GBHCT+SA model then calculating their free energies of binding using the PB implicit solvent model, binding poses similar to those observed in crystal structures were obtained. Rescoring of these poses according to their calculated binding energies resulted in improved correlations with experimental binding data. These correlations could be further improved by applying the postprocessing to several of the most highly ranked poses rather than focusing exclusively on the top-scored pose. The postprocessing protocol was successfully applied to the analysis of a set of Factor Xa inhibitors and a set of glycopeptide ligands for the class II major histocompatibility complex (MHC) Aq protein. These results indicate that the protocol for the postprocessing of docked protein−ligand complexes developed in this paper may be generally useful for structure-based design in drug discovery.
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| 12. |
- 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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| 13. |
- Nicholls, Ian A., et al.
(författare)
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Rational design of biomimetic molecularly imprinted materials : theoretical and computational strategies for guiding nanoscale structured polymer development
- 2011
-
Ingår i: Analytical and Bioanalytical Chemistry. - : Springer Science and Business Media LLC. - 1618-2642 .- 1618-2650. ; 400:6, s. 1771-1786
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Forskningsöversikt (refereegranskat)abstract
- In principle, molecularly imprinted polymer science and technology provides a means for ready access to nano-structured polymeric materials of predetermined selectivity. The versatility of the technique has brought it to the attention of many working with the development of nanomaterials with biological or biomimetic properties for use as therapeutics or in medical devices. Nonetheless, the further evolution of the field necessitates the development of robust predictive tools capable of handling the complexity of molecular imprinting systems. The rapid growth in computer power and software over the past decade has opened new possibilities for simulating aspects of the complex molecular imprinting process. We present here a survey of the current status of the use of in silico-based approaches to aspects of molecular imprinting. Finally, we highlight areas where ongoing and future efforts should yield information critical to our understanding of the underlying mechanisms sufficient to permit the rational design of molecularly imprinted polymers.
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| 14. |
- Rahm, Martin, et al.
(författare)
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The Molecular Surface Structure of Ammonium and Potassium Dinitramide : A Vibrational Sum Frequency Spectroscopy and Quantum Chemical Study
- 2011
-
Ingår i: The Journal of Physical Chemistry C. - : American Chemical Society (ACS). - 1932-7447 .- 1932-7455. ; 115:21, s. 10588-10596
-
Tidskriftsartikel (refereegranskat)abstract
- Vibrational sum frequency spectroscopy (VSFS) and quantum chemical modeling have been employed to investigate the molecular surface structure of ammonium and potassium dinitramide (ADN and KDN) crystals. Identification of key vibrational modes was made possible by performing density functional theory calculations of molecular clusters. The surface of KDN was found to be partly covered with a thin layer of the decomposition product KNO3, which due to its low thickness was not detectable by infrared and Raman spectroscopy. In contrast, ADN exhibited an extremely inhomogeneous surface, on which polarized dinitramide anions were present, possibly together with a thin layer of NH4NO3. The intertwined use of theoretical and experimental tools proved indispensable in the analysis of these complex surfaces. The experimental verification of polarized and destabilized dinitramide anions stresses the importance of designing surface-active polymer support, stabilizers, and/or coating agents, in order to enable environmentally friendly ADN-based solid-rocket propulsion.
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| 15. |
- Tejero, Ismael, et al.
(författare)
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Theoretical modeling of hydroxyl-radical-induced lipid peroxidation reactions
- 2007
-
Ingår i: Journal of Physical Chemistry B. - : American Chemical Society. - 1520-6106 .- 1520-5207. ; 111:20, s. 5684-5693
-
Tidskriftsartikel (refereegranskat)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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| 16. |
- Zhang, Ru Bo, et al.
(författare)
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Theoretical studies of damage to 3'-uridine monophosphate induced by electron attachment
- 2008
-
Ingår i: Chemistry - A European Journal. - Weinheim : Wiley-VCH-Verl.. - 0947-6539 .- 1521-3765. ; 14:9, s. 2850-2856
-
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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| 17. |
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| 18. |
- Maurina Morais, Eduardo, 1989
(författare)
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Synthesis of protic ionic liquids. Challenges and solutions for the synthesis of pure compounds.
