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1
GRECO, CLAUDIO. "A DFT and QM/MM Investigation on Models Related to the [FeFe]-Hydrogenase Active Site." Doctoral thesis, Università degli Studi di Milano-Bicocca, 2007. http://hdl.handle.net/10281/45775.
Full textAbstract:
In the present thesis, a theoretical investigation is described regarding hydroge-
nases - enzymes that are able to catalyze the reversible oxidation of molecular
hydrogen: H2
2H+ + 2e− . Such a very simple reaction could have fundamen-
tal importance for the possible future development of a hydrogen-based econ-
omy. However, the current approaches for molecular hydrogen oxidation imply
the use of very expensive platinum-containing catalysts, while H2 production at
industrial level still depends on hydrocarbons. In this framework, hydrogenases
represent a model for the development of new-generation catalysts, as they con-
tain only inexpensive transition metal cofactors (iron and/or nickel ions) and
are able to evolve hydrogen directly from acidic aqueous solutions supplied with
a convenient source of electrons.
The present work deals with the characterization of a specific class of hydro-
genases, termed [FeFe]-hydrogenases. These enzymes contain in their active site
a peculiar Fe6 S6 cluster - the so-called H-cluster - which can be ideally subdi-
vided in two distinct portions: a classical Fe4 S4 moiety, and a Fe2 S2 subcluster
(commonly termed [2Fe]H ) bearing CO and CN− ligands; these subclusters are
linked to each other through the sulphur atom of a cysteine residue. The two
iron atoms of the binuclear sub-site are termed proximal (Fep ) or distal (Fed ), de-
pending on their positions with respect to the Fe4 S4 moiety. Notably one of the
carbonyl groups included in the [2Fe]H subsite bridges the Fep and Fed centers,
and it moves to a semibridging position when the enzyme is in its completely
reduced form. The coordination environment of the iron ions included in the
binuclear cluster is completed by a bidentate ligand which has been proposed to
correspond either to a di(thiomethyl)amine (DTMA) or to a propanedithiolate
(PDT) residue.
Direct metal-hydrogen interaction at the binuclear sub-site is required for the
enzymatic activity of [FeFe]-hydrogenases; however, there is still some debate
about the way in which the interaction takes place, and about the catalytic
mechanism leading to H2 splitting/formation. In fact, despite the large number
of theoretical and experimental investigations carried out to clarify the catalytic
mechanism of [FeFe]-hydrogenases, a direct comparison between the two more
plausible routes for dihydrogen evolution/oxidation - i.e. a path involving the
formation of metal-bound terminal hydrides, as opposed to a route that implies
the presence of a hydride bridging Fep and Fed - was still lacking. Such study
has then been carried out in our laboratories, using computational models of
the H-cluster binuclear subsite in the context of a Density Functional Theory
(DFT) representation; this work is presented in Chapter 2. It turns out that H2 formation can take place according to reaction pathways that imply initial
protonation of the Fe(I)-Fe(I) form of [2Fe]H , leading to a formal Fe(II)-Fe(II)
hydride species, subsequent monoelectron reduction to an Fe(II)-Fe(I) species,
further protonation, and H2 release. A comparison of pathways involving either
the initial protonation of Fed or protonation of the Fep -Fed bond shows also
that the former pathway is characterized by smaller activation barriers, as well
as a downhill free-energy profile, suggesting that it could be the H2 production
pathway operative in the enzyme.
The next chapter in the present thesis is devoted to the characterization
of CO-mediated enzyme inhibition; indeed, the enzyme active site is able to
bind exogenous carbon monoxide, and such an interaction impairs the catalytic
process of H2 production/oxidation. Experimental and computational studies
have converged towards the assignment of a Fe(I)Fe(II) state to the CO-inhibited
binuclear sub-cluster, while there is still much debate about the disposition of
CO and CN− ligands around Fed in this form. Our analysis is carried out us-
ing a hybrid quantum mechanical/molecular mechanical (QM/MM) approach;
this means that an all-atom model of the enzyme is used for studying different
geometrical configurations of the active site. This allows us to show that the
protein environment surrounding the H-cluster plays a crucial role in influenc-
ing the mechanism of CO-inhibition; as a result, the CO-inhibited H-cluster is
expected to be characterized by a terminal CO ligand trans to the μ-CO group
on Fed .
A QM/MM approach is also used in order to unravel key issues regarding the
activation of the enzyme from its completely oxidized inactive state (Hox inact ,
an enzyme form in which the [2Fe]H subcluster attains the Fe(II)Fe(II) redox
state), and the influence of the protein environment on the structural and cat-
alytic properties of the H-cluster (see Chapter 4). Our results show that, in
Hox inact , a water molecule is bound to Fed . The computed QM/MM energy
values for water binding to the diferrous subsite are in fact over 17 kcal mol−1 ;
however, the affinity towards water decreases by one order of magnitude af-
ter a one-electron reduction of Hox inact , thus leading to release of coordinated
water from the H-cluster. The investigation of a catalytic cycle of the [FeFe]-
hydrogenase that implies formation of a terminal hydride ion and a DTMA
molecule acting as acid/base catalyst indicates that all steps have reasonable
reaction energies, and that the influence of the protein on the thermodynamic
profile of H2 production catalysis is not negligible; QM/MM results show that
the interactions between the Fe2 S2 subsite and the protein environment could
give place to structural rearrangements of the H-cluster functional for catalysis,
provided that the bidentate ligand that bridges the iron atoms in the binuclear subsite is actually a DTMA residue.
In the last two studies included in the present thesis (Chapter 5 and Chapter
6), DFT investigations are presented regarding the characterization of two syn-
thetic model complexes that represent structural and functional model of the
[2Fe]H cluster: Fe2 (S2 C3 H6 )(CO)6 and (S2 C3 H6 )[Fe2 (CO)5 P(NC4 H8 )3 ]. Both
of them are known to be able to catalyze proton reduction in an electrochemical
cell, but the details of the electrocatalytic mechanisms leading to H2 produc-
tion needed clarification. As for Fe2 (S2 C3 H6 )(CO)6 (a), it is showed that, in the
early stages of the catalytic cycle, a neutral μ-H adduct is formed; mono-electron
reduction and subsequent protonation can give rise to a diprotonated neutral
species (a-μH-SH), which is characterized by a μ-H group, a protonated sulfur
atom and a CO group bridging the two iron centers, in agreement with experi-
mental IR data indicating the formation of a long-lived μ-CO species. H2 release
from a-μH-SH and its less stable isomer a-H2 is kinetically unfavourable, while
the corresponding monoanionic compounds (a-μH-SH− and a-H2 − ) are more
reactive in terms of dihydrogen evolution, in agreement with experimental data.
As far as (S2 C3 H6 )[Fe2 (CO)5 P(NC4 H8 )3 ] (A) is concerned, experimental
results have suggested that the presence of the electron donor P(NC4 H8 )3 ligand
in A could favour the formation of a μ-CO species similar to that observed in the
enzymatic cluster. However, insight into the structural features of key catalytic
intermediates deriving from reduction and protonation of A was still lacking.
Thus, in Chapter 6 we present results obtained using Density Functional Theory
to evaluate structures, relative stabilities and spectroscopic properties of several
species relevant for the electrocatalytic H2 evolving process.
The results enable us to unravel the structure of the μ-CO complex ex-
perimentally detected after monoelectronic reduction of A. Moreover, we show
that the introduction of the large electron-donor ligand P(NC4 H8 )3 in the bio-
mimetic complex does not favour the stabilization of terminal-hydride adducts,
which are expected to be very reactive in terms of H2 production.
The comparison of our findings with previous theoretical and experimental
results obtained on similar model complexes suggests that the introduction of
an electron donor ligand as good as P(NC4 H8 )3 , but less sterically demanding,
could represent a better choice to facilitate the formation of μ-CO complexes
more closely resembling the structure of the enzymatic cluster.
2
Lockett, Lani Victoria. "Gas-Phase Photoelectron Spectroscopy and Computational Studies of [FeFe]-Hydrogenase Inspired-Catalysts for Hydrogen Production." Diss., The University of Arizona, 2009. http://hdl.handle.net/10150/193874.
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The work presented in this dissertation focuses on the [FeFe]-hydrogenase active site as inspiration for the design and synthesis of complexes capable of the electrocatalytic generation of molecular hydrogen from protons and electrons. The majority of work discussed uses gas-phase photoelectron spectroscopy (PES) and density functional theory (DFT) to probe and analyze the bonding and electron distribution in potential catalysts. These two techniques are also used to explore the nature of cyanide as a ligand, due to its presence and unknown role in these enzymes. This dissertation begins with the study of (η⁵-C₅H₅)Fe(CO)₂X (FpX) and (η⁵- C₅Me₅)Fe(CO)₂X (Fp*X) complexes where X = H⁻, Cl⁻, and CN⁻ to assess and compare their π-accepting abilities, which is contradicted in the literature. The shifts in ionization energies measured by PES provide a measure of the relative bonding effects. The results indicate cyanide is, overall, a weak π-acceptor, and the σ- and π-donor interactions are important to understanding the chemistry. The molecule [(μ-ortho-C₆H₄S₂)][Fe(CO)₃]₂ was examined, in part due to the delocalized π-orbitals of the C₆H₄S₂ ligand, which could facilitate the redox chemistry necessary for catalysis. Computations show that upon ionization, the complex adopts a semi-bridging carbonyl; termed “rotated structure”. The reorganization energy of this geometry change was determined, which may provide understanding of how the active site in the enzyme enables electron transfer to achieve this catalysis. Next complexes of the form (μ-SCH₂XCH₂S)[Fe(CO)₃]₂, where X=CH₂, O, NH, ᵗBuN, MeN, were explored in order to provide insight to the unknown atom at the central bridging position of the alkyl chain in the [FeFe]-hydrogenase enzyme. The likelihood of a rotated cationic structure is also shown, with reorganization energy values similar to that seen for [(μ-ortho-C₆H₄S₂)][Fe(CO)₃]₂. The final chapter explores the replacement of selenium for sulfur in (μ- X(CH₂)₃X)[Fe(CO)₃]₂ and (μ-X(CH₂)₂CH(CH₃)X)[Fe(CO)₃]₂, where X is either sulfur or selenium. The PES data show destabilization of the selenium complex ionizations compared to the sulfur complexes and a lower reorganization energy was calculated. The computed HOMO-LUMO gap energy for the selenium-based complex is roughly 0.17 eV smaller than for the sulfur analogs, which may indicate a lower reduction potential is needed.
3
Sakamoto, Takahiro. "Relationships between Gas-Phase Ionization Energies and Solution-Phase Oxidation Potentials: Applications to the Electrocatalytic Production of Hydrogen from Weak Acids." Diss., The University of Arizona, 2010. http://hdl.handle.net/10150/194534.
