Organic Chemistry

synthesis of anhydride

anhydrides are formed by condensation of 2 carboxylic acids for cyclic & linear anhydrides, replace -ACID at end of name w/ ANHYDRIDE anhydride formation also occurs via nucleophilic acyl substitution

carbons relative to carbonyl group nomenclature

another convention is naming carbons relative to carbonyl group. by this convention, carbon adjacent to carbonyl carbon is alpha. moving away from carbonyl, successive carbons are named beta, gamma, & delta carbons. this applies to both sides of carbonyl

gauche conformation

another type of staggered conformation 2 largest groups are 60 degrees apart

heterocycle

any cyclic compound w/ at least 1 heteroatom tryptophan, thymine (through resonance), & adenine all considered aromatic heterocycles

alpha hydrogens

are connected to the alpha carbon, which is a carbon adjacent to the carbonyl bc the ENOL form of carbonyl-containing carbanions is stabilized by resonance, these are acidic hydrogens that are easily lost

enamination

enamines are tautomers of imines (compound containing C=N bond). nitrogen in imine may or may not be bonded to alkyl group or another substituent through tautomerization (movement of hydrogen & double bond), imines can be converted into enamines imine form is thermodynamically favored over enamine form

acyl derivatives

encompasses all molecules with a carboxylic acid-derived carbonyl, including carboxylic acids, amides, esters, anhydrides, & others

enolate carbanion

enols are impt intermediates in many rxns of aldehydes & ketones. the enolate carbanion results from deprotonation of the alpha carbon by a strong base. the deprotonated enolate form can act as a nucleophile. common strong bases include the hydroxide ion, lithium diisopropyl amide (LDA), & potassium hydride (KH). a 1,3-dicarbonyl is particularly acidic bc there are 2 carbonyls to delocalize negative charge & as such, is often used to form enolate carbanions once formed, the nucleophilic carbanion reacts readily w/ electrophiles

heterolytic reactions

essentially the opposite of coordinate covalent bond formation: a bond is broken & both electrons are given to 1 of the 2 products

esterification

esters are hybrid btwn carboxylic acid & an ether (ROR'), which can be made by reacting carboxylic acids w/ alcohols under acidic conditions ESTERIFICATION is a CONDENSATION rxn w/ water as a side product. in acidic solns, the carbonyl oxygen can be protonated, which enhances the polarity of the bond, thereby placing additional positive charge on carbonyl carbon bc of protonated C=O bond, increasing its susceptibility to nucleophilic attack this condensation rxn occurs most rapidly w/ primary alcohols esterification rxns should NOT be carried out in water bc presence of water would most likely revert some of the desired esters back into carboxylic acids

naming cyclic esters

esters are named in same manner as salts of carboxylic acids & esters that are cyclic are called LACTONES & are named by replacing -OIC ACID w/ -LACTONE

hydrocarbon w/ 2 carbons

ethane

ubiquinone

ex of biologically active quinone also called COENZYME Q & is vital electron carrier associated w/ Complexes I, II, & III of electron transport chain ubiquinone is most oxidized form that this molecule takes physiologically. it can also be reduced to UBIQUINOL upon acceptance of electrons (2 ketones reduced to 2 hydroxyl groups). this oxidation reduction capacity allows molecule to perform its physiological function of electron transport the long alkyl chain of this molecule allows it to be lipid soluble, which allows it to act as electron carrier w/in phospholipid bilayer. also has conjugated rings, which stabilize molecule when accepting electrons

imine tautomerization

imines & related compounds can undergo tautomerization to form ENAMINES, which contain both a double bond & a nitrogen containing group this is analogous to the keto-enol tautomerization of carbonyl compound

mass spectrometry

involves ionization & fragmentation of compounds. these fragments are then run through magnetic field, which separates them by mass to charge ratio total molecular weight can thus be determined or the relative concentrations of diff fragments can be calculated & compared against reference values to identify the compound

chiral

object is considered chiral if its mirror image can't be superimposed on original object. this implies that molecule lacks internal plane of symmetry chirality can be thought of as handedness. although essentially identical, your left hand will not be able to fit into a right-handed glove

superheating

occurs when liquid is heated to temp above its BP w/o vaporization/boiling. superheating situations occur when gas bubbles w/in a liquid are unable to overcome combination of atmospheric pressure & surface tension

hydrocarbon w/ 8 carbons

octane

acetal & ketal formation

when aldehyde is mixed w/ diol (or 2 equivalents of alcohol), it forms an acetal when ketone is mixed w/ a diol (or 2 equivalents of alcohol), it forms a ketal

racemic mixture

when both (+) & (-) enantiomers are present in = concentration in these solns, rotations cancel each other out, & no optimal activity is observed. racemic mixtures have no handedness overall

phenols

when hydroxyl groups are attached to aromatic rings hydroxyl hydrogens of phenols are particularly acidic due to resonance w/in phenol ring possible resonance btwn ring & lone pairs of oxygen atoms in hydroxyl group to stabilize - charge on oxygen (stabilizing the anion) > hydrogen of alcohol more acidic than other alcohols phenols are slightly soluble in water, due to H bonding, as are some of its derivatives bc phenols are much more acidic than nonaromatic alcohols, they can form salts w/ inorganic bases such as NaOH when benzene rings contain 2 substituents, their relative positions must be indicated -2 groups on adjacent carbons are called ORTHO-, or simply O- -2 groups separated by a carbon are called META- or M- -2 groups on opposite sides of ring are called PARA, or P- presence of other substituents on ring has significant effects on acidity, boiling points, & melting points of phenols -as w/ other compounds, electron withdrawing substituents increase acidity & electron donating groups decrease acidity

ester nomenclature

carboxylic acid derivative hydroxyl group (-OH) replaced w/ an ALKOXY GROUP (-OR where R is a hydrocarbon chain) ester nomenclature is based on naming conventions for carboxylic acids 1st term is alkyl name of esterifying group, alkyl R group **2nd term is name of parent acid, w/ -OATE replacing the -oic acid suffix**

anhydride nomenclature

carboxylic acid derivative in formation of anhydride from 2 carboxylic acid molecules, 1 water molecule is removed. many anhydrides are cyclic, which may result from intramolecular dehydration of dicarboxylic acid anhydrides named by replacing ACID with ANHYDRIDE in name of corresponding carboxylic acid if anhydride is formed form only 1 type of carboxylic acid **if anhydride is not symmetrical, both carboxylic acids are named (w/o the suffix acid) before anhydride is added to the name**

amide nomenclature

carboxylic acid derivative. -OH replaced by an AMINO GROUP (nitrogen-containing group) amino nitrogen can be bonded to 0, 1, or 2 alkyl groups amides named similar to esters, except suffix becomes -AMIDE **substituents attached to N are labeled w/ a capital N- indicating that this groups is bonded to parent molecule via a nitrogen.** these substituents are included as prefixes in compound name & are not numbered

formation of amide

carboxylic acids can be converted into amides if the incoming nucleophile is ammonia (NH3) or an amine this can be carried out in either acidic or basic solns to drive the rxn forward amides exist in resonance state where delocalization of electrons occurs btwn the oxygen & nitrogen atoms

synthesis of carboxylic acids

carboxylic acids can be prepared via oxidation of aldehydes & primary alcohols oxidant is often a dichromate salt (Na2Cr2O7 or K2Cr2O7), chromium trioxide (CrO3), or potassium permanganate (KMnO4), but several other oxidizing agents can also work remember that secondary & tertiary alcohols can't be oxidized to carboxylic acids bc they already have at least 2 bonds to other carbons there are other methods of generating carboxylic acids outside scope of MCAT

reduction of carboxylic acids

carboxylic acids can be reduced to primary alcohols by use of lithium aluminum hydride (LiAlH4) aldehyde intermediates may be reduced in course of this rxn, but they too will be reduced to alcohol this rxn occurs by nucleophilic addition of hydride to carbonyl group LiAlH4 is strong reducing agent that can successfully reduce a carboxylic acid. a gentler reducing agent like sodium borohydride (NaBH4) is not strong enough to reduce carboxylic acids (no rxn will result)

physical properties

characteristics of processes that don't change composition of matter, such as melting/boiling point, solubility, odor, color, & density

alcohols w/ 2 hydroxyl groups nomenclature

alcohols w/ 2 hydroxyl groups are called DIOLS or GLYCOLS & are indicated w/ suffix -DIOL. entire hydrocarbon name is preserved, & -DIOL is added when naming diols, 1 must number each hydroxyl group for ex, ethane-1,2-diol is an ethane molecule w/ a hydroxyl group on each carbon. molecule's also known by common name, ethylene glycol mnemonic: VICInal diols are in the VICINity of each other, on adjacent carbons. GEMINal diols, like the GEMINi twins, are paired on the same carbon

electrophiles

"electron loving" w/ + charge or positively polarized atom that accepts an electron pair when forming new bonds electrophilicity is kinetic property while acidity is thermodynamic property but practically, electrophiles almost always act as Lewis acids in rxn nature of leaving group influences electrophilicity in species w/o empty orbitals. better leaving groups make it more likely that a rxn will happen if empty orbitals are present, an incoming nucleophile can make a bond w/ electrophile w/o displacing the leaving group electrophilicity & acidity are effectively identical properties when it comes to reactivity alcohols, aldehydes & ketones, carboxylic acids, & their derivatives act as acids & also as electrophiles more + charge (so carbocation more reactive than carbonyl carbon), better leaving groups, & less steric hindrance increase electrophilicity carboxylic acid derivatives in order of decreasing electrophilicity: acyl halides > anhydrides > carboxylic acids & esters > amides. DERIVATIVES OF HIGHER REACTIVITY CAN FORM DERIVATIVES OF LOWER REACTIVITY BY NUCLEOPHILIC RXN BUT NOT VICE VERSA derivatives of higher reactivity can form derivatives of lower reactivity but not vice versa, similar to acid base rxns

nucleophiles

"nucleus loving" species w/ other lone pairs or pi bonds that can form new bonds to electrophiles LOOK FOR CARBON, HYDROGEN, OXYGEN, OR NITROGEN (CHON) W/ A MINUS SIGN OR LONE PAIR TO IDENTIFY MOST NUCLEOPHILES nucleophilicity & basicity have similar definitions. **good nucleophiles tend to be good bases but nucleophile strength is based on relative rates of rxn w/ a common electrophile & is therefore a kinetic property. base strength is related to equilibrium position of a rxn & is therefore a thermodynamic property** ex of nucleophiles -anions -pi bonds -atoms w/ lone pairs as long as the nucleophilic atom is the same, the more basic the nucleophile, the more reactive it is -CHARGE: nucleophilicity increases w/ increasing electron density (more - charge) -ELECTRONEGATIVITY: nucleophilicity decreases as electronegativity increases bc these atoms are less likely to share electron density -STERIC HINDRANCE: bulkier molecules are less nucleophilic -SOLVENT: protic solvents can hinder nucleophilicity by protonating the nucleophile or through hydrogen bonding in polar protic solvents, nucleophilicity increases down the periodic table. in polar aprotic solvents, nucleophilicity increases up the periodic table for the halogens, in protic solvents, nucleophilicity decreases in the order: I- > Br- > Cl- > F- bc the protons in soln will be attracted to the nucleophile (F- is conjugate base of HF, a weak acid, so it'll form bonds w/ protons in soln & be less able to access electrophile) for halogens in aprotic solvents, nucleophilicity decreases in this order: F- > Cl- > Br- > I- bc there are no protons to attack nucleophile so nucleophilicity relates directly to basicity strong nucleophiles include HO-, RO-, CN-, & N3- NH3 & RCO2- are fair nucleophiles H2O, ROH, & RCOOH are weak nucleophiles for functional groups, amine groups tend to make good nucleophiles

