Molecule

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.

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.

V

POLARITY

As we have discussed, atoms with somewhat different electronegativity values bond covalently to form polar molecules. The degree of polarity in a molecule affects how strongly it is attracted to other molecules in a substance. This attraction, in turn, can influence the physical properties of the substance. Scientists can predict the polarity of a molecule if they know the electronegativity of the atoms that compose it. The arrangement of atoms in a molecule also affects its polarity.

Two atoms with no difference in electronegativity will form a nonpolar bond. In truly nonpolar molecules, the outer electrons of the atoms are distributed equally around the center of the molecule. This is the case for molecules formed of two bonded atoms of the same element, such as molecular hydrogen or oxygen. The outer electrons are also distributed equally around molecules such as methane (CH₄) and carbon dioxide (CO₂), in which a central atom bonds to identical atoms that are spaced equally apart from each other. Atoms that have very similar electronegativity values also form nonpolar bonds. A large number of molecules, called hydrocarbons, are composed of only hydrogen and carbon. These two elements have such similar electronegativity values that chemists consider hydrocarbon molecules to be nonpolar.

Atoms with more pronounced differences in electronegativity form polar molecules. The more electronegative atom pulls the shared electrons closer to it. Even atoms with similar electronegativity values can form a polar molecule, if they contain three or more atoms arranged nonsymmetrically. One end of the molecule has a small positive charge and one end has a small negative charge. This arrangement of charges forms what scientists call a dipole. A measurement of the strength of the dipole, called the dipole moment, depends on the size of the electrical charges, the distance between them, and how they are arranged.

If the electronegativity difference between two atoms is large, they will form an ionic compound rather than a molecular one. As we have seen, in this case one atom rips an electron from another atom. The atom—or group of atoms—that takes the negatively charged electron becomes a negative ion. The atom—or group of atoms—that gave the electron up becomes a positive ion. For example, sodium chloride (NaCl), which is table salt, is made up of positively charged sodium ions and negatively charged chlorine ions. There is no sharp dividing line between polar covalent bonds and ionic bonds. In an ionic substance, the positive ion often tugs at the electrons on the negative ion, distorting the ionic bond so that it acts a little like a covalent bond. The pure, nondistorted ionic bond and the nonpolar covalent bond are extreme types of bonds. Most bonds act more like a mix of ionic and covalent types.

VI

FORCES BETWEEN MOLECULES

Molecules can form compounds that are in any of the three main physical states of matter, that is, gases, liquids, or solids. In gases, the molecules are constantly moving and far apart. In solids, they are locked in position close together. In liquids, they are in between: the molecules are close together, but they can move or flow. Forces of attraction between molecules determine which state a substance will be in at a particular temperature and pressure. Forces of repulsion between molecules make it difficult to squeeze the molecules in a liquid or solid closer together. In general, forces between molecules are called intermolecular forces.

The state of a substance changes as its temperature and pressure change. The temperature determines the kinetic energy of the substance’s molecules. Kinetic energy is the energy of movement of the molecules, and more kinetic energy tends to drive molecules apart. This energy opposes the attractive intermolecular forces that tend to hold them together. As temperature increases, kinetic energy increases, and a substance will go from a solid, to a liquid, to a gas. Pressure works in the opposite manner, forcing molecules closer together so that intermolecular forces of attraction can bind the molecules together. Increasing pressure can make the distant molecules in gas squeeze together to form a liquid or make a liquid form a solid.

In gases, the molecules have very high kinetic energies, energies strong enough to overcome attractive forces and drive molecules apart. Gas molecules constantly move and will occupy the entire volume of any container. Gases expand or contract easily. When gas molecules are cooled, their kinetic energy decreases. Molecules condense, or form a liquid from vapor, at the substance’s condensation point (also its boiling point). This point is the temperature at which the kinetic energy is low enough that the intermolecular attractions can keep the individual molecules close to one another.

