Springer Publishing

Friday 11 November 2016

The Future of Canada's Oil and Energy Sector (oil, gas, mining, nuclear)

Aerial view of oil sands operations in Northern Alberta 
with the Athabasca River in the foreground. Image courtesy of CBC.

As a chemistry graduate student who analyzes the tailing pond waters of Northern Alberta's oil industries, I can say that I know some things about what is in the tailing ponds water.

I cannot say, however, that I know much about the politics of environment, health, rights, and bitumen--except for the injustices we hear in the media generally: Choruses of "No pipelines" and "increased consultation" being mowed down by "We're going to build it anyway".


Image result for #nodaplImage result for i love oil sands
We are surrounded by examples of how natural resource development and management (in Canada and US) are very divisive issues. Featured here are the #NODAPL protest against the Dakota Access Pipeline and a T-shirt logo. 


A reality is that pipelines bring jobs and revenue along with the bitumen, which are important to Canadians. Another reality is that pipelines bring disturbance and sometimes destruction to the environment we need and love. We need sources of energy. We need a clean environment. We need to execute decisions. We need to make the right decisions in broad consultation. Which do you think happens?

I felt that reading parliamentary transcripts (listening to audio/video) would be the best source of information when it came to understanding my country's decisions and how they arrive at them. So this is where I begin.

One week ago, I became interested in what was going on in Parliament regarding the Alberta Oil Sands operations. Much of my extended family lived and worked in Fort MacMurray and it has become the subject of my PhD work. With the recent hit the Canadian oil industry has taken, and the countless lives that have been effected by it, I was intensely curious about what the Government of Canada had in mind for this massive natural resource of ours.

Sure enough, the Standing Committee on Natural Resources was "having a time" chatting about this very issue, but also about the mineral mining sectors and nuclear energy. I was having some questions:

Was more money being put in to support natural resource development? The current Libéral Government campaigned openly about their future spending. Now that they've been elected, they are figuring out how they should spend money. Scientists know that money is being put into science, technology and innovation already which means more opportunities to develop knowledge into innovative technology. That's great for us...

Were measures being put into place that would ensure appropriate consultation with First Nations over the use of their land?

Would environmental assessment get a makeover? Would it include Professional Chemists?

From what I've read, all the above are being addressed and consulted on. There are also no signs of "shutting down" the oil sands or any other natural resource project amid the discussions. So many interesting and influential witnesses are being interviewed in Parliament and I am learning a lot. Full list is here under "witnesses".

Image result for innovation sustainability canadaI am looking forward to covering what is talked about in these meetings via blog posts. What will the decisions made do to Universities and their relationships to Industry and innovation? How much more money will I get!?? Will it be easier to make connections between communities, educational institutions, government and industries? Technology transfer? Knowledge mobilization? Innovation and sustainability in the era of climate change?


THINGS TO READ BEFORE JUMPING IN
Here are some things you should read prior to Meeting 4 (in order)


I am currently 29 meetings behind schedule, so you'll have to bear with me. The next meeting is November 15. Happy Remembrance Day in gratitude or our Veterans, Armed Forces and all others.

Thursday 2 June 2016

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!

Thursday 26 May 2016

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.

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.

Graphical abstract: 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

I read an alluring tweet today about a graphical abstract
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