| 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
-
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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| 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
-
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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| 11. |
- Maurina Morais, Eduardo, 1989
(författare)
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Synthesis of protic ionic liquids. Challenges and solutions for the synthesis of pure compounds.
- 2022
-
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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| 12. |
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| 13. |
- Sun, Bing, et al.
(författare)
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Ion transport in polycarbonate based solid polymer electrolytes : experimental and computational investigations
- 2016
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Ingår i: Physical Chemistry, Chemical Physics - PCCP. - : Royal Society of Chemistry (RSC). - 1463-9076 .- 1463-9084. ; 18:14, s. 9504-9513
-
Tidskriftsartikel (refereegranskat)abstract
- Among the alternative host materials for solid polymer electrolytes (SPEs), polycarbonates have recently shown promising functionality in all-solid-state lithium batteries from ambient to elevated temperatures. While the computational and experimental investigations of ion conduction in conventional polyethers have been extensive, the ion transport in polycarbonates has been much less studied. The present work investigates the ionic transport behavior in SPEs based on poly(trimethylene carbonate) (PTMC) and its co-polymer with epsilon-caprolactone (CL) via both experimental and computational approaches. FTIR spectra indicated a preferential local coordination between Li+ and ester carbonyl oxygen atoms in the P(TMC20CL80) co-polymer SPE. Diffusion NMR revealed that the co-polymer SPE also displays higher ion mobilities than PTMC. For both systems, locally oriented polymer domains, a few hundred nanometers in size and with limited connections between them, were inferred from the NMR spin relaxation and diffusion data. Potentiostatic polarization experiments revealed notably higher cationic transference numbers in the polycarbonate based SPEs as compared to conventional polyether based SPEs. In addition, MD simulations provided atomic-scale insight into the structure-dynamics properties, including confirmation of a preferential Li+-carbonyl oxygen atom coordination, with a preference in coordination to the ester based monomers. A coupling of the Li-ion dynamics to the polymer chain dynamics was indicated by both simulations and experiments.
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| 14. |
- 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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| 15. |
- 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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| 16. |
- 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
-
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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| 17. |
- Erdtman, Edvin, et al.
(författare)
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Theoretical study of 5-aminolevulinic acid tautomerization : a novel self-catalyzed mechanism
- 2008
-
Ingår i: Journal of Physical Chemistry A. - Washington DC : American Chemical Society. - 1089-5639 .- 1520-5215. ; 112:18, s. 4367-4374
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Tidskriftsartikel (refereegranskat)abstract
- 5-Aminolevulinic acid (5ALA) is the key synthetic building block in protoporphyrin IX (PpIX), the heme chromophore in mitochondria. In this study density functional theory calculations were performed on the tautomers of 5ALA and the tautomerization reaction mechanism from its enolic forms (5-amino-4-hydroxypent-3-enoic acid and 5-amino-4-hydroxypent-4-enoic acid) to the more stable 5ALA. The hydrated form 5-amino-4,4-dihydroxypentanoic acid was also studied. The lowest energy pathway of 5ALA tautomerization is by means of autocatalysis, in that an oxygen of the carboxylic group transfers the hydrogen atom as a "crane", with an activation energy of similar to 15 kcal/mol. This should be compared to the barriers of about 35 kcal/mol for water assisted tautomerization, and 60 kcal/mol for direct hydrogen transfer. For hydration of 5ALA, the water catalyzed activation barrier is found to be similar to 35 kcal/mol, approximately 5 kcal/mol lower than direct hydration.
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| 18. |
- 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
-
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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| 19. |
- Brinck, Tore, et al.
