| 1. |
- 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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| 2. |
- 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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| 3. |
- 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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| 4. |
- 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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| 5. |
- Chorell, Erik, et al.
(författare)
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Synthesis and application of a bromomethyl substituted scaffold to be used for efficient optimization of anti-virulence activity
- 2011
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Ingår i: European Journal of Medicinal Chemistry. - : Elsevier Masson SAS. - 0223-5234 .- 1768-3254. ; 46:4, s. 1103-1116
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Tidskriftsartikel (refereegranskat)abstract
- Pilicides are a class of compounds that attenuate virulence in Gram negative bacteria by blocking the chaperone/usher pathway in Escherichia coli. It has also been shown that compounds derived from the peptidomimetic scaffold that the pilicides are based on can prevent both Aβ aggregation and curli formation. To facilitate optimizations towards the different targets, a new synthetic platform has been developed that enables fast and simple introduction of various substituents in position C-7 on the peptidomimetic scaffold. Importantly, this strategy also enables introduction of previously unattainable heteroatoms in this position. Pivotal to the synthetic strategy is the synthesis of a C-7 bromomethyl substituted derivative of the ring-fused dihydrothiazolo 2-pyridone pilicide scaffold. From this versatile and reactive intermediate various heteroatom-linked substituents could be introduced on the scaffold including amines, ethers, amides and sulfonamides. In addition, carbon-carbon bonds could be introduced to the sp(3)-hybridized bromomethyl substituted scaffold by Suzuki-Miyaura cross couplings. Evaluation of the 24 C-7 substituted compounds in whole-bacterial assays provided important structure-activity data and resulted in the identification of a number of new pilicides with activity as good or better than those developed previously.
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| 6. |
- Khokarale, Santosh G., et al.
(författare)
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One-Pot, Metal-Free Synthesis of Dimethyl Carbonate from CO2 at Room Temperature
- 2020
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Ingår i: Sustainable Chemistry. - : MDPI. - 2673-4079. ; 1:3, s. 298-314
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Tidskriftsartikel (refereegranskat)abstract
- Herein, we report on the metal-free, one-pot synthesis of industrially important dimethyl carbonate (DMC) from molecular CO2 under ambient conditions. In this process, initially the CO2 was chemisorbed through the formation of a switchable ionic liquid (SIL), [DBUH] [CH3CO3], by the interaction of CO2 with an equivalent mixture of organic superbase 1,8-diazabicyclo-[5.4.0]-undec-7-ene (DBU) and methanol. The obtained SIL further reacted with methyl iodide (CH3I) to form DMC. The synthesis was carried out in both dimethyl sulfoxide (DMSO) and methanol. Methanol is preferred, as it not only served as a reagent and solvent in CO2 capture and DMC synthesis, but it also assisted in controlling the side reactions between chemical species such as CH3I and [DBUH]+ cation and increased the yield of DMC. Hence, the use of methanol avoided the loss of captured CO2 and favored the formation of DMC with high selectivity. Under the applied reaction conditions, 89% of the captured CO2 was converted to DMC. DBU was obtained, achieving 86% recovery of its salts formed during the synthesis. Most importantly, in this report we describe a simple and renewable solvent-based process for a metal-free approach to DMC synthesis under industrially feasible reaction conditions.
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| 7. |
- Vucetic, Nemanja, et al.
(författare)
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Tuned Bis-Layered Supported Ionic Liquid Catalyst (SILCA) for Competitive Activity in the Heck Reaction of Iodobenzene and Butyl Acrylate
- 2020
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Ingår i: Catalysts. - : MDPI. - 2073-4344. ; 10:9
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Tidskriftsartikel (refereegranskat)abstract
- A thorough experimental optimization of supported ionic liquid catalyst (SILCA) was performed in order to obtain a stable and efficient catalyst for the Heck reaction. Out of fifteen proposed structures, propyl imidazolium bromide-tetramethylguanidinium pentanoate modified SiO2 loaded with PdCl2 appeared to be the most stable and to have a good activity in the reaction between butylacrylate and iodobezene, resulting in a complete conversion in 40 min at 100 °C, in four consecutive experiments. This study elucidated on the stability of the catalytic system with an ionic liquid layer during the catalyst synthesis but also under reaction conditions. In the bis-layered catalyst, the imidazolium moiety as a part of internal layer, brought rigidity to the structure, while in external layer pentanoic acid gave sufficiently acidic carboxylic group capable to coordinate 1,1,3,3-tetramethylguanidine (TMG) and thus, allow good dispersion of Pd nanoparticles. The catalyst was characterized by means of XPS, FT-IR, TEM, ICP-OES, ζ-potential, EDX, TGA, and 13C NMR. The release and catch mechanism was observed, whereas Pd re-deposition can be hindered by catalyst poisoning and eventual loss of palladium.
