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Vibrational Properties of Quinones in Photosynthetic Reaction CentersZhao, Nan 12 August 2014 (has links)
Fourier transform infrared difference spectroscopy (FTIR DS) is widely used to study the structural details of electron transfer cofactors in photosynthetic protein complexes. In photosynthetic proteins quinones play an important role, functioning as a cofactor in light-driven electron transfer.
In photosystem I (PS I) phylloquinone (PhQ) functions as an intermediary in electron transfer. To investigate the properties of PhQ that occupies the, so called, A1 binding site in PS I, time-resolved step-scan FTIR DS, with 5µs time resolution at 77K has been used. By replacing PhQ in the A1 binding site with specifically isotope labeled version, information on the vibrational frequencies associated specifically with the quinone in the binding site were obtained, which could be compared to the vibrational properties of quinone in solution or quinones in other protein binding sites. To further aid in assessing the origin of bands in the spectra, quantum mechanics /molecular mechanics (QM/MM) ONIOM type calculations were undertaken. ONIOM is an acronym for Our own N-layered Integrated molecular Orbital and molecular Mechanics. We find that the phytyl tail of PhQ does not play an important role in the orientation of PhQ in the A1 binding site. We also find that PhQ, in both neutral and reduced states, is strongly hydrogen bonded.
To test and verify the applicability of our QM/MM approach, ONIOM calculations were also undertaken for ubiquinone and a variety of other quinones incorporated into the, so called, QA binding site in purple bacteria photosynthetic reaction centers. The calculated and experimental spectra agree well, demonstrating the utility and applicability of our ONIOM approach. Hydrogen bonding to the carbonyl groups of quinones in the QA binding site was shown to be relatively weak, and it was found that hydrogen bonding to neutral ubiquinone in purple bacterial reaction centers can be considered in purely electrostatic terms, contrary to the widely held belief that the hydrogen bonding amino acids should be treated quantum mechanically.
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Theoretical Investigation Of Unimolecular Reactions Of Cyclic C5h6 Compounds By Ab Initio Quantum Chemical MethodsKinal, Armagan 01 July 2004 (has links) (PDF)
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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Quantum Chemical Simulation Of Nitric Oxide Reduction By Ammonia (scr Reaction) On V2o5 / Tio2 Catalyst SurfaceSoyer, Sezen 01 September 2005 (has links) (PDF)
The reaction mechanism for the selective catalytic reduction (SCR) of nitric oxide by ammonia on (010) V2O5 surface represented by a V2O9H8 cluster was simulated by density functional theory (DFT) calculations. The computations
indicated that SCR reaction consisted of three main parts. In the first part ammonia activation on Brø / nsted acidic V-OH site as NH4+ species by a nonactivated process takes place. The second part includes the interaction of NO with pre-adsorbed NH4 + species to eventually form nitrosamide (NH2NO). The rate limiting step for this part as well as for the total SCR reaction is identified as NH3NHO formation reaction. The last part consists of the decomposition of NH2NO on the cluster which takes advantage of a hydrogen transfer mechanism
between the active V=O and V-OH groups.
Water and ammonia adsorption and dissociation are investigated on (101) and (001) anatase surfaces both represented by totally fixed and partially relaxed Ti2O9H10 clusters. Adsorption of H2O and NH3 by H-bonding on previously H2O and NH3 dissociated systems are also considered.
By use of a (001) relaxed Ti2O9H10 cluster, the role of anatase support on SCR reaction is investigated. Since NH2NO formation on Ti2O9H10 cluster requires lower activation barriers than on V2O5 surface, it is proposed that the role of titanium dioxide on SCR reaction could be forming NH2NO. The role of vanadium oxide is crucial in terms of dissociating this product into H2O and N2.
Finally, NH3 adsorption is studied on a V2TiO14H14 cluster which represents a model for vanadia/titania surface.
