Alkane
a hydrocarbon containing only single covalent bonds
Alkene
Alkyne
Alcohol
Ether
Ester
Amine
Aldehyde
Ketone
An organic compound with a carbonyl group of which the carbon atom is bonded to two other carbons.
Alkoxy
is an -OR group, an alkyl (or aryl) groupatttached to an oxygen atom.
Alkyl group
Carbonyl
carbon atom with a double bond to an oxygen atom
Hydroxyl
A functional group consisting of a hydrogen atom joined to an oxygen atom by a polar covalent bond. Molecules possessing this group are soluble in water and are called alcohols.
Acetyl
In organic chemistry, acetyl is a functional group, the acyl with chemical formula CH3CO. It is sometimes represented by the symbol Ac (not to be confused with the element actinium). The acetyl group contains a methyl group single-bonded to a carbonyl.
Gem-/Vic-
Vicinal on 2 different adjacent carbons
Geminal- on same carbon
Tosyl
a compound containing the functional group -SO3C6H4CH3, derived from toluenesulfonic acid.
Mesyl
a compound containing the functional group -SO3CH3, derived from methanesulfonic acid.
Carboxylic Acid
Amide (think of amino acid strucutre)
Anhydride
A functional group containing two carbonyls separated by an oxygen atom (RCOOCOR); often the condensation dimer of a carboxylic acid.
Aryl
organic halide in which the halogen atom is attached to an aromatic ring, such as a benzene ring
Halogens (fluorine, chlorine, bromine, iodine, astatine) are nonmetal elements that are highly electronegative and reactive.
Benzyl
benzyl is the substituent or molecular fragment possessing the structure C6H5CH2-. Benzyl features a benzene ring attached to a CH2 group.
Hydrazine
Vinyl
vinyl or ethenyl is the functional group ?CH=CH2, namely the ethylene (IUPAC ethene) molecule (H2C=CH2) minus one hydrogen atom. The name is also used for any compound containing that group, namely R?CH=CH2 where R is any other group of atoms.
Allyl
An allyl group is a substituent with the structural formula H2C=CH-CH2R, where R is the rest of the molecule
Nitrile
A nitrile is an organic chemical that contains a cyano functional group (subunit), CN-, in which the carbon and nitrogen atoms have a triple bond i.e. C?N-. The general chemical formula of a nitrile is RCN, where R is the organic group.
Epoxide
`
Enamine/Imine
An enamine is an unsaturated compound derived by the condensation of an aldehyde or ketone with a secondary amine. Enamines are considered to be nitrogen analogs of enols. If one of the nitrogen substituents is a hydrogen atom, H, it is the tautomeric for
Acyl
a functional group derived by the removal of one or more hydroxyl groups from an oxoacid,[1] including inorganic acids. It contains a double bonded oxygen atom and an alkyl group.
Aromatic
Aliphatic
In organic chemistry, hydrocarbons (compounds composed of carbon and hydrogen) are divided into two classes: aromatic compounds and aliphatic compounds also known as non-aromatic compounds.
Aliphatics can be cyclic, but only aromatic compounds contain an
Sulphone
an organic compound containing a sulfonyl group linking two organic groups.
Nitro
Nitro compounds are organic compounds that contain one or more nitro functional groups (?NO2). The nitro group is one of the most common explosophores (functional group that makes a compound explosive) used globally. The nitro group is also strongly elect
Acetal
An acetal is a functional group with the following connectivity R2C(OR')2, where both R' groups are organic fragments.
Ketal
term ketal is sometimes used to identify structures associated with ketones rather than aldehydes and, historically, the term acetal was used specifically for the aldehyde cases.
Hemiacetal
A functional group that contains a carbon atom bonded to one -OR group, one -OH group, an alkyl chain, and a hydrogen atom.
Hemiketal
A carbon atom bonded to two alkyl groups, an -OR group, and an -OH group
Meth
1
eth
2
prop
3
but-
4
pent-
5
hex-
6
hept-
7
oct-
8
non-
9
dec-
sec-butyl
isopropyl
isobutyl
tert-butyl
IUPAC RULES
IUPAC Rules:
1) Find the longest carbon chain.
� If there is a tie, the one with the most substituents is the parent chain.
2) The terminal carbon closest to a substituent is numbered #1.
� If there is a tie, look at the second substituent.
3) Order the s
Sigma bonds
First bond between 2 elements is always a sigma bond (?), it is the head to head overlap of two atomic orbitals
Pi bonds
The second and third bonds are always
pi (?) bonds and involve side-to-side overlap
of two p orbitals. Because pi bonds require
side-to-side overlap, the atoms must be fairly close to one another
As the radius of either atom increases, the p orbitals are
Q1. Which is stronger, a sigma bond or a pi
bond? Why?
Pi bonds themselves are weaker associations than are sigma bonds. However, a double bond (one sigma bond plus one pi bond) is stronger together than a single bond (one sigma bond only).
Also, triple bonds are much shorter, stronger bonds than are single b
Hybridization
Definition: Atoms, when bonded, hybridize (i.e., mix) their higher and lower energy valence electron orbitals to form "hybrid orbitals" with intermediate energy.
