OAT Organic Chemistry
Properties of amides
*Made by a combination of carboxylic acid and amine *Very stable but the reaction that makes them is reversible (hydrolysis) *CAN form hydrogen bonds to other amide molecule -amides are the MOST STABLE of all the acid derivatives...for the MCAT, you can consider their carbonyl carbons UNREACTIVE -primary and secondary amides can hydrogen bond and are thus water soluble as long as they lack long alkyl chains -tertiary amides do not have H-bonds and thus have minimal ability to form H-bonds (only off the carbonyl oxygen bc the nitrogen is too hindered)...thus, tertiary compounds are considered to have low water solubility high melting and boiling point, good water solubility
properties of esters
*Made by a combination of carboxylic acid and an alcohol *Water is a product *Colorless and pleasant odors (flowers & fruits) -Lower boiling points than carboxylic acids and alcohols -Most are colorless liquids at room temperature and have pleasant odors -Smaller ester molecules are soluble in water do not form hydrogen bonds since no OH group less polar and no lower melting and boiling point compared to carboxylic acids
SN1 reaction
*unimolecular nucleophilic substitution reactions: 2 steps 1. Leaving group leaves forming a positively charged carbocation (rate limiting step) *The rate of rxn depends only on the concentration of the substrate rate = k [R-L] R-L is the alkyl group containing the leaving group *Anything that accelerates the formation of the carbocation increase the rate of rxn 2. Nucleophile attacks the carbocation (unstable) *results in substitution product Unimolecular since the rate depends on one molecule (is first order) Rate determining step is the formation of a positively charged ion called a carbocation Good leaving group poor nucleophile
vacuum filtration
- The solvent is forced through the filter by a vacuum connected to the flask. - More often used when the solid is the desired product. Large amounts of solid
Tautomers
- Two isomers, which differ in the placement of a proton and the double bond
Nuclear Magnetic Resonance (NMR) Spectroscopy
- measures alignment of nuclear spin with an applied magnetic field, which depends on the magnetic environment of the nucleus itself - useful for determining the structure of a compound, including functional groups - nuclei may be in an α-state or β-state Used for hydrogen and carbon
Pentyl
-CH2CH2CH2CH2CH3 5 carbons
Butyl
-CH2CH2CH2CH3 4 carbons
Synthesis of alkynes
-Elimination of halides (E2) -Vicinal dihalide (alkane) ---(2 eq. KOH, ethanol or 2 NaNH2, NH3)--> alkyne -Vinylic halide (alkene) ---(NaNH2/NH3)--> alkyne
alcohol synthesis
-addition of water to double bonds -addition of gringard reagents to carbonyls -SN1 and SN2 reactions -reduction of carboxylic acids, aldehydes, ketones, and esters
Hydroboration of alkenes
-anti-markonikov -syn addition BH3 Step 1: B attaches to less sterically hindered carbon atom Step 2: oxidation hydrolysis produces alcohol that is anti markovnikov and syn addition
SN2 reaction
-bimolecular nucleophilic substitution reactions - only 1 step (concerted reaction) -nucleophile attacks the compound at the same time as the leaving group leaves -Nucleophile actively displaces the leaving group in a backside attack for this to occur, nucleophile must be strong & substrate can't be sterically hindered -concentrations of substrate & nucleophile have role in determining the rate --> rate = k[Nu][R-L] -Position of the substituents around the substrate carbon is inverted requires a strong nucleophile, adds antiperiplanar switching stereochemistry
ketone nomenclature
-e to -one Highest priority carbonyl group given lowest possible number
Creations of alcohols
1 SN1 and 2 (proton still allows it to act as LG) 2 electrophilic addition of water to a double bond 3 nucleophilic addition to carbonyl 4 oxidation and reduction
Aldehyde
1 alkyl group and 1 hydrogen bonded to a carbonyl in the middle Terminal group
a double bond is made up of
1 sigma 1 pi
Oxymercuration-Demurcuration
1) Hg(OAc)2, H2O 2) NaBH4 produces more substuited alcohol no rearrange,ents
Oxidative Cleavage of alkenes
1) O3 2) Zn, H20 (or CH3SCH3) Double bonds are oxidatively cleaved with ozone to make aldehydes and or ketones KMnO4 can be used too
Hydroboration-Oxidation
1. BH3, THF 2. H2O2, NaOH Anti Markovnikov Syn addition (OH and H are on the same side)
Electrophillic Aromatic Substitution
1. Br2/FeBr3 halogenation 2. I2/HNO3 halogenation (flourine too) 3. H2SO4/HNO3 sulfonation 4. H2SO4/SO3 sulfonation 5. H2SO4/HNO3 nitration 6. Acyl group+AlCl3 Acylation (Friedel-Crafts reaction)
Amide reduction into amine
1. LiAlH4 2. H3O+
Naming alkenes
1. count the number of carbons so that that double bond has the lowest possible number 2. choose the correct prefix 3. add the "ene" ending 4. write the # for the double bond at the start
Ketone
2 alkyl groups bonded to a carbon in the middle
Ether
2 alkyl groups bonded to oxygen Low boiling point slightly soluble in water Does not do hydrogen bonding
Condensation of 2 carboxylic acids
2 carboxylic acid molecules combine to an anhydride, reaction releases water Possible reagents: acetic anhydride, trifluroacetic anhydride, phosphorous pentachloride, DCC
