1,576 research outputs found

    Activating Methane and Other Small Molecules: Computational study of Zeolites and Actinides

    Get PDF
    Exploring the catalytic properties and reactivity of actinide complexes towards activation of small molecules is important as human activities have led to the increased distribution of these species in nature. Toward this end, it is important to have a computational protocol for studying these species, in this thesis we provide details on the performance of multiconfigurational pair-density functional theory (MC-PDFT) in actinide chemistry. MC-PDFT and Kohn-Sham Density Functional Theory (KS-DFT) perform well for these species with indications that the former can be used for species with even greater static electron correlation effect. In addition, we study the activity of organometallic trans-uranium complexes towards the electrocatalytic reduction of water. We conclude that, with a guided choice of ligand, neptunium complexes can provide similar reactivity when compared to organometallic uranium complexes.Conversion of methane to methanol has been a major focus of research interest over the years. This is largely due to the abundance of natural gas, of which methane is the major constituent. Copper-exchanged zeolites have been shown to be able to kinetically trap activated methane as strongly-bound methoxy groups, preventing over-oxidation to CO2, CO and HCOOH. In this stepwise process, there are three cycles; an initial activation step to form the copper oxo active site, methane C-H activation and lastly simultaneous desorption of methanol and re -activation of the active site.. We provide detailed description of the pathway for the formation of over oxidation products. It is observed that to ensure high selectivity to methanol and prevent further hydrogen atom abstraction by extra-framework species, the methyl group must be stabilized from the copper-oxo active sites. There is a temperature gradient between the steps in the methane-to-methanol conversion cycle which is an impediment to industrial adoption of this approach for methane-to-methanol conversion. To mitigate this, we have investigated the impact of heterometallic extra-framework motifs on the temperature gradients of each step. Using periodic DFT, we provide detailed descriptions of the mechanistic pathways for each of the three steps. We were subsequently able to design motif(s) with great methane C-H activities as well as the abilities to be formed and regenerated at nearly the same temperatures. We found [Cu-O-Ag] and [Cu-O-Pd] to be potential candidates for isothermal or near-isothermal operations of the methane-to-methanol conversion cycle. Finally, we provide insights to the changes in optical spectra of activated copper-exchanged zeolites, gaining an understanding of the evolution of these systems on a molecular level will provide opportunities to achieve improved reactivity

