Can anyone suggest books/papers which clearly explains pi-alkyl, pi-pi T shaped and pi-Sulphur interaction?
Dear S. Xavier
As we know that any molecule, be it protein or ligand, is made of atoms and atoms itself is made of nucleus (protons & neutrons) and electrons revolving around it S, P, D, F subshells.
Whenever we perform protein - ligand docking, what we basically check is the conformation of ligand with which it is binding to the receptor protein and try to quantify that binding energy between them using various force field equations.
Now, whenever the ligand interact with protein, at atomic level, it is the electrons which are being involved in formation of covalent or non-covalent bonding.
These pi-alkyl, pi-pi T shaped and pi-Sulphur interactions comes in the broad category of non-covalent interactions.
In pi-alkyl interactions there is interaction of pi- electron cloud over an aromatic group and electron group of any alkyl group.
In pi-pi T shaped interaction there is interaction of pi- electron cloud between two aromatic groups but in a T shaped manner, i.e, sidewise electron cloud of 1 ring and head on electron cloud of other ring.
In pi-sulphur interaction pi electron cloud of aromatic ring interact with lone pair of electron cloud of Sulphur atom.
Hope that will help you understand the above interactions.
regards
Tanuj Sharma
Dear S. Xavier
As we know that any molecule, be it protein or ligand, is made of atoms and atoms itself is made of nucleus (protons & neutrons) and electrons revolving around it S, P, D, F subshells.
Whenever we perform protein - ligand docking, what we basically check is the conformation of ligand with which it is binding to the receptor protein and try to quantify that binding energy between them using various force field equations.
Now, whenever the ligand interact with protein, at atomic level, it is the electrons which are being involved in formation of covalent or non-covalent bonding.
These pi-alkyl, pi-pi T shaped and pi-Sulphur interactions comes in the broad category of non-covalent interactions.
In pi-alkyl interactions there is interaction of pi- electron cloud over an aromatic group and electron group of any alkyl group.
In pi-pi T shaped interaction there is interaction of pi- electron cloud between two aromatic groups but in a T shaped manner, i.e, sidewise electron cloud of 1 ring and head on electron cloud of other ring.
In pi-sulphur interaction pi electron cloud of aromatic ring interact with lone pair of electron cloud of Sulphur atom.
Hope that will help you understand the above interactions.
regards
Tanuj Sharma
Hi,
As Tanuj explained, they are category of interaction which can be visualized using my visualization tools such as Discovery studio or Maestro.
- Badges
- Science topic
- Similar topics
- Bioinformatics
- Bioinformatics and Computational Biology