Neural-network approach to modeling liquid crystals in complex confinement

Finding the structure of a confined liquid crystal is a difficult task since both the density and order parameter profiles are nonuniform. Starting from a microscopic model and density-functional theory, one has to either (i) solve a nonlinear, integral Euler-Lagrange equation, or (ii) perform a direct multidimensional free energy minimization. The traditional implementations of both approaches are computationally expensive and plagued with convergence problems. Here, as an alternative, we introduce an unsupervised variant of the multilayer perceptron (MLP) artificial neural network for minimizing the free energy of a fluid of hard nonspherical particles confined between planar substrates of variable penetrability. We then test our algorithm by comparing its results for the structure (density-orientation profiles) and equilibrium free energy with those obtained by standard iterative solution of the Euler-Lagrange equations and with Monte Carlo simulation results. Very good agreement is found and the MLP method proves competitively fast, flexible, and refinable. Furthermore, it can be readily generalized to the richer experimental patterned-substrate geometries that are now experimentally realizable but very problematic to conventional theoretical treatments.

The key role of coligands in novel ruthenium(II)-cyclopentadienyl bipyridine derivatives: Ranging from non-cytotoxic to highly cytotoxic compounds

A new family of eight ruthenium(II)-cyclopentadienyl bipyridine derivatives, bearing nitrogen, sulfur, phosphorous and carbonyl sigma bonded coligands, has been synthesized. Compounds bearing nitrogen bonded coligands were found to be unstable in aqueous solution, while the others presented appropriate stabilities for the biologic assays and pursued for determination of IC50 values in ovarian (A2780) and breast (MCF7 and MDAMB231) human cancer cell lines. These studies were also carried out for the [5: HSA] and [6: HSA] adducts (HSA = human serum albumin) and a better performance was found for the first case. Spectroscopic, electrochemical studies by cyclic voltammetry and density functional theory calculations allowed us to get some understanding on the electronic flow directions within the molecules and to find a possible clue concerning the structural features of coligands that can activate bipyridyl ligands toward an increased cytotoxic effect. X-ray structure analysis of compound [Ru(eta(5)-C5H5)(bipy)(PPh3)][PF6] (7; bipy = bipyridine) showed crystallization on C2/c space group with two enantiomers of the [Ru(eta(5)-C5H5)(bipy)(PPh3)](+) cation complex in the racemic crystal packing. (C) 2015 Elsevier Inc All rights reserved.

The key role of coligands in novel ruthenium(II)-cyclopentadienyl bipyridine derivatives: ranging from non-cytotoxic to highly cytotoxic compounds

A new family of eight ruthenium(II)-cyclopentadienyl bipyridine derivatives, bearing nitrogen, sulfur, phosphorous and carbonyl sigma bonded coligands, has been synthesized. Compounds bearing nitrogen bonded coligands were found to be unstable in aqueous solution, while the others presented appropriate stabilities for the biologic assays and pursued for determination of IC50 values in ovarian (A2780) and breast (MCF7 and MDAMB231) human cancer cell lines. These studies were also carried out for the [5: HSA] and [6: HSA] adducts (HSA=human serum albumin) and a better performance was found for the first case. Spectroscopic, electrochemical studies by cyclic voltammetry and density functional theory calculations allowed us to get some understanding on the electronic flow directions within the molecules and to find a possible clue concerning the structural features of coligands that can activate bipyridyl ligands toward an increased cytotoxic effect. X-ray structure analysis of compound [Ru(η(5)-C5H5)(bipy)(PPh3)][PF6] (7; bipy=bipyridine) showed crystallization on C2/c space group with two enantiomers of the [Ru(η(5)-C5H5)(bipy)(PPh3)](+) cation complex in the racemic crystal packing.

Oxygen vacancies as active sites for water dissociation on rutile TiO2(110)

Through an interplay between scanning tunneling microscopy experiments and density functional theory calculations, we determine unambiguously the active surface site responsible for the dissociation of water molecules adsorbed on rutile TiO2(110). Oxygen vacancies in the surface layer are shown to dissociate H2O through the transfer of one proton to a nearby oxygen atom, forming two hydroxyl groups for every vacancy. The amount of water dissociation is limited by the density of oxygen vacancies present on the clean surface exclusively. The dissociation process sets in as soon as molecular water is able to diffuse to the active site.

