Molecule

I

Introduction

Molecule, smallest unit of a substance that shows all the chemical properties of that substance. A molecule is a group of atoms that are bound tightly together by strong chemical bonds called covalent bonds. Every molecule has a definite size. If a molecule is broken up into its atoms or into smaller groups of atoms by chemical processes, these pieces will not behave like the original molecule. A molecule can contain atoms of the same element or atoms of different elements. A substance made up of molecules that include two or more different chemical elements is called a molecular compound. An example of a molecular compound is water. Water is made of molecules that contain two hydrogen atoms and one oxygen atom. See also Atom.

Many substances on Earth are made of molecules. Millions of molecules join together to make up the cells in humans or in any other plant or animal. The food we eat, the air we breathe, the clothes we wear, and the wood, paint, and carpeting that we use in homes are all made of molecules. Millions of different molecules exist in nature or can be made by chemists. The nature of each molecule depends on the atoms that it contains and how they link to each other. For example, the oxygen that animals require is made of molecules that have two oxygen atoms bound together. If one oxygen atom binds to a carbon atom, the molecule is instead the poisonous gas carbon monoxide.

Scientists study molecules and their structures so they can better understand why substances behave the way they do. For example, molecular structure helps explain why water boils at a high temperature. Scientists and manufacturers also use their knowledge of molecules and molecular structures to make substances with desirable properties. Plastics, for instance, are laboratory-made substances that consist of enormous molecules containing thousands of atoms. By manipulating the molecular structure of plastics, chemists have created materials that stretch better, resist fading, or can be used in microwave ovens without melting. Similarly, pharmaceutical chemists use their knowledge of molecular structure to develop new drugs that more effectively ease pain or fight disease. The discovery of the structure of deoxyribonucleic acid (DNA), the molecule that contains the genetic blueprint for living organisms, opened the door to tremendous advances in medicine and industry. Knowledge of the structure of DNA has enabled physicians to understand and treat certain genetic diseases. Moreover, by manipulating DNA structure, scientists have been able to modify—or genetically engineer—organisms, creating, for example, bacteria that produce valuable drugs (see Genetic Engineering).

Although much of our world is composed of molecules, not all substances are molecular. As we will discuss later, metals do not consist of molecules; nor do ionic compounds, which are crystalline substances such as common table salt. The atoms in metals and ionic compounds form different arrangements from those of molecular structures.

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II

Molecular Formulas

Molecular formulas are a shorthand way of describing molecules and compounds. Chemists use formulas to talk and write about molecules and to indicate how molecules behave in chemical reactions. The molecular formula indicates, in special notation, which elements make up the molecule and how many atoms are needed of each element. Understanding these formulas is the first step toward understanding the language of chemistry.

Scientists use shorthand symbols for the elements in molecular formulas. These symbols can be found in the periodic table, a chart that arranges the elements according to their chemical properties (see Periodic Law). For example, H stands for hydrogen, C for carbon, and O for oxygen. To indicate a molecule, chemists write the number of atoms of each element in subscript to the right of the symbol. A water molecule, for example, contains two hydrogen atoms and one oxygen atom, and its formula is written as H₂O. A molecule of the compound ethane contains two carbon atoms and six hydrogen atoms, giving the molecular formula C₂H₆. A molecule of butane, C₄H₁₀, contains four carbon atoms and ten hydrogen atoms. The molecular formula of a compound is also called its chemical formula. Scientists also use chemical formulas to describe ionic compounds, which contain elements in definite proportions but do not actually contain molecules.

The empirical formula of a molecule is a simpler formula than the molecular formula. It is useful when scientists know only the ratio of atoms in a compound, for example, after performing a chemical analysis that reveals the weight of each element in the compound. The empirical formula looks similar to the molecular formula, but the subscripts only include information on the ratios of the elements with respect to each other and not on the actual number of atoms. For example, ethane’s molecular formula is C₂H₆, which shows that the ratio of carbon atoms to hydrogen atoms is 1 to 3, so its empirical formula is CH₃. An unknown sample with the empirical formula CH₃ may be ethane, but it cannot be butane, which has an empirical formula of C₂H₅. Water’s molecular formula is the same as its empirical formula, H₂O. Molecular formulas always have subscripts that are whole number multiples of the empirical formula of a compound. Chemists also use empirical formulas for ionic compounds.

The structural formula of a molecule provides even more information than does the molecular formula. It shows which groups of atoms bond to each other in a molecule. Structural formulas help differentiate between isomers, molecules that have the same molecular formula but different structures. For example, C₅H₁₂ may represent the substance pentane, with the structural formula CH₃-CH₂-CH₂-CH₂-CH₃, or it may represent isopentane (also called 2-methyl pentane), with the structural formula CH₃-CH₂-CHCH₃-CH₃.

