MOLECULES OF LIFE // LECTURE 1 // CH. 1 & 8.1 – 8.5
// ELECTRONIC STRUCTURE AND BONDING,
DELOCALIZATION
Organic molecule = molecule with C in it
➢ Learning goals for lectures 1 & 2
➢ The structure of an atom
Atoms are neutral → Number of protons equals the number of electrons
➢ The periodic table
→ Atomic number = number of protons
→ The number of neutrons can be different, but not the number of protons because that’s
fixed
➢ Electrons are distributed in shells around the core
,→ Hydrogen has 1 proton in the middle and as it has one electron it can all fit in the shell
and would be where the red dot is
→ Carbon has 6 protons, so also 6 electrons → 2 would fall in the first shell and the rest (4)
will go in the second shell
→ Louis said: Electrons are not only particles but they also have wave-like properties → This
complicates matters
➢ Shells contain subshells (Louis)
Subshells = atomic orbitals
→ Every atomic orbital can fit 2 electrons
→ So the atomic orbital in the first shell would be an S orbital and the number of atomic
orbitals is 1 with a maximum of 2 electrons
→ The second shell we will find an S orbital, but the second one is called P orbitals and we
find a total of 1 S orbital and 3 of the P orbitals and there would be 2 electrons for the S
orbitals and 6 for the P orbitals, giving us a total of 8
→ The third shell has S, P and D and we have 1, 3 and 5 number of atomic orbitals which
means that we have 2 plus 6 plus 10 = 18 maximum number of electrons
→ We mainly going to focus on valence electrons
➢ Ground-state electron configuration
3 rules of how these subshells are built up:
1. Aufbau principle → An electron goes into the atomic orbital with the lowest energy.
2. Pauli exclusion principle→ No more than two electrons can be in an atomic orbital.
3. Hund’s rule→ An electron goes into an empty degenerate orbital rather than pairing up.
→ The only thing that differentiates these shells is their energy levels
→ So the 1 S has the lowest energy, because it’s the most inner → So the more inner they
are, the more stable and the more closer they are to the positive charge of the protons
→ After the 1 S comes the 2 S, but now the 2 P orbitals is degenerative → So there are free
2 P orbitals that all have the same energy
→ Electrons always go to the lowest energy level they can go → Aufbau principle
→ Carbon has 6 electrons → So the first electron goes in to the lowest shell and we know
that a sub shell can only held 2 electrons → The 2nd electron will also go in to this shell →
Pauli exclusion principle → So now the inner shell (the 2 s atom orbital) is full → So the next
electron needs to go in to the 2 S shell and as the 2 S is lower in energy than the 2 P, the 4 th
electron needs also to go in the 2 S shell → Now we’re left with 2 electrons which we need
to fill → So the first one goes in one these 2 P orbitals → Hund’s rule comes in to effect →
So these 2 P orbitals have all the same energy and it’s preferently that you populate each of
them first with one than rather with 2 in there
,→ We can do this for a whole bunch of elements
→ One ‘streepje’ stands for one electron
→ It doesn’t matter with the 2p shells where you draw the second arrow (by oxygen for
example) → It’s just human nature to put it in to the 2p,x because it’s closer to the other
ones
➢ The octet rule
The octet rule = losing and gaining electrons
→ It turns out that atoms by themselves are not very stable
→ The atoms in the 8th period are stable and basically don’t react with anything because
they have a closed shell → Helium has a closed shell with 2 electrons etc. → So it turns out
that many atoms like to follow the octet rule
→ Octet rule = atoms are most stable when their outmost shell is filled
→ Sodium (Na) has 1 electron in its outer shell and it can get rid of this electron → When it
gets rid of this negative charge it becomes positive and it will be much happier because it’s
now more stable
→ F has 7 electrons and is only 1 electron away from having a complete octet and would
look like neon → So if you get 1 electron to it, it will become fully enclosed and happy
→ So hydrogen can do 2 things → It can lose an electron, which will make it a proton
(important for acids and bases) , but it can also gain an electron, which makes it a hydride
ion because it’s now charged
→ This is how atoms form molecules
➢ Ionic interactions
NaCl crystals form through ionic interactions
→ Electrostatic potential map shows you whether an atom is negative or positive
