Orgo
Enantiomeric excess
% of highest conc. enantiomer - % of lower conc. enantiomer
IR spectra are plotted as _____________ vs ______________
% transmittance vs wavenumber (cm^(1))
pKa of acid halide
-
pKa of +O-H
-2
∆G =
-RTln(Keq), where R = 8.314 J/mol*K Keq = [Products]/[Reactants] = [Equatorial]/[Axial]
Suffix for carboxylic acid Suffix for carboxylic acid salts Suffix for dicarboxylic acids
-oic acid -oate -dioic acids
Most hydrogen nuclei come into resonance ___ to ___ ppm downfield from TMS
0 to 10
Name the intermolecular forces from strongest to weakest
1) H-bonding (N, O, F) 2) Dipole-dipole 3) van der Waals/London dispersion
Gabriel synthesis
1) Potassium phthalimide + diethyl bromomalonate (SN2) 2) Base makes carbanion 3) SN2 w/ R-Br 4) NaOH, H2O, Δ opens ring and detaches part 5) H3O+, Δ gets rid of one CO2 and protonates the other
Good bases (5)
1) RO⁻ (oxides) 2) RC(triple bond)C⁻ (alkynides) 3) NH₂⁻ 4) H⁻ 5) ∆ OH⁻ for tertiary too!
van der Waals forces increase with...
1) Size (more important--the heavier, the stronger) 2) Shape: Ring > Straight Chains > Branched Chains (in order of decreased stacking ability)
Molecular vibrations measured by IR spectroscopy
1) Symmetric bend 2) Asymmetric bend 3) Symmetric stretch 4) Asymmetric stretch Also twisting and folding
Bulky bases (3)
1) t-BuO- 2) LDA 3) LiTMP
pKa of +N-H
10
Specific rotation is the rotation that ________ produce Opposite enantiomers produce
100% pure enantiomer (like only R or S) opposite rotation (like -10 instead of +10)
pKa of H2O
15.7
pKa of ROH
16
pKa of alpha H
20
pKa of alkyne H
25
How many stereoisomers?
2^n n = number of chiral centers
Number of hydrogens for saturated hydrocarbon
2n+2
pKa of NH3
35
1 kcal = ? J
4.184 J
pKa of alkene H
44
pKa of COOH
5
pKa of alkane H
50
A condensation reaction...
A chemical combination of two organic molecules that releases water
Universal indicator
A mixture of indicators which show different colors in solutions of different pHs ROYGBIV from very acidic to very basic
Racemic mixture
A mixture that contains equal amounts of the (+) and (-) enantiomers. Racemic mixtures are not optically active
Strecker synthesis
ALDEHYDE + NH4Cl + KCN NH4 attacks carbonyl carbon, generating an IMINE that is attacked by CN to make an aminonitrile which is hydrolyzed to make an amino acid
Organic phosphates
ATP, GTP, and those in DNA
Micelles
Absorb nonpolar organic molecules in their exterior, can be solvated w/ water due to exterior hydrophilic shell!
Aldehyde + alcohol (+ acid)
Acetal
Smallest ketone
Acetone (IUPAC name propanone)
Lewis definition of acids and bases
Acids are e- pair acceptors, bases are e- pair donors
Bronsted-Lowry definition of acids and bases
Acids are proton donors, bases are proton acceptors
Arrhenius definition of acids and bases
Acids have H, bases have OH
Nucleophilic substitution reactivity
Acyl chlorides > anhydrides > esters > amides > carboxylates
Why do carbonyl compounds have higher bp than corresponding alkane but lower bp than corresponding alcohol?
Alcohols participate in H-bonding
NMR shifts for H in: Alkyl groups Alkynes Alkenes Aromatics Aldehydes Carboxylic acids
Alkyl groups: 0-3 ppm Alkynes: 2-3 ppm Alkenes: 4.6-6 ppm Aromatics: 6-8.5 ppm Aldehydes: 9-10 ppm Carboxylic acids: 10.5-12 ppm
Ubiquinone (draw)
Also called Coenzyme Q: Biologically active quinone that is an electron carrier in Complexes I, II , and III of the electron transport chain Reduces to ubiquinol Long alkyl chain allows for molecule to be lipid soluble, carrying electrons within the phospholipid bilayer
Wavenumber
Analog of frequency used for infrared spectra instead of wavelength. f = c/λ whereas wavenumber = 1/λ
Alpha carbon
Any carbon attached directly to a carbonyl carbon
How does using base help with extracting an acid?
