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.

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

Propriedades física de molécilas orgânicas e compostos do tipo perovskita CdSiO3 e CaPbO3

In the first part of this work our concern was to investigate the thermal effects in organic crystals using the theory of the polarons. To analyse such effect, we used the Fröhlich s Hamiltonian, that describes the dynamics of the polarons, using a treatment based on the quantum mechanics, to elucidate the electron-phonon interaction. Many are the forms to analyzing the polaronic phenomenon. However, the measure of the dielectric function can supply important information about the small polarons hopping process. Besides, the dielectric function measures the answer to an applied external electric field, and it is an important tool for the understanding of the many-body effects in the normal state of a polaronic system. We calculate the dielectric function and its dependence on temperature using the Hartree-Fock decoupling method. The dieletric function s dependence on the temperature is depicted by through a 3D graph. We also analyzed the so called Arrhenius resistivity, as a functionof the temperature, which is an important tool to characterize the conductivity of an organic molecule. In the second part we analyzed two perovskita type crystalline oxides, namely the cadmium silicate triclinic (CdSiO3) and the calcium plumbate orthorhombic (CaPbO3), respectively. These materials are normally denominated ABO3 and they have been especially investigated for displaying ferroelectric, piezoelectric, dielectrics, semiconductors and superconductors properties. We found our results through ab initio method within the functional density theory (DFT) in the GGA-PBE and LDA-CAPZ approximations. After the geometry optimization for the two structure using the in two approximations, we found the structure parameters and compared them with the experimental data. We still determined further the angles of connection for the two analyzed cases. Soon after the convergence of the energy, we determined their band structures, fundamental information to characterize the nature of the material, as well as their dielectrics functions, optical absorption, partial density of states and effective masses of electrons and holes

Cálculos AB initio de propriedades estruturais, eletrônicas e ópticas de colmpostos CaXo3 (X=Si, Ge, Sn)

In this work we present a study of structural, electronic and optical properties, at ambient conditions, of CaSiO3, CaGeO3 and CaSnO3 crystals, all of them a member of Ca-perovskite class. To each one, we have performed density functional theory ab initio calculations within LDA and GGA approximations of the structural parameters, geometry optimization, unit cell volume, density, angles and interatomic length, band structure, carriers effective masses, total and partial density of states, dielectric function, refractive index, optical absorption, reflectivity, optical conductivity and loss function. A result comparative procedure was done between LDA and GGA calculations, a exception to CaSiO3 where only LDA calculation was performed, due high computational cost that its low symmetry crystalline structure imposed. The Ca-perovskite bibliography have shown the absence of electronic structure calculations about this materials, justifying the present work

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

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 estruturais e optoeletrônicas dos compostos SrSnO3, SrxBa1-xSnO3 e BaSnO3

In this work we present a study for the structural, electronic and optical properties, at ambient conditions of SrSnO3, SrxBa1

Estudo in silico das interações da protease NS3-NS2B de DENV-2 com o inibidor peptídico Bz-nKRR-H com finalidades terapêuticas

Dengue virus is an important patogen that causes Dengue desease in all world, and belongs to Flavivirus gender. The virus consists of enveloped RNA with a single strand positive sense, 11Kb genome. The RNA is translated into a polyprotein precursor, wich is cleaved into 3 structural proteins (C, prM e E) and 7 non-structural proteins (NS1, NS2A, NS2B, NS3, NS4A, NS4B e NS5). The NS3 is a multifunctional protein, that besides to promote the polyprotein precursor cleavage, also have NTPase, helicase and RTPase activity. The NS3 needs a hydrophilic segment of 40 residues from the transmembrane NS2B protein (who acts like cofator) to realize this functions. Actually, there's no vacines available on the market, and the treatment are just symptomatic. The tetrapeptide inhibitor Bz-Nle-Lys-Arg-Arg-H (Ki de 5,8-7,0 M) was showed as a potent inhibitor μ for NS3prot in Dengue virus. That is a inteligent alternative to treat the dengue desease. The present work aimed analyse the interactions of the ligand bounded to the activity site to provid a clear and depth vision of that interaction. 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 = 20 ε and 80 was used. The results demonstrate that the interaction energy of the system reached convergence at 13.5 A. Within a radius of 13,5A the most important residues were identified. Met49, Met84 and Asp81 perform interactions of hydrogen with the ligant. The Asp79 and Asp75 residues present high energy of attraction. Arg54, Arg85 and Lys 131 perform hydrogen interactions with the ligand, however, appear in BIRD graph having high repulsion energy with the inhibitor. The data also emphasizes the importance of residue Tyr161 and the involvement of the catalytic triad composed by Asp75, His51 and Ser135