→ These little balls with are hold together with these bonds is a crystal and you can see that
some of them are rather positive (the smaller sodium ions) and some are rather negative
(the larger chloride ions) → If they come together they will satisfy each other need to
become an octet → Ionic bond / interaction
→ This is the basis for inorganic chemistry
, ➢ Covalent bonds
Sharing electrons results in covalent bonds
→ Another way of become an octet
→ We have hydrogen on one side (which has 1 electron) and hydrogen on the other side
(with also 1 electron) → So in order to form a bond, they can share these electrons → This
is what we call a covalent bond → So the H – H symbolizes that the electrons are shared and
that each bond contains 2 electrons
→ Hydrogen can come together with chlorine because chlorine needs 1 electron to fill its
shell and complete the octet rule → So they can share their electrons and form a compound
H – Cl
→ Oxygen has 2 electrons which needs a partner → So we take 2 hydrogen atoms and we
form a simple molecule and we and up with H2O
➢ Polar and apolar covalent bonds
Electronegativity = the need to attract or give away electrons
→ The higher the electronegative, the easier it is to get a complete octet by taking an
electron
→ The electronegativity in the right and to the up
→ Polar means dissolve in water
→ Apolar bonds means that there is no polarity in the bond and there’s no/small difference
in electronegative between the atoms
→ Polar bonds exist because the difference in electronegativity is much higher
→ So the Cl in H – Cl is really pulling them in the right direction because it has more
electronegativity → So you get a partial positive and partial negative charge → Partial
charges are not complete charges, but we use them as a delta – which indicates that Cl has
more electrons that the H so the H must become partial positive charged (delta +)
→ Continuum of bonds
- If we go in the direction of electronegativity and the difference is more than 2.0 (like
with Li and F), we will call it an ionic bond
- If the difference is smaller than 0.5 it’s an Apolar bond
- Everything in between is a polar bond
,→ Greater dipole moment = more polar
→ So Lithium has a greater electronegativity → So it prefers to be positive → While the big
red boll is the hydrogen and is clearly negative and has a negative charge
→ The arrow indicates where the negative charge ends up
→ H – H is neutral because they both share happily their electrons
→ By H – F all the electrons are dragged to F which makes F partially negative and H partially
positive
➢ How many bonds and lone pairs for atoms?
→ If something has 1 electron, it can form 1 bond
→ Carbon has 4 valence electrons, so can form 4 bonds
→ Nitrogen has 5 valence electrons, but can’t form 5 bonds because we encounter anything
that can form more than 4 bonds → So 2 of these 5 electrons form an electron pair and we
call this a lone pair → This lone pair is already happy so it doesn’t need to share its electrons,
but the other 3 electrons want to form a bond → So that’s why N forms 3 bonds while
having 1 lone pair
→ Oxygen forms 2 bonds because the other 2 electrons all tied up in lone pairs
→ F, Br, Cl, I have 7 valance electrons and form 1 bond and the other 6 electrons are in lone
pairs
➢ Carbon forms 4 bonds (most of the times)
→ This C has only 3 bonds which means that it has a formal charge
→ Positive species are referred to as cat-ions and negative species are referred as an-ions
→ When the formal charge is 0 it’s an uncharged species which has a single electron and
that is called a radical → Radicals are reactive species because they have 1 unpaired
electrons and they want to make this a paired electron
, ➢ Nitrogen forms 3 bonds (most of the times)
➢ Oxygen forms 2 bonds (most of the times)
→ The positive charge is formally on the Oxygen, but if you look at the electrostatic
potential map, blue represents positive charge and positive charge everywhere but on the
oxygen
➢ Halogens and hydrogen form 1 bond
→ H has 1 electron so if there’s no electron left, it gets a positive charge
➢ Drawing molecules – Lewis structures
- 2nd → There’s a positive charge on the N because if you do the calculation you count
5 lone pairs but only 4 bonds and no free lone pair → So it gets a positive charge
- 3rd → Between the C and O there are 4 electrons → That means that in this case you
adjust a double bond between these
1. 4 for C and 1 for H and 6 for O → That gives a total of 14 electrons
