Organic Chemistry MCAT Uworld
Nucleophilic Acyl Substitution
1. Anhydride cleavage to a ester (if nuc was an alcohol) or amide (if nuc was a amide) and a carboxylic acid 2. Nucleophilic attack of carbonyl by alcohol 3. Carboxylic acid is the leaving group
L or D Chiral Center
Sugar is based on the configuration of the chiral center with the highest number R configuration = D sugar S configuration = L sugar
What is the anomeric carbon?
THe most oxidized carbon in a monosaccharide. C 1 in aldoses, C-2 in ketoses
Gas liquid chromatography
Technique used to separate molecules in a mixture based on their boiling points - Contains an injection port, mobile and stationary phase, a column in a heated oven, a detector, and computer analysis - The mobile phase is an inert gas (helium, or nitrogen) - The stationary phase is the liquid phase and coats the column - Volatility is the driving factor for the chromatography (more volatile solutions will elute out faster)
Benedicts test
Test for reducing sugars
Leaving groups for SN2
The Halogens are very good leaving groups - The larger the leaving group is the better the leaving group
Peptide Bond Formation
The amino group of one amino acid reacts with the carboxyl group of another amino acid to form a peptide bond - Releases H2O as a by products because it is a dehydration reaction
What occurs when UV chromophores absorb UV light
The energy from the UV light excited the electrons to a higher energy excited state
Minimum inhibitory concentration (MIC)
The lowest concentration necessary to inhibit the growth of a bacterium.
How many distinct fatty acids are released from a triacylglycerol
The number of distinct fatty acids released corresponds to the number of distinct hydrocarbon chains in the triacylglyceride.
Factors that affect boiling point
1. Relative strength of intermolecular forces - Stronger intermolecular force requires more strength to break apart (Ex. H bonding) 2. Boiling point increases with Molecular Weight 3. Symmetry affects (Branching decreases boiling point)
How are esters named?
1. State the prefix that corresponds to the alcohol alkyl chain 2. Followed by the name of the carboxylic acid
What is Fischer esterification?
Acid catalyzed reaction of an alcohol with a carboxylic acid 1. Acid catalyst protonates the carbonyl oxygen of the carboxylic acid making the carbonyl a good electrophile 2. Alcohol acts as a nucleophile and attacks the carbonyl carbon 3. Carboxylic -OH group gets protonated and leaves as water 4. An ester is formed
Hydrolysis of Triacylglycerols
Breaks the ester linkage releasing free fatty acids and glycerol
How to increase alcohols leaving group ability
Can be converted into a mesylate (-SO3CH3) in order to increase the leaving group ability
Amines
Can be primary, secondary, tertiary, or quartenary
SN1 reaction
Carbocation formation and then nucleophilic additions - More readily reacts with a tertiary alkyl halide because it will form a more stable carbocation - The nucleophile is generally more weak
Chiral Center
Carbon with four different substituents
Esters
Carboxylic acid derivatives formed by Fischer esterification
Mesylates and Tosylates
Commonly used sulfonates. - Improves leaving group ability of alcohol - The sulfonate ions are very weak bases and excellent leaving groups. When these are leaving groups, the reaction may proceed via Sn1 or Sn2 mechanism. - produced by the reaction of an alcohol with a base and methanesulfonyl chloride or p-toluenesulfonyl chloride, respectively.
Oxidizing agents
CrO3, PCC, H2CrO4 Can convert primary alcohols (OH) to aldehydes Can convert secondary alcohols to ketones Can convert aldehydes to carboxylic acids (except for PCC)
Dilution Factor
DF = Vt1/Vf1 x Vt2/Vf2
What does a reducing agent do ?
Decreases an atom's oxidation state and the number of bonds carbon has to electronegative atoms Increases the number of bonds to less electronegative atoms (hydrogen)
What are the products of retro aldol condensation dependent on?
