What is a condensed structure?
Harflerle yazilmis tek linelik name.
What is a line structure?
- Corners and line ends represent Cs.
- Hs on Cs are invisible unless the C is written out. Then, we must also draw the Hs.
- Hs are drawn on heteroatoms.
- Lone pairs on heteroatoms are not necessary, but lone pairs must be drawn if they’re on C or are involved in a reaction.
What is the charge of a 2 bonded N?
What is the charge of a 4 bonded N?
What is the charge of a 1 bonded O or S?
What is the charge of a 3 bonded O or S?
What is the charge of a 3 bonded C?
+, - or 0
What is the charge of a 2 bonded halogen?
Always show formal charges when drawing out molecules
How to find overall charge of molecule?
Add all formal charges.
What are constitutional isomers?
- Same molecular formula, different connectivity of their atoms.
- (chirals are excluded, as they’re optical isomers)
What are carbonyls?
Functional group containing C=O
Functional group: Thiol
Functional group: ether:
Functional group: sulfide:
Functional group: disulfide:
Functional group: amine
Functional group: imine:
Functional group: nitrile:
C triple bond N
Functional group: aldehyde
- End with -al (propanal)
Functional group: ketone
- End with -one
Functional group: carboxylic acid
Functional group: ester
- C double bonded to O
- Bonded to
- Bonded to C
- Example: methyl ethanoate (the one bonded to the O is the first one)
Functional group: thioester:
- C double bonded to O
- Bonded to
- Bonded to C
- Example: methyl ethanethiooate
Functional group: amide:
- C double bonded to O
- Bonded to N-R
Functional group: Carboxylic acid anhydride
- Bonded to O
- -oic anhydride
Functional group: phosphate
- P double bond O and single bond to 3 O
- One O bonds to a C
- Os can bond to other phosphates to form diphosphate etc.
How can we calculate degree of saturation for hydrocarbons?
- If DU = 0, saturated, alkane, no double bonds, no rings
- If DU = 1, unsaturated, 1 double bond or 1 ring
What is carboxylate?
- Conjugate base of carboxylic acid.
- Module 2 and 3
- Prefix for 3 carbon?
Prefix for 7 carbons?
Prefix for 4 carbons?
Prefix for 9 carbons?
Prefix for 10 carbons?
Rule for naming:
- If two numbering schemes lead to the same branch numbers, the alphabetically lower branch should get the lower number.
- If you have a ring, everything sticking off is a branch
How to we show that a group is attached to amine
What is resonance?
- The concept that electrons/bonds are delocalized over 3 or more atoms which cannot be depicted in a single simple lewis structure. Only electrons can be moved, not atoms.
- Total formal charge is always the same.
How do we figure out if there is resonance?
- Check if there is a negative charge on an atom.
- If an adjacent atom has a double or triple bond, there is resonance.
- Check if there is a positive charge on an atom
- Does an adjacent atom have a lone pair or a double or triple bond.
Resonance and stability
The more the different resonance structures, the stabler the molecule is.
How to decide whether a molecule is a major or minor contributor?
- Major contributor will have complete octets.
- Minimal formal charges
- And logical formal charges (the more electronegative atom has a negative charge)
List intermolecular interactions from strongest to weakest?
- Hydrogen bonding (lone pair of a very EN atom bonded to an H that is bonded to a FON)
- dispersion/lonon/van der waals (proportional to surface area)
Boiling point trends:
- Boiling point goes up as intermolecular forces goes up.
- If two molecules have the same intermolecular forces, the one with the greater number of C will have a higher boiling point.
- If they have the same number of C, the one with the more branches (higher surface area) will have the lower boiling point.
H bond and solubility
The molecule with H bonds will be the most soluble in water.
Solubility of hydrocarbons
Hydrophobic, so insoluble in water
Solubility of charged/ionic molecules:
Ion or dipole dipole interactions will be water soluble if their hydrophobic regions are small enough.
