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.

Elétrons fortemente correlacionados na vizinhança de uma transição de fase quântica

The aim of this work is to derive theWard Identity for the low energy effective theory of a fermionic system in the presence of a hyperbolic Fermi surface coupled with a U(1) gauge field in 2+1 dimensions. These identities are important because they establish requirements for the theory to be gauge invariant. We will see that the identity associated Ward Identity (WI) of the model is not preserved at 1-loop order. This feature signalizes the presence of a quantum anomaly. In other words, a classical symmetry is broken dynamically by quantum fluctuations. Furthermore, we are considering that the system is close to a Quantum Phase Transitions and in vicinity of a Quantum Critical Point the fermionic excitations near the Fermi surface, decay through a Landau damping mechanism. All this ingredients need to be take explicitly to account and this leads us to calculate the vertex corrections as well as self energies effects, which in this way lead to one particle propagators which have a non-trivial frequency dependence

Termoestatística quântica: uma abordagem via estatísticas não-gaussianas

Considering a quantum gas, the foundations of standard thermostatistics are investigated in the context of non-Gaussian statistical mechanics introduced by Tsallis and Kaniadakis. The new formalism is based on the following generalizations: i) Maxwell- Boltzmann-Gibbs entropy and ii) deduction of H-theorem. Based on this investigation, we calculate a new entropy using a generalization of combinatorial analysis based on two different methods of counting. The basic ingredients used in the H-theorem were: a generalized quantum entropy and a generalization of collisional term of Boltzmann equation. The power law distributions are parameterized by parameters q;, measuring the degree of non-Gaussianity of quantum gas. In the limit q

Bioquímica quântica na diferenciação dos níveis de ativação de receptores AMPA por agonistas parciais Wilardina

In the central nervous system (CNS) of mammalian, fast synaptic transmission between nerve cells is performed primarily by α-amino-3-hydroxy-5-methyl-4- isoxazolepropionic acid (AMPA) receptors, an ionotropic glutamate receptor that is related with learning, memory and homeostasis of the nervous system. Impairments in their functions are correlated with development of many brain desorders, such as epilepsy, schizophrenia, autism, Parkinson and Alzheimer. The use of willardiine analogs has been shown a powerful tool to understanding of activation and desensitization mechanisms of this receptors, because the modification of a single ligand atom allows the observation of varying levels of efficacy. In this work, taking advantage of Fluorine Willardiine (1.35Å), Hydrogen Willardiine (1.65Å), Bromine Willardiine (1.8Å) and Iodine Willardiine (2.15Å) structures co-crystalized with GluA2 with codes 1MQI, 1MQJ, 1MQH and 1MQG, we attempted to energetically differentiate the four ligands efficacy. The complexes were submitted to energetic calculations based on density functional theory (DFT), under the optics of molecular fractionation with conjugate caps (MFCC) method. Obtained results show a relationship between the energetic values and willardiines efficacy order (FW> HW > BrW > IW), also show the importance of E705, R485, Y450, S654, T655, T480 e P478 as the amino acids that contribute most strongly with the interaction of four partial agonists. Furthermore, we outlined the M708 behaviour, attracted by FW and HW ligands, and repels by BrW and IW. With the datas reported on this work, it is possible for a better understanding of the AMPA receptor, which can serve as an aid in the development of new drugs for this system.

Estudo in silico da interação da albumina de soro humano com o ibuprofeno

Currently, computational methods have been increasingly used to aid in the characterization of molecular biological systems, especially when they relevant to human health. Ibuprofen is a nonsteroidal antiinflammatory or broadband use in the clinic. Once in the bloodstream, most of ibuprofen is linked to human serum albumin, the major protein of blood plasma, decreasing its bioavailability and requiring larger doses to produce its antiinflamatory action. This study aimes to characterize, through the interaction energy, how is the binding of ibuprofen to albumin and to establish what are the main amino acids and molecular interactions involved in the process. For this purpouse, it was conducted an in silico study, by using quantum mechanical calculations based on Density Functional Theory (DFT), with Generalized Gradient approximation (GGA) to describe the effects of exchange and correlation. The interaction energy of each amino acid belonging to the binding site to the ligand was calculated the using the method of molecular fragmentation with conjugated caps (MFCC). Besides energy, we calculated the distances, types of molecular interactions and atomic groups involved. The theoretical models used were satisfactory and show a more accurate description when the dielectric constant ε = 40 was used. The findings corroborate the literature in which the Sudlow site I (I-FA3) is the primary binding site and the site I-FA6 as secondary site. However, it differs in identifying the most important amino acids, which by interaction energy, in order of decreasing energy, are: Arg410, Lys414, Ser 489, Leu453 and Tyr411 to the I-Site FA3 and Leu481, Ser480, Lys351, Val482 and Arg209 to the site I-FA6. The quantification of interaction energy and description of the most important amino acids opens new avenues for studies aiming at manipulating the structure of ibuprofen, in order to decrease its interaction with albumin, and consequently increase its distribution

