Location: Commodity Utilization Research
Title: Monte Carlo-based searching as a tool to study carbohydrate structure Authors
|Kiely, Donald -|
|Zhang, Jinsong -|
Submitted to: Carbohydrate Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: April 7, 2011
Publication Date: April 13, 2011
Citation: Dowd, M.K., Kiely, D.E., Zhang, J. 2011. Monte Carlo-based searching as a tool to study carbohydrate structure. Carbohydrate Research. 346:1140-1148. Interpretive Summary: A conformational search routine was developed to allow a directed search of the low-energy forms of flexible molecules. The program was used to study a number of carbohydrates with the molecular mechanics potential function MM3. For complicated molecules, the approach reduces the time it takes to find low-energy forms. By using examples already discussed in the literature, the method pointed to a number of problems and errors with prior reported results. The method should be of interest to researchers working to understand carbohydrate structure and the role that structure has on carbohydrate properties.
Technical Abstract: A torsion angle-based Monte-Carlo searching routine was developed and applied to several carbohydrate modeling problems. The routine was developed as a Unix shell script that calls several programs, which allows it to be interfaced with multiple potential functions and various functions for evaluating conformers. In its current form, the program operates with several versions of the MM3 and MM4 and has a module to calculate the hydrogen-hydrogen coupling constants. The routine was used to study the low-energy forms of the exo-cyclic substituents of the 1C4 chair form of beta-D-glucopyranose and the conformers of D-glucaramide, both of which had been previously been studied with MM3 by full-conformation searches. For these problems, the program found all previously reported low-energy structures. The routine was also used to find favorable conformers of 2,3,4,5-tetra-O-acetyl-N,N’-dimethyl-D-glucaramide and D-glucitol, the latter of which is believed to have many low-energy forms. Finally, the technique was used to study the inter-ring conformations of beta-gentiobiose, a beta-1->6-linked disaccharide of D-glucopyranose. The program easily found conformers in the ten previously identified low-energy phi-psi-omega regions for this disaccharide. In six of the ten regions, the program found the same previously identified local low-energy structure. In the remaining four regions, the search identified structures with slightly lower energies than those previously reported. The approach should be useful for extending modeling studies on acyclic monosaccharide structures and possibly larger oligomeric structures.