Molecular dynamics simulations of melting of perfect crystalline hexahydro-1,3,5-trinitro-1,3,5-s-triazine

The melting mechanism of superheated perfect crystalline hexahydro-1,3,5-trinitro-1,3,5-s-triazine (alpha-RDX) has been investigated using molecular dynamics simulations with the fully flexible force field developed by Smith and Bharadwaj [J. Phys. Chem. B 103, 3570 (1999)]. Sequential 50 ps equilibration simulations of the constant stress-constant temperature ensemble were performed at 10 K intervals over the range of 300-650 K, corresponding to a heating rate of 2.0 x 10(11) Ks. A solid-solid phase transition is observed between 480 and 490 K, followed by melting, which occurs between 500 and 510 K. The solid-solid phase transition, both displacive and rotational, is characterized by an abrupt decrease in the lengths of the unit cell edges a and b and an increase of the length of edge c. The molecular conformation in the new phase is AAE, although the axial nitro groups have different changes: one shift is more axial and the other is more equatorial. Phases other than alpha-RDX have been observed experimentally, however, there are insufficient data for comparisons to ascertain that the new phase observed here corresponds to a real phase. At the high heating rate (2.0 x 10(11) Ks) used in the simulations, the melted RDX reaches full orientational disorder at about 540 K and translational freedom at around 580 K. If the simulation at the melting temperature (510 K) is run sufficiently long complete rotational freedom is achieved in a few hundreds of picoseconds, while complete translational freedom requires much longer. These results show that given a sufficiently high heating rate, the system can exist for significant periods of time in a near-liquid state in which the molecules are not as free to rotate and diffuse as in the true liquid state. The bond lengths and bond angles undergo little change upon melting, while there are significant changes in the dihedral angles. The molecular conformation of RDX changes from AAE to EEE upon melting. The ramification of this for formulating force fields that accurately describe melting is that it is important that the torsional motions are accurately described.     

Molecular dynamics simulations of hexahydro-1,3,5-trinitro-1,3,5-s-triazine (RDX) using a combined Sorescu-Rice-Thompson AMBER force field

We present the results of molecular dynamics simulations of crystalline hexahydro-1,3,5-trinitro-1,3,5-s-triazine (RDX) using the SRT-AMBER force field (P. M. Agrawal et al., J. Phys. Chem. B 2006, 110, 5721), which combines the rigid-molecule force field developed by Sorescu-Rice-Thompson (D. C. Sorescu, B. M. Rice, and D. L. Thompson, J. Phys. Chem. B 1997, 101, 798) with the intramolecular interactions obtained from the Generalized AMBER Force Field (Wang et al., J. Comput. Chem. 2004, 25, 1157). The calculated crystal density at room conditions is about 10% lower than the measured value, while the lattice parameters and thermodynamic melting point are within about 5% at ambient pressure. The chair and inverted chair conformation, bond lengths, and bond angles of the RDX molecule are accurately predicted; however, there are some inaccuracies in the calculated orientations of the NO2 groups. The SRT-AMBER force field predicts overall reasonable results, but modifications, probably in the torsional parameters, are needed for a more accurate force field.     

High-pressure vibrational spectroscopy of energetic materials: hexahydro-1,3,5-trinitro-1,3,5-triazine

Vibrational spectroscopy has been used to investigate the room-temperature high-pressure phases of the energetic material hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX). The pressure-induced alterations in the spectral profiles were studied in a compression sequence to 30.2 GPa using Raman spectroscopy and to 26.6 GPa using far-infrared spectroscopy. At pressures near 4.0 GPa, several changes become immediately apparent in the Raman spectrum, such as large frequency shifts, mode splittings, and intensity changes, which are associated with a phase transition from alpha-RDX to gamma-RDX. Our study extends the kinetic stability of gamma-RDX to pressures near 18.0 GPa. Evidence for a new phase was found at pressures between 17.8 and 18.8 GPa and is based on the appearance of new vibrational bands and associated changes in intensity patterns. The new phase has vibrational characteristics that are similar to those of beta-RDX, suggesting the two polymorphs share a related crystal structure.     