Claisen Condensation
2 moles of ethyl acetate react under basic conditions to produce B-keto ester, ethyl 3-oxobutanoate addition of enolate anion to the carbonyl group of another ester and the displaceement of ethoxide ion
number of sterioisomers
2^n where n is the amount of chiral centers
Functional group region
4000-1400 cm-1 The left-hand two-thirds of an IR spectrum where most functional groups show absorption bands Wave number is related to functional groups and is used to identify functional groups
Triple bond
A chemical bond formed when atoms share three pairs of electrons 1 sigma 2 pi bonds
meso compound
A compound with chirality centers and an internal plane of symmetry causing it to be an achiral molecule Optically inactive Has R and S configuration
Anti aromatic
A cyclic, conjugated molecule that possesses 4n pi electrons
Anhydride
A functional group containing two carbonyls separated by an oxygen atom (RCOOCOR); often the condensation dimer of a carboxylic acid. Cannot form hydrogen bonds since they don't have an OH group, lower melting and boiling points Higher melting point than it's starting materials Polar but not soluble in water
Isoenzyme
A molecular form that originates at the level of the genes that encode the structures of the enzyme proteins in question.
isoelectric focusing
A specialized method of separating proteins by their isoelectric point using electrophoresis; the gel is modified to possess a pH gradient Molecules move until they reach the point where their pH=pI
column chromatography
Absorbent is in the form of a poured or packed column, which allows for separation Solvent and compounds move down the column due to the force of gravity Can be used to separate macromolecules
Two equivalents of alcohol are added
Acetal or ketal
Addition of water to alkene
Acidic conditions Double bond is protonated according to Markovnikovs rule forming the most stable carbocation Carbocation reacts with water forming a protonated alcohol, which loses a proton to yield alcohol
Anhydride synthesis
Acyl chloride reaction Cyclic anhydride self condensation Condensation of two carboxylic acids
Acyl halide conversion into anhydride
Acyl halide into carboxylate salt
Acyl halide Conversion into ester
Acyl halide reacts with alcohol Nucleophile is the oxygen in the alcohol
Acyl halide Conversion into amides
Acyl halide reacts with amine like ammonia Amine attacks carbonyl and displaces chloride
Nomenclature of anhydrides
Add anhydride instead of acid in carboxylic acid
Hydroboration of alkyne
Addition of boron to triple bond Syn addition Cis product ?
Broad peak at 3100-3500
Alcohol
KMnO4
Aldehyde to carboxylic acid
Oxidative reduction
Aldehydes can be oxidized with several reagents like: KMnO4, K2Cr2O7, CrO3, Ag2O, or H2O2 Product is a carboxylic acid
alkyl
Aliphatic compounds
Peak at around 2800
Alkane
Free Radical Halogenation
Alkanes react with halogens (F, Cl, Br, but not I) in the presence of heat or light to form a free radical. Chain rxn: 1) Initiation: the halogen starts as a diatomic molecule. It is homolytically cleaved by heat or UV light, resulting in free radicals. 2) Propagation: the halogen free radical removes an H from the alkane resulting in an alkyl radical. The alkyl radical may now react with a diatomic halogen creating an alkyl halide and a new halogen radical. Most products are formed here, can continue indefinitely. 3) Termination: either 2 radicals bond or a radical bonds to the wall of the container to end the chain rxn or propagation. -> Exothermic process. Alkyl radical stability is the same as carbocation stability: 3° > 2° > 1° > methyl. Alkyl radicals exhibit trigonal planar geometry. Bromine reacts slowly and produces most stable alkyl halide (most substituted) Chlorine reacts quickly and produces multiple products (does not discriminate what product is produced)
potassium permanganate oxidation of alkenes
Alkenes an be oxidized with KMnO4 to make varying products Cold dilute aqueous- 1,2 diol, syn addition Acidic conditions- complete cleavage of double bond Heat- terminal alkene—cleaved to form a carboxylic acid and CO2 Heat- nonterminal alkene-2 molar equivalents of carboxylic acid
Chromatography
Allows for separation and identification of individual compounds from a complex mixture based on their differing chemical properties Separates compounds based on how strongly they adhere to a stationary phase vs a mobile phase Sample put into absorbent and a fluid runs through it to displace it and let the sample travel up the plate Silica gel is usually the absorbent and is polar and hydrophilic The solvent is weakly polar Nonpolar compounds travel the fastest
Amine reduction from amide
Amides can be reduced with LiAlH to form amines
Amide is formed by
Amine and a carboxyl group or its acyl derivatives
Amine reduction from imines
Amines can be synthesized by reductive animation: where an aldehyde or ketone is reacted with ammonia. A primary amine, or secondary amine to form a primary, secondary, or tertiary amine When imine is reduced with hydrogen in the presence of a catalyst an amine is produced
alkyl group
An alkane with a hydrogen atom removed, e.g. CH3, C2H5; alkyl groups are often shown as 'R'.