Bonding of gold nanoclusters to oxygen vacancies on rutile TiO2(110)

Through an interplay between scanning tunneling microscopy (STM) and density functional theory (DFT) calculations, we show that bridging oxygen vacancies are the active nucleation sites for Au clusters on the rutile TiO2(110) surface. We find that a direct correlation exists between a decrease in density of vacancies and the amount of Au deposited. From the DFT calculations we find that the oxygen vacancy is indeed the strongest Au binding site. We show both experimentally and theoretically that a single oxygen vacancy can bind 3 Au atoms on average. In view of the presented results, a new growth model for the TiO2(110) system involving vacancy-cluster complex diffusion is presented.

Molecular modeling of asymmetric induction in heterogeneously catalyzed hydrogenation of the C=O bond

Modifiering av metallytor med starkt adsorberade kirala organiska molekyler är eventuellt den mest relevanta teknik man vet i dag för att skapa kirala ytor. Den kan utnyttjas i katalytisk produktion av enantiomeriskt rena kirala föreningar som behövs t.ex. som läkemedel och aromkemikalier. Trots många fördelar av asymmetrisk heterogen katalys jämfört med andra sätt för att få kirala föreningar, har den ändå inte blivit ett allmänt verktyg för storskaliga tillämpningar. Detta beror t.ex. på brist på djupare kunskaper i katalytiska reaktionsmekanismer och ursprunget för asymmetrisk induktion. I denna studie användes molekylmodelleringstekniker för att studera asymmetriska, heterogena katalytiska system, speciellt hydrering av prokirala karbonylföreningar till motsvarande kirala alkoholer på cinchona-alkaloidmodifierade Pt-katalysatorer. 1-Fenyl-1,2-propandion (PPD) och några andra föreningar, som innehåller en prokiral C=O-grupp, användes som reaktanter. Konformationer av reaktanter och cinchona-alkaloider (som kallas modifierare) samt vätebundna 1:1-komplex mellan dem studerades i gas- och lösningsfas med metoder som baserar sig på vågfunktionsteori och täthetsfunktionalteori (DFT). För beräkningen av protonaffiniteter användes också högst noggranna kombinationsmetoder såsom G2(MP2). Den relativa populationen av modifierarnas konformationer varierade som funktion av modifieraren, dess protonering och lösningsmedlet. Flera reaktant–modifierareinteraktionsgeometrier beaktades. Slutsatserna på riktning av stereoselektivitet baserade sig på den relativa termodynamiska stabiliteten av de diastereomeriska reaktant–modifierare-komplexen samt energierna hos π- och π*-orbitalerna i den reaktiva karbonylgruppen. Adsorption och reaktioner på Pt(111)-ytan betraktades med DFT. Regioselektivitet i hydreringen av PPD och 2,3-hexandion kunde förklaras med molekyl–yta-interaktioner. Storleken och formen av klustret använt för att beskriva Pt-ytan inverkade inte bara på adsorptionsenergierna utan också på de relativa stabiliteterna av olika adsorptionsstrukturer av en molekyl. Populationerna av modifierarnas konformationer i gas- och lösningsfas korrelerade inte med populationerna på Pt-ytan eller med enantioselektiviteten i hydreringen av PPD på Pt–cinchona-katalysatorer. Vissa modifierares konformationer och reaktant–modifierare-interaktionsgeometrier var stabila bara på metallytan. Teoretiskt beräknade potentialenergiprofiler för hydrering av kirala α-hydroxiketoner på Pt implicerade preferens för parvis additionsmekanism för väte och selektiviteter i harmoni med experimenten. De uppnådda resultaten ökar uppfattningen om kirala heterogena katalytiska system och kunde därför utnyttjas i utvecklingen av nya, mera aktiva och selektiva kirala katalysatorer.

