Chemical Search Traffic

Sorry to get all “meta” on you guys again, but I think this is somewhat interesting. There are four basic types of posts on this blog. The first are those that deal with the “nuts and bolts” of chemistry. These posts usually include chemical structures, schemes, and links to papers. The second are those that deal with the cultural aspects of chemistry—things like chemical history, lab management, departmental politics, and ethics. The third are posts that deal with blog housekeeping and the Internet, and the fourth are silly posts that have little intellectual value.

All four varieties deal with chemistry, although some misguided readers and commenters believe that only type-I posts qualify as chemical ones. I don’t feel inclined at the moment to explain to these people that the way chemical research gets done encompasses more than molecules and reaction conditions, so if you share their parochial attitude, I suggest that you find a different blog to read.

That said, I have tried to make an effort to incorporate more type-I material here. Back on April Fools’ Day, I posted three synthetic procedures as a homage to the great Org Prep Daily: amide coupling using HATU, methyl ester hydrolysis using LiOH, and a porphyrin preparation based on the work of J.S. Lindsey. That day saw some of the heaviest traffic in the history of ChemBark, and in the subsequent month, this site has gotten a significant number of hits (well over 100) based on searches directly related to these reactions. In fact, ChemBark comes up on the first page of results when you google “HATU”, “amide bond formation”, “methyl ester deprotection”, or “porphyrin synthesis”.

To me, it comes as no surprise that a lot of people are doing their literature searches using Google. SciFinder can be a pain in the butt sometimes, and more often that not, I find that the number of site licenses here are maxed out when I want to use it. On the other hand, Google is free, requires no special software, and is great for finding ubiquitous things like sample procedures for amide couplings. What surprises me is that of all the places that Google could have sent users, so many of them landed here. This either means that only a few sites are posting the information people are looking for or that there are a lot of people searching for this information. Maybe I should go back to the April Fools’ Day posts and insert references to score some cheap citations?

While surfing around chemistry pages, I often wonder why some professors put so much effort into traveling on the lecture circuit yet never think to spend time updating their own Web sites. It would seem that one of the main purposes of jetting around the world to present your research is to inform the community about your most recent results and convince them that what you are doing is interesting and valuable. Based on two days worth of travel, you “touch” an average of 50-250 people that are in your audience. In contrast, tens of thousands of chemists have access to the Internet, and Google will drive the ones who are especially interested in your field to your site. Why not spend a couple of hours jotting down synopses of your work in HTML?

And I imagine that if more professors blogged, they could easily establish online communities of experts that would process information more efficiently than anything else going. If a grad student can create a blog that attracts a couple of thousand readers a day, a big-name professor surely would attract ten times the traffic. That said, old habits die hard.  It might take a couple generations before online forums become as popular as today’s scientific talks and conferences, but it is going to happen. I have no doubt about that.

Previous Comments

1. milkshake Says:
   May 7th, 2007 at 6:32 am The famous Terrence Tao has his own blog, so do does lots of other high-profile academia people in math and high-energy physics. I think it is a cultural thingy, chemists are less computer-literate on average. (It would be great if somebody started the chemistry equivalent of arXiv).
2. Egon Willighagen Says:
   May 7th, 2007 at 6:37 am Milkshake, I the illiteracy is caused by the fact that many chemoinformatics thingies have disappointed them. I have seen computer literate organic chemists still disliking computer.About arXiv… there has been a Chemical Preprint Server, which dies silently because of too little usage. It worked for me though… I had a paper on it, and was asked to published it in a peer review journal not soon after.
3. Anonymous Says:
   May 7th, 2007 at 7:38 am You’re right, #2. Many Organic academics dislike computers, so I’d be pretty surprised if the likes of BMT, KCN or KBSharpless started a blog. Maybe the younger, more dynamic ones could do so.Anyway, and though the wealth of information contained in such a blog might prove invaluable, the way Organic chemists function is still far from being the “let’s share all our knowledge” fashion. In this world of competition for the best ideas, you wouldn’t want to discuss the paper you just read, which speaks of something really important and with profound implications + gave you 5 great ideas for research projects, with everyone in the Internet, would you?

   Further, I’ve got a question: is it me or some 90% of the academics in Org Chem have a Macintosh???

