MCAT ExamKrackers Organic Chemistry Notes
MCAT ExamKrackers Organic Chemistry Notes
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Date Created: 01/30/14
EXAMKRACKERS AUDIO OSMOSIS ORGANIC CHEMISTRY Lewis Dot Structures 0 Count total number of valence e for all 0 Two electronsbond 0 Arrange remaining around atoms to satisfy around octet rule Breaking octet rule 0 Atoms with more than octet of electrons must come from third period on periodic table since vacant d orbitals are required 0 Sulfur phosphorus o Boron beryllium may contain less than an octet Valence number of bonds an atom normally makes 0 Carbon tetravalent o Nitrogentrivalent 0 Oxygen divalent o Halogens monovalent Formal charge number of electrons on neutral atom minus how many electrons that atom has in the Lewis structure Fischer projection vertical lines are directed into plane of the page Dashed lines go into page Solid wedges come out of the page Newman projection staring down length of bond typically between 2 carbons Amides carbonyl compound 0 Bonded to a nitrogen Amine nitrogen bonded to carbons andor nitrogens Gemdihalide a ccompound with 2 halogens attached to the same carbon Single halogens attached to adjacent carbons vicdihalide Alcohol that has donated a proton alkoxide ion Carbon triple bonded to nitrogen nitrile Carboncarbon double bond attached to something else vinyl NO nitroso NO2 nitro Meth eth prop but pent hex hept oct non dec Npropyl and nbutyl are just NORMAL straight chains with 34 carbons Secbutyl and tertbutyl and both refer to first carbon on chain 0 Sec stands for secondary as in the first carbon on the chain is secondary o Tert stands for tertiary meaning attached to 3 other carbons Isobutyl shaped like a T with first carbona s primary Isopropyl shaped like a T with first carbon as secondary To name look for longest carbon chain with most substituents Carbon with double or triple bonds should get lowest number possible Order substituents alphabetically ignoring number prefixes Electrons are at their lowest energy level when they are closest to the nuclei Bond is formed when a pair of electrons can lower their energy by positioning themselves between the two nuclei Sigma bond electrons spend the msot time between the nuclei Pi bond electrons must occupy space above and beyond sigma bond because there is no room between the nuclei Sulfurgt phosphorusgt and silicon are highly unlikely to form double and triple bonds in this order Electrons in pi bond must have higher energy than sigma electrons Pi bond is more reactive than sigma bon Overall bond length of a double bond is shorter than a single bond and bond strentth is greater Bond strength and length are inversely related Orbital in s subshell has lower energy than orbital in p subshell Neutral carbon has 4 valance electrons 2 in s subshell and l in p subshell 0 Higher energy p orbitals combine with lower energy s orbitals combine to form a molecular orbital between the two Hybridized orbitals on oxygen in water sp3 Hydrogens in water s because hydrogen has only 1 valence electron 0 Carbon in 2 single bonds and 1 double bond sp2 Sp2 120 degrees Sp3 1095 degrees Lone pairs and ring structures can deform angles slightly Water bonds 1045 degree angles instead of 1095 expected angle Sp linear Sp2 trigonal planar Sp3 tetrahedralpyramidal or bent o Sp3 of ammonia pyramidal o Sp3 of methane tetrahedral Resonance occurs with delocalized electrons Molecule does not resonate back and foth o Weighted average of resonance structures 0 Actual benzene has no double bonds but they are partial double bonded in character as in the single bonds are shorter and stronger in character but still considered single bonds 0 Resonance stabilizes a molecule Actual molecule is most stable than any of the resonance structures 4 rules for resonance 0 Atoms must not be moved only electrons 0 Number of unpaired ele ctrons must remain constant 0 Resonance atoms must lie ins ame geometric plane This is why benzene is a at molecule 0 Only proper lewis structures can be resonance structures Ring structures must satisfy Huckel s rule ONLY RING STRUCTURES Even though most molecules are neutral they can have separation of charge 0 Center of charge of negatively charged electrons may not COINCIDE with center of charge of positively charged nuclei 0 A dipole moment is created when this happens Dipole moment is pointing fromn center