Molecular Modeling of the Structural and Dynamical Properties of Secondary Plant Cell Walls: Influence of Lignin Chemistry

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.

Molecular Dynamics Study of Hydrogen Bond Structure and Tensile Strength for Hydrated Amorphous Cellulose

Molecular dynamics (MD) simulations were conducted to investigate the hydrogen-bond (H-bond) structure and its impact on the tensile strength of hydrated amorphous cellulose. The study identifies a stable intramolecular H-bond between the hydroxyl group at position 3 and the ether oxygen at position 5 (OH3···O5). Intermolecularly, the hydroxyl groups at positions 2 (OH2) and 6 (OH6) form stable H-bonds. Young's modulus, maximum tensile strength, and corresponding strain were calculated as functions of moisture content, while the H-bond network, water cluster formation, and cellulose chain orientation during tensile simulations were analyzed to elucidate mechanical properties. The substitution effect of cellulose on Young's modulus is also examined, revealing that the substitution of OH3 for a hydrophobic group minimally affects Young's modulus, but substitutions at OH2 and OH6 significantly reduce tensile strength due to their roles as key intermolecular H-bond donor sites.

Origins of covalent linkages within the lignin-carbohydrate network of biomass

Covalent linkages between lignin and the surrounding carbohydrate network, often referred to as lignin-carbohydrate complexes (LCCs), have been proposed to affect the organization of the biomass microstructure and directly correlate with the recalcitrant nature of biomass. However, the existence and frequency of these LCC linkages remain controversial and largely unknown, primarily due to the harsh experimental techniques available to characterize them. During the predominant lignin polymerization pathway a reactive intermediate is formed. Though this intermediate can covalently bind to the surrounding cellulose/hemicellulose matrix, it has been traditionally assumed to react exclusively with water, leading to purely physical interactions between lignin and cellulose/hemicellulose in the cell wall. This work, for the first time, provides direct evidence of the molecular mechanism of the formation of benzyl ether and benzyl ester LCC linkages via the speculated lignin polymerization pathway. The formation of these LCC linkages showed thermodynamic favorability, while remaining kinetically facile, compared to the previously assumed mechanism of the lignin intermediate reacting with water. The present work suggests that the surrounding carbohydrate matrix could play a role in the organization of lignin deposition and these covalent linkages could be a key factor in biomass recalcitrance.

Physico-chemical interactions within lignocellulosic biomass and their importance in developing solvent based deconstruction methods

Fundamental understanding of physico-chemical interactions among the biopolymers in lignocellulosic biomass is crucial to develop atom-efficient deconstruction methods.

Importance of Water in Maintaining Softwood Secondary Cell Wall Nanostructure

Water is one of the principal constituents by mass of living plant cell walls. However, its role and interactions with secondary cell wall polysaccharides and the impact of dehydration and subsequent rehydration on the molecular architecture are still to be elucidated. This work combines multidimensional solid-state ¹³C magic-angle-spinning (MAS) nuclear magnetic resonance (NMR) with molecular dynamics modeling to decipher the role of water in the molecular architecture of softwood secondary cell walls. The proximities between all main polymers, their molecular conformations, and interaction energies are compared in never-dried, oven-dried, and rehydrated states. Water is shown to play a critical role at the hemicellulose–cellulose interface. After significant molecular shrinkage caused by dehydration, the original molecular conformation is not fully recovered after rehydration. The changes include xylan becoming more closely and irreversibly associated with cellulose and some mannan becoming more mobile and changing conformation. These irreversible nanostructural changes provide a basis for explaining and improving the properties of wood-based materials.

