Adri C. T. van Duin

ReaxFF Reactive Force Field for Molecular Dynamics Simulations of Hydrocarbon Oxidation

To investigate the initial chemical events associated with high-temperature gas-phase oxidation of hydrocarbons, we have expanded the ReaxFF reactive force field training set to include additional transition states and chemical reactivity of systems relevant to these reactions and optimized the force field parameters against a quantum mechanics (QM)-based training set. To validate the ReaxFF potential obtained after parameter optimization, we performed a range of NVT-MD simulations on various hydrocarbon/O2 systems. From simulations on methane/O2, o-xylene/O2, propene/O2, and benzene/O2 mixtures, we found that ReaxFF obtains the correct reactivity trend (propene > o-xylene > methane > benzene), following the trend in the C-H bond strength in these hydrocarbons. We also tracked in detail the reactions during a complete oxidation of isolated methane, propene, and o-xylene to a CO/CO2/H2O mixture and found that the pathways predicted by ReaxFF are in agreement with chemical intuition and our QM results. We observed that the predominant initiation reaction for oxidation of methane, propene, and o-xylene under fuel lean conditions involved hydrogen abstraction of the methyl hydrogen by molecular oxygen forming hydroperoxyl and hydrocarbon radical species. While under fuel rich conditions with a mixture of these hydrocarbons, we observed different chemistry compared with the oxidation of isolated hydrocarbons including a change in the type of initiation reactions, which involved both decomposition of the hydrocarbon or attack by other radicals in the system. Since ReaxFF is capable of simulating complicated reaction pathways without any preconditioning, we believe that atomistic modeling with ReaxFF provides a useful method for determining the initial events of oxidation of hydrocarbons under extreme conditions and can enhance existing combustion models.

Crenarchaeol: the characteristic core glycerol dibiphytanyl glycerol tetraether membrane lipid of cosmopolitan pelagic crenarchaeota.

The basic structure and stereochemistry of the characteristic glycerol dibiphytanyl glycerol tetraether (GDGT) membrane lipid of cosmopolitan pelagic crenarchaeota has been identified by high field two-dimensional (2D)-NMR techniques. It contains one cyclohexane and four cyclopentane rings formed by internal cyclisation of the biphytanyl chains. Its structure is similar to that of GDGTs biosynthesized by (hyper)thermophilic crenarchaeota apart from the cyclohexane ring. These findings are consistent with the close phylogenetic relationship of (hyper)thermophilic and pelagic crenarchaeota based 16S rRNA. The latter group inherited the biosynthetic capabilities for a membrane composed of cyclopentane ring-containing GDGTs from the (hyper)thermophilic crenarchaeota. However, to cope with the much lower temperature of the ocean, a small but key step in their evolution was the adjustment of the membrane fluidity by making a kink in one of the bicyclic biphytanyl chains by the formation of a cyclohexane ring. This prevents the dense packing characteristic for the cyclopentane ring-containing GDGTs membrane lipids used by hyperthermophilic crenarchaeota to adjust their membrane fluidity to high temperatures.

Linearly concatenated cyclobutane lipids form a dense bacterial membrane.

Lipid membranes are essential to the functioning of cells, enabling the existence of concentration gradients of ions and metabolites. Microbial membrane lipids can contain three-, five-, six- and even seven-membered aliphatic rings, but four-membered aliphatic cyclobutane rings have never been observed. Here we report the discovery of cyclobutane rings in the dominant membrane lipids of two anaerobic ammonium-oxidizing (anammox) bacteria. These lipids contain up to five linearly fused cyclobutane moieties with cis ring junctions. Such ‘ladderane’ molecules are unprecedented in nature but are known as promising building blocks in optoelectronics. The ladderane lipids occur in the membrane of the anammoxosome, the dedicated intracytoplasmic compartment where anammox catabolism takes place. They give rise to an exceptionally dense membrane, a tight barrier against diffusion. We propose that such a membrane is required to maintain concentration gradients during the exceptionally slow anammox metabolism and to protect the remainder of the cell from the toxic anammox intermediates. Our results further illustrate that microbial membrane lipid structures are far more diverse than previously recognized.

