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ORGO MCAT

Terms in this set (177)

formyl group
Formaldehyde
formic acid
acetyl group
acetaldehyde
acetic acid
acetone
acetylacetone
acetophenone
benzyl group
benzaldehyde
benzoic acid
benzoin
styrene
acryl group
acrolein
acrylic acid
carboxyl group
carboxylate ion
carbonate ion
carbonic acid
the highest priority functional group because it contains 3 bonds to oxygen
aldehyde
carbonyl group on terminal C
ketone
carbonyl group on non terminal C
ester
carboxilic acid derivative where OH is replaced with OR
amide
replace the OH group of a carboxylic acid with an amino group that may or may not be substituted
amine
Names of Straight-Chain Alkanes (1-30)
1. Methane
2. Ethane
3. Propane
4. Butane
5. Pentane
6. Hexane
7. Heptane
8. Octane
9. Nonane
10. Decane
11. Undecane
12. dodecane
13. tridecane
20. icosane
30. triacontane
alkane definition
hydrocarbon with no double or triple bonds
alkene
contains a double bond.

use suffix -ene
alkyne
contains a triple bond

use suffix -yne
alcohol
contains an OH group. use suffix "ol" or prefix "hydroxy"

alcohols have higher priority than double or triple bonds
diol
Contains 2 hydroxyl groups.

Geminal: If on same carbon

Vicinal: If on adjacent carbons
structural isomers
- share only a molecular formula

- have different physical and chemical properties
stereoisomers
- compounds with atoms connected in the same order but differing in 3D orientation
2^n rule
n = # of chiral centers

# of stereoisomers = 2^n
what are the 3 types oof conformational isomers
- anti

- gauche

- eclipsed
cyclohexane substituents
equatorial: in the plane of the molecule

axial: sticking up/down form the molecules plane
enantiomers
Nonsuperimposable mirror images. Opposite stereochemistry at every chiral carbon. Same chemical and physical properties, except for rotation of plane polarized light.
optical activity
The ability of a molecule to rotate plane-polarized light: d- or (+) = RIGHT, l- or (-) = LEFT.
racemic mixture
50:50 mixture of two enantiomers. Not optically active because the rotations cancel out.
meso compounds
Have an internal plane of symmetry, will also be optically inactive because the two sides of the molecule cancel each other out.
diastereomers
Stereoisomers that are NOT mirror image.
CIS // Trans
A subtype of diastereomers. They differ at some, but not all, chiral centers. Different chemical and physical properties.
relative configuration
Gives the stereochemistry of a compound in comparison to another compound. E.g. D and L.
absolute configuration
Gives the stereochemistry of a compound without having to compare to other compounds. E.g. S and R.
Cahn-Ingold-Prelog Priority Rules
Priority is given by looking at atoms connected to the chiral carbon or double-bonded carbons; whichever has the highest atomic # gets highest priority.
Z and E for alkenes
(Z): Highest priority on same side.

(E): Highest priority on opposite sides.
R and S for stereocenters
A stereocenter's configuration is determined by putting the lowest priority group in the back and drawing a circle from group 1-2-3.

(R): Clockwise

(S): Counterclockwise
Fischer Projections
Vertical lines go to back of page (dashes);
horizontal lines come out of the page (wedges).
Altering Fischer Projection
Switching 1 pair of substituents inverts the stereochemistry;switching2pairsretains stereochemistry. Rotating entire diagram 90° inverts the stereochemistry; rotating 180° retains stereochemistry.
bonding orbitals
Created by head-to-head or tail-to-tail overlap of atomic orbitals of the same sign. LOW energy HIGH stability
anti bonding orbitals
Created by head-to-head or tail-to-tail overlap of atomic orbitals of opposite signs. HIGH energy LOW stability
single bonds
1 sigma bond ; contains 2 e-
double bonds
1 sigma + 1 pi