(författare)
-
Green Energetic Materials, Chapter 2: "Theoretical Design of Green Energetic Materials: Predicting Stability, Detection, Synthesis and Performance"
- 2014
-
Ingår i: Green Energetic Materials. - 9781119941293 ; , s. 15-44
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Bokkapitel (övrigt vetenskapligt/konstnärligt)abstract
- Since the end of the 20th century it has been increasingly realised that the use, or production, of many energetic materials leads to the release of substances which are harmful to both humans and the environment. To address this, the principles of green chemistry can be applied to the design of new products and their manufacturing processes, to create green energetic materials that are virtually free of environmental hazards and toxicity issues during manufacturing, storage, use and disposal. Active research is underway to develop new ingredients and formulations, green synthetic methods and non-polluting manufacturing processes.Green Energetic Materials provides a detailed account of the most recent research and developments in the field, including green pyrotechnics, explosives and propellants. From theoretical modelling and design of new materials, to the development of sustainable manufacturing processes, this book addresses materials already on the production line, as well as considering future developments in this evolving field.Topics covered include:Theoretical design of green energetic materialsDevelopment of green pyrotechnicsGreen primary and secondary explosivesOxidisers and binder materials for green propellantsEnvironmentally sustainable manufacturing technologies for energetic materialsElectrochemical methods for synthesis of energetic materials and waste remediationGreen Energetic Materials is a valuable resource for academic, industrial and governmental researchers working on the development of energetic materials, for both military and civilian applications.
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| 20. |
- Karlsson, Rasmus, 1987-
(författare)
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Theoretical and Experimental Studies of Electrode and Electrolyte Processes in Industrial Electrosynthesis
- 2015
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Heterogeneous electrocatalysis is the usage of solid materials to decrease the amount of energy needed to produce chemicals using electricity. It is of core importance for modern life, as it enables production of chemicals, such as chlorine gas and sodium chlorate, needed for e.g. materials and pharmaceuticals production. Furthermore, as the need to make a transition to usage of renewable energy sources is growing, the importance for electrocatalysis used for electrolytic production of clean fuels, such as hydrogen, is rising. In this thesis, work aimed at understanding and improving electrocatalysts used for these purposes is presented.A main part of the work has been focused on the selectivity between chlorine gas, or sodium chlorate formation, and parasitic oxygen evolution. An activation of anode surface Ti cations by nearby Ru cations is suggested as a reason for the high chlorine selectivity of the “dimensionally stable anode” (DSA), the standard anode used in industrial chlorine and sodium chlorate production. Furthermore, theoretical methods have been used to screen for dopants that can be used to improve the activity and selectivity of DSA, and several promising candidates have been found. Moreover, the connection between the rate of chlorate formation and the rate of parasitic oxygen evolution, as well as the possible catalytic effects of electrolyte contaminants on parasitic oxygen evolution in the chlorate process, have been studied experimentally.Additionally, the properties of a Co-doped DSA have been studied, and it is found that the doping makes the electrode more active for hydrogen evolution. Finally, the hydrogen evolution reaction on both RuO2 and the noble-metal-free electrocatalyst material MoS2 has been studied using a combination of experimental and theoretically calculated X-ray photoelectron chemical shifts. In this way, insight into structural changes accompanying hydrogen evolution on these materials is obtained.
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| 21. |
- 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
-
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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| 22. |
- Falklöf, Olle, et al.
(författare)
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Inter-Excited-State Phosphorescence in the Four-Component Relativistic Kohn-Sham Approximation : A Case Study on Lumiflavin
- 2015
-
Ingår i: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 119:49, s. 11911-11921
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Tidskriftsartikel (refereegranskat)abstract
- Electronic transitions from one excited state to another excited state of different spin symmetry play important roles in many biochemical reactions. Although recent years have seen much progress in the elucidation of nonradiative (intersystem crossing) relaxation mechanisms for such transitions, there is presently a scarcity of data available to assess whether also radiative (phosphorescence) mechanisms are relevant for these processes. Here, we demonstrate that the well-established ability of quantum chemical methods to describe intersystem crossing events between excited states can be supplemented by the ability to also describe inter-excited-state phosphorescence. Specifically, by performing four-component relativistic time-dependent density functional theory calculations, we obtain rate constants for the radiative transitions from the absorbing 1(πHπL∗) singlet state of lumiflavin to the 3(πHπL∗), 3(nN2πL∗), and 3(πH-1πL∗) triplet states, and subsequently, we compare these results with rate constants calculated for the corresponding nonradiative transitions. Thereby, it is found that the radiative rate constants for these particular transitions are typically 2 to 5 orders of magnitude smaller than the nonradiative ones.