In a liquid, the molecules constantly move, although not as much, as fast, or as far as gas molecules do. Liquids take the shape of their container. They can expand or contract only slightly. As liquid molecules cool, they lose more kinetic energy and form a solid at the substance’s freezing point (also its melting point). At this temperature the kinetic energy is low enough that the molecules can form a rigid arrangement.

When molecules freeze into a solid, they form a molecular crystal. The molecules no longer move about the substance but only vibrate in place. Ice (H₂O) is an example of a molecular crystal. The bonds between molecules in a molecular crystal are weaker than the bonds that hold ionic crystals, such as table salt, together. Molecular crystals are usually softer and melt at lower temperatures than ionic crystals do, because it takes less energy to overcome their intermolecular attractions. Some molecules, such as those in glass and the long molecules of some plastics and proteins, can form a solid without freezing into a crystal structure. These molecules slow down and form amorphous materials, which behave as solids. Amorphous solids are more like very viscous liquids than crystals.

The intermolecular forces of attraction include dipole-dipole attractions, London forces, and hydrogen bonds. London forces are actually a weak form of dipole-dipole attraction, while hydrogen bonds are an especially strong type of dipole-dipole attraction. Molecules that have strong forces of attraction usually have higher boiling points and higher melting points than do molecules with a similar mass and weaker attractions.

Dipole-dipole attractions occur between polar molecules. In a polar molecule, one end (or pole) of the molecule is positively charged and the other end (the second pole) is negatively charged. These two oppositely charged poles form a dipole. The positive part of each polar molecule attracts the negative part of its neighboring molecules, and the negative part of each polar molecule attracts the positive part of its neighboring molecules. The more polar the molecules of a solid or liquid are, the stronger the attractive forces are between them and the harder it is to separate them. Molecules that are more polar tend to have higher melting points and boiling points than those of molecules that are less polar. Water, methanol (an alcohol), and ammonia are polar molecules that have dipole-dipole attractions.

London forces affect all molecules. London forces are also called induced dipole attractions or van der Waals forces. These attractions occur when nonpolar molecules become polar for a short time. Nonpolar molecules can briefly become polar because their electrons are in constant motion. This motion is usually balanced, or symmetrical, around a nonpolar molecule. If the electrons are briefly disturbed, however, their negative charge may increase at one part of the molecule, creating a positive charge on another part of the molecule. In such a case, the molecule becomes a dipole until the electrons rebalance. During the brief time that the molecule is a dipole, its charges can disturb electrons in neighboring molecules, turning them into dipoles as well. These temporary dipoles attract each other. For nonpolar molecules, such as methane and nitrogen molecules, the only intermolecular attractions are London forces. These forces are fairly weak, and therefore, nonpolar substances have low melting and boiling points. Many nonpolar substances are gases at room temperature.

Hydrogen bonds are an especially strong form of dipole-dipole attraction. They only occur between molecules containing hydrogen and elements that are highly electronegative, such as fluorine, oxygen, and nitrogen. A hydrogen atom has one positively charged proton in its nucleus and one electron. In molecules with hydrogen bonds, the strongly electronegative atom forms a covalent bond with hydrogen. In this bond, the electronegative atom pulls the bonding electrons very close, almost stripping the hydrogen atom of its one electron so that it becomes a bare proton. This arrangement leaves the hydrogen atom with a relatively large positive charge and the electronegative atom with a relatively large negative charge. The positively charged hydrogen atom attracts a negatively charged fluorine, oxygen, or nitrogen atom on a neighboring molecule or on the same molecule, thus creating a hydrogen bond.

The strong intermolecular attraction of the hydrogen bond is responsible for the unusual properties of water. For example, water boils at 100° C (212° F). Without hydrogen bonding, water would boil at –80° C (-112° F), and liquid water would not exist on Earth. Proteins often form hydrogen bonds between different parts of a single molecule. These bonds hold the protein in a folded-up shape. Hydrogen bonding is also important in the DNA molecules that make up an organism’s genetic code.