Carbon, for example, has two electrons in the s orbital and two electrons in the p orbital. H
sp hybridization
50% p character and 180 degree ideal bond angle
sp2 hybridization
33% s / 67% p
Trigonal Planar or Bent [120?]
sp3 hybridization
75% p character, 25% s
Tetrahedral, Trigonal Pyramidal, or Bent [109.5?]
sp3d hybridization
Trigonal Bipyramidal, Seesaw, T-Shaped, or Linear [90?/120? or 180?]
sp3d2 hybridization
Octahedral, Square Pyramidal, or Square Planar [90?]
Valence Shell Electron Pair Repulsion Theory:
The theory that predicts which shape molecules will take due to the repulsion of lone pairs of electrons. It is often abbreviated as VSEPR.
Bond Length and Bond Strength
Bond Length- shortest to longest
Triple bonds-> double bonds-> single bonds
Stability- least to most
Single->double->triple
Reactivity- least to most
single-> triple-> double
Bond strength- Weakest to strongest
single-> double-> triple
Dipole Moment
Any time charge is not evenly distributed within a bond (i.e., when the two atoms have non-identical electronegativities) that bond will have a dipole moment
q= charge and r= distance between charges
Molecules with two or more dipole moments can still hav
Forming and Breaking Bonds
Energy is released when bond is formed and is required when bond is broken
Heat of Combustion: When molecules are combusted, all of the bonds are broken and then reformed via a radical reaction. The less stable the bond, the greater will be the heat of co
Coordinate Covalent Bonds
A coordinate covalent bond is one in which both electrons shared in the bond are donated by one atom.
metal ion complexes, several Lewis bases "donate" their "free" pairs of electrons to an otherwise naked metal cation, which acts as a Lewis acid and "acc
Examples of Coordinate Covalent Bonds
Students will see two types of coordinate covalent bonds. The first one is illustrated any time a nucleophile with a lone pair abstracts a proton: NH3 + HCl -> NH4 + Cl- . The amine binds a fourth hydrogen, but the electron belonging to that hydrogen stay
The Octet Rule
Atoms of low atomic number (<20) tend to gain or lose electrons to obtain exactly eight electrons in their valence shell. This is the highly stable "noble gas configuration." This is why sodium forms the ion Na+ and not Na2+
o EXCEPTIONS to the octet rule
Valence
The number of bonds an atom "normally" makes: carbon and its family are tetravalent; nitrogen and its family are trivalent; oxygen and its family are divalent and fluorine and its family are monovalent.
The electrons in the outermost shell (main energy le
Formal Charge
The difference between the # of electrons in an atom's valence shell when it is in its ground/elemental state and the number assigned (lone-pair electrons and 1/2 of the bonding electrons) to it in a molecule.
Molecules prefer to get as close to 0 as poss
Resonance
Important Clarifications:
o Resonance structures are a "snapshot" of the different arrangements of electrons that contribute to the "actual structure."
o The actual structure is a weighted average (i.e., hybrid) of all of the contributors and does NOT loo
Drawing Resonance Structures
Drawing Resonance Structures:
o Atoms can never be moved.
o Single bonds can never be moved.
o All structures must obey the octet rule (excluding the exceptions outlined previously).
o All structures must have the same number of total valence electrons (i
Ranking Resonance Structures:
If determining the relative contribution of various resonance structures to the actual structure, the individual structure that contributes the most to the actual structure is the one that:
1) Allows the most atoms to have a full octet (unless atom is a c
Q12. Draw all possible resonance structures for a) an amide (R-CONH2) and b) the phosphate ion (PO43-).
In each case rank each structure in terms of its contribution to the actual structure.
The possible resonance structures are drawn below. For the amide, the most stable structure is the one to the far left because there is no separation of charge. Next in line is the middle structure because it places a positive formal charge on carbon, whe
Aromaticity:
Aromatic compounds are conjugated, unsaturated ring systems that exhibit greater stability than one would expect based on either resonance or conjugation alone.
For example, benzene shows far greater stability than other unsaturated compounds with three d
Lewis Dot STructure
Line-Bond Formula
Wedge-Dash Formula
Condensed formula
Fischer Projection
(horizontal lines project out of the page; vertical lines project into the page)
Newman Projection
Ball & Stick Model
Space Filling Model
Isomers
two molecules are isomers if they have the same molecular formula but are actually different compounds
The maximum number of optically active stereoisomers for any compound = 2^n, where n is the number of chiral centers.
Conformational Isomers
These are NOT true isomers! They are the same exact molecule. When a molecule twists or rotates around its bonds these are considered "conformers" NOT isomers.
Any compounds that have the same molecular formula and the same connectivity but that differ fr
Structural Isomers
Same formula, different bond-to-bond connectivity (For example: 2-methylpentane and 3-
methylpentane are both C6H14).
Stereoisomers
Same formula, same bond-to-bond connectivity, but different in the 3-D arrangement of their substituents
there are 2 types- enantiomers and diastereomers
Enantiomers
Two molecules with the same molecular formula and the same bond-to-bond connectivity that are non-identical, non-superimposable mirror images.
They contain at least one chiral center.
