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