05 August, 2014


Editing the Wikipedia today. Added a diagram for the page titled, Intramolecular Diels-Alder cycloaddition. Go check out the page and start editing! It's a bit difficult thinking of things to write that's specific for the intramolecular reaction, but a picture was missing and so I filled the gap.

"Corey 1978 gibberellic acid" by Marvinthefish - Own work. Licensed under Creative Commons Attribution-Share Alike 4.0 via Wikimedia Commons - https://commons.wikimedia.org/wiki/File:Corey_1978_gibberellic_acid.png#mediaviewer/File:Corey_1978_gibberellic_acid.png

Going through the guidelines on drawing chemical structures for Wikipedia (see here), I used ACS format, changed a "Me" to "CH3", included the stereochemistry and used ChemDraw (13.0). Maybe I need to take out the English, to make it "language neutral". Not even sure if I need things like reaction conditions and yield.

01 August, 2014

DNA - not like that!

DNA project 'to make UK world genetic research leader' says the headline.

But when one starts with left handed B-DNA...


Oh well at least they're not trying to sell us anything...like in this example

STOP the spread of left-handed B-DNA!

18 June, 2014

As SOON as publishable

What looks like a hand-drawn Figure 1. in this Journal of Organic Chemistry article. I can't spot any particular reason why it might be hand-drawn (as in, something clever which relates to the article itself). Any ideas? Also, that left-pointing retrosynthesis arrow seems inelegant to me. What's wrong with a standard reaction arrow?

13 May, 2014

Dorothy Hodgkin 12th May, 2014

Google's doodle on this day commemorated the "104th birthday"(is it still a birthday?) of Dorothy Hodgkin. I was happy to find I could recognise the molecule, before reading any further. I'm a real chemist (sounding like Pinocchio)! I particularly liked the Orange oxygen atoms :-)

Link to Google's explanation here (including  doodle drafts): http://www.google.com/doodles/dorothy-hodgkins-104th-birthday
...a pioneer of the field of X-ray crystallography. A 100 year old technique in chemistry which has revolutionized the way we understand the structure of the universe on a molecular level. By studying the patterns produced by X-rays, scientists are able to surmise the molecular structure of materials. A technique so important that it has had a direct role in producing multiple Nobel Laureates including Dorothy Hodgkin, who was awarded one in 1964 for her work on uncovering the complex structure of Penicillin G (the model in the doodle).

02 April, 2014


Skipping work* and heading in to London led to a wonderful day in Burlington House. A Wikipedia editing workshop was organised by the Royal Society of Chemistry and Wikimedia UK (a charity that supports and promotes Wikipedia and other Wikimedia projects).

*Looks back at original email application to attend* (paraphrased)

I want to learning more about editing and creating pages on Wikipedia would allow me to contribute more often than I do now. I have made a few small additions to pages, but feel I have been held back sometimes because of ignorance of the coding/formatting language (Just looked it up - "Wiki markup").

Editing wikipedia could give me the chance to have more interactions with the community of knowledgeable chemists around the world.

I would also like to learn more about linking, searching and applying chemical information on the internet. This would obvs be helpful to me in my career. Totes amazeballs,

 Stuff I need for the day: (from my notebook)
  • Laptop
  • Camera (photos below!)
  • Fob for work account (access to ChemDraw)
  • Notebook (Moleskine, unlined, pocket sized)
  • Chargers
  • Water
So after a fairly enjoyable trip in to foggy London (along with some commuters), I stopped for a coffee (I was a bit early). A couple were talking loudly about theology (existentialism was definitely a word they used) behind me. At that point I knew it was time to bathe in the scientific waters of the Royal Society of Chemistry. The walk up:
#UnionJack #Fortnum&Mason #BlackCab #RedPhoneBox
 I came to the door and pushed (or pressed, I can't remember).

