Lecture 24. Using Organic Spectroscopy to Solve Complex Structures


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Lecture 24. Using Organic Spectroscopy to Solve Complex Structures
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Nowick, James
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This is a graduate course in organic spectroscopy, focusing on modern methods used in structure determination of organic molecules. Topics include mass spectrometry; ultraviolet, chiroptical, infrared, and nuclear magnetic resonance spectroscopy.
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on there were going to have this week 1 of these oversaw me let me tell you what I'm what we're gonna do today so what we're going to do is to take the the problem number 2 from the homework and use it as a as a didactic example on work work through it and I wanted show you my philosophy do we have some extra copies here I know I made an offer so so what I wanna do today is take problem too from the homework and work through it as an example and really take my my approach on this and I think by now everyone's pretty much sort of on the ball I mean it for any of these these are problems that are dealing with structure solution of an unknown and that sort of half of what you get unity get some wacky product usually you kind of have an idea of where things are so you know you're working from some reaction you know what you put in there is not a natural products chemists and so you're you usually having a starting point and that's why I also think the analysis part is really really important but if you absolutely don't have an idea obviously the most important information is like molecular formula in getting degrees of on saturation I've started in the course with IR because I think it's really really important to get the functional groups in the molecule I and obviously can be mass spec and so forth from molecular formula where all I want us all on the same team page on NMR you go through a new letter the letter the peaks it's just the way we can all communicate In the other thing is read your spectrum when you're working on show you what I mean today you know really really enjoy down your thoughts and so forth carbon were numbering the peaks and again you're going to be getting information you're going to be thinking about symmetry when you're doing this you're going to be thinking about peak positions usually if it's available or go through the depth to the sign your clocks etc. next I'm not saying basically 2 quads ch ch to United's 3 usually next time I go to the HM we've already seen lots of situations where you have dire stereotyping protons and you're trying to put the framework of the molecule together and so the cozy is actually more useful once you've figured out stereo topic methylene sp and so forth cozy is going to build up fragments and it's really really useful to be keeping a scorecard as you go along of sort of water we know what don't we know what a rare fragments water interesting functional groups h NBC is super useful for putting the pieces together In you get a ton of information from ancient so it's really useful to work strategically around isolated things isolated mouthfuls original am quartz and carbon yields can be a real gem for this and finally I like to go ahead and use the nosy and Owyhee to address issues of Styria chemistry obviously obviously you're also going to news coupling constants when appropriate Class a also Jamestown found use so that's sort of a general philosophy and structure solving in I thought problem number 2 is is a useful useful example of this and I've handed out teapots of problem numbers 2 I've also handed out the low-level analysis that's pretty mechanical so we don't spend a lot of time so so when I looked at this let's say I got 15 age 18 0 3 and I always look and just say OK if it received 15 with oxygen is and so forth what would it be be 32 hydrogen is 32 minus 18 actors may divide by 2 rosettes that Klinsmann saturation so we get 7 degrees of unsaturated should the IOR and this 1 is really really interesting so the early on as a peak in 1783 and that service sends up a red flag it's you know it's we don't have like an acid chloride in there we're going to say you don't have you don't have any of these paired types of things words consistent with a N hydride say and so that starts to look like some sort of strange strained rain when we look at the 13 you're you're going to see there's nothing that's consistent with the key with a a sort of normal Tetonia here so we aren't thinking that's pretty typical for for like a gamma lack tone we see 1660 16 29 in the spectrum armor no conjugation can shift things to to lower lower wavelengths so that's that's kind of where I am starting out in looking at the data here now I know I want us to to focus on reading the animosity spectrum In I've given USA said to handouts 1 that you can work along with me but 1 where I've also done a lot of the low-level analysis and you should all From this week some work beyond that on the same and we will get you may find that the pants so I guess my philosophy and this 1 was I didn't want anyone to get wildly off base on this 1 in terms of molecular formula I wanted people to on on that wavelength so this spectrum was interesting so you went through and everything is everything is resolved to told no 1 hydrogen multiple and a couple of 3 hydrogen peaks there work there were some things that I thought were really really really interesting on this so I mean you can kind of see this in the hides them baffles here right this is a mouthful single here we have a Mathilde double it's already your thinking in CH 3 CH 2 CH 3 Ch for that this is like an isolated methyl right user these repeats if you've leaded letter all the way across right this is OK this is a alright we