Non-superimposable mirror image
� Remember the following regarding enan
Diastereomers
stereoisomers that are not mirror images
Two molecules with the same formula and the same bond-to-bond connectivity that are non-identical, but are NOT mirror images.
There are three kinds of diastereomers you must be familiar with for the MCAT: geometric
Geometric Isomers
The E/Z Convention: prioritize the two constituents on each carbon by molecular weight (as you do for R/S). If the two higher priority substituents are on the same side = Z. If the two higher priority substituents are on opposite sides = E
Remember the fo
Epimers
Diastereomers that differ at only one chiral center. Many pairs of carboydrates are
epimers (e.g., glucose and galactose).
Anomers
Molecules that differ only in their spatial orientation at the anomeric carbon of a ring structure.
If the anomeric OH/OR group and the CH2OH group are on the same side of the ring = Beta, if they are on the opposite side = Alpha.
Absolute COnfiguration
Assign priority to all four substituents based on molecular weight, with higher molecular weight atoms receiving higher priority.
Rotate the lowest priority substituent to the back (i.e., into the page).
If proceeding in order from one to three requires a
Chirality
Often referred to as "handedness." Any atom attached to four different substituents must be chiral.
Any atom with less than four substituents cannot be chiral (and therefore cannot be an enantiomer).
ALso no superimosable,
SOmething may have chiral carbon
Rotation of Plane-Polarized Light
Enantiomers rotate plane-polarized light. R and S enantiomers rotate this light to the same degree but in opposite directions. R enantiomers can rotate this light in a clockwise or counterclockwise direction, as can S enantiomers.
If a compound rotates li
Observed Rotation
the degree to which a sample rotates plane polarized light.
However, that rotation is not a universal constant for a particular molecule. Rather, it varies depending on concentration, length of the tube, etc
Specific Rotation
Specific Rotation takes these factors into account by dividing observed rotation by the length of the tube and the concentration. Specific rotation could therefore be described as "observed rotation per length, per concentration unit.
Polarimeter
A polarimeter is an
apparatus that measures the rotation of plane-polarized light as it passes through a sample
Plane-polarized light
Planepolarized light is light that exists in only a single plane. Normally, light waves are oriented in an infinite number of planes from zero to 360�.
A polarizer can sift out all of these leaving, for example, only vertically oriented waves.
Optically active vs Optically Inactive
To be optically active means that a substance does rotate planepolarized light.
Optically inactive compounds do not rotate plane-polarized light.
Racemic Mixture
A mixture that contains equal amounts of the (+) and (-) enantiomers. Racemic mixtures are not optically active.
Meso Compounds
Molecules with two or more chiral centers that contain a plane of symmetry. This symmetry cancels out their optical activity.
To recognize them, look for a center of symmetry. However, not all molecules with a plane of symmetry are meso compounds.
Next, c
Electron Flow
HIgh to low concentration in rxns, so form a full or partial negative charge to a species with a full or partial positive charge.
Bases and Nucleophiles attack electron poor species called electrophiles
For the MCAT focus on the function: if a species abs
Bases
Abstract protons/ hydrogens
Electron dense and have full or partial negative charge
strongest base forms strongest, stable bond with hydrogen, aka strong base favors conjugate acid
basicity describes how much molecule wants to react but nothing about how
Nucleophiles
Nucleophiles attack carbons or other central atoms
electron dense have have a full or partial negative charge
Reacts fastest with available electrophile and is a function of kinetics, how fast this is going to happen, just that they are good at reacting
N
Electrophiles
Electron poor species with full or partial positive charge
accepts electrons from nucleophiles or bases,
H+ ; R2C=O ; RX ; X2 ; HX ; R3C +
Leaving Groups
Atoms or molecules that leave parent molecule during a rxn, take both electronsform the bond with they leave
best leaving groups are those that are most stable after they leave
X ; -OCOR ; -H2O + ; -Tosyl ; -NH3 + ; -N2 + (diazonium)
E1 Reaction
(Elimination, Unimolecular)
Rate depends on the concentration of one species only and is thus first order.
1) The dissociation of the leaving group, resulting in formation of a carbocation [slow step].
2) The abstraction of a proton with collapse of the e
E2 Reaction
Elimination, Bimolecular
depeonds on 2 species, thus second order
Single step abstraction of a proton with collapse of electros to form a double bond and ejection of leaving group
SN1 Reaction
Nucleophilic substitution, unimolecular
KNow mechanism
Depends only on concentration of one species, is thus first order
1) The dissociation of the leaving group, resulting in formation of a carbocation [slow step].
2) Attack of the carbocation by the nuc
SN2 Reaction
Nucleophilic Substitution, Bimolecular
Rate depends on the concentration of 2 species, thus 2nd order
1) The single-step "back side attack" of the electrophile with simultaneous ejection of the leaving group.
E1, SN1, E2, SN2 Summaries
when something is less nucleophilic in protic solution, it means that in a protic solution that has high concentrations of Hydrogens, it doesn't react well. The hydrogens keep the nucleophile shielded, thus it cannot attack
take into account how stearic h
Alkanes
Carbon carbon or carbon hydrogen single bonds, gasoline, tar, crude oil, butane, methane, etc
Nomenclature- ane suffix
Physical Properties
- insoluble in water, low density, non-polar, oil or gas
o Melting and Boiling Point Trends: Master the trends liste
Alkanes- Cylic COmpunds
Ring Strain-
Cycloalkanes create ring strain because they force bond angles to deviate from the optimum tetrahedral angle of 109.5�.
