Organic Chemistry

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- First four alkanes are methane (CH4), Ethane (C2H6), Propane (C3H8), and Butane (C4H10)
- single Bonded
- Contain double and triple bonds respectively.
- contain Hydroxyl group (OH) 
- suffix ol or hydroxy if a higher priority group is present
- Diols contain two hydroxyl groups. 
* Geminal: 2 Hydroxyl groups on the same carbon
* Vicinal: on adjacent carbons
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- suffix al
- Common names include 
* formaldehyde for methanal (R = H)
* Acetyldehyde for ethanal ( R = CH3)
* Propionaldehyde for propanal (R = CH3CH2)
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- Dimethyl ketone
- Acetone
- ethylmethylketone
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- suffix one
- Acetone (dimethylketone; 2- propanone) ; smallest ketone; similar as the figure
- 2 pentanone (R= CH3CH2CH2)
- Naming ketones
- methylvinylketone
- Contain both carbonyl group C=O and hydroxyl group (OH)
- most oxidized group that appear on the MCAT
- Suffix: Oic acid
- Methanoic acid (Formic Acid) 
- Ethanoic acid (acetic acid)
- Propanoic Acid (Propanoic Acid)
- Carboxylic acid derivative
- OH is replaced with OR, an alkoxy group
- Carboxylic acid derivative
- OH is replaced with an amino group
- Carboxylic acid derivative
- formed by dehydration of 2 carboxylic acids
* Symmetric = same acid
* asymmetric = two different acids
* cyclic = intramolecular reaction of a dicarboxylic acid
- Share only a molecular formula
- They have different physical and chemical properties
- Same molecule, differ in rotation around single pi bonds.
- Anti staggered isomer has the lowest energy
- Staggered isomer has the highest energy
- Can be interconverted only by breaking bonds.
- consist of two categories:
* Enantiomers: nonsuperimposable mirror image and thus have opposite stereochemistry at every chiral carbon.
* Diasteromer: non- mirror image stereoisomers; differ at some but not all chiral centers. Ex) cis - trans isomers
- non- mirror image configurational isomer. 
- differ at some but not all chiral centers. Ex) cis - trans isomers
- Nearly identical physical properties and chemical properties
- They rotate plane polarized light in opposite directions and react differently in chiral environment
- 4 different group attach to the central carbon
- lack a plane of symmetry
- not superimposable
- Superimposable
- line of symmetry
- are essentially the molecular equivalent of a racemic mixture. 
- Racemix: when both (+) and (-) enantiomers are present in equal concentrations, no optical activity
- Has a plane of symmetry = no optical activity
- overall achiral ( mirror images that can be superimposed) and will not rotate plane polarized light.
- Z : same side
- E: Opposite side
- used for compounds with polysubstituded double bonds. 
- Part of relative configuration
- Used for chiral (stereogenic: 4 different groups bound to it in a non superimposable image) centers in molecules.
- (R) rotates to the right; clockwise
- (S) rotates to the left; counterclockwise
- Part of relative configuration
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- Sigma bonds, contains two electrons. 
* Permit free rotation
- Electron Acceptor in the formation of a covalent bond.
- Tend to be electrophile
- Vacant p-orbitals into which they can accept an electron pair.
- Positively polarized atoms.
- Electron Donor in the formation of a covalent bond. 
- Nucleophile
- Lone pair of electrons that can be donated, often anions; carrying a negative charge
- Proton Donor
Proton Acceptor
Ex) water can act as an acid by donating a proton or a base by accepting a proton .
- Measures the strength of an acid in a solution
- pKa can be calculated as -log Ka
* smaller pKa = stronger the acid = below -2
* Weak organic acids have a pKa between -2 and 20.
- lower pKa = stronger Acid = below -2
* -2 to 20 pKa is considered Weak Acid
- Larger pKa = More Basic
- Electron Donor; Good Bases
- Tend to have lone pairs or pi bonds that cane be used to form covalent bonds to electrophiles ( electron acceptors)
- (CHON) with a minus sign or lone pairs 
- Nucleophile strength is based on relative rates of reaction with a common electrophile; therefore, kinetic property.
- Charge: Increases with increasing electron density (more negative charge)
- Electronegativity: Decreases as electronegativity increases because these atoms are less likely to share electron density
- Steric Hindrance: Bulkier molecule = less nucleophilic
- Solvent: Protic solvents can hinder nucleophilicity by protonating the nucleophile or through hydrogen bonding.