Exhaustive Methylation - Hofmann Elimination
An amine is converted to a quaternary ammonium iodide salt by reacting with excess methyl iodide Treatment with silver oxide and water converts this to the ammonium hydroxide, which undergoes elimination to form an alkene and amine when heated Predominant alkene is is least substituted
Chemical shift
An arbitrary variable used to plot NMR spectra; measured in parts per million (ppm). Compared to TMS (peak at 0) Further left= downfield
Nucleophile
An atom (or group of atoms) that is attracted to an electron- deficient centre or atom, where it donates a pair of electrons to form a new covalent bond. Attracted to positive charges Better the base the better the nucleophile
substituent effect
An effect on the rate of reaction (or on the equilibrium constant) caused by the replacement of a hydrogen atom by another atom or group; effects include those caused by the size of the atom or group, called steric effects, and those effects caused by the ability of the group to withdraw or donate electron density, called electronic effects (inductive effects or resonance effects). First substituent on aromatic ring strongly influences the susceptibility of the ring to further aromatic substitution and what position an electrophile will go on Activating deactivating
Metalloenzyme
An enzyme that contains a mineral cofactor
Acyl chloride reaction
Anhydrides synthesized by acyl chloride and carboxylic salt
Friedel-Crafts Acylation
Aromatic ring acylated through electrophillic aromatic substitution.
Aromatic compound
Benzene ring Cyclic, conjugated, have 4n+2pi electrons
disubstituted
Benzene with 2 groups Cis and trans
Amine properties
Boiling point between alkane and alcohol Primary and secondary amines can form hydrogen bonds but tertiary amines cannot (have lower boiling points) N atom is sp3 hybridized, lone pair is important in the chemistry of amines Nitrogen inversion-enantiomers interconvert rapidly, inversion of sp3 orbital occupied by the lone pair Bronsted Bases, readily accept protons to make ammonium ions Lewis bases since they donate electrons
phenyl group
C6H5-, Benzene ring attached to a parent compound as a substituent
Peak at 1700
C=O
Propyl
CH2CH2CH3 3 carbons
Ethyl
CH2CH3 2 carbons
Methyl
CH3 1 carbon
Oxidation of alkynes
Can be cleaved with KMnO4 (produces 2 carboxylic acids) or Ozone (carboxylic acid and co2)
phosphate esters
Can form between a phosphate and a free hydroxyl group. Phosphate groups are often attached to proteins in this way. found in living systems in the form of phospholipids where glycerol is attatched to two carboxylic acids and one phosphoric acid
Ethers nomenclature
Chain numbered to give the ether group the lowest number Alphabetical order then add the word ether Cyclic ones naming begins at the oxygen and the rest of the substitutes are named with the lowest number
Methods of extraction are important for use in industry and research. One of the typical steps in an extraction is the use of either acid or base to treat an unknown mixture. This step is applied in order to
Change the water solubility of an unknown compound Adding acid or base to a mixture of unknown compounds is designed to change the water solubility. The loss or gain of protons will make the compound become ionic in nature, and thus soluble in water. On the other hand, compounds that are already ionic may become neutrally charged, resulting in lower solubility in water.
