MCAT Kaplan Orgo Review
semicarbazones
forms when H2NNHC(=O)NH2 replaces the oxygen of a carbonyl
angle strain
results when bond angles deviate from their ideal values by being stretched or compressed
torsional strain
results when cyclic molecules must assume conformations that have eclipsed or gauche interactions
nonbonded strain (van der Waals repulsion)
results when nonadjacent atoms or groups compete for the same space -dominant source of steric strain in the flagpole interactions of the cyclohexane boat conformation
methanoic acid
formic acid
Vacuum distillation
[purification methods] separates liquids when boiling points are GREATER than 150C (decreased pressure = decreased boiling point) -initial solutiion is placed in a heated distilling flask, where the components of the solution with the lowest boiling points will vaporize first. The vapor then condenses in the water-cooled condensor, and this distillate drips into the receiving flask. -allows us to not have to worry about degrading the product, since we don't have to go over 150*C
sigma bond
a bond formed when two atomic orbitals combine to form a molecular orbital that is symmetrical around the axis connecting the two atomic nuclei
pi bond
a bond that is formed when parallel orbitals overlap to share electrons.
Carboxylic acid salt
a carboxylate ion and the metal ion from the base that is the product of neutralization of a carboxylic acid
carbonyl group
a chemical group consisting of a carbon atom linked by a double bond to an oxygen atom
amino group
a chemical group consisting of a nitrogen atom bonded to two hydrogen atoms
condensation reaction
a chemical reaction in which two or more molecules combine to produce water or another simple molecule
Condensation reaction
a chemical reaction in which two or more molecules combine to produce water or another simple molecule -How amides, esters, and anhydrides are formed, in this case, the molecule being lost is water.
enol
a compound with a double bond and an alcohol group
staggered conformation
a conformation about a carbon-carbon single bond in which the atoms or groups on one carbon are as far apart as possible from atoms or groups on an adjacent carbon
gauche conformation
a conformation with a 60 degree dihedral angle between the largest groups
parts per million (ppm)
a method of expressing low concentrations; 1 ppm is equivalent to 1 milligram per liter.
bonding orbital
a molecular orbital that can be occupied by two electrons of a covalent bond if the signs of the wave functions are the same, a lower energy (more stable) bonding orbital is produced
antibonding orbital
a molecular orbital that is higher in energy than any of the atomic orbitals from which it was formed when signs of the wave functions are different, a higher-energy (less stable) antibonding orbital is produced
Bronsted-Lowry base
a molecule or ion that is a proton acceptor
Bronsted-Lowry acid
a molecule or ion that is a proton donor
chiral
a molecule that is not superimposable on its mirror image
boat conformation
a nonplanar conformation of a cyclohexane ring in which carbons 1 and 4 of the ring are bent toward each other
polypeptides
a polymer of amino acids joined together by peptide bonds.
amphoteric
a substance that can act as both an acid and a base Ex: bicarbonate/water
paper chromatography
a technique for separating dissolved compounds such as chlorophyll, carotene, and xanthophyll -medium is paper, which is composed of cellulose
magnetic resonance imaging (MRI)
a technique that uses magnetic fields and radio waves to produce computer-generated images that distinguish among different types of soft tissue; allows us to see structures within the brain
diol/glycol
alcohols with two hydroxyl groups -suffic is -diol, with the entire hydrocarbon name preserved
mass spectrometer
an instrument used to determine the relative masses of atoms by the deflection of their ions on a magnetic field
Four factors of nucleophilicity
charge, electronegativity, steric hindrance, solvent
protecting group
chemical modification of a func. group to "protect" it from reacting ex: non-reducing disaccharides
absolute configuration
describes the exact spatial arrangement of groups of atoms independent of other molecules.
Between a monocarboxylic acid, a dicarboxylic acid, and a dicarboxylic acid that has been deprotonated once, which will be the most acidic? Why?
dicarboxylic acid would be the most acidic, as the second carboxyl group is electron-withdrawing, and therefore contributes to even higher stability of the anion after loss of the first hydrogen. However, a monocarboxylic acid is more acidic than a deprotonated dicarboxylic acid because the carboxylate anion is electron donating, which destabilizes the product of the second deprotonation step, resulting in decreased acidity.
structural isomers
differ in the covalent arrangements of their atoms; may also differ in the location of double bonds
acetals
formed when hemiacetals react with alcohol the anomeric hydroxyl group is transformed into a alkoky group - making alpha and beta acetals with water as the leaving group -protecting group
How are peptide bond formed and cleaved?
formed: by a condensation reaction (loss of water) cleaved: hydrolytically by strong acid or base
dicarboxylic acids
have a carboxylic acid at each end of the molecule common in biological systems normal alkane name (ethane) with dioic acid as the suffix each COOH group effects the other COOH are electron withdrawing due to their electronegative oxygen - THEY ARE MORE ACIDIC THAN NORMAL CARBOXYLIC AICIDS - for the first hydrogen after the first hydrogen is removed the anion decreases the acidity of the remaining carboxylic acid second carboxylic to be deprotonated is less acidic than a normal carboxylic acid
chemical properties
have to do with the reactivity of the molecule with other molecules and result in changes in chemical composition. In organic chemistry, the chemical properties of a compound are generally dictated by the functional groups in the molecule.
What are the three intermolecular forces that affect solubility?
Hydrogen bonding dipole-dipole interactions van der Waals forces
How are hydroxyquinones produced?
Hydroxyquinones are produced by the oxidation of quinones adding a variable of additional hydroxyl groups.
Order of halogen nucleophilicity in a PROTIC solvent?
I- > Br- > Cl- > F- -protons in solution will be attracted to nucleophile. HF is conjugate base of HF, a weak acid, so it will form bonds w/ the protons in solution and be less able to access the electrophile to react.
What are the three specialized types of column chromatography? what does each use in order to separate the sample?
Ion-Exchange: -column is given a charge, which attracts molecules with the opposite charge Size Exclusion: -small pores are used; smaller molecules are trapped, while larger molecules pass through the column Affinity: -specific receptors or antibodies can trap the target in the column; the target must then be washed out using other solutions.
tautomers
Isomers that can interconvert by exchanging the location of a proton.
Aldehyde oxidation
KMnO4, CrO3, Ag2O or H2O2 makes carboxylic acid -most oxidizing agents will turn aldehydes into carboxylic acids; PCC, howver, is anhydrous and is not strong enough to oxidize past the point of an aldehyde
Which tautomer of aldehydes and ketones is thermodynamically favored: keto or enol?
Keto form is thermodynamically favored
What are cyclic esters called?
Lactones replace "-oic acid" with lactone
organic phase (layer)
Liquid layer that is a nonpolar organic liquid Dissolves nonpolar compounds Typically Ethers, Oils,
immiscible
Liquid solutes and solvents that are not soluble in each other Ex: -oil and water -oil and vinegar
Acidity of the alpha-hydrogen in beta-dicarboxylic acids
Note: that the alpha-hydrogens is less acidic than the hydroxyl hydrogen; the hydroxyl groups are left protonated in this example for demonstration purposes.
Electronegativity (nucleophilicity)
Nucleophilicity decreases as electronegativity increase bc these atoms are less likely to share their electrons
organic phosphates
Nucleotides with phosphate groups, such ATP, GTP, and those in DNA, b/c the the phosphate group is bonded to a carbon-containing molecules.
Hybridization of Carbon
On the MCAT, you will sometimes be tested about how much "s character" a certain hybrid bond has. To solve these problems, we simply need to determine what type of hybridization it is and use the name to solve the problem. For example, in sp3, we have one s and three p, so the bond therefore has 25% s character and 75% p character.
Enamination (Tautomerization)
On the left is the imine form, which is thermodynamically favored over the enamine form on the left
amides
Organic compounds whose molecules have a carbonyl nitrogen bond. They are the product formed in a reaction between a carboxylic acid and an amine.
oxidation-reduction (redox) reactions
Oxidation of one molecule is always accompanied by the reduction of another Electrons are often transferred as hydrogen atoms
Trend for oxidation and reduction reactions?
Oxidation reactions tend to feature an increase in the number of bonds to oxygen. oxidizing agents often contain metals bonded to a large number of oxygen atoms.
pyrophosphate
P2O7 (4-) aka PPi -an ester dimer of phosphate
pyrophosphate anion
P2O7 4-
Solvent (nucleophilicity)
Protic Solvents can hinder nucleophilicity by protonating the nucleophile or through hydrogen bonding. -protic solvents have hydrogens that can donate [H+] or hydrogen bond with solutes.
How are quinones generally produced?
Quinones are produced by oxidation of phenols
esters
R-COO-R -hybrid between a carboxylic acid and an ether (ROR') -can be made by reacting carboxylic acids with alcohols under acidic conditions.
naming of carboxylic acids
Replace the -e of the parent hydrocarbon with -oic acid.