Protic: - I- > Br- > Cl- > F
Aprotic: F- > Cl- > Br-> I-
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- Often ranked by electrophilicity.
- Anhydrides are the most reactive according to Kaplan.
- Higher reactivity can form derivatives of lower reactivity but not vice versa.
1) rate-limiting step in which the leaving group leaves, generating a positively charge carbocation.
2) The nucleophile attacks the carbocation resulting in the substitution product.
3) Product will usually be a racemic mixture.
4) rate = k [R-L] ; [R-L] is an alkyl group containing a leaving group
- Contains only one step
1) Nucleophile (Backside attack; must be strong and substrate cannot be statically hindered) attacks the compound at the same time as the leaving group leaves
2) Substrate will often be alkyl halides, Tosylate, or mesylate
3) Rate = k [Nu:] [R-L]; [R-L] is an alkyl group containing a leaving group
4) Inversion of relative configuration will correspond to change in absolute configuration from (R) to (S) or vice versa.
- Accepts an electron from another species.
- High Affinity for electrons such as O2, O3, and Cl2 or unusually high oxidation states (like Mn7+ in permanganate, MnO4-, and Cr6+ in chromate, CrO_4 ^2-)
- Oxidation reactions: inc. # of bonds to oxygen
- Oxidizing Agents: Metals bonded to large number of oxygen atoms.
Metals bonded to a large number of Oxygen atoms.
Metals bonded to a large number of Hydrides.
-Primary Alcohol Forms an aldehyde by Pyridinium Chlorochromate (PCC)
- Primary Alcohol is oxidized to a carboxylic acid by CrO3 (Jones Oxidation)
- Forms a Ketone by a Dichromate salt (Na_2Cr_2O_7 & K_2Cr_2O_7)
- Acetals: primary carbon with 1 OR and an OH atom
- Ketals: Secondary carbons with two OR groups. 
- Forms in the presence of a strong oxidizing agents.
- Acetals and Ketals are comparatively inert, are frequently used as protecting groups for carbonyl functionalities. 
- once a hemiacetal and hemiketal is formed, the hydroxyl group is protonated and released as a molecule of water; alcohol then attacks, forming an acetal or ketal.
- Make hydroxyl groups a better leaving groups for nucleophilic substitution
- They can act as a protecting group when we do not want alcohol to react.
- Serve as electron acceptor biochemically; Electron Transport Chain in both photosynthesis and aerobic respiration.
- Phylloquinone (Vitamin K1): important for photosynthesis and the carboxylation of some of the clotting factors in blood.
- Menanquinones (Vitamin K2)
- Share the same ring and carbonyl backbone as quinones but differ by the addition of one or more hydroxyl groups
- a) Tetrahydroxybenzoquinone; b) 5-hyroxynaphthoquinone; c) 1,2-dihydroxyanthraquinone
- Biologically active quinone (electron acceptor in photosynthesis and aerobic respiration)
- Reduced to ubiquinol upon the acceptance of electrons. 
- Long alkyl chain = lipid soluble = act as an electron carrier within the phospholipid bilayer.
- The oxygen in the alcohol functions as a nucleophile, attacking the carbonyl carbon, and generating a hemiacetal.
- Hemiacetals are unstable and the hydroxyl group is rapidly protonated and lost as water under acidic conditions, leaving behind a reactive carbocation.
- Ammonia (NH3) is added to the carbonyl, resulting in the elimination of water, and generating an imine. 
- Imine can undergo tautomerization and form enamine
- Example of condensation reaction since a small molecule is lost during the formation of a bond between two molecules.
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Cyanide functions as a nucleophile, attacking the carbonyl carbon and generating a cyanohydrin.
- Also H2O2
- Lithium aluminum hydride (LiAlH4)
- Sodium borohydride (NaBH4)
- Two isomers, which differ in the placement of a proton and the double bond
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- The kinetic enolate forms more quickly, irreversible, low temp, sterically hindered base, 
and is less stable than the thermodynamic enblate.
- Thermodynamic forms more slowly, reversible, weaker or smaller bases, higher tempreture
Imine from is the thermodynamically favored over the enamine form on the left.
- The aldol condensation involves two reaction series, the aldol addition reaction and the condensation reaction. Dehydration occurs through an elimination (technically, E1cB) mechanism to form an α, β-unsaturated aldehyde (enal) or ketone (enone), not the aldol.
