@phdthesis{Fischer2008,
  author    = {Fischer, Anna},
  title     = {"Reactive hard templating" : from carbon nitrides to metal nitrides},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-19777},
  school      = {Universit{\"a}t Potsdam},
  year      = {2008},
  abstract  = {Nanostructured inorganic materials are routinely synthesized by the use of templates. Depending on the synthesis conditions of the product material, either "soft" or "hard" templates can be applied. For sol-gel processes, usually "soft" templating techniques are employed, while "hard" templates are used for high temperature synthesis pathways. In classical templating approaches, the template has the unique role of structure directing agent, in the sense that it is not participating to the chemical formation of the resulting material. This work investigates a new templating pathway to nanostructured materials, where the template is also a reagent in the formation of the final material. This concept is described as "reactive templating" and opens a synthetic path toward materials which cannot be synthesised on a nanometre scale by classical templating approaches. Metal nitrides are such kind of materials. They are usually produced by the conversion of metals or metal oxides in ammonia flow at high temperature (T > 1000°C), which make the application of classical templating techniques difficult. Graphitic carbon nitride, g-C3N4, despite its fundamental and theoretical importance, is probably one of the most promising materials to complement carbon in material science and many efforts are put in the synthesis of this material. A simple polyaddition/elimination reaction path at high temperature (T = 550°C) allows the polymerisation of cyanamide toward graphitic carbon nitride solids. By hard templating, using nanostructured silica or aluminium oxide as nanotemplates, a variety of nanostructured graphitic carbon nitrides such as nanorods, nanotubes, meso- and macroporous powders could be obtained by nanocasting or nanocoating. Due to the special semi-conducting properties of the graphitic carbon nitride matrix, the nanostructured graphitic carbon nitrides show unexpected catalytic activity for the activation of benzene in Friedel-Crafts type reactions, making this material an interesting metal free catalyst. Furthermore, due to the chemical composition of g-C3N4 and the fact that it is totally decomposed at temperatures between 600°C and 800°C even under inert atmosphere, g-C3N4 was shown to be a good nitrogen donor for the synthesis of early transition metal nitrides at high temperatures. Thus using the nanostructured carbon nitrides as "reactive templates" or "nanoreactors", various metal nitride nanostructures, such as nanoparticles and porous frameworks could be obtained at high temperature. In this approach the carbon nitride nanostructure played both the role of the nitrogen source and of the exotemplate, imprinting its size and shape to the resulting metal nitride nanostructure.},
  language  = {en}
}
@phdthesis{Vranic2019,
  author    = {Vranic, Marija},
  title     = {3D Structure of the biomarker hepcidin-25 in its native state},
  doi       = {10.25932/publishup-45929},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-459295},
  school      = {Universit{\"a}t Potsdam},
  pages     = {xii, 135},
  year      = {2019},
  abstract  = {Hepcidin-25 (Hep-25) plays a crucial role in the control of iron homeostasis. Since the dysfunction of the hepcidin pathway leads to multiple diseases as a result of iron imbalance, hepcidin represents a potential target for the diagnosis and treatment of disorders of iron metabolism. Despite intense research in the last decade targeted at developing a selective immunoassay for iron disorder diagnosis and treatment and better understanding the ferroportin-hepcidin interaction, questions remain. The key to resolving these underlying questions is acquiring exact knowledge of the 3D structure of native Hep-25. Since it was determined that the N-terminus, which is responsible for the bioactivity of Hep-25, contains a small Cu(II)-binding site known as the ATCUN motif, it was assumed that the Hep-25-Cu(II) complex is the native, bioactive form of the hepcidin. This structure has thus far not been elucidated in detail. Owing to the lack of structural information on metal-bound Hep-25, little is known about its possible biological role in iron metabolism. Therefore, this work is focused on structurally characterizing the metal-bound Hep-25 by NMR spectroscopy and molecular dynamics simulations. For the present work, a protocol was developed to prepare and purify properly folded Hep-25 in high quantities. In order to overcome the low solubility of Hep-25 at neutral pH, we introduced the C-terminal DEDEDE solubility tag. The metal binding was investigated through a series of NMR spectroscopic experiments to identify the most affected amino acids that mediate metal coordination. Based on the obtained NMR data, a structural calculation was performed in order to generate a model structure of the Hep-25-Ni(II) complex. The DEDEDE tag was excluded from the structural calculation due to a lack of NMR restraints. The dynamic nature and fast exchange of some of the amide protons with solvent reduced the overall number of NMR restraints needed for a high-quality structure. The NMR data revealed that the 20 Cterminal Hep-25 amino acids experienced no significant conformational changes, compared to published results, as a result of a pH change from pH 3 to pH 7 and metal binding. A 3D model of the Hep-25-Ni(II) complex was constructed from NMR data recorded for the hexapeptideNi(II) complex and Hep-25-DEDEDE-Ni(II) complex in combination with the fixed conformation of 19 C-terminal amino acids. The NMR data of the Hep-25-DEDEDE-Ni(II) complex indicates that the ATCUN motif moves independently from the rest of the structure. The 3D model structure of the metal-bound Hep-25 allows for future works to elucidate hepcidin's interaction with its receptor ferroportin and should serve as a starting point for the development of antibodies with improved selectivity.},