Acyl Halide
Compounds with carbonyl groups attached to halides Most common reagent: SOCl
Isomers
Compounds with the same formula but different structures and connectivity
Ether Synthesis
Condensation of 2 molecules of an alcohol on the presence of an acid Williamson ether synthesis- produces asymmetric ethers from metal all oxide ions with primary alkyl halides and tostlates, alkoxides act as nucleophiles and displace non hindered halide or tosylate in SN2 rxn
Acyl Halide Hydrolysis
Conversion back to carboxylic acids
Jones reagent
CrO3, H2SO4 Converts primary alcohol to carboxylic acid
Alkane with mCPBA
Creates oxirane
Cyclic anhydride self-condensation
Cyclic anhydride formed by hearing carboxylic acid
OH group on acidity
Decreases acidity since it is an activating group
Physical properties of ketones and aldehydes
Dipole moment Carbonyl group is polar, higher bp than alkenes Cannot form hydrogen bonds
Bromination of alkene
Double bond attracts Br2 and displaces it so Br- is displaced, Br+ attaches to the double bond and a cyclic bronomium ion is formed, it is attacked by Br- Anti addition
Electrophillic addition to alkynes
Follows markovnikovs rule, can reduce to alkene
Free radical addition to alkynes
Free radical adds to triple bond with anti Markovnikov placement of halogen Product is trans Halogen adds to less substituted carbon the radical adds to the more substituted carbon
Acylation of anhydrides
Friedel-Crafts acylation occurs with anhydride in the presence of AlCl3 or other Lewis acid catalysts produces an aryl ketone and a carboxylic acid
reagents for decarboxylation
H3O+, heat
Sublimination
Heated solid turns directly into gas without becoming liquid Vapors condense on a cold finger where a pice of glassware with ice or cold water running through it Occurs best at low pressure most are preformed under a vacuum
Free Radical Addtion to alkene (HBr, ROOR) Propagation
Hydrogen halide addition (bromine) radical on the most stable carbon Anti markovnikov since the radical Br first adds to the double bond to produce the most stable free radical on the most substituted carbon. The hydrogen then adds to the free radical resulting in a less substituted product Adds to less substituted carbon
Reactions of anhydrides
Hydrolysis Conversion into amides Conversion into esters and carboxylic acids Acylation
Reduction of acyl halide
H₂ Pd/BaSO₄ Quinoline to reduce to aldehyde LAH to be reduced to alcohol
Huckel's Rule
If a compound has planar, monocyclic rings with 4n+2 pi electrons (n being any integer, including 0), it is by definition an aromatic compound. Number of pi electrons = number of pi bonds*2
Recrystallization
Impure crystals are dissolved in a minimum amount of hot solvent. As the solvent cools crystals re form and impurities are left in the solution Solvent must dissolve the product while hot only and remove impurities at any temperature Desired product should have solubility that depends on temp and would be more solubility at high temperatures
Acetal formation
In acidic conditions, an aldehyde or ketone will react with two molecules of alcohol to form an *acetal*(1st example in image). The brackets surrounding the H^+ indicate that the acid is a catalyst. Common acids used for this purpose include para-toluenesulfonic acid(TsOH) and sulfuric acid(H2SO4) (2nd example in image)
fingerprint region
In an IR spectrum, the region of 1400 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. Mostly bending
Soap
Is a salt, has a polar end (salt of a carboxylic acid, has Na or K) Long chain hydrocarbon with a highly polar end
Filtration
Isolates a suspended solid from a liquid Liquid/solid mixture is poured onto filter paper that only allows the solvent to pass through Separation of the solid (residue) from the liquid (filtrate) Solid stays on top of the filter paper
soponification
Long hydrocarbon carboxylic acids react with sodium and form salts/soaps They solubilize nonpolar organic compounds in aqueous solutions since they have a nonpolar tail and polar carboxylate head When placed in an aqueous solution, soap molecules arrange themselves into micelles where polar heads face outward where they can be solvated by water molecules, and the nonpolar hydrocarbon chains are inside the sphere protected from the solvent Nonpolar molecules like grease dissolve in the hydrocarbon interior of the Michelle
branched chain
Lower melting and boiling point than a straight chain
Pyrolysis
Molecule broken down by heat in the absence of oxygen Used to reduce weight of heavy oils to increase production or more desirable volatile compounds
Electrophoresis
Molecule placed in an electric field and it will either move toward the cathode or anode depending on its size and charge Separates macromolecules like proteins or DNA SIZE IS THE MOST IMPORTANT FACTOR small molecules travel faster
Alcohols with a lower molecular weight are
More soluable since they have a lower molecular weight and a shorter hydrocarbon chain
Synthesis of acyl chlorides
Most common are acid chlorides Prepared by reaction of carboxylic acid with thionyl chloride (SoCl2) Other reagents: pcl3 or pcl5
HPLC (high performance liquid chromatography)
Most widely used liquid chromatography Fractionation of drugs, hormones, lipids, carbohydrates, and proteins Liquid travels through a column and is under pressure
Narrow peak at 3000-3500
N-H
aldehyde nomenclature
Name longest parent chain with carbonyl group; replace "e" with "al"; # parent chain so carbonyl group has lowest #; determine location of substituents and add in front of parent chain
aldehyde nomenclature
Name longest parent chain with carbonyl group; replace "e" with "al"; # parent chain so carbonyl group has lowest #; determine location of substituents and add in front of parent chain Name so carbonyl is at C1 position In complicated molecules the suffix carbaldehyde can be used When a molecule has a higher priority group than the aldehyde, the prefix formyl is used
Amine reduction from nitriles
Nitriles can be reduced with hydrogen and a catalyst or LiAlH to produce primary amines
amine reduction from nitro compounds
Nitro compounds are easily reduced to primary amines Common reducing agents:iron or zinc and dilute hydrochloride acid Useful for aromatic compounds
H NMR
Nuclei are between 0 and 10 Bigger peak=more hydrogens, signifies that there are several equivalent hydrogens More downfield= hydrogen attached to electron withdrawing group
