Monday, February 18, 2013

Blog Syn #003: Benzylic Oxidation of Arylmethanes by IBX

(Disclaimer: The following experiments do not constitute rigorous peer review, but rather illustrate typical yields obtained and observations gleaned by trained synthetic chemists attempting to reproduce literature procedures. We've taken efforts to stay close to the original procedure, using similar glassware, equipment, and reagents wherever possible. Images have been cropped and scaled to fit in the allotted space, but have not been digitally altered otherwise.)

Update 2: 2/27/13 - Added Tamsyn NMR and email
Update 1: 2/25/13 - Added Phil NMR and email

Ref: Nicolaou, K. C.; Montagnon, T.; Baran, P. S.; Zhong, Y. L. J. Am. Chem. Soc. 2002124, 2245–2258.
Supporting Info

Experimenters: Three - B.R.S.M. and coworker (United Kingdom),  See Arr Oh (Somewhere, U.S.A.)

Recommendation: Pending Blog Syn repeat
Initial - Difficult to reproduce - little / no product observed or isolated.
*See below for Phil Baran's response and repeated reaction.



In Blog Syn's third installment, we examine a benzylic oxidation reaction pointed out by Chemjobber commenter Jose. Jose claims “0% conversion for multiple substrates with multiple chemists" using this reaction. The source paper is one of a four-part series penned by K.C. Nicolaou and Phil Baran describing the multitudinous uses of o-iodoxybenzoic acid (IBX) in organic synthesis. With Jose’s comment fully in mind, the Blog Syn Team members See Arr Oh and BRSM put the reaction to the test. 

A day in the library can save you a week in the lab, so let’s examine this paper’s impact using SciFinder: it's been cited 179 times from 2002-2013. Using the “Get Reactions" tool, coupled with SciFinder’s convenient new “Group by Transformation” feature, we identified 54 reactions from the citing articles that can be classified as “Oxidations of Arylmethanes to Aldehydes/Ketones" (the original reaction's designation). Of these 54 reactions, only four (4) use the conditions reported in this paper, and all four of those come from one article:  Binder, J. T.; Kirsch, S. F. Org. Lett. 20068, 2151–2153, which describes IBX as “an excellent reagent for the selective oxidation to generate synthetically useful 5-formylpyrroles.” Kirsch's yields range from 53-79% for relatively complex substrates, not too shabby.

Well, let’s see how things stack up for BRSM and See Arr Oh.


TRIAL 1 / 1a:


Experimenter: BRSM (and friend!)
Scale: 1 mmol (the paper claims 0.1 mmol to 1 mmol, without giving scales for specific entries. Used SI general procedure)
Example: 4-bromotoluene (table 5, entry 6)



Reagents: Aldrich fluorobenzene, 99%, borrowed and used as recieved;  Aldrich 4-bromotoluene, 98%, used as is; ACROS Extra Dry  DMSO, 99.7%  / AcroSeal'd bottle (almost new), IBX prepared according to JOC 1999, 4537, stored in freezer ~6 months. 

Observations:  A 1:1 mixture of DMSO:PhF was used at the suggested concentration of 1.25 M with respect to IBX as starting material wasn't soluble in DMSO. The reaction was carried out in a sealed tube that had been oven-dried for several days at 140 ºC and cooled under argon. IBX was found to be almost completely insoluble in this solvent system even at 90 ºC (Dry-Syn temperature). Stirred for 16 h, causing no apparent change to the white suspension. Worked up as described, except that saturated NaHCO3 solution was substituted for the 5% solution used by the authors. A white solid was recovered (177 mg). TLC after workup (20% ethyl acetate in petrol 40-60)  showed a faint new spot at Rf 0.5 that stained rapidly with KMnO4 dip without heating. 

Analysis: Crude 1H NMR showed trace product, with the balance being made up by starting material with traces of PhF and 2-iodobenzoic acid. As the mass recovery was good (177 mg crude back from 171 mg starting material) and the product aldehyde is not volatile (bp 240 ºC), it must be concluded that the reaction did not occur.



BRSM, crude NMR

Advice: As See Arr Oh and others have observed, the main problem with trying to repeat this work is the lack of an unambiguous Experimental procedure. Reactions were apparently carried out in either DMSO, or 1:2 DMSO:Fluorobenzene according to the paper, but the SI says that the ratio is substrate-dependent and that the reaction is faster if the amount of fluorobenzene is minimised. With such scant detail, it's pretty hard to say how precisely we repeated the reaction. Also, although I'm reasonably sure my IBX was good, I wonder what the authors used. As they don't state otherwise I presume that commercial IBX was used, if their general SI preamble is to be believed. I've never bought IBX, but I imagine it's packed out with lots of stabilisers, which might be important for the reaction. Would be interesting to try again with commercial IBX just to be sure.

Extra Credit: A lab-mate of mine tried a 1 mmol reaction on toluene (table 5, example 1), which was obtained from Fisher Scientific via our communal drying towers, using the same reagents and set-up as above. His tube was in the same Dry-Syn as mine, for the same time, and worked up identically. No colour change was observed and TLC against benzaldehyde seemed to indicate that no product had formed in the reaction before work-up. His crude NMR is a bit different to mine (presumably a lot of toluene was lost during workup and concentration), but still shows a serious lack of aldehydes. 

"Lab friend," toluene, with IBX

TRIAL 2: 


Experimenter: See Arr Oh
Scale: 1.0 mmol
Example: 2-methylnaphthalene (Table 5, Entry 10) 



Reagents: ACROS fluorobenzene, 99%, dried over 4A sieves; ACROS 2-methylnaphthalene, 97%, Alfa DMSO, 99.9% HPLC / ChemSeal bottle, IBX prepared in-house following JOC 1999, 4537, recrystallized, stored in freezer ~6 mos. IBX so prepared was active in enone dehydration reaction (see: Baran, Nicolaou ibid.)