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 teórico das propriedades eletrônicas e termodinâmicas de nanofitas quasiperiódicas BCN

Nanoscale materials composed of boron, nitrogen, and carbon have unique properties and may be useful in new technologies. In this thesis, we investigate some properties of BCN nanoribbons constructed according to the Fibonacci quasiperiodic sequence. We analyze properties such as structural stability, electronic density of states, electronic specific heat, band structure, and energy band gap. We have performed first-principles calculations based on density functional theory implemented in the SIESTA code. The results showed that nanoribbons present a fixed value of the formation energy. The electronic density of states was used to calculate the specific heat. We found an oscillatory behavior of the electronic specific heat, in the low temperature regime. We analyze the electronic band structure to determine the energy band gap. The energy band gap oscillates as a function of the Fibonacci generation index n. Our work suggest that appropriate choice of the building block materials of the quasiperiodic sequence, may lead to a tuneable band gap of the quasiperiodic nanoribbons.

Teoria do déficit de autocuidado análise da sua importância e aplicabilidade na prática de enfermagem

submeter a teoria do déficit de autocuidado de Orem a uma reflexão crítica. Metodologia: estudo teórico sobre os aspectos Importância e Aplicabilidade contidos no Modelo de Análise Crítica de Chinn e Kramer para análise crítica da teoria do déficit de autocuidado. Desenvolvido no período de outubro a dezembro de 2008. Resultados: o posicionamento da teoria do déficit de autocuidado está essencialmente relacionado à filosofia da enfermagem e demonstra potencial para influenciar ações de enfermagem, em especial relativas à educação para o autocuidado em pacientes portadores de cardiopatia isquêmica. Conclusões: a enfermagem, mediante a teoria do déficit de autocuidado, pode oferecer condições mais saudáveis e de maior autonomia ao indivíduo portador de cardiopatia isquêmica

Pensamento teórico e formação docente: apropriação de saberes da tradição lúdica na perspectiva da teoria da formação das ações mentais por etapas de P. Ya. Galperin

The study investigated the possibility of organizing a didactics unit for formation of hability of identifying and explaining the popular traditional games in the process of licensed formation in physical education. Had basic premised, the thesis formulated by Piorte Yakovleviche Galperin that the fundamental condition that mode determines the student s way of thinking and the theoretical structures thought. Is given by the method of organization activity that form the basis of guiding skills assimilates from this assumption the study defended the thesis that the contents of popular traditional games can be organizeds according the systemic functional-structural focus. As a method to plan a didactics unit that contributes to development of theoretical thought and the professional development of graduates in physical education. In this sense the general goal was studied and develop a training proposal of ability to identify and explain the popular traditional games for physical education teachers oriented to contribute to the development of theoretical thought. In the construction process of the thesis in a first moment was determined the invariant conceptual of popular traditional games from the method of analysis of activity, after was organized the content of popular traditional games according to the structural-functional systems revealing the essential properties elements and levels of relationship.These procedures provided to the construction elements of the concept popular traditional games, and was the basis for planning a didactical unit to the formation of ability to study. These strategies enable to build a set of prepositions to argue, as a result of the increases in the knowledge of the professional formation in physical education. The study was introduced the fallowing contributions; formulated a teaching proposal to develop the ability to identify popular traditional games, as a cultural and historical contribution and the development of an individual, in initial formation of physical education teacher, attuned to the demands of training and use of knowledge that requires this level of education, defined and organized the knowledge of popular traditional games , this enables a teaching able to raise the cognitive abilities and the theoretical concept of personality of graduated in physical education

PENSAMENTO TEÓRICO E FORMAÇÃO DOCENTE: apropriação de saberes da tradição lúdica na perspectiva da teoria da formação das ações mentais por etapas de P. Ya. Galperin