* The first step of aldol condensation involves a strong base like hydroxide abstracting a proton from the α-carbon (not the β-carbon) of a carbonyl compound (aldehyde or ketone) to form the enolate.
* The second step of aldol condensation involves the enolate attacking the aldehyde or ketone through a nucleophilic acyl addition mechanism (not substitution). Only carboxylic acid and its derivative can undergo nucleophilic acyl substitution.
- Examples are dehydration, nucleophilic addition , and aldol reaction.
Contains both aldehyde and alcohol functional groups.
ene + ol = double bond + hydroxyl group
Formation of esters from carboxylic acids and alcohols.
A reaction in which a part of a reactant is removed and a new multiple bond is introduced.
A reaction in which a molecule of water is eliminated
- suffix: dioic acid
- polar and can form hydrogen bonds.
- Acidity is due to resonance stabilization and can be enhanced by the addition of electronegative groups or a greater ability to delocalize charge.
- pKa: 4.8
Step 1: Nucleophilic Addition
Step 2: Elimination of the leaving group and reformation of the carbonyl.
- Carboxylic acid can be converted into amides if the incoming nucleophile is ammonia (NH3).
- Can be carried out in acidic or basic solution.
- Amides are named by replacing the oic acid with amide in the name of the parent carboxylic acid.
- Lactam
- replacing oic acid with lactam
- Lactone
- replacing oic acid with lactones
- Esterification is a condensation reaction with water as aside product. 
- Acidic conditions lead to carbonyl oxygen protonated = makes the electrophilic carbon even more nucleophilic attack.
Carboxylic acids can be reduced by LiAlH4, but not the less reactive NaBH4.
- Loss of CO2
- The intramolecular reaction proceeds via a six-membered ring transition state, and the product tautomerizes from the enroll to the more stable keto form. 
- Sponatenously occurs when heated.
- When a long chain of fatty acid (carboxylic acids) react with lye (sodium or potassium hydroxide), a salt is formed known as soap.
- Only a base ( such as NaOH) can catalyze the saponification of an ester
- A fatty acid would have a general formula of Rn_CO2H ; corresponding fatty acid salt.
- One hydroxide ion is required to hydrolyze one ester linkage of a triglycerol molecule
- Partially dissolve in polar and non polar solvents. The salt also contains the charged group CO2^-Na+
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- ortho-phtalic acid to ophthalmic anhydride
- Heat and the increased stability of the newly formed ring drive his intramolecular ring formation reaction forward.
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- Many antibiotics contain Beta-lactams.
- Many bacterias have developed Beta lactamasees, which break Beta lactam rings, as a resistance against these antibiotics. 
- Beta Lactams are sometimes given with Beta lactams inhibitors to increase their efficacy.
Cleavage reaction because it splits an anhydride in two.
Alcohols can act as a nucleophile resulting in the formation of esters.
Anhydrides can be reverted to carboxylic acids by exposing them to water
Different alcohol chains are swapped into and out of the esterifying group position
- Strong acid (protonating the carbonyl oxygen which inc. electrophiliciy) or base ( OH- will increase which would act as a nucleophile on the amide) is needed to catalyze the hydrolysis of amides, which are normally quite stable. 
- The attacking nucleophile is water (acidic environment) or hydroxide anion (basic environment)
- All R groups are naturally occurring amino acids in eukaryotes- except for Glycine- are optically active, and all are L-isomers.
- L- amino acids have (S) configuration except for cysteine, which is (R) because of the change in priority caused by sulfur 
- Amphoteric
- Amino groups can take on a positive charge by being protonated
- Carboxyl groups can take on negative charges by being deprotonated
- This double bond character between the nitrogen atom and the carbonyl carbon adds to the rigidity and stability of the backbone of proteins.
- The single bonds on either side of the peptide bond permit free rotation.
Peptide bonds are formed by condensation reaction in which water is lost and cleaved hydrolytic ally by strong acid or strong base.
- Generated from an aldehyde or ketone.
- Generates an amino acid
- Aldehyde
- Ammonium Chloride (NH_4Cl)
- Potassium Cyanide (KCN)
- water is used to hydrolyze the aminonitrile to form the amino acid.
- Condensation reaction: formation of an imine from a carbonyl containing compound and ammonia, with loss of water)
- Followed by nucleophilic addition (addition of a nitrile group) , 
- Followed by hydrolysis
- An amino acid is generated from phthalimide (nucleophile) and diethyl bromomalonate, using two SN2 reactions, hydrolysis, and decarboxylation.
