Submitted to: Carbohydrate Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: November 19, 2008
Publication Date: February 11, 2009
Citation: Schnupf, U., Willett, J.L., Bosma, W.B., Momany, F.A. 2009. DFT Conformation and Energies of Amylose Fragments at Atomic Resolution Part I: Syn Forms of Alpha-Maltotetraose. Carbohydrate Research. 344(1):362-373. Interpretive Summary: A thorough understanding of the conformational and energetic properties of carbohydrate molecules is essential for the design of new carbohydrate-based commercial products. This understanding is often hindered by the available experimental data and the large number of ways that the carbohydrate molecules can bend and fold. Alpha-Maltotetraose (DP-4) is a complicated system in terms of the number of possible molecular conformations, and we have used cutting edge theoretical methods to study the relative energies and structures of more than ninety DP-4 syn forms of these molecules. New and interesting molecular conformers have been identified from this study. Four glucose residue fragments of amylose have particular significance in nutritional and dietetic uses in enriched syrups, and are utilized as diagnostic testing materials for amylase enzymes. This work will lead to more efficient design methods for chemical modifications of starch that will result in biodegradable polymers with physical and structural properties useful for numerous commercial applications.
Technical Abstract: DFT optimization studies of ninety syn '-maltotetraose (DP-4) amylose fragments have been carried out at the B3LYP/6-311++G** level of theory. The DP-4 fragments studied include V-helix, tightly bent conformations, a boat, and a 1C4 conformer. The standard hydroxymethyl rotamers (gg, gt, tg) were examined at different locations in the residue sequence and their influence on the bridge conformations phi/psi values and conformer energy is described. Hydroxyl groups were considered to be homodromic, that is, they are either in the all clockwise, ‘c’, or all counterclockwise, ‘r’. Energy differences between conformations are examined in order to assess the stability of the different conformations and to identify the sources of energy that dictate amylose polymer formation. A small nearly cyclic compact structure is of low energy as one would expect when these flexible molecules are studied in vacuo. Many conformations in which the only differences are a single hydroxymethyl variation in the residue sequence, show similar energies and bridge conformations, with trends being a result of the hydroxymethyl as well as hydroxyl orientation. In general the ‘c’ structures are of lower energy than the ‘r’ structures, although this is only true for the in vacuo state. The solvent dependence on conformational preference of several low energy DP-4 structures was investigated via the continuum solvation method COSMO. These results suggest that the ‘r’ structures may be favored for fully solvated molecules.