Orgo Flashcards
What is a lactone?
circularized ester
What is a lactam?
circularized amide
What is another word for alkene?
olefin
What is another word for epoxide?
oxirane
What is another cyanohydrin?
carbon bonded to an alcohol and a CN
How are substituents ordered in a compound name?
in alphabetical order, not including the prefixes i.e. di, tri etc
How are compounds named when there is an alcohol in them?
so that lowest priority is given to the alcohol
What is the formula for unsaturation?
(2n + 2 + N - X - H) / 2
What are some general trends for electron donating groups?
alkyl groups i.e. CH3, Et etc
lone pair groups/atoms
What are some general trends for electron withdrawing groups?
halides
no lone pair
ie NO2
When does resonance stabilization occur?
in a conjugated system with 3 or more atoms that each have a p orbital
What are the 3 rules for resonance structures?
1) resonance structures can never be drawn through atoms that are truly spy hybridized
2) usually only involve electrons that are adjacent to a pi bond or an unhybridized p orbital
3) resonance structures of lowest energy are the most important
What 3 main criteria does evaluation of resonance structure rely on?
1) contributors in which the octet rule is satisfied for all toms are more important than for ones in which its not
2) contributors that minimize separation charge (formal charge) are better
3) if there are formal charges negatives should be on the more electronegative atoms and positives on the less electronegative atoms
What is a Bronsted-Lowry acid?
molecule that can donate a proton
Rank the stability of a carbocation from most to least stable
3 > 2 > 1 > Me
Rank the stability of a carbanion from most to least stable
Me > 1 > 2 > 3
What is a Bronstad-Lowry base?
accepts protons
What is a Lewis acid?
electron acceptor
What is a Lewis base?
electron donator
In general what is the order of relative acidity for organic compounds?
strong acids sulfonic acids carboxylic acids phenols alcohols and water aldehydes and ketons sp CH sp2 CH sp3 CH
What are the 6 strong acids (for the MCAT)?
HClO4 H2SO4 HNO3 HCl HBr HI
How do inductive effects affect acidity?
the closer an electron-withdrawing group is to the acidic proton, the greater the stabilizing effect and thus the greater the acidity
closer = better
more electronegative = better
electron-donating groups tend to destabilize and thus decrease acidity
Are nucleophiles Lewis acids or bases?
Lewis bases because they donate electrons
Are electrophiles Lewis acids or bases?
Lewis acids because they accept electrons
What are the general trends for nucelophilicity?
1) increases as negative charge increases
2) increases going down a group (larger, more polarizable)
3) increases going left across a period (less electronegative)
What is polarizability?
how easy it is for the electrons surrounding an atom to be distorted
generally down a group atoms become larger and more polarizable
What are some characteristics of a good leaving group?
weak C-LG bond (electronegative atoms or EWGs)
stable and unreactive products (low basicity, stable from resonance etc, large)
What is a better leaving group R-OH or R-OMs?
R-OMs
What is more reactive, a C-C double bond or a strained carbon ring?
C-C double bond
Do cyclopentane and cyclohexane undergo hydrogenation reactions under normal conditions?
no, they are relatively-strain free compared to smaller hydrocarbon rings
What are constitutional isomers?
same formula, different structure
What are conformational isomers?
same formula, same connectivity, different sigma bond rotation
ie eclipsed and staggered conformations
What are stereoisomers?
same formula, same connectivity, different 3D arrangements that cannot be changed by rotation of sigma bonds
If a compound rotates plane polarized light clockwise what is it classified as?
dextrorotatory
+
If a compound rotates plane polarized light counter clockwise what is it classified as?
levorotatory
-
When assigning absolute configuration how does priority work among isotopes?
assigned based on atomic weight
highest weight = highest priority
What are enantiomers?
non-superimposable mirror images
have the opposite absolute configuration at all chiral centres
have many identical physical properties
rotate plane polarized light in opposite directions (same magnitude)
What are diastereomers?
stereoisomers that aren’t enantiomers
opposite absolute configuration at some chiral centres i.e. only one needs to be the same
physical and chemical properties can vary dramatically
specific rotation is different, but there is no relationship between them
What are mess compounds?
need to have an even number of chiral centres and a line of symmetry
optically inactive
have chiral centres but are achiral
Do stereoisomers include E/Z configurations?
yes
How are enantiomers separated?
resolution
attach chiral probes which make them diasteromers than separate based on their different physical properties then release the probe
What are geometric isomers?
