Many elements can form two or more covalent bonds, but only a few are able to form extended chains of covalent bonds. The outstanding example is carbon, which can form as many as four covalent bonds and can bond to itself indefinitely. Carbon has six electrons in total, two of which are paired in an atomic orbital closest to the nucleus. The remaining four are farther from the nucleus and are available for covalent bonding. When there is sufficient hydrogen present, carbon will react to form methane, CH₄. When all four electron pairs occupy the four molecular orbitals of lowest energy, the molecule assumes the shape of a tetrahedron, with carbon at the centre and the four hydrogen atoms at the apexes. The C–H bond length is 110 picometres (1 picometre = 10^-12 metre), and the angle between adjacent C–H bonds is close to 110°. Such tetrahedral symmetry is common to many carbon compounds and results in interesting structural possibilities. If two carbon atoms are joined together, with three hydrogen atoms bonded to each carbon atom, the molecule ethane is obtained. When four carbon atoms are joined together, two different structures are possible: a linear structure designated n-butane and a branched structure called iso-butane. These two structures have the same molecular formula, C₄H₁₀, but a different order of attachment of their constituent atoms. The two molecules are termed structural isomers. Each of them has unique chemical and physical properties, and they are different compounds. The number of possible isomers increases rapidly as the number of carbon atoms increases. There are five isomers for C₆H₁₄, 75 for C₁₀H₂₂, and 6.2 × 10¹³ for C₄₀H₈₂. When carbon forms bonds to atoms other than hydrogen, such as oxygen, nitrogen, and sulfur, the structural possibilities become even greater. It is this great potential for structural diversity that makes carbon compounds essential to living organisms.

Even when the bonding sequence of carbon compounds is fixed, further structural variation is still possible. When two carbon atoms are joined together by two bonding pairs of electrons, a double bond is formed. A double bond forces the two carbon atoms and attached groups into a rigid, planar structure. As a result, a molecule such as CHCl=CHCl can exist in two nonidentical forms called geometric isomers. Structural rigidity also occurs in ring structures, and attached groups can be on the same side of a ring or on different sides. Yet another opportunity for isomerism arises when a carbon atom is bonded to four different groups. These can be attached in two different ways, one of which is the mirror image of the other. This type of isomerism is called optical isomerism, because the two isomers affect plane-polarized light differently. Two optical isomers are possible for every carbon atom that is bonded to four different groups. For a molecule bearing 10 such carbon atoms, the total number of possible isomers will be 2¹⁰ = 1,024. Large biomolecules often have 10 or more carbon atoms for which such optical isomers are possible. Only one of all the possible isomers will be identical to the natural molecule. For this reason, the laboratory synthesis of large organic molecules is exceedingly difficult. Only in the last few decades of the 20th century have chemists succeeded in developing reagents and processes that yield specific optical isomers. They expect that new synthetic methods will make possible the synthesis of ever more complex natural products.

Basic factors

The structure of ionic substances and covalently bonded molecules largely determines their function. As noted above, the properties of a substance depend on the number and type of atoms it contains and on the bonding patterns present. Its bulk properties also depend, however, on the interactions among individual atoms, ions, or molecules. The force of attraction between the fundamental units of a substance dictate whether, at a given temperature and pressure, that substance will exist in the solid, liquid, or gas phase. At room temperature and pressure, for example, the strong forces of attraction between the positive ions of sodium (Na⁺) and the negative ions of chlorine (Cl⁻) draw them into a compact solid structure. The weaker forces of attraction among neighbouring water molecules allow the looser packing characteristic of a liquid. Finally, the very weak attractive forces acting among adjacent oxygen molecules are exceeded by the dispersive forces of heat; oxygen, consequently, is a gas. Interparticle forces thus affect the chemical and physical behaviour of substances, but they also determine to a large extent how a particle will respond to the approach of a different particle. If the two particles react with each other to form new particles, a chemical reaction has occurred. Notwithstanding the unlimited structural diversity allowed by molecular bonding, the world would be devoid of life if substances were incapable of change. The study of chemical transformation, which complements the study of molecular structure, is built on the concepts of energy and entropy.

Energy and the first law of thermodynamics

The concept of energy is a fundamental and familiar one in all the sciences. In simple terms, the energy of a body represents its ability to do work, and work itself is a force acting over a distance.

Chemical systems can have both kinetic energy (energy of motion) and potential energy (stored energy). The kinetic energy possessed by any collection of molecules in a solid, liquid, or gas is known as its thermal energy. Since liquids expand when they have more thermal energy, a liquid column of mercury, for example, will rise higher in an evacuated tube as it becomes warmer. In this way a thermometer can be used to measure the thermal energy, or temperature, of a system. The temperature at which all molecular motion comes to a halt is known as absolute zero.

Energy also may be stored in atoms or molecules as potential energy. When protons and neutrons combine to form the nucleus of a certain element, the reduction in potential energy is matched by the production of a huge quantity of kinetic energy. Consider, for instance, the formation of the deuterium nucleus from one proton and one neutron. The fundamental mass unit of the chemist is the mole, which represents the mass, in grams, of 6.02 × 10²³ individual particles, whether they be atoms or molecules. One mole of protons has a mass of 1.007825 grams and one mole of neutrons has a mass of 1.008665 grams. By simple addition the mass of one mole of deuterium atoms (ignoring the negligible mass of one mole of electrons) should be 2.016490 grams. The measured mass is 0.00239 gram less than this. The missing mass is known as the binding energy of the nucleus and represents the mass equivalent of the energy released by nucleus formation. By using Einstein’s formula for the conversion of mass to energy (E = mc²), one can calculate the energy equivalent of 0.00239 gram as 2.15 × 10⁸ kilojoules. This is approximately 240,000 times greater than the energy released by the combustion of one mole of methane. Such studies of the energetics of atom formation and interconversion are part of a specialty known as nuclear chemistry.