Resonance of amides
Resonance between the carbonyl and lone pair on the nitrogen stabilizes this bond and restricts its motion
polar amino acids
Serine, Threonine, Cysteine, Asparagine, Glutamine
wash
Small amount of solute is used to extract and remove impurities rather than the compound of interest
What happens when butanoic acid is reaction with sodium borohydride? with lithium aluminum hydride
Sodium borohydride: not strong enough to reduce carboxylic acids, no reaction lithium aluminum hydride: will reduce to an alcohol, so it will produce 1-butanol.
Nucleophilic Acyl Substitution
Step 1: Nucleophilic Addition Step 2: Elimination of the leaving group and reformation of the carbonyl.
optical isomers (enantiomers: diasteriomers and enantiomers)
Stereoisomers that are non-superimposable mirror images of each other.
conformational isomers
Stereoisomers that differ by rotation about one or more single (sigma) bonds, usually represented using Newman projections.
How does steric hindrance affect the relative reactivity of aldehydes and ketones?
Steric hindrance is one of the two reasons that aldehydes are slightly more reactive than ketones. The additional alkyl group gets in the way of nucleophiles and makes for a higher-energy, crowded intermediate.
What are the reaction types used in the strecker synthesis?
Strecker synthesis is a condensation reaction -formation of an imine from a carbonyl-containing compound and ammonia, w/ loss of water) -followed by a nucleophilic addition (addition of the nitrile group) -finished by hydrolysis
How do strongly acidic and strongly basic conditions catalyze the hydrolysis of an amide? Strongly acidic conditions Strongly basic conditions
Strongly Acidic Conditions: -catalyze amide hydrolysis by protonating the oxygen in the carbonyl. This increases the electrophilicity of the carbon, making it more susceptible to nucleophilic attack Strongly Basic Conditions: -Greatly increase the concentration of OH- ions, which can act as a nucleophile on amide carbonyls.
Deprotection of alcohols
TBAF or H3O+
preparative TLC
TLC on a larger scale larger plate develops with a larger spot the sample splits into bands on individual compounds which can then be scarped off to yield pure compounds
What are tautomers?
Tautomers are isomers that can be interconverted by the movement of a hydrogen and a double bond.
Naming aldehydes
replace -e with -al
naming ketones
replace -e with -one
Iupac naming of alcohols
replace the -e ending of the alkane root with -ol. If the alcohol is the highest-priority functional group, the carbon atom attached to it receives the lowest possible number
naming ketones
replace the -e with the suffix -one. -when ketones are named as substituents, use either prefix oxo- or keto-
conjugation
requires alternating single and multiple bonds because this pater aligns a number of unhybridized p-orbitals down the backbone of the molecule
fractional distillation
separation of a liquid mixture into fractions differing in boiling point (and hence chemical composition) by means of distillation, typically using a fractionating column. -used to separate liquids with similar poiling points (within 25*C). -w/ increased SA in the distillation column, the distillate has more places on its way up the column. This allows for more refines separation of liquids with fairly close boiling points.
fischer esterification
the formation of an ester from a carboxylic acid and an alcohol in ACIDIC conditions -take a carboxylic acid 1: protonate ketone, 2: nucleophilic attack on a-carbon, move double bond towards oxygen. 4: OH group takes proton from attacking OH 5: water is then eliminated, with lone pairs from original ketone reforming.
Lewis Acid-base reaction
the formation of one or more covalent bonds between an electron-pair donor and an electron-pair acceptor
hybridization of orbitals
the mixing of several atomic orbitals to form the same total number of equivalent hybrid orbitals
chair conformation
the most stable conformation of cyclohexane, with one part puckered upward and another part puckered downward
phylloquinone
the plant form of vitamin K; also called vitamin K1.
acid dissociation constant (ka)
the ratio of the concentration of the dissociated form of an acid to the concentration of the undissociated form
Saponification
the reaction between a fat and a strong base to produce glycerol and the salt of a fatty acid (soap) -soaps can solvate nonpolar organic compounds in aqueous solutions b/c they have both a nonpolar tail and a polar carboxylate head.
stationary phase (absorbent)
the solid medium that the sample is placed on in chromatography
phosphodiester bond
the type of bond that links the nucleotides in DNA or RNA. joins the phosphate group of one nucleotide to the hydroxyl group on the sugar of another nucleotide
What is the C-N bond of an amide planar?
The C-N bond of an amide is planar b/c it has partial double-bond character due to resonance between lone pair on the nitrogen and the carbonyl group. Double bonds exist in a planar conformation, and restrict movement.
steric protection
The Prevention of the formation of alternative products using a protecting group such as a mesylate or tosylate.
What has a lower pKa: 3-pentanone of pentenal? Why?
The alpha-hydrogens of aldehydes are slightly more acidic than those of ketones due to the elctron donating characteristics of the second alkyl group in ketones. This extra alkyl group destabilizes the carbanion, which slighly disfavors the loss of the alpha-hydrogens in ketones as compared to aldehydes. Therefore, Pentanal is a stronger acid than 3-pentanone, and thus will have a lower pKa.
aqueous phase (layer)
water layer
enones
α,β-unsaturated carbonyls
peptide bond
The chemical bond that forms between the carboxyl group of one amino acid and the amino group of another amino acid
oxidizing agent
The electron acceptor in a redox reaction. -oxidizing agent is actually being reduced, since it is gaining electrons. So the oxidizing agent itself is OXIDIZING the molecule it reacts with Ex: 02, 03, cl2, mermanganate, MnO4-, Cro4(2-)
distillate
The liquid collected during distillation when the evaporated substance condenses
oxidation
The loss of electrons from a substance involved in a redox reaction.
esterification
The reaction of an alcohol with a carboxylic acid to produce an ester and water.
When nitrogen or nitrogen-containing derivatives react with aldehydes and ketones, what type of reaction happens, and what function group is formed?
The reaction that occurs is a condensation reaction b/c a small molecule is lost, and also a nucleophilic substitution reaction. This reaction results in the formation of a imine (or, for nitrogen-containing derivaties: oximes, hydrazones, or semicarbazones)
tautomerization
The rearrangement of bonds within a compound, usually by moving a hydrogen and forming a double bond
retro-aldol reaction
The reverse of an aldol condensation reaction, in which a carbon-carbon bond is cleaved with heat and base, yielding two aldehydes, two ketones, or one of each.
eluent
The solvent used in chromatography, after it has passed through the stationary phase
What characteristics of phosphoric acids make them good buffers?
The three hydrogens in phosphoric acid have very different pKa values. This allows phosphoric acid to pick up or give off protins in a wide pH range, making it a good buffer over most of the pH scale.
What must be true about the two solvents used for an extraction to work?
The two solvents must be immiscible (non soluble in one another) and must have different polarity or acid-base properties that allow a compound of interest t dissolve more easily in one than the other.
elute
To displace with solvent, as in thin-layer chromatography
resonance ozone
True electron density of ozone is somewhere between the two resonance forms, creating 1.5 bonds between each oxygen, and leaving each oxygen with a -1/2 charge
isomers
Two different molecules that have the same chemical formula
ketals
Two equivalents of an alcohol or a diol are reacted with a ketone using an acid catalyst Protects carbonyls from reducing agents (Ex LiAlH4)
synthesis of an anhydride via carboxylic acid condensation
Two molecules of carboxylic acid come together and lose a molecule of water in the formation of an anhydride.
vacuum distillation
Type of distillation used to distill a liquid with a boiling point over 150C.
What chemical properties of ubiquinone allow it to carry out its biological functions?
Ubiquinone has conjugated rings, which stabilize the molecule when accepting electrons. Additionally, the long alkyl chain in the molecule allow for lipid solubility, which allows the molecule to function in the phospholipid bilayer.
separatory funnel
Used to separate immiscible liquids, using the density of the layers, since the more dense layer will be on the bottom.
manipulations of fischer projections
What if our lowest priority group is pointing to the side and as such pointing out of the page? we have options -Make 0 switches assign priorities as normal 1-2-3 and 4 doesn't count since it will be left out then obtain R/S designation, !!! The true designation will be the opposite of what you just obtained!!! -make 1 switch swap lowest priority group with one of the groups on the vertical axis, obtain R/S and again this will be opposite since its a fischer -make 2 switches move lowest priority into the correct position stated above, then switch the other two as well and this will have the same designation as the initial molecule. This is the same as holding one substituent in place and rotating the other
When HCN reacts with an aldehyde or ketone, what functional group is produced? Is the product stable?
When HCN reacts with an aldehyde or a ketone, a cyanohydrin is produced, which is a stable product.