- 2022
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Licentiatavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The urgent need to diversify our energy matrix is responsible for a renewed interest in fuel cell technology, which can use hydrogen gas, a renewable green fuel, as an energy source. This technology is currently a commercially available option, however, it still requires technological improvements before it can be widely used for different applications. One way this technology could potentially be improved is by increasing its temperature range of operation by developing new, anhydrous proton conducting materials. Protic ionic liquids, which are organic salts with low melting temperatures, are interesting candidates for this application, since they can conduct protons in the operational conditions of fuel cells and without the need of water. These compounds can be synthesized by a simple acid-base neutralization reaction, but certain considerations must be taken in order to obtain high quality (dry and pure) protic ionic liquids. In this thesis, 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 consists of only glass and chemically resistant polymer(PTFE and PVDF) parts, which avoids other contaminants that can result from unwanted reactions involving the reagents with common laboratory tools (metallic objects, paper, plastic, etc.). The resulting ionic liquids were carefully analyzed by spectroscopic and thermal analysis 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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| 19. |
- Sauer, Christopher, 1993
(författare)
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Green Aromatics: Catalytic Valorisation of bio-derived 2,5-dimethylfuran over Zeolites and Zeotypes
- 2022
-
Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- This thesis discusses the use of biomass as a potentially green feedstock for the chemical industry in the urgent shift away from fossil resources. I elaborate on reasons why we cannot afford to burn virgin biomass for energy production, among them a variety of ecosystem services that forests and other lands provide. In addition, the utilisation of biomass should be focused on products that sequester and lock away carbon for more extended periods, e.g. timber, materials and chemicals. In particular, biomass can be used as an alternative "carbon neutral" feedstock for the chemical industry, where we can preserve the already existing chemical complexity in the bio-based molecules. One example is the upgrading of furans to benzene, toluene and xylene (BTX) aromatics with the help of zeolite catalysis. These aromatics are important commodity chemicals, where the shift to a bio-based resource could make use of already existing knowledge, catalyst and production infrastructure. However, research is necessary to understand these new feedstock molecules and their interaction with the catalysts and to enable the design of applicable catalysts. In order to study the interaction of the furans, in particular 2,5-dimethylfuran (2,5-dmf), I describe and discuss the development of an analytical methodology that utilises infrared spectroscopy and mass spectrometry for the on-line identification and quantification of product molecules during catalytic reactions. This on-line analysis method is then applied to the catalytic conversion of 2,5-dmf to aromatics over a range of zeolite and zeotype catalysts. In-depth studies with ammonia as a probe molecule of the catalytic active acid sites, as well as temperature programmed experiments with ammonia and 2,5-dmf give insights into product distribution, selectivity changes and deactivation of the catalyst. For example, olefins and aromatics are initially preferred products, while with increasing time on stream, the isomerisation of 2,5-dmf becomes dominant. The incorporation of Ga into the zeotype framework, resulting in a Ga-Silicate, shows how targeted catalyst design can increase overall aromatics production. This catalyst is also suitable for selective isomerisation of 2,5-dmf to 2,4-dimethylfuran, which has a rare substitution pattern. Finally, itwas found that the most valuable of BTX, p -xylene, can be produced more selectively when 2,5-dmf is pre-adsorbed onto zeolite ZSM-5 and then released during a temperature programmed product desorption.
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| 20. |
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| 21. |
- 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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| 22. |
- 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
-
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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| 23. |
- Erdtman, Edvin, et al.
(författare)
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Computational studies on Schiff-base formation : Implications for the catalytic mechanism of porphobilinogen synthase
- 2011
-
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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| 24. |
- Damas, Giane Benvinda, et al.
(författare)
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Carbon dioxide reduction mechanism on Ru-based electrocatalysts [Ru(bpy)(2)(CO)(2)](2+) : insights from first-principles theory
- 2021
-
Ingår i: Sustainable Energy & Fuels. - : Royal Society of Chemistry. - 2398-4902. ; 5:23, s. 6066-6076
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Tidskriftsartikel (refereegranskat)abstract
- Solar fuel production through the so-called artificial photosynthesis has attracted a great deal of attention to the development of a new world energy matrix that is renewable and environmentally friendly. This process is characterized by light absorption with enough photon energy to generate conduction electrons, which drive the carbon dioxide reduction to produce organic fuels. It is also common to couple Ru-complex electrocatalysts to form a more efficient and selective hybrid system for this application. In this work, we have undertaken a thorough investigation of the redox reaction mechanism of Ru-based electrocatalysts by means of density functional theory (DFT) methods under the experimental conditions that have been previously reported. More specifically, we have studied the electrochemistry and catalytic activity of the [Ru(bpy)(2)(CO)(2)](2+) coordination complex. Our theoretical assessment supports the following catalytic cycle: (i) [Ru(bpy)(2)(CO)(2)](2+) is transformed into [Ru(bpy)(2)(CO)](0) upon two-electron reduction and CO release; (ii) [Ru(bpy)(2)(CO)](0) is protonated to form the [Ru(bpy)(2)(CO)H](+) hydride complex; (iii) CO2 is activated by the hydride complex through an electrophilic addition to form the [Ru(bpy)(2)(CO)(OCHO)](+) intermediate; (iv) the resulting formic acid ligand is released in solution; and, finally, (v) the CO ligand is reattached to the complex to recover the initial [Ru(bpy)(2)(CO)(2)](2+) catalyst.
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| 25. |
- Napolitano, C., et al.
(författare)
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Synthesis, kinase activity and molecular modeling of a resorcylic acid lactone incorporating an amide and a trans-enone in the macrocycle
- 2012
-
Ingår i: Tetrahedron. - : Elsevier BV. - 0040-4020 .- 1464-5416. ; 68:27-28, s. 5533-5540
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Tidskriftsartikel (refereegranskat)abstract
- Details for the synthesis of a resorcylic acid lactone (RAL) incorporating a trans-enone and an amide in the macrocyclic ring are provided herein. The sequence included the assembly of three fragments by esterification, olefination, and lactamization. The RAL with the lactam was less potent as an inhibitor of kinases than other RALs investigated. The biological results were rationalized by docking and molecular dynamics simulations of the lactam bound to human ERK2 and comparison with hypothemycin. (c) 2012 Elsevier Ltd. All rights reserved.
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| 26. |
- Wiklander, Jesper G., 1974-, et al.