    Strategies for Red-Light Photoswitching

    Get PDF
    Vuorovaikutteiset, muotoutuvat ja jopa älykkäät molekyylirakenteet ovat avain uuden sukupolven lääkeaineisiin ja toiminnallisiin materiaaleihin. Valokytkimet eli yhdisteet, jotka isomeroituvat reversiibelisti valon vaikutuksesta johtaen makroskooppisten ominaisuuksien muutoksiin, ovat erottamaton osa tätä tulevaisuutta. Mahdolliset sovelluskohteet ulottuvat lääketieteestä elektroniikkaan ja robotiikkaan. Valitettavasti useimmat valokytkinrakenteet, esimerkiksi laajalti käytetyt atsobentseenit, absorboivat ultraviolettivaloa, joka on vahingollista monille materiaaleille ja erityisesti eläville soluille. Jotta valokytkinten koko potentiaali voidaan hyödyntää, tarvitaan harmittomalla näkyvällä valolla toimivia yhdisteitä. Puna- tai infrapunavalo olisi ihanteellinen ärsyke biologian alalla käytettäville kytkimille. Sama pätee myös molekyylimoottoreihin eli yhdisteisiin, jotka pyörivät valon vaikutuksesta yksisuuntaisesti. Lisäksi sekä kytkinten että moottorien tulisi isomerisoitua valon vaikutuksesta tehokkaasti ja nopeasti, termisten isomerisaatioreaktioiden tulisi olla sovelluskohteesta riippuen hitaita tai nopeita ja yhdisteiden tulisi toimia hyvin erilaisissa ympäristöissä. Näiden ominaisuuksien hallitsemiseksi on tärkeää ymmärtää niiden taustalla olevat mekanismit. Tässä väitöskirjassa tutkimme kolmea keinoa toteuttaa valokytkentä punaisella valolla: (i) atsobentseenien absorptiospektrin siirtäminen rakennetta muokkaamalla, (ii) uusien, valmiiksi punaista valoa absorboivien rakenteiden hyödyntäminen ja (iii) epäsuora valokytkentä punavalolla aktivoitavia katalyyttejä hyödyntäen. Tarkastelemme strategioita teoreettiselta kannalta ja osoitamme, että niistä jokainen mahdollistaa valokytkennän punaista valoa käyttäen. Kullakin strategialla on etunsa ja haasteensa tehokkaan, nopean ja kestävän valokytkennän toteuttamiseksi. Tästä johtuen yksi ihanteellinen valokytkinmalli ei voi saavuttaa kaikkia eri sovelluksille asetettuja tavoitteita, vaan tulevaisuuden haaste on löytää kuhunkin käyttöön paras ratkaisu. Samoja periaatteita voidaan soveltaa myös molekyylimoottoreihin, jolloin molekulaarisen tason yksisuuntainen kiertoliike voidaan saada aikaan näkyvällä valolla. Lisäksi punaisella valolla toimivien valokytkinten rakenteita hyödyntämällä moottorien rotaatiota saadaan tehostettua.Responsive, adaptive and even intelligent molecular systems have been identified as the key to next-generation pharmaceuticals and functional materials. Photoswitches, compounds that isomerise reversibly between two distinct ground-state species upon excitation with light and consequently give rise to a macroscopic effect, are an integral part of this future. Their potential application areas range from photopharmacology to optoelectronics and soft robotics. However, most conventional photoswitch structures such as azobenzenes absorb ultraviolet light, high-energy photons that are detrimental to many artificial materials and especially to living systems. To harness their full potential, photoswitches should function efficiently with visible light that is benign to the environment. Red or near-infrared light would be the ideal stimulus for switches utilised in biological context, as these wavelengths are least absorbed by living tissue. The same applies to light-driven molecular motors, compounds that exhibit unidirectional rotation upon photoexcitation. In addition to absorption in the red part of the visible spectrum, both switches and motors should exhibit efficient and fast photoisomerisation, favourable thermal isomerisation kinetics and tolerance towards different environments in order to be useful in real-life applications. In this light, it is crucial to understand the underlying fundamental mechanisms that govern these attributes. In this thesis, we explore three different approaches to realise photoswitching with red light: (i) synthetic modifications of azobenzenes, (ii) utilisation of new photoswitch cores that inherently absorb low-energy photons, and (iii) indirect isomerisation with red-light photocatalysts. We study each strategy from a theoretical viewpoint and demonstrate that they all provide means to induce isomerisation with red light, each with unique advantages and challenges in terms of promoting efficient, fast and robust switching. As a result, a single optimal photoswitch system cannot be designed; instead, the challenge lies in identifying the best design for each application. The same principles can also be applied to molecular motors, giving rise to visible-light-powered unidirectional rotary motion on a molecular level. We show that drawing inspiration from red-light-absorbing photoswitches has repercussions not only on the visible-light absorption but also on enhanced rotation dynamics

    DASH: Dynamic Attention-Based Substructure Hierarchy for Partial Charge Assignment

    Full text link
    We present a robust and computationally efficient approach for assigning partial charges of atoms in molecules. The method is based on a hierarchical tree constructed from attention values extracted from a graph neural network (GNN), which was trained to predict atomic partial charges from accurate quantum-mechanical (QM) calculations. The resulting dynamic attention-based substructure hierarchy (DASH) approach provides fast assignment of partial charges with the same accuracy as the GNN itself, is software-independent, and can easily be integrated in existing parametrization pipelines as shown for the Open force field (OpenFF). The implementation of the DASH workflow, the final DASH tree, and the training set are available as open source / open data from public repositories

    Exact two-component TDDFT with simple two-electron picture-change corrections: X-ray absorption spectra near L- and M-edges of four-component quality at two-component cost