a type of diasteromers
have different orientation around a ring or double bond
cis/trans (for double bonds or rings)
E/Z (only for double bonds)
What are epimers?
diasteromers that are opposite at only one chiral centre
ie L-glucose and D-glucose
What are anomers?
ring formations of epimers (which are diastereomers)
ie alpha-glucose and beta-glucose
What is the mobile phase in chromatography usually for?
it is usually a solvent and the mix to be separated
What is the stationary phase in chromatography usually for?
its usually something that the mix to be separated interacts with
What are the 4 options for the force driving the mobile phase in chromatography?
capillary action
gravity
pressure
magnet
What are the 5 physical properties used to separate compounds in chromatography? Will they work for enantiomer separation?
polarity size charge specific affinity volatility no they won't differ for enantiomers because they are physical properties
What is the stationary phase in thin layer chromatography?
silica (SiO2) coated glass plate (polar)
Which compounds move farthest in thin layer chromatography? Do they have a high or low Rf?
nonpolar compounds move farther than polar ones
they have a higher Rf
Explain column/flash chromatography
kind of like TLC using gravity and a column
column is filled with glass beads coated in silica (SiO2)
mixture of compounds to be separated are poured in and extra solvent is added periodically
compounds are collected at the bottom
nonpolar compounds come out first
polar compounds come out later because they interact with the silica
Explain size-based exclusion chromatography
large porous beads line a column
solvent with mixture is poured into the top
small molecules take a longer path so they come out later
large molecules take a shorter path and therefore come out first
used for separating polymers and monomers etc
Explain ionic exchange chromatography
column is lined with resin that is functionalized with charged groups (entire column is either negative or positive) i.e. Na+SO4-
mobile phase containing the mixture to be separated is put through
as it passes through the positively charged groups will replace the Na+ while the negatively charged and neutral species will pass right through
column can then be eluted with a concentrated sodium-containing solution to displace all the positively charged species
frequently used for separating proteins
Explain affinity chromatography
usually used to purify proteins or nucleic acids from cell lysates etc
large scale: column is packed with resin and sample is poured in
smaller scale: solid phase is mixed with sample in a small tube then centrifuged
solid phase with protein of interest goes to the bottom and supernatant can just be decanted
magnetic beads can also be used instead and held by a magnet while the solution is decanted
How are proteins of interest isolated using affinity chromatography?
either an antibody specific for the protein of interest is added and then protein A, G or L linked to a solid support is added (bind mammalian antibodies)
or an affinity tag can be used
added to the N or C terminus
i.e. His tags are 6-10 histidine AAs and will bind ions of resin such as nickel
done under high pH and His-tagged proteins can then be eluted under low pH conditions
Describe generally how HPLC (high performance liquid chromatography) works
mobile phase is pressurized
it is then injected by a syringe and carried to the column (4 different types)
sample is separated into individual flasks by retention time
components are detected and analyzed by UV/vis or mass spectrometry as the exit the column
increases speed and efficiency
What are the 4 types of HPLC? Which is the most common?
normal phase reverse phase size exclusion ion exchange *reverse phase is the most common (assume if not indicated on mcat)
How does normal phase HPLC work?
mobile phase is less polar, stationary phase in more polar
nonpolar compounds come out first
*like TLC or column chromatography
How does reverse phase HPLC work?
mobile phase is more polar than stationary phase
polar compounds come out first
*remember to assume this if its not indicated
How does size exclusion HPLC work?
mobile phase is a solvent and stationary phase is porous beads
large compounds come out first
How does ion exchange HPLC work?
mobile phase is solvent
stationary phase is charged resin
same charge as resin and neutral compounds come out first
What is something important to take into consideration before using gas chromatography?
you lose all of your sample, so don’t use it if you want the sample at the end
Explain how gas chromatography works
“separates” compounds based on their volatilities
sample is loaded and vaporized and carried along with an inert gas (usually helium)
moved through a column that has particles coated with liquid absorbent (viscous, high BP)
as components exit the column they are burned and a detector determines the number of components and their relative amounts
compounds with low volatility (high BP) move slowly because they turn to liquid or solid
compounds with high volatility (low BP) stay a gas and move faster (are out first)
What is fractional distillation?
usually used for liquids that have solid impurities
separates compounds with similar boiling points via volatility
column is packed with glass beads or steel sponge
mix is heated, boils, evaporates and condenses over and over and the vapour at the top becomes nearly purely the lower boiling component
it reaches the condenser (that uses cold water) and can then be collected as liquid
What is simple distillation?
