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Methoxylated ether lipids (MELs) are a subset of 1-O-alkyl-sn-glycerols that are found ubiquitously in nature in very low concentrations. The MELs occur in significantly higher amounts in the liver oil of shark and related cartilaginous fish species. These compounds have not been explored in a meaningful capacity and their function and physiological effects are therefore completely unknown. They can be described as a glycerol molecule ether-linked with a fatty hydrocarbon tail which can be saturated, monounsaturated, or polyunsaturated, possessing the methoxyl group. A remarkable omega-3 polyunsaturated DHA-like MEL derivative had been discovered in shark liver oil, and the main focus in the work described in this thesis was on its highly successful asymmetric synthesis. This synthetic task may be divided into two challenging parts. Firstly, the design and synthesis of a double-chiral synthon, regarded as the “head piece” of the MEL structure, and the control of its diastereomeric purity. Secondly the synthesis of the omega-3 polyunsaturated fatty chain regarded as the “tail” of the MEL structure and the considerable effort that went in to synthesizing and purifying compounds with up to six all-cis skipped double bond structures. The methodology developed in this work was used to synthesize the total of ten saturated, monounsaturated, and polyunsaturated MEL derivatives of which six are present in shark liver oil. A literature survey on the nature of skipped poly-yne/ene synthesis is contemplated in much detail in this thesis, both from the historical and experimental point of view. Some preliminary studies done mostly in the 1970’s showed interesting biological effects, such as anti-tumour, anti-bacterial and immune stimulating properties. These studies were all conducted with isolated mixtures of compounds or synthesized compounds with a mixture of diastereomers. Their low concentration in nature makes them difficult and arduous to isolate and study. This thesis describes a new synthetic strategy which allows access to any imaginable individual MEL compound in high diastereomeric purity which can hopefully rekindle interest in these mysterious compounds., Metoxýleruð eter lípíð (MEL) tilheyra undirflokki 1-O-alkýl-sn-glýseróla og finnast hvarvetna í náttúrunni í afar lágu magni, en koma fyrir í mun ríkari mæli í lifrarlýsi hákarla og annarra brjóskfiska. Þessi efni eru ekki mikið rannsökuð og virkni þeirra og tilgangur algerlega óþekktur. Þau hafa til að bera mettaðar eða ómettaðar kolvetniskeðjur (fituhalinn) settar metoxyl-hópnum, og eru þær tengdar sem eter inn á glýseról hluta sameindarinar (hausinn). Mjög áhugaverð MEL afleiða hefur fundist og verið greind í hákarlalýsi og hefur hún sömu kolefniskeðju og hin mikilvæga ómega-3 fjölómettaða fitusýra DHA. Megináhersla þessarar ritgerðar og rannsóknanna að baki henni fól í sér efnasmíðina á þessari heillandi ómega-3 fjölómettuðu MEL afleiðu og tókst hún með miklum ágætum. Henni má skipta í tvo meginþætti. Annars vegar efnasmíðin á svokölluðum haus-hluta þessara MEL efna með tvö hendin kolefni og rúmefnafræðilegur hreinleika hans; hins vegar efnasmíði fjölómettuðu kolvetniskeðjunnar með sex tvítengi og stjórnun á cis-skipaðri rúmefnafræði þeirra. Aðferðafræðinni var beitt til efnasmíða á samtals tíu MEL afleiðum, mettuðum, einómettuðum og fjölómettuðum og hafa sex þeirra fundist í hákarlalýsi. Í ritgerðinni eru efnasmíðar á fjölómettuðum alkýn og alken keðjum skoðaðar og tilraunum til smíða á slíkum efnum lýst í sögulegu samhengi. Nokkrar rannsóknir gerðar á MEL efnablöndum framkvæmdar á áttunda áratuginum sýndu fram á margvíslega lífvirkni, á borð við krabbameinsdrepandi, bakteríudrepandi og ónæmisvekjandi áhrif. Hinn lági styrkur þessara efna í náttúrunni gerir það að verkum að erfitt er að nálgast þau á hreinu formi til að rannsaka nánar. Þessi ritgerð lýsir nýrri synþetískri nálgun sem gerir efnasmíðar á þessum efnum mögulegar í háum efna- og rúmefnafræðilegum hreinleika. Þetta hefur vonandi það í för með sér að aukinn áhugi vakni aftur á þessum athyglisverðu efnum og þau þá rannsökuð meira og ýtarlegar., The Icelandic Center for Research (Rannís) grant number 174396

The research described in this thesis is part of a network project involving the growth of metal nanostructures on surfaces of solids, a Horizon 2020 project titled ELENA. The part of the project described here involved the use of various approaches including density functional theory (DFT), semi-empirical potential functions, and machine learned Gaussian approximation potentials (GAP) for determining the mechanism of adatom migration on surfaces of solids and interlayer transport. Minimum energy paths for the various elementary processes were calculated using the nudged elastic band method in order to identify the transition mechanisms and evaluate the corresponding activation energy. Particular focus was on processes involving the descent of adatoms that land on top of a growing close packed layer on platinum and gold crystals. These are the key transitions determining whether the surface grows layer-by-layer or forms three-dimensional islands. The optimal mechanism for such interlayer transport was identified taking into account the surface morphology, in particular the presence of kinks on the step edges. Also, calculations of Au adatom diffusion on the Si(100) surface were carried out. While exploratory calculations on all these systems were first carried out using semi-empirical potential functions, the principal results presented are based on more accurate DFT calculations that were carried out subsequently using the PBEsol electron density functional. The principal result for the Pt/Pt(111) and Au/Au(111) systems is that downstepping occurs most readily when there is a kink on the step edge, and the preferred mechanism involves a concerted two atom process that places an atom near but not into the kink sites. This is important for explaining the re-entrant layer-by-layer growth which has been experimentally observed previously for Pt(111) growth. The calculations for Au/Au(111) presented here predict similar behavior for the growth of the Au(111) surface. The importance of choosing a single reference point for the energy of the adatom, here chosen to be the adatom on an extended flat surface, is demonstrated. Also, two effects are identified leading to a depletion zone near the step edges, which has previously been observed experimentally. The calculations of a Au adatom on the Si(100)-2×1 surface reveal an unusual diffusion path. While the optimal binding site is in between the Si dimer rows, as has been deduced previously from experimental measurements, the optimal diffusion path involves promotion of the adatom to higher energy binding sites on top of a dimer row and then rapid skidding along the row before the adatom drops back down in between dimer rows to a low energy site. As a result, dimers of Au adatoms and possibly larger adatom clusters are predicted to form on top of dimer rows, rather than in between rows. On the basis of the calculations of binding sites and migration paths, kinetic Monte Carlo simulations of long time evolution were carried out and an effective activation energy for diffusion evaluated.

Publisher's version (útgefin grein), (Coumarin-4-yl)methyl (c4m) and p-hydroxyphenacyl (pHP)-based compounds are well known for their highly efficient photoreactions, but often show limited solubility in aqueous media. To circumvent this, we synthesized and characterized the two new c4m and pHP-based photoacid generators (PAGs), 7-[bis(carboxymethyl)amino]-4-(acetoxymethyl)coumarin (c4m-ac) and p-hydroxyphenacyl-2,5,8,11-tetraoxatridecan-13-oate (pHP-t), and determined their solubilities, stabilities and photolysis in aqueous media. The two compounds showed high solubilities in water of 2.77 mmol L−1±0.07 mmol L−1 (c4m-ac) and 124.66 mmol L−1±2.1 mmol L−1 (pHP-t). In basic conditions at pH 9, solubility increased for c4m-ac to 646.46 mmol L−1±0.63 mmol L−1, for pHP-t it decreased to 34.68 mmol L−1±0.62 mmol L−1. Photochemical properties of the two PAGs, such as the absorption maxima, the maximum molar absorption coefficients and the quantum yields, were found to be strongly pH-dependent. Both PAGs showed high stabilities s24h ≥95 % in water for 24 h, but decreasing stability with increasing pH value due to hydrolysis. The present study contributes to a clearer insight into the synthesis, solubilities, stabilities, and photolysis of c4m and pHP-based PAGs for further photochemical applications when high PAG concentrations are required, such as in polymeric foaming., K. A. gratefully acknowledges financial support by the Evonik Foundation. We thank the University of Stuttgart and the Fraunhofer‐Gesellschaft for provision of infrastructure and gratefully acknowledge generous financial support by the Carl Zeiss Foundation and the University of Stuttgart within the . The contribution by A.H. was made possible by SFB 902 and GRK 1986 of the Deutsche Forschungsgemeinschaft. Projekthaus NanoBioMater

Post-print (lokagerð höfundar), A direct optimization method for obtaining excited electronic states using density functionals is presented. It involves selective convergence on saddle points on the energy surface representing the variation of the energy as a function of the electronic degrees of freedom, thereby avoiding convergence to a minimum and corresponding variational collapse to the ground electronic state. The method is based on an exponential transformation of the molecular orbitals, making it possible to use efficient quasi-Newton optimization approaches. Direct convergence on a target nth-order saddle point is guided by an appropriate preconditioner for the optimization as well as the maximum overlap method. Results of benchmark calculations of 52 excited states of molecules indicate that the method is more robust than a standard self-consistent field (SCF) approach especially when degenerate or quasi-degenerate orbitals are involved. The method can overcome challenges arising from rearrangement of closely spaced orbitals in a charge-transfer excitation of the nitrobenzene molecule, a case where the SCF fails to converge. The formulation of the method is general and can be applied to non-unitary invariant functionals, such as self-interaction corrected functionals., The present work was funded by the Icelandic Research Fund (grant number 196070-052) and the University of Iceland Research Fund. AVI is supported by a doctoral fellowship from the University of Iceland.

Motivated by the use of tetrakis(dimethylamino)silane (TKDMAS) to produce silicon nitride-based deposits and its potential as a precursor for Focused Electron Beam Induced Deposition (FEBID), we have studied its reactivity towards low energy electrons in the gas phase and the composition of its deposits created by FEBID. While no negative ion formation was observed through dissociative electron attachment (DEA), significant fragmentation was observed in dissociative ionization (DI). Appearance energies (AEs) of fragments formed in DI were measured and are compared to the respective threshold energies calculated at the DFT and coupled cluster (CC) levels of theory. The average carbon and nitrogen loss per DI incident is calculated and compared to its deposit composition in FEBID. We find that hydrogen transfer reactions and new bond formations play a significant role in the DI of TKDMAS. Surprisingly, a significantly lower nitrogen content is observed in the deposits than is to be expected from the DI experiments. Furthermore, a post treatment protocol using water vapour during electron exposure was developed to remove the unwanted carbon content of FEBIDs created from TKDMAS. For comparison, these were also applied to FEBID deposits formed with tetraethyl orthosilicate (TEOS). In contrast, effective carbon removal was achieved in post treatment of TKDMAS. This approach only marginally affected the composition of deposits made with TEOS., The Icelandic Centre of Research (RANNIS), grant no. 13049305(1−3). MC acknowledges a doctoral grant from the University of Iceland Research Fund.

