DFT conformation and energies of amylose fragments at atomic resolution. Part 1: Syn forms of alpha-maltotetraose

Characterization of Cassava Starch and Its Structural Changes Resulting of Thermal Stress by Functionally-Enhanced Derivative Spectroscopy (FEDS)

Starch is one of the biopolymers that has been recognized as promising for its application as an eco-friendly substitute for conventional polymers due to its biodegradable nature, low cost, and considerable abundance from renewable vegetal-type resources. In particular, the use of cassava starch as raw material in the manufacture of packaging materials has increased in recent years. Consequently, the analytical study of the quality and features of starch and its derivatives throughout their entire life cycle have gained importance, with non-destructive sample methods being of particular interest. Among these, spectroscopic methods stand out. The aim of this study was evaluated using spectroscopic techniques (i.e., mid-infrared spectroscopy (MIRS) and functional-enhanced derivative spectroscopy (FEDS)) for the monitoring of the effect of the thermal stress of starch in conjunction with computational tools such as density-functional theory (DFT). It is concluded that the FEDS technique in conjunction with DFT calculations can be a useful tool for the high-precision spectral analysis of polymers subjected to small thermal perturbations. In addition, it is demonstrated that small changes produced by thermal stress can be monitored by infrared spectroscopy in conjunction with FEDS at wavenumber range between 3800 and 3000 cm−1, which would allow for the implementation of spectral techniques instead of thermal techniques for out-lab evaluations and for the study of the thermal stress of biomaterials.

Bioinformatics and molecular modeling in glycobiology

The field of glycobiology is concerned with the study of the structure, properties, and biological functions of the family of biomolecules called carbohydrates. Bioinformatics for glycobiology is a particularly challenging field, because carbohydrates exhibit a high structural diversity and their chains are often branched. Significant improvements in experimental analytical methods over recent years have led to a tremendous increase in the amount of carbohydrate structure data generated. Consequently, the availability of databases and tools to store, retrieve and analyze these data in an efficient way is of fundamental importance to progress in glycobiology. In this review, the various graphical representations and sequence formats of carbohydrates are introduced, and an overview of newly developed databases, the latest developments in sequence alignment and data mining, and tools to support experimental glycan analysis are presented. Finally, the field of structural glycoinformatics and molecular modeling of carbohydrates, glycoproteins, and protein-carbohydrate interaction are reviewed.

Comparison of different force fields for the study of disaccharides

Eighteen empirical force fields and the semi-empirical quantum method PM3CARB-1 were compared for studying beta-cellobiose, alpha-maltose, and alpha-galabiose [alpha-D-Galp-(1-->4)-alpha-D-Galp]. For each disaccharide, the energies of 54 conformers with differing hydroxymethyl, hydroxyl, and glycosidic linkage orientations were minimized by the different methods, some at two dielectric constants. By comparing these results and the available crystal structure data and/or higher level density functional theory results, it was concluded that the newer parameterizations for force fields (GROMOS, GLYCAM06, OPLS-2005 and CSFF) give results that are reasonably similar to each other, whereas the older parameterizations for Amber, CHARMM or OPLS were more divergent. However, MM3, an older force field, gave energy and geometry values comparable to those of the newer parameterizations, but with less sensitivity to dielectric constant values. These systems worked better than MM2 variants, which were still acceptable. PM3CARB-1 also gave adequate results in terms of linkage and exocyclic torsion angles. GROMOS, GLYCAM06, and MM3 appear to be the best choices, closely followed by MM4, CSFF, and OPLS-2005. With GLYCAM06 and to a lesser extent, CSFF, and OPLS-2005, a number of the conformers that were stable with MM3 changed to other forms.