just 1 ADB the accepted do in yes each of June so we should all With the other thing that was really interesting about this you look at this position here it's a 3 hydrogen it's a Mathilde now and it's a matter for 1 interesting position because you're going to have something shifting you down to about 2 1 that's 0 like Zoellick Alford to Aqaba Neil position the other thing is if you look at it you can see it on the people print out you can see it reflected the heights that is shorter than the other methyl saying Let's so this guy's a double it I think .period J was what 1 . 2 words for 1 . 1 heard somewhere somewhere around there I mean this is classic a little leg the Homola like type of coupling Cimmino something's going on with this methyl group if feel like there's 1 other weather a couple of other interesting features on the spectrum so number C is interesting letters say seems interesting for a number of reasons his position as is very interesting we'll see in just a moment that he's not from the ancient QC he's is not associated with a double bond right we have to Al protons in fact these guys these guys are kind of interesting because they're both double its J is equal to 9 . 9 hurts immediately you're starting to think maybe assists Cissell came right sisters about 10 yards typically trends about about 17 per hour put it on started jotting down ideas and thinking taking kind of putting down ?question mark appearance and going along this guy is interesting because he's a double it but there's a little something more going on with him in so here's here's the expansion of C didn't give you a hand out on that you've got it on your on your Maine propped on a main problem if you want initially you might think that this is a double that of doublets and that might be you cholera .period apparent double double its notice there's really a little little something funny going on here it's what we're actually going to see that it's a tablet of for text the outer winds just aren't resolved again the Jays about 1 . 2 or 1 . 1 . 1 per cent it's just just barely at the resolution that you're going to see splitting because your line with should typically about a Hertz which means you just barely have things resolve out I kiss the other thing that's interesting is down and this this region right in the aliphatic region between the deal alike around the alone-like methyl so we won't necessarily necessarily know this In terms of what's what's happening at this point but we're going to see it later so this is really interesting we've got these multiple it's here they're very nicely resolved at least for these 3 here so you can see that you have a double of quartets are a quartet of doublets rather and that another quartet of doublets and a triplet of doublets you can see this from the heights of the peaks that you're getting basically this 1 3 3 1 type of pattern with some tending in words you can see some coupling partners so you're dealing with a situation where you've got 3 big J values in 1 of them to big J values in another them then you've got a smaller J. This is like the types of things we've seen in the past with Germinal couplings and axial axial couplings that sort of an interesting reading these guys have just 1 big J and a bunch of little couplings that sorrow at manifold anyone recognize this pattern here In a double that of cortex you notice the 1 3 3 and then of course you're 1 is sort of hiding under here but you see that heights and then another 1 3 3 and 1 is hiding under there so again that's a sort of a neat neat things as to what's happening in a in terms of actually understanding it will as we start to get into the structure in the cozy world will be able to understand this a lot better but this is what I like to do initially is just just come up with their own read on things you know I went through it went through the carbon and numbered at you're basically numbering numbering 1 15 sold that's all written out there for