Publisher's version (útgefin grein), Silicon nanowires (SiNWs) are known to exhibit a large piezoresistance (PZR) effect, making them suitable for various sensing applications. Here, we report the results of a PZR investigation on randomly distributed and interconnected vertical silicon nanowire arrays as a pressure sensor. The samples were produced from p-type (100) Si wafers using a silver catalyzed top-down etching process. The piezoresistance response of these SiNW arrays was analyzed by measuring their I-V characteristics under applied uniaxial as well as isostatic pressure. The interconnected SiNWs exhibit increased mechanical stability in comparison with separated or periodic nanowires. The repeatability of the fabrication process and statistical distribution of measurements were also tested on several samples from different batches. A sensing resolution down to roughly 1 mbar pressure was observed with uniaxial force application, and more than two orders of magnitude resistance variation were determined for isostatic pressure below atmospheric pressure., Reykjavík University

To gain information about the function of nucleic acids, their structure and dynamics need to be investigated. Electron paramagnetic resonance (EPR)- and fluorescence spectroscopies are highly sensitive and valuable techniques to study nucleic acids. These methods require incorporation of spin- and fluorescent labels prior to measurements. This doctoral dissertation focuses on the synthesis of rigid spin- and fluorescent labels and their incorporation into DNA and RNA for the study of structure and dynamics of nucleic acids by EPR- and fluorescence spectroscopies. The first part of the thesis describes a protecting group strategy to address a longstanding problem associated with spin-labeling by chemical synthesis of nucleic acids, namely reduction of nitroxides during solid-phase synthesis. A benzoyl group was used to protect the nitroxide by reducing the nitroxide to the corresponding hydroxylamine, followed by benzoylation. The method was used to incorporate the rigid spin label Çm into RNA with quantitative spin-labeling efficiency. This protecting-group strategy can be used as a general method to incorporate nitroxide spin-labels into nucleic acids by the phosphoramidite approach. The second part of this thesis focuses on labeling of specific nucleic acids with rigid spin- and fluorescent labels, namely Ç, Çm and Çmf. The rigid spin labels Ç and Çm were incorporated into DNA and RNA, respectively, for measurements in the research group of Prof. Thomas F. Prisner at the Goethe University in Frankfurt, by pulsed electron-electron double resonance (PELDOR) spectroscopy. Furthermore, Çmf, the fluorescent derivative of Çm, was incorporated into various RNAs to investigate them by fluorescence spectroscopy, by the research group of Prof. Josef Wachtveitl at the Goethe University in Frankfurt. The third part of the thesis describes the design and synthesis of the new rigid spin labels Ċ and Ċm for DNA and RNA, respectively, that are carbazole-derived nitroxides and analogues of cytidine. Crystal structure analysis indicated that Ċ and Ċm are more rigid than the rigid spin labels Ç and Çm. Ċ and Ċm were incorporated into several oligonucleotides and showed to be non-perturbing of duplex structure. These new rigid spin labels are promising candidates for future studies of DNA and RNA structures and dynamics by pulsed EPR methods., Til að fá vitneskju um virkni kjarnsýra er nauðsynlegt að rannsaka byggingu og hreyfingu þeirra. Litrófsgreiningar sem byggja á rafeindasegulómun (e. electron paramagnetic resonance, EPR) og fljúrljómun eru mjög næmar og gagnlegar aðferðir til að rannsaka kjarnsýrur. Til að unnt sé að beita slíkum mæliaðferðum er nauðsynlegt að innleiða meðseglandi- og flúrljómandi merki inn í kjarnsýrurnar. Þessi doktorsritgerð lýsir efnasmíði á stífum spuna- og flúrljómandi merkjum og innleiðingu þeirra inn í DNA og RNA til rannsókna á byggingu og hreyfingu kjarnsýra með EPR- og flúrljómunarlitrófsgreiningum. Fyrsti hluti ritgerðarinnar lýsir hvernig tekið var á þrálátu vandamáli sem tengist spunamerkingu kjarnsýra, nánar tiltekið afoxun nítroxíða þegar kjarnsýrur eru smíðaðar á föstu efni (e. solid-phase synthesis). Bensóýl hópur var notaður til að vernda nítroxíðið með því að afoxa það í hýdroxýlamín, sem í kjölfarið var bensóýlað. Þessi aðferð var notuð til að innleiða stífa spunamerkið Çm ólaskað inn í RNA. Þessa verndunaraðferð ætti að nýtast almennt til að innleiða nítroxíð spunamerki inn í kjarnsýrur með fosfóramidíð efnasmíðum (e. phosphoramidite approach). Í öðrum hluta ritgerðarinnar er fjallað um merkingu ákveðinna kjarnsýra með stífum spuna- og flúrljómandi merkjum, nánar tiltekið Ç, Çm og Çmf. Stífu spunamerkin Ç og Çm voru innleidd í DNA og RNA sameindir til rannsókna í rannsóknarhópi prófessor Thomas F. Prisner við Goethe Háskólann í Frankfurt, með PELDOR (e. pulsed electron-electron double resonance) litrófsgreiningu. Þar að auki var Çmf, flúrljómandi afleiðan af Çm, innleidd í ýmsar RNA sameindir til rannsókna með flúrljómun í rannsóknarhópi prófessor Josef Wachtveitl við Goethe Háskólann í Frankfurt. Loks lýsir þriðji hluti ritgerðinnar hönnun og smíði á nýjum stífum spunamerkjum, Ċ og Ċm, fyrir DNA og RNA, sem hafa karbasól byggingu og eru afleiður af sýtidíni. Kristalgreining bendir til að Ċ og Ċm séu enn stífari en spunamerkin Ç og Çm. Ċ og Ċm voru innleidd í ýmis fákirni (e. oligonucleotides) og var sýnt fram á að Ċ og Ċm raska ekki byggingu tvístrendinga (e. duplex). Þessi nýju stífu spunamerki eru vænleg fyrir rannsóknir á byggingu og hreyfingu DNA og RNA með púlsuðum EPR mælingum., The Icelandic Centre of Research (Rannís) University of Iceland Teaching Assistantship Grant Collaborative Research Centre 902

Publisher's version (útgefin grein), Multilayer structures comprising of SiO2/SiGe/SiO2 and containing SiGe nanoparticles were obtained by depositing SiO2 layers using reactive direct current magnetron sputtering (dcMS), whereas, Si and Ge were co-sputtered using dcMS and high-power impulse magnetron sputtering (HiPIMS). The as-grown structures subsequently underwent rapid thermal annealing (550-900 degrees C for 1 min) in N-2 ambient atmosphere. The structures were investigated using X-ray diffraction, high-resolution transmission electron microscopy together with spectral photocurrent measurements, to explore structural changes and corresponding properties. It is observed that the employment of HiPIMS facilitates the formation of SiGe nanoparticles (2.1 +/- 0.8 nm) in the as-grown structure, and that presence of such nanoparticles acts as a seed for heterogeneous nucleation, which upon annealing results in the periodically arranged columnar self-assembly of SiGe core-shell nanocrystals. An increase in photocurrent intensity by more than an order of magnitude was achieved by annealing. Furthermore, a detailed discussion is provided on strain development within the structures, the consequential interface characteristics and its effect on the photocurrent spectra., M-ERA. NET project PhotoNanoP UEFISCDI Contract no. 33/2016, PCE project UEFISCDI Contract no. 122/2017 and by Romanian Ministry of Research and Innovation through NIMP Core Program PN19-03, contract no. 21 N/08.02.2019 and by the Technology Development Fund of the Icelandic Centre for Research, grant no. 159006-0611., "Peer Reviewed"

Publisher's version (útgefin grein), Molybdenum nitrogenase is one of the most intriguing metalloenzymes in nature, featuring an exotic iron-molybdenum-sulfur cofactor, FeMoco, whose mode of action remains elusive. In particular, the molecular and electronic structure of the N2-binding E4 state is not known. In this study we present theoretical QM/MM calculations of new structural models of the E4 state of molybdenum-dependent nitrogenase and compare to previously suggested models for this enigmatic redox state. We propose two models as possible candidates for the E4 state. Both models feature two hydrides on the FeMo cofactor, bridging atoms Fe2 and Fe6 with a terminal sulfhydryl group on either Fe2 or Fe6 (derived from the S2B bridge) and the change in coordination results in local lower-spin electronic structure at Fe2 and Fe6. These structures appear consistent with the bridging hydride proposal put forward from ENDOR studies and are calculated to be lower in energy than other proposed models for E4 at the TPSSh-QM/MM level of theory. We critically analyze the DFT method dependency in calculations of FeMoco that has resulted in strikingly different proposals for this state. Importantly, dinitrogen binds exothermically to either Fe2 or Fe6 in our models, contrary to others, an effect rationalized via the unique ligand field (from the hydrides) at the Fe with an empty coordination site. A low-spin Fe site is proposed as being important to N2 binding. Furthermore, the geometries of these states suggest a feasible reductive elimination step that could follow, as experiments indicate. Via this step, two electrons are released, reducing the cofactor to yield a distorted 4-coordinate Fe2 or Fe6 that partially activates N2. We speculate that stabilization of an N2-bound Fe(i) at Fe6 (not found for Fe2 model) via reductive elimination is a crucial part of N2 activation in nitrogenases, possibly aided by the apical heterometal ion (Mo or V). By using protons from the sulfhydryl group (to regenerate the sulfide bridge between Fe2 and Fe6) and the nearby homocitrate hydroxy group, we calculate a plausible route to yield a diazene intermediate. This is found to be more favorable with the Fe6-bound model than the Fe2-bound model; however, this protonation is uphill in energy, suggesting protonation of N2 might occur later in the catalytic cycle or via another mechanism., RB acknowledges support from the Icelandic Research Fund, Grants No. 141218051 and 162880051 and the University of Iceland Research Fund. The Max Planck society is acknowledged for funding. Serena DeBeer is thanked for support. Some of the computations were performed on resources provided by the Icelandic High Performance Computing Centre at the University of Iceland.

