Hydrogen bond

The hydrogen bond is also referred to as hydrogen bridge, and, as its name implies, it involves a hydrogen atom. Indeed, this is a particular case of a dipole-dipole interaction (an interaction established between polar molecules) that includes a hydrogen atom, and requires specific conditions to be established.

There are two requirements that have to occur in order to be established a hydrogen bond. Therefore, not all polar molecules having hydrogen atoms have the ability to establish this type of interaction... The first requirement that must be acomplished is the existence of a very electronegative atom in one of the involved molecules. When I say "very electronegative" I 'm referring to one of the 3 most electronegative atoms - oxygen, nitrogen or fluorine. This atom will function as an "acceptor" of hydrogen, due to the fact that it is very electronegative, and thus it will have a very high electron density on it, presenting a partial negative charge. The second condition that needs to occur is the existence of a hydrogen atom covalently bonded to a very electronegative atom. In this case, the latter acts as a "donor" of hydrogen, and the hydrogen will present partial positive charge because it is attached to a very electronegative atom.

So, what happens is an electrostatic attraction between opposite partial charges, settling the hydrogen bridge. In biochemistry, the hydrogen bonds, like the remaining non-covalent forces, are very important. The best known example concerns the interaction between complementary nitrogenous bases in DNA.

And now... despite having already written this in another post , I can not resist telling it again: ;)

Do you know how an electron commits suicide?

It jumps from the hydrogen bridge!

Dipole-dipole interaction

The dipole-dipole interaction, unlike the ionic bond (recently explained here in the blog ... ) involves non ionizable functional groups, ie without total positive or negative charges. It involves regions with partial charges...

It is a type of electrostatic interaction established between polar molecules, or at least between polar regions of biomolecules. As explained on a previous post about the concept of electronegativity, the presence of atoms with different electronegativities in a specific region of a molecule, will lead to inequalities in the distribution of the electronic cloud, which will, in turn, create regions with less electron density (and hence with partial positive charges) and regions with higher electron density (and hence with partial negative charges).

Thus, a region with a partial positive charge tends to interact electrostatically with a region of a partial negative charge, through a dipole-dipole bond.

Ionic bond

The ionic bond, also called salt bridge, it is, perhaps, the easiest non-covalent bond type to understand. As the name implies, it is an interaction that occurs between ions, i.e., between positive and negative charges. In biochemistry, the concept of ion is slightly different, because in a biomolecule (a protein, for example) we can have multiple regions with negative and/or positive charges. For this to happen just it is only necessary the presence of ionizable functional groups...

Therefore, when one biomolecule has a region with a negative charge (a phosphoryl or carboxyl group, for example), it can establish electrostatic interactions with a region of a biomolecule that presents a positive charge (e.g., amine or imidazole functional groups). This electrostatic attraction that occurs between the opposite charges is the ionic bond.

It is a type of interaction that occurs between polar molecules or at least between ionizable polar regions of biomolecules. As examples, we have the case of an interaction between a lysine and a glutamate in the interior of a protein or the interaction between DNA and histones, among many others...

Intermolecular forces and melting/boiling point

One thing that tends to make confusion to my students is the relationship between non-covalent intermolecular forces and the melting/boiling point of a substance. In fact, how one can explain in a molecular point of view, the existence of the liquid and solid states? The answer lies precisely by the existence of intermolecular forces. Both states are characterized by a higher order spatial distribution of the molecules compared to the gaseous state. This order is a consequence of the attractions between the different molecules that make up a substance. Thus, in the liquid state, each molecule establishes various interactions (non-covalent!) with neighboring molecules, and in the solid state the amount of interactions is further increased.

When it is reached the melting/boiling point, which is going on is a transition from a state in which there are more intermolecular forces to one where there are fewer. In other words, what is being done is to provide energy to break the non-covalent forces established between the molecules, by increasing their kinetic energy.

Therefore, the greater the intensity of the non-covalent forces existing between the molecules, the greater the amount of energy required to break these interactions, and thus the higher the melting/boiling point.

I often ask to my students what happens when it is reached the boiling point of a substance, and the answer that I invariably get is: "You are breaking the bonds." The problem comes when I ask what kind of bonds, because usually their tendency is to say the covalent bonds. I, playfully, then tell them that if so, the water in the gaseous state is no longer H₂O, and then they realize that indeed that what it is cleaved are not the covalent bonds but the non-covalent ones.

In short, there is a direct relationship between intermolecular forces and melting/boiling point, and the greater the sum of these forces, the higher the melting/boiling point of a substance.

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Electronegativity

In order to understand the concept of electronegativity, it is necessary to take into account the following idea... The molecules are highly dynamic, and electrons are in constant motion around the atoms, representing the so-called "electron cloud". The movement of electrons around an atoms is directly conditioned by its characteristics. That is, if an atom has a greater ability to take over the electronic cloud, the electrons will be located predominantly on him. Electronegativity concerns exactly with this capability. Therefore, the more electronegative an atom is, the greater the portion of the electron cloud on it. Consequently, the more electronegative atoms tend to have negative partial charges, because at every moment there will be more electrons on them than on other atoms .

It is this asymmetry that is created in the distribution of the electron cloud that causes the molecules to become polar. Thus, in general , the presence of different atoms with different electronegativities in a molecule causes the molecule becomes polar, or at least the region where this happens to become polar .

In the case of biochemistry , since carbon and hydrogen have similar electronegativities, the regions of the molecules that contain only these two atoms are nonpolar , while the presence of oxygen, nitrogen , fluorine , phosphorus , etc., tend to render that region polar .