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[MatSQ Tip] How to Model Complicated Molecule

2021-02-25 09:27:39

The previous module tip showed how to model simple molecules using the 'Chemical Database' and the 'Draw Molecule' menu.

However, molecules widely used in real research are not simple. Rhodamine 6G, for example, is utilized in diverse biotechnology applications (i.e., fluorescence microscope, flow cytometry, and enzyme-linked immunosorbent assay (ELISA)). This fluorescent dye has a complicated structure because it consists of many benzene rings, functional groups, and a charge.

In this module tip, we will learn details of the 'Draw Molecule' menu and the modeling of Rhodamine 6G as an example.



Molecule Modeling

The 'Draw Molecule' menu is very intuitive. The bottom toolbar includes ring-shaped hydrocarbons such as benzene, cyclopentadiene, and cyclohexane. Users can quickly add ring-shaped structural formulas by click and drag.



To draw a Rhodamine 6G molecule, you can start by making an anthracene structure, the backbone of the Rhodamine 6G. In the process, some carbon might have more than four bonds due to the overlapped conjugation. Conjugation means a state in which three or more orbitals overlap in succession.


This error can get solved by clicking the bond line and changing the number of bonds. The ‘Single Bond ' tool allows adjusting multiple bonds.

You can add various functional groups combining the 'Single Bond ', 'Chain ' and 'Element' tool. 원The functional group is attached where you click and drag. If you click an atom position, keeping select an element from the left sidebar, the atom will be replaced with the selected component. When a mistake occurs, you can use the 'Erase ' tool to delete atoms, bonds, functional groups, or all.

If you use various tools in the ‘Draw Molecule’, you can easily draw very complicated structural formulas.



Rhodamine 6G has a plus charge at the right-top nitrogen. The ‘Charge Plus ' tool makes plus charge where the selected atom position.




Figure Tool

These tools are useful for creating figures to be inserted into general documents, including papers.

Note that the information entered with this tool is not reflected in the 3D structure builder.


Reaction Arrow Tool: A tool for drawing reaction arrows. You can add + sign by clicking the right-bottom triangle.



R-Group Label Tool: A tool to add Alkyl Group.

S-Group: A tool for drawing polymer units. Select the desired repeating unit and select the 'Type: SRU polymer'



In this module tip, we deeply learned how to use the 'Draw Molecule' menu. Many functions in the 'Draw Molecule' menu make the modeling of complex molecules easy. Model molecules in Materials Square and get the properties of the molecules you want!



Example Video



🍀Do you need more information?

[Modules] Structure Builder

[MatSQ Tip] Molecule modeling in Materials Square