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| 23. |
- Saenz-Mendez, Patricia, et al.
(författare)
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Theoretical study of sequence selectivity and preferred binding mode of psoralen with DNA
- 2007
-
Ingår i: Research Letters in Physical Chemistry. - : Hindawi Limited. - 1687-6873 .- 1687-6881. ; , s. Article number 60623-
-
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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| 24. |
- Ye, Chen, et al.
(författare)
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Optimizing photon upconversion by decoupling excimer formation and triplet triplet annihilation
- 2020
-
Ingår i: Physical Chemistry Chemical Physics. - : Royal Society of Chemistry (RSC). - 1463-9076 .- 1463-9084. ; 22:3, s. 1715-1720
-
Tidskriftsartikel (refereegranskat)abstract
- Perylene is a promising annihilator candidate for triplet-triplet annihilation photon upconversion, which has been successfully used in solar cells and in photocatalysis. Perylene can, however, form excimers, reducing the energy conversion efficiency and hindering further development of TTA-UC systems. Alkyl substitution of perylene can suppress excimer formation, but decelerate triplet energy transfer and triplet-triplet annihilation at the same time. Our results show that mono-substitution with small alkyl groups selectively blocks excimer formation without severly compromising the TTA-UC efficiency. The experimental results are complemented by DFT calculations, which demonstrate that excimer formation is suppressed by steric repulsion. The results demonstrate how the chemical structure can be modified to block unwanted intermolecular excited state relaxation pathways with minimal effect on the preferred ones.
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| 25. |
- Erdtman, Edvin, et al.
(författare)
-
Modelling the behavior of 5-aminolevulinic acid and its alkyl esters in a lipid bilayer
- 2008
-
Ingår i: Chemical Physics Letters. - Amsterdam : North-Holland Publishing Co. - 0009-2614 .- 1873-4448. ; 463:1-3, s. 178-182
-
Tidskriftsartikel (refereegranskat)abstract
- 5-Aminolevulinic acid (5ALA) and ester derivates thereof are used as prodrugs in photodynamic therapy (PDT). The behavior of 5ALA and three esters of 5ALA in a DPPC lipid bilayer is investigated. In particular, the methyl ester displays a very different free energy profile, where the highest barrier is located in the region with highest lipid density, while the others have their peak in the middle of the membrane, and also displays a considerably lower permeability coefficient than neutral 5ALA and the ethyl ester. The zwitterion of 5ALA has the highest permeability constant, but a significant free energy minimum in the polar head-group region renders an accumulation in this region.