III

Bonds Within the Molecule

The bonds that hold a molecule together form because of the structure of the atoms in the molecule. Atoms are made of a nucleus surrounded by a cloud of electrons. The nucleus contains positively charged particles called protons and, in almost all atoms, neutral particles called neutrons. The electrons in an atom arrange themselves in shells, like the layers of an onion, around the atom’s nucleus. Each shell can contain a certain number of electrons, and electrons normally fill the shells closest to the nucleus first. Atoms bond with each other to form molecules by sharing their valence, or outermost, electrons.

Each chemical element has a characteristic number of electrons. For example, a carbon atom has six electrons and a neon atom has ten electrons. The first, or innermost, shell of each of these atoms can contain two electrons, and it is full for both of them. The second shell—which is the outermost shell for both of these elements—can contain eight electrons. Carbon has only four electrons in its outer shell, so it needs four more electrons to fill this layer. Neon has eight electrons in its outer shell, so its outer shell is full. Atoms are very stable when their outermost electron shell is full. Neon and the other so-called noble gases all have full outer electron shells. They are extremely stable and rarely react with other elements. Atoms of other elements bond with each other to fill their outermost shell of electrons and thus attain the stable configuration of the noble gases.

When two atoms bond by sharing some of their outer electrons, the atoms create a covalent bond, forming a molecule. To create a covalent bond, two atoms share a pair of electrons; in most cases, each atom contributes one of the shared electrons. Each atom becomes more stable, because the covalent bond has effectively provided each atom with one more electron in its outer shell. This type of bond, in which one pair of electrons is shared, is called a single bond. Sometimes, two atoms share two or three pairs of electrons with each other. These bonds are called double or triple bonds, respectively.

Two hydrogen atoms, each of which contains one electron, form the simplest covalent bond and the simplest molecule. In the resulting hydrogen molecule, the electrons are much more likely to be located between the hydrogen nuclei than on the far side of either one. The bond is strong because the positively charged nuclei are attracted to the negatively charged electrons between them. The electrons belong to the molecule as a whole. However, each hydrogen atom now has a complete outer shell of two electrons. The formula H₂ describes a hydrogen molecule, a discrete unit. When a molecule contains just two atoms, such as the hydrogen molecule does, it is called a diatomic molecule. Some atoms can form covalent bonds with more than one other atom and thus create a larger molecule.

Atoms form molecules with covalent bonds when they have similar electronegativity values. Electronegativity is a measure of how strongly an atom attracts electrons. If atoms A and B form a molecule with a covalent bond and atom B is slightly more electronegative than atom A is, the molecule’s electrons will shift slightly toward atom B. The side of the molecule near atom A will have a slight positive charge, while the side closer to atom B will have a slight negative charge. This arrangement results in a polar molecule, which is similar to a tiny magnet.

If the electronegativity difference is very large between atoms A and B, the atoms will not bond covalently. Instead, atom B will effectively steal an electron from atom A. As a result, atoms A and B become electrically charged atoms, or ions. Atom B is now a negative ion, while atom A becomes a positive ion. Although the two atoms do not share electrons to form a covalent bond, they are strongly attracted to each other because of their opposite charges. Based on this electrical attraction, they form an ionic bond, and together with other ions, they form an ionic compound. Atoms do not form individual molecules in an ionic compound. Instead, all the ions are mutually attracted. They build up a lattice structure to form a crystal.

When the atoms that join together are all metallic elements, they form a metal. Any number of metal atoms can bond together in a metallic crystal. To form metallic bonds, each atom releases its outer electrons to the metal. The remainder of the atom becomes part of a crystal structure, surrounded by a sea of electrons shared by the entire metal. Metals conduct electricity because these outer electrons can move easily throughout the structure.

IV

Sizes and Shapes

Molecules come in many sizes and shapes. They range in size and complexity from the tiny, diatomic molecules (of which the hydrogen molecule is the smallest) to enormous molecules with thousands and thousands of atoms, such as DNA and plastics molecules. The size and shape of a molecule depends on the number of atoms it contains and how the atoms are arranged. For large molecules, the shape also depends on the flexibility of the molecule. Long chains of atoms can coil up into a variety of shapes.

The size and shape of the molecules in a substance determine many properties of the substance. For example, small molecules tend to separate from each other more easily than larger molecules do, unless other attractive forces are involved. This means that substances made of small molecules usually boil or evaporate into gases at lower temperatures than do substances made of similar, larger molecules. Air is a gas that mainly contains small molecules of nitrogen and oxygen. These molecules boil at extremely low temperatures.