Pretreatment of Corn Stover Using an Extremely Low-Liquid Ammonia (ELLA) Method for the Effective Utilization of Sugars in Simultaneous Saccharification and Fermentation (SSF) of Ethanol

Extremely low-liquid ammonia (ELLA) pretreatment using aqueous ammonia was investigated in order to enhance the enzymatic saccharification of corn stover and subsequent ethanol production. In this study, corn stover was treated with an aqueous ammonia solution at different ammonia loading rates (0.1, 0.2, and 0.3 g NH3/g biomass) and various liquid-to-solid (L/S) ratios (0.55, 1.12, and 2.5). The ELLA pretreatment was conducted at elevated temperatures (90–150 °C) for an extended period (24–120 h). Thereafter, the pretreated material was saccharified by enzyme digestion and subjected to simultaneous saccharification and fermentation (SSF) tests. The effects of key parameters on both glucan digestibility and xylan digestibility were analyzed using analysis of variance (ANOVA). Under optimal pretreatment conditions (L/S = 2.5, 0.1 g-NH3/g-biomass, 150 °C), 81.2% glucan digestibility and 61.1% xylan digestibility were achieved. The highest ethanol yield achieved on the SSF tests was 85.4%. The ethanol concentration was 14.5 g/L at 96 h (pretreatment conditions: liquid-to-solid ratio (L/S) = 2.5, 0.1 g-NH3/g-biomass, 150 °C, 24 h. SSF conditions: microorganism Saccharomyces cerevisiae (D5A), 15 FPU/g-glucan, CTech2, 3% w/v glucan, 37 °C, 150 rpm).

Stochastic model of lignocellulosic material saccharification

The processing of agricultural wastes towards extraction of renewable resources is recently being considered as a promising alternative to conventional biofuel production. The degradation of agricultural residues is a complex chemical process that is currently time intensive and costly. Various pre-treatment methods are being investigated to determine the subsequent modification of the material and the main obstacles in increasing the enzymatic saccharification. In this study, we present a computational model that complements the experimental approaches. We decipher how the three-dimensional structure of the substrate impacts the saccharification dynamics. We model a cell wall microfibril composed of cellulose and surrounded by hemicellulose and lignin, with various relative abundances and arrangements. This substrate is subjected to digestion by different cocktails of well characterized enzymes. The saccharification dynamics is simulated in silico using a stochastic procedure based on a Gillespie algorithm. As we additionally implement a fitting procedure that optimizes the parameters of the simulation runs, we are able to reproduce experimental saccharification time courses for corn stover. Our model highlights the synergistic action of enzymes, and confirms the linear decrease of sugar conversion when either lignin content or crystallinity of the substrate increases. Importantly, we show that considering the crystallinity of cellulose in addition to the substrate composition is essential to interpret experimental saccharification data. Finally, our findings support the hypothesis of xylan being partially crystalline.

Leftover wastes generated by agriculture, such as inedible leaves and stalks of plants, represent an abundant and unexploited raw material that contains energy in the form of sugar polymers. Their breakdown and processing into bio-ethanol is recently being considered as a promising candidate for renewable fuel production. However, it is still poorly understood, how the microscopic structure and composition of plant waste materials impact their enzymatic digestion. Various experimental pre-processing methods are currently being tested to determine their effect on the material composition and structure, and the sugar conversion. In this study, we present a computational model to complement such experimental approaches. We simulate a microscopic plant fragment typically found in plant waste materials, whose structure and composition can be tailored. This fragment is then subjected to enzymatic digestion, whose dynamics is tracked in silico. The model reproduces experimentally observed time courses for plant fragments of known composition. It additionally provides new hypotheses for interpreting complex experimental results.

Dynamical Water Ingress and Dissolution at the Amorphous-Crystalline Cellulose Interface

The use of cellulose has considerable promise in a wide range of industrial applications but is hampered by degradation in mechanical properties due to ambient moisture uptake. Existing models of equilibrium moisture content can predict the impact of these effects, but at present, the dynamical, atomic-scale picture of water ingress into cellulose is lacking. The present work reports nonequilibrium molecular simulations of the interface between cellulose and water aimed at capturing the initial stages of two simultaneous dynamical processes, water ingress into cellulose and cellulose dissolution into water. These simulations demonstrate that the process depends on the temperature and chain length in the amorphous region, where high temperatures can induce more mass exchange and short chains can easily detach from amorphous cellulose. A cooperative mechanism that involves both chemical and physical aspects, namely, hydrogen bonding and chain intertwining, respectively, is proposed to interpret the incipient dual ingress/dissolution process. Outcomes of this work will provide a foundation for cellulose functionalization strategies to impede moisture uptake and preserve the mechanical properties of nanocellulose in applications.

