Ab Initio Molecular Dynamics Investigation of Xylan Hydrolysis

Chapter 1

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Ab Initio Molecular Dynamics Investigation of Xylan Hydrolysis Haitao Dong and Xianghong Qian* Department of Mechanical Engineering, Colorado State University, Fort Collins, Colorado 80523, USA *[email protected]

Ab initio molecular dynamics (CPMD) coupled with metadynamics (MTD) simulations were used to investigate the free-energy surfaces of acid-catalyzed hydrolysis reactions of xylobiose disaccharide in the gas phase and in aqueous solution. Water and water structures were found to play a critical role in the hydrolysis reaction barrier. Proton partial desolvation associated with its migration to the ether linkage site, the protonation of the ether bond, and the subsequent breaking of the C-O bond were found to be the rate-limiting steps. The significant contribution to the reaction barrier caused by partial proton desolvation and migration could partially explain the biphasic phenomenon in xylan hydrolysis and highlight the importance of mass transport during biomass pretreatment.

Introduction Cellulosic biomass represents an abundant renewable resource for producing bio-based products and biofuels. Cellulosic biomass is mainly composed of hemicelluloses (~15%–32%), cellulose (~30%–50%) and lignin (~15%–25%). Hemicelluloses (mostly xylan) are natural polymers of β-D-xylose and other minor sugars, whereas cellulose is made of β-D-glucose. Lignin is a polymer composed of non-fermentable phenyl-propene monomer units. Both xylose and glucose sugar monomers are connected via the β-1,4 ether linkage to form xylan and cellulose, respectively. The typical biochemical platform for converting biomass to biofuels such as ethanol includes a thermochemical pretreatment step followed by enzymatic hydrolysis and fermentation. © 2010 American Chemical Society In Computational Modeling in Lignocellulosic Biofuel Production; Nimlos, M., et al.; ACS Symposium Series; American Chemical Society: Washington, DC, 2010.


Before enzymatic hydrolysis and fermentation, cellulosic biomass must be pretreated to hydrolyze hemicelluloses, increase the material porosity, and render the biomass substrates more susceptible to enzymatic digestion (1). Thermochemical pretreatment opens up the biomass structure and has long been recognized as a critical step in producing cellulose with acceptable enzymatic digestibility (2). Not only is pretreatment the most costly step, it also has a significant impact on the cost of both prior (e.g., size reduction) and subsequent (enzymatic hydrolysis and fermentation) operations (3, 4). Various technologies, including dilute acid (5, 6), alkaline (7, 8), hot water or steam (9, 10), ammonia fiber explosion (AFEX) (11, 12), and lime (13, 14) pretreatment methods have been developed to accomplish this goal (15). Dilute sulfuric acid (~0.5%–3.0% sulfuric acid by weight) is one of the most common and cost-effective agents used in pretreatment to hydrolyze hemicelluloses and relocate lignin (7, 16–25). Typically, dilute-acid pretreatment is carried out at an elevated temperature of 430-500K. During dilute-sulfuric-acid pretreatment, hemicelluloses (mostly xylan) are hydrolyzed to monomer sugars, the majority of which are β-D-xylose. During this process, a small amount of β-D-glucoses are also released from hemicellulose xyloglucan and possibly from cellulose. Depending on the severity (temperature, acidity, and processing time) of the acid pretreatment, some xylose and glucose molecules undergo an undesirable degradation process that lowers the biomass conversion efficiency. 2-Furaldehyde (Furfural) (26–29) and 5-(hydroxymethyl)-2-furalde (HMF) (27, 28, 30–33) are major degradation products from xylose and glucose, respectively, in an acidic environment. Besides these two major products, there are several other degradation products (48, 50, 53–57). The xylose and glucose molecules could also react with each other in an acidic environment to form various disaccharides or even oligomers, particularly at higher sugar concentrations. Sugar yields decrease as temperature and acidity increase because of acid-catalyzed sugar degradation. However, at lower temperature and acidity, the processing time is much longer due to the presence of both fast and slow biphasic xylan de-polymerization reactions (17, 19). So far our understanding of the biphasic phenomenon of xylan hydrolysis in the complex biomass matrix is very limited. However, laboratory evidence (34) supports the theory that xylan hydrolysis without the presence of other biomass components (mainly cellulose and lignin) is fast and does not exhibit biphasic kinetics. It is postulated that mass transport plays an important role in xylan hydrolysis. Here, we attempt to understand the reaction-free energy and barrier for xylan hydrolysis and associated crucial rate-limiting step(s). Because xylan hydrolysis and sugar degradation/ condensation reactions are both catalyzed by proton during dilute-acid pretreatment, the knowledge of their relatively reaction-free energies and reaction barriers is tremendously valuable for optimizing pretreatment conditions. In this chapter, we focus on the xylan hydrolysis reaction using β-1,4-linked xylobiose hydrolysis as an example. The reaction free energy ΔG and the reaction barrier ΔEa are extremely useful parameters for quantifying a chemical reaction. They determine the thermodynamic equilibrium constant K, the kinetic reaction rate constant k, both of which are needed to quantify the xylan hydrolysis, sugar degradation 2 In Computational Modeling in Lignocellulosic Biofuel Production; Nimlos, M., et al.; ACS Symposium Series; American Chemical Society: Washington, DC, 2010.