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The transfer of electrons to and from a molecule is one of the more fundamental and important chemical processes. One such important example is the reduction-oxidation (redox) cycles in catalysts and enzymes. In the hydrogenase enzymes, adding and removing electrons is one of the key processes for generating H₂ from water molecules. Finding a direct free energy relation between the vertical ionization energies (IE(V)) measured spectroscopically by gas-phase photoelectron spectroscopy and the oxidation potentials (E(1/2)) measured thermodynamically in solution by cyclic voltammetry (CV) for molecules is an important aspect for developing effective catalysts. In this study, a series of organometallic compounds such as metallocenes were used for investigating the free energy relationships and catalysts inspired by the active sites of [FeFe]-hydrogenases enzymes were evaluated for their ability to produce H₂ from electrocatalytic reduction of weak acids. The first part of the dissertation explores metallocenes of the form (η⁵-C₅H₅)₂M (M= Fe, Ru, Os, Co, Ni) as the model for developing the free energy relation between gas phase ionization energies (IE(V)) and solution oxidation potentials (E(1/2)). It was found that computing the electronic properties of Cp₂Fe, Cp₂Ru, and Cp₂Os using VWN-Stoll and OPBE density functional theory (DFT) functional was successful with root mean square deviation (RMSD) of 0.02 eV between the experimental and calculated ionization energies. However, calculated ionization energies of Cp₂Co and Cp₂Ni were less successful with RMSD of 0.3 eV between the experimental and calculated ionization energies. Introduction of the B3LYP or M06 hybrid DFT functionals yielded much improved results (0.1 eV) over the previous combinations of DFT functional for Cp2Co and Cp2Ni. The energy relation between the two experimental measurements was established and further computational studies revealed that the solvation energy was the largest energy contribution between IE(V) and E(1/2) in the five studied metallocenes. The RMSD of the calculated oxidation potentials, after adjusting for the error in gas-phase ionization energies, was 0.09 V. The second part of the dissertation explores a series of catalysts inspired by the active sites of [FeFe]-hydrogenase enzymes; μ-(2,3-pyrazinedithiolato)diironhexacarbonyl (PzDT-cat), Fe₂(μ-X₂C₅H₈O)(CO)₆ (where X = S, Se, Te), and Fe₂(μ-1,3-SC₃H₆X)(CO)₆ (where X = Se and Te) for their ability to produce H₂ from weak acids utilizing the computational techniques and knowledge gained from the metallocene study. Even though the overall electronic perturbation from μ-(1,2-benzenedithiolato)diironhexacarbonyl (BDT-cat) to μ-(2,3-pyridinedithiolato)diironhexacarbonyl (PyDT-cat) to PzDT-cat is found to be small, the reduction potential of PzDT-cat was found to be 0.15 V less negative than that of BDT-cat resulting in less energy required for initiating electrocatalytic H₂ production over the BDT-cat and PyDT-cat. Lower reorganization energy has been achieved by substitutions of larger chalcogens at the Fe₂S₂ core. However, the electrocatalytic production of H₂ from acetic acid in acetonitrile was found to be diminished upon going from analogous S to Se to Te species. This is ascribed to the increase in the Fe–Fe bond distance with a corresponding increase in the size of the chalcogen atoms from S to Se to Te, disfavoring the formation of a carbonyl-bridged structure in the anion which is thought to be critical to the mechanism of H₂ production.
4
Dogaru, Daniela. "Hydrogenase inhibition by O2 density functional theory/molecular mechanics investigation /." Cleveland, Ohio : Cleveland State University, 2008. http://rave.ohiolink.edu/etdc/view?acc_num=csu1231721611.
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Thesis (Ph.D.)--Cleveland State University, 2008.Abstract. Title from PDF t.p. (viewed on Apr. 13, 2009). Includes bibliographical references (p. 102-109). Available online via the OhioLINK ETD Center. Also available in print.
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Dogaru, Daniela. "Hydrogenase Inhibition by O2: Density Functional Theory/Molecular Mechanics Investigation." Cleveland State University / OhioLINK, 2008. http://rave.ohiolink.edu/etdc/view?acc_num=csu1231721611.
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6
Guo, Zhen, and 郭臻. "Density functional theory studies of selected hydrogen bond assisted chemical reactions." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2009. http://hub.hku.hk/bib/B42182335.
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Guo, Zhen. "Density functional theory studies of selected hydrogen bond assisted chemical reactions." Click to view the E-thesis via HKUTO, 2009. http://sunzi.lib.hku.hk/hkuto/record/B42182335.
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Chohan, Urslaan. "Modelling early stages of hydrogen embrittlement and surface oxidation of iron using density functional theory." Thesis, University of Manchester, 2018. https://www.research.manchester.ac.uk/portal/en/theses/modelling-early-stages-of-hydrogen-embrittlement-and-surface-oxidation-of-iron-using-density-functional-theory(52c00a91-b779-4c0a-9dc7-688916f7bf57).html.
Full textAbstract:
In this project, I have modelled the adsorption and diffusion of hydrogen and oxygen on and through the three low-index planes of two phases of iron, namely the body-centred cubic ferromagnetic alpha iron, alpha-Fe, and face-centered cubic gamma iron phase, gamma-Fe. This was done using spin-polarised Density Functional Theory, and the minimum energy path for the diffusion calculation was derived from potential energy surfaces created from a tight 3D mesh through the crystal. It was found that oxygen and hydrogen atoms strongly chemisorb on the (110) phase. Oxygen strongly chemisorbs on alpha-Fe(110) at the quasi-threefold site, with a surface stretch ~500 cm-1 for higher coverage. The structural changes at the highest coverage (>0.5 ML) indicated the incipient formation of FeO(111) from the O-Fe(110) overlay. Studying the electronic properties of the formation of FeO(111) yields an understanding of the earliest stage of oxide formation. Hydrogen was found to strongly chemisorb on the (110) surface of alpha-Fe. The hydrogen adsorbs at the quasi-threefold site with an adsorption energy of ~3 eV/H atom and surface stretches at ~1100 cm-1 for higher coverages. The (111) surface of gamma-Fe has been found to have the highest barrier for bulk-like diffusion. The bulk-diffusion barrier for hydrogen through gamma-Fe is ~0.7 eV for the (111) surface, which is ~0.2 eV higher than the (110) surface. The presence of magnetism in the (001) surface of gamma-Fe resulted in a lowering in the bulk-like diffusion barrier, with an ~0.2 eV barrier in the ferromagnetic surface as opposed to the ~0.6 eV in the non-magnetic surface. The high barrier for the (111) surface of gamma-Fe demonstrates that producing textured austenitic steel components with this surface exposed to the hydrogen source may work to lower the hydrogen damage in these samples. The strong effect of magnetism in lowering the barrier for diffusion demonstrates the importance of avoiding ferromagnetic austenitic steel alloys in environments where hydrogen is in abundance. These results may be applied in the process of development of Gen IV fission and fusion reactors. Ferritic and austenitic steels are ideal candidates for a number of components in these reactors, such as the first wall/breeding blanket. There is an abundance of presence of hydrogen in nuclear reactors. Hydrogen may enter the metallic matrix through diffusion processes, leading to the embrittlement of these components. Additionally, oxygen is readily present in the environment, which may oxidise components. In this project, I have modelled the adsorption and diffusion of hydrogen and oxygen on and through the three low-index planes of two phases of iron, namely the body-centred cubic ferromagnetic alpha iron, alpha-Fe, and face-centered cubic gamma iron phase, gamma-Fe. This was done using spin-polarised Density Functional Theory, and the minimum energy path for the diffusion calculation was derived from potential energy surfaces created from a tight 3D mesh through the crystal. It was found that oxygen and hydrogen atoms strongly chemisorb on the (110) phase. Oxygen strongly chemisorbs on alpha-Fe(110) at the quasi-threefold site, with a surface stretch ~500 cm-1 for higher coverage. The structural changes at the highest coverage (>0.5 ML) indicated the incipient formation of FeO(111) from the O-Fe(110) overlay. Studying the electronic properties of the formation of FeO(111) yields an understanding of the earliest stage of oxide formation. Hydrogen was found to strongly chemisorb on the (110) surface of alpha-Fe. The hydrogen adsorbs at the quasi-threefold site with an adsorption energy of ~3 eV/H atom and surface stretches at ~1100 cm-1 for higher coverages. The (111) surface of gamma-Fe has been found to have the highest barrier for bulk-like diffusion. The bulk-diffusion barrier for hydrogen through gamma-Fe is ~0.7 eV for the (111) surface, which is ~0.2 eV higher than the (110) surface. The presence of magnetism in the (001) surface of gamma-Fe resulted in a lowering in the bulk-like diffusion barrier, with an ~0.2 eV barrier in the ferromagnetic surface as opposed to the ~0.6 eV in the non-magnetic surface. The high barrier for the (111) surface of gamma-Fe demonstrates that producing textured austenitic steel components with this surface exposed to the hydrogen source may work to lower the hydrogen damage in these samples. The strong effect of magnetism in lowering the barrier for diffusion demonstrates the importance of avoiding ferromagnetic austenitic steel alloys in environments where hydrogen is in abundance. These results may be applied in the process of development of Gen IV fission and fusion reactors. Ferritic and austenitic steels are ideal candidates for a number of components in these reactors, such as the first wall/breeding blanket. There is an abundance of presence of hydrogen in nuclear reactors. Hydrogen may enter the metallic matrix through diffusion processes, leading to the embrittlement of these components. Additionally, oxygen is readily present in the environment, which may oxidise components.
9
Aurlien, Ragnhild. "A Density Functional Theory Study of Hydrogen Transfer and Rotational Barriers in Vitamin E-like Molecules." Thesis, Norges teknisk-naturvitenskapelige universitet, Institutt for fysikk, 2011. http://urn.kb.se/resolve?urn=urn:nbn:no:ntnu:diva-12798.
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A study of the antioxidant property of two vitamin E simplifications with density functional theory has been done. In one of the simplifications the phytyl tail and the methyl group on the heterocyclic ring in vitamin E is replaced by two hydrogen atoms, simplification A. In the other simplification the heterocyclic ring is replaced by two hydrogen atoms, simplification B. Three main investigations have been done; rotation of the hydroxyl group on the different isoforms of the two simplifications, hydrogen transfers from the alpha-isoform of the simplifications to three different radicals OOH, OOCH3, and OOC2H5, and a rotation of the hydroxyl group with a hydrogen bond to OOH and OOCH3 for simplification B. The BLYP exchange correlation functional is found to underestimate hydrogen transfer energy barriers, which is improved with the B3LYP functional. This problem did not occur for the rotation of the hydroxyl group. The energy barriers for the rotation of the hydroxyl group is found to be smallest for the alpha-isoform, and simplification A gives lower rotational barriers than simplification B. Simplification A also results in smaller energy barriers for hydrogen transfers. The hydrogen transfer to OOC2H5 with the B3LYP functional resulted in hydrogen barriers of 0,411 eV for simplification B and 0,231 eV for simplification A. Thus simplification B is found to be less reactive than simplification A, which is explained by the electron donating property of the heterocyclic ring not included in simplification B. Since simplification B is less reactive than simplification A, it is concluded to be a poorer antioxidant than simplification A, and a poor model for vitamin E.
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Edwards, Angela Celeste. "Probing the Hydrogen Bonding Interaction at the Gas-Surface Interface using Dispersion Corrected Density Functional Theory." Thesis, Virginia Tech, 2015. http://hdl.handle.net/10919/71784.
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he interactions of the chemical warfare agent sulfur mustard with amorphous silica were investigated using electronic structure calculations. In this thesis, the binding energies of sulfur mustard and mimic species used in the laboratory were calculated using density functional theory and fully ab initio calculations. The wB97XD and B97D functionals, which include functions to account for long-range dispersion interactions, were compared to experimental trends. The hydroxylated amorphous silica surface was approximated using a gas-phase silanol molecule and clusters containing a single hydroxyl moiety.