Beta state nmr
Nuclei with magnetic moments that are aligned against the field
synthesis of anhydrides
Nucleophilic attack on a carboxylic acid, leaving of leaving group, reformation of carbonyl
Bimolecular Elimination (E2)
Occurs in one step Rate is dependent on the concentration of the substrate and the base Base removed a proton and a halide anti to the proton leaves, results in double bond Zaitsev's rule- The more substituted product is the major one Steric hinderance does not affect E2 rxns and highly substituted carbon chains form more stable alkenes (SN2 does not do this) Strong bulky bases are favored
HNMR coupling/splitting
Occurs when 2 magnetically different protons are within three bonds of each other
ortho position
On Carbon 2 in ring structure
Meta position
On Carbon 3 in ring structure
monosubstituted
One group Is equatorial because larger groups should be at a position with less strain
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. RCONH2
Making aldehydes and ketones
Oxidation of alcohols Oxidative cleavage of alkenes Friendless Crafts acylation of benzenes
Aldehyde and ketone reactions
Oxidized or reduced to form carboxylic acids or alcohols
Best reagent for primary alcohol to aldehyde
PCC
Polar aprotic
Polar lacks an acidic proton, lack hydroxyl and amine groups
KMnO4
Potassium permanganate is a very strong oxidizing agent. It will oxidize primary alcohols and aldehydes to carboxylic acids, secondary alcohols to ketones, form diols from alkenes, and oxidatively cleave carbon-carbon multiple bonds.
Oxidation of alcohols
Primary alcohols can be oxidized to aldehydes using PCC and further oxidized to carboxylic acids using KMnO₄, Na₂Cr₂O₇, or CrO₃. Secondary alcohols can be oxidized to ketones using any of these oxidants.
Spectroscopy
Process of measuring the frequencies of electromagnetic radiation (light) absorbed and emitted by a molecule -frequencies of light absorbed and emitted are related to the energy levels of the molecule and different types of motion, including rotation, vibration of bonds, and electron movement Different types measure different types of motion, allows for the identification of specific functional groups and how they are connected within a molecule
Friended crafts acylation
Produces ketones in the presence of AlCl3
One equivalent of alcohol added to aldehyde or ketone
Product is hemiacetal or hemiketal
ester
RCOOR dehydration product of carboxylic acids abd alcohols
Acyl halide
RCOX Oh of carboxyl replaced by halogen Cannot form hydrogen bonds Lower melting and boiling point since less polar
HBr, peroxide (ROOR)
Radical Addition using peroxide anti-markovnikov Br Br goes to less subsisted carbon
Disproportionation
Radical transfers a hydrogen atom to another radical producing an alkane and an alkene
Alkyne Reduction
React with lindlar's catalyst and quinoline for cis addition H2 also, Sodium and liquid ammonia (-33C) for trans addition
Unimolecular Elimination
Reaction of alkenes 2 steps Rate is dependent on the concentration of the substrate Elimination of a leaving group results in the formation of a double bond 1 step: leaving group departs and a carbocation forms 2nd step: proton is removed by the base and a double bond forms Favored: like E1 protic solvent, branched carbon chain (more likely to form where more substitution is), good leaving group, weak nucleophile First order
LiAlH4 (stronger) and NaBH4 (milder)
Reduce aldehydes and ketones to alcohols
Quantum level with the lowest energy
S
sterioisomers
Same formula, same connections, different arrangement in space cis trans meso enantiomers, diastereomers conformational isomers
Rate of SN2
Second order; depends on concentrations of both Nu and R-LG rate = k[substrate][nucleophile] Substrate must be unhindered, methyl >primary>secondary substrates are the most stable, tertiary substrates are not in SN2 rxns Occurs in polar aprotic solvents like acetone, DMSO Weak bases for a good leaving group Strong nucleophile usually - charged
PCC
Secondary alcohol to ketone
Blotting
Separates biological macromolecules The sample which is proteins, DNA, or RNA are transferred onto a substrate like nitrocellulose Visualization stain helps isolate the sample Southern blot-dna Northern blot-rna Western blot-proteins
Centrifugation
Separates components by density using high speed spinning Greater mass and density compounds settle towards the bottom of the test tube and lighter compounds are at the top
Simple distillation
Separates liquids that have a boiling point below 150 degrees C and are 25 degrees C different Apparatus is a distilling flask containing the two liquids and a distillation column consisting of a thermometer and a condenser with a flask to collect the distilate
Fractional distillation
Separates liquids that have boiling points that are very similar less than 25C apart Fractioning column is used, filled with inert objects like glass beads, have large surface area so the vapors can condense on them, re evaporate, and condense further up the column. Occurs until the vapor near the top is composed of one component that condenses on the distillation column and collects in the receiving flask
Acidity of carboxylic acids
Significantly increased by the substitution of highly electronegative halogens onto the carbon chain Especially strong when electronegative groups are on the alpha carbon More electronegative groups=more acidic
Nucleophilic Acyl Substitution
Step 1: Nucleophilic Addition Step 2: Elimination of the leaving group and reformation of the carbonyl. Acyl halides are very reactive, the electron withdrawing effect of the halogen makes the carbonyl carbon more susceptible to nucleophillic attack Halides are good LGs Nucleophilic attack is followed by reformation of the carbonyl Acyl halides readily undergo nucleophillic substitution including hydrolysis Reactions: hydrolysis, conversion into anhydrides, conversions into esters, conversions into amides
Alkyl benzene
Substituted benzene
Ketone nomenclature
Suffix -one Location of carbonyl must be specified except in cyclic ketones where it is assumed to be at 1 When listing the carbonyl as a substituent, the prefix oxo is used
Tf pi bonds cannot exist without sigma bond
T
Jones Reagent, KMnO4
Takes primary OH to COOH converts secondary OH to ketones
base peak
Tallest peak in a mass spectrum.