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| 26. |
- Arvidsson, Adam, 1990
(författare)
-
Partial methane oxidation from electronic structure calculations
- 2017
-
Licentiatavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Investigating catalytic reactions with computational methods is a powerful approach to understand fundamental aspects of catalytic reactions and find ways to guide catalytic design. Partial methane oxidation is one example of a reaction with intriguing challenges, where a detailed atomistic approach may help to unravel the bottlenecks of this, as of yet, inefficient reaction. Although methane only needs one oxygen atom for conversion to methanol, the direct oxidation is difficult; it is in fact so difficult that at many oil extraction sites, the methane that inevitably accompanies the crude oil is flared into carbon dioxide and water as gas-phase methane is too inconvenient to store and transport.The main challenge with partial oxidation of methane is to selectively control the oxidation and steer it towards methanol and prevent over-oxidation to CO2. There exist natural enzymes that can partially oxidize methane to methanol at ambient pressure and temperature, although very slowly. One inorganic analogue to these naturally occurring enzymes are zeolites, a porous material that can readily be synthesized and that have been shown to convert methane to methanol at ambient conditions with a high selectivity (>90 %). This has been realized for zeolites ion-exchanged with different metals, such as iron, cobalt, nickel, and copper. Although there have been many attempts to determine the active site for the reaction, there is still no consensus. One candidate that has been put forth is a [Cu-O-Cu]2+ motif experimentally characterized in the ZSM-5 zeolite. In this thesis, partial oxidation of methane is investigated, focusing on this dimer motif. By combining density functional theory calculations with microkinetic modelling, the catalytic performance of the dimer motif is investigated with a simple reaction mechanism for copper, but also with the copper atoms exchanged with nickel, cobalt, iron, silver, or gold. From these results, it is clear that this particular dimer site is a relevant candidate only for copper, and can be excluded in the continued search for active sites in nickel, cobalt, and iron ion-exchanged ZSM-5.To further understand how methanol is formed and interacts with Cu-ZSM-5, experimental and calculated infrared frequencies are compared for methanol and other adsorbates. The partial oxidation of methane is also studied for other systems with oxidants other than oxygen. In particular, methane oxidation with H2S to CH3SH and H2 is explored on molybdenum sulfide clusters.
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| 27. |
- Borg, O. Anders, et al.
(författare)
-
Electron-transfer induced repair of 6-4 photoproducts in DNA : a computational study.
- 2007
-
Ingår i: Journal of Physical Chemistry A. - Washington, DC : American Chemical Society. - 1089-5639 .- 1520-5215. ; 111:12, s. 2351-2361
-
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. |
- Grand, André, et al.
(författare)
-
*H and *OH radical reactions with 5-methylcytosine
- 2007
-
Ingår i: Journal of Physical Chemistry A. - Washington, D.C. : American Chemical Society. - 1089-5639 .- 1520-5215. ; 111:37, s. 8968-8972
-
Tidskriftsartikel (refereegranskat)
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| 30. |
- Karlsson, Magnus, et al.
(författare)
-
Homology Models and Molecular Modeling of Human Retinoic Acid Metabolizing Enzymes Cytochrome P450 26A1 (CYP26A1) and P450 26B1 (CYP26B1)
- 2008
-
Ingår i: Journal of Chemical Theory and Computation. - Columbus, Ohio : American Chemical Society. - 1549-9618 .- 1549-9626. ; 4:6, s. 1021-1027
-
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. |
- Labet, Vanessa, et al.
(författare)
-
Proton catalyzed hydrolytic deamination of cytosine : a computational study
- 2008
-
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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| 32. |
- List, N. H., et al.
(författare)
-
Beyond the electric-dipole approximation : A formulation and implementation of molecular response theory for the description of absorption of electromagnetic field radiation
- 2015
-
Ingår i: Journal of Chemical Physics. - : American Institute of Physics (AIP). - 0021-9606 .- 1089-7690. ; 142:24
-
Tidskriftsartikel (refereegranskat)abstract
- We present a formulation of molecular response theory for the description of a quantum mechanical molecular system in the presence of a weak, monochromatic, linearly polarized electromagnetic field without introducing truncated multipolar expansions. The presentation focuses on a description of linear absorption by adopting the energy-loss approach in combination with the complex polarization propagator formulation of response theory. Going beyond the electric-dipole approximation is essential whenever studying electric-dipole-forbidden transitions, and in general, non-dipolar effects become increasingly important when addressing spectroscopies involving higher-energy photons. These two aspects are examined by our study of the near K-edge X-ray absorption fine structure of the alkaline earth metals (Mg, Ca, Sr, Ba, and Ra) as well as the trans-polyenes. In following the series of alkaline earth metals, the sizes of non-dipolar effects are probed with respect to increasing photon energies and a detailed assessment of results is made in terms of studying the pertinent transition electron densities and in particular their spatial extension in comparison with the photon wavelength. Along the series of trans-polyenes, the sizes of non-dipolar effects are probed for X-ray spectroscopies on organic molecules with respect to the spatial extension of the chromophore.
