Module 3: Structure And Reactions Of Organice Molecules Flashcards
Orbital
An area surrounding a nucleus in which an electron has a 95% probability of being within
Order of orbitals
1s 2s 2p 3s 3p 4s 3d 4p 5s
How many electrons does an S orbital contain?
2
How many electrons does a p orbital contain?
6
How many electrons does a d orbital contain?
10
Which side of the periodic table contains elements with outermost orbitals of s?
Left
Which side of the periodic table contains atoms with outermost orbitals of p?
Right
How do atoms interact to form a molecule?
Via their outermost orbitals
Chemical bond
A region of high electron density
Where electrons are repelling each other, and nuclei and electrons and attracting
Octet rule
Atoms try to complete their octets (8 valence electrons) by sharing electrons
Which row of the periodic table always obeys the octet rule?
Row 2
Which row of the periodic table can disobey the octet rule?
Row 3
If an atom has an excessive d orbital, which part of the periodic table is it likely from?
Row 3
Five steps for drawing a Lewis structure
- Count valence electrons for each atom
- Assemble bonding framework using single covalent bonds
- Place three nonbonding pairs of electrons on each outer atom
- Assign remaining valence electrons to inner atoms
- Minimise formal charges on all atoms
Formal charge= ?
Valence electrons on free atom - electrons assigned in Lewis structure
How do we minimise formal charges?
By converting lone pairs into shared pairs (double bond)
Resonance hybrid
A structure that describes chemical bonding in a molecule where there are multiple Lewis structure possibilities
Resonance hybrid
The representation of two or more resonance structures of a molecule.
What does resonance provide in organic molecules?
Stability
VSEPR
Valence shell electron pair repulsion
A theory that states a molecule has the shape which allows pairs to be as far away form each other as possible
Or electron pair repulsions are minimised
Shape and bond angles of molecule with two regions of electron density
Linear
180 degrees
Shape and bond angles of molecule with three regions of electron density
Trigonal planar
120 degrees
Shape and bond angles of molecule with four regions of electron density
Tetrahedral
109 degrees
Shape and bond angles of molecule with five regions of electron density
Trigonal bipyramidal
120 and 90 degrees
Shape and bond angles of molecule with six regions of electron density
Octahedral
90 degrees
Which element (not in the 3rd row) does not obey the octet rule?
Boron
Why are bond angles sometimes slightly different than normal shape would predict?
Lone electron pairs have bigger regions of electron density than bonding pairs
This increases the bond angles between lone pairs and bonding pairs
And decreases the bond angles between separate bonding pairs
Valence bond theory
Half-filled atomic orbitals overlap to form new orbitals in a bond between atoms.
σ (bond)
Sigma bond (for molecular orbitals)
Hybrid orbital
A new orbital formed from mixing two other orbitals that is suitable for bonding.
How does the energy level of a hybrid orbital relate to the energy levels of the atomic orbitals?
In the middle of them
Hybrid orbitals of one molecule have the same energy as each other
sp^3 hybridisation
Hybrid orbitals used in any C molecule with a tetrahedral shape
sp^2 hybridisation
Hybrid orbitals used in any C molecule with a trigonal planar shape
What does a line with two arrows through it mean in an energy diagram?
A full orbital- lone pair of electrons (non-bonding)
Why is boron so reactive?
It has an empty p orbital which is highly attractive to electrons
Multiple bonding
When more than two electrons are involved in bonding two atoms
How many electrons involved in a double bond?
4
How many electrons involved in a triple bond?
6
If the bond angles around a central atom are 120 degrees, how many hybrid orbitals do we need to form?
Three
If the bond angles around a central atom are 105 degrees, how many hybrid orbitals do we need to form?
Four
How is a double bond formed via orbitals?
Two p orbitals form a Pi bond while two ps^2 orbitals form a sigma bond
You can’t have a Pi bond without _____ because?
Sigma bonds, because they pull the p orbitals together
Triple bonding involves____?
Two pi bonds and a sigma bond
Chiral organic compound
Contains an asymmetric carbon (or >1)
Stereocentre
An asymmetric carbon of a molecule
What shape will a chiral molecule be?
Tetrahedral with sp^3 orbitals
How do enantiomers of a compound differ?
In their interactions with other chiral compounds
What makes a stereocentre asymmetric?