Base will associate with H, leaving A- behind. The A- will be more soluble in the aqueous layer b/c it's charged
Affinity chromatography
Beads are coated w/ a receptor that binds the protein of interest (high affinity), then eluted by washing the column w/ a free receptor that competes w/ the bead bound receptor and frees protein or by changing pH or salinity levels to disrupt bond b/w ligand & protein
Decalin
Bicyclic molecule
pKa trend
Bigger, more EN atoms are more acidic! (lower pKa)
Retro-aldol
Break link between ketones (acid/base cat)
Amphoteric
Can act as acid or base
Vinyl group
Carbon double bond with extra C
Highest priority functional group
Carboxylic acid
Cis alkenes have ______ heats of combustion than trans
Cis are less stable than trans, so cis have lower heats of combustion
Aliphatic
Containing only C and H (includes proline and methionine)
HCN + aldehyde (+ acid)
Cyanohydrin
IR peaks: 1900-2200 medium, 1600-1680 weak
C≡C or C≡N C=C
Peptide bond synthesis occurs with ____
DCC
Hyperconjugation
Delocalization of charge by the interaction of an empty p-orbital (often of a carbocation) with an adjacent, eclipsed sigma bond
Since the compounds in TLC are usually white, how do we see them?
Developed plate is placed under UV light or substances are stained (but this destroys them)
Types of stereoisomers
Enantiomers and diastereomers
Michael Addition
Enolate attacks an α,β-unsaturated carbonyl double bond
Aldol Condensation
Enolate ion attacks the carbonyl carbon directly Can do the E1cb after to get rid of alcohol
Which preference is best for big groups in chair cyclohexane?
Equatorial
How do we use distillation to make alcoholic drinks?
Ethanol boils at a lower temp than water; it is the condensate
3 solubility-based separation methods
Extraction, filtration, recrystallization
True/False: a single extraction with a larger volume of water us better than multiple with a smaller volume
False
Slow step in SN1/E1
First one, making the carbocation
What kind of distillation should be used if BPs are less than 25 deg apart and why?
Fractional The fractionation column increases surface area so vapor condenses on extra surfaces + refluxes back down until rising heat makes it evaporate again to do it all again higher up the column (refined sep)
Aldehyde + water (+ acid or base)
Gem-diol
Gravity filtration vs vacuum filtration
Gravity filtration is used for when the desired product is in solution (usually hot to keep product dissolved) where as vacuum filtration has the desired product being a solid
3 intermolecular forces that affect solubility
H bonds, dipole-dipole interactions, + van der Waals (London) forces
Phosphoric acid
H3PO4 Sometimes referred to as inorganic phosphate (Pi). At pH 7 exists as HPO4 (2-) and H2PO4-
Meso compounds
Have two or more chiral centers, but also have an internal line of symmetry that make them achiral. An even number of chiral centers must have opposite configurations
Hoffman/Zaitsev = thermodynamic/kinetic control?
Hoffman = lower Ea = kinetic control Zaitsev = overall lowest G = thermodynamic control
Cahn-Ingold-Prelog priority rules
How to determine priority for R/S or cis/trans
Markovnikov's Rule
Hydrogen will add to the least substituted carbon of the double bond
IR spectroscopy is best for...