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| 33. |
- Matxain, Jon M, et al.
(författare)
-
New solids based on B12N12 fullerenes
- 2007
-
Ingår i: The Journal of Physical Chemistry C. - Washington, DC : American Chemical Society. - 1932-7447 .- 1932-7455. ; 111:36, s. 13354-60
-
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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| 34. |
- Musa, Klefah A K, et al.
(författare)
-
Mechanism of Photoinduced Decomposition of Ketoprofen
- 2007
-
Ingår i: Journal of Medicinal Chemistry. - Washington, DC : American Chemical Society. - 0022-2623 .- 1520-4804. ; 50:8, s. 1735-1743
-
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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| 35. |
- Musa, Klefah A. K., et al.
(författare)
-
Theoretical assessment of naphazoline redoxchemistry and photochemistry
- 2007
-
Ingår i: Journal of Physical Chemistry B. - Washington, DC : American Chemical Society. - 1520-6106 .- 1520-5207. ; 111:15, s. 3977-3981
-
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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| 36. |
- Saenz-Mendez, Patricia, et al.
(författare)
-
Theoretical prediction of binding modes and hot sequences for allopsoralen-DNA interaction
- 2007
-
Ingår i: Chemical Physics Letters. - Amsterdam : Elsevier. - 0009-2614 .- 1873-4448. ; 450:1-3, s. 127-131
-
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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| 37. |
- Sebastian, Eider San, et al.
(författare)
-
Metal ion dependent adhesion sites in integrins : A Combined DFT and QMC Study on Mn2
- 2007
-
Ingår i: Journal of Physical Chemistry B. - Washington, DC : American Chemical Society. - 1520-6106 .- 1520-5207. ; 111:30, s. 9099-9103
-
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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| 38. |
- Singh, Shivangi, 1996
(författare)
-
Investigating hydrothermal stability and influence of water on the activity of Cu-CHA catalysts for NH3-SCR
- 2024
-
Licentiatavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Selective catalytic reduction of nitrogen oxides (NOx) with NH3 as a reducing agent (NH3- SCR) is a leading technology for diesel exhaust emission control. Cu-exchanged zeolites with the chabazite structure (Cu-CHA) have emerged as the preferred catalysts thanks to its high activity and hydrothermal stability. Hydrothermal stability is related to dealumination, i.e. removal of aluminum from the zeolite framework to form extraframework aluminum, at high temperatures in the presence of water vapor. Copperexchanged chabazite (Cu-CHA) zeolites have higher hydrothermal stability compared to H-chabazite (H-CHA). To understand the delayed dealumination of Cu-CHA catalysts, we have investigated the reaction paths for dealumination in H-CHA and Cu-CHA using density functional theory (DFT) calculations combined with microkinetic modeling. We find that Cu-CHA and H-CHA follow similar four-step hydrolysis processes, yet the dealumination of Cu-CHA has higher energy barriers, suggesting stabilization of the CHA structure by Cu ions. Furthermore, the preferred reaction product upon complete dealumination of Cu-CHA is a copper-aluminate like species bound to the zeolite framework. The microkinetic analysis quantifies the increased stability of Cu-CHA as compared to H-CHA. In addition to the high-temperature dealumination, we investigated the role of water on low-temperature SCR by experimentally measuring the activity and reaction order of water. The reaction order of water is found to be increasingly negative with increasing water pressure. DFT calculations reveal that water blocks the active Cu-sites and a DFT-based microkinetic model reproduces the measured change of reaction order with water pressure.