IUPAC naming procedure

1. identify the longest carbon chain containing the highest-order functional group 2. number the chain 3. name the substituents 4. assign a number to each substituent 5. complete the name

acetyl

2 carbon unit w/ 1 carbon in a carbonyl group

enantiomers

2 molecules that are nonsuperimposable mirror images of each other have same connectivity but opposite configurations at every chiral center in molecule enantiomers have identical physical & chemical properties w/ 2 notable exceptions: optical activity (rotates plane-polarized light in opposite drxns) & react differently in chiral environments assuming concentration & path lengths are equal, 1 enantiomer will rotate plane-polarized light to same magnitude but in opposite drxn of its mirror image

ring strain

Energy created in a cyclic molecule. cycloalkanes can be either fairly stable or fairly unstable compounds depending on ring strain can arise from 3 factors: angle strain, torsional strain, & nonbonded strain (sometimes referred to as steric strain)

hydroquinone vs hydroxyquinone

HYDROQUINONE is benzene ring w/ 2 hydroxyl groups HYDROXYQUINONE contains 2 carbonyls & a variable # of hycroxyl groups

plotting IR spectra

IR spectra are plotted as percent TRANSMITTANCE, amount of light that passes through the sample & reaches the detector, vs. wavenumber in IR spectrum, percent transmittance is plotted vs. frequency equation relating absorbance, A, & percent transmittance, %T is A = 2 - log%T -this means max absorptions appear as bottoms of valleys on spectrum in IR spectrum for aliphatic alcohol, large broad peak at 3300 cm^-1 due to presence of hydroxyl group. sharper peak at 3000 cm^-1 due to carbon-hydrogen bonds in alkane portion of molecule

R / S designation of Fischer projection

If lowest priority group is pointing to the side & as such, pointing out of the page make 0 switches. determine order of substituents as normal, draw circle 1>2>3, obtain R/S designation, FLIP this designation

double & triple bond nomenclature

MCAT doesn't explicitly test rxns of alkenes & alkynes, but their suffixes are -ene & -yne which signify double & triple bonds many of these compounds will also have common names that have to be known **double & triple bond is named like a substituent & is indicated by lower-numbered carbon involved in the bond** number may precede the molecule name, as in 2-butene, or it may be placed near suffix, as in but-2-ene. both are correct if there are MULTIPLE multiple bonds, the numbering is generally separated form the suffix, as in 1,3-butadiene **alkenes & alkynes considered to be tied for priority except in cyclic compounds, where alkenes have higher priority**

spin-spin coupling (splitting)

Occurs when we have 2 protons in close proximity to each other that are not magnetically identical the magnetic environments of the nonidentical protons can affect each other so each proton experiences 2 diff magnetic environments to determine # of peaks present, use the N+1 RULE. if proton has n protons that are ****3 bonds away, it will be split into n + 1 peaks (but do NOT include protons attached to oxygen or nitrogen)**** the magnitude of this splitting, measured in hertz, is called the COUPLING CONSTANT, J peaks that have more than 4 shifts generally referred to as MULTIPLET

preparative TLC

TLC on a larger scale. as large plate develops, larger spot of sample splits into bands of individual compounds, which can then be scraped off & washed to yield pure compounds

steric hindrance

The prevention of a reaction at a particular location in a molecule due to size of substituent groups STERIC PROTECTION can be used as tool in synthesis of desired molecules & prevention of formation of alternative products -bulky groups make it impossible for nucleophile to reach most reactive electrophile > nucleophile attacks another region **-temporarily mask leaving group w/ sterically bulky PROTECTING GROUP during synthesis to prevent it from reacting (can be removed w/ acidic workup)** **for ex, reduction of molecule w/ both carboxylic acids & aldehydes or ketones can result in reduction of all functional groups. to prevent this. aldehyde or ketone first converted to nonreactive acetal or ketal, which serves as the protecting group, & the rxn can proceed** another protective reaction is the reversible reaction of alcohols to tert-butyl ethers

ultraviolet (UV) spectroscopy

UV spectra obtained by passing UV light through sample that's usually dissolved in inert, nonabsorbing solvent, & recording the absorbance the absorbance is then plotted against wavelength. the absorbance is caused by electronic transitions btwn orbitals ****biggest piece of info we get from this technique is wavelength of max absorbance, which tells us extent of conjugation w/in conjugated systems: the more conjugated the compound, the lower the energy of the transition & the greater the wavelength of max absorbance**** conjugation shifts the absorption spectrum, resulting in higher maximum wavelengths (lower frequencies) -large conjugated molecules may even absorb light in visible range, leading to color. bc technique for UV spectroscopy can be used at visible wavelengths, it's sometimes called UV-Vis spectroscopy UV spectroscopy is most useful for studying compounds containing double bonds or heteroatoms w/ lone pairs that create conjugated systems

staggered conformation

a conformation about a carbon-carbon single bond in which the atoms or groups on one carbon are as far apart as possible from atoms or groups on an adjacent carbon. no overlap of atoms along the line of sight

jones oxidation

an even stronger chromium containing oxidizing agent is chromium trioxide (CrO3) dissolved w/ dilute sulfuric acid in acetone this oxidizes primary alcohols to carboxylic acids & secondary alcohols to ketones

strecker synthesis

a way to synthesize amino acid w/ aldehyde or ketone starts w/ an aldehyde, ammonium chloride (NH4Cl), & potassium cyanide (KCN) STEP 1: the carbonyl oxygen is protonated, increasing the electrophilicity of the carbonyl carbon. then, ammonia can attack the carbonyl carbon, forming an imine. the imine carbon is also susceptible to nucleophilic addition reactions, so CN- anion from KCN attacks, forming a NITRILE group (-C triple bonded to N) -mnemonic: niTRIles have a TRIple bond btwn N & C the final molecule at end of step 1 is an AMINONITRILE, a compound containing an amino group (-NH2) & a nitrile group STEP 2: nitrile nitrogen is protonated, increasing the electrophilicity of the nitrile carbon. this is similar to protonating the oxygen of a carbonyl a water molecule attacks, leading to creation of a molecule w/ both imine & hydroxyl moieties on the same carbon. this imine is attacked by another equivalent of water. a carbonyl is formed, kicking off ammonia & creating the carboxylic acid functionality. this step is performed in aqueous acid & can be accelerated by use of heat the starting material for the Strecker synthesis is a planar carbonyl containing compound, so the product of this pathway is a racemic mixture. the incoming nucleophiles are able to attack form either side of the carbonyl. thus, both L & D-amino acids can be generated through this process **Strecker synthesis is 2 step process to form amino acids. 1st step is aminonitrile formation followed by protonation of aminonitrile & attack by water to turn nitrile into carboxylic acid

absolute conformation

absolute conformation of chiral molecule describes the exact spatial arrangement of these atoms or groups, independent of other molecules

ethane parent alkane common names

acetaldehyde & acetic acid

achiral

achiral objects have mirror images that CAN be superimposed, such as a fork **a simple 180 degree rotation around a vertical axis allows compounds to be superimposed upon their mirror images**

acid-base reaction

acid & base react, resulting in formation of conjugate base of the acid & conjugate acid of the base reaction proceeds as long as reactants are more reactive, or stronger, than the products formed

Bronsted-Lowry acid & bases

acid is species that can donate a proton (H+) & a base can accept a proton some molecules like water can act as either Bronsted-Lowry acids or bases, making them AMPHOTERIC -water can act as acid by donating proton to base & becoming its conjugate base OH- -water can act as base by accepting proton to become its conjugate acid H3O+ degree to which molecule acts as acid or base is dependent upon properties of soln. water can only act as base in acidic soln & only as acid in basic soln other ex of amphoteric molecules include Al(OH)3, HCO3-, HSO4-

transesterification

alcohols can act as nucleophiles & displace the esterifying group on an ester in this rxn, 1 ester is simply transformed to another

lewis acid

electron acceptor in the formation of a covalent bond also tend to be electrophiles & have vacant p orbitals into which they can accept an electron pair or are positively polarized atoms

production of aldehydes & ketones

aldehyde can be obtained from partial oxidation of a primary alcohol, although only by PYRIDINIUM CHLOROCHROMATE (PCC). w/ any stronger oxidants, aldehydes will continue to be oxidized to carboxylic acids ketone can be obtained from oxidation of secondary alcohol. this can be performed w/ reagents ranging from sodium or potassium dichromate salts (Na2Cr2O7 / K2Cr2O7) to chromium trioxide (CrO3) to PCC. -when oxidizing secondary alcohol, no concern for oxidizing too far bc rxn will stop @ ketone stage

aldol condensatioin

aldehyde or ketone acts both as electrophile (in its keto form) & a nucleophile (in its enolate form) & the end result is formation of carbon-carbon bond -in aldol condensations, it's same nucleophilic addition rxn seen before w/ carbonyl compounds, just w/ the carbonyl containing compound acting as both a nucleophile & an electrophile step 1: aldol formation when acetaldehyde (ethanal) is treated w/ catalytic amount of base, an enolate ion is produced. enolate is more nucleophilic than enol bc it's - charged the nucleophilic enolate ion (deprotonated aldehyde or ketone) can react w/ electrophilic carbonyl group of another keto form of acetaldehyde molecule. the key to this rxn is that both species are in the same flask product is 3-hydroxybutanal, which is an ex of an ALDOL (molecule that contains both ALDehyde & alcohOL functional groups) mechanism is still called aldol rxn even when reactants are ketones step 2: aldol condensation: -w/ strong base & high temps, dehydration occurs by an E1 or E2 mechanism: we kick off water molecule & form a double bond, producing an alpha, beta unsaturated carbonyl aldol condensations are most useful if we use only 1 type of aldehyde or ketone. if there are multiple aldehydes or ketones, we can't easily control which will act as nucleophile & which will act as electrophile, & a mixture of products will result. this can be prevented if 1 of the molecules has no alpha hydrogens bc the alpha carbons are quaternary (like benzaldehyde) this rxn is referred to as a CONDENSATION REACTION bc 2 molecules are joined w/ loss of small molecule. this type of rxn is also a DEHYDRATION RXN bc the small molecule that's lost is water

alcohols as protecting groups

aldehydes & ketones can be reacted w/ 2 equivalents of an alcohol or a diol (dialcohol), forming ACETALS (primary carbons w/ 2 -OR groups & a hydrogen atom) or KETALS (secondary carbons w/ 2-OR groups) -this is first step of protection of aldehydes & ketones using dialcohols carbonyls are very reactive w/ strong reducing agents like LiAlH4. acetals & ketals don't react w/ LiAlH4 so they protect aldehydes & ketones from rxn after reducing other functionalities in molecule, acetal or ketal can be reverted back to carbonyl & a dialcohol w/ aqueous acid, a step called DEPROTECTION

aldehyde & ketone reduction

aldehydes & ketones can undergo reduction to form alcohols this is often performed w/ HYDRIDE REAGENTS. the most common are LITHIUM ALUMINUM HYDRIDE (LiAlH4) & SODIUM BOROHYDRIDE (NaBH4) which is often used when milder conditions are needed

aldehyde & ketone oxidation

aldehydes occupy middle of oxidation-reduction spectrum. they're more oxidized than alcohols but less than carboxylic acids. ketones on the other hand are as oxidized as secondary carbons get when aldehydes are further oxidized, they form carboxylic acids. any oxidizing agent stronger than PCC can perform this rxn, such as potassium permanganate (KMnO4), chromium trioxide (CrO3), silver (I) oxide (Ag2O), & hydrogen peroxide (H2O2)

alpha carbon & alpha hydrogens

alpha carbon is adjacent to the carbonyl carbon & the hydrogens connected to the alpha carbon are termed the ALPHA HYDROGENS through induction, oxygen pulls some of the electron density out of these C-H, weakening them. this makes it relatively easy to deprotonate the alpha carbon of an aldehyde or ketone the acidity of alpha hydrogens is augmented by resonance stabilization of conjugate base -alpha hydrogens are acidic bc of resonance stabilization & electronegative carbonyl oxygen specifically, when alpha hydrogen is removed, the extra electrons that remain can resonate btwn the alpha carbon, the carbonyl carbon, & the carbonyl oxygen. this increases the stability. this increases the stability of enolate intermediate. through this resonance, the - charge can be distributed to the more electronegative oxygen atom the electron withdrawing oxygen atom thereby helps stabilize the CARBANION (molecule w/ a negatively charged carbon atom) when in basic solutions, alpha hydrogens will easily deprotonate *****the alpha hydrogens of ketones tend to be slightly less acidic than those of aldehydes due to electron donating properties of additional alkyl group in ketone. this property is the same reason that alkyl groups help stabilize carbocations, but in this case, they destabilize carbanion***** electron withdrawing groups like oxygen stabilize organic anions while electron donating groups like alkyl groups destabilize organic anions

