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Carbohydrates are an essential part of the diet in humans and animals. Grains, fruits, and vegetables are natural sources of carbohydrates that provide energy to the body, particularly through glucose, a simple sugar that is a component of starch and an ingredient in many staple foods. The stoichiometric formula (CH2O)n, where n is the number of carbons in the molecule represents carbohydrates. In other words, the ratio of carbon to hydrogen to oxygen is 1:2:1 in carbohydrate molecules. This...

Chemistry of Carbohydrates

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Carbohydrates are an essential part of the diet in humans and animals. Grains, fruits, and vegetables are natural sources of carbohydrates that provide energy to the body, particularly through glucose, a simple sugar that is a component of starch and an ingredient in many staple foods. The stoichiometric formula (CH2O)n, where n is the number of carbons in the molecule represents carbohydrates. In other words, the ratio of carbon to hydrogen to oxygen is 1:2:1 in carbohydrate molecules. This...

Chemistry of Carbohydrates

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Monte Carlo-based searching as a tool to study carbohydrate structure.

Michael K Dowd¹, Donald E Kiely, Jinsong Zhang

¹Southern Regional Research Center, ARS, USDA, 1100 Robert E. Lee Blvd., New Orleans, LA 70124, USA. michael.dowd@ars.usda.gov

Carbohydrate Research

|May 4, 2011

Summary

A new Monte Carlo routine efficiently models carbohydrate structures by exploring torsion angles. This computational method successfully identified known low-energy forms and discovered novel conformations for various sugars and disaccharides.

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Area of Science:

Computational Chemistry
Carbohydrate Chemistry
Molecular Modeling

Background:

Accurate conformational analysis of carbohydrates is crucial for understanding their biological roles.
Previous methods often relied on exhaustive searches, which can be computationally intensive.
Developing efficient computational tools is essential for advancing carbohydrate modeling.

Purpose of the Study:

To develop and implement a novel torsion angle-based Monte Carlo searching routine for carbohydrate modeling.
To apply this routine to identify low-energy conformers of various carbohydrate molecules.
To assess the routine's efficiency and accuracy compared to existing methods.

Main Methods:

A Unix shell script-based Monte Carlo routine was developed, utilizing multiple potential functions and molecular mechanics programs (MM3, MM4).
The routine incorporates a module for calculating hydrogen-hydrogen coupling constants.
The method was applied to study exo-cyclic substituents of β-D-glucopyranose, conformers of D-glucaramide, and related derivatives, as well as β-gentiobiose.

Main Results:

The routine successfully identified all previously reported low-energy structures for β-D-glucopyranose and D-glucaramide.
Favorable conformers were found for 2,3,4,5-tetra-O-acetyl-N,N'-dimethyl-D-glucaramide and D-glucitol.
For β-gentiobiose, the routine located known low-energy regions and identified structures with potentially lower energies than previously reported.

Conclusions:

The developed torsion angle-based Monte Carlo routine is an effective tool for carbohydrate conformational searching.
The approach demonstrates efficiency in finding known low-energy conformers and discovering new ones.
This method holds promise for future modeling studies of monosaccharides, oligosaccharides, and related complex carbohydrates.