and condensation products. For a reversible chemical reaction A + B → C + D, where A and B are reactants and C and D are products, the relations between the equilibrium constant K and free energy ΔG, reaction rate constant k, and activation barrier ΔEa are shown in Equations 1 and 2, respectively. Here, R is the gas constant and T is the absolute temperature in Kelvin. A is a prefactor depending on collision frequency.

Equation 2 is the Arrhenius equation. It is an empirical relationship. It is generally assumed that prefactor A and ΔEa are either not dependent or only weakly dependent on temperature. The prefactor A can be determined statistically as well as experimentally by plotting the natural logarithm of measured k with respect to 1/T. Chemical reactions are complex dynamical processes involving the breaking and forming of chemical bonds and the transfer of electrons. Therefore, only electronic methods based on first-principles quantum calculations are generally able to describe these processes. The common dynamical methods, such as classical molecular dynamics (MD) simulations based on solving Newton’s equation of motion, are unable to describe these chemical and electron transfer processes. Due to its dynamic nature, the reacting system changes state dramatically over a relatively short period of time, making static quantum mechanical computational methods inadequate. Ab initio MD simulation methods such as CPMD (35) are the leading techniques for investigating chemical reactions and processes. CPMD is a predictive technique that requires no empirical parameter and is one of the most accurate available. CPMD unifying molecular dynamics and density functional theory (36) have been successfully and extensively applied to investigate water structure, proton transfer processes, and several chemical reactions (37–51), many of which have been extensively tested and validated by available experimental data. While many chemical reactions and processes occur on the time scale of femtoseconds (fs) (10-15 s) to picoseconds (ps) (10-9 s), a significant number occur on nanoseconds (ns) (10-9 s) or even much longer time scales. Chemical reactions occur when the system migrates from one local equilibrium minimum to another, overcoming the usually large energy barriers that separate reagents from products (52). The probability of such an event occurring spontaneously is inversely related to the exponential of the reaction energy barrier. Depending on the reaction energy barrier, this process could easily exceed 50 ps CPU time, which is the limit our current computing technology can afford. The typical approach of quantum chemistry to overcome this problem is to determine the local minima and saddle points on the potential energy surface to find the possible equilibrium structures and reaction pathways as used in Gaussian (53). These calculations are computationally very demanding, require much 3 In Computational Modeling in Lignocellulosic Biofuel Production; Nimlos, M., et al.; ACS Symposium Series; American Chemical Society: Washington, DC, 2010.


insight, and are generally very difficult. During the past few years, a new MTD method was developed by Parrinello and coworkers (52, 54), based on the ideas of extended Lagrangian (54–57) and coarse-grained, non-Markovian dynamics (54), which allow very efficient exploration of the reactive system’s free-energy surface (FES). It is suitable for implementation in ab initio MD simulation codes and has been incorporated into CPMD. This MTD method assumes that several collective coordinates that distinguish reactants from products are able to characterize the reaction process. These collective coordinates (e.g., distances between atoms and coordination numbers) must include the relevant modes that cannot be sampled within the typical time scale of the ab initio MD simulation (~50 ps). This method is a significant leap forward in simulating chemical reactions and has been successfully applied to several chemical and biological systems (58–70). In this work, CPMD-MTD will be used to explore the free-energy surfaces of xylobiose hydrolysis reactions. The reaction pathways, barriers, and rate constants can also be determined. Our earlier work (27–29, 71) demonstrated the unique capability of CPMD (35, 55) for studying sugar reactions both in the absence and presence of explicit surrounding water molecules. Our calculations show that water and water structure play an important role in sugar reaction pathways. Water molecules can compete with the hydroxyl groups on the sugar ring for a proton. Moreover, water molecules can extract a proton from the carbocation intermediates to terminate the reaction. These results suggest that solvent molecules play a crucial role for both sugar reactions and xylan hydrolysis. Our results show that the size of the water cluster surrounding the sugar molecule has a significant effect on the reaction barrier.

Method Metadynamics is an extended Lagrangian method designed to accelerate the energy barrier-crossing progress, which has been a major drawback for MD simulations that are limited in a sub-microsecond time scale (52, 54). The basic assumption of this method is that the FES depends on n (n

Ab Initio Molecular Dynamics Investigation of Xylan Hydrolysis

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