MCAT Organic Chemistry Review Materials
MCAT Organic Chemistry Review Materials
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Alcohols All alcohols undergo hydrogen bonding Because they undergo hydrogen bonding alcohols tend to have higher boiling points than alkanes or alkenes of similar molecular weight Also because of their hydrogen bonding small sized alcohols with carbon chains of 3 carbons or fewer are soluble in water Alcohols can lose a hydrogen ion from the OH group attached to their carbon chain That s another way of saying that alcohols can act as acids You should know that some alcohols are more acidic than others In order to tell which alcohol is more acidic look at the alcohol and see whether it s a primary secondary or tertiary alcohol Then remember this when it comes to alcohol the order of acidity is primary more than secondary and secondary more than tertiary Alcohols can lose a whole molecule of water An alcohol can lose its OH group plus another atom of hydrogen and that means it s losing a molecule of H20 When an alcohol or any other molecule loses some molecule of H20 we say it s been dehydrated When alcohols undergo dehydration they formed alkenes Some alcohols are dehydrated more readily than others The order in which alcohols are willing to give up water and become an alkene is just the opposite of the order of their willingness to give up hydrogen So when talking about how willing an alcohol is to be dehydrated remember this order tertiary more than secondary and secondary more than primary Alcohols can lose an H2 molecule and when they do they re said to be oxidized When an alcohol molecule loses H2 and is therefore oxidized it ends up with the double bonded oxygen Just where that double bonded oxygen will be depends on whether the alcohol was a primary secondary or tertiary alcohol When oxidized primary alcohols become aldehydes and secondary alcohols become ketones Remember that the common oxidizing agents used are KMNO4 and K2CR207 You should know that it s hard to oxidize a tertiary alcohol When a tertiary alcohol is subjected to oxidation a carbon and hydrogen are lost The resulting ketone has a carbon chain that is shorter by one carbon than the original alcohol An alcohol can have its OH replaced by a halide like chlorine bromine or iodine If the alcohol is a primary alcohol the halide goes right on to the carbon that had the OH group attached to it This is called a substitution reaction This is a one step process in which the halide knocks off the leading group in the rate determining step A different reaction occurs with tertiary alcohols This is a two step process which leads to the formation of a carbocation in the rate determining step Sometimes rearrangement occurs when a secondary alcohol is halogenated to form a more stable carbocation Both reactions are known as substitution reactions because chlorine substitutes for an OH group So when do we use SN1 and SN2 SN1 favors tertiary alcohols while SN2 is most likely to occur with primary alcohols Secondary alcohols use either mechanisms but generally favor SN1 The only other things you need to know about substitution reactions is that for SN1 the rate depends only on the concentration of the alcohol while the rate of SN2 depends on concentration of both the alcohol and the halide Know also that an inversion occurs during SN2 and rearrangement often occurs during SN1 Amino Acids Another important derivative of ammonia is the amino acid An amino acid is basically a carboxylic acid with an amino group attached somewhere on the carbon chain Amino acids are important because they form proteins A protein is a chain of amino acids linked together You need to know how two amino acids link themselves together They do this by linking the carboxyl carbon of one amino acid to the nitrogen of another and in the process a molecule of water is lost The link between two amino acids is called a peptide bond Amino acids can link together with peptide bonds to form very long chains called polypeptide chains or proteins We said that each peptide bond involves the removal of one molecule of water Now if we started with a protein and wanted to get amino acids out of it we have to break the peptide bonds To do that we would have to put in a molecule of water There are about 20 different amino acids that are important in building proteins You should be somewhat familiar with them So listen to these names but don t try to memorize them glycine alanine valine leucine isoleucine phenylalanine methionine aspartic acid asparagine glutamic acid glutamine lysine arginine histidine serine threonine tyrosine tryptophan cysteine and proline When you look at an amino acid you ll see that the carboxylic acid group and the NH3 group are attached to a carbon atom called the alpha carbon This means that most biologically significant amino acids are alpha amino acids The amino acid proline is not considered an alpha amino acid That is because its amino group is attached not only to the alpha carbon but also to another carbon to form a ring called an imino ring So proline is an exception to that rule In most alpha amino acids the alpha carbon is a chiral center In other words the alpha carbon has four different things bonded to it The carboxyl group an amino group a hydrogen and a side chain This means the molecule is chiral which means that it would be optically active and it will rotate the plane of polarized light Glycine is an exception In the Glycine molecule the side chain is just another hydrogen atom So glycine s alpha carbon does not have four different things bonded to it It has a carboxyl group an amino group a hydrogen and another hydrogen atom That s why glycine is not optically active