Understanding Plant Biomass via Computational Modeling

Plant biomass, especially wood, has been used for structural materials since ancient times. It is also showing great potential for new structural materials and it is the major feedstock for the emerging biorefineries for building a sustainable society. The plant cell wall is a hierarchical matrix of mainly cellulose, hemicellulose, and lignin. Herein, the structure, properties, and reactions of cellulose, lignin, and wood cell walls, studied using density functional theory (DFT) and molecular dynamics (MD), which are the widely used computational modeling approaches, are reviewed. Computational modeling, which has played a crucial role in understanding the structure and properties of plant biomass and its nanomaterials, may serve a leading role on developing new hierarchical materials from biomass in the future.

Molecular Insight into the Cosolvent Effect on Lignin-Cellulose Adhesion

Understanding and controlling the physical adsorption of lignin compounds on cellulose pulp are key parameters in the successful optimization of organosolv processes. The effect of binary organic-aqueous solvents on the coordination of lignin to cellulose was studied with molecular dynamics simulations, considering ethanol and acetonitrile to be organic cosolvents in aqueous solutions in comparison to their monocomponent counterparts. The structures of the solvation shells around cellulose and lignin and the energetics of lignin-cellulose adhesion indicate a more effective disruption of lignin-cellulose binding by binary solvents. The synergic effect between solvent components is explained by their preferential interactions with lignin-cellulose complexes. In the presence of pure water, long-lasting H-bonds in the lignin-cellulose complex are observed, promoted by the nonfavorable interactions of lignin with water. Ethanol and acetonitrile compete with water and lignin for cellulose oxygen binding sites, causing a nonlinear decrease in the lignin-cellulose interactions with the amount of the organic component. This effect is modulated by the water exclusion from the cellulose solvation shell by the organic solvent component. The amount and rate of water exclusion depend on the type of organic cosolvent and its concentration.

Enzymes to unravel bioproducts architecture

Enzymes are essential and ubiquitous biocatalysts involved in various metabolic pathways and used in many industrial processes. Here, we reframe enzymes not just as biocatalysts transforming bioproducts but also as sensitive probes for exploring the structure and composition of complex bioproducts, like meat tissue, dairy products and plant materials, in both food and non-food bioprocesses. This review details the global strategy and presents the most recent investigations to prepare and use enzymes as relevant probes, with a focus on glycoside-hydrolases involved in plant deconstruction and proteases and lipases involved in food digestion. First, to expand the enzyme repertoire to fit bioproduct complexity, novel enzymes are mined from biodiversity and can be artificially engineered. Enzymes are further characterized by exploring sequence/structure/dynamics/function relationships together with the environmental factors influencing enzyme interactions with their substrates. Then, the most advanced experimental and theoretical approaches developed for exploring bioproducts at various scales (from nanometer to millimeter) using active and inactive enzymes as probes are illustrated. Overall, combining multimodal and multiscale approaches brings a better understanding of native-form or transformed bioproduct architecture and composition, and paves the way to mainstream the use of enzymes as probes.

