Unsupervised learning of representative local atomic arrangements in molecular dynamics data

Roncoroni, Fabrice; Sanz-Matı́as, Ana; Sundararaman, Siddharth

doi:10.48550/arxiv.2302.01465

Cited by 2 publications

(7 citation statements)

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“…Force-field parameters 44,45 were validated in our previous work on the same system. 17 The graphene was frozen in place by setting the forces to zero in order to ensure neutral and charged simulations were comparable. These MD setup was kept for the MTD and US simulations.…”

Section: Methodsmentioning

confidence: 99%

“…Umbrella sampling trajectories were analyzed with an unsupervised learning methodology recently developed by us. 17 In this protocol, between 5000 and 10000 local atomic arrangements were extracted from each US trajectory, which when there aligned while taking into account possible permutations between similar elements (e.g. THF -O).…”

Section: Methodsmentioning

confidence: 99%

“…Our metadynamics simulations project the full free energy landscape onto only a few collective variables, however, multiple molecular conformations may satisfy these constraints (Ca-B coordination number and Ca-Ca distance, in this case). Data-mining techniques (dimensionality reduction, hierarchical clustering and permutation-invariant alignment 17 -details in Methods and SI) applied to selective umbrella sampling of local minima in the free energy landscape reveal a rich variety of solvated isomeric structures, summarized in Fig. 1 d.…”

Section: In the Bulk Electrolytementioning

confidence: 99%

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Ca-dimers and solvent layering determine electrochemically active species in Ca(BH$_4$)$_2$ in THF

Sanz-Matìas¹,

Roncoroni²,

Sundararaman³

2023

Preprint

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Divalent ions, such as Mg, Ca, and Zn, are being considered as competitive, safe, and earthabundant alternatives to Li-ion electrochemistry. However, the challenge remains to match electrode and electrolyte materials that stably cycle with these new formulations, based primarily on controlling interfacial phenomena. We explore the formation of electroactive species in the electrolyte Ca(BH4)2 in THF through molecular dynamics simulation. Free-energy analysis indicates that this electrolyte has a majority population of neutral Ca dimers and monomers, albeit with diverse molecular conformations as revealed by unsupervised learning techniques, but with an order of magnitude lower concentration of possibly electroactive charged species, such as the monocation, CaBH + 4 , which we show is produced via disproportionation of neutral Ca(BH4)2 complexes. Dense layering of THF molecules within 1 nm of the electrode surface (modeled here using graphite) hinders the approach of reducible species to within 0.6 nm and instead enhances the local concentration of species in a narrow intermediate-density layer from 0.7-0.9 nm. A dramatic increase in the monocation population in this intermediate layer is induced at negative bias, supplied by local dimer disproportionation. We see no evidence to support any functional role of fully-solvated Ca 2+ in the electrochemical activity of this electrolyte. The consequences for performance and alternative formulations are discussed in light of this molecular-scale insight.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: In the Bulk Electrolytementioning

confidence: 99%

See 1 more Smart Citation

Ca-dimers and solvent layering determine electrochemically active species in Ca(BH$_4$)$_2$ in THF

Sanz-Matìas¹,

Roncoroni²,

Sundararaman³

2023

Preprint

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show abstract

“…[11][12][13][14][15][16] Furthermore, mining the large quantities of compositional and conformational data produced by these simulations presents its own challenge. Here we rely on recently developed unsupervised learning approaches 17 to provide a faster path to extracting molecular-scale insight and guidance for future experiments to validate our predictions.…”

Section: Introductionmentioning

confidence: 99%

“…Umbrella sampling trajectories 740 were analyzed with an unsupervised learning methodology recently developed by us. 17 In this protocol, between 5000 and 10000 local atomic arrangements were extracted from each US trajectory, which when there aligned while taking into account possible permutations between simi-745 lar elements (e.g. THF -O).…”

mentioning

confidence: 99%

Ca-dimers and solvent layering determine electrochemically active species in Ca(BH4)2 in THF

Sanz-Matı́as

Roncoroni

Sundararaman

2023

Preprint

Self Cite

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Divalent ions, such as Mg, Ca, and Zn, are being considered as competitive, safe, and earth-abundant alternatives to Li-ion electrochemistry. However, the challenge remains to match elec- trode and electrolyte materials that stably cycle with these new formulations, based primarily on controlling interfacial phenomena. We explore the formation of electroactive species in the electrolyte Ca(BH4)2 in THF through molecular dynamics simulation. Free-energy analysis indicates that this electrolyte has a majority population of neutral Ca dimers and monomers, albeit with diverse molecular conformations as revealed by unsupervised learning techniques, but with an order of magnitude lower concentration of possibly electroactive charged species, such as the monocation, CaBH4+, which we show is produced via disproportionation of neutral Ca(BH4)2 complexes. Dense layering of THF molecules within 1 nm of the electrode surface (modeled here using graphite) hinders the approach of reducible species to within 0.6 nm and instead enhances the local concentration of species in a narrow intermediate-density layer from 0.7-0.9 nm. A dramatic increase in the monocation population in this intermediate layer is induced at negative bias, supplied by local dimer disproportionation. We see no evidence to support any functional role of fully-solvated Ca2+ in the electrochemical activity of this electrolyte. The consequences for performance and alternative formulations are discussed in light of this molecular-scale insight.

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Unsupervised learning of representative local atomic arrangements in molecular dynamics data

Cited by 2 publications

References 0 publications

Ca-dimers and solvent layering determine electrochemically active species in Ca(BH$_4$)$_2$ in THF

Ca-dimers and solvent layering determine electrochemically active species in Ca(BH$_4$)$_2$ in THF

Ca-dimers and solvent layering determine electrochemically active species in Ca(BH4)2 in THF

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