and it does not rotate the plane of polarized light Since amino acids have both a carboxylic acid group which tends to give up a hydrogen ion and an imino which tends to take up a hydrogen ion they can end up with both a negative charge on the carboxyl group and a positive charge on the imino group If we take an amino acid and put it in a very acidic environment the amino group will end up taking on a hydrogen ion and it will be positively charged But the carboxyl group may not give up its hydrogen ion in such an acidic environment And so it may not be negatively charged In a very acidic environment therefore an amino acid tends to have a positive charge at the imino group but it doesn t have a negative at the carboxyl group On the other hand if we take an amino acid and put it in a very basic environment the carboxyl group will end up giving away a hydrogen ion and it will be negatively charged But the imino group may not take on a hydrogen ion and it may be neutral In a very basic environment therefore an amino acid tends to have a negative charge at the carboxyl group but it doesn t have a positive at the imino group When the surrounding pH is low the amino acid tends to be positively charged because the imino group takes up a hydrogen ion When the surrounding pH is high the amino acid tends to be negatively charged because the carboxyl group gives up a hydrogen ion If the pH is not too high and not too low then the amino acid has both have a positive and negative charge It s a dipolar ion That pH at which an amino acid is balanced so that the carboxyl group is negatively charged and the imino group is positively charged is called the isoelectric point Each amino acid has its own isoelectric point The isoelectric point is the pH at which the amino acid is a dipolar ion In some amino acids the side chain has a tendency to give up a hydrogen ion Those amino acids are called acidic amino acids It also happens that in some amino acids the side chain has a tendency to take up a hydrogen ion Those amino acids are called basic amino acids So when we say an amino acid is basic it means two things It means that its side chain has a group on it that tends to take up a hydrogen ion It also means that at pH 70 or lower its side chain will be positively charged because it has taken up a hydrogen ion When we say an amino acid is acidic that means two things It means that its side chain has a group on it that tends to give up a hydrogen ion and it also means that at pH 7 0 or higher its side chain will be negatively charged because it has given up a hydrogen ion If an amino acid s side chain is charged negatively or positively at neutral pH it is called hydrophilic That is because its charge allows it to dissolve in water So remember that acidic and basic amino acids are hydrophilic which means they can dissolve easily in W21t I39 It also happens that some amino acids are polar molecules even though their side chains are not charged Since any polar molecule is hydrophilic a polar amino acid is hydrophilic Amino acids get together to form proteins and when they do hydrophilic amino acids tend to be located on the outside of proteins and hydrophobic amino acids tend to be located on the inside that s because the hydrophilic amino acids can interact nicely with water but the hydrophobic ones cannot Something you should know about cysteines is that because they contain sulfur Two cysteine molecules usually get together to form a molecule of cystine They do this by linking their sulfurs to each other That is called a sulfide linkage You should know which amino acids are polar non polar acidic or basic Non polar Alanine valine proline leucine isoleucine phenylalanine methionine tryptophan Polar Glycine serine asparagine threonine cysteine tyrosine and glutamine Acidic Aspartic acid and glutamic acid Basic Arginine lysine and histidine When we talk about a protein s primary structure we are talking about the particular sequence of amino acids along the polypeptide chain that creates the protein molecule Most protein molecules fold in on themselves in some regular pattern like an alpha helix or a beta sheet And when we say secondary structure we are talking about the patterns in which a protein folds When we say tertiary structure we re talking about the way of protein folds in on itself in three dimensions Some protein molecules are composed of several polypeptide chains wound up and wrapped up together to form something we call a single molecule When we say quaternary structure we re talking first of all about proteins that have more than one polypeptide chain and we are talking specifically about the way the different chains bond to each other Aldehydes and Ketones Let us now talk a little about aldehydes and ketones First of all the C double bond 0 group is called a carbonyl group Second of all the carbonyl group is polar since oxygen is more electronegative than carbon Therefore aldehydes and ketones are slightly polar molecules In respect to solubility aldehydes and ketones are like alcohols Small sized aldehydes and ketones are soluble in water and the bigger ones are not When it comes to melting points and boiling points remember that the greater the molecular weight the higher the melting and boiling points the more branching the lower the boiling point You should remember that since aldehydes and ketones are polar they tend to have higher boiling points than alkanes and alkenes of similar molecular weight On the other hand they do not undergo hydrogen bonding which means that their boiling points are a little lower than alcohols of similar molecular weight Nucleophile is an atom or a radical group that is anxious to get rid off electrons It wants to give away some