structure of Organic Molecule Flashcards
understading the Bonding and shape in organic molecules
what does the periodic table show
Number or electrons, neutrons and protons
Mass of a mole of atoms
Group-Available for bonding
Period (shells)
Name/symbol
what does the group in the periodic table tell?
indicates number of electrons in ‘outer shell’
Available for bonding
what’s the trend of the atomic radius in the periodic table
atomic radius generally decreases as you move from left to right across a period (due to increasing nuclear charge) and increases as you move down a group (due to the increasing number of electron shells).
what’s the trend for the non metabolic characteristics in the periodic table
As you move diagonally across the periodic table, non-metallic characteristics increase due to higher electronegativity and smaller atomic size.
what’s the trend in the periodic table for metabolic characteristics
As you move diagonally across the periodic table from bottom left to top right, metabolic characteristics generally decreases due to higher electronegativity, smaller atomic size, and increased tendency to gain electrons, impacting metabolic rates and reactivity.
what’s the trend in the periodic table for Electronegativity, electron affinity, and ionization energy
Electronegativity, electron affinity, and ionization energy generally increase across periods in the periodic table from left to right. This trend occurs due to a greater nuclear charge and decreasing atomic size, resulting in stronger attraction for electrons and a higher energy requirement to remove electrons.
what doe the first ionisation tell?
The amount of energy required to remove an electron from a neutral atom in its gaseous phase(The lower this energy is, the more readily the atom
becomes a cation)
what are 3 factors affecting the ionisation energy
1 -The charge on the nucleus
2 -The distance of the electron from the nucleus
3 -The number of electrons between the outer electrons and the nucleus
why does The number of electrons between the outer electrons and
the nucleus affect the ionisation energy
The inner electrons shells shield the outer electrons shells and
reduce the effect of the nuclear “pull” on those outer electrons.
The shielding provided by the inner electrons means it will take
less energy to free outer electrons from their orbitals
Ionization energy of an outer electron is reduced by the effects of
shielding.
This lessening of the pull of the nucleus by inner electrons is
known as screening or shielding.
Describes why the electron affinity decreases down a group of elements
Generally decreases down a group of elements
Each atom is larger than the atom above it
An added electron is further away from the atom’s
nucleus compared to its position in the smaller atom
With a larger distance between the negatively-charged
electron and the positively-charged nucleus, the force of
attraction is relatively weaker
Describes why the electron affinity increases when it moves from left to right across the period
Moving from left to right across a period
Atoms become smaller as the forces of attraction
become stronger.
This causes the electron to move closer to the
nucleus, thus increasing the electron affinity from left
to right across a period.
describe what is electron affinity
the ability of an atom to accept an electron
describe what is electronegativity
Measures an atom’s strength to attract and form bonds with
electrons
describe why as you move to the right across a period of elements,
electronegativity increases
When the valence shell of an atom is less than half full, it requires
less energy to lose an electron than gain one and thus, it is easier to
lose an electron.
Conversely, when the valence shell is more than half full, it is easier
to pull an electron into the valence shell than to donate one
explain why the electronegativity decreases down the group
this is because there is an increased distance between the valence
electrons and nucleus
what is the most electronegative element ?
fluorine
when are ionic bond formed?
onic bonds are formed when the electronegativity
difference between the atoms is > 1.7
when are covalent bonds, formed?
Covalent bonds are formed when the electronegativity
difference between the atoms is < 1.7
what does an ionic bond do?
transfer electron(s)
what does a covalent bond do?
share electrons
are electrons shared equally in covalent bonds?
Unless difference = 0, there is unequal sharing of the
electrons
when are polar covalent bond made?
PCBs are formed when the electronegativity difference between the atoms is between 0.4 and around 1.7
Non-polar covalent bonds - difference is less than 0.4
What makes a compound polar?
Bond polarity-Must contain polar bonds (dipole)
Symmetry -Molecule must not be symmetrical (needs to have overall dipole)
except Water- is polar
CO2 is non polar
why is polarity a desirible propertie in drugs?
1-More likely to be dissolved, required for gut absorption
2-Stay dissolved once administered intravenously
what do phospholipids, contain?
Hydrophilic head- Polar head group
Hydrophobic tail- Mainly chains of C and H
Form important molecules (Cell membranes)
what is a dative covalent bond
An atom donates two electrons to form a new bond
what’s a dipole?
A pair of equal and oppositely charged or magnetized poles
separated by a distance
what are Dipole-dipole interactions?
Electrostatic interactions
Permanent dipole (molecule with polarised bond)-Attracted to other molecules with permanent dipoles
what is hydrogen bond?
Weak bonds
But stronger than D-D and VdW
Formed between Electron rich atoms (like N, O and F)
In water this is contributes to the high boiling point
can form lattices
what are vander waals forces
can also be called London dispersion forces
These are weak interactions between molecules
Temporary dipoles
Where the electrons are unevenly distributed
Leads to polarization of neighbouring molecules
what is intramolecular? and examples
exist or takes place within a molecule
ionic
covalent
metallic
what is intermolecular?examples
existing or taking place between molecules
(nonbonding)
ion-dipole
Hbond
Dipole-dipole
ion-induced dipole
dipole induced dipole
Dispersion (London)
what can electrons be describe as?
(Electrons are not discrete particles)
Can be described as both particles or waves
Impossible to locate precise position of an electron
Possible to indicate a region where the electron is most
likely to be found
This region is called an Orbital
what drug interaction (with proteins) are driven by bonding?
Weak interactions like H-bonding
Other polar and hydrophobic interactions
AND shape
what is orbital hybridisation and what does it do?
Atoms hybridise or ‘mix’ their atomic orbitals
-Optimise the geometry
-Minimise the energy
what can hybrid orbital contain?
Hybrid orbitals may contain bonding
or non-bonding pairs of electrons
what does the wedge and hash symbolise
Wedge – pointing towards you
Hash – pointing out to the back
what affects bond length
Depend on the bonding situation
Bond length decreases as π character increases
what affects the bond angles
Depends on…
types of atom
Bonds and lone pairs
hybridisation
different spatial arrangements of the same molecule that can rotate along single bonds.(double and triple bonds can’t rotate)thermal energy is used to rotate
what is The VSEPR ?
The VSEPR (Valence Shell Electron Pair Repulsion) theory in chemistry explains molecular geometry based on the idea that electron pairs around a central atom repel each other and therefore arrange themselves to minimize repulsion. It predicts molecular shapes by considering the number of electron pairs (bonding and non-bonding) around the central atom and arranging them to be as far apart as possible, leading to specific geometries such as linear, trigonal planar, tetrahedral, trigonal bipyramidal, and octahedral, among others.
although conformers cannot be separated as separate structure, what is the energy difference between the structures?
30 kJmol –1
