Den kopparbindande egenskapen hos prionproteiner är sannolikt kopplad till proteinets funtion. Det mänskliga prionproteinet innehåller ett kopparbindande oktapeptidområde, där PHGGGWGQ-sekvensen upprepas fyra gånger i följd. Syftet med detta arbete är att undersöka strukturen och dynamiken i oktapeptidområdet genom att använda teoretiska metoder. Med kvantkemisk strukturoptimering genomfördes en detaljerad jämförelse av växelverkan mellan flera katjoner och det kopparbindande området. Enligt dessa beräkningar är rodium(III) en möjlig ersättare för koppar(II) i NMR-specktroskopiska koordinationsstudier. Alternativa solvatiseringsmodeller i molekyldynamiksimuleringar har också jämförts. Periodiska randvillkor är mest lämpade för användning i de system som undersöks i detta arbete. Molekyldynamiksimuleringar användes för att jämföra oktapeptidområdets struktur och dynamik med och utan kopparjoner. Växelverkan mellan aminosyrornas ringar påverkar starkt strukturen i detta område i frånvaro av kopparjoner. Fyra olika icke-bindande och bindande modeller har studerats, vilka skiljer i sin beskrivning av växelverkan mellan koppar och proteinet. Teoretiska EXAFS spektra beräknades från dem simulerade strukturerna. Spektra som genererats för den bindande modellen är nästan identiska med experimentiella resultat, vilket stöder användandet av den bindande modellen. Detta arbete visar att kopparjoner interagerar med histidin imidazolringens Nδ, deprotonerade amidkväven hos de därpå följande glycinerna samt karbonylsyret hos den andra glycinen. Simuleringarna kunde visa att kopparjonen inte stabilt binder några axiella vattenmolekyler i lösning, till skillnad från en kristallstruktur av koordinationsstrukturen. Indolringen hos tryptofan interagerar direkt med kopparjonen genom stabiliserande katjon-π växelverkan utan direkt medverkan av någon vattenmolekyl. Växelverkan mellan indolringen och kopparjonen var väldefinierad och observerades kunna ske på båda sidor av koordinationsplanet. Molekyldynamiksimuleringarna med kopparjoner och oktapeptidområdet visade hur närvaron av kopparjoner ledde till ett mer strukturerat oktapeptidområde. / The copper-binding ability of the prion protein is thought to be closely related to its function. The human prion protein contains a copper-binding octapeptide region, where the octapeptide PHGGGWGQ is repeated four times consecutively. This work focuses on investigation of the structure and the dynamics of the octapeptide region by means of theoretical methods. Quantum chemical structural optimization allowed a detailed comparison of the interaction of several cations at the copper coordination site. These calculations identified rhodium(III) as a potent substitute for copper(II) that could be used to study the coordination site with NMR-spectroscopic methods. Solvation models that could be used in molecular dynamics simulations as an alternative to periodic boundary conditions were evaluated. Periodic boundary conditions are the best method for modeling the aqueous bulk in the kind of systems that are studied in this work. Molecular dynamics simulations were used to compare the behavior of the octapeptide region in the absence and presence of copper ions. Interaction between nonpolar rings strongly influences the structure of the region in the absence of copper ions. Four different non-bonded and bonded models for describing the interaction between copper and the protein were evaluated. Theoretical EXAFS spectra were calculated from the simulated structures. The results obtained for the bonded model are nearly identical with experimental data, which validates the use of the bonded model. This work thus shows strong evidence for copper(II) ions interacting with the octapeptide region through the histidine imidazole Nδ, the deprotonated nitrogen atoms of the following two glycine residues and the carbonyl oxygen atom of the second glycine residue. Notably, the simulations show that the axial sites of the copper ion do not stably coordinate water molecules in solution, as opposed to the crystal structure reported for the coordination site. Instead, the tryptophan indole ring interacted directly with the copper ion through stabilizing cation-π interaction without water mediation. The interaction of the indole ring with the copper ion was well-defined and was observed to occur on both sides of the coordination plane. The investigations of the interaction between copper ions and the octapeptide region with molecular dynamics simulations show how the presence of copper ions results in a more structured octapeptide region. / QC 20100816