Cyclohexane in its chair conformation has zero ring strain.
Cycloalkanes with more or less than six carbons exhibit increa
Axial vs. Equatorial
red=axial
blue= equatorial
On the chair conformation of cyclohexane the axial substituents rise vertically from the ring and the equatorial substituents extend horizontally.
Large substituents are more stable (i.e., lower energy) when in the equatorial po
Combustion of an Alkane
a radical, exothermic chain reaction with oxygen; high energy of activation.
CH4 + 2O2 -> CO2 + 2H2O + Heat
From highest to lowest, heat of combustion is as follows: cyclopropane, cyclobutane,
cyclooctane, cyclohexane. Cyclooctane comes before cyclohexane
Radicals
The heterolytic cleavage of bonds during reactions results in paired electrons on just one of the atoms.
A homolytic cleavage sends ONE electron to one species and ONE to another, generating radicals.
Radicals also form as a result of damage to the molecu
Synthesis of an Alkane from an Alkene:
Formed from alkenes through rxn with H2 with metal catalyst
Syn addition- H2 added to same side
anti- new bonds formed on opposite sides
CH2=CH2 + H2/Pd(catalyst) -> CH3CH3
Alkenes
Focus on general characteristics of alkenes and seeing them prat of beta-oxidation, dehyrdation of alcohols,etc.
Anything with a double bond
Alkenesact as nucleophiles, the pi electrons will attack, leaving a carbocation on one of the carbons as a carboca
Alkynes
SImilar to alkenes in how they react,
has triple bond
Benzene
6 membered rign with alternated double and single bonds, its a conjugated pi system
Ph, C6H5, Ar
-A phenyl group, Ph, is attactched to a primary chain, a benzyl group has CH2 attaching the benzene to the ring, and aryl is ANY aromatic ring system
-C6H5, A
Alcohols
Any species with -PH funcitonal group
Can act as nucleophiles or as lewis acidwhen oxidized to a carbonyl group
Nomenclature- Alcohols have -ol suffix, butanol, cycloheanol, 1,3-hexanediol
Boiling Point- Goes up with increasing molecular weight and decrea
Hydrogen BOnding
Hydrogen bond/acceptors: F, O, or N when bonded to a H, can act as either a hydrogen bond donor or hydrogen bond acceptor
F, O, N atom with lone pairs that are not attached to a H, (ROR, RCOR, etc), cannot act Hydrogen bond acceptors
Alcohols have much hi
Alcohol Acidity
Less acidic than water
Acidity increases form tertiary to secondary to primary, meaning a primary is mostly like to give it's H
Both trends are explained by the fact that alkyl substituents are weak electron donating groups. When we look at the conjugate
Formation of an Alkyl Halide from an Alcohol via SN2 Reaction
Via SN2: CH3OH + HCl -> CH3OH2 + + Cl- -> CH3Cl + H2O
KNOW MECHANISM
o STEPS:
1) The alcohol acts as a nucleophile, attacking the electrophilic halide hydrogen and forming the good leaving group water plus a halide ion.
2) The halide ion attacks the centr
Formation of an Alkyl Halide from an Alcohol via SN1 Reaction
Via SN1: R3COH + HCl -> R3COH2 + + Cl- -> R3C+ + H2O -> R3CCl
KNOW MECHANISM
o STEPS:
1) The alcohol acts as a nucleophile, attacking the electrophilic halide hydrogen and forming the good leaving group water plus a halide ion.
2) The good leaving group w
Oxidation of an Alcohol
FOcus on recognizing oxidizing agents themselves and general characteristics, like how secondary alcohols can only form ketones and tertiary alcohols cannot be oxidized at all.
1? Alcohols -> Aldehydes -> Carboxylic Acids
2? Alcohols -> Ketones
3? Alcohol
Common Oxidizing Agents
O3, C32O7, CrO4, KMnO4, JOnes, COllins, PCC, PDC
Reduction Synthesis of an Alcohol
Reducing agents like NaBH4, LiAlH4 and H2/pressure reduce a carbonyl to an alcohol
NaBH4 can only reduce aldehydes and ketones
LiAlH4 and H2/ pressure can reduce aldehydes, ketones, carboxylic acids, and esters
Pinacol Rearrangment (Polyhydroxyl Alcohols)
Vic-diol _ hot acid-> ketone or aldehyde
Vicinal- diol (OH Neighbors) + Acid ( H3O+)
KNOW MECHANISM
Two hydroxyl groups must be in the Vicinal position and the carbons bearing those 2 hdroxyl groups must be tri or tetra substituted by R groups.
