Organic Chemistry Flashcards
Geminal diols
Diols with hydroxyl groups on the same carbon
Vicinal diols
Diols with hydroxyl groups on adjacent carbons
Methanal common name
Formaldehyde
Ethanal common name
Acetaldehyde
Propanal common name
Propionaldehyde
3C ketone common name
Acetone
Priority of substituents
Carboxylic acid > anhydride > ester > amide > aldehyde > ketone > alcohol > alkene ≥ alkyne > alkane
Porphyrin
The structure that makes up heme. It is made up of pyrrole rings (5 membered ring with a N)
Constitutional isomers
Also called structural isomers. Structures with similar molecular formulas, but different physical and chemical properties
Stereoisomers
Structures with the same chemical formula and connectivity, but differ in orientation
*A molecule with n chiral centers will have 2ⁿ stereoisomers
Conformational isomers
Structures that differ in rotation around sigma bonds. Varying degrees of rotation around single bonds creates different levels of strain
Angle strain
Strain caused when the molecule is stretched or compressed. Bond angles are not ideal.
Torsinal strain
Strain caused by gauche or eclipsed interactions
Non-bonded strain
Strain caused by non-adjacent atoms competing for space
Axial position
Perpendicular to the plane (sticking up or down)
Equitorial position
Parallel to the plane (sticking out)
Relative configuration
relationship of the configuration of one chiral molecule to another. Ex/ Cis, Trans, E/Z
Absolute configuration
exact spatial arrangement of the atoms or groups on a chiral molecule. Ex/ R/S
Chiral molecule
mirror image of a molecule can not be superimposed (4 different substituents)
Achiral molecule
mirror image can be superimposed (only 3 different substituents)
Dextrorotatory (d)
(+) rotating to the right
Levorotatory (l)
(-) rotating to the left
Specific rotation
The change in orientation of plane polarized light as it passes through a sample of a cmpd. This does not have to do with D and L configurations, only (+) and (-)
[α] = α[observed] / c x l c = concentration in g/mL l = length of path in dm (deci = 10⁻¹)
Racemic mixture
When both (+) and (-) enantiomers are present in equal concentrations. *The rotations cancel each other out and there is no optical activity
Diastereomer
Non-mirror image configurational isomers. They are molecules with at least 2 chiral center and differ at some but not all of them
Cis-tras (geometric) isomers
Type of diastereomer where the substituents differ in their position around an immovable bond. Cis is same side, trans is opposite
Meso compounds
Molecules with chiral centers but contain an internal plane of symmetry (optically inactive). They are super imposable mirror images
E and Z form
Used to describe compounds with polysubstituted double bonds. Priority of substituents has to be assigned on each side of the bond (L and R). Then the E and Z designations are assigned if these highest priority substituents are on the same side or opposite sides of the bond (top or bottom)
Fischer projection
Horizontal lines indicate bonds that project out of the page (wedges). Vertical lines indicate bonds that project into the page (dashes)
Hybridization
describes how bonds with different energy orbitals make up the same type of bond
Hybrid orbital theory
In order for a molecule to form equal bonds, electrons occupy hybrid orbitals that are formed from pre-existing orbitals
Derivative
a compound that can be imagined to arise, or actually be synthesized, from a parent compound by replacement of one atom with another atom or group of atoms
Acid dissociation constant
Ka = [H+][A-] / [HA]
pKa = -log(Ka)
The more acidic a molecule, the smaller the pKa. The more basic a molecule, the higher the pKa
Nucleophile
Like to form new bonds to electrophiles (donate e-, Lewis bases). Nucleophilicity increases as electronegativity, and leaving group quality, decreases. Ex/ Anions, pi bonds, *alcohols&amines (require a neutral or basic solvent)
Polar solvents
Dissolve nucleophiles and allow for reactants to mix together. They assist in the movement of e-
Nonpolar solvents
Do not allow for dissolution of nucleophiles. They are best used to halt enzymatic activity.
