De aminoácidos a proteínas: medidas e cálculos ab initio de propriedades estruturais e eletrônicas de polimorfos cristalinos de glicina e a interação entre Clorotetraciclina e o receptor TetR

Abstract

Glycine is the simplest among all naturally occurring amino acids, presenting an hydrogen atom in its side chain and for this reason it is the only non-chiral. In its gaseous phase, glycine appears in a non-ionic structure, whereas in solution or crystal, it takes an ionic or zwitterionic form. Although at molecular level, there is no L- or D-glycine, it presents great versatility in its crystalline phase related to the existence of several polymorphs, which the three most studied are: α-, β- or γ-glycine, containing four, two and three molecules per unit cell, respectively. First principles calculations based on the density functional theory within the generalized gradient approach (DFT-GGA) using the PBE functional were performed. Three different approaches for accounting core electrons were used: (i) all electron (AE); (ii) ultra-soft pseudopotencials (USP); and (iii) norm-conserving pseudopotentials. Lattice parameters are in good greement with those previously published from both experimental and theoretical works. The crystal stability was studied by both the energy per molecule and Mulliken populational analysis, accounting also for the core electron binding energy. This way, the stability sequence was taken as α > β > γ, being the α polymorph the most stable structure, which is in agreement with the previously published results by Chisholm et. al. (J. A. Chisholm et. al., Crystal Growth & Design 5(4), 1437, 2005) from DFT simulations. However, this result confronts experimental results, which account for the γ > α > β stability sequence. Optical absorption was computed, showing that γ-glycine presents the lowest dependence with the incident radiation polarization amongst all polymorphs studied. All glycine phases presented indirect band gaps. Optical absorption and X-ray photoelectron spectroscopy (XPS) experiments were made for α-glycine grown by the standard solvent slow evaporation method using ultrapure commercially-obtained glycine powder (> 99%) and Milli-Q water. The absorption spectra showed the existence of a 5, 11 ± 0.02 eV direct energy band gap, and the XPS showed the binding energy for core electrons for non-hydrogen atoms and also showed the presence of chlorine and sodium atoms in α-glycine crystals. These experimental results were interpreted by comparison with first principles calculations. The calculated absorption spectra showed great dependence with the incident radiation polarization, due to the molecular space arrangement, which generates the greatest electric dipole within 100 direction. XPS was interpreted analyzing the partial density of states for every element and functional group obtained by AE calculations, and also by comparing 1s orbital energies for non-hydrogen atoms. The difference between theoretically predicted binding energies was lower than 5%. Luminescence spectra were obtained for temperatures varying from 4 K to 300 K for α-glycine crystals. Time-dependent density functional theory calculations were performed in order to assign molecular signature for the 3,4 eV peak in the luminescence spectra. The present dissertation also includes calculations for binding energies between the Tetracycline (Tc) antibiotic with its binding site at the protein Tet responsive to Tc (TetR). Tc are a family of broad spectrum antibiotics, which exhibits activity against several gam-positive and gram-negative bacteria. The interaction energies were computed for all Tc interacting residues of Tetr, constrained to their atomic positions obtained experimentally, with structure available at Protein Data Bank within ID 2TCT. Energy calculations were performed within DFT-GGA using the hybrid functional proposed by Becke-Lee-Yang-Parr (BLYP) and taking the double numerical plus polarization (DNP) basis set with an orbital cutoff of 4.9 ˚A. Our results are in overall good agreement with previously proposed interaction energies, though Met177 presents a great discrepancy, related to fact that calculations lead to greater interaction intensity than it is expected experimentally. Despite this fact, our results suggest that the methodology employed can be extended to other systems with relative confidence and also, which changes can be made in order to increase the antibiotic activity