- useful for energy
- contains a very negative charge
- when bonded to other phosphate groups in a nucleotide triphosphate, this creates repulsion with adjacent phosphate groups, increasing the energy of the bond. 
- Inorganic phosphate can be resonance- stabilized.
- Measures absorption of infrared waves by specific bonds, which vibrate... results in 
- Infrared light is passed through a sample, and the absorbance is measured
- finger print region: Molecule as a whole, 1500 to 400 cm^-1
- No absorption from symmetric bond (ex: O_2 or triple bond in acetylene C_2H_2)
- Enantiomers have identical IR bc they have the same functional groups, but they have opposite specific rotations but that doesn't have an effect on IR
- OH: broad, wide peak 
* Alcohol: 3300 cm^-1
* Carboxylic Acids: 3000 cm^-1
- Carbonyl (C=O): sharp deep peak around 1700 cm^-1
- N-H bonds are in the same region as OH bonds around 3300 cm^-1, but have a sharp peak instead of a broad one.
- A system of connected p-orbitals with delocalized electrons in molecules with alternating single and multiple bonds, which in general may lower the overall energy of the molecule and increase stability.
- Lone pairs, radicals or carbenium ions may be part of the system.
- Higher order bonds tend to have higher absorption frequencies, so loss of double bond could decrease the frequency of the group.
- Certain atomic nuclei have magnetic moments that are oriented at random. Their magnetic moments tend to align either with or against the direction of this applied field. 
- Aligned with the field = Alpha state = low energy
- using radio frequency pulses, excite some lower energy nuclei into the Beta state (Higher Energy) 
- Ex) Magnetic Roesonance imaging (MRI)
- Diagnostic tool that uses proton NMR
- Shows the relative density of specific types of protons
- A dark area on a T1- weighted MRI tends to correspond to water
- Light area indicates fattier tissue
- Frequency vs. absorption energy
- Arbitrary variable called chemical shift (sigma ), with units of parts per million (ppm)
- Chemical shift is plotted on the x-axis; increases towards left (downfield) 
- Tetramethlsilane (TMS) : provides a reference peak. The signal for 1H (proton) atom is assigned sigma = 0
- Most hydrogen (1H) nuclei come into resonance 0 to 10 ppm downfield from TMS.
- Each nuclei gives rise to a separate peak
- Number of peaks = protons in different environment
- Height of each peak is proportional to the number of protons it contains.
- Integration: Area under the peak (a) to (b) is 1:3
- The position of the peak (upfield or downfield) is due to shielding or deshielding effects and reflects the chemical environment of the protons
- (a) is downfield due to electronegative cl atoms and an oxygen atom that pull electron density away from the surrounding atoms... deshielding the proton
- Represents the number of adjacent hydrogens. 
- n+1 rule: if a proton has n protons that are three bonds away,
- Alkyl groups: 0 to 3 ppm
- Alkynes: 2 to 3 ppm
- Aromatic: 6 to 8.5
- Aldehydes: 9 to 10 ppm
- Carboxylic Acids: 10.5 to 12 ppm
- Two protons close to one another have an effect on the other's magnetic environment 
- This results in splitting peaks to doublets, triplets, or multiplets
- n+1 rule
- coupling constant, J, measured in hertz; frequency of distance between subpeaks
- Frequency (c/wavelength)
- Inversely proportional to wavelength
- use a separatory funnel to separate solvents based on their relative densities; denser is drained first
- Aqueous phase (water or polar isoburic acid) & organic phase (diethyl ether; nonpolar)
- More common for the organic layer to be on top
- When the acid dissociates, the anion formed will be more soluble in the aqueous layer than the original protonated acid; thus adding a base will help to extract an acid into the aqueous phase
- Depends on the law of solubility; like dissolves like.
- 3 intermolecular forces that affect solubility
1) Hydrogen bonding: compounds like acids and alcohols; will move most easily in aqueous layer
2) Dipole Dipole: less likely to move in aqueous layer
3) Van der Waals: With only these interactions, compounds are less likely to move into the aqueous layer.
- Isolates a solid from a liquid
- Solid (residue), and the flask full of liquid that passed through the filter (filtrate)
- Gravity Filtration: Solvent's own weight pulls it through the filter
- Vacuum Filtration: Solvent is forced through the filter by a vaccum connected to the flask, used when Solid is the desired product
- Method for further purifying crystals in solution.
