The relation between lignin sequence and its 3D structure

Advancing plant cell wall modelling: Atomistic insights into cellulose, disordered cellulose, and hemicelluloses - A review

The complexity of plant cell walls on different hierarchical levels still impedes the detailed understanding of biosynthetic pathways, interferes with processing in industry and finally limits applicability of cellulose materials. While there exist many challenges to readily accessing these hierarchies at (sub-) angström resolution, the development of advanced computational methods has the potential to unravel important questions in this field. Here, we summarize the contributions of molecular dynamics simulations in advancing the understanding of the physico-chemical properties of natural fibres. We aim to present a comprehensive view of the advancements and insights gained from molecular dynamics simulations in the field of carbohydrate polymers research. The review holds immense value as a vital reference for researchers seeking to undertake atomistic simulations of plant cell wall constituents. Its significance extends beyond the realm of molecular modeling and chemistry, as it offers a pathway to develop a more profound comprehension of plant cell wall chemistry, interactions, and behavior. By delving into these fundamental aspects, the review provides invaluable insights into future perspectives for exploration. Researchers within the molecular modeling and carbohydrates community can greatly benefit from this resource, enabling them to make significant strides in unraveling the intricacies of plant cell wall dynamics.

Computational study on the impact of linkage sequence on the structure and dynamics of lignin

Lignin, one of the most abundant biopolymers on Earth, is of great research interest due to its industrial applications including biofuel production and materials science. The structural composition of lignin plays an important role in shaping its properties and functionalities. Notably, lignin exhibits substantial compositional diversity, which varies not only between different plant species but even within the same plant. Currently, it is unclear to what extent this compositional diversity plays on the overall structure and dynamics of lignin. To address this question, this paper reports on the development of two models of lignin containing all guaiacyl (G) subunits with varied linkage sequences and makes use of all-atom molecular dynamics simulations to examine the impact of linkage sequence alone on the lignin's structure and dynamics. This work demonstrates that the structure of the lignin polymer depends on its linkage sequence at temperatures above and below the glass transition temperature ( T g ), but the polymers exhibit similar structural properties as it is approaching the viscous flow state (480 K). At low temperatures, both of lignin models have a local dynamics confined in a cage, but the size of cages varies depending on structural differences. Interestingly, at temperatures higher than T g , the different linkage sequence leads to the subtle dynamical difference which diminishes at 480 K.

Cloning, expression and application of a novel laccase derived from water buffalo ruminal lignin-degrading bacteria

Water buffalo is the only mammal found to degrade lignin so far, and laccase plays an indispensable role in the degradation of lignin. In this study, multiple laccase genes were amplified based on the water buffalo rumen derived lignin-degrading bacteria Bacillus cereus and Ochrobactrum pseudintermedium. Subsequently, the corresponding recombinant plasmids were transformed into E. coli expression system BL21 (DE3) for induced expression by Isopropyl-β-D-thiogalactopyranoside (IPTG). After preliminary screening, protein purification and enzyme activity assays, Lac3833 with soluble expression and high enzyme activity was selected to test its characteristics, especially the ability of lignin degradation. The results showed that the optimum reaction temperature of Lac3833 was 40 °C for different substrates. The relative activity of Lac3833 reached the highest at pH 4.5 and pH 5.5 when the substrates were ABTS or 2,6-DMP and guaiacol, respectively. Additionally, Lac3833 could maintain high enzyme activity in different temperatures, pH and solutions containing Na+, K+, Mg2+, Ca2+ and Mn2+. Importantly, compared to negative treatment, recombinant laccase Lac3833 treatment showed that it had a significant function in degrading lignin. In conclusion, this is a pioneering study to produce recombinant laccase with lignin-degrading ability by bacteria from water buffalo rumen, which will provide new insights for the exploitation of more lignin-degrading enzymes.