Nucleophilic addition reaction mechanism
When the nucelophilie attacks, it forms a covalent bond to the carbon, breaking the pi bond in the carbonyl. The electrons from the pi bond are pushed onto the oxygen. Oxygen happily accepts them due to its electronegativity Breaking the pi bond forms a tetrahedral intermediate. Any time a carbonyl is formed ask "can I reform it" If no good leaving group is present then you cannot reform it. If a leaving group is present then yes it can reform. Generally O- will accept a proton from the solvent to form a hydroxyl group resulting in an alcohol
electrophiles
"Electron-loving" atoms with a positive charge or positive polarization; can accept an electron pair when forming new bonds with a nucleophile.
d-orbital shape
4 leaf clover
succinic anhydride
5-membered cyclic anhydride.
gamma-lactam
5-membered nitrogen-containing ring not easily hydrolyzed under any conditions
delta-lactam
6-membered nitrogen containing ring not easily hydrolyzed under any conditions
epsilon-lactam
7-membered nitrogen containing ring
What causes the relatively high acidity of carboxylic acids?
carboxylic acids are particularly acidic due to the electron withdrawing oxygen atoms found in the functional group and the high stability of the carboxyate anion, which is resonance stabilized by delocalization with two electronegative oxygen atoms.
physical properties
characteristics of processes that don't change the composition of matter, such as melting point, boiling point, solubility, odor, color, and density.
tosylates
contain the functional group -SO3C6H4CH3, which is derived from toluenesulfonic acid
pKa
=-logKa more acidic molecules have a smaller (or even negative) pKa more basic molecules will have a larger pka
international union of pure and applied chemistry
The body responsible for the standardization of chemical nomenclature and usage
carboxylate anion stability
The negative charge from deprotonation is stabilized through resonance.
backside attack
The nucleophile approaches from the side opposite the leaving group -for this to occur the nucleophile must be strong, and the substrate cannot be sterically hindered, therefore, the less substituted the carbon, the more reactive it is in sn2 reactions.
Soap micelle
The polar heads interact with the hydrophilic environment; the nonpolar tails are oriented toward the interior of the micelle.
enolization/ tautomerization
The process by which the carbonyl oxygen of a ketone gets protonated to form an enol. Conversion forms from alpha racemization
transesterification
The process that transforms one ester to another when an alcohol acts as a nucleophile and displaces the alkoxy group on an ester.
what are the axis labels in an IR plot?
X-axis: Wavenumber (increases from right-left Y-axis: Transmittance (%)
ethanal
acetaldehyde
ethanoic acid
acetic acid
pKas of common organic molecules
alkane: ~50 Alkene: ~42 Hydrogen (H2): 42 Amine (NH3): ~35 Alkyne: ~25 Ester: ~25 Ketone/Aldehyde: ~20-24 Alcohol: ~17 Water: ~16 Carboxylic Acid: ~4 Hydronium Ion: ~-1.7
cysteine
all amino acids have (s) configurations, except for cysteine.
single bonds
all single bonds are sigma bonds
L- and D- amino acids
amino acids whose stereochemistry is the same as the stereochemical standards L- and D-glyceraldehyde, respectively
beta-lactam
an antibiotic with a beta lactam ring all PCN and cephalosporins always suspect beta lactamase if had an abx in past 90 days and sick again or still sick
hereroatoms
any atom in organic chemistry that isn't carbon or hydrogen
alpha-carbon
any carbon attached directly to a carbonyl carbon
chain-terminating
appear at end of C chain ex) aldehydes
integration NMR
area under the peaks in NMR, used to measure the number of protons in a peak
negatively charged amino acids
aspartate, glutamate
deshielding
*Stronger magnetic field -Chemical shift is increased due to removed electron density
mesylate
*contain functional group -SO3CH3 -derived from methanesulfonic acid -prepared using methylsulfonyl chloride and an alcohol in presence of a base -mesyl and tosyl groups can serve as protecting groups when we don't want alcohols to react -will not react with many of the other reagents that would attack alcohols
hydrazones
- forms when NNH2 replaces the oxygen of the carbonyl
What characteristics make inorganic phosphate so useful for energy transfer biologically?
-inorganic phosphates contain a very negative charge. When bonded to other phosphate groups in nucleotide triphosphate, this creates repulsion with adjacent phosphate groups, increasing the energy of the both -also, inorganic phosphate can be resonance-stabilized.
pKas of phosphoric acid
2.15, 7.20, 12.32 great buffer - covers whole pH scale
dehydration reaction
A chemical reaction in which molecules combine by removing water
what suffixes are used for aldehydes and ketones; How are carbonyl groups names as a substituent?
Aldehydes: suffix -al, Ketones: suffix -one Carbonyl groups of both aldehydes and ketones are labeled as oxo- substituents ( ketones may also be called keto- substituents)
Given an alkane, an aldehyde, and an alcohol with equal-length carbon chains, which will have the highest boiling point? Why?
Alkane will have the lowest boiling point, followed by the aldehyde and than the alcohol. The boiling point of the aldehyde is elevated by its dipole, but the boiling point of an alcohol is further elevated by hydrogen bonding.
When will an acid-base reaction proceed, based on the strength of the reactants and products?
An acid-base reaction will proceed when the acid and base react for form conjugate products that are weaker than the reactants Strong-> weak for both acid and base
molecular vibrations measured by infrared spectroscopy
Bond bending and stretching; twisting and folding can also occur.
toluenesulfonic acid
CH3 C6 H4 SO3 H -these compiunds are produced by reactions of alcohols with p-toluenesulfonyl chloride
methanesulfonic acid
CH3 SO3 H
propanoic acid
CH3CH2COOH
ethanoic acid (acetic acid)
CH3COOH (weak)
what is one method for forming an aldehyde?
Can be formed by the oxidation of primary alcohols using PCC. Other strong oxidizing agents will fully oxidize to a carboxylic acid, so PCC has to be used.
What is one method for forming a ketone?
Can be formed by the oxidation of secondary alcohols with varying oxidizing agents. Ex: PCC, Na2Cr2O7, K2Cr2O7
stereoisomers
Compounds with the same structural formula but with a different arrangement of the atoms in space.
aldol
Contains both aldehyde and alcohol functional groups.
inorganic phosphate
Derived from phosphoric acid, the molecule that forms high-energy bonds for energy storage in nucleotide triphosphates like ATP; also used for enzyme regulation. -inorganic in that its not attached to carbon at all
ring strain
Energy created in a cyclic molecule by angle strain, torsional strain, and nonbonded strain; determines whether a ring is stable enough to stay intact.
common ketones
Ethyl methyl ketone and acetone (dimethyl ketone)
If we are given a solution of ether, with a boiling point of 308 K and methylene chloride, with a boiling point of 313K which type of distillation should be used to separate them?
Fractional distillation, since the boiling points are within 25*C of one another.
What functional group is formed when an aldehyde is oxidized? what are some common oxidizing agents that assist this reaction?
Functional Group: Yields a carboxylic acid Oxidizing agents: KMnO4, CrO3, Ag2O, H2O2
glycine
Gly, G simplest amino acid, with an H for its R group, not optically active.
nonpolar aliphatic amino acids
Glycine, alanine, valine, leucine, isoleucine, proline, methionine.
semicarbazide
H2N-NH-C(O)NH2
hydrazine
H2N-NH2
conjugated molecules
Have unhybridized p orbitals that can also be excited by ultraviolet light Shifts the absorption spectrum, *resulting in higher maximum wavelengths* Ex: -benzene has three broad absorbances, which mark the energy level transitions; found at 180, 200, and 255 nm wavelengths.
intermolecular anhydride formation
Heat and the increased stability of the newly formed ring drive this intramolecular ring formation reaction forward.
hydroxyl group (-OH)
In an organic molecule, a functional group consisting of a hydrogen atom bonded to an oxygen atom.
extractions
Manual removal of impurities and comedones.
IUPAC nomenclature
Met-, eth-, prop-, but-, pent-, hex-, hept-, oct-, non-, dec- (sec-butyl, isopropyl, isobutyl, tertbutyl)
hydroxylamine
NH2OH
hydride reagents
NaBH4, LiAlH4; only LiAlH4 can reduce carboxylic acids/esters/acetates to alcohols
esters
RCOOR -common carboxylic acid derivatives. -OH groups is replaced with an alkoxy group (-OR, where R is a hydrocarbon chain)
reduction of a carboxylic acid to a primary alcohol
Reaction occurs by nucleophilic addition of hydride and proceeds through an aldehyde intermediate, but will be further reduced all the way to an alcohol. Ex: LiAlH4 NaBH4 is not a strong enough reducing agent to reduce carboxylic acids.
cleavage reaction
Reaction that splits an anhydride into 2 molecules Typically via nucleophilic acyl substitution via strong nucleophile *creating a carboxylic acid derivative (nucleophile specific) and carboxylic acid*
Naming alcohols
Replace -e with -ol When alcohol not highest priority group, named as substituent with prefix hydroxy-
azimuthal quantum number
Second quantum number, designated l. Tells us the shapes of the electron orbitals 0 to n-1
menaquinones
The forms of vitamin K synthesized by bacteria and found in animals.
half-chair conformation
The unstable conformation halfway between the chair conformation and the boat conformation. Part of the ring is flat in the half-chair conformation.
saponification of a triacylglycerol
Treating triacylglycerols with NaOH will produce fatty acid salts (soap) as well as glycerol
What are common biologically active amphoteric species?