- Solvent chosen should be one in which the product is soluble only at high temperatures; when the solution cools, only the desired product will recrystallize
- Takes advantage of differences in boiling point to separate two liquids by evaporation and condensation.
- This condensate then drips down into a vessel. 
- Because ethanol boils at a lower temprature than water, we can use distillation to make beverages with high ethanol content.
- Simple (less than 25 C difference), Vacuum ( boiling point over 150 C), and Fractional ( Less than 25 C apart)
- Liquids that boil below 150 C and have atleast 25C difference in boiling temperature. 
- Consists of a distilling flask (containing combined solution), distillation column ( thermometer, condenser, and receiving flask to collect the distillate.
- Distill a liquid with a boiling point over 150 C
- By using a vacuum, we lower the ambient pressure, so that the liquid can boil at lower temperature. 
- Liquids boil when their vapor pressure = ambient pressure.
- Two liquids with similar boiling points, Less than 25 C apart 
- Fractional column connects the distillation flask to the condenser
- Surface area is increased by the inclusion of inert objects like glass beads or steel wool; allows for more refined separation of liquids with fairly close boiling points.
- Uses chemical and physical properties to separate and identify compounds from a complex mixture based on how strongly they adhere to the solid. 
- Sample onto a solid medium called the stationary phase; then run the mobile phase , usually a liquid or a gas through the stationary phase. 
- Ex) Thin Layer (TLC), Column Chromatography (Ion exchange, size-exclusion, affinity), Gas, and High performance liquid chromatography
- Varying only in the medium used for the stationary phase.
- Thin layer of silica gel or alumina adherent to an inert carrier sheet is used
- Spotting: well defined spot of the sample directly onto the silica or paper plate
- Eluent (shallow pool of solvent at the bottom of the jar): solvent will creep up the plate by capillary action; silica gel which is polar and hydrophilic 
- Mobile phase: organic solvent of weak to moderate polarity; more non polar the sample, further up the plate it will move.
- Exaction opposite of Thin Layer (TLC)
- stationary phase is non polar so polar molecules move up the plate quickly
- When using Thin Layer Chromatography (TLC) is performed, Rf is the relatively constant for a particular compound in a given solvent
- Can be used to identify unknown compounds.
- More polar the solution, lower the Rf
- uses an entire column filled with silica or aluminum beads as an adsorbent, allowing for much greater separation.
- Flash Column Chromatography: one can force the solvent through the column using gas pressure. 
- The more similar the sample is to the mobile phase, the faster it elutes; the more similar it is to the stationary phase, the more slowly it will elute
- Used in biochemistry to separate and collect macromolecules such as proteins or nucleic acids. 
- Ion Exchange, Size Exclusion, and Affinity chromatography
- Beads in the column are coated with charged particles so they can attract opposite charges. 
- Positive charged compounds will attract and hold a negative charged backbone of DNA or protein
- EX) Lactoferrin, a milk protein, is a valuable antimicrobial agent that is extracted from a pasteurized; due to likely be charged, charged proteins will stick to the column.
- Beads used in the column contain tiny pores of varying sizes.
- Large compounds can't fit into the pores, so they will move around them and travel through the column faster. 
- A common approach in protein purification is to use an ion exchange column followed by a size exclusion column.
- Separate a biological effector from solution
- Creating a column with high affinity for that protein.
- Coating beads with a receptor that binds the protein or specific antibody to the protein, protein retained in the column. 
- Common stationary phase molecules include: nickel, used in separation of genetically engineered proteins with histidine tags, antibodies or antigens, and enzyme substrate analogues
- Also known as vapor-phase chromatography (VPC)
- The fluent is a gas (usually helium or nitrogen) instead of a liquid
- The adsorbent is a crushed metal or polymer inside a 30 foot column.
- The gaseous compounds travel through the column at different rates because they adhere to the adsorbent in the column to different degrees and will separate in space by the time they reach the end of the column. 
- The injected compound must be volatile: low melting point, subsumable solids or vaporizable liquids.
- It is common to separate molecules using GC and then to inject the pure molecules into a masss spectrometer (run through a magnetic field, which separates them by mass to charge ratio) for molecular weight determination.
- similar to gas chromatography, but uses liquid under pressure instead of gas
- The whole process is under computer control, hence higher performance
- HPLC uses high pressure and columns uses gravity.
- When cyclic hemiacetals and acetals are formed, the ring carbon atom derived from the carbonyl group in the open chain of a monosaccharide; ( the carbon atom that bears two oxygen substituents).