Recent temperature programmed desorption experiments performed in UHV concluded that sulfur mustard and its less toxic mimics undergo molecular adsorption to amorphous silica. Hydrogen bonding can occur between surface silanol groups and either the sulfur or chlorine atom of the adsorbates, and the calculations indicate that the binding energies for the two hydrogen bond acceptors are similar. The adsorption of sulfur mustard and its mimics on silica also exhibits the presence of significant van der Waals interactions between alkyl of the adsorbates and the surface. These interactions, in combination with the formation of a hydrogen bond between a surface silanol group and the Cl or S atoms of the adsorbates, provide remarkably large binding energies.Master of Science
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Kim, Duck Young. "Ab initio Lattice Dynamics : Hydrogen-dense and Other Materials." Doctoral thesis, Uppsala universitet, Institutionen för fysik och materialvetenskap, 2009. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-9535.
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This thesis presents a theoretical study of materials under high pressure using ab initio lattice dynamics based on density functional theory and density functional perturbation theory using both super-cell and linear response approach. Ab initio lattice dynamics using super-cell approach is applied to compare our theoretical predictions with experimental findings. Phonon dispersion curves of fcc α-γ cerium are calculated and compared with inelastic X-ray scattering data. Pressure dependency of phonon density of states in two cubic phases TiO2 allows us to assign the observed cubic phase in experiments to be of fluorite rather than pyrite structure. Dynamical stability of cotunnite TiO2 phase at low pressure can explain the observed quenching phenomena in experiments. Our calculated O2 vibron mode in both ε-ζ phases of solid oxygen supports the hypothesis that both phases are iso-structural. Hydrogen-dense materials attract great attention not only because they open a path to study phenomena related to metallization (superconductivity) of solid hydrogen but also because they are closely related to important industrial applications (hydrogen storage). Using linear response method, we find that metallic fcc-AlH3 is dynamically stabilized in the range of 72-106 GPa and can persist at ambient pressure if finite temperature effects are considered. For SiH4, we test dynamical stability, Raman spectra, zero point energy, and utilize GW calculations for self energy correction. We find that a metallic tetragonal phase of SiH4 can be assigned to the experimentally observed one. Our ab initio lattice dynamics calculations based on density functional perturbation theory predict that fcc-YH3 is a pressure-induced superconductor with a high transition temperature of 40 K at 17.7 GPa. With increasing pressure this material undergoes a superconductor-metal-superconductor transition and the underlying mechanism of this transition can simultaneously explains also the observed metal-insulator transition at 25 GPa in YH3-δ.
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Muscenti, Thomas Michael. "Density Functional Theory Study of Rutile SiO₂ Stishovite: An Electron Pair Description of Bulk and Surface Properties." Thesis, Virginia Tech, 2004. http://hdl.handle.net/10919/10179.
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The bulk structure and the nonpolar, stoichiometric (110) surface of stishovite, rutile structure type SiO₂, has been studied using a first principles, density functional method. The geometric and electronic structure, including the density of states, charge density, and electron localization function for both the bulk and the surface have been examined. The electron pair properties of both bulk and surface-layer atoms were found to be similar to molecular analogs. The analogs allowed for the description of surface electronic structure using simple molecular models. The adsorption of hydrogen fluoride was studied on the (110) surface. The geometry optimized and electronic structure have been found for various initial geometries. Relaxed structures of certain initial geometries give dissociated hydrogen fluoride upon geometry optimization.Master of Science
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Qian, Zhao. "Atomistic Modelling of Materials for Clean Energy Applications : hydrogen generation, hydrogen storage, and Li-ion battery." Doctoral thesis, KTH, Tillämpad materialfysik, 2013. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-129220.
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In this thesis, a number of clean-energy materials for hydrogen generation, hydrogen storage, and Li-ion battery energy storage applications have been investigated through state-of-the-art density functional theory. As an alternative fuel, hydrogen has been regarded as one of the promising clean energies with the advantage of abundance (generated through water splitting) and pollution-free emission if used in fuel cell systems. However, some key problems such as finding efficient ways to produce and store hydrogen have been hindering the realization of the hydrogen economy. Here from the scientific perspective, various materials including the nanostructures and the bulk hydrides have been examined in terms of their crystal and electronic structures, energetics, and different properties for hydrogen generation or hydrogen storage applications. In the study of chemisorbed graphene-based nanostructures, the N, O-N and N-N decorated ones are designed to work as promising electron mediators in Z-scheme photocatalytic hydrogen production. Graphene nanofibres (especially the helical type) are found to be good catalysts for hydrogen desorption from NaAlH4. The milestone nanomaterial, C60, is found to be able to significantly improve the hydrogen release from the (LiH+NH3) mixture. In addition, the energetics analysis of hydrazine borane and its derivative solid have revealed the underlying reasons for their excellent hydrogen storage properties. As the other technical trend of replacing fossil fuels in electrical vehicles, the Li-ion battery technology for energy storage depends greatly on the development of electrode materials. In this thesis, the pure NiTiH and its various metal-doped hydrides have been studied as Li-ion battery anode materials. The Li-doped NiTiH is found to be the best candidate and the Fe, Mn, or Cr-doped material follows.QC 20130925
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Hussain, Tanveer. "Computational Insights on Functional Materials for Clean Energy Storage : Modeling, Structure and Thermodynamics." Doctoral thesis, Uppsala universitet, Institutionen för fysik och astronomi, 2013. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-206938.
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The exponential increase in the demands of world’s energy and the devastating effects of current fossil fuels based sources has forced us to reduce our dependence on the current sources as well as finding cleaner, cheaper and renewable alternates. Being abundant, efficient and renewable, hydrogen can be opted as the best possible replacement of the diminishing and harmful fossil fuels. But the transformation towards the hydrogen-based economy is hindered by the unavailability of suitable storage medium for hydrogen. First principles calculations based on density functional theory has been employed in this thesis to investigate the structures modelling and thermodynamics of various efficient materials capable of storing hydrogen under chemisorption and physisorption mechanisms. Thanks to their high storage capacity, abundance and low cost, metal hydride (MgH2) has been considered as promising choice for hydrogen storage. However, the biggest drawback is their strong binding with the absorbed hydrogen under chemisorption, which make them inappropriate for operation at ambient conditions. Different strategies have been applied to improve the thermodynamics including doping with light and transitions metals in different phases of MgH2 in bulk form. Application of mechanical strain along with Al, Si and Ti doping on MgH2 (001) and (100) surfaces has also been found very useful in lowering the dehydrogenation energies that ultimately improve adsorption/desorption temperatures. Secondly, in this thesis, two-dimensional materials with high surface area have been studied for the adsorption of hydrogen in molecular form (H2) under physisorption. The main disadvantage of this kind of storage is that the adsorption of H2 with these nanostructures likes graphane, silicene, silicane, BN-sheets, BC3 sheets are low and demand operation at cryogenic conditions. To enhance the H2 binding and attain high storage capacity the above-mentioned nanostructures have been functionalized with light metals (alkali, alkaline) and polylithiated species (OLi2, CLi3, CLi4). The stabilities of the designed functional materials for H2 storage have been verified by means of molecular dynamics simulations.
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Kinaci, Alper. "First Principles Investigation Of Hydrogen Storage In Intermetallic Systems." Master's thesis, METU, 2007. http://etd.lib.metu.edu.tr/upload/3/12608548/index.pdf.
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The design and production of efficient metal-hydrides for hydrogen storage is a long standing subject. Over the years, many different types of intermetallic hydride systems were studied and some of them came out to be operable. However, none of them meet all the storage criteria perfectly. In this study, total energies, hydrogen storage capacity and stability of AB (A = Al, Be, Cu, Fe, Ni, Sb, V and B = Ti) type intermetallics were investigated with the goal of spotting a potential hydrogen storage material. The relation between thermodynamic properties and the atomic and the electronic structure of hydrides are also pointed out. For this task, first principles pseudopotential method within the generalized gradient approximation (GGA) to density functional theory (DFT) was used. Calculations correctly predict experimentally determined structures except for CuTiH. Moreover, the atomic and cell parameter were found within the allowable error interval for DFT. In CuTi intermetallic, a structure having considerably lower formation energy than experimentally found mono-hydride was determined. This contradiction may be due to metastability of the experimental phase and high activation energy for the hydrogen movement in the system. It was found that AlTi and SbTi are not suitable candidates for hydrogen storage since their hydrides are too unstable. For the other intermetallic systems, the stability of the hydrides decreases in the order of VTi, CuTi, NiTi, BeTi, FeTi. For VTi, FeTi and NiTi, a change in metallic coordination around hydrogen from octahedron to tetrahedron is predicted when tetra-hydride (MTiH4) is formed. Additionally, at this composition, FeTi and NiTi have hydride structures with positive but near-zero formation energy which may be produced with appropriate alteration in chemical makeup or storage parameters. VTi is a promising intermetallic by means of storage capacity in that even VTiH6 is found to have negative formation energy but the hydrides are too stable which can be a problem during hydrogen desorption.
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Samsonov, V. M., V. V. Zubkov, and I. V. Grinev. "Comparative Study of Hydrogen Adsorption in Slit-like Pores of Carbon Adsorbents and on Fullerene Molecules." Thesis, Sumy State University, 2013. http://essuir.sumdu.edu.ua/handle/123456789/35172.
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Adsorption of hydrogen in slit-like pores of carbon adsorbents and on fullerene molecules was
investigated using the classical density functional theory. Hydrogen adsorption in a gap between two
graphene walls was calculated at different temperatures and pressures. The obtained results agree with
the data found using the Dubinin theory of the volume pore filling and with the available molecular
dynamics results. It has been shown that conventional carbon adsorbents corresponding to the slit-like
model and fullerene materials should have approximately equal storage capacities. However, such a
capacity is sufficient for practical storage and use of hydrogen at low temperatures only (at about 20 K),
and at room temperatures some special active sites of adsorption should be used to solve the problem
under consideration.
When you are citing the document, use the following link http://essuir.sumdu.edu.ua/handle/123456789/35172
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Graça, Araújo Carlos Moysés. "Hydrogen Storage Materials : Design, Catalysis, Thermodynamics, Structure and Optics." Doctoral thesis, Uppsala universitet, Institutionen för fysik och materialvetenskap, 2008. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-8574.
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Hydrogen is abundant, uniformly distributed throughout the Earth's surface and its oxidation product (water) is environmentally benign. Owing to these features, it is considered as an ideal synthetic fuel for a new world energetic matrix (renewable, secure and environmentally friendly) that could allow a sustainable future development. However, for this prospect to become a reality, efficient ways to produce, transport and store hydrogen still need to be developed. In the present thesis, theoretical studies of a number of potential hydrogen storage materials have been performed using density functional theory. In NaAlH4 doped with 3d transition metals (TM), the hypothesis of the formation of Ti-Al intermetallic alloy as the main catalytic mechanism for the hydrogen sorption reaction is supported. The gateway hypothesis for the catalysis mechanism in TM-doped MgH2 is confirmed through the investigation of MgH2 nano-clusters. Thermodynamics of Li-Mg-N-H systems are analyzed with good agreement between theory and experiments. Besides chemical hydrides, the metal-organic frameworks (MOFs) have also been investigated. Li-decorated MOF-5 is demonstrated to possess enhanced hydrogen gas uptake properties with a theoretically predicted storage capacity of 2 wt% at 300 K and low pressure. The metal-hydrogen systems undergo many structural and electronic phase transitions induced by changes in pressure and/or temperature and/or H-concentration. It is important both from a fundamental and applied viewpoint to understand the underlying physics of these phenomena. Here, the pressure-induced structural phase transformations of NaBH4 and ErH3 were investigated. In the latter, an electronic transition is shown to accompany the structural modification. The electronic and optical properties of the low and high-pressure phases of crystalline MgH2 were calculated. The temperature-induced order-disorder transition in Li2NH is demonstrated to be triggered by Li sub-lattice melting. This result may contribute to a better understanding of the important solid-solid hydrogen storage reactions that involve this compound.