negative charge So nucleophile is basically the opposite of electronegativity the opposite of electron affinity When you see some atom or radical with an unshared pair of electrons think nucleophile Aldehydes and ketones can gain a nucleophile because the carbonyl carbon is slightly positive nucleophiles like it And aldehydes and ketones are prime targets for nucleophiles A reaction in which a nucleophile attacks a carbonyl carbon first is called nucleophilic addition So when an aldehyde or a ketone undergoes nucleophilic addition here is what happens The nucleophile itself becomes bonded to the carbonyl carbon A hydrogen gets attached to the carbonyl oxygen and the double bond between C and 0 turns into a single bond You need to know other nucleophilic addition reactions at the carboxyl bond When an alcohol is added to an aldehyde a hemi acetyl is formed If another alcohol is added an acetyl is formed If the alcohol is added to a ketone instead a hemi ketyl and ultimately a ketyl is formed Another example of a nucleophilic addition is an aldyl condensation in which two carbonyls condense to form an aldyl Aldehydes can lose a hydrogen ion and get an OH group instead If we take an aldehyde and expose it to oxygen in the presence of an oxidizing agent the aldehyde will lose the hydrogen that is attached to its carbonyl carbon and gain an OH instead That means the aldehyde has turned into a carboxylic acid When this happens we say that the aldehyde has been oxidized Remember that the two oxidizing agents you will probably see are KMnO4 and KZCRZO7 Also remember that ketones are less susceptible to nucleophilic addition and oxidation than are aldehydes The carbons that are next to the carbonyl carbons are called alpha carbons If you take a hydrogen ion off an alpha carbon you are left with a negatively charged anion called a carbanion Carbanion is a carbon chain compound that is missing a hydrogen ion Now when a carbanion is formed by removing a hydrogen ion from an alpha carbon we end up with a resonant structure which is very stable This is important because the resonant structure makes the alpha carbon more willing to give up a hydrogen atom Now the alpha hydrogen on an aldehyde is more acidic than the alpha hydrogen on a ketone In other words aldehydes are better at giving away hydrogens than are ketones Carbonyls exist as tautomers Tautomers are different forms of the same thing The two tautomers for a carbonyl are the keto form and enol form At equilibrium both of these forms exist So this equilibrium is referred to as keto enol tautomerism Ammonia Now let us talk about ammonia The nitrogen atom on the ammonia molecule has an unshared pair of electrons which is the reason that ammonia is a base Ammonia can turn into an amine An amine is just ammonia in which one or more of the hydrogens has been replaced by an alkyl or an aryl group Like ammonia amines are polar and therefore have a dipole moment Primary and secondary amines can form hydrogen bonds So amines have higher boiling points than similar non polar compounds that cannot form hydrogen bonds You should also know that the nitrogen in an amine forms SP1 hybrid orbitals Usually one of these orbitals is occupied by an unshared pair of electrons In alkylation we add an alkyl halide like CH3Cl to ammonia When this happens we get a primary amine A primary amine can be alkylated to and that gives us a secondary amine Then if a secondary amine is alkylated you get a tertiary amine Now if a tertiary amine is alkylated you get something called a quaternary ammonium salt The amines are bases for the same reason that ammonia is They have an extra electron pair Now when a chain type molecule like an alkyl group is substituted for hydrogen it tends to make the amine more basic than ammonia On the other hand when a benzene type molecule like an aryl group is substituted for hydrogen it tends to make the amine less basic than ammonia As we said a while ago an acid chloride can react with ammonia to form an amide Well an amine can also react with an acid chloride to form what is called a substituted amide Alkanes and Alkenes If all of the carbon atoms in a molecule are linked together by single bonds the molecule is called an alkane An alkene means a hydrocarbon chain in which at least two of the carbons are connected by a double bond In order to name alkanes or alkenes we count the carbons in the carbon chain If the number of carbons is one you say meth if it is two you say eth three you say prop four you say but five you say pent six you say hex seven you say hept eight you say oct nine you say non ten you say dec Then you add ane for an alkane and ene for an alkene If the molecule is an alkene put a number in front of it The number in front of an alkene s name indicates the carbon in the molecule where the double bond begins To find this number you count the carbons starting from the end nearest the double bond Now if for example a molecule is called 2 methylheptane that means that on the second carbon of a heptane there is a methyl group attached For alkenes that have another group attached we have to make the name a little more descriptive So if there is methyl group stock on carbon number 2 of a 3 octane we call this molecule 2 methyl 3 octene Remember that when you are counting the length of a carbon chain you must count the longest continuous chain even if is not straight across the page A carbon chain can be branched having all kinds of branches attached to it The branches might be long or short assuming all kinds of shapes and configurations You should know about three special kinds of branches and be able to recognize them An iso group is a branch that ends with the carbon bonded to two methyl groups and