Wood–Moisture Relationships Studied with Molecular Simulations: Methodological Guidelines

This paper aims at providing a methodological framework for investigating wood polymers using atomistic modeling, namely, molecular dynamics (MD) and grand canonical Monte Carlo (GCMC) simulations. Atomistic simulations are used to mimic water adsorption and desorption in amorphous polymers, make observations on swelling, mechanical softening, and on hysteresis. This hygromechanical behavior, as observed in particular from the breaking and reforming of hydrogen bonds, is related to the behavior of more complex polymeric composites. Wood is a hierarchical material, where the origin of wood-moisture relationships lies at the nanoporous material scale. As water molecules are adsorbed into the hydrophilic matrix in the cell walls, the induced fluid–solid interaction forces result in swelling of these cell walls. The interaction of the composite polymeric material, that is the layer S2 of the wood cell wall, with water is known to rearrange its internal material structure, which makes it moisture sensitive, influencing its physical properties. In-depth studies of the coupled effects of water sorption on hygric and mechanical properties of different polymeric components can be performed with atomistic modeling. The paper covers the main components of knowledge and good practice for such simulations.

Lignin-polysaccharide interactions in plant secondary cell walls revealed by solid-state NMR

Lignin is a complex aromatic biopolymer that strengthens and waterproofs plant secondary cell walls, enabling mechanical stability in trees and long-distance water transport in xylem. Lignin removal is a key step in paper production and biomass conversion to biofuels, motivating efforts to re-engineer lignin biosynthesis. However, the physical nature of lignin's interactions with wall polysaccharides is not well understood. Here we show that lignin self-aggregates to form highly hydrophobic and dynamically unique nanodomains, with extensive surface contacts to xylan. Solid-state NMR spectroscopy of intact maize stems, supported by dynamic nuclear polarization, reveals that lignin has abundant electrostatic interactions with the polar motifs of xylan. Lignin preferentially binds xylans with 3-fold or distorted 2-fold helical screw conformations, indicative of xylans not closely associated with cellulose. These findings advance our knowledge of the molecular-level organization of lignocellulosic biomass, providing the structural foundation for optimization of post-harvest processing for biofuels and biomaterials.

Biopolymer nanofibrils: structure, modeling, preparation, and applications

Biopolymer nanofibrils exhibit exceptional mechanical properties with a unique combination of strength and toughness, while also presenting biological functions that interact with the surrounding environment. These features of biopolymer nanofibrils profit from their hierarchical structures that spun angstrom to hundreds of nanometer scales. To maintain these unique structural features and to directly utilize these natural supramolecular assemblies, a variety of new methods have been developed to produce biopolymer nanofibrils. In particular, cellulose nanofibrils (CNFs), chitin nanofibrils (ChNFs), silk nanofibrils (SNFs) and collagen nanofibrils (CoNFs), as the four most abundant biopolymer nanofibrils on earth, have been the focus of research in recent years due to their renewable features, wide availability, low-cost, biocompatibility, and biodegradability. A series of top-down and bottom-up strategies have been accessed to exfoliate and regenerate these nanofibrils for versatile advanced applications. In this review, we first summarize the structures of biopolymer nanofibrils in nature and outline their related computational models with the aim of disclosing fundamental structure-property relationships in biological materials. Then, we discuss the underlying methods used for the preparation of CNFs, ChNFs, SNF and CoNFs, and discuss emerging applications for these biopolymer nanofibrils.

Cellulose Nanofiber-Graphene Oxide Biohybrids: Disclosing the Self-Assembly and Copper-Ion Adsorption Using Advanced Microscopy and ReaxFF Simulations

The self-assembly of nanocellulose and graphene oxide into highly porous biohybrid materials has inspired the design and synthesis of multifunctional membranes for removing water pollutants. The mechanisms of self-assembly, metal ion capture, and cluster formation on the biohybrids at the nano- and molecular scales are quite complex. Their elucidation requires evidence from the synergistic combination of experimental data and computational models. The AFM-based microscopy studies of (2,2,6,6-tetramethylpiperidine-1-oxylradical)-mediated oxidized cellulose nanofibers (TOCNFs), graphene oxide (GO), and their biohybrid membranes provide strong, direct evidence of self-assembly; small GO nanoparticles first attach and accumulate along a single TOCNF fiber, while the long, flexible TOCNF filaments wrap around the flat, wide GO planes, thus forming an amorphous and porous biohybrid network. The layered structure of the TOCNFs and GO membrane, derived from the self-assembly and its surface properties before and after the adsorption of Cu(II), is investigated by advanced microscopy techniques and is further clarified by the ReaxFF molecular dynamics (MD) simulations. The dynamics of the Cu(II)-ion capture by the TOCNF and GO membranes in solution and the ion cluster formation during drying are confirmed by the MD simulations. The results of this multidisciplinary investigation move the research one step forward by disclosing specific aspects of the self-assembly behavior of biospecies and suggesting effective design strategies to control the pore size and robust materials for industrial applications.

