ASCOT: A web tool for the digital construction of energy minimized Ag, CuO, TiO2 spherical nanoparticles and calculation of their atomistic descriptors

Abstract

ASCOT (an acronym derived from Ag-Silver, Copper Oxide, Titanium Oxide) is a user-friendly web tool for digital construction of electrically neutral, energy-minimized spherical nanoparticles (NPs) of Ag, CuO, and TiO₂ (both Anatase and Rutile forms) in vacuum, integrated into the Enalos Cloud Platform (https://www.enaloscloud.novamechanics.com/sabydoma/ascot/). ASCOT calculates critical atomistic descriptors such as average potential energy per atom, average coordination number, common neighbour parameter (used for structural classification in simulations of crystalline phases), and hexatic order parameter (which measures how closely the local environment around a particle resembles perfect hexatic symmetry) for both core (over 4 Å from the surface) and shell (within 4 Å of the surface) regions of the NPs. These atomistic descriptors assist in predicting the most stable NP size based on lowest per atom energy and serve as inputs for developing machine learning models to predict the toxicity of these nanomaterials. ASCOT's automated backend requires minimal user input in order to construct the digital NPs: inputs needed are the material type (Ag, CuO, TiO₂-Anatase, TiO₂-Rutile), target diameter, a Force-Field from a pre-validated list, and the energy minimization parameters, with the tool providing a set of default values for novice users.

Keywords: Ag; Anatase; Automation; CuO; Descriptors; Energy Minimization; Nanoparticle; Rutile; Tenorite; TiO2.

Graphical abstract

Fig. 1

Unit cells of a) Ag (native silver), b) CuO (tenorite), c) TiO₂ (Anatase) and d) TiO_{2 (}Rutile) and spherical NPs built using these unit cells via ASCOT.

Fig. 2

Calculation of the minimum number of unit cells per x, y, z direction (= N₁, N₂, N₃) that are needed to make a spherical NP with radius R_user. The unit cell vectors a, b, c are illustrated with pink, green and brown colours respectively.

Fig. 3

Graphical illustration of the NP construction algorithm for an imaginary material consisting of red and green atoms with stoichiometry 2:1. The Parallelograms of this Figure show the boundaries of each unit cell which is replicated in space to make a larger parallelogram. Only the atoms inside the diameter of our NP are kept to construct our NP. If the stoichiometry of the atoms inside the sphere is different from the stoichiometry of the unit cell, the atoms that are in abundance are deleted to get the structure we will use for the next step of energy minimization. To find the outer atoms which are candidates to be deleted in order to achieve the desired stoichiometry (indicated as blue spheres in the bottom right step), an outer shell of 0.02 Å thickness was used.

Fig. 4

Geometrically constructed Native Silver NP created by ASCOT after inserting 5 nm diameter as input.

Fig. 5

Conversion of a triclinic box to orthorhombic one and increase on its edge 10 Å to avoid NP self-interactions.

Fig. 6

A TiO₂ (Anatase) NP made by ASCOT having its diameter equal to 7.4 nm and a sketch of the Shell Average Potential Energy per atom as a function of the radius beyond which shell starts (see Burk et al. [44]). The blue point is the point of the maximum curvature of the Shell Average Potential Energy per atom which Burk et al. used to determine the borderline between the core (dark sphere) and the shell (the region between the outer and the inner sphere) according to the Kneedle algorithm .

Fig. 7

Graphical User Interface of ASCOT with a description of the NP generation and optimization Stages and its derived files, demonstrated as implementation of the construction of spherical CuO NPs having diameter equal to 5 nm, and the energy minimisation step. The descriptors are then automatically calculated for the energy minimised NPs.

Fig. 8

(a) Geometrically constructed spherical TiO₂-Anatase NP of 3.5 nm diameter, (b) Energy-minimized spherical TiO₂-Anatase NP of 3.5 nm initial diameter using a COMB3 type Force-Field and (c) Energy-minimized spherical TiO₂-Anatase NP of 3.5 nm initial diameter using a MEAM type Force-Field of Zhang and Trinkle .

Fig. 9

The average potential energy (a), the average coordination number (b) and the average CNP number (c) per atom as a function of the diameter of Rutile and Anatase NPs. Solid and dashed lines illustrate the descriptor values for the Anatase and the Rutile phases of TiO₂ NPs respectively. The whole NP, the core of the NP and the shell of NP descriptors are illustrated with blue, orange, and grey line colours respectively in (a-c). Anatase and Rutile NPs having diameter equal to 5 nm are also illustrated (d), with the Ti and O illustrated with grey and red coloured balls, respectively.

Fig. 10

Crystal growth of TiO₂-Rutile NP starting from a diameter of 5 nm (left), growing into a NP having diameter equal to 5.2 nm (middle) and 5.4 nm (right). Ti and O are illustrated with grey and red colours, respectively.

Fig. 11

The average potential energy (a), the average coordination number (b) and the average CNP number (c) per atom as a function of the diameter of Ag NPs. Solid and dashed lines illustrate the descriptors values for the Force-Fields of Ackland et al. and Girifalco and Weizer , respectively. The whole NP, the core of the NP and the shell of NP descriptors are illustrated with blue, orange, and grey colours respectively in (a-c). An Ag NP having diameter equal to 9 nm is also illustrated (d).

Fig. 12

The average potential energy (a), the average coordination number (b) the average CNP number (c) per atom as a function of the diameter of CuO NPs for the COMB3 Force-Field , the magnitude of the hexatic order parameter (d) and its phase (e). The whole NP, the core of the NP and the shell of NP descriptors are illustrated with blue, orange, and grey colours, respectively, in (a-e). A CuO NP geometrically constructed having diameter equal to 5 nm is also illustrated (f) with the Cu and O shown as green and red respectively).