(författare)
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Towards a synthetic avidin mimic
- 2011
-
Ingår i: Analytical and Bioanalytical Chemistry. - : Springer Science and Business Media LLC. - 1618-2642 .- 1618-2650. ; 400:5, s. 1397-1404
-
Tidskriftsartikel (refereegranskat)abstract
- A series of streptavidin-mimicking molecularly imprinted polymers has been developed and evaluated for their biotin binding characteristics. A combination of molecular dynamics and NMR spectroscopy was used to examine potential polymer systems, in particular with the functional monomers methacrylic acid and 2-acrylamidopyridine. The synthesis of copolymers of ethylene dimethacrylate and one or both of these functional monomers was performed. A combination of radioligand binding studies and surface area analyses demonstrated the presence of selectivity in polymers prepared using methacrylic acid as the functional monomer. This was predicted by the molecular dynamics studies showing the power of this methodology as a prognostic tool for predicting the behavior of molecularly imprinted polymers.
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| 27. |
- Borg, O. Anders, et al.
(författare)
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Electron-transfer induced repair of 6-4 photoproducts in DNA : a computational study.
- 2007
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Ingår i: Journal of Physical Chemistry A. - Washington, DC : American Chemical Society. - 1089-5639 .- 1520-5215. ; 111:12, s. 2351-2361
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Tidskriftsartikel (refereegranskat)abstract
- The mechanism employed by DNA photolyase to repair 6-4 photoproducts in UV-damaged DNA is explored by means of quantum chemical calculations. Considering the repair of both oxetane and azetidine lesions, it is demonstrated that reduction as well as oxidation enables a reversion reaction by creating anionic or cationic radicals that readily fragment into monomeric pyrimidines. However, on the basis of calculated reaction energies indicating that electron transfer from the enzyme to the lesion is a much more favorable process than electron transfer in the opposite direction, it is suggested that the photoenzymic repair can only occur by way of an anionic mechanism. Furthermore, it is shown that reduction of the oxetane facilitates a mechanism involving cleavage of the C−O bond followed by cleavage of the C−C bond, whereas reductive fragmentation of the azetidine may proceed with either of the intermonomeric C−N and C−C bonds cleaved as the first step. From calculations on neutral azetidine radicals, a significant increase in the free-energy barrier for the initial fragmentation step upon protonation of the carbonylic oxygens is predicted. This effect can be attributed to protonation serving to stabilize reactant complexes more than transition structures.
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| 28. |
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| 29. |
- Guedes, Rita Cardoso, et al.
(författare)
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Photophysics, photochemistry, and reactivity : Molecular aspects of perylenequinone reactions
- 2007
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Ingår i: Photochemical and Photobiological Sciences. - Cambridge : Royal Society of Chemistry. - 1474-905X .- 1474-9092. ; 6:10, s. 1089-1096
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Tidskriftsartikel (refereegranskat)abstract
- Density functional theory (DFT) and time-dependent density functional theory (TD-DFT) were used to elucidate the photochemistry and photophysics of eight different perylenequinones (PQ). The objective of this work has been to quantitatively investigate the photodynamic therapeutic potential of this family of compounds and give an overview of their photoreactivity. The effects of solvation were evaluated through single-point calculations using the integral equation formalism of the polarised continuum model. It is concluded that the eight studied perylenequinones can generate singlet oxygen (in aqueous solution) and superoxide radical anions, and that the autoionisation of two nearby PQ molecules is possible.
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| 30. |
- Karlsson, Magnus, et al.
(författare)
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Homology Models and Molecular Modeling of Human Retinoic Acid Metabolizing Enzymes Cytochrome P450 26A1 (CYP26A1) and P450 26B1 (CYP26B1)
- 2008
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Ingår i: Journal of Chemical Theory and Computation. - Columbus, Ohio : American Chemical Society. - 1549-9618 .- 1549-9626. ; 4:6, s. 1021-1027
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Tidskriftsartikel (refereegranskat)abstract
- Homology models of cytochrome P450 26A1 and cytochrome P450 26B1 were constructed using the crystal structures of human, CYP2C8, CYP2C9, and CYP3A4 as templates for the model building. The homology models generated were investigated for their docking capacities against the natural substrate all-trans-retinoic acid (atRA), five different tetralone-derived retinoic acid metabolizing blocking agents (RAMBAs), and R115866. Interaction energies (IE) and linear interaction energies (LIE) were calculated for all inhibitors in both homology models after molecular dynamics (MD) simulation of the enzyme-ligand complexes. The results revealed that the homologues had the capacity to distinguish between strong and weak inhibitors. Important residues in the active site were identified from the CYP26A1/B1-atRA complexes. Residues involved in hydrophobic interactions with atRA were Pro113, Phe222, Phe299, Val370, Pro371, and Phe374 in CYP26A1 and Leu88, Pro118, Phe222, Phe295, Ile368, and Tyr272 in CYP26B1. Hydrogen bonding interactions were observed between the atRA carboxylate group and Arg 90 in CYP26A1 and with Arg76, Arg95, and Ser369 in CYP26B1.
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| 31. |
- Musa, Klefah A. K., et al.
(författare)
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Theoretical assessment of naphazoline redoxchemistry and photochemistry
- 2007
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Ingår i: Journal of Physical Chemistry B. - Washington, DC : American Chemical Society. - 1520-6106 .- 1520-5207. ; 111:15, s. 3977-3981
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Tidskriftsartikel (refereegranskat)abstract
- The imidazoline derivative naphazoline (2-(1-naphtylmethyl)-2-imidazoline) is an α2-adrenergic agonist used as non-prescription eye and nasal preparations. Besides its functionality in generating vascoconstriction and decongestion in the patient, the toxicity, ROS generating capability, and recently also possible antioxidant capacity of the compound have been reported in the literature. In the current work the structural and electronic features of the drug are explored, using computational chemical tools. Electron affinities, ionization potentials, and excitation energies are reported, as well as charge and spin distributions of various forms of the drug. The difference in photochemical behavior between the protonated and unprotonated (basic) species is explained by the molecular orbital distributions, allowing for efficient excitation quenching in the basic structure but clear naphthalene to imidazolene charge transfer upon HOMO→ LUMO excitation in the protonated form, enabling larger intersystem crossing capability to the imidazole localized excited triplet and a resulting higher singlet oxygen quantum yield.