Polar protic solvent
Has the ability to hydrogen bond
Polar aprotic solvent
Can not hydrogen bond
Electrophiles
Have a positive charge or (+) polarized atom that accepts an e- pair when forming bonds with a nucleophile. Electrophile strength is determined by a molecules ability to accept and e- pair. Ex/ carbonyls, carbocation
Electrophillic addition
when a nucleophile attacks an electrophile that is a double or triple bond
Electrophilic aromatic substitution
process where an electrophile attacks an aromatic ring forming a carbocation. That carbocation is electrophilic and can undergo substitution with a base
Heterolytic reactions
opposite of coordinate covalent bond formation where a bond is broken and both e- are given to 1 of the products
SN1 reaction
Unimolecular substitution. The 1st step generates the carbocation and a leaving group (rate limiting)
Carbocation stability: tertiary > secondary > primary
SN2 reaction
Bimolecular substitution. The only step in the rxn occurs when the nucleophile attacks the compound and the leaving group leaves at the same time
It is called a concerted reaction because it only has 1 step (rate limiting)
Chemoselectivity
The preferential reaction of one functional group compared to others in a molecule. This is the most reactive region in a molecule. Ex/ a reducing reagent will react with a carboxylic acid over a alcohol in the same molecule
Steric protection
used as a tool in the synthesis of desired molecules by preventing the formation of alternative products
Electron withdrawing groups
Increase acidity
Electron donating groups
Decrease acidity. Ex/ -CH3, -OCH3, -OH, -NH2
Mesylate
Used to make alcohols good leaving groups because it is relatively inert and does not contain an acidic proton. Contains the functional group -SO₃CH₃
Tosylate
Used to make alcohols good leaving groups because it is relatively inert and does not contain an acidic proton. It contains the group - SO₃C₆H₄CH₃
Acetal
Primary carbon with 2 -OR groups and a H atom. Formed when 2 equivalents of an alcohol attacks an aldehyde
Ketal
Secondary carbon with 2 -OR groups. Formed when 2 equivalents of an alcohol attacks a ketone
Quinone
produced when a phenol is treated with an oxidizing agent
Hydroxyquinone
same structure as quinones except they have 1 or more hydroxy groups attached
Ubiquinone
Biologically active quinone associated with complexes I, II, III of the ETC. It is lipid soluble due to the long alkyl chain
Acetylation
Reaction that occurs when an acetyl group (RC=O) is attached to a group
Imine
Formed when ammonia attacks a carbonyl and water is lost. It has a N that is doubled bonded to a C
Tautomers
2 isomers that differ in the placement of a proton and double bond
α-racemization
if an aldehyde or ketone has a chiral α-carbon, it will become a racemic mixture during tautomerization
Enamine
tautomer of imine
Aldol condensation
where an aldehyde or ketone acts as a electrophile (keto form) and then a nucleophile (enolate form) to form a C-C bond
Retro-aldol reaction
This is a reverse of the condensation reaction where 1 molecule is broken into 2 by breaking the bonds between the α and β carbons of the carbonyl (a C-C bond)
Gringard reaction
This is an organometallic chemicalreactionin which alkyl, vinyl, or aryl-magnesium halides (Grignard reagent) add to a carbonyl group in an aldehyde or ketone
Methanoic acid common name
Formic acid
Ethanoic acid common name
Acetic acid
Dimer
pairs of molecules connected by H bonds
Lactams
amides that are cyclic
Lactones
cyclic esters
Decarboxylation
intermolecular reaction that occurs with β-keto acids and β-dicarboxylic acids. It results in the loss of a carboxyl group in a carboxylic acid as CO₂
Saponification
Long chain carboxylic acids are reacted with NaOH (or LiOH) to form salts (R-COO-Na+) capable of solvating nonpolar organic cmpds. The longer the chain in the salt, the better the emulsifying agent (soap)
Fisher esterification
under acidic conditions, carboxylic acids and alcohols condense into esters
Reactivity of carboxylic acid derivitives
