RSS Feeds: Don't Fear The Reader

As scientists, how do we keep up with the literature?

Julian G. West  Science ,  2017 ,  355 , 1090 (DOI: 10.1126/science.355.6329.1090)

Julian G. West Science, 2017, 355, 1090 (DOI: 10.1126/science.355.6329.1090)

About a year ago, I gave a very informal presentation to my PhD group on how to keep up with the literature. Over the years I started using alerts for every project: Google Scholar citation alerts for related articles and SciFinder alerts for keywords or chemical structures. I also mentioned RSS feeds but acknowledged that I had no idea how they worked and they intimidated me. My coworker Kyle, introduced me to The Old Reader and I’m never going back.

I used to browse journals in my spare time by opening individual tabs for each journal.

My computer has been slow lately and can’t handle the massive amounts of RAM that Firefox gobbled up. The Old Reader (and other RSS aggregators) are an easy way to browse the article titles/TOC graphics of lots of journals in ONE TAB, which means I spend more time browsing and less time loading.

Back in the day, Google used to provide a really good RSS feed aggregator called Google Reader, and when that service shut down The Old Reader sprung up. I’d consider myself a beginner (I’ve only used The Old Reader for about 4 months) but so far it’s been easy to use and made my literature browsing more efficient and enjoyable. The service is free for up to 100 RSS feeds, but currently I only use about 25 and that’s more than enough.

When I’ve got some free time at work you might find something like this on my laptop screen.

When I’ve got some free time at work you might find something like this on my laptop screen.

Adding new feeds is super easy.

You can see that I have a list of journals and science blogs. To add a new journal I normally just google search “journal of [BLANK] rss feed” and add the web address manually (here is the one for my blog). There is an “add a subscription” search feature, but it can be hit-or-miss. Once you’ve added it you can drag it into groups to keep your feed organized. Another helpful feature is in the top right, where you can show all posts of a journal or only show the unread articles.

A Dance With Dragons by George RR Martin

A Dance With Dragons by George RR Martin

I’ve also uploaded my feed here, it can give you some basic organic chemistry journals/blogs feeds to get you started (full disclosure, my own blog is on it too!). To use it just download my opml file, and upload it by clicking “upload” in the top right of the screen next to your name. Make sure to customize it with the journals/blogs that you’re interested it.

One last thing about RSS feed anxiety.

As you can see, I’m falling behind on some of the journals (582 unread Chem Comm articles??), but in my opinion the point of an RSS feed is not to read every single article - it’s to provide inspiration. By exposing myself to articles I might not see with my regular alerts I’m helping become a more balanced scientist. This is especially true with the “general” journals in my feed like Science/Nature. As an organic chemist I used to get burnt out after my usual literature browsing of JACS/OL/JOC/JMedChem, but now I can easily pop over to see some general work.

As I said earlier, I’m no expert. If you have any tips/tricks that I didn’t list or feel like trashing my journal choices (or the fact that I grouped them by IF) please leave a comment below :)

Happy reading!

Maps vs. University

I'm a bit of a map nerd...

If somebody is talking about their hometown, I'll usually suggest we take a look on Google maps.  The satellite and street views can't compare to to an actual visit, but it's free and you can learn a lot!  I love the excitement people have showing me the places they grew up, their favourite restaurants, or whatever buildings/monuments make their hometown special.

I also love playing GeoGuessr, a game where where you're dropped somewhere random in the world and can only walk around using Google street view.  You have to guess where you are just by looking at the stuff around you.  Which side of the road are people driving on?  What climate is it?  What language is on the signs?  What units?  This game is truly addictive.

This fascination with maps has motivated to talk about two universities that I love:

1. The University of Western Ontario (now Western University)

The original name of my alma mater is the University of Western Ontario.  Let's look at the following map:

Map courtesy of Google Maps and modified (crudely) by me.

Map courtesy of Google Maps and modified (crudely) by me.

"Hmmmm," you might say, "that university isn't in the west of Ontario at all."

That's very astute, dear reader.  The name is confusing without the proper context.

The school adopted its name in 1923 and makes sense based on the population distribution.  I can't find data for 1923, but here's what it looked like in 2006.

Map courtesy of Statistics Canada.

Map courtesy of Statistics Canada.

If you ignore the less populated regions (and the University of Windsor!) the name starts to make sense.

However, the school's name was changed in 2012 to "Western University", which doesn't make any sense at all!  If they asked me I would have called it University of London 2.

2. University of California, Santa Barbara

This is the school where I'm completing my PhD and it's arguably the most beautiful campus in the world.  After getting accepted to UCSB, I remember reading all about Santa Barbara during one of London's frequent thunderstorms.