If tri-sub
Protection of Alcohols
2 common examples
KNOW MECHANISM
TMS: ROH + TMS-> RO-Si(CH3)3
Protection by MOM: ROH + Base-> RO- + CH3OCH2Cl (MOMCl)-> ROCH2OCH3 (RO-MOM)
Acidification will remove either protectiong group to restore alcohol
https://www.youtube.com/watch?v=KsdZsWOsB84
Reaction with SOCl2 and PBr3
ROH + SOCl2 -> RCl
ROH + PBr3 -> RBr
Common bases Et3N, or pyridine, C6H5N
Formation of Tosylates/ Mesylates
Tosyl-Cl + ROH -> Tosyl-OR + HCl
KNOW MECHANISM
1) The alcohol attacks the tosyl or mesyl halide via SN2, kicking off a halide ion.
2) A hydrogen is abstracted by the halide ion, quenching the charge on the oxygen
Mesylates and Tosylates are desirable bec
Dehydration of an Alcohol: Synthesis of an Alkene
o CH3CH2OH + H2O <-> CH3CH2OH2 + <-> CH2=CH2
KNOW MECHANISM
This is an equilibrium reaction. The alkene is favored by hot, concentrated acid; the alcohol is favored by cold, dilute acid.
The major product is the most substituted, most stable alkene
o STEP
Grignard Synthesis
Grignard Synthesis: Production of an alcohol with extension of the carbon chain
KNOW MECHANISM
o CH3COCH3 + CH3MgBr -> CH3COH(CH3)2
Use H3O+ to protonate the O atom
Produces an alcohol by adding RMgX (most frequently RMgBr; called an organometallic compou
Ethers
AN oxygen bonded to two R-groups in the R-O-R format
Nomeclature- ethers referred by common names wherein each -R group is named separately (Methyl ethyl ether, dietheylether, methyl propyl ether
IUPAC- STandard naming of longer of 2 -R groups as the pare
Epoxdies
Cylic ethers involving one O and 2 C in a 3 membered ring
Severe ring strain, thus highly reactive
Acid catalyzes rxn by protonation Oxygen and makig it a better elacing group
KNOW MECHANISM
Electronegativity
The greater the difference in the electronegativity of two atoms in a bond, the more polar the bond.
example-
Comparing electronegativity, we see that the partial positive charge on the carbon in a C=O bond is greater than the partial positive charge on t
Electron Donating and Withdrawing Groups
o To determine if a group is electron donating or withdrawing:
1) Look at the first atom from the point of attachment. Compare its electronegativity to the atoms bound to it. If it is more electronegative, it will bear a partial negative charge and if it
Electron donating Groups
electron donating group (EDG) or electron releasing group (ERG) is an atom or functional group that donates some of its electron density into a conjugated ? system via resonance or inductive effects, thus making the ? system more nucleophilic.
Alkyl group
Electron Withdrawing Groups
An electron withdrawing group or EWG draws electrons away from a reaction center. Makes it less nucleophilic
When this center is an electron rich carbanion or an alkoxide anion, the presence of the electron-withdrawing substituent has a stabilizing effect
SN1/SN2 and E1/E2
Review these patterns
SN1 competes with E1
SN2 competes with E2
SN1 does not compete with SN2 or E1 does not compete with E2
a 3' carbon must react via SN1 or E1 mechanism ALWAYS just on the MCAT
Acidity
ALways look at the stability of the conjugate base
STability or lack thereof will be affected by EDG or EWG.
Alcohols are weaker acids than water due to donating effect of the R groups
RESONANCE STABILIZATION, if there is resonance, it makes it more acidi
Bascity
EDG increases bascitity,
EWG decrease Bascitity
Bascity vs. Nucleopohilicity
Steric Hindrance favors bascitity over Nucleophilicity
- Nucleophiles must have VERY little hindrance,
-primary nucleophiles most common
-secondary atoms can often as as bases or nucleophiles
-tertirary atoms will only act as bases
Reactivity (low stabili
Electrophilicity
Electrophiles are always electron poor
they will ALWAYS have a full or partial positive charge
Always attacked by electron rnich species
Carbocations
MEchanism will always proceed through the most stable carbocation (unless peroxide is present)
Carbocation Stability:
Tertiary > SEcondary > Primary
Steric Hindrance
If more than one mechanism, intermediate, electrophile or nucleophile is possible
The one that invloves least steric hindrance will be favored
Count your carbons
Make sure each product has right number of carbons. Pay attention to those rxns that add to or take awa from length of the carbon.
Polar Protic Solvents
Polar protic solvents are capable of intermolecular hydrogen binding
Polar protic solvents solvate both cations and anions well
cationsare solvated by ion-dipole interactions
anions are solvated by hydrogen bonding
Affects nucleophlicity:
- In polar proti
Polar Aprotic Solvents
Polar aprotic solvens exibit diple-dipole
Solvents solvate only cations well
Anions are not well solvated because the solvent cannot hydrogen bond to them
DOwn a column of the periodic table increases nucleophilicty in aprotic solvents
Chromatography
Separation of one or more compounds by dissolving them in a mobile phase and passing that phrase through or across a stationary phase
Substances in mobile phase interact to varying degrees based on their polarity
More interaction= slower movement
Substanc
Thin-Layer CHromatography
TLC is a solid-liquid partitioning technique in which the mobile liquid phase ascends a thin layer of absorbent (generally silica, SiO2).