About 90% of all chemicals are produced with the help of catalysts, substances with the ability to accelerate reactions without being consumed. Metal oxides play a prominent role in catalysis, since they are able to act reversibly in many chemical processes. Zink oxide (ZnO) is used to catalyse a number of industrially important reactions. For many of these reactions water is present as a reactant, product, or byproduct. The surface structure has a significant impact on the catalytic activity. However, currently, no experimental method simultaneously offers the spatial and temporal resolution to directly follow a catalytic process. This thesis explores surface structure dependent dynamical behavior for ZnO surfaces, nanoparticles, and water interfaces, using the computational chemistry method Molecular Dynamics, which enables detailed studies of structural and dynamical processes. Quantum mechanical (QM) calculations have been performed to obtain the energetics of the materials as a function of structure. This data has been used to parametrize reactive force-fields (ReaxFF), since the catalytic processes require both far larger and longer simulations than the capabilities of QM calculations on current computers. The simulations show that when steps are present on the surface, during crystal growth of ZnO, the creation of energetically favorable structures is accelerated. At the ZnO - water interface, structures that favor hydrogen bonding is promoted. At low, monolayer, coverage water adsorbs both molecularly and dissociatively, whereas at high coverage dissociated adsorption is favored. During evaporation from the monolayers, the ratio of dissociated and molecular water is preserved. Surface steps stabilizes the dissociated state as well as increases the rate of dissociation. The dynamical properties of ZnO nanoparticles were explored using Raman measurements and simulation. In both simulation and experiment certain vibrations were suppressed in the nanoparticles, compared to bulk. The simulations show that a narrow surface region lack the bulk-specific vibrations.

With the retreating sources of carbon based fuels, thermoelectric materials can play an important role in the future of environmentally friendly power generators. Sb based framework have in some cases shown some promising properties as thermoelectric materials. The physical properties may be modified with doping or incorporation of new elements. Zn4Sb3 and Cd4Sb3 are structurally related with a Sb-based network and Zn/Cd occupying the rest of the positions. Both structures undergo order-disorder α–β transition of the Zn/Cd positions, at 254 K and ~355 K respectively. The previously ordered interstitial atoms become distributed in the structure and the two high temperature phases are isostructural (R-3c). Cd4Sb3 was synthesized from melt-quench, flux synthesis with Sn, Bi and In. The syntheses made with In resulted in interstitial-free β-Cd4Sb3 with the composition Cd11.7In1.5Sb10. This compound exhibits no phase transitions until decomposition. ZnSnSb2 and InSb both exhibit the cubic sphalerite structure. ZnSnSb2 is metallic and InSb narrow band-gap semiconductor. Attempts were made to fine-tune the electrical properties by probing the mutual solid solubility range. The formula [ZnSnSb2]x[2(InSb)]1-xSn4 and 0<X<1 with 0.1 increments for the whole composition range was used. Resistivity changes from semiconducting to metallic conduction between x=0.9 and x=0.8. In the attempt to dope Zn4Sb3 by In a novel metastable compound with the composition Zn9Sb6In2 was found. Another novel phase was discovered with the composition Zn5Sb4In2-δ (δ=0.15).  The two phases have the same Sb-framework with a CuAl2 structure. Zn and In arrangements fill the square antiprisms formed by the stacking of 32434 nets in anti configuration. The filling of the antiprisms in the two phases are different, in Zn9Sb6In2 the antiprisms have two filling arrangements, an In or Zn3 triangles. In Zn5Sb4In2-δ the antiprisms are filled with an In and a Zn that occupies a split position to form a hetero-atomic dimers.

There is a strong driving force to increase the competitiveness of the pulping industry by finding new business opportunities. In this context full utilisation of the wood raw material used in conventional pulping mills is of vital importance. One focus area is to increase the utilisation areas of lignin. LignoBoost is a new method to obtain kraft lignin of high purity. The aim of the project was to investigate and increase the ability of LignoBoost kraft lignins to bind metals in aqueous solutions. The metal binding property of kraft lignins was evaluated using copper (II) ions. The metal binding capacities were 1.76 mg Cu2+/g LignoBoost softwood kraft lignin, 0.96 mg Cu2+/g LignoBoost hardwood kraft lignin and 1.12 mg Cu2+/g condensed softwood kraft lignin. The metal binding capacities of the softwood and hardwood kraft lignins from LignoBoost were lower than expected, when compared to the metal binding capacities of other lignins found in literature. The highest copper binding capacity of a kraft lignin found in literature was almost 50 times greater than that of the LignoBoost softwood kraft lignin.   The Mannich reaction was used to increase the nitrogen content in softwood lignin, and thereby increase its electron-donating capacity. An increase in electron-donating capacity should promote its metal binding capacity.   The Mannich reaction occurs in the vacant ortho position of the phenolic groups of lignin, introducing an aminomethyl group at that position. The only vacant ortho position in the phenol unit for reaction is in the guaicyl unit. Softwood lignin underwent a Mannich reaction, since softwood contains a greater number of guaiacyl units than hardwoods.   A screening of the products from this Mannich reaction on LignoBoost softwood kraft lignin was performed to optimise the reaction conditions. The reaction time, temperature, amount of formaldehyde and dimethylamine were varied. The Mannich products were evaluated by elemental analysis. The conditions giving the highest nitrogen content in the product were used further in a Mannich reaction of condensed softwood kraft lignin. The condensed softwood kraft lignin (7 g) was treated with dimethylamine (0.35 mol) and formaldehyde (0.35 mol) at 80°C for 24 hours.   The metal binding experiment could not be carried out with Mannich-modified condensed softwood kraft lignin since the lignin dissolved in the copper solution.   When introducing nitrogen functionalities into lignin the electron-donating capacity should increase. An increase in donor groups should promote the metal binding capacity of the lignin. A problem that occurred when introducing aminomethyl groups was an increase in solubility of the lignin. Water solubility of the lignin derivative is undesirable in the envisaged utilization area, metal binding in, for example mine deposits, from where contaminated water may be a concentrated source of heavy metals.