pi bonds are created by sharing of e- between two unhybridized p-orbitals that align side-by-side
triple bonds
1 sigma +2 pi
which type of bonds are less flexible
Multiple bonds are less flexible than single bonds because rotation is not permitted in the presence of a p bond. Multiple bonds are shorter and stronger than single bonds, although individual p are weaker than s bonds
conjugation
Occurs when single and multiple bonds alternate, creating a system of unhybridized p orbitals down the backbone of the molecule through which p electrons can delocalize
resonance
Describes the delocalization of electrons in molecules that have conjugated bonds
Lewis Acid
e- acceptor. has vacant orbitals or + polarized atoms
Lewis Base
e- donor. Has a lone pair of e-, are often anions
Bronsted-Lowry Acid
proton donor
Bronsted-Lowry Base
proton acceptor
Amphoteric Molecules
Can act as either acids or bases, depending on reactionconditions.
Ka
Acid dissociation constant. A measure of acidity. It is the equilibrium constant corresponding to the dissociation of an acid, HA, into a proton and its conjugate base.
pKa
An indicator of acid strength. pKa decreases down the periodic table and increases with EN.

p𝐾a = −log(𝐾a)
alpha carbon
A carbon adjacent to a carbonyl.
alpha hydrogen
Hydrogen connected to an a-carbon.
nucleophiles
"Nucleus-loving". Contain lone pairs or pi bonds. They have high EN and often carry a NEG charge. Amino groups are common organic nucleophiles.
nucleophilicity
A kinetic property. The nucleophile's strength. Factors that affect nucleophilicity include charge, EN, steric hindrance, and the solvent.
electroophiles
"Electron-loving". Contain a + charge or are positively polarized. More positive compounds are more electrophilic.
leaving group
Molecular fragments that retain the electrons after heterolysis. The best LG can stabilize additional charge through resonance or induction. Weak bases make good LG.
Sn1 Reactions
Unimolecular nucleophilic substitution. 2 steps. In the 1st step, the LG leaves, forming a carbocation. In the 2nd step, the nucleophile attacks the planar carbocation from either side, leading to a racemic mixture of products.

Rate = 𝑘 [substrate]
SN2 reactions
Bimolecular nucleophilic substitution. 1 concerted step. The nucleophile attacks at the same time as the LG leaves. The nucleophile must perform a backside attack, which leads to inversion of stereochemistry. (R) and (S) is also changed if the nucleophile and LG have the same priority level. SN2 prefers less-substituted carbons because steric hindrance inhibits the nucleophile from accessing the electrophilic substrate carbon.

Rate = 𝑘 [nucleophile] [substrate]
oxidation number
The charge an atom would have if all its bonds were completely ionic.
oxidation
Raises oxidation state. Assisted by oxidizing agents.
oxidizing agent
Accepts electrons and is reduced in the process.
reduction
Lowers oxidation state. Assisted by reducing agents.
reducing agent
Donates electrons and is oxidized in the process.
Chemoselectivity
preferential reaction of one functional group in the presence of other functional groups based off of steric hindrance properties
polar protic solvents
acetic acid, H2O, ROH, NH3
polar aprotic solvents
DMF, DMSO, Acetone, Ethyl acetate
phenols
Benzene ring with -OH groups attached. Named for the relative position of the -OH groups:

