Bonded interactions¶
The intra-molecular or bonded interactions consist of energy components that are short range in nature and usually applied within the molecule to maintain the geometrical structure of the molecule.
Bonded interactions consist of several energy components as follows:
- Bond interaction. Also called the 1-2 interaction. It describes interaction between two bonded atoms.
- Angle interaction. Also called the 1-3 interaction. It describes interaction two atoms that are bonded to a common atom.
- Dihedral (tortional) interaction. Also called the 1-4 interaction. It describes the angular interaction drawn between planes 1,2,3 and 2,3,4.
Diagram below shows the summary of these interactions.
- Improper interaction. This is a type of dihedral interaction that is imposed on certain molecular functional group to preserve a particular geometry of three atoms around a central atom. Example of these functional groups are carbonate and carbonyls, to maintain a planar conformation (where alpha = 0 degree).
Diagram below illustrates how these interactions are applied on a molecular structure (salicylic acid).
So far, we have discussed the ‘direct’ bonded interactions, depending on the type of FFs, there are other types of cross component bonded interactions.
For instance, the bond-bond interaction, where the cross component interactions are described in terms of the bond distances between two succesive bonds 1-2 and 2-3. Other cross components may also involve a more extensive geometries such as angle-angle, bond-angle and even angle-torsion interactions.