"I really can't wait to live in Santa Barbara," I thought to myself..

Map courtesy of the City of Goleta and modified (crudely) by me.

Map courtesy of the City of Goleta and modified (crudely) by me.

The school (Lab on the map) encircles the undergrads that live in Isla Vista.  I don't live in Santa Barbara, I actually live in Goleta.  I had no idea when I moved here that Santa Barbara proper is actually about 15-20 min away depending on traffic on the 101.

The school would be more accurately named UC Goleta or UC Isla Vista.  There's a movement to change the school's mascot to a mapache (raccoon) and I could get behind a school name change as well.

If you looked closely at the last map, you'll see that technically UCSB is touching Santa Barbara at the airport.  Take a look at this monstrosity:

Map courtesy of the Santa Barbara County Surveyor and modified (crudely) by me.

Map courtesy of the Santa Barbara County Surveyor and modified (crudely) by me.

This is called a Shoestring Annexation and it has a pretty interesting history.  A sneaky Mayor used a strip over the ocean to "steal" the airport to collect its taxes; the loophole was plugged immediately after.

In summary, the schools that I attend are wonderful but their names don't make sense.  Now if you'll excuse me, I'm going to play a few rounds of GeoGuessr before bed.

The Cult of Molecular Sieves

At some point in during my MSc degree, our postdoc inducted me into the Molecular Sieves Cult (lets also call this MSC for short).  I needed dry solvent and the postdoc handed me a printed copy of Drying of Organic Solvents: Quantitative Evaluation of the Efficiency of Several Desiccants.  This paper has been the second most useful one in my career (after NMR Chemical Shifts of Common Laboratory Solvents as Trace Impurities).

CC Image courtesy of Robert Montgomery on Flickr

CC Image courtesy of Robert Montgomery on Flickr

Here is where I should probably put my conflict of interest:

My group job is to refill and maintain our solvent purification system (SPS).
Fewer people use it = Less work for me

I joined the MSC long before this group job though.  As the Paper says, mol sieves and time are better or equal to distillation or the neutral alumina in a SPS.  You also avoid the danger of distillation and the large startup cost for an SPS; all you need is some cheap mol sieves and a bottle!  I have big bottles of dry DCM, MeOH, and toluene that believers in the lab use (but never refill...) and small bottles of MeCN, EtOH, iPrOH, and ethylene glycol.

I believe that 3A mol sieves are essential to every lab and I hope to convert others to the MSC, but now I'm going to talk about the dark side of our cult.

Acetone

The most memorable blog post I've ever read is by the Curly Arrow titled Anhydrous Solvents Part 3: Acetone and Molecular Sieves - Bad idea!  It's a great post and essential reading for MSC members.  In short: mol sieves are slightly basic and over time it'll Aldol the heck out of acetone to make heavy, greasy crap.

THF & Other Ethers

The point of mol sieves is that you can set it and forget it.  Forgetting ethers in a bottle on the shelf for long periods of time can lead to peroxide formation, so I avoid using it or only dry the amount that I'll need for that week.

DMF & Triethylamine

These tend to turn brown over time.  If I were to buy an SPS the only solvents I would have are DMF (since it loooves water) and THF (for BuLi reactions).  If you need very dry triethylamine just do what I do: Go to Zakarian's lab and use his solvent still ;)

Example 13C NMR (100 MHz, CDCl3) with trace CHCl3 at 77.20 ppm.

Example 13C NMR (100 MHz, CDCl3) with trace CHCl3 at 77.20 ppm.

A Note about CDCl3:

Like most people in the MSC, as soon as I crack open a cold CDCl3 with the boys I dump in pile of mol sieves.  Say goodbye to water in your 1H NMR (unless your compound is still wet) and since it's basic it should in theory mop up any DCl.

One very hot summer, I was trying to assign some very small peaks in my 13C NMR.  I found a tiny peak hidden in the residual solvent peak and called it a day.  In the coming weeks, the peak was growing.  I ran a blank 13C NMR and then went back and reassigned my spectrum.

The problem is that our lab gets hot during heat waves.  Like really, really hot (35 C)!  I never found these peaks during "winter" or non-heat-wave-summer.  I suspect that when heated, the water trapped in the sieves was doing a base-catalyzed hydrogen exchange.  This is just a theory, and I haven't put in the effort to replicate it.  They also upgraded our lab so it doesn't get as hot now - just in time for me to graduate :/

CC Image courtesy of Daniel (refletsdevert) on Flickr

CC Image courtesy of Daniel (refletsdevert) on Flickr

Don't let these exceptions scare you from mol sieves, they're amazing as long as you are using the right solvents.  If you have strong feelings about the MSC or any solvent-specific knowledge please let me know in the comments below!

