A study of neolignan compounds with biological activity against Paracoccidioides brasiliensis by using quantum chemical and chemometric methods

Métodos quimiométricos (estatísticos) são empregados para classificar um conjunto de compostos derivados de neolignanas com atividade biológica contra a Paracoccidioides brasiliensis. O método AM1 (Austin Model 1) foi utilizado para calcular um conjunto de descritores moleculares (propriedades) para os compostos em estudo. A seguir, os descritores foram analisados utilizando os seguintes métodos de reconhecimento de padrões: Análise de Componentes Principais (PCA), Análise Hierárquica de Agrupamentos (HCA) e o método de K-vizinhos mais próximos (KNN). Os métodos PCA e HCA mostraram-se bastante eficientes para classificação dos compostos estudados em dois grupos (ativos e inativos). Três descritores moleculares foram responsáveis pela separação entre os compostos ativos e inativos: energia do orbital molecular mais alto ocupado (EHOMO), ordem de ligação entre os átomos C1'-R7 (L14) e ordem de ligação entre os átomos C5'-R6 (L22). Como as variáveis responsáveis pela separação entre compostos ativos e inativos são descritores eletrônicos, conclui-se que efeitos eletrônicos podem desempenhar um importante papel na interação entre receptor biológico e compostos derivados de neolignanas com atividade contra a Paracoccidioides brasiliensis.

Structure-activity relationship of compounds which are anti-schistosomiasis active

O método do orbital molecular AM1 foi empregado para calcular um conjunto de descritores moleculares para vinte neolignanas sintéticas com atividade anti-esquistossomose. O método de reconhecimento de padrão (análise de componentes principais ACP, análise de conglomerados AC e análise de discriminante) foi utilizado para obter a relação entre a estrutura molecular e a atividade biológica. O conjunto de moléculas foi classificado em dois grupos de acordo com seus graus de atividade biológica. Estes resultados permitem que, projete-se racionalmente novos compostos, potenciais candidatos à síntese e à avaliação biológica.

Modelamento do transporte eletrônico em dispositivos moleculares

No presente trabalho, simulamos as propriedades de transporte e espectro de absorção do composto orgânico Vermelho de Etila. Este é o primeiro estudo teórico de um indicador específico de pH utilizado como nanodispositivo, com base na teoria quântica e no modelo de transporte não-difuso. A distribuição de carga ao longo da molécula é determinada através da técnica, Ab initio, como uma função de um campo elétrico externo. Baseado em um modelo de multiníveis ressonantes também calculamos a corrente como função da tensão de polarização. O acúmulo de carga e a corrente apresentam comportamento semelhante, como a condução do tipo ressonante e curvas carga-tensão e corrente-tensão assimétricas. Os principais resultados sugerem que o sistema presente poderia funcionar como um transistor molecular bi-direcional. Estendemos esta metodologia de análise para outro dispositivo molecular, mas composto de três terminais. Para este sistema, nossa descoberta principal é a resistência diferencial negativa (RDN) na carga Q como uma função do campo elétrico externo. Para explicar este efeito RDN, aplicamos um modelo capacitivo fenomenológico, também baseado em um sistema de multiníveis localizados (que podem ser os LUMOs – Lowest Unoccupied Molecular Orbital – Orbitais moleculares desocupados mais baixos). A capacitância descreve, por efeito de carregamento, a causa do bloqueio de Coulomb (BC) no transporte. Mostramos que o efeito BC dá origem a uma RDN para um conjunto adequado de parâmetros fenomenológicos como: taxa de tunelamento e energia de carregamento. O perfil da RDN obtida nas duas metodologias, ab initio e fenomenológica, estão em comum acordo.