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Cavalleri, Matteo. "Local Structure of Hydrogen-Bonded Liquids." Doctoral thesis, Stockholm : Fysikum, Univ, 2004. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-286.
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Ståhle, Jonas. "Computational chemical investigation of factors affecting the reactivity of the hetero Diels-Alder reaction." Thesis, KTH, Skolan för kemivetenskap (CHE), 2012. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-94476.
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Recent research has shown that small hydrogen bonding catalysts can catalyze the hetero Diels-Alder reaction. In this thesis such hydrogen bonding catalysts in conjunction with varying functional groups and their effect on the hetero Diels-Alder reaction have been investigated. The influence of the different solvents has been investigated as well. The activation barriers for the different region- and stereo isomeric pathways have been compared in order to determine the stereo specificity of the reactions. These calculations have been done using the B3LYP functional for the geometry optimizations and then M06-2X for single point calculations. For the solvated cases the cPCM model and the M06-2X functional were used. It was shown that for the catalyzed systems bulkier groups in the endo position tend to have a lower activation barrier, allowing for control over the stereoselectivity. Electron withdrawing groups have an activating effect and are also synergistic with the hydrogen bonding catalysts. The solvent with the lowest dielectric constant gave the lowest activation barrier.
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Lousada, Patrício Cláudio Miguel. "Reactions of aqueous radiolysis products with oxide surfaces : An experimental and DFT study." Doctoral thesis, KTH, Tillämpad fysikalisk kemi, 2013. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-119780.
Full textAbstract:
The reactions between aqueous radiolysis products and oxide surfaces are important in nuclear technology in many ways. In solid-liquid systems, they affect (and at the same time are dependent on) both the solution chemistry and the stability of materials under the influence of ionizing radiation. The stability of surface oxides is a factor that determines the longevity of the materials where such oxides are formed. Additionally, the aqueous radiolysis products are responsible for corrosion and erosion of the materials. In this study, the reactions between radiolysis products of water – mainly H2O2 and HO radicals – with metal, lanthanide and actinide oxides are investigated. For this, experimental and computational chemistry methods are employed. For the experimental study of these systems it was necessary to implement new methodologies especially for the study of the reactive species – the HO radicals. Similarly, the computational study also required the development of models and benchmarking of methods. The experiments combined with the computational chemistry studies produced valuable kinetic, energetic and mechanistic data. It is demonstrated here that the HO radicals are a primary product of the decomposition of H2O2. For all the materials, the catalytic decomposition of H2O2 consists first of molecular adsorption onto the surfaces of the oxides. This step is followed by the cleavage of the O-O bond in H2O2 to form HO radicals. The HO radicals are able to react further with the hydroxylated surfaces of the oxides to form water and a surface bound HO• center. The dynamics of formation of HO• vary widely for the different materials studied. These differences are also observed in the activation energies and kinetics for decomposition of H2O2. It is found further that the removal of HO• from the system where H2O2 undergoes decomposition, by means of a scavenger, leads to the spontaneous formation of H2. The combined theoretical-experimental methodology led to mechanistic understanding of the reactivity of the oxide materials towards H2O2 and HO radicals. This reactivity can be expressed in terms of fundamental properties of the cations present in the oxides. Correlations were found between several properties of the metal cations present in the oxides and adsorption energies of H2O, adsorption energies of HO radicals and energy barriers for H2O2 decomposition. This knowledge can aid in improving materials and processes important for nuclear technological systems, catalysis, and energy storage, and also help to better understand geochemical processes.QC 20130322
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Oftadeh, M., M. Gholamian, and H. H. Abdallah. "Investigation of Interaction Hydrogen Sulfide with (5,0) and (5,5) Single-Wall Carbon Nanotubes by DFT Method." Thesis, Sumy State University, 2012. http://essuir.sumdu.edu.ua/handle/123456789/35161.
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In the present study the interaction of Hydrogen Sulfide with inside and outside single-wall carbon
nanotube of (5,0) and (5,5) was investigated. This study was conducted using DFT at B3LYP/6-31G* level
of theory. Computational calculations were performed in the gaseous phase in Gaussian 09. The geometry
of all molecules under investigation was determined by optimizing all geometrical variables without any
symmetry constraints. The harmonic frequencies were computed from analytical derivatives for all species
in order to define the minimum-energy structures. The adsorption energies, the thermodynamic properties,
HOMO-LUMO energy gaps and partial charges of the interacting atoms were also studied during two rotation
kinds of H2S molecules vertical and horizontal to the main axes of nanotube.
When you are citing the document, use the following link http://essuir.sumdu.edu.ua/handle/123456789/35161
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Ma, Zhu. "First-principles study of hydrogen storage materials." Diss., Atlanta, Ga. : Georgia Institute of Technology, 2008. http://hdl.handle.net/1853/22672.
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Thesis (Ph. D.)--Physics, Georgia Institute of Technology, 2008.Committee Chair: Mei-Yin Chou; Committee Member: Erbil, Ahmet; Committee Member: First, Phillip; Committee Member: Landman, Uzi; Committee Member: Wang, Xiao-Qian.
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Choudhury, Pabitra. "Theoretical and experimental study of solid state complex borohydride hydrogen storage materials." [Tampa, Fla] : University of South Florida, 2009. http://purl.fcla.edu/usf/dc/et/SFE0003164.
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Vastine, Benjamin Alan. "Understanding mechanisms for C-H bond activation." [College Station, Tex. : Texas A&M University, 2008. http://hdl.handle.net/1969.1/ETD-TAMU-2679.
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Kim, Ki Chul. "Thermodynamics of metal hydrides for hydrogen storage applications using first principles calculations." Diss., Georgia Institute of Technology, 2010. http://hdl.handle.net/1853/34688.
Full textAbstract:
Metal hydrides are promising candidates for H2 storage, but high stability and poor kinetics are the important challenges which have to be solved for vehicular applications. Most of recent experimental reports for improving thermodynamics of metal hydrides have been focused on lowering reaction enthalpies of a metal hydride by mixing other compounds. However, finding out metal hydride mixtures satisfying favorable thermodynamics among a large number of possible metal hydride mixtures is inefficient and thus a systematic approach is required for an efficient and rigorous solution. Our approaches introduced in this thesis allow a systematic screening of promising metal hydrides or their mixtures from all possible metal hydrides and their mixtures. Our approaches basically suggest two directions for improving metal hydride thermodynamics. First, our calculations for examining the relation between the particle size of simple metal hydrides and thermodynamics of their decomposition reactions provide that the relation would depend on the total surface energy difference between a metal and its hydride form. It ultimately suggests that we will be able to screen metal hydride nanoparticles having favorable thermodynamics from all possible metal hydrides by examining the total surface differences. Second, more importantly, we suggest that our thermodynamic calculations combined with the grand canonical linear programming method and updated database efficiently and rigorously screen potential promising bulk metal hydrides and their mixtures from a large collection of possible combinations. The screened promising metal hydrides and their mixtures can release H2 via single step or multi step. Our additional free energy calculations for a few selected promising single step reactions and their metastable paths show that we can identify the most stable free energy paths for any selected reactant mixtures. In this thesis, we also demonstrate that a total free energy minimization method can predict the possible evolution of impurity other than H2 for several specified mixtures. However, it is not ready to predict reaction thermodynamics from a large number of compounds.
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Janke, Svenja Maria. "Theoretical Description of Hydrogen Atom Scattering off Noble Metals." Doctoral thesis, Niedersächsische Staats- und Universitätsbibliothek Göttingen, 2016. http://hdl.handle.net/11858/00-1735-0000-0028-87A3-4.
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Srepusharawoot, Pornjuk. "Computational Studies of Hydrogen Storage Materials : Physisorbed and Chemisorbed Systems." Doctoral thesis, Uppsala universitet, Materialteori, 2010. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-132875.
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This thesis deals with first-principles calculations based on density functional theory to investigate hydrogen storage related properties in various high-surface area materials and the ground state crystal structures in alkaline earth dicarbide systems. High-surface area materials have been shown to be very promising for hydrogen storage applications owing to them containing numerous hydrogen adsorption sites and good kinetics for adsorption/desorption. However, one disadvantage of these materials is their very weak interaction with adsorbed hydrogen molecules. Hence, for any feasible applications, the hydrogen interaction energy of these materials must be enhanced. In metal organic frameworks, approaches for improving the hydrogen interaction energy are opening the metal oxide cluster and decorating hydrogen attracting metals, e.g. Li, at the adsorption sites of the host. In covalent organic framework-1, the effects of the H2-H2 interaction are also found to play a significant role for enhancing the hydrogen adsorption energy. Moreover, ab initio molecular dynamics simulations reveal that hydrogen molecules can be trapped in the host material due to the blockage from adjacent adsorbed hydrogen molecules. In light metal hydride systems, hydrogen ions play two different roles, namely they can behave as "promoter" and "inhibitor" of Li diffusion in lithium imide and lithium amide, respectively. By studying thermodynamics of Li+ and proton diffusions in the mixture between lithium amide and lithium hydride, it was found that Li+ and proton diffusions inside lithium amide are more favorable than those between lithium amide and lithium hydride. Finally, our results show that the ground state configuration of BeC2 and MgC2 consists of five-membered carbon rings connected through a carbon atom forming an infinitely repeated chain surrounded by Be/Mg ions, whereas the stable crystal structure of the CaC2, SrC2 and BaC2 is the chain type structure, commonly found in the alkaline earth dicarbide systems.Felaktigt tryckt som Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology 712
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Nyberg, Borrfors André. "Energy Decomposition Analysis of Neutral and Anionic Hydrogen Bonded Dimers Using a Point-Charge Approach." Thesis, KTH, Tillämpad fysikalisk kemi, 2020. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-288970.
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En stor samling dimolekylära vätebindningar med formen A – H … B, där AH är en alkyn, alkohol eller tiol och B = [Br–, Cl–, NH3, HCN] beräknas och utvärderas med Kohn-Sham täthetsfunktionalteori tillsammans med bassetet m062x/6-311+g(2df.2p). Dessa komplex utvärderas även med en punktladdningsmodell (som använder samma metod och basset), där atomerna i vätebindningsmottagaren B byts ut mot laddningar som passats för att återskapa laddningsfördelningen runt molekylen, med målet att separera och isolera de elektrostatiska och polariserande energikomponenterna från de totala interaktionsenergierna. Med hjälp av detta tillvägagångssätt visade det sig att vätebindningars komplexeringsenergi (i.e. interaktionsenergin med energikostnaden för att deformera atomkärnornas rymdgeometri borttagen), oberoende av karaktären hos monomeren AH eller B, till stor del består av elektrostatik och polarisation, medan laddningsutbyte, dispersion, och andra resttermer endast utgör en liten del av den totala interaktionen. Fördelningen mellan elektrostatik och polarisation varierar beroende på typen av monomerer i vätebindningen, men deras summa, den resulterande punktladdningsenergin, korrelerar linjärt (ΔECompl = 0.85ΔEPC ) med R2 = 0.995 över energiomfånget 0 < ΔECompl < 50 kcal mol–1. Detta blir ännu mer anmärkningsvärt då inkluderingen av komplexeringsenergierna från halogenbindningar i samma korrelation inte förändrar korrelationskoefficienten avsevärt, vilket indikerar att båda bindningstyperna består av samma energikomponenter även då bindningarna i sig är väldigt olika.A large set of dimeric hydrogen bonds of the type A – H … B, where AH is an alkyne, alcohol, or thiol and B = [Br–, Cl–, NH3, HCN] are computed and evaluated using Kohn-Sham density functional theory together with the m062x/6-311+g(2df.2p) basis set. These complexes are also evaluated using a point charge (PC) approach (using the same method and basis set), where the atoms of the hydrogen bond acceptor B are substituted for charges that are optimized to reproduce the charge distribution of the molecule, with the purpose of separating and isolating the electrostatics- and polarization energy components of the interaction energies. Using this approach it was discovered that the complexation energy of hydrogen bonds (i.e.the interaction energy with the energy cost of nuclear deformation corrected for), independent on the nature of either monomer AH or B, are largely made up of electrostatics and polarization, while charge transfer, dispersion, and other rest terms only make up a small fraction of the total interaction. The composition of electrostatics and polarization vary depending on the type of monomers in the hydrogen bond, but their sum, the PC interaction energy, correlates linearly (ΔECompl = 0.85ΔEPC ) with R2 = 0.995 over an energy span of 0 < ΔECompl < 50 kcal mol–1. This is made even more remarkable by the inclusion of halogen bonded complexation energies in the same correlation without changing the correlation coefficient significantly, indicating that the two bond types are comprised of the same components even though they are remarkably different in origin.
