Molecule

History

Formation

Characteristics

Molecular bonding

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It was not until knowledge about atoms and elements was gained that the make-up of the millions of different substances around scientists was understood. All the scientific knowledge known today indicates that these different substances are made from only 92

different kinds of atoms that make up the naturally occurring elements.

These atoms are able to join together in millions of different combinations and arrangements to form all the substances in the universe. A molecule is formed when two or more of the same or different kinds of atoms join together. The newly formed substance is called a compound. Although the identity of the elements stays the same because the number of protons is the same, the physical and chemical properties of the compound are different from the properties of the elements from which they formed because the arrangement of the outermost electrons is different.

For centuries chemists and physicists believed that it was possible to transmute one element, such as lead, into another, such as gold. When the corpuscular theory of matter was developed and accepted (which could explain but not predict chemical changes in terms of transmutations), this belief was strengthened. By the middle of the eighteenth century, however, virtually all chemists and physicists believed that transmutations of matter into other kinds of matter were not possible. But lack of knowledge about the elements, the basic building blocks of all matter, hindered any real understanding of the nature of matter and the formation of new substances.

During the period between 1789 and 1803, French chemist Antoine-Laurent Lavoisier (1743–1794) defined the elements as substances that could not be separated by fire or some other chemical means and British chemist John Dalton (1766–1844) defined atoms as small, indestructible and invisible particles. These ideas cleared the way for understanding the

makeup of all the substances in the universe. Dalton assumed that each kind of element had its own kind of atom, which was different from the atoms of all other elements. He also assumed that chemical elements kept their identity during all chemical reactions.

During the early nineteenth century, chemical experiments centered mainly around taking measurements of substances involved in chemical reactions both before and after the reaction. It was found that elements always reacted to form a new substance in the same ratio. If different ratios of the reacting substances were used, different substances were produced. Dalton’s atomic theory went on to say that chemical compounds are the new substances that form when atoms combine with each other; that a specific compound always has the same kinds of atoms in the same ratio; and that chemical reactions do not involve a change in the atoms themselves but in the way they are arranged.

In 1809, French chemist Joseph-Louis Gay-Lussac (1778–1850) and others began doing numerous experiments with gases by measuring the amounts of the gases that actually reacted. They found that two volumes of hydrogen reacted with one volume of oxygen to form two volumes of water. They also found that one volume of hydrogen gas reacted with one volume of chlorine gas to form two volumes of hydrogen chloride gas. In 1811, Italian physicist and chemist Amedeo Avogadro (1776–1856) hypothesized that equal volumes of different gases, when at the same temperature and pressure, contained the same number of particles. These experimental results and theories eventually led to the determination of the number of atoms in the substances. The name molecule was later assigned to particles made up of more than one atom, which may be of the same or different atoms.

Of all the naturally occurring substances around us every day, there are only 92 that cannot be chemically changed to simpler substances. Two or three of these substances are so rare in nature that their natural occurrence is questionable. There are also 19 other known substances (and several others at various stages of discovery and confirmation) that are artificially made in sophisticated instruments like cyclotrons. Together, these 111 pure substances are called elements. The atoms of the 92 naturally occurring elements are the building blocks for all of the substances in the universe.

When atoms join together in various combinations of kind and number, they form molecules. When molecules are made from two or more different kinds of atoms, the substances are called compounds. If molecules are made from only one kind of atom, the substances are elements. New combinations of the atoms produce new molecules and therefore different substances.

Special kinds of chemical formulas, called molecular formulas, are used to represent the kinds of atoms and the number of each kind of atom in a molecule. The simplest molecules are composed of just two atoms (usually a single atom is not referred to as a molecule), which may be the same or different. Oxygen gas (O 2 ), hydrogen gas (H 2 ), and nitrogen gas (N 2 ), are

made up of molecules composed of just two atoms of oxygen, hydrogen, or nitrogen respectively. Since these substances are composed of only one kind of atom, they are elements. Carbon monoxide (CO) is a gas with molecules composed of one atom of carbon and one atom of oxygen and carbon dioxide (CO 2 ) is a gas with molecules composed of one atom of carbon and two atoms of oxygen. Water molecules (H 2 O) are composed of one atom of oxygen and two atoms of hydrogen. These substances are compounds because the molecules that make it up have two kinds of atoms. Many molecules, especially those in living things such as sugar, fat, or protein molecules and molecules of deoxyribonucleic acid (DNA) or ribonucleic acid (RNA), are much larger and more complex.