4. No charge
// ELECTRONIC STRUCTURE AND BONDING,
DELOCALIZATION
Organic molecule = molecule with C in it
➢ Learning goals for lectures 1 & 2
➢ The structure of an atom
Atoms are neutral → Number of protons equals the number of electrons
➢ The periodic table
→ Atomic number = number of protons
→ The number of neutrons can be different, but not the number of protons because that’s
fixed
➢ Electrons are distributed in shells around the core
,→ Hydrogen has 1 proton in the middle and as it has one electron it can all fit in the shell
and would be where the red dot is
→ Carbon has 6 protons, so also 6 electrons → 2 would fall in the first shell and the rest (4)
will go in the second shell
→ Louis said: Electrons are not only particles but they also have wave-like properties → This
complicates matters
➢ Shells contain subshells (Louis)
Subshells = atomic orbitals
→ Every atomic orbital can fit 2 electrons
→ So the atomic orbital in the first shell would be an S orbital and the number of atomic
orbitals is 1 with a maximum of 2 electrons
→ The second shell we will find an S orbital, but the second one is called P orbitals and we
find a total of 1 S orbital and 3 of the P orbitals and there would be 2 electrons for the S
orbitals and 6 for the P orbitals, giving us a total of 8
→ The third shell has S, P and D and we have 1, 3 and 5 number of atomic orbitals which
means that we have 2 plus 6 plus 10 = 18 maximum number of electrons
→ We mainly going to focus on valence electrons
➢ Ground-state electron configuration
3 rules of how these subshells are built up:
1. Aufbau principle → An electron goes into the atomic orbital with the lowest energy.
2. Pauli exclusion principle→ No more than two electrons can be in an atomic orbital.
3. Hund’s rule→ An electron goes into an empty degenerate orbital rather than pairing up.
→ The only thing that differentiates these shells is their energy levels
→ So the 1 S has the lowest energy, because it’s the most inner → So the more inner they
are, the more stable and the more closer they are to the positive charge of the protons
→ After the 1 S comes the 2 S, but now the 2 P orbitals is degenerative → So there are free
2 P orbitals that all have the same energy
→ Electrons always go to the lowest energy level they can go → Aufbau principle
→ Carbon has 6 electrons → So the first electron goes in to the lowest shell and we know
that a sub shell can only held 2 electrons → The 2nd electron will also go in to this shell →
Pauli exclusion principle → So now the inner shell (the 2 s atom orbital) is full → So the next
electron needs to go in to the 2 S shell and as the 2 S is lower in energy than the 2 P, the 4 th
electron needs also to go in the 2 S shell → Now we’re left with 2 electrons which we need
to fill → So the first one goes in one these 2 P orbitals → Hund’s rule comes in to effect →
So these 2 P orbitals have all the same energy and it’s preferently that you populate each of
them first with one than rather with 2 in there
,→ We can do this for a whole bunch of elements
→ One ‘streepje’ stands for one electron
→ It doesn’t matter with the 2p shells where you draw the second arrow (by oxygen for
example) → It’s just human nature to put it in to the 2p,x because it’s closer to the other
ones
➢ The octet rule
The octet rule = losing and gaining electrons
→ It turns out that atoms by themselves are not very stable
→ The atoms in the 8th period are stable and basically don’t react with anything because
they have a closed shell → Helium has a closed shell with 2 electrons etc. → So it turns out
that many atoms like to follow the octet rule
→ Octet rule = atoms are most stable when their outmost shell is filled
→ Sodium (Na) has 1 electron in its outer shell and it can get rid of this electron → When it
gets rid of this negative charge it becomes positive and it will be much happier because it’s
now more stable
→ F has 7 electrons and is only 1 electron away from having a complete octet and would
look like neon → So if you get 1 electron to it, it will become fully enclosed and happy
→ So hydrogen can do 2 things → It can lose an electron, which will make it a proton
(important for acids and bases) , but it can also gain an electron, which makes it a hydride
ion because it’s now charged
→ This is how atoms form molecules
➢ Ionic interactions
NaCl crystals form through ionic interactions
→ Electrostatic potential map shows you whether an atom is negative or positive