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| 39. |
- van den Bossche, Maxime, 1989
(författare)
-
Methane oxidation over palladium oxide. From electronic structure to catalytic conversion
- 2017
-
Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Understanding how catalysts work down to the atomic level can provide ways to improve chemical processes on which our contemporary economy is heavily reliant. The oxidation of methane is one such example, which is important from an environmental point of view. Methane is a potent greenhouse gas and natural and biogas vehicles need efficient catalysts to prevent slip of uncombusted fuel into the exhaust. Commercial catalysts for methane oxidation are often based on palladium or platinum. Metallic palladium, however, is easily converted to palladium oxide when the engine is operated at oxygen rich conditions. In this thesis, various aspects of complete methane oxidation over PdO(101) are investigated with computational methods based on density functional theory (DFT). PdO(101) is the active surface for methane oxidation, and firstly, the reaction intermediates CO and H are studied in detail. Possible pathways for H2 adsorption, dissociation and eventual water formation are investigated, in connection to core-level spectroscopy experiments. Similarly, the adsorption configurations for carbon monoxide on clean and oxidized palladium are examined with a combination of DFT calculations, core-level and infrared spectroscopy. Secondly, a detailed kinetic model is constructed that describes the catalytic conversion of CH4 to CO2 and H2O over PdO(101). This is done in a first-principles microkinetics framework, where the kinetic parameters are obtained by applying density functional and transition state theory. The kinetic model provides a fundamental understanding of findings from reactor experiments, such as the rate limiting steps and poisoning behaviour, and shows qualitatively different behaviour of adsorbates on oxide as compared to metal surfaces. Lastly, limitations of the commonly used class of generalized gradient functionals are illustrated in the computation of several properties of adsorbates on metal oxide surfaces. These include core-level shifts and thermodynamic and reactive properties of adsorbates on the PdO(101) surface. Similarly, the description of several molecular and cooperative adsorption processes are also found to be sensitive to the applied exchange-correlation functional on the BaO(100), TiO2(110) and CeO2(111) surfaces.
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| 40. |
- Angelin, Marcus, et al.
(författare)
-
Rocket scientist for a day : Investigating alternatives for chemical propulsion
- 2012
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Ingår i: Journal of Chemical Education. - : American Chemical Society (ACS). - 0021-9584 .- 1938-1328. ; 89:10, s. 1301-1304
-
Tidskriftsartikel (refereegranskat)abstract
- This laboratory experiment introduces rocket science from a chemistry perspective. The focus is set on chemical propulsion, including its environmental impact and future development. By combining lecture-based teaching with practical, theoretical, and computational exercises, the students get to evaluate different propellant alternatives. To complete the task, they need to use several important curricular concepts, such as the breaking and formation of bonds, redox reactions, and thermodynamics. They also apply basic computational electronic structure calculations to investigate the energetic content of hitherto nonexisting alternatives. Finally, actual chemical rocket propulsion is demonstrated through the assembly and testing of a model rocket motor, employing a commercially available kit. The full experiment was developed for upper-level high school classes and is completed in a 3-h lab period. The experiment, or parts of it, has also been successfully used both in undergraduate programs and continuing education for teachers.
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| 41. |
- Katona, Gergely, 1975, et al.
(författare)
-
Raman-assisted crystallography reveals end-on peroxide intermediates in a nonheme iron enzyme.
- 2007
-
Ingår i: Science (New York, N.Y.). - : American Association for the Advancement of Science (AAAS). - 1095-9203 .- 0036-8075. ; 316:5823, s. 449-53
-
Tidskriftsartikel (refereegranskat)abstract
- Iron-peroxide intermediates are central in the reaction cycle of many iron-containing biomolecules. We trapped iron(III)-(hydro)peroxo species in crystals of superoxide reductase (SOR), a nonheme mononuclear iron enzyme that scavenges superoxide radicals. X-ray diffraction data at 1.95 angstrom resolution and Raman spectra recorded in crystallo revealed iron-(hydro)peroxo intermediates with the (hydro)peroxo group bound end-on. The dynamic SOR active site promotes the formation of transient hydrogen bond networks, which presumably assist the cleavage of the iron-oxygen bond in order to release the reaction product, hydrogen peroxide.