Observations: Combined all reagents in oven-dried pressure tube under N2 stream. White suspension in 1:1 DMSO / fluorobenzene. Heated to 85-90˚C on sand bath. Suspension turns peach-orange, then deep yellow. Heated 19 h. TLC at 19 h shows faint spot at Rf 0.5 (5% MTBE / Hept). Workup: bicarb wash, extract with MTBE 3x, washed with H2O, dried over Na2SO4, concentrated to yellow solid, 220 mg.

Analysis: Crude 1H NMR: <5% product observed. 

SAO, Crude NMR

Advice: Supporting Information indicates a "substrate dependent ratio [of fluorobenzene:DMSO] with fluorobenzene conc. being minimized." My reaction never went completely into solution, despite attempts to sonicate / shake flask. It's possible that a different ratio of solvent may have promoted the reaction, but I'm skeptical.

SAO, Crude solid
SAO, Unreacted mixture


Author Response: Sent over by Prof. Phil Baran, Feb 10, 2013 (highlights mine): 

"...my recollection was that the IBX we made was ALWAYS completely soluble in DMSO at higher temperature (80 degrees I recall), and dissolved in DMSO prior to use in the oxidation reaction.. I always tried to do my reactions in pure DMSO. In addition, we never ordered IBX, it was always made freshly before use, ensuring that it was made with an internal heating temperature of 73 degrees Celsius to get the optimal yield and purity of product.  IBX quality was discerned by 1H NMR in DMSO prior to use. I'd recommend you try these reactions without the fluorobenzene, which was used with certain substrates that were not soluble in pure DMSO at elevated temperature.  


It's unfortunate that the SI was not clear enough for you and your colleagues to repeat it, but I can assure you that this reaction IS reproducible and was done independently by several highly qualified chemists within the Nicolaou laboratory prior to publication.  There might also be value in reproducing one of the substrates reported in one of the other literature examples that use IBX for benzylic oxidation (the 2006 Org. Lett., page 2151 you mention for example). In addition to the papers that use stoichiometric IBX others have found catalytic versions also capable of benzylic oxidation."

[Update(2/25/13) - Tamsyn Montagnon was indadvertently left off the original email chain.]

2/12/13
"It is right to suggest doing these reactions without fluorobenzene - I think a lot of the issue is that simple alkanes are pretty tricky in these reactions, because they aren't soluble in DMSO so you get little micelles floating on the surface and not reacting – ironically, this is a reaction that works better on more complicated substrates that have more functionality to assist in solubilizing them....FB certainly hinders the reaction (again probably a facet of creating almost a two phase reaction mixture)......and IBX is most certainly completely soluble in DMSO at RT, let alone elevated temps, anybody that has ever oxidized an alcohol with IBX knows this - IBA on the other hand is not, it crashes out during IBX oxidations and hinders the work of IBX (probably by being more Lewis acidic and sequestering non-productively substrate - if you add extra equivs of IBX once you have IBA in a reaction (in alcohol oxidations, dehydrogenations, benzylic oxidations whatever) you don't push it to completion you just end up with more IBA crashed out. The fact that they made a "Dess Martin" from their IBX means nothing ...God knows what oxidant you get if you heat up an IBX/IBA mixture in (Ac)2O."


TRIAL 3: 


B.R.S.M. (again) - We decided to re-run the reaction, given Prof. Baran's helpful suggestions.



Based on these comments, I decided that I'd have to remake the IBX fresh to their specifications in order to test the reaction properly. At first, I made IBX using the second procedure in the Oxone JOC paper (i.e. using 3 equiv. Oxone and a more dilute reaction mixture). I repeated the reaction on the scale (5g) and concentration given in the paper. On Phil's suggestion, I also used a thermometer and a great deal of time to ensure that the internal temperature was held at 70-73 degrees C. As promised, this batch contained no 2-iodobenzoic or 2-iodosobenzoic acid, but it did have around 5% of some other impurity I couldn't identify. The prep supposedly delivers 99% analytically pure IBX, so I was a little disappointed.

BRSM's new IBX batch

It's interesting to note at this point that the NMR data for IBX given in the Org. Synth. prep for Dess-Martin seems a little odd; two of the aromatic protons have coupling constants of 14.8 Hz, which seems inexplicably large to me. The chemical shifts given in the Org. Synth. prep do match the literature, but I can't find coupling constants given anywhere else for IBX to compare. Mine are not that large. Strange. Also, all batches of IBX I have analyzed by NMR have a broad peak around 10, which I'd always put down the the OH, but this doesn't seem to be mentioned in the literature. 

**This batch was totally soluble in neat DMSO at RT**

I checked my 2-iodobenzoic acid starting material by NMR - it was pure and free from impurities. I really wanted to make "perfect" IBX to give the benzylic oxidation a fair hearing, so I borrowed some 2-IBA and some Oxone from another group and tried again. I produced another batch, essentially identical to the first one, which is to say, ~95% pure by NMR. My colleague and I re-ran our benzylic oxidations on PhMe and 4-Br-PhMe with this "new" IBX. Based on the authors' recommendations we used neat DMSO. The IBX didn't dissolve immediately, although the literature (Tet. Lett.) says that it can take 10-15 mins stirring to go in. We starting heating straight after adding it and about 10 mins later, at an oil bath temp of 40 degrees C, we obtained clear solutions. 