you so don't don't bother to try that try to follow along here 8 9 10 11 12 13 14 15 you can almost get your Kwok by inspection there usually low remember quartz have much slower relaxation time so with normal relaxation the wager mechanization is returning to the city access you also don't have hydrogen Sundance you know getting a nuclear over House effect here no more and no line in number 10 interesting there . 4 parts per million a partner see 13 a market that's right at the limits of where 1 can practically start to use HMM BC to figure out what's lining up with what you can but you have to be really careful do expansions increased a number of points in the In the virtual domain in the F 1 the main to 1024 and worked pretty hard work were actually not that indeed this will see later on in a moment when we come to the agent BC will actually be able to figure it out because 9 and 10 Avery very distinct I went through and again this is all on you're sort of quick and dirty Yum 34 page handout went through and basically on that hand out assigned urea seems C-1 and C-2 received 465 9 ended up being close this particular 1 was done with adept 45 adept 45 was the 1 we talked about at the end where you have that they wipe pulse of 45 degrees that gives you your defines methyl Filene's and Mathilde not done too much you can see pretty much you can pick out your financing can pick out your winnings 11 and 13 methylene 12 14 and 15 of the metals and then you have some Sorensen these and again this is started started the lower low level analysis on it I just went through my my HM QC and collate and this is going to be this last page of that 2nd hand out really is going
to be the are Rosetta stone for taking it from here so I went through
and did the low-level analysis in line things up and again if you're having having any trouble visually just just get out of or if you're working on a computer on on an iPad using Acrobat you can use command you win it'll it'll slap agreed but it's very easy the trace over interest out alright so that that takes us through our preliminary analysis In end let's see if I want to say Let's go to the let's go to the cozy posing next and I think fears were all start Our real analysis on this issue so I have a couple of expansions that are useful weakened muck around we can muck around entirely on the spectrum but others start on get this guy out of the way so we've got Alcan region here this to double its with Jay of 9 . 9 Hirtzer are crossing with each other so we have 3 A and 6 B and 380 In 6 B and of course a diagonal runs right through right through the cozy like so and so we've got a 380 Cross 6 days so I'm pretty sure at this point that we're talking about an Algerian that's coupled together I guess what medium let me put down maybe 80 start of a summary from the pH and you say so see 1 is a quiet seemed to is a quiet see story H A C 4 c 5 these requirements C 6 H B B this is all just from our HM QC analysis C 7 8 C In guests I guess the thing that was sort of interesting I try to keep a note of what's interesting this is at 81 ppm for the carbon in 4 . 8 ppm so that's probably connected to an oxygen I think probably probably can be pretty confident that that's connected to an oxygen let's see we have age age see it is in the squad 10 h deed see 11 years G and HJ see 12 H 3 OK so that's that's 1 of the the Mosul's there see 13 H. F HIT see 14 a 3 L and see 15 aged 3 E so that's the 1 that's the 1 that's 2 . 1 ppm the 1 that I think is that it is in some way a little like because it can't be if itself into a carbon Yelets just going to be an isolated natural right is going to be a metal he tone so we can't get a Mathilde the tone and be a double-edged if you've ever seen the only case she could have something that looked like a double it would be if you had Split field a few Shiming was off on the instrument all of your pizza would be splits into 2 peaks and Cedar TMS would be splitter chloroform anything that looked like a methyl singling in general that'll occur curfew have too little sampling year-round inured to brief you have found if you have something wrong with the shimmying ,comma OK so at this point at this point I'm really really ready for some more serious analysis In other words build up the structure at this point get get as many fragments as many fragments as I can so we have c 3 age here were pretty sure I maybe output a dotted line just indicate that we can be absolutely confident there's a double bond you could conceivably have a double bond connected to another another double bond alright let's see we have a bunch of a bunch of unknowns if that's the case we've got led Serie C 1 there's gotta be a carbon dealers seemed to has gotta be a carbon he'll see foreign again I'm pretty sure we're talking about that than being double bonded were not going to be able to do anything with the 15 h 3 indeed actually well will come back to to will come back to these underscore current see 12 H 3 the nineties are going to sort of be problem children so let's work through
let's work through the expansion of the cozy if this point right so very very mechanically I'd go through and I would go and label might be exceeded the F G H I J K L and then just put the numbers here 7 this change In let C 13 F in and 11 g it's nice to have 1 of the staff these 1805 . 