Question

True or false? The following ligand can act as a bidentate ligand? c1ccc2nc3ccccc3nc2c1

Short answer

True. The given ligand has two nitrogen atoms with lone pairs, allowing it to act as a bidentate ligand.

Step-by-step solution

1. Interpret the SMILES notation of the ligand

The given SMILES notation is: c1ccc2nc3ccccc3nc2c1. Let's break down the structure: - The lower-case 'c' represents a carbon atom in an aromatic ring. - The numbers (1, 2, 3) are used to indicate the connection between two atoms. - 'n' represents a nitrogen atom So the SMILES notation represents a molecular structure with three fused aromatic rings, with nitrogen atoms in the second and third rings.

2. Identify the molecular structure by drawing it

Now, we draw the molecular structure based on the SMILES notation:  We have drawn the molecular structure. Aromatic carbon atoms are highlighted in gray, while nitrogen atoms are in blue.

3. Identify possible donor atoms in the ligand

In order to act as a bidentate ligand, there must be two or more lone pair donor atoms within the ligand structure. Nitrogen atoms are common lone pair donor atoms that can bind to metal ions. In our structure, there are two nitrogen atoms.

4. Determine the ligand's ability to act as a bidentate ligand

Since there are two nitrogen atoms with lone pairs in the ligand structure, it is possible for the ligand to act as a bidentate ligand. Therefore, the answer is True, the given ligand can act as a bidentate ligand.

Key concepts

SMILES Notation

SMILES (Simplified Molecular Input Line Entry System) notation is a way to represent a chemical structure using a string of text. This system is very popular in computational chemistry, as it allows chemists to describe complex molecules concisely. Each atom is represented by its own letter, for example, 'C' for carbon, 'N' for nitrogen.
Lower-case letters, like 'c', specifically denote atoms in aromatic rings. SMILES also uses numbers to indicate the connectivity between atoms. These come into play when atoms are bonded across different parts of the molecule, such as in ring formations or bridged structures.
Reading SMILES notation requires understanding these conventions, which allows for the accurate depiction of molecular structures, like the ligand in question.

Aromatic Rings

Aromatic rings are a class of cyclic, planar structures with delocalized pi-electron systems that provide stability. This delocalization is often represented by a circle within the ring in traditional chemical structures. Aromatic compounds, like benzene, exhibit unique properties such as increased stability and specific bonding patterns.
In the SMILES notation, 'c' represents a carbon atom in such aromatic rings. Aromatic rings are often seen in complex organic molecules, forming the structural backbone that can influence the molecule's reactivity and interaction with other compounds.
The ligand described in the exercise contains three fused aromatic rings, which are indicated by multiple 'c' characters in the SMILES notation. These rings contribute to the planarity and potential reactivity of the ligand.

Nitrogen Atoms

Nitrogen atoms play a crucial role in coordination chemistry and the formation of bidentate ligands. As common donors in ligands, nitrogen atoms can donate lone pairs of electrons to form coordinate bonds with metal ions.
In the SMILES notation and the provided molecular structure, 'n' represents nitrogen atoms. In our ligand example, these nitrogen atoms appear in the second and third aromatic rings. They can use their lone electron pairs to bind with metal ions, making them ideal donor atoms in bidentate ligands.
Understanding the position and availability of nitrogen atoms is vital in predicting the behavior and functionality of ligands in coordination chemistry.

Coordination Chemistry

Coordination chemistry revolves around the complex formation between a central atom (often a transition metal) and surrounding ligands. Ligands are ions or molecules capable of donating pairs of electrons to the metal atom. This donation forms a coordinate covalent bond.
Bidentate ligands, like the one in the exercise, have two atoms that can donate electron pairs. These ligands form more stable complexes due to their ability to "bite" the metal atom at two points, effectively forming a chelate.
The nitrogen atoms in our ligand act as these two donor atoms, fulfilling the criteria for bidentate ligand formation. Coordination complexes play vital roles in biology and industry, serving functions from oxygen transport in hemoglobin to catalysis in chemical reactions. Understanding the interaction of ligands helps in designing and applying these complexes effectively.