Determining the atomic structure of nanoclusters is a challenging task and a critical one for understanding their chemical and physical properties. To fully understand the properties of a nanocluster, it is necessary to know the positions of the atoms in the nanocluster. Recently, the high-resolution aberration-corrected scanning transmission electron microscope (AC-STEM) technique has provided valuable information about such systems. While the AC-STEM experimental equipment is highly developed, the analysis of the images in terms of the atomic structure of the clusters is still often qualitative rather than quantitative. In this work, a general method applicable in studies of irregular atomic structures has been developed for quantitative analysis of AC-STEM images of nanoclusters. An objective function formed by a linear combination of a measure of the agreement of a simulated image with the measured AC-STEM image plus an approximate description of the atomic interactions is used in a global optimization algorithm to extract the atomic coordinates. The method is first illustrated by analyzing synthetic images generated from regular as well as irregular structures of Au55 nanocluster. As the method does not rely on the alignment of atoms, all the structures can be successfully determined even when a significant level of noise is added to the images. The method is then applied to an experimental AC-STEM image of a Au55 nanocluster, a particularly challenging case since the atomic structure is irregular. Analysis of the local structure shows that the cluster is a combination of a part with icosahedral structure elements and a part with local atomic arrangement characteristic of a crystal packing, including a segment of a flat surface facet. The energy landscape of the cluster is explored in calculations of minimum energy paths between the optimal fit structure and other candidates generated in the analysis. This reveals low energy barriers for conformational changes, showing that such transitions can occur on laboratory timescale even at room temperature and lead to considerable changes in the AC-STEM image. Furthermore, the paths reveal additional cluster configurations, some with lower DFT energy and providing nearly as good fit to the experimental image. Detailed analysis of AC-STEM images using theoretical modeling requires a reliable, quantitative measure of the extent to which a simulated image agrees with an experimentally measured image. A simple sum of pixel-by-pixel squared errors turns out to be unreliable and a more advanced measure is needed. A method based on the Speeded Up Robust Features (SURF) algorithm is applied to match simulated images to an experimental AC-STEM image of a Au55 nanocluster. The method provides a quantitative measure that more closely corresponds to a visual assessment of image similarity, Ákvörðun á uppröðun atóma í nanóklösum er erfitt verkefni en mjög mikilvægt til að öðlast skilning á efna- og eðlisfræðilegum eiginleikum þeirra. Nýleg mælitækni, spegilvilluleiðrétt og skannandi gegnumlýsingar rafeindasmásjá (e. aberration corrected scanning transmission electron microscope, AC-STEM) hefur gefið mikilvægar upplýsingar um slík kerfi. Þótt mælitækin séu háþróuð er úrvinnslan á mæligögnunum, sem er tvívíð mynd af klasanum á atómskala, oft ónákvæm og ekki magnbundin enn sem komið er. Í verkefninu er þróuð aðferðafræði til að vinna úr myndum sem koma úr AC-STEM mælingum. Þar er mat á samræminu milli útreiknaðrar myndar við mældu myndinarinnar ásamt mati á orku nanóklasans notað í bestunarreikningum til að ákvarða hnit atómanna. Fyrst er aðferðin prófuð fyrir líkön af AC-STEM myndum fyrir bæði reglulega og óreglulega Au55 nanóklasa. Ekki er nauðsynlegt að atómin myndi raðir í klasanum og einnig er hægt að finna réttu hnitin þótt suð sé til staðar. Þá er aðferðinni beitt á mælda AC-STEM mynd af Au55 klasa. Þetta er sérstaklega krefjandi dæmi því staðsetning atómanna er óregluleg í þessum klasa. Greining á staðbundinni uppröðun atómanna sýnir að klasinn er samsettur úr tveimur hlutum, annar með strúktúreiningar sem einkenna íkósahedru og hinn dæmigerður fyrir atóm í kristal og þar er jafnframt að finna bút af flötu yfirborði. Orkulandslag klasans er kannað með reikningum á lágmarksorkuferlum milli strúktúrsins sem gefur besta samsvörun við mælingarnar og annarra strúktúra sem einnig sýna góða samsvörun. Í ljós kemur að orkuhólarnir milli þessara strúktúra eru gjarnan lágir og slíkar umraðanir atómanna geta því greiðlega átt sér stað á meðan á mælingunum stendur og þar með haft áhrif á AC-STEM myndina. Ferlarnir leiða einnig í ljós nýja strúktúra sem sumir hafa lægri DFT orku og gefa næstum jafn góða samsvörun við myndina sem fékkst með mælingunum. Ítarleg úrvinnsla á ACSTEM myndum með útreikningum fyrir líkön af strúktúrum krefst þess að áreiðanlegt tölulegt mat sé hægt að leggja á hversu góð samsvörunin er. Í ljós kemur að einföld summa af kvaðrati frávikanna í styrk allra dílanna á myndinni er ekki góður mælikvarði á gæðin. Aðferð sem byggist á hraðaðri greiningu á afgerandi kennileitum (speeded up robust features, SURF) er þróuð og notuð til að bera saman reiknaðar myndir og mælda fyrir Au55 klasann. Þessi aðferð gefur magnbundið mat á samsvörunina sem samræmist vel niðurstöðum sem fást við skoðun myndanna.

Dissertation submitted in partial fulfillment of a Philosophiae Doctor degree in Chemistry, The oxygen reduction reaction (ORR) is of central importance in the development of more efficient and durable fuel cells and computer simulations can be used to help explain and predict properties of ORR catalysts. In this thesis, various simulation methods are used, their accuracy tested, and some new tools developed for simulations of different types of ORR catalysts. The first part of the thesis presents a ReaxFF reactive force field study of the oxidation of platinum nanoparticles, the catalyst currently used in most fuel cells. The simulations make use of a grand-canonical Monte Carlo simulation approach to study the mechanism of oxidative nanoparticle degradation. Electrochemical oxidation phase diagrams are constructed and they show that stable surface oxides can form under fuel cell operating conditions. Furthermore, clusters of Pt6O8 stoichiometry are identified as the primary oxidation product and this provides a detailed, atomic scale mechanism for the degradation of platinum nanoparticle ORR catalysts. In the second part of the thesis, metal-free ORR catalysts are studied, namely nitrogen-doped graphene (NG). There, electron density functional theory calculations are used to estimate the thermodynamics of possible reaction paths and provide an estimate of the overpotential. Various density functional approximations are tested against high level diffusion Monte Carlo calculations on the binding and migration of an *O adatom on graphene, an important intermediate in the ORR. It is found that generalized-gradient approximation (GGA) functionals have low accuracy while some hybrid functionals and a self-interaction corrected GGA functional give good agreement with the reference calculation. A hybrid functional is then used to calculate the free energy of ORR intermediates to estimate the overpotential for various catalyst structures and compositions. While overpotentials are initially found to be unfavorable, the presence of water molecules at the catalyst surface is estimated to reduce the calculated overpotentials significantly. This shows that proper inclusion of the aqueous electrolyte is important. From this conclusion, a significant challenge arises as inclusion of many solvent molecules makes the simulated system too large for electronic structure calculations. In the third part of the thesis, a new methodology is developed to make it possible to include the aqueous electrolyte in simulations by using a hybrid simulation approach where part of the system — the catalyst as well as the reacting species and nearby water molecules — are included in the electronic structure calculation, while the rest of the aqueous electrolyte is described using a potential energy function. The separation between the two regions is made to lie through the aqueous phase in order to make it easier to describe the interaction between atoms on opposite sides of the boundary. Therein, the challenge is to enforce the boundary in such a way that atoms and molecules do not wander from one region to another. A new method referred to as scattering-adapted flexible inner region ensemble separator (SAFIRES) is developed for this purpose. It represents an improvement on a previous algorithm called FIRES. With SAFIRES, the boundary between the two regions is flexible and adjusts automatically but particles cannot move between the regions. It is demonstrated that using SAFIRES, the energy, atomic forces, and probability distribution for the location of atoms are reproduced accurately compared to results of simulations where where no boundary is present. The SAFIRES algorithm dynamically changes the time step in the iterative algorithm for time evolution to identify and enforce elastic collisions of atoms with the boundary separating the two regions. A new propagator is introduced to simulate the time evolution of the system with or without a connection to a heat bath. Tests are carried out by simulating a Lennard-Jones liquid, a Lennard-Jones liquid/solid interface, and water described using a potential energy function. With the SAFIRES method, along with the recently developed, self-consistent polarizable hybrid simulation methodology, the stage is set for proper inclusion of the aqueous phase at the electrode surface in future electrochemistry simulations., Supported by a PhD fellowship from the University of Iceland research fund

Notkun verndarhópa á virka hópa aminosýra í litlum peptíðum gefur tækifæri til að breyta girðieiginleikum viðkomandi peptíðs við málmjónir. Alkýlun á karboxýlhóp C-enda peptíðsins beinir girðingu málmjónarinnar í fjórgirta κ4[NH2,N,N,=O] komplexa. Með stýringu á samsetningu peptíðsins er hægt að mynda kelaða hringi umhverfis málmjónina í misstórum hringjastærðum; Hægt er að mynda fjórgirðandi peptíð, κ4[n,5,5] (þar sem n = 5, 6, 7, eða 8 atóm) með misstórum hringjum á hliðarkeðju N-endans sem leiðir til mismunandi rúmfræðilegrar girðingar málmsins og væntanlega breytilegra efnaeiginleika. Fjögur trípeptíð með alkýlaða karboxylhópa voru smíðuð, α-Asp(OtBu)AlaGly(OMe), β- Asp(OtBu)AlaGly(OMe), TrpAlaGly(OMe), HisAlaGly(OMe), og γ-Glu(OMe)Cys(SMe)- Gly(OMe) til þess að mynda palladium og nickel komplexa í fjórgirtu umhverfi. Girðieiginleikar alkýleraðra trípeptíða voru rannsakaðir með spennutítrunum og NMR mælingum í vatni. Sýrustigsháð girðing tenglanna við [Pd(en)(H2O)2]2+ var greind og myndaðir komplexar staðfestir með NMR greiningum. Út frá þessum niðurstöðum voru tilraunir hannaðar til að smíða Pd(II) komplexa með trípeptíðunum α- Asp(OtBu)AlaGly(OMe), β-Asp(OtBu)AlaGly(OMe), og TrpAlaGly(OMe). Þessir komplexar voru einangraðir og greindir að fullu. Tenglarnir mynda þrí- og fjórgirta komplexa með Pd(II). Þrígirtu komplexarnir höfðu fjórða tengilinn frá upphafsefninu. Skiptihvörf á þessum fjórða tengli sýndu að hægt væri að fjarlægja rétt valinn tengil og trípeptíðið myndaði þá fjórgirt lokaefni með ferningslaga byggingu. Byggingar komplexanna voru reiknaðar með DFT reikningum þar sem kristalbyggingar fengust ekki. Hvarfgirni með litlum sameindum eins og ethylen, sýrum, formati, og episúlfíði var skoðuð, en komplexarnir hvörfuðust ekki við ethylene. Þeir brotna niður í sýru og við súrar aðstæður. Asetaldehýð myndaðist í hvarfi við ethylene við súrar aðstæður. Pd(II) er mjúk Lewis sýra og myndar auðveldlega súlfíð; Pd-trípeptíð komplexarnir tóku auðveldlega brennistein frá episúlfíði og mynduðu alken við hvötunaraðstæður. Hvarf við format leiddi til rof málmsins frá tenglinum og afoxun í Pd(0). Ni(II) komplexar með tenglunum, α-Asp(OtBu)AlaGly(OMe), β-Asp(OtBu)AlaGly(Ome), og TrpAlaGly(OMe) voru smíðaðir og greindir með litrófsgreiningum, frumefna og massagreiningum. Komplexarnir hafa bjagaða ferningslaga byggingu samkvæmt DFT reikningum. Alkýlhópar tenglanna reyndust viðkvæmari fyir sýrustigi í hvörfum með Ni(II) en með Pd(II) og C-endi trípeptíðsins gekkst undir vatnsrof við mildar aðstæður. Rafefnafræði komplexanna var mæld í vatni og sýndi óafturkræfa hegðun fyrir alla þrjá komplexa., The use of protecting groups on amino acid and peptides affords opportunities to change preferred coordination behaviors to metal centers. Alkylating the C-terminus carboxylate allows directed tripeptide coordination, forming tetradentate κ4[NH2,N,N,=O] complexes. Changing tripeptide composition enables the formation of chelates of various ring sizes, and depending on the N-terminus side chains, tetradentate κ4[n,5,5] (where n = 5, 6, 7, or 8 membered rings) coordination geometries can be achieved. The alkylated tripeptide compounds α-Asp(OtBu)AlaGly(OMe), β-Asp(OtBu)Ala- Gly(OMe), TrpAlaGly(OMe), HisAlaGly(OMe), and γ-Glu(OMe)Cys(SMe)Gly(OMe) were synthesized as ligands to coordinate to palladium and nickel to form neutral tetradentate complexes. The coordination of select alkylated tripeptides to palladium was first established by potentiometric and NMR spectroscopic data. pH-dependent complexation was analyzed and coordination properties to [Pd(en)(H2O)2]2+ were inferred from their NMR spectra. Building on aqueous NMR studies, Pd(II) complexes with the tripeptides α-Asp(OtBu)- AlaGly(OMe), β-Asp(OtBu)AlaGly(OMe), and TrpAlaGly(OMe) were synthesized and characterized. The ligands form tri- and tetradentate complexes with Pd(II). For tridentate coordination complexes, ligand exchange reactions, occupying the fourth coordination sphere, showed that sufficiently labile ligands may be removed to form the tetradentate coordination mode, which adopt a square planar geometry with tetradentated ligands. The complex coordination geometry was established using 1H and 13C NMR, and infrared spectroscopy, and supported using DFT calculations. Reactivity of palladium tripeptide complexes with small molecules such as ethylene, acids, CO and formates, and episulfides were investigated. Complexes were found to be rather inert towards ethylene coordination and decompose in acid and under acidic conditions; in the presence of ethylene, acetaldehyde was formed only after complex decomposition. Reactivity with CO and CO surrogates such as formates results in the dissociation of the ligand and reduces the metal to Pd(0). Pd(II) is a soft Lewis acid and thiophilic; when reacted with thiirenes, Pd-tripeptide complexes abstracted sulfur from the episulfide at modest catalytic rates. Ni(II) complexes with the ligands, α-Asp(OtBu)AlaGly, β-Asp(OtBu)AlaGly, and TrpAlaGly were synthesized and characterized using infrared and 1H, 13C NMR spectroscopy, mass spectrometry and elemental analysis. The complexes were predicted using DFT calculations to have square planar geometries. The esters of these ligands proved highly pH sensitive and hydrolyze fully at moderately basic conditions. The electrochemistry of the complexes was investigated in water to reveal irreversible redox behavior of all three complexes.