Intermolecular forces of repulsion result from the negative charge of each molecule’s outer electrons. This negative charge repels the negative charge of every other molecule’s outer electrons. Forces of repulsion only comes into effect when the molecules are close together, as in a liquid or solid. They prevent molecules from getting too close to each other, making it difficult to compress a molecular liquid or solid.

VII

MACROMOLECULES

Macromolecules are giant molecules with many atoms and very large masses for a molecule. Nearly all macromolecules include the element carbon as a building block, because it is the only element that readily forms giant chains or networks by bonding to other carbon atoms and other elements (Chemistry, Organic). Chemists can create macromolecules in laboratories or in factories. Most of the synthetic (laboratory-made) macromolecules are polymers, molecules created by linking together many identical units, called monomers. Living organisms build polymers and other complex macromolecules through natural processes.

A polymer’s properties depend on its size, its monomers, the strength of its bonds, and whether links form between different parts of the molecule. Larger molecules tend to have higher melting points, so macromolecules tend to be solid at room temperature. The type of monomer or monomers affects the polymer structure and its properties. The repeating monomer unit may be polar or nonpolar, depending on the types of atoms it contains and whether they form polar bonds. If the monomers are polar, attractions can form between different parts of the molecule or between the monomers and other molecules. The bonds between the units may be stable, or they may break easily in water or in other substances. Hydrogen bonds linking two parts of a polymer can make it hold a special shape or strengthen it.

Synthetic polymers include the plastics polystyrene, polyester, nylon (a polyamide), and polyvinyl chloride. These polymers differ in their repeating monomer units. Scientists build polymers from different monomer units to create plastics with different properties. For example, polyvinyl chloride is tough and nylon is silklike. Synthetic polymers usually do not dissolve in water or react with other chemicals. Strong synthetic polymers form fibers for clothing and other materials. Synthetic fibers usually last longer than natural fibers do.

Living organisms produce three main types of biological polymers: polysaccharides, proteins, and nucleic acids. Polysaccharides are made of linked sugar molecules, such as fructose and glucose. Plants use sugars to make polysaccharides, such as starch and cellulose, to store energy and form cell walls. Animals eat plants to gain energy from the plants’ sugars and polysaccharides. These molecules are important sources of energy for both plants and animals.

Proteins consist of amino acids linked together. There are 20 different amino acids, which can combine in a myriad of ways to form the protein molecules an organism needs. Protein chains can curl or twist in upon themselves and hold a special form because of hydrogen bonds and other bonds between parts of the molecule. Proteins perform a variety of functions in a living organism. They form the enzymes that make chemical reactions possible in the human body. The protein hemoglobin carries oxygen to cells. Other proteins in the cells use the oxygen to break down the sugar glucose to create the energy the body needs. Proteins also form important bodily structures. Proteins are, for instance, the important part of muscles that enables limbs to bend and the heart to pump. They also form fingernails and hair to protect the skin.

Nucleic acids are macromolecules found in the cell’s nucleus and cytoplasm. There are two classes of nucleic acids: deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). DNA forms an organism’s genetic code—the set of hereditary instructions that govern the activities of every cell. The DNA instructions serve as “blueprints” for all the proteins a cell needs to make. RNA enables a cell to use the DNA blueprints to build proteins. In nucleic acids, sugars link together with phosphorus and oxygen atoms (which together form the phosphate group) to form the macromolecule’s backbone. Nitrogen-containing side chains, called bases, link to the sugars of the backbone. The sequence of the bases forms the code that the cell uses to make proteins. During cellular replication—when a cell divides into two “daughter” cells—the DNA code is copied so that each daughter has a complete set of the original genetic code.

A

Discovery of Molecules

Until the 1800s chemists did not understand the difference between ionic and molecular compounds. They considered anything that contained more than one element to be a compound. Investigators, such as British scientists Michael Faraday and Henry Cavendish, began to differentiate the two when they realized that some compounds, when dissolved in water, made the water conduct electricity more easily, while others did not. Cavendish gave himself electric shocks to measure the conductivity of these water solutions. His results were surprisingly accurate.