Transporte eletrônico e quiralidade molecular: um estudo de dispositivos orgânicos em sistemas de dois terminais

No presente trabalho, investigamos o transporte eletrônico molecular em dois compostos orgânicos, o Ponceau SS (PSS) e o Oligo-(para)fenileno-vinileno (PPV) através de cálculos ab initio e função de Green de não equilíbrio (FGNE). Estes métodos demonstraram equivalência para a descrição destes dispositivos moleculares. Fizemos cálculos quânticos para o Hamiltoniano derivado de Hartree-Fock (HF) e obtivemos as propriedades de corrente-voltagem (I-V) para as duas estruturas moleculares. Com o método FGNE conseguimos modelar o transporte através de um sistema de multiníveis eletrônicos obtendo a corrente descrevendo as regiões de ressonância e a assimetria do sistema. Como resposta o PSS demonstrou assimetria para polarizações direta e reversa e a ressonância é alcançada mostrando que o dispositivo opere como um transistor molecular bi-direcional. Para o PPV investigamos também as propriedades geométricas através da conexão entre transporte eletrônico e o grau de quiralidade molecular que foi calculado usando o índice quiral que depende apenas das posições atômicas. Obtivemos que moléculas quirais e propriedades estruturais podem induzir uma assimetria no transporte eletrônico, resultando num processo de retificação. Também obtivemos que a resposta elétrica (I-V) e momento de dipolo elétrico são proporcionais ao grau de quiralidade molecular. Estes resultados sugerem que o transporte eletrônico neste sistema pode ser explorado na avaliação do seu grau de quiralidade.

Measuring Quantum Capacitance in Energetically Addressable Molecular Layers

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Stretching of BDT-gold molecular junctions: thiol or thiolate termination?

It is often assumed that the hydrogen atoms in the thiol groups of a benzene-1,4-dithiol dissociate when Au-benzene-1,4-dithiol-Au junctions are formed. We demonstrate, by stability and transport property calculations, that this assumption cannot be made. We show that the dissociative adsorption of methanethiol and benzene-1,4-dithiol molecules on a flat Au(111) surface is energetically unfavorable and that the activation barrier for this reaction is as high as 1 eV. For the molecule in the junction, our results show, for all electrode geometries studied, that the thiol junctions are energetically more stable than their thiolate counterparts. Due to the fact that density functional theory (DFT) within the local density approximation (LDA) underestimates the energy difference between the lowest unoccupied molecular orbital and the highest occupied molecular orbital by several electron-volts, and that it does not capture the renormalization of the energy levels due to the image charge effect, the conductance of the Au-benzene-1,4-dithiol-Au junctions is overestimated. After taking into account corrections due to image charge effects by means of constrained-DFT calculations and electrostatic classical models, we apply a scissor operator to correct the DFT energy level positions, and calculate the transport properties of the thiol and thiolate molecular junctions as a function of the electrode separation. For the thiol junctions, we show that the conductance decreases as the electrode separation increases, whereas the opposite trend is found for the thiolate junctions. Both behaviors have been observed in experiments, therefore pointing to the possible coexistence of both thiol and thiolate junctions. Moreover, the corrected conductance values, for both thiol and thiolate, are up to two orders of magnitude smaller than those calculated with DFT-LDA. This brings the theoretical results in quantitatively good agreement with experimental data.

Influence of Mg on the structural and optical properties of LiNbO3 thin films grown by polymeric precursor method

A polymeric precursor solution was used to deposit pure and Mg doped LiNbO3 thin films on sapphire substrates by spin-coating. The effects of magnesium addition on crystallinity, morphology and optical properties of the annealed films were investigated. X-ray diffraction patterns indicate the oriented growth of the films. Phi-scan diffraction evidenced the epitaxial growth with two in-plane variants. AFM studies show that the films are very homogeneous, dense and present smooth surfaces. The refractive index and optical losses obtained by the prism coupling method were influenced by the magnesium addition.

