Análise conformacional de amino dissacarídeos via dinâmica molecular de Car-parrinello

Abstract

The building blocks of oligosaccharides are more diverse in nature than proteins and nucleic acids. These blocks called carbohydrates, hydrates of carbon or saccharides, often differ with respect to each other only in their stereochemistry and the pattern of linkages between the residues which can be very heterogeneous. The information capacity of carbohydrates is much greater than proteins, particularly due the branched structures. It has been assumed that carbohydrates contain hidden codes for biological recognition. Consequently, determination of the structure of these saccharides is a difficult but important problem. Experimentally this determination is made mainly by two techniques: X-ray diffraction and nuclear magnetic resonance spectroscopy (NMR). The more flexible the molecule is, the harder it is to induce crystallization. If a carbohydrate is flexible, it must not only show a three-dimensional characteristic shape. Thus, the conformation of carbohydrates consists in both spatial and temporal components. The result is numerous structural models that often diverge even for a same substance. Thus, new tools need to be developed. One of these is the molecular modeling that supported by the technological advancement has stood out as a methodology. The successful application of a theoretical model is strongly related to the degree which the interatomic properties of a given molecule can be approximated by the mathematical description. The molecular dynamics of Car-Parrinello, a quantum-classical dynamics, is a robust method to perform quantum calculations in a relatively short time, and so it was chosen. Four different types of amino disaccharide were simulated at room temperature (300K) using the functional PBE and Vanderbilt ultra-soft pseudopotential. The calculations were carried out in the gas phase (isolated molecule). It was determined geometric and electronic parameters such as bond length and bond angles, dihedral angle and hydrogen bonds. Disaccharides showed different behavior, especially in relation to the main dihedral angles that characterize saccharide’s conformation and by forming intramolecular hydrogen bonds. These parameters are important to understand the behavior of disaccharides, as well as the respective polysaccharides.