Surface geometry of Cu{531}

We present a combined quantitative low-energy electron diffraction (LEED) and density-functional theory (DFT) study of the chiral Cu{531} surface. The surface shows large inward relaxations with respect to the bulk interlayer distance of the first two layers and a large expansion of the distance between the fourth and fifth layers. (The latter is the first layer having the same coordination as the Cu atoms in the bulk.) Additional calculations have been performed to study the likelihood of faceting by comparing surface energies of possible facet terminations. No overall significant reduction in energy with respect to planar {531} could be found for any of the tested combinations of facets, which is in agreement with the experimental findings.

Direct probing of photoinduced electron transfer in a self- assembled biomimetic [2Fe2S]-hydrogenase complex using ultrafast vibrational spectroscopy

A pyridyl-functionalized diiron dithiolate complex, [μ-(4-pyCH2−NMI-S2)Fe2(CO)6] (3, py = pyridine(ligand), NMI = naphthalene monoimide) was synthesized and fully characterized. In the presence of zinc tetraphenylporphyrin (ZnTPP), a self-assembled 3·ZnTPP complex was readily formed in CH2Cl2 by the coordination of the pyridyl nitrogen to the porphyrin zinc center. Ultrafast photoinduced electron transfer from excited ZnTPP to complex 3 in the supramolecular assembly was observed in real time by monitoring the ν(CO) and ν(CO)NMI spectral changes with femtosecond time-resolved infrared (TRIR) spectroscopy. We have confirmed that photoinduced charge separation produced the monoreduced species by comparing the time-resolved IR spectra with the conventional IR spectra of 3•− generated by reversible electrochemical reduction. The lifetimes for the charge separation and charge recombination processes were found to be τCS = 40 ± 3 ps and τCR = 205 ± 14 ps, respectively. The charge recombination is much slower than that in an analogous covalent complex, demonstrating the potential of a supramolecular approach to extend the lifetime of the chargeseparated state in photocatalytic complexes. The observed vibrational frequency shifts provide a very sensitive probe of the delocalization of the electron-spin density over the different parts of the Fe2S2 complex. The TR and spectro-electrochemical IR spectra, electron paramagnetic resonance spectra, and density functional theory calculations all show that the spin density in 3•− is delocalized over the diiron core and the NMI bridge. This delocalization explains why the complex exhibits low catalytic dihydrogen production even though it features a very efficient photoinduced electron transfer. The ultrafast porphyrin-to-NMIS2−Fe2(CO)6 photoinduced electron transfer is the first reported example of a supramolecular Fe2S2-hydrogenase model studied by femtosecond TRIR spectroscopy. Our results show that TRIR spectroscopy is a powerful tool to investigate photoinduced electron transfer in potential dihydrogen-producing catalytic complexes, and that way to optimize their performance by rational approaches.

Tetrachlorocarbonyliridates: Water-Soluble Carbon Monoxide Releasing Molecules Rate-Modulated by the Sixth Ligand

A new family of compounds is presented as potential carbon monoxide releasing molecules (CORMs). These compounds, based on tetrachlorocarbonyliridate(III) derivatives, were synthesized and fully characterized by X-ray diffraction, electrospray mass spectrometry, IR. NMR, and density functional theory calculations. The rate of CO release was studied via the myoglobin assay. The results showed that the rate depends on the nature of the sixth ligand, trans to CO, and that a significant modulation on the release rate can be produced by changing the ligand. The reported compounds are soluble in aqueous media, and the rates of CO release are comparable with those for known CORMs, releasing CO at a rate of 0.03-0.58 mu M min(-1) in a 10 mu M solution of myoglobin and 10 mu M of the complexes.