Estrutura eletrônica de derivados de politieno[3,4-b]-tiofeno-co-benzoditiofeno para aplicação em camadas ativas de células solares orgânicas

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Determination of chlorine in food samples via the AlCl molecule using high-resolution continuum source molecular absorption spectrometry in a graphite furnace

Determination of chlorine using the molecular absorption of aluminum mono-chloride (AlCl) at the 261.418 nm wavelength was accomplished by high-resolution continuum source molecular absorption spectrometry using a transversely heated graphite tube furnace with an integrated platform. For the analysis. 10 mu L of the sample followed by 10 mu L of a solution containing Al-Ag-Sr modifier, (1 g L-1 each), were directly injected onto the platform. A spectral interference due to the use of Al-Ag-Sr as mixed modifier was easily corrected by the least-squares algorithm present in the spectrometer software. The pyrolysis and vaporization temperatures were 500 degrees C and 2200 degrees C, respectively. To evaluate the feasibility of a simple procedure for the determination of chlorine in food samples present in our daily lives, two different digestion methods were applied, namely (A) an acid digestion method using HNO3 only at room temperature, and (B) a digestion method with Ag, HNO3 and H2O2, where chlorine is precipitated as a low-solubility salt (AgCl), which is then dissolved with ammonia solution. The experimental results obtained with method B were in good agreement with the certified values and demonstrated that the proposed method is more accurate than method A. This is because the formation of silver chloride prevented analyte losses by volatilization. The limit of detection (LOD, 3 sigma/s) for Cl in methods A and B was 18 mu g g(-1) and 9 mu g g(-1), respectively, 1.7 and 3.3 times lower compared to published work using inductively coupled plasma optical emission spectrometry, and absolute LODs were 2.4 and 1.2 ng, respectively. (C) 2012 Elsevier B.V. All rights reserved.

Probing unoccupied electronic states in aqueous solutions

Water is one of the most common compounds on earth and is essential for all biological activities. Water has, however, been a mystery for many years due to the large number of unusual chemical and physical properties, e.g. decreased volume during melting and maximum density at 4 °C. The origin of the anomalies behavior is the nature of the hydrogen bond. This thesis will presented an x-ray absorption spectroscopy (XAS) study to reveal the hydrogen bond structure in liquid water. The x-ray absorption process is faster than a femtosecond and thereby reflects the molecular orbital structure in a frozen geometry locally around the probed water molecules. The results indicate that the electronic structure of liquid water is significantly different from that of the solid and gaseous forms. The molecular arrangement in the first coordination shell of liquid water is actually very similar as the two-hydrogen-bonded configurations at the surface of ice. This discovery suggests that most molecules in liquid water have two-hydrogen-bonded configurations with one donor and one acceptor hydrogen bond compared to the four-hydrogen-bonded tetrahedral structure in ice. This result is controversial since the general picture is that the structure of liquid water is very similar to the structure of ice. The results are, however, consistent with x-ray and neutron diffraction data but reveals serious discrepancies with structures based on current molecular dynamics simulations. The two-hydrogen-bond configuration in liquid water is rigid and heating from 25 °C to 90 °C introduce a minor change in the hydrogen-bonded configurations. Furthermore, XAS studies of water in aqueous solutions show that ion hydration does not affect the hydrogen bond configuration of the bulk. Only water molecules in the close vicinity to the ions show changes in the hydrogen bond formation. XAS data obtained with fluorescence yield are sensitive enough to resolved electronic structure of water molecules in the first hydration sphere and to distinguish between different protonated species. Hence, XAS is a useful tool to provide insight into the local electronic structure of a hydrogen-bonded liquid and it is applied for the first time on water revealing unique information of high importance.

Studies of pure rotational spectra of isolated molecules and molecular adducts using pulsed jet Fourier transform microwave (PJ-FTM) spectroscopy

This thesis focuses on studying molecular structure and internal dynamics by using pulsed jet Fourier transform microwave (PJ-FTMW) spectroscopy combined with theoretical calculations. Several kinds of interesting chemical problems are investigated by analyzing the MW spectra of the corresponding molecular systems. First, the general aspects of rotational spectroscopy are summarized, and then the basic theory on molecular rotation and experimental method are described briefly. ab initio and density function theory (DFT) calculations that used in this thesis to assist the assignment of rotational spectrum are also included. From chapter 3 to chapter 8, several molecular systems concerning different kind of general chemical problems are presented. In chapter 3, the conformation and internal motions of dimethyl sulfate are reported. The internal rotations of the two methyl groups split each rotational transition into several components line, allowing for the determination of accurate values of the V3 barrier height to internal rotation and of the orientation of the methyl groups with respect to the principal axis system. In chapter 4 and 5, the results concerning two kinds of carboxylic acid bi-molecules, formed via two strong hydrogen bonds, are presented. This kind of adduct is interesting also because a double proton transfer can easily take place, connecting either two equivalent or two non-equivalent molecular conformations. Chapter 6 concerns a medium strong hydrogen bonded molecular complex of alcohol with ether. The dimer of ethanol-dimethylether was chosen as the model system for this purpose. Chapter 7 focuses on weak halogen…H hydrogen bond interaction. The nature of O-H…F and C-H…Cl interaction has been discussed through analyzing the rotational spectra of CH3CHClF/H2O. In chapter 8, two molecular complexes concerning the halogen bond interaction are presented.