5 millimeter pencils because they they really really help you work in crowded spaces it's 12 In and 14 hailed here and let's see 15 year their selected just go ahead and seven-city attending the 15 EU 13 F 11 injury dates 13 on I 11 J 12 K In end food chain so far so we got our cozy here so 7 is interesting so we've got our gonna diagonal probably a good idea to get in the habit of destroying a line on it so you can have it as a point of reference I'm a big fan of keeping my Spector's square I tried a particularly with Proton Proton techniques guest on to really keep my spectrum where it helps me out helps me get better control I like the instrument to enter my my values through the the keyboard rather than just grabbing the cursor OK so we've got some interesting stuff going on here so we've got 7 C cost 15 East so that's kind of interesting remember that was the pair that's the Olmaliq Mathilde and it's we know that that's a little properly because if you have a methyl next directly next to a C H U J value is going to be close to 7 2 7 if there were a couple of Elektra negative Adams might be 6 refined but it's not going to be 1 and we notice that 7 with 7 seventh-seeded also swept into this double that of quartet survived at least look like a double of double it's so the other 1 that's interesting so we don't yet know How old 15 I use connecting in here the other 1 that's really interesting as we get 7 C 10 88 and that's kind of nice because that's giving us that's giving us some connectivity at this at this point so if we start to now we can build up build up a framework for the molecule assuming I can find my marker it will take the take the back of marker so OK so we've got CAT H H for over here we've got 7 it's C Over here some somehow we don't really know we probably have an oxygen on here somehow that's the 15 agency is tying into this so we really don't know exactly what's going on right now alright we continue to build up build framework here and so we get a date said Tandy and we get a H To Abner and let's see we get of 14 Els Ted Tandy and so if we look at that and continue to work to build up our framework show all I'm sorry we get 14 14 L 2 tending right so we get seemed 10 H B and C 14 H 3 L and so at this point we sort of wanna keep track of a valances writer valances fall this methyl groups we have a valence here we have a valence here we have a valence here we have a villains on the oxygen and we're going to continue to build build up Our framework so we move into this crowded region I just did it on this on this expansion here you could easily easily go to another to another expansion so we get we get some interesting once we get our
mn 13 F 11 we get 13 F crosses 13 on a sewer GM and all so that's not particularly useful and it looks like and we see the car arbitary 1 over here it looks like we get 13 after crosses a date and so that that's interesting because now that allows us to to continue to build up our chain and so at this point were building out to sea 13 H F h I so it's kind of like solving a puzzle here we have a valence over there and there we just continue continue across here we get GE cross on a G cross J. over here so let's see 11 change Cross 11th GA that's trivial because that's just a germinal have aligned for that out for while and then we get another 1 which is 11 g us Cross 13 on OK so that that basically gives us and so that's G and J and so that basically completes this fragment everything else we're going to to see here is going to be going to the redundancy you've got this off diagonal peak year of H. cross on a crosses 13 on In so that just reinforces the information we have over here and then we have odd last crossed peak is but is Jay Cross but of course I so 11 Jerry crosses 11 Our 13 high-efficiency incorrectly all right so that basically takes us as far as we can go based on the connectivity and we still have still have better like that for a right this is where we want so this is after this point is where we really have to score card up here of visa a problem children this is sort of where we don't know what to put in yet In its where we won a focus now invariably it ends up being marks an isolated peaks that are the ones that are the problems but there are also the ones that are tremendously beneficial In the agent BC in the reason they're tremendously beneficial is this problem of having your isolated peaks of of of having to win 3 bonds ch coupling both show up and show up not guaranteed to show up in the HM QC in NBC means that you really want to be looking toward isolated peaks to help serve as a linchpin of let me show you how this works here so here our H. B you can pretty much go ahead and cross out all of the G-8 coupled peaks the HM QC tight across speaks the ones I sometimes jokingly referred to as vampire bites so I think but see I think I got them got them all there 1 more hanging out down here he been let's see 1 more hour for worst see over there alright I wanna be good about this so again I'm going to be very slavishly transcribed 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 for my carbon axis and if I just do my letters 3 M A 6 B 7 C standing 15 III it's 13 marker is getting close to the dollar sharper 1 but Eleven the ADA
