Lecture 06. Fragmentation in EIMS: Alkanes, Alkenes, Heteroatom Compounds, Carbonyl Compounds

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Lecture 06. Fragmentation in EIMS: Alkanes, Alkenes, Heteroatom Compounds, Carbonyl Compounds
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Lecture 06. Alkanes, Alkenes, Heteroatom and Carbonyl Compounds
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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.
Alkali Spectrometer Carbonylverbindungen Spaltfläche Methylgruppe Chemistry Molecule Electron Lipide Mass spectrometry Chemical compound Naturstoff Setzen <Verfahrenstechnik> Hydride Walking Katalase Food additive Wine tasting descriptors Emission spectrum Taxis Functional group Radical (chemistry) Iron Cycloalkane Methylphenidate Zellmigration Chemical structure Nitrosamine Biomolecular structure
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Ionenbindung Chain (unit) Stannane Species Reaction mechanism Oolite Spaltfläche Wursthülle Chemistry Molecule Electron Ausgangsgestein Library (computing) Öl Setzen <Verfahrenstechnik> Stickstoffatom Doppelbindung Walking Formaldehyde Minimale Hemmkonzentration Carbon (fiber) Katalase Protonation River source Chemical reaction CHARGE syndrome Ash (analytical chemistry) Ampicillin Hydrogen Initiation (chemistry) Functional group Radical (chemistry) Azo coupling Clay Can (band) Butcher Silicon Mixing (process engineering) Cobaltoxide Lymphangioleiomyomatosis Extract
Chain (unit) Chemistry Alpha particle Atomic orbital Molecule Electron Cycloalkane Trauma (medicine) Doppelbindung Alkylation Katalase Solution Chemical reaction Alcohol Stockfish Ash (analytical chemistry) Electronic cigarette Food additive Emission spectrum Lone pair Ampicillin Acid Hydroxyl radical Azo coupling Chemical compound Repeated sequence (DNA) Cobaltoxide Lymphangioleiomyomatosis Chewing gum Stereoselectivity Sense District Ionenbindung Species Reaction mechanism Oolite Geochemistry Spaltfläche Wursthülle Methylgruppe Ham Heroin Common land Acetaldehyde Process (computing) Potenz <Homöopathie> Mixture Phase (waves) Meat Carbon monoxide Rearrangement reaction Carbon (fiber) Carbonylverbindungen Spawn (biology) CHARGE syndrome Water Hydrogen Drop (liquid) Metabolic pathway Radical (chemistry) Functional group Lake
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some method groups and the following groups and you really even with a very high Highfield a spectrometer not going to be able to to see a lot of distinction between these structures but the big difference in mess that commentary is that fragmentation will occur at 26 they give you secondary and tertiary public and irons Miller so if we look for example on the next step them on the spectrum of one-man on Dec 18 and now we know what we see a break in the usual pattern in other words the peaked at 71 is enhanced and the peaked at 57 years diminished and the other thing that's interesting is for all intents and purposes you don't see the molecular ion did very very small and of course the reason for this is now you've got to undesirable break points in the molecule similar cleavage over here and did you know a pendant can I a 2nd Penta probable Cat am and that's going to be give rise to your enhanced the at 71 and conversely the future ways to break the smile molecule to give you a bureau ,comma and because of that came had 2 positions you could break was Saturday but that he had 2 positions you can break with method 1 that he and has wants to have peaked at 57 is diminished and if you look hard to currency European 27 was also enhanced right here you have this sort downward so a person with a mass spectrometry with with Minister MS spectrometer could look at this molecule and say this is for methyl on Dec 18 rather than saying 5 Mathilde on Dec came and this becomes important marine natural products were often you get lipid type groups with unusual patterns as well as in identifying with instructions the I of you know that absolutely absolutely still stabilization of the radical is less important than stabilization of a Carvel Qatar radicals are unhappy Koble cannons are really the radicals have at least 1 electron in the they can what's essentially P 1 little wears purple Qatar and so have no electrons there so they're much more hectic plus you have charged to stabilize other questions yes abc's I would I would imagine young I would imagine you probably well With the methyl there's no simple migration so if you look at it to pinching O'Connor and there's no simple migration that will give you rise I guess what you need is I don't I don't know the answer today that I know in cyclo taxi His cycle had sold hobble Catalan chemistry if you can get a 1 2 0 hydride shift that gives you a tertiary yeah it'll occur if you can get a 1 to Alkol shift of the year tertiary Shiites say if you can find the 1 2 methyl shift it'll probably it will probably occur but in this
