Prin Chem Honor Lab II
Prin Chem Honor Lab II CHM 218H
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Structure and Nomenclature of Molecules Possessing Carbonyl Groups There are a number of molecular types in organic chemistry that include the CO carbonyl group In this module we will discuss four of them ketones aldehydes esters and carboxylic acids This module is done last because each has a different although related nomenclature system A commonality to all of these molecular types is how the first two molecules in the series are named As you ve already seen one and two carbon alkanes are named methane and ethane respectively Each molecule can be named based on this system All can also be named using an older nomenclature system much like the arenes have two systems Some also have a nonsystematic common name like grain alcohol for ethanol The systematic names are based on the names for the carboxylic acids and so that is where we begin Carboxylic acids Carboxylic acids have been known for millennia and so many received common names that where then used to develop systematic names for other carbonyl containing molecules Carboxylic acids typically have low volatility because of strong hydrogen bonding but their vapors are typically sharp and unpleasant They are also generally toxic For example formic acid is the sting in an ant bite H C C O I ll H C C COH O O O O O II II II C C HCOH CH3COH CH3 CHZC OH HOC COH H methanoic acid ethanoic acid propanoic acid ethanedioic acid formic acid acetic acid propionic acid benzoic acid oxalic acid In general the modern system of nomenclature is used for all monocarboxylic acids consisting of 3 carbons or more the terms methanoic and ethanoic acid are rarely used Likewise the common names are used almost exclusively for the 26 carbon dicarboxylic acids For benzene rings with functional groups the benz beginning is always used although there is a very clunky IUPAC name The modern system of naming acids begins by using the names of alkanes as their base 1 Find the longest carbon chain that includes the carbon to which the 7COOH group is attached 2 Name the molecule as if it were an alkane starting from the carbon in the 7COOH group This is an important point you must include the carbonyl acid carbon in the counting L V Change the nal e to ic acid Numbering is unnecessary because the 7COOH group is always aterminal group 4 If the carboxylic acid contains other attached groups the molecule is M named as a carboxylic acid and numbering begins with the carbonyl carbon Unsubstituted carboxylic acids never need numbers since the acid group appears on the end of the chain In RH if CH3CH2CH2CH2CH2COH CH3CHCH2CH2COH hexanoic acid 4hydroxypentanoic acid Aldehydes Aldehydes are molecules that end in COH ie the 70H group in an acid is replaced by an H They typically result in nature from the oxidation of alcohols and usually have a sharp disagreeable odor Formaldehyde is atypical example of this Cinnamonaldehyde represents an aldehyde with a sharp pleasant odor picture provided in Arenes notes Substituted aldehydes are named as in the case for carboxylic acids 1 Name the corresponding carboxylic acid by any system 2 For IUPAC naming replace oic acid with al 3 For the older system replace ic acid with aldehyde Preferred names are underlined CC39 H CI C gH o o CC HCH CH3CH2CH H H methanal propanal formaldehyde propionaldehyde benzaldehyde m In esters the OH is replaced by an OR group where R is some organic group Thus they have the general formula RCOOR where the R groups may be the same or different Esters generally produce pleasant odors scents that are mild The scents associated with fruits are frequently either an ester or a mixture of esters That scents are frequently blends of several compounds accounts for the fact that fruit avored things eg gum rarely taste exactly like the real thing Wikipedia lists many examples http enwikipedia orgwiki Ester several of which are used as nomenclature examples below We ll begin with ethyl formate HCOOCH2CH3 a component of lemon mom and strawberry avors HiIJOCHZCH3 1 Name the portion of the molecule containing the carbonyl group as if it was a carboxylic acid In this case the acid would be formic acid Replace ic acid by ate Now we have formate 2 Name the R group as if it were a substituent on another molecule In this case the R group is ethyl 3 The ester is named by placing the R group name first and ester group second in this case ethyl formate H H I II ll CH3 