C NMR Spectroscopy
The application of nuclear magnetic resonance regarding the 13C isotope within the molecules of a substance
Why is it harder to oxidize tertiary alcohols
They do not have a hydrogen attached to the carbon with the hydroxyl group -alcohol oxidation involves removal of hydrogen and if there isn't one it is harder to occur
Tf molecules without dipoles such as symmetrical molecules do not absorb IR light like O2 and Br2
True
Tf pi bond formed by the overlap of two p orbitals
True
SDS-PAGE
Type of chromatography used to separate proteins based on mass.
Infrared Spectroscopy (IR)
Used to determine chemical structure because different bonds will absorb different wavelengths of light. Measures molecular vibrations Passing infrared light through a sample and recording the frequencies where light is absorbed Absorption frequencies correspond to stretching, bending, and rotation Frequencies can be split into functional group regions and frequency regions -
Acid chloride
Very reactive acyl halide, good electron withdrawing power from the Cl makes the carbonyl carbon more susceptible to nucleophillic attack Cl is a good leaving group
Free radical substitution
When a halogen replaces a H in a reaction. 3 steps I,P,T Initiation-diatomic hydrogen is cleaved by uv light or peroxide. Free radicals on right side Propagation- radical produces another radical that can continue the rxn one radical on left and right sides Termination- 2 free radicals combine to make a stable molecule, both free radicles on the left Free radicals attack at more substituated carbon such as a tertiary Depends on stability of the intermediate and the number of hydrogens present
UV spectroscopy
[spectroscopy] involves passing uv light through a chemical sample and plotting absorbance v wavelength Detects conjugation (alkenes and aromatics)
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 Head to head overlap 2 electrons All single bonds
Alkynes
a carbon compound with a carbon-carbon triple bond. Shorter chain compound is a gas Higher boiling point Internal alkynes have higher boiling points Terminal alkynes are acidic
Cycloalkene
a cyclic hydrocarbon that contains a double bond
antibonding orbital
a molecular orbital that is higher in energy than any of the atomic orbitals from which it was formed
Bonding orbital
a molecular orbital that is lower in energy than any of the atomic orbitals from which it was formed
thin layer chromatography
a separation technique that involves the separation of small molecules as they move through a silica gel Identification not seperation Substance can be identified by how far it travels Rf value is the distance a compound travels/distance the solvent traveled
Distillation
a separation technique that is based on differences in the boiling points of the substances involved Seperation of one liquid from another through vaporization and condensation Mixture of liquids is heated slowly and the compound with the lower boiling point is vaporized, condensed on a water cooled distillation column and separated Used for miscible liquids
aprotic solvent
a solvent that has no acidic protons; a solvent with no O-H or N-H groups Nucleophile basicity strength is used
mass spectrometry
a technique that separates particles according to their mass Based on how it ionizes and decomposed under specific conditions Net charge mass and abundance of each particle is found First ion formed is the +1 one which is just the removal of a single electron Unit is m/z Tallest peak belongs to most common ion (base peak)
acyl halides to amines
acyl halides are converted into amides by nucleophillic substitution with amines amine lika ammonia attacks the carbonyl group, displacing the chloride produces amide and ammonium chloride
Grignard Addition to Ester
add to the carbonyl groups of esters to form ketones 2 equivalents of grignard reagent: produce tert alcohol
KMnO4
adds hydroxide groups (syn addition)
transesterification
alcohols act as nucleophiles and displace alkoxy groups on esters -transforms ester into another
Claisen Condensation reagents
alcoxide base OR- HCl to quench it
Terminal functional groups
aldehydes and carboxylic acids
Combustion of alkanes
alkane + oxygen -> carbon dioxide + water + heat react with oxygen gas to make carbon dioxide and water in combustion reactions -release energy when C—C bonds are broken in combustion reactions
amine nomenclature
alkyl groups are named before the amine and smaller substituents are give a position of N ex: N,N-dimethylcyclopentylamine Longest chain attached to nitrogen is the backbone Replace e with amine
direct (alkylation of ammonia )
alkyl halide reacts with ammonia to produce alkylammonium halide salts
aliphatic compounds
all compounds that are not aromatic aka alkyl (R)
hydrolysis of amides
amides are hydrolized under acidic conditions through nucleophillic substitution to produce carboxylic acids
ammonia + acetic anhydride
ammonium carboxylate
Cycloalkane
an alkane that is a ring or cyclic structure Prefix cyclo Numbered at greatest point I'd substitution
Conversion of anhydrides into esters and carboxylic acids
anhydride and alcohol react to form esters produces an ester and carboxylic acid
anhydride conversion into amides
anhydride cleaved by ammonia, producing an amide and a carboxylic acid
conversion of anhydrides into amides