case I don't think there's 1 area and then by the time you go to a highly branch compound so here's an example where you really do only have have you do see the tertiary peak predominating so here's another isomer highly branched isomer and you'll notice that the peak that predominates is absolutely that Turkey people cobbled Tadiran and again you don't you don't see the implies you don't see the molecular you have have great great question so the 1st thing that people often do ears blow off the region they suspect the molecular ions areas now the 2nd thing is let's say you have a little bit of information remember the nitrogen role that I mentioned the fact that in the EI mass spectrum if a compound has an odd number of nitrogen as 1 nitrogen a three-night regions were primary regions the molecular weight is off not just the mass of making up molecules so In this spectrum we were seeing peaks at 43 pizzas 57 etc. so if you know all my molecule has no nitrogen and then you see only on peaks you say Oh wait a 2nd these all have to be fragmented fragments so if you have some additional information for example you say OK I know my compound is really natural product that has no no regions in it but I'm only seeing a peek at 171 in the I'm aspect and remember it's all reversed and see I'm aspect is reporting proton which is what that's what then you'd say OK but that can't be the molecular and that's really important because otherwise you got yourself stuck in his mind-set saying all this is the molecular and how do I get this how do I get this structure y I want talk for a moment about AL teams and then move on to head a rat ,comma it's so Al Kinzer are the most militant intuitive because canes have no Nova Paul obvious place to take that on electron out we have to be thinking about sigma bonds molecular orbitals by the time we get to AL teams we can say OK the highest occupied molecular orbitals apply or middle will take an electron helped we'll get a radical can have and we really can remind ourselves that there are going to be to residents structures Stewart and the chemistry of about teens is very similar to the chemistry of but now at least we sort of have a way of thinking about it and we can think about things as a home Oolitic cleavage mechanism often give in little like Pavel Qadir so let me just right sort of a generic compounds mentioned that we had now seen over here and now I've taken the Elstein and I have generated the radical can generated the molecular ion 1 of the very fundamental reactions of radicals is home cleavage home Oolitic cleavage means you take this font and you break it equally home letting you take 1 electron you send it 1 way you take 1 elect you send it the other way solid drum idle fish shook Kerberos that you've been using hopefully sense of organic chemistry for this type of for this type of wrecked reactions and I'll take away minus are prime down not so we don't see that because that's a radical and this gives rise to a mail alike and so on the whole series of peaks the whole series of peaks that you might see for Al-Qaeda 43 57 61 you will see largely diminished by 2 foreign Al 41 55 etc. going up going the series so the case of Alcan's we were talking about C A N age To and plus 1 plus here we're talking about C & H 2 and minus 1 now the AL team tennis and not get a ride it out as a mechanism but you can write a Kurd Barham mechanism to walk radical all over the molecule by a series of 1 2 hydride shifts and so the Al Qaim tends not to state quite so you can't you might think alike could tell where the Al team is in the molecule but this vibrates throughout the molecule so you can pinpoint where the allocation is so let me just put out for comparison and contrast let me put up 1 don't guess seen son the flip side of the page this year and so for 1 day don't saying you see a peaked at 41 by this new pathway and 455 5th for 1 word at
60 yards 69 and so forth and of course you do still see the 43 page so you do also see the other half and while a 57 consoles so the peak at peak at 41 for example is simply this cleavage mechanism I talked about and I can at least in lease right it and as 1 2 3 4 5 6 7 8 9 10 11 12 I can write it there to resonance structures 1 with the primary positive charge and the other the major contributor with the secondary positive charge but I can write occurred are mechanisms showing the home Oolitic cleavage pathway To give rise to deal with troubled continent what's your questions on this point would be peaks with the circles are other pathways that involve for example loss of a hydrogen atoms and so we're not we're not talking about we're not going to talk about every absolutely every every mechanism so for example this peak at 42 although some of it comes from the small amount of C 13 isotopic Amir also has to correspond to a species that is a radical cattle with the formula of C C C 3 8 6 but we're not going to to talk about the the mechanism of formation all right and they could this place what I'd like to do is to move on to Harrow Adams containing compounds and what I think is needed about how 0 Adam containing compounds is we really can make since Of the chemistry from dust a few mechanisms so in addition to the whole political cleavage we can also think of paralytic cleavage mechanisms and hydrogen abstraction fragmentation however still I'll greater generic federal Adam containing compound as part of why we're showing a here on why it is going to be a generic enough that I mean that this could be an alcohol and ease their halide mean but also the OR group on of an Esther and so later on in the homework said you'll get esters and we'll see mechanisms involving the carbon also mechanisms involving the OR group and will also stay made in our 2 groups alright so the general just as we can think of the molecular ions as kicking out 1 of the electrons from the long hair and so for example we we can envision a home Oolitic cleavage mechanism as much as we envisioned the home Oolitic cleavage in the case of our Balanchine's for Allen well around teams so we can envision a whole cleavage unless they could be enhanced my molecule here so I'm drawing in the alpha carving the