In the case of PhMe, the results were similar, with perhaps a larger aldehyde peak in the crude NMR, although given the volatility of the toluene we couldn't really measure conversion accurately. Benzaldehyde was also visible by TLC, which it wasn't for the first run. My colleague attempted a column but no aldehyde could be isolated. For the 4-Br-PhMe (which I ran) the results were quite different from last time. The mass recovery was worse - only 100 mg back from 171mg, compared to perfect recovery last time - although the same scale and workup were used. Also, the crude NMR was messier and didn't seem to contain as much unreacted SM. Still apparently <5% aldehyde, though. And the literature boiling point is ~240 degrees, so I doubt I lost it. 


TRIAL 4: 


(Update: 2/21/13) See Arr Oh here again: noting suggestions made by Prof. Baran and various commenters, I re-set a 1.0 mmol reaction, this time in pure DMSO with 0.1 volume of H2O under a lab air environment. I observed the material going mostly into solution (60 degrees), and a lemon-yellow color evolved inside of 2 hours.

Checking the reaction by TLC at 12 hours, however (see Just Like Cooking) did not indicate a much better result than I had obtained previously. Perhaps, as suggested, my IBX is simply too old; commenters' suggestions to re-make a new batch, recrystallize, or test IBX by iodometric titration are all under consideration. 

I have heard that BRSM may be running the reaction with other co-solvents / conditions, so keep those fingers crossed!

*Author Addendum: One week after our initial post, Prof. Phil Baran wrote in with a successfully duplicated reaction and a much more elaborate experimental write-up. Below, I've reproduced his email and pictures in their entirety.


"I write regarding your entry on IBX oxidation of aryl methyl groups which your team found to be irreproducible.  I have subsequently had a student run this reaction under the published conditions and the results, documented with pictures of everything, are below.  I would like to mention that in the future it is very easy for you or any of your readers to contact me directly with any questions – those experiencing trouble could have emailed me anytime. Looking back on those days, well over a decade ago, I remember KC watching Yong-Li (one of the most incredible chemists I've ever worked with) and I do these reactions and us sharing TLC plates with him in our excitement. It was fun to do this reaction again and it brought back nice memories :)

Since your blog is quite new, I think it might be nice if in the future you give the authors a week or so to respond to claims of irreproducibility. After all, the paper has been out for over a decade so would an extra week hurt? You are, I suppose, in search of the truth. And the truth cannot always be realized with "Speed and Aplomb" as your blog advertises.  Incidentally, my colleague Jin-Quan Yu has also reproduced his reaction and sent you all the evidence that it is, in fact, completely reproducible (not "moderately" so as is stated on your website).  

I understand that your blog is meant to be helpful but you should also remember (as Yong-Li, a 10 year Merck Process veteran reminded me the other day) that many reactions have a "window" of reproducibility. In the current case it might be with regards to the quality of the IBX used (your spectrum of "good" IBX does not look very good - see attached for an example of what good IBX looks like) and the actual internal temperature employed.  If you are doing the reaction on something as volatile as toluene or 2-methylnapthalene then you must ensure that the entire flask, vial, or sealed tube is at 80-100 degrees or the SM will simply "hang out" at the the cooler part of the vessel. That's precisely why you and your colleagues saw little or no product because the SM was never actually exposed to the IBX (high or low quality it should have worked to some extent). Seems obvious in retrospect, and thats probably why it wasn't explicitly stated in the SI. That was our mistake.

Over the years my students have run dozens (if not hundreds) of literature reactions that either did not work in their hands or gave significantly lower yields of product than reported – before around 1995 many papers had no SI or procedures to speak of (except maybe JOC). I think all experienced organic chemists have seen this. That's why journals like Org. Syn. and Org. Proc. Res. Dev. exist. General procedures in an SI are mostly general guidelines. In the full paper we did give a number of examples of different conditions and it is up to the chemist to decide on the best ones for a given substrate (as the Kirsch group did in 2006 when they successfully oxidized several complex benzylic substrates at 110 degrees in DMSO with IBX).  

Your blog will remind the community of the importance of documenting even the most minute and subtle details and pictures of reaction setups of new reactions.  General procedures are clearly not always enough and, ideally, a Supporting Information should resemble an Organic Synthesis prep. Our group will certainly keep this in mind in the future and I suspect most of the academic community will too. And again, I am available day or night to anyone (anonymous or not) that has questions about anything I have co-authored.

Thanks for pushing the field in a positive direction.

Best Wishes,

phil

p.s. Tamsyn will also be emailing you again soon (you ignored her first email with suggestions) with her pictures of a reproduced reaction from a different lab.

–––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––

The following is the procedure, TLC, NMRs (of IBX, 2-methylnapthalene, and product), and reaction setup used for 2-methylnapthalene (the substrate that you obtained "0% yield" on).

To a 1.25M solution of 2-methylnapthalene (distilled, 22 mg) in DMSO/PhF (5:1) was added IBX (NMR spectrum attached) and the reaction was heated to 95 degrees for 24 hours (TLC performed with 9:1 Hexanes:EtOAc). The vial was wrapped in foil and submerged as low as possible in the oil bath to prevent the volatile SM from escaping.  As a control, if the reaction was done with pure DMSO and submerged only halfway, the napthalene refluxed at the top of the vial (confirmed by cooling it and watching the 2-methylnapthalene crystallize) and <10% conversion was observed since the reaction cannot take place if all reactants are not in solution.  After 24 hours the reaction was worked up exactly as described in the SI (using 5% NaHCO3) and extracted with EtOAc. A silica column was run and 16mg of pristine product (65%) was obtained.  I'm certain if this is done on larger scale and/or the solvent ratio is modified slightly a much higher yield can be obtained. This was essentially the first time (aside from the pure DMSO reaction) this student did this reaction and it will be the last."

