Ch. 1 3D Molecular Structure


In this chapter, we will see that it is sometimes insufficient to describe the structure of a molecule in a planar, two-dimensional way which is usually used in textbooks, because atoms that make up a molecule are arranged three dimensionally.
Three-dimensional structure of organic compounds highly depends on the shapes and characteristics of hybridized atomic orbitals of the carbon atom. Here we will see sp3 and sp2 hybridized orbitals, which are related deeply to the stricture of molecules.
Models are useful tools to see the shape of molecules. Molecular models that are commercially available will be classified based on their characteristics.
Sometimes a compound may have two or more names. Similarly, there are several nomenclatures (notations) for stereochemistry of organic compounds. The nomenclature based on the sequence rule will be also introduced because this method corresponds to the systematic nomenclature and is most widely utilized.

Goal of this chapter

At the end of the study of this chapter, you will be able to understand the followings:

  1. Organic compounds are three-dimensional, and cannot be properly reproduced on a two-dimensional sheet of paper. Their geometry depends on hybridization of their carbon atoms, and there are three types of hybridization - sp3, spand sp.
  2. Such three-dimensional structures result in configurational isomers. Those are identical in their structural formula but differed in three-dimensional spatial arrangement of atoms. A pair of enantiomers (enantio isomers) similar to the relation between the left hand and the right hand is one of the examples.
  3. Molecular models will help your understanding of three-dimensional structure of molecules. There are several types of molecular models, and each of them has own characteristics. It must be instructive for you to practically use them if available.
  4. 4 Structure of molecules is not always fixed; rotation about bonds can results in change of their structures.

New terms and concepts

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1.1 Isomerism and Isomer

1.3 The atomic orbital of carbon atom and the hybridization of the orbitals

1.4 Multiple bond

1.5 The molecular models and the shape of molecules

1.6 Sequence rule


S1.1  molecular formula, rational formula, structural formula

molecular formula: describe only number and a kind of atoms contained in a molecule
rational formula: simply describe functional groups (including multiplex bonds) contained in a molecule
structural formula: exactly describe the order of atoms in a molecule by means of bond.

go to 1.1 Isomerism, isomers

S1.2  hybridization of carbon atom

1) sp3hybridization … tetrahedral (e.g. methane, ethane)
2) sp2hybridization … trigonal planar (e.g. ethylene, benzene)
3) sp hybridization … linear (e.g. acetylene)

go to 1.3 Atomic orbitals of carbon atoms; hybridization

go to 1.4 Multiple bonds

S1.3  Variety of molecular models

The molecular models can be classified into following three types.
1) space filling model (e.g. Stuart model)
2) skeletal model (e.g. Dreiding model)
3) ball and stick model (e.g. HGS model)

go to 1.5 Molecular models and geometry of molecule

S1.4  Sequence rules

(1) If the atom of the ligand directly bonded to a central atom (the first atom) has greater atomic numbers than that of other ligands, the ligand has a higher priority.
(2) In the case of a tie atomic numbers, atoms attached to the first atom (the second atoms; not always only one atom) must be considered. If the priority is not determined at this stage, the third or forth atoms must be taken into account in turn.
(3) For a multiple bond, replica atoms are considered. Thus, an atom that is multiply bonded to another atom is considered as if it attaches to the same number of other atoms with the multiplicity of the atom.


S1.5  Priority of representative ligands (lower to higher)

go to 1.6 Nomenclature of stereochemistry