Water, bicarbonate, dihydrogen phosphate, etc.
Hydroxy-
When the alcohol is not the highest priority group, it is named as a substituent w/ prefix hydroxy-
ethanoic anhydride
acetic anhydride
propanone
acetone
Why are the alpha-hydrogens of aldehydes and ketones acidic?
acidic due to both inductive effects and resonance effects. The electronegative oxygen atom pulls electron density from the C-H bond, weakening it. Once deprotonated, the resonance stabilization of the negative charge between the alpha-carbon and the carbonyl carbon, and electron-withdrawing carbonyl oxygen increases the stability of this form.
sp3 hybridized orbitals
atomic orbitals that are achieved by mathematically averaging one s orbital with three p orbitals to form four hybridized atomic orbitals
Retro-aldol mechanism
bond between the alpha and beta carbons are broken -results in an aldehyde and ketone
Steric Hindrance (nucleophilicity)
bulkier molecules are less nucleophilic
configurational isomers
can be interconverted only be breaking bonds
Nitrile
carbon triple bonded to nitrogen
hydration of carbonyl
carbonyl is hydrated by water, then protonated, resulting in a geminal diol
Methanal
common name: formaldehyde
amino acid
compound with an amino group on one end and a carboxyl group on the other end
carboxylic acid
contain a carbonyl group and a hydroxyl group bonded to the same carbon
coordinate covalent bonds
covalent bonds in which one of the atoms furnishes both of the electrons for the bond
vicinal diols
diols with hydroxyl groups on adjacent carbons
geminal diols
diols with hydroxyl groups on the same carbon -aka hydrates
induction
distribution of charges across sigma bonds. Electrons are attracted to atoms that are more electronegative, generating a dipole across the sigma bond. -responsible for the dipole character of the carbonyl group, as well as the increased dipole character of carboxylic acids.
Naming aldehydes
drop e add al
what is responsible for the increased rate of hydrolysis in beta-lactams?
due to high levels of ring strain, which is due to both torsional strain (eclipsing interactions) and angle strain (deviation from 109.5*)
p-orbital shape
dumbbell shaped
spin quantum number (m sub s)
either +1/2 or -1/2, indicating the spin orientation of an electron
covalent
electrons are shared between atoms (similar electronegativities) - can be single, double, triple
ionic bonding
electrons are transferred from one atom to another and the resulting ions are held together by electrostatic interactions
Acyl derivatives
encompass all molecules with a carboxylic acid-derived carbonyl, including carboxylic acids, amides, esters, anhydrides, and others.
ethyl ethanoate
ethyl acetate
hybrid orbitals
form by "mixing" of atomic orbitals to create new orbitals of equal energy, called degenerate orbitals.
aminonitrile
formed in the step one process of the strecker synthesis compound containing an amino group and a nitrile group amino group is from the CN and the nitrile group is from the original ammonia/imine
reduction
gain of electrons
eclipsed conformation (eclipsed or totally eclipsed)
highest energy no separation. or 120 separation.
phthalic anhydride
hydrolyzes to phthalmic acid in water
molecular orbital diagram
in MO theory, an energy-level diagram showing the relative energies and electron occupancy of the molecular orbitals for a molecule
What properties account for the differences in reactivity seen between anhydrides, esters, and amides with nucleophiles?
induction has some effect on the reactivity of the carbonyl in these three functional groups differences in resonance also explain the increased reactivity of anhydrides. steric effects could also be significant, depending on the specific leaving group present.
enantiomers
isomers that are mirror images of each other
relative configuration of a chiral molecule
its configuration in relation to another chiral molecule
What are cyclic amides called?
lactams
filtrate
liquid that has passed through a filter after a filtration
condensate
liquid that results when gas is cooled
positively charged amino acids
lysine, arginine, histidine
Spectroscopy
measures the energy differences between the possible states of a molecular system by determining the frequencies of electromagnetic radiation absorbed by the molecules`
common aldehydes
methanal (formaldehyde) ethanal (acetaldehyde) propanal (propionaldehyde) butanal (butanal) benzaldehyde (valeraldehyde)
Name Alkanes 1-10
methane ethane propane butane pentane hexane heptane octane nonane decane
Recrystallization
method for purifying crystals in solution -first dissolve product in minimum amount of hot solvent and let it recrystallize as it cools. After cools, only the desired product will recrystallize out of solution, excluding the purities.
downfield
movement toward the left in an NMR spectrum -more electronegative atoms shift protons downfield b/c of deshielding.
naming lactams
named by replacing -oic acid, with -lactam
cyanohydrin formation
nucleophilic attack cyanide functions as a nucleophile, attacking the carbonyl carbon and generating a cyanohydrin.
Charge (nucleophilicity)
nucleophilicity increases with increasing electron density (more negative charge)
specific rotation equation
observed rotation / [solution] x tube length (dm)
chair flip
one chair conformation is converted to the other briefly passes through the half chain conformation all axial groups become equatorial all equatorial groups become axial dashed lines remain dashed wedges remain wedges conversion is slowed if there is bulky groups attached bulkiest group will favor the equatorial position
double bond
one pi bond on top of an existing sigma bond
molecular orbitals
orbitals that apply to the entire molecule
Nonpolar Aromatic Amino Acids
phenylalanine, tyrosine, tryptophan
developed
placing the absorbent upright in a developing chamber usually a beaker with a lip or a wide-mouthed jar.
conjugation
presence of alternating single and multiple bonds. -implies that all of the atoms involved in these bonds are either sp2 or sp hybridized, and therefore have unhybridized p-orbitals. When p-orbitals align, they can delocalize pi electrons through resonance, forming clouds of electron density above and below the plane of the molecule
Cahn-Ingold-Prelog priority rules
priority is given by looking at the atoms connected to the chiral carbon or double-bonded carbons - whichever has the highest atomic number gets highers priority - if there is a tie, one moves outward from the chiral carbon or double bond until the tie is broken
propanal
propionaldehyde
propanoic acid
propionic acid
Examples of protic and aprotic solvents
protic: carboxylic acids, ammonia/amines, water/alcohols aprotic: DMF, DMSO, acetone
spin-spin coupling (splitting)
proton NMR Hs on adj atoms, interfere w/ each other's magnetic envrm protons' peak slit into n+1 subpeaks n = # of protons that are 3 bonds away from the proton of interest`
chemically equivalent protons
protons with the same connectivity relationship to the rest of the molecule
configuration of a stereoisomer
refers to the spatial arrangement of the atoms or groups in the molecule
size exclusion chromatography
relies on porous beads; larger molecules elute first because they are not trapped in small pores
dextrorotatory
rotates plane-polarized light in a clockwise direction (+) (d-) and (+)
optical activity
rotation of the plane of polarized light
sp2 hybridization
s, p, p orbital and 3 hybrid orbitals, trigonal-planar (120) 33% s, and 66% p character seen in alkenes
Ketone Reduction
secondary alcohol
stereospecific
single reactant forms an unequal mixture of stereoisomers -happens via sn2 reaction, where the configuration of the reactant determines the configuration of the product due to the reaction mechanism.
s-orbital shape
spherical (1 orientation x 2 electrons = 2 electrons)
diastereomers
stereoisomers that are not mirror images of each other
cis-trans isomers (geometric isomers)
stereoisomers that differ only with respect to their cis or trans arrangement on a ring or double bond
Nucleophilic acyl substitution: amide to carboxylic acid
strong acid or base is needed to catalyze the hydrolysis of amides, which are normally quite stable
transmittance
the amount of light that passes through the sample and reaches the detector
magnetic quantum number
symbolized by m, indicates the orientation of an orbital around the nucleus ranges from -l to +l
principal quantum number
symbolized by n, indicates the main energy level occupied by the electron
mass spectrometry
technique based of the detection of vaporized molecules and their ionized (charged) fragments; detection and display of the spectra are based on the mass-to-mass charge ratios of the ions; method is specific for qualitative analysis and useful for quantitative analysis
When doing an extraction, is it better to do three extractions w/ 10mL or one extraction w/ 30mL?
three extractions with 10 mls. More of the compound of interest would be extracted with multiple sequential extractions than one large one
affinity chromatography
uses a bound receptor or ligand and an eluent with free ligand or a receptor for the protein of interest
triple bond
two pi bonds on top of an existing sigma bond
acetal and ketal formation
two. eq. of alcohol => acetal or a ketal in aldehyde => H is characteristic
distilling flask
used as a container of the solution to be change from gas to liquid/liquid to gas in the distillation process.