Electrochemical deposition finds applications in the electronics- and protective coating industries. The technique is a versatile tool for the synthesis of alloys and thin films. Knowledge of the fundamental aspects of the electrode processes enables the design of nanostructured materials. In this thesis, electrodeposition processes in solutions containing metal ion complexes were studied and new methods for the preparation of metal/metal-oxide coatings were developed and evaluated. Metal/metal oxide coatings were electrodeposited from aqueous solutions containing metal complexes of hydroxycarboxylic acids under reducing conditions. The mass changes of the working electrode were monitored in-situ with the electrochemical quartz crystal microbalance (EQCM) technique and ellipsometry was used to detect the formation of Cu2O. The coatings were further characterized with XRD, XPS, SEM, TEM, and Raman spectroscopy. Electrochemical methods, including reduction of Sb/Sb2O3 in an organic electrolyte, were also used to study the properties of the deposited materials. Nanostructured coatings of Cu/Cu2O were obtained during spontaneous potential or current oscillations in alkaline Cu(II)-citrate solutions. The oscillations were due to local pH variations induced by a subsequent chemical step and comproportionation between Cu and Cu2+. Well-defined layers of Cu and Cu2O could be prepared by a galvanostatic pulsing technique, allowing independently controlled thickness of several hundred nanometers. Coatings, containing Sb and co-deposited, nanograins of Sb2O3, with a thickness of up to 200 nm were prepared from poorly buffered Sb(III)-tartrate solutions. Galvanostatic cycling showed that the latter material could be reversibly charged and discharged in a Li-ion battery for more than 50 cycles with a capacity of 660 mAh/g. The results show that precipitations of metal oxides can occur due to local pH increases during electrochemical deposition from metal complexes with ligands containing hydroxyl groups. The ability to deposit metal oxides using cathodic deposition relies on a sufficiently slow reduction of the oxide.

In discussions of heterogeneous catalysis and other surface-related phenomena, the dynamical properties of the catalytic material are often neglected, even at elevated temperatures. An example is the three-way catalyst (TWC), used for treatment of exhaust gases from combustion engines operating at several hundred degrees Celsius. In the TWC, reduced ceria (CeO2-x) is one of the key components, where it functions as an oxygen buffer, storing and releasing oxygen to provide optimal conditions for the catalytic conversion of the pollutants. In this process it is evident that dynamics plays a crucial role, not only ionic vibrations, but also oxygen diffusion. In this thesis, the structure and dynamics of several ionic crystalline compounds and their surfaces have been studied by means of Molecular dynamics (MD) simulations and Lattice dynamics (LD) calculations. The main focus lies on CeO2-x, but also CeO2, MgO and CaF2 have been investigated. The presence of oxygen vacancies in ceria is found to lead to significant distortions of the oxygen framework around the defect (but not of the cerium framework). As a consequence, a new O-O distance emerges, as well as a significantly broadened Ce-O distance distribution. The presence of oxygen vacancies in ceria also leads to increased dynamics. The oxygen self-diffusion in reduced ceria was calculated from MD simulations in the temperature range 800-2000 K, and was found to follow an Arrhenius behaviour with a vacancy mechanism along the crystallographic <100> directions only. The cation and anion vibrational surface dynamics were investigated for MgO (001) using DFT-LD and for CaF2 (111) in a combined LEED and MD study. Specific surface modes were found for MgO and increased surface dynamics was found both experimentally and theoretically for CaF2, which is isostructural with CeO2. Many methodological aspects of modeling dynamics in ionic solids are also covered in this thesis. In many cases, the representation of the model system (slab thickness, simulation box-size and the choice of ensemble) was found to have a significant influence on the results.