Computational insight into energetic cage derivatives based on hexahydro-1,3,5-trinitro-1,3,5-triazine

Four novel cage compounds were designed by introducing –N(NO₂)CH₂–, –N(NO₂)O–, –N(NO₂)N(NO₂)–, and –N=N– linkages into the RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine) skeleton. Their molecular geometry, electronic structure, heat of formation, and detonation properties were systematically studied using density functional theory (DFT). In addition, the most stable dimers of the four compounds were constructed to further investigate their stability based on intermolecular interactions. It is found that the unconventional CH⋯O interactions would be the dominant driving force when the title compounds form crystals. Compared with the traditional explosives, the compounds with higher detonation properties and lower impact sensitivity will be considered as promising candidates for high energy density compounds. Our results indicate that our innovative design strategy is extremely useful for developing novel energetic compounds.     

Crystal structure of the high-pressure phase of hexahydro-1,3,5-trinitro-1,3,5-triazine (gamma-RDX)

The crystal structure of the high-pressure phase of hexahydro-1,3,5-trinitro-1,3,5-triazine (gamma-RDX), which is stable above 4 GPa at room temperature, was investigated by using infrared spectroscopy and powder X-ray diffraction measurements followed by Rietveld refinements using a diamond anvil cell (DAC). Although gamma and alpha phases were found to belong to the same space group Pbca, they exhibited a different crystal packing. The molecular structure of the gamma phase exhibited the same conformation as that of the alpha phase; however, the torsion angles of N-NO2 changed marginally.     

High pressure Raman spectroscopy of single crystals of hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX)

To gain insight into the high-pressure polymorphism of RDX, an energetic crystal, Raman spectroscopy results were obtained for hydrostatic (up to 15 GPa) and non-hydrostatic (up to 22 GPa) compressions. Several distinct changes in the spectra were found at 4.0 +/- 0.3 GPa, confirming the alpha-gamma phase transition previously observed in polycrystalline samples. Detailed analyses of pressure-induced changes in the internal and external (lattice) modes revealed several features above 4 GPa: (i) splitting of both the A' and A' ' internal modes, (ii) a significant increase in the pressure dependence of the Raman shift for NO2 modes, and (iii) no apparent change in the number of external modes. It is proposed that the alpha-gamma phase transition leads to a rearrangement between the RDX molecules, which in turn significantly changes the intermolecular interaction experienced by the N-O bonds. Symmetry correlation analyses indicate that the gamma-polymorph may assume one of the three orthorhombic structures: D2h, C2v, or D2. On the basis of the available X-ray data, the D2h factor group is favored over the other structures, and it is proposed that gamma-phase RDX has a space group isomorphous with a point group D2h with eight molecules occupying the C1 symmetry sites, similar to the alpha-phase. It is believed that the factor group splitting can account for the observed increase in the number of modes in the gamma-phase. Spatial mapping of Raman modes in a non-hydrostatically compressed crystal up to 22 GPa revealed a large difference in mode position indicating a pressure gradient across the crystal. No apparent irreversible changes in the Raman spectra were observed under non-hydrostatic compression.     

Ab initio based force field and molecular dynamics simulations of crystalline TATB

An all-atom force field for 1,3,5-triamino-2,4,6-trinitrobenzene (TATB) is presented. The classical intermolecular interaction potential for TATB is based on single-point energies determined from high-level ab initio calculations of TATB dimers. The newly developed potential function is used to examine bulk crystalline TATB via molecular dynamics simulations. The isobaric thermal expansion and isothermal compression under hydrostatic pressures obtained from the molecular dynamics simulations are in good agreement with experiment. The calculated volume-temperature expansion is almost one dimensional along the c crystallographic axis, whereas under compression, all three unit cell axes participate, albeit unequally.     