ortho - right next to each other

meta -- skip a carbon in between

para -- opposite ends of each other
what do alcohols increase
boiling and melting points
are phenols acidic or basic
Phenols are more acidic than other alcohols because the aromatic ring can delocalize the charge of the conjugate base
quinones
Synthesized through oxidation of phenols. Quinones are resonance-stabilized electrophiles. Vitamin K1 (phylloquinone) and Vitamin K2 (the menaquinones) are examples of biochemically relevant quinones
hydroxyquinones
roduced by oxidation of quinones, adding a variable
number of hydroxyl gruops
Ubiquinone
Also called coenzyme Q. Another biologically active quinone that acts as an electron acceptor in Complexes I, II, and III of the electron transport chain. It is reduced to ubiquinol
primary alcohol
Can be oxidized to aldehydes only by pyridinium: chlorochromate (PCC); they will be oxidized all the way to
carboxylic acids by any stronger oxidizing agents
secondary alcohols
Can be oxidized to ketones by any common oxidizing agent
mesylates
Contain the functional group -SO3CH3
Tosylates
Contain the functional group -SO3C6H4CH3
how are aldehydes and ketones protected?
by converting them into acetals or ketals
acetal
A 1° carbon with two -OR groups and an H atom
ketal
A 2° carbon with two -OR groups
deprotection
The process of converting an acetal or ketal back to a carbonyl by catalytic acid
aldehyde properties
Are terminal functional groups containing a carbonyl bonded to at least one hydrogen. Nomenclature: suffix -al. In rings, they are indicated by the suffix -carbaldehyde.
ketone properties
Internal functional groups containing a carbonyl bonded to two alkyl chains. In nomenclature, they use the suffix -one and the prefix oxo- or keto-.
carbonyl properties
A carbon-oxygen double bond. The reactivity of a carbonyl is dictated by the polarity of the double bond. The carbon has a partial positive so it is electrophilic. Carbonyl containing compounds have a HIGHER BP than equivalent alkanes due to dipole interactions. Alcohols have HIGHER BP than carbonyls due to hydrogen bonding.
oxidation properties
Aldehydes and ketones are commonly produced by oxidation of primary and secondary alcohols, respectively. Weaker, anhydrous oxidizing agents like pyridinium chlorochromate (PCC) must be used for synthesizing aldehydes, or the reaction will continue oxidizing to a carboxylic acid.
aldehydes in ox/red
Aldehydes can be oxidized to carboxylic acids using an oxidizing agent like KMnO4, CrO3, Ag2O, or H2O2. They can be reduced to primary alcohols via hydride reagents (LiAlH4, NaBH4).
ketones in ox/red
Ketones cannot be further oxidized, but can be reduced to secondary alcohols using the same hydride reagents.
alpha carbon
The carbon adjacent to the carbonyl is the a-carbon. The hydrogens attached to the a-carbon are the a-hydrogens
alpha hydrogens
Relatively acidic and can be removed by a strong base. The e- withdrawing O of the carbonyl weakens the C-H
bonds on a-hydrogens. The enolate resulting fromdeprotonation can be stabilized by resonance with thecarbonyl.
ketones principles with alpha carbons
Ketones are less reactive toward nucleophiles because of steric hindrance and a-carbanion de-stabilization. The presence of an additional alkyl group crowds the transition step and increases energy. The alkyl group also donates e- density to the carbanion, making it less stable.
tautomers
Isomers that can be interconverted by moving a hydrogen and a double bond. Keto / Enol are tautomers.
Michael addition enolate chemistry
An enolate attacks an a,b-unsaturated carbonyl, creating a bond.
kinetic enblate
Favored by fast, irreversible reactions at LOW TEMP, with strong, sterically hindered bases.
thermodynamic enolate
Favored by slower, reversible reactions at HIGH TEMP with weaker, smaller bases.
Enamine
Tautomers of imines. Like enols, enamines are the less common tautomer
Imine
how does aldol condensation work?
starts with an aldol addition to create an aldol and create a new C--C bond.