Depend on the substituents on the carbonyl carbon and the B-carbon. - If the carbonyl carbon is bonded to a hydrogen before the reaction it will turn into an aldehyde, and if it is not it will turn into a ketone - If the B-carbon is bonded to a H it will become an aldehyde
Splitting pattern
Determined by the n+1 rule - n is the number of non-equivalent hydrogen atoms on adjacent carbons
Diastereomers
Differ at one or more stereocenters but have the orientation of at least one stereocenter in common - Differ in magnitude and differ in direction
What occurs in a highly conjugated system and its change in color
Difference in energy between between the ground and excited state of the electrons is equal to the energy of a particular wavelength or visible light - Determined by the electronic structure of a molecule
Which techniques separate based on boiling point
Distillation and Gas Chromatography
electron withdrawing groups vs. electron donating groups
EDG: Anything with electrons to donate • - CH3CH2... • - OR • - O- • - OH • - N-R1-R2 EWG: Lacks electrons so want to take them away • - Br, Cl, I • - Ketone • - Aldehyde • - Ester • - Carboxylic Acid • - Nitrile (triple bonded N) • - Sulfonic Acid (S double bonded to 2 O's, and 1 OH) • - Nitro (NO2) • - Protonated amine (NR1R2H)) • - Alkyl trihalide
EDG/EWG on carbocations
Electron Donating Group helps to stabilize carbocations because they donate electrons towards the positive charge Electron withdrawing groups destabilizes carbocations because it withdraws electrons from the carbon causing a partial positive charge
inductive effect
Electrons are donated through sigma bonds - Electronegative atoms or electron withdrawing substituents pull electrons away from an adjacent atom toward themselves = create larger dipoles - greater partial charges - Better leaving groups
Organic Layer
Fatty acids are insoluble in aqueous layer and are soluble in organic layer because non-polar
Electron delocalization
For a molecule to absorb UV or visible light its electrons must be sufficiently delocalized so that the energy difference between the ground and excited state correspond to the energy of the light being absorbed - Delocalization achieved by a highly conjugated system (system with alternating double and single bonds) - Larger system corresponds to a higher energy wavelength absorbed - Pi electrons are delocalized through the p-orbitals which create a extended network of conjugated pi bonds which are resonance stabilized
Acylation between anhydride and amine
Form amide and carboxylic acid
What are anhydrides?
Formed through the condensation reaction of two carboxylic acid
Furanose vs. Pyranose
Furanose: Five membered rings (4 C and 1 O) Pyranose: Six membered rings (5 C and 1 O)
Enantiomers
Have specific rotation of equal magnitude but opposite directions - would have specific rotations of +40 and -40 Have the same chemical and physical properties
Extraction
Like dissolves like is the driving force for extraction processes - Two immiscible solvents (will not remains mixed) can be used to separate solutes according to difference in polarity - Entails organic solvent to an aqueous mixture - With gentle shaking hydrophobic (nonpolar) solutes separate into the organic layer - polar/charged substances remain in the aqueous later
Types of scales on a graph
Linear, Logarithmic, or combination of both Log scales display changes in order of magnitude: 1 step is equal to 10 fold 2 step is 100 fold 3 steps is 1000 fold
hemiacetal
Originates from an aldehyde and consists of a carbon bonded to a hydroxyl group (OH), and alkyl group (OR), and an H atom
how is a pi bond vs. sigma bond formed
Pi bond: Side by side overlap of p orbitals Sigma bond: Direct end to end overlap of atomic orbitals
Primary vs. Secondary vs. Tertiary Alcohols
Primary alcohols are more likely to undergo Sn1 reactions as compared to secondary or tertiary - There is more steric hindrance with secondary and tertiary - Primary alcohols are more acidic - Form a stable tertiary carbocation
What is fractional distillation?
Purification technique that separates molecules based on their boiling point
Structure of purines & pyrimidines
Purines = Adenine and Guanine - Bigger and double carbon-nitrogen ring with four nitrogen atoms Pyrimidines = Cysteine, Thymine, and Uracil - Smaller and single carbon-nitrogen ring with two nitrogen atoms
how to form an anhydride
Reaction between a carboxylic acid and an acid chloride
What is transesterification?