1,3,5-trinitro-1,3,5-triazine decomposition and chemisorption on Al(111) surface: first-principles molecular dynamics study

We have investigated the decomposition and chemisorption of a 1,3,5-trinitro-1,3,5-triazine (RDX) molecule on Al(111) surface using molecular dynamics simulations, in which interatomic forces are computed quantum mechanically in the framework of the density functional theory (DFT). The real-space DFT calculations are based on higher-order finite difference and norm-conserving pseudopotential methods. Strong attractive forces between oxygen and aluminum atoms break N-O and N-N bonds in the RDX and, subsequently, the dissociated oxygen atoms and NO molecules oxidize the Al surface. In addition to these Al surface-assisted decompositions, ring cleavage of the RDX molecule is also observed. These reactions occur spontaneously without potential barriers and result in the attachment of the rest of the RDX molecule to the surface. This opens up the possibility of coating Al nanoparticles with RDX molecules to avoid the detrimental effect of oxidation in high energy density material applications.     

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.     

Determination of N-nitroso derivatives of hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) in soils by pressurized liquid extraction and liquid chromatography-electrospray ionization mass spectrometry

To aid in the evaluation of the potential toxicity of N-nitroso derivatives of hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX), we describe a pressurized liquid extraction (PLE) followed by liquid chromatography-electrospray ionization-mass spectrometry (LC-ESI-MS) method for determination of RDX and its N-nitroso derivatives: hexahydro-1-nitroso-3,5-dinitro-1,3,5-triazine (MNX), hexahydro-1,3-dinitroso-5-nitro-1,3,5-triazine (DNX), and hexahydro-1,3,5-trinitroso-1,3,5-triazine (TNX) in soils. Sandy loam soil was spiked with RDX and its N-nitroso derivatives (MNX, DNX, and TNX). Acetonitrile was used as the PLE extraction solvent at 100 degrees C and 1500 psi for 15 min. Florisil was used to cleanup extracts following PLE. Instrumental analysis employed LC-ESI-MS, in which 1mM acetic acid was added to the mobile phase to facilitate formation of acetate adduct ions [M+CH(3)COO](-). The method detection limits (MDLs) for RDX, MNX, DNX, and TNX were 1.46, 1.46, 1.69, and 1.93 ng/g, respectively. High recovery (91.1-108.3%), good precision (RSD: 3.2-12.4%), and reproducibility were achieved. This method proved effective and was applied to monitor the reductive biotransformation of MNX in soils with the presence of earthworms (Eisenia fetida).     

Paramfit: Automated optimization of force field parameters for molecular dynamics simulations

The generation of bond, angle, and torsion parameters for classical molecular dynamics force fields typically requires fitting parameters such that classical properties such as energies and gradients match precalculated quantum data for structures that scan the value of interest. We present a program, Paramfit, distributed as part of the AmberTools software package that automates and extends this fitting process, allowing for simplified parameter generation for applications ranging from single molecules to entire force fields. Paramfit implements a novel combination of a genetic and simplex algorithm to find the optimal set of parameters that replicate either quantum energy or force data. The program allows for the derivation of multiple parameters simultaneously using significantly fewer quantum calculations than previous methods, and can also fit parameters across multiple molecules with applications to force field development. Paramfit has been applied successfully to systems with a sparse number of structures, and has already proven crucial in the development of the Assisted Model Building with Energy Refinement Lipid14 force field. © 2014 Wiley Periodicals, Inc.     

A polarizable empirical force field for molecular dynamics simulation of liquid hydrocarbons

Electronic polarizability is usually treated implicitly in molecular simulations, which may lead to imprecise or even erroneous molecular behavior in spatially electronically inhomogeneous regions of systems such as proteins, membranes, interfaces between compounds, or mixtures of solvents. The majority of available molecular force fields and molecular dynamics simulation software packages does not account explicitly for electronic polarization. Even the simplest charge‐on‐spring (COS) models have only been developed for few types of molecules. In this work, we report a polarizable COS model for cyclohexane, as this molecule is a widely used solvent, and for linear alkanes, which are also used as solvents, and are the precursors of lipids, amino acid side chains, carbohydrates, or nucleic acid backbones. The model is an extension of a nonpolarizable united‐atom model for alkanes that had been calibrated against experimental values of the density, the heat of vaporization and the Gibbs free energy of hydration for each alkane. The latter quantity was used to calibrate the parameters governing the interaction of the polarizable alkanes with water. Subsequently, the model was tested for other structural, thermodynamic, dielectric, and dynamic properties such as trans/gauche ratios, excess free energy, static dielectric permittivity, and self‐diffusion. A good agreement with the experimental data for a large set of properties for each considered system was obtained, resulting in a transferable set of polarizable force‐field parameters for CH₂, CH₃, and CH₄ moieties. © 2014 Wiley Periodicals, Inc.     