SM

SM in DMSO-d6
Fluorobenzene

DMSO-d6

All SM before reaction.

IBX in DMSO-d6
Rxn, showing 95 deg C

Close up on oil bath w/vials

TLC

Final product

Final pdt NMR, CDCl3
*See Arr Oh here: We at Blog Syn thank Prof. Baran for his willingness to re-run the reaction, and for sending over visual evidence. Once we have a chance to run it in our hands with the improved conditions, we will reconsider the above recommendation.

Author Addendum II: Dr. Tamsyn Montagnon has also written in with a duplicated reaction. Below, I've reproduced her email and pictures in their entirety:

"You may want to consider the following:

[1] Good IBX really is NOT hard to make. It should be free flowing, crystalline with a definite sparkle. See attached 1H NMR.

[2] There is in your discussion a throw away comment about the 2-methylnaphthalene not being volatile. Have you never showered and then left your hair to dry at room temperature? – water evaporates at RT, just as 2-methylnaphthalene does at 95 ºC. I suggest to you that at the working temperatures of this reaction, the biggest problem may be substrate evaporation (or “hanging out” on the colder parts of the flask as Phil said).

[3] As Phil also said every reaction has a window. I think we can all agree that the window for this reaction is pretty narrow and that what you are seeking in your blog-site work are wide windows, ones that aren’t so sensitive to the many variables in play. This, however, is a more complex discussion than you are making out to be.

[4] We need fluorobenzene to reflux in these reactions and in so-doing wash substrate back into the reaction from the walls of the vessel, but it clearly slows/inhibits the reaction also – so, we need to tune this balance carefully and with patience. Scale will have a big influence on how well this process works.

[5] Likewise, IBX decomposes under the reaction conditions (heating in a DMSO solution) so again we have to balance this with the need for higher temperatures to initiate the reaction when trying to find the best conditions for each substrate.

[6] I also believe the method used in isolation of the products is critical here. The reaction by-products are solids onto which the products stick (these hypervalent iodine compounds are all very oxaphilic Lewis acids). Without care, the layers are hard to separate and material gets lost in amongst the solid residue and poorly separated layers.

Moving on to the test reaction I conducted this week. Unfortunately, I work in a lab with extremely limited resources and therefore I have encountered some problems; the most important being we have no fluorobenzene on site, a lag time of a month on all orders we place for chemicals and very little money for consumables. For these reasons, I had to conduct the reaction with benzene instead of fluorobenzene – as you’ll appreciate I kept the scale small, because I really wasn’t keen on large scale benzene refluxing. It has to be said though that it is rather an important 5 ºC at the given reaction temperatures that we are talking about here (benzene refluxes at 80 ºC and fluorobenzene at 85 ºC), but despite this I obtained significant product (in contrast to your claim of no product). I also used 1-methylnapthalene not 2-methylnapthalene because this is all that we had.

Photos are attached of all relevant reagents/ set up etc.

Otherwise, I carried out the reaction exactly as Phil described in his procedure except that I added the IBX (3 equiv.) in four evenly spaced portions (be careful not to open up a hot reaction and loose all the substrate in the course of these additions though!). Also, with regard to the work up, I prefer to extract with diethyl ether because EtOAc or DCM drag IBX/by-product residues into the organic phase. I also tend to filter through a small pad of celite (after addition of diethyl ether) to remove solids.

I obtained 27 mg, 48 % of the desired aldehyde (1H NMR attached) and recovered 20 mg, 40 % unreacted start material."



Starting materials
1-methylnaphthalene NMR

IBX NMR
Reaction setup

TLC, crude reaction

Pdt NMR, CDCl3
*We at Blog Syn thank Dr. Montagnon for her willingness to duplicate the reaction and for sending over visual evidence. We will incorporate her reaction into our final assessment.

Roundup:


This reaction clearly requires mojo. We observe a fairly substantial difference between the authors’ results and ours; a quick poll around the blogosphere suggests others also have trouble with this reaction. An unclear Supporting Info, a highly-variable reagent, and possible physical phenomena (IBX solubility, temperature control, etc) could potentially explain our experimental results. 

Given Blog Syn’s credo, we must deem this reaction Difficult to reproduce.

Thanks to B.R.S.M. (and friend) for synthetic runs, and for the second round based on Dr. Baran's advice. Readers, have you run this before, successfully? Please discuss your secrets in the Comments section.

57 comments:

  1. I tried this a few times, never got any product over 5%. We tried different people making the IBX, buying IBX, hell I think we even roped in another lab down the hall to see what we were missing.

    My PI just assumed it was b/c I wasn't super awesome like Phil. Oh well, maybe I will forward him this post.

    ReplyDelete
  2. MOAR! I actually learn something about organic chemistry.

    And really consider Kickstarter, or compatible, to cover your costs and get more people involved.

    ReplyDelete
  3. 1) I wonder about the role of water in this reaction. It may be possible that traces of water are necessary... so not so dry DMSO could be better.

    2) About IBX and Nicolaou... I tried once to reproduce the conversion from cheap cycloheptAnone to expensive 2-cyccloheptEnone. According to them (JACS 2002, 2245) is possible to do that step in 88% yield avoiding the cycloheptenDIEN-one. NO WAY. Conversion in each attempt (fresh and good IBX) was low and selectivity poor, so you end up having a tedious mixture of three cycloheptxxxones. When commenting that to my boss, he said "ah, yeah, we tried that in the past and didn't work at all". End-game: Sigma-Aldrich was happy to sell us our desired product.

