Atoms, Orbitals and Bonds
All substances around us consist of molecules. A molecule is a three dimensional structure of atoms that are connected to each other through bonds. A good understanding of these concepts is a requirement for learning organic chemistry, so we will briefly go over these in this article.
Structure of an Atom
Atoms consist of a nucleus surrounded by "clouds" of electrons. The nucleus contains particles called protons, which have a positive charge, and neutrons, which are not charged. The electrons surrounding the nucleus have a negative charge. An atom is electrically neutral when it contains an equal amount of protons and electrons.
The amount of protons in the nucleus of an atom determines its atomic number. The atomic number plays a decisive role in the binding behavior of the atom and also determines its element. All known elements can be found in the periodic table. The element carbon, for example, always has six protons in its nucleus.
Atoms are additionally classified on the basis of their mass. The mass number of an atom is simply the sum of protons and neutrons. Electrons have too little mass to count. Not every atom of the same element has the same amount of mass. Usually a carbon atom has a mass number of 12 (noted as 12C), but carbon atoms with a mass number of 13 and 14 also exist (noted as 13C and 14C).
Atoms with a different mass number are called isotopes of each other. Carbon consists for 99% of 12C, with the last remaining percentage consisting of 13C and 14C. The weighted average of all these isotopes is called the relative atomic mass, expressed in atomic mass units (denoted as u). The relative atomic mass of carbon is 12.011 u.
Orbitals
Electrons move around the nucleus, but not all at the same position since they would all repel each other due to their negative charge. Instead, electrons distribute themselves in shells around the nucleaus. Each shell is further subdivided in orbitals, which can contain two electrons each. This is also known as the Pauli exclusion principle.
There are different types of orbitals, each with their own shape and energy level. Starting at the lowest energy level there are s-orbitals (spherical), p-orbitals, d-orbitals and f-orbitals. The higher the atomic number, the more electron shells and orbitals are needed to accomodate all the associated electrons.
Schematic representation of the 1s-, 2s- and three 2p-orbitals. Image from Wikipedia.
Electrons distribute themselves over the available orbitals in such a way as to fill the lower energy levels first. This is called the aufbau principle. The further the electron shell is from the nucleus, the higher the energy level. The first four shells divided as follows:
- Shell 1: one s-orbital, max. 2 electrons.
- Shell 2: one s-orbital and three possible p-orbitals, max. 8 electrons.
- Shell 3: 1×s, 3×p, 5×d, max. 18 electrons.
- Shell 4: 1×s, 3×p, 5×d, 7×f, max. 32 electrons.
A carbon atom with six protons has to distribute six electrons across the various orbitals. The first two will go into the s-orbital of shell 1 (called 1s), the next two go into the s-orbital of shell 2 (called 2s) and the last two each go into one of the three p-orbitals of shell 2 (called 2p). The electrons in the outer shell (shell 2 in this case) are also known as valence electrons. These outer electrons will go on to form bonds with other atoms.
Bonds
An atom is most stable when the outer shell contains exactly eight electrons (or two in the case of hydrogen). This phenomenon is also called the octet rule. To achieve this, an atom can either give away, absorb or share electrons. This results in the creation of bonds. There are various kinds of bonds, but for now we are only interested in ionic bonds and covalent bonds.
Ionic bonds
Elements such as Sodium and Lithium, and all other elements in the first group, have one electron in their outer shell. They can easily give away an electron to reach a stable situation. For elements in group 17, such as Chlorine, its the opposite. They only have to absorb one electron to be stable. When Sodium gives an electron away (and becomes positively charged) and Chlorine absorbs an electron (and becomes negatively charged) an ionic bond forms between these two elements. Together they form the common compound edible salt.
In other words, ionic bonds are bonds whereby the atoms are held together by the attraction between the positive charge of the one atom and the negative charge of the other.
Covalent bonds
The situation where atoms share their electrons with each other is called a covalent bond. As an example, Fluorine only needs one electron to reach a total of eight electrons in its outer shell. Therefore two fluorine atoms could both share one of their outer electrons. This way both of them are stable with eight electrons in their outer shell. This sharing of electrons binds them together.
Organic chemistry primarily deals with covalent bonds.