Carboxylic acids are tough to analyze. Hydrocarbon (petroleum) carboxylic acids are particularly tough to analyze. Of the carboxylic acids that have been saved in databases to date, there appear to be differences among databases (as expected).
So, I analyzed what was in the LIPIDMAPS database. I get the feeling this database is well-curated.
LIPIDMAPS contains 25,120 carboxylic acids with deficiencies in the 1000-2000 amu range.
I wanted to compare this number and range with that available on PubChem, but I haven't found a way to search for carboxylic acids in PubChem yet without overloading things and returning no results!
Stay tuned for updates.
Springer Publishing
Thursday, 26 May 2016
Friday, 5 February 2016
Tetranitratoethane
Once again, we come to a graphical abstract feast!
They make it look so cubic and symmetric! Ladies and gentlemen: This is tetranitratoethane.

By the way, "tetranitratoethane" in Google Scholar only brings up this paper! No theoretical papers? Strange. What are some synonyms?
The crystal space group was P21/c, which is claimed to be orthorhombic in the paper, although it seems to be monoclinic everywhere else. The molecular point group looks like it could almost be S2n, but all I can see is maybe an inversion point.
An updated graphical abstract might look like this:
Yes, I am still afraid of nitro explosives going kapow. Also, a 1.4 cm long molecule is huge.
References:
D Fischer, T M Klapötke and J Stierstorfer, Chem. Commun., 2016, 52, 916 (DOI: 10.1039/c5cc09010e)
They make it look so cubic and symmetric! Ladies and gentlemen: This is tetranitratoethane.
By the way, "tetranitratoethane" in Google Scholar only brings up this paper! No theoretical papers? Strange. What are some synonyms?
The crystal space group was P21/c, which is claimed to be orthorhombic in the paper, although it seems to be monoclinic everywhere else. The molecular point group looks like it could almost be S2n, but all I can see is maybe an inversion point.
An updated graphical abstract might look like this:
Yes, I am still afraid of nitro explosives going kapow. Also, a 1.4 cm long molecule is huge.
References:
D Fischer, T M Klapötke and J Stierstorfer, Chem. Commun., 2016, 52, 916 (DOI: 10.1039/c5cc09010e)
Monday, 18 January 2016
Perturbing the Copper(III)–Hydroxide Unit through Ligand Structural Variation or How to Really Annoy Copper(III)–Hydroxide with Pippi by Making the Activation Energy Heavier than a Log
Perturbing the Copper(III)–Hydroxide Unit through Ligand Structural Variation
or
How to Really Annoy Copper(III)–Hydroxide with Pippi by Making the Activation Energy Heavier than a Log
How to Really Annoy Copper(III)–Hydroxide with Pippi by Making the Activation Energy Heavier than a Log
Yo, anybody seen a see-saw yet in a graphical abstract?
No. No. No. No.
Well, let's just put an end to THAT, then!
https://t.co/fGW3ATFxGp
— ErgodicOrNot (@ChemProfCramer) January 18, 2016
Well, I took the bait and here is what I saw:Personally, it was much too simplified. Even if I had sparrho's new tool, it would take a bit of thinking for me to remember what the paper was about.
Because there is so much information that couldn't be captured in this graphical abstract (as there is in almost every graphical abstract), I decided to spruce it up a little by including references to the ligand(s), tunneling, hydrogen abstraction etc....
So Cu(III) hydroxide becomes terribly disappointed with the prospect of having to give up a hydrogen so easily. Pippi was always surprising!
References:
Perturbing the Copper(III)–Hydroxide Unit through Ligand Structural Variation
Debanjan Dhar, Gereon M. Yee, Andrew D. Spaeth, David W. Boyce, Hongtu Zhang, Büsra Dereli, Christopher J. Cramer, and William B. Tolman
Journal of the American Chemical Society 2016 138 (1), 356-368
DOI: 10.1021/jacs.5b10985Friday, 27 November 2015
Antisapstains, including chlorophenols!
Sapstain is the grey/blue stain in wood caused by wood-staining fungi Grosmannia clavigera.
Antisapstains are a small group of chemicals used in wood treatment and pulp mills. They are covered by law. Canadian Law (BC regulation) defines the following substances as antisapstains:
http://www.canlii.org/en/bc/laws/regu/bc-reg-300-90/latest/bc-reg-300-90.html
DDAC IPBC TCMTB



Cu-8

As well as Chlorophenol,Which is further defined as the sum of chlorophenols and chlorophenates
2-chlorophenol, 3-chlorophenol, 4-chlorophenol and deprotonated forms.
Table of abbreviations, names, SMILES, CAS and chemical formula.