4. European Chemist Says:
   May 7th, 2007 at 7:39 am That was me, btw (forgot to log in, hehe).
5. Greg Says:
   May 7th, 2007 at 10:09 am I agree – Google has been getting better and better about finding scientific literature.EC, I’m not sure why you say that Organic academics dislike computers. Yes, most do use Macs. This is likely because Chemdraw was the first chemistry drawing program and it was only available for macintosh.
6. excimer Says:
   May 7th, 2007 at 10:31 am Paul, I think another interesting trend is the use of wikis for intergroup information,. According to my boss, they’re becoming more and more popular nowadays to store information for groups, especially for large groups. Our group has the unfortunate distinction of having two labs which are separated by a large distance, so being able to figure out if the TGA over there is up and running, or if a particular chemical is there or not, before wasting twenty minutes is a nice thing, indeed.
7. aa Says:
   May 7th, 2007 at 10:37 am Further, I’ve got a question: is it me or some 90% of the academics in Org Chem have a Macintosh???Ya what’s up with that? My boss uses a Mac, and is die-hard about it. he converted a few lab members to the cult as well… I’d say that its 70:30 Mac:PC when visiting profs bring their own computers to give talks, which is a huge difference compared to Mac’s market share in laptops. where does this come from? i have no clue myself, considering that a lot of chemical software doesn’t have good mac compatibility (bielstein for OS-X as an example)
8. Kutti Says:
   May 7th, 2007 at 11:23 am I have a Mac and I love it and I´d happy to see Macs at our university as well. Unfortunately, the number of Macs here in Germany is still very low. What is still very annoying is the fact that there is no good NMR software for Macintosh. I mean why didn´t they develop MestreC for Mac?
9. ZAL Says:
   May 7th, 2007 at 11:46 am My former boss is another hardcore Mac fan. Nothing wrong about that, but very often we had communication problems between his computer and the PCs of our group, in particular by transferring .doc files with ChemDraw graphics embedded in them, which was very annoying as you may understand.
   @ Kutti: there is an old program for Mac called “SwaN-NMR”, a colleague of mine used it to process NMR spectra and it should be freeware. It should be possible to download it from: www.inmr.net, but I did not try so check if it is really for free.
10. ZAL Says:
    May 7th, 2007 at 11:49 am Sorry, I just realized they are also selling software there, so please do not consider the previous post as any type of advertisement (positive or negative)!
11. Phlogiston Says:
    May 7th, 2007 at 11:52 am Chemists are a smart bunch and we know that Mac is vastly superior to a PC. Besides…you can now buy Macs that can dual boot into either OS-X or Windows. Problem solved. Interestingly, windows runs faster on the new Macs (especially the dual-core) than it does on a top of the line Dell.
12. blatnoi Says:
    May 7th, 2007 at 11:58 am “In this world of competition for the best ideas, you wouldn’t want to discuss the paper you just read, which speaks of something really important and with profound implications + gave you 5 great ideas for research projects, with everyone in the Internet, would you?”Yes, that’s certainly an important point to consider, but I hope we can change that. The true test will come when someone posts a paper on the Organometallic blog that gives “me” in particular great new ideas that are directly related to my own research project. It’s a lot easier over at ‘Totally Synthetic’ since once you make the thing, it’s not like someone else can really use your total synthesis to advance their own research quite as dramatically.

    “I mean why didn´t they develop MestreC for Mac?”

    Because MestreC is Spanish and Spanish people are cool and know what they are doing. They don’t write no code for no Mac.

13. Ψ*Ψ Says:
    May 7th, 2007 at 12:31 pm I’d love to see academic websites updated more frequently. It would make choosing literature stalking victims so much easier…
14. IC Says:
    May 7th, 2007 at 12:40 pm There is a new version of MestreC called MestReNova ( www.mestrec.com ). It is a dramatically improved with respect to ease of use and transfers of spectra to Word, PowerPoint etc. There will also be a Mac OS-X version soon.
15. Kyle Finchsigmate Says:
    May 7th, 2007 at 1:00 pm I frustratingly spent about 100 hours making an interactive website with movies and active content only to have my boss relegate it to a link on his website. How the hell can you expect to be taken seriously when it looks like your web page was written in 1997 and not touched since?
16. Hap Says:
    May 7th, 2007 at 1:43 pm “Spanish people are cool and know what they’re doing. They don’t write no code for no Mac.”You must have something mixed up there, because the people who wrote the code for my PC apparently seem neither cool nor competent (well, they are/were semi-competent – it works, mostly). Between sticky keys that are programmed in SuperGlue and computers where no one could afford to ground the USB ports, I would say that the union of the set (competent, PC manufacturers/programmers) is not the set (competent).
17. blatnoi Says:
    May 7th, 2007 at 2:03 pm That’s why I put a very confusing triple negative in that sentence. It was just so that if someone were to call me on it (and since I don’t really know anything about writing code), I could hide behind the fact that whatever it was that I wrote, it wasn’t really what I was saying.So, are you impressed?
18. Greg Says:
    May 7th, 2007 at 3:28 pm Word document/Chemdraw compatibility was solved with Office 2003 (win) and 2004 (mac). It’s perfectly compatible.For mac NMR software there are several options. The best is FREE! Jeol provides their very powerful Delta software for free (you have to register it). It is the full and complete version that runs on their spectrometers. It takes a little learning to use it. The NMR jocks I know use this regularly to process their 3D data as it’s so much better than Varian’s software.
19. Molecular Probes Says:
    May 7th, 2007 at 3:48 pm I want to make a series of sulfonated fluorescein and rhodamine derivatives. Molecular Probes sells these compounds (”Alexa fluores”) for a ridiculous amount of money and I would go broke if I had to purchase the compounds from them. Recently I made roughly 400,000$ (literally) worth of a product from M. Probes starting from 100$ worth of chemicals I purchased from Alfa and two days of work. I now give this compound out for free to the molecular imaging community. Paul please protect my IP address/identity from Probes….I am interested in hearing any ideas you have for introducing sulfonate groups into fluorescein and rhodamine. I have never sulfonated anything (I have gone the other way though and reduced sulfonyl groups). Has anyone ever sulfonated dyes before? You can believe that Probes has never published their synthetic prep but you can rest assured that when I find out how to make this stuff I am going to distribute it for free.

