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| 3. |
- 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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| 4. |
- 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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| 5. |
- 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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| 6. |
- 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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| 7. |
- 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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| 8. |
- 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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| 9. |
- Sauer, Christopher, 1993
(författare)
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Green Aromatics: Catalytic Valorisation of bio-derived 2,5-dimethylfuran over Zeolites and Zeotypes
- 2022
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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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| 10. |
- Bushnell, Eric A. C., et al.
(författare)
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The first branching point in porphyrin biosynthesis : a systematic docking, molecular dynamics and quantum mechanical/molecular mechanical study of substrate binding and mechanism of uroporphyrinogen-III decarboxylase
- 2011
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Ingår i: Journal of Computational Chemistry. - New York : John Wiley & Sons. - 0192-8651 .- 1096-987X. ; 32:5, s. 822-834
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Tidskriftsartikel (refereegranskat)abstract
- In humans, uroporphyrinogen decarboxylase is intimately involved in the synthesis of heme, where the decarboxylation of the uroporphyrinogen-III occurs in a single catalytic site. Several variants of the mechanistic proposal exist; however, the exact mechanism is still debated. Thus, using an ONIOM quantum mechanical/molecular mechanical approach, the mechanism by which uroporphyrinogen decarboxylase decarboxylates ring D of uroporphyrinogen-III has been investigated. From the study performed, it was found that both Arg37 and Arg50 are essential in the decarboxylation of ring D, where experimentally both have been shown to be critical to the catalytic behavior of the enzyme. Overall, the reaction was found to have a barrier of 10.3 kcal mol−1 at 298.15 K. The rate-limiting step was found to be the initial protontransfer from Arg37 to the substrate before the decarboxylation. In addition, it has been found that several key interactions exist between the substrate carboxylate groups and backbone amides of various activesite residues as well as several other functional groups.
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