R group
used to represent one of 20 possible side chains found in amino acids of living systems Ex: Lysine
spotting
when the sample is placed directly onto the absorbent itself (like the silica or paper plate)
Ortho-
when the two substituent groups are on adjacent carbons
para-
when the two substituent groups on an aromatic compound are on opposite sides of the ring.
meta-
when the two substituent groups on an aromatic compound are separated by a carbon
Hydrolysis of amides
Amides can be hydrolyzed under highly acidic conditions via nucleophilic substitution. The acidic conditions allow the carbonyl oxygen to become protonated, making the molecule mores susceptible to nucleophilic attack by a water molecule. The product of this reaction is a carboxylic acid and ammonia. Don't forget hydrolysis can also occur if conditions are basic enough. The reaction is similar to an acid-catalzed reaction, except that the carbonyl oxygen is not protonated and the nucleophile is a hydroxide ion. The product of this reaction would be the deprotonated carboxylate anion.
methanoic acid (formic acid)
(HCOOH) Simplest of organic acids. Not used by embalmers but used by ants, wasps and other stinging insects.
acid anhydrides
(RCO)2O -oic anhydride e.g. ethanoic anhydride
heterolytic reactions
- A bond is broken and both electrons are given to one of the two products. - The best leaving group is able to stabilize the extra electrons. * Weak bases (conjugate bases of strong acids such as I-, Br-, and Cl-) make good leaving groups
ubiquinone
- Biologically active quinone (electron acceptor in photosynthesis and aerobic respiration) - Reduced to ubiquinol upon the acceptance of electrons. - Long alkyl chain = lipid soluble = act as an electron carrier within the phospholipid bilayer.
anhydrides
- Carboxylic acid derivative - formed by dehydration of 2 carboxylic acids * Symmetric = same acid * asymmetric = two different acids * cyclic = intramolecular reaction of a dicarboxylic acid
reverse phase chromatography
- Exact opposite of Thin Layer (TLC) - stationary phase is non polar so polar molecules move up the plate quickly
simple distillation
- Liquids that boil below 150 C and have atleast 25C difference in boiling temperature. - Consists of a distilling flask (containing combined solution), distillation column ( thermometer, condenser, and receiving flask to collect the distillate.
quinone
- Serve as electron acceptor biochemically; Electron Transport Chain in both photosynthesis and aerobic respiration. - Phylloquinone (Vitamin K1): important for photosynthesis and the carboxylation of some of the clotting factors in blood. - Menanquinones (Vitamin K2)
three examples of hydroxyquinones
- Share the same ring and carbonyl backbone as quinones but differ by the addition of one or more hydroxyl groups - a) Tetrahydroxybenzoquinone; b) 5-hyroxynaphthoquinone; c) 1,2-dihydroxyanthraquinone
Kinetic and Thermodynamic Enolates
- The kinetic enolate forms more quickly, irreversible, low temp, sterically hindered base, and is less stable than the thermodynamic enolate. - Thermodynamic forms more slowly, reversible, weaker or smaller bases, higher temperature
Hemiacetal formation mechanism
- The oxygen in the alcohol functions as a nucleophile, attacking the carbonyl carbon, and generating a hemiacetal. - Hemiacetals are unstable and the hydroxyl group is rapidly protonated and lost as water under acidic conditions, leaving behind a reactive carbocation.
resonance in the peptide bond
- This double bond character between the nitrogen atom and the carbonyl carbon adds to the rigidity and stability of the backbone of proteins. - The single bonds on either side of the peptide bond permit free rotation.
Michael Addition
- an enolate attacks an α,β-unsaturated carbonyl, creating a bond
lactones
- cyclic esters - named by the number of carbons in the ring and the Greek letter of the carbon forming the bond with the oxygen
twist boat conformation of cyclohexane
- little angle strain but has both steric and torsional strain
Triacylglycerols (triglycerides)
- storage lipids involved in human metabolic processes - contain three fatty acid chains esterified to a glycerol molecule
Common names of aldehydes
- suffix al - Common names include * formaldehyde for methanal (R = H) * Acetyldehyde for ethanal ( R = CH3) * Propionaldehyde for propanal (R = CH3CH2)
What is a retro-aldol reaction? What conditions favor retro-aldol reactions?
-A retro-aldol reaction is the reverse of an aldol reaction where instead a bond between the alpha and beta carbons of a carbonyl is broken. This can be favored by the addition of base and heat. In this reaction, a bond between the alpha and beta carbons of a carbonyl is broken
ultraviolet (UV) spectroscopy
-A technique that measures absorbance of ultraviolet light of various wavelengths passing through a sample. -UV spectra are obtained by passing UV light through a sample that is usually dissolved in an inert solvent, and recording the absorbance, or change in absorbanceover time, which is then plotted against wavelength.
If we are given a solution of bromobenzene, with a boiling point of 156 degrees C and camphor; with a boiling point of 204 which type of distillation should be used to separate them?
-Can't use fractional distillation, b/c the boiling points aren't that close to one another -w/ such high boiling points, you should use vacuum distillation, b/c the decreased ambient pressure would allow them to boil at a lower temperature, so you don't degrade the desired product.
Hydrogen Bonding in carboxylic acids
-Carboxylic acids are polar because they contain a carbonyl group and can also form hydrogen bonds because they contain a hydrogen bonded to a very electronegative atom (in this case the hydroxyl oxygen) -Carboxylic acids display particularly strong intermolecular attractions because both the hydroxyl oxygen and carbonyl oxygen can participate in hydrogen bonding. This plays into carboxylic acids tending to form dimers; which are pairs of molecules connected y two hydrogen bonds. -multiple hydrogen bonds elevate the boiling and melting points of carboxylic acids past those of corresponding alcohols. Boiling points also increase with increasing molecular weight
Distillation separates compounds based on what property?
-Distillation takes advantage of differences in boiling point in order to separate solutions of miscible (soluble) liquids
reducing agent
-Donates electrons and becomes oxidized. -mostly gives electrons in the forms of protons, but itself is being oxidized. Ex: sodium, magnesium, aluminum, zinc, which all have low electronegativities and ionization energies. Also metal hydries such as NaH, CaH2, LiAlH4, and NaBH4, are also good reducing agents b/c they have H-ions
In what was is gas chromatography distinct from all of the other techniques that were discussed?
-Gas chromatography is simply the same technique of mobile and stationary phase performed with a gaseous eluent (instead of liquid) -stationary phase is usually a crushed metal or polymer
fischer projections
-Horizontal lines indicate bonds that project out from the plane of the page -Vertical lines indicate bonds going into the plane of the page -point of intersection = carbon atom
Isobutyric acid and diethyl ether
-Isobutyric acid is more polar than diethyl ether and can exhibit hydrogen bonding, so it will congregate in the aqueous layer -diethyl ether will remain in the organic layer
imine formation
-Nitrogen and nitrogen-based groups are good nucleophiles b/c there is a lone pair of e- on N which react w/ electrophilic carbonyls of aldehydes and ketones -Ammonia adds to the carbon atom & water is lost producing an imine *NH3 reacts with carbon forming a tetrahedral and breaking the pi bond *the e- from the pi bond are accepted by the O in carbonyl group *2 of the H from NH3 react with O to form water (leaves) *NH is left double bonded to C
Examples of nucleophiles
-OH and H₂O; the oxygen, in both cases. ex. water in hydrolysis
What two peaks would you expect to see in the IR spectrum of a carboxylic acid?
-OH peak (~3000 cm^-1) -C=O peak (~1700 cm^-1)
Synthesis methods of carboxylic acids
-Oxidation of primary alcohol w/ strong oxidizing agent Ex: K2Cr2O7, CrO3, KMnO4, NaCr2O7
esters
-RCOOR -are the dehydration synthesis products of other carboxylic acid derivatives and alcohols
What are the four main reactants in the Gabriel synthesis of an amino acid?
-Starts with potassium phthalimide and diethyl bromomalonate -followed by an alkyl halide. -Water is then used to hydrolyze the resulting compound to form the amino acid. While acids and bases are used at various times as catalysts, they are not the main reactants.
How are HOMO and LUMO related to absorption wavelength?
-The smaller the difference in energy between the HOMO and the LUMO, the longer the wavelengths that can be absorbed by the molecule.