The energy released by the combustion of methane is about 900 kilojoules per mole. Although much less than the energy released by nuclear reactions, the energy given off by a chemical process such as combustion is great enough to be perceived as heat and light. Energy is released in so-called exothermic reactions because the chemical bonds in the product molecules, carbon dioxide and water, are stronger and stabler than those in the reactant molecules, methane and oxygen. The chemical potential energy of the system has decreased, and most of the released energy appears as heat, while some appears as radiant energy, or light. The heat produced by such a combustion reaction will raise the temperature of the surrounding air and, at constant pressure, increase its volume. This expansion of air results in work being done. In the cylinder of an internal-combustion engine, for example, the combustion of gasoline results in hot gases that expand against a moving piston. The motion of the piston turns a crankshaft, which then propels the vehicle. In this case, chemical potential energy has been converted to thermal energy, some of which produces useful work. This process illustrates a statement of the conservation of energy known as the first law of thermodynamics. This law states that, for an exothermic reaction, the energy released by the chemical system is equal to the heat gained by the surroundings plus the work performed. By measuring the heat and work quantities that accompany chemical reactions, it is possible to ascertain the energy differences between the reactants and the products of various reactions. In this manner, the potential energy stored in a variety of molecules can be determined, and the energy changes that accompany chemical reactions can be calculated.

Entropy and the second law of thermodynamics

Some chemical processes occur even though there is no net energy change. Consider a vessel containing a gas, connected to an evacuated vessel via a channel wherein a barrier obstructs passage of the gas. If the barrier is removed, the gas will expand into the evacuated vessel. This expansion is consistent with the observation that a gas always expands to fill the volume available. When the temperature of both vessels is the same, the energy of the gas before and after the expansion is the same. The reverse reaction does not occur, however. The spontaneous reaction is the one that yields a state of greater disorder. In the expanded volume, the individual gas molecules have greater freedom of movement and thus are more disordered. The measure of the disorder of a system is a quantity termed entropy. At a temperature of absolute zero, all movement of atoms and molecules ceases, and the disorder—and entropy—of such perfectly compacted substances is zero. (Zero entropy at zero temperature is in accord with the third law of thermodynamics.) All substances above absolute zero will have a positive entropy value that increases with temperature. When a hot body cools down, the thermal energy it loses passes to the surrounding air, which is at a lower temperature. As the entropy of the cooling body decreases, the entropy of the surrounding air increases. In fact, the increase in entropy of the air is greater than the decrease in entropy of the cooling body. This is consistent with the second law, which states that the total entropy of a system and its surroundings always increases in a spontaneous reaction. Thus the first and second laws of thermodynamics indicate that, for all processes of chemical change throughout the universe, energy is conserved but entropy increases.

Application of the laws of thermodynamics to chemical systems allows chemists to predict the behaviour of chemical reactions. When energy and entropy considerations favour the formation of product molecules, reagent molecules will act to form products until an equilibrium is established between products and reagents. The ratio of products to reagents is specified by a quantity known as an equilibrium constant, which is a function of the energy and entropy differences between the two. What thermodynamics cannot predict, however, is the rate at which chemical reactions occur. For fast reactions an equilibrium mixture of products and reagents can be established in one millisecond or less; for slow reactions the time required could be hundreds of years.

Rates of reaction

When the specific rates of chemical reactions are measured experimentally, they are found to be dependent on the concentrations of reacting species, temperature, and a quantity called activation energy. Chemists explain this phenomenon by recourse to the collision theory of reaction rates. This theory builds on the premise that a reaction between two or more chemicals requires, at the molecular level, a collision between two rapidly moving molecules. If the two molecules collide in the right way and with enough kinetic energy, one of the molecules may acquire enough energy to initiate the bond-breaking process. As this occurs, new bonds may begin to form, and ultimately reagent molecules are converted into product molecules. The point of highest energy during bond breaking and bond formation is called the transition state of the molecular process. The difference between the energy of the transition state and that of the reacting molecules is the activation energy that must be exceeded for a reaction to occur. Reaction rates increase with temperature because the colliding molecules have greater energies, and more of them will have energies that exceed the activation energy of reaction. The modern study of the molecular basis of chemical change has been greatly aided by lasers and computers. It is now possible to study short-lived collision products and to better determine the molecular mechanisms that fix the rate of chemical reactions. This knowledge is useful in designing new catalysts that can accelerate the rate of reaction by lowering the activation energy. Catalysts are important for many biochemical and industrial processes because they speed up reactions that ordinarily occur too slowly to be useful. Moreover, they often do so with increased control over the structural features of the product molecules. A rhodium phosphine catalyst, for example, has enabled chemists to obtain 96 percent of the correct optical isomer in a key step in the synthesis of L-dopa, a drug used for treating Parkinson’s disease.