It is possible for all the different substances in the universe to be produced from only 92 naturally occurring elements because there are endless ways to combine these 92 kinds of atoms, which are the building blocks for all molecules. The 26 letters of the alphabet can be compared to the 92 different kinds of atoms. Different words can be formed in many different ways: by using different letters, such as dog and dig and dodge and dug and dugout; or by using the same letters with different arrangements, such as dog and God and good; or mate and tame and meat, or met and meet and teem. Because of all these possibilities, the 26 letters of the alphabet form all the millions of words of the English language. Similarly, new substances form when different kinds or different numbers of atoms join, or when the same kinds of atoms join in different arrangements. And, just like the letters of the alphabet, the 92 naturally occurring elements form all the millions of different substances in the entire universe including all the various metals, plastics, materials for building, fabrics, all parts of all living things, etc. It is the kind, number, and arrangement of atoms within the molecule that determines what the substance is.

All molecules have a definite mass and size that are dependent on the atoms from which the molecule is made. The mass is equal to the sum of the masses of all the individual atoms in the molecular structure. The size is not only dependent on the atomic components of the molecule, but also on the arrangement of the atoms within the molecule and how tightly they are joined together.

When atoms join other atoms to form molecules, the chemical and physical properties of the compounds are different from those of the elements from which they were formed. These include such things as color, hardness, conductivity, state (solid, liquid, gas), etc. When letters are used to form new words, such as dog, God and good from the letters g, o, and d, the meanings of the new words cannot be discovered by observing or studying either the letters g, o, and d, or the other words. The new words formed have new and different meanings. This is also true when new molecules form. The properties of the new substances cannot be found by studying the properties of the elements from which they formed or the properties of other similar molecules.

The molecular formula for sugar is C 6 H 12 O 6 , which indicates that a sugar molecule is made up of six atoms of carbon, 12 atoms of hydrogen, and six atoms of oxygen. Carbon is an element that is black and often is found in powder form. It is well known as the major component of coal or the black that appears on burnt toast. Pure hydrogen is a the lightest gas known and pure oxygen is a gas present in the air and needed for living things to breathe and for fires to burn. When these three substances chemically combine in the ratio of C 6 H 12 O 6 to form sugar, which is a white, crystalline solid that has a sweet taste and is soluble in water, the properties of the sugar are unlike those of the pure elements from which it was formed. However, if sugar is reacted under extreme conditions (a chemical change), the original substances, carbon, hydrogen, and oxygen could be recovered.

Hydrogen and oxygen atoms can join to form water molecules. Once again, the properties of water (often used to extinguish fires) are completely different from the properties of oxygen gas (needed to support burning). These same two elements, hydrogen and oxygen, also form another common substance, hydrogen peroxide, with a molecular formula of H 2 O 2 . Hydrogen peroxide, in its undiluted form, can cause serious burns. When diluted, it is often used for bleaching and as an antiseptic in cleansing wounds. These properties are completely different from the properties of the elements from which it is made, hydrogen and oxygen, as well as from the similar molecule, water. One could not boil potatoes in H 2 O 2 instead of H 2 O without deadly effects. The properties of hydrogen peroxide differ greatly from those of hydrogen, oxygen, and water because each of the substances has its own specific number, kind, and arrangement of atoms.