The thin layer absorbent acts as a polar stationary phase for the sample to interact with.
A very small sample is spo
Rf Value
The Rf value is equal to the distance traveled by the solute/distance traveled by the nonpolar solvent (usually hexane).
The least polar compound would be expected to have the highest Rf value due to its high solubility in hexane.
Rf= distance traveled by
Column Chromatography
Mixture to be separated through a column packed with charged glass beads or some other polar matrix
Solution is collected in fractions at the bottom of the column
involves a stationary phase of finely-divided alumina or silica gel in a vertical glass tube
Ion-Exchange Chromatography
Column or stationary phase is coated with cations or anions
Mixture is passed through and oppositely charged ions adhere to the column
Target molecules can then be eluted by washing with a salt solution
Make the beads the oppisote ion of the protein you w
Affinity Chromatography
Used to isolate a specific molecule or product based on a very specific affinity or binding interaction
Example- Molecules in mixture react via acid-base neutralization with molecules on the column. To elute the bound target molecule, one must disrupt the
Gas Chromatography
Liquid is used as the stationary phase
Mixture is dissolved into a heated gas and passed through the liquid
Various components reach the exit port at different rates based on 1) boiling point and 2) polarity
Only consider polarity if two substances have a
IR Spectroscopy
If a bond that has a dipole, exposing that bond in a external electric field will cause atoms to move within that field like a charged particle attached to a spring, infrared radiation is used to create an oscillating electric field, which in turn causes
IR Absorbances: Carbonyl
C=O
1700 cm?�
sharp, deep
IR Absorbances: Alcohol
3300 cm?�
broad, separate from CH
IR Absorbances: Saturated Alkane
2800 cm?�
sharp, deep
IR Absorbances: Carboxylic Acid
3000 cm?�
broad, overlaps CH
IR Absorbances: Amine
3300 cm?�
broad, shallow
IR Absorbances: Amide
3300 cm?�
broad, deep
IR Absorbances: Nitriles
2250 cm?�
sharp, deep
UV Spectroscopy
Energy difference between 2 adjacent molecular orbitals, is the amount of energy created by electromagnetic radiation in UV spectrum
When a molecule is exposed to UV radiation, electrons within that molecule will often absorb that energy and excite to the
Mass Spectrometry
The molecules of the sample are bombarded with electrons causing them to both break apart into smaller pieces and ionize
This produces fragments iwth different masses and charges
These fragments are accelerated through a narrow curved magnet called a flig
NMR Spectroscopy
Used to differentiate molecules based on differing chemical environments of Hydrogen Nuclei (H-NMR) or differing carbon nuclei (C13-NMR)
H-NMR is tested about 90% of the time
An atom must have either an odd atomic number or an odd mass number to register
Reading H-NMR Spectra
Peaks: Each peak represents all of the hydrogens in a molecule that share an indistinguishable chemical enviornment, aka equivalent hydrogens
Spin-SPin SPlitting: Presence of neighbors, non equivalent H attached to neighboring carbon, causes splitting of
Isopropanol H-NMR spectrum
1-bromopropane H-NMR spectrum
Tert-butyl alcohol H-NMR spectrum
Reading C��-NMR Spectra
Important difference from H-NMR:
-- No spin-spin splittings (all peaks are singlets)
-- No integration (area under curve is not relative to number of carbons)
Absorbance range:
- 0 - 220 ppm
-- 220 ppm is downfield- deshielded
-- 0 ppm is upfield= sheilde
Extraction
Purpose: Use to separate two compounds or to remove a desired product from a rxn mixture
Two liquids, a polar and non-polar are used.
The separation depends on the target molecule having differential solubility in two solvents
How it works:
--- The two so
Improving Separation
Seperation can be aided by repitation
Fractional Extraction: Extracting with 5 mL 10 separate times will produce a much better separation than extracting with 50 mL all at once
Addition of an acid to protonate the product
Addition of a base to deprotonate
Gravity Filtration
Physical separation of a solid (either crystallized product or solid impurities) from a liquid by passing it through filtration paper
Fluted filter paper is recommended, it increases surface area for filtration
Whether you would want to filter hot or cold
Vacuum Filtration
Vacuum filtration is performed with a Hirsch or Buchner funnel.
A vacuum is created inside of the flask which creates suction to pull the filtrate through the filter paper.
The filter usually has holes in it which are covered by the filter paper.