-Andre

Teaching an Old DA New Tricks

Javier first introduced me to this project in December 2015.  Around this time I had just finished published my methodology project and had been working on a total synthesis of (±)-sunken costataxine.  It didn't hurt that the new project was funded by MedImmune, which meant I wouldn't have to grade lab reports/exams!

The idea was simple:

  1. Antibody–drug conjugates are mostly made through a thio-Michael addition between a thiol and maleimide
  2. The thiol–maleimide bond are reversible (like velcro)
  3. The same maleimides could react with diene through a strong Diels–Alder adduct (like superglue)
My thiol-maleimide = velcro metaphor falls apart because these shoes look awesome. CC Image courtesy of ashleigh290 on Flickr

My thiol-maleimide = velcro metaphor falls apart because these shoes look awesome.
CC Image courtesy of ashleigh290 on Flickr

Maleimides attached to powerful drugs are common (I count at least 10 in the pipeline).  They're synthesized on large scale, and there's more on the way.  Many groups are making maleimides with new combinations of toxic drugs, solubilizing PEGs, cleavable linkers, and self-immolative spacers.
This part of project reminded me of the proverb, "If all you have is a hammer [thiol], everything looks like a nail [maleimide]".  Now we have many maleimides so:

If you have a lot of nails, you should make a really good hammer
— Andre

Enter the Diels–Alder reaction!

I know what you're thinking: "The Diels–Alder reaction has been around for 90 years, surely there's nothing new you can do with it."

That's a good point, and it's one reason why this project was hard to sell.  The recent literature is full of useful examples of the inverse electron-demand Diels–Alder reaction (I consider this to be New Coke), but we want to bring back the normal electron-demand Diels–Alder reaction (Coca-Cola Classic).  The main concerns were that good dienes aren't stable and that the rates wouldn't be fast enough.

Maleimide is an amazing dienophile and we're not the only ones working on this:
Dr. Molly Shoichet used the Diels–Alder reaction between furan and maleimide to make hydrogels or conjugates.  This is very cool work but it doesn't quite meet our requirements - the rates aren't known and the conversions needed to form gels/conjugates don't need to be quantitative.
Dr. Anna Grandas Sagarra's group has a lot of cool papers, but my favourite is the reaction between a trans-3,5-hexadiene + maleimide to produce conjugates.  The reaction is in water, which accelerates the reaction, and the yield is 90—95%!  The kinetics aren't known and they use concentrations too high for antibody chemistry (1 mM vs 30 umol).

Turbodiene CC Image courtesy of  j4p4n  on openclipart and modified by me in ChemDraw

Turbodiene
CC Image courtesy of j4p4n on openclipart and modified by me in ChemDraw

Emboldened by these examples we chose some turbo-charged dienes from the literature.  The dienes need to be stable in water, start from cheap starting materials, and easy to make (this makes it scalable/accessible to other labs - it's not laziness!)

After the literature search phase I ended up making 3 different cyclopentadienes, and all have a special place in my heart.  Mono-substituted cyclopentadiene tends to dimerize, it's kind of the wildcard of the group.  Spiroheptadiene was easy to make and has a rich history in total synthesis, so it's the brainy one.  Pentacyclopentadiene (Cp*H) smells like buttered popcorn, so it's the fun one.

I was also inspired by some very cool 3-alkoxyfurans developed by Dr. Tom Sheppard's lab at University College London (the old London, not London Ontario).  This super powerful furan is an excellent dienophile becau — OK YOU GOT ME, I just wanted to do some gold chemistry.  I share an office with Dr. Liming Zhang's students and they make it look so cool!  I was able to trade a drum of acetone for a few milligrams of gold and the long-ish synthesis was so satisfying.  Since it's the only furan in the series, it's the black sheep of the lot.

I'm not going to go over the details, but attaching these dienes to antibodies was easy and they reacted really well with maleimide!  The Diels–Alder bond is more stable than the thiol–maleimide, so I think we'll be seeing much more normal electron-demand Diels–Alder bioconjugations in the future.

This whole project has been a dream!  We had a bioconjugation problem and a clever solution.  I was given pretty much free rein on designing the dienes, which meant I read a lot of DA papers in bioconjugate chemistry, polymer chemistry, and regular old organic synthesis.  We shipped the good ones across the country to my fantastic collaborators at MedImmune, where they took care of all of the biochemistry stuff.

So many fields of chemistry use the DA reaction as molecular glue, hopefully our work makes it a bit easier.