    I find it annoying that I can buy fluorescein from Alfa for $0.1/g but the disuldonic acid salt from M. Probes costs around $100/mg (!). Doesn’t that seem obnoxious?

    Any suggestions would be appreciated.

20. Molecular Probes Says:
    May 7th, 2007 at 3:51 pm P.S. I would appreciate any suggestions that are based on experience. I can sit down and read the dye literature and see what people have used (fuming H2SO4 and so on) but what I would really like is actual experience or practical advice.
21. Wavefunction Says:
    May 7th, 2007 at 4:03 pm Kutti, there’s a pretty good NMR program for Mac which I extensively use and can highly recommend: iNMRhttp://www.inmr.net/
22. Bobo Says:
    May 7th, 2007 at 5:24 pm “I want to make a series of sulfonated fluorescein and rhodamine derivatives. Molecular Probes sells these compounds Recently I made roughly 400,000$ (literally) worth of a product from M. Probes starting from 100$ worth of chemicals I purchased from Alfa and two days of work”Molecular probes is expensive because it sells to biologists who dont know squat about chemistry. It also certifies its stuff for biological assay (can you?).

    Also, Molecular Probes is a sketchy outfit because many of its products dont deliver as advertised. They staff a largely incompetent group of scientists that hmmmm how should I say this….well it is Chembark so I’ll just say it – they (allegedly) steal or coopt ideas in the literature, stamp their 1% difference on it and sell the junk at exorbitant rates. So, nobody will cry much if you do undercut them. The chemistry you’re doing is old school. What are you, an ambitious undergrad looking to fund his own blog?

23. Molecular Probes Says:
    May 7th, 2007 at 6:03 pm Look, I want useful advice, not blubbering. Obviously you have nothing useful to contribute (Bobo) so why not just keep quiet and let the intelligent people speak up.It doesn’t help me when someone tells me it is “old school chemistry”. You either know it or you don’t.