enolate formation

alpha hydrogens are much more acidic than in regular C-H bond due to resonance stabilization of enol form > they can be easily deprotonated w/ strong base, forming an enolate the enolate then becomes strong nucleophile & alkylation can result if good electrophiles are available

cis-trans isomers

also called geometric isomers specific subtype of diastereomers in which substituents differ in their position around an immovable bond, such as a double bond or around a ring structure in simple compounds w/ only 1 substituent on either side of immovable bond, we use terms cis & trans for more complicated compounds w/ polysubstituted double bonds, (E)/(Z) nomenclature is used instead

gas chromatography (GC)

also known as vapor phase chromatography (VPC) similar to other types of chromatography except eluent is gas (usually helium or nitrogen) instead of liquid adsorbent is crushed metal or polymer inside a 30 foot column. this column is coiled & kept inside oven to control its temperature. mixture is then injected into column & vaporized. gaseous compounds travel through compounds at diff rates bc they adhere to adsorbent in column to diff degrees & will separate in space by time they reach end of column. the injected compounds must be VOLATILE: low melting point, sublimable solids or vaporizable liquids. the compounds are registered by a detector, which records them as a peak on a chart. it's common to separate molecules using GC & then to inject the pure molecules into mass spectrometer for molecular weight determination

amide synthesis

amides are generally synthesized by rxn of other carboxylic acid derivatives w/ either ammonia or an amine loss of hydrogen from nucleophile is required for this rxn to take place so only primary & secondary amines will undergo this rxn amides may or may not participate in hydrogen bonding depending on # of alkyl groups that they have bonded & therefore their boiling points may be lower or on same level as boiling points of carboxylic acids

hydrolysis of amides

amides can be hydrolyzed under highly acidic conditions via nucleophilic substitution the acidic conditions allow the carbonyl oxygen to become protonated, making the molecule more susceptible to nucleophilic attack by a water molecule. the product of this rxn is a carboxylic acid & ammonia bc this is the reverse of the condensation rxn by which amides are formed hydrolysis can also occur if conditions are basic enough. the rxn is similar to an acid-catalyzed rxn, except that the carbonyl oxygen is not protonated & the nucleophile is a hydroxide ion. the product of this rxn would be the deprotonated carboxylate anion

naming cyclic amides

amides that are cyclic are called LACTAMS & are named by replacing -OIC ACID w/ -LACTAM. they may also be named by indicating the specific carbon that's bonded during cyclization. ex: beta-lactam, gamma-lactam

formation of carboxylic acid derivatives

amides, esters, & anhydrides are all formed by CONDENSATION rxns w/ a carboxylic acid, a rxn that combines 2 molecules into 1 while losing a small molecule which is water in this case -water is created from hydroxyl group of carboxylic acid & a hydrogen associated w/ the incoming nucleophile

anhydride cleavage

as w/ carboxylic acids, nucleophilic acyl substitution involves nucleophilic attack of carbonyl carbon w/ displacement of a leaving group all carboxylic acid derivatives can participate in nucleophilic substitution rxns at diff relative rates, anhydrides are most reactive toward nucleophiles, followed by esters & then amides. 1 ex is formation of amides from nucleophilic substitution rxn btwn ammonia & any carboxylic acid or derivative. ammonia + anhydride is not only a nucleophilic substitution rxn but also a CLEAVAGE REACTION bc it splits an anhydride in 2. -in this rxn, ammonia acts as nucleophile, 1 of the carbonyl carbons acts as the electrophile, & a carboxylic acid is the leaving group alcohols can also act as nucleophiles toward anhydrides. this nucleophilic substitution rxn will result in formation of esters & carboxylic acids anhydrides can also be reverted to carboxylic acids by exposing them to water. for these rxns to be useful, the anhydride should be symmetric, otherwise 1 forms a mixture of products

heteroatoms

atoms besides carbon & hydrogen, like oxygen, nitrogen, phosphorus, or halogens

nuclear magnetic resonance (NMR) spectroscopy

based on fact that certain atomic nuclei have magnetic moments that are oriented at random. when nuclei are placed in magnetic field, their magnetic moments tend to align either w/ or against drxn of this applied field ****nuclei w/ magnetic moments that are aligned w/ field are said to be in the ALPHA STATE (lower energy). the nuclei can then be irradiated w/ radiofrequency pulses that match the energy gap btwn the 2 states, which will excite some lower energy nuclei into the BETA STATE (higher energy).**** the absorption of this radiation leads to excitation at diff frequencies, depending on an atom's magnetic environment. in addition, the nuclear magnetic moments of atoms are affected by nearby atoms that also possess magnetic moments MRI is noninvasive diagnostic tool that uses proton NMR

ion exchange chromatography

beads in column coated w/ charged substances so they attract or bind compounds that have opposite charge after all compounds have moved through column, salt gradient used to elute charged molecules that have stuck to column

pi bond

bonding molecular orbital formed when 2 unhybridized p orbitals line up in a parallel side by side fashion, their electron clouds overlap electron density exists above & below the plane of the molecule, restricting rotation about a double bond 1 pi bond on top of an existing sigma bond is a DOUBLE BOND **a sigma bond & 2 pi bonds form a TRIPLE BOND** **pi bonds can't exist independently of a sigma bond**. only after the formation of a sigma bond will p orbitals on adjacent carbons be parallel & in position to form the pi bond **while double bonds are stronger than single bonds overall, individual pi bonds are weaker than sigma bonds so it's possible to break only 1 of the bonds in a double bond, leaving a single bond intact** -pi bonds are weaker than single bonds bc s orbitals have more overlap than p orbitals. bond strength related to amount of overlap & p orbitals have less overlap bc they're parallel

hydrocarbon w/ 4 carbons

butane

wash

can use reverse extraction w/ small amt of solute to extract & remove impurities, rather than compound of interest. wash with nonpolar liquids (e.g. hexanes) to clean a polar substance or with polar liquids (e.g water) to clean an organic substance

michael addition

carbanion attacks an alpha,beta unsaturated carbonyl compound, a molecule w/ a multiple bond btwn the alpha & beta carbons next to a carbonyl rxn proceeds due to resonance stabilization of the intermediates

2. number the chain

carbon #1 will be closest to highest-priority functional group if functional groups all have same priority, numbering the chain should make the numbers of the substituted carbons as low as possible just like straight chains, rings are numbered starting at point of greatest substitution, continuing in the direction that gives the lowest numbers to the highest-priority functional groups **if there's a tie btwn assigning priority in a molecule with double and triple bonds, double bond takes precedence**

carbonyl group

carbon double bonded to an oxygen

chiral center

carbon with four different substituents and lacks a plane of symmetry carbon has an asymmetrical core of optical activity known as the chiral center a carbon w/ 3 diff substituents has a plane of symmetry & is therefore ACHIRAL

diastereomers

chiral molecules that share same connectivity but aren't mirror images of each other bc they differ at SOME BUT NOT ALL of their multiple chiral centers SO diastereomers are required to have multiple chiral centers diastereomers have diff chemical properties but may behave similarly in some rxns bc have same functional groups bc they have diff arrangement in space, they will consistently have diff physical properties diastereomers rotate plane-polarized light, but knowing specific rotation of 1 diastereomer gives no indication of rotation of another diastereomer

diol reactivity

commonly used as protecting group for aldehydes or ketones diols are nucleophiles bc of lone pairs on oxygens in hydroxyl groups

p orbital

composed of 2 lobes located symmetrically above the nucleus & contains a NODE, an area where the probability of finding an electron is 0, at the nucleus dumbbell that can be positioned in 3 diff orientations, along the x, y, or z axis. this is why there are 3 p orbitals

d orbital

composed of 4 symmetrical lobes & contains 2 nodes 4 of the d orbitals are clover shaped & the 5th looks like a donut wrapped around the center of a p orbital

optical activity

compound is optically active (chiral) if it has the ability to rotate plane-polarized light in order to have optical activity, molecule must not only have chiral centers but also must lack plane of symmetry ordinary light is unpolarized, which means it consists of waves vibrating in all possible planes perpendicular to its drxn of propagation a polarizer allows light waves oscillating only in particular drxn to pass through, producing plane-polarized light a compound that rotates the plane of polarized light to the right, or clockwise, is DEXTROROTATORY (d-) & labeled (+) compound that rotates light towards left or counterclockwise is LEVOROTATORY (l-) & labeled (-) drxn of rotation can't be determined from structure of molecule & must be determined experimentally amount of rotation depends on # of molecules that light wave encounters. this depends on 2 factors, concentration of optically active compound & length of tube through which light passes chemists have set standard conditions of 1 g/mL for concentration & 1 dm (10 cm) for length to compare optical activities of diff compounds rotations measured @ diff concentrations & tube lengths can be converted to standardized SPECIFIC ROTATION using: [alpha] = alpha observed / c x l -[alpha] is specific rotation in degrees -alpha observed is observed rotation in degrees -c is concentration in g/mL -l is path length in dm

hydrocarbons

compounds that contain only carbon & hydrogen atoms

aldehydes nomenclature

contains carbonyl group & is CHAIN-TERMINATING, meaning they appear @ end of parent chain no leaving groups connected to carbonyl chain. only connected to hydrogen atoms bc it's terminal functional group that takes precedence over many others, it's generally attached to carbon #1 named by replacing -e of parent alkane w/ suffix -AL when aldehyde is @ position 1, we don't need to include this # in chemical name if aldehyde is attached to a ring, the suffix -CARBALDEHYDE is used instead METHANAL, ETHANAL, & PROPANAL are referred to almost exclusively by their common names, FORMALDEHYDE, ACETALDEHYDE, & PROPIONALDEHYDE rather than their IUPAC names

anhydride formation

condensation dimers of carboxylic acids. acid anhydrides synthesized by condensation rxn btwn 2 carboxylic acids, w/ 1 molecule of water lost in condensation have general formula RC(O)OC(O)R phthalic & succinic anhydrides are cyclic anhydrides arising from intramolecular condensation or dehydration of diacids certain cyclic anhydrides can be formed simply by heating carboxylic acids. the rxn is driven forward by increased stability of the newly formed ring. as such, only anhydrides w/ 5 or 6 membered rings are easily made -just as w/ all anhydride formations, the hydroxyl group of 1 -COOH acts as the nucleophile, attacking the carbonyl on the other -COOH anhydrides often have greater boiling points than their related carboxylic acids, based solely on their much greater weight

configuration

configuration of stereoisomer refers to spatial arrangement of the atoms or groups in molecule

unimolecular nucleophilic substitutions (SN1) reactions

contain 2 steps 1st step is rate-limiting step in which leaving group leaves, generating a positively charged CARBOCATION nucleophile then attacks carbocation, resulting in substitution product the more substituted the carbocation, the more stable it is bc the alkyl groups act as electron donors, stabilizing the + charge bc the formation of the carbocation is the rate-limiting step, the rate of the rxn depends only on the concentration of the substrate rate = k[R-L] where R-L is an alkyl group containing a leaving group this is a first order rxn: anything that accelerates the formation of the carbocation will increase the rate of an SN1 rxn > prefer tertiary to secondary carbons as reactive sites, & secondary to primary bc SN1 rxn passes through a planar intermediate before the nucleophile attacks, the product will usually be a racemic mixture. incoming nucleophile can attack carbocation from either side, resulting in varied stereochemistry prefer POLAR PROTIC SOLVENTS bc they stabilize carbocation intermediate