ID of functional groups
n+1 rule
If a signal is split by n neighboring equivalent protons, it will be split into n+1 peaks
Amine + aldehyde
Imine + water
Strong oxidizing agents
KMnO₄ and the Cr⁶⁺ reagents
Kinetic vs thermodynamic enolate
Kinetic is with strong, sterically hindered base at LOW TEMP Thermo is with weaker, smaller bases at HIGH TEMP
Naming cyclic amides
Lactams Use B- in front to denote the letter of carbon forming bond w/ N (this tells you how big the ring is) Ex. B-lactam, gamma-lactam
Naming cyclic esters
Lactone Use B- in front to denote the letter of carbon forming bond w/ N (this tells you how big the ring is) Ex. B-propiolactone, gamma-butyrolactone
Strong reducing agent
LiAlH₄
Gas chromatography
Main difference is that eluent (usually He or N2) is an inert gas instead of a liquid. Stationary phase is a thin layer of material inside the column. Vaporize the liquid (MUST BE VOLATILE-low melting pt) before separation. Molecules are separated based on POLARITY + BP. Typically the polarity of the stationary phase matches that of the solute. Detector records material as peaks on a chart)
Saponification
Mixing long-chain carboxylic acids (fatty acids) with a strong base results in a salt called a soap plus glycerol
Ion-exchange chromatography
Molecules separated based on net surface charge by a saline
Chair flip process
Move everything over by one Axial --> equatorial Equatorial --> axial BUT up/down stays the same!
Weak reducing agent
NaBH₄
Common name of a ketone
Name alkyl groups on either side alphabetically and then add ketone Ex. 2-butanone is ethylmethylketone
Naming anhydrides
Names of parent acid(s) in alphabetical order followed by anhydride Ex. ethanoic propanoic anhydride)
Torsional strain
Neighboring carbons possess hydrogens that overlap in space
Enantiomers
Non-superimposable mirror images Opposite configuration at all chiral centers
IR peaks: 3300 broad, 3300 sharp , 1750 sharp
OH, NH, C=O
Geminal/vicinal
On the same carbon/on adjacent carbons
Why do you need to beware of reactions of organometallics with acidic hydrogens?
Organometallics act as STRONG BASES You'll RUIN the organometallic :(
Hydroxyquinone (draw)
Oxidation of quinones
Why do E2 reactions have an anti-coplanar (or diaxial) requirement?
Pi-orbitals need to overlap to create a double bond
SN2 prefers this solvent
Polar aprotic solvents because they can't H-bond and decrease nucleophilicity
SN1 prefers this solvent
Polar protic solvents because they stabilize the TS
What is the point of a boiling chip in distillation?
Provides surface area which allows for the liquid to smoothly boil
What is released in phosphodiester synthesis?
Pyrophosphate (PPi, P2O7 (4-)) Can be hydrolyzed to 2 inorganic phosphates
R vs S isomers
R: CW S: CCW
Relative vs absolute configuration
Relative: gives stereochem of compound in relation to another compound (ie D and L) Absolute: gives stereochem of compound by itself (ie R and S)
Size-exclusion chromatography
Relies on porous beads; larger molecules elute first because they are not trapped in small pores
Retardation factor
Rf = distance spot moved / distance solvent front moved
All amino acids have __ stereochem except _____
S (L), cysteine
Reagents used to transform alcohols into alkyl halides
SOCl₂ and PBr₃ (Always SN2, so only 1° and 2° alcohols)
Stereoisomers
Same connectivity, different arrangement
Diastereomers
Same connectivity, not mirror images Opposite configuration at some but not all chiral centers
Chromatography
Separates protein mixes on the basis of their affinity for a stationary phase or a mobile phase
What kind of distillation should be used if BPs are under 150 deg and are at least 25 deg apart and why?
Simple Temp isn't so high that compounds degrade
How are stereoisomers and conformational isomers different?
Stereoisomers cannot be made to be identical through rotation of single bonds
Conformational isomers
Stereoisomers that differ by rotation about one or more single bonds, usually represented using Newman projections
E2: Strong or weak Nu? TS or intermediate? Concerted or 2-step mech? Unsubstituted or highly substituted LG? Stereochemistry?
Strong TS Concerted Highly substituted Anti-coplanar (180°)
SN2: Strong or weak Nu? TS or intermediate? Concerted or 2-step mech? Unsubstituted or highly substituted LG? Stereochemistry?