used to eliminate trace impurities or separate compounds that have large boiling point differences
doesn’t have a column, you just boil and condense what you want
is less specific
What are extractions used for?
separating a complex mix of organic molecules via solubility
What will be in the aqueous layer of an extraction to begin with?
inorganic salts
strong acids and bases
alcohols, amines and carboxylic acids that are less than 5C
What will move into the aqueous layer of an extraction if you add 5% NaHCO3?
weak acids will move in
because HCO3 is a weak base and will deprotonate them
What will move into the aqueous layer of an extraction if you add 10% NaOH?
very weak acids will move in
because it is a stronger base and will deprotonate them
What will move into the aqueous layer of an extraction if you add 5% HCl?
weak bases will move in
because it is a strong acid and will deprotonate them
What is generally left in the organic layer of an extraction at the end?
nonpolar compounds
can be isolated by evaporation if the non polar compound was what you wanted
How are enantiomers resolved?
use a resolving agent i.e. tartaric acid to create diastereomers which will have different physical properties
separate and the cleave off the tartaric acid
What is mass spectroscopy and what is it used for?
very specific
is used to find a molecule’s molecular weight or formula
involves molecules being ionized by bombardment with electrons and then being put in an electric field
What is deuterium?
hydrogen that has an extra neutron and thus weighs 2
What is UV/vis spectroscopy and what is it used for?
used to study the structure of metals and conjugated organic molecules
the more conjugation the longer the wavelength of max absorption will be
shorter wavelength and higher energy than IR
usually for covalent bonds
What is IR spectroscopy and what is it used for?
used different wavelengths to vibrate covalent bonds in order to identify functional groups
What is IR spectroscopy data measured in?
wavenumber, which is indirectly proportional to wavelength and directly proportional to frequency and energy
usually graph goes from 1000 to 4000 cm^-1
What is usually found in the 600-1600cm^-1 range on IR data?
nothing useful, this is the fingerprint region
Where are CH bonds found in an IR?
spikes at 2800-3300 cm^-1
Where are C-C double bonds found in an IR?
1650 cm^-1
How does stiffness affect bond vibration in IR?
more stiff bonds resonate at higher frequencies
Where are C-C triple bonds found in an IR?
2200 cm^-1
How does atomic mass affect bond vibration in IR?
atoms with higher mass have lower frequency
ie C would be higher than O
Where are most common functional groups found on an IR?
1600-3500 cm^-1
Describe an OH on an IR graph
strong broad peak (because of H-bonding) from 3600-3200 cm^-1
Describe an NH bond on an IR graph
little bit wide, moderately strong peak from 3150-2500
Describe a carbonyl bond on an IR
strong spike around 1700
Describe an alkene on an IR
variably strong around 1650
Describe a CN triple bond on an IR
variably strong, around 2200
Describe a CC triple bond on an IR
variably strong, less strong than CN
around 2200
What is usually the difference between aliphatic and aromatic CH bonds on an IR?
aliphatic CH bonds are usually a little less than 3000
aromatic CH bonds are usually a little more than 3000
Where are CH bonds found in general in an IR?
3300-2700
Where are sp3 carbons on an IR?
3000-2850
Where are sp2 carbons on an IR?
3150-3000
Where are sp carbons on an IR?
3300
Which side is downfield on an NMR? Are these shielded or deshielded?
downfield is to the left
this is deshielded
What is HNMR for?
it uses light energy and absorption for the structural info of the hydrogens in a molecule
What does the number of peaks in an HNMR tell you?
the number of non-equivalent hydrogens
What is the area under a peak of an HNMR proportional to?
RELATIVELY proportional to the number of Hs of that type
What does splitting tell you on an HNMR?
of non-equivalent H neighbours + 1
What do shift values on an HNMR tell you?
tell you about the environment of the H i.e. the shielding
What is shielding?
the electrons around an H make a magnetic field which shields it, therefore giving it more energy for absorption, moving it upfield
What is happening to a deshielded H?
electrons are being pulled away from it, creating less of a personal magnetic field
shifted downfield on an HNMR
What affect do heteroatoms have of Hs in an HNMR?
they block so you can only see Hs on one C away
What are heteroatoms?
any atom that isn’t carbon or hydrogen
What affects the shielding of an H?
electronegativity of neighbouring atoms
hybridization
acidity and hydrogen bonding
How does acidity affect the shielding of Hs?
deshields them
acidic Hs are downfield on an HNMR
How does electronegativity of neighbouring atoms affect the shielding of Hs?
near electronegative atoms Hs are more deshielded
How does hybridization affect the shielding of Hs?
sp are most deshielded > sp2 > sp3 are the most shielded
greater the s character the more deshielded
Where are aldehyde Hs found on an HNMR?