carboxylic acids nomenclature

contains both a carbonyl group (C=O) & a hydroxyl group (-OH) on a terminal carbon terminal functional group so their associated carbon is usually #1 this is the most oxidized functional group on MCAT w/ 3 bonds to oxygen so all other groups are named as substituents w/ prefixes carboxylic acids replace -e at end of name of parent alkane w/ suffix -OIC ACID common name for methanoic acid is FORMIC ACID. ethanoic acid is ACETIC ACID. propionic acid is PROPANOIC ACID

ketones

contains carbonyl group & found in middle of carbon chains, so we will always have to assign a # to the carbonyl carbon when naming ketones (except propanone, which must have the ketone on carbon 2 by default) no leaving groups connected to carbonyl chain. only connected to alkyl chains replace -e in name of parent alkane w/ suffix -ONE ketones commonly named by listing alkyl groups in alphabetical order, followed by ketone, such as ethylmethylketone PROPANONE common name is ACETONE & is smallest possible ketone molecule ***in more complex molecule w/ a higher-priority group that takes precedence over the carbonyl, name ALDEHYDES & ketones as substituents using the prefix OXO- in reference to carbonyl oxygen*** **sometimes ketones may also be indicated w/ prefix KETO-**

lewis base

electron donor in formation of covalent bond Lewis bases tend to be nucleophiles & have lone pair of electrons that can be donated & are often anions, carrying a negative charge

bimolecular nucleophilic substitution (SN2) reactions

contains only 1 step, in which the nucleophile attacks the compound @ the same time as the leaving group leaves bc this rxn has only 1 step, it's a CONCERTED rxn rxn is called bimolecular bc this single rate-limiting step involves 2 molecules in SN2 rxns, the nucleophile actively displaces the leaving group in a BACKSIDE ATTACK. for this to occur, nucleophile must be strong & substrate can't be sterically hindered. therefore, the less substituted the carbon, the more reactive it is in SN2 rxns, which is opposite trend for SN1 rxns -methyl & primary carbons are preferred over secondary, & tertiary carbons won't react single step of an SN2 rxn involves 2 reacting species: the substrate (often an alkyl halide, tosylate, or mesylate) & the nucleophile. thus , concentrations of both have role in determining the rate rate = k [Nu:] [R-L] SN2 rxns are accompanied by an inversion of relative configuration. position of substituents around substrate carbon will be inverted if nucleophile & leaving group have same priority in their respective molecules, this inversion will also correspond to a change in absolute config from R to S or vice versa this is an ex of a STEREOSPECIFIC rxn, 1 in which the configuration of the reactant determines the configuration of the product due to the rxn mechanism prefer POLAR APROTIC SOLVENTS bc protic solvents weaken nucleophiles

naming cyclic carboxylic acids

cyclic carboxylic acids are named by listing the cycloalkane w/ the suffix CARBOXYLIC ACID salts of carboxylic acids are named beginning with the cation, followed by the name of the acid with the ending -OATE replacing -OIC ACID

chair flip

cyclohexane can undergo a CHAIR FLIP in which 1 chair form is converted to the other. in this process, the cyclohexane molecule briefly passes through a 4th conformation called the HALF-CHAIR CONFORMATION. after the chair flip, all axial groups become equatorial & all equatorial groups become axial. all dashes remain dashes & all wedges remain wedges

hydrocarbon w/ 10 carbons

decane

decarboxylation

decarboxylation describes complete loss of carboxyl group as carbon dioxide. this is common way of getting rid of carbon from parent chain 1,3-dicarboxylic acids & other beta-keto acids may spontaneously decarboxylate when heated. beta-keto acids & beta-dicarboxylic acids can decarboxylate bc they can form cyclic transition state that permits simultaneous hydrogen transfer & loss of carbon dioxide. bc both the electrophile & nucleophile are in the same molecule, rxn proceeds through 6 membered ring in its transition state. the enol that's initially formed from destruction of ring tautomerizes to more stable keto form

ester formation

dehydration synthesis of other carboxylic acid derivatives & alcohols ethyl acetate, derivewd from the condensation of acetic acid & ethanol, is called ethyl ethanoate according to IUPAC nomenclature bc they lack hydrogen bonding, esters usually have lower boiling points than their related carboxylic acids triacylglycerols are esters of long chain carboxylic acids (fatty acids) & glycerol

nucleophilic substitution reactions

demonstrate nucleophile-electrophile reactions in both SN1 & SN2 rxns, a nucleophile forms a bond w/ a substrate carbon & a leaving group leaves just like acid-base rxns, nucleophilic attack will only occur if reactants are more reactive than the products, so the nucleophile must be more reactive (stronger base) than the leaving group

NMR spectroscopy values to know

deshielded aldehyde: 9-10 ppm hydrogen of aromatic ring: 6-8.5 ppm hydrogens on sp3 hybridized carbons: 0-=3 ppm sp2 hybridized carbons: 4.6-6 ppm sp hybridized carbons: 2-3 ppm Alkyl groups: 0 to 3 ppm Alkynes: 2 to 3 ppm Alkenes: 4.6 to 6 ppm Aromatics: 6 to 8.5 ppm Aldehydes: 9 to 10 ppm Carboxylic acids: 10.5 to 12 ppm when electronegative groups, higher #s & more downfield

aldehyde & ketone isomers

due to acidity of alpha hydrogen, aldehyde & ketones exist in solution as a mixture of 2 isomers: the familiar KETO form & the ENOL form the ENOL form gets its name from presence of a carbon carbon double bond (the en-component) & an alcohol (the -ol component) the 2 isomers, which differ in placement of proton & double bond, are called TAUTOMERS. the equilibrium btwn the tautomers lies far to the keto side, so there will be many more keto isomers in soln. keto form is thermodynamically favored tautomers are not resonance structures bc they differ in their connectivity of atoms

beta dicarboxylic acids

dicarboxylic acids in which each carboxylic acid is positioned on beta carbon of the other. there are 2 carboxylic acids separated by a single carbon these compounds are notable for high acidity of the alpha hydrogens located on carbon btwn the 2 carboxyl groups. loss of this acidic hydrogen produces a carbanion, which is stabilized by electron withdrawing effect of both carboxyl groups the hydroxyl hydrogen is the most acidic proton on a carboxylic acid. however, in 1,3-dicarbonyls, the alpha hydrogen is also quite acidic. this also applies to alpha hydrogens in beta-diketone, beta-ketoacids, beta-dialdehydes, & other molecules that share the 1,3-dicarbonyl structure

vicinal diols

diols with hydroxyl groups on adjacent carbons

geminal diols

diols with hydroxyl groups on the same carbon geminal diols, or HYDRATES, are not commonly seen bc they spontaneously dehydrate (lose a water molecule) to produce carbonyl compounds w/ functional group C=O

carbonyl dipole

dipole of carbonyl is stronger than dipole of an alcohol bc the double bonded oxygen is more electron withdrawing than single bond to oxygen in hydroxyl group in solution, dipole moments associated w/ polar carbonyl groups increase intermolecular attractions, causing an elevation in boiling point relative to their parent alkanes ***however, even though carbonyls are more polar than alcohols, their elevation in boiling point is less bc no hydrogen bonding is present***

induction

distribution of charge across sigma bonds. electrons are attracted to atoms that are more electronegative, generating dipole across sigma bond. the less electronegative atom gets slightly + charge & the more electronegative atom acquires slightly - charge this effect is relatively weak & gets increasingly weaker as 1 moves further away w/in molecule from the more electronegative atom. this effect is responsible for dipole character of the carbonyl group, as well as the increased dipole character (& therefore susceptibility to nucleophilic attack) of carboxylic acids, which contain an additional oxygen atom in their leaving group. this also explains overall relative reactivity of 2 anhydrides, esters, & amides toward nucleophilic attack. anhydrides have 2 electron withdrawing groups, which leave a significant partial + charge on electrophilic carbon. this effect is smaller in amides bc nitrogen is less electronegative than oxygen & the dipole is not as strong ****resonance & conjugation are much more powerful than induction**** & also affect reactivity of molecule

hydrocarbon w/ 12 carbons

dodecane

methane parent alkane common names

formaldehyde & formic acid

molecular orbitals

formed when 2 atomic orbitals combine obtained mathematically by adding or subtracting the wave functions of the atomic orbitals, which is not on MCAT, but exam may ask for visualization of molecular orbitals if the signs of the wave functions are the same, a lower energy & more stable BONDING ORBITAL is produced if signs are diff, a higher energy & less stable ANTIBONDING ORBITAL is produced like atomic orbitals, molecular orbitals contain a maximum of 2 electrons

functional groups as acids & bases

functional groups that act as acids include alcohols, aldehydes, ketone (at the alpha-carbon), carboxylic acids, & most carboxylic acid derivatives. these compounds are easier to target w/ basic (or nucleophilic) reactants bc they readily accept a lone pair amines & amides are the main functional groups that act as bases. nitrogen atom of amine can form coordinate covalent bonds by donating lone pair to lewis acid

substituents

functional groups that aren't part of parent chain

acid strength

generally, bond strength decreases down periodic table (atomic radius increases in size) & acidity therefore increases the more electronegative an atom, the higher the acidity when these 2 trends oppose each other, low bond strength takes precedence

kinetic & thermodynamic enolates

given a ketone that has 2 diff alkyl groups, each of which may have alpha hydrogens, 2 forms of the enolate can form, w/ the carbon carbon double bond btwn the carbonyl carbon & either the more or less substituted carbon the equilibrium btwn these forms is dictated by the kinetic & thermodynamic control of the rxn. the kinetically controlled product is formed more rapidly but is less stable. this form has double bond to less substituted alpha carbon. this product is formed by removal of alpha hydrogen from less substituted alpha carbon bc it offers less steric hindrance thermodynamically controlled product is formed more slowly but is more stable & features the double bond being formed w/ the more substituted alpha carbon. this is formed by removal of alpha hydrogen from more substituted alpha carbon *****kinetic product is favored in rxns that are rapid, irreversible, at lower temps, & w/ a strong, sterically hindered base***** if rxn is reversible, kinetic product can revert to original reactant & react again to form thermodynamic product. *****thermodynamic product is favored w/ high temps, slow, reversible rxns, & weaker, smaller bases*****

alkyl halides nomenclature

halogens are common substituents on alkanes alkyl halides are indicated by prefix: fluoro- chloro- bromo- iodi-

dicarboxylic acids

have a carboxylic acid group on each end of the molecule common in biological systems the. smallest dicarboxylic acid is oxalic acid, w/ 2 carbons next 5 straight chain dicarboxylic acids are malonic, succinic, glutaric, adipic, & pimelic acids their IUPAC names have suffix DIOIC ACID, such as ethanedioic acid, propanedioic acid, butanedioic acid, pentanedioic acid, hexanedioic acid, & heptanedioic acid in dicarboxylic acids, each -COOH group influences the other -COOH group. carboxylic acids are electron withdrawing due to electronegative oxygen atoms they contain. net result is that dicarboxylic acids are more acidic than analogous monocarboxylic acids -however, when 1 proton is removed from molecule, the carboxylate anion is formed, resulting in immediate decrease in acidity of remaining carboxylic acid. this makes sense bc if 2nd group is deprotonated, it would create doubly charged species w/ 2 negative charges repelling each other. due to this instability, the 2nd proton is LESS acidic (harder to remove) than the analogous proton of a monocarboxylic acid

alcohols

have general formula ROH w/ the functional group -OH referred to as the HYDROXYL group alcohols seen as protic solvents, reactants, products, & prime examples of hydrogen bonding > higher melting & boiling points than those of analogous hydrocarbons -more hydroxyl groups = more H bonding = higher BP/MP & solubility in water named in IUPAC system by replacing -e ending of root alkane w/ -ol -when alcohol is not highest priority group, it's named as substituent w/ the prefix hydroxy- common naming practice is to name alkyl group as derivative, followed by ALCOHOL **hydroxyl hydrogen is weakly acidic & alcohols can dissociate into protons & alkoxide ions in same way that water dissociates into protons & hydroxide ions** ***presence of more alkyl groups in nonaromatic alcohols produce less acidic molecules bc alkyl groups donate electron density & destabilize a - charge. additionally, alkyl groups help stabilize + charges, explaining why more substituted carbocations have higher stability than less substituted carbocations***