a hydrogen atom The smallest possible iso group is an isopropyl group So if we attach a chlorine to the fourth side of an isopropyl group we would have isopropyl chloride and if we attach another carbon atom we would have an isobutyl group A tert butyl group is a branch that ends with the carbon bonded to three methyl groups The smallest possible tert group is a tert butyl group So if attach an OH group to the fourth side of the group we would have tert butyl alcohol A sec butyl group is a branch that ends with the carbon attach to a hydrogen on one side a methyl group on another and the methyl group on the third The smallest possible sec group is a sec butyl group If on the fourth side we would attach a fluorine atom we would have sec butyl fluoride Solubility Any molecule s solubility in things depends a lot on whether it is a polar molecule or a non polar molecule Remember that when it comes to polarity and non polarity like dissolves like So polar molecules are soluble in other polar molecules and non polar molecules are soluble in other non polar molecules Alkanes and alkenes are non polar molecules Water on the other hand is a polar molecule So alkanes and alkenes are not soluble in water Boiling and Melting Point For alkanes and alkenes higher molecular weight tends to mean higher melting points and boiling points Since the boiling points of alkanes and alkenes tend to be higher when molecular weight is higher it turns out that the shorter molecules are gases at room temperature and the larger ones tend to be liquids in room temperature Very big alkanes and alkenes with chains that have more than 17 carbons on them are solids at room temperature Now there is one more thing you should know about boiling points of alkanes and alkenes it has to do with branching If two molecules have the same number of carbons so their molecular weights are about the same but one molecule is a straight chain and the other is a branched chain The branched molecule will have a lower boiling point than the straight chain molecule So the two things to remember are one increasing the molecular weight of an alkane or alkene carbon chain increases its melting and boiling points and two branching tends to lower the boiling point Now that we have talk a little about how molecular weight and branching affect the properties of alkanes and alkenes let us talk some about what alkanes and alkenes do Let us start with things that alkanes do Alkanes undergo a reaction called a halogenation and you should know a little about this halogenation reaction This is what happens in halogenation An alkane meets up with the molecule of a halogen like uorine or bromine and one of the alkanes hydrogens get substituted by one of the halogen atoms The halogenation of an alkane is a chain reaction There are three steps involved in this chain reaction Step 1 or chain initiating step is simple In this step a halogen molecule is split in to two atoms under the in uence of ultraviolet light Now each of the 2 atoms has an unpaired electron At step 2A the alkane comes on the scene Let us say that in this case the alkane is methane and the halogen is bromine One of the bromine atoms robs a hydrogen atom off of the alkane and forms a molecule of hydrogen bromide That means the alkane is missing a hydrogen It also leaves the alkane with an unpaired electron The little dot next to the CH3 indicates that this robbed alkane molecule has an unpaired electron The robbed alkane molecule is called an alkyl free radical Remember that these alkyl free radicals are not stable They are looking for something to react with In this case the alkyl free radical reacts with another molecule of halogen to form CH3Cl At the end step of 2B we are left with our halogenated alkane and a single halogen atom This single halogen atom can now react with another molecule of alkane and thereby repeat step 2A Once step 2A has been repeated step 2B can be repeated then step 2A can be repeated again and step 2B can be repeated again and so on and so on Eventually the reaction terminates when a radical reacts with another radical If a carbon is attached to only one other carbon we call them primary carbons If a carbon is attached to two other carbons we call it a secondary carbon If a carbon is attached to three other carbons it is a tertiary carbon In forming a free radical the hydrogen is more likely to be taken from the carbon that will leave the most stable free radical So the hydrogen is more likely to be taken from a tertiary carbon than from a secondary carbon and it is more likely to be taken from a secondary carbon than from a primary carbon It is important to remember with respect to alkyl free radicals the order of stability which is tertiary more than secondary more than primary Another way of saying this is it takes less energy to form a tertiary alkyl radical than it does to form a secondary alkyl radical and it takes less energy to form a secondary alkyl radical than it takes to form a primary alkyl radical If enough heat is supplied for activation energy alkanes can burn or combust That means they react with oxygen to form carbon dioxide and water So there are two reactions alkanes can undergo halogenation by UV light and combustion Sometimes alkanes will form rings You need to remember that the angles in the ring produce something called angle strain Angle strained tends to make a ring unstable The more angle strain the less stable the ring The less angle strain the more stable the ring When we are talking about rings with fewer than seven carbons the simple rule is the more carbons in the ring the less the angle strain and of course the less the angel strain the more stable the ring Cyclohexane is an important ring that