Ab Initio Screening Approach for the Discovery of Lignin Polymer Breaking Pathways

Mar, Brendan D.; Qi, Helena W.; Liu, Fang; Kulik, Heather J.

doi:10.1021/acs.jpca.5b03503

Cited by 17 publications

(22 citation statements)

References 83 publications

(181 reference statements)

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“…Only cleavage at bonds D or E corresponds to single homolytic bond cleavage, whereas the opening of the five-membered ring results in significant rearrangement after formation of a radical. This latter observation is consistent with our earlier studies of the ring-opening in the β-β and β-5 dimers 59 . We thus characterize the eight cleavage pathways in terms of bonds cleaved that lead to a final product distribution.…”

Section: A Overview Of Spirodienone Cleavage Pathwayssupporting

confidence: 94%

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Depolymerization Pathways for Branching Lignin Spirodienone Units Revealed with ab Initio Steered Molecular Dynamics

Mar

Kulik

2017

J. Phys. Chem. A

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Lignocellulosic biomass is an abundant, rich source of aromatic compounds, but direct utilization of raw lignin has been hampered by both the high heterogeneity and variability of linking bonds in this biopolymer. Ab initio steered molecular dynamics (AISMD) has emerged both as a fruitful direct computational screening approach to identify products that occur through mechanical depolymerization (i.e., in sonication or ball-milling) and as a sampling approach. By varying the direction of force and sampling over 750 AISMD trajectories, we identify numerous possible pathways through which lignin depolymerization may occur in pyrolysis or through catalytic depolymerization as well. Here, we present eight unique major depolymerization pathways discovered via AISMD for the recently characterized spirodienone lignin branchinglinkage that may comprise around 10% weight of all lignin in some softwoods. We extract representative trajectories from AISMD and carry out reaction pathway analysis to identify energetically favorable pathways for lignin depolymerization. Importantly, we identify dynamical effects that could not be observed through more traditional calculations of bond dissociation energies. Such effects include thermodynamically favorable recovery of aromaticity in the dienone ring that leads to near-barrierless subsequent ether cleavage and hydrogen bonding effects that stabilize newly formed radicals. Some of the most stable spirodienone fragments that reside at most 1 eV above the reactant structure are formed with only 2 eV barriers for C-C bond cleavage, suggesting key targets for catalyst design to drive targeted depolymerization of lignin.2

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Section: A Overview Of Spirodienone Cleavage Pathwayssupporting

confidence: 94%

“…In all cases, however, the homolytic ring-opening cleavage of bond C occurs followed by a number of different events that depend upon the AP topology. This observation highlights the benefit of sampling of AP choices as a means to discover depolymerization pathways, as we have previously observed in other lignin motifs 59 .…”

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confidence: 76%

Depolymerization Pathways for Branching Lignin Spirodienone Units Revealed with ab Initio Steered Molecular Dynamics

Mar

Kulik

2017

J. Phys. Chem. A

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“…The diversity of the monomer (oligomer) coupling and polymerization mechanisms makes the study of this polymer a difficult task (Boerjan et al, 2003 ). The breaking pathways of lignin (Mar et al, 2015 ) are of great interest since it has been found as one of the principal responsible for biomass recalcitrance in biofuel production (Batalha et al, 2015 ). Lignin varies between species and also between cellular types inside the same tree/plant (Campbell and Sederoff, 1996 ; Neutelings, 2011 ).…”