then it undergoes a dehydration to give a conjugate
what is an aldol
contains both an aldehyde and an alcohol
aldol nucleophile
The nucleophile is the enolate formed from the deprotonation of the a-carbon.
aldol electrophile
The electrophile is the aldehyde or ketone in the form of the keto tautomer.
dehydration of an aldol
After the aldol is formed, a dehydration reaction (loss of water molecule) occurs. This results in an a,b- unsaturated carbonyl.
retro-aldol reactions
Reverse of aldol reactions. Catalyzed by heat and base. Bond between alpha - and beta -carbon is cleaved.
where carboxylic acid is always located
they are always terminal groups
nomenclature of carboxylic acid
Suffix -oic acid. Salts are named with the suffix -oate, and dicarboxylic acids are -dioic acids
physical properties of carboxylic acids
Carboxylic acids are polar and hydrogen bond well, resulting in high BP. They often exist as dimers in solution.
acidity of carbon acids
The acidity of a carb acid is enhanced by the resonance between its oxygen atoms. The acidity can be further enhanced by substituents that are electron-withdrawing, and decreased by substituents that are electron-donating
beta dicarboxylic acids
Like other 1,3-dicarbonyl compounds, they have an a- hydrogen that is also highly acidic
which proton on a carbox acid is the most acidic
the alpha proton
oxidation reaction of carbon acids
Carboxylic acids can be made by the oxidation of 1° alcohols or aldehydes or the oxidation of 1° or 2° alkyl groups using an oxidizing agent like KMnO4, Na2Cr2O7, K2Cr2O7, or CrO3.
nucleophilic acyl substitution of carbon acids
A common reaction in carboxylic acids. Nucleophile attacks the electrophilic carbonyl carbon, opening the carbonyl and forming a tetrahedral intermediate. The carbonyl reforms, kicking off the L.G.
nucleophiles in carbon acids
Ammonia / Amine: Forms an amide. Amides are given the suffix -amide. Cyclic amides are called lactams. Alcohol: Forms an ester. Esters are given the suffix - oate. Cyclic esters are called lactones.
Carboxylic Acid: Forms an anhydride. Both linear and cyclic anhydrides are given the suffix anyhydride.
reduction of carbon acids
Carboxylic acids can be reduced to a 1° alcohol with a strong reducing agent like LiAlH4. Aldehyde intermediates are formed, but are also reduced to 1° alcohols. NaBH4 is not strong enough to reduce a carboxylic acid
decarboxylation of carbox acids
beta-dicarboxylic acids and other beta-keto acids can undergo spontaneous decarboxylation when heated, losing a carbon as CO2. This reaction proceeds via a six-membered cyclic intermediate
saponification
Mixing long-chain carboxylic acids (fatty acids) with a strong base results in the formation of a salt we call soap. Soaps contain a hydrophilic carboxylate head and hydrophobic alkyl chain tail. They organize in hydrophilic environments to form micelles. A micelle dissolves nonpolar organic molecules in its interior, and can be solvated with water due to its exterior shell of hydrophilic groups.
micelle
Polar heads, non-polar tails. The non-polar tails dissolve non-polar molecules such as grease -- fatty acids
amides condensations
The condensation product of carboxylic acid and ammonia or an amine. Amides are given the suffix -amide. The alkyl groups on a substituted amide are written at the beginning of the name with the prefix N-. Cyclic amides are called lactams, named with the Greek letter of the carbon forming the bond with the N.
ester condensation
The condensation products of carboxylic acids with alcohols, i.e., a Fischer Esterification. Esters are given the suffix -oate. The esterifying group is written as a substituent, without a number. Cyclic esters are called lactones, named by the number of carbons in the ring and the Greek letter of the carbon forming the bond with the oxygen. Triacylglycerols include three ester bonds between glycerol and fatty acids.
anhydrides condensation
The condensation dimers of carboxylic acids. Symmetric anhydrides are named for the parent carb acid, followed by anhydride. Asymmetric anhydrides are named by listing the parent carb acids alphabetically, followed by anhydride. Some cyclic anhydrides can be synthesized by heating dioic acids. Five- or six-membered rings are generally stable.
steric hindrance principle
Describes when a reaction cannot proceed (or significantly slows) because substituents crowd the reactive site. Protecting groups, such as acetals, can be used to increase steric hindrance or otherwise decrease the reactivity of a particular portion of a molecule
induction principle
Refers to uneven distribution of charge across a s bond because of differences in EN. The more EN groups in a carbonyl-containing compound, the greater its reactivity
conjugation principle
Refers to the presence of alternating single and multiple bonds, which creates delocalized p electron clouds above and below the plane of the molecule. Electrons experience resonance through the unhybridized p-orbitals, increasing stability. Conjugated carbonyl-containing compounds are more reactive because they can stabilize their transition states.