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Relativistická teorie elektronového transportu v magnetických vrstvách / Relativistic Theory of Electron Transport in Magnetic LayersSýkora, Rudolf January 2012 (has links)
Title: Relativistic Theory of Electron Transport in Magnetic Layers Author: Rudolf Sýkora Department / Institute: Institude of Theoretical Physics Supervisor of the doctoral thesis: doc. RNDr. Ilja Turek, DrSc., Department of Condensed Matter Physics Abstract: We review the density-functional theory (DFT) in detail using the Levy Lieb ap- proach. The Kohn Sham scheme is discussed, starting from the simplest spinless non- relativistic case, then including spin and considering potential spin magnetism, and finally deriv- ing the full Kohn Sham Dirac relativistic scheme. The Linear Muffin-Tin Orbital (LMTO) method for electronic-structure calculation is presented, together with mentioning the necessary changes to include the spin-orbit (SO) interaction effects to an otherwise scalar-relativistic (SR) theory. Derivation of an electronic-conductance formula for a layered system is given, based on the Landauer scattering picture and using simple non-equilibrium Green functions. The formal- ism is applied to layered metallic systems of light elements Co, Ni, Cu elements, and to layered systems with a tunnelling barrier, Fe/MgO/Ag and Fe/GaAs/Ag. The effects of the SO interac- tion on the Giant Magnetoresistance (GMR) ratio and/or the Tunnelling Anisotropy Magnetore- sistance (TAMR) for these systems are discussed....
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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 CCHViana, Marco Antonio de Abreu 06 August 2013 (has links)
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Previous issue date: 2013-08-06 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES / 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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Estudos da relação quantitativa estrutura-atividade (QSAR) de adutos de Morita-Baylis-Hillman bioativos contra Leishmania amazonensis / Quantitative Structure-Activity Relationship (QSAR) Studies of Morita-Baylis- Hillman Adducts bioactive against Leishmania amazonensis.Alencar Filho, Edilson Beserra de 14 December 2012 (has links)
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Previous issue date: 2012-12-14 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES / The Morita-Baylis-Hillman Adducts (MBHA) is a class of molecules studied
by our research group on synthetic, theoretical and bioactivity aspects. In this work,
we present Quantitative Structure-Activity Relationship (QSAR) models involving 32
aromatic MBHA. Initially, the most stable conformations of thirty-two MBHA were
investigated by theoretical methods, which were used to construct models. For this
study, were obtained potential energy curves using AM1 semi-empirical method,
considering rotational degrees of freedom (sigma bonds). From these curves, the
less energy conformation to each molecule was selected and optimized at B3LYP/6-
31+G(d) level, considering solvent effects through Polarizable Continuum Model
(PCM). Proton Nuclear Magnetic Ressonance data are in agreement with the
conformational study. Intramolecular Hydrogen Bonds (IHB) are presents in the most
of the studied compounds, according to structural characterization and QTAIM
calculations. Curiously, compounds that showed hydrogen bonds involving the nitro
and hydroxyl groups have the best values of biological activity (IC50). An explanation
is based on redox mechanism of action of nitrocompounds. NBO (Natural Bond
Orbital) charges and LUKO (Lowest Unoccupied Kohn-Sham Orbitals) analysis at the
ortho-nitro group are in agreement with these analyses. Considering quantum
calculations and structural observations, four descriptors were selected a priori and
submitted to a QSAR study using PLS (Partial Least Squares) and MLR (Multiple
Linear Regression) modeling. A second QSAR approach was made from the another
set of descriptors obtained through the online platform E-DRAGON, which were
submitted to a variable selection method. The quality parameters obtained for models
indicate that both are robust and predictive. / Os Adutos de Morita-Baylis-Hillman (AMBH) compreendem uma classe de
moléculas investigadas por nosso grupo de pesquisas nos aspectos sintéticos,
teóricos e de bioatividade. Neste trabalho, apresentamos modelos de Relação
Quantitativa entre a Estrutura Química e a Atividade Leishmanicida (QSAR)
envolvendo 32 AMBH aromáticos. Deste modo, inicialmente foram investigadas as
conformações mais estáveis de cada composto através de métodos teóricos, as
quais foram utilizadas na construção dos modelos. Foram obtidas curvas de energia
potencial utilizando o método semi-empírico AM1, considerando graus de liberdade
rotacionais (ligações sigma). A partir destas curvas, a conformação de menor
energia para cada molécula foi selecionada e otimizada ao nível B3LYP/6-31+G(d),
considerando os efeitos do solvente aquoso usando PCM ( Polarizable Continuum
Model ). Dados espectroscópicos de Ressonância Magnética Nuclear de prótons
corroboraram o estudo conformacional. Ligações de Hidrogênio Intramoleculares
(LHI) se mostraram presentes na maioria das moléculas estudadas, conforme
caracterização estrutural e cálculos QTAIM ( Quantum Theory Atoms in Molecules ).