Strong TS Concerted (making/breaking bond at same time) Unsubstituted Inversion
How to cleave peptide bonds
Strong acid or base
Constitutional isomers
Structural isomers: same molecular formula, different connectivity
Three polar aprotic solvents
THF, DMSO, DMF
______ is used to calibrate NMR to 0 ppm
Tetramethylsilane (TMS) SKIP THIS WHEN COUNTING PEAKS
High performance liquid chromatography (HPLC)
The P used to stand for pressure. HPLC is a type of liquid chromatography that uses high pressure to pass the solvent phase through a more finely ground stationary phase. This gives HPLC higher resolving power than regular column chromatography
Transmittance
The amount of light that passes through the sample onto the detector
Element effect for leaving group stability
The best leaving groups are more EN and bigger
Spin-spin coupling
The interaction between spin states of non-equivalent nuclei that results in a group of peaks in an NMR spectrum
Why do carboxylic acids have higher bp than corresponding alkanes and alcohols?
They are polar and H-bond well
Hammond Postulate
Transition state resembles the structure (and energy) of the reactant or product that is closest to it in energy
Naming amides
Use N to denote alkyl groups attached to nitrogen atom Ex. N, N-dimethylpropanamide
Naming esters
Use suffix -oate Substituent on one side, and then the other, counting the carbonyl carbon Ex. isopropyl propanoate
Preparative TLC
Used for purification of compound. Larger spot of sample splits into bands of individual compounds which are then scraped off + washed to reveal pure ones
Reverse phase chromatography
Uses a nonpolar card with a polar solvent
Column chromatography
Uses beads of a polar compound, like silica or alumina (stationary phase), with a nonpolar solvent (mobile phase) Different compounds migrate at different speeds
What kind of distillation should be used if BPs are over 150 deg and why?
Vacuum Vacuum lowers ambient (air) pressure, which decreases the temp the compound must reach to boil (remember liquids boil when vapor pressure equals ambient pressure)
Fischer projection
Vertical lines are into the page (dash) Horizontal lines are out of the page (wedge)
Quinone (draw)
Vitamin E and K Produced by oxidation of phenols
Reverse of extraction
Wash: add small amount of solute to dissolve impurities away from organic product
______ is removed during peptide synthesis
Water
E1: Strong or weak Nu? TS or intermediate? Concerted or 2-step mech? Unsubstituted or highly substituted LG? Stereochemistry?
Weak Intermediate 2-step Highly substituted Non-specific (no anti-coplanar)
SN1: Strong or weak Nu? TS or intermediate? Concerted or 2-step mech? Unsubstituted or highly substituted LG? Stereochemistry?
Weak Intermediate 2-step Highly substituted Racemic
When do you use a prefix for a functional group?
When it's not highest priority
Z vs E isomers
Z: cis (THINK: ciz) E: trans
Ka =
[H+][A-]/[HA]
Optical activity equation
[alpha] = alpha * c * l, where [alpha] = specific rotation alpha = observed rotation c = concentration (g/mL) l = length (dm) + = CW = d - = CCW = l
UV spectroscopy measures...
absorbance of UV light of various wavelengths passing through a sample, which causes movement of electrons between orbitals Don't need to interpret data for MCAT
UV spectra are plotted as _____________ vs ______________
absorbance vs wavelength
NMR spectroscopy measures...
alignment of nuclear spin with an applied magnetic field
Observed rotation
alpha = [alpha]*ee, where alpha = observed rotation [alpha] = specific rotation ee = enantiomeric excess
Amino acids are ______, meaning that they can act as acids or bases
amphoteric
Cyclo- and iso- are/aren't included in alphabetizing?
are
Distillation separates compounds according to differences in their ________
boiling points
Soaps contain a hydrophilic ______ head and a hydrophobic ______ tail
carboxylate, alkyl
Absorption of visible light gives ______
complementary color
UV spectroscopy is best for...
compounds w/ double bonds or heteroatoms w/ lone pairs that create conjugated systems
Is the compound with the lowest BP the condensate or the distillate?
condensate b/c it goes to the gas phase first and then condensates
Heat of combustion of alkanes ______ with branching
decreases
Diastereomers have ________ physical properties
different This includes cis/trans
Constitutional isomers have ________ physical properties
different (melting pt, boiling pt, etc.)