carbon that's directly attached to the head all-atom and the data carbon carbon 1 over and mention of mechanism just like we saw before the radical pattern from the Algerian where the bond 1 over from the art electron breaks sending 1 electron to former double bond and the other electron To the other carbon so in such a mechanism will generate a radical and of course the radical you won't see and will also generate a species with a double bond to the library and a positive charge on the life of the people say the other mechanism were gonna see is a header cleavage is paralytic cleavage mechanism that means the 2 electrons go in 1 direction paralytic cleavage mixed cleavage in other words the electrons don't go 1 in 1 way 1 of the other they both go in the same way and for simplicity of just right where Group like so so here we are back at our need to write and write in the rest of the molecule so you can think of the white group remember that's enough oxygen or nitrogen or something with a positive charge you can think of it as a leaving group and the leaving group takes its electrons and leaves much as you've seen in regular Carvel can regular cat and instead of radical cat chemistry where in an essay 1 type of reaction were you 1 reaction the 1st step is the leading group believes with its parent electrons and you get ah plus you get a couple jelly other mechanism that can occur that's along the same lines so another header Oolitic cleavage mechanism is after a hydrogen atom abstraction fragmentation and you can end up With the proton on your leaving group and so all right this is all are Y aid With a positive shows why and in that case again you can take a year off electrons and you're reading group can leave the 3rd common mechanism that will see is a hydrogen atom abstraction fragmentation mechanism and the point that I'll make here is that in addition defragmenting radicals also have a propensity to pull off hydrogen stew extract Adams it's 1 of the reactions of radicals if you've already studied perhaps as an undergraduate tribunal tin hydride chemistry were you have maybe AID in initiator to generate a radical a radical change mechanism New Year's tribunal to tonight lies 1 of the key steps in your chain mechanism is going to be the radical plucked off the church group you will have a hydrogen in your molecule the radical can pluck off the hydrogen it's really quite indiscriminate about where it plucks it off remember not only is it a free radical but it's also a very hot free radical and silicon can go ahead In plucked off that hydrogen it makes you feel like a freshman once again where you have to keep track of all because you're seeing so many unfamiliar species you have to keep track of formal charges and keep track of your order like and so now we have a positive charge on why and this can under show further fragmentation either by way of a home cleavage over here say home we violated the head of the National here but the the in the abstract this sounds very very complicated so what I'd like to do is to render it concrete and I have a handout so transparencies what
this this is your homework at helping you with what you have in October fell below here but if
you want we can just we can just leave no no part of what I'd like what I'd like to do is to convince you that these very few mechanisms I showed you actually account for all the peaks so lucky alright so here are right the 1st thing you'll notice is that our compound has a molecular weight of 102 but our implies is missing this is not uncommon for alcohol then what you can think of is if you generate the radical catalog and you do a whole Miletic cleavage so we have a math fell a hydrogen and 80 the group attached to the Alpha carbon if we cleave the hydrogen and all Miletic cleavage and you'll often see people do an abbreviated mechanism where they just write 1 Fisher took part and parcel with that of course is this odd electron comes in over here and we lose hydrogen itself we do minus . like so then and I tell you what I will even be a good person and writing in all my lone pairs of electrons to help you out then that species is our species at 101 so here we see a tiny peaked at 101 if I in Avery slavish fashion simple repeat this process indulges put the hydrogen down here but my methyl over here if I in a very slavish fashion repeat this process and lose and Mathilde doctor the methyl radical you know I have 1 too 3 4 5 6 years should have it's what they do 1 2 3 4 5 6 2 3 4 5 6 I lost lost my hydrogen to is the but I had occurred in here take off 1 2 3 4 5 I added 7 self easiest solution is just cut it off the here I lose lose the methyl group and they end up with this species should have 1 2 3 4 5 so that explains their peaked at 87 loss of a Mathilde 87 over there if I do the same and I'm going to skip the mechanism but obviously if I just do -minus .period that's going to take us to protonated acetaldehyde side and that's going to be a key 45 alright so that actually takes care of 3 different key peaks In the spectrum also you 1 more pathway and that's our abstraction fragmentation halfway so if I go ahead and began with I write our species and I'll just write it a slightly different way just to make it make it suggestive so if I now now writer our species the hydrogen the oxygen can pluck off a hydrogen it's all draw fish up inefficient and just for the sake of not having fish Oaks fly everywhere I won't drop Fisher back that carbon but you can if you like just 2 other radical and carbon and now the there a couple of ways that we can go if for example Water leaves and at this point we have are paralytic cleavage water is leaving taking its pair of electrons with it's all just put a pair of electrons onto water like so so we get a radical cannot I'm over here that radical caravans going to be at 84 in fact it's very common to see minus 17 an alcohol so that a common cleavage pathway and if I further go ahead isn't loser methyl radical then all and a single fish hook
