Isomers and Molecular Shape

Isomers

Isomers are chemicals with the same formula, same number of atoms, and same types of atoms, but with different arrangements. Isomers are prevalent in organic chemistry because carbon can be reconfigured into many forms, unlike inorganic compounds.

  • Isomerism: The key is that one molecule can take on many forms, resulting in a nearly infinite number of ways to arrange organic compounds.

*Isomers are the reason why life on Earth is carbon-based.

SciFinder

It is impossible to search Google if you know only the structure of a molecule but not the name. SciFinder is a service that offers a structured search capability where you can draw the structure and search for it.

Organic Chemistry

Organic chemistry is the chemistry of carbon. Anything that carbon can build, life can use.

  • Criterion: For a compound to be organic, it has to be directly bonded to hydrogen or derived from chemicals that are directly bonded to hydrogen.

  • Exception: Oxalic acid (C2H2O_4) is technically organic even though there is no carbon directly bonded to hydrogen because life makes it from more complex molecules.

Vitalism

Scientists once believed that organic chemicals could only be extracted from living things and could not be made from scratch because organic compounds are made using the life force coming from the soul of the living thing. This is called vitalism hypothesis, but it was disproven when urea was synthesized in the lab.

Degree of Unsaturation

Degree of unsaturation indicates the presence of multiple bonds or rings in a molecule.

  • Double bond: One degree of unsaturation.

  • Ring: One degree of unsaturation.

Isomerization

The process of converting one isomer to another is called isomerization. The enzyme that catalyzes this process is called an isomerase.

Isomers vs. Resonance Structures

Isomers are different from resonance structures.

  • Resonance Structures: Only the double bonds move; no atoms move. Only the electrons move. The hydrogens do not move. In reality, these two structures are the same. Representing a structure with multiple resonance structures is useful, since either one alone would be misleading.

  • Isomers: The isomers are real, and you can separate isomers.

Examples of Isomers

  • Glucose and fructose (C6H{12}O_6) are isomers. Fructose is sweeter than glucose.

  • Omeprazole and esomeprazole are isomers. Esomeprazole is a purified activating region of Omeprazole, meaning more effective.

  • An isomer of a certain painkiller and anti-inflammatory drug was found to destroy the fetus.

Iso

Iso means the same. Isomer, isoceles, etc.

Resonance Structures are not Real

Resonance structures are not real.

Molecular Shape

Two variables determine a molecular structure: bond length and bond angle.

Bond Length

Bond length is measured from the center to center of the two atoms.

  • Factors influencing bond length:

    • The C-H bond is longer than the O-H bond because oxygen is smaller than carbon.

    • Bond length increases down the column of the periodic table as the size of the atom increases (e.g., HBr > HCl > HF).

Average Bond Lengths

  • H-H: 74 picometers

  • C-I: 213 picometers

Molecular Geometry

  • Tetrahedron: This is the most distance that any atom can space itself on a sphere. sp^3 hybridized. Bond angle is 109.5 degrees.

  • Trigonal Planar: sp^2 hybridized. Bond angle is 120 degrees.

  • Linear: sp hybridized.

Bond Strain

Planar geometry or square planar arrangement does not occur because of bond strain. Because of bond strain, there is energy stored in that bond. This energy will be violently released if you manage to cut that bond.

Condensed Structure

In the condensed structure, all atoms are drawn, but the bond lines are removed. If you depict something in parentheses, it means that the groups in the parentheses are bonded together.