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.

Propriedades ópticas de nanocristais de SiGe: efeitos de dopagem e desordem

We have used ab initio calculations to investigate the electronic structure of SiGe based nanocrystals (NC s). This work is divided in three parts. In the first one, we focus the excitonic properties of Si(core)/Ge(shell) and Ge(core)/Si(shell) nanocrystals. We also estimate the changes induced by the effect of strain the electronic structure. We show that Ge/Si (Si/Ge) NC s exhibits type II confinement in the conduction (valence) band. The estimated potential barriers for electrons and holes are 0.16 eV (0.34 eV) and 0.64 eV (0.62 eV) for Si/Ge (Ge/Si) NC s. In contradiction to the expected long recombination lifetimes in type II systems, we found that the recombination lifetime of Ge/Si NC s (τR = 13.39μs) is more than one order of magnitude faster than in Si/Ge NC s (τR = 191.84μs). In the second part, we investigate alloyed Si1−xGex NC s in which Ge atoms are randomly positioned. We show that the optical gaps and electron-hole binding energies decrease linearly with x, while the exciton exchange energy increases with x due to the increase of the spatial extent of the electron and hole wave functions. This also increases the electron-hole wave functions overlap, leading to recombination lifetimes that are very sensitive to the Ge content. Finally, we investigate the radiative transitions in Pand B-doped Si nanocrystals. Our NC sizes range between 1.4 and 1.8 nm of diameters. Using a three-levels model, we show that the radiative lifetimes and oscillator strengths of the transitions between the conduction and the impurity bands, as well as the transitions between the impurity and the valence bands are strongly affected by the impurity position. On the other hand, the direct conduction-to-valence band decay is practically unchanged due to the presence of the impurity

Novos protocolos teóricos utilizados nos estudos das ligações hidrogênio-hidrogênio, na estabilidade do tetraedrano, seus derivados e das reações de diels-alder e na quantificação da afinidade de fármacos

This thesis was performed in four chapters, at the theoretical level, focused mainly on electronic density. In the first chapter, we have applied an undergraduate minicourse of Diels-Alder reaction in Federal University of Rio Grande do Norte. By using computational chemistry tools students could build the knowledge by themselves and they could associate important aspects of physical-chemistry with Organic Chemistry. In the second chapter, we studied a new type of chemical bond between a pair of identical or similar hydrogen atoms that are close to electrical neutrality, known as hydrogen-hydrogen (H-H) bond. In this study performed with complexed alkanes, provides new and important information about their stability involving this type of interaction. We show that the H-H bond playing a secondary role in the stability of branched alkanes in comparison with linear or less branched isomers. In the third chapter, we study the electronic structure and the stability of tetrahedrane, substituted tetrahedranes and silicon and germanium parents, it was evaluated the substituent effect on the carbon cage in the tetrahedrane derivatives and the results indicate that stronger electron withdrawing groups (EWG) makes the tetrahedrane cage slightly unstable while slight EWG causes a greater instability in the tetrahedrane cage. We showed that the sigma aromaticity EWG and electron donating groups (EDG) results in decrease and increase, respectively, of NICS and D3BIA aromaticity indices. In addition, another factor can be utilized to explain the stability of tetra-tert-butyltetrahedrane as well as HH bond. GVB and ADMP were also used to explain the stability effect of the substituents bonded to the carbon of the tetrahedrane cage. In the fourth chapter, we performed a theoretical investigation of the inhibitory effect of the drug abiraterone (ABE), used in the prostate cancer treatment as CYP17 inhibitor, comparing the interaction energies and electron density of the ABE with the natural substrate, pregnenolone (PREG). Molecular dynamics and docking were used to obtain the CYP1ABE and CYP17-PREG complexes. From molecular dynamics was obtained that the ABE has higher diffusion trend water CYP17 binding site compared to the PREG. With the ONIOM (B3LYP:AMBER) method, we find that the interaction electronic energy of ABE is 21.38 kcal mol-1 more stable than PREG. The results obtained by QTAIM indicate that such stability is due a higher electronic density of interactions between ABE and CYP17