Acidity of carboxylic acids
-They hydroxyl hydrogen of a carboxylic acid is quite acidic. This results in a negative charge that remains after the hydrogen is removed and resonance stabilization occurs between both of the electronegative oxygen atoms. -Carboxylic acids are relatively acidic, with pKa values on the order of 4.8 for ethanoic acid and 4.9 for propanoic acid. -They are acidic in for organic compounds but do not compare to strong acids like HCL(PKa= -8) and HSO4- (1.99) -groups like -NO2 or halides are electron-withdrawing, INCREASING acidity -groups like -NH2 and -OCH3 are electron-donating, DECREASING acidity.
receiving flask
-Where distillate is collected, can be put in an ice bath for further condensation
amphoteric
-a substance that can act as both an acid and a base -amino acids w/ their acidic carboxyl group and basic amino group can act as both acid and base.
formation of a carbanion
-alpha hydrogens of ketones tend to be slightly less acidic than those of aldehydes due to the electron-donating properties of the additional alkyl group in a ketone.
lewis acid
-an atom, ion, or molecule that accepts an electron pair to form a covalent bond -tend to be electrophiles with empty p-orbitals to which they can accept an electron pair
lewis base
-an atom, ion, or molecule that donates an electron pair to form a covalent bond -tend to be nucleophiles, which have lone pair of electrons that can be donated, and are often anions
anhydride cleavage
-anhydrides are most reactive bc of resonance stabilization and e- withdrawing oxygens -works well with ammonia, alcohol, or water -CLEAVES to form new product + carboxylic acid
node
-area where probability of finding an e- is zero
phenols
-aromatic alcohols -Hydroxyl groups can be attached to aromatic rings (these hydroxyl hydrogens are very acidic due to possible resonance b/w the ring & the lone pairs on the O atom) -Two groups on adjacent carbons are called ortho- or o- -Two groups separated by a carbon is called meta- or m- -Two groups on opposite sides of the ring are called para- or p-
residue
-at the end of the filtration, the solid part that is left (usually the compound you want, or could be a drying agent you used to remove water)
why does a carbonyl have a significant dipole moment?
-because oxygen is more electronegative, and thus pulls electrons away from the carbon, making the carbon electrophile and a good target for nucleophiles. -more impactful than alcohols
Intermolecular Hydrogen bonding in alcohols
-capable of intermolecular hydrogen bonding, which results in significantly higher melting and boiling points than those of analogous hydrocarbons
anhydrides
-carboxylic acid derivative -had water molecule removed during formation -formed from 2 carboxylic acid molecules -named by replacing acid with anhydride in the name of the carboxylic acid if anhydride is formed from only 1 type of carboxylic acid -if anhydride is not symmetrical, both carboxylic acids are named before the anhydride is added to the name (ex: ethanoic propanoic anhydride) ex: pentanoic acid becomes pentanoic anhydride
decarboxylation of carboxylic acids: Loss of CO2
-complete loss of the carboxyl group as carbon dioxide. -1,3-dicaroxylic acids and beta-keto acids may spontaneously decarboxylte when heated.
Which one of the following molecules is detectable by UV spectroscopy: propane, propene, propanone.
-conjuagated systems and other molecules w/ pi or nonbonding electrons can give absorbances on a UV spectroscopy plot -therefore, propane would not appear, but propene and propanone would
carboxylic acids
-contain a carbonyl group (C=O) and a hydroxyl group (OH) on a terminal carbon -very oxidized (have 3 bonds to O) -named by replacing -e in the name of the parent alkane with -oic acid
ketones
-contain carbonyl group somewhere in the middle of the carbon chain -always assign a number to the carbonyl carbon -named by replacing -ane in the name of the parent alkane with the suffix -one -give the carbonyl carbon the lowest possible # since it is the highest priority group
Bimolecular nucleophilic substitution (SN2) reactions
-contains one step, in which the nucleophile attacks the compound at the same time as the leaving group leaves -concerted, since it works in once motion -reaction is bimolecular b/c this single rate-limiting step involves two molecules Rate = k[Nu:][R-L]
naming cyclic carboxylic acids
-cyclic carboxylic acids are named by listing the cycloalkane with the suffix carboxylic acid -salts of carboxylic acids are named beginning with the cation, followed by the name of the acid with the ending -oate replacing -oic acid.
beta-dicarboxylic acids
-dicarboxylic acids in which each carboxylic acid is positioned on the beta carbon of the other -the two carboxylic acids are separated by a single carbon -very acidic due to the alpha carbons located between the two -loss of an alpha carbon produces a carbanion - which is stabilized by the electron withdrawing effect of both carboxyl groups
What properties of molecules do thin-layer chromatography, paper chromatography, and standard column chromatography take advantage of to separate compounds?
-each method uses differences in charge and polarity to separate compound.
Unimolecular nucleophilic substitution (SN1) reactions
-first step is the rate-limiting step, in which the leaving group leaves, generating a positively charge carbocation -b/c formation of carbocation is rate limiting, the rate of the reaction depends only on the concentration of the substrate rate = k[R-L] where R-L is an alkyl group containing a leaving group, first order reaction
hydroxyquinones
-have 2 carbonyls and a variable number of hydroxyl groups -named by indicating the position of the OH group with a number & indicating the total number of OH groups by a prefix (di- or tri-) with the substituent name hydroxyl- (ex: 1,2-dihydroxyanthraquinone) - To convert phenols to hydroxyquinones, they must be converted to quinones to an oxidation step first and then another oxidation is required to further oxidize the quinones (total of 2 oxidation steps)
aldehydes
-have a carbonyl group found at the end of the carbon chain (attached to C1) -named by replacing -e of the parent alkane with suffix -al
Naming cyclic Aldehydes
-if the aldehyde is attached to a ring, the suffic -carbaldehyde is used instead.
Hydration of an aldehyde (base and acid catalyzed)
-in the presence of water, aldehydes and ketones react to form geminal diols.
volatile
-injected compounds in gas chromatography, which have low melting points, sublimable solids or vaporizable liquids.
What does Infrared (IR) spectroscopy measure? what is IR spectroscopy generally used for?
-measure absorption of infrared light by specific bonds, which vibrate -these vibrations cause changes in the dipole moment of the molecule that can be measured -once the bonds in a molecular are determined, one can infer the presence of a number of functional groups to determine the identity of the molecule.
leaving groups
-molecular fragments that retain e- after heterolysis -Weak bases are more stable w/ extra electrons -->good leaving groups
boiling points for various alcohols
-molecules with more than one hydroxyl group show greater degrees of hydrogen bonding -boiling point increases w/ more -OH b/c more H-bonding.
conjugation in a carbonyl-containing compound
-multiple resonance structures allows for the stabilization of a positive charge once the nucleophile has bonded, making these compounds more susceptible to nucleophilic attack
nucleophiles
-nucleus loving -negatively charged so they are attracted to the + nucleus -have lone pairs or π bonds that can be used to form covalent bonds to electrophiles
superheating
-occurs when a liquid is heated to a temperature above its boiling point without vaporization -occurs when gas buble within a liquid are unable to overcome the combination of atmospheric pressure and surface tension.
pyridinium chlorochromate (PCC)
-oxidizes primary alcohols to aldehydes -lacks the water necessary to hydrate the aldehyde so it cannot oxidize it any further -oxidizes secondary alcohols to ketones
pyridinium chlorochromate (PCC)
-oxidizes primary alcohols to aldehydes (stops before oxidizing all the way to a carboxylic acid). -lacks the water necessary to hydrate the aldehyde so it cannot oxidize it any further. -oxidizes secondary alcohols to ketones.
dimers
-pairs of molecules connected by two hydrogen bonds -carboxylic acids tend to form dimers b/c of hydrogen bonding
quinones
-phenols treated with oxidizing agents -Named by indicating the position of the carbonyls numerically & adding quinone to the name of parent phenol -Serve as electron acceptors in e- transport chain
chemoselectivity
-preferential reaction of one functional group in the presence of other functional groups
structure of the mesylate anion
-prepared using methylsulfonyl chloride and an alcohol in the presence of a base
steric hindrance
-prevention of reactions at a particular location within a molecule due to the size of substituent groups
steric hindrance
-prevention of reactions at a particular location within a molecule due to the size of substituent groups Ex: -Sn2 reactions will not occur at tertiary carbons.
ubiquinol
-reduced form of ubiquinone after it accepts electrons
alpha-hydrogens
-relatively acidic -can be removed by a strong base -made more acidic by the electron withdrawing oxygen of the carbonyl
cyanohydrins
-stable compounds produced when the nucleophile cyanide anion attacks the carbonyl carbon atom (after H dissociates) in aldehydes and ketones -form when the O has been reprotonated -Gains stability from the newly formed C-C bond (C-CN) *HCN dissociates into H+ and CN- *CN- reacts w/ carbonyl carbon breaking the pi bond and causing O to accept those e- from the pi bond *H+ then reacts with the - charged O forming an OH group
ion exchange chromatography
-stationary phase is made of either negatively or positively charged beads (attract & bind compounds that have opposite charge) -salt is added to elute proteins stuck to column
what are the products of the transesterification reaction between isopropyl butanoate and ethanol?
-the ethyl group of ethanol will replace the isopropyl group of isopropyl butanoate, resulting in ethyl butanoate and 2-propanol
extraction
-the transfer of a dissolved compound (the desired product) from a starting solvent into a solvent in which the product is more soluble -based on the concept that like dissolves like (i.e. polar and polar, nonpolar and nonpolar)
What are the reactions types in the Gabriel Synthesis?
-two Sn2 reactions -hydrolysis -decarboxylation
How would you oxidize a primary alcohol to a carboxylic acid?