Functionalization of group-14 two-dimensional materials

The great success of graphene has boosted intensive search for other single-layer thick materials, mainly composed of group-14 atoms arranged in a honeycomb lattice. This new class of two-dimensional (2D) crystals, known as 2D-Xenes, has become an emerging field of intensive research due to their remarkable electronic properties and the promise for a future generation of nanoelectronics. In contrast to graphene, Xenes are not completely planar, and feature a low buckled geometry with two sublattices displaced vertically as a result of the interplay between sp² and sp³ orbital hybridization. In spite of the buckling, the outstanding electronic properties of graphene governed by Dirac physics are preserved in Xenes too. The buckled structure also has several advantages over graphene. Together with the spin-orbit (SO) interaction it may lead to the emergence of various experimentally accessible topological phases, like the quantum spin Hall effect. This in turn would lead to designing and building new electronic and spintronic devices, like topological field effect transistors. In this regard an important issue concerns the electron energy gap, which for Xenes naturally exists owing to the buckling and SO interaction. The electronic properties, including the magnitude of the energy gap, can further be tuned and controlled by external means. Xenes can easily be functionalized by substrate, chemical adsorption, defects, charge doping, external electric field, periodic potential, in-plane uniaxial and biaxial stress, and out-of-plane long-range structural deformation, to name a few. This topical review explores structural, electronic and magnetic properties of Xenes and addresses the question of their functionalization in various ways, including external factors acting simultaneously. It also points to future directions to be explored in functionalization of Xenes. The results of experimental and theoretical studies obtained so far have many promising features making the 2D-Xene materials important players in the field of future nanoelectronics and spintronics.

Effective Saccharification of Corn Stover Using Low-Liquid Aqueous Ammonia Pretreatment and Enzymatic Hydrolysis

Low-liquid aqueous ammonia (LLAA) pretreatment using aqueous ammonia was investigated to enhance enzymatic saccharification of corn stover. In this method, ground corn stover was simply contacted with aqueous ammonia mist (ammoniation step), followed by pretreatment at elevated temperature (90⁻150 °C) for an extended period (24⁻120 h) at different solid/liquid (S/L) ratios (0.29, 0.47 or 0.67), termed a pretreatment step. After that, excess (unreacted) ammonia was removed by evaporation, and the pretreated material was immediately saccharified by an enzyme without a washing step. The effects of key reaction parameters on both glucan digestibility and XMG digestibility were evaluated by analysis of variance (ANOVA). Under the best pretreatment conditions [S/L = 0.47, 0.16 (g NH₃)/(g biomass), 90 °C, 24 h], LLAA pretreatment enhanced enzymatic digestibility from 23.1% for glucan and 11.3% for XMG (xylan + galactan + mannan) of untreated corn stover to 91.8% for glucan and 72.6% for XMG in pretreated solid.