you should know about Confirmations are the different spatial configurations of a molecule You should know 2 confirmations for cyclohexane chair and boat The chair confirmation is more stable than the boat form The way to represent confirmations is by drawing Newman projections Remember that when the methyl groups in a molecule are closer together they produce greater esteric strain In the case of alkenes we are dealing with double bonds which cannot rotate So if there are two molecules attached to the alkene on the same side of the double bind and two molecules attached on opposite sides of the double bond we have two different alkenes even though they may have the same formula The alkene with the molecules on the same side of the double bond is called the cys isomer of the alkene The alkene with the molecules on the opposite sides of the double bond is called the trans isomer of the alkene So the point is this if you are looking at an alkene and the two double bounded carbons have 2 like constituents attached to them what you call them depends on where the constituents are attached If the light constituents are on the same side you say cys isomer If the light constituents are on the opposite sides you say trans isomer Remember that a cys isomer is a dipole A cys isomer is a dipole because charge is not symmetrically distributed around the carbon carbon double bond If you think about the upper and lower sides of the double bond you will realize that one side is going to be a little positive and one side is going to be a little negative Trans isomers on the other hand are not dipoles That is because the polar bonds are arranged so that the centers of positive and negative charge are in the same place You need to know that when we are dealing with alkenes we can get rid off of the double bond by adding things to the double bonded carbons The thing that is usually added is a hydrogen halide like hydrogen chloride hydrogen bromide or hydrogen iodide and the reaction is known as electrophilic addition This reaction is called an electrophonic addition because the hydrogen is added to the double bond first Ether Let s talk a little about ether An ether molecule is an oxygen molecule with two R groups on each side An ether molecule does not however form a straight line Instead it forms a bond angle at the oxygen atom This means that charge is not symmetrically distributed and the ether molecule has a dipole moment It is a polar molecule with the negative charge on oXygen s end Ethers are somewhat soluble in water and the reason is that their polarity lets them form hydrogen bonds with water molecules They are also weak bases and you need to know that they can be cleaved by acids Carboxylic Acids Carboxylic acids are called so because the OH group has a tendency to give up a hydrogen ion When it does it is called a carboxylate ion The carboxylate ion is a resonant structure and since resonance creates stability carboxylic acids are more acidic than alcohols phenols aldehydes and ketones One of the important reasons that carboxylic acids are so acidic is that the carboxylate ion is stabilized by resonance Because carboxylic acids have twice the hydrogen bonding their boiling points are higher than the boiling points of alcohols When it comes to solubility carboxylic acids are more or less like alcohols Small sized carboxylic acids with carbon chains of four carbons or fewer are soluble in water Halogenation makes a carboxylic acid even more acidic You should know that carboxylic acid can gain a halogen on the alpha carbon When we have got a carboxylic acid and we put a chlorine on the alpha carbon we get a stronger acid than we had before and it is now called an acid chloride This happens in the presence of SOCl2 A carboxylic acid can be turned into an alcohol This happens in the presence of LiAlH4 Carbohydrates Carbohydrates are composed only of carbon hydrogen and oxygen And when we talk about carbohydrates these three elements are always present in this ratio CnH2nOn So we can always tell when we are dealing with carbohydrate just by noting that the molecule is made only of carbon hydrogen and oxygen And the number of carbons is equal to the number of oxygens And the number of hydrogens is twice the number of carbons The simplest carbohydrates in the world are monosaccharides Some monosaccharides contain three carbons Some contain five carbons and some contain six carbons If a monosaccharide contains three carbons it is called a triose If it contains five carbons it is called a pentose If it contains six carbons it s called a hexose Glucose and fructose are two hexoses Glucose has a C double bond O group on its terminal carbon which makes it an aldehyde We call glucose an aldose or an aldohexose Fructose has a C double bond O group on the carbon that is next to the terminal carbon which makes it a ketone We call fructose a ketose or a ketohexose Every hexose is either an aldohexose or a ketohexose In fact every monosaccharide is either a ketose or an aldose whether it is a triose a pentose or a hexose Hexoses assume the conformation of both a straight chain molecule and a ring So a glucose can turn itself from a straight chain structure to a ring structure The ring structure of glucose is called glucopyranose The glucopyranose ring contains five carbons and one oxygen The sixth carbon is bonded to the ring Hexoses are chiral molecules because four of their carbons are asymmetric Every hexose can exist as a D dextro or L levo isomer Here is what that means When you re looking at a Fischer Projection of a hexose look at carbon number five and see whether the OH is on the right or the left If the OH is on the right then you re looking at the D isomer If the OH is