Computerized Molecular Modeling of Carbohydrates

Abstract

Computerized molecular modeling continues to increase in capability and applicability to carbohydrates. This chapter covers nomenclature and conformational aspects of carbohydrates, perhaps of greater use to carbohydrate-inexperienced computational chemists. Its comments on various methods and studies might be of more use to computation-inexperienced carbohydrate chemists. New work on intrinsic variability of glucose, an overall theme, is described.

Combining Computational Chemistry and Crystallography for a Better Understanding of the Structure of Cellulose

“…125 That number of stable structures is a significant decrease from the 729 structures that are generated by putting each of the five OÀ ÀH groups and the C-6À ÀO group into each of the three staggered orientations (729 ¼ 3 6 ). This can be accomplished with several modeling protocols, including energy minimizations at each point on a grid, unconstrained minimization, and various forms of MD simulation.…”

Comparison of Methods for Bulk Automated Simulation of Glycosidic Bond Conformations

“…If a donor and acceptor cannot be distinguished (e.g., in sucrose), the residue located at the left side in CSDB Linear encoding [ 27 ] was considered as a donor. The used hydrogen-based definition for Ramachandran plotting was pointed out as optimal for graphic representation torsional maps [ 28 ].…”

Three-Dimensional Structures of Carbohydrates and Where to Find Them

“…To date, the following theoretical models and methods are applied for in silico design of carbohydrate three-dimensional structure [ 112 , 113 , 114 , 115 , 116 ]: Molecular mechanics (MM) and molecular dynamics (MD) calculations [ 117 ]; Monte Carlo simulations [ 118 , 119 ]; Semi-empirical methods [ 120 , 121 , 122 , 123 ]; Ab initio simulations based on density functional theory (DFT) [ 124 , 125 , 126 , 127 , 128 ]; Hybrid QM/MM and QM/QM and ONIOM (“our own N-layered integrated molecular orbital and molecular mechanics”) approaches [ 129 , 130 , 131 , 132 , 133 , 134 ]. …”