    3) I must say as well that a colleague of mine could make her desired cyclooctaDIENone from the cyclooctAnone using this method. But she had to "get expertise"... IBX from second method of the JOC, adjusting equivalents.... etc. Presence of iodoso-species in IBX were not good for this reaction.

    ReplyDelete
    Replies
    1. And good to see you here Santi,
      This reaction is weird, but it (under some kind of magic condition) work.

      substitute magic with whatever variable come up in your mind

      Delete
  4. It'd be interesting if someone from Prof. Baran's lab who has done this successfully could post a successful run in the same "open lab book" format you use. Your efforts are interesting, but together with a successful reaction it'd be potentially quite instructive.

    (Obviously it may be that nobody from the Baran lab is reading this or has time, but a guy can hope.)

    ReplyDelete
    Replies
    1. We can hope! I really wanted this one to work; we did the first reactions over a week ago, but waited in order to test out Prof Baran's suggestions before going live. I made two new IBX batches for this post in order to give the reaction a fair trial. These reactions probably do work, but apparently not with the published proceedure. I'd love to know what we're doing wrong!

      Delete
    2. I assure you, they are reading this.

      Delete
  5. It's a relief to see this post. I tried to repeat this IBX oxidation in my grad school a few years ago. I freshly prepared my IBX through both means: KBrO3 and oxone. None gave me significant conversion with toluene as substrate. I ended up changing my synthetic route. My 2 cents: is it possible that some metal contamination in IBX helped the authors getting higher conversion?

    ReplyDelete
    Replies
    1. That's a very interesting question, given the recent surge in "metal-free" reactions that ended up having ppb levels of Cu and Pd in the bicarbonate bases...

      Delete
    2. Unfortunately Prof. Baran's suggestion to try the 2006 Org. Lett paper substrates/methodolgy is useless as that paper doesn't give ANY experimental detail other than a picture of the IBX oxidation w/ reagents, molar equivalents, and temps. The SI in that paper is silent wrt to the reaction other than showing NMR data.

      Delete
    3. Here's the link: http://pubs.acs.org/doi/suppl/10.1021/ol060664z

      Delete
  6. Keep up the great work guys, I think this is an extraordinarily valuable contribution to the chem blogosphere! And who knows, maybe Blog Syn will help authors think a little about the quality of their method sections and SI.

    ReplyDelete
  7. I think it is quite possible that the IBX used in Baran work was made by the old KBrO3 + H2SO4 route and contained bromide/bromate impurities. Br radical is quite a good agent to bring about benzylic bromination and oxidative solvolysis of benzyl bromides in DMSO with heating is a good way of making aldehydes. I would try to re-run the reaction in the presence of a) 20mol% of KBr b) 20 mol% of KBrO3

    by the way, KBrO3 alone is not too shabby for oxidizing benzylic positions as long as you rund the reaction at reflux in water during the day - sunlight is critical for starting the radical chain. Oxidation of undesired enantiomer of chloramphenicol base (to a racemizable aminoketone) with aqueous KBrO3 is done industrially, with floodlight illumination

    ReplyDelete
  8. IBX, prepared by the oxone prep (95% purity has always worked for me), or IBX-MPO is my standard for oxidation of ketones to enones and I have used it successfully multiple times on various substrates, although I never tried benzylic oxidation.
    Tips:
    As mentioned above, it needs water to react...I use wet DMSO. As Phil said, use only enough co-solvent to dissolve your substrate if DMSO won't do it. Also, IBX starts decomposing not much above 90 degrees...I try to keep my reactions at 80 or below. Finally, while milkshake may call me a wimp, the KBrO3 prep makes IBX that is shock sensitive.

    ReplyDelete
    Replies
    1. Anon (and Follower, below): Ah, the Schreiber paper: https://www.broadinstitute.org/chembio/lab_schreiber/pubs/pdffiles/193.pdf

      I don't doubt that water also accelerates the reaction, however, the SI explicitly states: "All reactions were carried out under an argon atmosphere with dry solvents under anhydrous conditions, unless otherwise specified."

      No one would doubt the value of trace O2 in the solvent for these oxidations, either...but, again, this doesn't jive with the SI as written.

      Delete
    2. Entry 3 in Table 5 of the paper shows that the addition of water (100 eq) has no effect on the reaction (same conditions w/ effectively the same yield as anhydrous conditions).

      A large number of chemist-hours have clearly been wasted by the synthetic community trying to reproduce the claims in this paper. I find it interesting that a decade later, there is not a single reported reaction in SciFinder which confirms the claims AND reports synthetic details.........

      Delete
    3. Actually ALL IBX procedures afford shock sensitive materials and should be treated with some degree of caution. I would never heat IBX that wasn't first dissolved in DMSO, and even then I would do it behind a blast shield. The commercial versions of IBX have stabilizers added to improve stability, but I would still be wary of heating IBX on anything but a small scale. It's been a long time since I've worked with IBX, but I seem to recall that you can make 0.2 or 0.3 M DMSO solutions of the stuff if you just stir at room temp for a while (~20-30 min). It's worth the wait.

      When I was a first year grad student in K.C.'s group we submitted an Org. Synth. prep on the room-temperature oxidation of TMS enol ethers to enones using IBX-MPO complex. (Interestingly enough, percent conversion in this reaction depended on solubility of your substrate in DMSO.) Our submission included the Oxone prep of IBX and during safety checking by some process chemists it was found that this "safe" IBX explosively decomposed during bomb calorimetry, taking the instrument with it. I recall that they also observed some shock sensitivity. Rightfully so, they refused to put IBX in their reactors from that point forward and our submission was ultimately rejected on safety grounds.

      I also know of a really bad accident that happened during the preparation of DMP from IBX on a large scale. The reaction violently erupted, shattering the flask and the suspected cause was the heating of undissolved IBX after the chemist's stirrer stopped functioning.