Paul Ricouer: entre hermenêutica e crítica das ideologias

This work exposes the Paul Ric ur s thought in relation to the contemporary complaint between the hermeneutics and the ideologies criticism. It shows, in this direction, the unity between text and action according to Ric ur s perspective. The philosophical view of Ric ur, It affirms, is far from any eclecticism, but if it characterizes for a dynamic style, explained here from the analogies with the movement of the particles, of the quantum physics, which help to excuse to the make a mistake idea of compilation and eclecticism, resultant of superficial readings of its texts. In deep, this work nothing more it is that a contribution to the construction of a theory of the reading of the text of this notable philosopher

Espectro das ondas de spin lineares e não-lineares em multicamadas magnéticas anisotrópicas

Conselho Nacional de Desenvolvimento Científico e Tecnológico

Papel de sinais cromáticos na identificação de parceiros sexuais em sagüi comum (callithrix jacchus)

The literature concerning color vision shows a trichromatic advantage in detecting ripe fruits and young leaves, but there are contradictory results. There is also the suggestion of this type of vision being adapted to perceive socio-sexual signals. Indeed, Old World primates utilize the skin color of conspecifics as a factor of attraction. But in New World primates there is no record of a coloration signal in the body that can be utilized by other group members. The present study aims to: 1- test whether there is a relation between coloration of body regions and ovulatory cycle in female Callithrix jacchus; 2- Determine if this species uses visual signals to choose mates that are sexually receptive. We collected feces from six females during one month to quantify progesterone concentration by EIA. Body region coloration was measured using a portable spectrometer and modeled to obtain the quantum catch of each photoreceptor, the opponency channels and chromatic distance between the points in units of JND. We recorded the behavior of six males exposed to three pairs of females with a cycling and a non-cycling female in each pair using a transparent plexiglass apparatus. The color of different body regions presented a correlation between progesterone concentration and the yellow-blue and red-green visual axes, with the genitalia as the region showing the highest correlation. The visual axis more apt to see the color variations was the yellow-blue in dichromats, and in trichromats were the red-green to face, yellow-blue to abdomen and both chromatic axes to genitalia. There was no difference in the signal detectability between trichromats and dichromats, but the perception pattern differed between the phenotypes, with a better signal detection by the dichromat phenotype 562 and the trichromat phenotype 543/562. During the behavioral experiments males presented longer gaze duration in periods of experimental manipulation and gaze duration was always longer towards cycling females compared to non-cycling females. Male locomotion during experimental manipulation was greater than in the control only during the periovulatory period of the female, indicating greater excitement. The behavior of cycling females was more active than the behavior of the non-cycling ones regarding locomotion and touching of the plexiglass division of the apparatus. Male gaze duration to cycling females increased with decreasing progesterone concentration, but none of the coloration parameters was correlated to the mate preference exhibited. This coloration signal can transmit information to animals of the group about fertility of female. Different from the intense red of the genitalia swellings of Old World primates, marmoset female genitalia became more bluish-green in the fertile period. Males chose fertile females and were able to visually identify the periovulatory period of females. Choice is related to progesterone concentration, but our results do not show relation between coloration and mate preference. Maybe some behavioral measure is associated with the choice

Sinalização cromática da condição reprodutiva de fêmeas de segui comum (Callithrix jacchus)

