Comparison of the simulations of cellulosic crystals with three carbohydrate force fields. (3rd March 2016)

• Record Type: Journal Article
• Authors: Miyamoto, Hitomi; Schnupf, Udo; Crowley, Michael F.; Brady, John W.
• Is Part Of: Carbohydrate research. Volume 422(2016)
• Page Start: 17
• Page End: 23
• Publication Date: 2016-03-03
• Subjects: Molecular mechanics calculations -- Molecular dynamics simulations -- Carbohydrate force fields -- Conformational energy calculations; Carbohydrates -- Periodicals; Chemistry, Organic -- Periodicals; Biochemistry -- Periodicals; Carbohydrates -- Periodicals; Chimie organique -- Périodiques; Glucides -- Périodiques; Biochemistry; Carbohydrates; Chemistry, Organic; Periodicals; Electronic journals; 507.78
• DOI: 10.1016/j.carres.2016.01.001
• Languages: English
• ISSNs: 0008-6215

Abstract

Highlights: MD simulations of small molecule crystals were used to evaluate 3 common force fields. The force fields (ff) used were CHARMM (C35), GLYCAM06, and CSFF. The small molecule analogs of cellulose were simulated to see which ff is best. All of the ffs did a reasonable job of modeling the crystal structures. None of the three ffs was found to be clearly superior to the others. Graphical abstract: Abstract: Three independently developed molecular mechanics force fields for carbohydrates have been used to simulate a suite of small molecule analogs of cellulose for which crystal structures have been reported, as a test to determine which might be best for simulations of cellulose itself. Such evaluation is necessary since the reported cellulose crystal structure is not stable in molecular dynamics simulations with any available force field. The present simulations found that all three resulted in small deviations from the reported crystal structures, but that all were reasonably accurate and none was clearly superior to the others for the entire suite of structures examined.