      Delete
  9. further to Santi Barrosso's comment I saw a paper a while back (possibly S.Schreiber?) where they reported a reaction that would only work with one batch of their DMP it turned out to be slightly wet so they ended up adding a minute amount of water and the reaction started working again with whatever batch of stock DMP they had, could be the case here? *speculation*

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    Replies
    1. no it is not the case, IBX is not acetylated. I remember that Schreiber group paper - nothing earth-shattering. People have been starting Dess-Martin with a drop of tBuOH much before, and what works even better for activation is a small amount of pyridine. (Pyridine also keeps TES ethers and other highly acid sensitive protecting groups from coming off by DMP)

      Delete
    2. yeah it really wasn't earth shattering! but just popped into my head. Cheers for the tips with the DMP heard of some of those before now I think about it...damn my brain!

      Delete
  10. Unrelated to this post, but I (and other chemists more technically talented than me) have had trouble reproducing the synthesis of O-(2,4-Dinitrophenyl)hydroxylamine as reported in this paper: http://pubs.acs.org/doi/abs/10.1021/jo034456l.

    According to the paper, the product is made is >90% yield and excellent purity upon deprotection with hydrazine. I was never able to reproduce this result after trying about a dozen times using the original procedure and various modifications (source of hydrazine, etc.). I'd love to know if it was just us me being a crappy chemist or if there was something truly wrong with the reaction/procedure.

    This reagent was also used in Kurti's recent paper (http://pubs.acs.org/doi/full/10.1021/ja309637r) on amination of boronic acids (although they have a commercial source for their reagent).

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  11. Hot Diggity Dog! I am exceedingly glad to see these results- they are wholly consistent with ours, it's good to know we weren't hacks. If the reaction works, I suspect it is a due to trace impurities in the IBX; good for a follow-up paper if anyone is in the market! The paucity of refs for reactions using those conditions certainly says something....

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  12. Nicolaou, K.C.; Baran, P.S. Angew. Chem. Int. Ed. 2002, 41, 2678-2720.

    "In the midst of their desperation and hope,
    Yong-Li Zhong and Phil postulated that raising the temperature
    might persuade the lactol to reveal its primary alcohol,
    thus rendering it susceptible to oxidation by DMP. They
    proceeded to design, in complete secrecy (from K.C.N.), an
    experiment in which hydroxylactol 132 was to be heated in
    refluxing benzene with excess DMP! It is fair to say at this
    junction that had they informed me of their intention to heat
    DMP at such temperatures, I would have most likely
    instructed them against this course of action in light of the
    assumption that DMP could possibly be explosive at high
    temperatures. Their plot was, therefore, perfect and they got
    away with it..." "...That was when I (K.C.N.) heard
    about their daring escapades with high-temperature DMP
    oxidations. In retrospect I am, of course, glad that I did not
    interfere with this part of the expedition which brought us
    within striking distance of the ™Minotaur" the CP molecules"

    "Upon increasing the
    reaction temperature to 90 C, remarkably efficient conversion
    to 215 was observed. In fact, this result was initially
    received with considerable skepticism by one us (KCN).
    Could it be that inadequate experimental technique led to this
    bizarre finding or had we discovered another unique reaction?
    And how is it that no one had ever reported such
    reactions with iodine(v )-based reagents or hypervalent iodine
    compounds in general? It was time to consider this issue from
    a more global perspective."

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    Replies
    1. Perhaps you didn't pay enough to Charon to get across the river to the land of reactions, that laboratory in the sky, where the yields are always 100% and they are all reproducible.

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  13. This is totally outside my expertise, but the fact that something weird is going on with IBX before you even use it seems to be a red flag. Figuring out the explanation might give you the answer and would probably be worth doing in any case. (Could this have anything to do with tautomerism of IBX?)

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  14. How lucky I am to come across your website on a reaction which I have been trying to attempt during my work. I have a nitrated benzocycloheptenone which I thought could be a trial to see if I can achieve selective benzylic oxidation (that was the primary aim). After doing the initial reaction with 3 equivalents of IBX, using a small amount of fluorobenzene in DMSO (not dried or anything) at around 88 deg C over two days I landed up with something. After further investigations, we concluded that we had a benzotropone. We also tried this reaction with a phenol group installed on the benocycloheptenone. The reaction seems to give similar results (yet to be fully investigated). The Nicolaou paper also delves in enone formation, so I assume that is what is happening in my substrate rather than benzylic oxidation. Hope my two cents about this reaction helps....Looking forward to hearing from others as it would be really interesting for me if this reaction works either ways...

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  15. This is a wonderful blog, thanks for all your work! Are you planning on doing some reactions that you expect to be reproducible or is this blog only for dodgy stuff? I really hope that it's the former; this could show how well written and helpful the supporting information can be!

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    Replies
    1. Dear Anon - No, we'd like to expand the blog to include anything reproducible. The Blog Syn mission isn't to chastise or condemn, only to ensure that a prep performed in your lab works just as well in mine.

      If you have any reactions to suggest, please don't hesitate!

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    2. I would like to see those palladium catalyzed cyanation papers that claim to use DMF as cyanide source being reproduced...

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  16. I think gippgig is on to something. Inconsistency in the dissolution behavior of the IBX makes me suspicious.

    The Org Syn prep contains a footnote describing the iodometic titration of the reagent to determine its activity. Might be worth checking the activity of your IBX via that method before each reaction to ensure it has not degraded, as Baran did note in his response they used freshly prepared stuff.

