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United States Department of Agriculture

Agricultural Research Service

Research Project: Influence of Structure and Moisture on Cotton Fiber Properties

Location: Cotton Structure and Quality Research

Title: In defense of adiabatic phi/psi mapping for cellobiose and other disaccharides

Author
item French, Alfred

Submitted to: Cellulose
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: March 25, 2011
Publication Date: March 10, 2011
Citation: French, A.D. 2011. In defense of adiabatic phi/psi mapping for cellobiose and other disaccharides. Cellulose. 18:889-896, DOI 1007/s10570-011-9538-7.

Interpretive Summary: Although properties of carbohydrate materials vary greatly, they are all very similar chemically. Despite that similarity in elemental composition, different carbohydrates have different shapes, and it is widely thought that many of the physical properties of carbohydrate materials can be traced back to their molecular shapes. One of the tools to study the shapes of these molecules is computerized molecular modeling. The present paper presents arguments regarding the details of how to carry out such modeling studies after a challenge in the literature.

Technical Abstract: Thorough conformational study of cellobiose requires consideration of numerous arrangements of the exocyclic groups. Therefore, it is customary to prepare a number of structures with different arrangements of hydroxyl and hydroxymethyl groups. These “starting geometries” are then given different values of the glycosidic linkage torsion angles Phi and Psi' At each increment of Phi and Psi'' the energy is calculated. Usually, the final product is an “adiabatic” contour plot of the lowest energy at each Phi/Psi point after considering all of the starting geometries. The present paper advocates for adiabatic maps despite the statement by Schnupf and Momany (preceding paper) that adiabatic maps are not of interest because they contain sparse details about the structures at each minimum. Similar information is computed by their method and adiabatic mapping, and comparable details can be provided from adiabatic studies. Although Schnupf and Momany presented maps from calculations in vacuum and in water that considered all of their calculated energies, they favored the presentation of two to four maps for each of 36 individual minima, each with its own zero of relative energy. However, previous work showed that more structures are needed to provide the lowest energies at each point in Phi/Psi space. Following their preferred strategy would result in even more maps when the added structures are considered. The need to map individual minima can be avoided by starting calculations with the same exocyclic orientations at each Phi/Psi point instead of using the preceding optimized structure to start the next energy minimization. Using the same orientations at each point allows periodic maps that depict barriers between minima.

Last Modified: 10/1/2014
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