good oxidizing agents

have high affinity for electrons (such as O2, O2, & Cl2) or unusually high oxidatin states (like Mn7+ in MnO4- & Cr6+ in CrO4-2) common way to synthesize carboxylic acid is to use strong oxidizing agent such as PCC or KMnO4 oxidizing agents often contain metals bonded to large # of oxygen atoms

good reducing agents

have low electronegativities & ionization energies or contain a hydride ion (H-) & include sodium, magnesium, aluminum & zinc, which have low electronegativities & ionization energies metal hydrides, such as NaH, CaH2, LiAlH4, & NaBH4 are good reducing agents bc they contain H- ion aldehydes & ketones will be reduced to primary & secondary alcohols, respectively. this rxn is exergonic but exceedingly slow w/o a catalyst amides can be reduced to amines using LiAlH4. this same reducing agent will reduce carboxylic acids to primary alcohols & esters to a pair of alcohols reduction rxns tend to favor increase in # of bonds to hydrogen & reducing agents often contain metals bonded to large # of hydrides many common oxidizing & reducing agents include transition metals bc they can take on many diiff oxidation states. their low ionization energies & presence of d orbitals allows them to give up & accept electrons easily

chemical properties

have to do w/ reactivity of the molecule w/ other molecules & result in changes in chemical composition in organic chem, chemical properties of compound generally dictated by functional grps in molecule

hydrocarbon w/ 7 carbons

heptane

hydrocarbon w/ 6 carbons

hexane

separating racemic mixture

how do you separate mixture if enantiomers have same chemical & physical properties? reacting 2 enantiomers w/ a single enantiomer of another compound will lead to 2 diastereomers for ex, if 2 enantiomers w/ 1 chiral carbon labeled (+) & (-) react w/ (+) enantiomer of another compound, 2 products would result: (+,+) & (-,+). bc the 2 products differ @ some but not all chiral centers, they're diastereomers. diastereomers have diff physical properties & these diff enable 1 to separate these products by common lab techniques such as crystallization, filtration, distillation, etc. once separated, these diastereomers can be reacted to regenerate original enantiomers

cyanohydrin formation

hydrogen cyanide (HCN)is classic nucleophile. the -CN acts as nucleophile & carbonyl carbon is electrophile HCN has both triple bonds & an electronegative nitrogen atom, rendering it relatively acidic w/ pKa of 9.2. after hydrogen dissociates, the nucleophilic cyanide anion can attack the carbonyl carbon atom rxns w/ aldehydes & ketones produce stable compounds called CYANOHYDRINS once oxygen has been reprotonated. the cyanohydrin gains its stability from the newly formed C-C bond

IR absorptions to memorize

hydroxyl group (O-H) absorbs with broad/wide peak around 3300 cm^-1 for alcohols & 3000 cm^-1 for carboxylic acids -the carbonyl of a carboxylic acid pulls some of the electron density out of the O-H bond, shifting absorption to lower wavenumber carbonyl (C=O), absorbs around 1700 cm^-1 w/ sharp peak bond btwn any atom & hydrogen always has relatively high absorption frequency & as we add more bonds btwn carbon atoms, absorption frequency increases N-H bonds are in same region as O-H bonds (around 3300 cm^-1) but have sharp peak instead of broad one like O-H C-C 1200-1400 cm^-1 C-H 2800-3000 cm^-1 on MCAT< all info comes from frequencies btwn 1400 & 4000 cm^-1. everything lower in fingerpring scope is out of scope

Preparation of mesylates and tosylates

hydroxyl groups of alcohols are fairly poor leaving groups for nucleophilic substitution rxns however, they can be protonated, or reacted to form much better leaving groups called mesylates & tosylates. tosylates & mesylates displace the OH- to make new structure that's easily removed MESYLATE is a compound containing the functional group -SO3CH3, derived from METHANESULFONIC ACID -mesylates are prepared using methylsulfonyl chloride & an alcohol in the presence of a base TOSYLATES contain the functional group -SO3C6H4CH3 derived from TOLUENESULFONIC ACID -these compounds are produced by rxn of alcohols w/ p-toluenesulfonyl chloride, forming esters of toluenesulfonic acid in addition to making hydroxyl groups of alcohols into better leaving groups for nucleophilic substitution rxns, mesyl & tosyl groups can also serve as protecting groups when we do not want alcohols to react -these groups are protective bc they don't react w/ many other reagents that would attack alcohols, especially oxidizing agents -reacting alcohol to form mesylate or tosylate is sometimes performed before multistep rxns in which desired products do not derive from alcohol

carboxylate anion

hydroxyl hydrogen of carboxylic acid is quite acidic, resulting in - charge that remains after the hydrogen is removed & resonance stabilization occurs btwn both of the electronegative oxygen atoms delocalization of the - charge results in a very stable carboxylate ion -the more stable the conjugate base is, the easier it is for the proton to leave, & thus the stronger the acid carboxylic acids are relatively acidic, w/ pKa around 5, but not compared to strong acids. substituents on carbon atoms near a carboxyl group influence anion stability & therefore affect acidity -groups like -NO2 or halides are electron withdrawing & increase acidity -in contrast, -NH2 or -OCH3 are electron donating groups that destabilize the - charge, decreasing acidity of compound the closer the substituent groups are to the carboxyl group, the greater the effect will be

rings with multiple substituents nomenclature

if both groups are located on same side of ring, the molecule is called CIS if they're on opposite sides of ring, it's called TRANS these terms also used for molecules w/ double bonds

polar solvents

if solvent is not given, assume rxn occurs in polar solvent polar solvents, whether protic or aprotic, can dissolve nucleophiles & assist in any rxn in which electrons are moved protic solvents can hydrogen bond. common protic solvents: -carboxylic acids -ammonia/amines -water/alcohols aprotic solvents can't can't hydrogen bond. common aprotic solvents -dimethylformamide (DMF) -dimethylsulfoxide (DMSO) -acetone

reactivity of carboxylic acid derivatives

in nucleophilic substitution rxn, reactivity of carbonyl is determined by its substituents anhydrides are most reactive, followed by esters (which are essentially tied w/ carboxylic acids), then finally amides due to structures -anhydrides have resonance stabilization & 3 electron withdrawing oxygen atoms, so they're the most electrophilic -esters lack 1 electron withdrawing oxygen & are slightly less reactive -amides have electron donating group & are least reactive towards nucleophile

aldehydes & ketones in water

in presence of water, aldehydes & ketones react to form GEMINAL DIOLS (1,1-diols) in this case, the nucleophilic oxygen in water attacks electrophilic carbonyl carbon this hydration rxn normally proceeds slowly but we can increase rate by adding small amt of catalytic acid or base

reactivity of aldehydes & ketones

in rxns, aldehydes & ketones both act as electrophiles, making good targets for nucleophiles. this is due to electron w/drawing properties of carbonyl oxygen, leaving partial + charge on carbon generally, aldehydes are more reactive toward nucleophiles than ketones bc they have less steric hindrance & fewer electron-donating alkyl groups carbonyl carbon is the most common electrophile seen on the MCAT

carboxylic acid derivatives

include esters, amides, & anhydrides

oxidation

increase in oxidation state, which means a loss of electrons in orgo, often easier to view oxidation as increasing # of bonds to oxygen or other heteroatoms (atoms besides carbon & hydrogen) oxidation of carbon atom occurs when bond btwn carbon & atom that's less electronegative than carbon is replaced by bond to atom that's more electronegative than carbon -usually means decreasing # of bonds to hydrogen & increasing # of bonds to other carbons, nitrogen, oxygen, or halides **can organize diff functional groups by "levels" of oxidation:** -level 0 (no bonds to heteroatoms): alkanes. least oxidized carbon -level 1: alcohols, alkyl halides, amines -level 2: aldehydes, ketones, imines -level 3: carboxylic acids, anhydrides, esters, amides -level 4 (4 bonds to heteroatoms): carbon dioxide. most oxidized carbon

filtration

isolates solid from a liquid at end of filtration, left w/ solid, called the RESIDUE & the flask full of liquid that passes through filter, known as FILTRATE filtration can be modified depending on whether substance of interest is solid or is dissolved in filtrate -GRAVITY FILTRATION, in which solvent's own weight pulls it through filter, is more common when product of interest is in filtrate. hot solvent generally used to keep product dissolved in liquid -VACUUM FILTRATION, in which solvent is forced through filter by vacuum connected to flask, is more often used when solid is desired product

lactam & lactone reactivity

lactams & lactones are cyclic amides & esters certain lactams & lactones are more reactive to hydrolysis bc they contain more strain. ring strain & therefore the reactivity of beta lactams is increased by fusion to a 2nd ring the 4 membered structure of a beta lactam also forces a trigonal pyramidal bond geometry on the nitrogen atom in the ring, which reduces resonance, making hydrolysis more likely

structural isomers

least similar of all isomers only thing structural / constitutional isomers share is their molecular formulas, so their molecular weights are the same aside from this similarity, structural isomers are widely varied w/ diff chemical & physical properties

stereoisomers

like structural isomers & all isomers, stereoisomers have same chemical formula but unlike structural isomers, stereoisomers also share same atomic connectivity. they have same structural backbone stereoisomers differ in how these atoms are arranged in space (their wedge & dash pattern) & all isomers that aren't structural isomers are stereoisomers largest distinction w/in this class of isomers is btwn CONFORMATIONAL & CONFIGURATIONAL isomers for any molecule w/ n chiral centers, there are 2^n possible stereoisomers, so if compound has 2 chiral carbons, it has max of 4 possible stereoisomers

alcohol reactions

main reactions for alcohols include oxidation, preparation of mesylates & tosylates, & protection of carbonyls by alcohols

gabriel synthesis

malonic-ester synthesis. another way of synthesizing amino acids in this method, potassium phthalimide (protected form of ammonia that prevents multiple alkylations due to steric hindrance of phthalimide group) is reacted w/ diethyl bromomalonate. phtalimide is acidic & exists in solution as a nucleophilic anion. diethyl bromomalonate contains a secondary carbon bonded to bromine, a good leaving group. this setup sounds like SN2 rxn, w/ phthalimide as the nucleophile, the (secondary) substrate carbon as the electrophile, & bromine as the leaving group, this rxn generates a phthalimidomalonic ester bulkiness of using large nucleophile creates steric hindrance, which prevents the substrate carbon from undergoing multiple substitutions. instead, in the presence of base, this carbon (which is the alpha carbon btwn 2 carbonyls) can easily be deprotonated. the molecule as a whole can then act as a nucleophile, attacking the substrate carbon of a bromoalkane. this is another ex of SN2 rxn. the nucleophile is the large, deprotonated phthalimidomalonic ester, the electrophile is the substrate carbon, & the leaving group is the bromide anion next, this molecule is hydrolyzed w/ strong base & heat. much like converting a cyclic anhydride into a diolic acid, the phthalimide moiety is removed as phthalic acid (w/ 2 carboxylic acids). the malonic ester is hydrolyzed to a dicarboxylic acid w/ an amine on the alpha carbon finally, the dicarboxylic acid, which is a 1-3, dicarbonyl, can be decarboxylated through addition of acid & heat. the loss of a molecule of carbon dioxide results in formation of complete amino acid. like the strecker synthesis, the gabriel synthesis starts w/ a planar molecule. thus, product is racemic mixture of L & D amino acids

nucleophilic acyl substitution

many rxns in which carboxylic acids & their derivatives participate proceed via a single mechanism: nucleophilic acyl substitution this mechanism is similar to nucleophilic addition to aldehyde or ketone but the key diff focuses on existence of leaving group in carboxylic acids & their derivatives in this case, after opening the carbonyl via nucleophilic attack & forming tetrahedral intermediate, the carbonyl can reform, thereby kicking off the leaving group in these rxns, the nucleophilic molecule replaces the leaving group of an acyl derivative. these rxns are favored by good leaving group -remember weak bases, which are often conjugate bases of strong acids, make good leaving groups these rxns are favored: -in basic soln, which makes the nucleophile more nucleophilic -in acidic soln, which makes the electrophile more electrophilic -by good leaving groups (weak bases)

nucleophilic addition to carbonyl

many rxns of aldehydes, ketones, & more complex molecules share this general rxn mechanism C=O bond is polarized w/ partial + on carbonyl carbon & partial - on oxygen > carbonyl carbon is electrophile when nucleophile attacks, it forms covalent bond to the carbon, breaking the pi bond in the carbonyl. the electrons from the pi bond are pushed into oxygen atom. oxygen happily accepts these electrons due to its electronegativity breaking pi bond forms tetrahedral intermediate. any time a carbonyl group is opened, ask if you can reform the carbonyl. -if no good leaving group is present (as w/ aldehydes & ketones), carbonyl will not reform. generally, O- will accept a proton from the solvent to form a hydroxyl group, resulting in an alcohol. -however, if a good leaving group is present (as w/ carboxylic acids & its derivatives), the carbonyl double bond can reform, pushing off the leaving group

anti conformation

most energetically favorable of staggered conformation the 2 largest groups are ANTIPERIPLANAR (in same plane but on opposite side, 180 degrees apart from each other)