of positive to center of negative charge 0 Mu d between centers of chargetotal charge q of either center NOT CHARGE OF BOTH CENTERS Strongest kind of dipoledipole force is hydrogen bond 0 Hydrogen bonds are still far WEAKER bonds 0 Dipole moment is a vector 0 Dipole moments of bond may add up to 0 and thus cancel Thus a molecule with polar bonds dipole moments may not be polar overall Momentary dipoles only forces that cause nonpolar molecules to be attracted to one another 0 London Dispersion forces 0 Van der Waals forces I This may also refer to ALL types of dipole forces I Must look at context in which it is used 0 O Iso same Isomers have same molecular formula but are not same compound Newman projection with anti gauche eclipsed 0 Anti has two largest groups as far as possible as possible 0 Gauche groups exactly opposite are NOT the biggest groups Different compounds with same molecular formula are isomers If isomers have different bondbond connections they are structural isomers 0 Two dichlorobutanes but one has both halogens attached to first carbon whereas the other has one attached to each carbon 0 Obviously same molecular formula but different connections 0 Have different molecular and physical properties Chirality almost always have 4 different substituents attached Absolute configurations 0 Number substituents from highest to lowest priority based upon atomic weight o Counterclockwise S o Clockwise R o If one carbon is double bonded to an oxygen it is considered to be bonded to two oxygens for the purpose of priority assignment Relative configuration requires comparison of 2 chiral molecules 0 If they have same relative configuration it means similar substituents are in same place in terms of their chiral centers 0 Relevant in terms of snl and sn2 reactions in which half of the configurations are retained and completely inverted respectively Chiral compounds rotate plane polarized light 0 When photon strikes a molecule it refracts rotating the electric field When same photon strikes mirror image it rotates back exactly the same distance Mirror image cancels out the rotation Achiral molecules are their own mirror image and thus mirror images cannot be separated from compound so these never have opportunity to rotate planepolarized light Enantiomers rotate in same degree but in same directions Clockwise d Counterclockwise both of tehse l are called observed rotation 0 Specific rotation observed rotation with parameters such as concentration etc Light is an electromagnetic wave where each photon creates an electric field and a magnetic field perpendicular to each other and to direction of photon movement Enantiomers and diastereomers are the two types of stereoisomers Enantiomers have SAME physical amp chemical properties except way they rotate plane polarized light and the way they react to other chiral compounds Racemic mixture mixture of enantiomers Resolution separating a racemic mixtures Cistrans isomers are diastereomers Occurs when two atoms are connected by a bond that cannot rotate about its axis and 2 carbons have an identical substituent Cis isomers have dipole moments HIGHER BOILING POINTS HIGHER HEATS OF COMBUSTION Trans isomers more symmetrical AND TEND TO HAVE HIGH MELTING POINTS E HIGHEST PRIORITY ATOMS ARE ON DIFFERENT SIDES Z HIGHEST PRIORITY ATOMS ARE ON SAME SIDE In labeling EZ divide the double bond vertically and label and then compare the highest priority groups of each one horizontally Meso compounds more than one chiral carbon and an internal plane of symmetry 0 Cannot have enantiomers Methyl carbon is attached to 3 hydrogens Physical properties of alkanes o The more carbons the higher the meltingboiling point 0 True waxes are ether 0 Branching increases the melting point but decrease the boiling point I This is because breanching chains are more compact which weakens van der Waals forces and lowers the boiling point while same compound structure allows same alkane to pack easily and form a solid 0 Alkanes are less dense than water Specific gravity 07 insoluble in water Think of oil spill 0 When alkane is attached to polar group the polarity and solubility go down Ring strain is 0 for cyclohexane OOO OOO Effects of ring strain can be seen using a bomb calorimeter With ring strain will exhibit a high heat of combustion per CH2 group when placed here Ring strain gives molecule higher energyCH2 group Cyclohexane