Curiosamente, os compostos que apresentaram Ligações de Hidrogênio envolvendo
o grupo nitro (NO2) e a hidroxila (OH) possuem melhores valores de atividade
biológica (menor IC50). Uma explicação está baseada no mecanismo de ação redox
de nitrocompostos. Observação das cargas NBO ( Natural Bond Orbitals ) e análise
dos orbitais de fronteira LUKO ( Lowest Unoccupied Kohn-Sham Orbitals ) ao nível
do grupo orto-nitro estão de acordo com estas análises. Considerando os cálculos
quânticos, bem como observações estruturais, quatro descritores foram
selecionados a priori e submetidos a um estudo QSAR ( Quantitative Structure-
Activity Relationships ) utilizando modelagem PLS ( Partial Least Squares ) e MLR
( Multiple Linear Regression ). Uma segunda abordagem QSAR foi realizada a partir
de outro conjunto de descritores obtidos através da plataforma online E-DRAGON,
os quais foram submetidos ao método de seleção de variáveis OPS ( Ordered
Predictor Selection ). Os parâmetros de qualidade obtidos para os modelos indicam
que ambos são robustos e preditivos.
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Structural Properties Electronic and Vibrational Crystals Aspartic Acid (Asp): Computer Simulations in Formalism DFT / Propriedades Estruturais, EletrÃnicas e Vibracionais de Cristais do Ãcido AspÃrtico (Asp): SimulaÃÃes Computacionais no Formalismo DFTAgmael MendonÃa Silva 20 February 2015 (has links)
FundaÃÃo Cearense de Apoio ao Desenvolvimento Cientifico e TecnolÃgico / Computer simulations within the Density Functional Theory (DFT) formalism were accomplished to find the structural, electronic and vibrational properties of aspartic acid (Asp) crystals in the L-anhydrous, L-monohydrated, and DL-anhydrous phases. Aspartic acid is a non-essential amino acid with a role in the fadigue resistance mechanism. It also works as an excitatory neurotransmitter in the brain, contributes to eliminate any excess of toxins from the cells and is capable to affect RNA synthesis. The computer codes CASTEP (for crystals) and GAUSSIAN (for molecules) were employed in the present study. For the aspartic acid crystals, LDA and GGA-PBE exchange-correlation functional were used in the simulations, the last one taking into account empirical corrections for dispersive forces (PBE+TS) following the scheme proposed by Tkatchenko and Scheffler. Molecular calculations were carried out using the Gaussian09 program with the hybrid exchange-correlation functional B3LYP and the 6-311+G(d,p) basis set. The molecules were simulated in the gaseous phase and solvated in water within the Polarizable Continuum Model (PCM). Crystalline (optimized unit cells) and molecular (smallest energy conformations) structures obtained from the calculations were compared with experimental results and other theoretical computations. For the L-Asp anhydrous crystal, the optical and vibrational infrared (IR) and Raman spectra were contrasted with experimental measurements, and its band structure suggests it is a semiconductor. For the monohydrated L-Asp crystal, an indirect gap 0,1 eV larger than the gap of the anhydrous crystal is caused due to the role of water in its electronic structure. The DL-Asp anhydrous crystal, on the other hand, exhibits a wide direct band gap, which suggests possible optoelectronic uses. Effective masses obtained for all crystals exhibit an anisotropy which must affect their electronic transport properties, with electric conduction more likely along a direction parallel to the molecular planes for the L-Asp anhydrous system. The analysis of the
density of electronic states revealed the contributions per atom and per functional group to the valence and conduction band states. A nice agreement was found between the theoretical
IR and Raman spectra and the experimental data for the L-Asp anhydrous crystal, allowing for an adequate interpretation of the normal modes involved in each spectral feature. / SimulaÃÃes computacionais no formalismo DFT (Density Functional Theory) foram realizadas para a determinaÃÃo das propriedades estruturais, eletrÃnicas e vibracionais de cristais de Ãcido aspÃrtico (Asp) nas formas cristalinas L-Asp anidro, L-Asp monohidratado e DL-Asp anidro. O Ãcido aspÃrtico à um aminoÃcido nÃo essencial com papel na fisiologia da resistÃncia fÃsica, atuando como neurotransmissor excitatÃrio no cÃrebro, contribuindo para a eliminaÃÃo do excesso de toxinas nas cÃlulas, alÃm de ser capaz de afetar a sÃntese de RNA. Os cÃdigos CASTEP (para cristais) e GAUSSIAN (para molÃculas) foram utilizados no presente estudo. Para os cristais de Ãcido aspÃrtico, os funcionais de troca e correlaÃÃo LDA e GGA-PBE foram empregados nas simulaÃÃes, este Ãltimo incluindo correÃÃes empÃricas para interaÃÃes dispersivas (PBE+TS) de acordo com o esquema de Tkatchenko e Scheffler. Os cÃlculos moleculares foram realizados utilizando o programa Gaussian09 com o funcional hibrido de troca e correlaÃÃo B3LYP e o conjunto de base 