Acid anhydrides > carboxylic acids > esters > amides
Transesterification
when an alcohol acts as a nucleophile, attacks an ester, and displaces the esterifying group (becomes a alcohol)
Hydrolysis
cleavage of a bond with the addition of water
Strecker synthesis
A mechanism that uses aldehydes to form amino acids in the lab. The identity of the aldehyde determines the identity of the amino acid
Gabriel synthesis
Process of using alkyl halides to produce primary amines. Primary amines can be used to make amino acids
Spectroscopy
measures the energy differences between states of a molecular system by determining the frequencies of EMR absorbed
IR spectroscopy
measures molecular vibrations which are seen as bending, stretching, or a combination of different types
Range: 40 - 4000 cm⁻¹ (2500 - 25,000 nm)
Hydroxyl IR frequency
(broad peak) - 3300 for alcohols and 3000 for carboxylic acids
Carbonyl IR frequency
(sharp peak) - 1700
Amine IR frequency
(sharp peak) - 3300
UV spectroscopy
measures the wavelength of absorbance when UV light is passed through a dissolved substance. It is most useful for studying compounds with double bonds or heteroatoms with lone pairs that create conjugated systems
Conjugated molecules
those with unhybridized p orbitals
Extraction
the transfer of a dissolved compound from a starting solvent into a solvent where the product is soluble
Immiscible
layers that do not mix
Aqueous phase
contains polar solutes
Organic phase
contains nonpolar solutes
Sequestration
This is the removal of ions from solution by another type of molecule or ion through complex formation
Distillation
separates liquids based on differences in boiling points by evaporation and condensation
Simple distillation
The max BP is 150℃ and there needs to be a 25℃ difference between the 2 liquids
Vacuum distillation
used when we want to distill a liquid with a BP over 150℃
Superheating
occurs when the liquid is heated past its BP without vaporization
Fractional distillation
used when we want to separate 2 liquids with similar BP (less than 25℃ apart)
Chromatography
Physical and chemical properties are used to separate and identify compounds in a mixture based on affinity to the stationary phase. Most chromatography techniques use a polar stationary phase and a nonpolar mobile phase.
Lower the affinity —> faster the elution
Higher the affinity —> slower the elution
Stationary phase
The solid medium or absorbant
Thin layer chromatography
Uses a silica gel (polar, hydrophilic) or alumina adherent for the stationary phase to separate non-volatile mixtures based on polarity. Polar stationary phase, nonpolar mobile phase
Retention factor
distance spot moved / distance solvent front moved
Column chromatography
Similar to TLC except that it uses a column filled with an absorbent (like silica). It allows for greater absorption
Ion exchange chromatography
column chromatography that uses beads in the column coated with charged substances that attack or bind compounds with the opposite charge
Size exclusion chromatography
Uses beads in the column that contain tiny pores of varying sizes. Large compounds can not fit so they move around them and travel faster. Small compounds are slowed down and retained longer
Affinity chromatography
uses a compound in the column that has a high affinity for the target compound
Gas chromatography (GC)
The eluent is a gas. The absorbent is a crushed metal or polymer in a column. Molecules with the lowest MW and weakest intermolecular bonds will migrate fastest and be the first peak on a GC trace
Stereospecific
A reaction preferentially yields a specific conformation of product over the other. Ex/ Sn2 rxn
Resolving agents
A chiral molecule. Can be used to separate racemic mixtures by introducing a new chiral center to each
Normal phase high performance liquid chromatography (HPLC)
Polar stationary phase, nonpolar mobile phase. Molecules with similar polarity to the stationary phase have longer retention times
Reverse phase HPLC
Nonpolar stationary phase, polar mobile phase. The only type of chromatography that reverses the affinity for each phase
