Organic Chemistry
Enol Form
ene + ol = double bond + hydroxyl group
Formula for the number of possible peptides that contain one each of n amino acids
n! - Ex) tripeptide = 3*2*1 = 6
When an aldehyde or ketone with a alpha hydrogen is treated with a strong base such as LDA
It forms the more nucleophilic enblate carboanion.
Kinetic Energy
KE avg = 3/2 NkT
Good Reducing Agents
Metals bonded to a large number of Hydrides.
Good Oxidizing Agents
Metals bonded to a large number of Oxygen atoms.
How are peptide bonds formed and cleaved?
Peptide bonds are formed by condensation reaction in which water is lost and cleaved hydrolytic ally by strong acid or strong base.
Aldehyde Nomenclature: Propanal
Propionaldehyde
Nucleophile in protic and aprotic solvents
Protic: - I- > Br- > Cl- > F Aprotic: F- > Cl- > Br-> I-
Bronsted Lowry Base
Proton Acceptor
Nucleophilic Acyl Substitution
Step 1: Nucleophilic Addition Step 2: Elimination of the leaving group and reformation of the carbonyl.
An Acid-Base reaction will proceed when ...
The acid and Base react to form conjugate products that are weaker than the reactants.
Aldehyde Nomenclature: Pentanal
Valeraldehyde
Chiral center
- 4 different group attach to the central carbon - lack a plane of symmetry - not superimposable
Heterolytic Reactions
- A bond is broken and both electrons are given to one of the two products. - The best leaving group is able to stabilize the extra electrons. * Weak bases (conjugate bases of strong acids such as I-, Br-, and Cl-) make good leaving groups
Geminal Diol
- A compound with two hydroxyl groups on the same carbon due to a hydration reaction, water adds to a carbonyl. -
Conjugated Systems
- 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.
Oxidizing Agents and Reactions
- 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.
Acetals and Ketal Formation
- 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.
Protecting Groups of Acetals and Ketals
- 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.
Would acid dissolve better in aqueous acid or aqueous base?
- Acid dissolves better Aqueous base to form conjugated base, being more highly charged
What are the four reactants in the Strecker synthesis of an amino acid
- Aldehyde - Ammonium Chloride (NH_4Cl) - Potassium Cyanide (KCN) - water is used to hydrolyze the aminonitrile to form the amino acid.
Amino Acid
- 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
Aldehyde oxidation
- Also H2O2
Gas Chromatography (GC)
- 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.
Zwitterion
- Amino groups can take on a positive charge by being protonated - Carboxyl groups can take on negative charges by being deprotonated
Imine Formation
- 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.
Aldehyde vs. Ketones Terminal group
- An aldehyde has a terminal functional group due to the one hydrogen - Ketone has two alkyl groups so it's never a terminal group.
Gabriel Synthesis
- An amino acid is generated from phthalimide (nucleophile) and diethyl bromomalonate, using two SN2 reactions, hydrolysis, and decarboxylation.
Newman's Projection
- Anti staggered isomer has the lowest energy - Staggered isomer has the highest energy
Ion Exchange 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.
Size Exclusion Chromatography
- 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.
Ubiquinone
- 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.
Configurational Isomer
- 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
Organic Phosphate
- Carbon containing molecules with phosphate groups - Most common example are nucleotides, like those in DNA, ATP, or GTP.
Oxidation State Order of Increase
- Carboxylic Acid > Aldehydes, Ketones, and imines, which in turn are more oxidized than alcohols, alkyl halides, and amines. - Oxidation increases as the number of bonds to oxygen increases or other heteroatom (atoms besides carbon and oxygen)
Formation of an Amide by Nucleophilic Acyl Substitution
- 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.
Ester
- Carboxylic acid derivative - OH is replaced with OR, an alkoxy group
Amides
- Carboxylic acid derivative - OH is replaced with an amino group
Anhydrides
- Carboxylic acid derivative - formed by dehydration of 2 carboxylic acids * Symmetric = same acid * asymmetric = two different acids * cyclic = intramolecular reaction of a dicarboxylic acid
Nuclear Magnetic Resonance (NMR)
- 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)
Nucleophilicity is determined by 4 major factors:
- 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.
Reaction type for Strecker Synthesis
- 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
Carboxylic Acids and Derivatives
- 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)
Alkenes and Alkynes
- Contain double and triple bonds respectively.
Double Bonds
- Contain one sigma bond and one pi bond. - Pi bonds are created by sharing of electrons between two unhybridized p-orbitals that align side by side. - Pi bonds do not permit rotations
Triple Bonds
- Contain one sigma bond and two pi bonds. - Pi bonds do not permit rotations
Mechanism of SN2 Reaction
- 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.