HCIC CC OCH CH CH3COCH2CH3 CH3CO CH2CI CC 2 3 CH3 H H ethyl acetate isobutylacetate ethylbenzoate peach pineapple raspberry cherry raspberry strawberry essence di Niobe Essence di Niobe is a fruity ester used in the manufacture of perfumes Ethyl acetate is also sold as acetonefree nail polish remover m Ketones are molecules whose carbonyls occur along the inside of a carbon chain They have the general formula RCO R where the R groups may be the same or different Ketones are frequently fragrant and are considered between esters and aldehydes in terms of pleasantness They are frequently used as solvents and are found in nature in a number of places For example muscone is the primary contributor to the odor of musk while acetophenone is found in apple cheese apricot banana beef and cauli ower As you ve guessed ketones are indicated by the one ending 1 IUPAC system Name the parent alkane by the standard rules replacing the e ending with one 2 In molecules that require numbering numbering should begin such that the carbonyl carbon gets the lowest possible number unless there is an aldehyde or carboxylic acid group Those always occupy the number 1 position 3 Common system Name each group bound to the carbonyl as a substituent Then use those substituent names as pre xes to the word ketone Usually they are placed in order of increasing size Cu CH3 C CH3 propanone dimethyl ketone acetone 3 CH3 CH2C CH3 butanone methylethylketone 0 ll CHz CHi ICHZ C CH 2 CH2 CH2 CHZ CH2 CH2 CH2 CH CH CH2 CH3 3methylcyclopentadecanone muscone O CH CH II CH3 C C CH CH CH phenylethanone methylphenylketone acetophenone CH3 0 CH3 CH C CH3 3methylbutan0ne methylisopropylketone EFT Summary Commands H1 spectra 0 Place sample in spinner to measured depth Place in the nmr and turn the air off using the elbow switch then on You should hear a quotpurrquot at this point 0 Enter the PNMR program 0 Select Hl parameters ltnu hlgt Commands within ltgt are meant to be typed in the small command line towards bottom of screen End the command with an quotenterquot Parameters should be nsl rg 5 for neat samples rg30 for 2 samples and for 198 ethyl benzene standard 1 Acquire data ltzggt The computer will ask for a file name Hit return to use the default name The FID should be above base line and yellow If red reduce rg If there is no signal or very little increase rg or run standard to find problem 2 Enter NUTS program Nut commands are just two letters in the main program with NO following enter If you mistakenly enter a subprogram hit enter to get back to the main program If the NUTS program is doing strange things quit it and restart the NUT S application program 3 Process the data Ctrl F2 To use the default data file hit return when it asks for the data file name 4 Trim the phase ap 5 Integrate the spectrum ai 6 Plot the spectrum pl 7 If at any point you have trouble run the 198 ethyl benzene standard to see if the problem is with the instrument or if it is with your sample If it is the instrument problem contact JW L Integration tricks for EFT spectra If the integration scale is either too large or too small you can correct it by usmg the following procedure use puts you use on the left to adjust the enter If you want to put a numerical value on the integration puts you a cursor on one V up a where you can put the value you want on the integration of this peak Other peaks Phasing tricks for the EFT spectra If the phasing of the spectrum is not good You can manually phase the spectrum by step action 39 1 close the nuts clears any bad information window and restart out a new one 2 Do the basic If the spectrum looks good at processing the same this stage do not phase Just way as usual integrate and plot control F2 for proton spectra 3 use the command This will put you in a manual PH phase subroutine Hold down the left mouse and drag it left and right to do a first order correction Hold the right mouse down and drag it left and right to make a second order correction exits the manual phase subm enu 4 enter Clearing carry over information from your window step action 39 1 under the view unclick the appropriate items such as clipboard neak label C13 Spectra 0 Place sample in spinner to measured depth Place in the nmr and turn the air off then on You should hear a quotpurrH at this point 0 Enter the PNMR program 0 Select Cl3 parameters ltnu Cl3gt Commands within ltgt are meant to be typed in the small command line towards bottom of the screen End each command with an quotenterquot