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...

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Autores: Perera, Isuri N., Dobhal, Garima S., Pringle, Jennifer M., O'Dell, Luke A., Tawfik, Sherif Abdulkader, Walsh, Tiffany R., Pozo Gonzalo, Cristina
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
id ES_4e793f2d07f810ed9fbe667baa461599
oai_identifier_str oai:digital.csic.es:10261/365699
network_acronym_str ES
network_name_str España
repository_id_str
dc.title.none.fl_str_mv Supplementary information for A case study using spectroscopy and computational modelling for Co speciation in a deep eutectic solvent [Dataset]
title Supplementary information for A case study using spectroscopy and computational modelling for Co speciation in a deep eutectic solvent [Dataset]
spellingShingle Supplementary information for A case study using spectroscopy and computational modelling for Co speciation in a deep eutectic solvent [Dataset]
Perera, Isuri N.
Computational model
Cobalt
http://metadata.un.org/sdg/7
Ensure access to affordable, reliable, sustainable and modern energy for all
cobalt
title_short Supplementary information for A case study using spectroscopy and computational modelling for Co speciation in a deep eutectic solvent [Dataset]
title_full Supplementary information for A case study using spectroscopy and computational modelling for Co speciation in a deep eutectic solvent [Dataset]
title_fullStr Supplementary information for A case study using spectroscopy and computational modelling for Co speciation in a deep eutectic solvent [Dataset]
title_full_unstemmed Supplementary information for A case study using spectroscopy and computational modelling for Co speciation in a deep eutectic solvent [Dataset]
title_sort Supplementary information for A case study using spectroscopy and computational modelling for Co speciation in a deep eutectic solvent [Dataset]
dc.creator.none.fl_str_mv Perera, Isuri N.
Dobhal, Garima S.
Pringle, Jennifer M.
O'Dell, Luke A.
Tawfik, Sherif Abdulkader
Walsh, Tiffany R.
Pozo Gonzalo, Cristina
author Perera, Isuri N.
author_facet Perera, Isuri N.
Dobhal, Garima S.
Pringle, Jennifer M.
O'Dell, Luke A.
Tawfik, Sherif Abdulkader
Walsh, Tiffany R.
Pozo Gonzalo, Cristina
author_role author
author2 Dobhal, Garima S.
Pringle, Jennifer M.
O'Dell, Luke A.
Tawfik, Sherif Abdulkader
Walsh, Tiffany R.
Pozo Gonzalo, Cristina
author2_role author
author
author
author
author
author
dc.contributor.none.fl_str_mv Australian Government
Perera, Isuri N. [0000-0001-6861-2781]
Dobhal, Garima S. [0000-0003-3538-0026]
Pringle, Jennifer M. [0000-0002-2729-2838]
O'Dell, Luke A. [0000-0002-7760-5417]
Tawfik, Sherif Abdulkader [0000-0003-3592-1419]
Walsh, Tiffany R. [0000-0002-0233-9484]
Pozo Gonzalo, Cristina [0000-0002-7890-6457]
Pozo Gonzalo, Cristina [cpg@deakin.edu.au, cpozo@icb.csic.es]
Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]
dc.subject.none.fl_str_mv Computational model
Cobalt
http://metadata.un.org/sdg/7
Ensure access to affordable, reliable, sustainable and modern energy for all
cobalt
topic Computational model
Cobalt
http://metadata.un.org/sdg/7
Ensure access to affordable, reliable, sustainable and modern energy for all
cobalt
description 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.
publishDate 2024
dc.date.none.fl_str_mv 2024
2024
2024
dc.type.none.fl_str_mv info:eu-repo/semantics/dataset
http://purl.org/coar/resource_type/c_ddb1
format dataset
dc.identifier.none.fl_str_mv http://hdl.handle.net/10261/365699
url http://hdl.handle.net/10261/365699
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv Perera, Isuri N.; Dobhal, Garima S.; Pringle, Jennifer M.; O'Dell, Luke A.; Tawfik, Sherif Abdulkader; Walsh, Tiffany R.; Pozo Gonzalo, Cristina. A case study using spectroscopy and computational modelling for Co speciation in a deep eutectic solvent. http://dx.doi.org/10.1039/d4cp01471e. http://hdl.handle.net/10261/365690
https://doi.org/10.1039/d4cp01471e
https://www.rsc.org/suppdata/d4/cp/d4cp01471e/d4cp01471e1.pdf
Sí
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv Royal Society of Chemistry (UK)
publisher.none.fl_str_mv Royal Society of Chemistry (UK)
dc.source.none.fl_str_mv reponame:DIGITAL.CSIC. Repositorio Institucional del CSIC
instname:Consejo Superior de Investigaciones Científicas (CSIC)
instname_str Consejo Superior de Investigaciones Científicas (CSIC)
reponame_str DIGITAL.CSIC. Repositorio Institucional del CSIC
collection DIGITAL.CSIC. Repositorio Institucional del CSIC
repository.name.fl_str_mv
repository.mail.fl_str_mv
_version_ 1869407758926741504
spelling Supplementary information for A case study using spectroscopy and computational modelling for Co speciation in a deep eutectic solvent [Dataset]Perera, Isuri N.Dobhal, Garima S.Pringle, Jennifer M.O'Dell, Luke A.Tawfik, Sherif AbdulkaderWalsh, Tiffany R.Pozo Gonzalo, CristinaComputational modelCobalthttp://metadata.un.org/sdg/7Ensure access to affordable, reliable, sustainable and modern energy for allcobaltUnder 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.Figure S1: UV-vis spectra of 0.1 mol L-1 CoCl2.6H2O and CoSO4.7H2O in EG:ChCl (4.5:1).; EPR spectroscopy: Figure S2; FTIR spectroscopy: Figures S3, S4; H NMR Spectroscopy: Figures S5, S6, S7; Further details on Force Field Molecular Dynamics Simulations: Simulated Annealing protocol, Production runs: Table S1; AIMD system construction: Table S2, Figure S8, S9, S10, S11, S12.Peer reviewedRoyal Society of Chemistry (UK)Australian GovernmentPerera, Isuri N. [0000-0001-6861-2781]Dobhal, Garima S. [0000-0003-3538-0026]Pringle, Jennifer M. [0000-0002-2729-2838]O'Dell, Luke A. [0000-0002-7760-5417]Tawfik, Sherif Abdulkader [0000-0003-3592-1419]Walsh, Tiffany R. [0000-0002-0233-9484]Pozo Gonzalo, Cristina [0000-0002-7890-6457]Pozo Gonzalo, Cristina [cpg@deakin.edu.au, cpozo@icb.csic.es]Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]202420242024info:eu-repo/semantics/datasethttp://purl.org/coar/resource_type/c_ddb1application/pdfhttp://hdl.handle.net/10261/365699reponame:DIGITAL.CSIC. Repositorio Institucional del CSICinstname:Consejo Superior de Investigaciones Científicas (CSIC)InglésPerera, Isuri N.; Dobhal, Garima S.; Pringle, Jennifer M.; O'Dell, Luke A.; Tawfik, Sherif Abdulkader; Walsh, Tiffany R.; Pozo Gonzalo, Cristina. A case study using spectroscopy and computational modelling for Co speciation in a deep eutectic solvent. http://dx.doi.org/10.1039/d4cp01471e. http://hdl.handle.net/10261/365690https://doi.org/10.1039/d4cp01471ehttps://www.rsc.org/suppdata/d4/cp/d4cp01471e/d4cp01471e1.pdfSíinfo:eu-repo/semantics/openAccessoai:digital.csic.es:10261/3656992026-05-22T06:33:51Z
score 15,81155

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