Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA.
J Chem Phys. 2013 Jun 7;138(21):214108. doi: 10.1063/1.4808025.
A fundamental understanding of the intermolecular forces that bind polysaccharide chains together in cellulose is crucial for designing efficient methods to overcome the recalcitrance of lignocellulosic biomass to hydrolysis. Because the characteristic time and length scales for the degradation of cellulose by enzymatic hydrolysis or chemical pretreatment span orders of magnitude, it is important to closely integrate the molecular models used at each scale so that, ultimately, one may switch seamlessly between quantum, atomistic, and coarse-grained descriptions of the system. As a step towards that goal, four multiscale coarse-grained models for polysaccharide chains in a cellulose-Iα microfiber are considered. Using the force matching method, effective coarse-grained forces are derived from all-atom trajectories. Performance of the coarse-grained models is evaluated by comparing the intrachain radial distribution functions with those obtained using the all-atom reference data. The all-atom simulation reveals a double peak in the radial distribution function for sites within each glucose residue that arises from the distinct conformations sampled by the primary alcohol group in the glucose residues. The three-site and four-site coarse-grained models have sufficient degrees of freedom to predict this double peak while the one-site and two-site models do not. This is the first time that coarse-grained models have been shown to reproduce such subtle, yet important, molecular features in a polysaccharide chain. The relative orientations between glucose residues along the polysaccharide chain are evaluated and it is found that the four-site coarse-grained model is best at reproducing the glucose-glucose conformations observed in the all-atom simulation. The success of the four-site coarse-grained model underscores the importance of decoupling the pyranose ring from the oxygen atom in the glycosidic bond when developing all-atom to coarse-grained mapping schemes for polysaccharides.
对将多糖链结合在一起的分子间力的基本理解对于设计克服木质纤维素生物质水解抗性的有效方法至关重要。由于纤维素通过酶水解或化学预处理降解的特征时间和长度尺度跨越多个数量级，因此重要的是要密切整合在每个尺度上使用的分子模型，以便最终可以在系统的量子、原子和粗粒度描述之间无缝切换。作为实现这一目标的一步，考虑了纤维素-Iα微纤维中多糖链的四个多尺度粗粒化模型。使用力匹配方法，从全原子轨迹推导出有效的粗粒化力。通过将链内径向分布函数与使用全原子参考数据获得的分布函数进行比较，评估粗粒化模型的性能。全原子模拟揭示了每个葡萄糖残基内位点的径向分布函数中的双峰，这是由葡萄糖残基中的伯醇基团采样的不同构象引起的。三位点和四位点粗粒化模型具有足够的自由度来预测这种双峰，而一位点和二位点模型则不能。这是首次表明粗粒化模型能够在多糖链中再现这种微妙但重要的分子特征。评估了多糖链上葡萄糖残基之间的相对取向，发现四位点粗粒化模型最能再现全原子模拟中观察到的葡萄糖-葡萄糖构象。四位点粗粒化模型的成功突出了在开发多糖的全原子到粗粒化映射方案时将吡喃糖环与糖苷键中的氧原子解耦的重要性。