o Exists as several conformers same molecular formula and connectivityb ut different orientation 0 Conformers are chair half chair twist and boat 0 Important ones to know are chair and boat 0 Twist is lower in energy than boat 0 Boat is in higher energy than chair conformation o For hydrogen neither axialequatorial is favored from an energy position Alkanes are not very reactive 0 Do not react with strong acidsbases o If add enough energy they will react violently with oxygen Combustion a reaction with oxygen Energy of activation of combustion with alkanes is very high but once the reaction begins the reaction is exothermic enough to be selfperpetuating 0 Products are water and carbon dioxide 0 Radical reaction 0 Exothermic high activation energy 12 does not typically react with alkanes to form alkyl halides Halogenation requires heat or light to initiate reaction 0 Chain reaction I Halogen molecule alone will not react with alkane Halogen ishomolytically cleaved this creates 2 radicals I The unpaired radical is neutral but is highly reactive and is very unstable I Never exists in high concentration I Radical reaction initiation propagation termination 0 Net reaction is sum of initiation and propagation I l halogen l alkane 1 alkyl halide 1 hydrogen halide 0 Termination steps are important when there are few reactants available 0 Usually results in mixed products like multi halogenated alkyol halides and alkyl halides halogenated at different carbons o Exothermic 0 Reactivity of alkyl radicals is same as reactivity of carbocations Methyl are most reactive o Iodine is least reactive halogen and most selective o Bromine prefers to add tertiary while uorine reacts with any primary or secondary or tertiary Alkenes 0 Pi bond occupies space above and below sigma bond 0 Inductively electronwithdrawing 0 Greater molecular weight higher the boiling point and density Slightly more soluble in water than alknes not very soluble in water 0 Typically oat on water as they are less dense o Easily dissolve in solvents with low polarity Synthesizing alkenes 0 Via elimination reaction 0 E1 or E2 mechanism 0 El occurs in two steps and E2 occurs in one step E2 reaction 0 E2 dehydrohalogenation 0 Strong bulky base is added to alkyl halide I Base is too bulky to act as nucleophile I As a base it must accept a proton Dehydration of alcohol 0 El reaction IMPORTANT Add a hot concentrated acid to an alcohol Has a carbocation intermediate Leaves an alkene Acid is actually a catalyst here 0 Maj or product is most substituted alkene Catalytic hydrogenation 0 Two hydrogens are added one to each carbon in double bond 0 SYN addition hydrogens add to same side of alkene o Erythro similar functional groups are on same side in a fischer projection OOOOO Threo func gropus on different sides on Fischer project Catalyst is heterogeneous Exothermic reaction CATALYST DOES NOT CHANGE THERMODYNAMICS OFA REACTIONENDOEXO o Hydrogenation of an alkyne makes an alkene Oxidation of an alkene 0 Adding ozone O3 which is high energy 0 Cleaves through double bond leaving 2 separate molecules with carbonyl groups 0 Permanganate with HEAT also splits alkene in two I If aldehydes is formed it is oxidized to carboxylic acid I Without heat permanganate followed by a base makes a glycol in hydroxylation o Glycol diol o OsO4 also produces a glycol when added to alkene Electrophilic addition 0 Electrophile will usually have a positive or partial positive charge 0 Add to alknees by attacking pi bond electron cloud 0 Add via Markovnikov s rule I Electrophiles hydrogen ions add to elast substituted carbon of alkene this is because it forms the most stable carbocation 0 Whenever a carbocation is formed a skeleton rearrangement may occur Peroxides HBr will add antimarkovnikov where hydrogen adds to most substituted carbon 0 Radical reaction where bromine radical adds before the hydrogen 0 Occurs with HBr not HCl not HI not HF Adding water to an alkene o Reversing dehydration of an alcohol 0 Cold dilute acid cause addition of water to an alkene I Electrophilic addition 0 Carbocation is formed hydroxyl group is added and alcohol is formed 0 MARKOVNIKOV ADDITION I Rearrangement must be possible Oxymercuration o Prevents carbonskeletal rearrangement during hydration o Organiometallic compound bonds to both doublebonded carbons 0 Water attacks from opposite side in an anti addition 0 Forms an alcohol 0 