    Get PDF
    X-ray absorption spectroscopy (XAS) has gained popularity in recent years as it probes matter with high spatial and elemental sensitivities. However, the theoretical modeling of XAS is a challenging task since XAS spectra feature a fine structure due to scalar (SC) and spin-orbit (SO) relativistic effects, in particular near L and M absorption edges. While full four-component (4c) calculations of XAS are nowadays feasible, there is still interest in developing approximate relativistic methods that enable XAS calculations at the two-component (2c) level while maintaining the accuracy of the parent 4c approach. In this article we present theoretical and numerical insights into two simple yet accurate 2c approaches based on an (extended) atomic mean-field exact two-component Hamiltonian framework, (e)amfX2C, for the calculation of XAS using linear eigenvalue and damped response time-dependent density functional theory (TDDFT). In contrast to the commonly used one-electron X2C (1eX2C) Hamiltonian, both amfX2C and eamfX2C account for the SC and SO two-electron and exchange-correlation picture-change (PC) effects that arise from the X2C transformation. As we demonstrate on L- and M-edge XAS spectra of transition metal and actinide compounds, the absence of PC corrections in the 1eX2C approximation results in a substantial overestimation of SO splittings, whereas (e)amfX2C Hamiltonians reproduce all essential spectral features such as shape, position, and SO splitting of the 4c references in excellent agreement, while offering significant computational savings. Therefore, the (e)amfX2C PC correction models presented here constitute reliable relativistic 2c quantum-chemical approaches for modeling XAS. © 2023 The Authors. Published by American Chemical Society.2/0135/21; NN4654K; Ministerstvo Školství, Mládeže a Tělovýchovy, MŠMT: RP/CPS/2022/007; Agentúra na Podporu Výskumu a Vývoja, APVV: APVV-19-0516, APVV-21-0497; Norges Forskningsråd: 262695, 314814, 315822; Horizon 2020: 945478, SASPRO

    Production and characterisation of dipolar Bose–Einstein condensates

    Get PDF
    Remarkable progress in the field of ultracold atoms has enabled the study of a great variety of topics in many-body quantum mechanics. The precise control of key parameters, such as interactions, temperature, density, internal and external degrees of freedom, dimensionality and the trapping geometry makes them a powerful and flexible experimental platform. The ability to create degenerate samples of atoms which feature long-range and anisotropic dipole–dipole interactions besides the more conventional short-range and isotropic contact interactions drew considerable attention, enabling the creation of quantum droplets and a supersolid phase. This thesis reports on experimental and theoretical progress in investigating dipolar many-body quantum systems. We present an overview of our experimental apparatus and the techniques used for obtaining a Bose–Einstein condensate (BEC) of erbium. We then discuss our experimental sequence for producing a quantum degenerate gas, creating a quasi-pure BEC with 2.2 x 10^5 atoms. To optimise the production of erbium BECs, we explore density- and temperature-dependent losses in 166Er and identify six previously unreported resonant loss features. Finally, to enable studies of density-dependent phenomena, we present a theoretical investigation of dipolar condensates in box-like traps, where we explore stability and how one can use it to replicate properties of an infinite, homogeneous system to study dipolar physics. We found that traps with hard walls trigger roton-like density oscillations even if the bulk of the system is far from the roton regime, so smoother potentials are better suited to recreate homogeneous conditions. This sets the ground for future experiments, where the atoms will be loaded into a box trap to enable studies of systems which are tightly trapped in one direction but homogeneous in the other two

    Precision mass measurements for the astrophysical rp-process and electron cooling of trapped ions