The study investigated the possibility of organizing a didactics unit for formation of hability of identifying and explaining the popular traditional games in the process of licensed formation in physical education. Had basic premised, the thesis formulated by Piorte Yakovleviche Galperin that the fundamental condition that mode determines the student s way of thinking and the theoretical structures thought. Is given by the method of organization activity that form the basis of guiding skills assimilates from this assumption the study defended the thesis that the contents of popular traditional games can be organizeds according the systemic functional-structural focus. As a method to plan a didactics unit that contributes to development of theoretical thought and the professional development of graduates in physical education. In this sense the general goal was studied and develop a training proposal of ability to identify and explain the popular traditional games for physical education teachers oriented to contribute to the development of theoretical thought. In the construction process of the thesis in a first moment was determined the invariant conceptual of popular traditional games from the method of analysis of activity, after was organized the content of popular traditional games according to the structural-functional systems revealing the essential properties elements and levels of relationship.These procedures provided to the construction elements of the concept popular traditional games, and was the basis for planning a didactical unit to the formation of ability to study. These strategies enable to build a set of prepositions to argue, as a result of the increases in the knowledge of the professional formation in physical education. The study was introduced the fallowing contributions; formulated a teaching proposal to develop the ability to identify popular traditional games, as a cultural and historical contribution and the development of an individual, in initial formation of physical education teacher, attuned to the demands of training and use of knowledge that requires this level of education, defined and organized the knowledge of popular traditional games , this enables a teaching able to raise the cognitive abilities and the theoretical concept of personality of graduated in physical education

"Eu pensei que ia sair daqui falando inglês": um estudo sistêmico-funcional sobre papéis sociais atribuídos por alunos de um curso de Letras/Inglês

Research in the area of teacher training in English as a Foreign Language (CELANI, 2003, 2004, 2010; PAIVA, 2000, 2003, 2005; VIEIRA-ABRAHÃO, 2010) articulates the complexity of beginning teachers classroom contexts aligned with teaching language as a social and professional practice of the teacher in training. To better understand this relationship, the present study is based on a corpus of transcribed interviews and questionnaires applied to 28 undergraduate students majoring in Letters/English emphasis, at a public university located in the interior of the Western Amazon region, soliciting their opinions about the reforms made in the curriculum of this Major. Interviews and questionnaires were used as data collection instruments to trace a profile of the students organized in Group 1, with freshmen and sophomore undergraduates who are following the 2009 curriculum, and Group 2, with junior and senior undergraduates who are following the 2006 curriculum. The objectives are to identify, to characterize and to analyze the types of pronouns, roles and social actors represented in the opinions of these students in relation to their teacher training curriculum. The theoretical support focuses on the challenge of historical and contemporary routes from English teachers initial education programs (MAGALHÃES; LIBERALLI, 2009; PAVAN; SILVA, 2010; ALVAREZ, 2010; VIANA, 2011; PAVAN, 2012). Our theoretical perspective is based on the Systemic Functional Grammar of Halliday (1994), Halliday and Hasan (1989), Halliday and Matthiessen (2004), Eggins (1994; 2004) and Thompson (2004). We focus on the concept of the Interpersonal meaning, specifically regarding the roles articulated in the studies by Delu (1991), Thompson and Thetela (1995), and in the Portuguese language such as Ramos (1997), Silva (2006) and Cabral (2009). Moreover, we ascribe van Leeuwen s (1997; 2003) theory of Representation of Social Actors as a theoretical framework in order to identify the sociological aspect of social actors represented in the students discourse. Within this scenario, the analysis unfolds on three levels: grammatical (pronouns), semantic (roles), and discursive (social actors). For the analysis of interpersonal realizations present in the students opinions, we use the computational program WordSmith Tools (SCOTT, 2010) and its applications Wordlist and Concord to quantify the occurrences of the pronouns I, You and They, which characterize the roles and social actors of the corpus. The results show that the students assigned the following roles to themselves: (i) apprentice to express their initial process of English language learning; (ii) freshman to reveal their choice of Major in Letters/English emphasis; (iii) future teacher to relate their expectations towards a practicing professional. To assign the roles to professors in the major, the students used the metaphor of modality (I think) to indicate the relationship of teacher training, while they are in the role of a student and as a future teacher. From these evidences the representation of the students as social actors emerges in roles such as: (i) active roles; (ii) passive roles and (iii) personalized roles. The social actors represented in the opinions of the students reflect the inclusion of these roles assigned to the actions expressed about their experiences and expectations derived from their teacher training classroom