As social animals, primates use different sensory modalities (acoustic, chemical, tactile and visual) to convey information about social and sexual status to conspecifics. Among these modalities, visual signals are widely used, especially color signals, since primates are the mammalian group that displays the greatest variety of colors in their skin and fur. Studies with Old World primate species suggest that hormonal variations are related to variations in the colors of individual faces and genitals. Therefore, chromatic cues can be used by conspecifics to identify the reproductive condition of an individual. To date, studies with the same approach are unknown for New World species. However, behavioral and physiological studies suggest that different New World primate species seem to perceive reproductive conditions such as the timing of female conception and gestation. Thus, in this study, our aim was to: i) identify whether there are chromatic cues on the skin of female common marmosets, (Callithrix jacchus) that indicate their reproductive condition; ii) define whether this chromatic variation can be perceived by all visual phenotypes known in this species; iii) identify if these chromatic cues can be perceived under different light intensity levels (dim, intermediate and high). For this, we selected 13 female common marmosets in four distinct reproductive conditions: pregnant female preceding parturition, postpartum mothers, noncycling and cycling females. The coloration of the skin in genital and thigh areas in females was measured using a spectrophotometer. Using mathematical models of visual perception, we calculated the values of quantum catch for each photoreceptor type known in this species, the visual opponency channels and color contrast between those body spots. Our results indicate the occurance of chromatic variations in the genital area during the weeks that precede and follow parturition, forming a U-pattern of variation perceptible to males and females in natural conditions of low and high luminosity. Furthermore, we observed distinct color patterns in the genital skin of pregnant and cycling females that indicate their reproductive conditions. Finally, we present evidence of color contrast in noncycling females that is higher than that of pregnant ones. This study suggests that there is a chromatic xii variation in the genital skin of females that can be perceived by conspecifics and that may be related to hormonal changes typical of pregnancy and the ovarian cycle

Análise sobre diferentes abordagens de configuração eletrônica de elementos apresentados em livros de química

This study aimed to identify and review of the conceptual differences presented by authors of books, focusing on the theme of electronic configuration. It shows the changing concepts of electronic configuration, its implications for the cognitive development of students and their relations with the contemporary world. We identified possible obstacles in books generated in the search for simplifications, situations of different concepts of energy in the electron configuration for sublevels. For this analysis was carried out in several books, and some other general chemistry and inorganic chemistry without distinguishing between level of education, whether secondary or higher. It was found that some books for school books corroborated with higher education, others do not. To check the consistency of what was discussed, it was a survey of 30 teachers, it was found divergent points of responses, particularly with respect to the energy sublevels and authorship of the diagram which facilitated the electron configuration. It was found that the total 22professores, ie, 73,33% answered correctly on the energy sublevel more calcium (Ca) and 80%, ie, 24 teachers responded incorrectly on the iron. As for the authorship of the diagram used to facilitate the electronic configuration, we obtained 93, 33% of teachers indicated that they followed a diagram, and this was called "Diagram of Linus Pauling," teacher 01, 3,33%, indicated that the diagram was authored by Madelung and 01, 3,33%, did not respond to question. Was observed that it is necessary a more detailed assessment of ancient writings, as the search for simplifications and generalizations, not so plausible, lead to errors and consequences negative for understanding the properties of many substances. It was found that quantum mechanics combined with spectroscopic data should be part of a more thorough analysis, especially when it extends situations atoms monoelectronicpolieletrônicos to describe atoms, because factors such as effective nuclear charge and shielding factor must be taken into consideration, because interactions there is inside an atom, described by a set ofquantum numbers, sometimes not taken into account

Estudo teórico QTAIM e DFT dos compostos de coordenação: efeito quelato, titanocenos e ligação química

This work is a study of coordination compounds by quantum theory of atoms in molecules (QTAIM), based on the topological analysis of the electron density of molecular systems, both theoretically and experimentally obtained. The coordination chemistry topics which were studied are the chelate effect, bent titanocene and chemical bond in coordination complexes. The chelate effect was investigated according to topological and thermodynamic parameters. The exchange of monodentate ligands on polydentate ligands from same transition metal increases the stability of the complex both from entropy and enthalpy contributions. In some cases, the latter had a higher contribution to the stability of the complex in comparison with entropy. This enthalpic contribution is explained according to topological analysis of the M-ligand bonds where polidentate complex had higher values of electron density of bond critical point, Laplacian of electron density of bond critical point and delocalization index (number of shared electrons between two atoms). In the second chapter, was studied bent titanocenes with bulky cyclopentadienyl derivative π-ligand. The topological study showed the presence of secondary interactions between the atoms of π-ligands or between atoms of π-ligand and -ligand. It was found that, in the case of titanocenes with small difference in point group symmetry and with bulky ligands, there was an nearly linear relationship between stability and delocalization index involving the ring carbon atoms (Cp) and the titanium. However, the titanocene stability is not only related to the interaction between Ti and C atoms of Cp ring, but secondary interactions also play important role on the stability of voluminous titanocenes. The third chapter deals with the chemical bond in coordination compounds by means of QTAIM. The quantum theory of atoms in molecules so far classifies bonds and chemical interactions in two categories: closed shell interaction (ionic bond, hydrogen bond, van der Waals interaction, etc) and shared interaction (covalent bond). Based on topological parameters such as electron density, Laplacian of electron density, delocalization index, among others, was classified the chemical bond in coordination compounds as an intermediate between closed shell and shared interactions