Lignin developmental patterns and Casparian strip as apoplastic barriers: A review

Lignin and Casparian strips are two essential components of plant cells that play critical roles in plant development regulate nutrients and water across the plants cell. Recent studies have extensively investigated lignin diversity and Casparian strip formation, providing valuable insights into plant physiology. This review presents the established lignin biosynthesis pathway, as well as the developmental patterns of lignin and Casparian strip and transcriptional network associated with Casparian strip formation. It describes the biochemical and genetic mechanisms that regulate lignin biosynthesis and deposition in different plants cell types and tissues. Additionally, the review highlights recent studies that have uncovered novel lignin biosynthesis genes and enzymatic pathways, expanding our understanding of lignin diversity. This review also discusses the developmental patterns of Casparian strip in roots and their role in regulating nutrient and water transport, focusing on recent genetic and molecular studies that have identified regulators of Casparian strip formation. Previous research has shown that lignin biosynthesis genes also play a role in Casparian strip formation, suggesting that these processes are interconnected. In conclusion, this comprehensive overview provides insights into the developmental patterns of lignin diversity and Casparian strip as apoplastic barriers. It also identifies future research directions, including the functional characterization of novel lignin biosynthesis genes and the identification of additional regulators of Casparian strip formation. Overall, this review enhances our understanding of the complex and interconnected processes that drive plant growth, pathogen defense, regulation and development.

Comparison of the Interaction and Structure of Lignin in Pure Systems and in Asphalt Media by Molecular Dynamics Simulations

Lignin is a class of organic aromatic polymers contributing to the rigidity and strength of plants and has been proposed as a modifier to improve asphalt performance on road pavement. However, contradicting experimental results on the lignin miscibility in asphalt were found from different studies, and lignin has been found to self-assemble in different solutions. Thus, investigating the interaction and microstructure of lignin in asphalt media in molecular detail is necessary. Molecular dynamics (MD) simulations using both the LAMMPS program with the OPLS-aa force field and the NAMD program with the CHARMM force field have been conducted on pure lignin (including lignin monomer, dimer, and polymer with 17 and 31 units) and their mixtures with model asphalt molecules at different temperatures. Consistent results were observed from both programs and force fields in terms of density, hydrogen bonds, diffusion coefficient, radius of gyration, and radial distribution function. Glass transition was observed in the pure lignin systems based on density and diffusion coefficient calculations at different temperatures. Lignin can form intramolecular hydrogen bonds and intermolecular hydrogen bonds with other lignin and 1,7-dimethylnapthalene in the asphalt mixture, which has dependence on temperature and lignin chain length. Correlating the lignin size and chain length using the power-law relationship showed that lignin polymers in pure systems are in quasi-relaxed structures at different temperatures; lignin molecules stay in quasi-relaxed structures in asphalt mixtures at high temperatures but in collapsed structures at low temperatures. Implementing lignin monomer, dimer, and polymer into the model asphalt mixture can improve its density. Although lignin in different chain lengths aggregates in asphalt, lignin can modify the packing between different components in asphalt media at different temperatures. The work suggests that temperature can significantly influence the miscibility of lignin polymer in asphalt and that lignin can function as both a modifier and a resin in asphalt.

Atomistic Simulations of Polydisperse Lignin Melts Using Simple Polydisperse Residue Input Generator

Understanding the physics of lignin will help rationalize its function in plant cell walls as well as aiding practical applications such as deriving biofuels and bioproducts. Here, we present SPRIG (Simple Polydisperse Residue Input Generator), a program for generating atomic-detail models of random polydisperse lignin copolymer melts i.e., the state most commonly found in nature. Using these models, we use all-atom molecular dynamics (MD) simulations to investigate the conformational and dynamic properties of polydisperse melts representative of switchgrass (Panicum virgatum L.) lignin. Polydispersity, branching and monolignol sequence are found to not affect the calculated glass transition temperature, Tg. The Flory-Huggins scaling parameter for the segmental radius of gyration is 0.42 ± 0.02, indicating that the chains exhibit statistics that lie between a globular chain and an ideal Gaussian chain. Below Tg the atomic mean squared displacements are independent of molecular weight. In contrast, above Tg, they decrease with increasing molecular weight. Therefore, a monodisperse lignin melt is a good approximation to this polydisperse lignin when only static properties are probed, whereas the molecular weight distribution needs to be considered while analyzing lignin dynamics.