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| 32. |
- Saenz-Mendez, Patricia, et al.
(författare)
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Theoretical prediction of binding modes and hot sequences for allopsoralen-DNA interaction
- 2007
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Ingår i: Chemical Physics Letters. - Amsterdam : Elsevier. - 0009-2614 .- 1873-4448. ; 450:1-3, s. 127-131
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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| 33. |
- Saenz-Mendez, Patricia, et al.
(författare)
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Theoretical study of sequence selectivity and preferred binding mode of psoralen with DNA
- 2007
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Ingår i: Research Letters in Physical Chemistry. - : Hindawi Limited. - 1687-6873 .- 1687-6881. ; , s. Article number 60623-
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Tidskriftsartikel (refereegranskat)abstract
- Psoralen interaction with two models of DNA was investigated using molecular mechanics and molecular dynamics methods. Calculated energies of minor groove binding and intercalation were compared in order to define a preferred binding mode for the ligand.We found that both binding modes are possible, explaining the low efficiency for monoadduct formation from intercalated ligands. A comparison between the interaction energy for intercalation between different base pairs suggests that the observed sequence selectivity is due to favorable intercalation in 5'-TpA in (AT)n sequences.
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| 34. |
- Sebastian, Eider San, et al.
(författare)
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Metal ion dependent adhesion sites in integrins : A Combined DFT and QMC Study on Mn2
- 2007
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Ingår i: Journal of Physical Chemistry B. - Washington, DC : American Chemical Society. - 1520-6106 .- 1520-5207. ; 111:30, s. 9099-9103
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Tidskriftsartikel (refereegranskat)abstract
- The theoretical study of relative energies of different spin states of Mn2+ has been carried out for the isolated cation and for structures in which the cation is coordinated to ligands that represent the first coordination shell in a protein environment that contains a metal ion dependent adhesion site (MIDAS, found in the ligand binding domain of protein LFA-1). The calculations determine whether the ligand field generated by a prototype protein environment affects the relative energies between high, intermediate, and low spin states. Geometry optimizations and vibrational frequency calculations were carried out at the B3LYP/SKBJ+* level of theory. Single point calculations were performed at the B3LYP/6-311++G(2df,2p) and diffusion monte carlo (DMC) levels for the refinement of the electronic energies. These calculations reveal important differences in the relative energies between high/low spin complexes obtained by B3LYP and DMC and show that although both DFT and DMC show similar trends, a higher level method such as DMC is necessary for a quantitative description of the interactions between Mn2+ and its natural ligands. (G)s of acetate-type ligand binding reactions were calculated that show that the higher the spin of the manganese complex, the lower the affinity for the ligand.
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| 35. |
- Wojas, Natalia
(författare)
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The dynamic surface nature of calcite and its role in determining the adsorptive stability toward hydrophobizing carboxylic fatty acids
- 2021
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Calcium carbonate has attracted a lot of interest over the centuries. Nowadays, mainly as mineral pigment and filler, it has a wide use in technological applications ranging from paper, construction, polymers, and environmental solutions to consumer goods. Amongst these uses, the filler pigment is required to display either hydrophilicity (for applications in aqueous colloidal systems, including, for example, in paper and emulsion paints), or, in contrast, oleophilicity (for applications in contact with oil-based systems, such as plastics and volatile solvent-containing sealants). To achieve oleophilicity, and resulting hydrophobicity, the filler is surface treated, typically using carboxylic fatty acids. In this thesis, effects of humidity and fatty carboxylic acids vapor on CaCO3 surface wettability and nanomechanical properties were studied, with the aim to gain knowledge on layer packing density and order, as well as resistance to water exposure and mechanical wear. A better understanding of the dynamic nature of the calcite surface presented in this work allows the industry to increase sustainable control over materials production and storage. First, a setup combining an atomic force microscope (AFM) with a humidifier was used to map nanomechanical properties of growing surface domains (hydrated form of CaCO3) formed by ion dissolution, diffusion, and redeposition, a process that is not reversible upon drying. Secondly, AFM and contact angle goniometer measurements showed that the stability of the calcite surface improves with increasing carboxylic acid chain length (C2 to C18). Meanwhile, X-ray photoelectron spectroscopy and vibrational sum frequency spectroscopy techniques demonstrated that a coherent layer with maximum packing density of carboxylate and carboxylic acid species was achieved with the use of stearic acid (C18) with high enough vapor pressure and exposure time. The AFM images successfully visualized that a complete C18 monolayer is capable of countering nano-wear of the calcite surface despite the humidity (under the range of loads investigated in this work) and the layer has self-healing properties, while calcite displayed high abrasive wear. Further, when calcite coated by a highly packed monolayer of C18 was covered with a water droplet, a large contact angle hysteresis resulted in a coffee ring effect (CRE). That is leading to formation of hillocks at the contact line consisting of dissolved fatty carboxylic acid and possibly calcium bicarbonate Ca(HCO3)2 molecules transported from the bare calcite region that also is created next to the droplet edge. Interestingly, C18 coated calcite remained considerably more stable in the case where a water droplet saturated with octanoic acid was used instead of water; thus, it was concluded that the CRE can be contained via reduction of the liquid surface tension and contact angle hysteresis.