H bonding and solubility
- Alcohols, acids, amines are very soluble. (both donors and acceptors of h bonds)
- Ketones, ethers and aldehydes are soluble but not so much (just acceptors of H bonds)
Which are H bond acceptors only?
Which are H bond donors and acceptors?
How to decide if a molecule is polar?
- If all bonds are nonpolar, then nonpolar
- If molecule has 1 polar bond, then polar
- If molecule has multiple polar bonds and the dipole moments oppose each other, then the molecule is nonpolar. BUT make sure you check whether they oppose each other in a 3D space.
- What are conformational isomers?
- Various 3D arrangements of atoms that can be interconverted solley by rotations around single bonds. No moving electrons. Just spinning electrons.
How to depict conformers?
- Using Newman projections.
- The dot is the front carbon, the circle is the back carbon. There are no invisible Hs.
What are more stable newman projections?
- If the Hs are lined up directly behind each other, this is a high energy conformation.
- This is called ECLIPSED.
- If the Hs are not lined up, this is the lower energy conformation. This is called staggered.
What is staggered?
Lowest energy possible with the Hs not lined up directly behind each other.
What is eclipsed?
When the Hs are lined up directly behind each other in newman projections
What are gauche interactions?
- When methyl groups or something are next to each other but not lined up with each other (eclipsing)
- THis is higher in energy than staggered, but definitely lower in energy than eclipsed conformers.
What does cis mean?
On the same face of the ring (top or bottom)
What does trans mean?
On the opposite faces of the ring (top or bottom)
What does axial mean?
Sticking up or down parallel to an axis.
What does equatorial mean?
Sticking to the sides of the ring (east, west)
What is a chair flip?
Everything that was axial becomes equatorial, but top/up remains the same.
What are the rules for chair configuration?
- Bulkier groups prefer equatorial positions. Given a choice, put smaller groups axial and bigger groups equatorial.
- Carbons are bigger than non carbons.
- Branched is bigger than non branched
- T-butyl group is huge. There is extreme preference to but this as equatorial (c bonded to 3 methyl groups)
How do I choose the higher energy chair configuration?
- If not equatorial, then higher energy.
- If everything is axial, cis one is higher energy due to diaxial interactions.
What is anti conformation?
- When the angle between the two largest groups in the newman projection is 180 degrees.
- What are stereoisomers?
- All atoms are connected in the same order, but with different arrangement of atoms/bonds in 3D space.
- Conformers are a type of stereoisomer that can be interconverted by rotating around single (sigma) bonds.
- Can’t be enantiomers without an asymmetric carbon.
What are enantiomers?
- Mirror image, non super imposable stereoisomers
- Boiling point, melting point, solubility are equal, but they rotate plane polarized light in opposite directions.
What are diastereomers?
Opposite configuration at 1 or more but not all stereocenters.
What are epimers?
Opposite configuration of one out of many chiral centers.
What is meso?
- Molecules with an internal plane of symmetry, which makes R S the same as S R.
- Meso compounds are always R S
- A cross with the top being arms away from you and the sides being arms towards you.
- Common for sugars.
If there is no rotation of plane polarized light, what can we infer?
- Achiral molecules
- OR racemic mixture
Nomenclature based on light rotation
- d (+) is to the right
- l is to the left (-)
- But there is no obvious correlation between 3D arrangement and direction of light rotation
What is chiral?
A molecule that has an enantiomer.
What is achiral?
A molecule whose mirror image is superimposable.
How to give names to molecules using R/S system?
- Rank priority of 4 groups (larger atomic number = higher priority, double bond is counted as bonded to that molecule twice)
- Place #4 in the back, or if it is the highest priority, switch S to R in the end
- Draw arrows 1-2-3, if clockwise R, if counterclockwise S
How to do E-Z nomenclature?
- Draw bisecting line across double bond
- Assign priorities to each “end” using the same rules as R/S
- If they’re on the same side, Z (zusammen)
- If they’re on opposite sides, E (entgagen)
What must happen for a reaction to occur?
