Week 4 (Molecules-molecular orbitals. Symmetry and isomerism) Flashcards
Problems with the Lewis model
(paramagnetism)
The Lewis model for covalent bonding was a brilliant but
flawed model.
e.g. it could not account for the magnetism of O2
Paramagnetism, weak attraction of a substance to an external magnetic field, caused by presence of a unpaired electrons in the substance.
In the Lewis model all electrons are paired, yet O2 is magnetic, a property that implies the presence of unpaired
electrons.
A more sophisticated model is therefore needed to explain these properties.
.
Molecular orbital theory
We combine atomic orbitals (AOs) of elements in a molecule to create
molecular orbitals (MOs)
Then fill, Molecular Orbital diagram with electrons like we would fill an Atomic Orbital
diagram using Hund’s first rule and the Pauli exclusion principle
Nuclei of given molecule placed at equilibrium distance and electrons added.
Linear Combinations of Atomic Orbitals (LCAO)
(wavefunctions)
Wave-particle duality-
particles, e.g electrons, can be treated as waves. For electrons these called wavefunctions.
Waves can be added together, provide constructive
interference (bigger wave), destructive interference (smaller wave).
By combining the Atomic Orbital
wavefunctions of two or more interacting
atoms we can make Molecular Orbitals
either constructively or destructively
Linear Combinations of Atomic Orbitals (LCAO)
The simplest approximation to MOs is to consider them to result from…
simple linear combinations of AOs.
Form MO by adding (constructive interference) or subtracting the appropriate atomic orbitals.
Isomerism Definition:
What are the types
existence of molecules have same
no. of same kinds of atoms (and hence the same formula) but differ in chemical and physical properties
- structural isomers (constitutional isomers)
- stereoisomers
Structural isomers defintion
(3 types)
Structural isomers have same molecular formula, but different bonding arrangement of atoms.
- Chain isomerism
- Functional group isomerism
- Position isomerism
Structural isomers
- Chain isomerism:
occurs when chains are branched.
The longer the
chain, more branching is possible and therefore more possible
structural isomers.
Structural isomers
functional group isomerism:
same molecular mass, but contain different functional groups due to
isomerism.
Structural isomers
Position isomerism:
In this case, the alkyl (carbon) chain stays the
same, with the functional group(s) moving round the skeleton.
- NOT same as functional group isomerism, as functional groups remain constant
Stereoisomers definition:
what the 2 types
molecules with the same molecular formula and sequence of bonded atoms.
Differ in the three-dimensional orientations of their
atoms in space
Chiral and Achiral molecules
Achiral molecules,
superimposable on their
mirror image
Chiral molecules, non
super imposable on their
mirror image (like hands)
Chirality
molecules that have a “handedness” i.e. nonsuperimposable by any rotation or movement (termed “translation” in
chemistry).
The “handedness” comes from the fact that you cannot rotate or move a left hand onto a right hand.
This means the hands are “chiral” (from the Greek word for hand)
A Racemic mixture
a 50/50 mix of two enantiomers
Each chiral centre will be either R (r for right) or S (Latin for left is sinister). To determine
whether an enantiomer is R or S there is a system called…
the Cahn-Ingold-Prelog rules.
Alternatively the enantiomers can be labelled (+) or (-). This is determined by how they…
polarise light.
Why are enantiomers are often referred to as “optical isomers”
Light from lamp can be polarised using a filter.
If the polarised light passes through an optically active molecule it can be rotated.
Enantiomers
will rotate the light in different directions.
If there is a racemic mixture of enantiomers (50/50) there will be no angle of rotation observed.
Chiral centres (2):
Chiral centres are tetrahedral atoms (usually carbons) that have four different substituents
Chiral centres can
be denoted with a
star
Diastereoisomers
Diastereoisomers are stereoisomers that are not mirror images of each
other.
Cis isomers - “cis” means the nonhydrogen groups on same side
of hexagon of carbons
Trans isomers - “trans” means, “ “ on other sides
of hexagon of carbons
Diastereoisomers
This can also happen across…
alkenes as they do not rotate.
(not just typically sterosiosmers)
Can diastereoisomers be both chiral and achiral?