ring strain principle
Increased strain in a molecule can make it more reactive. b-lactams are prone to hydrolysis because they have significant ring strain. Ring strain is due to torsional strain from eclipsing interactions and angle strain from compression bond angles below 109.5°
cleavage in nucleophilic acyl substitution
Anhydrides can be cleaved by the addition of a nucleophile. Addition of ammonia or an amine results in an amide and a carboxylic acid. Addition of an alcohol results in an ester and a carboxylic acid. Addition of water results in two carboxylic acids.
Transesterification in nucleophilic acyl substitution
The exchange of one esterifying group for another on an ester. The attacking nucleophile is an alcohol.
amides nucleophilic acyl substitution rxns
Can be hydrolyzed to carboxylic acids under strongly acidic or basic conditions. The attacking nucleophile is water or the hydroxide anion.
amino acid structure
The a-carbon of an amino acid is attached to four groups: an amino group, a carboxyl group, a hydrogen atom, and an R group. It is chiral in all amino acids except glycine.
amino acid stereochemistry
All amino acids in eukaryotes are L-amino acids. They all have (S) stereochemistry except cysteine, which is (R).
which amino acids are not chiral and have R sterochem.
GLYCINE and CYSTINE
amphoteric substance amino acids
Amino acids are amphoteric, meaning they can act as acids or bases. Amino acids get their acidic characteristics from carboxylic acids and their basic characteristics from amino groups. In neutral solution, amino acids tend to exist as zwitterions (dipolar ions).
aliphatic amino acids
Non-aromatic. Side chain contains only C and H. Gly, Ala, Val, Leu, Ile, Pro. Met can also be considered aliphatic.
peptide bonds in amino acids
pForm by condensation reactions and can be cleaved hydrolytically. Resonance of peptide bonds restricts motion about the C-N bond, which takes on partial double bond character. A strong acid or base is needed to cleave a peptide bond. Formed when the N-terminus of an AA nucleophilically attacks the C-terminus of another AA.
polypeptides amino acids
Made up of multiple amino acids linked by peptide bonds. Proteins are large, folded, functional polypeptides.
Strecker synthesis of alpha amino acids
Generates an amino acid from an aldehyde. An aldeyhyde is mixed with ammonium chloride (NH4Cl)
and potassium cyanide. The ammonia attacks the carbonyl carbon, generating an imine. The imine is then attacked by the cyanide, generating an aminonitrile. The aminonitrile is hydrolyzed by two equivalents of water, generating an amino acid.
Gabriel synthesis of alpha amino acids
Generates an amino acid from potassium phthalimide, diethyl bromomalonate, and an alkyl halide.
Phthalimide attacks the diethyl bromomalonate, generating a phthalimidomalonic ester. The phthalimidomalonic ester attacks an alkyl halide, adding an alkyl group to the ester. The product is hydrolyzed, creating phthalic acid (with two carboxyl groups) and converting the esters into carboxylic acids. One carboxylic acid of the resulting 1,3-dicarbonyl is removed by decarboxylation.
phosphoric acid
Sometimes referred to as a phosphate group or inorganic phosphate, denoted Pi. At physiological pH, inorganic phosphate includes molecules of both hydrogen phosphate (HPO42-) and dihydrogen phosphate (H2PO4-).
phosphoric acid structure
Contains 3 hydrogens, each with a unique pKa. The wide variety in pKa values allows phosphoric acid to act as a buffer over a large range of pH values.
phosphodiester bond
Phosphorus is found in the backbone of DNA, which uses phosphodiester bonds. In forming these bonds, a pyrophosphate (PPi, P2O74-) is released. Pyrophosphate can then be hydrolyzed to two inorganic phosphates. Phosphate bonds are high energy because of large negative charges in adjacent phosphate groups and resonance stabilization of phosphates.
organic phosphates
Carbon containing compounds that also have phosphate groups. The most notable examples are nucleotide triphosphates (such as ATP or GTP) and DNA.
chromatography
Separates two or more molecules from a mixture. Includes liquid chromatography, gas chromatography, size-exclusion chromatography, ion-exchange chromatography, affinity chromatography, and thin-layer chromatography.
distillation
Separates liquids according to differences in their boiling points. The liquid with the lowest BP vaporizes first and is collected as the distillate.
simple distillation
Can be used if the boiling points are under 150°C and are at least 25°C apart.
vacuum distillation
Should be used if the boiling points are over 150°C to prevent degradation of the product. The vacuum lowers the air pressure, which decreases the temp the liquid must reach in order to boil.
fractional distillation
Should be used if the boiling points are less than 25°C apart because it allows more refined separation of liquids by BP.
extraction definition
Combines two immiscible liquids, one of which easily dissolves the compound of interest.