    Thanks in advance

24. Klug Says:
    May 7th, 2007 at 6:27 pm Paul, this is your blog and your decision. But I would be loathe to let “MP” comment/get advice on this blog.Assuming that we’re not being trolled and leaving Molecular Probes’ pricing ethics aside, I think it is bad juju to be taking food out of the mouths of other chemists.
25. eugene Says:
    May 7th, 2007 at 11:09 pm “But I would be loathe to let “MP” comment/get advice on this blog.”But, but… putting sulfonates on things selectively without using fuming sulfuric acid!? I finally thought that maybe, finally maybe, it’s my time to shine! Oh well, I guess I’ll shine some other time. That stuff isn’t published yet anyways.
26. peach Says:
    May 8th, 2007 at 2:31 am so what’s the macos x beilstein story? do you guys run it on parallels? is there an up-to-date crossfire version coming anytime ever?
27. Paul Says:
    May 8th, 2007 at 5:24 am I think this is the first time in the history of the Internet that a threadjack effectively ended a Mac vs. PC flame war.All topics of discussion are fair game on this site, so long as nothing irrelevant of a personal nature is posted in a comment. That said, The Wall is the best forum to launch topics that aren’t related to the subject of a post or any of the previous comments in a discussion thread.
28. HB Says:
    May 8th, 2007 at 1:30 pm I think even the more computer-literate Professors don’t want to blog because of the stigma attached to it. It is rightfully seen as ill-informed turds with campy, ludicrous themes and pseudonyms making much ado about nothing. Face it, chemistry blogs are mostly fluff.Also when you travel the lecture circuit, you get to travel. The advantage there over blogging is apparent.
29. excimer Says:
    May 8th, 2007 at 3:42 pm must…resist…urge…to…feed….troll….Hey did anyone read that Org. Lett ASAP today? Apparently bridged bromonium ions are crap. I haven’t read the whole thing yet, though.
30. Kutti Says:
    May 8th, 2007 at 4:32 pm @Wavefunction: Thanks a lot for that pointer! I will see whether this software works for me. On the other hand, I think due to the fact that one can use Parallels or Bootcamp on the Intel Macs makes it also easier to use a Mac without having the problem of running software that only exists for Win.
31. programmer Says:
    May 8th, 2007 at 5:52 pm I can’t get why it’s important if a software is free. When you publish a paper, will it be more easily accepted if your work has been done using freeware? Doesn’t your boss allow you to spend money for research?
32. Darksyde Says:
    May 8th, 2007 at 10:45 pm in response to Programmer: Yes. Because you know the formulae that are used for the crunching are not proprietary.I’m biased, of course. I use free software wherever I can. Which means everything except pulling chromatography info.
33. programmer Says:
    May 9th, 2007 at 1:57 am I see no hidden formula in ChemDraw. They talked about NMR: the formulae for Fourier Transform, phase correction, integration, etc… are on all the text-books… All instruments come with some sort of proprietary software: do you de-install it after the purchase?
34. Mitch Says:
    May 10th, 2007 at 12:08 pm The building of the chemical infrastructure for the eventual full emergence of chemical professionals to the web is being developed and thought about by chemical web developers. Out of curiosity, what does the community think would be a useful tool for chemists on the internet?Mitch
35. krp Says:
    May 12th, 2007 at 9:42 pm This topic led me to ask for your suggestions to a concern that I have for some time now.Let me explain my situation a bit.

    I am a postdoc at a small university. I have tried my luck to get some position in “academia”. It did not work out as we (me and my current supervisor) thought. But as you know, putting the package together is very time consuming, and I do not want to go through the same process next year. For all I know, I may not have access to the data bases since I am planning to take shelter in Industry for a while. I am worried as to some body will get the same research ideas (?) and send me again back to where I started this year. Believe me – getting the similar ideas is not that simple either as some of them are so precious. Is there any way that I can start some website of my own or blog and post all my research ideas there hoping that no body will dare to copy them…or at least I will have track of those who visited the site or blog. Or is there any such place that I am not aware of where you can post the ideas alone securely. I wish there is some kind of journal just for publishing the ideas first so that no body will scoop.

    Do you have any other suggestions for protecting my research ideas which have already been sent to quite a few schools as research proposals?

    Thanks in advance.

    KRP

36. Mitch Says:
    May 13th, 2007 at 4:43 pm Posting them on the internet would not be a good idea.
37. krp Says:
    May 13th, 2007 at 8:15 pm Mitch, thank you.Any other suggestions?

    KRP

38. Paul Says:
    May 13th, 2007 at 11:53 pm Posting the ideas on the Internet is probably the best way to ensure that someone works on them. We’re not living in the days of Diels and Alder, where you could claim a research area for yourself. And that’s a good thing, because it is unfair to expect that we should halt the progress of science for an individual’s personal benefit. That said, if anyone uses your ideas, the ethical thing for them to do would be to acknowledge that fact. But, as we have seen, there are plenty of unethical people in our profession.Bottom line: if you don’t want people working on your ideas, don’t tell *anyone* about them. But, if you are genuinely excited about them and just want someone to work on them, post them on the Internet. This reminds me of one of my favorite all-time quotations:

    “There is no limit to what a man can do so long as he does not care a straw who gets the credit for it.” — C.E. Montague

39. Anonymous Says:
    May 14th, 2007 at 7:13 am Paul,Thank you. Actua;;y I was doing some search related to the issue that I listed above. You are right by posting on blog it might work the other way round.

    But there are still honest people around.

    Check this:

    http://dererumnatura.us/archiv…..tists.html

    Thank you for your suggestions.

    Best,

    KRP

40. Anonymous Says:
    May 14th, 2007 at 7:19 am sorry for the typos in the above message as it was posted in haste.Just thought of bringing this site to the notice :

    http://usefulchem.wikispaces.com/