1H NMR Spectroscopy

most hydrogen (^1N nuclei) come into resonance 0 to 10 ppm downfield from TMS ****each distinct set of nuclei gives rise to separate peak, so if multiple protons are CHEMICALLY EQUIVALENT, having same magnetic environment, they will lead to same peak**** height of peaks is proportional to # of protons it contains & analyzing area under the peaks is called INTEGRATION ****atoms that pull electron density away from surrounding atoms DESHIELD proton from magnetic field & it goes further downfield**** -electron donating groups shield ^1H nuclei & give it a position further upfield

hydrocarbon w/ 5 carbons

pentane

infrared (IR) spectroscopy

measures molecular vibrations, which can be seen as bond stretching, bonding, or combination of diff vibrational modes to record an IR spectrum, infrared light is passed through a sample & the absorbance is measured. by determining what bonds exist w/in a molecule, we hope to infer the functional groups in the molecule the infrared light range runs from lambda = 700 nm to 1 mm, but the useful absorptions for spectroscopy occur at wavelengths of 2500 to 25,000 nm. on an IR spectrum, we use analog of frequency called WAVENUMBER. wavenumber = 1/lambda. the standard range corresponding to 2500 to 25,000 nm is 4000 to 400 cm^-1. when light of these wavenumbers is absorbed, the molecules enter excited vibrational states, such as symmetric bend, asymmetric bend, symmetric stretch, asymmetric stretch, twisting, & folding more complex vibration patterns, caused by motion of molecule as a whole, can be seen in the 1500 to 400 cm^-1 range, called the FINGERPRINT REGION bc the specific absorbance pattern is characteristic of each individual molecule, but don't need to use this region on MCAT for an absorption to be recorded, the vibration must result in change in bond dipole moment. this means that molecules that don't experience a change in dipole moment such as those composed of atoms w/ same electronegativity or molecules that are symmetrical, don't exhibit absorption so don't show up on IR spectra -no absorption from O2 or Br2 but do get absorption from HCl or CO -symmetric bonds, such as triple bond in acetylene (C2H2) will also be silent ****IR spectroscopy measures absorption of infrared light by specific bonds, which vibrate. these vibrations cause changes in dipole moment of molecule that can be measured. symmetric bonds or molecules with atoms of same electronegativity don't show****

acid dissociation constant (Ka)

measures strength of acid in soln in dissociation of an acid HA (HA <> H+ + A-), the constant is given by Ka = [H+][A-] / [HA] pKa can be calculated as: pKa = -logKa more acidic molecules will have a smaller or even negative pKa & more basic molecules will have lalrger pKa acids w/ pKa below -2 are considered strong acids & weak organic acids often have pKa values btwn -2 & 20

sp2

merging 1 s orbital w/ 2 p orbitals > 3 sp2 orbitals formed. this is hybridization seen in alkenes. 3rd p orbital of each carbon is left unhybridized & this is the orbital that participates in the pi bond. 3 sp2 orbitals are oriented 120 degrees apart

sp3

merging 3 p orbitals & 1 s orbital forms sp3 orbital. all 4 point towards vertices of a tetrahedron to minimize repulsion w/ angle btwn bonds = 109.5 degrees this has 25% s character & 75% p character hybridization's accomplished by promoting 1 of the 2s electrons into 2pz orbital. this produces 4 valence orbitals, each w/ 1 electron which can be mathematically mixed to model hybrid orbitals in ethene, 2 sp2 hybridized orbitals will participate in C-H bonds & the other hybrid orbital will line up w/ the pi bond & form the sigma component of the C=C double bond

hydrocarbon w/ 1 carbon

methane

recrystallization

method for further purifying crystals in solution. in this process, dissolve product in minimum amt of hot solvent & let it recrystallize as it cools solvent chosen for this process should be 1 in which product is soluble only at high temps, so when soln cools, only desired product will recrystallize out of soln, excluding the impurities

leaving groups

molecular fragments that retain electrons after heterolysis the best leaving groups will be able to stabilize the extra electrons from heterolytic rxn -weak bases are more stable w/ an extra set of electrons & therefore make good leaving groups, such as conjugate bases of strong acids like I-, Br-, & Cl- leaving group ability can be augmented by resonance & inductive effects from electron withdrawing groups: these help delocalize & stabilize negative charges alkanes & hydrogen ion will almost never serve as leaving groups bc they form very reactive, strongly basic anions think of nucleophiles & leaving groups serving opposite functions. in substitution rxns, the weaker base (the leaving group) is replaced by the stronger base (the nucleophile)

newman projection

molecule is visualized along a line extending through a carbon-carbon bond axis

meso compound

molecule w/ chiral centers that has internal plane of symmetry > not optically active & overall achiral essentially molecular equivalent of a racemic mixture

chair conformation

most stable conformation of cyclohexane & minimizes all 3 types of strain **the hydrogen atoms that are perpendicular to the plane of the ring (sticking up or down) are called AXIAL & those parallel (sticking out) are called EQUATORIAL** the axial-equatorial orientations alternate around the ring **-if the wedge on C-1 is an axial group, the dash on C-2 will also be axial, the wedge on C-3 will be axial, etc.** **for substituted rings, the bulkiest group will favor the equatorial position to reduce nonbonded strain (flagpole interactions) w/ axial groups in molecule** in rings w/ more than 1 substituent, the preferred chair form is determined by LARGER group, which will prefer the equatorial position.

alcohol nomenclature

named by replacing -E at end of name of corresponding alkane with suffix -OL chain's numbered so carbon attached to hydroxyl group (-OH) gets the lowest possible number, even when there is a multiple bond present. hydroxyl group takes precedence over multiple bonds bc of the higher oxidation state of the carbon. if alcohol is not the highest-priority functional group, then it's named as a hydroxyl substituent (HYDROXY-) alcohols often referred to by their common names, rather than their IUPAC names. in this version, name of alkyl group is followed by the word alcohol, such as ETHYL ALCOHOL (rather than ETHANOL) & ISOPROPYL ALCOHOL (rather than 2-PROPANOL)

5. complete the name

names always begin w/ names of substituents in alphabetical order, w/ each substituent preceded by its number. prefixes like di-, tri-, & tetra- & n- & tert- are ignored while alphabetizing nonhyphenated roots that ARE part of the name such as iso, neo, or cyclo are part of the alphabetization numbers are separated from each other w/ commas & from words with hyphens finish name w/ name of backbone chain, including suffix for functional group of highest priority

imine formation

nitrogen & nitrogen based functional groups act as good nucleophiles due to lone pair of electrons on nitrogen, & react readily w/ electrophilic carbonyls of aldehydes & ketones in simplest case, ammonia adds to carbon atom & water is lost, producing an IMINE, a compound w/ N=C -bc a small molecule is lost during the formation of a bond btwn 2 molecules, this is an ex of a CONDENSATION RXN -bc nitrogen replaces the carbonyl oxygen, this is also an ex of a NUCLEOPHILIC SUBSTITUTION some common ammonia derivatives that react w/ aldehydes & ketones are HYDROXYLAMINE (H2N-OH), HYDRAZINE (H2N-NH2), & the SEMICARBAZIDE (H2N-NH-C(O)NH2). these form OXIMES, HYDRAZONES, & SEMICARBAZONES

amide vs amine

nitrogen atom bonded to one side of a carbonyl group are classified as amides. Amines are a basic functional group. Amines and carboxylic acids can combine in a condensation reaction to form amides

hydrocarbon w/ 9 carbons

nonane

oxidation reduction (redox) reactions

oxidation states of reactants change

4. assign a number to each substituent

pair the substituents that you have named to the corresponding #s in the parent chain multiple substituents of same type get both the di-, tri-, tetra- prefixes & also a carbon designation even if they're on the same carbon

phosphate

phosphoric acid okforms high energy bonds that carry energy in adenosine triphosphate (ATP) phosphoric acid (H3PO4) sometimes referred to as a PHOSPHATE GROUP or INORGANIC PHOSPHATE, denoated Pi -at physiological pH, ****inorganic phosphate includes molecules of both hydrogen phosphate (HPO4^2-) & dihydrogen phosphate (H2PO4-). **** in addition to energy carrying nucleotide phosphates, phosphorus is also found in backbone of DNA in PHOSPHODIESTER BONDS linking the sugar moieties of the nucleotides -when a ****new nucleotide is joined to growing strand of DNA by DNA polymerase, it releases an ester dimer of phosphate, referred to as PYROPHOSPHATE (P2O7^4-) denoted PPi.**** -the hydrolytic release of this molecule provides the energy for the formation of the new phosphodiester bond. ****pyrophosphate is unstable in aqueous soln & is hydrolyzed to form 2 molecules of inorganic phosphate****, which can then be recycled to form high energy bonds in ATP or for other purposes ****nucleotides, such as ATP, GTP, & those in DNA, are referred to as ORGANIC PHOSPHATES due to presence of phosphate group bonded to carbon containing molecule**** inorganic phosphate so useful for energy transfer biologically bc it carries very - charge, repulsion w/ other phosphates it's bonded to in nucleotide triphosphate increases energy of bond, & can also be resonance stabilized -energy released when phosphate or pyrophosphate is cleaved is quite high phosphoric acid is unique bc it has 3 acidic hydrogens, each w/ its own pKa. phosphoric acid most properly refers to form that predominates ins strongly acidic conditions, H3PO4-. In mildly acidic conditions, it loses proton to become dihydrogen phosphate H2PO4-. it will readily lose 2nd proton to become hydrogen phosphate, HPO4^2- in weakly basic solns. the form that exists in strongly basic solns is phosphate, PO4^3- -at physiological pH< dihydrogen phosphate & hydrogen phosphate predominate in nearly = proportions variety of pKa values that span nearly entire pH scale makes phosphates good buffers bc they can pick up or give off hydrogens depending on pH of soln

stereoselectivity

preference for the formation of one stereoisomer when several are possible occurs in rxns where 1 configuration of product is more readily formed due to product characteristics this occurs often bc diff products have diff traits which affect relative stability if there's more than 1 product, major product generally determined by diff in strain or stability btwn 2 molecules. products w/ conjugation are significantly more stable than those w/o

chemoselectivity

preferential reaction of 1 functional group in the presence of other functional groups which site is reactive site of a molecule depends on the type of chemistry that's occurring **a redox reagent will tend to act on highest priority functional group** **for a reaction involving nucleophiles & electrophiles, rxns also tend to occur @ highest priority functional group** the more oxidized the functional group, the more reactive it is in both nucleophile-electrophile & oxidation-reduction rxns nucleophile wants good electrophile w/ the more oxidized carbon (more electronegative groups around it) which experiences the larger partial + > carboxylic acids & their derivatives are 1st to be targeted by nucleophile, followed by aldehyde or ketone, followed by alcohol or amine **aldehydes generally more reactive toward nucleophiles than ketones bc they have less steric hindrance** carbonyl carbon has + polarity due to electronegativity of oxygen so it becomes an electrophilic target for nucleophiles