→ These little balls with are hold together with these bonds is a crystal and you can see that
some of them are rather positive (the smaller sodium ions) and some are rather negative
(the larger chloride ions) → If they come together they will satisfy each other need to
become an octet → Ionic bond / interaction
→ This is the basis for inorganic chemistry
, ➢ Covalent bonds
Sharing electrons results in covalent bonds
→ Another way of become an octet
→ We have hydrogen on one side (which has 1 electron) and hydrogen on the other side
(with also 1 electron) → So in order to form a bond, they can share these electrons → This
is what we call a covalent bond → So the H – H symbolizes that the electrons are shared and
that each bond contains 2 electrons
→ Hydrogen can come together with chlorine because chlorine needs 1 electron to fill its
shell and complete the octet rule → So they can share their electrons and form a compound
H – Cl
→ Oxygen has 2 electrons which needs a partner → So we take 2 hydrogen atoms and we
form a simple molecule and we and up with H2O
➢ Polar and apolar covalent bonds
Electronegativity = the need to attract or give away electrons
→ The higher the electronegative, the easier it is to get a complete octet by taking an
electron
→ The electronegativity in the right and to the up
→ Polar means dissolve in water
→ Apolar bonds means that there is no polarity in the bond and there’s no/small difference
in electronegative between the atoms
→ Polar bonds exist because the difference in electronegativity is much higher
→ So the Cl in H – Cl is really pulling them in the right direction because it has more
electronegativity → So you get a partial positive and partial negative charge → Partial
charges are not complete charges, but we use them as a delta – which indicates that Cl has
more electrons that the H so the H must become partial positive charged (delta +)
→ Continuum of bonds
- If we go in the direction of electronegativity and the difference is more than 2.0 (like
with Li and F), we will call it an ionic bond
- If the difference is smaller than 0.5 it’s an Apolar bond
- Everything in between is a polar bond
,→ Greater dipole moment = more polar
→ So Lithium has a greater electronegativity → So it prefers to be positive → While the big
red boll is the hydrogen and is clearly negative and has a negative charge
→ The arrow indicates where the negative charge ends up
→ H – H is neutral because they both share happily their electrons
→ By H – F all the electrons are dragged to F which makes F partially negative and H partially
positive
➢ How many bonds and lone pairs for atoms?
→ If something has 1 electron, it can form 1 bond
→ Carbon has 4 valence electrons, so can form 4 bonds
→ Nitrogen has 5 valence electrons, but can’t form 5 bonds because we encounter anything
that can form more than 4 bonds → So 2 of these 5 electrons form an electron pair and we
call this a lone pair → This lone pair is already happy so it doesn’t need to share its electrons,
but the other 3 electrons want to form a bond → So that’s why N forms 3 bonds while
having 1 lone pair
→ Oxygen forms 2 bonds because the other 2 electrons all tied up in lone pairs
→ F, Br, Cl, I have 7 valance electrons and form 1 bond and the other 6 electrons are in lone
pairs
➢ Carbon forms 4 bonds (most of the times)
→ This C has only 3 bonds which means that it has a formal charge
→ Positive species are referred to as cat-ions and negative species are referred as an-ions
→ When the formal charge is 0 it’s an uncharged species which has a single electron and
that is called a radical → Radicals are reactive species because they have 1 unpaired
electrons and they want to make this a paired electron
, ➢ Nitrogen forms 3 bonds (most of the times)
➢ Oxygen forms 2 bonds (most of the times)
→ The positive charge is formally on the Oxygen, but if you look at the electrostatic
potential map, blue represents positive charge and positive charge everywhere but on the
oxygen
➢ Halogens and hydrogen form 1 bond
→ H has 1 electron so if there’s no electron left, it gets a positive charge
➢ Drawing molecules – Lewis structures
- 2nd → There’s a positive charge on the N because if you do the calculation you count
5 lone pairs but only 4 bonds and no free lone pair → So it gets a positive charge
- 3rd → Between the C and O there are 4 electrons → That means that in this case you
adjust a double bond between these
1. 4 for C and 1 for H and 6 for O → That gives a total of 14 electrons
4. No charge