6-311+G(d,p). As molÃculas foram simuladas em fase gasosa e em meio aquoso (modelo de solvataÃÃo contÃnuo PCM). As estruturas cristalinas (cÃlulas unitÃrias otimizadas) e moleculares (conformaÃÃes de menor energia) obtidas nos cÃlculos foram comparadas com resultados experimentais e outros cÃlculos teÃricos. No caso do cristal L-Asp anidro, a absorÃÃo Ãptica e os espectros vibracionais IR e Raman tambÃm foram confrontados com medidas experimentais, e sua estrutura de bandas sugere um possÃvel carÃter semicondutor. No caso do cristal L-Asp monohidratado, um gap indireto 0,1 eV maior do que o do cristal anidro reflete o impacto da Ãgua sobre a estrutura eletrÃnica desse cristal. O cristal DL-Asp anidro, por outro lado, exibe um gap direto largo, o que sugere possÃveis usos em optoeletrÃnica. As massas efetivas obtidas para todos os cristais revelam uma anisotropia das propriedades de transporte eletrÃnico, sendo a conduÃÃo elÃtrica mais favorÃvel na direÃÃo paralela aos planos moleculares para o caso L-Asp anidro. A anÃlise da densidade de estados eletrÃnicos permitiu estabelecer a contribuiÃÃo por Ãtomo e por grupo
funcional para os estados das bandas de valÃncia e conduÃÃo e um Ãtimo acordo foi obtido entre os espectros vibracionais IR e Raman teÃricos e experimentais do cristal L-Asp anidro, permitindo uma adequada interpretaÃÃo dos modos normais envolvidos em cada pico espectral.
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Structure électronique et compétition de phases dans les semi-conducteurs Cu-(In,Ga)-Se, Ga-Se et In-Se : calculs premiers principes basés sur divers potentiels d'échange-corrélation / Electronic structure and competition of phases in Cu-(In,Ga)-Se, Ga-Se and In-Se semiconductors : first-principles calculations based on different exchange-correlation potentialsYoussef Srour, Juliana 14 December 2016 (has links)
Afin de pouvoir utiliser les nouveaux matériaux semi-conducteurs dans les domaines de l’électronique et de l’optique, il faut parvenir à comprendre leur «structure électronique», ou plus précisément le positionnement des niveaux d’énergie des électrons impliqués dans l’absorption / émission d’un photon. Les propriétés électroniques, sensibles à la composition chimique et à la structure du matériau, sont théoriquement accessibles en résolvant les équations de la mécanique quantique sur ordinateur. Ce travail porte sur des simulations théoriques de la structure électronique de semi-conducteurs binaires constitués d'indium (ou du gallium) et de sélénium, ainsi que de leurs "dérivés" à base de cuivre. La stabilité relative des phases cristallographiques de certains composés In-Se et Ga-Se a été évaluée, ce qui a permis d’expliquer certaines tendances connues et de formuler des prédictions. Les résultats obtenus seront particulièrement utiles dans le domaine du photovoltaïque. Les simulations numériques ont été réalisées dans le cadre de la théorie de la fonctionnelle de la densité (DFT), visant les structures cristallines d'équilibre et les propriétés électroniques de quelques semi-conducteurs binaires ou (pseudo)ternaires à base de Cu, In, Ga et Se. Les systèmes étudiés possèdent la même structure à courte portée (environnement tétraédrique des cations et anions) mais diffèrent à longue portée. Les composés binaires (Ga/In)Se, (Ga/In)2Se3 constituent des références importantes dans les diagrammes de phases des systèmes à base de (Cu, In, Se) et (Cu, Ga, Se), au sein desquels figurent les phases potentiellement utiles dans le domaine du photovoltaïque. Le travail comprend deux chapitres d'introduction et trois chapitres exposant des résultats nouveaux / In order to optimally use new semiconductor materials in electronics or optics, one needs to understand their “electronic structure”, that is, the mutual placement of the electron energy levels concerned by the processes of absorption / emission of a photon. The electronic properties, which depend on the material’s chemical composition and crystal structure, may be assessed by theory via solving quantum-mechanical equations on a computer. The present work deals with theory simulations of electronic structure done for several binary semiconductors consisting of indium (or gallium) and selenium, moreover for their “derivatives” containing copper. As a result, the relative stability of crystallographic phases of some Ga-Se and In-Se compounds has been assessed, explaining the known trends and making predictions. The results are expected to be useful for current works in photovoltaics. The numerical simulations have been performed within the density functional theory (DFT), aimed at the equilibrium crystal structures and electronic characteristics of several binary or (pseudo)ternary semiconductors based on Cu, In, Ga and Se. The compounds under study share similar short-range order features (tetrahedral environment of both cations and anions), differently assembled on a long-range scale. The binary compounds (Ga/In)Se, (Ga/In)2Se3 mark important end points at the phase diagrams of the (Cu,In,Se) and (Cu,Ga,Se) systems that cover a number of phases relevant, e.g., for applications in photovoltaics. The work comprises two chapters of introduction and three outlining novel results