    Inconsistent dissolution behavior could also indicate distinct crystal forms of IBX, which may have different solubility properties. Looking at the Org Syn and JOC preps, there's nothing to dismiss the possibility that you don't get different crystal forms of this reagent via the cooling crystallization.

    I worked with with iodosobenzene (PhI=O) for a while and remember that its structure was polymeric as a solid. To get it to do the reaction I needed, I had to add MeOH to break the poolymeric structure and form PhI(OMe)2. Could also be that IBX has some polymeric versus monomeric character that is poorly controlled in the IBX prep, resulting in variable activity in reactions. In those cases addition of water may be critical to controlling solubility or reactivity of the IBX.

    So many variables, so little time. Fun to speculate though.

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    Replies
    1. Also, what about titrating your "failed" reactions? Do you actually have active IBX left?

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  17. Here's a procedure I recently used that worked exactly as advertised: Nakamura, et al. JACS 2012, 134, 19366-19369. Starting material was easy to prepare, ligand was available in 1-2 steps, and I used materials right out of our stockroom without further purification. Products could be very useful for the synthesis of chiral catalysts. The procedure worked just as well on >1g scale as it did on the smaller reported scale.

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  18. Can someone post a balance chemical equation?

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  19. Maybe we should consider an alternative iodine(V)-based oxidant: Look in Zhdankin et al., JOC 2005, 70, 6484. To make it, all you need to do is (1) take 2-iodobenzoic acid and make the acyl chloride, (2) make the isopropyl ester, (3) stir the ester in a mixture of DCM/concentrated bleach/dry ice and stir overnight. I made (and still have) gram quantities of the oxidant in less than two days. The oxidant has two I-O double bonds, if you were wondering. (I haven't verified how potent or pure the oxidant is aside from NMR, but I did effect the oxygen-atom transfer of iron(II) compounds with this reagent, and it gave a similarly clean result to iodosobenzene.)

    This paper has some interesting insights. One, they can oxidize alcohols to ketones or aldehydes...with a catalyst of TFA, BF3.Et2O, or KBr. (Milkshake's bromine-based oxidant hypothesis above seems intriguing here). Two, they suggest ligand exchange is important; TFA likely generates a trifluoroacetate-iodine(V) reactive species in the catalysis. Three, the solubility of the oxidant is much better than iodosobenzene since it is no longer a polymer, and they have appreciable solubility in chloroform and acetonitrile.

    Anyway, maybe I'll try some of this chemistry with Zhdankin's reagent. (I'm not even an organic chemist, but who cares, trying chemistry outside my project once in a while can be fun.)

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  20. A couple thoughts --
    with these 'small' starting materials might it be better to try sealed tube?
    as Baran points out you may be losing the starting material.

    can you use KI starch strips to check oxidant?

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    Replies
    1. Just be careful - IBX is explosive at elevated temperatures.

      Delete
  21. Very decent of Prof. Baran to contribute and show us where the problem is. I regularly do a reaction in a sealed vessel and didn't even realise it may need to be fully submerged. Learn something new every day.

    Perhaps in future a photo of the reaction set-up ought to be included to help identify problems like this?

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  22. Are you kidding me? That procedure has nothing in common what-so-ever with the original publication. Via what route was the pristine via-NMR IBX made?? Can someone still in a lab run p-bromotoluene (bp= 184 -185 C!)? I have run hundreds of sealed-tube reactions and reflux on the tube walls has always been sufficient....

    That said, I am exceedingly impressed Phil B was so conscientious and forthcoming, and it clearly illustrates his research ethics which in my experience are far, far from the norm. He should be truly and honestly commended for that. I am also exceeding sorry for precipitating what must have been a truly hellish week for that grad student- mea culpa!

    Glad to see that Blog Syn had made a significant addition to the literature, and look forward to more of the same.

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    Replies
    1. Chemists greatly pride themselves in their work and admitting faults is tough, but still, redemption can be a bitch and having to do this at all is sad.

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    2. Hellish week? The reaction is dump and stir. If you follow the above procedure with good IBX it will work. The 2-methylnapthalene doesn't need to be distilled. It can be used straight out of any decent bottle--that stuff is a rock. Same goes for the DMSO and fluorobenzene. I didn't know what to believe so I just ran it myself last night. My colleague also reproduced it with a different bottle of IBX. idk why it didn't work the first time.

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    3. Dear Anon 9:37 - Perhaps you could send over a write-up and pictures of your successful reactions. I would be glad to have another potential collaborator.

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  23. 'Pristine' IBX can be made by the published route (J. Org. Chem. 1999, 64, 4537-4538) but-as this blog is a testament to-the real procedure is slightly modified:

    IBX (>99%, 1HNMR, EA)

    2-iodobenzoic acid (5.0 g, 0.20 mol) was added to an aqueous solution of Oxone (37.2 g, 0.061 mol, 3 eq, 200 mL) in a 0.5 L flask. The suspension was set to 70 °C (internal temperature). Care must be taken to keep the internal temperature below 72 °C. The suspension was stirred for 2 hours then removed from the oil bath and cooled slowly to room temperature. Once at room temperature the flask was cooled to 0 °C for 1 hour by an ice bath. The solid formed was filtered, washed four times with 100 mL of ice cold water, then washed two times with 100 mL of acetone. The resulting solid was dried under vacuum to provide IBX.

    Key details: -unlike the paper reports, the reaction is not complete in 1 hour and you should stir for 2-2.5 hours
    -even slightly elevated temperature (75 degrees or so) produces byproducts

    I've scaled that up to 50g with the same purity of IBX obtained on all occasions. IBX made this way was also used by Anon 9:37 and his coworker successfully.

    IBX NMR: http://postimage.org/image/ri2sievv7/

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    Replies
    1. Thank you for the input. I'll run mine this way in the future.