Thermal decomposition of RDX from reactive molecular dynamics

We use the recently developed reactive force field ReaxFF with molecular dynamics to study thermal induced chemistry in RDX [cyclic-[CH(2)N(NO(2))](3)] at various temperatures and densities. We find that the time evolution of the potential energy can be described reasonably well with a single exponential function from which we obtain an overall characteristic time of decomposition that increases with decreasing density and shows an Arrhenius temperature dependence. These characteristic timescales are in reasonable quantitative agreement with experimental measurements in a similar energetic material, HMX [cyclic-[CH(2)N(NO(2))](4)]. Our simulations show that the equilibrium population of CO and CO(2) (as well as their time evolution) depend strongly of density: at low density almost all carbon atoms form CO molecules; as the density increases larger aggregates of carbon appear leading to a C deficient gas phase and the appearance of CO(2) molecules. The equilibrium populations of N(2) and H(2)O are more insensitive with respect to density and form in the early stages of the decomposition process with similar timescales.

Evaluation of B3LYP, X3LYP, and M06-class density functionals for predicting the binding energies of neutral, protonated, and deprotonated water clusters

In this paper we assess the accuracy of the B3LYP, X3LYP, and newly developed M06-L, M06-2X, and M06 functionals to predict the binding energies of neutral and charged water clusters including (H2O)n, n = 2-8, 20), H3O(+)(H2O)n, n = 1-6, and OH(-)(H2O)n, n = 1-6. We also compare the predicted energies of two ion hydration and neutralization reactions on the basis of the calculated binding energies. In all cases, we use as benchmarks calculated binding energies of water clusters extrapolated to the complete basis set limit of the second-order Møller-Plesset perturbation theory with the effects of higher order correlation estimated at the coupled-cluster theory with single, double, and perturbative triple excitations in the aug-cc-pVDZ basis set. We rank the accuracy of the functionals on the basis of the mean unsigned error (MUE) between calculated benchmark and density functional theory energies. The corresponding MUE (kcal/mol) for each functional is listed in parentheses. We find that M06-L (0.73) and M06 (0.84) give the most accurate binding energies using very extended basis sets such as aug-cc-pV5Z. For more affordable basis sets, the best methods for predicting the binding energies of water clusters are M06-L/aug-cc-pVTZ (1.24), B3LYP/6-311++G(2d,2p) (1.29), and M06/aug-cc-PVTZ (1.33). M06-L/aug-cc-pVTZ also gives more accurate energies for the neutralization reactions (1.38), whereas B3LYP/6-311++G(2d,2p) gives more accurate energies for the ion hydration reactions (1.69).

Confined water dissociation in microporous defective silicates: mechanism, dipole distribution, and impact on substrate properties.

Interest in microporous materials has risen in recent years, as they offer a confined environment that is optimal to enhance chemical reactions. Calcium silicate hydrate (C-S-H) gel, the main component of cement, presents a layered structure with sub-nanometer-size disordered pores filled with water and cations. The size of the pores and the hydrophilicity of the environment make C-S-H gel an excellent system to study the possibility of confined water reactions. To investigate it, we have performed molecular dynamics simulations using the ReaxFF force field. The results show that water does dissociate to form hydroxyl groups. We have analyzed the water dissociation mechanism, as well as the changes in the structure and water affinity of the C-S-H matrix and water polarization, comparing the results with the behavior of water in a defective zeolite. Finally, we establish a relationship between water dissociation in C-S-H gel and the increase of hardness due to a transformation from a two- to a three-dimensional structure.

Initiation Mechanisms and Kinetics of Pyrolysis and Combustion of JP-10 Hydrocarbon Jet Fuel

In order to investigate the initiation mechanisms and kinetics associated with the pyrolysis of JP-10 (exo-tricyclo[5.2.1.0(2,6)]decane), a single-component hydrocarbon jet fuel, we carried out molecular dynamics (MD) simulations employing the ReaxFF reactive force field. We found that the primary decomposition reactions involve either (1) dissociation of ethylene from JP-10, resulting in the formation of a C(8) hydrocarbon intermediate, or (2) the production of two C(5) hydrocarbons. ReaxFF MD leads to good agreement with experiment for the product distribution as a function of temperature. On the basis of the rate of consumption of JP-10, we calculate an activation energy of 58.4 kcal/mol for the thermal decomposition of this material, which is consistent with a strain-facilitated C-C bond cleavage mechanism in JP-10. This compares well with the experimental value of 62.4 kcal/mol. In addition, we carried out ReaxFF MD studies of the reactive events responsible for oxidation of JP-10. Here we found overall agreement between the thermodynamic energies obtained from ReaxFF and quantum-mechanical calculations, illustrating the usefulness of ReaxFF for studying oxidation of hydrocarbons. The agreement of these results with available experimental observations demonstrates that ReaxFF can provide useful insights into the complicated thermal decomposition and oxidation processes of important hydrocarbon fuels.

