Supplementary information for A case study using spectroscopy and computational modelling for Co speciation in a deep eutectic solvent [Dataset]
Under a Creative Commons license BY 3.0.-- Force Field Molecular Dynamics Simulations: For all simulations, pressure was controlled using the Berendsen barostat with a time constant of 1.0 ps and compressibility of 4.5x10-5 bar-1.12 Temperature was controlled using the Nosé-Hoover thermostat with a...
| Autores: | , , , , , , |
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| Tipo de recurso: | conjunto de datos |
| Fecha de publicación: | 2024 |
| País: | España |
| Institución: | Consejo Superior de Investigaciones Científicas (CSIC) |
| Repositorio: | DIGITAL.CSIC. Repositorio Institucional del CSIC |
| OAI Identifier: | oai:digital.csic.es:10261/365699 |
| Acceso en línea: | http://hdl.handle.net/10261/365699 |
| Access Level: | acceso abierto |
| Palabra clave: | Computational model Cobalt http://metadata.un.org/sdg/7 Ensure access to affordable, reliable, sustainable and modern energy for all cobalt |
| Sumario: | Under a Creative Commons license BY 3.0.-- Force Field Molecular Dynamics Simulations: For all simulations, pressure was controlled using the Berendsen barostat with a time constant of 1.0 ps and compressibility of 4.5x10-5 bar-1.12 Temperature was controlled using the Nosé-Hoover thermostat with a time constant of 0.2 ps.13, 14 Coloumbic and van der Waals cut-offs of 1.6 nm were used and long range electrostatics were calculated using the Particle-mesh Ewald method.15, 16 A timestep of 1 fs was used. Simulated Annealing protocol: Several simulated annealing protocols were trialled with longer quenching times, and lower top temperatures. Here, we failed to see a convergence of the radial distribution functions (RDFs) and therefore, the structuring. This was particularly when the radial distribution functions of Co- (solvent atom) were constructed which showed that the cobalt coordination environment could get easily trapped in an energy minima which could not be recovered after another cycle of heating and cooling. The SA protocol that showed the least variations in the RDFs was used for further annealing. This involved heating the system up from 300 K to 1200 K in 200 ps, keeping the temperature at 1200 K for 3 ns and cooling down to 300 K in 6 ns. After this, a 300 ps simulation under a constant number, volume and temperature ensemble (NVT) was run at 300 K during which the RDFs for cycles were recorded. Production runs: For our production runs, three representative states were taken from each simulated annealing cycle. Trajectories were visualised using Visual Molecular Dynamics (VMD).17 RDFs were calculated using the gmx rdf utility. Analysis of coordination numbers and H-bonding was done using in-house python codes which utilised MDAnalysis. H-bonding was calculated by using a cut-off of donor oxygenacceptor oxygen distance of 3 Å and an angle cut-off of acceptor oxygen-donor oxygen-hydrogen of 30o or less. CN histograms for the first-shell used atom-atom cut-offs for Co-Cl, Co-O(EG), Co-NA, Co-Ow and Co-O(SO4) using the distance at which the respective RDFs were at a minimum after the initial peak. Second-shell CN was calculated using cut-offs from the minimum after the first peak to the minimum after the second peak in the RDFs. |
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