  language  = {en}
}
@phdthesis{VillatoroLeal2018,
  author    = {Villatoro Leal, Jos{\´e} Andr{\´e}s},
  title     = {A combined approach for the analysis of biomolecules using IR-MALDI ion mobility spectrometry and molecular dynamics simulations of peptide ions in the gas phase},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-419723},
  school      = {Universit{\"a}t Potsdam},
  pages     = {133},
  year      = {2018},
  abstract  = {The aim of this doctoral thesis was to establish a technique for the analysis of biomolecules with infrared matrix-assisted laser dispersion (IR-MALDI) ion mobility (IM) spectrometry. The main components of the work were the characterization of the IR-MALDI process, the development and characterization of different ion mobility spectrometers, the use of IR-MALDI-IM spectrometry as a robust, standalone spectrometer and the development of a collision cross-section estimation approach for peptides based on molecular dynamics and thermodynamic reweighting. First, the IR-MALDI source was studied with atmospheric pressure ion mobility spectrometry and shadowgraphy. It consisted of a metal capillary, at the tip of which a self-renewing droplet of analyte solution was met by an IR laser beam. A relationship between peak shape, ion desolvation, diffusion and extraction pulse delay time (pulse delay) was established. First order desolvation kinetics were observed and related to peak broadening by diffusion, both influenced by the pulse delay. The transport mechanisms in IR-MALDI were then studied by relating different laser impact positions on the droplet surface to the corresponding ion mobility spectra. Two different transport mechanisms were determined: phase explosion due to the laser pulse and electrical transport due to delayed ion extraction. The velocity of the ions stemming from the phase explosion was then measured by ion mobility and shadowgraphy at different time scales and distances from the source capillary, showing an initially very high but rapidly decaying velocity. Finally, the anatomy of the dispersion plume was observed in detail with shadowgraphy and general conclusions over the process were drawn. Understanding the IR-MALDI process enabled the optimization of the different IM spectrometers at atmospheric and reduced pressure (AP and RP, respectively). At reduced pressure, both an AP and an RP IR-MALDI source were used. The influence of the pulsed ion extraction parameters (pulse delay, width and amplitude) on peak shape, resolution and area was systematically studied in both AP and RP IM spectrometers and discussed in the context of the IR-MALDI process. Under RP conditions, the influence of the closing field and of the pressure was also examined for both AP and RP sources. For the AP ionization RP IM spectrometer, the influence of the inlet field (IF) in the source region was also examined. All of these studies led to the determination of the optimal analytical parameters as well as to a better understanding of the initial ion cloud anatomy. The analytical performance of the spectrometer was then studied. Limits of detection (LOD) and linear ranges were determined under static and pulsed ion injection conditions and interpreted in the context of the IR-MALDI mechanism. Applications in the separation of simple mixtures were also illustrated, demonstrating good isomer separation capabilities and the advantages of singly charged peaks. The possibility to couple high performance liquid chromatography (HPLC) to IR-MALDI-IM spectrometry was also demonstrated. Finally, the reduced pressure spectrometer was used to study the effect of high reduced field strength on the mobility of polyatomic ions in polyatomic gases. The last focus point was on the study of peptide ions. A dataset obtained with electrospray IM spectrometry was characterized and used for the calibration of a collision cross-section (CCS) determination method based on molecular dynamics (MD) simulations at high temperature. Instead of producing candidate structures which are evaluated one by one, this semi-automated method uses the simulation as a whole to determine a single average collision cross-section value by reweighting the CCS of a few representative structures. The method was compared to the intrinsic size parameter (ISP) method and to experimental results. Additional MD data obtained from the simulations was also used to further analyze the peptides and understand the experimental results, an advantage with regard to the ISP method. Finally, the CCS of peptide ions analyzed by IR-MALDI were also evaluated with both ISP and MD methods and the results compared to experiment, resulting in a first validation of the MD method. Thus, this thesis brings together the soft ionization technique that is IR-MALDI, which produces mostly singly charged peaks, with ion mobility spectrometry, which can distinguish between isomers, and a collision cross-section determination method which also provides structural information on the analyte at hand.},