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| 36. |
- Zhang, Ru bo, et al.
(författare)
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Effects of OH radical addition on proton transfer in the guanine-cytosine base pair
- 2007
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Ingår i: Journal of Physical Chemistry B. - Washington, DC : American Chemical Society. - 1520-6106 .- 1520-5207. ; 111:23, s. 6571-6576
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Tidskriftsartikel (refereegranskat)abstract
- Double proton transfer (PT) reactions in guanine-cytosine OH radical adducts are studied by the hybrid density functional B3LYP approach. Concerted and stepwise proton-transfer processes are explored between N1(H) on guanine (G) and N3 on cytosine (C), and between N4(H) on C and O6 on G. All systems except GC6OH display a concerted mechanism. 8OHGC has the highest dissociation energy and is 1.2 kcal/mol more stable than the nonradical GC base pair. The origin of the interactions are investigated through the estimation of intrinsic acid-basic properties of the *OH-X monomer (X = G or C). Solvent effects play a significant role in reducing the dissociation energy. The reactions including *OH-C adducts have significantly lower PT barriers than both the nonradical GC pair and the *OH-G adducts. All reactions are endothermic, with the GC6OH --> GC6OHPT reaction has the lowest reaction energy (4.6 kcal/mol). In accordance with earlier results, the estimated NBO charges show that the G moiety carries a slight negative charge (and C a corresponding positive one) in each adduct. The formation of a partial ion pair may be a potential factor leading to the PT reactions being thermodynamically unfavored.
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| 37. |
- Zhang, Ru Bo, et al.
(författare)
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Radical-induced damage in 3'dTMP : Insights into a mechanism for DNA strand cleavage
- 2007
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Ingår i: Journal of Chemical Theory and Computation. - Washington, DC : American Chemical Society. - 1549-9618 .- 1549-9626. ; 3:3, s. 803-810
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Tidskriftsartikel (refereegranskat)abstract
- DNA strand scission and base release in 3‘dTMP, induced by H and OH radical addition to thymine, is studied at the DFT B3LYP/6-31+G(d,p) level in the gas phase and in solution. In particular the mechanism of H atom transfer subsequent to radical formation, from C2‘ on the sugar to the C6 site on the base, is explored. Bulk solvation is found to lower the barrier by up to 5 kcal mol-1 and the reaction energy by up to 12 kcal mol-1 for the hydroxyl radical adducts. The strengths of the N1−C1‘(N1-glycosidic bond) and C3‘−O(P) bonds are calculated, showing that homolytic bond breaking processes are largely favored in both cases. The barrier for C3‘−O(P) bond rupture is approximately 18.2 kcal mol-1, and its breakage is preferred by 10−15 kcal mol-1 over that of N1-glycosidic bond cleavage in both the gas phase and solvents, which is consistent with the changes in C3‘−O(P) and N1−C1‘ bond lengths during the H transfer reactions. Mulliken spin densities, NPA charges, and vertical electron affinities are calculated to clarify the reactive properties of the intramolecular H-transfer radicals.
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| 38. |
- Co, Michelle, 1975-, et al.
(författare)
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Degradation effects in the extraction of antioxidants from birch bark using water at elevated temperature and pressure
- 2012
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Ingår i: Analytica Chimica Acta. - : Elsevier BV. - 0003-2670 .- 1873-4324. ; 716, s. 40-48
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Tidskriftsartikel (refereegranskat)abstract
- Experiments with birch bark samples have been carried to enable a distinction between extraction and degradation effects during pressurised hot water extraction. Two samples, E80 and El 80, contained birch bark extracts obtained after extraction at 80 and 180 degrees C for up to 45 min, respectively. Two other samples, P80 and P180, were only extracted for 5 min at the two temperatures and were thereafter filtered and hydrothermally treated at 80 and 180 degrees C, respectively. During the latter treatment, samples were collected at different times to assess the stability of the extracted compounds. An offline DPPH (2,2-diphenyl-1-picrylhydrazyl) assay, as well as a high performance liquid chromatographic separation coupled to an electrochemical detector, were used to determine the antioxidant capacity of the processed samples. The results obtained with the different techniques were compared to assess the yield of the extraction and degradation processes. In addition, an online hyphenated system comprising high performance liquid chromatography coupled to diode-array; electrochemical; and tandem mass spectrometric detection (HPLC-DAD-ECD-MS/MS) was used to study the compositions of the extracts in more detail. The results for the samples processed at 80 degrees C showed that the extraction reached a steady-state already after 5 min, and that the extracted compounds were stable throughout the entire extraction process. Processing at 180 degrees C, on the other hand, gave rise to partly degraded extracts with a multitude of peaks in both the diode array and electrochemical detectors, and a higher antioxidant capacity compared to for the extracts obtained at 80 degrees C. It is concluded that HPLC-DAD-ECD is a more appropriate technique for the determination of antioxidants than the DPPH assay. The mass spectrometric results indicate that one of the extracted antioxidants, catechin, was isomerised to its diastereoisomers; (+)-catechin, (-)-catechin, (+)-epicatechin, and (-)-epicatechin.
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| 39. |
- Bannan, T. J., et al.