Section: Discussionmentioning

confidence: 99%

Waterproofing in Arabidopsis: Following Phenolics and Lipids In situ by Confocal Raman Microscopy

et al. 2016

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Waterproofing of the aerial organs of plants imposed a big evolutionary step during the colonization of the terrestrial environment. The main plant polymers responsible of water repelling are lipids and lignin, which play also important roles in the protection against biotic/abiotic stresses, regulation of flux of gases and solutes, and mechanical stability against negative pressure, among others. While the lipids, non-polymerized cuticular waxes together with the polymerized cutin, protect the outer surface, lignin is confined to the secondary cell wall within mechanical important tissues. In the present work a micro cross-section of the stem of Arabidopsis thaliana was used to track in situ the distribution of these non-carbohydrate polymers by Confocal Raman Microscopy. Raman hyperspectral imaging gives a molecular fingerprint of the native waterproofing tissues and cells with diffraction limited spatial resolution (~300 nm) at relatively high speed and without any tedious sample preparation. Lipids and lignified tissues as well as their effect on water content was directly visualized by integrating the 1299, 1600, and 3400 cm−1 band, respectively. For detailed insights into compositional changes of these polymers vertex component analysis was performed on selected sample positions. Changes have been elucidated in the composition of lignin within the lignified tissues and between interfascicular fibers and xylem vessels. Hydrophobizing changes were revealed from the epidermal layer to the cuticle as well as a change in the aromatic composition within the cuticle of trichomes. To verify Raman signatures of different waterproofing polymers additionally Raman spectra of the cuticle and cutin monomer from tomato (Solanum lycopersicum) as well as aromatic model polymers (milled wood lignin and dehydrogenation polymer of coniferyl alcohol) and phenolic acids were acquired.

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“…Computational approaches to complement available structural data have yielded insights with respect to lignin interaction with its immediate biological environment, , its thermal degradation, − or chemical modification − and solvation. , However, these simulations often use a homogeneous lignin polymer, which is not representative of heterogeneous lignin synthesis products that demonstrate wide variation in size and composition. , To model this morphological diversity, recent work has developed lignin topological libraries that emulate the distributions of sizes and linkages seen in isolated lignin populations. , …”

Section: Introductionmentioning

confidence: 99%

Automated Transformation of Lignin Topologies into Atomic Structures with LigninBuilder

Vermaas

Dellon

Broadbelt

et al. 2018

ACS Sustainable Chem. Eng.

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Lignin is an abundant aromatic heteropolymer found in secondary plant cell walls and is a potential feedstock for conversion into bioderived fuels and chemicals. Lignin chemical diversity complicates traditional structural studies, and so, relatively little experimental evidence exists for how lignin structure exists in aqueous solution or how lignin polymers respond to changes in their chemical environment. Molecular modeling can address these concerns; however, prior computational structural lignin models typically did not capture lignin heterogeneity, as only a few polymers were considered. LigninBuilder creates a framework for building structural libraries for lignin from existing topological libraries, permitting significantly greater diversity of lignin structures to be sampled at atomic detail. As a demonstration of its capabilities, LigninBuilder was applied to three libraries of lignin from hardwood, softwood, and grass, and the resulting polymer structures were simulated in an aqueous environment. The lignins adopted compact globular structures, as would be expected for polymers in poor solvents. The differences between the libraries were largest when quantifying the packing of nonadjacent aromatic residues, with greater branching within the polymer resulting in poorer aromatic packing. Individual lignin polymers were also found to undergo rapid conformational changes, with the dwell time within a state growing as the square of the molecular weight. This first application of LigninBuilder demonstrates the potential for atomic-level insight into lignin interactions. LigninBuilder is distributed as a plugin to the visualization software VMD, lowering the barrier for modeling lignin structure in diverse environments.

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Ab Initio Screening Approach for the Discovery of Lignin Polymer Breaking Pathways

Cited by 17 publications

References 83 publications

Depolymerization Pathways for Branching Lignin Spirodienone Units Revealed with ab Initio Steered Molecular Dynamics

Depolymerization Pathways for Branching Lignin Spirodienone Units Revealed with ab Initio Steered Molecular Dynamics

Waterproofing in Arabidopsis: Following Phenolics and Lipids In situ by Confocal Raman Microscopy

Automated Transformation of Lignin Topologies into Atomic Structures with LigninBuilder

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