In by now these guys should be coming becoming good good friends or at least worthy adversaries 13 on 11 J union 12 K 14 jails so the isolated peaks are the ones that I generally start with you don't have that analyze absolutely everything itself on the and maybe but but initially I'm going through and sort of looking OK we've got 1 2 3 need and this is a little confusing 1 2 6 be remembered small or put a question mark their small couplings small couplings skin can end up being confusing here and then 1 15 III now this last 1 really really a but the guests are right so at this point I guess I'm trying to trying to figure out what's going on with which see 1 carbon and so this this 1 is interested so we have snaffled was so solo like mad for and that's really really useful we know that that Mathilde isn't directly connect it to see what right we know it's a little like we're seeing a little like coupling we don't have for the Tony and yet it's isolated that's telling us something that's telling us that as we build up this structure we do now stick R C 15 a off here so that's useful we know it's gonna be on a double bonds ,comma we've got these 2 guys here the 1 2 3 a M 1 2 6 billion we're pretty sure we had assists a South Canaan and so that's going to help us out Over here because now remember those have hydrogen on you can't have H a on the same carbon is a math you can't have H beyond the same problem as a methyl because you'd see a coupling of about 7 herds all we're saying is this very cost so we got this guy over here and these guys have hydrogen is when I'm not certain what I like to do do something like this I don't know if it's carbon 3 carbon 6 connected to carbon I could probably look it up in practice and see which has a bigger coupling constant because 1 of these if it is really coupling is very small the others pretty big and 2 and 3 bond couplings can be surprising but if I go see 3 6 h a HBO later on I can make make certain whether and similarly here I don't know if I have see 3 years and 564 oversee 5 over there but I have that all right let's continue here so I want to move on to carbon number to copy number 2 with another is another Carbondale and carbon number 2 was really interesting we get to nice speaks here to to 10 days and chew 214 L it said that 2 of 14 Ellis another real we don't share because you've got this Mathilde Over here and this Mathilde is isolated here by 10 so I know that that that carbon deal in order to get that crossed speak with 14 that Carbondale seemed to pass the bill Over here In we have 1 Valence now we can find out later by the process of elimination I wish we were seeing across peaked between see and carbon to that's going to depend on the diet he'd roll angle but we use up 1 carbon with a key town here that explains our 1660 it's a conjugate Carboneau we have a lack tone we can close this or we can wait wait till later on for a process of elimination here let's continue our build there's nothing too much else that's going to come in useful off of our off of our Al I'll go through we've got a little bit of useful stuff we've got 3 to to 11 J for this 1 and we got 3 to 12 K go grab my shop repair 3 to 11 the GAA 3 to 12 New and so
far are not quite sure what to do with that it's going to be useful because we're trying to connect we've got this fragment here the answer struggling at this point how the hell out of put them together and let me show you these and we could go ahead and put them in a moment but but I'll show you where things where things come in very very nicely in just just a moment 12 is interesting 12th Kennedy so this is starting this 1 is that that's very interested because we have an isolated from here and so we've got this problem here were taken care Of this guy we've taken care of this guy we've taken care of this guy we've taken care of this guy we have 2 carbons left and we know that the isolated isolated Mathilde it is not directly coupled over here and what's very nice about it that is it really leaves you with the process of elimination but let me show you how beautiful this work so here's your see-through C 12 H 3 please but let me show you how beautifully this works so let me switch tracks at this point I wanna go directly off of that isolated Mathilde so that isolated methyl ends up being a lovely lovely Lynch here you go and you see it's for at 12 K we go ahead we get and let's see if we get OK then we have an interesting 1 year or so so we have 11 to 12 K is up here it is up up there there we have this crossed there as I said 9 and 10 are really really close to each other you might be able to
expand and get this resolved media not depends how good respect if I were running this in the lab I might go down do some additional expansion but what's really nice at this point is you know what that tennis taken out of commission 10 is now completely isolated over here and so this 12 K ends up being this fantastic linchpin that's putting together the molecule because 12 K is crossing with 3 years and so that helps us a sign that 3 has that this 1 so that resolves that which means 6 this once a 6 a and B year this 1 its crossing with Fuller so that linchpin puts in our connectivity hero at this point we have 2 valence sees that left are left to be filled and it really isn't very hard because we have to villains laughter on this part of the molecule so in other words now were also crossing were also crossing with 11 and so that puts in this year and that's puts that therefore connectivity and so we can go through and check on some other aspects of connectivity but I think at this point I want us we can go for example we see some duplicate information off of offer of 7 and so for example by a similar logic is 97 sealed orders some ambiguity we've got some cross peaks over here like 5 to 15 the better giving us information we now