Atoms, Isotopes, Ions, and Molecules: The Building Blocks

Covalent Bonds and Other Bonds and Interactions

Another way to satisfy the octet rule by sharing electrons between atoms to form covalent bonds. These bonds are stronger and much more common than ionic bonds in the molecules of living organisms. We commonly find covalent bonds in carbon-based organic molecules, such as our DNA and proteins. We also find covalent bonds in inorganic molecules like H2O, CO2, and O2. The bonds may share one, two, or three pairs of electrons, making single, double, and triple bonds, respectively. The more covalent bonds between two atoms, the stronger their connection. Thus, triple bonds are the strongest.

The strength of different levels of covalent bonding is one of the main reasons living organisms have a difficult time in acquiring nitrogen for use in constructing their molecules, even though molecular nitrogen, N2, is the most abundant gas in the atmosphere. Molecular nitrogen consists of two nitrogen atoms triple bonded to each other and, as with all molecules, sharing these three pairs of electrons between the two nitrogen atoms allows for filling their outer electron shells, making the molecule more stable than the individual nitrogen atoms. This strong triple bond makes it difficult for living systems to break apart this nitrogen in order to use it as constituents of proteins and DNA.

Forming water molecules provides an example of covalent bonding. Covalent bonds bind the hydrogen and oxygen atoms that combine to form water molecules as Figure shows. The electron from the hydrogen splits its time between the hydrogen atoms' incomplete outer shell and the oxygen atoms' incomplete outer shell. To completely fill the oxygen's outer shell, which has six electrons but which would be more stable with eight, two electrons (one from each hydrogen atom) are needed: hence, the well-known formula H2O. The two elements share the electrons to fill the outer shell of each, making both elements more stable.

Link to Learning

View this short video to see an animation of ionic and covalent bonding.

Polar Covalent Bonds

There are two types of covalent bonds: polar and nonpolar. In a polar covalent bond, Figure shows atoms unequally share the electrons and are attracted more to one nucleus than the other. Because of the unequal electron distribution between the atoms of different elements, a slightly positive (δ+) or slightly negative (δ–) charge develops. This partial charge is an important property of water and accounts for many of its characteristics.

Water is a polar molecule, with the hydrogen atoms acquiring a partial positive charge and the oxygen a partial negative charge. This occurs because the oxygen atom's nucleus is more attractive to the hydrogen atoms' electrons than the hydrogen nucleus is to the oxygen’s electrons. Thus, oxygen has a higher electronegativity than hydrogen and the shared electrons spend more time near the oxygen nucleus than the hydrogen atoms' nucleus, giving the oxygen and hydrogen atoms slightly negative and positive charges, respectively. Another way of stating this is that the probability of finding a shared electron near an oxygen nucleus is more likely than finding it near a hydrogen nucleus. Either way, the atom’s relative electronegativity contributes to developing partial charges whenever one element is significantly more electronegative than the other, and the charges that these polar bonds generate may then be used to form hydrogen bonds based on the attraction of opposite partial charges. (Hydrogen bonds, which we discuss in detail below, are weak bonds between slightly positively charged hydrogen atoms to slightly negatively charged atoms in other molecules.) Since macromolecules often have atoms within them that differ in electronegativity, polar bonds are often present in organic molecules.

Nonpolar Covalent Bonds

Nonpolar covalent bonds form between two atoms of the same element or between different elements that share electrons equally. For example, molecular oxygen (O2) is nonpolar because the electrons distribute equally between the two oxygen atoms.

Figure also shows another example of a nonpolar covalent bond—methane (CH4). Carbon has four electrons in its outermost shell and needs four more to fill it. It obtains these four from four hydrogen atoms, each atom providing one, making a stable outer shell of eight electrons. Carbon and hydrogen do not have the same electronegativity but are similar; thus, nonpolar bonds form. The hydrogen atoms each need one electron for their outermost shell, which is filled when it contains two electrons. These elements share the electrons equally among the carbons and the hydrogen atoms, creating a nonpolar covalent molecule.