This thesis is an investigation into the hydrogenous behavior of Zintl phases. Zintl phases are comprised of an active metal (i.e alkali, alkaline earth, and rare earth) and a p-block element. The discussion gives an overview of the influence hydrogen affects the electronic and geometric structure of Zintl phases and subsequent properties. Incorporation of hydrogen into a Zintl phase is categorized as either polyanionic or interstitial Zintl phase hydrides. In the former the hydrogen covalently bonds to the polyanion and in the latter the hydrogen behaves hydridic, coordinates exclusively with the active metal, leading to an oxidation of the polyanion. Synthesis of hydrogenous Zintl phases may be through either a direct hydrogenation of a Zintl phase precursor or by combining active metal hydrides and p-block elements. The latter strategy typically leads to thermodynamically stable hydrides, whereas the former supports the formation of kinetically controlled products.  Polyanionic hydrides are exemplified by SrAlGeH and BaAlGeH. The underlying Zintl phases SrAlGe and BaAlGe have a structure that relates to the AlB2 structure type. These Zintl phases possess 9 valence electrons for bonding and, thus, are charge imbalanced species. Connected to the charge imbalance are superconductive properties (the Tc of SrAlGe and BaAlGe is 6.7 and 6.3 °C, respectively). In the polyanionic hydrides the hydrogen is covalently bonded as a terminating ligand to the Al atoms. The Al and Ge atoms in the anionic substructure [AlGeH]2- form corrugated hexagon layers. Thus, with respect to the underlying Zintl phases there is only a minimal change to the arrangement of metal atoms. However, the electronic properties are drastically changed since the Zintl phase hydrides are semiconductors.  Interstitial hydrides are exemplified by Ba3Si4Hx (1 < x < 2) which was obtained from the hydrogenation of the Zintl phase Ba3Si4. Ba3Si4 contains a Si46- “butterfly” polyanion. Hydrogenation resulted in a disordered hydride in which blocks of two competing tetragonal structures are intergrown. In the first structure the hydrogen is located inside Ba6 octahedra (I-Ba3Si4H), and in the second structure the hydrogen is located inside Ba5 square pyramids (P-Ba3Si4H2). In both scenarios the “butterfly anions appear oxidized and form Si44- tetrahedra. Hydrogenation may also be used as a synthesis technique to produce p-block element rich Zintl phases, such as silicide clathrates. During hydrogenation active metal is removed from the Zintl phase precursor as metal hydride. This process, called oxidative decomposition, was demonstrated with RbSi, KSi and NaSi. Hydrogenation yielded clathrate I at 300 °C and 500 °C for RbSi and KSi, respectively. Whereas a mixture of both clathrate I and II resulted at 500 °C for NaSi.  Low temperature hydrogenations of KSi and RbSi resulted in the formation of the silanides KSiH3 and RbSiH3. These silanides do not represent Zintl phase hydrides but are complex hydrides with discrete SiH3- complex species. KSiH3 and RbSiH3 occur dimorphic, with a disordered α-phase (room temperature; SG Fm-3m) and an ordered β-phase (below -70 °C; SG = Pnma (KSiH3); SG = P21/m ( RbSiH3)). During this thesis the vibrational properties of the silyl anion was characterized. The Si–H stretching force constants for the disordered α-phases are around 2.035 Ncm-1 whereas in the ordered b-forms this value is reduced to ~1.956 Ncm-1. The fact that SiH3- possesses stronger Si-H bonds in the α-phases was attributed to dynamic disorder where SiH3- moieties quasi freely rotate in a very weakly coordinating alkali metal ion environment.

A sustainable solution for meeting the energy demands at our planet is by utilizing wind-, solar-, wave-, thermal-, biomass- and hydroelectric power. These renewable and CO2 emission-free energy sources are highly variable in terms of spatial and temporal availability over the Earth, introducing the need for an appropriate method of storing and carrying energy. Hydrogen has gained significant attention as an energy storage- and carrier media because of the high energy density that is exploited within the ‘power-to-gas’ process chain. A robust way of producing sustainable hydrogen is via electrochemical water splitting. In this work the search for new heterogeneous catalyst materials with the aim of increasing energy efficiency in water splitting has involved methods of both electrochemical water splitting and chemical water oxidation. Some 21 compounds including metal- oxides, oxofluorides, oxochlorides, hydroxide and metals have been evaluated as catalysts. Two of these were synthesized directly onto conductive backbones by hydrothermal methods. Dedicated electrochemical cells were constructed for appropriate analysis of reactions, with one cell simulating an upscale unit accounting for realistic large scale applications; in this cell gaseous products are quantified by use of mass spectrometry. Parameters such as real time faradaic efficiency, production of H2 and O2 in relation to power input or overpotentials, Tafel slopes, exchange current density and electrochemical active surface area as well as turnover numbers and turnover frequencies have been evaluated. Solubility, possible side reactions, the role of the oxidation state of catalytically active elements and the nature of the outermost active surface layer of the catalyst are discussed. It was concluded that metal oxides are less efficient than metal based catalysts, both in terms of energy efficiency and in terms of electrode preparation methods intended for long time operation. The most efficient material was Ni-Fe hydroxide electrodeposited onto Ni metal foam as conductive backbone. Among the other catalysts, Co3Sb4O6F6 was of particular interest because the compound incorporate a metalloid (Sb) and redox inert F and yet show pronounced catalytic performance. In addition, performance of materials in water splitting catalysis has been discussed on the basis of results from electron microscopy, solubility experiments and X-ray diffraction data.