minus CH 3 . now that's going to give rise to power I think the last species that we were supposed to see which is served peaked at 69 so go ahead you know don't that really been injuries where that paralytic OK beautiful beautiful question so the question is can we also have lost all of always died and the answer is you have a tiny amount Over here not enough to to give a big piece but you actually anticipated my next remark and if we flipped for the next Beckham so the problem is that the OH radicals is really really unstable you have to have an up oxygen has an incomplete architect and so that's bad but the other thing that army that's bad about about it is you get no hyper conjugated stabilization of the radical now if we look at this Easter here on the next play page then you can see this mechanism so I'll just use this as a chance To what to show this to you so you also see a home Oolitic cleavage mechanism of all leave that to you to write on your own and if we apply a header related cleavage here the weaving group takes its 2 electrons and leaves sell this radical this oxygen centered radical is more stable than a hydroxyl radical so we lose 73 are molecule was 130 to start with see it but now we get 8 Carbol cat I'm here that you there in a concerted fashion that were stepwise fashion almost certainly rearranges to the church people cobbled which is this and so the answer is in the alcohol you may have a little bit of it but not enough to really see in this case we haven't even more so this year in some cases you'll see a direct so I think yet in the end the alcohol if you look there's a teeny tiny peaked at 85 and it's not clear whether it's big enough whether it's the 13 isotope about whether whether it is whether it's this alright I'll leave it to you or I will talk about the next 1 in discussion section but I want to finish up by talking of carbonyl it's because we've gotten all but 1 of the mechanisms here and the key mechanism for carbon geochemistry so for carbon compounds and that's the whole family out the hides the tones etc fosters and animated acids the whole bloody family you can think of this in a couple of ways you have a whole melodic cleavage pathway and in the whole Miletic cleavage pathway it's the same as before you picture taking your electron out of a lone pair the reason is the lone pairs of the highest occupied molecular orbitals in the molecule in a whole Miletic cleavage pathway you break a bond like so you lose are done you lose erratic and you get an is solely a mile In many cases so that'll cost you part of the molecule in many cases you'll see a further fragmentation where are you now have a heroin it pleases you lose carbon-monoxide and you get same call this part crimes so I will stick with that and you get our prime plus as the cobbled this same chemistry that occurs here can in in Friedel craft solution phase chemistry so for example if I set out to do a Friedel crafts installation reaction with a compound that could easily fragment to give a church futile alkyl Carbo Qatar and I might end up seeing Friedel crafts alkylation competing with the Friedel crafts a selection of the worst loss of carbon monoxide from my silly in the gas phase were molecules are hot it's even more prevalent the other key reaction of carbonyl compounds is them aquifer the rearrangement that's a charge accelerated retrofitting reaction 4 and new reaction is a Paris a quick-reaction it's very much akin to the deal's older reaction in the forward direction it brings together in Al Qaim component and a component with a double bond in the reverse direction you just push electrons in the opposite way and I'll show you how I like to think of the Lafferty rearrangement sometimes you'll see it written with Fish Stocks Chelsea a written as a radical reaction to me this makes much more sense to think of it as a Paris cyclic reaction so here I've written a powerful chain hanging off of my radical cattle and if we simply move electrons in a ring in pairs In 6 electron Paris a quick process much like you're going to learn in the event ranking our class in 2 0 1 if you haven't already done a mail you can get a very nice I guess I'll call that crime you can get a very nice curve mechanism the kicks out milking but 1 1 moment to show you this pathway so you will
see in this compound you will see examples of the whole Miletic cleavage the home cleavage with loss of carbon-monoxide I'll let you figure those all out but I just want to show you the McLeod for the pathway here we are at 1 2 3 4 5 6 0 to Hexham known and if I just write Monica Lafferty rearrangement like so I lose probe penal that's minus 42 we started with the weight of 100 And so let me just right my the the resulting product and so we come to a peak at 58 and there we see 58 so as I said you will also see all these other pathways we've talked about you'll see the whole Miletic cleavage and further loss of Seattle
we'll see some abstraction fragmentation well no let you figure all that out of homework and I should point out on the preceeding problem on the main problem In addition to seeing the pathways of that we've talked about in addition to seeing for example the whole balletic cleavage pathway you will see a further retro Union pathway giving rise to what actually is the strongest in the molecule so will talk more about the use of foreign


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