Table compares water, methane and carbon dioxide molecules. In water, oxygen has a stronger pull on electrons than hydrogen resulting in a polar covalent O-H bond. Likewise in carbon dioxide the oxygen has a stronger pull on electrons than carbon and the bond is polar covalent. However, water has a bent shape because two lone pairs of electrons push the hydrogen atoms together so the molecule is polar. By contrast carbon dioxide has two double bonds that repel each other, resulting in a linear shape. The polar bonds in carbon dioxide cancel each other out, resulting in a nonpolar molecule. In methane, the bond between carbon and hydrogen is nonpolar and the molecule is a symmetrical tetrahedron with hydrogens spaced as far apart as possible on the three-dimensional sphere. Since methane is symmetrical with nonpolar bonds, it is a nonpolar molecule.
Whether a molecule is polar or nonpolar depends both on bond type and molecular shape. Both water and carbon dioxide have polar covalent bonds, but carbon dioxide is linear, so the partial charges on the molecule cancel each other out.

Hydrogen Bonds and Van Der Waals Interactions

Ionic and covalent bonds between elements require energy to break. Ionic bonds are not as strong as covalent, which determines their behavior in biological systems. However, not all bonds are ionic or covalent bonds. Weaker bonds can also form between molecules. Two weak bonds that occur frequently are hydrogen bonds and van der Waals interactions. Without these two types of bonds, life as we know it would not exist. Hydrogen bonds provide many of the critical, life-sustaining properties of water and also stabilize the structures of proteins and DNA, the building block of cells.

When polar covalent bonds containing hydrogen form, the hydrogen in that bond has a slightly positive charge because hydrogen’s electron is pulled more strongly toward the other element and away from the hydrogen. Because the hydrogen is slightly positive, it will be attracted to neighboring negative charges. When this happens, a weak interaction occurs between the hydrogen's δ+ from one molecule and another molecule's δ– charge on the more electronegative atoms, usually oxygen or nitrogen, or within the same molecule. Scientists call this interaction a hydrogen bond. This type of bond is common and occurs regularly between water molecules. Individual hydrogen bonds are weak and easily broken; however, they occur in very large numbers in water and in organic polymers, creating a major force in combination. Hydrogen bonds are also responsible for zipping together the DNA double helix.

Like hydrogen bonds, van der Waals interactions are weak attractions or interactions between molecules. Van der Waals attractions can occur between any two or more molecules and are dependent on slight fluctuations of the electron densities, which are not always symmetrical around an atom. For these attractions to happen, the molecules need to be very close to one another. These bonds—along with ionic, covalent, and hydrogen bonds—contribute to the proteins' three-dimensional structure in our cells that is necessary for their proper function.

Career Connection

Pharmaceutical Chemist Pharmaceutical chemists are responsible for developing new drugs and trying to determine the mode of action of both old and new drugs. They are involved in every step of the drug development process. We can find drugs in the natural environment or we can synthesize them in the laboratory. In many cases, chemists chemically change potential drugs from nature chemically in the laboratory to make them safer and more effective, and sometimes synthetic versions of drugs substitute for the version we find in nature.

After a drug's initial discovery or synthesis, the chemist then develops the drug, perhaps chemically altering it, testing it to see if it is toxic, and then designing methods for efficient large-scale production. Then, the process of approving the drug for human use begins. In the United States, the Food and Drug Administration (FDA) handles drug approval. This involves a series of large-scale experiments using human subjects to ensure the drug is not harmful and effectively treats the condition for which it is intended. This process often takes several years and requires the participation of physicians and scientists, in addition to chemists, to complete testing and gain approval.

An example of a drug that was originally discovered in a living organism is Paclitaxel (Taxol), an anti-cancer drug used to treat breast cancer. This drug was discovered in the bark of the pacific yew tree. Another example is aspirin, originally isolated from willow tree bark. Finding drugs often means testing hundreds of samples of plants, fungi, and other forms of life to see if they contain any biologically active compounds. Sometimes, traditional medicine can give modern medicine clues as to where to find an active compound. For example, mankind has used willow bark to make medicine for thousands of years, dating back to ancient Egypt. However, it was not until the late 1800s that scientists and pharmaceutical companies purified and marketed the aspirin molecule, acetylsalicylic acid, for human use.

Occasionally, drugs developed for one use have unforeseen effects that allow usage in other, unrelated ways. For example, scientists originally developed the drug minoxidil (Rogaine) to treat high blood pressure. When tested on humans, researchers noticed that individuals taking the drug would grow new hair. Eventually the pharmaceutical company marketed the drug to men and women with baldness to restore lost hair.

A pharmaceutical chemist's career may involve detective work, experimentation, and drug development, all with the goal of making human beings healthier.