|French, Alfred - Al|
Submitted to: Molecular Simulation
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/4/2007
Publication Date: 4/1/2008
Citation: French, A.D., Johnson, G.P. 2008. Roles of starting geometries in quantum mechanics studies of cellobiose. Molecular Simulation.Vol. 34, No. 4, April 2008, 365–372.
Interpretive Summary: To better understand the interactions of materials such as cotton fiber with their surroundings, chemists and materials scientists often resort to models of the molecules. In the past few decades the models have become more realistic and useful because their properties have been described in computer software. In this work, electronic structure theory, also called quantum mechanics, was used to predict the probabilities of the various shapes of cellobiose, the shortest prototype of the main molecule in cotton, cellulose. The probabilities of the various overall shapes of cellobiose depended on the orientations of the hydroxyl and primary alcohol groups that are part of the two glucose units that compose cellobiose. To find the most probable structure, it is necessary to examine a large number of different arrangements of these groups. This work was done for two reasons. Other scientists have not fully considered the orientations of the hydroxyl and primary alcohol groups, so this paper stresses that importance. Secondly, the calculation of the energy (or probability), although it required years of computer time, can be improved upon but the improved methods will take even more computer time. Therefore, the current work can help to reduce the number of different arrangements that need to be considered. The work is mostly of interest to other scientists who are studying computer models of molecules that contain carbohydrates.
Technical Abstract: A relaxed HF/6 31G(d) energy surface was constructed for the fraction of phi,psi space that contains most geometries from crystals of molecules similar to cellobiose. Two regions around other minima were examined with unconstrained B3LYP/6 31+G(d) minimizations, as were two sub regions covered by the map. More than 100 different exo cyclic group arrangements ("starting geometries"), selected for stability and low energies, were tested at each phi,psi point and in the four sets of unconstrained minimizations. Twenty four unique structures gave the lowest energy at one or more of the 81 phi,psi grid points. Structures from the unconstrained minimizations covered wide ranges of phi,psi space. Also, the large range of relative energies resulting from the different starting geometries for the unconstrained minimizations was comparable to the range of energies on the relaxed map where some conformations were held in high energy phi,psi shapes by the mapping. Thus, exo cyclic group orientations and the phi and psi torsion angles are both important factors in determining the likely structures of a disaccharide.