-use of a strong oxidizing agent, like chromium (6) Ex: sodium and potassium dichromate salts (Na2Cr2O7 and K2Cr2O7) -will fully oxidie alcohols to carboxylic acids, and secondary alcohols to ketones.
gravity filtration
-used when the product of interest is in the filtrate -hot solvent is used to maintain solubility
vacuum filtration
-used when the product of interest is the solid -vacuum is connected to the flask to pull the solvent through more quickly
Jones oxidation
-uses chromium trioxide dissolved in dilute sulfuric acid and acetone (stronger oxidizing agent) -oxidizes primary alcohols to carboxylic acids -oxidizes secondary alcohols to ketones
partitioning
-when different characteristics of molecules in a sample migrate at different rate b/c or their different physical and chemical properties, causing them to migrate at different speeds through the medium.
Electron transitions in UV vis
-works b/c molecules w/ pi electrons or nonbonding electrons can be excited by UV light to higher antibonding orbitals. -molecules w/ lower energy gap between the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) are more easily excited and can absorb longer wavelengths (lower frequencies) w/ lower energies.
mechanism of sn1 reaction
1) rate-limiting step in which the leaving group leaves, generating a positively charge carbocation. 2) The nucleophile attacks the carbocation resulting in the substitution product. 3) Product will usually be a racemic mixture. 4) rate = k [R-L] ; [R-L] is an alkyl group containing a leaving group
Under what conditions will a carboxylic acid spontaneously decarboxylate?
1,3-dicarboxylic acids will spontaneously decarboxylate when heated, due to the stable cyclic intermediate step.
to determine the absolute configuration at a chiral center
1. assign priority by atomic number 2. arrange the molecule with the lowest-priority substituent in the back (or invert the sterochemistry by switching the two substituents) 3. draw a circle around the molecule from highest to lowest priority 4. clockwise = R counterclockwise = S
five steps of iupac nomenclature
1. identify longest carbon chain 2. number the chain 3. name substituents 4. assign a number to substituents 5. complete the name
5 amino acid groups
1. nonpolar aliphatic (nonaromatic) 2. Aromatic 3. Polar 4. Negatively charged (acidic) 5. Positively charged (basic)
peptide bond formation and cleavage
1. undergo condensation reactions to form peptides 2. reverse reaction, hydrolysis of the peptide bond, is catalyzed by a strong acid or base.
What are the four reactants in the Strecker Synthesis of an amino acid?
1: An aldehyde 2: Ammonium chloride (NH4Cl) 3: Potassium cyanide These three are used to make the aminonitrile 4: H2O is used to hydrolyze the aminonitrile to form the amino acid
Steps to problem solving in organic chemistry
1: Know your Nomenclature 2: Identify the Functional Groups 3: Identify the Other Reagants 4: Identify the most reactive functional groups(s) 5: Identify the First Step of the Reaction 6: Consider Stereospecificity/Stereoselectivity
What are the three absorption peaks you should know for the MCAT?
1: O-H peak (3300cm^-1 for alcohol, 3000 cm^-1 for carboxylic acids. 2: Carbonyl (C=O, around 1700 cm^-1, sharp/deep peak) 3: N-H (same region as O-H bond around 3300cm^-1), but has a sharp peak instead of a broad one.
meso compound
A compound with chirality centers and an internal plane of symmetry causing it to be an achiral molecule
Levorotary, (l-) or (-) Rotation
A counterclockwise rotation of plane polarized light by a stereoisomer (i.e., l- or (-)- methamphetamine).
imine
A double bond between a carbon and a nitrogen
imine
A double bond between a carbon and a nitrogen -susceptible to nucleophilic addition reactions, so CN- can attack, forming a nitrile group
Carbonyl
A double bond between a carbon and an oxygen. -includes aldehydes, ketones, carboxylic acids, esters, amides, anhydrides, etc.
High Performance Liquid Chromatography (HPLC)
A form of chromatography in which a small sample is put into a column that can be manipulated with sophisticated solvent gradients to allow very refined separation and characterization; formerly called high-pressure liquid chromatography.
phosphate group
A functional group consisting of a phosphorus atom covalently bonded to four oxygen atoms
hemiacetal
A functional group that contains a carbon atom bonded to one -OR group, one -OH group, an alkyl chain, and a hydrogen atom.
acetal/ketal
A functional group that contains a carbon atom bonded to two- OR groups, an alkyl chain, a hydrogen atom.
mobile phase of chromatography
A liquid (or a gas in gas chromatography) that is run through the stationary phase in chromatography. -solvent usually
beta-state (higher energy)
A magnetic state seen in NMR spectroscopy in which nuclei have been irradiated with radiofrequency pulses to bring them to a higher-energy state.
alpha-state (lower energy)
A magnetic state seen in NMR spectroscopy in which nuclei have magnetic moments that are aligned with an incident magnetic field, thus having lower energy.
Strecker synthesis
A method of synthesizing amino acids that uses condensation between an aldehyde and hydrogen cyanide, followed by hydrolysis.
Gabriel (Malonic-Ester) Synthesis
A method of synthesizing amino acids that uses potassium phthalimide and diethyl bromomalonate followed by an alkyl halide; two substitution reactions are followed by hydrolysis and decarboxylation. -an amino acid is generated from phthalimide and diethyl bromomalonate, using two Sn2 reactions, hydrolysis, and decarboxylation. -also starts with a planar molecule, thus, product is a racemic mixture of L- and D- amino acids.
newman projection
A method of visualizing a compound in which the line of sight is down a carbon-carbon bond axis.
racemic mixture
A mixture that contains equal amounts of the (+) and (-) enantiomers. Racemic mixtures are not optically active.
achiral
A molecule that either does not contain a chiral center or contains chiral centers and a plane of symmetry; as such, it has a superimposable mirror image.
sp2 hybridization orbitals
A molecule with these orbitals has trigonal planar geometry, and the one unhybridized p-orbital can be used to form a pi-bond
sp hybridization orbitals
A molecule with this geometry has linear geometry, and the two unhybridized p-orbitals can be used to form pi bonds 50% s and 50% p character 180 degrees apart
oxidation state
A positive or negative whole number that represents the "charge" an atom in a compound would have if all shared electrons were assigned to the atom with a greater attraction for those electrons.
filtration
A process that separates materials based on the size of their particles.
distillation
A process that separates the substances in a solution based on their boiling points -separates by evaporation and conensation -liquid w/ lower boiling point will vaporize first, and the vapors will rise up the distillation column to condense in a water-cooled condenser -heating temp is kept lowso that the liquid w/ higher boiling point will not be able to boil, and therefore will remain a liquid in the initial container.
Retardation Factor (Rf)
A ratio used in thin-layer chromatography to identify a compound; calculated as how far the compound traveled relative to how far the solvent front traveled.
Aldol condensation
A reaction in which an aldehyde or ketone acts as both the electrophile and nucleophile, resulting in the formation of a carbon-carbon bond in a new molecule called an aldol.
Coenzyme Q (Ubiquinone)
A small non-protein electron carrier in the electron transport chain.
carbanion
A strongly nucleophilic species with a negatively charged carbon atom having only three bonds. The carbon atom has a nonbonding pair of electrons.
chromatography
A technique that is used to separate the components of a mixture based on the tendency of each component to travel or be drawn across the surface of another material. -used physical and chemical properties to separate and identify compounds from a complex mixture.
infrared (IR) spectroscopy
A technique that measures molecular vibrations at different frequencies, from which specific bonds can be determined; functional groups can be inferred based on this information infrared light range runs from wavelengths of 700nm to 1mm
Nuclear Magnetic Resonance (NMR) Spectroscopy
A technique that measures the alignment of magnetic moments from certain molecular nuclei with an external magnetic field; can be used to determine the connectivity and functional groups in a molecule.
Thin Layer Chromatography (TLC)
A type of chromatography that uses silica gel or alumina on a card as the medium for the stationary phase. -silica gel is polar and hydrophobic, so nonpolar compounds dissolve in the organic solvent and move quickly as the solvent moves up the plate, whereas polar molecules stick to the gel and don't travel as far.
Gas Chromatography (GC) also known as vapor-phase chromatography (VPC)
A type of chromatography used to separate vaporizable compounds; the stationary phase is a crushed metal or polymer and the mobile phase is a nonreactive gas. -sample is injected into the column and movs with the gaseous mobile phase through a stationary liquid or solid ohase; a computer identifies the sample components
totally eclipsed conformation
A type of conformation in which the two largest groups are 0 degrees apart; the most energetically unfavorable conformation
anti conformation
A type of staggered conformation in which the two largest groups are antiperiplanar to each other; the most energetically favorable conformation
E/Z isomerism
A type of stereoisomerism in which different groups attached to each carbon of a C=C double bond may be arranged differently in space because of the restricted rotation of the C=C bond.
distillation column
A vertical pipe in which crude oil is separated into several components.
NMR spectrum of dichloromethyl methyl ether
A: dichloromethyl proton B: Methyl protones
What makes glycine unique among the amino acids?
All amino acids, except glycine, have chiral a-carbons. Because the R group of glycine is a hydrogen atom. It is not chiral and therefore is not optically active.