Direct optimization methods for the calculation of ground and excited electronic states are presented for both total density and orbital-density-dependent functionals. The methods have been developed for various types of basis sets including localized atomic orbitals, plane waves and real space grid. The algorithms have been implemented in combination with the projector-augmented-wave method to represent inner electrons of the atoms. The direct optimization method is shown to be more robust and faster than the conventional self-consistent field approach in calculations of both ground and excited states. An assessment of the Perdew-Zunger self-interaction correction (PZ-SIC) to the energy functional has also been made and its performance compared to the commonly used generalized gradient approximation (GGA). PZ-SIC is found to systematically improve the description of the atomization and ionization energy as well as the band gaps of insulators, but needs to be scaled by a half. PZ-SIC can be especially important for the accurate description of systems containing transition metals as is illustrated by the excellent results obtained for the Mn dimer, a system where results of GGA calculations are qualitatively incorrect. However, PZ-SIC does not substantially improve the excitation energy of small organic molecules as the correction there tends to cancel out when the energy of ground and excited states is compared. The efficient and practical implementation of PZ-SIC presented here paves the way for the development of more accurate orbital-density-dependent functionals., Aðferðir til að reikna út grunn og örvuð rafeindaástönd með beinni bestun hafa verið þróaðar, bæði fyrir felli háð heildarrafeindaþéttni sem og almennari felli háð þéttni svigrúmanna. Aðferðirnar hafa verið þróaðar fyrir ýmsar gerðir grunna svo sem staðbundin atómsvigrúm, planbylgjur og grind í raunrúminu. Þær hafa verið innleiddar með ’projector-augmented-wave’ aðferðinni til að lýsa áhrifum innri rafeinda atómanna. Beina bestunin reynist vera áreiðanlegri og hraðvirkari en þær aðferðir sem áður hafa verið notaðar bæði hvað varðar reikninga á grunnástöndum sem og örvuðum ástöndum. Áhrif sjálfsvíxverkunarleiðréttingar Perdew og Zunger (PZ-SIC) á útkomu reikninganna hefur einnig verið könnuð og niðurstöðurnar bornar saman við almennu stigulnálgunina (GGA). PZ-SIC leiðréttingin reynist bæta kerfisbundið útreiknaða sundrunarorku sameinda sem og jónunarorku og einnig orkugeil einangrara, en þarf að skalast niður í helming. Reikningar á eiginleikum kerfa með hliðarmálmatóm geta batnað sérlega mikið með PZ-SIC leiðréttingunni og þar er Mn tvennan sérlega afgerandi tilfelli þar sem reikningar með PZ-SIC gefa mjög góða niðurstöðu á sama tíma og GGA gefur verulega rangar niðurstöður. Hins vegar hefur PZ-SIC ekki mikil áhrif á útreiknaða örvunarorku lítilla lífrænna sameinda þar eð leiðréttingin á grunn og örvaða ástandinu styttist þar að miklu leiti út. Sú skilvirka innsetning á PZ-SIC sem er framsett hér opnar leiðina fyrir þróun á nákvæmari fellum háðum svigrúmaþéttni., Fellowship from the University of Iceland, the University of Iceland Research Fund and the Icelandic Research Fund.

Fragmentation of transient negative ions of tryptophan molecules formed through electron transfer in collisions with potassium atoms is presented for the first time in the laboratory collision energy range of 20 up to 100 eV. In the unimolecular decomposition process, the dominating side-chain fragmentation channel is assigned to the dehydrogenated indoline anion, in contrast to dissociative electron attachment of free low-energy electrons to tryptophan. The role of the collision complex formed by the potassium cation and tryptophan negative ion in the electron transfer process is significant for the mechanisms that operate at lower collision energies. At those collision times, on the order of a few tens of fs, the collision complex may not only influence the lifetime of the anion but also stabilize specific transition states and thus alter the fragmentation patterns considerably. DFT calculations, at the BHandHLYP/6-311++G(3df,2pd) level of theory, are used to explore potential reaction pathways and the evolvement of the charge distribution along those., F.F.d.S., T.C., and A.R. acknowledge the Portuguese National Funding Agency FCT-MCTES for IF-FCT IF/00380/2014, SFRH/BD/52538/2014, and PD/BD/114449/2016 and together with P.L.-V. the research grants PTDC/FIS-AQM/31215/2017 and PTDC/FIS-AQM/31281/2017. This work was also supported by Radiation Biology and Biophysics Doctoral Training Programme (RaBBiT, PD/00193/2012); UIDB/00068/2020 (CEFITEC) and UIDB/04378/2020 (UCIBIO). M.J.C. and A.G. also thank FCT-MCTES UIDB/04046/2020 and UIDP/04046/2020, and A.G. thanks the SFRH/BPD/89722/2012 grant. G.G. is partially funded by the Spanish Ministerio de Ciencia, Innovacion y Universidades (project no. PID2019-104727RB-C21) and CSIC (Project LINKA20085). O.I. acknowledges the Icelandic Center of Research (RANNIS) and the University of Iceland Research Fund for financial support. The authors thank Ragnar Bjornsson for fruitful discussions while preparing this manuscript., Pre-print

Rafeindasegullitrófsgreiningu (e. Electron Paramagnetic Resonance, EPR) er reglubundið beitt í rannsóknum á byggingu og hreyfingu kjarnsýra til að fá upplýsingar um starfsemi þeirra og hlutverk. Innleiðing meðseglandi kjarna á ákveðinn stað í kjarnsýrum er nauðsynleg fyrir EPR mælingar og er það gert með aðferð sem kallast staðbundin spunamerking. Þessi doktorsritgerð lýsir betrumbótum á staðbundinni spunamerkingu á kjarnsýrum með notkun stífra spunamerkja. Fyrsti hluti ritgerðarinnar lýsir þróun á aðferð til verndunar nítroxíð stakeinda til að koma í veg fyrir afoxun þeirra þegar spunamerktar kjarnsýrur eru útbúnar með efnasmíði. Notast var við bensóylverndað hýdroxylamín til verndunar á nítroxíðinu. Þessi aðferð var notuð til að innleiða stífa spunamerkið Ç inn í DNA kjarnsýrur og lofar góðu sem almenn aðferð til þess að innleiða spunamerki í kjarnsýrur með fosfóramíðít efnasmíði. Í öðrum hluta ritgerðarinnar er efnasmíði á spunamerkjunum EÇ og EÇm lýst, en bæði eru stöðug við afoxandi aðstæður. Þessi spunamerki eru ætluð til notkunar við innan-fruma EPR mælingar á kjarnsýrum. Bæði spunamerkin eru stíf, sem gerir mögulegt að fá nákvæmar upplýsingar um byggingu og hreyfingu kjarnsýra með EPR. EÇ var innleitt í DNA og EÇm í RNA með kjarnsýruefnasmíði. EÇm afoxaðist að hluta til á meðan á RNA smíðinni stóð en þá afoxun var unnt að koma í veg fyrir með fyrrnefndri bensóyl verndun nítroxíðsins. Sýnt var fram á að EÇ og EÇm breyttu ekki byggingu DNA og RNA tvíliða. Þriðji hluti ritgerðarinnar lýsir efnasmíðum á o-bensókvinón afleiðum af ísóindólíni og þéttingu þeirra með o-fenýlentvíamínum til að mynda ísóindólín-fenasín afleiður. Í kjölfarið voru þær oxaðar í fenasín-tví-N-oxíð nítroxíð og kannað hvort unnt væri að nota þær til spunamerkinga án samgildra tengja á tvístrendum DNA og RNA kjarnsýrum sem innihalda basalausar stöður. Ósetið fenasín-N,N-tvíoxíð tetrametýlísóindólín nítroxíð sýndi mikla sækni í basalausa stöðu í DNA á móti basanum C., Electron paramagnetic resonance (EPR) spectroscopy is routinely used to study the structure and dynamics of nucleic acids to obtain information about their functions. Incorporation of a paramagnetic center into nucleic acids is necessary prior to EPR measurements. This doctoral dissertation focuses on improvements in nitroxide spin-labeling of nucleic acids for structure determination using rigid spin labels. The first part of this thesis describes the development of a protecting group strategy for nitroxide radicals to circumvent their reduction during the chemical synthesis of DNA. Specifically, a benzoylated hydroxylamine was used as a protected form of the nitroxide. This method was used to incorporate the rigid spin label Ç into DNA oligonucleotides and represents a general strategy for spin labeling nucleic acids using the phosphoramidite method. In the second part of the thesis, the synthesis of the reduction-resistant spin labels EÇ and EÇm is described, nitroxides that will facilitate application of EPR spectroscopy for the investigation of nucleic acids within cells. Both labels possess rigidity for extracting detailed information about structure and dynamics by EPR. EÇ and EÇm were incorporated into DNA and RNA, respectively, by oligonucleotide synthesis. Partial reduction of EÇm during RNA synthesis was observed but was circumvented by using the aforementioned benzoyl protecting group strategy. EÇ and EÇm were shown to be non-perturbing of duplex DNA and RNA structures, respectively. The third part of this thesis describes the synthesis of o-benzoquinone derivatives of isoindoline and their condensation with o-phenylenediamines to form isoindoline-phenazines. Subsequent oxidation gave phenazine-di-N-oxide radicals that were evaluated for noncovalent spin-labeling of duplex DNA and RNA containing abasic sites. No specific binding was observed for RNA, but an unsubstituted phenazine-N,N-dioxide tetramethyl isoindoline nitroxide showed high binding affinity and specificity towards abasic sites in duplex DNA opposite to C.