  language  = {en}
}
@phdthesis{DereseYenesewMidiwoetal.2003,
  author    = {Derese, Solomon and Yenesew, Abiy and Midiwo, Jacob O. and Heydenreich, Matthias and Peter, Martin G.},
  title     = {A new isoflavone from stem bark of Millettia dura},
  issn      = {1011-3924},
  year      = {2003},
  language  = {en}
}
@phdthesis{Rackwitz2016,
  author    = {Rackwitz, Jenny},
  title     = {A novel approach to study low-energy electron-induced damage to DNA oligonucleotides},
  school      = {Universit{\"a}t Potsdam},
  pages     = {137},
  year      = {2016},
  language  = {en}
}
@phdthesis{Gebauer2008,
  author    = {Gebauer, Denis},
  title     = {A novel view on the early stage of crystallization},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-19818},
  school      = {Universit{\"a}t Potsdam},
  year      = {2008},
  abstract  = {This thesis provides a novel view on the early stage of crystallization utilizing calcium carbonate as a model system. Calcium carbonate is of great economical, scientific and ecological importance, because it is a major part of water hardness, the most abundant Biomineral and forms huge amounts of geological sediments thus binding large amounts of carbon dioxide. The primary experiments base on the evolution of supersaturation via slow addition of dilute calcium chloride solution into dilute carbonate buffer. The time-dependent measurement of the Ca2+ potential and concurrent pH = constant titration facilitate the calculation of the amount of calcium and carbonate ions bound in pre-nucleation stage clusters, which have never been detected experimentally so far, and in the new phase after nucleation, respectively. Analytical Ultracentrifugation independently proves the existence of pre-nucleation stage clusters, and shows that the clusters forming at pH = 9.00 have a proximately time-averaged size of altogether 70 calcium and carbonate ions. Both experiments show that pre-nucleation stage cluster formation can be described by means of equilibrium thermodynamics. Effectively, the cluster formation equilibrium is physico-chemically characterized by means of a multiple-binding equilibrium of calcium ions to a 'lattice' of carbonate ions. The evaluation gives GIBBS standard energy for the formation of calcium/carbonate ion pairs in clusters, which exhibits a maximal value of approximately 17.2 kJ mol^-1 at pH = 9.75 and relates to a minimal binding strength in clusters at this pH-value. Nucleated calcium carbonate particles are amorphous at first and subsequently become crystalline. At high binding strength in clusters, only calcite (the thermodynamically stable polymorph) is finally obtained, while with decreasing binding strength in clusters, vaterite (the thermodynamically least stable polymorph) and presumably aragonite (the thermodynamically intermediate stable polymorph) are obtained additionally. Concurrently, two different solubility products of nucleated amorphous calcium carbonate (ACC) are detected at low binding strength and high binding strength in clusters (ACC I 3.1EE-8 M^2, ACC II 3.8EE-8 M^2), respectively, indicating the precipitation of at least two different ACC species, while the clusters provide the precursor species of ACC. It is proximate that ACC I may relate to calcitic ACC -i.e. ACC exhibiting short range order similar to the long range order of calcite and that ACC II may relate to vateritic ACC, which will subsequently transform into the particular crystalline polymorph as discussed in the literature, respectively. Detailed analysis of nucleated particles forming at minimal binding strength in clusters (pH = 9.75) by means of SEM, TEM, WAXS and light microscopy shows that predominantly vaterite with traces of calcite forms. The crystalline particles of early stages are composed of nano-crystallites of approximately 5 to 10 nm size, respectively, which are aligned in high mutual order as in mesocrystals. The analyses of precipitation at pH = 9.75 in presence of additives -polyacrylic acid (pAA) as a model compound for scale inhibitors and peptides exhibiting calcium carbonate binding affinity as model compounds for crystal modifiers- shows that ACC I and ACC II are precipitated in parallel: pAA stabilizes ACC II particles against crystallization leading to their dissolution for the benefit of crystals that form from ACC I and exclusively calcite is finally obtained. Concurrently, the peptide additives analogously inhibit the formation of calcite and exclusively vaterite is finally obtained in case of one of the peptide additives. These findings show that classical nucleation theory is hardly applicable for the nucleation of calcium carbonate. The metastable system is stabilized remarkably due to cluster formation, while clusters forming by means of equilibrium thermodynamics are the nucleation relevant species and not ions. Most likely, the concept of cluster formation is a common phenomenon occurring during the precipitation of hardly soluble compounds as qualitatively shown for calcium oxalate and calcium phosphate. This finding is important for the fundamental understanding of crystallization and nucleation-inhibition and modification by additives with impact on materials of huge scientific and industrial importance as well as for better understanding of the mass transport in crystallization. It can provide a novel basis for simulation and modelling approaches. New mechanisms of scale formation in Bio- and Geomineralization and also in scale inhibition on the basis of the newly reported reaction channel need to be considered.},