on the left then you re looking at the L isomer Fructose can also form a ring structure and it is called fructofuranose Since fructose is ketohexose its ring conformation will contain four carbons and one oxygen Two carbon atoms will be bonded to the ring When two monosaccharides get together they form a disaccharide And when it comes to the hexoses you should know that a molecule of D glucose and the molecule of D fructose get together to form a disaccharide called sucrose You should also know the following combinations of D glucose If two D glucose molecules get together they will make a molecule of maltose Lots of D glucose molecules linked together can make either cellulose or glycogen The difference between cellulose and glycogen has to do with the way the glycosidic bond is formed between the glucose molecules If D glucose molecules are linked up by something called an alpha 1 4 glycosidic bond then the result is glycogen When we say alpha 1 4 glycosidic bond we only mean that the glycosidic bond links carbon number one of one glucose molecule to carbon number four of the next The alpha means that the glycosidic bond arises below the carbon number one If D glucose molecules are linked together by a beta 14 glycosidic bond then the result is cellulose The body stores its glucose in the form of glycogen which is made of many glucose molecules linked together by alpha 14 glycosidic bonds If these glycosidic linkages are broken glucose is generated There are two steps in breaking these linkages Step One Orthophosphate comes and splits the linkage between one glucose molecule and the next leaving glucose one phosphate and the rest of the glycogen molecule Step Two The phosphate is separated from the glucose by hydrolysis to yield a glucose molecule and a molecule of phosphate When these two steps are complete we are left with a molecule of glucose that has been split off from a long molecule of glycogen The rest of the glycogen molecule keeps undergoing the same two steps over and over again And glucose molecules are removed one at a time by the breakage of glycosidic bonds Hydrogen Bonding Hydrogen is not very electronegative So when it gets involved in a bond it does not take the electrons it is sharing with some other atom Therefore the other atom gets to take the electron The other atom therefore tends to be partially negative and the hydrogen atom tends to be partially positive The hydrogen oxygen bond is polar for the reason we just talked about The bond between the positive hydrogens of one molecule and the negative oxygens of another is called a hydrogen bond Here is what hydrogen bonding is in a molecule that has hydrogen bonded to oxygen the hydrogen is positive and the oxygen is negative When a bunch of those molecules get together a link is formed between the positive hydrogen of one molecule and the negative oxygen of the next We called that link a hydrogen bond If a substance has an OH group and undergoes hydrogen bonding it means two things One the substance will have a higher boiling point because the hydrogen bonds tend to hold the molecules together And two the substance will be more soluble in water because the hydrogen bonds between the substance and water tend to help the substance mix well with water Spectroscopy You should have a little familiarity with infrared and nuclear magnetic resonance spectroscopy and their use in structural identification of organic compounds Infrared spectroscopy The infrared spectrometer is used to detect the presence or absence of functional groups So the infrared spectrum helps to reveal the structure of a compound by telling you what groups are present or absent from the molecule This is how it works Think of a molecule as containing atoms connected by springs Imagine that the molecule is constantly Vibrating and that its bonds are always stretching and bending Now remember that when the molecule absorbs infrared light each bond absorbs energy and increases the amplitude of its Vibration When the molecule is somehow connected to an IR spectrometer the increase amplitude shows up as a set of absorption bonds and the nature of each absorption bond indicate the presence of a particular functional group An important point is that molecules that have dipole moments showed deep absorption bonds A carbonyl group for example which has dipole moment will show a deep absorption bond just remember that a given functional group produces a distinct absorption bond So there tends to be a commonality among the infrared spectra of all alcohols carboxylic acids aldehydes and esters Here are lists of bonds and their IR frequency ranges listen but do not try to memorize them Aldehyde 1740 to 1720 Ketone 1725 to 1680 Carboxylic acid 1725 to 1720 Esters 1700 to 1630 Alkanes 3095 to 2850 Alkynes near 3300 Aromatic near 3030 Amine 3500 to 3300 Amide 3500 to 3140 Alcohol 3650 to 3200 Nuclear magnetic resonance NMR spectroscopy NMR spectroscopy helps identify molecules on the basis of CH bonds In regard to NMR just remember these three little facts 1 NMR spectroscopy works through subjecting the molecule to a magnetic fields and b electro magnetic radiation 2 When a molecule is subjected to NMR testing it produces signals which show up as peaks on a graph Identical groups of hydrogen atom show identical peaks and are said to be equivalent 3 NMR spectroscopy works by measuring the spin spin interactions between hydrogen atoms that are attached to adjacent carbon atoms If two peaks in an NMR graph are split it is called spin spin splitting or spin spin coupling So instead of getting two true peaks we get two peaks each of which is split The splitting is due to the fact that the hydrogens on one carbon are affected by the hydrogens