Reaction between an ester and an alcohol where the ester OR group is replaced with the alcohol OR group. - Can be acid catalyzed or base-catalyzed
Decarboxylation
Reaction that removes a carboxyl group from a carboxylic acid with a B-carbonyl releasing the carboxyl (COOH) group as CO2
Oxidation of Organic Molecules
Requires a decrease in the amount of C-H bonds and an increase in the number of C-O bonds Ex. Tertiary carbon cannot be oxidized further
How to separate enantiomers in a racemic mixture:
Requires the addition of a resolving agent to change their physical properties by creating a pair of diastereomers
retro aldol condensation
Reverse of an aldol condensation Either the aldol product or the dehydration product is heated and treated with base causing the carbon carbon bond between the a and the B to break - 2 products are formed: 2 ketones/2 aldehydes/or one of each
Rf value equation
Rf = Distance compound traveled from origin/ Distance from origin to solvent front A larger Rf value means a more non-polar compound A smaller Rf value means a more polar compound
S/L and R/D
S rotation always go with L R rotation always goes with D
Isomers
Same chemical formula BUT have different connectivity (constitutional isomers) same connectivity but different arrangement (diastereomers)
How are ketone selectively reduced
Selectively reduced into a secondary alcohol by NaBH4 NaBH4 - Selective for reactive carbonyls - aldehydes and ketones - WILL not reduce esters or carboxylic acids
How are carboxylic acids selectively reduced?
Selectively reduced to primary alcohols by Borane (BH3)
TLC (thin layer chromatography)
Separates components of a mixture based on polarity and can be used to monitor reactions - Stationary phase = polar - Mobile phase = non-polar - If the mixture absorbs UV light to excite to a higher energy level then that could be indicated by the TLC
Mass spectroscopy
Separates ions according to their mass-charge ratio - m/z - Ex. If there were two charges it would be the molecular weight over the amount of charges.
Different types of distillation
Separates liquid molecules based on their boiling points Simple distillation: Best for boiling points that have a difference betweeen 25 and 150 degrees apart Fractional Distillation: Best for boiling points that have a difference <25 degrees apart Vacuum Distillation: Best for boiling points that have a different of >150 degrees apart
Reversed Phase High Performance Liquid Chromatography
Stationary phase is a non-polar compound Mobile phase = polar compound - Polar compounds would move faster through the column and non-polar would have longer retention times
stereocenters vs stereoisomers
Stereocenters: how many SINGLE chiral centers in a molecule Stereoisomers: number of single chiral centers superscripted to 2 formula = 2^n
Geometric Isomers
Stereoisomers that arise from disubstituted double bonds - Classified as cis or trans based on the relative position of the non-hydrogen substituents - separated by gas chromatography - Slightly different boiling points
steric hindrance
The prevention of a reaction at a particular location in a molecule by substituent groups around the reactive site.
Aldol Condensation Reaction
Two carbonyl compounds (ketones or aldehydes) are joined together by nucleophilic addition to form an aldol product 1. The reaction begins with deprotonation of the α-carbon on one of the substrates, forming a resonance-stabilized enolate intermediate 2. Nucleophilic addition of the enolate to the other carbonyl substrate yields the aldol product, and then deprotonation of the α-carbon 3. followed by -OH elimination, yields the conjugated product, an α,β-unsaturated carbonyl compound.
Which molecules can be seen under UV light on during TLC
UV chromophores can be visualized with UV light - These are double bonds, triple bonds, carbonyls, and conjugated systems
What are boiling chips used for?
Used to evenly heat a liquid and prevent superheating - Use in a distillation would prevent the mixture from abruptly forming large bubbles that could spill over
tollens test
Used to identify the presence of aldehydes and hydroxy ketones - Utilizes oxidizing agent Ag(NH3)2 to oxidize aldehydes to carboxylic acids - Ketones must undergo tautomerization via enediol intermediate to produce an aldehyde under basic conditions - Forms a positive silver mirror deposited on the glassware
Conformational Isomers
Versions of the same molecule that form when an atoms rotates about its bond - must be the same specific rotation
Aqueous layer
Water
Polar compounds
Water, Acetone, Methanol
Good leaving groups are
Weak Bases that are able to accept electrons - halide ions (I-, Br-, Cl-) - water (H2O) - sulfonates such as p-toluenesulfonate (OTs) and methanesulfonate (OMs)
Markovnikov's Rule
When adding to an alkene, put the H on the C with the most H's already. ("The rich get richer") The halide will add to the most substituted positions
Chemical Shifts
When an electron cloud is around a proton it shields them from the external magnetic field - This causes an upfield shift (small chemical shift) An electronegative substituents withdraws electrons and de-shields the neighboring protons causing a downfield signal - An electronegative atom causes a downward shift (to the left)
How to increase the solubility of carboxylic acid in water?