Proton NMR is good for:
- Determine the relative number of protons and their relative chemical environments - Showing how many adjacent protons there are by splitting patterns. - Inferring certain functional groups
Magnetic Resonance Imaging
- 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
Naming Ketones: 2-propanone
- Dimethyl ketone - Acetone
Racemix Mixture
- Displays no optical activity - when both (+) and (-) enantiomers are present in equal concentrations. - Ex) A solution containing 2M (R)-2-butanol and 2 M (S)-2-butanol
Vacuum Distilation
- 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.
Lewis Acid
- 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.
Lewis Base
- Electron Donor in the formation of a covalent bond. - Nucleophile - Lone pair of electrons that can be donated, often anions; carrying a negative charge
Nucleophiles
- 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.
Reverse- phase chromatography
- Exaction opposite of Thin Layer (TLC) - stationary phase is non polar so polar molecules move up the plate quickly
Alkanes
- First four alkanes are methane (CH4), Ethane (C2H6), Propane (C3H8), and Butane (C4H10) - single Bonded
Oxidation of a Secondary Alcohol
- Forms a Ketone by a Dichromate salt (Na_2Cr_2O_7 & K_2Cr_2O_7)
Wavenumber (1/wavelength) is directly proportional to:
- Frequency (c/wavelength) - Inversely proportional to wavelength
A typical NMR Spectrum
- 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
Reduction of Carbon
- Gains Electrons - When an atom that is more electronegative than carbon is replaced with less electronegative than carbon - Means increasing the number of bonds to Hydrogen and decreasing the number of bonds to carbons, nitrogen, oxygen and halides
Aminonitrile
- Generated from an aldehyde or ketone. - Generates an amino acid
What are some features of good leaving groups?
- Good leaving groups can stabilize the extra electrons that result from heterolysis. - Weak bases (conjugate bases of strong acids such as I-, Br-, and Cl-) are good leaving groups. - Resonance stabilization also improve leaving groups
What trends increase electrophilicity?
- Greater positive charge increases electrophilicity, and better leaving groups increase it by making the reaction to proceed.
Filtration
- 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
How must the nucleophile and leaving group be related in order substitution reaction to proceed?
- It will proceed when the nucleophile is a strong base (more reactive) than the leaving group. - Acid catalyst is required if the leaving group is a hydroxide ( bad leaving group) so it can get protonated to water (good leaving group) .
Amides that are cyclic are known as
- Lactam - replacing oic acid with lactam
Esters that are cyclic are known as
- 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.
Simple distillation
- 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.
Reduction by Hydride Reagents
- Lithium aluminum hydride (LiAlH4) - Sodium borohydride (NaBH4)
Decarboxylation of Carboxylic Acids
- 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.
Protecting Groups for alcohols
- 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.
Penicillin, Beta-Lactam- Containing Antibiotics
- 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.
Infrared (IR) Spectroscopy
- 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
Acid Dissociation constant, Ka
- 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.
Recrystallization
- 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
Proton NMR (1H-NMR)
- 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
Ultraviolet (UV) spectroscopy
- Most useful for studying compounds containing double bonds and/ or heteroatom with lone pairs, or pi bonds or non bonding electrons that create conjugated systems (molecules with unhybridized p-orbitals). - HOMO (Highest Occupied Molecular Orbital) - LUMO (Lowest Unoccupied Molecular Orbital) * The smaller the difference, the longer the wavelength that can be absorbed * Only after absorbing UV light is an electron is excited from the HOMO to the LUMO.
3-butene-2-one
- Naming ketones - methylvinylketone
Enantiomer
- Nearly identical physical properties and chemical properties - They rotate plane polarized light in opposite directions and react differently in chiral environment
How do the definitions of nucleophile and electrophile differ from those of Lewis Acids and Lewis Base?
- Nucleophilicity and electrophilicity are based on relative rates of reactions therefore are kinetic properties. - Acidity and Basicity are measured by the position of equilibrium in a protonation or deprotonation reaction and are therefore thermodynamic properties.
IR Absorption Frequencies
- 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.
Carboxylic Acid Derivatives
- Often ranked by electrophilicity. - Anhydrides are the most reactive according to Kaplan. - Higher reactivity can form derivatives of lower reactivity but not vice versa.
Bronsted Lowry Acid
- Proton Donor
Proton NMR splitting of the peak
- 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
Conformational Isomer
- Same molecule, differ in rotation around single pi bonds.