Yes
Achiral molecules are
superimposable on their
mirror image
Chiral molecules are non
super imposable on their
mirror image (like hands)
Organic compounds
Defintion:
a large class of chemical compounds in which
one or more atoms carbon, covalently linked to atoms of other elements,
most commonly hydrogen, oxygen, or nitrogen.
Carbons can “catenate” or form covalent bonds with other carbons to from chains and rings of
carbons.
Why is it being able to draw stable carbon compounds efficiently and accurately is therefore very important?
Counting only molecules that are under 30 Carbon atoms, there are many
combinations of atoms that are possible to create stable compounds.
It has been calculated that there are (10^63) stable compounds are possible.
There aren’t enough carbon atoms in the universe to make them all.
What varies across stable organic compounds
very different properties.
What are all the different ways that carbon can bond for amino acids (8)
2 carbon chain
3 carbon chain
9 carbons
chain
rings
straight chain
branched chain
ring and chain
All have similar properties:
all soluble in water, all both acidic and basic
(amphoteric), all be joined with other amino
acids to form proteins
This is because the chemistry of organic
molecules depends much less on the number or
the arrangement of carbon or hydrogen atoms
than on the other types of atoms (O,N, S, P, Si…)
in the molecule.
We call parts of molecules containing small
collections of these other atoms (O,N, S, P, Si…)
functional groups, simply because they are groups of atoms that determine the way the molecule works.
All amino acids contain two functional groups: an
amino (NH2or NH) group and a carboxylic acid (CO2H)
group (some contain other functional groups
as well)
The hydrocarbon framework is made up of chains and rings of carbon atoms, and acts as…
a support fro the functional groups.
The functional groups detemines what? (2)
the way the moelcule works both chemically and biologically
When molecules get larger we need different ways of drawing them
What are the 3 guidlines:
1) Draw chains of atoms as zig - zags
2) Miss out the Hs atatched to carbon atoms, along with C- H bonds (unless there’s a good reason not to).
3) Miss out the capital Cs representing carbon atoms (unless good reason not to).
Every kink (corner) in chain is carbon atom.
Sometimes “R” is used to represent a …
a functional
group. For example, for all amino acids
In order to discuss and answer questions about symmetry in chemistry, we need
a notation that we can use to write 3D molecules in 2 dimensions.
dashed line means
the bond is going into
the page / screen
The wedged line means
the bond is coming out
of the page / screen
These bonds (regualr line) are in the
same plane as the page
/ screen
Dashed lines - means bond is going into the page
Wedged - out
It is important to be able to specify the carbon-carbon bond types
3 types
Alkane (single bond) sp^3
Alkene (double bond) sp^2
Alkyne (triple bond) sp
What is the resulting wave-function for a molecular orbital?
Equation:
The resulting wavefunction is a combination of the two atomic wavefunctions:
waterpotential sign, sub (sigma) = waterpotential sign, sub(A) + waterpotential sign, sub(B)
this is if constructive interfernce occurs
The out-of-phase combination must also be considered. A further molecular orbital is produced, this time through destructive interference of the wavefunctions.
Equation: now instead subtract A from B
and add a * to sigma sign to indicate deconstructive.
Destructive interference of wave functions:
Here there is a nodal plane between the two nuclei. A nodal plane indicates that the value of the wavefunction
is 0 in this region i.e. there is no probability of finding the electron in this region of space.
This combination is higher in energy than the (sigma)s bonding orbital and is referred to as an antibonding, (simga)s*
Molecular orbital diagrams
what are the 2 types of bonds:
sigma - all single bonds
pi - only double and triple bonds
so if you have a double bond, 1 will be sigma and the other pi, likewise if you have triple bond, 1 sigma other 2 pi bonds.
Molecular orbital diagrams
what is the difference between bonds and antibonds?
bonds- stabilising interactions between 2 atoms
antibonds- destabilising interactions between 2 atoms
Molecular orbital diagrams
Magnetic properties:
Diamagnetic: no unpaired electrons
Paramagnetic: at least one unpaired electron
Molecular orbital diagrams
How do you calculate bond order?
It represents the number of chemical bonds between 2 atoms (e.g bond order of 1 for single bonds, 2 for double, etc).
Note that bond order does not need to be a whole number, intermediate bond orders are a result of resonance.
Equation: 1/2 (electrons found in the bonding orbital electrons) - (electrons found in the antibonding orbital electrons)
