University of Tennessee/Oak Ridge National Laboratory , Center for Molecular Biophysics, P.O. Box 2008, Oak Ridge, Tennessee 37831-6164, United States.
J Phys Chem B. 2014 Mar 20;118(11):3026-34. doi: 10.1021/jp407953p. Epub 2014 Mar 5.
Understanding biomass structure and dynamics on multiple time and length scales is important for the development of cellulosic biofuels. To this aim, we have developed a coarse-grain (CG) model for molecular dynamics (MD) simulations of cellulose fibrils in explicit water based on target observables from fully atomistic simulations. This model examines the significance of the presence of explicit solvent and compares results with the previous, implicit solvent CG cellulose models. The present, constraint-free CG model is used to generate a series of noncrystalline fibril structures using a coupling parameter, λ, between fully crystalline and fully amorphous potentials. By exploring various structural parameters, including the root-mean-square deviation, root-mean-square fluctuations, radius of gyration, and persistence length, we find the crystalline-to-amorphous state transition takes place at λ ≈ 0.386. The persistence length of cellulose fibril in the transition region corresponds to that of native cellulose fibrils. The transition between crystalline and amorphous fibrils occurs at larger values of λ in explicit water than in the implicit case. Detailed analysis of individual energetic contribution to the transition reveals that the nonbonded interactions, in particular, that of cellulose-water interaction, plays a significant role in the observed crystalline to amorphous transition of cellulose fibril. The present study thus highlights the importance of solvent presence that cannot be adequately described with the previous implicit solvent model. The present method provides an accurate and constraint-free approach for deriving a variety of structures of cellulose in water, with a wide range of crystallinity, suitable for incorporation into large-scale models of lignocellulosic biomass.
理解生物质在多个时间和长度尺度上的结构和动态对于纤维素生物燃料的发展非常重要。为此，我们基于全原子模拟的目标观测值，为纤维素原纤维在显式水中的分子动力学（MD）模拟开发了一种粗粒度（CG）模型。该模型检验了显式溶剂存在的重要性，并将结果与之前的、隐式溶剂 CG 纤维素模型进行了比较。本研究中，无约束的 CG 模型使用全晶态和全非晶态之间的耦合参数 λ 生成了一系列非晶原纤维结构。通过探索各种结构参数，包括均方根偏差、均方根涨落、回转半径和持久长度，我们发现晶态到非晶态的转变发生在 λ≈0.386 处。在转变区域内，纤维素原纤维的持久长度与天然纤维素原纤维的持久长度相对应。在显式水中，晶态和非晶态原纤维之间的转变发生在比隐式情况更大的 λ 值处。对转变的单个能量贡献的详细分析表明，非键相互作用，特别是纤维素-水相互作用，在纤维素原纤维的观察到的晶态到非晶态转变中起着重要作用。因此，本研究强调了溶剂存在的重要性，这是以前的隐式溶剂模型无法充分描述的。本研究提供了一种准确且无约束的方法，用于推导纤维素在水中的各种结构，具有广泛的结晶度，适合纳入木质纤维素生物质的大规模模型中。