Studies of degradation of organic solar cell materials using electrical scanning probe microscopy

Intense research is being done in the field of organic photovoltaics in order to synthesize low band-gap organic molecules. These molecules are electron donors which feature in combination with acceptor molecules, typically fullerene derivarntives, forming an active blend. This active blend has phase separated bicontinuous morphology on a nanometer scale. The highest recorded power conversionrnefficiencies for such cells have been 10.6%. Organic semiconductors differ from inorganic ones due to the presence of tightly bonded excitons (electron-hole pairs)resulting from their low dielectric constant (εr ≈2-4). An additional driving force is required to separate such Frenkel excitons since their binding energy (0.3-1 eV) is too large to be dissociated by an electric field alone. This additional driving force arises from the energy difference between the lowest unoccupied molecular orbital (LUMO) of the donor and the acceptor materials. Moreover, the efficiency of the cells also depends on the difference between the highest occupied molecular orbital (HOMO) of the donor and LUMO of the acceptor. Therefore, a precise control and estimation of these energy levels are required. Furthermore any external influences that change the energy levels will cause a degradation of the power conversion efficiency of organic solar cell materials. In particular, the role of photo-induced degradation on the morphology and electrical performance is a major contribution to degradation and needs to be understood on a nanometer scale. Scanning Probe Microscopy (SPM) offers the resolution to image the nanometer scale bicontinuous morphology. In addition SPM can be operated to measure the local contact potential difference (CPD) of materials from which energy levels in the materials can be derived. Thus SPM is an unique method for the characterization of surface morphology, potential changes and conductivity changes under operating conditions. In the present work, I describe investigations of organic photovoltaic materials upon photo-oxidation which is one of the major causes of degradation of these solar cell materials. SPM, Nuclear Magnetic Resonance (NMR) and UV-Vis spectroscopy studies allowed me to identify the chemical reactions occurring inside the active layer upon photo-oxidation. From the measured data, it was possible to deduce the energy levels and explain the various shifts which gave a better understanding of the physics of the device. In addition, I was able to quantify the degradation by correlating the local changes in the CPD and conductivity to the device characteristics, i.e., open circuit voltage and short circuit current. Furthermore, time-resolved electrostatic force microscopy (tr-EFM) allowed us to probe dynamic processes like the charging rate of the individual donor and acceptor domains within the active blend. Upon photo-oxidation, it was observed, that the acceptor molecules got oxidized first preventing the donor polymer from degrading. Work functions of electrodes can be tailored by modifying the interface with monomolecular thin layers of molecules which are made by a chemical reaction in liquids. These modifications in the work function are particularly attractive for opto-electronic devices whose performance depends on the band alignment between the electrodes and the active material. In order to measure the shift in work function on a nanometer scale, I used KPFM in situ, which means in liquids, to follow changes in the work function of Au upon hexadecanethiol adsorption from decane. All the above investigations give us a better understanding of the photo-degradation processes of the active material at the nanoscale. Also, a method to compare various new materials used for organic solar cells for stability is proposed which eliminates the requirement to make fully functional devices saving time and additional engineering efforts.

