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5.9: Bond polarity, inter- and intramolecular interactions

So far, we have been considering covalent bonds in which the sharing of electrons between atoms is more or less equal, but that is not always the case. Because of their atomic structures, which arise from quantum mechanical principles (not to be discussed here), different atoms have different affinities for their own electrons. When an electron is removed or added to an atom (or molecule) that atom/molecule becomes an ion. Atoms of different elements differ in the amount of energy it takes to remove an electron from them; this is, in fact, the basis of the photoelectric effect explained by Albert Einstein, in another of his 1905 papers162. Each type of atom (element) has a characteristic electronegativity, a measure of how tightly it holds onto its electrons. If the electronegativities of the two atoms in a bond are equal or similar, then the electrons are shared more or less equally between the two atoms and the bond is said to be non-polar (meaning without direction). There are no stable regions of net negative or positive charge on the surface of the resulting molecule. If the electronegativities of the two bonded atoms are unequal, however, then the electrons will be shared un-equally. On average, there will be more electrons more of the time around the more electronegative atom and fewer around the less electronegative atom. This leads to partially negatively and positively-charged regions to the bonded atoms - the bond has a direction. Charge separation produces an electrical field, known as a dipole. A bond between atoms of differing electronegativities is said to be polar.

In biological systems atoms of O and N will sequester electrons when bonded to atoms of H and C, the O and N become partly negative compared to their H and C bonding partners. Because of the quantum mechanical organization of atoms, these partially negative regions are organized in a non-uniform manner, which we will return to. In contrast, there is no significant polarization of charge in bonds between C and H atoms, and such bonds are termed non-polar. The presence of polar bonds leads to the possibility of electrostatic interactions between molecules. Such interactions are stronger than van der Waals interactions but much weaker than covalent bonds; like covalent bonds they have a directionality to them – the three atoms involved have to be arranged more or less along a straight line. There is no similar geometric constraint on van der Waals intermolecular interactions.

Since the intermolecular forces arising from polarized bonds often involve an H atom interacting with an O or an N atom, these have become known generically (at least in biology) and perhaps unfortunately as hydrogen or H-bonds. Why unfortunate? Because H atoms can take part in covalent bonds, but H-bonds are not covalent bonds, they are very much weaker. It takes much less energy to break an H-bond between molecules or between parts of (generally macro-) molecules that it does to break a covalent bond involving a H atom.


162 Albert Einstein: Why Light is Quantum:


  • Michael W. Klymkowsky (University of Colorado Boulder) and Melanie M. Cooper (Michigan State University) with significant contributions by Emina Begovic & some editorial assistance of Rebecca Klymkowsky.