anhydride cleaved by ammonia, producing an amide and a carboxylic acid carboxylic acid further reacts with ammonia to form ammonium carboxylate
Hydrolysis of anhydrides
anhydrides are converted to carboxylic acids when exposed to water produces two molecules of the same carboxylic acid
anhydride conversion into esters and carboxylic acids
anhydrides react with alcohols to form esters produces one ester and one molecule of carboxylic acid
Holoenzyme
apoenzyme + cofactor
Arenes
aromatic hydrocarbons
phenol
benzene with OH group
Decarboxylation
carboxylic acid loses CO2 Occurs in beta keto acids and 1,3 diacids
Ester formation
carboxylic acid w/ alcohol under acidic conditions to form esters and water
nomenclature of amines
classified according to the number of alkyl groups that nitrogen is bound to primary amine: attatched to one alkyl group RNH2 secondary amine: attatched to 2 alkyl groups R2NH tertiary amine:bound to three alkyl groups R3N quaternary ammonium compound: R4N+ suffix -amine is used instead of the -e of the alkane prefix -amino is used to for naming compounds of a higher priority OH or CO2H group
flash column chromatography
column chromatography where the solvent is sped up moving down the column by applying gas pressure -the solvent drips out of the end of the column and fractions are collected in flasks or test tubes -fractions have bands corresponding to the different compounds and when the solvents are evaporated the compound is isolated
phthalimide
condensation product of phthalic acid and ammonia, good Nu when deprotonated
synthesis of esters
conversion of acyl chlorides into esters conversion of anydrides into esters and carboxylic acids condensation of carboxylic acids and alcohols
Hoffmann Rearrangement
converts amides to primary amines with the loss of the carbonyl carbon as a molecule of CO2 formation of nitrene (nitrogen analog of carbene) nitrene attatched to the carbonyl carbon, rearranges to form isocyanate, which is hydrolized to amine when under aqueous conditions
alkylation of ammonia
direct alkylation and gabriel synthesis
electron donating groups
donate electrons and thus stabilize positive charge. Decrease acidity Increase pKa Alkyl groups
Apoenzyme
enzyme without its cofactor
Keto-enol tautomerism
equilibrium between a keto form and an enol form (alcohol) of a chemical
Reduction of ester
esters reduced to primary alcohol with LiAlH
Williamson Ether Synthesis
formation of an ether from the reaction of an alkoxide ion with an alkyl halide - Br is involved can be methyl or ethyl bromide SN2
Fisher Esterification
formation of ester from carboxylic acid and an alcohol initiated by an acid catalyst acid catalyst protonates the alcohol --> forms oxonium ion --> protonates carboxylic acid --> carboxylic acid open to nucleophilic attack by the alcohol --> water eliminated yields protonated ester
aldehyde as a substituent
formyl
Gas Chromatography
gas flowing through a coated tube separates compounds by their size, weight, and chemical reactivity with the coating of the tube or column Gases are identified using retention times how long it takes for the gas to travel through the column
cis-trans isomers
have the same covalent bonds but differ in spatial arrangements Compounds differ in position of substitutents attached to the two carbons that form a double bond Cis Same side both up or down Trans different sides one up one down
coupling (splitting)
in NMR spectroscopy, a phenomenon that occurs when there are protons in such close proximity to each other that their magnetic moments affect each other's appearance in the NMR spectrum by subdividing the peak into subpeaks 2 protons near each other = doublet, two peaks of equal intensity Peaks for number of adjacent proton +1
Enantiomers
isomers that are mirror images of each other
Hydration of alkenes
markovinik, OH is at most sunstuited carbon
conversion of carboxylic acids and alcohols
mixture of carboxylic acids and alcohols condense into esters, releases water sulfuric acid as a catalyst
melting point
more carbonds means higher melting point, branching means higher melting point
ester nomenclature
named as alkyl or aryl alkanoates -alkyl chain attatched to the non-carbonyl oxygen is named as a functional group -carboxylic acid suffix -oic acid is replaced by -oate
amide nomenclature
named by replacing -oic acid with -amide alkyl substituents on the N atom are prefixes, location is specified by the letter N
ester conversion into amides
nitrogen bases like ammonia (reagent), act as a nucleophile, attack the electrophilic carbonyl carbon atom, displacing the ester functional group to make an alcohol and amide
conversion of esters into amides
nitrogen bases like ammonia act as nucleophiles act as and attack the electrophilic carbonyl carbon atom, displacing the ester to yield an amide and alcohol
Amine
nitrogen containg compound
Alpha state NMR
nuclei with magnetic moments that are aligned with the field (lower energy)
reduction of amines
obtained from other nitrogen containing functionalities through reduction reactions using reducing agents can be reduced from nitro compounds, nitriles, imines, and amides
para position
on carbon 4 in ring structure
Coenzyme
organic cofactor
Molecular ion peak
parent ion peak--peak furthest to the RIGHT-represents the initial molecular cation=molecular weight of the original molecule.