Alcohol may also be used as the solvent in this reaction Hydrating alkene with anti Markovnikov addition 0 Hydroboration BH3 and then peroxides o REMEMBER PEROXIDES CAUSE ANTIMARKOVNIKOV Halogenation of an alkene o Electrophilic 0 As they are more reactive alkenes do not need to create a readical in order to make them react with halogen 0 Anti addition 0 One halogen adds to each but on opposite sides Benzene is a at sixcarbon ring 0 Bonds have only partial doublebond character as pi electrons are delocalized around the ring 0 Undergoes electrophilic substitution not addition I Addition would destroy its resonance leading to a more unstable molecule and such reactions are unlikely to occur Ortho on either side directly Meta two carbons away Para directly across the ring from the substituent If substituent is electronwithdrawing it deactivates and directs next substituent to add at meta position I Oxygens withdraw electrons via double bonds I Nitrogens with 4 bonds they withdraw electrons I Halogens are actually electron withdrawing but NOT meta directed OOOO OOOO I Carbonyls nitriles Cyanide o If it is electrondonating it activates ring and directs to add ortho or para I Halogens are the exception here I Oxygens donate electrons via single bonds I Nitrogens with only 3 bonds donate electrons I Alkyl groups are electron donating I Benzene SNl Occurs in 2 steps First step is the slow step Usually alkyl halide is tertiary for no backside attack Halogen acts as the leaving group and a small nucleophile bonds to the carbocation Rate depends solely on the concentration of the substrate alkyl halide Carbocation attens out and nucleophile can add to either side If it were chiral product would be a racemic mixture Works best in polar solvents which would STABILIZE THE CARBOCATION Does not occur often with secondary I Carbocations are too unstable Skeletal carbocation rearrangement is possible Snl and El usually occur together to form mixed products 0 OOOOOOOOO O Sn2 Occurs in 1 step Alkyl group is NOT bulky Nucleophile is a nonbulky strong base Halogen is dislodged after the nucleophile comes in Inversion of relative configuration occurs Rate depends upon nucleophile and the substrate Requires primary secondary carbon as substrate 0 If base is too strong and substratebase is sterically hindred an e2 reaction will occur Nucleophilicity 0 Base bonds to a proton and a nucleophile bonds to a carbon 0 Good base is often a good nucleophile I Base is always a better nucleophile than its conjugate acid Less bulkiness in the base nucleophile Negative chargeamppolarizability nucleophile Electronegativitiy reduces nucleophilicity o Nucleophilicity increases going down and to the left on the periodic table Nucleophile and 5 S s o Sn2 requires strong nucleophile whereas it is unimportant in snl o Substrate tertiary snl and rest sn2 o Solvent polar solvent increase rate of snl by stabilizing carbocation but inhibit sn2 by stabilizing nucleophile o Speed sn2 depends on nucleophile and substrate whereas snl depends only on substrate 0 Stereochemistry snl racemic and sn2 inversion o Skeleton in sn2 no carbocation rearrangement as there is no carbocation Alcohol organic compounds containing a hydroxyl group CO bond is longer than OH bond Bond angle is closer to 1095 degree angle due to bulk of alkyl group Lower molecular weight alcohols are miscible with water because alcohol can hydrogen bond and are also less dense than water Boiling points decrease with branching Alcohols are very weak acids weaker than water in most cases Primary alcohols are most acidic followed by secondary then tertiary Alkyl group in alcohol is electron donating Phenol is benzene with a hydroxyl group Conjugate base of alcohol alkoxide ion We can synthesize alcohol by adding Grignard reagent to a carbonyl group Grignard is organometallic compound Metal has a partial positive charge because metals like to lose electrons leaving alkyl group with negatively charged OOO OOOOOOO carbon Negative charge thus makes a nice nucleophile Grignard is nucleophile attacking carbonyl carbon Oxygen is protonated in an acid bath afterwards Reduce ketonealdehydes to make alcohol via NaBH4 and LiAlH4 These two are salts that make ions when placed in water Both are eager to donate a hydride ion H Acid bath protonates oxygen afterwards o NaBH4 only reduces to primary and secondary alcohols o LiAlH4 will reduce esters