Getting creative with PubChem molecular similarity graphs

PubChem has the ability to graph the molecules in a search result by Tanimoto similarity. The result is displayed as a hierarchical graph. Below is a snippet of a PubChem substructure search I made using a generalized steroid scaffold (take cholic acid, remove stereochemistry symbols and peripheral oxygens): SMILES: [CH]1CC[CH]2[C]1([CH](C[CH]3[CH]2[CH](C[CH]4[C]3(CC[CH](C4))C)))C

~51,000 results

You can save this data as a GML file. GML is a lightweight graph format that saves connectivity information and usually seems pretty easy to load into graph readers.

I loaded this hierarchical data into yEd, a free graph editor. I applied a circular layout regime, BCC compact, with no special requirements and voila: The data concerning steroid-like molecules in PubChem comes out looking like this!

Need I say that this format looks very appealing?! Next I want to colour-code based on molecular weight and use this data for some mass spectrometry-based problems!

Carboxylic acids (not including proteins) in databases

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.

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)

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

I read an alluring tweet today about a graphical abstract

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.5b10985

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.

	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

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

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,

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!