Molecule

• 1. Introduction

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  A molecule is a group of two or more atoms held together by attractive forces called chemical bonds. That sounds tidy. The reality is that scientists argued for centuries over what should count as one, and they still hedge. Depending on context, the term may or may not include ions that satisfy the same criterion. In quantum physics, organic chemistry, and biochemistry, the distinction from ions gets dropped entirely. The word itself is younger than the idea behind it, coined by one man to settle a confusion about gases. So what exactly holds atoms together, why do rocks and metals not qualify, and how did a French physicist finally prove these things are real? Those are the questions ahead.

• 2. A Word Born In Latin

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  Latin gave the word its root. According to Merriam-Webster and the Online Etymology Dictionary, "molecule" derives from the Latin "moles", meaning a small unit of mass. The word entered French in 1678, from Neo-Latin, a diminutive of the Latin term for mass or barrier. Until the late 18th century it was used only in its Latin form. It gained popularity through discussions of the natural philosophy of Rene Descartes. Amedeo Avogadro is the figure who actually created the word "molecule" as we now use it. His 1811 paper carried the title "Essay on Determining the Relative Masses of the Elementary Molecules of Bodies". In it, according to Partington's A Short History of Chemistry, he argued that the smallest particles of gases are not necessarily simple atoms. They are made of a certain number of atoms united by attraction to form a single molecule. That distinction between an atom and a bonded cluster gave chemistry a vocabulary it had been missing.

• 3. From Atoms To Quantum Bonds

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  Around 450 BC, Empedocles imagined fundamental elements of fire, earth, air, and water, plus forces of attraction and repulsion that let them interact. The Greek philosophers Leucippus and Democritus argued that the universe was made of atoms and voids. A fifth element, the incorruptible quintessence aether, was treated as the building block of the heavenly bodies. Aristotle accepted this viewpoint and passed it to medieval and renaissance Europe. Robert Boyle gave the idea a more concrete shape in 1661. In his treatise The Sceptical Chymist, he proposed that matter is composed of clusters of particles he called "corpuscles", and that chemical change comes from rearranging those clusters. In 1789, William Higgins published views on combinations of what he called "ultimate" particles, foreshadowing the concept of valency bonds. The French chemist Marc Antoine Auguste Gaudin, in 1833, used "volume diagrams" to lay out Avogadro's hypothesis. These diagrams showed semi-correct geometries such as a linear water molecule and correct formulas such as H2O. The 20th century brought quantum physics into the question. In 1917, an unknown American undergraduate chemical engineer named Linus Pauling was learning the Dalton hook-and-eye bonding method, the mainstream description of bonds at the time. Dissatisfied, he turned to the emerging field of quantum physics. In 1927, the physicists Fritz London and Walter Heitler applied quantum mechanics to the exchange forces of the hydrogen molecule. Their valence bond treatment, published jointly, brought chemistry under quantum mechanics. Pauling, freshly holding his doctorate, visited Heitler and London in Zurich on a Guggenheim Fellowship. In 1931 he published "The Nature of the Chemical Bond", using quantum mechanics to calculate bond angles and rotation. He developed hybridization theory to explain bonds in molecules such as CH4, where four sp3 hybridised orbitals overlap with hydrogen's 1s orbital to yield four sigma bonds of equal length and strength.

• 4. Proving They Exist

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  In 1926, the French physicist Jean Perrin received the Nobel Prize in physics for proving, conclusively, that molecules exist. He did it by calculating the Avogadro constant using three different methods, all involving liquid phase systems. First he used a gamboge soap-like emulsion. Second he carried out experimental work on Brownian motion. Third he confirmed Einstein's theory of particle rotation in the liquid phase. Each independent route converged on the same number, which is what made the case conclusive. Definitions had lagged behind this kind of proof for a long time. Earlier definitions were less precise, treating molecules as the smallest particles of a pure substance that still retain its composition and chemical properties. That definition breaks down for rocks, salts, and metals, which are large crystalline networks rather than discrete molecules. The refinement of the concept ran through Robert Boyle, Amedeo Avogadro, Jean Perrin, and Linus Pauling, and the field is today known as molecular physics or molecular chemistry.