Preparation and Adsorption Properties of Lignin/Cellulose Hydrogel

With the development of global industry, industrial wastewater pollution has caused serious environmental problems, and the demand for green and sustainable adsorbents is increasingly strong in the society. In this article, lignin/cellulose hydrogel materials were prepared using sodium lignosulfonate and cellulose as raw materials and 0.1% acetic acid solution as a solvent. The results showed that the optimal adsorption conditions for Congo red were as follows: an adsorption time of 4 h, a pH value of 6, and an adsorption temperature of 45 °C. The adsorption process was in line with the Langmuir isothermal model and a quasi-second-order kinetic model, which belonged to single molecular layer adsorption, and the maximum adsorption capacity was 294.0 mg/g. The optimal adsorption conditions for Malachite green were as follows: an adsorption time of 4 h, a pH value of 4, and an adsorption temperature of 60 °C. The adsorption process was consistent with the Freundlich isothermal model and a pseudo-second-order kinetic model, which belonged to the chemisorption-dominated multimolecular layer adsorption with the maximum adsorption capacity of 129.8 mg/g.

Valorization of homogeneous linear catechyl lignin: opportunities and challenges

Lignin is the dominant aromatic renewable polymer on earth. Generally, its complex and heterogeneous structure hinders its high-value utilization. Catechyl lignin (C-lignin), a novel lignin discovered in the seed coats of vanilla and several members of Cactaceae, has received increasing attention due to its unique homogeneous linear structure. Obtaining substantial amounts of C-lignin either by gene regulation or effective isolation is essential to advance C-lignin's valorization. Through a fundamental understanding of the biosynthesis process, genetic engineering to promote the accumulation of C-lignin in certain plants was developed to facilitate C-lignin valorization. Various isolation methods were also developed to isolate C-lignin, among which deep eutectic solvents (DESs) treatment is one of the most promising approaches to fractionate C-lignin from biomass materials. Since C-lignin is composed of homogeneous catechyl units, depolymerization to produce catechol monomers demonstrates a promising way for value-added utilization of C-lignin. Reductive catalytic fractionation (RCF) represents another emerging technology for effective depolymerizing C-lignin, leading to a narrow distribution of lignin-derived aromatic products (e.g., propyl and propenyl catechol). Meanwhile, the linear molecular structure predisposes C-lignin as a potential promising feedstock for preparing carbon fiber materials. In this review, the biosynthesis of this unique C-lignin in plants is summarized. C-lignin isolation from plants and various depolymerization approaches to obtaining aromatic products are overviewed with highlights on RCF process. Exploring new application areas based on C-lignin's unique homogeneous linear structure is also discussed with its potential for high-value utilization in the future.

Biomass carbon mining to develop nature-inspired materials for a circular economy

A transition from a linear to a circular economy is the only alternative to reduce current pressures in natural resources. Our society must redefine our material sources, rethink our supply chains, improve our waste management, and redesign materials and products. Valorizing extensively available biomass wastes, as new carbon mines, and developing biobased materials that mimic nature's efficiency and wasteless procedures are the most promising avenues to achieve technical solutions for the global challenges ahead. Advances in materials processing, and characterization, as well as the rise of artificial intelligence, and machine learning, are supporting this transition to a new materials' mining. Location, cultural, and social aspects are also factors to consider. This perspective discusses new alternatives for carbon mining in biomass wastes, the valorization of biomass using available processing techniques, and the implementation of computational modeling, artificial intelligence, and machine learning to accelerate material's development and process engineering.