Dutch chemist Jacobus Hendricus Van’t Hoff (who received the first Nobel Prize in chemistry in 1901) and Swedish chemist Svante August Arrhenius explained why different water solutions conduct electricity differently. Van’t Hoff determined that salts—such as sodium chloride (NaCl), or table salt, and potassium chloride (KCl)—split into two particles when they dissolve in water, while substances such as glucose do not split apart when they dissolve. Arrhenius realized that the dissolved salts not only split, but they split into two electrically charged particles, or ions. The ions move through the water to conduct electricity. Substances such as glucose do not split and thus dissolve into uncharged compound particles that do not conduct electricity, that is, into molecules.

VIII

STUDYING MOLECULES

Scientists study molecules to determine why substances made up of molecules behave the way they do. They study the structure of molecules; that is, how atoms and electrons are arranged within molecules. The molecular structure can help explain a substance’s properties, such as how the substance behaves if it is heated or compressed or mixed with another substance.

When chemists understand the relationships between a molecule’s structure and the properties of the substance containing the molecule, they can create new molecules with better properties or molecules that copy natural substances. For example, pharmaceutical chemists study molecular structures to develop new drugs. Some drugs that dull pain work by fitting into slots on nerves in the body. A scientist can examine the structure of molecules that fit the slot to develop a similarly shaped molecule that works better. Scientists have used their understanding of molecules and molecular structure to make many useful materials, such as the plastics nylon and Teflon, vitamins, pharmaceuticals, and artificial skin and bones. Scientists can also determine whether a substance is likely to be harmful by comparing its molecular structure with the structures of other molecules that are known to be harmful. Chemists use many tools to study molecules, including lasers, nuclear magnetic resonance (NMR), X-Ray systems (see X Ray), spectroscopes, and computers.

Scientists have recently developed devices that allow them to study a single molecule at a time. Lasers and magnets can hold a molecule in place, and devices such as scanning tunneling microscopes (see Microscope: Scanning Probe Microscopes) can create images of the atoms in a molecule. Single molecule studies can verify the molecular structures that have been deduced by other means and further reveal how molecules work. Some scientists have used particle traps to hold a single DNA molecule at each end and then pull it apart or twist it. Scientists may someday be able to make tiny devices out of one or a few molecules, devices that are even smaller than the tiny micromachines now in use.

NMR systems give scientists information about the positions of atoms in a molecule and so help reveal which molecules are present in a substance. The NMR system creates a magnetic field, an area of space that exerts a force on other magnets. The nuclei of hydrogen atoms and several other atoms act like small magnets. Scientists can use the NMR device to measure the strength of these small magnets, which helps them learn how hydrogen atoms are positioned within molecules that make up a substance.

X rays are high-energy electromagnetic waves (see Electromagnetic Radiation). Scientists can use X rays to study the relationships between atoms in compounds, especially bond distances, that is, the distance between two bonded atoms. When X rays pass near electrons, they diffract, or bend. Chemists can use the angles of diffraction, or the amount of bending, to create a three-dimensional map of a molecule.

Chemists also use spectroscopy to help determine a molecule’s structure. When scientists shine a light on a sample, the molecules in the sample will absorb and emit certain wavelengths of light depending on the atoms and groups of atoms in the molecule. A spectroscope reveals which wavelengths, or colors, of light the molecules absorb or emit. Certain groups of atoms commonly found together in molecules absorb certain wavelengths of light. If a molecule absorbs the wavelength usually absorbed by a particular group of atoms, it very likely contains that group.

Computers have improved these tools and made two new methods of studying molecules, molecular modeling and combinatorial chemistry possible. In molecular modeling, chemists use computers to simulate the structure and motion of macromolecules. In combinatorial chemistry, a chemist can use robotic tools (see Robots) to make a huge number of slightly different molecules. This set of molecules helps the chemist search for a useful molecule. Both of these tools are particularly useful to pharmaceutical and biological chemists.

Contributed By:
Donald K. Brandvold

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