    Get PDF
    Precision mass measurements of rare isotopes with decay half-lives far below one second are of importance to a variety of applications including studies of nuclear structure and nuclear astrophysics as well as tests of fundamental symmetries. The first part of this thesis discusses mass measurements of neutron-deficient gallium isotopes in direct vicinity of the proton drip line. The reported measurements of 60-63Ga were performed with the MR-TOF-MS of TRIUMF's Ion Trap for Atomic and Nuclear Science (TITAN) in Vancouver, Canada. The measurements mark the first direct mass determination of 60Ga and yield a 61Ga mass value three times more precise than the literature value from AME2020. Our 60Ga mass value constrains the location of the proton dripline in the gallium isotope chain and extends the experimentally evaluated IMME for isospin triplets up to A=60. The improved precision of the 61Ga mass has important implications for the astrophysical rapid proton capture process (rp-process). Calculations in a single-zone model demonstrate that the improved mass data substantially reduces uncertainties in the predicted light curves of Type I X-ray bursts. TITAN has demonstrated that charge breeding provides a powerful means to increase the precision and resolving power of Penning trap mass measurements of radioactive ions. However, the charge breeding process deteriorates the ion beam quality, thus mitigating the benefits associated with Penning trap mass spectrometry of highly charged ions (HCI). As a potential remedy for the beam quality loss, a cooler Penning trap has been developed in order to investigate the prospects of electron cooling the HCI prior to the mass measurement. The second part of this thesis reports exploratory studies of electron cooling of singly charged ions in this cooler Penning trap. Comparison of measured ion energy evolutions to a cooling model provides a detailed understanding of the underlying cooling dynamics. Extrapolation of the model enables the deduction of tentative estimates of the expected cooling times for radioactive HCI

    Dynamics of the photo-induced desorption and oxidation of CO on Ru(0001) with different (O, CO) coverages

    Get PDF
    244 p.Carbon monoxide (CO) is a neurotoxic gas emitted for instance in combustion reaction. Therefore it hasbeen sought for air treatment solution, where CO oxidation is a straight forward choice. In ultra highvacuum conditions the ruthenium has been found to be very inactive for CO oxidation. Experimentally ithas been shown the opening of a new reaction path for CO oxidation on ruthenium surfaces by means offem to second laser irradiation. Accurate simulations of the photo-reaction dynamics are required to give aproper characterization of this kind of experiments. This thesis is dedicated to the study of the photo induced desorption and oxidation of CO molecules, coadsorbed with oxygen (O) adatoms on Ru(0001)with different surface coverages. We began with the characterization of three (O, CO) mixed surface coverages on Ru(0001). We first found the adsorption configuration of minimum energy for each surface coverage, then we computed the desorption potential of a CO molecule, and found the minimum energy path to CO oxidation on all three surface coverages. Then we ran ab-initio molecular dynamics with electronic friction simulations, and we have been able to show the complexity of the reaction path to oxidize the CO molecule, and explain its low probability of occurrence. Next, we showed the importance of surface deformations on the desorption and oxidation probabilities of CO, and on the adsorbat emotion. Then, we have shown in detail and characterized the different mechanisms of CO oxidation.Finally we created a potential energy surface based on neural networks and showed that it is a very promising tool to solve the problem of the computational cost of ab-initio molecular dynamics simulations