For each of the derivatives below, list the nucleophile used to form the derivative in an acyl substitution reaction and the name of the cyclic form of that functional group amide ester anhydride
Amide -Formed by reacting w/ Ammonia (NH3) or amine -Cyclic form is called a Lactam Ester -formed by reacting an alcohol -Cyclic form is called a Lactone Anhydride -formed by reacting with another carboxylic acid -Cyclic form is called an Anhydride still
For each of carboxylic acid derivatives below, list the relevant nucleophile that reacts with a carboxylic acid to generate the derivative, the derivative's suffix, and the name of the derivative in cyclic form. Amide Ester Anhydride
Amide: -Formed from COOH by NH3 or amine -Suffix: -amie -Cyclic naming: Lactam Ester: -Formed by COOH by an Alcohol -Suffix: -oate -Cyclic naming: Lactone Anhydride: -Formed by -COOH by another carboxylic acid -Suffix: anhydride -Cyclic naming: anhydride
zwitterion
Amphoteric (reacts as acid or base) compound with no net electric charge.
The aldol condensation can be classified under many categories of reactions. List some of these reaction types, and provide a short description of each.
An aldol condensation is a 1: condensation reaction, b/c two molecules are joined to form a single molecules w/ the loss of a small molecule 2: a dehydration reaction, in which a molecule of water is lost 3: a nucleophile-electrophile reaction, in which a nucleophile pushes an electron pair to form a bond with an electrophile.
Strecker Synthesis: Step 2
An amino acid is generated from the amino acid -starting material for strecker synthesis is a planar carbonyl-containg compound, therefore, product is a racemic mixture, therefor both the L- and D- amino acids can be generated through this process.
enamine
An amino group attached to a carbon that is double-bonded to another carbon.
Strecker synthesis: Step 1
An aminonitrile is generated from an aldehyde or ketone
wavenumber
An analog of frequency used for infrared spectra instead of wavelength. -units of inverse cm (cm^-1)
chemical shift
An arbitrary variable used to plot NMR spectra; measured in parts per million (ppm).
tetramethylsilane
An internal standard for all NMR data -marks 0ppm
carbocation
An organic ion in which a carbon atom has a positive charge
Of amides, esters, and anhydrides, rank which groups are the most reactive?
Anhydrides are the most reactive, followed by esters, and then finally amides. Anhydrides w/ their resonance stability and 3 electron withdrawing oxygens, are the most electrophilic Esters lack one electron-withdrawing carbonyl oxygen and are slightly less reactive Amides have an electron-donating group, are the least reactive towards nucleophiles.
hydrogen bond
Attraction between a slightly positive hydrogen atom and a slightly negative atom.
A chemistry student reacts butanone and butanal each with PCC and KMnO4, what are the expected products of each
Butanone: Reacts with neither PCC or KMnO4 b/c ketones cannot be oxidiazed with common oxidizing reagent that cannot break the c-c bond Butanal: is oxidized by KMnO4 to form butanoic acid, but does not react with PCC, which is not a strong enough oxidant
What is an inorganic phosphate?
Carbon-containing molecules w/ phosphate groups: Ex: -nucleotides, like those in DNA, ATP or GTP
organic Functional Groups
Carboxylic Acid Prefix: Carboxy- Suffix: -oic acid anhydride Prefix: alkanoyloxycarboyl- suffix: anhydride Ester prefix: alkoxycarbonyl suffix: -oate amide prefix: carbamoyl- or amido- suffix: -amide aldehyde Prefix: oxo- Suffix: -al ketone prefix: oxo- or keto- suffix: -one alcohol prefix: hydroxy- suffix: -ol alkene: prefix: alkenyl- suffix: -ene alkyne: prefix: alkynl- suffix: -yne alkane: prefix: alkynyl- suffix: -ane
proteins
Chains of amino acids that are formed by long polypeptide chains.
Naming esters
Change the -anol of he alcohol to -yl and the -oic acid of the parent acid to -oate. CH₃COOCH₃ Methanol + Ethanoic Acid → Methyl Ethanoate
column chromatography
Chromatography in which the substances to be separated are introduced onto the top of a column packed with an adsorbent (as silica gel or alumina), pass through the column at different rates that depend on the affinity of each substance for the adsorbent and for the solvent or solvent mixture, and are usually collected in solution as they pass from the column at different times -sample is added to the top of the column, and a solvent is poured over it. The more similar the sample is to the mobile phase, the faster it elutes; the more similar it is to the stationary phase, the more slowly it will elute (if at all).
lactams
Cyclic amides. Amides are the most stable of the carboxylic acid derivatives but β-lactams are highly reactive due to large ring strain. Good electrophiles. Found in several antibiotics. β-lactam: 4-membered ring (N attached to carbonyl C and β-C). γ-lactam: 5-membered ring δ-lactam: 6-membered ring
Conformations of Cyclohexane
Cyclohexane can adopt many conformations. We will explore two conformations: the chair conformation and the boat conformation. In both conformations, the bond angles are fairly close to 109.5°, and therefore, both conformations possess very little angle strain. The significant difference between them when comparing torsional strain
axial and equatorial positions in cyclohexane
During a chair flip, axial components become equatorial and vice versa. However, components pointing "up" (wedge) remain up and components pointing "down" (dash) remain down.
What effects do additional substituents have on the acidity of carboxylic acids?
Electron withdrawing substituents make the anion more stable and therefore increase acidity. Electron donating substituents destabilize the anion, causing the carboxylic acid to be less acidic. The closer the substituent is to the carboxylic acid on the molecule. the stronger the effect will be.
Which role does the enolate carbanion play in organic reactions: nucleophile, electrophile, oxidizing agent, or reducing agent?
Enolate carbanions act as nucleophiles
synthesis of a carboxylic acid via oxidation of a primary alcohol
Ex: K2Cr2O7, CrO3, KMnO4, NaCr2O7
Order of halogen nucleophilicity in an Aprotic Solvent
F- > Cl- > Br- > I- -in aprotic solvents, nucleopilicity relates directly to basicity
What functional group is formed when aldehydes and ketones are reduced? What are some common reducing agents that assist this reaction?
Functional Group: Yields an alcohol (not covered on MCAT, but in some cases it can be reduced all the way to an alkane) Oxidizing agents: LiAlH4, NaBH4
phosphoric acid
H3PO4 weak acid -extremely important biochemically -forms the high-energy bonds that carry energy in adenosine triphosphate (ATP)
Naming Amides
Highest priority: "amide" suffix Name of R group as prefix with "N-" Lower priority: "carbamoyl or amido" prefix
Naming of amides
Highest priority: "amide" suffix Name of R group as prefix with "N-" Lower priority: "carbamoyl or amido" prefix
naming amides
Highest priority: "amide" suffix Name of R group as prefix with "N-" Lower priority: "carbamoyl or amido" prefix -named by replacing the -oic acid suffix w/ -amide. Alkyl substituents on the nitrogen are listed as prefixes, and their location is specified with the letter N-
naming esters
Highest priority: "oate" suffix Name of R group as prefix O-R Lower priority: "alkoxycarbonyl" prefix
naming esters
Highest priority: "oate" suffix Name of R group as prefix O-R Lower priority: "alkoxycarbonyl" prefix -named by placing the esterifying group (substituent bonded to the oxygen) as a prefix; the suffix -oate replace -oic acid.
Naming anhydrides
Highest priority: "oic anhydride" suffix name of alkyl groups attached to the anhydride as a prefix in alphabetical order if they are different Lower priority: "alkanoyloxycarbonyl" prefix
naming anhydrides
Highest priority: "oic anhydride" suffix name of alkyl groups attached to the anhydride as a prefix in alphabetical order if they are different Lower priority: "alkanoyloxycarbonyl" prefix
What is the major historical distinction between HPLC and column chromatography? what is the major distinction now?
Historically: -HPLC was performed at high pressures, whereas column chromatography uses gravity to pull solution through the column Now: -HPLC is performed with sophisticated and variable solvent and temperature gradients, allow for much more specific separation of compounds than column chromatography; HIGH PRESSURE NO LONGER REQUIRED.
nucleophilic substitution reactions
In Sn1 & Sn2 reactions, a nucleophile forms a bond with a substrate carbon and a leaving group leaves
fingerprint region
In an IR spectrum, the region of 1500 to 400 cm-1 where more complex vibration patterns, caused by the motion of the molecule as a whole, can be seen; it is characteristic of each individual molecule.
Would acid dissolve better in aqueous acid or aqueous base?
In aqueous BASE, b/c it will dissociate to form the conjugate base, and being highly charged, will become more solube the like dissolves like applies to polarity; acids and bases dissolve more easily in solutions with OPPOSITE acid-base characteristics.
protic and aprotic solvents
In polar protic solvents, nucleophilicity increases DOWN the periodic table In polar aprotic solvents, nucleophilicity increases UP the periodic table
