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Bond stretching and three-center angle bending potentials have been developed to extend an existing rigid-bond 1,3,5-triamino-2,4,6-trinitrobenzene molecular dynamics force field [D. Bedrov, O. Borodin, G. D. Smith, T. D. Sewell, D. M. Dattelbaum, and L. L. Stevens, J. Chem. Phys. 131, 224703 (2009)] for simulations requiring fully flexible molecules. The potentials were fit to experimental vibrational spectra and electronic structure predictions of vibrational normal modes using a combination of zero kelvin eigenmode analysis for the isolated molecule and power spectra for the isolated molecule and crystal. A reverse non-equilibrium molecular dynamics method [F. Müller-Plathe, J. Chem. Phys. 106, 6082 (1997)] was used to obtain the room temperature, atmospheric pressure thermal conductivity along three directions in a well-defined, non-orthogonal basis. The thermal conductivity was found to be significantly anisotropic with values 1.13 ± 0.07, 1.07 ± 0.07, and 0.65 ± 0.03 W m(-1) K(-1) for directions nominally parallel to the a, b, and c lattice vectors, respectively.

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The anisotropic thermal conductivity was determined for initially defect-free and defective crystals of 1,3,5-triamino-2,4,6-trinitrobenzene (TATB), a material that exhibits a graphitic-like packing structure with stacked single-molecule-thick layers, using the reverse non-equilibrium molecular dynamics method and an established TATB molecular dynamics force field. Thermal conduction in TATB is predicted to be substantially higher and more anisotropic than in other related organic molecular explosives, with conduction along directions nominally in the plane of the molecular layers at least 68% greater than conduction along the direction exactly perpendicular to the layers. Finite-size effects along the conduction directions were assessed. The conductivity along directions nominally in the plane of the molecular layers was found to be insensitive to the supercell length along the conduction direction-a result commensurate with the estimated phonon mean free path, ∼6 Å. A small decrease in the conductivity normal to the layers was found for longer supercells and is likely due to increased phonon scattering as a result of dynamic structural transitions in the crystal. The thermal conductivity of TATB crystals containing vacancy defects was also determined and the variation of conductivity with crystal density was found to be both linear and anisotropic, with the introduction of vacancy defects leading to a greater percentage reduction in conduction for the direction perpendicular to the molecular layers.

We demonstrate the capability of creating robust density functional tight binding (DFTB) models for chemical reactivity in prebiotic mixtures through force matching to short time scale quantum free energy estimates. Molecular dynamics using density functional theory (DFT) is a highly accurate approach to generate free energy surfaces for chemical reactions, but the extreme computational cost often limits the time scales and range of thermodynamic states that can feasibly be studied. In contrast, DFTB is a semiempirical quantum method that affords up to a thousandfold reduction in cost and can recover DFT-level accuracy. Here, we show that a force-matched DFTB model for aqueous glycine condensation reactions yields free energy surfaces that are consistent with experimental observations of reaction energetics. Convergence analysis reveals that multiple nanoseconds of combined trajectory are needed to reach a steady-fluctuating free energy estimate for glycine condensation. Predictive accuracy of force-matched DFTB is demonstrated by direct comparison to DFT, with the two approaches yielding surfaces with large regions that differ by only a few kcal mol.