In the current contribution we present a comprehensive study on the heteronuclear carbonyl complex H2FeRu3(CO)13 covering its low energy electron induced fragmentation in the gas phase through dissociative electron attachment (DEA) and dissociative ionization (DI), its decomposition when adsorbed on a surface under controlled ultrahigh vacuum (UHV) conditions and exposed to irradiation with 500 eV electrons, and its performance in focused electron beam induced deposition (FEBID) at room temperature under HV conditions. The performance of this precursor in FEBID is poor, resulting in maximum metal content of 26 atom % under optimized conditions. Furthermore, the Ru/Fe ratio in the FEBID deposit (≈3.5) is higher than the 3:1 ratio predicted. This is somewhat surprising as in recent FEBID studies on a structurally similar bimetallic precursor, HFeCo3(CO)12, metal contents of about 80 atom % is achievable on a routine basis and the deposits are found to maintain the initial Co/Fe ratio. Low temperature (≈213 K) surface science studies on thin films of H2FeRu3(CO)13 demonstrate that electron stimulated decomposition leads to significant CO desorption (average of 8–9 CO groups per molecule) to form partially decarbonylated intermediates. However, once formed these intermediates are largely unaffected by either further electron irradiation or annealing to room temperature, with a predicted metal content similar to what is observed in FEBID. Furthermore, gas phase experiments indicate formation of Fe(CO)4 from H2FeRu3(CO)13 upon low energy electron interaction. This fragment could desorb at room temperature under high vacuum conditions, which may explain the slight increase in the Ru/Fe ratio of deposits in FEBID. With the combination of gas phase experiments, surface science studies and actual FEBID experiments, we can offer new insights into the low energy electron induced decomposition of this precursor and how this is reflected in the relatively poor performance of H2FeRu3(CO)13 as compared to the structurally similar HFeCo3(CO)12., The authors acknowledge the fruitful and productive environment provided by the COST Action CELINA CM1301 and we would like to take the opportunity to extend our thanks to Prof. Petra Swiderek for running this Action exceptionally well. Marc Hanefeld and Michael Huth acknowledge financial support by the Deutsche Forschungsgemeinschaft (DFG) through Priority Program SPP 1928, project HU 752/12-1. DHF thanks the National Science Foundation for support of this work through the linked collaborative grants CHE-1607621 and CHE-1607547. OI acknowledges supported from the Icelandic Center of Research (RANNIS) Grant No. 13049305(1-3) and the University of Iceland Research Fund. RKTP acknowledges a doctoral grant from the University of Iceland Research Fund and financial support from the COST Action CM1301; CELINA, for short term scientific missions (STSMs).

A new 1.2 Å crystal structure of vanadium nitrogenase, isolated under turnover conditions, recently revealed a light atom ligand (OH or NH) replacing the bridging S2B sulfide of the FeV cofactor. QM/MM calculations on the new structure now reveal the light-atom ligand to be a bridging hydroxo group, probably derived from water binding to the cofactor., R. B. acknowledges support from the Icelandic Research Fund, grants 141218051 and 162880051, and the University of Iceland Research Fund. R. B. thanks Oliver Einsle for useful discussions. Open Access funding provided by the Max Planck Society

We present first experiments on electron beam induced deposition of silacyclohexane (SCH) and dichlorosilacyclohexane (DCSCH) under a focused high-energy electron beam (FEBID). We compare the deposition dynamics observed when growing pillars of high aspect ratio from these compounds and we compare the proximity effect observed for these compounds. The two precursors show similar behaviour with regards to fragmentation through dissociative ionization in the gas phase under single-collision conditions. However, while DCSCH shows appreciable cross sections with regards to dissociative electron attachment, SCH is inert with respect to this process. We discuss our deposition experiments in context of the efficiency of these different electron-induced fragmentation processes. With regards to the deposition dynamics, we observe a substantially faster growth from DCSCH and a higher saturation diameter when growing pillars with high aspect ratio. However, both compounds show similar behaviour with regards to the proximity effect. With regards to the composition of the deposits, we observe that the C/Si ratio is similar for both compounds and in both cases close to the initial molecular stoichiometry. The oxygen content in the DCSCH deposits is about double that of the SCH deposits. Only marginal chlorine is observed in the deposits of from DCSCH. We discuss these observations in context of potential approaches for Si deposition., CWH likes to thank Luc van Kessel, Kerim Arat and Sebastiaan Lokhorst for their assistance with the Monte Carlo simulations of Figure 10. OI acknowledges supported from the Icelandic Center of Research (RANNIS) Grant No. 13049305(1-3) and the University of Iceland Research Fund. RKTP acknowledges a doctoral grant from the University of Iceland Research Fund and financial support from the COST Action CM1301; CELINA, for short term scientific missions (STSMs)

Here we present a combined experimental and theoretical study on the fragmentation of o- and p-tetrafluorohydroquinone upon low energy electron attachment. Despite an identical ring-skeleton and identical functional groups in these constitutional isomers, they show distinctly different fragmentation patterns, a phenomenon that cannot be explained by distinct resonances or different thermochemistry. Using high-level quantum chemical calculations with the computationally affordable domain localized pair natural orbital approach, DLPNO–CCSD(T), we are able to provide a complete and accurate description of the respective reaction dynamics, revealing proton shuttling and transition states for competing channels as the explanation for the different behavior of these isomers. The results represent a “schoolbook example” of how the combination of experiment and modern high-level theory may today provide a thorough understanding of complex reaction dynamics by computationally affordable means., (This work was supported by the Icelandic Center of Research (RANNIS) Grant No. 13049305 and 141218051 and the University of Iceland Research Fund.

Publisher's version (útgefin grein), The factors affecting the self-assembly process in low molecular weight gelators (LMWGs) were investigated by tuning the gelation properties of a well-known gelator N-(4-pyridyl)isonicotinamide (4PINA). The N—H···N interactions responsible for gel formation in 4PINA were disrupted by altering the functional groups of 4PINA, which was achieved by modifying pyridyl moieties of the gelator to pyridyl N-oxides. We synthesized two mono-N-oxides (INO and PNO) and a di-N-oxide (diNO) and the gelation studies revealed selective gelation of diNO in water, but the two mono-N-oxides formed crystals. The mechanical strength and thermal stabilities of the gelators were evaluated by rheology and transition temperature (Tgel) experiments, respectively, and the analysis of the gel strength indicated that diNO formed weak gels compared to 4PINA. The SEM image of diNO xerogels showed fibrous microcrystalline networks compared to the efficient fibrous morphology in 4PINA. Single-crystal X-ray analysis of diNO gelator revealed that a hydrogen-bonded dimer interacts with adjacent dimers via C—H···O interactions. The non-gelator with similar dimers interacted via C—H···N interaction, which indicates the importance of specific non-bonding interactions in the formation of the gel network. The solvated forms of mono-N-oxides support the fact that these compounds prefer crystalline state rather than gelation due to the increased hydrophilic interactions. The reduced gelation ability (minimum gel concentration (MGC)) and thermal strength of diNO may be attributed to the weak intermolecular C—H···O interaction compared to the strong and unidirectional N—H···N interactions in 4PINA., We thank the University of Iceland Research Fund and the Science Institute for funding. D.G. thanks the University of Iceland for the Doctoral Research and Teaching Assistantship grant. We thankfully acknowledge Jonathan Steed, Durham University, Durham, UK for rheology experiments, Sigurjur Sveinn Jonsson, ISOR-Iceland for X-ray powder diffraction analysis, and Sigridur Jonsdottir, University of Iceland for NMR and mass spectroscopy. We thank Rannís Iceland for granting an infrastructure grant for a single-crystal X-ray diffractometer.

Publisher's version.(útgefin grein), Fabrication and sensor application of a simple plasmonic structure is described in this paper. The sensor element consists of nano-patterned gold film brought about from two-dimensional periodic photoresist templates created by holographic laser interference lithography. Reflectance spectroscopy revealed that the sensor exhibits significant refractive index sensitivity. A linear relationship between shifts in plasmonic resonances and changes in the refractive index were demonstrated. The sensor has a bulk sensitivity (SB) of 880 nm/refractive index unit and work under normal incidence conditions. This sensitivity exceeded that of many common types of plasmonic sensors with more intricate structures. A modeled spectral response was used to study the effect of its geometrical dimensions on plasmonic behavior. A qualitative agreement between the experimental spectra and modeled ones was obtained., This research was supported in part by the UT System Texas Nanoelectronics Research Superiority Award funded by the State of Texas Emerging Technology Fund. Additional support was provided by the Texas Instruments Distinguished University Chair in Nanoelectronics endowment., "Peer Reviewed"