The groups attached to it are different
Optical rotation
Polarises and rotates light by cutting out specific wavelengths
Passes the light through a chiral compound in solution
If the light rotates 90 degrees, the molecule is an enantiomer
Which three things are displayed when describing optical rotation?
Degrees of rotation
Temperature
Light used
+ and - enantiomers
+ when light is rotated to the right
- when light is rotated to the left
What is the result of a chiral compound containing a 1:1 of enantiomers in optical rotation?
What is this mixture called?
No rotation of light
Racemic mixture/ racemate
A solution containing one enantiomer is called?
Enantiopure
How do we identify R and S isomers? 4 steps
- Identify stereocentre
- Assign priorities to the four substituents
- Visualise molecule with lowest priority substituent in the back
- R: 1-3 bond arrangement is clockwise, L: 1-3 bond arrangement is anticlockwise
Relationship between R and S, and + and - enantiomers
Don’t always match up/ unrelated
Diastereomers
Any stereoisomer that isn’t an enantiomer
It has more than one stereocentre
How many diastereomers will a molecule with n stereocentres have?
2^n
What does a half-headed arrow represent?
One electron transferred
What does a full-headed arrow represent?
Two electrons are transferred
What does the direction of a half or full-headed arrow show?
Transfer of electrons to a delta positive area/ proton
Homolytic bond cleavage
Bond is broken by each of two electrons being transferred to a different atom
What are the species generated from a homolytic bond cleavage?
Radicals
In a double bond, which bond is cleaved first?
Pi bond
How is an alkene isomerised?
Pi bond is cleaved, rotation about the bond occurs, then bond forms again
Heterolytic bond cleavage
Both electrons are transferred from the bond to the same atom
What does heterolytic bond cleavage generate?
Charged intermediates
Electrophilic
Seeking electrons
Nucleophilic
Can donate a pair of electrons to form a bond
Leaving group
Group/ atom which separates from a molecule by breaking the bond
Nucleophilic substitution reaction
Leaving group (X) is replaced by nucleophile
Nucleophilic elimination reaction
Nucleophile acts as a base and pulls hydrogen atom from carbon (peripheral to leaving group)
Leaving group’s bond is broken and electrons from that bond form a double bond, turning alkane into an alkene
Production of adrenaline is what kind of reaction?
Nucleophilic substitution
SN1
Substitution nucleophilic first order
Two step reaction
- Leaving group leaves (X)
- Nucleophile attaches
SN2
Substitution nucleophilic second order reaction
One step reaction: X leaves as nucleophile attaches
Rate law for SN1
rate = k[C-X]
Rate law for SN2
Rate = k[C-X][Nu:-]
For SN2, does it matter which side the nucleophile attaches from?
Yes- opposite to leaving group, as needs to happen simultaneously
(if it approaches from X side, X acts as a barrier and the nucleophile can’t get enough energy)
Does SN2 have any reaction intermediates or transition states?
One transition state: C-X bond is breaking, Nu-C bond is forming
Which have higher Gibbs energy in a nucleophilic reaction- products or reactants?
Reactants
Which step is slower in an SN1 reaction?
First step- X leaves slowly
Is independent of nucleophile
First transition state in SN1 reaction
C-X bond is stretched to breaking point
nucleophile is not yet attached
Why is the second step of SN1 fast?
The carbon is now a carbocation, because the negative X group has left
This means it is charged and accessible, so the nucleophile doesn’t have to collide with a particular orientation
Reaction intermediate of SN1 reaction
Carbocation (positive carbon group with no X or nucleophile attaches)
Reacts with any nucleophile it collided with- doesn’t have to be a good one
Has a short lifetime
Second transition state of SN1 reaction
C-Nu bond is forming
When will SN1 be a three step process? Why?
When H2O is the solvent (anything aqueous)
H2O provides one extra proton (H atom) to the carbocation, so it has a positive charge
the third step involves deprotonation by a base (can be H2O)
Inversion of configuration
R to S or S to R
What happens to stereochemistry in SN2 mechanism?
Nucleophile attaches opposite to the leaving group, so stereochemistry is inverted
Which nucleophilic substitution is stereospecific?
SN2
Why does SN1 mechanism produce both R and S enantiomers?
