[Module Tip] Molecule Modeling in Materials Square - Materials Square
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[Module Tip] Molecule Modeling in Materials Square

2021-02-17 06:55:21

In computational science, a basis set is used to describe wavefunctions. A basis set is a set of several functions. Among diverse basis sets, plane waves and atomic orbitals are typically used.

While Quantum Espresso adopts a plane wave basis set, DFT codes for chemistry (e.g., Gaussian, Qchem, GAMESS, etc.) adopt an atomic orbital basis set. The plane-wave basis is appropriate for describing crystal systems under periodic boundary conditions because it uses plane waves with periodicity. However, this method is inefficient in calculating single atoms or small molecules which occupy local space. The atomic orbital basis, which describes the wavefunctions using local functions, is suitable for single atoms or small molecules. [1]

There is a difference in modeling methods between the plane wave basis code and atomic orbital basis code. For example, the plane-wave basis sets should add an optional vacuum to describe an isolated system. On the other hand, the atomic orbital basis sets regard all structures as isolated systems. 
Easy and convenient modeling is possible by using a new function of Materials Square


Chemical Database

Recently, the ‘Structure Builder’ module has been updated: the ‘Chemical’ tab in the ‘Database’ menu and the ‘Draw Molecule’ icon in the ‘Modeling’ tab.

Materials Square provides the PubChem[2] database which is the world-famous chemical database. You can bring a molecular structure by searching the compound’s name (both its IUPAC name but and common name).


Example Video (Chemical Database)



Draw Molecule

The ‘Draw Molecule’ menu in the ‘Modeling’ tab has been released.

Through the ‘Draw Molecule’ menu allows intuitive modeling using structural formulas and SMILE.

An optimization process is essential to convert the drawn 2D structural formula to 3D. It applies MMFF94 Forcefield[3] of Open Babel. At this step, you should select the optimization precision and speed from 'Relax Mode'. 

It is recommended to select the ‘Best’ or ‘Normal’ mode because typical optimization processes consume a short time of under 28 seconds. However, optimization of a large system may not finish within 28 seconds, and consequently, the following error message appears. 

In this case, you should use ‘Fast’ mode to optimize the molecule.


Example Video (Draw Molecule)



In this module tip, we learned how to model single molecules in Materials Square. You can calculate the properties of single molecules by connecting simulation engines to the modeled molecular structure. 

GAMESS, the DFT code on the atomic orbital basis, will soon be updated in Materials Square to meet the growing demands and expectations in the field of chemistry. Also, theme type MD modules for polymer properties are scheduled to be released.

Perform your DFT research based on an atomic orbital basis using Materials Square's convenient GUI and fast computing environment!



🍀 Need More Information?

[Modules] Structure Builder


[1] Lee, J. G. (2016). Computational materials science: an introduction. CRC press.
[2] Kim, S., Chen, J., Cheng, T., Gindulyte, A., He, J., He, S., ... & Bolton, E. E. (2021). PubChem in 2021: new data content and improved web interfaces. Nucleic Acids Research49(D1), D1388-D1395.
[3] Halgren, T. A. (1999). MMFF VI. MMFF94s option for energy minimization studies. Journal of Computational Chemistry20(7), 720-729.