Electron crystallography is complementary to X-ray crystallography. Single crystal X-ray diffraction requires the size of a crystal to be larger than about 5 × 5 × 5 μm3 while a TEM allows a million times smaller crystals being studied. This advantage of electron crystallography has been used to solve new structures of small crystals. One method which has been used to collect electron diffraction data is rotation electron diffraction (RED) developed at Stockholm University. The RED method combines the goniometer tilt and beam tilt in a TEM to achieve 3D electron diffraction data. Using a high angle tilt sample holder, RED data can be collected to cover a tilt range of up to 140o.  Here the crystal structures of several different compounds have been determined using RED. The structure of needle-like crystals on the surface of NiMH particles was solved as La(OH)2. A structure model of metal-organic layers has been built based on RED data. A 3D MOF structure was solved from RED data. Two halide perovskite structures and two newly synthesized aluminophosphate structures were solved. For those beam sensitive crystals characterized here, sample cooling down to -170oC was used to reduce the beam damage. The low temperature not only reduces electron beam damage, but also keeps the structure more stable in the high vacuum in a TEM and improves the quality of the diffraction data. It is shown that cooling can improve the resolution of diffraction data for MOFs and zeolites, for samples undergoing phase changes at low temperature, the data quality could be worse by cooling. In summary, cooling can improve the ED data quality as long as the low temperature does not trigger structural changes. / <p>At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 1: Manuscript. Paper 3: Submitted.</p>

This thesis presents the synthesis, properties, and applications of two important classes of metal-organic frameworks (MOFs); lanthanide MOFs and hierarchical porous zeolitic imidazolate frameworks (ZIFs). The materials have been characterized using a wide range of techniques including diffraction, imaging, various spectroscopic techniques, gas sorption, dynamical light scattering (DLS) and thermogravimetric analysis (TGA). In Chapter 1, the unique features of MOFs and ZIFs as well as their potential applications are summarized. In Chapter 2, different characterization techniques are presented. Chapter 3 describes a family of new isoreticular lanthanide MOFs synthesized using tri-topic linkers of different sizes, H3L1-H3L4, denoted SUMOF-7I-IV (Ln) (SU; Stockholm University, Ln = La, Ce, Pr, Nd, Sm, Eu and Gd, Paper I). The SUMOF-7I-III (Ln) contain permanent pores and exhibit exceptionally high thermal and chemical stability. The luminescence properties of SUMOF-7IIs are reported (Paper II). The influences of Ln ions and the tri-topic linkers as well as solvent molecules on the luminescence properties are investigated. Furthermore, the potential of SUMOF-7II (La) for selective sensing of Fe (III) ions and the amino acid tryptophan is demonstrated (Paper III).  Chapter 4 presents a simple, fast and scalable approach for the synthesis of hierarchical porous zeolitic imidazolate framework ZIF-8 and ZIF-67 using triethylamine (TEA)-assisted approach (Paper IV). Organic dye molecules and proteins are encapsulated directly into the ZIFs using the one-pot method. The photophysical properties of the dyes are improved through the encapsulation into ZIF-8 nanoparticles (Paper IV). The porosity and surface area of the ZIF materials can be tuned using the different amounts of dye or TEA. To further simplify the synthesis of hierarchical porous ZIF-8, a template-free approach is presented using sodium hydroxide, which at low concentrations induces the formation of zinc hydroxide nitrate nanosheets that serve as in situ sacrificial templates (Chapter 5, Paper V). A 2D leaf-like ZIF (ZIF-L) is also obtained using the method. The hierarchical porous ZIF-8 and ZIF-L show good performance for CO2 sorption. / <p>At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 2: Manuscript. Paper 5: Manuscript.</p>