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[MatSQ Tip] How to Find Stable Molecule Geometry: Conformational Isomer

2021-05-11 10:10:27

One chemical formula can represent various molecules according to the atomic arrangement. The molecules with the same formula but different structures are called the 'structural isomers (constitutional isomers).' Besides, some molecules can have different properties according to the atom arrangement in the space, although the same chemical formula. Stereoisomers are molecules that have the same bonding state but disparate stereoscopic structures. Among them, isomers that can build the same structure by rotating atom groups are called conformational isomers.

 

The Molecule Builder supports the diverse functions for molecular modeling. For example, a helpful function is the 'Conformers' that find the conformers (conformational isomers).

Finding the conformers is meaningful. The energy stability can be varied according to the inter-angles of the atoms in the 3D space. If the number of atoms is large, it is difficult to find a stable conformer due to the many possibilities.

We can solve this problem by geometry optimization instead of finding conformers. However, some cases would fail in finding the global minimum (ground state) because the calculation terminated at the local minimum. It is not easy to induce a new minimum found through structure modification since 2D structures cannot include the angle information.

For these cases, we should examine the conformers to determine which atomic arrangement the molecule can have through 'Conformer search.' And it is recommended to perform the optimization with DFT from the desired structure among various conformers.

 

In this module tip, we'll learn how to use the 'Conformers' function of the Molecule Builder.

 

 

1. Drawing Molecule

We require to draw a 2D structure in the Ketcher tab of the Molecule Builder. For more information on this, refer to the previous module tips, 'Molecular Modeling in Materials Square' and 'How to Model Complex Molecules.'

이This module tip will show you modeling the 'Ethane' and 'Butane' as examples for conformer search.

 

 

 

 

2. Conformer search

The conformation search is immediately processed after clicking the 'Conformers' button on the top of the Molecule Builder module. The 3D converting is performed together. Therefore, It can be performed only to the 2D structure, which not conducted the 3D convert. The conformation search is proceeded using the 'Confab' algorithm of the 'Generate multiple conformers' function of the 'Open Babel.'[1]

The obtained conformers and the relative energy of each conformer can be checked on the right-side list.

Select the conformer with relative energy is 0.000 kcal/mol and move to the 'Visualizer' tab to see the most stable molecule geometry. In some cases, it may be easier to find the global minimum when performing optimization calculations with DFT from other structures with relative energy close to 0.000 kcal/mol.

 

1) Ethane

The 'staggered' conformation is the most stable structure. We can find the staggered structure by performing the geometry optimization with the MMFF94 forcefield from the 3D button. However, after pressing the 'Conformers' button and looking at the relative energy data together, you can certainly see that the staggered conformation is the most stable structure.

 

 

 

2) Butane

This molecule has a small molecular weight; therefore, the most stable configuration can be found even when optimizing the MMFF94 forcefield. From the relative energy obtained during the conformer search, we can determine that the 'Anti' conformation that has the angle of 180° between the two methyl groups is the most stable.

 

 

 

If the algorithm found too many conformers, only the top 10 stable structures energetically will be added to the list.

 

 

In this module tip, we learned how to find the conformational isomers of molecules using the 'Conformers' function of the 'Molecule Builder' module. Use the conformer search function to find possible atomic arrangements in a molecule, and start DFT calculation from the desired structure to efficiently find the ground-state molecular structure.

Start molecular modeling in Materials Square!

 

 

Example Video

 

 

🍀Need more information?

>Blog
[MatSQ Tip] Molecule Modeling in Materials Square
[MatSQ Tip] How to model complicated molecule
[MatSQ Tip] How to Model Polymer in 3D: Molecule Builder

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[Modules] Molecule Builder

 


[1] https://open-babel.readthedocs.io/en/latest/3DStructureGen/multipleconformers.html

 

 


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