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Spektroskopické a teoretické studium supramolekulárních komplexů symetrických porfyrinů s chirálními guesty / Spektroskopické a teoretické studium supramolekulárních komplexů symetrických porfyrinů s chirálními guestyBřezina, Václav January 2014 (has links)
Certain types of porphyrins can be used as achiral agent for determination of enantiomeric excess (ee) of chiral molecules. Particular organic chiral molecule (guest) and porphyrin (host) form host-guest complex while inducing nonequiv- alency of particular proton resonances in symmetrical host. It causes splitting of NMR signals linearly dependent on ee of guest. In this work we investigated com- plexation of di-brombenzylated oxoporphyrin with chiral camphorsulfonic acid. NMR titration revealed that they form complex with 1:1 stoichiometry with as- sociation constant K ≈ 5 × 104 l/mol. We confirmed linear dependence of split- ting of host β-protons on ee of guest. Low temperature measurements revealed two conformations of host-guest complex with population around 0.7:0.3 (at −60 ◦ C). DFT quantum mechanical computations at BLYP/3-21G* level revealed also two conformations with population 0.79:0.21. NMR shifts were computed on this geometries with method GIAO/PBE1PBE/6-31G(2df,2pd) and compared to experimental values. 1
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Exchange-Correlation Kernels Within Time-Dependent Density Functional Theory For Ground-State and Excited-State PropertiesNepal, Niraj, 0000-0002-7281-3268 January 2020 (has links)
The exact exchange-correlation kernel is a functional derivative of the exact time-dependent exchange-correlation (XC) potential with respect to the time-dependent density, evaluated at the ground-state density. As the XC potential is not known, the exact kernel is also unavailable. Therefore, it must be modeled either using many-body perturbation theory or by satisfying the exact constraints for various prototype systems such as the paradigm uniform electron gas (UEG). The random phase approximation (RPA) neglects the kernel, therefore, fails to provide the accurate ground- and excited-state properties for various systems from a simple uniform electron gas to more complex periodic ones. There are numerous corrections to RPA available, including kernel-corrected RPA, often called the beyond-RPA (bRPA) methods.
In this work, we employed various bRPA methods for a diverse set of systems together with RPA. At first, we applied RPA based methods to study the phase stability of the cesium halides. Cesium halides phase stability is one of the stringent tests for a density functional approximation to assess its accuracy for dispersion interaction. Experimentally, CsF prefers the rocksalt (B1) phase, while the other halides CsCl, CsBr, and CsI prefer the cesium chloride (B2) phase. Without dispersion interaction, PBE and PBE0 predict all halides to prefer the B1 phase. However, all RPA based methods predict the experimental observations. The bRPA methods usually improve the quantitative prediction over RPA for the ground-state equilibrium properties of cesium halides. Next, we explored binary intermetallic alloys, where we showed that RPA successfully predicts the accurate formation energies of weakly bonded alloys. However, a kernel corrected RPA is needed when dealing with strongly bonded alloys with partially filled d-band metals. We utilized the renormalized ALDA (rALDA) and rAPBE kernel as bRPA methods.
Exact constraints and appropriate norms such as the uniform electron gas are very useful to construct various approximations for the exchange-correlation potentials in the ground-state, and the exchange-correlation kernel in the linear-response theory within the TDDFT. These mathematical formulations not only guide us to formulate more robust nonempirical methods, but they also have more predictive power. We showed the importance of these constraints by calculating plasmon dispersion of the uniform electron gas using the non-local, energy-optimized (NEO) kernel using only a few constraints. More predictive power comes with more constraint satisfaction. As a result, we developed a new wavevector- and frequency-dependent exchange-correlation kernel that satisfies all the constraints that it should satisfy with a real frequency. It gives accurate ground-state correlation energy and describes the charge density wave in low-density UEG. It also predicts an accurate plasmon dispersion with a finite lifetime at wavevectors less than the critical one, where the plasmon dispersion meets the electron-hole continuum. / Physics
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