When converted to carboxylate anions by a base
How does reduced pressure help with distillation
With reduced pressure boiling point can be achieved at lower temperatures
Can esters undergo B-carboxylation
Yes. It must be transformed ester + H20 --> carboxylic acid and alcohol - A cyclic transition state that incorporate both the carbonyls releases CO2 and forms an enol
Vacuum Distillation
[purification methods] separates liquids when boiling points are GREATER than 150C - under reduced pressures (decreased pressure = decreased boiling point)
How to calculate specific rotation
[α] = αobs/cxl [α] = specific rotation (degrees) αobs = observed rotation (degrees) c = concentration (g/ml) l = path length (dm)
Gabriel Synthesis (malonic ester synthesis)
a chemical reaction that transforms primary alkyl halides into primary amines. Traditionally, the reaction uses potassium phthalimide - Produces L and D amino acids
enone
alpha beta unsaturated carbonyl
Sterols
compounds containing a four-ring carbon structure with any of a variety of side chains attached. - Dissolves best in non polar solvents
mutarotation
one anomeric form shifts to another, with the straight-chain form as an intermediate
PCC
oxidation of primary/secondary alcohol to aldehyde/ketone, respectively
Aldehydes to carboxylic acids
oxidized via most oxidizing agents KMnO4 CrO3 Ag2O H2O2
Saponification
the hydrolysis of an ester with a strong base to produce a salt of the carboxylic acid and an alcohol
Difference between aldose and ketose
- If the carbonyl is an aldehyde (double bond at the end of the chain the sugar is an aldose - If the carbonyl is a ketone at the end of the chain the sugar
Tautomerization
- Isomerization that involves transfer of hydrogen atoms from one position to another within a molecule and the movement of a double bond to an adjacent atom - Involves keto form (C = O) = major - To enol form = minor
What does acid do in the Fischer Esterification
- Strong acids donate their protons to other molecules providing the molecule with an increased positive charge enhancing esterification - Also forms a stable carbocation intermediate - Creates a good leaving - Increases carbonyl electrophilicity
Mass Spectroscopy analysis and what does lowering the pH do?
- The Signal Intensity or the height of the data peak corresponds to the relative quantity of ions at each mass to charge ratio m/z - Ions that have multiple charges have a smaller m/z ratio because denominator has increased translating to a greater signal intensity - Lowering the pH of the solvent increases the concentration of protons and results in a greater number of multiply charge molecules
Acid chloride
-COCl
How many equivalents of base are needed to hydrolyze one ester linkage
1 equivalent of base. There are three esters in triacylglycerol meaning 3 equivalent are needed for that.
base catalyzed aldol condensation
1) base abstracts an alpha-hydrogen: leaving enolate ion 2) enolate ion acts as nucleophile, attacks carbonyl carbon: forms alkoxide ion 3) alkoxide ion is stronger base than hydroxide ion; removes proton from water and completes aldol aldol is unstable and easily dehydrated to an enal +H2O+OH-. enal stabilized by double bonds
Different functional groups absorb IR radiation at different intensities and different frequencies. Name some
3650-3200 (O-H) 3300 (sp C-H) 3100 (sp2 C-H) 2900-3000 (sp3 C-H) 1810-1650 (C=O) 1600- 1475 (C=C)
B-lactam ring
4-membered cyclic amides - Trigonal pyramidal geometry (reducing resonance) - Reduced resonance causes the nitrogen to have the sp3 hybridization - Bond angles are less than 109.5 = significant ring strain
Hemiketals
A carbon atom bonded to two alkyl groups, an -OR group, and an -OH group - From ketoses
High Performance Liquid Chromatography (HPLC)
A liquid solvent (mobile phase) carries the sample through a column filled with adsorbent material (stationary phase) - Guiding principle for separation is polarity - Molecules with a polarity similar to stationary phase have longer retention time - stationary phase = polar - Mobile phase = non-polar
Stecker Synthesis
A method for the synthesis of amino acids by the reaction of an aldehyde with ammonium chloride in the presence of potassium cyanide - Produces L and D amino acids
Racemic Mixture
A mixture that contains equal amounts of the (+) and (-) enantiomers. Racemic mixtures are not optically active. Have a specific rotation of 0 because they cancel out
How does cholesterol affect membrane fluidity?
