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What is a condensed structure?
Harflerle yazilmis tek linelik name.
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What is a line structure?
- Skeleton
- 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.
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What is the charge of a 2 bonded N?
-1
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What is the charge of a 4 bonded N?
+1
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What is the charge of a 1 bonded O or S?
-1
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What is the charge of a 3 bonded O or S?
+1
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What is the charge of a 3 bonded C?
+, - or 0
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What is the charge of a 2 bonded halogen?
+.
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Note
Always show formal charges when drawing out molecules
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How to find overall charge of molecule?
Add all formal charges.
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What are constitutional isomers?
- Same molecular formula, different connectivity of their atoms.
- (chirals are excluded, as they’re optical isomers)
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What are carbonyls?
Functional group containing C=O
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Functional group: Thiol
-SH
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Functional group: ether:
C-O-C
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Functional group: sulfide:
C-S-C
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Functional group: disulfide:
C-S-S-C
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Functional group: amine
C-N-R
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Functional group: imine:
C=N-R
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Functional group: nitrile:
C triple bond N
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Functional group: aldehyde
- End with -al (propanal)
- C=O
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- H
- -COH
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Functional group: ketone
- O
- =
- C-C-C
- End with -one
- -C(CO)C
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Functional group: carboxylic acid
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Functional group: ester
- C double bonded to O
- Bonded to
- O
- Bonded to C
- Example: methyl ethanoate (the one bonded to the O is the first one)
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Functional group: thioester:
- C double bonded to O
- Bonded to
- S
- Bonded to C
- Example: methyl ethanethiooate
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Functional group: amide:
- C double bonded to O
- Bonded to N-R
- -amide
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Functional group: Carboxylic acid anhydride
- C=O
- Bonded to O
- C=O
- -oic anhydride
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Functional group: phosphate
- P double bond O and single bond to 3 O
- PO4
- -phosphate
- One O bonds to a C
- Os can bond to other phosphates to form diphosphate etc.
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How can we calculate degree of saturation for hydrocarbons?
- (2C+2)-H/2
- If DU = 0, saturated, alkane, no double bonds, no rings
- If DU = 1, unsaturated, 1 double bond or 1 ring
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What is carboxylate?
- Conjugate base of carboxylic acid.
- Module 2 and 3
- Prefix for 3 carbon?
- Prop
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Prefix for 7 carbons?
Hept
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Prefix for 4 carbons?
But
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Prefix for 9 carbons?
Non
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Prefix for 10 carbons?
Dec
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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
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How to we show that a group is attached to amine
N-
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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.
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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.
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Resonance and stability
The more the different resonance structures, the stabler the molecule is.
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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)
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List intermolecular interactions from strongest to weakest?
- Ionic
- Hydrogen bonding (lone pair of a very EN atom bonded to an H that is bonded to a FON)
- Dipole-dipole
- dispersion/lonon/van der waals (proportional to surface area)
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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.
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H bond and solubility
The molecule with H bonds will be the most soluble in water.
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Solubility of hydrocarbons
Hydrophobic, so insoluble in water
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Solubility of charged/ionic molecules:
Ion or dipole dipole interactions will be water soluble if their hydrophobic regions are small enough.
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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)
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Which are H bond acceptors only?
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Which are H bond donors and acceptors?
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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.
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Module 4
- 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.
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How to depict conformers?
- Using Newman projections.
- The dot is the front carbon, the circle is the back carbon. There are no invisible Hs.
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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.
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What is staggered?
Lowest energy possible with the Hs not lined up directly behind each other.
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What is eclipsed?
When the Hs are lined up directly behind each other in newman projections
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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.
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What does cis mean?
On the same face of the ring (top or bottom)
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What does trans mean?
On the opposite faces of the ring (top or bottom)
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What does axial mean?
Sticking up or down parallel to an axis.
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What does equatorial mean?
Sticking to the sides of the ring (east, west)
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What is a chair flip?
Everything that was axial becomes equatorial, but top/up remains the same.
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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)
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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.
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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.
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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.
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What are diastereomers?
Opposite configuration at 1 or more but not all stereocenters.
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What are epimers?
Opposite configuration of one out of many chiral centers.
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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
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Fisher projection:
- A cross with the top being arms away from you and the sides being arms towards you.
- Common for sugars.
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If there is no rotation of plane polarized light, what can we infer?
- Achiral molecules
- OR racemic mixture
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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
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What is chiral?
A molecule that has an enantiomer.
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What is achiral?
A molecule whose mirror image is superimposable.
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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
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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)
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What must happen for a reaction to occur?
Reactants must collide in the correct orientation with enough energy.
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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.
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What is endergonic?
Requires input of energy
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What is exergonic?
Outputs energy
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What is the top of the hill in an energy graph?
Transition state
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What is the bottom of a hill in an energy graph?
Intermediate.
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What is Keq?
Conc. of products / conc of reactants
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When is Keq bigger than one?
More products than reactants, exergonic reaction
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When is Keq smaller than one?
More reactants than products, endergonic reaction
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Reactions with lower activation energy
- Are faster
- Not the rate determining step
- Position of equilibrium DOES NOT change with catalysts
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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
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Carbocation stability:
- 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
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What is the inductive effect?
E- shift toward a positive charge through sigma bonds.
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What is Markovnikov’s rule?
The carbocation with higher stability (more c bonded to it) will be preferentially formed.
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Remember
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.
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What is the Hammond postulate?
The transition state looks more like whatever it is closer to in energy.
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What is the Bronsted Lowry definition of acids and bases?
- Acids are proton donors
- Bases are proton acceptors.
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Remember
You must have a free lone pair to act as a base.
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The lower the PkA,
The stronger the acid, the more deprotonated at equilibrium (loves giving away protons)
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Henderson Hasselbalch
PH = Pka + [deprotonated]/[protonated]
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When pH > PkA
Molecule is predominantly deporonated
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When ph < pKA
Molecule is predominantly protonated
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When pH = PKa
Molecule is 50:50 deprotonated to protonated
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For amine bases
- Deprotonated: 0
- Protonated: +
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For acids:
- Protonated: 0
- Deprotonated: -
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If pH = Pka + 1
90 % deprotonated
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If pH = pKa + 2
99 % deprotonated
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If pH = Pka -1
90% protonated
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If Ph = pKa - 2
99% protonated
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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
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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.
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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)
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What is zwitterion?
Contains both + and - charges and net charge is 0
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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.
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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.
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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.
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What are alpha protons?
Protons next to a C double bonded to O.
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