      Delete
    2. I can confirm this. Exact same reaction, 20 mmol scale, 71.2 C internal temp. I ran mine for about 5 hours, cooled it to 0 C for 15 min, washed with room temp water and acetone. 78% yield, and that's with some slipping through filter paper, and some getting sucked up by the high-vac (I was in a bit of a hurry ha..)

      Proton NMR: http://s23.postimage.org/dhqcyu1p7/IBX_HNMR.jpg
      Zoomed In: http://s24.postimage.org/at8vunjfp/IBX_HNMR_zoom.jpg

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    3. Actually, Anon, note that your IBX looks a lot like BRSM's IBX. It's "dry" IBX...see what happens by NMR when you add 1 drop of H2O. (answer: it starts to look like Phil and Tamsyn's).

      I think there's a lot more at work here than we think. Check back here later for our updated assessment.

      Delete
    4. Anon 4:35 here.
      I'll rerun proton with H2O and D2O tomorrow and see how it turns out. I have noticed some differences, namely splitting patterns. I'm also doing a couple runs with 4-bromotoluene per Prof. Baran's comments. Tried these reactions about 5 months ago and failed, so I have somewhat of a vested interest in this. I'll email with data/results/photos.

      Delete
  24. What does the vapor pressure of 2-methylnaphthalene need to be in order to be entirely volatilized 150 degrees below it's boiling point? Does it sublime? Does anyone really have an oil bath deep enough to run a 200 mL reaction like this? Ironically, this may work better on more complex substrates, like Baran's student suggested, both because they're more soluble in DMSO, and they're less likely to vaporize, but most people wouldn't be willing to try because it didn't work in the model system.

    The prep for IBX reminds me a lot of making dibutylboron triflate. You needed a crazy strong vacuum, because you started to see impurities come in at higher distillation temps. That meant a well maintained pump, and using copious amounts of teflon grease and clamps to seal the (massive) apparatus. The good stuff was water white and froze at ~-10C, but most people couldn't get there.

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  25. Hello guys,
    Thanks a lot for doing this and bringing attention to the issue of reproducibility.

    I have one suggestion. Given you do not write now posts on a reaction but rather update the existing one, would it be possible to somehow indicate the updated parts? Perhaps, some kind of color variations or nested "update boxes". A label like "version 3, 28/02/13" at the beginning would be also useful.

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    Replies
    1. A very fair assessment. I've added an "Update" statement at top, and will figure out some way to differentiate the headings. Thanks!

      Delete
  26. i think phil baran and his lab deserve a large amount of praise for this, as do the folks behind blog-syn (though that should go without saying). it's hard to imagine a more positive outcome than an independent group trying to reproduce notoriously tricky reaction, failing, and then getting detailed notes from the experimentalist that elucidate how to successfully run such a reaction. it was their own "mojo" that got them into this situation in the first place, but this is peer review at its best (better than jacs, obviously).
    as an overarching point while i appreciate the full and non-vitriolic response from baran and his lab, this should be more cautionary than redemptive. get it right the first time. and second time, and third time.
    on a separate note, i agree with baran that the experimentalists should have a reasonable time to respond; for better or worse, blog-syn in its early stages is a tribunal, so should hear the case of the defendant before passing judgement to the internet people.
    please, keep em coming.

    ReplyDelete
    Replies
    1. Aaron - Thanks for the constructive feedback. As the risk of going in circles, I left a comment on Pipeline that bears repeating: for Blog Syn #002 and #003, we reached out to the authors very early in the process. I sent emails to Profs. Yu and Baran on 1/29/13, and their posts went live on 2/12 and 2/18. Is 2-3 weeks "unreasonable?"

      Thanks,
      SAO

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    2. any chance i can get my last name removed there? autocompleted.

      Delete
  27. Kudos to blog syn et al. That being said, I would like to comment on the idea that the original authors should be able to respond to blog syn before a post goes live. If this is done, I think the original post and the author response should go live together. I do not think blog syn should have to run a method, ask the original group what they think, take pointers, try again, and then make a first post so to speak with pointers from the authors. If this is truly a vetting of important procedures, shouldn't the procedure as written in the SI be tested on its own with amendments added later? I realize that could seem a bit vindictive but it may also globally improve the state of SIs if people know their original procedure can be validated (or not, as the case may be) using the words as written with all amendments noted after the fact. I'm a big fan of testing methods and global improvements in SI.

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  28. (Jose, as anonymous):

    Damn nice work! It is ironic that we were *too* rigorous in our trials and therefor pooched the rx.... good to know for the future!

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  29. I think Anon 7:57 has a fair point. By publishing the original article (which leads to the idea of irreproducibility), a fair number of people will have that idea stuck in their heads. I feel that it is incomplete at this stage and could be left until the authors respond and you give it another try. While this would require longer times for each post, I feel like there would be less confusion and a complete "story" to each reaction.

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    Replies
    1. Dear Anon7:38 - I believe Anon7:57 was actually arguing the counterpoint.

      Again (not to repeat myself overmuch) we have ALWAYS reached out to authors long before we publish a post. Lead time for #001 was only 1 day, but we learned better, and gave Profs. Yu and Baran >2 weeks to respond.

      There's no guarantee that each professor we contact will choose to repeat the reaction in their hands vs. just giving advice, so we publish posts after we've 1) heard back from them, and 2) attempted (once) to "re-do" the reaction.

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  30. If you follow the above procedure with good IBX it will work. The 2-methylnapthalene doesn't need to be distilled. It can be used straight out of any decent bottle--that stuff is a rock. Thanks!
    Phase Transfer Catalysts

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