• 5. When Atoms Do Not Make Molecules

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  Most familiar solid substances on Earth are not made of molecules. Sand, clay, pebbles, rocks, boulders, bedrock, the molten interior, and the core of the Earth all contain many chemical bonds, yet they form crystals or ionic compounds rather than identifiable molecules. No typical molecule can be defined for salts or for covalent crystals. These are often built from repeating unit cells, extending in a plane as in graphene, or three-dimensionally as in diamond, quartz, and sodium chloride. Most metals follow the same theme of repeated unit-cellular structure; they are condensed phases held by metallic bonding, so solid metals are not made of molecules. Glasses complicate the picture further. They are solids in a vitreous disordered state, held together by chemical bonds with no definable molecule and none of the regularity that marks salts, crystals, and metals. The substances of life sit on the other side of the line. Proteins, amino acids, the nucleic acids DNA and RNA, sugars, carbohydrates, fats, and vitamins are all molecules. Nutrient minerals such as iron sulfate are ionic compounds, and so they are not.

• 6. How Atoms Hold Together

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  Covalent bonding holds most molecules together. A covalent bond involves the sharing of electron pairs between atoms, called shared pairs or bonding pairs, balanced between attraction and repulsion. Several non-metallic elements exist only as molecules in the environment rather than as free atoms; hydrogen is one example. Ionic bonding works by a different mechanism. It is the electrostatic attraction between oppositely charged ions, the primary interaction in ionic compounds. Atoms that lose electrons become cations, and atoms that gain electrons become anions, a transfer termed electrovalence in contrast to covalence. In the simplest case the cation is a metal atom and the anion is a nonmetal atom, though ions can be more complicated, such as molecular ions like NH4+ or SO42-. At normal temperatures and pressures, ionic bonding mostly creates solids without separate identifiable molecules. But vaporization or sublimation of such materials does produce separate molecules, where the electron transfer is still full enough for the bond to count as ionic rather than covalent.

• 7. Reading A Molecule

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  A chemical formula fits onto a single typographic line of element symbols, numbers, and symbols such as parentheses, brackets, and plus and minus signs. An empirical formula gives the simplest integer ratio of the elements. Water always holds a 2:1 ratio of hydrogen to oxygen, and ethanol always holds carbon, hydrogen, and oxygen in a 2:6:1 ratio. That ratio does not pin down a unique molecule. Dimethyl ether shares ethanol's ratios, and such molecules with the same atoms in different arrangements are called isomers. Acetylene shows the gap between the two formula types; its molecular formula is C2H2 while its simplest integer ratio is CH. Molecular mass is calculated from the formula and expressed in daltons, each equal to one twelfth of the mass of a neutral carbon-12 atom. Some molecules outgrow the page entirely. Most are far too small to see, with building blocks for organic synthesis measuring a few angstroms to several dozen, around one billionth of a meter. The smallest is diatomic hydrogen, H2, with a bond length of 0.74 angstroms. At the other extreme, biopolymers such as DNA reach macroscopic sizes, and an atomic force microscope can trace small molecules and even the outlines of individual atoms.

• 8. An Operational Idea

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  The hydrogen molecule-ion, H2+, is the simplest of all molecules, and its single one-electron bond is the simplest of all chemical bonds. With two positively charged protons and one negatively charged electron, it has no electron-electron repulsion, so its Schrodinger equation can be solved more easily. Fast digital computers later opened approximate solutions for more complicated molecules, a central aspect of computational chemistry. IUPAC tries to draw a firm line. It suggests an arrangement of atoms must correspond to a depression on the potential energy surface deep enough to confine at least one vibrational state. That rule depends only on the strength of the interaction, not its nature. It even admits the helium dimer, He2, which has one vibrational bound state and is so loosely bound that it is only likely to be observed at very low temperatures. Whether an arrangement counts as a molecule is, in the end, an operational definition. A molecule is not a fundamental entity the way an elementary particle is. It is the chemist's way of making a useful statement about the strengths of atomic-scale interactions in the world we observe.