Reactants must collide in the correct orientation with enough energy.
Alkene addition mechanisms:
- No intermediate (single step reaction), concerted addition to one face of the double bond (H2 with Pt or something) cis addition
- Intermediate (triangle), stepwise addition to opposite faces (cyclic bromonium ion (+) with (-)
- Intermediate (carbocation + sp2 + p hybridization) stepwise addition to either face. (HCl,), H is added first to either side in either orientation, the other C becomes +. We understand which C it gets added to through Markovnikov’s rule. The Markovnikov’s rule states that H gets added to the C with more Hs.
What is endergonic?
Requires input of energy
What is exergonic?
What is the top of the hill in an energy graph?
What is the bottom of a hill in an energy graph?
What is Keq?
Conc. of products / conc of reactants
When is Keq bigger than one?
More products than reactants, exergonic reaction
When is Keq smaller than one?
More reactants than products, endergonic reaction
Reactions with lower activation energy
- Are faster
- Not the rate determining step
- Position of equilibrium DOES NOT change with catalysts
How do catalysts work?
- Make rxns go faster but are not consumed
- DO NOt change the position of equilibrium, stabilize the transition state and lower the Ea
- The more carbons around a carbocation, the more it is stabilized by the inductive effect.
- Tertiary is more stable than secondary which is more stable than primary which is more stable than methyl
What is the inductive effect?
E- shift toward a positive charge through sigma bonds.
What is Markovnikov’s rule?
The carbocation with higher stability (more c bonded to it) will be preferentially formed.
Resonance is a more powerful stabilizer than induction. If you’re asked which molecule is more stable, check if any have resonance. IF not, tertiary is most stable.
What is the Hammond postulate?
The transition state looks more like whatever it is closer to in energy.
What is the Bronsted Lowry definition of acids and bases?
- Acids are proton donors
- Bases are proton acceptors.
You must have a free lone pair to act as a base.
The lower the PkA,
The stronger the acid, the more deprotonated at equilibrium (loves giving away protons)
PH = Pka + [deprotonated]/[protonated]
When pH > PkA
Molecule is predominantly deporonated
When ph < pKA
Molecule is predominantly protonated
When pH = PKa
Molecule is 50:50 deprotonated to protonated
For amine bases
- Deprotonated: 0
- Protonated: +
- Protonated: 0
- Deprotonated: -
If pH = Pka + 1
90 % deprotonated
If pH = pKa + 2
99 % deprotonated
If pH = Pka -1
If Ph = pKa - 2
Why are most drugs bases?
- Neutral (uncharged) molecules can cross membranes and charged molecules cannot.
- Acids are nearly 100% deprotonated (-) at 7.4
- Bases are only 90% protonated (+) at 7.4
What is the isoelectric group?
- PI = PH at which the average net charge = 0
- For aminoacids with acidic side chains, the PIs will be the midpoint of the two lowest pKas.
- For amino acids with basic side chains, PI will be the midpoint of the two highest Pkas.
- For amino acids with non ionizable side chains, PI = midpoint of the acid and base PkAs.
How do we recognize organic acids?
- Contain a positively polarized H (binded to O or S)
- Or H bonded to C next to a carbonyl (C=O)
What is zwitterion?
Contains both + and - charges and net charge is 0
How do we decide the relative strength of organic acids?
The more stable the resulting base (lower energy, through induction or resonance) the stronger the acid.
Inductive effect and acid strength
- EN molecules (such as Cl, F etc.) bonded to C cause inductive effect and stabilize the - charge on the conjugate base, thus making the acid stronger.
- This has a positive relationship with proximity to negative charge, electronegativity of the atoms, and the number of electronegative atoms.
How to judge the relative strength of organic bases?
- Conjugate bases of weak acids are strong bases. The weaker the acid, the stronger the base.
- Nitrogens with lone pairs are good bases. AMIDES aren’t, since their electrons are tied up in resonance.
What are alpha protons?
Protons next to a C double bonded to O.