Molecular dynamics simulations of aqueous pullulan oligomers.
Molecular dynamics simulations of aqueous pullulan oligomers.
复制标题
水性支链淀粉低聚物的分子动力学模拟。
DOI：
10.1021/bm049463d
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发表时间：
2005
期刊：
影响因子：
--
通讯作者：
Brant,DavidA
中科院分区：
文献类型：
--
作者：
Jaud,Simon;Tobias,DouglasJ;Brant,DavidA
Molecular dynamics (MD) simulations have been used to model small-angle X-ray scattering (SAXS) data on aqueous solutions of four oligomeric segments of the glucan pullulan: the trimer G3(comprising one polymer repeating unit), the hexamer (G3)2, the nonamer (G3)3, and the dodecamer (G3)4. The AMBER* force field was used in conjunction with the GB/SA continuum solvation model to calculate both the mean global dimensions of the oligomers from the limiting small angle scattering behavior and the shorter range structural information implicit in the Debye scattering function at larger scattering angles. This same force field and solvation treatment were employed earlier by Liu et al. (Macromolecules1999,32, 8611−8620) with apparent success in a rotational isomeric state (RIS) treatment of the same experimental data. The present work discloses that, despite numerical success in modeling the SAXS data, the RIS treatment, which includes only the interactions within dimeric segments of the polymer chain, fails to account accurately for excluded volume effects at the range of 3−12 sugar residues in the polymer backbone. It is suggested that MD simulations using continuum solvation models can be used to circumvent errors inherent in the computationally efficient RIS treatments of polymer nano- and picosecond dynamics while at the same time avoiding the heavy computational requirements of all-atom methods.