Enhanced flocculation of aluminum oxide particles by lignin-based flocculants in dual polymer systems

Lignin is an abundant phenolic polymer produced vastly in pulping processes that could be further valorized. In this work, anionic (AKLs) and cationic (CKLs) lignin-based polymers were made by polymerizing kraft lignin (KL) with acrylic acid (AA) or [2-(methacryloyloxy) ethyl] trimethyl-ammonium chloride (METAC), respectively. In the polymerization reactions, various molar ratios of AA or METAC to KL were applied to produce AKLs and CKLs with different characteristics. The produced AKLs and CKLs were used in single and dual systems to flocculate aluminum oxide in suspension. To assess the interaction of these lignin-based polymers with the aluminum oxide particles; the zeta potential, adsorption, and flocculation of the colloidal systems were evaluated comprehensively. The flocculation performance of the lignin-derived polymers was compared with that of the homopolymers of AA and METAC (PAA and PMETAC) and commercially used flocculants. In single polymer systems, among the anionic synthesized polymers and homopolymers, KL-A4 (an AKL) was the best flocculant for the aluminum oxide suspensions owing to its largest molecular weight (330 × 10³ g/mol) and highest charge density (-4.2 mmol/g). Remarkably, when KL-A4 and KL-C4 (the CKL with the highest molecular weight and charge density) were used subsequently in a dual polymer system, a larger adsorbed mass and a more viscous adlayer were formed than those of single polymer systems on the surface of aluminum oxide particles. The synergy between KL-A4 and KL-C4 was even stronger than that between homopolymers, which led to more significant adsorption on the aluminum oxide surface and, consequently, more efficient flocculation, producing larger (22 μm) and stronger flocs, regardless of the agitation intensity used in the systems.

Fractionation and characterization of lignin from sugarcane bagasse using a sulfuric acid catalyzed solvothermal process

Conversion of lignocellulosic residue to bioenergy and biofuel is a promising platform for global sustainability. Fractionation is an initial step for isolating lignocellulosic components for subsequent valorization. The aim of this research is to develop the solvothermal fractionation of sugarcane bagasse to produce high purity lignin. The physio-chemical structure of isolated lignin from this process was determined. In this study, a central composite design-based response surface methodology (RSM) was used to optimize an acid promoter for isolating lignin from sugarcane bagasse using a solvothermal fractionation process. The reaction was carried out with sulfuric acid, at a concentration of 0.01-0.02 M and a reaction temperature of 180-200 °C for 30-90 min. The optimal conditions for the experiment were obtained at the acid concentration of 0.02 M with a temperature of 200 °C for 90 min in methyl isobutyl ketone (MIBK)/methanol/water (35% : 25% : 40% v/v%). The results showed that 88% of lignin removal was done in the solid phase, while 87% of lignin recovery was conducted in the organic phase. Furthermore, the changes in the physico-chemical characteristics of solid residue and lignin recovery were analyzed using various techniques. GPC analysis of recovered lignin from the organic fraction showed a lower M w (1374 g mol-1) and polydispersity index (1.75) compared to commercial organosolv lignin. The major lignin degradation temperature of commercial organosolv lignin was estimated to be 410 °C, whereas BGL showed two main degradations at 291 °C and 437 °C, which could point to potential relationships with the degradation of β-O-4 cross-links. The results indicated that recovered lignin was mostly cross-linked by β-O-4 cross-links. In addition, Py-GC/MS and 2D HSQC NMR gave more information regarding the compositional and structural features of recovered lignin. The development of the sulfuric acid catalyzed solvothermal process in this study provides efficient extraction of high-value organosolv lignin from sugarcane bagasse and the production of recovered lignin in the organic phase with low contamination from other contents. The lignin characteristic data can contribute to the development of lignin valorization in value-added applications.