Novel algorithms for electronic structure based molecular dynamics with linear system-size scaling

Die vorliegende Arbeit behandelt die Entwicklung und Verbesserung von linear skalierenden Algorithmen für Elektronenstruktur basierte Molekulardynamik. Molekulardynamik ist eine Methode zur Computersimulation des komplexen Zusammenspiels zwischen Atomen und Molekülen bei endlicher Temperatur. Ein entscheidender Vorteil dieser Methode ist ihre hohe Genauigkeit und Vorhersagekraft. Allerdings verhindert der Rechenaufwand, welcher grundsätzlich kubisch mit der Anzahl der Atome skaliert, die Anwendung auf große Systeme und lange Zeitskalen. Ausgehend von einem neuen Formalismus, basierend auf dem großkanonischen Potential und einer Faktorisierung der Dichtematrix, wird die Diagonalisierung der entsprechenden Hamiltonmatrix vermieden. Dieser nutzt aus, dass die Hamilton- und die Dichtematrix aufgrund von Lokalisierung dünn besetzt sind. Das reduziert den Rechenaufwand so, dass er linear mit der Systemgröße skaliert. Um seine Effizienz zu demonstrieren, wird der daraus entstehende Algorithmus auf ein System mit flüssigem Methan angewandt, das extremem Druck (etwa 100 GPa) und extremer Temperatur (2000 - 8000 K) ausgesetzt ist. In der Simulation dissoziiert Methan bei Temperaturen oberhalb von 4000 K. Die Bildung von sp²-gebundenem polymerischen Kohlenstoff wird beobachtet. Die Simulationen liefern keinen Hinweis auf die Entstehung von Diamant und wirken sich daher auf die bisherigen Planetenmodelle von Neptun und Uranus aus. Da das Umgehen der Diagonalisierung der Hamiltonmatrix die Inversion von Matrizen mit sich bringt, wird zusätzlich das Problem behandelt, eine (inverse) p-te Wurzel einer gegebenen Matrix zu berechnen. Dies resultiert in einer neuen Formel für symmetrisch positiv definite Matrizen. Sie verallgemeinert die Newton-Schulz Iteration, Altmans Formel für beschränkte und nicht singuläre Operatoren und Newtons Methode zur Berechnung von Nullstellen von Funktionen. Der Nachweis wird erbracht, dass die Konvergenzordnung immer mindestens quadratisch ist und adaptives Anpassen eines Parameters q in allen Fällen zu besseren Ergebnissen führt.

Molecular Charge-Transfer Cross Sections and Their Correlation with Reactant Ion Structures

Charge-transfer cross sections have been obtained by using time-of-flight techniques, and results correlated with reaction energetics and theoretical structures computed by self-consistent field-molecular orbital methods. Ion recombination energies, structures, heats of formation, reaction energy defects, and 3.0-keV charge-transfer cross sections are presented for reactions of molecular and fragment ions produced by electron bombardment ionization of CH30CH, and CH$l molecules. Relationships between experimental cross sections and reaction energetics involving different ion structures are discussed.

Experimental and Theoretical Electron Density Analysis of Copper Pyrazine Nitrate Quasi-Low-Dimensional Quantum Magnets

The accurate electron density distribution and magnetic properties of two metal-organic polymeric magnets, the quasi-one-dimensional (1D) Cu(pyz)(NO3)2 and the quasi-two-dimensional (2D) [Cu(pyz)2(NO3)]NO3·H2O, have been investigated by high-resolution single-crystal X-ray diffraction and density functional theory calculations on the whole periodic systems and on selected fragments. Topological analyses, based on quantum theory of atoms in molecules, enabled the characterization of possible magnetic exchange pathways and the establishment of relationships between the electron (charge and spin) densities and the exchange-coupling constants. In both compounds, the experimentally observed antiferromagnetic coupling can be quantitatively explained by the Cu-Cu superexchange pathway mediated by the pyrazine bridging ligands, via a σ-type interaction. From topological analyses of experimental charge-density data, we show for the first time that the pyrazine tilt angle does not play a role in determining the strength of the magnetic interaction. Taken in combination with molecular orbital analysis and spin density calculations, we find a synergistic relationship between spin delocalization and spin polarization mechanisms and that both determine the bulk magnetic behavior of these Cu(II)-pyz coordination polymers.