While the molecular formula gives the basic information about what atoms are joined together and how many of each kind of atom, this formula does not give the whole story. The arrangement of the atoms within the molecule must also be considered since different arrangements of the same atoms within a molecule produce different substances. The molecular formulas for ethyl alcohol (formed from the fermentation of grains and fruits and present in all wines and liquors) and for methyl ether (sometimes used in refrigeration but not the same ether used as an anesthetic) are identical, C 2 H 6 O. However, the chemical properties are very different. This is because the atoms are arranged differently within the molecule. Molecular formulas cannot convey this information. Different kinds of formulas, called structural formulas, are needed to show molecular arrangements. In the case of ethyl alcohol, the oxygen atom is joined to a carbon atom and to a hydrogen atom. However, in the case of methyl ether, the oxygen atom is joined to two carbon atoms. This different arrangement of atoms within the molecule is responsible for imparting different chemical properties to the compound. Thus, the new chemical properties are not only dependent on how many of each kind of atom have joined together, but on how these atoms are arranged within the molecule.

Much of the research in the field of chemistry today involves the formation of new substances by trying to change atoms within a molecule or the arrangement of the same atoms. This latter is a particularly important area when the arrangement of the atoms is changed from what is called a right-handed molecule to a left-handed molecule or vice-versa. Molecules such as these behave as they do because of their shape, much like gloves fit either the right or the left hand because of their shape. Some of the current research on new fat-free commercial products, such as ice cream or cooking oil, involves right-or left-handed versions of the original fat molecules. These mirror images of the original molecules cannot be absorbed or used by the body because of the different shape of the molecule. Yet because they are often so similar, enough of the original properties of the fat remain intact to make it useful as a substitute. So far, the taste and their inability to withstand high temperatures in cooking are problematic.

Similarly, many powerful drugs in use today have both right- and left-handed versions. Most drugs contain both forms of the molecules because this mixture is cheaper and easier to produce. However, often only one version gives the desired effect while frequently the other produces unwanted side effects. Although it is chemically much more difficult and more expensive to produce drugs of only one handedness, patients needing these drugs are finding the purer, single-handed version much easier to tolerate. Drug companies are beginning to pay attention and research is being done to produce drugs of only one handedness at a reasonable cost.

When compounds are formed, the identity of the atoms, which is associated with the number of protons in the nucleus, does not change. For example, oxygen atoms are still oxygen atoms whether they are part of oxygen gas molecules, water molecules, carbon dioxide molecules, etc., because the number of protons is unchanged.

But unlike mixtures, where two or more substances are mixed together but there is little or no interaction among the atoms of the various substances, there is interaction among the atoms within molecules. New compounds are formed when the atoms within the molecule form a chemical bond. These bonds are a sort of glue that holds the atoms together within the molecule. Bonds involve only the outermost electrons of the atoms, that is, those in the highest shell or energy level. It is this change in electron arrangements that is responsible for the new properties observed when compounds are formed. There are two major types of bonds, ionic and covalent.

An ionic bond forms when the outermost electrons are transferred from one atom to another. One atom loses one or more electrons and another atom

KEY TERMS

Atom— Small, indestructible particles, composed of protons, neutrons, and electrons, from which all elements are made.

Chemical bond— The force or glue that holds atoms together in chemical compounds.

Compound— A pure substance that consists of two or more elements, in specific proportions, joined by chemical bonds. The properties of the compound may differ greatly from those of the elements it is made from.

Covalent bond— A chemical bond formed when two atoms share a pair of electrons with each other.

Element— A pure substance that can not be changed chemically into a simpler substance.

Ionic bond— The attractive forces between positive and negative ions that exist when electrons have been transferred from one atom to another.

Metallic bond— The forces that exist between the atoms in metals due to mobile electrons moving throughout the structure.

Molecular formula— Shorthand method for representing the composition of molecules using symbols for the type of atoms involved and subscripts for the number of atoms involved.

Molecule— Particles formed when two or more atoms join together to form new substances.

Structural formula— The chemical representation of a molecule that shows how the atoms are arranged within the molecule.

gains these electrons. Sodium metal is a soft, shiny, and very reactive metal that is stored under kerosene to keep it from reacting with the oxygen in the air. Sodium atoms have only one electron at the highest energy level. They would be more stable if they got rid of this electron. Chlorine is a very poisonous green gas involved in the purifying process of swimming pools and responsible for the characteristic smell around them. Chlorine has seven electrons at the highest energy level. It would be much more stable with eight electrons at this level. When sodium and chlorine come in contact with each other, there is an instantaneous reaction. Neutral atoms of sodium metal give up one electron with their negative charge and form particles, called ions, with net charges of +1. Neutral atoms of chlorine gain negatively-charged electrons from sodium atoms and form particles, also called ions, with net charges of -1.

