pyCOFBuilder: A Python Package for Automated Creation of Covalent Organic Framework Models Based on the Reticular
Felipe L Oliveira1, Pierre M Esteves1
1Instituto de Química, Universidade Federal do Rio de Janeiro, Av. Athos da Silveira Ramos, 149, CT A-622, Cid. Univ., Rio de Janeiro, Rio de Janeiro 21941-909, Brazil.
Journal of Chemical Information and Modeling
|March 30, 2024
Summary
This study introduces pyCOFBuilder, an open-source Python package that simplifies the creation of covalent organic framework (COF) structures for computational research, accelerating materials discovery.
Area of Science:
- Materials Science
- Computational Chemistry
- Supramolecular Chemistry
Background:
- Covalent organic frameworks (COFs) offer high surface area and tunable properties, making them promising for diverse applications.
- Experimental exploration of the vast COF structural space is challenging and time-consuming.
- Computational high-throughput studies are valuable but require efficient structure generation methods.
Purpose of the Study:
- To develop an accessible tool for generating covalent organic framework (COF) structures.
- To facilitate computational studies of COFs by automating structure generation.
- To provide a user-friendly software package for exploring COF topologies and chemistries.
Main Methods:
- Introduction of pyCOFBuilder, an open-source Python package.
- Implementation of functionalities for generating COF structures based on the reticular approach.
- Description of the software's features and capabilities for creating diverse COF models.
Main Results:
- pyCOFBuilder enables the facile generation of COF structures.
- The software supports the creation of COFs with varied topologies and chemical compositions.
- Demonstrated utility in accelerating the computational exploration of COF materials.
Conclusions:
- pyCOFBuilder addresses the challenge of COF structure generation for computational studies.
- The package streamlines the process, making COF research more accessible.
- Freely available on GitHub, promoting wider adoption in the scientific community.
Related Concept Videos
02:00Molecular Models
38.3K
Physical models representing molecular architectures of chemical compounds play essential roles in understanding chemistry. The use of molecular models makes it easier to visualize the structures and shapes of atoms and molecules.
38.3K
02:46Covalent Bonding and Lewis Structures
49.2K
Compared to ionic bonds, which results from the transfer of electrons between metallic and nonmetallic atoms, covalent bonds result from the mutual attraction of atoms for a “shared” pair of electrons.
49.2K
02:27Predicting Molecular Geometry
34.3K
VSEPR Theory for Determination of Electron Pair Geometries
34.3K
02:18Network Covalent Solids
13.5K
Network covalent solids contain a three-dimensional network of covalently bonded atoms as found in the crystal structures of nonmetals like diamond, graphite, silicon, and some covalent compounds, such as silicon dioxide (sand) and silicon carbide (carborundum, the abrasive on sandpaper). Many minerals have networks of covalent bonds.
To break or to melt a covalent network solid, covalent bonds must be broken. Because covalent bonds are relatively strong, covalent network solids are typically...
To break or to melt a covalent network solid, covalent bonds must be broken. Because covalent bonds are relatively strong, covalent network solids are typically...
13.5K
01:18Structure of Benzene: Molecular Orbital Model
9.0K
According to the molecular orbital (MO) model, benzene has a planar structure with a regular hexagon of six sp2 hybridized carbons. As shown in Figure 1, each carbon is bonded to three other atoms with C–C–C and H–C–C bond angles of 120°. The C–H bond length is 109 pm, and the C–C bond length is 139 pm which is midway between the single bond length of sp3 hybridized carbons (154 pm) and sp2 hybridized carbons (133 pm).
9.0K
02:04Covalently Linked Protein Regulators
6.8K
Proteins can undergo many types of post-translational modifications, often in response to changes in their environment. These modifications play an important role in the function and stability of these proteins. Covalently linked molecules include functional groups, such as methyl, acetyl, and phosphate groups, and also small proteins, such as ubiquitin. There are around 200 different types of covalent regulators that have been identified.
These groups modify specific amino acids in a protein....
These groups modify specific amino acids in a protein....
6.8K