Parameters should be ns16 rg 100 for all neat samples and for the 396 nButanol standard If no one is waiting for the instrument you can enter a large number for ns and then ltzggt and got to steps 2 and3 Repeat 3 until the spectra quot looks good then plot it Hit Q in PNMR to stop data collection If you use an ns gt64 you must wait until no one else has a sample to run If you use ns gt1000 you must wait until the evening 1 Acquire data ltzggt The computer will ask for a file name Hit return to use the default name The FID should be above the base line and yellow 2 Enter the NUTS program Nut commands are just two letters in main program with NO following enter 3 Process the data Ctrl F3To use the default data file hit return when it asks for the data file Use line broadening of 2 when it asks Line broadening LB2 4 Adjust scale by using scroll bar on right 5 Plot the data pl DEPT Spectra 1 After you have gotten a good Cl3 spectrum on your sample Enter the PNMR program Type ltDEPTgt in the command line followed by return The program will ask you for the Name of file Just hit return if you wish to use the file Myidept for your data If you want to call it something else do so but remember what you called it 2 The program now acquires three sets of data So just wait When it is done it will put up another question box This just gives you time to read the processing instructions Hit return when you39ve read them 3 Enter the NUTS program Nut commands are just two letters in main program with NO following enter 4 Process the data first spectrum al quotaH one 5 Phase it if necessary ap 6 Now put all three of the spectra of the screen Cntrl Fl 1 7 Adjust scale by using scroll bar on right 8 Plot the data p Tuning the NMR The commands on the previous page assume the NMR is quottunedquot and TMS has been used to set the instrument scale to zero You can determine if these have been done by taking the 198 ethyl benzene standard spectrum A well separated quartet indicates good quottuningquot or the correct shims have been set The TMS signal at zero indicates the offset poteniometer is set correct If the instrument is not tuned you have two options 1 Ask someone who is more familiar with the instrument to tune it for you IWL would be glad to 2 For those of you bold enough to do so tune it yourself This is done by putting in the 198 sample be sure to see that it is spinning well and the sample is set at the right depth If you start to tune the instrument and at any time you see no FID or a very unusual FID stop and report the problem to IWL i Type in the command ltSHIMgt and follow the directions It will first take a minute or two to find the correct gain They system will then guide you in the tuning of the Y and curvature values on the potentiometers on the tuning tray Follow the directions carefully If at any time you make a mistake in setting the pots keep going and it will eventually correct your mistake but each mistake adds a couple of minutes to the time it takes very time you make a mistake The whole process takes about 27 minutes and the shim program will stop when you have tuned the instrument ii Set the TMS zero by taking a Hl spectrum 198 Process through NUTS in the usual way Note where the TMS line is in ppm Go back to PNMR and use the command ltfogt It will ask for the TMS reading in ppm then where you want it set put in 0 then it will tell you where to set the offset potentiometer on the tuning tray Make this adjustment and the next spectrum you take and process should have ppm scale set right Page 1 of 6 Picture illustrating the HH coupling in ethyl benzene and the calculation of the 3 bond coupling constant between the methyl group and the methylene group the conversion of ppm to Hz and the use of PascalOs triangle to get the intensity ratios of multiplet peaks J H 541W LAW 213 cu 1quot cu a l f I 1 I cu 11 I L I quotM f 39 hark 4 3 732 MM Ila 3 Lana f wt 1 fr 5 I4 Lilo I I awn Alli0 J l J l A rtnu bula t y t w q 1 I l 43quot I a rim ll ll l l l 7 H 7 7 t 7 v it 7 12 7739 TV a r 2 V a 12mm W m Pjyft g 39ZDMLmzwuuml Ol l Y 7 7 7 Whma Ln 6 Na lm L Mtgmml rag 41 a r Mimiu are l i r f L x I 1 39u x I 1 l Jg I 1 hi 39 quot0quot and h 3 bmu ffl 1 9 s H l ml 0913 All A ml 3911 3 It a h m 1 i a I 1 1 39 Lumm m MW Hm ltif EVInl gt leD218h218hlect 6htm ltendit 2142008 Page 2 of 6 leD218h218hlect 6htm 2142008 Page 3 of 6 Picture of the spectrum of the H spectrum of chloroform in dueterated acetone and labeling peaks Splitting of the CH peak in acetone