and acetates to alcohol as well Thus stronger reducing reagent Alcohol can be oxidized to make ketone aldehydes or carboxylic acid Primary oxidizes to aldehydes or carboxylic acid Secondary oxidizes to ketone Hydroxyl group by itself is a terrible leaving group If we add acid halide to alcohol it protonates hydroxyl group and halide acts as nucleophile 0 Use SOCl2 as halide Ether polar aprotic solvent with low reactivity and dissolves a wide range of solvents without reacting When adding hydrogen halide ether is split Epoxide reactive ether in a ring similar to a triangle Reactive because it has much angle strain Order of acidity weakest to strongest alkane alkene H2 NH3 alkyne aldehydes alcohol water carboxylic acid Carbonyls pi electrons are pulled towards oxygen Oxygen might even accept one pair of the electrons and take on a negative charge Carbonyl carbon has a partial positive charge Carbonyl carbon makes 3 sigma bonds and is sp2 hybridized Compound is at at carbonyl carbon Aldehydes similar chemistry to ketones Simplest one is formaldehyde methanol Simplest ketone is acetone or 2 propanone Higher boiling points than similar weight ethers but lower boiling points than alcohols Good solvents for alcohols and means short chain aldehydesketones are soluble in water Aldehydes and ketones are susceptible to Nucleophilic attack Like to undergo Nucleophilic addition because they don t have good leaving groups May also behave as a BronstedLowry acid They donate the alpha hydrogen When conjugate base is stabilized acid gets stronger Oxygen in carbonyl is willing to take on an electron from the carbonyl bond Stabilized by resonance Aldehydes and ketones are weaker acids than alcohol Tautomers structural isomers where a proton has shifted Exist in equilibrium These are NOT resonance structures Tautomerizatoin is reaction with equilibrium favoring aldehydesketone Aldehydesketone in alcohol intermediate compound is hemiacetal or hemiketal Catalyzed by acid or base Can take it one step further by adding another equivalent of alcohol to form an acetal or ketal Can only be catalyzed by acid not base because acid creates water as the leaving group We can reverse this reaction just by adding acid Germinal diol carbonyl carbon has oxygen replaced by two hydroxyl groups Aldol condensation aldehydesketone reacts with itself and behaves both as acid and as Nucleophilic addition substrate Can be catalyzed by acidbase Alpha hydrogen is removed forming negatively charged alpha carbon on enolate ion and this attacks carbonyl on other aldehydesketone Aldol is then formed in the end This much is called aldol addition The condensation part a second alpha hydrogen is removed with hydroxyl group Conjugation double bonds separated by just one single bond More stable than isolated double bond systems A double bond between alpha and beta carbon of carbonyl is conjugated Here electrophile may add to carbonyl oxygen Following with nucleophile that adds to beta carbon Carboxylic acids common names formic acetic and benzoic acid 0 Strong organic acids but weak compared to strong inorganic acids Weaker than hydronium ion for instance 0 Spreading negative charge over a larger area always stabilizes Follow same meltingboiling point trends as hydrocarbons with much higher melting and boiling points due to hydrogen bonding Chains with 8 or more carbons are generally solid Carboxylic acids like to undergo Nucleophilic substitution True for derivates of these as well Add PCl3 PCl5 or SOCl2 to carboxylic acid get Nucleophilic substitution Acid chloride is left behind Called an acyl chloride and donates an alpha hydrogen Acid chloride is more acidic than an aldehyde 0 Chloride ion is a good leaving group 0 Alcohol acid chloride ester 0 Carboxylate acid chloride anhydride Amines ammonia derivatives with one or more alkyl or aryl groups bound to hydrogen Ammonia primary and secondary amines form hydrogen bonds Hydrogen bonds formed by amines are not as strong as those formed by alcohols Act as nucleophile or as lewis base Electron donating groups strengthen basicity of amines Nitrogen is willing to make a fourth bond by taking on a positive charge 0 Like to be nucleophiles 0 Add to carbonyl carbon in presence of an acid 0 Amine attacks carbonyl carbon but nal result is complete replacement of carbonyl oxygen with nitrogen Product is called an imine o Amine can react with any of