Discovering what’s in a name at the CCDC
August 11, 2015
A guest blog by Thom, one of CCDC’s co-funded summer students
This summer I decided to enhance (and help fund!) my Chemistry degree in Edinburgh by entering the world of crystallography for a few months, including a week’s visit to the home of the CSD in Cambridge.
My week of experience at the CCDC has opened my eyes to the tireless work and expertise which maintains and develops such an immense, and impressive, catalogue of data. The CCDC is truly a machine: its gears turning under the constant flow of deposits, while its developers work to refine the already sophisticated editorial process through the production and utilisation of immaculate pieces of software.
My summer placement aims to help crystallographers and chemists at the University to share their unpublished structures through the CSD as Private Communications. With Prof Simon Parsons, Dr Gary Nichol, Dr Stephen Moggach and others providing over 450 structures to the cause I think it is fair to say it will be a busy summer! During my week at the CCDC, I worked through 76 deposits. This mainly involved learning how to use CCDC’s internal system to process depositions and create the CSD entries and assisting in the scientific validation process, making sure the structures are consistent with their CIFs. A big part of this is naming the variety of compounds I came across (who knew hyphenating was such a skill? (see below)) and checking the chemical connectivity automatically generated from the coordinates in the CIF was chemically accurate. There were stark contrasts in the lengths and complexity of the compounds names, from the monstrous beast of bis(1-(5-t-butyl-2-oxido-3-((hydroxyimino)methyl)benzyl)piperidinium)-bis(μ-1-(5-t-butyl-2-(oxido)-3-(((oxido)imino)methyl)benzyl)piperidiniumato)-di-copper bis(trifluoromethanesulfonate) chloroform solvate (CSD Refcode OHEZOS) to the beautiful simplicity of di-t-butylsilanediol (CSD Refcode COLTAY06). Gratifyingly all these structures and indeed chemical names are already available via the CCDC’s freely available Get Structures service with many more to come in the weeks ahead!
CSD refcode OHEZOS
CSD refcode COLTAY06
Additionally, I was shown some of the more advanced features of CSD software, equipping me with new structural chemistry skills as I go through my degree. I’m sure the expertise I’ve gained here will help me greatly in the future.
The CCDC staff are also incredibly friendly. Even though many were busy making preparations for the upcoming CSD50 event, they always took the time to see if I needed assistance (often imparting wisdom on whether a structure should contain a ‘bis’ or a ‘di’) and were extremely approachable, knowledgeable and welcoming.
Lastly, I would like to say thank you for a thoroughly enjoyable week and I sincerely hope that the gears of the CCDC machine keep on turning for at least another 50 years!
We are delighted to be collaborating with Edinburgh University, several other institutions and many individual crystallographers to share more structures through the CSD. Fifty years of the CSD has taught us all that real impact comes when data are shared and combined to allow the creation of new knowledge. This is not possible without individual depositions. Each structure shared has its own story to tell and role to play in making the collection of structures an even more powerful resource.
The crystallographers of Edinburgh University are not alone in having unpublished crystal structures just waiting to be shared with the world. If, like them, you have a collection of unpublished crystal structures then please do let us know; we would love to collaborate with you to make sure these are shared with the world.
Suzanna Ward – CSD manager
CSD System (45)