Throughout these changes, the number of protons and neutrons in the nucleus and all of the innermost electrons around the nucleus stay the same. Only an insignificant amount of the mass of the atom is associated with electrons, so the mass of the atom also stays essentially the same. However, a chemical change has occurred and the original properties of the atoms have changed because of the new arrangement of the electrons. The newly formed sodium ion and the chloride ion are electrically attracted or bonded to each other because opposite charges attract each other. The substance formed is ordinary table salt, which is a white, salty, crystalline solid, properties that are very different from the original elements of sodium and chlorine. The bond that formed is called an ionic bond and sodium chloride is called an ionic compound. An ionic bond is formed when the glue between atoms is the force of attraction between opposite charges. In fact, salt crystals are formed by the very neat and orderly arrangement of alternating sodium and chloride ions. Ionic bonds are most often formed between atoms of metals and atoms of non-metals.

Often, the outermost electrons of an atom are shared with the outermost electrons of another atom. Electrons move around the nucleus of an atom at very high speeds and, when electrons are shared between two atoms, the nuclei move so close together that the shared electrons spend part of their time near both nuclei simultaneously. This sharing of electrons by the nuclei of two atoms simultaneously is the glue that is holding them together within the molecule. This type of bond is called a covalent bond. Electrons that are shared can be contributed by either or both atoms involved in the bond formation.

Carbon atoms have four outermost electrons and need eight to be more stable. If one carbon atom shares each of its outermost electrons with a hydrogen atom, which needs only two electrons to become more stable, a molecule of methane is formed. The formula for the new substance formed is CH 4 . Methane is often called marsh gas because it forms in swamps and marshes from the underwater decomposition of plant and animal material. It is widely distributed in nature and about 85% of natural gas is methane.

When things are shared, like sharing the sofa with a friend, they are not always shared equally. This is also true of electrons involved in covalent bonds. At times, the electrons involved in bonding are shared equally between the nuclei of two atoms and the bond is called a pure covalent bond. More often, however, the sharing is unequal and the electrons spend more time around the nucleus of one atom than of the other. The bond formed is called a polar covalent bond. Usually covalent bonds (both pure covalent and polar covalent) form when atoms of non-metallic elements bond to atoms of other non-metallic elements.

The glue or bonding that holds atoms of metals close to each other is usually referred to as a metallic bond. It is formed because the outermost electrons of the metal atoms form a sort of sea of electrons as they move freely around the nuclei of all the metal atoms in the crystal. These mobile electrons are responsible for the electrical and heat conductivity of the metals.

See also Compound, chemical; Element, chemical; Formula, chemical; Formula, structural.

BOOKS

Emsley, John. Nature’s Building Blocks: An A-Z Guide to the Elements. Oxford: Oxford University Press, 2002.

Moog, Richard Samuel. Chemistry: A Guide Inquiry. New York: Wiley, 2005.

Siekierski, Slawomir. Concise Chemistry of the Elements. Chichester, UK: Horwood Publishing, 2002.

Tro, Nivaldo J. Introductory Chemistry. Upper Saddle River, NJ: Pearson Education, 2006.

OTHER

Bader, Richard F.W., Department of Chemistry, McMaster University. “Atoms and Molecules.” <http://www.chemistry.mcmaster.ca/bader/aim/> (accessed October 17, 2006).

Department of Chemistry, Wellesley College. “Alphabetical Listing of Molecules.” <http://www.wellesley.edu/Chemistry/Flick/molecules/newlist.html> (accessed October 17, 2006).

School of Chemistry, University of Bristol. “Molecules with Silly or Unusual Names.” <http://www.chm.bris.ac.uk/sillymolecules/sillymols.htm> (accessed October 17, 2006).

Leona B. Bronstein