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Dziekan, Thomas. "Electronic Transport in Strained Materials." Doctoral thesis, Uppsala University, Department of Physics and Materials Science, 2008. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-8471.
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In this thesis the conductivity of strained materials has been investigated using density functional theory and a semiclassical transport theory based on the Boltzmann equation.
In transition metals trends are reproduced without adjustable parameters. The introduction of one temperature dependent cross section allowed the reproduction of resistivity trends between 10 and 1000K.
The effect of strain on transition metals in bcc and fcc structure was studied deforming the unit cell along the tetragonal deformation path. The anisotropy of the conductivity varied on wide range of the c/a-ratio. The orbitals at the Fermi level determined the principal behavior. Pairs of elements with permutated number of electrons and holes in the 4d band showed similar behavior. The concept of the tetragonal deformation was also applied on semiconductors.
The deformation of Vanadium in X/V superlattices (X=Cr,~Fe,~Mo) due to Hydrogen loading depends on the properties of X. It was found that counteracting effects due to the presence of Hydrogen influence the conductivity.
It is shown that a small magnetic moment of the V host reduces the hydrogen solubility. Depending on the magnitude of the tetragonal distortion of V, the hydrogen dissolution becomes favored for larger moments.
Finally, extra charge filling of the bandstructure of Cr and Mo decreases the Fermi velocity and increases the density of states at the Fermi energy.
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Larsson, Peter. "Computational Studies of Nanotube Growth, Nanoclusters and Cathode Materials for Batteries." Doctoral thesis, Uppsala universitet, Materialteori, 2009. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-108261.
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Density functional theory has been used to investigate cathode materials for rechargeable batteries, carbon nanotube interactions with catalyst particles and transition metal catalyzed hydrogen release in magnesium hydride nanoclusters. An effort has been made to the understand structural and electrochemical properties of lithium iron silicate (Li2FeSiO4) and its manganese-doped analogue. Starting from the X-ray measurements, the crystal structure of Li2FeSiO4 was refined, and several metastable phases of partially delithiated Li2FeSiO4 were identified. There are signs that manganese doping leads to structural instability and that lithium extraction beyond 50% capacity only occurs at impractically high potentials in the new material. The chemical interaction energies of single-walled carbon nanotubes and nanoclusters were calculated. It is found that the interaction needs to be strong enough to compete with the energy gained by detaching the nanotubes and forming closed ends with carbon caps. This represents a new criterion for determining catalyst metal suitability. The stability of isolated carbon nanotube fragments were also studied, and it is argued that chirality selection during growth is best achieved by exploiting the much wider energy span of open-ended carbon nanotube fragments. Magnesium hydride nanoclusters were doped with transition metals Ti, V, Fe, and Ni. The resulting changes in hydrogen desorption energies from the surface were calculated, and the associated changes in the cluster structures reveal that the transition metals not only lower the desorption energy of hydrogen, but also seem to work as proposed in the gateway hypothesis of transition metal catalysis.
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Rashid, Shaan. "Dual-spray Synthesis and Reactions." Thesis, Université d'Ottawa / University of Ottawa, 2017. http://hdl.handle.net/10393/35726.
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By using two electrospray emitters containing different solutions (“dual-spray”) we have recently conducted in-source hydrogen/deuterium exchange (HDX) reactions and synthesized organometallic species. For dual-spray HDX reactions, peptide and protein solutions were electrosprayed through one emitter and the deuterating agent D2O through the secondary electrospray emitter. Clear shifts in isotope distributions indicated hydrogen-deuterium exchange occurring within the ion source. By ion mobility, simultaneous deuterium exchange for two isobaric species, the oxytocin monomer and dimer, was observed. Lysozyme has a linear relation between the charge state and the average number of exchanges, indicating that lysozyme becomes increasingly unfolded as the charge state increases. Based on deuterium uptake data and the lack of a temperature dependence, the dual-spray HDX reaction is thought to occur mostly in the gas phase. Tris(2,2’-bipyridine)ruthenium(II) and similar complexes containing the 1,10-phenanthroline ligand were formed by spraying a ligand solution and the ruthenium trichloride solution through two independent ESI emitters. This was confirmed by comparing ion mobility drift time, mass spectra, and CID fragmentation with the reference standard compounds. Tris(2,2’-bipyridine)iron(II), tris(1,10-phenantroline)iron(II) and mixed ligand complexes of iron(II) formed by dual-spray showed two additional hydrogens bonded to the complex. By CID, these unique gas phase complexes showed similar initial ligand loss to the reference standards however the secondary ligand loss showed dissimilar dissociation channels and energetics. Using DFT calculations, geometry optimizations for the [Fe(phen)3 + 2H]2+ complex and its fragment ions were done. After the initial ligand loss, the additional hydrogens are believed to transfer to the central iron atom. The relative energy of the dissociation channels showed good agreement with experimental breakdown curves.
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Daramola, Oludamilola A. "Theoretical Characterization of Ammonia Oxidation Species on Platinum Clusters." Ohio University / OhioLINK, 2011. http://rave.ohiolink.edu/etdc/view?acc_num=ohiou1321547233.
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Yu, Fu-Chen. "Reactivation Mechanism Studies on Calcium-Based Sorbents and its Applications for Clean Fossil Energy Conversion Systems." The Ohio State University, 2011. http://rave.ohiolink.edu/etdc/view?acc_num=osu1298957301.
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Knight, Christopher J. "Hydrogen bond topology order/disorder transitions in ice and the behavior of defects in a disordered ice lattice /." Columbus, Ohio : Ohio State University, 2009. http://rave.ohiolink.edu/etdc/view?acc%5Fnum=osu1236788109.
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Blomqvist, Andreas. "Insights into Materials Properties from Ab Initio Theory : Diffusion, Adsorption, Catalysis & Structure." Doctoral thesis, Uppsala universitet, Materialteori, 2010. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-131331.
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In this thesis, density functional theory (DFT) calculations and DFT based ab initio molecular dynamics simulations have been employed in order to gain insights into materials properties like diffusion, adsorption, catalysis, and structure. In transition metals, absorbed hydrogen atoms self-trap due to localization of metal d-electrons. The self-trapping state is shown to highly influence hydrogen diffusion in the classical over-barrier jump temperature region. Li diffusion in Li-N-H systems is investigated. The diffusion in Li3N is shown to be controlled by the concentration of vacancies. Exchanging one Li for H (Li2NH), gives a system where the diffusion no longer is dependent on the concentrations of vacancies, but instead on N-H rotations. Furthermore, exchanging another Li for H (LiNH2), results in a blockade of Li diffusion. For high-surface area hydrogen storage materials, metal organic frameworks and covalent organic frameworks, the hydrogen adsorption is studied. In metal organic frameworks, a Li-decoration is also suggested as a way to increase the hydrogen adsorption energy. In NaAlH4 doped with transition metals (TM), the hypothesis of TM-Al intermetallic alloys as the main catalytic species is supported. The source of the catalytic effect of carbon nanostructures on hydrogen desorption from NaAlH4 is shown to be the high electronegativity of the carbon nanostructures. A space-group optimized ab initio random structure search method is used to find a new ground state structure for BeC2 and MgC2. The fast change between the amorphous and the crystalline phase of GeSbTe phase-change materials is suggested to be due to the close resemblance between the local amorphous structure and the crystalline structure. Finally, we show that more than 80% of the voltage in the lead acid battery is due to relativistic effects.Felaktigt tryckt som Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology 702
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Viana, Marco Antonio de Abreu. "Ligações de hidrogênio usuais e não usuais: um estudo comparativo das propriedades moleculares e topológicas da densidade eletrônica em HCCH --- HX e HCN --- HX com X = F, CI, CN e CCH." Universidade Federal da Paraíba, 2013. http://tede.biblioteca.ufpb.br:8080/handle/tede/7117.
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The aim of this work was to study two kinds of intermolecular hydrogen bonding, the non-usual that is represented by the interaction between acetylene and the HX species (C2H2 --- HX) and the usual that is represented by the interaction between hydrogen cyanide and HX species, with X = F, Cl, CN, and HCCH. This interaction promotes changes in the structural, electronic and vibrational properties of the species involved. In this work, we employe d not onlycomputational-quantum methods MP2/6-311 + + G (d, p) and DFT/B3LYP/6-311 + + G (d, p) in order to study the structural, electronic and vibrational properties of those two types of intermolecular hydrogen bonding, but also we employed QTAIM and NBO methods to complement our research. The results have shown no significant differences between the two correlated methods employed for both types of hydrogen bonded complexes, leading us to suggest the use of the DFT/B3LYP method for studies of similar systems to those studied here, due to the lower computational demand. The increase in bond length of the HX species are enhanced due to formation of more linear complexes than T-complexes, in both calculation levels. The intermolecular bond length values in the complex HCN --- HX are smaller than in the complexes HCCH --- HX, and the values from MP2 and DFT/B3LYP are very close in each individual type of hydrogen complex, suggesting that the linear complexes are more stabilized by the formation of hydrogen bonding than the T-complexes, which can be proved by the values of the binding energy of hydrogen in HCN --- HX. Concerning the redshift effect in the harmonic vibrational mode of species HX, due to the formation of intermolecular bond, the values obtained for linear complexes hydrogen are higher than for the corresponding T-complexes, considering both calculation levels. Values were evaluated from the increase in the intensity values of the stretch mode HX bond formation due to intermolecular and, according to the model CCFOM, the term load flow is responsible for the effect on the increase of HX intensity. We also highlight the new vibrational modes, emphasizing the stretch mode of the intermolecular bond. From studies employing QTAIM, it was possible to obtain the values of electron density and the Laplacian electron density and evaluate these parameters in critical points in HX and intermolecular hydrogen bonding, thus confirming the formation of hydrogen bonded complexes. We evaluated the energy difference between π orbitals and lone pair of nitrogen (in HCN), for the species receiving proton and sigma antibonding for the hydrogen of HX, using the method of natural bond orbital variation.