Affinity Chromatography
- 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
Quinone
- 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)
Structural Isomer
- Share only a molecular formula - They have different physical and chemical properties
Three Examples of Hydroxyquinones
- 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
Single Bonds
- Sigma bonds, contains two electrons. * Permit free rotation
Nucleophilic Acyl Substitution: Amide to carboxylic acid
- 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)
Achiral
- Superimposable - line of symmetry
Distillation
- 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)
Aldol Condensation Reaction
- 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.
Kinetic and Thermodynamic Enolates
- 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
Hemiacetal Formation
- 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.
Phosphoric Acids
- The three hydrogens in phosphoric acid have very different pKa values. - This allows phosphoric acid to pick up or give off protons in wide pH range, making it a good buffer over most pH scale.
Resonance in the peptide bond
- 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.
Tautomers
- Two isomers, which differ in the placement of a proton and the double bond
Fractional Distillation
- 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.
Spin-Spin coupling
- 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
Immiscible
- Two solvents that do not mix - used in Extraction - Ex) Isobutyric acid and diethyl ether
(R) and (S) Nomenclature
- 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
Chromatography
- 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
Thin-Layer And Paper 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.
Saponification
- 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+
Anomeric Carbon
- 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).
Retardation Factor
- 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
(E) and (Z) Designations of Alkenes
- Z : same side - E: Opposite side - used for compounds with polysubstituded double bonds. - Part of relative configuration
Bond Strength decreases down the periodic table
- acidity increases. - Also Higher electronegative an atom, higher the acidity.
Meso Compound
- 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.
Alcohols
- 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
Naming Ketones: 2-butanone
- ethylmethylketone
pKa
- lower pKa = stronger Acid = below -2 * -2 to 20 pKa is considered Weak Acid - Larger pKa = More Basic
Diastereomers
- non- mirror image configurational isomer. - differ at some but not all chiral centers. Ex) cis - trans isomers
Intramolecular anhydride formation
- ortho-phtalic acid to ophthalmic anhydride - Heat and the increased stability of the newly formed ring drive his intramolecular ring formation reaction forward.
Carboxylic Acid characteristics
- 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
High Performance Liquid Chromatography (HPLC)
- 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.
Common Names of Aldehydes
- suffix al - Common names include * formaldehyde for methanal (R = H) * Acetyldehyde for ethanal ( R = CH3) * Propionaldehyde for propanal (R = CH3CH2)
Common Names for Ketones
- suffix one - Acetone (dimethylketone; 2- propanone) ; smallest ketone; similar as the figure - 2 pentanone (R= CH3CH2CH2)
Common Names of Dicarboxylic Acid
- suffix: dioic acid
Extraction
- 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.
Inorganic phosphate
- 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.
Column Chromatography
- 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
Oxidation of Primary Alcohol
-Primary Alcohol Forms an aldehyde by Pyridinium Chlorochromate (PCC) - Primary Alcohol is oxidized to a carboxylic acid by CrO3 (Jones Oxidation)
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.
Mechanism of SN1 Reaction
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
Dehydration Reaction
A molecule of water is lost
Nucleophile-electrophile Reaction
A nucleophile pushes an electron pair to form a bond with an electrophile.
Dehydration reaction
A reaction in which a molecule of water is eliminated
Elimination reaction
A reaction in which a part of a reactant is removed and a new multiple bond is introduced.
Aldehyde Nomenclature: Ethanal
Acetaldehyde
Nucleophilic Acyl Substitution: Anhydride to Ester and Carboxylic Acid
Alcohols can act as a nucleophile resulting in the formation of esters.
Nucleophilic Acyl Substitution: Anhydride to Carboxylic Acid
Anhydrides can be reverted to carboxylic acids by exposing them to water
Aldehyde Nomenclature: Butanal
Butyraldehyde
Summary of Functional Groups
Carboxylic acid > anhydride > Ester > Amide > Aldehyde > Ketone > Alcohol > alkene or alkyne > alkane
Reduction of a carboxylic acid to a primary alcohol
Carboxylic acids can be reduced by LiAlH4, but not the less reactive NaBH4.
Nucleophilic Acyl Substitution: Anhydride to Amide and Carboxylic Acid
Cleavage reaction because it splits an anhydride in two.
Aldol reaction
Contains both aldehyde and alcohol functional groups.
Cyanohydrin or Hydrogen Cyanide (HCN)
Cyanide functions as a nucleophile, attacking the carbonyl carbon and generating a cyanohydrin.
Nucleophilic Acyl Substitution: Transesterification
Different alcohol chains are swapped into and out of the esterifying group position
Amphoteric
Ex) water can act as an acid by donating a proton or a base by accepting a proton .
Aldehyde Nomenclature: Methanal
Formaldehyde
Esterification reaction
Formation of esters from carboxylic acids and alcohols.
Enamination
Imine from is the thermodynamically favored over the enamine form on the left.