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| 42. |
- Artemenko, A., et al.
(författare)
-
Reference XPS spectra of amino acids
- 2021
-
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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| 43. |
- 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
-
Ingår i: Colloids and interfaces. - : MDPI. - 2504-5377. ; 5:1
-
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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| 44. |
- Brinck, T, et al.
(författare)
-
Green Energetic Materials, Chapter 7: "Green propellants Based on Dinitramide Salts: Mastering Stability and Chemical Compatibility Issues"
- 2014
-
Ingår i: Green Energetic Materials, kapitel 7. - 9781119941293 ; , s. 179-204
-
Bokkapitel (övrigt vetenskapligt/konstnärligt)abstract
- Since the end of the 20th century it has been increasingly realised that the use, or production, of many energetic materials leads to the release of substances which are harmful to both humans and the environment. To address this, the principles of green chemistry can be applied to the design of new products and their manufacturing processes, to create green energetic materials that are virtually free of environmental hazards and toxicity issues during manufacturing, storage, use and disposal. Active research is underway to develop new ingredients and formulations, green synthetic methods and non-polluting manufacturing processes.Green Energetic Materials provides a detailed account of the most recent research and developments in the field, including green pyrotechnics, explosives and propellants. From theoretical modelling and design of new materials, to the development of sustainable manufacturing processes, this book addresses materials already on the production line, as well as considering future developments in this evolving field.Topics covered include:Theoretical design of green energetic materialsDevelopment of green pyrotechnicsGreen primary and secondary explosivesOxidisers and binder materials for green propellantsEnvironmentally sustainable manufacturing technologies for energetic materialsElectrochemical methods for synthesis of energetic materials and waste remediationGreen Energetic Materials is a valuable resource for academic, industrial and governmental researchers working on the development of energetic materials, for both military and civilian applications.
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| 45. |
- Hertzog, Manuel, 1989, et al.
(författare)
-
Enhancing Vibrational Light-Matter Coupling Strength beyond the Molecular Concentration Limit Using Plasmonic Arrays
- 2021
-
Ingår i: Nano Letters. - : American Chemical Society (ACS). - 1530-6984 .- 1530-6992. ; 21:3, s. 1320-1326
-
Tidskriftsartikel (refereegranskat)abstract
- Vibrational strong coupling is emerging as a promising tool to modify molecular properties by making use of hybrid light-matter states known as polaritons. Fabry-Perot cavities filled with organic molecules are typically used, and the molecular concentration limits the maximum reachable coupling strength. Developing methods to increase the coupling strength beyond the molecular concentration limit are highly desirable. In this Letter, we investigate the effect of adding a gold nanorod array into a cavity containing pure organic molecules using FT-IR microscopy and numerical modeling. Incorporation of the plasmonic nanorod array that acts as artificial molecules leads to an order of magnitude increase in the total coupling strength for the cavity with matching resonant frequency filled with organic molecules. Additionally, we observe a significant narrowing of the plasmon line width inside the cavity. We anticipate that these results will be a step forward in exploring vibropolaritonic chemistry and may be used in plasmon based biosensors.
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| 46. |
- Ye, Chen, et al.
(författare)
-
Annihilation Versus Excimer Formation by the Triplet Pair in Triplet-Triplet Annihilation Photon Upconversion
- 2019
-
Ingår i: Journal of the American Chemical Society. - : American Chemical Society (ACS). - 0002-7863 .- 1520-5126. ; 141:24, s. 9578-9584
-
Tidskriftsartikel (refereegranskat)abstract
- The triplet pair is the key functional unit in triplet-triplet annihilation photon upconversion. The same molecular properties that stabilize the triplet pair also allow dimers to form on the singlet energy surface, creating an unwanted energy relaxation pathway. Here we show that excimer formation most likely is a consequence of a triplet dimer formed before the annihilation event. Polarity-dependent studies were performed to elucidate how to promote wanted emission pathways over excimer formation. Furthermore, we show that the yield of triplet-triplet annihilation is increased in higher-viscosity solvents. The results will bring new insights in how to increase the upconversion efficiency and how to avoid energy-loss channels.
