Molecule

A molecule consists of two or more atoms that have bonded together. A great deal of matter is made up of molecules, including Earth’s oceans and the air that people breathe. Scientists estimate that the first molecule was formed approximately 250,000 to 300,000 years after the big bang. They believe that the first molecule to form was the helium hydride ion (HeH⁺), a positively charged ion containing hydrogen and helium, which together account for the vast majority of atoms created during the big bang.

Over time, atoms of other elements began to form, including oxygen and carbon, as well as heavier elements such as gold and silicon. Hydrogen atoms began bonding with these other elements to form different molecules, such as water (H₂O) and various hydrocarbons. The most abundant molecules in biological systems are those that contain carbon, hydrogen, nitrogen, oxygen, phosphorus, and sulfur.

Brief History

Perhaps the biggest contribution to the discovery of the molecule was made by English scientist John Dalton (1766–1844). During the early 1800s, Dalton developed what was later known as his atomic theory of matter. The principles of this theory included the following proposals: (1) that all matter was composed of atoms; (2) that atoms could not be cut, subdivided, created, or destroyed; (3) that all atoms of a specific element were identical in mass; (4) that compounds were created from combinations of whole numbers of atoms; and (5) that chemical reactions were caused by atoms either separating or combining.

Dalton’s second and third principles were later disproved, the second when scientists discovered that atoms could, in fact, be subdivided into even smaller subatomic particles called protons, neutrons, and electrons. The third principle was refuted by the discovery of isotopes, which are atoms of the same element that have different masses and properties.

Overview

In their most basic form, molecules are simply two or more atoms bonded together through chemical interactions. It does not matter whether those two atoms are of the same element or not; two individual oxygen atoms can bond together to create the molecule O₂ (oxygen gas), while four hydrogen atoms and one carbon atom can bond together to create the molecule CH₄ (methane). Some other examples of common molecules are C₆H₁₂O₆ (glucose), PO₄ (phosphate), and H₂O₂ (hydrogen peroxide). Molecules come in many different shapes, sizes, and arrangements, characteristics that dramatically affect how they react with one another.

Whenever molecules are composed of more than a single element, they are referred to as molecular compounds. Examples include methane, glucose, phosphate, and hydrogen peroxide, as shown above, as well as calcium oxide (CaO) and potassium sulfide (K₂S). As a result, all compounds are molecules, but not all molecules are compounds.

Individual atoms form larger molecules through chemical bonding. The two main types of bonding that occur between atoms are covalent bonding and ionic bonding. Covalent bonding occurs when two atoms share two, four, or six electrons between them. (Two shared electrons form a single covalent bond, and certain atoms have the ability to form double or even triple bonds.) Examples of covalent bonds include those found in diatomic carbon (C₂) or molecular oxygen (O₂).

Because molecules such as C₂ and O₂ are formed from atoms of the same element, there is no difference in the amount of pull that each one has on their electrons. For two atoms to bond together, their outermost electrons, called valence electrons, need to be either shared or transferred from one to the other. The atom with the stronger pull on its electrons is said to be more electronegative. As mentioned above, covalent bonding occurs whenever two atoms, of either the same element or different ones, share their valence electrons. In the case of C₂ and O₂, because both atoms are from the same element, there is no difference in electronegativity, and the electrons can be shared evenly as a result.

Ionic bonding is a process in which one atom gives up one or more electrons to another. Under these circumstances, the atom giving up, or donating, its electrons will almost always have a lower amount of electronegativity than the atom receiving, or accepting, the electrons. This process creates two oppositely charged ions: the donor atom becomes a positively charged ion, or cation, and the acceptor atom becomes a negatively charged ion, or anion. The two ions are then held together by the attraction between their opposite charges, thus creating an ionic compound.

Individual molecules can be classified as either polar or nonpolar. In a polar molecule, the electrons are not evenly shared between the individual atoms. Water is a perfect example of this. Oxygen is more electronegative than hydrogen, so the oxygen atom pulls the electrons of the hydrogen atoms closer to it, leaving the positively charged nucleus of each hydrogen atom exposed. As a result, one end of the molecule—the oxygen atom—develops a slight negative charge, while the exposed nuclei of the hydrogen atoms at the other end cause them to develop a slight positive charge.

In nonpolar molecules, electrons are shared equally among the individual atoms, and unshared electrons remain largely in place around their respective atoms. Methane is an example of a nonpolar molecule. It consists of one carbon atom and four hydrogen atoms, the latter bonded to the former via equivalent and equidistant carbon-hydrogen bonds to form a symmetrical tetrahedral molecule. As a result, no polar regions form on the molecule.

Nonpolar molecules tend to be hydrophobic, meaning they do not mix well with water, due to the polar nature of the water molecule. Likewise, polar molecules tend to be hydrophilic, meaning that they do mix well with water, because the negative regions of the polar molecule are attracted to the positive regions of the water molecule, and vice versa.

In biological systems, whether a molecule is hydrophobic or hydrophilic is very important. For instance, the membrane of a living cell is composed primarily of a lipid bilayer that is hydrophilic on each outer surface and hydrophobic in the middle, which helps separate the outside of the cell from the inside. In the physical world, water’s polar nature allows for the creation of hydrogen bonds, which are the main reason that water remains in a liquid rather than gaseous state at room temperature.

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