by 2 bond coupling to D D has spin of 1 so has three states and splits neighboring nuclei into three peaks C12 chloroform peaks C13 peaks and splitting side bands are identi ed quotL 119 phat Tugfiwa 1 all1 14 2 anu w 7 w ML r H mm 1 um 7 ltif lvrnl gt I a d u u 3 quott 1 HM I u vl D I gum F f Winn 7 o if l 565 i a x l quoto 5 4 1M ltenditgt ltif lsupportErnptyParas gt ltlendifgt ltlif lsupportErnptyParas gt ltlendifgt leD218h218hlect 6htm 2142008 lt if supportErnptyParas gt lt endif gt lt if supportErnptyParas gt lt endif gt The chloroform peaks are magnified to show integration of C 13 peaks to get C 13 atomic abundance in natural carbon lt if supportErnptyParas gt lt endif gt lt if supportErnptyParas gt lt endif gt lt if supportErnptyParas gt lt endif gt i 13914 i quotM VM V 39t39quot7 1 1 i7 9457 i a H 1 1 1 i I 1 1 395Y J 1 1 13 10752 a I 5 ii 1 1 w K 1 58 5 J 9 4 5 L L ND ley Page 4 of 6 lt if Vm1 gt 062 1 1 1 39 V I 1 39 3 1 N 2 am 14 p it A w W a g 1 1 1 iv I 1 g 1 39 39 HIV M1 139 M 39 quot 11111111111111111 1111 1W1 1 1111111 11111111111111va1 1 IL l l 11 1 1 1 1 I 1 u I 1 1 1 1 z x 1 1 x 1 z39ll l I 4X14 I39Y H I 11 39l 1 95 0 85 80 75 70 65 60 PPM l I V USER DATE012407 1343 F1 60010 SW1Z 1000 10F 3600 1 1PTSId 4096 EX 22mm 1PW 175 usec iPD 10 sec 1NA 32 1L8 00 1 WinNuts Temp di r39 quotI 17 n EH z I quotW g39 a L i I u I I39 I F i i I i 15quot quot IL 1 I I q an a I3 I E5 39 39 1 Ii39i Hquot 1quot quotquot i ii arrn Inquot Malt Ln 1quot II quot LI139quotquotquot 1 f sl39l 1 1 In E 395 Hi I 1 P g a 39 w W g FYIn v awlngl39a H 1t w w a FZI39J quot Ll u Iu h Elf 1 4 leD218h218h lect 6htm lt endif gt 2142008 Page 5 of 6 The acetone CH peak coupled to 2 D in a 12321 pentet is expanded to get the 2 bond HD coupling constant Mp Ml WM 3X4 y t i H A J J t y 4 J 1 Wm H e r ii39iBJ 9r u MAYA 7 u xid 7 Jvl39UnKJ 4 u Jquot 2 ltif EVInlgt ltendit leD218h218hlect 6htm 2142008 Page 6 of 6 leD218h218hlect 6htm 2142008 Structure and Nomenclature of Substituted Alkanes In the Alkanes notes you learned about two systems of naming molecules Here we expand those systems to allow us to name molecules with heteroatom nonCH substituents We ll also encounter a third nomenclature method It is the oldest of the ways to name compounds and not a system at all It dates from the days before the existence of atoms and elements was postulated Thus each compound was given a unique name frequently based on some physical characteristic e g appearance odor or source While most of these names have fallen out of use eg sulfuric acid is no longer called oil ofvz39m39ol or zinc oxide owers ofzz39nc some survive eg plaster of Paris calcium sulfate and a few have even been incorporated into systematic naming e g benzene which appears in a later handout Alcohols The term alcohol has an interesting origin Like many words in science beginning with al this term has an Arabic origin Al means the Thus alchemy is the chemistry The last two syllables come from the word for an early eye shadow made of antimony powder The word for the process by which this powder was made is very similar to the word for the powder itself The process is essentially distillation Medieval Europeans learned of distillation through the operation of making liquor Of course the active ingredient of liquors is ethanol but at the time the name of the process by which ethanol was concentrated was given to the chemical itself Hence the original name of ethanol was alcohol Molecules containing one or more 70H groups are so common in nature that many have common names FOI example OH CH CH HO OH HO CH IOH CHsoH CHscHon CH3 CH3 CHzCHZ CH2 CH2 wood alcohol grain alcohol rubbing alcohol glycerin methyl alcohol ethyl alcohol isopropyl alcohol ethylene glycol glycerol methanol ethanol 2propanol l2ethanediol 123propanetriol The modern system of naming alcohols begins by using the names of alkanes as their base 1 Find the longest carbon chain that includes the carbon to which the 0H groups is attached 2 Name the molecule as if it were an alkane starting from the end closest to the 70H group L V Change the nal e to ol and put the 70H location prior to that chain name using numbers if required to remove ambiguity The examples just given also include their systematic names When more than one 70H functionality is present use the endings diol triol etc OH For example C39H contains the 3carbon alkane propane The 70H group is 3c CH3 bound to the middle 2 carbon and so this alcohol is named 2propanol The older systematic