on neighboring carbons Separation and Distillation You need to know how to separate and purify organic compounds from mixtures So you need to be familiar with the different methods of purifying and isolating substances which are thin layer chromatography extraction distillation and recrystallization Thin Layer Chromatography TLC This is a quick and easy procedure to separate mixtures of organic compounds based on phase distribution a mobile phase and a stationary phase TLC indicates the number of compounds in the mixture This is how it works Suppose we were given a mixture X and we wanted to identify how many compounds it contains Here is what we do take an adsorbent paper and place it on a glass plate This is the stationary phase Then dissolve the compound in an organic solvent like benzene This is the mobile phase We then take a sample of the unknown solution and add a drop of the sample near the edge of the plate Place the plate in a container with a small amount of an eluting solvent The solvent will then migrate up the plate by capillary action carrying with it the components of the mixture at different rates In the end we will find several spots on the plate each representing different compounds So if for mixture X we found three different spots it means that it contains three unknown compounds Extraction An extraction is a procedure used to isolate individual components of a mixture by repeatedly adding an aqueous solvent to extract different compounds An extraction involves the distribution of a solute between two immiscible solvents Each of the solvents has different acid base properties that isolate specific types of compounds Let us look back at mixture X The TLC chromatography indicated that the mixture contained three compounds Now we want to know what types of compounds are in the mixture If one of the compounds is moderately basic like an amine it will be extracted from the solution by HCl So if we add HCl to the solution and shake vigorously we will see two layers in the solution We drain off the phase containing the base If we now take the remaining solution and mix it with weak base like sodium carbonate it will extract compounds such as carboxylic acids We once again removed the layer we are interested in and proceed with the extraction If we take the solution and mix it with a strong base like sodium hydroxide it will separate out phenols So for mixture X we have identified three substances an amine a phenol and a carboxylic acid Distillation Distillation is used to purify a volatile liquid product It is based on the ability of substances to turn into gasses Here is how distillation works Take the solution and put it in a ask and heat the liquid until it boils The vapors in the ask are collected in a receiver ask and allowed to recondense The nonvolatile impurities remain in the original ask We can also separate two or more liquids in a ask if they have vastly different boiling points The lower boiling mixture will separate first followed by the higher boiling mixture Recrystallization Recrystallization is used to purify solid compounds To do this we take a solid and dissolve it in a hot solvent to disrupt its crystalline structure We will need an appropriate solvent that will dissolve the solid at its boiling point The best solvents are generally those that dissolve the impurities Remember like dissolves like Filter the solutions so that the impurities are removed with the hot solvent Then the pure crystals are allowed to reform Carbon Learning organic chemistry means learning a lot about carbon Carbon has one pair of electrons in the 2s subshell and two unpaired electrons in the 2p subshell If it were not for hybridization carbon would be able to form only two covalent bonds but because of hybridization it can form four covalent bonds When carbon hybridizes it takes an electron out of its 2s subshell and puts it unpaired into a p subshell The carbon atom ends up with four new hybrid orbitals and there is an unpaired electron in each Because the four hybrid orbitals came originally from ls orbital and 3p orbitals we call this kind of hybridization sp3 hybridization Carbon can form a carbon carbon double bond and you need to know a little about how this bond is formed When a carbon carbon double bond is formed this is what happens two carbon atoms undergo hybridization but instead of forming four sp orbitals they form three sp orbitals and leave lp orbital as a pure p orbital Then in order to form two bonds between them each carbon atom donates one electron from one of its sp2 orbitals and each carbon atom donates one electron from its pure p orbital Those two bonds together make the double bond The bond between the sp2 orbitals is called a sigma bond The bond between the pure p orbitals is called a pie bond Double bonds are shorter than single bonds but stronger Triple bonds are even shorter and stronger The double and triple bonds do not rotate around their axis but a single bond can A covalent bond can be polar which means simply that it sort of has a positive end and a negative end because its shared pair of electrons are not being shared equally Think of a molecule of CH4 In this molecule hydrogen is less electronegative than carbon So for each of the four CH bonds carbon is a little negative and hydrogen is a little positive Notice that the molecule as a whole has no net positive or negative end because of symmetry The center of positive charge is right in the middle at the carbon and the center of negative charge is also right in the middle at the carbon Now think about the CH3Cl molecule The hydrogens in this molecule are less electronegative than carbon So for each of the three C H bonds carbon is a little negative and