high performance liquid chromatography (HPLC)

previously called high PRESSURE liquid chromatography eluent is liquid & it travels through column of defined composition. there are variety of stationary phases that can be chosen depending on target molecule & quantity of material that needs to be purified. this is fairly similar to column chromatography bc the various compounds in soln will react differently w/ adsorbent material. small sample injected into column & separation occurs as it flows through. compounds pass through detector & are collected as solvent flows out of end of apparatus interface is similar to that used for GC bc entire process is computerized but uses liquid under pressure instead of gas. bc whole process is under computer control, sophisticated solvent gradients & temperature can be applied to column to help resolve various compounds in sample, hence higher performance of HPLC over regular column chromatography

oxidation of alcohols

primary alcohols can be oxidized to aldehydes by PYRIDINIUM CHLOROCHROMATE (PCC), a mild anhydrous oxidant -w/ other oxidizing agents, aldehydes are rapidly hydrated to form GEMINAL DIOLS (1,1-diols) which can be easily oxidized to carboxylic acids -oxidation of primary alcohols w/ strong oxidizing agent like chromium (VI) will produce a carboxylic acid. in the process, chromium (VI) is reduced to chromium (III) -common chromium containing oxidizing agent is sodium & potassium dichromate salts secondary alcohols can be oxidized to ketones by PCC or any stronger oxidizing agent tertiary alcohols can't be oxidized bc they're already as oxidized as they can be w/o breaking a carbon-carbon bond. -tertiary alcohols are oxidized w/ difficulty bc there is no hydrogen attached to the carbon w/ the hydroxyl group & oxidation requires removing a hydrogen so carbon can make another bond with oxygen -oxidation of tertiary alcohol will only happen in extreme conditions that cleave a carbon-carbon bond

Cahn-Ingold-Prelog priority rules

priority assigned based on the atom bonded to the double bonded carbons the higher the atomic #, the higher the priority if atomic #s are equal, priority is determined by next atoms outwards. priority determined by combination of atoms attached to these atoms **if there's a double bond, it's counted as 2 individual bonds to that atom**

enolization

process of interconverting from keto to enol tautomer is called ENOLIZATION, or more generally TAUTOMERIZATION. by extension, any aldehyde or ketone w/ a chiral alpha carbon will rapidly become a racemic mixture as the keto & enol forms interconvert, a phenomenon known as ALPHA-RACEMIZATION 1st step in base-catalyzed keto-enol tautomerization is formation of C- by removing proton from carbon that's alpha to carbonyl. normally this proton's not removable but allowed bc of electronegativity of carbonyl oxygen

quinones

produced from treatment of phenols w/ oxidizing agents **quinones are named by indicating the position of the carbonyl numerically & adding 'quinone' to the name of the parent phenol** ex: 1,4 benzoquinone due to conjugated ring system, these molecules are resonance-stabilized electrophiles these aren't necessarily aromatic bc they lack classic aromatic conjugated ring structure. some quinones do have aromatic ring, but this isn't always the case quinones serve as electron acceptors biochemically, specifically in the electron transport chain in both photosynthesis & aerobic respiration vitamin K1 is common name of quinone molecule also called PHYLLOQUINONE which is impt for photosynthesis & carboxylation of some clotting factors in blood vitamin K2 similarly corresponds to class of molecules called MENAQUINONES. these quinone molecules can be further oxidized to form class of molecules called hydroxyquinones w/ variable # of hydroxyl groups

hydrocarbon w/ 3 carbons

propane

affinity chromatography

protein of interest bound by creating a column w/ high affinity for that protein. this can be accomplished by coating beads w/ receptor that binds protein or specific antibody to the protein. in either case, protein is retained in column *****common stationary phase molecules include nickel, which is used in separation of genetically engineered proteins w/ histidine tags, antibodies or antigens, & enzyme substrate analogues, which mimic natural substrate for enzyme of interest***** once protein is retained in column, it can be ****eluted by washing column w/ free receptor (or target or antibody), which will compete w/ bead bound receptor & ultimately free protein from column****. eluents can also be created w/ varying pH or salinity level that disrupts bonds btwn ligand & protein of interest. only drawback of elution step is that recovered substance can be bound to eluent. if for ex, the eluent was an inhibitor of an enzyme, it could be difficult to remove

reduction

refers to decrease in oxidation state so a gain in electrons increasing # of bonds to hydrogen reduction of carbon occurs when bond btwn carbon atom & atom that's more electronegative than carbon is replaced by bond to atom that's less electronegative than carbon, usually means increasing # of bonds to hydrogen & decreasing # of bonds to other carbons, nitrogen, oxygen, or halides

relative configuration

relative config of chiral molecule is its configuration in relation to another chiral molecule (often through chemical interconversion) can use relative configuration to determine whether molecules are enantiomers, diastereomers, or the same molecule retained in a reaction if bonds of stereocenter aren't broken

conjugation

resonance delocalization of electrons occurs in molecules that have conjugated bonds conjugation requires alternating single & multiple bonds bc this pattern aligns a # of unhybridized p orbitals down the backbone of the molecule **all atoms involved in these bonds are either sp2 or sp hybridized & therefore have unhybridized p orbitals. when these p orbitals align, they can delocalize pi electrons through resonance, forming clouds of electron density above & below plane of molecule** -pi electrons delocalized through this p orbital system adds stability to the molecule in carbonyl containing compounds, conjugation can be established w/ the carbonyl group itself. alpha,beta unsaturated carbonyls (or ENONES) are common example this type of electron sharing makes for very stable compounds bc these compounds have multiple resonance structures. **this characteristic allows for stabilization of a + charge once the nucleophile has bonded, making these compound more susceptible to nucleophilic attack**

resonance structures

resonance structures are drawn as various transient forms of the molecule takes equilibrium. however, these forms aren't in any sort of equilibrium **electron density is distributed throughout, making the true form a hybrid of the resonance structures** **if the stability of various resonance forms differs, then true electron density favors the most stable form** **particular resonance structures can be favored bc they lack formal charges or form full octets on highly electronegative atoms, like oxygen & nitrogen** stabilization of + & - charges through induction & aromaticity can also favor certain resonance structures resonance structures differ in placement of electrons in hybridized p orbitals & require bond conjugation to delocalize electrons in a molecule

nonbonded strain (van der waals repulsions)

results when NONADJACENT atoms or groups compete for the same space nonbonded strain is dominant source of steric strain in FLAGPOLE INTERACTIONS of cyclohexane boat conformation to alleviate their strain, cycloalkanes attempt to adopt various nonpolanar conformations. -cyclobutane puckers into slight "V" shape -cyclopentane adopts envelope conformation -cyclohexane exists mainly in 3 conformations called the CHAIR, BOAT, & TWIST OR SKEW-BOAT FORMS

angle strain

results when bonded angles deviate from their ideal values by being stretched or compressed

torsional strain

results when cyclic molecules must assume conformations that have eclipsed or gauche interactions

retro aldol reaction

reverse of aldol condensation to push the rxn in a retro aldol drxn, aqueous base is added & heat is applied. the retro aldol rxn is useful for breaking bonds btwn the alpha & beta carbons of a carbonyl. this rxn is facilitated if the intermediate can be stabilized in the enolate form, just as in the forward rxn. by breaking bond btwn alpha & beta carbons of a carbonyl, can form 2 aldehydes, 2 ketones, or 1 aldehyde & 1 ketone

isomers

same molecular formula but diff chemical structure

chromatography

separates compounds based on how strongly they adhere to solid, or stationary, phase (how easily they come off into mobile phase) place sample onto solid medium called STATIONARY PHASE, or ADSORBENT. then, run MOBILE PHASE, usually a liquid (or gas in gas chromatography) through stationary phase depending on characteristics of substances in sample & polarity of mobile phase, it will adhere to stationary phase w/ differing strengths, causing diff substances to migrate at diff speeds -this is called PARTITIONING, & it represents an equilibrium btwn the 2 phases. diff compounds will have diff PARTITIONING COEFFICIENTS & will elute at diff rates. this results in separation w/in stationary phase, allowing us to isolate each substance individually diff media can be used as stationary phase, each 1 exploiting diff properties that allow us to separate out desired compound. on MCAT, property most commonly used is polarity -in TLC, silica gel is highly polar stationary phase -in column chromatography, size & charge both have role in how quickly compound moves through stationary phase chromatography is based on speed at which compounds move through media but we can also measure how far each substance travels in given amt of time (TLC) or how long it takes to elute (column or gas chromatography)

hydroxyquinone

share same ring & carbonyl backbone as quinones but differ by addition of 1 or more hydroxyl groups. many have biological activity & some are used in synthesis of medication bc of resonance, hydroxyquinones behave like quinones w/ electron donating groups, making these slightly less electrophilic (although still quite reactive) when naming these compounds, position of hydroxyl groups is indicated by a #, & the total # of hydroxyl groups if there is more than 1 is indicated by prefix, such as di- or tri- w/ the substituent name hydroxy-

thin layer chromatography

similar to paper chromatography, varying only in media used for stationary phase. for paper chromatography, medium is paper composed of cellulose. for TLC, thin layer of silica gel or alumina adherent to inert carrier sheet is used sample to separate is placed directly onto adsorbent. this is called SPOTTING. plate is then DEVELOPED, which involves placing adsorbent upright in developing chamber, usually a beaker w/ a lid or a wide mouthed jar. at bottom of jar is shallow pool of solvent, called the ELUENT. spots of sample must be above level of solvent or they will dissolve in solvent solvent creeps up plate by capillary action, carrying various compounds in sample w/ it. for TLC, silica gel is polar & hydrophilic while mobile phase is usually organic solvent of weak to moderate polarity, so it doesn't bind well to gel. bc of this, nonpolar compounds dissolve in organic solvent & move quickly as solvent moves up plate, whereas more polar molecules stick to the gel. thus, the more nonpolar the sample is, the further up the plate it will move spots of individual compounds usually white, so developed plate can be placed under UV light to show compounds that are UV-sensitive. iodine, phosphomolybdic acid, or vanillin can be used to stain the spots but this will destroy the compounds so they can't be recovered compounds generally identified using RETARDATION FACTOR (RF), which is relatively constant for particular compound in given solvent Rf = distance spot moved / distance solvent front moved

carboxylic acid physical properties

similar to those of aldehydes & ketones bc they contain carbonyl groups however, additional hydroxyl group permits carboxylic acids to hydrogen bond & provides another acidic hydrogen that can participate in rxns carboxylic acids are polar bc they contain carbonyl group & can also form hydrogen bonds bc they contain a hydrogen bonded to a very electronegative atom (in this case, the hydroxyl oxygen) their acidity is due to resonance stabilization & can be enhanced by addition of electronegative groups or greater ability to delocalize charge. carboxylic acids display particularly strong intermolecular attractions bc both the hydroxyl oxygen & carbonyl oxygen can participate in hydrogen bonding -as a result, carboxylic acids tend to form DIMERS: pairs of molecules connected by 2 hydrogen bonds. multiple hydrogen bonds elevate the boiling & melting points of carboxylic acids past those of corresponding alcohols. boiling points increase w/ increasing molecular weight

alkanes

simple hydrocarbon molecules w/ the formula CnH(2n+2) ends in -ANE

s orbital

spherical & symmetrical, centered around the nucleus

reverse phase chromatogrphy

stationary phase is nonpolar, so polar molecules move up plate quickly while nonpolar molecules stick more tightly to stationary phase

conformational isomers

stereoisomers also called conformers differ in rotation around single (sigma) bond of all isomers, conformational isomers are the most similar. they're the same molecule but @ diff points in their natural rotation around single (sigma) bonds conformational isomers arise from fact that varying degrees of rotation around single bonds can create diff levels of strain these conformations are easy to see when molecule is depicted in a NEWMAN PROJECTION conformational interconversion energy barriers are small & easily overcome @ room temperature but @ low temps if molecules don't possess sufficient energy to cross energy barrier, they may not rotate at all

configurational isomers

stereoisomers that can be interconverted only by breaking & reforming covalent bonds 2 categories of configurational isomers are ENANTIOMERS & DIASTEREOMERS. both can be considered OPTICAL ISOMERS bc the diff spatial arrangement of groups in these molecules affects the rotation of plane-polarized light

