Molecular Bonds

What is a covalent bond?

Protons and neutrons form the nucleus, whilst the electrons occuyp different orbitals around the nucleus. In a shell with several orbitals, the elctrons first fill each orbital, but they prefer to form pairs. A free electron can form a pair with another free electron from a second atom, creating a covalent bond. 

In some atoms, the number of covalent bonds is determined by the number of covalent bonds. For instance, carbon will always make four covalent bonds as they have four free electrons, while oxygen make two as they only have two single electrons.

Atoms can form both single and double bonds. Double bonds allow to make the same amount of covalent bonds with less then four atoms, making them more stable than single bonds. The structure will also vary.  

What is an asymmetric atom? What does charility mean?

An asymmetric atom is defined as an atom within a molecule that contains four different atoms / groups of atoms bonded to it. For instance, an asymmetric carbon atom is a carbon atom bound to f our different atom. Molecules with asymmetric atoms can exist as two different, mirror-image, forms, creating what we call chirality. The two forms are called stereoisomers. 

The different stereoisomers have the same chemical composition, but they are mirrored eachother. They are isolated molecules where the atomic connection is identical, but the placement of the atoms may vary. This can lead to consequences, for example, in the 1950s and 60s, thaliodomide was used to alleviate morning sickness. During the same time period many babies were born with limb malformations. It turned out that the S-stereoisomer is a teratogenic agent, causing abnormalities in fetuses.

How can covalent bonds affect the property of the larger molecule?

There are two main ways that covalent bonds can affect the property of the larger molecule: either being polar or non-polar. This is determined by electronnegativity. If the electronnegativity is similar, the bond is nonpolar, if not, the bond between them is polar and thus an electric dipole.

An example of this is H₂O. Water molecules occur in a V-shape, and has a partial negative charge at the oxygen end and partial positives at the hydrogen atoms. Due to the V-shape of the molecule, the partial charges create an electric dipole. If they were linear, the charges would cancel themselves out, thus not being a dipole.

What are non-covalent interactions?

Non-covalent interactions do not involve shared electrons. They are less stable than covalent bonds, which means it required less energy to disrupt them. In macromolecules, non-covalent interactions are used to stabilize the 3D-structure. Interactions between macromolecules involve many non-covalent bonds.

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Non-covalent interactions are very important, as there is strenght in numbers! They lay the groundwork for molecular complementarity, which determines the 3D structure of macromolecules and the binding between them.

What are ionic (electrostatic) interactions?

Electrons can be tranferred from one atom to another. Gaining or losing electrons change atom into ions. Cations are positively charged ions that lack electrons, while anions are negativily charged and have an excess of electrons.

Cations and anions interact by ionic interactions. In solid from, cations and anions can be arranged in specific patterns and form crystals. These vary in size and complexity.

Water dipoles are very effective at dissolving these crystals, by forming cages around them.

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What are hydrogen bonds?

Hydrogen atoms have a partially positive charge, that allows them to interact with electrons from another atom. The hydrogen atom is partially positively charged when it’s bonded to an atom with a higher electronnegativity. Hydrogen bonds are often used in nucleic acids.

What are Van der Waals interactions?

Electrons are constantly moving, which creates a transient difference in charge. Such transient dipoles cause Van der Waals interactions! Transient dipoles and van der Waals interactions occur both in polar and non-polar molecules. They are very weak, and can only act at very short distances.

What are hydrophobic interactions?

Nonpolar molecules are hydrophobic. This means that water molecules do not form bonds with the nonpolar molecules, but instead form “cages” around them. Merging these cages require less water molecules, making it more energetically favourable. This is called the hydrophobic effect. It’s rather a way to repel the water molecules in between them instead of being attracted to each other.

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Hydrophobic interactions are different from the other non-covalent interactions, as it relies on their properties instead of difference in charge (dipole properties and ions).

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