hydrogen is a little positive Chlorine is more electronegative than carbon So in the C Cl bond carbon is a little positive and chlorine is a little a negative In this molecule the center of positive charge is toward the bottom of the molecule and the center of negative charge is toward the top That means this molecule is polar If in a whole molecule the center of positive charge and the center of negative charge are in different places then that molecule is polar Another way of saying that a molecule is polar is to say that the molecule is a dipole When a molecule is a dipole then it has something called a dipole moment You will not have to know exactly what a dipole moment means Remember that water is a dipole You might think from the formula H20 that water would not be a dipole since it has two hydrogen atoms attach to one oxygen atom but water is a polar molecule that is because the molecule is bent due to hybridization and does not form a straight line if the water molecule formed a straight line like the CO2 molecule then it would not be a dipole Stereochemistry Two or more compounds with the same number and kinds of atoms are called isomers They have the same molecular formula Structural isomers are isomers that differ in the orders in which carbon or other atoms are attached to one another Stereoisomers are isomers with the same structural formula which means they have the same atoms attached to each other In a pair of stereoisomers the bonding patterns are the same They differ only in their configuration in space There are two types of stereoisomers optical isomers and geometric isomers Optical isomers rotate plain polarized light They are optically active Remember that only chiral molecules are optically active Any carbon atom with four different substituents bonded to it is called a chiral center and the molecule to which it belongs is called a chiral molecule Every chiral molecule has an enantiomer and enantiomer is a mirror image of the chiral molecule Remember however that enantiomers are not identical because they are not super imposable on each other Chiral molecules do not have enantiomers Let us review what we just learned 1 A chiral molecule is a molecule with the chiral center and the chiral center is a carbon with four different things attached to it 2 If a molecule is chiral it is not super imposable on its mirror image which means the molecule and its mirror image molecule are not the same 3 The chiral molecule and its mirror image are called enantiomers 4 An a chiral molecule is super imposable on its mirror image molecule which means the molecule and its mirror image are in fact identical Chiral molecules do not give rise to enantiomers Remember that every chiral molecule and its enantiomer are optically active Polarized light can be rotated to the right or to the left If a particular chiral molecule rotates polarized light to the right then its enantiomer rotates the plain to the left Similarly if a given chiral molecule rotates the plain of polarized light to the left it has an L configuration and its enantiomer which rotates the plain of polarized light to the right has a D configuration In order to figure out the configuration of enantiomers look at one enantiomer and examine the chiral carbon and its four different substituents Look at the flat atom on each substituent and find the one that has the lowest atomic weight of the four then when you find it rotate it to the back Look at the remaining three atoms and assign each one a priority number based on its atomic weight Assign priority one to the substituent whose first atom has the highest atomic weight Assign priority two to the substituent whose first atom has the second highest atomic weight Assign priority three to the substituent whose first atom has the lowest atomic weight With your finger point to the substituents in numerical order one two three If your finger is moving clockwise you are looking at the R enantiomer If your finger is moving counterclockwise you are looking at the S enantiomer Remember that absolute configuration does not tell you anything about the direction in which a particular enantiomer rotates the plain of polarized light A chiral molecule may have more than just one chiral center When a pair of chiral molecules is not mirror images of each other they are no longer enantiomers They are called diastereomers Diastereomers have different physical and chemical properties and can be separated by methods such as crystallization chromatography and distillation When equal amounts of enantiomers and diastereomers are mixed together the resultant mixture is called a racemic mixture and has no optical activity The opposite rotational effects of the enantiomers cancel each other out Therefore the net effect is zero optical rotation Geometrical isomers differ in their orientation about a double bond or ring Geometric isomers are not optically active An example of this is cis and trans isomers Hydrocarbons are molecules that are made of carbon and hydrogen only Phenols You should know a little about phenol Phenol itself undergoes hydrogen bonding with other phenol molecules and with water too So phenol itself is a kind of soluble in water and it tends to have a high boiling point Phenols have an OH group attached to their benzene ring So just like alcohols phenols can lose a hydrogen ion In other words phenols can act as acids In fact phenols are more acidic than alcohols Phenols with substituted groups that withdraw electrons from the ring such an N02 and CN stabilize the ion and make the phenol more acidic Groups that donate electrons such as alkyl groups destabilize the ion and make the phenol less acidic
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