Antisapstains are a small group of chemicals used in wood treatment and pulp mills. They are covered by law. Canadian Law (BC regulation) defines the following substances as antisapstains:
http://www.canlii.org/en/bc/laws/regu/bc-reg-300-90/latest/bc-reg-300-90.html
DDAC IPBC TCMTB
Cu-8
As well as Chlorophenol,Which is further defined as the sum of chlorophenols and chlorophenates
2-chlorophenol, 3-chlorophenol, 4-chlorophenol and deprotonated forms.
Table of abbreviations, names, SMILES, CAS and chemical formula.
| DDAC | didecyldimethyl ammonium chloride | CCCCCCCCCC[N+](C)(C)CCCCCCCCCC.[Cl-] | 7173-51-5 | C22H48NCl | |
|---|---|---|---|---|---|
| IPBC | 3-iodo-2-propynyl butylcarbamate | CCCCOC(=O)NCC#CI | 55406-53-60 | C8H12INO2 | |
| TCMTB | 2-(thiocyanomethylthio)-benzothiazole | N#CSCSC1=Nc2ccccc2S1 | 21564-17-0 | C9H6N2S3 | |
| Cu-8 | copper-8-quinolinolate | [O-]c1cccc2cccnc12.Cu | 10380-28-6 | C9H6NOCu |
Tuesday, 27 October 2015
Open Science Working List
| academia.edu | www.academia.edu/ | social network |
|---|---|---|
| altmetrics | http://www.altmetric.com | measuring scholarly impact |
| authorclaim | http://authorclaim.org/ | measuring researcher impact |
| citeulike | http://www.citeulike.org | citation bookmarking |
| crossref | http://www.crossref.org | article metadata search doi resolver |
| crowdometer | http://crowdometer.org/ | |
| datacite | https://www.datacite.org/ | doi provider |
| depsy | http://depsy.org | measuring scholarly impact |
| faculty of 1000 | http://f1000.com/ | |
| Fast Track Impact | http://fasttrackimpact.com | research impact |
| figshare | http://figshare.com/ | data repository |
| github | https://github.com/ | computer programming |
| Global Research Identifier Database (GRID) | www.grid.ac | database |
| google scholar | scholar.google.com/ | measuring researcher impact |
| hypothesis | https://hypothes.is | annotation organize collaborate |
| impactstory | https://impactstory.org/ | measuring scholarly impact |
| journal of brief ideas | beta.briefideas.org/ | journal |
| journalreview.org | https://www.journalreview.org/ | |
| kudos | www.growkudos.com | research impact |
| mendeley | https://www.mendeley.com/ | citation bookmarking |
| microsoft academic search | http://academic.research.microsoft.com/ | measuring researcher impact |
| mozilla science lab | https://www.mozillascience.org/ | |
| open access infrastructure for research in europe | https://www.openaire.eu/ | |
| open knowledge | https://okfn.org/ | data repository |
| open researcher and contributor id | http://orcid.org/ | researcher identification |
| open science framework (OSF) | http://osf.io | research publishing framework |
| papercritic | http://www.papercritic.com/ | monitoring feedback and conversation |
| peerj | https://peerj.com/ | |
| plos impact explorer | http://altmetric.com/interface/plos.html | scientific conversation impact |
| plum analytics | http://plumanalytics.com/ | measuring scholarly impact |
| public library of science | https://www.plos.org/ | library journal |
| publons | https://publons.com/ | scientific review |
| pubpeer | https://pubpeer.com/ | |
| readermeter | http://readermeter.org/ | impact |
| researcherid | www.researcherid.com/ | researcher identification |
| researchgate | http://www.researchgate.net/ | social network |
| rio journal | http://riojournal.com/ | journal |
| Securing a Hybrid Environment for Research Preservation and Access, SHERPA | http://www.sherpa.ac.uk | repository development |
| sciencecard | http://50.17.213.175/ | measuring researcher impact |
| scienceopen | https://www.scienceopen.com/ | publishing network |
| scinote | scinote.net | electronic lab notebook |
| slideshare | www.slideshare.net/ | |
| sparrho | https://www.sparrho.com/ | recommender search engine |
| the new reddit journal of science | https://www.reddit.com/r/science/ | journal |
| the winnower | https://thewinnower.com/ | journal |
| wikipathways | www.wikipathways.org/ | |
| wikipedia | https://www.wikipedia.org/ | |
| wiktionary | https://en.wiktionary.org/ | |
| zenodo | http://zenodo.org/ | data repository |
the content mine,contentmine.org,
journal of open humanities data,
science.ai
journal of open humanities data,
science.ai
Scihub, http://sci-hub.io, http://sci-hub.cc
The open journal, http://theoj.org,
Protocols.io, https://www.protocols.io
Pubchase, www.pubchase.com,
Monday, 19 October 2015
PubPeer - Scientific Conversation
PubPeer, The Online Journal Club, is a program that is involved in carrying on the conversation of science, mostly after work has been published.