Picked up my name badge and headed in to start up my computer and get Wikipedia editing. One of the first things I learn is WP is a better abbreviation for Wikipedia than "Wiki" according to Charles Matthews, one of the Wikipedians teaching us. Interesting. We will build the house of the future.
If those vertices were carbon atoms, the structure would be unstable.
 After setting up Userpages, everyone listened to talks from Wikipedians and from representatives from the RSC. Charles Matthews went through one article in particular in order to explain topics around conflicts of interest. The article doesn't matter, just that it contained some advertising copy. He walked us through how to edit so that the final article was more neutral and clear. The afternoon was set aside for free editing of any page (or pages) you liked. I chose the page on actaplanin, because it was tagged previously as a chemistry page which needed an image. I also looked up the 1984 research on this antibiotic carried out by Eli Lilly, and a patent. Using my newly acquired Wikipedia skillz, I updated the page. I think I did an OK job for a beginner! Still lots to add and clarify, when I have time. The part I found most difficult was knowing when to stop. I've started a list of articles to edit, but it's growing rapidly. Maybe the way to go about this is to recruit more people.
"Arty" shot of Nelson's column

 *I'm a good fish and actually booked the day off 4-6weeks previously.

03 March, 2014

Experimental pancakes

Aim: Delicious pancakes for Pancake Tuesday
Date: Monday 3rd March 2014
Procedure: Plain white flour (300g, “essential Waitrose”) and salt (<1g, NaCl) was weighed out using the balance. This was passed through a sieve into a 2L circular bowl. A small depression was made in the centre of the flour. Eggs (three, medium-size hen eggs(free-range)) were cracked open and poured into the centre of the flour. Sunflower oil (22ml (1 ½ tablespoons)) was added next, followed by milk (100ml, semi-skimmed cow’s milk, 1.7% w/v fat content, ~5°C). The mixture was stirred vigorously using a whisk until all solid flour had become incorporated and a viscous paste formed.
Milk (100ml) was added to the paste and stirring continued for 2min. Milk was then added until a total of 450ml had been added, stirring continuously (may use a dropping funnel clamped above, if desired). The viscous liquid – the batter – was placed in the fridge overnight at 4°C ± 1°.
The next day, the batter was poured on to a hot pan and heated until delicious. 

Recommendations: Lemon juice (10ml. From Eureka lemon. Contains water, limonene, citric acid...) was added to the “pancake”, followed by sucrose (10g). Order of addition found to be a controversial issue.
Use fork or spoon to place in mouth. Masticate, swallow and digest. Smile. It’s Pancake Tuesday!

Suggestions for future experiments: To be updated


13 January, 2014

A trip to the dentist

Back in work today after a trip to the dentist. Still feeling the affects of this pretty little molecule:

My voltage-gated Na channels in my neurons are starting to fire again, my lip and face are getting their feeling back and my liver is doing its thing, grinding this puppy into glycine deriviatives and adding oxygen atoms!

Lots of chemistry going on down at your local dentist. My jaw is now packed with an amalgam of mercury, silver, tin, copper and who knows what other metals (I'm hoping for ruthenium, one of my favourite metals! Unlikely) The dentist, using caution, described it as a "silver" filling. Having just yesterday finished reading "Bad Science" by Ben Goldacre, I can understand why the general public are a bit more scared of mercury fillings (Oooh just thought of a science-based joke : What do you call holes in your teeth after you've been to the dentist? Hg wells! Needs improvement, but I do like the different levels - the science fiction, the non-obvious acronym for mercury, Wells died just around the time lidocaine was discovered (first marketed in 1949, Wells died in 1946). My work is done for the day after that.)

When I arrived at work there was an email from the British Dental Journal (published by Nature) and I browsed through the list of article titles. Fluoride in water was one of the links. Sugar also comes up. Interesting, because I had not really thought about the effect of sugar on teeth when dietary sugar was being discussed in the media (at least, in the UK media) recently. Maybe I should try cut down on the ol' sugar. I do have a bit of a sweet tooth. Quote from the sugar article :

The Newcastle University study, commissioned by the WHO and published last month in the Journal of Dental Research, recognises the benefit of this threshold by showing that when less than 10% of total calories in the diet is made up of free sugars there are much lower levels of tooth decay. The new research findings go even further, suggesting that halving this threshold for sugars to less than 5% of calories – around five teaspoons a day - would bring further benefits, minimising the risk of dental cavities throughout life.