carboxylic acid derivatives to create an amide which is an amine attached to a carbonyl 0 Acid chlorides are most reactive then followed by anhydride then ester then amide Amide is most stable of them all Alkyl halide will react with ammonia to make primary amine Nitriles carbon is partially positive Can be hydrolyzed in acid to give a carboxylic acid Can be reduced to give amines Fatty acids long chained carboxylic acids Be able to draw structure of an amino acid Alpha amino acids are used to make proteins Nearly all organisms use same 20 alpha amino acids 0 10 of common amino acids are essential to humans Two amino acids attached by one peptide bond dipeptide Isoelectric point of amino acid when amino acid starts with negatively charged carboxylic acid and positive amine zwitterions Four characteristics dipolar creates high melting point water solubility large dipole moments and makes amino acid less acidic than most carboxylic aids but less basic than most amines Isoelectric point is pH at which this amino acid exists as a zwitterion Carbohydrates are a one to one ratio of carbon to hydrogen Glucose is a hexose Makes glycogen starch cellulose and chitin Plants store glucose as starch Plant cell walls are made of cellulose Beta linkages in cellulose and chitin Alpha linkages in others Humans absorb only D glucose NMR protonNMR usually on the MCAT Uses constant frequency photon source and changes magnetic field til resonance is detected If no electrons around nucleus all protons would exhibit resonance at same field strength Protons shielded from external mag Field by electrons require a stronger external magnetic field to exhibit resonance 0 Electron withdrawing groups deshield protons allowing them to resonate at lower field strength Numbers increase to the left Larger numbers indicate a weaker magnetic field strength To left is called downfield Carbonyl proton has peak at around 95 ppm IMPORTANT o Spinspin splitting occurs when neighboring hydrogens that are stereochemically different from each other I such hydrogens are enantiotropic to each other Each peak splits in same number of peaks as non enantiotropic neighbors plus 1 Group of peaks with more hydrogens has greater total area under the peak Horizontal line called integral trace can be drawn at spectrum and will rise and stay at new height each time it reaches top of new peak and extent it rises is proportional to this amount of hydrogen A rise of 2 represents twice as many hydrogens as a rise of 1 IR spectroscopy infrared Perpendicularly oriented constantly changing magnetic field 0 Elastic component tends to increase frequency 0 Carbonyls register strongly Deep sharp dip at 1700 cm l which is unit called wavenumber Number of waves in each centimeter Alcohols are at 32003600 with very broad peaks Fingerprint region each compound has unique IR spectrum which is between 6001400 No polar bonds make weaker signals Chromatography resolution of a mixture by passing it over a surface that adsorbs compound in mixture at different rates Moving phase and stationary phase Stationary phase is the surface and moving is some type of solution As moving phase moves over stationary compounds with greater affinity for stationary move more slowly More polar have greater affinity for stationary phase In column chromatography solution with mixture is dripped down a column of glass beads Paper chromatography know it Thin layer chromatography Gas chromatography mixture dissolved in heated carrier gas Results recorded as peaks Distillation separation based upon boiling points Unless azeotrope boiling point of mixture is same as boiling point of compound in mixture with lowest boiling point Poured into condensing ask Should be done slowly Crystallization crystals tend to form from pure substances Mixture to be purified is melted and crystallized many times Extraction based upon solubilities Nonpolar layer and aqueous layer Nonpolar layer usually contains mixture Acid is added and apparatus with both layers is shaken vigorously Acid protonates mixture in nonpolar mixture Protonated bases settle out in aqueous which is drawn off Next weak base is added and shaken Weak base Deprotonates strong acids which settle in aqueous and are drawn off Strong base is added and apparatus is shaken Deprotonates weak acids which then also settle out in aqueous solution
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