Nuts and Bolts
Essentially, it appears to work by searching articles based on DOI or other unique identifier (e.g. PubMed ID) through the PubPeer interface. Once the article is found, you can provide comments on it.
Getting started
You become a member by inputting the DOI of a paper you published, selecting which author you are, then providing your institutional email address. ResearchGate is another service that requires an institutional email address to get started.
Providing Commentary
Of course there are guidelines on how to provide appropriate commentary through PubPeer.
The Browser Extension
I, as a good scientist, installed the browser extension. I tried it out searching the keyword "naphthenic acids". No PubPeer results on the first page. I also searched "cancer", "pubpeer" and "metabolomics" and there was no PubPeer commentary on any article on the first page.
Finally, I went to the PubMed featured comment for the day (Oct. 2, 2015) and saw the following page. The yellow bar above the article title shows how many comments are on PubPeer.
To access the PubPeer comment, you click on the white words "1 comment on PubPeer". You are then taken to PubPeer's webspace to explore the comment. The comment at PubPeer is pretty much the same comment below the article in PubMed Commons.
Commenting
I posted my first comment on PubPeer concerning an article about the synthesis of yaku'amide. This is how it looks!
Future
Will they permanently archive commentaries and/or commentary chains with DOIs? What is the difference between PubPeer and PubCommons in PubMed? How is PubPeer different than Disqus?
I know there are subtle differences, but I am still waiting to hear back from those organizations. Until then, PubPeer remains another excellent tool for scientific commentary just waiting to explode!
I know there are subtle differences, but I am still waiting to hear back from those organizations. Until then, PubPeer remains another excellent tool for scientific commentary just waiting to explode!
Monday, 5 October 2015
Sparrho - Scientific Recommendation

Sparrho ("sparrow") is a scientific recommendation service.
When I began playing with Sparrho, I got the feeling that it was similar to Google Scholar, but I knew it was different. I just couldn't tell how.
So I asked Sparrho myself!
@matthwmaclennan we do personal rec of other scientific content types (+ articles/patents)...
— Sparrho (@sparrho) September 28, 2015
@matthwmaclennan ...and these rec are not only based on articles u've published, so we can rec even if you haven't published anything before
— Sparrho (@sparrho) September 28, 2015
@matthwmaclennan that's great, thanks for the shoutout! Let us know if u need anything (pics, slides etc) to make ur life easier :)
— Sparrho (@sparrho) September 28, 2015
Thanks so much! I also got an invitation to receive some "sparrhoswag". I'm not sure what it is, but it sounds good. Now I am trying to navigate sparrho.
--
Be it known that I am obsessed with naphthenic acids in oil sands process waters!
How can sparrho help me?
--
Well, the interface is sleek-looking, purple and starry! I am looking into a fascinating world. As I type in and save keywords, I am building a repertoire of articles of which I can mark as relevant (checkmark) or irrelevant (X) for my purposes. It's like I am building a research topic channel. I can immediately share articles over a variety of networks and link to the location of the article online.
The only thing is the 1D, 2D, 3D network graph logos that confuse me a bit.
THIS is how Sparrho is different from Google Scholar.
The 1-D graph image is a search which contains only the exact keywords you've entered for your channel.
Okay, let me go back to Sparrho then and play the game!
The Game
A 2-D search returns over 400 hits! Excellent. I tend to get hits concerning various aspects of naphthenic acids chemistry: biodegradation, toxicity, structure determination, etc. Extremely useful. If an article is currently considered "noise" to a channel, I can mark it as irrelevant. I can also dig up the articles I have marked by clicking HISTORY button on the top right. I can change the status of an article to which I have already applied relevance status (for that particular channel).
A 3-D search produces 261 hits, which is less than 403, but doesn't mean the search has somehow failed. On the contrary, it succeeded by returning exactly the number of results it is supposed to return for the keywords and relevance scores supplied! Perhaps it suggests that my channel's keywords are quite 'directed' and do not have a diffuse set of connotations or definitions. I saw here some articles related to climate change and the Athabasca oil sands, as well as articles concerning oil sands soil nitrogen availability, and honouring indigenous treaty rights.
When you click on the information about an article, a pleasant green window pops down underneath called "People who read this also read", showing articles that can be called as such.
Summary
I am very excited to learn how to use Sparrho more effectively. I can envisage the 3-D search being extremely useful for academics who are charged with research that is very nebulous, publicly involved and has a lot of angles by which to approach: In fact this is all PhD projects, no matter how pessimistic you may feel! Using Sparrho can open you up to new research that is still directed toward your primary research interests and goals! Although I am developing analytical methods to characterize naphthenic acids, my efforts are directly related to policy and the wider industry. I believe it is my job to understand and be able to effectively manage the milieu in which my research is situated so I can have an impact there. Sparrho is helping.
P.S.: sparrhoswag?
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