O objeto de estudo deste trabalho foi a ligação de hidrogênio intermolecular de dois tipos, a não-usual representada pela interação entre o acetileno e espécies HX (C2H2---HX) e a usual representada pela interação entre o ácido cianídrico e espécies HX, com X=F, Cl, CN e HCCH. Esta interação provoca mudanças nas propriedades estruturais, eletrônicas e vibracionais das espécies envolvidas. Neste trabalho empregamos os métodos quântico-computacionais MP2/6-311++G(d,p) e DFT/B3LYP/6-311++G(d,p) para estudar as propriedades estruturais, eletrônicas e vibracionais dos dois tipos de ligação de hidrogênio intermolecular, além de complementar nossa investigação empregando os métodos QTAIM e NBO. Os resultados não mostraram diferenças significativas entre os dois métodos correlacionados empregados para ambos os tipos de complexos de hidrogênio, nos levando a sugerir o emprego do método DFT/B3LYP para estudos de sistemas semelhantes aos aqui estudados, devido a menor demanda computacional. Os valores de incremento no comprimento de ligação das espécies HX são mais acentuados devido à formação dos complexos lineares do que dos complexos-T, em ambos os níveis de cálculo. Os valores de comprimento de ligação intermolecular nos complexos HCN---HX são menores do que nos complexos HCCH---HX, sendo os valores MP2 e DFT/B3LYP bem próximos em cada tipo individual de complexo de hidrogênio, sugerindo que os complexos lineares são mais estabilizados pela formação da ligação de hidrogênio do que os complexos-T, fato que pode ser comprovado pelos valores da energia de ligação de hidrogênio em HCN---HX. Com respeito ao efeito redshift no modo vibracional harmônico das espécies HX, devido à formação da ligação intermolecular, os valores obtidos para os complexos de hidrogênio lineares são maiores do que para os correspondentes complexos-T, considerando ambos os níveis de cálculo. Foram avaliados os valores do incremento nos valores de intensidade do modo de estiramento de HX devido à formação da ligação intermolecular e, de acordo com o modelo CCFOM, o termo de fluxo de carga é o responsável pelo efeito no aumento da intensidade de HX. Foram ainda destacados os novos modos vibracionais, dando ênfase ao modo de estiramento da ligação intermolecular. Dos estudos empregando a QTAIM foi possível obter os valores da densidade eletrônica e do Laplaciano da densidade eletrônica e avaliar os valores desses parâmetros nos pontos críticos de ligação em HX e na ligação de hidrogênio intermolecular, comprovando dessa forma a formação dos complexos de hidrogênio. Com os estudos empregando o método dos orbitais naturais de ligação foi avaliada a diferença de energia entre os orbitais π (no acetileno) e o orbital do par de elétrons livres do nitrogênio (em HCN), para as espécies receptoras de próton, e o orbital sigma antiligante do hidrogênio em HX.
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Berg, Lotta. "Exploring non-covalent interactions between drug-like molecules and the protein acetylcholinesterase." Doctoral thesis, Umeå universitet, Kemiska institutionen, 2017. http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-129900.
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The majority of drugs are small organic molecules, so-called ligands, that influence biochemical processes by interacting with proteins. The understanding of how and why they interact and form complexes is therefore a key component for elucidating the mechanism of action of drugs. The research presented in this thesis is based on studies of acetylcholinesterase (AChE). AChE is an essential enzyme with the important function of terminating neurotransmission at cholinergic synapses. AChE is also the target of a range of biologically active molecules including drugs, pesticides, and poisons. Due to the molecular and the functional characteristics of the enzyme, it offers both challenges and possibilities for investigating protein-ligand interactions. In the thesis, complexes between AChE and drug-like ligands have been studied in detail by a combination of experimental techniques and theoretical methods. The studies provided insight into the non-covalent interactions formed between AChE and ligands, where non-classical CH∙∙∙Y hydrogen bonds (Y = O or arene) were found to be common and important. The non-classical hydrogen bonds were characterized by density functional theory calculations that revealed features that may provide unexplored possibilities in for example structure-based design. Moreover, the study of two enantiomeric inhibitors of AChE provided important insight into the structural basis of enthalpy-entropy compensation. As part of the research, available computational methods have been evaluated and new approaches have been developed. This resulted in a methodology that allowed detailed analysis of the AChE-ligand complexes. Moreover, the methodology also proved to be a useful tool in the refinement of X-ray crystallographic data. This was demonstrated by the determination of a prereaction conformation of the complex between the nerve-agent antidote HI-6 and AChE inhibited by the nerve agent sarin. The structure of the ternary complex constitutes an important contribution of relevance for the design of new and improved drugs for treatment of nerve-agent poisoning. The research presented in the thesis has contributed to the knowledge of AChE and also has implications for drug discovery and the understanding of biochemical processes in general.
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Bonfanti, M. "REACTIONS AT SURFACES: BEYOND THE STATIC SURFACE APPROACH IN QUANTUM DYNAMICS." Doctoral thesis, Università degli Studi di Milano, 2012. http://hdl.handle.net/2434/167911.
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Thanks to the peculiar electronic properties of gas-solid interfaces, surfaces play an important role in many chemical processes. In my thesis, I considered few different reactions at surfaces and addressed the problem of their description by means of quantum dynamical methods. In particular, the focus of the work is on the inclusion of surface motion in the dynamical models. This problem is very challenging for state-of-art quantum methods, due to the unfavorable scaling with the number of degrees of freedom. To avoid this computational limit a variety of methods were adopted, ranging from a static approach in a low dimensional Time Dependent Wave Packet (TDWP) calculations to a full dynamical description of dissipation in the framework of Multi-Configuration Time-Dependent Hartree method (MCTDH).
I considered three different physical problems. The first one is the exothermic, collinearly-dominated Eley-Rideal H2 formation on graphite. In particular, I focused on the importance of the model used to describe the graphitic substrate, in light of the marked discrepancies present in available literature results. To this end, I considered the collinear reaction and computed the Potential Energy Surface (PES) for a number of different graphitic surface models using Density Functional Theory (DFT) for different dynamical regimes. I performed quantum dynamics with wave-packet techniques down to the cold collision energies relevant for the chemistry of the interstellar medium. Results show that the reactivity at moderate-to-high collision energies sensitively depends on the shape of the PES in the entrance channel, which in turn is related to the adopted surface model. At low energies I ruled out the presence of any barrier to reaction, thereby highlighting the importance of quantum reflection in limiting the reaction efficiency.
In a second part of my work, I studied the effect of lattice displacement on the interaction of H2 with the Cu(111) surface using the Specific Reaction Parameter (SRP) approach to DFT. I systematically investigated how the motion of the surface atoms affects some features of the PES, such as the dissociation barrier height and the barrier geometry corresponding to some representative reaction pathways, and the anisotropy of the potential at these geometries. This analysis allowed the identification of the surface degrees of freedom that are likely to be most relevant for H2 dissociation. In particular, I found that the lattice coordinate displacements that have the largest effect on the H2/Cu(111) DFT-SRP barrier heights and locations concern the motion of the 1st layer and 2nd layer Cu atoms in the Z direction, and motion of the 1st layer atoms in the directions parallel to the surface. Whereas the first degree of freedom mostly affects the barrier geometry, the second and third motions can lower or raise the barrier height. The latter effect cannot be described with the usual surface oscillator dynamical models employed in the past to include surface motion, and its dynamical influence on the dissociative adsorption needs to be further investigated.
In the third part of the thesis I addressed the problem of including dissipative effects in the reaction dynamics of hydrogen sticking and scattering on surfaces. I considered dissipative baths with different spectral properties and represented them with a linear chain of coupled harmonic oscillators, exploiting an equivalent effective-mode representation that has recently been developed. I studied the system dynamics with MCTDH, aiming on one hand to an accurate description of dissipation at a short time scale, and on the other hand to a simplified but qualitatively correct behavior of the long time dynamics. In this framework, I found a very useful scheme to represent the long time dynamics of the system without incurring in unwanted Poincaré's recurrences. I used this method to obtain the sticking probability of one hydrogen atom scattered by a simple one dimensional Morse potential. The methodology developed in this work is going to be extended to the more realistic problem of hydrogen sticking on graphitic surfaces.
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Mohammadhosseini, Ali. "A search for optimal structure of carbon-based porous adsorbents for hydrogen storage : numerical modeling approach." Thesis, Aix-Marseille, 2013. http://www.theses.fr/2013AIXM4736.
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Le but principal de cette étude était la recherche de structures optimales de charbons activés capables d"atteindre l'objectif de stockage d'hydrogène fixé par le département de l"énergie américain (DOE) pour les applications mobiles en utilisant l"adsorption physique à la température ambiante et aux pressions en-dessous de120 bars. L'hydrogène est destiné à être stocké dans une cuve rempliée d"adsorbants et doit être utilisé dans les véhicules alimentés principalement par des piles à combustible. Les adsorbants à base de carbone connus ont une capacité de stockage faible. Par conséquent, dans ce travail, j'ai défini les paramètres responsables de l'insuffisance de capacité de stockage de ces matériaux. Une attention particulière a été accordée à la géométrie locale des pores des adsorbants. J'ai étudié la structure locale des pores des adsorbants à base de carbone et je présente le principe de la conception d"architectures tridimensionnelles de nouvelles structures de carbone ainsi que la capacité d'adsorption de l'hydrogène par ces structures, lesquelles constituent une classe prometteuse de matériaux pour le stockage d'hydrogène et qui n'ont pas été étudiées jusqu'ici. Hormis la maximisation de la densité de l'hydrogène absorbée par cette famille de structures, mon but était de caractériser l'adsorption dans cette nouvelle catégorie d'adsorbants. Cela permet d"apporter des informations quant à la méthodologie à utiliser pour ajuster les propriétés physiques de ces matériaux afin d'optimiser leurs propriétés de stockage. Les résultats obtenus semblent montrer que cet objectif est atteint et confirment que mon approche constitue une bonne base pour de futures recherchesThe main goal of research presented in this thesis has been a search for optimal carbon-based porous structure capable to achieve the hydrogen storage capacity defined by US Department of Energy (DOE) for mobile applications at room temperature by adsorption at medium-level pressures below 120 bars. The hydrogen is assumed to be stored in a tank filled with adsorbents to be used in transport application, mainly fuel-cell driven vehicles. The known carbon-based adsorbents have low storage capacity. Therefore in this work, I have defined the basic parameters which are responsible for the capacity deficiency of such materials. Special attention has been paid to local pore geometry of adsorbents. I have investigated the pore local structure of carbon-based adsorbents and I present the basis of design and hydrogen adsorption capacity in three-dimensional architecture of new carbon frameworks, a promising class of potential hydrogen storage materials that have not been studied so far. Apart from maximizing the density of hydrogen taken up by this family of structures, I have aimed at characterization of this new category of adsorbents. This is hoped to lead to a guidance how their physical properties can be designed, or `tuned', to optimize their storage properties, and the obtained results seem to achieve this aim and thus provide a good basis for future research
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Burkert, Till. "Materials for Magnetic Recording Applications." Doctoral thesis, Uppsala University, Department of Physics, 2005. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-5800.
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In the first part of this work, the influence of hydrogen on the structural and magnetic properties of Fe/V(001) superlattices was studied. The local structure of the vanadium-hydride layers was determined by extended x-ray absorption fine structure (EXAFS) measurements. The magnetic ordering in a weakly coupled Fe/V(001) superlattice was investigated using the magneto-optical Kerr effect (MOKE). The interlayer exchange coupling is weakened upon alloying with hydrogen and a phase with short-range magnetic order was observed.