Nonpolar Layer: Organic layer, dissolves nonpolar compounds.

Polar Layer: Aqueous (water) layer. Dissolves compounds with hydrogen bonding or polarity.
wash solubility definiton
The reverse of an extraction. A small amount of solvent that dissolves impurities is run over the compound of interest.
filtration definition
Isolates a solid (residue) from a liquid (filtrate)

Gravity Filtration: Use 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. A vacuum is connected to the flask to pull the solvent through more quickly.
recrystallization definition
The product is dissolved in a minimum amount of hot solvent. If the impurities are more soluble, the crystals will reform while the flask cools, excluding the impurities.
what does inferred spectroscopy do?
Measures absorption of infrared light, which causes molecular vibration
(stretching, bending, twisting, and folding). Plotted as % transmittance vs.
wavenumber 1/lamda
what does ultraviolet spectroscopy do?
UV spectroscopy is most useful for studying compounds containing double bonds and/or heteroatoms with lone pairs that create conjugated systems.

Measures the absorption of UV light, which causes movement of electrons between molecular orbitals. UV spectra are generally plotted as percent transmittance or absorbance vs. Wavelength.
HOMO and LUMO of uv spec
To appear on a UV spectrum, a molecule must have a small enough energy difference between its HOMO and
LUMO to permit an electron to move from one orbital to the other. The smaller the difference between HOMO and LUMO, the longer the wavelengths a molecule can absorb.
what does nuclear magnetic resonance (NMR) spectroscopy
NMR spectroscopy measures alignment of nuclear spin with an applied magnetic field, which depends on the magnetic environment of the nucleus itself. It is useful for determining the structure (connectivity) of a compound, including functional groups.

Generally plotted as frequency vs. absorption energy. They are standardized by using chemical shift (d), measured in parts per million (ppm) of spectrophotometer frequency.
TMS of NMR
NMR spectra are calibrated using tetramethylsilane (TMS), which has a chemical shift of 0 ppm
Integration of NMR
Area under the curve. Proportional to the number of protons contained under the peak.
deshielding of NMR
Occurs when electron-withdrawing groups pull electron density away from the proton's nucleus, allowing it to be more easily affected by the magnetic field. Deshielding moves a peak further downfield
downfield of NMR
LEFT. Deshielded by EWG or EN atom nearby.
upfield of NMR
RIGHT. More shielded, by EDG or less EN atom nearby.
spin-spin coupling of NMR
When hydrogens are on adjacent atoms, they interfere with each other's magnetic environment, causing spin-spin coupling (splitting). A proton's (or a group of protons') peak is split into n+ 1 subpeaks, where n is the number of protons that are three bonds away from the proton of interest. Splitting patterns include doublets, triplets, and multiplets.
mass spectrometry
Used to determine the molecular weight and aid in determining molecular structure. The charged molecule collides with an electron, resulting in the ejection of an electron from the molecule, making it a radical
base peak of mass spec
Tallest peak (not always the intact molecule)
molecular ion peak with mass spec
Peak that represents the molecule.
M+1 Peak with mass spec
Relative abundance of 13C. Found in relative abundance of 1.1%. So, if M+1 has an m/z value of 4.4, that means there are 4 carbons. 4.4/1.1 = 4.
M+2 Peak with mass spec
Relative abundance of either 81Br or 37Cl. Br has a 1:1 ratio relative to the M peak. Cl has a 3:1 ratio relative to the M peak.
what are the derivatives of carboxylic acid
ester -- where OH is replaced with OR

amide -- where OH is replaced with an amino group
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