An active field of research in magnetism today involves studies of solitons -- localised magnetic textures possessing particle-like properties. They are considered promising for various applications but are also intriguing from a fundamental point of view. Most of the effects related to magnetic solitons, including in particular skyrmions, can be described in classical spin-lattice models. In this context, effective tools for materials and device design are needed in order to calculate properties, such as thermal stability, lifetime, critical velocity, characteristic dynamical modes and much more. This thesis is devoted to the development of new methodology and the implementation and verification of a new software framework for the simulation of atomistic spin systems. Going beyond the widely known approaches of Monte Carlo and Landau-Lifshitz-Gilbert (LLG) dynamics, this thesis describes the recently developed geodesic nudged elastic band (GNEB) method and harmonic transition state theory in a consistent mathematical framework. The minimum mode following (MMF) method, which can be used to seek out first order saddle points in the energy landscape, is formulated for magnetic systems. Such saddle point searches are an essential part in identifying possible transition processes between magnetic configurations and therefore in estimating the rates of transitions between magnetic states, which determine the states' lifetimes. Using the MMF method, a mitosis-like skyrmion duplication -- or inversely a merger -- transition was found and could be reproduced in LLG dynamics simulations using an external magnetic field pulse. The entire set of methods discussed in this thesis has been implemented into a novel, open source software framework. Using scripting and graphical user interfaces, including powerful real-time visualisation features, the methods can now be used easily in conjunction with and complementary to one another. The implementation, including high performance parallelisation schemes, is described and a key set of its features are demonstrated. The software framework is applied to a variety of challenging problems in two- and three-dimensional systems. In two dimensions, complex higher-order skyrmionic textures are studied using the GNEB method and mitosis-like transitions identified. Three-dimensional systems are shown to host a large variety of complex spin textures, including a novel three-dimensionally localised state -- the magnetic globule. This state is composed of two coupled quasi-monopoles, also known as Bloch points, and may form stable spin textures in a wide range of parameters and in various situations. The software framework presented here brings simulations of atomic scale magnetic systems to a higher level and represents a significant step in the modernisation of computational tools in magnetism. It brings benefits in productivity and ease of use and improves accessibility of recent and novel methodology., Ein zur Zeit aktives Forschungsfeld im Bereich des Magnetismus bezieht sich auf sogenannte Solitonen -- lokalisierte magnetische Texturen mit teilchenartigen Eigenschaften. Sie werden für diverse Anwendungen als vielversprechend angesehen, sind aber auch von einem fundamentalen Blickwinkel aus interessant. Die meisten Effekte im Zusammenhang mit magnetischen Solitonen, insbesondere Skyrmionen, können im Rahmen klassischer Spin-Gitter Modelle beschrieben werden. In diesem Kontext werden effektive Werkzeuge für das Entwerfen von Materialien und Anordnungen benötigt, um Eigenschaften wie thermische Stabilität, Lebenszeit, kritische Geschwindigeit, charakteristische dynamische Eigenmoden und viel mehr zu berechnen. Diese Arbeit widmet sich der Entwicklung neuer Methodik und dem Implementieren und Verifizieren einer neuen Software für die Simulation atomistischer Spin-Systeme. Über die weithin bekannten Ansätze der Monte Carlo-Methode und Landau-Lifshitz-Gilbert (LLG) Dynamik hinaus werden die kürzlich entwickelte "geodesic nudged elastic band" (GNEB) Methode und die "harmonic transition state theory" in einem konsistenten mathematischen Rahmen beschrieben. Die "minimum mode following" (MMF) Methode, welche verwendet werden kann, um Sattelpunkte in der Energielandschaft ausfindig zu machen, wird für magnetische Systeme formuliert. Solche Sattelpunktsuchen spielen eine wichtige Rolle in der Identifikation möglicher Über\-gangs\-prozesse zwischen magnetischen Konfigurationen und somit in der Bestimmung der Übergangsraten, welche die Lebenszeiten magnetischer Zustände bestimmen. Mit der MMF-Methode wurde eine mitoseartige Skyrmionverdoppelung -- invers betrachtet eine Kollision -- gefunden und in LLG Dynamik-Simulationen mit Hilfe eines magnetischen Feld-Pulses reproduziert. Die gesamte Menge der Methoden, welche in dieser Arbeit diskutiert werden, wurde in einer neuen, frei verfügbaren Software implementiert. Mithilfe von Skripten und grafischen User-Interfaces, einschließlich Echtzeitvisualisierung, können die Methoden nun leicht zusammen und komplementär zu einander verwendet werden. Die Implementierung wird einschließlich hochperformanter Parallelisierungen beschrieben und die wichtigsten Merkmale werden demonstriert. Die Software wird auf eine Vielzahl herausfordernder Probleme in zwei- und dreidimensionalen Systemen angewandt. In zwei Dimensionen werden komplexe skyrmionische Texturen höherer Ordnung unter Verwendung der GNEB-Methode studiert und weitere mitoseartige Übergänge identifiziert. Es wird gezeigt, dass dreidimensionale Systeme eine große Vielzahl komplexer Spin-Texturen ermöglichen, einschließlich eines neu entdecken dreidimensional lokalisierten Zustandes -- dem "magnetic globule". Dieser Zustand besteht aus zwei aneinander gekoppelten Quasimonopolen, auch Bloch-Punkte genannt, und kann in einem großen Parameterbereich und in diversen Situationen stabile Spin-Texturen formen. Die hier vorgestellte Software bringt Simulationen von magnetischen Systemen auf der atomistischen Skala auf ein höheres Niveau und stellt einen nennenswerten Schritt in der Modernisierung der numerischen Werkzeuge im Magnetismus dar. Sie bringt Vorteile in Produktivität und einfacher Benutzung und verbessert die Zu\-gänglich\-keit kürzlich entwickelter, sowie neuer Methodik., Staðbundin segulástönd, svokallaðir einfarar, hafa agnaeiginleika og eru mikið rannsökuð í dag. Vonir standa til að hægt verði að nota þau á ýmsan hátt í framtíðar tækni en grundvallar eiginleikar þeirra eru einnig mjög áhugaverðir. Að mestu leiti er hægt að lýsa slíkum ástöndum með klassískum spuna-grindar líkönum. Mikilvægt er að hafa skilvirkar aðferðir til að reikna út hina ýmsu eiginleika svo sem varmafræðilegan stöðugleika, líftíma, krítískan hraða, eiginhætti o.sv.frv. Þessi ritgerð fjallar um þróun aðferðafræði, innsetningu og beitingu nýs hugbúnaðar fyrir tölvureikninga á spunakerfum á atómskala. Til að komast umfram það sem hægt er að gera með algengum aðferðum svo sem Monte Carlo og Landau-Lifshitz-Gilbert (LLG) tímaferlum, byggir ritgerðin á heilsteyptri framsetningu á 'geodesic nudged elastic band' (GNEB) aðferðinni og kjörsveifilsnálgun á virkjunarástandskenningunni (HTST). 'Minimum mode following' (MMF) aðferðin til að finna fyrsta stigs söðulpunkta er útvíkkuð fyrir segulkerfi. Slíkar söðulpunktaleitir eru mikilvægar til að finna mögulega hvarfganga fyrir breytingar úr einu segulástandi í annað sem er nauðsynlegur undanfari þess að meta hvarfhraða og þar með líftíma segulástanda. Með MMF aðferðinni var fundinn hvarfgangur þar sem skyrmeind skiptist upp í tvær skyrmeindir, eða öfugt -- að tvær skyrmeindir renna saman í eina -- og sýnt fram á að hægt væri að kalla fram slíkan hvarfgang í LLG reikningum á tímaframvindu þegar beitt er segulsviðspúlsi. Hinar ýmsu aðferðir sem fjallað er um í ritgerðinni hafa verið innleiddar í nýjum hugbúnaðarpakka. Með skriftum og sjónrænu viðmóti sem og öflugri rauntíma myndgerfingu er auðvelt að bbeita hinum ýmsu aðferðum og nýta kosti hverrar um sig. Innsetningu aðferðanna er lýst sem og lykil eiginleikum hugbúnaðarins. Hugbúnaðinum er beitt á ýmis krefjandi verkefni sem tengjast tví- og þrívíðum kerfum. Í tvívíðum kerfum eru skyrmeindir rannsakaðar með GNEB aðferðinni og hún notuð til að greina skiptingu skyrmeindar. Fyrir þrívíð kerfi er sýnt fram á að ýmis flókin segulkerfi geta myndast, þar með nýtt þrívítt segulkerfi sem nefnt hhefur verið 'globule'. Þetta ástand felur í sér tvö tengd einskaut, þ.e. Bloch punkta, og það getur verið stöðugt fyrir mörg stikugildi og við ýmsar aðstæður. Hubúnaðurinn gerir atómskala reikninga á segulkerfum auðvelda og felur í sér stórt skref til að nútímavæða þau tól sem hægt er að nota í tölvureikningum á segulkerfum. Hann sameinar kosti þess að vera auðveldur í notkun og eykur aðgengi að nýrri- og endurbættri aðferðafræði.

The research focused on multiphoton dynamics and fragment formation for HBr, DCl, and bromomethanes, using mass resolved multiphoton ionization (MR-MPI) and velocity map imaging (VMI) techniques. Data interpretations were based on analysis of (2+n)REMPI spectra, kinetic energy release spectra (KERs) and angular distributions of ions formed. Experiments for HBr revealed perturbations due to interactions between triplet and singlet states, seen as line-shifts (LS) and line-intensity (LI) alterations in MR-REMPI spectra, and intensity anomalies in VMI data. DCl studies revealed five new Rydberg states, and eight new vibrational states of the ion-pair state, as well as strong perturbation effects between singlet sigma Rydberg and singlet sigma ion-pair state, seen as LS and LI effects, and chlorine isotope shifts. Comparison with analogous data for HCl was performed. Highly perturbed spectral region of four Rydberg states in CH and CD, caused by interaction with a repulsive state, was inspected via multiphoton photodissociation of bromoform in MR-REMPI. In addition to LS and LI effects, linewidth (LW) broadenings, were evident. Four band origins were assigned. A number of Rydberg states of CH3Br in two-photon excitation region of 66 000 – 80 000 cm-1 were resonantly excited. The multiphoton dynamics was explored with both one- and two-colour excitation schemes. One-, two- and three- photon initial excitations were found to form ground state fragments CH3 and Br/Br*, whereas CH3 Rydberg states along with Br/Br* were found to be the major products following three-photon excitations prior to ionization. Interaction between Rydberg and ion-pair states is found to be evident., Rannsóknirnar fólust einkum í að kanna áhrif fjölljóseindaörvunar á rofferli HBr, DC l og brómometan sameinda með massagreiningu (MR-MPI aðferð) og myndgreiningu (VMI). Túlkun mæligagna fólst í greiningu á fjölljóseindarófum ((2+n)REMPI róf) sem og á hraða- (KERs) og hornháðum dreifimynstrum jóna sem myndast. Athuganir á HBr sýndu truflanir vegna víxlverkana á milli þrístigs- og einstigs-orkuástanda sameindarinnar, sem birtust í formi hliðrunar (LS áhrif) og styrkbreytinga (LI áhrif) litrófslína í MR-REMPI litrófum sem og í formi óreglulegra mynstra í VMI myndum. Samkvæmt DCl mæligögnum fundust fimm ný Rydberg orkuástönd og átta ný titringsástönd jón-para forms sameindarinnar. Sterk víxlverkunaráhrif greindust milli einstigs Rydberg ástanda og jón-para ástandsins sem birtist í formi LS og LI áhrifa og sem samsætuhliðranir. Framkvæmdur var samanburður við sambærileg gögn frá HCl. Óreglulegt mynstur REMPI litrófa fyrir sameindabrotin CH og CD sem mynduðust við fjölljóseindarof bromoforms báru vitni um hraðvirka rofnun fjögurra Rydberg ástanda. LS og LI áhrif sem og breikkun litrófslína báru þessu vitni. Orka viðkomandi ástanda var auðkennd. Fjölmörg Rydberg ástönd CH3Br sameindarinnar voru orkuörvuð á tveggja ljóseinda bylgjutölusviðinu 66 000 – 80 000 cm-1 . Rofferli voru könnuð með aðferðum eins- og tvílita fjölljóseindaörvana. Einnar-, tveggja og þriggja ljóseinda örvanir sameindarinnar leiddu allar til myndunar sameindabrotanna CH3 og Br í grunn-rafeindaástöndum. Meginrofferli sameindarinnar var hins vegar myndun CH3 Rydberg ástanda ásamt bróm frumeindum í kjölfar þriggja ljóseinda örvunarinnar. Vísbendingar um víxlverkun milli Rydberg ástanda og jón-para ástanda fundust.

