Samenvatting Molecules of Life, Vakcode: WBBY047-05
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Course
Molecules of Life (WBBY04705)
Institution
Rijksuniversiteit Groningen (RuG)
Book
Organic Chemistry
This summary includes all the information that you need for the course Molecules of Life. The summary is 143 pages long, because it contains a lot of information, but also a lot of describing pictures which means that you can go fast through it. By reading and understanding this summary you don't e...
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
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