Optical energy storage properties of Sr(2)MgSi(2)O(7):Eu(2+),R(3+) persistent luminescence materials

The details of the mechanism of persistent luminescence were probed by investigating the trap level structure of Sr(2)MgSi(2)O(7):Eu(2+),R(3+) materials (R: Y, La-Lu, excluding Pm and Eu) with thermoluminescence (TL) measurements and Density Functional Theory (DFT) calculations. The TL results indicated that the shallowest traps for each Sr(2)MgSi(2)O(7):Eu(2+),R(3+) material above room temperature were always ca. 0.7 eV corresponding to a strong TL maximum at ca. 90 A degrees C. This main trap energy was only slightly modified by the different co-dopants, which, in contrast, had a significant effect on the depths of the deeper traps. The combined results of the trap level energies obtained from the experimental data and DFT calculations suggest that the main trap responsible for the persistent luminescence of the Sr(2)MgSi(2)O(7):Eu(2+),R(3+) materials is created by charge compensation lattice defects, identified tentatively as oxygen vacancies, induced by the R(3+) co-dopants.

Modelagem molecular na caracterização eletrônica de oligopeptídeos e na descrição quântica da interação fármaco-receptor

In this dissertation, the theoretical principles governing the molecular modeling were applied for electronic characterization of oligopeptide α3 and its variants (5Q, 7Q)-α3, as well as in the quantum description of the interaction of the aminoglycoside hygromycin B and the 30S subunit of bacterial ribosome. In the first study, the linear and neutral dipeptides which make up the mentioned oligopeptides were modeled and then optimized for a structure of lower potential energy and appropriate dihedral angles. In this case, three subsequent geometric optimization processes, based on classical Newtonian theory, the semi-empirical and density functional theory (DFT), explore the energy landscape of each dipeptide during the search of ideal minimum energy structures. Finally, great conformers were described about its electrostatic potential, ionization energy (amino acids), and frontier molecular orbitals and hopping term. From the hopping terms described in this study, it was possible in subsequent studies to characterize the charge transport propertie of these peptides models. It envisioned a new biosensor technology capable of diagnosing amyloid diseases, related to an accumulation of misshapen proteins, based on the conductivity displayed by proteins of the patient. In a second step of this dissertation, a study carried out by quantum molecular modeling of the interaction energy of an antibiotic ribosomal aminoglicosídico on your receiver. It is known that the hygromycin B (hygB) is an aminoglycoside antibiotic that affects ribosomal translocation by direct interaction with the small subunit of the bacterial ribosome (30S), specifically with nucleotides in helix 44 of the 16S ribosomal RNA (16S rRNA). Due to strong electrostatic character of this connection, it was proposed an energetic investigation of the binding mechanism of this complex using different values of dielectric constants (ε = 0, 4, 10, 20 and 40), which have been widely used to study the electrostatic properties of biomolecules. For this, increasing radii centered on the hygB centroid were measured from the 30S-hygB crystal structure (1HNZ.pdb), and only the individual interaction energy of each enclosed nucleotide was determined for quantum calculations using molecular fractionation with conjugate caps (MFCC) strategy. It was noticed that the dielectric constants underestimated the energies of individual interactions, allowing the convergence state is achieved quickly. But only for ε = 40, the total binding energy of drug-receptor interaction is stabilized at r = 18A, which provided an appropriate binding pocket because it encompassed the main residues that interact more strongly with the hygB - C1403, C1404, G1405, A1493, G1494, U1495, U1498 and C1496. Thus, the dielectric constant ≈ 40 is ideal for the treatment of systems with many electrical charges. By comparing the individual binding energies of 16S rRNA nucleotides with the experimental tests that determine the minimum inhibitory concentration (MIC) of hygB, it is believed that those residues with high binding values generated bacterial resistance to the drug when mutated. With the same reasoning, since those with low interaction energy do not influence effectively the affinity of the hygB in its binding site, there is no loss of effectiveness if they were replaced.

