Timescale prediction of complex multi-barrier pathways using flux sampling molecular dynamics and 1D kinetic integration: Application to cellulose dehydration

Abstract

Reactive molecular dynamics simulations, especially those employing acceleration techniques, can provide useful insights on the mechanism underlying the transformation of buried organic matter, yet, so far, it remains extremely difficult to predict the timescales associated to these processes at moderate temperatures (i.e. when such timescales are considerably larger than those accessible to MD). We propose here an accelerated method based on flux sampling and kinetic integration along a 1D order parameter that can considerably extend the accessible timescales. We demonstrate the utility of this technique in an application to the dehydration of crystalline cellulose at temperatures ranging from 1900 K to 1500 K. The full decomposition is obtained at all temperatures apart from T=1500 K, showing the same distribution of the main volatiles (H 2 O, CO and CO 2 ) as recently obtained using replica exchange molecular dynamics. The kinetics of the process is well fitted with an Arrhenius law with E a = 93 kcal/mol and k 0 = 9 × 10 19 s −1 , which are somehow larger than experimental reports. Unexpectedly, the process seems to considerably slow down at lower temperatures, severely departing from the Arrhenius regime, probably because of an inadequate choice of the order parameter. Nevertheless, we show that the proposed method allows considerable time sampling at low temperature compared to conventional MD.

Simulating the Geological Fate of Terrestrial Organic Matter: Lignin vs Cellulose

“…As observed for reactive MD simulations at much higher temperatures, 42,67 cellulose entirely disintegrates into small molecules, mostly light tar molecules, in the very early stages of the REMD simulation (Figure 3a). These molecules further react to form even smaller (gas) species, which dominate in mass after ∼100 ps.…”

“…The As observed for reactive MD simulations at much higher temperatures, 42,67 cellulose entirely disintegrates into small molecules, mostly light tar molecules, in the very early stages of the REMD simulation (Fig. 3(a)).…”

Replica Exchange Molecular Dynamics Simulation of Organic Matter Evolution: From Lignin to Overmature Type III Kerogen

“…More precisely, we use the Atmani et al parameterization, which contains the C–C parameters from the Reax2013 parameterization, the C–H parameters from Shin et al, and the C–O parameters trained from an extended database . In addition to the work described above, this forcefield was also used to investigate the kinetics of the dehydration of cellulose, the natural evolution of cellulose, and the carbon nucleation from deep hydrothermal fluids . The MD and REMD simulations are performed using the large-scale atomic/molecular massively parallel simulator (LAMMPS) package .…”

Development of Atomistic Kerogen Models and Their Applications for Gas Adsorption and Diffusion: A Mini-Review

“…Kineticbased methods, rather than thermodynamic-based methods like REMD could also be considered. In this regard, Valdenaire et al 165 have recently proposed a method based on first passage times and kinetic integration to accelerate the RMD simulation of cellulose pyrolysis. Although promising, the obtained gain in time scale was insufficient to consider such methods for geological evolution so far.…”