ketone as a substituent
prefix oxo-
Gabriel synthesis
primary alkyl halides to primary amines 1st step: creation of a phthalimide, a nitroge source based on ammonia with more controlled reactivity
Hydrolysis of esters
produces carboxylic acids and alcohols acidic conditions: first step is protonation of carbonyl oxygen, followed by water attacking carbonyl carbon basic conditions: nucleophile is OH-, attacks the carbonyl carbon, produces triacylglycerols, saponification
SN1 rate
rate = k[substrate] Formation of carbocation is rate determining step First order Rate is not dependent on the nucleophile Rate can be increased by structural factors, more substituted alkane like tertiary alkane are more stable, more stable carbocation Primary and methyl substrates are not in SN1 reactions More polar solvents are also better for SN1 reactions like polar protocol solvents h2o and alcohol Weaker bases as leaving groups so they can leave easily Nucleophile and be strong or weak
Ester reactions
react with nucleophiles at the carbonyl carbon -almost all reactions are nucleophillic substitution(where carbonyl is retained) or nucleophillic addition(carbonyl is lost) Hydrolysis, cpnversion into amides, transesterfication, gringard addition, claisen condensation, reduction
conversion of acyl chlorides into esters (synthesis of esters)
reaction of acid chlorides with alcohols aromatic esters require a base catalyst
Catalytic Hydrogenation of Alkenes
reducing an alkene by adding molecular hydrogen to double bond with aid of metal catalyst. e.g. pt, pd, ni. takes place on surface of metal so it does syn addition (added to the same face of the double bond)
Carboxylic acid nomenclature
replace -e of alkane with -oic acid
Pi bonds
result of the overlap of two parallel electron cloud densities Weaker than sigma bonds Formed from overlap of 2 p orbitals
Constitutional isomers
same molecular formula, different connectivity Have different chemical and physical properties
agarose gel electrophoresis
separates DNA molecules by size
vacuum distillation
separates liquids when boiling points are GREATER than 150C (decreased pressure = decreased boiling point) Temperatures of liquids are at least 25C apart
keto-enol tautomerization
shift from a carbonyl to an alkene with an alcohol. It is a reaction at equilibrium; these structures are not resonance structures
Alkane
single bond C-H Includes methane ethane propane and butane
Gravity filtration
solvents own weight pulls it through the filter, more commonly used when the product of interest is in the filtrate. Usually done with hot solvent Desired product is the liquid
protic solvent
solvents with protons in solution, e.g. water or alcohol. large atoms tend to be better nucleophiles in here because they can shed the solvating protons around them and are more polarizable
Hybridization in a Double Bond
sp2
Diastereomers
stereoisomers that are not mirror images One difference
electron withdrawing groups
strongly electronegative and pull electron density away from rest of the molecule, and stabilize negative charge. Increase acidity Decrease pKa Electronegative atoms like flourine
Synthesis of amides
synthesized by the reaction of acid chlorides with amines or by the reaction of acid anhydrides with ammonia
Double bonds
the sharing of two pairs of electrons between two atoms 1 sigma 1 pi bond
Extraction
the transfer of a dissolved compound from a starting solvent into a solvent in which the product is more soluble Most impurities will be left behind in the first solvent Two solvents are immiscible (2 layers form that do not permanently mix) Two layers mix together by shaking and venting any gas formed so the solute can pass from one layer to another Separates substances based on solubility in aqueous vs organic solvents Proud it will go into the layer of solvent it is the most like and that layer is then collected and a separately funnel is used to separate it. Once the compound is isolated in a pure solvent the product is obtained by evaporation Compounds with hydrogen bonding move into the aqueous layer Compounds with dipole dipole or London dispersion forces are less likely to move into aqueous layer Adding base helps extract acid into the aqueous layer
Carboxylic acid reduction
they are reduced by LiAlH4 (but not NaBH4) to an alcohol
Diol
two hydroxyl groups
Nomenclature of acyl halides
yl halide