| 1. |
- 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
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Ingår i: Journal of the American Chemical Society. - : American Chemical Society (ACS). - 0002-7863 .- 1520-5126. ; 144:26, s. 11736-11747
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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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| 2. |
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| 3. |
- 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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| 4. |
- 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
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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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| 5. |
- Wiklander, Jesper G., 1974-, et al.
(författare)
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Towards a synthetic avidin mimic
- 2011
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Ingår i: Analytical and Bioanalytical Chemistry. - : Springer Science and Business Media LLC. - 1618-2642 .- 1618-2650. ; 400:5, s. 1397-1404
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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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| 6. |
- 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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| 7. |
- 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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| 8. |
- 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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| 9. |
- 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
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Ingår i: The Journal of Physical Chemistry C. - : American Chemical Society (ACS). - 1932-7447 .- 1932-7455. ; 115:21, s. 10588-10596
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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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| 10. |
- Tejero, Ismael, et al.
(författare)
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Theoretical modeling of hydroxyl-radical-induced lipid peroxidation reactions
- 2007
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Ingår i: Journal of Physical Chemistry B. - : American Chemical Society. - 1520-6106 .- 1520-5207. ; 111:20, s. 5684-5693
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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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