Lecture 4 - Covalent and non-covalent bonding Flashcards
Atoms want complete….
outer valence shells
Hydrogen has one electron in it’s outer valence shell. It will either…
- lose it and become a proton
- share the electron to form a covalent bond
Atoms with nearly empty or complete shells tend to…
ionise easily to form salts.
Give an example of a salt and why/how it forms.
NaCl
- Chlorine has seven outer valence electrons. It will gain one electron to get a full shell.
- Sodium has one electron in its outer valence shell. It wants to lose the electron.
- Sodium and chlorine form a salt in this way.
Basic definition of covalent bond
the electrostatic attraction between positively charged nuclei of the bonding atoms and the shared pair of negatively charged electrons.
Explain covalent bonding in hydrogen.
Both hydrogen atoms have an unpaired electron in the 1s orbital. When the two atoms get close together the two 1s orbitals overlap and merge into a single bond orbital that contains both electrons.
Two important points about covalent bonding
Electrons must have opposite spins and each electron is able to exist in any part of the bond orbital and so belongs to both atomic nuclei.
Explain why the formation of a bond is accompanied by excess energy release and therefore what bond dissociation energy is
The molecule formed is at a lower energy than two atoms on their own. Therefore, the formation of a bond is accompanied by excess energy being released. To break the bond, the energy must be put back in- this is the bond dissociation energy (a measure of how strong the bond is)
How does orbital overlap effect strength of bond?
greater overlap of orbitals= stronger bond
What is a sigma bond?
- single bond
- strongest type of covalent bond
- orbitals overlap head on.
Give an example of S-S sigma bonds and the shape you would get.
- The simplest example is in dihydrogen. Two 1s atomic orbitals- one from each hydrogen atom will overlap to form a sigma bond. A single bond.
- The new molecular orbital in H2 (sigma s-s) has a shape that you would get from merging two s orbitals- sausage shaped
see notes
Sigma bonds can also form with an s and a p orbital. Draw this. Explain the shape of the sigma s-p orbital formed. What is the smaller lobe involved in?
The new molecular orbital formed has two lobes- one is much larger than the other. The smaller lobe is involved in substitution reactions.
Sigma bonds can also form with an s and an sp orbital. Draw this and describe the shape of the new sigma s-sp hybrid molecular orbital formed. What is the smaller lobe used for?
The new molecular orbital- sigma s-sp hybrid has two lobes. One lobe is bigger than the other. The smaller lobe is involved in substitution reactions.
What is a Pi bond?
- Covalent bonds formed from the sideways overlap of two p orbital lobes on one atom with two p orbital lobes on another
The node between the lobes in a p orbital have no electron density. What is the effect of this?
In a pi bond when the two p orbitals overlap there is a plane between the molecular orbitals with no electron density.
Pi bonds form with an existing sigma bond. What is the result of this?
double/triple bond is formed
Why is a Pi bond weaker than a sigma bond?
There is less of an overlap between p orbitals in a pi bond because of their parallel orientation, in contrast to sigma bonds where the bond is formed by the head on overlap of orbitals.
Lone pairs of electrons affect the shape of molecules. Explain this concept using ammonia an example (refer to hybridization)
- For nitrogen to form ammonia it is hybridized. Creates four sp3 hybrid orbitals. Three of the orbitals are filled with paired electrons. The fourth is home to two unpaired electrons- a lone pair of electrons. The lone pair behaves like a bond. The ammonia molecule adopts a tetrahedral shape- one arm is occupied by the lone pair. The result of this is a molecule shaped like a pyramid. The lone pair has a stronger repulsion than the sigma bonds which compresses the bond angle to 107. Reduces the bond angle by 2.5
What is a hydrogen bond?
A hydrogen bond is a partially electrostatic attraction between a hydrogen which is bonded to a more electronegative atom (hydrogen bond donor) and another atom with a lone pair of electrons (hydrogen bond acceptor)
What does the strength of the hydrogen bond depend upon?
the environments and geometries of the donor and acceptor atoms.
Hydrogen bonds do have some covalent nature. Explain
- they have direction
- bond distances are shorter than would be expected of van der waals.
In hydrogen bonds, the more electronegative the donor….
the more covalent the nature of the bond.
Hydrogen bonds increase…
- melting points
- boiling points
- solubility
- viscosity
What is the hydrogen bond donator?
The atom covalently bonded to hydrogen
What is the hydrogen bond acceptor?
Electronegative atom with lone pair of electrons not covalently bonded to hydrogen
- where are the hydrogen bond donors in this molecule?
- where are the hydrogen bond acceptors?
- Why are some of the nitrogen NOT hydrogen bond acceptors?
- N-H bond - bond donors
- oxygen, fluorine are hydrogen bond acceptors.
- The nitrogen are not H bond acceptors because the their lone pair is not available due to the mesomeric effect.
Why is solid ice less dense than liquid water?
The network of hydrogen bonds in ice keep the water molecules apart. Makes it less dense.
What are Van der Waals forces?
Really weak forces found between gaseous molecules and almost all liquids and solids. The forces attract neutral molecules together.
Three ways Van der Waals forces arise….
- permanent dipole-dipole interactions
- molecules with a permanent dipole can distort the electric charge/induce a dipole in a nearby molecule. These will then attract.
- London forces/dispersion forces- electrons move around atoms randomly. At any given time there may be more electrons on one side of the atom than the other. This leads to an instantaneous dipole. The instantaneous dipole can induce polarization in adjacent molecules.
Hydrophobic interactions refers to…
segregation of water and non-polar substances.
What is an amphiphile?
both hydrophobic and hydrophilic domains. E.g. detergents.
How does a micelle form?
- Amphiphilic molecules form micelles in water.
- They arrange in such a way that the hydrophilic head unit is found on the outside and the hydrophobic tails face inside.
Proteins will contain amino acids with hydrophobic elements. What is the effect of this?
- Proteins will contain amino aids with hydrophobic elements. As a result when proteins fold into 3D shapes it is common to have a hydrophobic core composed of these amino acids.
- Charged and polar amino acids that can interact with water molecules are found on the outside. Hydrophobic side chains will face inside. This effects folding.
Primary structure of a protein
Polypeptide chain made up of amino acids held together by covalent peptide bonds.
Secondary structure of protein
Alpha helix and beta pleated sheet. Formed as a result of patterns of hydrogen bonds between polypeptide chain.
Tertiary structure of protein
3D shape of the molecule. Alpha helix and beta sheet are folded. Mainly due to hydrophobic interactions but also as a result of ionic, hydrogen bonding and disulphide bridges
Quaternary structure of protein
two or more polypeptide chains assembled to form one unit.
Beta pleated sheet
- Hydrogen bonds form between partially negatively charged oxygen atoms in the carboxyl group (hydrogen bond acceptor) and partially positively charged hydrogen in the amine group (hydrogen bond donors)
- The result= beta pleated sheet.
Alpha helix
The partially negatively charged oxygen atom in the carboxyl group forms a hydrogen bond with the hydrogen atom bonded to the nitrogen in the amine group four residue along the polypeptide chain. The result is an alpha helix