    Band structure renormalization at finite temperatures from first principles

    Get PDF
    In dieser Doktorarbeit untersuchen wir den Einfluss von Elektron-Phonon-Wechselwirkungen (EPW) auf die Bandlueckenrenormierung in kristallinen Festkoerpern bei endlichen Temperaturen. Das Hauptziel besteht darin, den Einfluss der Kernbewegung und der thermischen Ausdehnung des Gitters auf die Bandstruktur in einer Vielzahl von Materialien zu quantifizieren. Zu diesem Zweck wird der Temperatureinfluss auf das EPW in harmonischen Naeherungen unter Verwendung der stochastischen Abtastmethode und vollstaendig anharmonisch durch Durchführung von ab initio Molekulardynamiksimulationen (aiMD). Die Bandluecke bei endlichen Temperaturen wird aus der thermodynamisch gemittelten Spektralfunktion extrahiert, die unter Verwendung der Bandentfaltungstechnik berechnet wird. Waehrend die Verwendung von aiMD bereits fuer Berechnungen von EPW verwendet wurde, wurde die Kombination von aiMD und Bandentfaltung zur Behandlung der Bandluecken renormalisierung erst kuerzlich verwendet. In dieser Doktorarbeit haben wir eine verbesserte Bandentfaltungstechnik verwendet, um die Berechnung effektiv zu verwalten. Diese verbesserte Methode enthaelt mehrere methodische Neuerungen, die dazu dienen, den Rechenaufwand zu verringern und das statistische Rauschen in den Endergebnissen zu minimieren. Die aktualisierte Methode wurde gruendlich bewertet, dokumentiert und mit einer benutzerfreundlichen Oberflaeche gestaltet. Wir praesentieren eine umfassende Untersuchung der numerischen Aspekte der thermodynamischen Mittelung, der Schaetzung von Fehlerbalken und der Bewertung der Konvergenz in Bezug auf die Groesse der Simulationssuperzelle. Unser etabliertes Protokoll ermoeglicht die Berechnung der Bandlückenrenormierung bei endlichen Temperaturen, was in guter Uebereinstimmung mit frueheren theoretischen Studien und experimentellen Daten steht.In this thesis, we investigate the influence of electron-phonon interactions (EPI) on the band gap renormalization in crystalline solids at finite temperatures. The main goal is to identify the impact of the nuclear motion and the lattice thermal expansion on the band structure in a wide range of materials. For this purpose, the temperature influence on the EPI is calculated in the harmonic approximations by utilizing the stochastic sampling methodology and fully anharmonically, by performing ab initio molecular dynamics simulations (aiMD). The band gap at finite temperatures is extracted from the thermodynamically averaged spectral function, which is calculated using band-unfolding technique. While utilization of aiMD was already used for calculations of EPI the combination of aiMD and band-unfolding to treat the band gap renormalization was used only recently. In this thesis, we employed an improved band unfolding technique in order to effectively manage the calculations. This improved method incorporates several methodological innovations that serve to mitigate computational cost and minimize statistical noise in the final results. The updated method was thoroughly benchmarked, documented, and designed with a user-friendly interface. We present a comprehensive examination of the numerical aspects of thermodynamic averaging, the estimation of error bars, and the evaluation of convergence with respect to the size of the simulation supercell. Our established protocol enables the calculation of band gap renormalization at finite temperatures, which is in good agreement with prior theoretical studies and experimental data

    Studies of Molecular Precursors Used in FEBID Fabrication of Nanostructures

    Get PDF
    The adoption of nanotechnology is increasingly important in many aspects of our daily life influencing the clothes we wear and most of the electronic devices we use while also underpinning the development of drugs and medical techniques that we will need at some point in our lives. The methods by which nanoscale devices are fabricated is changing from a 'top down' etching based procedure to a 'bottom up' molecule by molecule deposition and assembly. The focus of the present research is the development, design, and analysis of new precursors for focused electron beam induced deposition (FEBID) and extreme ultraviolet nanolithography (EUVL) through a large pool of experimental and computational resources. The research is divided into two areas: gas - phase analysis of precursors (largely used for fragment and radicals' analysis, and molecular design) and surface and deposition science (physical deposition of precursors, simulation analysis of surface - molecule interactions and characterization of deposition processes to obtain optimal process parameters for molecular structures). It is necessary to collect data such as cross sections of electron - molecule interactions e.g., dissociative ionization (DI) and dissociative electron attachment (DEA) to provide accurate simulations that can be used to improve the FEBID and EUVL while understanding surface processes such as molecular absorption and diffusion to determine the structure and purity of the nanostructures formed by these methods. The objective of this thesis is to provide a gas - phase and deposition analysis of potential and widely used precursors for FEBID and EUVL at the nanoscale. To achieve this the experimental technique of velocity sliced map imaging (VsMI) was used in conjunction with theoretical tools such as density functional theory (DFT) simulations using Gaussian 16 software and evaluation of cross-section data for molecular dissociation at low electron energies of 0 - 20 eV using Quantemol-N. Results of the gas - phase analysis of negative ionic fragments formed by DEA and DI with their appearance, dissociation and ionization energies, angular distributions and kinetic energies, cross-sections for DEA fragmentation at low energy and excited states calculations at values up to 10 eV are presented. These results are used as the inputs to the models of the FEBID processes. The electronic, structural, and kinetic properties of several FEBID precursors are explored, and FEBID method used to create nanostructures using a Zeiss MeRiT SEM with GEMINI column operated at 20 kV. Analysis of the deposits was performed using EDX and atomic force microscopy (AFM) analysis as well as electron stimulated desorption (ESD) and temperature programmed desorption (TPD). Complementary simulations of the dynamics of processes at the surface were studied using MBN Explorer and surface - molecule interactions with great results in simulating the deposition process of islands and structures (results presented in Chapter 8)
    corecore