9-10ppm
**Where are aromatic Hs found on an HNMR?
6.5-8
**Where are vinyl Hs found on an HNMR?
5-6
Where are halogen, beside an amine or beside an ether Hs found on an HNMR?
2.5-4
**Where are alkyl (normal) Hs found on an HNMR?
just above 0-2
Where are carboxylic acids Hs found on an HNMR?
10-13
Where are alcohol Hs found on an HNMR?
2-5
Where are benzylic Hs found on an HNMR?
2.5-3.5
Where are alkyne Hs found on an HNMR?
2
Name 6 oxidizing agents. What will they reduce alcohols to?
H2CrO4 CrO42- Cr2O72- MnO4- CrO3 PCC they will all reduce primary alcohols to carboxylic acids except for PCC (aldehyde) they will all reduce secondary alcohols to ketones
What happens in a nucleophilic addition reaction?
pi bond is broken
2 sigma bonds are formed
Name 2 reducing agents. What do they usually do?
NaBH4
LiAlH4
usually add a hydride to a carbonyl, making an alcohol
What kind of solvent is used when using a Grignard reagent?
aprotic solvent (because they’re very basic)
What are mesyls and tosyls used for?
protecting alcohols or amino groups
have SO3- attached to some Cs
What is used to form an imine?
weakly acidic conditions and an aldehyde or ketone with a primary amine
What is used to form an examine?
catalyzed with acid
aldehyde or ketone with a secondary amine
(can be reversed with aqueous acid)
What is an aldol condensation reaction?
when the enolate of one carbonyl compound reacts with the carbonyl of another carbonyl compound
forms a beta-hydroxycarbonyl compound
“crossed” when two different carbonyl compounds are used
requires strong acid
What is the thermodynamic control of aldol reactions?
use an unencumbered base and run at room temp
enolate is formed by removing protons from the more sterically crowded alpha-carbon
What is the kinetic control of aldol reactions?
use a bulky base and low temperatures
enolate is formed at the less substituted alpha-carbon
What two things can be done with the product of an aldol condensation reaction?
treat with a strong base to reverse the reaction (called a retro-aldol reaction)
or
undergo dehydration using heat to form an alpha,beta-unsaturdated carbonyl compound
How can carboxylic acids be reduced to primary alcohols?
using LiAlH4
but NOT NaBH4
Why are carboxylic acids that have carbonyl groups beta to the carboxylate unstable?
because they can undergo decarboxylation
What is acyl substitution?
also called nucleophilic addition-elimination reactions
a new pi bond is formed and 2 sigma bonds break
go through a tetrahedral intermediate
What is esterification?
carboxylic acid and alcohol react in the presence of a catalytic amount of acid to form an ester
What is saponification?
basica hydrolysis of a triacylglyceride
get glycerol and 3 fatty acids
What is used to make acid halides?
SOCl2 or PX3 (X= Br, Cl)
How is an acid anhydride made?
condensation of two carboxylic acids or addition of a carboxylic acid to an acid halide
Can amides be prepared directly from carboxylic acids?
no because they are very basic and will deprotonate the carboxylic acid first
Put the carboxylic acid derivatives in order of relative reactivity (most to least reactive)
acid chloride > acid anhydride > esters > amides
What is an SN2 mechanism?
only one step "backside attack" has a pentavalent transition state product is inverted rxn rate depends on both the nucleophile and electrophile don't want bulky Nu, should be strong less substituted substrates react faster than more substituted ones methyl > 1 > 2 >> 3 use polar, aprotic solvents
What is an SN1 mechanism?
two steps
has a carbocation intermediate
3 > 2 > 1 > methyl
results in a racemic mixture
rxn rate only depends on electrophile (leaving group needs to leave)
use ptotic solvents (stabilize the carbocation)
non-basic, weaker Nu, often the solvent itself (solvolysis)
What is Strecker synthesis?
synthetic synthesis of amino acids using ammonium and cyanide salts
(goes through an imine)
What is Gabriel-malonic ester synthesis?
synthetic synthesis of amino acids using the N in pthalamide and an alpha-bromomalonic-ester
What is DCC coupling?
used for artificially synthesizing peptides
DCC converts the OH of the carboxylate group in an amino acid to a good leaving group