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| 8. |
- Luong, N. Tan, 1995-
(författare)
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Water film-mediated mineralogical transformations and photocatalytic reactions
- 2023
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Mineral particles capture water vapor in the atmosphere in the form of water films that are only few monolayers thick. Water films form nanoscale hydration environments that mediate a wide range of important reactions in nature and technology. This thesis explored two important phenomena that commonly occur within the confines of water films: mineralogical transformations (Topic 1) and photocatalytic decomposition of organics (Topic 2). These transformations were chiefly identified by vibrational spectroscopy, X-ray diffraction, X-ray photoelectron spectroscopy and (Transmission and Scanning) electron microscopy. Interpretations of reaction mechanisms were partially supported by chemometrics, kinetic and thermodynamic modeling, as well as molecular simulations.Mineralogical transformations (Topic 1) resolved in this thesis involved the hydroxylation (Papers I, II) and carbonation (Paper III) of periclase (MgO), and the oxidation of rhodochrosite (MnCO3) (Paper IV). Two types of MgO nanocubes with contrasting physical properties were used to resolve nucleation- and diffusion-limited hydroxylation reactions to brucite and carbonation reactions to amorphous magnesium carbonate (AMC). While nucleation-limited reactions completely transformed (8 nm) small and aggregated MgO nanocubes to brucite, the reactions became diffusion-limited in larger (32 nm) monodispersed MgO nanocubes because of brucite surface nanocoatings (Paper I). Additionally, brucite nanosheets grew under (GPa-level) crystallization pressures because of the important volumetric expansion of the reaction, which took place in a complex network of microporosity between the small and within the larger MgO nanocubes. Brucite stacking mechanisms, explored in Paper II, focused on the early stages of MgO-water interaction in water films of different thicknesses. These were suggested to involve the stacking and (epitaxial-like) growth of precursor Mg(OH)2 nanosheets in water films. Carbonation reactions explored in Paper III completely hampered hydroxylation reactions studied in Papers I and II, and produced AMC nanocoatings grown over an unreacted MgO core. Finally, oxidation-driven reactions involving rhodochrosite in Paper IV produced MnO2, Mn3O4, and MnOOH nanocoatings with growth rates being scaled with water loadings.Photocatalytic decomposition reactions of organics (Topic 2) were focused on the case of oxalate bound to TiO2 nanoparticles (Paper V). Photodecomposition rates scaled with humidity in oxygenated water films, and were explained by the combination of hole transfer (HT), ligand-to-metal charge transfer (LMCT), and the formation of hydroxyl radicals and reactive oxygen species. Decreasing rates in oxygen-free water films were, on the other hand, explained by water-driven charge localization, which eventually limited radical production and charge transfers via HT and LMCT. The reactions involved limited HT and LMCT processes which also competed with a charge recombination process across all humidity ranges.This thesis provides new insight into two key types of transformations mediated by water films on minerals. This knowledge can be used to understand the reactivity of mineral (nano)particles exposed to variations in atmospheric humidity and oxygen content, which are both highly relevant to a wide range of settings in nature and technology. It can also advance new ideas in the study of mineral growth, especially within the confines of nanometer-thick water films.
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| 9. |
- Khokarale, Santosh G., et al.