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| 47. |
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| 48. |
- Londero, Elisa, 1982, et al.
(författare)
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Desorption of n-alkanes from graphene: a van der Waals density functional study
- 2012
-
Ingår i: Journal of Physics Condensed Matter. - : IOP Publishing. - 0953-8984 .- 1361-648X. ; 24:42, s. 424212-
-
Tidskriftsartikel (refereegranskat)abstract
- A recent study of temperature-programmed desorption (TPD) measurements of small linear alkane molecules (n-alkanes, with formula CNH2N+2) from C(0001) deposited on Pt(111) shows a linear relationship of the desorption energy with increasing n-alkane chain length N. We here present a van der Waals density functional study of the desorption barrier energy of the ten smallest n-alkanes (of carbon chain length N = 1–10) from graphene. We find linear scaling with N, including a non-zero intercept with the energy axis, i.e. an offset at the extrapolation to N = 0. This calculated offset is quantitatively similar to the results of the TPD measurements. From further calculations of the polyethylene polymer we offer a suggestion for the origin of the offset.
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| 49. |
- Das, Sambit Kumar, 1994-, et al.
(författare)
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Simulating non-adiabatic dynamics of photoexcited phenyl azide : Investigating electronic and structural relaxation en route to the formation of phenyl nitrene
- 2024
-
Ingår i: Chemistry - A European Journal. - 0947-6539 .- 1521-3765. ; 30:7
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Tidskriftsartikel (refereegranskat)abstract
- Excited state molecular dynamics simulations of the photoexcited phenyl azide have been performed. The semi-classical surface hopping approximation has enabled an unconstrained analysis of the electronic and nuclear degrees of freedom which contribute to the molecular dissociation of phenyl azide into phenyl nitrene and molecular nitrogen. The significance of the second singlet excited state in leading the photodissociation has been established through electronic structure calculations, based on multi-configurational schemes, and state population dynamics. The investigations on the structural dynamics have revealed the N−N bond separation to be accompanied by synchronous changes in the azide N−N−N bond angle. The 100 fs simulation results in a nitrene fragment that is electronically excited in the singlet manifold.
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- Öhrn, Anders
(författare)
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Development and Application of a First Principle Molecular Model for Solvent Effects
- 2008
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- A considerable part of chemistry in nature and industry, takes place in an environment of other molecules. Reactions, transitions, interactions or other chemical processes are almost always modified by the environment. These modifications or environment effects depend ultimately on the interactions between the molecules, the so called intermolecular interactions. The special case of effects induced by a solvent, such as water, are called solvent effects, and are widely studied and used to fine-tune properties of chemical processes. In this thesis, solvent effects are studied theoretically. Fundamental questions of how certain effects come about, that is their molecular origin, can be addressed through computer simulations. A new model with this purpose is formulated in the thesis. The model is developed from fundamental relations and well-established knowledge of intermolecular interactions, statistical mechanics and quantum mechanics. No experimental data are used as input into the model, rather the model proceeds from theoretical first principles. In the discussion of the model, special attention is given to the question of the balance between the various approximations. The model is found to accurately reproduce well-determined experimental data for a few test systems. The model is also used to study solvation and photophysical processes for which experiment is presently unable to elucidate the molecular origin. Noteworthy results from these studies are: asymmetric solvation of the quadrupolar para-benzoquinone, interface specific effects to the spectra of indole at the air/water interface, polarization-repulsion couplings in the solvation of monatomic ions and significant dependence of the molecular structure of urea on the properties of the environment.
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