The second part is concerned with first-principles calculations of magnetic materials, with a focus on magnetic recording applications. The uniaxial magnetic anisotropy energy (MAE) of Fe, Co, and Ni was calculated for tetragonal and trigonal structures. Based on an analysis of the electronic states of tetragonal Fe and Co at the center of the Brillouin zone, tetragonal Fe-Co alloys were proposed as a material that combines a large uniaxial MAE with a large saturation magnetization. This was confirmed by experimental studies on (Fe,Co)/Pt superlattices. The large uniaxial MAE of L10 FePt is caused by the large spin-orbit interaction on the Pt sites in connection with a strong hybridization between Fe and Pt. Furthermore, it was shown that the uniaxial MAE can be increased by alloying the Fe sublattice with Mn. The combination of the high-moment rare-earth (RE) metals with the high-TC 3d transition metals in RE/Cr/Fe multilayers (RE = Gd, Tb, Dy) gives rise to a strong ferromagnetic effective exchange interaction between the Fe layers and the RE layer. The MAE of hcp Gd was found to have two principal contributions, namely the dipole interaction of the large localized 4f spins and the band electron magnetic anisotropy due to the spin-orbit interaction. The peculiar temperature dependence of the easy axis of magnetization was reproduced on a qualitative level.
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Estejab, Ali. "Mathematical and Molecular Modeling of Ammonia Electrolysis with Experimental Validation." Ohio University / OhioLINK, 2018. http://rave.ohiolink.edu/etdc/view?acc_num=ohiou1514834805432007.
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He, Tianwei. "Computational discovery and design of nanocatalysts for high efficiency electrochemical reactions." Thesis, Queensland University of Technology, 2020. https://eprints.qut.edu.au/203969/1/Tianwei_He_Thesis.pdf.
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This thesis reports a computational discovery and design of highly efficient electrocatalysts for various of electrochemical reactions. The method is based on the Density Functional Theory (DFT) by using Vienna ab initio simulation package (VASP). This project is a step forward in developing the low-cost, high activity, selectivity, stability and scalability for the electrochemical reactions, which could make a contribution to the global-scale green energy system for a clean and sustainable energy future.
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Sun, Yuemei. "Simulation de réactions chimiques en catalyse hétérogène : l'hydrogène sur la surface (111) du palladium." Thesis, Lyon, École normale supérieure, 2014. http://www.theses.fr/2014ENSL0923.
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Dans ce travail, nous avons étudié l’adsorption dissociative de l’hydrogène sur Pd(111) ainsi que la diffusion d’un atome de l’hydrogène sur ce même surface. A l’aide de la théorie de la fonctionnelle de la densité, nous avons mené une étude systématique de l’effet du recouvrement en surface sur l’énergétique de la dissociation de H2 sur une surface de Pd(111) couverte par des atomes de l’hydrogène. Un résultat surprenant que nous avons trouvé est que les atomes adsorbés ont non seulement un effet de poison mais peuvent aussi promouvoir la dissociation de H2 s’ils sont adsorbés sur des sites loin de la molécule d’hydrogène qui dissocie. En ce qui concerne la diffusion d’un atome d’ hydrogène sur Pd(111), nous avons déterminé le coefficient de diffusion par des simulations de dynamique moléculaire en utilisant la formule d’Einstein à différente température de la surface, Ts=500K, 300K and 250K. Une méthode de la dynamique moléculaire accélérée a été développée afin d’étudier la diffusion à bases températures. Dans notre approche, l’accélération se fait moyennant l’augmentation de l’énergie cinétique de l’atome qui diffuse suivant une distribution Maxwell-Boltzmann qui correspond à une température plus élevée et la correction de l’échelle de temps d’une façon consistante. Pour tester la validité de notre approche, nous avons effectué des simulations pour la diffusion d’un atome d’hydrogène sur Pd(111) à Ts=300K and Ts=100K. Les résultats obtenus par la méthode accélérée est en bon accord avec ceux de la simulation standard. Par la méthode accélérée, l’échelle de temps peut être étendu à l’ordre de micro-secondesIn this thesis, we studied dissociative adsorption of hydrogen on Pd(111) with particular attention paid to the surface coverage effect and the diffusion of a hydrogen adatom on Pd(111). With the help of DFT calculations, we carried out a systematic investigation of the effect of H-adatoms on the dissociation energetics of H2 on H-covered Pd(111) surfaces at various coverages. A quite surprising finding is that the H-adatoms do not only have a poisoning effect but can also promote H2 dissociation when they are adsorbed on sites which are sufficiently far from the dissociating H2 molecule. The macroscopic diffusion coefficient of an H-adatom on Pd(111) is determined from molecular dynamics simulations with the help of Einstein formula for different surface temperatures, i.e., Ts=500K, 300K and 250K. An accelerated molecular dynamics method was developed in order to study the diffusion at low surface temperatures. In our approach, the acceleration is achieved by increasing the kinetic energy of the diffusing atom according to the Maxwell-Boltzmann distribution at a higher temperature and correcting the time scale in a consistent way. For testing the validity of our method, we performed simulations for the diffusion of H adatom on Pd(111) surface at T=300K and T=100K. The diffusion coefficient obtained from the accelerated MD method is in agreement with that obtained from the direct MD and TST methods. And the physical time scale can be extended to the order of microseconds
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Kinal, Armagan. "Theoretical Investigation Of Unimolecular Reactions Of Cyclic C5h6 Compounds By Ab Initio Quantum Chemical Methods." Phd thesis, METU, 2004. http://etd.lib.metu.edu.tr/upload/12605124/index.pdf.
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Thermodynamic stabilities of eighteen cyclic C5H6 isomers were explored computationally both on singlet and triplet state potential energy surfaces (PES). All isomers have singlet ground states except for bicyclo[2.1.0]pent-5-ylidene (B5) having no stable geometry on the singlet C5H6 PES. Cyclopenta-1,3-diene (M1) is the most stable cyclic C5H6 isomer while cyclopent-1,4-diylidene is the least stable one among all. Cyclopenta-1,2-diene (M2) and cyclopentyne (M3) have biradical characters of 46.9 and 21.5%, respectively.
Seven unimolecular isomerization reactions occurring among several of these molecules were investigated by DFT and ab initio methods. The conversion of bicyclo[2.1.0]pent-2-ene (B1) and tricyclo[2.1.0.02,5]-pentane (T1) into 1,3-cyclopentadiene (M1) are shown to be concerted processes whose reaction paths pass through TSs with a high degree of biradical character. The reaction enthalpies (DH0) are predicted to be -47.7 kcal/mol for B1 and -63.8 kcal/mol for T1 at UB3LYP/6-31G(d) level. The activation enthalpy (DH0¹) for the ring opening of B1 was calculated by the CR-CCSD(T) method to be 25.2 kcal/mol, in good agreement with experiment. Furthermore, the DH0¹
for the ring opening of T1 was obtained by the CR-CCSD(T) method to be 48.2 kcal/mol. The self-conversion of M1 via 1,5-hydrogen shift is a facile and concerted reaction with aromatic TS. The DH0¹
estimations of B3LYP and CC methods are 25.24 and 28.78 kcal/mol, respectively. For 1,2-hydrogen shift reactions of cyclopent-3-enylidene (M4) and cyclopenten-2-ylidene (M5), the single point CC calculations predicted the DH0¹
values of 3.13 and 10.12 kcal/mol, as well as, the DH0 values of -71.28 and -64.05 kcal/mol, respectively. The reason of M5 being more stable than M4 is due to the conjugation of the carbene carbon and the double bond in M5. The reaction path of cyclobutylidene methylene to cyclopentyne rearrangement is found to be rather shallow. The DH0¹
and DH0 values predicted by the RCCSD(T) method to be 3.65 and -5.72 kcal/mol, respectively. Finally, triplet state isomerization of bicyclo[2.1.0]pent-5-ylidene to cyclopenta-1,2-diene, as well as, its parent reaction, cyclopropylidene to 1,2-propadiene were investigated at several levels of theory including DFT, CASSCF and CC methods. The UCCSD(T) method estimated a moderate barrier whose value is 8.12 kcal/mol for the isomerization of 3B5 with the reaction enthalpy of -44.63 kcal/mol.
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Norberg, Daniel. "Quantum Chemical Studies of Radical Cation Rearrangement, Radical Carbonylation, and Homolytic Substitution Reactions." Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis, 2007. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-8178.
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Paglia, Gianluca. "Determination of the structure of y-alumina using empirical and first principle calculations combined with supporting experiments." Thesis, Curtin University, 2004. http://hdl.handle.net/20.500.11937/2341.
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Aluminas have had some form of chemical and industrial use throughout history. For little over a century corundum (α-Al2O3) has been the most widely used and known of the aluminas. The emerging metastable aluminas, including the γ, δ, η, θ, κ, β, and χ polymorphs, have been growing in importance. In particular, γ-Al2O3 has received wide attention, with established use as a catalyst and catalyst support, and growing application in wear abrasives, structural composites, and as part of burner systems in miniature power supplies. It is also growing in importance as part of the feedstock for aluminium production in order to affect both the adsorption of hydrogen fluoride and the feedstock solubility in the electrolytic solution. However, much ambiguity surrounds the precise structure of γ-Al2O3. Without proper knowledge of the structure, understanding the properties, dynamics and applications will always be less than optimal. The aim of this research was to contribute towards settling this ambiguity. This work was achieved through extensive computer simulations of the structure, based on interatomic potentials with refinements of promising structures using density functional theory (DFT), and a wide range of supporting experiments. In addition to providing a more realistic representation of the structure, this research has also served to advance knowledge of the evolution of the structure with changing temperature and make new insights regarding the location of hydrogen in γ-Al2O3.Both the molecular modelling and Rietveld refinements of neutron diffraction data showed that the traditional cubic spinel-based structure models, based on m Fd3 space group symmetry, do not accurately describe the defect structure of γ-Al2O3. A more accurate description of the structure was provided using supercells of the cubic and tetragonal unit cells with a significant number of cations on c symmetry positions. These c symmetry based structures exhibited diffraction patterns that were characteristic of γ-Al2O3. The first three chapters of this Thesis provide a review of the literature. Chapter One provides a general introduction, describing the uses and importance of the aluminas and the problems associated with determining the structure of γ-Al2O3. Chapter Two details the research that has been conducted on the structure of vi γ-Al2O3 historically. Chapter Three describes the major principles behind the computational methods employed in this research. In Chapter Four, the specific experimental and computational techniques used to investigate the structure of γ-Al2O3 are described. All preparation conditions and parameters used are provided. Chapter Five describes the methodology employed in computational and experimental research. The examination of the ~ 1.47 billion spinel-based structural possibilities of γ-Al2O3, described using supercells, and the selection of ~ 122,000 candidates for computer simulation, is detailed. This chapter also contains a case study of the structure of κ-Al2O3, used to investigate the applicability of applying interatomic potentials to solving complex structures, where many possibilities are involved, and to develop a systematic procedure of computational investigation that could be applied to γ-Al2O3. Chapters Six to Nine present and discuss the results from the experimental studies.Preliminary heating trials, performed to determine the appropriate preparation conditions for obtaining a highly crystalline boehmite precursor and an appropriate calcination procedure for the systematic study of γ-Al2O3, were presented in Chapter Six. Chapter Seven details the investigation of the structure from a singletemperature case. Several known structural models were investigated, including the possibility of a dual-phase model and the inclusion of hydrogen in the structure. It was demonstrated that an accurate structural model cannot be achieved for γ-Al2O3 if the cations are restricted to spinel positions. It was also found that electron diffraction patterns, typical for γ-Al2O3, could be indexed according to the I41/amd space group, which is a maximal subgroup of m Fd3 . Two models were presented which describe the structure more accurately; Cubic-16c, which describes cubic γ-Al2O3 and Tetragonal-8c, which describes tetragonal γ-Al2O3. The latter model was found to be a better description for the γ-Al2O3 samples studied. Chapter Eight describes the evolution of the structure with changing calcination temperature. Tetragonal γ-Al2O3 was found to be present between 450 and 750 °C. The structure showed a reduction in the tetragonal distortion with increasing temperature but at no stage was cubic γ-Al2O3 obtained. Examination of the progress of cation migration indicates the reduction in the tetragonal nature is due to ordering within inter-skeletal oxygen layers of the unit cell, left over from the breakdown of the hydroxide layers of boehmite when the transformation to γ-Al2O3 occurred. Above 750 °C, δ-Al2O3 was not observed, but a new phase was identified and designated γ.-Al2O3.The structure of this phase was determined to be a triple cell of γ-Al2O3 and is herein described using the 2 4m P space group. Chapter Nine investigates the presence of hydrogen in the structure of γ-Al2O3. It was concluded that γ-Al2O3 derived from highly crystalline boehmite has a relatively well ordered bulk crystalline structure which contains no interstitial hydrogen and that hydrogen-containing species are located at the surface and within amorphous regions, which are located in the vicinity of pores. Expectedly, the specific surface area was found to decrease with increasing calcination temperature. This trend occurred concurrently with an increase in the mean pore and crystallite size and a reduction in the amount of hydrogen-containing species within the structure. It was also demonstrated that γ-Al2O3 derived from highly crystalline boehmite has a significantly higher surface area than expected, attributed to the presence of nano-pores and closed porosity. The results from the computational study are presented and discussed in Chapter Ten. Optimisation of the spinel-based structural models showed that structures with some non-spinel site occupancy were more energetically favourable. However, none of the structural models exhibited a configuration close to those determined from the experimental studies. Nor did any of the theoretical structures yield a diffraction pattern that was characteristic of γ-Al2O3. This discrepancy between the simulated and real structures means that the spinel-based starting structure models are not close enough to the true structure of γ-Al2O3 to facilitate the derivation of its representative configuration.Large numbers of structures demonstrate migration of cations to c symmetry positions, providing strong evidence that c symmetry positions are inherent in the structure. This supports the Cubic-16c and Tetragonal-8c structure models presented in Chapter Seven and suggests that these models are universal for crystalline γ-Al2O3. Optimisation of c symmetry based structures, with starting configurations based on the experimental findings, resulted in simulated diffraction patterns that were characteristic of γ-Al2O3.