Protons near EN atoms produce a _______ shift
downfield THINK: deshield = downfield
Keq =
e^(-ΔG/RT), where R = 8.314 J/mol*K
Common names for methanal, ethanal, and propanal
formaldehyde, acetaldehyde, propionaldehyde
Common names for methanoic acid, ethanoic acid, and propanoic acid
formic acid, acetic acid, propionic acid
NMR spectra are plotted as _________ vs _________
frequency vs energy absorption (chemical shift δ in ppm)
With a neutral nucleophile and bad backside, ___ can favor E1 over SN1
heat
Draw the big daddy flowchart
http://lightcat-files.s3.amazonaws.com/pdfs/fgjUSGRmTna3LiOlT0K7_13A-ORGO-06j-Big%20Daddy%20Mechanism%20Flowchart.pdf
Nuclei with magnetic moments that are aligned with the field are said to be...
in the a-state (lower energy)
Bulk increases/decreases basicity?
increases
In a Fischer projection, rotating 90 deg ______ stereochem
inverts
The more a proton's electron density is pulled away, the _____ it can shield itself from the applied magnetic field
less
Superheating occurs when...
liquid is heated to above its boiling pt without vaporization--can happen when gas bubbles in a liquid can't overcome Patm and surface tension
Nuclei with odd _____, odd ______, or both will have a magnetic moment when placed in a magnetic field
mass numbers, atomic numbers
Mass spectrometry separates ions by their ________ ratio. It's then used to determine ________
mass-to-charge molecular weight
In recrystallization, the product is dissolved in a _____ amount of hot/cold? solvent and left to recrystallize as the flask cools, excluding the _______
minimum hot impurities
IR spectroscopy measures...
molecular vibrations via a change in dipole moment (bond stretching or bending) after absorbing IR radiation, looking at wavenumber (cm^(-1)) Diatomic molecules do not absorb b/c don't have dipole moment Best for ID of the functional groups present in molecules!
Molecules with a lower energy gap between HOMO and LUMO are _____ excited and can absorb _______ wavelengths (_______ frequencies) with ______ energy
more easily longer, lower lower
In the SN2 reaction, a _______ nucleophile reacts with an ________ LG to produce substitution in ______ step(s)
negatively charged accessible one
In the SN1 reaction, a _______ nucleophile reacts with an ________ LG to produce substitution in ______ step(s)
neutral inaccessible two
For E2, the number of ________ determines the number of possible products
non-equivalent B-carbons with at least one hydrogen
The more ______ a compound is, the farther it will move up the TLC gel and the ______ its Rf will be
nonpolar higher
Mobile phase is _______
nonpolar (usually the solvent that moves down the card/column)
Protic solvents hinder __________, so ____ and ____ reactions prefer them
nucleophiles, SN1 and E1
Stationary phase is _______
polar
E1 rate
rate = k[RX]
SN1 rate
rate = k[RX]
E2 rate
rate = k[RX][Nu]
SN2 rate
rate = k[RX][Nu]
Extraction is performed in a _______
separatory funnel
Stationary phase in TLC
silica gel (polar)
Filtration isolates a _______ (________) from a _______ (________) using a paper filter
solid (residue) from a liquid (filtrate)
Questions about boiling/melting points of molecules are always referring to the...
strength of IMF's between molecules
In the E2 reaction, a _______ nucleophile reacts with an ________ LG to produce beta-elimination in ______ step(s)
strong inaccessible one
The height of/area under a NMR peak is proportional to ______
the number of chemically equivalent protons
Conformational isomers have ________ physical properties
the same
Enantiomers have ________ physical properties
the same (aside from optical activity)
Symmetric stretches do not show up in IR spectra b/c...
they involve no net CHANGE in dipole moment
Extraction combines...
two immiscible liquids Nonpolar layer: organic layer (diethyl ether, on TOP) Polar layer: aqueous layer
All molecules have _______ forces
van der Waals
Strong acids are _____ bases
weak
In the E1 reaction, a _______ nucleophile reacts with an ________ LG to produce beta-elimination in ______ step(s)
weak inaccessible two
PCC is a... It can add one oxygen to ___ alcohols
weak oxidizing agent 1° (can't make beyond aldehydes)
Cis and trans for chairs is based on _________, not _________
whether substituents are facing up/down not axial/equatorial
In neutral solutions, amino acids exist as _______
zwitterions
Gibbs free energy equation
ΔG = ΔH - TΔS