CHARMM force field and molecular dynamics simulations of protonated polyethylenimine

As a gene delivery vector, polyethylenimine (PEI) shows one of the highest transfection efficiencies, while effectively protecting DNA from enzyme degradation. The distinctive charge pattern of protonated PEI is widely considered responsible for fundamental process such as DNA condensation into PEI/DNA polyplexes (which are able to enter cells via endocytosis), proton sponge effect (which triggers the release of polyplexes from endosome), and release of DNA from polyplexes (to be further processed inside the nucleus). Our investigations are largely motivated by the crucial need for a realistic molecular mechanics force field (FF) for PEI, and, accordingly, we focus on two major issues: (1) development of a new atomistic (CHARMM) FF for PEI in different protonation states, rigorously derived from high‐quality ab initio calculations performed on model polymers, and (2) molecular dynamics investigations of solvated PEI, providing a detailed picture of the dynamic structuring thereof in dependence on their size and protonation state. The modeled PEI chains are essentially described in terms of gyration radius, end‐to‐end distance, persistence length, radial distribution functions, coordination numbers, and diffusion coefficients. They turn out to be more rigid than in other computational studies and we find diffusion coefficients in fair agreement with experimental data. The developed atomistic FF proves adequate for the realistic modeling of the size and protonation behavior of linear PEI, either as individual chains or composing polyplexes. © 2017 Wiley Periodicals, Inc.     

Trace level analysis of hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) and its biodegradation intermediates in liquid media by solid-phase extraction and high-pressure liquid chromatography analysis

The use of solid-phase extraction for the analysis of liquid media containing low microg/L levels of hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX), mononitroso-RDX (MNX), dinitroso-RDX (DNX), and trinitroso-RDX (TNX) is examined. Aqueous samples (100 mL) consisting of water and a microbiological basal medium are spiked with known concentrations of RDX, MNX, DNX, and TNX. The compounds are extracted from the liquid media using a Porapak RDX cartridge and then eluted from the cartridge with 5 mL of acetonitrile. The eluent is concentrated to 1 mL before analysis by high-pressure liquid chromatography (HPLC). The method detection limits for RDX are 0.1 microg/L in water and 0.5 microg/L in the basal medium after a 100-fold concentration. For MNX, DNX, and TNX, the method detection limits are approximately 0.5 microg/L in water and approximately 1 microg/L in the basal medium after a 100-fold concentration. Interferences in the basal medium and a contaminant in the standard made quantitation for MNX and TNX, respectively, is less accurate below the 1 microg/L level. Solid-phase extraction of the liquid media gave good recoveries of nitramines and nitroso intermediates from a microbiological basal medium, allowing HPLC detection of RDX and the nitroso intermediates in the low microg/L (ppb) range.     

Development of dissociative force field for all-atomistic molecular dynamics calculation of fracture of polymers

A dissociative force field for all-atomistic molecular dynamics calculations has been developed to investigate impact fracture of polymers accompanying dissociation of chemical bonds of polymer main chain. Energy of dimer molecules was evaluated as a function of both bond-length b and bond-angle θ by CASPT2 calculations, whose quality is enough to describe dissociation of chemical bonds. Because we found that the bond dissociation energy D decreases with increasing bond-angle, we employed the Morse-type function V_Bond(b, θ) = {D − V_Angle(θ)}[1 − exp{−α(b − b₀) − β(b − b₀)²}] where a quartic function V_Angle(θ) = k₁(θ − θ₀) + k₂(θ − θ₀)² + k₃(θ − θ₀)³ + k₄(θ − θ₀)⁴ . This function reproduced well the CASPT2 potential energy surface in a wide range of b and θ. The parameters have been obtained for four popular glassy polymers, polyethylene, poly(methyl methacrylate), poly(styrene), and polycarbonate. © 2019 Wiley Periodicals, Inc.     