Because the nucleophile attaches to the carbocation (no X group), so it can approach from either side
Which kind of carbon molecules almost always goes via SN2?
Methyl
Which kind of carbon molecule almost always goes via SN1?
Tertiary (3 R side chains/ 3 additional carbons)
Why is SN1 faster with a higher number of alkyl groups?
First transition state (C-X bond breaking) can be stabilised by electrons from alkyl groups
The more alkyl groups, the more they can stabilise
Why is SN2 faster with a lower number of alkyl groups?
The less alkyl groups, the less steric hinderance of the nucleophile trying to approach the carbon
What two components of a secondary carbon reaction determine whether it goes via SN1 or SN2?
Leaving group X
Solvent
What does SN1 require that SN2 doesn’t? Why?
A good leaving group
In SN2, strong nucleophile can make up for a poor leaving group because it’s done in one step
What makes a good leaving group? Three examples
A weak base (conjugate acid is strong)
Cl-
Br-
I-
Which of I:-, Br:- and Cl:- is the best leaving group? Why?
I:- because it has the fastest rate of C-X cleavage, due to its longer weaker bonds (bigger atomic number)
Example of bad leaving group
Why?
HO:-
Strong base forms strong bond with carbon. Slow rate of C-X cleavage
How can HO:- or RO:- be converted into better leaving groups?
Protonation under strongly acidic conditions
O bonds a second H atom, making the leaving group H2O
A much better leaving group with weaker C-O bond- because electrons move closer and to O from C
In which substitution reaction is a good nucleophile essential? Why?
SN2
Has to bump electrophile off the carbon
Example of a good nucleophile, and a neutral nucleophile
Good: HO:-
Neutral: H2Ö
Why is (CH3)3 CO:- a poor nucleophile?
Three methyl groups gives molecule a large size - they don’t allow the O:- to get close enough to the electrophilic carbon
In which solvents is SN1 fastest? Why?
Polar solvents, particularly those which hydrogen-bond
First transition state is stabilised by hydrogen bonds- making bond cleavage (first step) faster and easier
Which solvents are best for SN2 reactions? Why?
Polar solvents that don’t do hydrogen bonding
Solvent sphere (circle of H+ bonds) can hinder the nucleophile- and hinder the process of nucleophile bonding to the carbon
What are elimination mechanisms determined by?
Base strength
Strong base: E2
Weak base: E1
Describe E1 mechanism
Step 1: C-X bond cleaved, forming carbocation
Step 2: nucleophile bonds to H atom and pulls it from the carbocation. Electrons from C-H bond form a Pi bond (double bond) to the central carbon- forming an alkene
Controlling factors of E1 reaction (same as SN1) (3)
Strong base not required
H-bonding polar solvents speed up reaction
Most common when leaving group is on tertiary carbon
Which two nucleophilic reactions often co-occur? What is the ratio of these two reactions controlled by?
E1 and SN1
Relative rates of the fast step of each reaction (does not depend on leaving group)
Describe E2 mechanism
Nucleophile pulls proton off and X leaves (forming alkene bond) in same step
Second order reaction
Where does the nucleophile collide in E2 reaction?
At the carbon peripheral to the leaving group
Does E2 need a strong base, or does it not matter?
Yes- protons aren’t as easy to pull off since X is still attached
Why is E2 possible for 1, 2 and 3 carbon compounds?
The protons are easily accessible in any compound- on the outside
What does ENu represent?
A molecule with an electrophilic portion and a nucleophilic portion
Two steps of addition reaction to an alkene
- Slow addition of the electrophilic to the double bond
2. Fast attack by a nucleophile at the carbocation intermediate
Which part of an addition to alkene requires the highest energy?
The first step- slow and rate-determining
Which carbon of unsymmetrical carbon does the nucleophile attack in an alkene addition reaction? Why?
The carbon with more alkyl groups donating electrons
The alkyl groups stabilise the positive charge of the carbocation (onto which the nucleophile attacks)
This takes less energy to form
How can a non polar molecule (e.g. Br2) react with an alkene by addition?
As it approaches the double bond- which is electron rich- a dipole is induced
Turning one Br more positive and one more negative (electron dense)
How is the carbocation stabilised in addition to an alkene?
Br (electrophilic) snaps shut by forming single bond with each carbon (two)
This forms a bromonium ion for example
