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Text of the page (random words):
javier lopez rohan narayan donna blackmond and phil baran after the team s initial work developing the psi reagents for the stereocontrolled synthesis of phosphorothioate linkages much work remained to build out the p v platform both to include other types of desired p linkages but also to develop a protocol for using the novel reagents on an automated oligo synthesizer the development of these additional reagents ps2 po and racps all proceeded in different ways the challenges overcome in the syntheses of the ps2 and racps reagents were a simpler story so i ll direct you to finding that info in the publication on the other hand there is the p o reagent to the best of our knowledge there had never been a published p v reagent capable of forming a phosphodiester bond between two nucleosides with phosphoramidite like kinetics i e crazy quick the initial hit for such a reagent came in july of 2018 followed by my famous last words shouldn t take long to find the perfect p o reagent although the hit was exciting it required kotbu as a base and wasn t compatable with dbu or organic bases that would be amendable to an automated oligo synthesizer to address this we evaluated new p o reagents on several criteria 1 could they be made synthesis 2 could they be reacted with a nucleoside to afford a monomer loading 3 could they be coupled via an organic base with a second nucleoside to afford a dinucleotide coupling we had two ways of making the reagents either synthesizing 1 3 mercaptopropanols and reacting them with pocl 3 or by generating analogous compounds with 1 3 diols and pscl 3 followed by an interesting atom transposition using tbai we found a lot of things that could work and plenty that couldn t but only one scaffold was able to accomplish all 3 of our goals p o 5 the diphenyl scaffold after this discovery we investigated the aryl electronics and stereochemistry of the diphenyl backbone attempts to modulate the coupling efficiency through the aryl electronics proved negligible the stereochemistry was a more interesting questions because the first synthesis of this reagent used a racemic mixture of the mercaptopropanol generating a racemic mixture of p o reagents which upon loading onto a chiral nucleoside revealed a mixture of the possible isomers that one could imagine we began synthesizing single isomer versions of these reagents and observed that the syn scaffold epimerized into an inactive form during the loading step further investigation of the anti backbone revealed that the r r substituted system gave the fastest coupling times we next looked into the synthesis of this reagent the stereochemistry could be programed in via a noyori reduction and using pfp as a leaving group provided suitable physical properties to afford a solid reagent despite this success the reagent still had two flaws it wasn t stable enough could only survive about a week on the benchtop and it was still a mixture of isomers with one reacting much faster than the other sitting around the lab one day we thought to ourselves why don t start with the original psi a reagent we knew reacted at lighting speed and swap the s for o it seemed rather straightforward in practice we were never able to do this successfully on the psi reagent itself so we tried it on the psi loaded monomers instead although we could succesfuly perform s o transpositions on these monomers there were always side reactions associated with the transformation ultimately leading us to abandon this approach third times a charm as they always say so revisiting the idea of performing the s o transposition on the reagent itself we knew we the reagent formed with pftp psi was too reactive after making the p o version of itself so after generating psi alternatives with different leaving groups we found that we could successfully perform this transposition to generate a stable reagent most notably the 4 bromothiphenol version there s plenty more to the story we evaluated the kinetics of the p v molecules demonstrating that they are on par with phosphoramidite chemistry we developed a novel universal linker capable of performing oligo synthesis under the unusual basic conditions found in the p v protocol and we even took a trip to cambridge ma to visit our collaborators at bms and see and learn first hand how they were making oligonucleotides also if you ve read this far it s fair to assume you re a fan of the p v approach to oligos so check out our perspective on p v chemistry that was also just published in acs central science if you re still reading and want to follow the next steps of the p v story keep an eye out on elsiebio com or drop one of us a line to check out how were using the p v technology among other things to develop the next generation of oligonucleotide therapeutics and replace dogma with data kyle and the p v team posted by baranlab at 5 37 am 1 comment email this blogthis share to x share to facebook share to pinterest thursday april 15 2021 ika guest post on classic alternating current mode electrasyn 2 0 software update to support alternating polarity in constant voltage reaction mode author information chuanjun jiao ika works inc 3550 general atomics court ms g02 321 san diego ca 92121 1122 united states email charles jiao ika net note this report is not related to the recently added new function rapid alternating polarity rap the change described here is relevant only when the default alternating polarity function is used together with a reference electrode currently only alternating polarity function is supported to be used with a reference electrode and rap function is not compatible with a reference electrode in addition further software update is not necessary to a unit in which the rap function is already installed since the latest software supporting the rap function already includes this change background recently the reid group at university of strathclyde reported a mechanistic study of electrochemical benzylic oxidation with the use of electrasyn 2 0 chemelectrochem 2020 7 2771 during their study the group observed unexpected product distribution change when alternating polarity was applied during a constant voltage experiment with electrasyn 2 0 the report describes their careful investigation of this phenomenon and casts a practical consideration on users of ika electrasyn 2 0 here is the key points of their report unexpected outcome was obtained under the condition of constant potential reaction mode reference electrode on alternating polarity on during alternating polarity the same magnitude of current would be expected in both positive and negative phase however the observed current magnitude was totally different between these two phases this asymmetric current distribution affected electrochemical reaction resulting in unexpected product selectivity change therefore electrasyn 2 0 might have an engineering concern summary of ika investigation ika conducted a series of experiments to clarify the nature of this phenomenon and to improve electrasyn 2 0 the detail of our internal investigation can be found in detail of our investigation in this document here we would like to provide a summary of our investigation we verified asymmetric current distribution in the same setting described in the report constant voltage reference electrode on alternating polarity on this asymmetric current distribution was observed only when reference electrode is on