At low temperatures there is increased fluidity At high temperature there is decreased fluidity
Alpha or beta sugar
Alpha is when it points down vs. Beta where it points up
Polarity Ranking of the Functional Groups
Amide > Carboxylic Acid > Alcohol > Ketone ~ Aldehyde > Amine > Ester > Ether > Alkane
aromatic heterocycle
Any cyclic compound containing a heteroatom (atom other than carbon or hydrogen)
Imine vs. Enamine Formation
Imine are formed when a ketone/aldehyde (C=O) reacts with a primary amine (Acid catalyzed) Enamines are formed when a ketone/aldehyde (C=O) reacts with a secondary amine (Acid catalyzed)
Bonding and nonbonding orbitals in ground state and excited state
In the ground state π electrons from double bonds are in the π bonding molecular orbital, and non bonding electrons are in the n bonding orbital When excited the electrons are excited to the LUMO (lowest unoccupied molecular orbital) called the π* antibonding orbital
Membrane fluidity
Increased phospholipid tail length, decreases membrane fluidity Increased temperature, increased membrane fluidity Increased temperature, cholesterol causes decreased membrane fluidity Decreased temperature, cholesterol causes increased membrane fluidity Increased saturation, decreases membrane fluidity
Absorption of what type of light leads to vibration and rotations
Infrared Light
What is mass spectrometry?
Ionizes molecules and detects their molecular weight - Molecular ions are broken into fragments- analyzed through another round of MS - Ion mass abundance vs. the mass to charge ratio (m/z) - Mass spectrum used to identify the mass of a molecules fragments - Ex. 3 fragments (2 units used of something)
D vs. L amino acids
L is drawn with a dashed H D is drawn with a wedge H - Natural occurring amino acids are in the L formation (except glycine) because D amino aids cannot be incorporated into proteins
What are hydride reagents?
LiAlH4 and NaBH4 - common reducing agents - Acts as a nucleophile and attacks an electrophilic atom - LiAlH4 - will reduce carbonyl compounds to alcohol - Aldehydes/Esters/Carboxylic acids reduced to primary alcohols - Ketones reduced to secondary alcohol
Triacylglycerols (triglycerides)
Made up of three fatty acids and a glycerol molecule connected through ester linkage
What techniques give rise to molecular ion peaks
Mass Spectroscopy
Does intramolecular force of intermolecular force increase boiling point
More intermolecular forces increases boiling point
IR in aromatics
O-H stretch phenol (3200 to 3650) C-C stretch phenol (1475 to 1600) N-H stretch amide (3060 to 3550) C=O amide (1650)
SN2 reaction
Occur when a nucleophile attacks an electrophile causing the leaving group to leave in the same step - Take place more readily on the less substituted carbon - Less sterically hindered --> nucleophile easier attack the electrophilic substrate - Halide leaving group ability increases as the size of the halide increases
Fluorescence
Occurs when a photo in the ultraviolet or visible region is absorbed by a fluorophore - Photon have enough energy to excite certain electrons to higher energy states - After excitation electrons loses some of its energy as heat - The remaining energy is emitted as a longer wavelength (less energy)
Oxidation Reduction Reaction
Occurs when electrons are transferred from one atom to another - A molecule is oxidized when it loses electrons and the number of carbon-heteroatom bonds increase - A molecule is reduced when it gains electrons and the number of carbon-heteroatom bonds decreases Ex. In the ETC, ubiquinone receives two electrons from NADH reducing carbonyl carbons to hydroxyls and forms an aromatic ring
What is decarboxylation?
Occurs with B-dicarbonyl compounds - Removal of a CO2 group
SN2
One step process (fast) - More readily reacts with primary because less steric hinderance - Requires a strong nucleophile (generally bears a negative charge)
Protecting Groups
Organic molecules that are functional groups that tend to be stable under reducing and oxidizing conditions
