Molecules of life 2021
Lecture 1
Life is because of molecules. Biology cell biology biochemistry (nucleic acids
(DNA/RNA), peptides/proteins).
Molecules are the building blocks of life. Biochemistry under the loop: nucleobases, amino
acids, sugars and morphine.
An inorganic compound (salts or minerals) can become organic when treated with heat.
Understanding organic molecules is important: lidocaine = local anesthetic, diclofenac = pain
medication, B4PyMPM = OLED screens.
The structure of an atom: nucleus (protons (+ charged) + neutrons (neutral)) + an electric
cloud (negative). Neutral atoms: #protons = #electrons. Electrons make up most of the
volume important for molecule formation.
A closer look at the periodic table: periods and
downwards are the groups.
Isotopes: same number of protons but different
number of neutrons.
Niels Bohr stated that protons and neutrons are
depicted in the center, and electrons fly around it.
1st shell 2é, 2nd shell 8é, 3rd shell 18é, 4th shell 32é
Electrons are distributed in shells around the core. Shells contain subshells: atomic orbitals.
Relative energy of atomic orbitals: 1s < 2s < 2p < 3s < 3p < 3d.
Core electrons are electrons in the inner shell(s). Valence electrons are electrons in the
outmost shell.
, Ground-state electron configuration: 3 rules
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
Losing and gaining electrons: the octet rule. Noble gases do not react under normal
circumstances (group from helium). This has to do with the octet rule: atom is most stable if
the outer shell is filled or empty.
NaCl crystals form through ionic interactions.
Sharing electrons results in covalent bonds. You have polar and apolar
covalent bonds. Greater dipole moment = more polar. The
electronegativity increases when you go up and to the right in the periodic
table.
When deltaE = bigger dan 2 ionic
When deltaE = between 0.5 and 2 polar bond
When deltaE = lower than 0.5 apolar bond
How many bonds and lone pairs for atoms?
Carbon forms 4 bonds (most of the times).
Nitrogen forms 3 bonds (most of the times) with one lone pair
Oxygen forms 2 bons (most of the times) with 2 lone pairs
Halogens and hydrogen form 1 bond with 3 lone pairs
Formals charge = # of valence electrons – (# lone pair electrons + # of bonds)
Drawing a molecule from its chemical formula:
1. Determine the total number of valence electrons (when there is a formal charge, the
negative should be added, when it is positive moet je m aftrekken)
2. Distribute the atoms
3. Form bonds and fill octets with lone pairs
4. Check for formal charges
Lecture 1
Life is because of molecules. Biology cell biology biochemistry (nucleic acids
(DNA/RNA), peptides/proteins).
Molecules are the building blocks of life. Biochemistry under the loop: nucleobases, amino
acids, sugars and morphine.
An inorganic compound (salts or minerals) can become organic when treated with heat.
Understanding organic molecules is important: lidocaine = local anesthetic, diclofenac = pain
medication, B4PyMPM = OLED screens.
The structure of an atom: nucleus (protons (+ charged) + neutrons (neutral)) + an electric
cloud (negative). Neutral atoms: #protons = #electrons. Electrons make up most of the
volume important for molecule formation.
A closer look at the periodic table: periods and
downwards are the groups.
Isotopes: same number of protons but different
number of neutrons.
Niels Bohr stated that protons and neutrons are
depicted in the center, and electrons fly around it.
1st shell 2é, 2nd shell 8é, 3rd shell 18é, 4th shell 32é
Electrons are distributed in shells around the core. Shells contain subshells: atomic orbitals.
Relative energy of atomic orbitals: 1s < 2s < 2p < 3s < 3p < 3d.
Core electrons are electrons in the inner shell(s). Valence electrons are electrons in the
outmost shell.
, Ground-state electron configuration: 3 rules
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
Losing and gaining electrons: the octet rule. Noble gases do not react under normal
circumstances (group from helium). This has to do with the octet rule: atom is most stable if
the outer shell is filled or empty.
NaCl crystals form through ionic interactions.
Sharing electrons results in covalent bonds. You have polar and apolar
covalent bonds. Greater dipole moment = more polar. The
electronegativity increases when you go up and to the right in the periodic
table.
When deltaE = bigger dan 2 ionic
When deltaE = between 0.5 and 2 polar bond
When deltaE = lower than 0.5 apolar bond
How many bonds and lone pairs for atoms?
Carbon forms 4 bonds (most of the times).
Nitrogen forms 3 bonds (most of the times) with one lone pair
Oxygen forms 2 bons (most of the times) with 2 lone pairs
Halogens and hydrogen form 1 bond with 3 lone pairs
Formals charge = # of valence electrons – (# lone pair electrons + # of bonds)
Drawing a molecule from its chemical formula:
1. Determine the total number of valence electrons (when there is a formal charge, the
negative should be added, when it is positive moet je m aftrekken)
2. Distribute the atoms
3. Form bonds and fill octets with lone pairs
4. Check for formal charges