in other words this issue does not occur when reference electrode is off this is simply originated from how voltage is controlled in electrasyn 2 0 accordingly electrasyn 2 0 does not have engineering concern software update although we confirmed that elecrasyn2 0 does not have any engineering flaw we updated electrasyn 2 0 software to enable equal current distribution in the above experimental conditions constant voltage reference electrode on alternating polarity on when this setting change is needed a user needs to enable this function only when constant voltage reaction mode with reference electrode on and alternating polarity on effect on past research the issue only occurs when constant voltage reaction mode with reference electrode on and alternating polarity on in other conditions current and voltage control is accurate and experimental data is reliable detail of our investigation ika electrasyn 2 0 provides many functions that satisfy different requirements for electrosynthesis among those functions constant voltage is a reaction mode where the reaction is executed at a fixed voltage this reaction mode is generally more selective than constant current mode though the reaction time tends to be longer alternating polarity is an option that periodically switches anode and cathode this option is useful when electrode fouling is observed switching polarity helps to alleviate accumulation of deposit both constant voltage and alternating polarity are routinely used for electrosynthesis the recent report by the reid group described a mechanistic study in synthetic organic electrochemical method development with the use of electrasyn 2 0 chemelectrochem 2020 7 2771 in this report unexpected product selectivity change was observed in electrochemical benzylic c h oxidation of toluene derivatives by employing constant voltage alongside alternating polarity function equipped in electrasyn 2 0 during those experiments it was observed that the magnitude of the current during the second half of alternating period was greater than during the first half giving an asymmetric current over time response this is not desired because alternating polarity is simply an electrode cleaning technique and should not alter the magnitude of current further in depth investigation of cell potential with alternating polarity revealed that the voltage during the negative phase was not controlled the set voltage was 1 5v which means the reaction voltage should alternate between 1 5v and 1 5v however the observed voltage was clearly not in this case in additional tests a rapid degradation of nhpi was observed in alternating polarity experiments due to this unexpectedly high current input such degradation leads to the unexpected product selectivity accordingly the group published their findings to highlight an equipment engineering concern that is likely to influence and inform optimization strategies for a wide range of synthetic organic electrochemical methods under development to ensure product quality and to further improve eletrasyn2 0 ika has conducted a thorough inspection of the instrument as well as detailed investigation of this issue it turned out that the varied cell potential was caused by the way electrasyn 2 0 controls voltage against the reference electrode method of voltage control in the default setting of electrasyn 2 0 potential difference between working electrode we and reference electrode re is controlled when reference electrode is on such setting remains unchanged during the experiments in the electrasyn 2 0 apparatus the working electrode we is installed to the left side of the reaction cell and the counter electrode ce is installed to the right side however we and ce do not necessarily indicate anode and cathode in electrolysis we can be both anode and cathode for example if 1 2 v is applied we will play the role of anode and the voltage should be set as 1 2 v between we and re on the other hand if 1 2 v is applied we will play the role of cathode alternating polarity during alternating polarity what is expected is the cycle of applying 1 2 v between we and re and then 1 2v between ce and re however in the current electrasyn 2 0 software the voltage control remains between we and re during the entire period this means that applying 1 2v between we and re may induce completely different reaction resulting in the observed asymmetric current behavior in other words if electrasyn 2 0 could switch we and ce during alternating polarity the problem of asymmetric current will be solved this function was installed in an updated software software update after our investigation in software development the aforementioned voltage control method was implemented users are provided with the option of enabling disabling the alternate polarity with the latest software version 0 0 026 0 0 027 the new software version was validated by using following test in the first test the solution containing 0 114 m bu 4 nclo 4 with acetone mecn 1 1 ratio was used as pointed out by the reid group constant potential mode with reference electrode on and alternating polarity on gave asymmetric current blue circle in figure 15 when the setting is changed as illustrated above totally symmetric current was observed orange circle this test was conducted with another solution verifying symmetric current behavior in this case as well accordingly we have concluded that alongside the existing function an updated software version 0 0 026 0 0 027 will enable electrasyn 2 0 to perform a constant voltage reaction with reference electrode under alternating polarity conditions we thank dr marc reid his colleagues and all our users for supporting electrasyn 2 0 and providing valuable feedback posted by baranlab at 12 56 pm no comments email this blogthis share to x share to facebook share to pinterest monday october 5 2020 adventures in p v chemistry our two recent p v based projects that were just published in jacs and acs central science were a lesson of teamwork and sometimes serendipity that we would like to describe in the following blogpost having worked on the p v reagent platform since its inception i have spent a considerable amount of time sitting in front of the only nmr spectrometer at scripps capable of detecting the 31 p nucleus since these blog posts are supposed to be the behind the scenes version of papers we publish i thought i would take this time to walk you through the fun journey from the baran lab to the molecular biology building where one of our nmr labs is you begin by leaving the 4 th floor of the beckman center for the chemical sciences traversing the intricate hogwarts style staircases down to the lobby after exiting the building and making a daring leap over the crosswalk between the two buildings it s time to go further into the depths of the mbb building okay back to the science as you can see in the figure below the loading and coupling events between the p v reagents and alcohol nucleophiles proceeds with a rather boring and predictable outcome via 31 p nmr over the course of 3 years hundreds of compounds have undergone this reaction sequence regardless of the compound in question the only observable peaks are 100 ppm for the loading and 55 ppm for the coupling products the reactions between nitrogen and sulfur nucleophiles were never observed this led us to the realization that the p v reagents could potentially solve the challenge associated with serine selective functionalization as highlighted in the chart below a...