The prim
Distillation
Separate two substances by simple distillation, must have boiling points at least 25'c apart
Simple Distillation
Heat mixture in a flask
Liquid with lower boiling point evaporates first, enters a collecting arm, cools and drops into a collecting flask
Cooling the condensing arm or placing the collecting flask on ice can improve the separation process
Fractional Distillation
A fractionating column is placed between the heating flask and the condensing arm
Mixture is heated to slightly above the boiling point of the more volatile liquid
Gas rises through a column of glass beads or metal shards
Causes any impurities in the vapo
Vacuum Distillation
Air inside apparatus is evacuated to create a vacuum
Vacuum distillation is used because it dramatically lowers the boiling point, allowing you to work at more manageable temperatures with substances that have much higher boiling points at atmospheric pre
Recrystallization
When the desired product that still contains impurities is dissolved in the minimum amount of hot solvent necessary to create solution
The solution is then cooled as slowly as possible
Because pure substances usually crystallize at a higher temperature th
Carbonyl Functional Group
For the MCAT, you can treat most carbonyl analogues, such as S=O or N=O, as you would carbonyls. However, it is quite possible that the MCAT would require you to use your basic knowledge of electronegativity, bond polarity, atomic radius, etc., to predict
Alpha Hydrogens
Hydrogens on a carbon adjacent to a carbonyl carbon are acidic due to resonance stabilization of the conjugate base
When there are two carbonyls separated by a single carbon, Hydrogens on the middle carbon are even more acidic
The greater the partial posi
Electron Withdrawing Group
An electron withdrawing group will make the carbonyl better at stabilizing the conjugate base and therefore the strongest electron withdrawing group would indicate the strongest acid (because it produces the most stable conjugate base).
1) closer the EWG
Electron Donating Groups
donate electrons and thus stabilize positive charge; make a molecule more basic; decrease acidity of alcohols
An electron donating group on the carbonyl carbon will decrease its partial positive charge and thereby make it less able to stabilize the conjug
Aldehydes and Ketones
An aldehyde is any compound containing a carbonyl with one or more hydrogen substituents on the carbonyl carbon.
A ketone is any compound containing a carbonyl with two carbon substituents on the carbonyl carbon.
Aldeyhdes and ketones can act as H-bond re
Aldehydes and Ketones Nomenclature
Aldehydes are named with the -al ending;
ketones are named with the -one ending.
In either case, the parent chain must be the longest chain that includes the carbonyl.
Aldehyde carbons are always considered carbon #1 for numbering purposes.
If a ketone mu
Keto-Enol Tautomerization
This is the process by which an alpha hydrogen adjacent to an aldehyde or ketone becomes bonded to the carbonyl oxygen, while the double bond is switched from the carbon oxygen bond to the bond between the carbonyl carbon and the alpha carbon
What you sho
Formation of Acetals/Hemiacetals and Ketals/Hemiketals
Students seem to have a difficult time remembering the structure of these four species and telling them apart.
Acetals/ketals have two -OR substituents and hemiacetals/hemiketals have one -OR substituent plus one alcohol substituent (-OH group).
The MCAT
Protecting Ketones/Aldehydes from Reaction
o Ketones or aldehydes can be prevented from reaction with a nucleophile or base by conversion to an acetal or ketal (which are unreactive in all but acidic conditions). Any terminal diol with at least two carbons will work.
o STEPS:
1) One end of the dio
Halogenation of an Aldehyde or Ketone
o Substitution of a Br, Cl or I for one of the alpha hydrogens on an aldehyde or ketone.
Multiple halogenations often occur.
o STEPS:
1) A base abstracts an alpha hydrogen, leaving a carbanion.
2) The carbanion attacks a diatomic halogen.
Aldol Condensation
o The condensation of one aldehyde or ketone
with another aldehyde or ketone.
o STEPS:
1) A base abstracts an alpha hydrogen,
creating a carbanion.
2) The carbanion will attack any carbonyl
carbon in the solution.
3) The oxygen is protonated to form an
al
?-? Unsaturated Carbonyls
An aldehyde or ketone with a double bond between the alpha and beta carbons.
In terms of the MCAT, you should think of an ?-?-unsaturated carbonyl as an electrophile. Nucleophiles either attack the beta carbon directly, or attack the carbocation that exis
Carboxylic Acids
Any compound with a carbonyl containg a hydroxyl substituent on the carbon
Nomenclature for Carboxylic acids:
--end with an "-oic Acid"
-- When loses proton, it has an "-ate" ending, ex- formic acid-> formate
Common names: HCOOH- Formic acid, CH?COOH- Ace
Nucleophilic Attack of Carbonyls
RCOOH + H?O -> RCOOH?? + Nu:- ? RCONu + H?O
Decarboxylation
Loss of CO2 from beta-keto carboxylic acid, leaves behind a resonance stabilized carbanion
This is usually done by catalysis by a base
The carboxylate ion usually retakes the hydrogen from the base, forming a keto-enol tautomer.
Esterification
RCOOH + ROH -> RCOOR + H2O
Reaction of an alcohol with a carboxylic acid to form an ester.
You've probably realized by now that the hydroxyl group will never leave without being protonated first to form the "good leaving group water"; thus this reaction r
Triacyglycerol Mechanism
Follows esterification to form triacylglycerols
Acid Chlorides
Any Compound containing a carbonyl with a chlorine substituent on the carbonyl carbon
Nomenclature
- oyl chloride for the ending, ex- propanoyl chloride
- Formyl Chloride, Acetyl Chloride, Benzoyl Chloride
Formation of Acid Chlorides
RCOOH + PCl? ? RCOCl + H?O
Normally use PCl?, PCl?, SOCl? to form Acid Chloride
Remember: Addition of Chloride ion Cl- to a carboxylic acid does NOT produce an acid chloride due to Cl- being already stable on it's own.