(författare)
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A method for extracting calibrated volatility information from the FIGAERO-HR-ToF-CIMS and its experimental application
- 2019
-
Ingår i: Atmospheric Measurement Techniques. - : Copernicus GmbH. - 1867-1381 .- 1867-8548. ; 12:3, s. 1429-1439
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Tidskriftsartikel (refereegranskat)abstract
- The Filter Inlet for Gases and AEROsols (FIGAERO) is an inlet specifically designed to be coupled with the Aerodyne High-Resolution Time-of-Flight Chemical Ionization Mass Spectrometer (HR-ToF-CIMS). The FIGAERO-HR-ToF-CIMS provides simultaneous molecular information relating to both the gas- and particle-phase samples and has been used to extract vapour pressures (VPs) of the compounds desorbing from the filter whilst giving quantitative concentrations in the particle phase. However, such extraction of vapour pressures of the measured particle-phase components requires use of appropriate, well-defined, reference compounds. Vapour pressures for the homologous series of polyethylene glycols (PEG) ((H-(O-CH 2 CH 2 ) n -OH) for n = 3 to n = 8), covering a range of vapour pressures (VP) (10 -1 to 10 -7 Pa) that are atmospherically relevant, have been shown to be reproduced well by a range of different techniques, including Knudsen Effusion Mass Spectrometry (KEMS). This is the first homologous series of compounds for which a number of vapour pressure measurement techniques have been found to be in agreement, indicating the utility as a calibration standard, providing an ideal set of benchmark compounds for accurate characterization of the FIGAERO for extracting vapour pressure of measured compounds in chambers and the real atmosphere. To demonstrate this, single-component and mixture vapour pressure measurements are made using two FIGAERO-HR-ToF-CIMS instruments based on a new calibration determined from the PEG series. VP values extracted from both instruments agree well with those measured by KEMS and reported values from literature, validating this approach for extracting VP data from the FIGAERO. This method is then applied to chamber measurements, and the vapour pressures of known products are estimated. © 2019 Author(s).
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| 40. |
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| 41. |
- Guo, Y. D., et al.
(författare)
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Identification of highly oxygenated organic molecules and their role in aerosol formation in the reaction of limonene with nitrate radical
- 2022
-
Ingår i: Atmospheric Chemistry and Physics. - : Copernicus GmbH. - 1680-7316 .- 1680-7324. ; 22:17, s. 11323-11346
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Tidskriftsartikel (refereegranskat)abstract
- Nighttime NO3-initiated oxidation of biogenic volatile organic compounds (BVOCs) such as monoterpenes is important for the atmospheric formation and growth of secondary organic aerosol (SOA), which has significant impact on climate, air quality, and human health. In such SOA formation and growth, highly oxygenated organic molecules (HOM) may be crucial, but their formation pathways and role in aerosol formation have yet to be clarified. Among monoterpenes, limonene is of particular interest for its high emission globally and high SOA yield. In this work, HOM formation in the reaction of limonene with nitrate radical (NO3) was investigated in the SAPHIR chamber (Simulation of Atmospheric PHotochemistry In a large Reaction chamber). About 280 HOM products were identified, grouped into 19 monomer families, 11 dimer families, and 3 trimer families. Both closed-shell products and open-shell peroxy radicals (RO2 center dot) 2 were observed, and many of them have not been reported previously. Monomers and dimers accounted for 47% and 47% of HOM concentrations, respectively, with trimers making up the remaining 6 %. In the most abundant monomer families, C10H15-17NO6-14, carbonyl products outnumbered hydroxyl products, indicating the importance of RO2 center dot termination by unimolecular dissociation. Both RO2 center dot autoxidation and alkoxy-peroxy pathways were found to be important processes leading to HOM. Time-dependent concentration profiles of monomer products containing nitrogen showed mainly second-generation formation patterns. Dimers were likely formed via the accretion reaction of two monomer RO2 center dot , and HOM-trimers via the accretion reaction between monomer RO2 center dot and dimer RO2 center dot. Trimers are suggested to play an important role in new particle formation (NPF) observed in our experiment. A HOM yield of 1.5%(+1.7%)(-0.7%) was estimated considering only first-generation products. SOA mass growth could be reasonably explained by HOM condensation on particles assuming irreversible uptake of ultra-low volatility organic compounds (ULVOCs), extremely low volatility organic compounds (ELVOCs), and low volatility organic compounds (LVOCs). This work provides evidence for the important role of HOM formed via the limonene +NO3 reaction in NPF and growth of SOA particles.
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| 42. |
- Guo, Y., et al.
(författare)
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Reversible Structural Isomerization of Nature's Water Oxidation Catalyst Prior to O-O Bond Formation
- 2022
-
Ingår i: Journal of the American Chemical Society. - : American Chemical Society (ACS). - 0002-7863 .- 1520-5126. ; 144:26, s. 11736-11747
-
Tidskriftsartikel (refereegranskat)abstract
- Photosynthetic water oxidation is catalyzed by a manganese-calcium oxide cluster, which experiences five "S-states" during a light-driven reaction cycle. The unique "distorted chair"-like geometry of the Mn4CaO5(6)cluster shows structural flexibility that has been frequently proposed to involve "open" and "closed"-cubane forms from the S1 to S3states. The isomers are interconvertible in the S1 and S2states, while in the S3state, the open-cubane structure is observed to dominate inThermosynechococcus elongatus (cyanobacteria) samples. In this work, using density functional theory calculations, we go beyond the S3+Yzstate to the S3nYz•→ S4+Yzstep, and report for the first time that the reversible isomerism, which is suppressed in the S3+Yzstate, is fully recovered in the ensuing S3nYz•state due to the proton release from a manganese-bound water ligand. The altered coordination strength of the manganese-ligand facilitates formation of the closed-cubane form, in a dynamic equilibrium with the open-cubane form. This tautomerism immediately preceding dioxygen formation may constitute the rate limiting step for O2formation, and exert a significant influence on the water oxidation mechanism in photosystem II.