A molecular mechanics force field for lignin

A CHARMM molecular mechanics force field for lignin is derived. Parameterization is based on reproducing quantum mechanical data of model compounds. Partial atomic charges are derived using the RESP electrostatic potential fitting method supplemented by the examination of methoxybenzene:water interactions. Dihedral parameters are optimized by fitting to critical rotational potentials and bonded parameters are obtained by optimizing vibrational frequencies and normal modes. Finally, the force field is validated by performing a molecular dynamics simulation of a crystal of a lignin fragment molecule and comparing simulation-derived structural features with experimental results. Together with the existing force field for polysaccharides, this lignin force field will enable full simulations of lignocellulose.     

Enthalpies of mixing predicted using molecular dynamics simulations and OPLS force field

Enthalpy of mixing (EOM) is one of the most basic thermodynamic properties of mixtures. To assess feasibility of predicting EOM using force field simulation methods, fifteen (15) representative binary mixtures were investigated using MD simulations based on OPLS and TIP4P force fields. The simulation conditions and errors were carefully examined. The precision level of 0.04 kJ/mol was obtained for calculated EOM data. However, the predictions, measured by deviations from experimental data, were only qualitatively correct. Among various factors influencing the accuracy of predictions, force field quality representing interactions among different molecules plays the most significant role. Using methanol/benzene and ethanol/benzene as examples, we demonstrated that non-additive interaction terms between polarizable atoms can be used to significantly improve the quality of predictions. In addition, it appears that charge-dependent LJ parameters are required in order to represent the polarization effects accurately.     

Hydration of calcium oxide surface predicted by reactive force field molecular dynamics

In this work, we present the parametrization of Ca-O/H interactions within the reactive force field ReaxFF, and its application to study the hydration of calcium oxide surface. The force field has been fitted using density functional theory calculations on gas phase calcium-water clusters, calcium oxide bulk and surface properties, calcium hydroxide, bcc and fcc Ca, and proton transfer reactions in the presence of calcium. Then, the reactive force field has been used to study the hydration of the calcium oxide {001} surface with different water contents. Calcium oxide is used as a catalyzer in many applications such as CO(2) sequestration and biodiesel production, and the degree of surface hydroxylation is a key factor in its catalytic performance. The results show that the water dissociates very fast on CaO {001} bare surfaces without any defect or vacancy. The surface structure is maintained up to a certain amount of water, after which the surface undergoes a structural rearrangement, becoming a disordered calcium hydroxyl layer. This transformation is the most probable reason for the CaO catalytic activity decrease.     

A vibrational molecular force field of model compounds with biological interest. I. Harmonic dynamics of crystalline urea at 123 K

Normal coordinate calculations have been performed for urea and deuterated urea in the crystalline state. We have used the modified Urey–Bradley–Shimanouchi intramolecular potential energy function and a rather sophisticated intermolecular energy function to reproduce I.R. and Raman frequencies with an average error of 2 cm^–1. The general agreement between the calculation and experiment suggests that intermolecular interactions must be taken into account to determine reliable intramolecular parameters of the potential energy function, mainly the barrier to internal rotation around the C? N bond. The intermolecular energy function, which consists of the Buckingham function and an explicit harmonic function for hydrogen-bonding, then has the merit to reproduce quite well the observed frequencies of lattice vibrations.     

New all-atom force field for molecular dynamics simulation of an AlPO(4)-34 molecular sieve

A force field of the triclinic framework of AlPO(4)-34, important in methanol-hydrocarbon conversion reactions, was developed using an empirical potential function. Molecular dynamics simulation of an AlPO(4)-34 triclinic framework segment of 1216 atoms, containing the template molecules isopropylamine and water, was performed with explicit consideration of atomic charges. The average RMS difference between instantaneous positions of the framework atoms during 1 ns simulation and their positions in the structure determined from single crystal X-ray diffraction was calculated, and the average structure of the flexible framework was determined. The computed Debye-Waller factors and simulated FTIR spectra are in good agreement with the experimental data. The new force field permits detailed molecular dynamics simulations of flexible, charged aluminophosphate molecular sieves which should lead to a better understanding of the catalytic processes and the crucial role played by templating molecules.