3. name the substituents

substituent name will be placed @ beginning of compound name as prefix, followed by the name of the longest chain only highest-priority functional group will determine suffix for compound & must be part of parent chain carbon chain substituents are named like alkanes, w/ the suffix -YL replacing -ANE. **the prefix n- simply indicates that this is "normal" or in other words, a straight chain alkane.** bc this prefix will not always be present, it's safe to assume alkane substituents will be normal unless otherwise specified if there are multiple substituents of the same type, we use the prefixes di-, tri-, tetra-, & so on. these prefixes included directly before the substituent's name

carboxylic acid reactions

synthesis of carboxylic acids nucleophilic acyl substitution amides esters: esterification anhydrides reduction decarboxylation saponification

hybridization

the mixing of several atomic orbitals to form the same total number of equivalent hybrid orbitals HYBRID ORBITALS are formed by mixing diff types of orbitals

1. identify the longest carbon chain containing the highest-order functional group

this is the PARENT CHAIN & will be used to determine root of name double & triple bonds btwn carbons must be considered when identifying highest-order functional group highest-order functional group has the most oxidized carbon & provides the suffix -the more oxidized a carbon, the higher priority it has in the molecule. **oxidation state increases w/ more bonds to HETEROATOMS & decreases w/ more bonds to hydrogen** **if there are 2 or more chains of equal length, the more substituted chain is parent chain**

eclipsed conformation

to convert from anti to gauche conformation, the molecule must pass through an ECLIPSED conformation in which the 2 largest groups are 120 degrees apart & overlap w/ the hydrogen atoms on the adjacent carbons when the 2 largest groups directly overlap each other w/ 0 degree separation, the molecule is TOTALLY ECLIPSED & in its highest-energy state totally eclipsed conformations are the least favorable energetically bc the 2 largest groups are SYNPERIPLANAR (in same plane on the same side)

sp

to form a triple bond, we need 2 of the p orbitals to form pi bonds & the 3rd p orbital will combine w/ the s orbital to form 2 sp orbitals these orbitals orient 180 degrees apart > linear structure in molecules w/ sp hybridized carbons the 2 pi bonds can be between the carbon & 1 other atom (forming triple bond) or btwn carbon & 2 diff atoms (forming 2 double bonds in a row). in both, molecule is linear about the sp hybridized carbon

NMR spectrum

typical NMR spectrum is a plot of frequency vs absorption of energy bc diff NMR spectrometers operate a diff magnetic field strengths, a standardized method of plotting the NMR spectrum has been adopted. the standardized method, which is the only 1 seen on MCAT, uses ****arbitrary variable called CHEMICAL SHIFT w/ units of PARTS PER MILLION (PPM) of spectrometer frequency**** -the chemical shifit is plotted on x axis & it increases toward the left (referred to as DOWNFIELD) to make sure that we know just how far downfield compounds are, we use ****TETRAMETHYLSILANE (TMS) as calibration standard to mark 0 ppm****. the signal for its ^1H atom is assigned chemical shift = 0. when counting peaks, make sure to skip the TMS peak NMR most commonly used to study ^1H nuclei (protons), although any atom possessing a nuclear spin (w/ an odd atomic number, odd mass number, or both) can be studied -MCAT only tests knowledge of ^1H-NMR

hydrocarbon w/ 11 carbons

undecane

fischer esterification

under acidic conditions, mixtures of carboxylic acids & alcohols condensing into esters esters can also be obtained from rxn of anhydrides w/ alcohols

(R) & (S) nomenclature

used for chiral (stereogenic) centers in molecules step 1: assign priority to the 4 substituents step 2: orient molecule so atom w/ lowest priority is @ back of molecule. if this is difficult, any time 2 groups are switched on a chiral carbon, the stereochemistry is inverted so can switch lowest priority group w/ group @ back of molecule. now we have changed molecule to opposite config, so remember to switch final answer (R to S or vice versa) step 3: draw circle from substituent #1 > 2> 3. can skip lowest priority group bc it goes into back of page. if circle is COUNTERCLOCKWISE, atom is S. if it's CLOCKWISE, it's R mnemonic: Right is R

(E) & (Z) nomenclature

used for compounds w/ polysubstituted double bonds to determine (E)/(Z) designation, start by identifying highest-priority substituent attached to each double-bonded carbon alkene is named (Z) if 2 highest-priority substituents on each carbon are on same side of double bond & (E) if they're on opposite side mnemonic: Z is "Z"ame side. E is "E"pposite side

fractional distillation

used to separate 2 liquids w/ similar BPs less than 25C apart fractionation column connects distillation flask to condenser. fractional column is column in which surface area is increased by inclusion of inert objects like glass beads or steel wool. as vapor rises up in column, it condenses on these surfaces & refluxes back down until rising heat causes it to evaporate again, only to condense again higher in column. each time condensate evaporates, vapor consists of higher proportion of compound w/ lower BP. by time top of column is reaches, only desired product drips down receiving flask

normal phase HPLC

used to separate nonpolar compounds consists of polar stationary phase & nonpolar mobile phase

reverse phase HPLC

used to separate polar compounds & consists of nonpolar stationary phase & polar mobile phase

vacuum distillation

used when we want to distill liquid w/ a BP over 150 degrees C. by using vacuum, we lower ambient pressure, thereby decreasing temp that liquid must reach in order to have sufficient vapor pressure to boil (bc liquids boil when their vapor pressure = ambient pressure). this allows us to distill compounds w/ higher BPs at lower temps so we don't degrade product *same setup as simple distillation but w/ a vacuum adaptor

column chromatography

uses entire column filled w/ silica or aluminum beads as adsorbent, allowing for much greater separation. gravity moves solvent & compounds down column. to speed up process, 1 can force solvent through column using gas pressure, a technique called flash column chromatography. in column chromatography, the solvent polarity can also be changed to help elute desired compound eventually, solvent drips out at end of column & diff fractions that leave column can be collected over time. each fraction will contain diff compounds after collection, solvent can be evaporated, leaving behind compounds of interest

Fischer projection

way to represent 3D molecules **horizontal lines indicate bonds that project out from the plane of the page (wedges)** **vertical lines indicate bonds going into plane of page (dashes)** point of intersection of lines represents a carbon atoms to determine config w/ Fischer projection, follow same (R)/(S) rule & make sure lowest priority group points into page **benefit of Fischer projection is lowest-priority group can be on top or bottom of molecule & still project into the page** another advantage is we can manipulate Fischer projections w/o changing the compound. rotating Fischer projection in plane of page by 90 degrees will invert stereochemistry of molecule by extension, interchanging any 2 pairs of substitutents will revert compound back to original stereochemistry rotating Fischer projection in plane of page by 180 degrees also retains stereochemistry of molecule

extraction

way to separate out desired product. transfer of dissolved compound (desired product) from starting solvent into a solvent in which the product is more soluble, leaving impurities behind in first solvent when performing extractions, 2 solvents have to be IMMISCIBLE, meaning they form 2 layers that don't mix. the 2 layers are temporarily mixed by shaking so solute can pass from 1 solvent to the other water is aqueous phase/layer & nonpolar layer is organic phase/layer -****compounds that can hydrogen bond will move easily into aqueous layer & compounds w/ only dipole dipole interactions are less likely to move into aqueous layer**** after 2 layers are mixed, they will separate on their own. in order to isolate 2 phases, use SEPARATORY FUNNEL where gravitational forces cause denser layer to sink to bottom of funnel, where it can be removed by turning stopcock at bottom after extraction, shake to remix & then extract. ****multiple extractions w/ fresh water more effective for obtaining the most product rather than a single extraction w/ a large volume of water**** ****once desired product has been isolated in solvent, can obtain product alone by evaporating solvent, usually by using a ROTARY EVAPORATOR (ROTOVAP)**** adding bases can help extract acid into aqueous phase bc anion formed will be more soluble in aqueous layer than original protonated acid bc it's charged. acids & bases dissolve more easily in solns w/ opposite acid-base characteristics

aldehydes & ketones w/ 1 equivalent of alcohol

when 1 equivalent of alcohol (the nucleophile in the rxn) is added to an aldehyde or ketone, the product is a HEMIACETAL or HEMIKETAL, respectively hemiacetals & hemiketals can be recognized by retention of hydroxyl group. this "halfway" step (hence the hemi- prefix) is the endpoint in basic conditions

aldehyde & ketones w/ 2 equivalents of alcohol

when 2 equivalents of alcohol are added to aldehydes & ketones, rxn proceeds to completion, resulting in formation of an ACETAL or KETAL this rxn proceeds by nucleophilic substitution rxns (SN1) & is catalyzed by anhydrous acid the hydroxyl group of hemiacetal or hemiketal is protonated under acidic conditions & lost as molecule of water. a carbocation is thus formed & another equivalent of acid attacks carbocation, resulting in formation of acetal or ketal acetals & ketals, which are comparatively inert, are frequently used as protecting groups for carbonyl functionalities

Lewis acids + bases

when Lewis acids & bases interact, they form COORDINATE COVALENT BONDS covalent bonds in which both electrons in the bond came from same starting atom (the Lewis base)

saponification

when long chain carboxylic acids react w/ sodium or potassium hydroxide, a salt is formed this process called SAPONIFICATION occurs by mixing fatty acids w/ lye (sodium or potassium hydroxide), resulting in formation of a slat that we know as SOAP & a glycerol -soap is a SALT of a carboxylate anion w/ a LONG hydrocarbon tail subsequent acidification of the soap regenerates the fatty acids soaps can solvate nonpolar organic compounds in aqueous solns bc they contain both a nonpolar tail & a polar carboxylate head when placed in aqueous solution, soap molecules arrange themselves into spherical structures called micelles. polar heads face outward, where they can be solvated by water, & the nonpolar hydrocarbon chains are oriented toward inside of sphere, protected from solvent. nonpolar molecules, such as grease, dissolve in the hydrocarbon interior of the spherical micelle. the micelle as a whole then dissolves in water due to polarity of its exterior surface

sigma bond

when molecular orbital is formed by head to head or tail to tail overlap can be formed by head to head overlap of 2 s orbitals, 2 p orbitals, 1 s & 1 p orbital, or hybridized orbitals electron density is btwn the 2 nuclei of the bonding atoms all SINGLE BONDS are sigma bonds, accommodating 2 electrons

distillation

when product is liquid that's soluble in solvent, use distillation that ****takes advantage of diff in boiling points to separate 2 liquids by evaporation & condensation**** ****liquid w/ lower boiling point will vaporize first & the vapors will rise up distillation column to condense in water-cooled condenser. this CONDENSATE then drips down into vessel. end product is called DISTILLATE.**** the heating temp is kept low so liquid w/ higher BP will not be able to boil & will remain liquid in original container SIMPLE DISTILLATION is least complex version of distillation & proceeds just as described -should only be used to separate liquids that boil below 150 degrees & have at least a 25 degree C diff in boiling points -these restrictions prevent temp from becoming so high that compounds degrade & provide large enough diff in BPs that 2nd compound won't accidentally boil off in distillate -apparatus for this technique consists of a DISTILLING FLASK containing combined liquid soln, a DISTILLATION COLUMN consisting of thermometer & CONDENSER, & a RECEIVING FLASK to collect the distillate -****sometimes additional equipment such as boiling chip, ebulliator, or magnetic stirrer will be introduced to break surface tension & prevent superheating****