(författare)
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Metal free synthesis of ethylene and propylene carbonate from alkylene halohydrin and CO2 at room temperature
- 2019
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Ingår i: RSC Advances. - : The Royal Society of Chemistry. - 2046-2069. ; 9:58, s. 34023-34031
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Tidskriftsartikel (refereegranskat)abstract
- Herein we describe a metal free and one-pot pathway for the synthesis of industrially important cyclic carbonates such as ethylene carbonate (EC) and propylene carbonates (PC) from molecular CO2 under mild reaction conditions. In the actual synthesis, the alkylene halohydrins such as alkylene chloro- or bromo or iodohydrin and organic superbase, 1,8-diazabicyclo-[5.4.0]-undec-7-ene (DBU) reacted equivalently with CO2 at room temperature. The syntheses of cyclic carbonates were performed in DMSO as a solvent. Both 1,2 and 1,3 halohydrin precursors were converted into cyclic carbonates except 2-bromo- and iodoethanol, which were reacted equivalently with DBU through n-alkylation and formed corresponding n-alkylated DBU salts instead of forming cyclic carbonates. NMR analysis was used to identify the reaction components in the reaction mixture whereas this technique was also helpful in terms of understanding the reaction mechanism of cyclic carbonate formation. The mechanistic study based on the NMR analysis studies confirmed that prior to the formation of cyclic carbonate, a switchable ionic liquid (SIL) formed in situ from alkylene chlorohydrin, DBU and CO2. As a representative study, the synthesis of cyclic carbonates from 1,2 chlorohydrins was demonstrated where the synthesis was carried out using chlorohydrin as a solvent as well as a reagent. In this case, alkylene chlorohydrin as a solvent not only replaced DMSO in the synthesis but also facilitated an efficient separation of the reaction components from the reaction mixture. The EC or PC, [DBUH][Cl] as well as an excess of the alkylene chlorhydrin were separated from each other following solvent extraction and distillation approaches. In this process, with the applied reaction conditions, >90% yields of EC and PC were achieved. Meanwhile, DBU was recovered from in situ formed [DBUH][Cl] by using NaCl saturated alkaline solution. Most importantly here, we developed a metal free, industrially feasible CO2 capture and utilization approach to obtain EC and PC under mild reaction conditions.
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| 10. |
- Mousavinejad, Atiyeh, et al.
(författare)
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Nickel-Based Metal–Organic Frameworks to Improve the CO2/CH4 Separation Capability of Thin-Film Pebax Membranes
- 2020
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Ingår i: Industrial & Engineering Chemistry Research. - : American Chemical Society (ACS). - 0888-5885 .- 1520-5045. ; 59:28, s. 12834-12844
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Tidskriftsartikel (refereegranskat)abstract
- Incorporating metal–organic frameworks (MOFs) into the thin layer of thin-film composite (TFC) membranes is an effective way of improving the CO2/CH4 separation performance. In this study, porous polyethersulfone (PES) membranes were surface-coated with a novel CO2-permeable layer consisting of CO2-philic Pebax and nickel-based MOF particles. The MOF particles were synthesized using nickel(II) acetate tetrahydrate as a metal source and 2-amino-1,4-dicarboxybenzene (NH2-BDC) as an organic linker. The properties and performance of the MOFs and synthesized membranes were assessed using analytical techniques including differential scanning calorimetry (DSC), thermogravimetric analysis (TGA), field-emission scanning electron microscopy (FE-SEM), and dynamic light scattering (DLS). DLS analysis showed that the MOF particle size range was in a range of 350–650 nm. Moreover, cross-sectional FE-SEM images depicted that a uniform and dense Pebax layer was shaped on top of the PES substrate. Well dispersion of the particles was demonstrated by surface FE-SEM imaging. DSC analysis showed that embedding Ni-NH2-BDC MOF particles into the Pebax-1657 film increased the crystallinity degree and the glass-transition temperature (Tg) of resulted membranes. To evaluate the membrane’s separation performance, permeation experiments were performed with CO2, CH4, and CO2/CH4 mixtures at ambient temperature. Embedding 5 wt % Ni-based MOF particles improved the CO2 permeability and CO2/CH4 selectivity from 19.05 Barrer and 32.2 to 31.55 Barrer and 94, respectively, compared to MOF-free membranes. Loading MOF particles into the Pebax matrix also improved the real gas separation factor. The obtained results demonstrate the great potential of the fabricated TFC membranes for gas separation.
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