Impact of metal ionic characteristics on adsorption potential of Ficus carica leaves using QSPR modeling

The present study describes Quantitative Structure Property Relationship (QSPR) modeling to relate metal ions characteristics with adsorption potential of Ficus carica leaves for 13 selected metal ions (Ca⁺², Cr⁺³, Co⁺², Cu⁺², Cd⁺², K⁺¹, Mg⁺², Mn⁺², Na⁺¹, Ni⁺², Pb⁺², Zn⁺², and Fe⁺²) to generate QSPR model. A set of 21 characteristic descriptors were selected and relationship of these metal characteristics with adsorptive behavior of metal ions was investigated. Stepwise Multiple Linear Regression (SMLR) analysis and Artificial Neural Network (ANN) were applied for descriptors selection and model generation. Langmuir and Freundlich isotherms were also applied on adsorption data to generate proper correlation for experimental findings. Model generated indicated covalent index as the most significant descriptor, which is responsible for more than 90% predictive adsorption (α = 0.05). Internal validation of model was performed by measuring [Formula: see text] (0.98). The results indicate that present model is a useful tool for prediction of adsorptive behavior of different metal ions based on their ionic characteristics.

Conformations of Low-Molecular-Weight Lignin Polymers in Water

Low-molecular-weight lignin binds to cellulose during the thermochemical pretreatment of biomass for biofuel production, which prevents the efficient hydrolysis of the cellulose to sugars. The binding properties of lignin are influenced strongly by the conformations it adopts. Here, we use molecular dynamics simulations in aqueous solution to investigate the dependence of the shape of lignin polymers on chain length and temperature. Lignin is found to adopt collapsed conformations in water at 300 and 500 K. However, at 300 K, a discontinuous transition is found in the shape of the polymer as a function of the chain length. Below a critical degree of polymerization, Nc =15, the polymer adopts less spherical conformations than above Nc. The transition disappears at high temperatures (500 K) at which only spherical shapes are adopted. An implication relevant to cellulosic biofuel production is that lignin will self-aggregate even at high pretreatment temperatures.

Poroelastic model for adsorption-induced deformation of biopolymers obtained from molecular simulations

Molecular simulation of adsorption of water molecules in nanoporous amorphous biopolymers, e.g., cellulose, reveals nonlinear swelling and nonlinear mechanical response with the increase in fluid content. These nonlinearities result from hydrogen bond breakage by water molecules. Classical poroelastic models, employing porosity and pore pressure as basic variables for describing the "pore fluid," are not adequate for the description of these systems. There is neither a static geometric structure to which porosity can sensibly be assigned nor arrangements of water molecules that are adequately described by giving them a pressure. We employ molar concentration of water and chemical potential to describe the state of the "pore fluid" and stress-strain as mechanical variables. A thermodynamic description is developed using a model energy function having mechanical, fluid, and fluid-mechanical coupling contributions. The parameters in this model energy are fixed by the output of the initial simulation and validated with the results of further simulation. The poroelastic properties, e.g., swelling and mechanical response, are found to be functions both of the molar concentration of water and the stress. The basic fluid-mechanical coupling coefficient, the swelling coefficient, depends on the molar concentration of water and stress and is interpreted in terms of porosity change and solid matrix deformation. The difference between drained and undrained bulk stiffness is explained as is the dependence of these moduli on concentration and stress.

Supramolecular Interactions in Secondary Plant Cell Walls: Effect of Lignin Chemical Composition Revealed with the Molecular Theory of Solvation

Plant biomass recalcitrance, a major obstacle to achieving sustainable production of second generation biofuels, arises mainly from the amorphous cell-wall matrix containing lignin and hemicellulose assembled into a complex supramolecular network that coats the cellulose fibrils. We employed the statistical-mechanical, 3D reference interaction site model with the Kovalenko-Hirata closure approximation (or 3D-RISM-KH molecular theory of solvation) to reveal the supramolecular interactions in this network and provide molecular-level insight into the effective lignin-lignin and lignin-hemicellulose thermodynamic interactions. We found that such interactions are hydrophobic and entropy-driven, and arise from the expelling of water from the mutual interaction surfaces. The molecular origin of these interactions is carbohydrate-π and π-π stacking forces, whose strengths are dependent on the lignin chemical composition. Methoxy substituents in the phenyl groups of lignin promote substantial entropic stabilization of the ligno-hemicellulosic matrix. Our results provide a detailed molecular view of the fundamental interactions within the secondary plant cell walls that lead to recalcitrance.