Índice de aromaticidade baseado na deslocalização, degenerescência e densidade (D3BIA) para acenos e moléculas homoaromáticas

The aromaticity index is an important tool for the investigation of aromatic molecules. This work consists on new applications of the aromaticity index developed by teacher Caio Lima Firme, so-called D3BIA (density, delocalization, degeneracy-based index of aromaticity). It was investigated its correlation with other well-known aromaticity indexes, such as HOMA (harmonic oscillator model of aromaticity), NICS (nucleus independent chemical shielding), PDI (para-delocalization index), magnetic susceptibility (), and energetic factor in the study of aromaticity of acenes and homoaromatic species based on bisnoradamantanyl cage. The density functional theory (DFT) was used for optimization calculations and for obtaining energetic factors associated with aromaticity and indexes HOMA and NICS. From quantum theory of atoms in molecules (QTAIM) it was obtained the indexes D3BIA, PDI and . For acenes, when the over-mentioned indexes were applied it was observed no correlation except for D3BIA and HOMA (R2=0.752). For bisnoradamantenyl dication and its derivatives, it was obtained a good correlation between D3BIA and NICS. Moreover, it was evaluated solely one of the factors used on D3BIA calculation, the delocalization index uniformity (DIU), so as to investigate its possible influence on stability of chemical species. Then, the DIU was compared with the formation Gibbs free energy of some pairs of carbocations, isomers or not, which each pair had small difference in point group symmetry and no difference among other well-known stability factors. The obtained results indicate that DIU is a new stability factor related to carbocations, that is, the more uniform the electron density delocalization, the more stable the is carbocation. The results of this work validate D3BIA and show its importance on the concept of aromaticity, indicating that it can be understood from degeneracy of atoms belonging the aromatic site, the electronic density in the aromatic site and the degree of uniformity of electron delocalization

Efeito do campo elétrico em nanocones formados por aln e BN: um estudo por primeiros princípios

The development of computers and algorithms capable of making increasingly accurate and rapid calculations as well as the theoretic foundation provided by quantum mechanics has turned computer simulation into a valuable research tool. The importance of such a tool is due to its success in describing the physical and chemical properties of materials. One way of modifying the electronic properties of a given material is by applying an electric field. These effects are interesting in nanocones because their stability and geometric structure make them promising candidates for electron emission devices. In our study we calculated the first principles based on the density functional theory as implemented in the SIESTA code. We investigated aluminum nitride (AlN), boron nitride (BN) and carbon (C), subjected to external parallel electric field, perpendicular to their main axis. We discuss stability in terms of formation energy, using the chemical potential approach. We also analyze the electronic properties of these nanocones and show that in some cases the perpendicular electric field provokes a greater gap reduction when compared to the parallel field

Propriedades termo-eletrônicas da molécula do DNA

Conselho Nacional de Desenvolvimento Científico e Tecnológico

Integrais de linha intervalares: fundamentos e aplicações

A necessidade de uma precisão e de uma aproximação dos resultados numéricos zeram com que diversas teorias surgissem: dentre elas, destacamos a Matemática Intervalar. A Matemática Intervalar surgiu na década de 60 com os trabalhos de pesquisa de Moore (MOORE, 1959) , em que ele propôs trabalhar com uma Matemática baseada na noção de intervalo real e não mais com um número como aproximação. Com isso, surgiu a necessidade de revisitar e reformular os conceitos e resultados da Matemática Clássica utilizando como base a noção de intervalo de Moore. Uma das áreas da Matem ática Clássica que tem tido muitas aplicações em engenharias e ciências é a Análises Numérica, onde um dos seus pilares é o Cálculo Integral e em particular as integrais de linha. Assim, é muito desejável se ter um cálculo integral dentro da própria Matemática Intervalar. No presente trabalho apresenta-se uma noção de Integral de Linha Intervalar baseada na extensão de integração proposta por Bedregal em (BEDREGAL; BEDREGAL, 2010). Para a fundamentação apresenta-se incialmente uma introdução sobre a pespectiva em que o trabalho foi realizado, considerando alguns aspectos histórico-evolutivos da Matemática Clássica. Os conceitos de Integrais de Linha Clássica, bem como algumas das suas aplicações mais importantes. Alguns conceitos de Matemática Intervalar necessários para o entendimento do trabalho. Para nalizar propomos uma aplicação da integral de linha em um experimênto clássico da mecânica quântica (a difração de um elétron em uma fenda) que graças ao fato de ser a Matemática Intervalar utilizada, nos dá um foco mais detalhado e mais próximo da realidade