Molecular shape can affect properties such as the elasticity and rigidity of a substance. Shape can also determine how molecules function in living organisms. The shapes of large protein molecules are especially important in animals and plants. Many protein molecules work by fitting together with other molecules, in much the same way that a lock and key fit together. For example, inside your nose are protein molecules shaped to fit with the molecules of particular odors. Certain scent proteins fit with the molecules that give chocolate its odor, while another set of scent proteins fit with the molecules that make bananas smell as they do. Similarly, the protein hemoglobin, which is found in our red blood cells, has a shape that fits exactly with oxygen molecules, enabling the red blood cells to carry oxygen throughout the body. If a protein has the wrong shape, it will not work properly. For example, the disorder sickle-cell anemia results when hemoglobin molecules are deformed and cannot pass through the capillaries readily.

The size and shape of a molecule depend on the type and number of atoms that make up the molecule and how they are arranged. The smallest molecules—such as hydrogen, oxygen, and water molecules—contain only a few atoms. These molecules are smaller than one-millionth of a meter at their widest point. Scientists usually measure them in Angstroms (Å), where one Å is 10^-10 (or 1/10,000,000,000) meters. The hydrogen molecule, made of two hydrogen atoms, is about 1.5 Å. The oxygen molecule, made of two oxygen atoms, is slightly larger, since oxygen atoms are slightly larger than hydrogen atoms are.

Many carbon-containing molecules, such as proteins and plastics, are made of long chains of thousands of atoms. Although such molecules are thousands of times longer than the smallest molecules, they are still microscopic in width. Some of the longest natural molecules are the DNA molecules found in the cells of every living organism. The longest human DNA molecule, when fully stretched out, spans about 9 cm (about 4 in). However, DNA molecules twist and curl such that 46 can pack into the microscopic nucleus of a human cell.

Chemists can predict the shape of small molecules if they know the number and type of atoms in the molecule. In any two-atom molecule, the shape will be linear, meaning the two atoms form a line. Among molecules that contain more than two atoms, the simplest have one central atom that bonds to two or more surrounding atoms, which do not bond to any other atoms. The shape of the resulting molecule depends on the number of atoms in the molecule and the number of valence electrons in the central atom. Each of the central atom’s valence electrons pairs up, with either another electron in its own shell or one in the shell of another atom. This pairing forms a more stable atom. When two valence electrons from the central atom pair up, they are called a nonbonding pair. When a valence electron pairs with an electron in another atom, it forms a covalent bond.

Each pair of electrons in the valence shell of a molecule stays together, but it repels the other electron pairs because of their similar electric charge. Each electron pair therefore moves as far away from the other electron pairs as possible. In simple molecules, this movement determines the shape of the molecule. If all the electrons in the central atom’s valence shell pair with electrons from other atoms, the molecule will form a shape with the surrounding atoms as far apart from each other as possible. In a molecule with three atoms, for instance, the two surrounding atoms are furthest apart when the three atoms form a straight line. For a molecule with four atoms, the central atom lies in the middle of a triangle formed by the three surrounding atoms. For a molecule with five atoms, the four surrounding atoms form a tetrahedron, a four-sided shape that looks like a pyramid with a triangle base. The central atom lies at the center of the tetrahedron. The atoms of some elements can bond to five or six surrounding atoms.

Some simple molecules, such as water molecules, do not form these shapes. They form slightly different shapes, because their central atom has two or more valence electrons that link up with each other into nonbonding pairs. Each nonbonding pair acts like a phantom atom. As a result, the surrounding atoms do not move as far apart from each other as possible, but instead move as far apart from each other and from the nonbonding pairs as possible. For example, a molecule with three atoms can form the shape normally formed by a molecule with four atoms, because the one missing surrounding atom is replaced by a nonbonding pair. This is the case for water. In a water molecule, the central oxygen atom bonds to two surrounding hydrogen atoms and is left with one nonbonding pair in its valence shell. Instead of forming a straight line, the water molecule follows the pattern for a molecule with four atoms, with a central atom in the middle of a triangle formed by the surrounding atoms. Since one point of the triangle is missing, the water molecule forms a V shape. The three atoms form a molecule that is bent, not linear. A molecule will also form a different shape if two atoms share more than one pair of electrons.

Complex molecules form when one or more of the atoms surrounding a central atom links to other atoms. These atoms can in turn link to still other atoms. The molecule’s shape can be described as a series of the previously mentioned shapes linked together. Molecules can form shapes such as rings, chains, or networks. Chains can curl and twist into themselves to form bloblike shapes. For example, the proteins called enzymes form long chains that twist into special shapes that speed up chemical reactions. Enzymes work because of their special shape. Other molecules fit into grooves within the enzyme. The folded shape of the enzyme brings the “captive” molecules so close together that they react with each other. This is one way that enzymes speed up chemical reactions.