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HydroNanoConstruct: A Web Application for Digital Construction, Crystal Growth Investigation, and Atomistic
Panagiotis D Kolokathis1, Anastasios Sourpis2, Dimitris Mintis2,3
1NovaMechanics MIKE, Piraeus 18545, Greece.
Abstract:
HydroNanoConstruct is a web application with a graphical user interface (GUI) that enables the digital construction and analysis of hydrated metal/metalloid oxide (ΜΟ) nanoparticles (NPs). The tool supports (a) building hydrated ΜΟ NPs from crystallographic information files (CIFs) of MOs by adding hydrogen cations, hydroxyl anions, and water molecules to the surface atoms, preserving the bulk material's coordination numbers for the metal/metalloid atoms, (b) performing energy minimization on the digitally constructed hydrated MO NPs to obtain realistic structures, (c) embedding the hydrated MO NP into a simulation box filled with water molecules to incorporate solvent effects, and (d) running multiple molecular dynamics and energy minimization cycles to compute atomistic descriptors, including surface energy (in vacuum and in water) and the potential energy of the bulk material. The tool is freely available via the EosCloud Platform at https://eoscloud.entelos.eu/ssbd4chem/nanoconstruct/.
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