Computational protocol: Formation of the prebiotic molecule NH2CHO on astronomical amorphous solid water surfaces: accurate tunneling rate calculations††Electronic supplementary information (ESI) available: Geometric details, lists of calculated rate constants. See DOI: 10.1039/c6cp05727fClick here for additional data file.

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Protocol publication

[…] The ASW surface was prepared by classical molecular dynamics (MD) simulations with NAMD. The initial sample is produced by VMD version 1.9.2 containing 9352 TIP3P water molecules. These were simulated in a slab of 85 Å × 85 Å and a thickness of approximately 36 Å. Periodic boundary conditions were applied along all three Cartesian axes with about 70 Å of vacuum between the slabs. This system was treated as a canonical ensemble, equilibrated at 300 K using a Langevin thermostat for 100 ps. After that, the thermostat was instantaneously quenched to 10 K and the system was left for 20 ps to produce a thermally equilibrated bulk amorphous water at low temperature. A hemisphere with a radius of 34 Å was cut out of the slab to be used in the following QM/MM calculations.A large sample of different binding sites on the surface was generated. The HNCO molecule was placed at 113 positions on a regular 2D-grid with a step size of 2 Å covering a circular area with a radius of 12 Å. In each of the 113 points, the molecule was placed 2 Å above the surface. Water molecules with at least one atom within 6 Å were treated by QM (typically about 23 molecules), water molecules within 12 Å were optimized (typically about 161). All other molecules of the hemispheric model were frozen. […]

Pipeline specifications

Software tools NAMD, VMD
Application Protein structure analysis
Chemicals Hydrogen