  language  = {en}
}
@phdthesis{Jehannin2015,
  author    = {Jehannin, Marie},
  title     = {About the role of physico-chemical properties and hydrodynamics on the progress of a precipitation reaction},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-88364},
  school      = {Universit{\"a}t Potsdam},
  pages     = {xii, 130},
  year      = {2015},
  abstract  = {The size and morphology control of precipitated solid particles is a major economic issue for numerous industries. For instance, it is interesting for the nuclear industry, concerning the recovery of radioactive species from used nuclear fuel. The precipitates features, which are a key parameter from the post-precipitate processing, depend on the process local mixing conditions. So far, the relationship between precipitation features and hydrodynamic conditions have not been investigated. In this study, a new experimental configuration consisting of coalescing drops is set to investigate the link between reactive crystallization and hydrodynamics. Two configurations of aqueous drops are examined. The first one corresponds to high contact angle drops (>90°) in oil, as a model system for flowing drops, the second one correspond to sessile drops in air with low contact angle (<25°). In both cases, one reactive is dissolved in each drop, namely oxalic acid and cerium nitrate. When both drops get into contact, they may coalesce; the dissolved species mix and react to produce insoluble cerium oxalate. The precipitates features and effect on hydrodynamics are investigated depending on the solvent. In the case of sessile drops in air, the surface tension difference between the drops generates a gradient which induces a Marangoni flow from the low surface tension drop over the high surface tension drop. By setting the surface tension difference between the two drops and thus the Marangoni flow, the hydrodynamics conditions during the drop coalescence could be modified. Diols/water mixtures are used as solvent, in order to fix the surface tension difference between the liquids of both drops regardless from the reactant concentration. More precisely, the used diols, 1,2-propanediol and 1,3-propanediol, are isomer with identical density and close viscosity. By keeping the water volume fraction constant and playing with the 1,2-propanediol and 1,3-propanediol volume fractions of the solvents, the mixtures surface tensions differ up to 10 mN/m for identical/constant reactant concentration, density and viscosity. 3 precipitation behaviors were identified for the coalescence of water/diols/recatants drops depending on the oxalic excess. The corresponding precipitates patterns are visualized by optical microscopy and the precipitates are characterized by confocal microscopy SEM, XRD and SAXS measurements. In the intermediate oxalic excess regime, formation of periodic patterns can be observed. These patterns consist in alternating cerium oxalate precipitates with distinct morphologies, namely needles and "microflowers". Such periodic fringes can be explained by a feedback mechanism between convection, reaction and the diffusion.},
  language  = {en}
}
@phdthesis{Bai2010,
  author    = {Bai, Shuo},
  title     = {Active hydrogels with nanocomposites},
  address   = {Potsdam},
  pages     = {VI, 109 Bl. : Ill., graph. Darst.},
  year      = {2010},
  language  = {en}
}
@phdthesis{Asfaw2005,
  author    = {Asfaw, Mesfin},
  title     = {Adhesion of multi-component membbranes and strings},
  address   = {Potsdam},
  pages     = {102 S. : graph. Darst.},
  year      = {2005},
  language  = {en}
}
@phdthesis{Steeples2016,
  author    = {Steeples, Elliot},
  title     = {Amino acid-derived imidazolium salts: platform molecules for N-Heterocyclic carbene metal complexes and organosilica materials},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-101861},
  school      = {Universit{\"a}t Potsdam},
  pages     = {139},
  year      = {2016},
  abstract  = {In the interest of producing functional catalysts from sustainable building-blocks, 1, 3-dicarboxylate imidazolium salts derived from amino acids were successfully modified to be suitable as N-Heterocyclic carbene (NHC) ligands within metal complexes. Complexes of Ag(I), Pd(II), and Ir(I) were successfully produced using known procedures using ligands derived from glycine, alanine, β-alanine and phenylalanine. The complexes were characterized in solid state using X-Ray crystallography, which allowed for the steric and electronic comparison of these ligands to well-known NHC ligands within analogous metal complexes. The palladium complexes were tested as catalysts for aqueous-phase Suzuki-Miyaura cross-coupling. Water-solubility could be induced via ester hydrolysis of the N-bound groups in the presence of base. The mono-NHC-Pd complexes were seen to be highly active in the coupling of aryl bromides with phenylboronic acid; the active catalyst of which was determined to be mostly Pd(0) nanoparticles. Kinetic studies determined that reaction proceeds quickly in the coupling of bromoacetophenone, for both pre-hydrolyzed and in-situ hydrolysis catalyst dissolution. The catalyst could also be recycled for an extra run by simply re-using the aqueous layer. The imidazolium salts were also used to produce organosilica hybrid materials. This was attempted via two methods: by post-grafting onto a commercial organosilica, and co-condensation of the corresponding organosilane. The co-condensation technique harbours potential for the production of solid-support catalysts.},
  language  = {en}
}