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Hernandez, Jean-Alexis. "Ab initio modeling of dense water ices at extreme conditions of pressure and temperature." Thesis, Lyon, 2017. http://www.theses.fr/2017LYSEN028/document.
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Dans cette thèse, nous étudions la stabilité et les propriétés des glaces d’eau de haute pression (entre 5 et 300 GPa) et de haute température (entre 300 et 2000 K) comportant ou non des inclusions de NaCl dans leur structure cristalline. Pour attendre ces conditions propres aux intérieurs des exoplanètes océans, nous utilisons une approche théorique basée sur des dynamiques moléculaires ab initio. Nous montrons que l’analyse de la dynamique des liaisons entre hydrogènes et oxygènes permet de distinguer toutes les phases de la glace présentant une structure cubique volume-centrée. En particulier, nous présentons la première description ab initio de la phase plastique, et nous mettons en évidence la présence de multiples transitions dans la phase superionique. Ensuite, nous montrons que jusqu’à 5.9 % en masse de NaCl peuvent être inclus dans la structure de la glace à 1600 K. L’inclusion des ions Na+ et Cl- stimule le désordre orientationel des molécules d’eau par rapport à la glace d’eau pure. À partir de 2.5 % en masse de NaCl, la conduction superionique s’étend à l’ensemble de la gamme de pression étudiée, et la symétrisation des liaisons hydrogènes se produit à plus haute pression. Enfin, nous décrivons les structures de cœur des dislocations vis ayant des vecteurs de Burgers <110> et <111> dans la glace X à 80 GPa, ce qui constitue une étape préliminaire importante à la construction de lois rhéologiques pour les glaces cubiques de haute pressionIn this thesis we study the stability and the properties of pure and NaCl-bearing dense water ices at high pressure (between 5 and 300 GPa) and high temperature (between 300 and 2000 K). To reach these conditions that correspond to the interiors of ocean exoplanets, we employ a theoretical approach based on ab initio molecular dynamics simulations. We show that a detailed analysis of the hydrogen bond dynamics allows to distinguish all the different ice phases presenting a body-centered cubic sub-lattice of oxygen atoms. In particular, we present the first ab initio description of the plastic phase of water ice. We also reveal the multiple transitions that occur in the superionic domain. Next, we show that ice VII' can incorporate up to 5.9 wt% NaCl in its structure at 1600 K. The inclusion of Na+ and Cl- ions enhances the orientation disorder of the water molecules in comparison to the pure ice. From 2.5 wt% NaCl, superionic conduction expands over the entire pressure range studied, and the hydrogen symmetrisation is shifted towards higher pressures. Last, we describe the <110> and <111> screw dislocation core structures of ice X at 80 GPa. This constitutes a first step towards the construction rheological laws for high-pressure cubic ices
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Nordlund, Dennis. "Core Level Spectroscopy of Water and Ice." Doctoral thesis, Stockholm : Fysikum, Univ, 2004. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-181.
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Paglia, Gianluca. "Determination of the structure of y-alumina using empirical and first principle calculations combined with supporting experiments." Curtin University of Technology, Department of Applied Physics & Department of Applied Chemistry, 2004. http://espace.library.curtin.edu.au:80/R/?func=dbin-jump-full&object_id=14992.
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Aluminas have had some form of chemical and industrial use throughout history. For little over a century corundum (α-Al2O3) has been the most widely used and known of the aluminas. The emerging metastable aluminas, including the γ, δ, η, θ, κ, β, and χ polymorphs, have been growing in importance. In particular, γ-Al2O3 has received wide attention, with established use as a catalyst and catalyst support, and growing application in wear abrasives, structural composites, and as part of burner systems in miniature power supplies. It is also growing in importance as part of the feedstock for aluminium production in order to affect both the adsorption of hydrogen fluoride and the feedstock solubility in the electrolytic solution. However, much ambiguity surrounds the precise structure of γ-Al2O3. Without proper knowledge of the structure, understanding the properties, dynamics and applications will always be less than optimal. The aim of this research was to contribute towards settling this ambiguity. This work was achieved through extensive computer simulations of the structure, based on interatomic potentials with refinements of promising structures using density functional theory (DFT), and a wide range of supporting experiments. In addition to providing a more realistic representation of the structure, this research has also served to advance knowledge of the evolution of the structure with changing temperature and make new insights regarding the location of hydrogen in γ-Al2O3.Both the molecular modelling and Rietveld refinements of neutron diffraction data showed that the traditional cubic spinel-based structure models, based on m Fd3 space group symmetry, do not accurately describe the defect structure of γ-Al2O3. A more accurate description of the structure was provided using supercells of the cubic and tetragonal unit cells with a significant number of cations on c symmetry positions. These c symmetry based structures exhibited diffraction patterns that were characteristic of γ-Al2O3. The first three chapters of this Thesis provide a review of the literature. Chapter One provides a general introduction, describing the uses and importance of the aluminas and the problems associated with determining the structure of γ-Al2O3. Chapter Two details the research that has been conducted on the structure of vi γ-Al2O3 historically. Chapter Three describes the major principles behind the computational methods employed in this research. In Chapter Four, the specific experimental and computational techniques used to investigate the structure of γ-Al2O3 are described. All preparation conditions and parameters used are provided. Chapter Five describes the methodology employed in computational and experimental research. The examination of the ~ 1.47 billion spinel-based structural possibilities of γ-Al2O3, described using supercells, and the selection of ~ 122,000 candidates for computer simulation, is detailed. This chapter also contains a case study of the structure of κ-Al2O3, used to investigate the applicability of applying interatomic potentials to solving complex structures, where many possibilities are involved, and to develop a systematic procedure of computational investigation that could be applied to γ-Al2O3. Chapters Six to Nine present and discuss the results from the experimental studies.
Preliminary heating trials, performed to determine the appropriate preparation conditions for obtaining a highly crystalline boehmite precursor and an appropriate calcination procedure for the systematic study of γ-Al2O3, were presented in Chapter Six. Chapter Seven details the investigation of the structure from a singletemperature case. Several known structural models were investigated, including the possibility of a dual-phase model and the inclusion of hydrogen in the structure. It was demonstrated that an accurate structural model cannot be achieved for γ-Al2O3 if the cations are restricted to spinel positions. It was also found that electron diffraction patterns, typical for γ-Al2O3, could be indexed according to the I41/amd space group, which is a maximal subgroup of m Fd3 . Two models were presented which describe the structure more accurately; Cubic-16c, which describes cubic γ-Al2O3 and Tetragonal-8c, which describes tetragonal γ-Al2O3. The latter model was found to be a better description for the γ-Al2O3 samples studied. Chapter Eight describes the evolution of the structure with changing calcination temperature. Tetragonal γ-Al2O3 was found to be present between 450 and 750 °C. The structure showed a reduction in the tetragonal distortion with increasing temperature but at no stage was cubic γ-Al2O3 obtained. Examination of the progress of cation migration indicates the reduction in the tetragonal nature is due to ordering within inter-skeletal oxygen layers of the unit cell, left over from the breakdown of the hydroxide layers of boehmite when the transformation to γ-Al2O3 occurred. Above 750 °C, δ-Al2O3 was not observed, but a new phase was identified and designated γ.-Al2O3.
The structure of this phase was determined to be a triple cell of γ-Al2O3 and is herein described using the 2 4m P space group. Chapter Nine investigates the presence of hydrogen in the structure of γ-Al2O3. It was concluded that γ-Al2O3 derived from highly crystalline boehmite has a relatively well ordered bulk crystalline structure which contains no interstitial hydrogen and that hydrogen-containing species are located at the surface and within amorphous regions, which are located in the vicinity of pores. Expectedly, the specific surface area was found to decrease with increasing calcination temperature. This trend occurred concurrently with an increase in the mean pore and crystallite size and a reduction in the amount of hydrogen-containing species within the structure. It was also demonstrated that γ-Al2O3 derived from highly crystalline boehmite has a significantly higher surface area than expected, attributed to the presence of nano-pores and closed porosity. The results from the computational study are presented and discussed in Chapter Ten. Optimisation of the spinel-based structural models showed that structures with some non-spinel site occupancy were more energetically favourable. However, none of the structural models exhibited a configuration close to those determined from the experimental studies. Nor did any of the theoretical structures yield a diffraction pattern that was characteristic of γ-Al2O3. This discrepancy between the simulated and real structures means that the spinel-based starting structure models are not close enough to the true structure of γ-Al2O3 to facilitate the derivation of its representative configuration.
Large numbers of structures demonstrate migration of cations to c symmetry positions, providing strong evidence that c symmetry positions are inherent in the structure. This supports the Cubic-16c and Tetragonal-8c structure models presented in Chapter Seven and suggests that these models are universal for crystalline γ-Al2O3. Optimisation of c symmetry based structures, with starting configurations based on the experimental findings, resulted in simulated diffraction patterns that were characteristic of γ-Al2O3.
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Shi, Hongting. "Defect structure and optical properties of alkaline earth fluorides." Doctoral thesis, [S.l.] : [s.n.], 2007. http://deposit.ddb.de/cgi-bin/dokserv?idn=984572015.
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