Carbon Cluster Formation during Thermal Decomposition of Octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine and 1,3,5-Triamino-2,4,6-trinitrobenzene High Explosives from ReaxFF Reactive Molecular Dynamics Simulations

We report molecular dynamics (MD) simulations using the first-principles-based ReaxFF reactive force field to study the thermal decomposition of 1,3,5-triamino-2,4,6-trinitrobenzene (TATB) and octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) at various densities and temperatures. TATB is known to produce a large amount (15-30%) of high-molecular-weight carbon clusters, whereas detonation of nitramines such as HMX and RDX (1,3,5-trinitroperhydro-1,3,5-triazine) generate predominantly low-molecular-weight products. In agreement with experimental observation, these simulations predict that TATB decomposition quickly (by 30 ps) initiates the formation of large carbonaceous clusters (more than 4000 amu, or approximately 15-30% of the total system mass), and HMX decomposition leads almost exclusively to small-molecule products. We find that HMX decomposes readily on this time scale at lower temperatures, for which the decomposition rate of TATB is about an order of magnitude slower. Analyzing the ReaxFF MD results leads to the detailed atomistic structure of this carbon-rich phase of TATB and allows characterization of the kinetics and chemistry related to this phase and their dependence on system density and temperature. The carbon-rich phase formed from TATB contains mainly polyaromatic rings with large oxygen content, leading to graphitic regions. We use these results to describe the initial reaction steps of thermal decomposition of HMX and TATB in terms of the rates for forming primary and secondary products, allowing comparison to experimentally derived models. These studies show that MD using the ReaxFF reactive force field provides detailed atomistic information that explains such macroscopic observations as the dramatic difference in carbon cluster formation between TATB and HMX. This shows that ReaxFF MD captures the fundamental differences in the mechanisms of such systems and illustrates how the ReaxFF may be applied to model complex chemical phenomena in energetic materials. The studies here illustrate this for modestly sized systems and modest periods; however, ReaxFF calculations of reactive processes have already been reported on systems with approximately 10(6) atoms. Thus, with suitable computational facilities, one can study the atomistic level chemical processes in complex systems under extreme conditions.

Catalyzed growth of carbon nanotube with definable chirality by hybrid molecular dynamics-force biased Monte Carlo simulations

Metal-catalyzed growth mechanisms of carbon nanotubes (CNTs) were studied by hybrid molecular dynamics-Monte Carlo simulations using a recently developed ReaxFF reactive force field. Using this novel approach, including relaxation effects, a CNT with definable chirality is obtained, and a step-by-step atomistic description of the nucleation process is presented. Both root and tip growth mechanisms are observed. The importance of the relaxation of the network is highlighted by the observed healing of defects.

Development of a ReaxFF reactive force field for glycine and application to solvent effect and tautomerization.

Tautomerization of amino acids between the neutral form (NF) and the zwitterionic form (ZW) in water has been extensively studied, often using glycine as a model to understand this fundamental process. In spite of many advanced studies, the tautomerization reaction remains poorly understood because of the intrinsic complexities of the system, including multiple accessible reaction pathways, charge transfer, and variations of solvation structure. To establish an accurate model that can be used for molecular dynamics simulations, a ReaxFF reactive force field has been developed for glycine. A training set for the ReaxFF hydrocarbon potential was augmented with several glycine conformers and glycine-water complexes. The force field parameters were optimized to reproduce the quantum mechanically derived energies of the species in the training set. The optimized potential could accurately describe the properties of gas-phase glycine. It was applied to investigate the effect of solvation on the conformational distribution of glycine. Molecular dynamics simulations indicated significant differences in the dominant conformers in the gas phase and in water. This suggests that the tautomerization of glycine occurs through a conformational isomerization followed by the proton transfer event. The direct reaction mechanism of the NF → ZW proton transfer reaction in water, as well as mechanisms mediated by one or two water molecules, were investigated using molecular dynamics simulations. The results suggest that the proton transfer reaction is most likely mediated by a single water molecule. The ReaxFF potential developed in this work provides an accurate description of proton transfer in glycine and thus provides a useful methodology for simulating proton transfer reactions in organic molecules in the aqueous environment.