Electron paramagnetic resonance (EPR) spectroscopy is a well known technique that is routinely used to investigate the structure and dynamics of nucleic acids. EPR requires incorporation of paramagnetic centers at specific sites, called site-directed spin labeling (SDSL). Spin labeling of nucleic acids can be carried out by two approaches, either by forming a covalent bond between spin label and the nucleic acid or by noncovalent binding of the spin label to the nucleic acid. This PhD dissertation is focused on advancing noncovalent and site-directed spin labeling (NC-SDSL) of nucleic acids. Our approach is based on ligand-receptor interactions, where the spin label binds to an abasic site of nucleic acids through formation of Watson-Crick base pairing with an orphan base on the opposing strand and pi- stacking interaction. A series of purine-based spin labels were prepared. Both 1,1,3,3- tetramethylisoindolin-2-yloxyl and 2,2,6,6-tetramethylpiperidine-1-oxyl (TEMPO) were conjugated with either the C2- or C6-position of the purines, yielding nitroxide derivatives of guanine, adenine or 2,6-diaminopurine. The binding of these spin- labeled purines to abasic sites in duplex nucleic acids was evaluated by EPR spectroscopy. The isoindoline-derived spin labels showed full binding to abasic sites in RNA duplexes and emerged as superior binders when compared to TEMPO-derived spin labels. The guanine-derived Ǵ bound fully to both DNA and RNA duplexes at lower temperature when paired with cytosine (C). Ǵ bound much more efficiently to RNA than DNA and showed even extensive binding at 20 °C (Kd = 6.15 x 10-6 M). Adenine-derived spin label 28 was also bound fully at low temperature (-30 °C) to abasic sites in both DNA and RNA duplexes when paired with T and U, respectively, but showed only minor binding at 20 °C (< 5%). Thus, Ǵ and 28 allow noncovalent and site directed spin labeling of abasic sites in nucleic acids, using any of the pyrimidines as orphan bases on the opposing strand. The spin label that bound with the highest efficiency (Ǵ) was chosen to investigate further various aspects of noncovalent spin labeling. Ǵ was found to bind to abasic sites in DNA/RNA hybrids, either to the DNA- or the RNA-strand. Ǵ showed only a minor flanking sequence effect upon binding to abasic sites in RNA, with binding affinities within a factor of two of each other. For a given base on the 5’-end, the highest binding was observed when a U was on the 3’-side. When the abasic site was placed close to the duplex end, the affinity of the spin label was reduced, presumably due to the increased flexibility at base pairs in the vicinity of the duplex terminus. Abasic sites in the fourth position from the duplex end had the same affinity as abasic sites towards the middle of the duplex. A distance measurement between two spin labels was performed on a Ǵ- labeled 22-mer RNA duplex using pulsed electron-electron double resonance (PELDOR) spectroscopy in collaboration with Prof. Thomas Prisner (Goethe University, Germany). The PELDOR data showed a strong orientation dependence and a distance of 31.3 ± 3.5 Å, similar to the distance of ca. 29 Å, obtained by molecular modelling. The noncovalent binding of purine-derived spin labels to the DNA triplex containing one nucleotide gap as binding site in phosphate- as well as magnesium containing-buffer was also evaluated by EPR spectroscopy. The nitroxide connected to N6-position of purine (28-31) had less binding to triplex DNA (IV-VI), whereas Ǵ bound almost fully to the triplex DNA V and VI in magnesium containing buffer. This project was pursued in collaboration with Prof. Clemens Richert’s research group at University of Stuttgart, Germany who provided the triplex DNA motifs., Rafeindaspunalitrófsgreining (e. electron paramagnetic resonance (EPR) spectroscopy) er vel þekkt aðferð sem er reglubundið beitt í rannsóknum á byggingu og hreyfingu kjarnsýra. EPR mælingar grundvallast á því að koma meðseglandi kjarna fyrir á ákveðnum stað innan kjarnsýra, þ. e. staðbundnum spunamerkingum (e. site directed spin-labeling, SDSL). Spunamerkingaraðferðin sem hér er lýst byggist á víxlverkun milli tengils og viðtaka, þar sem spunamerkið binst við basalausa stöðu (basaeyðu) í tvíþátta kjarnsýrum, annars vegar með Watson-Crick basapörun við staka basann á mótstæða strendingnum og hins vegar með pí-stöflun við aðliggjandi basa. Safn púrín-tengdra spunamerkja var útbúið með bæði 1,1,3,3-tetrametýlísóindólín-2-ýloxýl og 2,2,6,6-tetrametýlpiperidín-N-oxýl (TEMPO) merkihópum, sem voru tengdir inn á C2- eða C6-stöðuna á púríni. Þannig fengust nítroxíð afleiður gúaníns, adeníns eða 2,6-díamínópúríns. Tengigeta þessara spunamerktu púrína við basaeyðu í tvíþátta kjarnsýrum var mæld með EPR mælingu. Afleiður ísóindólín spunamerkjanna tengdust fullkomlega við slíkar eyður í tvíþátta RNA og mun betur en TEMPO afleiðurnar. Gúanín afleiðan Ǵ tengdist að fullu við bæði tvíþátta DNA og RNA við lágt hitastig, þegar hún var pöruð við sýtósín (C). Ǵ tengdist betur við RNA en DNA og sýndi jafnvel mikla bindingu við 20 °C (Kd = 6,15∙10-6 M). Adenín-afleidda spunamerkið 5 sýndi einnig hámarks tengingu við lágt hitastig (-30 °C) við basaeyðuna á tvíþátta DNA og RNA á móti T annars vegar og U hins vegar. Spunamerkið Ǵ var síðan valið til að rannsaka nánar ýmsa þætti spunamerkingar án samgildra tengja. Í ljós kom að Ǵ tengdist basaeyðum í DNA/RNA blendingum, annaðhvort við DNA- eða RNA strendinginn. Basarnir við hliðina á basalausu stöðunni höfðu aðeins lítil áhrif á tengingu Ǵ við eyðuna í RNA. Þegar slík eyða var staðsett nálægt endandum á tvíþátta kjarnsýrunni, minnkaði sækni spunamerkisins, væntanlega vegna aukins hreyfanleika basapara sem staðsett eru í nánd við endann. Fjarlægðamæling milli tveggja spunamerkja var framkvæmd á Ǵ-merktu tvíþátta RNA með notkun PELDOR (e. pulsed electron-electron double resonance) í samvinnu við Prof. Thomas Prisner við Goethe Háskólann í Frankfurt, Þýskalandi. PELDOR mælingarnar voru háðar innbyrðis afstöðu (e. orientation dependence) spunamerkjanna og gáfu fjarlægðina 31,3 ± 3,5 Å, sem reyndist í góðu samræmi við fjarlægðina í líkönum (29 Å)., The university of Iceland research fund

Nanomagnetic systems and transitions between magnetic states are currently an active topic of research. Spintronics is, in particular, a new branch of science and technology where spin degrees of freedom and spin currents are used in an analogous way as electron current in electronic devices. The development of techniques for constructing magnetic systems with near atomic-scale precision opens the possibility of using quantum coherence in magnetic states for quantum computing devices. Quantum mechanical tunneling from one magnetic state to another is an important topic in that context. In this thesis, the tunneling between magnetic states is studied from the point of view of instanton theory. An instanton is an optimal tunneling path, corresponding to a solution to the equation of motion in imaginary time. A method for finding instantons in magnetic systems at finite temperature is presented. It is used to find the crossover temperature from over-the-barrier transition mechanism to tunneling. In some cases, the crossover is abrupt, a first order transition, while in other cases it is more gradual, a second order transition. The latter is referred to as thermally assisted tunneling. A test problem including a single spin with an easy axis and applied transverse magnetic field is studied where the crossover changes from first to second order as the strength of the applied magnetic field is increased. The instanton is used to estimate the crossover temperature as well as the activation energy for thermally activated tunneling as a function of temperature. A general expression is presented for the crossover temperature in second-order transitions where the only input is the second derivative of the energy of the system with respect to the orientation of the magnetic moments at the first order saddle point in the energy surface. The over-the-barrier transition rate and crossover temperature for tunneling are estimated for a monomer and dimer of a molecular magnet containing a Mn4 group and the results found to agree well with experimental data. An application to the annihilation of a magnetic skyrmion shows that a crossover temperature for tunneling can be obtained at over 1 K for a certain range of values for the parameters in the Hamiltonian., Segulástönd eru notuð til að skrá og geyma upplýsingar. Eftir því sem stærð seguleininganna er minnkuð til að auka geymslugetuna, verður mikilvægara að gæta að líftíma segulástandanna. Í ritgerðinni er greint frá kennilegum rannsóknum á þeim möguleika að umbreyting úr einu segulástandi í annað gerist með skammtafræðilegu smugi og almenn líking er leidd út til að meta við hvaða hitastig smug verður ráðandi hvarfgangur. Aðferð til að finna líklegustu smugferla, þ.e. svokallaðar snareindir, er þróuð og notuð til að meta virkjunarorku fyrir varmafræðilega eflt smug sem fall af hitastigi. Aðferðunum er beitt á ýmis segulkerfi, svo sem sameindasegla og skyrmeindir í þunnum segulhúðum.

Microscopic magnetic particles can be found in a wide range of systems, from asteroids in outer space and minerals in the Earth’s crust to living organisms on land and in the ocean. Often they determine critical functional properties of these systems and form the basis of modern technology such as high-density data storage devices. An essential task for fundamental magnetism and applications is to describe the behavior of such particles at a given temperature and in the presence of an applied magnetic field. In this thesis, a theoretical method is developed for estimating the lifetime of magnetic states of microscopic particles based on harmonic transition state theory. It represents an extension of Stoner-Wohlfarth theory by introducing the effect of temperature. An analytical expression for the lifetime is presented as a function of magnetic field strength and temperature for certain field directions. This theory is applied in the calculations of switching field distribution of sub-micron CoPt islands with out-of-plane anisotropy and in the estimation of nucleation volume for magnetization reversal in such islands. After considering magnetization reversal of a single island, collections of micromagnetic particles in elements of spin ice systems are analyzed. Micromagnetic, dipole-dipole and dumbbell numerical models for the description of the interaction between islands in spin ice magnetic elements are compared. The lifetime of magnetic states in one and two hexagonal rings of a kagome spin ice system is calculated and found to compare well with reported results of experimental measurements. The magnetization reversal processes in an element of the shakti lattice are quantitatively described using various paths on the energy surface with estimation of the energy variation along each path for a range in the value of the lattice constant., Örsmæðar segulagnir koma fyrir víða, allt frá loftsteinum í himinhvolfinu til steinda í jarðskorpunni, og í lifandi verum á láði og legi. Oft á tíðum gegna þær lykilhlutverki og eru t.a.m. grundvöllurinn fyrir nútíma tækni svo sem í háþéttni gagnageymslum. Mikilvægt er að skilja grundvallareiginleika slíkra agna og geta metið líftíma segulástandanna við tiltekið hitastig og ytra segulsvið. Í þessari ritgerð er þróuð aðferð til að meta líftíma segulástanda örsmæðar segulagna með því að nota virkjunarástandskenninguna innan kjörsveifilsnálgunarinnar. Þar með er Stoner-Wohlfarth aðferðin útvíkkuð til að taka áhrif hitastigs með í reikninginn. Einföld líking er leidd út fyrir líftímann sem fall af hitastigi og styrkleika segulsviðsins fyrir tilteknar stefnur sviðsins. Þessari aðferð var beitt í reikningum á vendisviðsdreifinu smárra CoPt eyja með þverstæðan stefnuás til að meta kjarnarúmmálið fyrir umseglun eyjanna. Eftir að umselgun stakra eyja hafði verið rannsökuð voru greindir eiginleikar eyjaklasa sem eru einingar í spunaís. Tvískautsog handlóðarnálganir til að lýsa víxlverkun milli eyja í spunaíseiningum voru bornar saman við míkrósegulreikninga. Líftími segulástanda í einum og tveimur sexhringjum kagome spunaíss var reiknaður og niðurstöðunum bar vel saman við birtar mæliniðurstöður. Umseglun í einingu af shakti spunaís var lýst ítarlega með ýmsum hvarfleiðum á orkuyfirborðinu og mati á orkunni eftir ferlunum fyrir ýmis gildi á grindarfastanum.