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| 43. |
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| 44. |
- Le Breton, Michael, 1986, et al.
(författare)
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Application of a FIGAERO ToF CIMS for on-line characterization of real-world fresh and aged particle emissions from buses
- 2019
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Ingår i: Aerosol Science and Technology. - : Informa UK Limited. - 0278-6826 .- 1521-7388. ; 53:3, s. 244-259
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Tidskriftsartikel (refereegranskat)abstract
- © 2019, © 2019 The Author(s). Published with license by Taylor & Francis Group, LLC. On-line chemical characterization of real-world particle emissions from 13 transit buses was performed using a chemical ionization mass spectrometer (CIMS) equipped with a filter inlet for gases and aerosols (FIGAERO). In addition to the fresh emissions the emissions were artificially aged using a potential aerosol mass reactor (Go:PAM). The buses studied were running on different fuel types (diesel, compressed natural gas, and rapeseed methyl ester) and exhaust after-treatment systems (selective catalytic reduction (SCR), exhaust gas recirculation (EGR), and a three-way catalyst). When evaluating emissions from passing exhaust plumes using the FIGAERO ToF-CIMS, two technical features were highlighted from this work, the use of high mass calibrants and the factor enhancement method to be able to filter important compounds from mass spectra including hundreds of species. Here, acetate was used as the reagent ion to enable detection of highly oxygenated species in the exhaust particle emissions with potential high toxicity and/or secondary organic aerosol formation (SOA) potential. The acetate ionization scheme accounted for 4% to 46% of the total emitted particulate mass through identification of 61 species in the spectra. For aged emission the various fuel types provided overlapping species that could explain up to 19% of the aged emissions. This is hypothesized to come from the oxidation of engine lubrication oil, thus a common source for various fuels which was further supported by laboratory measurements. Specific markers from the SCR technology, such as urea oxidation products and further byproducts from hydrolysis were identified and attributed to reactions of isocyanic acid.
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| 45. |
- Le Breton, Michael, 1986, et al.
(författare)
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Chlorine oxidation of VOCs at a semi-rural site in Beijing: significant chlorine liberation from ClNO2 and subsequent gas- and particle-phase Cl-VOC production
- 2018
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Ingår i: Atmospheric Chemistry and Physics. - : Copernicus GmbH. - 1680-7316 .- 1680-7324. ; 18:17, s. 13013-13030:18, s. 13013-13030
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Tidskriftsartikel (refereegranskat)abstract
- Nitryl chloride (ClNO2) accumulation at night acts as a significant reservoir for active chlorine and impacts the following day's photochemistry when the chlorine atom is liberated at sunrise. Here, we report simultaneous measurements of N2O5 and a suite of inorganic halogens including ClNO2 and reactions of chloride with volatile organic compounds (Cl-VOCs) in the gas and particle phases utilising the Filter Inlet for Gas and AEROsols time-of-flight chemical ionisation mass spectrometer (FIGAERO-ToF-CIMS) during an intensive measurement campaign 40 km northwest of Beijing in May and June 2016. A maximum mixing ratio of 2900 ppt of ClNO2 was observed with a mean campaign nighttime mixing ratio of 487 ppt, appearing to have an anthropogenic source supported by correlation with SO2, CO and benzene, which often persisted at high levels after sunrise until midday. This was attributed to such high mixing ratios persisting after numerous e-folding times of the photolytic lifetime enabling the chlorine atom production to reach 2.3 x 10(5) molecules cm(-3) from ClNO2 alone, peaking at 09:30 LT and up to 8.4 x 10(5) molecules cm(-3) when including the supporting inorganic halogen measurements. Cl-VOCs were observed in the particle and gas phases for the first time at high time resolution and illustrate how the iodide ToF-CIMS can detect unique markers of chlorine atom chemistry in ambient air from both biogenic and anthropogenic sources. Their presence and abundance can be explained via time series of their measured and steady-state calculated precursors, enabling the assessment of competing OH and chlorine atom oxidation via measurements of products from both of these mechanisms and their relative contribution to secondary organic aerosol (SOA) formation.
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| 46. |
- Li, J. J., et al.
