CÃlculo ab initio de propriedades optoeletrÃnicas da L-alanina

CoordenaÃÃo de AperfeiÃoamento de NÃvel SuperiorSÃo apresentados aqui cÃlculos de primeiros princÃpios realizados para a obtenÃÃo de propriedades Ãpticas e eletrÃnicas da molÃcula e do cristal de L-alanina. No caso da molÃcula, foi efetuada a otimizaÃÃo da geometria para trÃs conformaÃÃes e usando trÃs mÃtodos diferentes: aproximaÃÃo de Hartree-Fock na base 6-31++G(d,p), aproximaÃÃo de Hartree-Fock na base 6-311++G(3d,3p) e teoria do funcional da densidade (funcional de troca e correlaÃÃo B3LYP) na base 6-31++G(d,p). A partir da otimizaÃÃo das geometrias para diferentes conformaÃÃes, foram obtidas a energia total, momentos de dipolo e quadrupolo, polarizabilidades, propriedades termodinÃmicas, modos normais de vibraÃÃo, espectros Raman, infravermelho e VCD, nÃveis de energia eletrÃnicos e orbitais HOMO e LUMO, com comparaÃÃes com resultados experimentais ao longo do trabalho. Para o cristal de L-alanina, a geometria dos Ãtomos na cÃlula unitÃria foi otimizada usando as aproximaÃÃes LDA e GGA, determinando-se a estrutura de bandas, massas efetivas, funÃÃo dielÃtrica, absorÃÃo, refletividade e Ãndice de refraÃÃo. Estes dados sÃo usados na investigaÃÃo do espectro de luminescÃncia do cristal de L-alanina puro e dopado com manganÃs. Os cÃlculos ab initio permitem associar os picos de fotoluminescÃncia no visÃvel a processos de natureza excitÃnica relacionados a nÃveis de polaron e impurezas aprisionadoras de portadores. Calculando as transiÃÃes vertical e adiabÃtica entre os estados excitados e o estado fundamental de uma molÃcula de L-alanina simples na forma zwitteriÃnica, o pico estreito da fotoluminescÃncia no ultravioleta à atribuÃdo a transiÃÃes intramoleculares nas molÃculas de L-alanina fracamente interagentes dentro do cristal, o que deixa uma assinatura molecular especÃfica do aminoÃcido. Jà o estudo da fotoluminescÃncia integrada do cristal dopado com Mn2+ revela um forte quenching da luminescÃncia provocado pela presenÃa do Ãon metÃlico nos interstÃcios da cÃlula unitÃria. Resultados de cÃlculos ab initio preliminares indicam que tal quenching esta relacionado ao modo como a distribuiÃÃo de energias excitÃnicas muda quando o Ãon e inserido num interstÃcio da cÃlula unitÃria.Ab initio calculations for the molecule and crystal of L-alanine are presented. Geometry optimizations were performed for three L-alanine molecular conformers using three different methods: Hartree-Fock approximation with a 6-31++G(d,p) basis, Hartree-Fock approximation with a 6-311++G(3d,3p) basis and Density Functional Theory (B3LYP exchange-correlation functional) with a 6-31++G(d,p) basis. From the geometry optimizations, total energies, dipole and quadrupole moments, polarizabilities, thermodynamical properties, normal modes, Raman, infrared and VCD spectra, energy levels and frontier molecular orbitals were obtained and comparisons with experimental results were carried out. For the L-alanine crystal, geometry optimization was performed within the framework of DFT (LDA and GGA), and band structures, effctive masses, dielectric function, absorption, reflectivity and refraction index were calculated. Those results were employed to investigate the photoluminescence spectra of undoped and Mn-doped L-alanine crystals. The ab initio results allow assignment of the photoluminescence peaks in the visible region to lattice-related processes of exciton nature associated with polaron levels and defect trapping centers for carriers. By evaluating the vertical and adiabatic transitions between the ground state and excited states of a single L-alanine molecule in the zwitterion form, the very thin photoluminescence peak in the ultraviolet region is assigned to intramolecular transitions in the weakly interacting L-alanine molecules forming the crystals, being a signature of the type of the crystalline amino acid. In the case of Mn-doped alanine crystal, the integrated photoluminescence intensity is shown to be dramatically quenched by the intersticial manganese, with a decrease greater than 65% for higher doping. Preliminar ab initio calculations indicate that this quenching is related to the change of exciton energy levels due to the charge redistribution in the unit cell when manganese ions are present

Quantum Biochemistry and MM-PBSA Description of the ZIKV NS2B-NS3 Protease: Insights into the Binding Interactions beyond the Catalytic Triad Pocket

The Zika virus protease NS2B-NS3 has a binding site formed with the participation of a H51-D75-S135 triad presenting two forms, active and inactive. Studies suggest that the inactive conformation is a good target for the design of inhibitors. In this paper, we evaluated the co-crystallized structures of the protease with the inhibitors benzoic acid (5YOD) and benzimidazole-1-ylmethanol (5H4I). We applied a protocol consisting of two steps: first, classical molecular mechanics energy minimization followed by classical molecular dynamics were performed, obtaining stabilized molecular geometries; second, the optimized/relaxed geometries were used in quantum biochemistry and molecular mechanics/Poisson–Boltzmann surface area (MM-PBSA) calculations to estimate the ligand interactions with each amino acid residue of the binding pocket. We show that the quantum-level results identified essential residues for the stabilization of the 5YOD and 5H4I complexes after classical energy minimization, matching previously published experimental data. The same success, however, was not observed for the MM-PBSA simulations. The application of quantum biochemistry methods seems to be more promising for the design of novel inhibitors acting on NS2B-NS3