On the Use of Molecular Dynamics Simulations for Elucidating Fine Structural, Physico-Chemical and Thermomechanical Properties of Lignocellulosic Systems: Historical and Future Perspectives

Krishnamurthy Prasad,Mostafa Nikzad,Shammi Sultana Nisha,Igor Sbarski

doi:10.3390/jcs5020055

Krishnamurthy Prasad, Mostafa Nikzad + Show 2 more

Open Access

https://doi.org/10.3390/jcs5020055

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Abstract

The use of Molecular Dynamics (MD) simulations for predicting subtle structural, thermomechanical and related characteristics of lignocellulosic systems is studied. A historical perspective and the current state of the art are discussed. The use of parameterised MD force fields, scaling up simulations via high performance computing and intrinsic molecular mechanisms influencing the mechanical, thermal and chemical characteristics of lignocellulosic systems and how these can be predicted and modelled using MD is shown. Individual discussions on the MD simulations of the lignin, cellulose, lignin-carbohydrate complex (LCC) and how MD can elucidate the role of water on the surface and microstructural characteristics of these lignocellulosic systems is shown. In addition, the use of MD for unearthing molecular mechanisms behind lignin-enzyme interactions during precipitation processes and the deforming/structure weakening brought about by cellulosic interactions in some lignocellulosic systems is both predicted and quantified. MD results from relatively smaller systems comprised of several hundred to a few thousand atoms and massive multi-million atom systems are both discussed. The versatility and effectiveness of MD based on its ability to provide viable predictions from both smaller and massive starting systems is presented in detail.

Highlights

They constructed the lignocellulosic model (Figure 2) by incorporating 1 out of 4 separate lignin units within a polysaccharide unit comprised of cellulose chains and hemicellulose layers (Figure 2)
While the overall work in the Molecular Dynamics (MD) simulation of lignocellulosic phase is limited, similar to the use of MD for lignin simulations as in Section 2.2.2, the work that has been conducted has been able to estimate critical aspects that drive the thermomechanical properties of lignocellulosic systems
Owing to their simple methodology, MD simulations are an excellent way to visualize, model and predict molecular interactions. These molecular interactions are a critical influence on the overall bulk material properties

Summary

Molecular Dynamics and Associated Force Fields

Molecular dynamics (MD) simulations, first developed in the late 1970s for protein folding and conformational analyses, have advanced from simulating several hundreds of atoms to systems with several thousand or even millions of atoms [1,2,3]. An additional term is needed with the torsional terms to ensure planarity for some types of bonding systems such as sp hybridized carbon atoms in carbonyls or aromatic rings This extra component describes the positive contribution to the energy of those out-of-plane motions and is shown in Equation (11) where λ is the improper angle corresponding to the deviation from planarity. This implies that the simulation operators are obliged to employ significant physical approximations to describe in a tractable manner, the intermolecular interactions, which limits their accuracy They are called empirical potentials or empirical force fields, and depending on the procedure followed to develop them and the set of input data used to optimize their parameters, different force fields applicable to different systems or problems are obtained. As of today all leading force fields provide quite reasonable results for a wide range of properties of isolated molecules, pure liquids, and aqueous solutions [7,8,9,10,11,12,13,14,15]

Molecular Dynamics Ensembles

Lignocellulosics

Mechanical Behavior Prediction of Lignocelluloics Using MD

Lignins

Findings

Conclusions