(författare)
-
Characterization of Aerosol Aging Potentials at Suburban Sites in Northern and Southern China Utilizing a Potential Aerosol Mass (Go:PAM) Reactor and an Aerosol Mass Spectrometer
- 2019
-
Ingår i: Journal of Geophysical Research-Atmospheres. - : American Geophysical Union (AGU). - 2169-897X .- 2169-8996. ; 124:10, s. 5629-5649
-
Tidskriftsartikel (refereegranskat)abstract
- Aerosol mass spectrometry was used to characterize submicron aerosols before and after aging in a Gothenburg Potential Aerosol Mass (Go:PAM) reactor at two suburban sites in China, one in northern China at Changping (CP), Beijing, and a second in southern China at Hong Kong (HK). Organic aerosol (OA) dominated in the ambient nonrefractory particulate matter <1m (NR-PM1) for both CP (42-71%) and HK (43-61%), with a large contribution from secondary OA factors that were semivolatile oxygenated (SVOOA) and low-volatility oxygenated (LVOOA). Under constant OH exposure, OA enhancement (78-98%) dominated the NR-PM1 mass increment at both sites, while nitrate was enhanced the most among the inorganic species (7-9%). Overall, the CP site exhibited higher OA oxidation potential and more enhancement of SVOOA than LVOOA (7.5 vs. 2.7g/m(3)), but the reverse was observed in HK (0.8 vs. 2.6g/m(3)). In CP, more enhancement of the less oxygenated SVOOA suggests that aerosol aging was more sensitive to the abundant locally emitted primary OA and volatile organic compound precursors. On the contrary, the more formation of the highly oxidized LVOOA in HK indicates that aerosol aging mainly escalated the degree of oxygenation of OA as ambient aerosol was already quite aged and there was a lack of volatile organic compound precursors. The comparative measurements using the same oxidation system reveal distinct key factors and mechanisms that influence secondary aerosol formation in two suburban locations in China, providing scientific insights to assist formulation of location-specific mitigation measures of secondary pollution. Plain Language Summary Atmospheric submicron particles have significant impacts on the climate and human health. A large part of these particles are formed secondarily through successive aging of primary emissions. To study such aging processes, we used a reactor that can provide highly oxidizing conditions to simulate the oxidation of ambient aerosols at accelerated rates. An online mass spectrometer was connected after the reactor to measure changes in aerosol mass concentration and chemical composition between the ambient samples and the oxidized ones. We presented the first comparative measurements of the aging potentials of ambient aerosols in two suburban sites in northern and southern China (Changping District in Beijing, and Hong Kong). Results showed that generally aerosols at the Changping site had higher aging potentials after passing through the oxidation reactor, probably due to more local emissions of precursors, while air masses in Hong Kong were already in a higher oxidation state with lower aging potentials, mainly because of strong impacts from long-range transported pollution sources. Distinct aerosol aging pathways related to different ambient precursors were observed at the two sites. Understanding of the different characteristics of aerosol aging processes can lead to advances in air quality modeling and pollution management.
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| 47. |
- Mohr, Claudia, et al.
(författare)
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Molecular identification of organic vapors driving atmospheric nanoparticle growth
- 2019
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Ingår i: Nature communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 10
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Tidskriftsartikel (refereegranskat)abstract
- Particles formed in the atmosphere via nucleation provide about half the number of atmospheric cloud condensation nuclei, but in many locations, this process is limited by the growth of the newly formed particles. That growth is often via condensation of organic vapors. Identification of these vapors and their sources is thus fundamental for simulating changes to aerosol-cloud interactions, which are one of the most uncertain aspects of anthropogenic climate forcing. Here we present direct molecular-level observations of a distribution of organic vapors in a forested environment that can explain simultaneously observed atmospheric nanoparticle growth from 3 to 50nm. Furthermore, the volatility distribution of these vapors is sufficient to explain nanoparticle growth without invoking particle-phase processes. The agreement between observed mass growth, and the growth predicted from the observed mass of condensing vapors in a forested environment thus represents an important step forward in the characterization of atmospheric particle growth.
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| 48. |
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| 49. |
- Artemenko, A., et al.
(författare)
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Reference XPS spectra of amino acids
- 2021
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Konferensbidrag (refereegranskat)abstract
- In this report we present XPS data for five amino acids (AAs) (tryptophan, methionine, glutamine, glutamic acid, and arginine) with different side chain groups measured in solid state (powder form). The theoretically and experimentally obtained chemical structure of AAs are compared. Here, we analyse and discuss C 1 s, N 1 s, O 1s and S 2p core level binding energies, FWHMs, atomic concentrations of the functional groups in AAs. The experimentally obtained and theoretically calculated ratio of atomic concentrations are compared. The zwitterionic nature of methionine and glutamine in solid state was determined from protonated amino groups in N 1s peak and deprotonated carboxylic groups in the C 1s spectrum. The obtained XPS results for AAs well correspond with previously reported data.
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| 50. |
- Barišić, Antun, et al.
(författare)
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Experimental Data Contributing to the Elusive Surface Charge of Inert Materials in Contact with Aqueous Media
- 2021
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Ingår i: Colloids and interfaces. - : MDPI. - 2504-5377. ; 5:1
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- We studied the charging of inert surfaces (polytetrafluoroethylene, i.e., PTFE; graphite; graphene; and hydrophobic silica) using classical colloid chemistry approaches. Potentiometric titrations showed that these surfaces acquired less charge from proton-related reactions than oxide minerals. The data from batch-type titrations for PTFE powder did not show an effect of ionic strength, which was also in contrast with results for classical colloids. In agreement with classical colloids, the electrokinetic results for inert surfaces showed the typical salt level dependence. In some cases, the point of zero net proton charge as determined from mass and tentatively from acid–base titration differed from isoelectric points, which has also been previously observed, for example by Chibowski and co-workers for ice electrolyte interfaces. Finally, we found no evidence for surface contaminations of our PTFE particles before and after immersion in aqueous solutions. Only in the presence of NaCl-containing solutions did cryo-XPS detect oxygen from water. We believe that our low isoelectric points for PTFE were not due to impurities. Moreover, the measured buffering at pH 3 could not be explained by sub-micromolar concentrations of contaminants. The most comprehensive explanation for the various sets of data is that hydroxide ion accumulation occurred at the interfaces between inert surfaces and aqueous solutions.
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