In the case of van der Waals interactions, the atoms and molecules involved retain their hold on their electrons, they remain distinct and discrete. There are cases, however, where atoms come to "share" each other's electrons. This sharing involves pairs of electrons, one from each atom. When electron pairs are shared, the atoms stop being distinct in that their shared electrons are no longer restricted to one or the other. In fact, since one electron cannot even in theory be distinguished from any other electron, they become a part of the molecule’s electron system156. This sharing of electrons produces what is known as a covalent bond. Covalent bonds are ~20 to 50 times stronger than van der Waals interactions. What exactly does that mean? Basically, it takes much more energy to break these bonds. While the bonded form of atoms in a molecule is always more stable than the unbounded form, it may not be stable enough to withstand the energy delivered through collisions with neighboring molecules. Different bonds between different atoms in different molecular contexts differ in terms of bond stability; the bond energy refers the energy needed to break a particular bond. A molecule is stable if the bond energies associated with bonded atoms within the molecule are thigh enough to survive the energy delivered to the molecule through either collisions with neighboring molecules or the absorption of energy (light).
When atoms form a covalent bond, their individual van der Waals surfaces merge to produce a new molecular van der Waals surface. There are a number of ways to draw molecules, but the space-filling or van der Waals surface view is the most realistic (at least for our purposes). While realistic it can also be confusing, since it obscures the underlying molecular structure, that is, how the atoms in the molecule are linked together. This can be seen in this set of representations of the simple molecule 2-methylpropane157. As molecules become larger, as is the case with many biologically important molecules, it can become impossible to appreciate their underlying organization based on a van der Waals surface representation.
Because they form a new stable entity, it is not surprising (perhaps) that the properties of a molecule are quite distinct from, although certainly influenced by, the properties of the atoms from which they are composed. To a first order approximation, a molecule’s properties are based on its shape, which is dictated by how the various atoms withjn the molecule are connected to one another. These geometries are imposed by each atom’s quantum mechanical properties and (particularly as molecules get larger, as they so often do in biological systems) the interactions between different parts of the molecule. Some atoms, common to biological systems, such as hydrogen (H), can form only a single covalent bond. Others can make two (oxygen (O) and sulfur (S)), three (nitrogen (N)), four (carbon (C)), or five (phosphorus (P)) bonds.
In addition to smaller molecules, biological systems contain a number of distinct types of extremely large molecules, composed of thousands of atoms; these are known as macromolecules. Such macromolecules are not rigid; they can often fold back on themselves leading to intramolecular interactions. There are also interactions between molecules. The strength and specificity of these interactions can vary dramatically and even small changes in molecular structure can have dramatic effects.
Molecules and molecular interactions are dynamic. Collisions with other molecules can lead to parts of a molecule rotating around a single bond158. The presence of a double bond restricts these kinds of movements; rotation around a double bond requires what amounts to breaking and then reforming one of the bonds. In addition, and if you have mastered some chemistry you already know this, it is often incorrect to consider bonds as distinct entities, isolated from one another and their surroundings. Adjacent bonds can interact forming what are known as resonance structures that behave as mixtures of single and double bonds. Again this restricts free rotation around the bond axis and acts to constrain molecular geometry. As we we will see later on with the peptide bond, which occurs between a carbon (C) and a nitrogen (N) atom in polypeptide chain, is an example of such a resonance structure. Similarly, the ring structures found in the various “bases” present in nucleic acids produces flat structures that can pack one top of another. These various geometric complexities combine to make predicting a particular molecule’s three dimensional structure increasingly difficult as its size increases.