naming system uses the following steps and generally applies to smaller alcohols 1 Identify the organic group to which the alcohol is bound and name it as an alkane substituent group under the older system 2 Add the word alcohol to complete the name CIH ThuS CH has the CH3CHCH3 group attached to the 70H group This group is H3C CH3 isopropyl and so the alcohol becomes isopropyl alcohol A common mistake made is to combine the two systems Thus isopropanol is a tempting but incorrect name for this alcohol Halide compounds Constructing the names of these compounds follows a similar path to that of the alcohols Since all of the halide unknowns in this course contain bromine will use those as our examples 1 Find the longest carbon chain that includes the carbon to which the 7X groups is attached 2 Name the molecule as if it were an alkane starting from the end closest to the 7X group 3 Number the carbons The name begins with the number of the carbon to which the halide is bound followed by the halogen written as halo e g bromo followed by the alkane name Multiple halides carry the Greek pre xes di tri etc 4 When multiple different groups are bound to the alkane they are named alphabetically Numbering begins with the substituent which appears closest to the end of the chain When this is a tie the name closest to the beginning of the alphabet gets the lower number Br Following the alcohol example clH has the CH3CHCH3 group attached to the iBr H3C CH3 group This group is isopropyl and so3 the alcohol becomes isopropyl bromide A slightly more 139 I complicated example would be CHsE CH3 This contains the 3carbon alkane propane The CH iBr group is bound to the middle 2 casrbon as is a methyl group and so this alcohol is named Br 2bromo2methylpropane Likewise 313 lj 13 is 22dibromopropane I Br Which two of the cl to c4 alcohols will give three peaks in the carbon spectrum How will you tell them apart Which two of the cl to c4 alcohols will give four peaks in the carbon spectrum How will you tell them apart Introduction to NMRProton NMR fulluwmg 4 ways m nuclel m the integra nn ufthe peaks Each unhesewm be dxscussedm tum spemm r FHV H methannl andtbutanW rm mm r r alum e1 ectmn density refB samgle B ref v amgl V 61000000 MB mppm 1000000 6 mppm Mltk 39dlm qttwdxxchhuac1nmxtecmqAes1dhhtml mmn chermcal shms generally run fmm o m 12 ppm and are referenced fmm TMStetIamethy1 s11ane whens kmwn as the we eld regmn RCOOH ROH RCHo m2 ArH RCHR39 RCH2 ROCHZR39 CHZOR CHgAr Rc0 CHIR 2 39 Rco CH3 RCH 8 7 6 5 4 3 Z 1 0 Chemical shi ppm Table of H1 Substituent parameters on tetrahedral C methane shift 23 ppm Sample Calculation Predict the chemical shifts in ethanol CH 3CH 20H predicted shifts 23 29762 382 exp 369 23 6235 120 exp 123 the chemical shift of the OH depends on concentration solvent H bonding and can appear any where from5 to 5 Coupling Interaction of the nucleus with neighboring nuclei Results in a pattern of peaks For the simplest and common spectra number of peaks is n1 where n is the number of neighboring equivalent 112 nuclei NOTE the restriction on the use of this rule Coupling ConstantsThe separation between peaks in Hz caused by coupling Coupling in proton spectra is primarily due to coupling of the protons to neighboring protons with different chemical shifts Ifthe protons doing the splitting have the same coupling constant splitting will result in 2n1 peaks where n is the number of neighboring protons The intensity of the peaks will follow Pascal triangle Thus a triplet will indicate two neighboring protons a quartet will indicate three neighboring protons etc The coupling constant associated with this splitting is denoted as a HH coupling through three bonds 3JH H The magnitude of the constant is about 515 Hz and independent of the magnetic eld of the spectrometer DecouplingRemoving the coupling information by irradiating the molecule at the neighboring nuclei s frequency Carbon spectra are usually run with hydrogen decoupling on The reason for this will be gone into in detail in the next lecture But as a result peaks in a quotnormalquot C13 spectrum do not show coupling Similarly protons on an oxygen usually rapidly exchange with other OH protons and are exchange decoupled and usually but not always show up as single decoupled peaks Integration the area under a NMR peaks or a set of peaks The integration is proportional to the number of nuclei involved in the absorption 1 Solve the following structures from their proton spectra ddoublet