Sistemas Nanoestruturados: Heteroestruturas Quasi-Periódicas de Nitretos e Cálculos Ab initio em Polimorfos CaCO3

The physical properties and the excitations spectrum in oxides and semiconductors materials are presented in this work, whose the first part presents a study on the confinement of optical phonons in artificial systems based on III-V nitrides, grown in periodic and quasiperiodic forms. The second part of this work describes the Ab initio calculations which were carried out to obtain the optoeletronic properties of Calcium Oxide (CaO) and Calcium Carbonate (CaCO3) crystals. For periodic and quasi-periodic superlattices, we present some dynamical properties related to confined optical phonons (bulk and surface), obtained through simple theories, such as the dielectric continuous model, and using techniques such as the transfer-matrix method. The localization character of confined optical phonon modes, the magnitude of the bands in the spectrum and the power laws of these structures are presented as functions of the generation number of sequence. The ab initio calculations have been carried out using the CASTEP software (Cambridge Total Sequential Energy Package), and they were based on ultrasoft-like pseudopotentials and Density Functional Theory (DFT). Two di®erent geometry optimizations have been e®ectuated for CaO crystals and CaCO3 polymorphs, according to LDA (local density approximation) and GGA (generalized gradient approximation) approaches, determining several properties, e. g. lattice parameters, bond length, electrons density, energy band structures, electrons density of states, e®ective masses and optical properties, such as dielectric constant, absorption, re°ectivity, conductivity and refractive index. Those results were employed to investigate the confinement of excitons in spherical Si@CaCO3 and CaCO3@SiO2 quantum dots and in calcium carbonate nanoparticles, and were also employed in investigations of the photoluminescence spectra of CaCO3 crystal

Tetrachlorocarbonyliridates: Water-Soluble Carbon Monoxide Releasing Molecules Rate-Modulated by the Sixth Ligand

A new family of compounds is presented as potential carbon monoxide releasing molecules (CORMs). These compounds, based on tetrachlorocarbonyliridate(III) derivatives, were synthesized and fully characterized by X-ray diffraction, electrospray mass spectrometry, IR. NMR, and density functional theory calculations. The rate of CO release was studied via the myoglobin assay. The results showed that the rate depends on the nature of the sixth ligand, trans to CO, and that a significant modulation on the release rate can be produced by changing the ligand. The reported compounds are soluble in aqueous media, and the rates of CO release are comparable with those for known CORMs, releasing CO at a rate of 0.03-0.58 mu M min(-1) in a 10 mu M solution of myoglobin and 10 mu M of the complexes.

Estudo do transporte eletrônico em nanoestruturas baseadas em carotenoides e tétrades com fulereno C60

Neste Trabalho é apresentado um estudo teórico da estrutura eletrônica de uma molécula de fulereno C60 com junções em quatro terminais baseados em grupos doadores de elétron – etratiofulvaleno (TTF) – e grupos aceitadores de elétrons – fenilpropanodinila (FPP) e dispositivos moleculares baseados em derivados dos Carotenoides. O mecanismo de transporte investigado para os derivados dos Carotenoides foram utilizados para o melhor entendimento das curvas de Fowler- Nordheim (FN) e Millikan-Lauritsen (ML) para os sistemas baseados em fulereno C60. Em todos os casos foi possível confirmar que a análise empírica de Millikan-Lauritsen (ML) também é suficiente para descrever em todos os aspectos a espectroscopia de voltagem de transição (TVS). Para estudar os sistemas, foram feitas otimizações de geometria sistematicamente e observado uma transferência eletrônica calculada por métodos derivados de Hartree-Fock e Teoria do Funcional Densidade (DFT). Os resultados apresentados mostram um estudo detalhado do rearranjo de carga molecular para a estrutura, que sob a ação de um campo elétrico externo apontou que o transporte de carga está diretamente ligado ao tipo de junção que esse sistema é submetido de forma que a voltagem aplicada é intensa o bastante para criar um potencial de saturação nos sistemas em estudo: fulereno C60 com três terminais de tetratiofulvaleno e um terminal de fenil-propanodinila (C60-(TTF)₃-FPP); fulereno C60 com quatros terminais de fenil-propanodinila (C60-(FPP)₄). Os resultados mostram que se tem um retificador molecular que pode trabalhar corretamente como um retificador macroscópico.

Estudo químico quântico relativístico das propriedades eletrônicas e estruturais dos compostos Aun(n=1-5), AuOn-e AuSn - (n=1-2) e AuH

Pós-graduação em Ciência e Tecnologia de Materiais - FC