Understanding how edge misfit dislocations (MDs) form in a GeSi/Si(001) film has been a long standing issue. The challenge is to find a mechanism accounting for the presence of these dislocations at the interface since they are not mobile and cannot nucleate at the surface and glide towards the interface. Furthermore, experiments can hardly detect the nucleation and early stages of growth because of the short time scale involved. Here we present the first semi-quantitative atomistic calculation of the formation of edge dislocations in such films. We use a global optimization method and density functional theory calculations, combined with computations using potential energy functions to identify the best mechanisms. We show that those previously suggested are relevant only for a low film strain and we propose a new mechanism which accounts for the formation of edge dislocations at high film strain. In this one, a 60° MD nucleates as a “split” half-loop with two branches gliding on different planes. One branch belongs to the glide plane of a complementary 60° MD and therefore strongly favors the formation of the complementary MD which is immediately combined with the first MD to form an edge MD., This work has been supported in part by the Academy of Finland through its COMP CoE (T.A.-N., nos 251748 and 284621) and FiDiPro (E.M. and H.J., no. 263294) grants. We acknowledge computational resources provided by the Aalto Science-IT project and CSC IT Center for Science Ltd in Espoo, Finland. E.M. wishes to thank Oleg Trushin, David Rodney and Emmanuel Clouet for helpful discussions.

In single electron collisions with the heteronuclear metal carbonyl compound HFeCo3(CO)12 we observe the formation of long-lived negative ion states up to about 20 eV, 11 eV above its ionization energy. These transient negative ions (TNIs) relax through dissociation (dissociative electron attachment, DEA), losing up to all 12 CO ligands, demonstrating their resilience towards reemission of the captured electron – even at such very high energies. This is unique in DEA and we hypothesize that this phenomenon is rooted in the orbital structure enabling a scaffold of multi-particle, electronically excited resonances. We support this with calculated MO-diagrams revealing dense bands of energy levels near the HOMO–LUMO gap. HFeCo3(CO)12 is a promising focused electron beam induced deposition (FEBID) precursor and we argue that its unusual DEA behavior relates to its exceptional performance in FEBID. This may be general to a class of molecules with high potential for nano-fabrication by FEBID., This work was supported by the Icelandic Center of Research (RANNIS) Grant No. 13049305(1-3) and the University of Iceland Research Fund. RKTP acknowledges a doctoral grant from the University of Iceland Research Fund and nancial support from the COST Action CM1301; CELINA, for short term scientic missions (STSMs). R. B. acknowledges support from the Icelandic Research Fund, Grant No. 141218051.

We apply particle-in-cell simulations with Monte Carlo collisions to study the influence of the singlet metastable states on the ion energy distribution in single and dual frequency capacitively coupled oxygen discharges. For this purpose, the one-dimensional object-oriented particlein-cell Monte Carlo collision code oopd1 is used, in which the discharge model includes the following nine species: electrons, the neutrals O(3 P) and O ( Σ− 2 X g 3 ), the negative ions O−, the positive ions O+ and O+ 2 , and the metastables O(1 D), O2( ) a ∆g 1 and O2(b Σ+ g 1 ). Earlier, we have explored the effects of adding the species O2(a ∆g 1 ) and O2(b Σ+ g 1 ), and an energy-dependent secondary electron emission yield for oxygen ions and neutrals, to the discharge model. We found that including the two molecular singlet metastable states decreases the ohmic heating and the effective electron temperature in the bulk region (the electronegative core). Here we explore how these metastable states influence dual frequency discharges consisting of a fundamental frequency and the lowest even harmonics. Including or excluding the detachment reactions of the metastables O2(a ∆g 1 ) and O2(b Σ+ g 1 ) can shift the peak electron temperature from the grounded to the powered electrode or vice versa, depending on the phase difference of the two applied frequencies. These metastable states can furthermore significantly influence the peak of the ion energy distribution for O+ 2 -ions bombarding the powered electrode, and hence the average ion energy upon bombardment of the electrode, and lower the ion flux., This work was partially supported by the Icelandic Research Fund Grant No. 163086 and the Swedish Government Agency for Innovation Systems (VINNOVA) Contract No. 2014-04876.

Many factors may contribute to loss of current efficiency (CE) in aluminum reduction and one of them is a presence of impurities. In this work, the effect of phosphorus on CE is studied in a laboratory cell at different current densities. Due to a growing trend toward higher amperage in retrofitted industrial cells, a study is performed both at a representative industrial current density (0.8 A/cm(2)) and at a high current density (1.5 A/cm(2)). More resolution was obtained at phosphorus levels comparable to typical industrial concentration in aluminum reduction cell (0-220 mg/kg). It is shown that the effect of phosphorus on the CE is more significant at high current density. Trend lines for the whole concentration range btw. 0 and 630 mg/kg showed a decrease of 1.1% in CE per 100 mg/kg for the high current density and 0.67% per 100 mg/kg at the low current density. The detrimental effect was more pronounced for relatively low phosphorus contents up to 220 mg/kg. A trend line for that smaller range revealed a reduction of 2.5% per 100 mg/kg of phosphorus at 1.5 A/cm(2), while at 0.8 A/cm(2) a reduction of 0.92% per 100 mg/kg of phosphorus was obtained. This indicates that increasing amperage in retrofitted cells may amplify the detrimental effect of impurities on the current efficiency., Funding for this work was provided by Alcoa Fjardaal and HRV Engineering. Assistance from Manolescu and Sintef staff is gratefully acknowledged., "Peer Reviewed"

Studying human metabolism is crucial for the understanding of diseases and improvement of therapy as metabolic alterations are central to a number of human diseases. A variety of experimental disciplines, such as biochemistry, biophysics and systems biology are involved in the elucidation of metabolic pathways. The work presented in this thesis is divided into three main studies, which expand the knowledge of human metabolism using systems biology and biochemical techniques. In the first study presented in this thesis, constraint-based modeling was used to investigate metabolic changes during epithelial to mesenchymal transition (EMT), which is a developmental process where epithelial cells dedifferentiate into mesenchymal-like cells. Dysregulation of EMT has been associated with cancer metastasis. Context-specific genome-scale metabolic models were derived from a generic human metabolic model using transcriptomic and extracellular metabolomics data from isogenic breast epithelial cell lines (D492 and D492M), which allowed in silico predictions of the metabolic changes during EMT. The models revealed differences in the central carbon metabolism along with different utilization of amino acids in the two cell lines. In silico gene essentiality analysis predicted that components of the SLC7A5 subunit of the large neutral amino acid transporter LAT1 was exclusively essential for mesenchymal cell survival. This study presented a platform for further studies on EMT. Further, the predicted metabolic targets can aid the development of novel cancer therapeutics. In the second study, the effects of a novel human metabolic enzyme, gluconokinase, was investigated. Despite the presence of gluconate in human bio-fluids and its widespread use in food and pharmaceutical industry, the details of gluconate metabolism in humans is relatively unexplored. Reactions specific for consumption of gluconate were added to a red blood cell metabolic model, in order to evaluate the impact of gluconate on human metabolism. It was found that adding gluconokinase to the model affects NADPH production in red blood cells, which in turn is closely associated with oxidative stress regulation and fatty acid metabolism in the cells. The computational simulations demonstrated that gluconokinase activity has significant effects on the overall metabolism of the cell and is worth investigating further. In the final study, kinetic parameters of human gluconokinase were determined using isothermal titration calorimetry (ITC) along with the mechanism of the reaction. The results establish that the reaction follows a ternary complex mechanism with ATP being the first binding substrate and gluconate displaying substrate inhibition. This study demonstrated that ITC could be used as a tool to determine mechanisms of enzyme catalyzed reactions along with kinetic parameters. The studies presented in this thesis emphasize that traditional biochemical assays and advanced systems biology methods are complementary tools, which allow a more complete understanding of human metabolism., Rannsóknir á efnaskiptum eru nauðsynlegar til að skilja undirliggjandi forsendur sjúkdóma og til að efla lyfjameðferðir þar sem breytingar í efnaskiptaferlum eru miðlægar í mörgum sjúkdómum. Margar aðferðafræðilegar nálganir á borð við lífefnafræði, lífeðlisfræði og kerfislíffræði eru notaðar til greininga efnaskiptaferlum. Þessari ritgerð er skipt í þrjá hluta sem fjalla á ólíkan hátt um efnaskipti í mannafrumum með kerfislíffræðilegum- og lífefnafræðilegum aðferðum. Fyrsta rannsóknin fjallar um notkun skorðaðra efnaskiptalíkana til rannsókna á breyttum efnaskiptaferlum við bandvefsumbreytingu (epithelial to mesenchymal transition - EMT). EMT er vel þekkt ferli í fósturþroskun þar sem þekjuvefs frumur umbreytast í bandvefslíkar frumur. Brenglun á EMT ferlinu hefur verið tengt myndun meinvarpa í brjóstakrabbameinum. Sérhæfð efnaskiptalíkön byggð á gögnum um genatjáningu og mælingar á upptöku og seytingu næringarefna frá brjóstaþekjufrumulínunni D492 og bandvefslíkri dóttufrumulínu hennar D492M. Með notkun þessara efnaskiptalíkana er mögulegt að spá fyrir um breytingar í innanfrumu efnaskiptaferlum sem verða við bandvefsumbreytingu. Líkönin benda til þess að munur sé í miðlægum kolefnis efnaskiptum ásamt breytilegri nýtingu amínósýra milli frumulínanna tveggja. Greiningu á lífsnauðsynlegum genum fyrir hvora frumulínu „in Silico“ bendir til þess að SLC7A5 undireiningin í LAT1 amínósýruferjunni sé nauðsynlegur fyrir lifun bandvefslíkra frumna en ekki nauðsynlegur fyrir þekjuvefsfrumur. Aðferðafræðin sem notast var við í þessari rannsókn getur nýst við frekari rannsóknir á bandvefsumbreytingu. Gögnin sem kynnt eru í þessari rannsókn má nýta til að spáð fyrir um ný möguleg lyfjamörk til krabbameins meðferða. Í annari rannsókninni er fjallað um nýlega skilgreint efnaskiptaensím í mönnum, glúkonókínasa. Þrátt fyrir tilvist glúkonats í líkamsvessum og útbreidd a notkun þess í matar- og lyfjaiðnaði, hafa efnaskipti glúkonats í mönnum verið lítt rannsökuð. Efnahvörf sem miða að niðurbroti glúkonats var bætt við efnaskiptalíkan rauðra blóðkorna til þess að meta vægi glúkonats í efnaskiptum manna. Með því að bæta við efnaskiptaferlum fyrir niðurbrot glúkonats komu fram breytingar á NADPH framleiðslu, sem er tengt við stýringu oxunarálags og fitusýruefnaskiptum þeirra. Tölvulíkönin sýna fram á að glúkonókínasa virkni hefur marktæk áhrif á efnaskiptaferla og er vert frekari rannsókna. Seinasta rannsóknin snýst um að mæla parametra hreyfiorkunnar fyrir glúkónokínasa með skammtastilltri jafnhita-varmamælingu (ITC) ásamt greiningu hvarfgangs. Niðurstöðurnar sýna að hvarfgangurinn myndar þríundarklósamband við ATP sem fyrsta hvarfefni og að glúkonat sýnir hvarfefnahindrun. Þessi rannsókn sýnir að skammtastillt jafnhitavarmamæling getur verið gagnlegt til að ákvarða hvarfgang ensím-hvataðra hvarfa ásamt því að skilgerina parametra hreyfiorkunnar. Rannsókninar sem notaðar eru í þessari ritgerð renna stoðum undir að hefðbundin lífefnafræði og kerfislíffræði eru samfallandi aðferðir sem leyfa dýpri og öflugri skilning á efnaskiptaferlum.