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About TopIso3D Viewer

TopIso3D Viewer is a free software with a user-friendly graphical interface, that generates three-dimensional maps to analyze descriptors based on the Quantum Theory of Atoms in Molecules (QTAIM), applied in periodic and non-periodic systems. The software also automates the launching of topological analysis calculations through the Topond package and generates a report that facilitates the identification of the values of the calculated descriptors, in the Bond Critical Points (BCP), facilitating the classification of chemical interactions. The map projects created can be stored in the form of HTML files, for later consultation through any type of browser.
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TopIso3D Viewer was developed for the community of Crystal package and Topond software users, running, in this Version 1, only on Linux operating system. For its use, the optimized system wave functions file (fort.9), generated by the Crystal17© Package, is required. TopIso3D Viewer is ready to be downloaded, in the form of an executable file, compressed in .zip format, through the "Download Software" button above. Once the download is finished, the folder must be unzipped and the executable file must be used from this folder. The TopIso3D Viewer Manual v. 1 is also available for download.

Some projects

Some projects prepared by our team and the TopIso3D community are available below. They provide information about the analyzed systems and the optimization conditions through the Crystal17© Package. The project can be accessed through the link in the map type.

Urea Molecule

Electron density map

OPTIMIZATION PARAMETERS:

Functional: HSE06; Basis set: pob-TZVP-rev2 (all elements); TOLDEE: 10; TOLINTEG: 10 10 10 10 20; SHRINK: 8 8;

TOPISO3D PARAMETERS:

SURFRHOO; Slices: 100; Opacity: 0.1; Isosurfaces: 10; Min: 0.01 a.u.; Max: 0.5 a.u.

Urea Crystal

Electron density map

OPTIMIZATION PARAMETERS:

Functional: HSE06; Basis set: pob-TZVP-rev2 (all elements); TOLDEE: 10; TOLINTEG: 10 10 10 10 20; SHRINK: 8 8;

TOPISO3D PARAMETERS:

SURFRHOO; Slices: 100; Opacity: 0.1; Isosurfaces: 10; Min: 0.01 a.u.; Max: 0.5 a.u.

MgO

Lap. of electron density map

OPTIMIZATION PARAMETERS:

Functional: B3LYP; Basis set: Mg_8-511G_harrison_1994, O_m-6-311G(d)_Heyd_2005; TOLDEE: 9; TOLINTEG: 7 7 7 7 9; TOLDEG: 0.003; TOLDEX: 0.012; SHRINK: 12 12;

TOPISO3D PARAMETERS:

SURFLAPP; Slices: 100; Opacity: 0.2; Isosurfaces: 7; Min: -0.5 a.u.; Max: 0.5 a.u.

Metallic Cu

Beck ELF map

OPTIMIZATION PARAMETERS:

Functional: PWGGA; Basis set: Cu_86-4111(41D)G_doll_2000; TOLDEE: default; TOLINTEG: default; TOLDEG: default; TOLDEX: default; SHRINK: 12 12;

TOPISO3D PARAMETERS:

SURFELFB; Slices: 100; Opacity: 0.1; Isosurfaces: 5; Min: 0 a.u.; Max: 0.2 a.u.

Li2O

Electron density map

OPTIMIZATION PARAMETERS:

Functional: B3LYP; Basis set: Li_5-11(1d)G_baranek_2013_LiNbO3, O_6-31d1_corno_2006; TOLDEE: default; TOLINTEG: default; TOLDEG: default; TOLDEX: default; SHRINK: 8 8;

TOPISO3D PARAMETERS:

SURFELFB; Slices: 100; Opacity: 0.1; Isosurfaces: 5; Min: 0 a.u.; Max: 0.1 a.u.

K4Nb6O17

Electron density map

OPTIMIZATION PARAMETERS:

Functional: B3LYP-D3; Basis set: O_8-411d11f_mahmoud_2013, K_SC_HAYWSC-31(1d)G_baranek_2013_KNbO3, Nb_SC_HAYWSC-31(31d)G_baranek_2013_KNbO3; TOLDEE: 10; TOLINTEG: 10 10 10 10 20; TOLDEG: 0.0001; TOLDEX: 0.0004; SHRINK: 4 4;

TOPISO3D PARAMETERS:

SURFELFB; Slices: 100; Opacity: 0.1; Isosurfaces: 2; Min: 0.010 a.u.; Max: 0.015 a.u.

We encourage our users to submit projects so that we can share and publicize their work.

Our Team

We are a multidisciplinary team of professors and researchers from public higher education institutions in different states of Brazil, with expertise in computational chemistry, simulation of crystalline solid systems, theoretical and experimental applications of new materials and cheminformatics. Below you can find more information about the members of this team.

Main Authors Team

Ary Maia
Anderson Reis
Jeronimo Silva

Contributions Team

Julio Sambrano
Gilherme Fabris

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Divulgation

Some articles that used TopIso3D Viewer, in the literature. You can use the link to access them.

JCIM - 10.1021/acs.jcim.3c00302 (2023)

TopIso3DViewer: Enhancing Topological Analysis through 3D Isosurfaces.

FlatChem 35 (2022) 100410

Inorganic graphenylene-like silicon carbide as anode material for Na batteries.

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