The initial conversion pathways of linkages and their linked monomer units in lignin pyrolysis were investigated comprehensively by ReaxFF MD simulations facilitated by the unique VARxMD for reaction analysis. The simulated molecular model contains 15 920 atoms and was constructed on the basis of Adler’s softwood lignin model. The simulations uncover the initial conversion ratio of various linkages and their linked aryl monomers. For linkages and their linked monomer aryl rings of α-O-4, β-O-4 and α-O-4 & β-5, the Cα/Cβ ether bond cracking dominates the initial pathway accounting for at least up to 80% of their consumption. For the linkage of β–β & γ-O-α, both the Cα–O ether bond cracking and its linked monomer aryl ring opening are equally important. Ring-opening reactions dominate the initial consumption of other 4-O-5, 5-5, β-1, β-2, and β-5 linkages and their linked monomers. The ether bond cracking of Cα–O and Cβ–O occurs at low temperature, and the aryl ring-opening reactions take place at relatively high temperature. The important intermediates leading to the stable aryl ring opening are the phenoxy radicals, the bridged five-membered and three-membered rings and the bridged six-membered and three-membered rings. In addition, the reactivity of a linkage and its monomer aryl ring may be affected by other linkages. The ether bond cracking of α-O-4 and β-O-4 linkages can activate its neighboring linkage or monomer ring through the formed phenoxy radicals as intermediates. The important intermediates revealed in this article should be of help in deepening the understanding of the controlling mechanism for producing aromatic chemicals from lignin pyrolysis.

Initial reaction mechanisms of lignin pyrolysis were studied by large-scale ReaxFF molecular dynamics simulations (ReaxFF MD) facilitated by the first GPU-enabled code (GMD-Reax) and the unique reaction analysis tool (VARxMD). Simulations were performed over wide temperature ranges both for heat up at 300–2100 K and for NVT at 500–2100 K with a large lignin model, which contained 15920 atoms and was constructed based on Adler’s softwood lignin model. By utilizing the relatively continuous observation for pyrolysate evolution in slow heat up simulations, three stages for lignin pyrolysis are proposed by pyrolysate fractions. The underlying mechanisms for the three stages are revealed by analyzing the species structure evolution and the reactions of linkages, aryl units, propyl chains, and methoxy substituents. Stage I is characterized with the complete decomposition of source lignin molecules at low temperatures dominated by breaking of α-O-4 and β-O-4 linkages. The temperature in stage II is relatively high where cracking of all the linkages occurs, accompanied by conversion of propyl chains and methoxy substituents. Stage III mapping to high temperature shows the formation of heavy pyrolysates by recombination reactions of five-, six-, or seven-membered aliphatic rings. The heterocyclic oxygen-containing rings are revealed as important intermediates for the aryl monomer ring opening into aliphatic rings of five-membered, seven-membered, or even larger. The pathways for small molecule formation observed in this work are broadly in agreement with the literature. This work demonstrates a new methodology for investigating the overall behaviors and the underlying complex mechanisms of lignin pyrolysis.

•Cellulose pyrolysis is simulated with large-scale models by GPU-based ReaxFF MD.•Chemical mechanisms studied with the unique VARxMD for reaction analysis.•Overall spectrum of product tendency and underlying detailed reactions revealed.•Simulated product evolution (500–1400 K) agrees well with Py-GC/MS (673–1073 K).•A reaction scheme for major pyrolyzates is obtained.Mechanism investigation of cellulose pyrolysis is remarkably useful for efficient utilization of biomass. In this paper, a new methodology rooted in the first GPU enabled ReaxFF MD simulation program (GMD-Reax) and the unique cheminformatics based reaction analysis tool (VARxMD) was employed to investigate the initial reaction mechanism of cellulose pyrolysis. Both the overall spectrum product evolution and underlying detailed chemical reactions of cellulose pyrolysis have been revealed. A reaction scheme of cellulose pyrolysis with detailed reaction pathways for major pyrolyzates has been obtained that is not readily accessible by experiments. The simulated evolution tendencies of the major pyrolysis products (glycolaldehyde, levoglucosan and water) with temperature at 500–1400 K agrees well with the Py-GC/MS experimental observations at 673–1073 K. Compared with the large temperature discrepancy imposed by the widely used simulation strategy of artificially increased temperature in ReaxFF MD, the very close temperature range between the simulations and experiments suggests that cellulose is a good model system to validate the ReaxFF force field in predicting the behavior and chemistry events in pyrolysis of complex molecular systems. The computational approach of large model simulation facilitated by efficient computation of GMD-Reax, and chemical reaction analysis capability of VARxMD can shed new light on the detailed chemical mechanisms of pyrolysis for cellulose and other biomass.

•This article presents the algorithms and applications of VARxMD.•VARxMD allows analysis of chemical reactions for ReaxFF MD for the first time.•Reactions generated directly from 3D coordinates and bond orders by bonding analysis.•VARxMD has been applied in pyrolysis of large scale coal models and an HDPE model.ReaxFF MD (Reactive Force Field Molecular Dynamics) is a promising method for investigating complex chemical reactions in relatively larger scale molecular systems. The existing analysis tools for ReaxFF MD lack the capability of capturing chemical reactions directly by analyzing the simulation trajectory, which is critical in exploring reaction mechanisms. This paper presents the algorithms, implementation strategies, features, and applications of VARxMD, a tool for Visualization and Analysis of Reactive Molecular Dynamics. VARxMD is dedicated to detailed chemical reaction analysis and visualization from the trajectories obtained in ReaxFF MD simulations. The interrelationships among the atoms, bonds, fragments, species and reactions are analyzed directly from the three-dimensional (3D) coordinates and bond orders of the atoms in a trajectory, which are accomplished by determination of atomic connectivity for recognizing connected molecular fragments, perception of bond types in the connected fragments for molecules or radicals, indexing of all these molecules or radicals (chemical species) based on their 3D coordinates and recognition of bond breaking or forming in the chemical species for reactions. Consequently, detailed chemical reactions taking place between two sampled frames can be generated automatically. VARxMD is the first tool specialized for reaction analysis and visualization in ReaxFF MD simulations. Applications of VARxMD in ReaxFF MD simulations of coal and HDPE (high-density polyethylene) pyrolysis show that VARxMD provides the capabilities in exploring the reaction mechanism in large systems with complex chemical reactions involved that are difficult to access manually.