MOST REACTIVE CARBOXYLIC ACID DERIVA
Anyhydride
Compound with two acyl groups connected to one another by a single oxygen
Nomenclature:
--Poic Anhydride ex benzoic acid-> benzoic anhydride
-- Common names- Formic Anhydride, acetic anhydride, acetic formic anhydride
VERY GOOD ELECTROPHILES, due to highl
Acetic Formic Anhydride
Amides
Any compound containg a carbonyl with an anime sbustituent
Nomeclature- change oic ending to amide- ex- benzoic Acid-> benzamide
Properties:
--- Most stable of all acid derivatives, for MCAT, carbonyl carbons are unreactive cause NH2 is NOT good leaving g
Hofmann Degradation
Primary Amides (amides with only H on the nitrogen) react in strong, basic solutions of Cl2 or Br2 to form primary amines
MEchanism uses decarboxlyation, thus shortening the length of the carbon chain
This rxn allows you to add an amine to a tertiary carb
Esters
Any compound containg OR on carbonyl carbon
Nomenclature- Use -oate- example- Methyl Penanoate
--- know methy formate, methyl acetate, methyl benzoate
--- Esters act as H-bond recipients, but not donors, slightly soluble in water, but less soluble than ac
Transesterification
Reaction of existing ester with an Alcohol, creating a dfiferetn ester
Uses Acid catalysis
RCOORa + RbOH ?RCOORb + RaOH
Saponification (Hydrolysis of an Ester)
Hydrolysis of an ester to yield an alcohol and the salt of a carboxylic acid.
o STEPS:
1) The hydroxide ion (NaOH or KOH) attacks the carbonyl carbon and pushes the C=O electrons uponto the oxygen.
2) The electrons collapse back down and kick off the -OR
Acetoacetic Ester Synthesis
Formation of a ketone from a ?-keto ester.
o STEPS:
1) A base abstracts the acidic alpha hydrogen, leaving a carbanion.
2) The carbanion attacks an alkyl halide (R-X), resulting in addition of the -R group to the alpha carbon.
3) Hot acid during workup ca
Inorganic Esters
Referred to as oxo acids, such as phosphoric acid, sulfuric acid, nitric acid
Be familiar with those structures
GTP, ATP, UTP,- inorganic triphosphate esters
FADH2, NADH= Disphopshate Esters
FMN, DNA, RNA= Monophosphate esters
Phosphoric Acid
H?PO?
Sulfuric Acid
H?SO?
Nitric Acid
HNO?
ATP
GTP
UTP
Substitution of Acid Derivatives
Mechanism Notes-
--- A nucleophile can be added to a carboxylic acid or acid derivative via carbonyl carbon
--- Sometimes, will it result in substitution of that nucleophile for the existing substituent
--- The intermediate is an oxygen anion that collaps
Stability of Carboxylic Acid Derivatives
- Amide > Ester > Carboxylic Acid > Anhydride > Acid Chloride
Amines
An amine is any organic compound that contains a basic nitrogen atom
Can act as either a base or a nucleophile:
--normally with primary or secondary amines acting as nucleophiles
--tertiary acting as a base.
Amine Basicity:
---Decreases from tertiary to p
Amine Nomenclature
1)Name the alkane to which the N is attached (e.g., propane)
2) Add "amine" in place of the "e" on the end of "ane" (e.g., propanamine). It is also acceptable to separate the substituent name (e.g., propyl amine)
3) If the amine is secondary, the longest
Tautomerization
An enamine and imine interchange via a proton shift analogous to the keto-enol tautomerization
Synthesis of Alkyl Amines
NH3 + CH3Br -> NH2CH3 + HBr
o Formation of an alkylamine from an amine and an alkyl halide
o STEPS:
1) Ammonia acts as a nucleophile, attacking the alkyl halide via SN2 and kicking off the halide ion.
2) The halide ion acts as a base, abstracting a hydrog
Gabriel Synthesis
making primary amines through Sn2 rxn of phthalimide with an alkyl halide followed by cleavage w hydrazine (NH?NH?)
Formation of a primary amine from a primary alkyl halide; avoids the side products of alkyl amine synthesis.
Reduction Synthesis of Amines
o Reduction of amides, imines, nitriles, and nitro groups via common reducing agents such as LiAlH4, NaBH4, and H2/catalyst with pressure.
Nitro groups can be reduced to the associated primary amine via all of the above listed reducing agents. Most O-Chem
Addition of Amines to Carbonyls (Formation of Enamines and Imines)
o Amines add to aldehydes and ketones to form imines and enamines.
o STEPS:
1) The amine acts as a nucleophile, attacking the electrophilic carbonyl carbon.
2) The oxygen is protonated twice, creating the good leaving group water.
3) A base abstracts a hy
Formation of Imine
� Primary amines yield imines
STEPS:
1) The amine acts as a nucleophile, attacking the electrophilic carbonyl carbon.
2) The oxygen is protonated twice, creating the good leaving group water.
3) A base abstracts a hydrogen from the nitrogen and kicks off
Formation of Enamine
� Secondary amines yield enamines
STEPS:
1) The amine acts as a nucleophile, attacking the electrophilic carbonyl carbon.
2) The oxygen is protonated twice, creating the good leaving group water.
3) A base abstracts a hydrogen from the nitrogen and kicks