have but what I want to do right now is to move into this final stage of determining history chemistry of knowledge or at 1st thing I'm going to do is redraw In all drive to give us a connectivity and similar work in our anomalies .period so see 13 h effort age on is on the top and C 8 and destroying in a particular way C 8 H H and see 11 hg age In C 9 and C 4 To see 5 C 1 carbon meals since 6 it's the authority H A C 12 H 3 K see 15 H 3 E and we continue to see 7 8 see we have a volunteer see 10 inch D. C 14 H 3 L seemed to carbon meal In the oxygen for a long time however it now in terms of where where I go with something like this generally in terms of figuring out Styria chemistry unjust going to go ahead and start by drawing a cycle hexane during that pride the 1 thing I can and can't do kindness clearly and the great thing is you can take a stab at Stary can and very quickly you're not question I'm going to get absolute stereo chemistry but very quickly all see if you have your relatives during a chemistry right so let's just take a stay out so here is that whole unsaturated bring them over here are right and let's take a stand all put in an angular methyl 1 axial methyl let's see 12 it's 3 and let me just start the 1 thing I can do is draw cheers and when you're once you're dealing with a five-member bring you sort of fake it and so you can draw like Tony here and we have a substituent here In a substituent here and what I would probably do is start with this guy over here and see how see how things work out N so we've got let's see we've got 7 over here we've got 8 over here we've got to hand over here are so let's see let's see how things worked out on the NOV alright so this in week the bottom and we use of very very nice express the bottom and we we've got this clear shot at 7 C and he really really answers things for so you radiates 7 and if you look at this as lovely enhancement of you've got a subtraction artifact on neural like methyl that's pretty normal you see a clear enhancement of 13 I. it looks like 8 h has some Jake coupling to wait maybe some some of maybe a tiny bit of enhancement but also something going on ,comma J. coupling because it's not the same multiplicity and we've got 12 OK so that's interesting because we've got our 7 see here and you radiator ham and 12 OK lights up like a Christmas tree 1 3 axial interactions are very nice forgetting and a weasel my hand out that was the 1 I showed it was just like to point something I think Angstrom let's see we have Tendoy over here so that's interesting because that it is really giving us the rest of the hysteria chemistry and the molecule that's giving us we need this 1 center over here but we pretty much pretty much have everything Everything that we need we really can't have a translated and then let's see we have on the back I guess that's it was at that so each on over here tried dried up here so we get that we the age all I that's very nice we look at our other experiments experiments and this one's kind of complementary your radiate 10 and it looks like we have Jake coupling to 8 C it's alright coupling you notice that aren't I face thing we looks like we get a little 1 to 13 on a little hard to tell what's going on here subtraction artifact and we get 7 say so in other words we right we radiate HT we get 7 6 so that's good that's kind of out of office now the last thing here are at this 1 this 1 is kind of a mess because we're coming in will see on the next page in so I'm trying to hit at this point 14 L you'll see on the next page what's going on so we got see 14 it's 3 L methyl he isn't on the next page I assumed did a little bit and so this is the same same experiment and you can see remember what I said stuff to hit peaks that are close to each other so we're hitting here were hitting 14 but we have a little bit of incomplete selectivity so we're hitting 12 OK just a little bit and so you can see mostly were hitting 14 here and you're getting this very very nice and no E 2
10 days OK that sort of makes sense were radiating this methyl groups were getting in and out we overdid here that makes sense they're close to each other it looks like we're also getting in on Over here 2 13 a half In a day so OK so member I sort of was wondering about the started chemistry of this 0 8 h is is on going down and let's see this is 13 on the back here and so 13 F is Equatorial so we get that nice we over there and so that kind of finishes Upper Styria chemistry on molecule and so just just good idea snap it with a camera so so Justice Justice sum up what we basically did was after going through this mechanical part of 1 labeling our residences was really try to put together fragments as completely as possible look at those isolated peaks and tried to use those as linchpins the type of thing together keep our wits about us about chemical shifts and our observations of things like little like coupling and then use NO we use and J values we didn't even go through a big Jason Little Jay's but you'll see they all fit into this axial axial coupling axial advertorial general coupling model so anyway that's the general just for sort of hardcore structures solving and medium-size molecule


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