www.ccdc.cam.ac.uk

The newsletter of The Cambridge Crystallographic Data Centre

CrystallineNovember 2013

CCDC in the DRCIn June 2013, CCDC staff members JuliettePradon and Peter Galek spent another week atthe University of Kinshasa delivering severaltalks and workshops about the CSD System, aswell as running an electronic structure theoryworkshop where the interface to MOPAC inMercury was used to probe moleculargeometries, energies of interactions, and theJahn-Teller effect. This was to lay thegroundwork for two research projects, whichhave just commenced;

- Albert Lundemba Singa is an MSc student whostarted the second year of his Masters studyin September 2013. His research project isbased at the University of Kinshasa and isfinancially sponsored by the CCDC. It consistsof a comparative study of the interactiongeometries and energies of hydrogen bonds totraditional acceptors with those to functionalgroups involving the element selenium.

- Didi Bibelayi Dikima is a PhD student whoseresearch project is based at the University ofKinshasa, to include several visits to the CCDC

in Cambridge. This too is financially sponsoredby the CCDC and co-supervised by JuliettePradon with the scientific support of otherCCDC staff members. His work will be on theuse of the CSD and QM calculations toinvestigate sigma-hole and H-bond interactionsmade by selenium and possibly tellurium.

These two research projects will help to showhow the CSD System can be used in thedeveloping world to do valuable, publishable,cutting-edge research at a minimal cost,helping us to fulfil our charitable objectives ofenabling structural chemistry understanding,discovery and development worldwide. In July2013 the CCDC became a member of theHumanitarian Centre, an umbrella organisationfor Cambridge-based charities andorganisations that are involved in thedeveloping world.

The CCDC is very much looking forward tosome fruitful results from the DRC very soon.

The CCDC has formed a friendly connectionwith Professor Zéphirin G. Yav of the ChemistryDepartment of the University of Kinshasa in theDemocratic Republic of the Congo (DRC).Contacts with Professor Yav date back to 2007/8,when a Cambridge Structural Database (CSD)System licence was granted to his laboratory aspart of a collaboration with Professor Luc vanMeervelt at K.U. Leuven, Belgium. In 2012, theCCDC’s Director Colin Groom and JuliettePradon spent a week at the University ofKinshasa as part of a year-long, British Councilfinanced Science Training Laboratory project,entitled “Using New Information andCommunication Technologies”. They delivered aseries of seminars and workshops on the use ofthe CSD System to an audience consisting ofacademic staff and other researchers.

The CCDC is now delighted to be entering into aresearch collaboration with Professor Yav in thearea of structural chemistry. Yav has beenProfessor of Physical and Biophysical Chemistryat the University of Kinshasa for almost 30 years.

The building housing the Chemistry Department at Kinshasa University Juliette and Professor Yav enjoy some refreshment

www.ccdc.cam.ac.uk

The CCDC is a charitable organisation andas such we are delighted to be given theopportunity to sponsor scientificmeetings and training workshops. On

many occasions we lead training workshopsourselves; indeed in 2013 alone we havecontributed to over ten schools and workshops.Below we hear from Sebastien Suarez whoattended the Cambridge Structural DatabaseSystem training workshop we led at this year’sACA in Hawaii. You can read more about theCellCheckCSD feature Sebastian refers to on theCCDC website:http://www.ccdc.cam.ac.uk/Solutions/FreeSoftware/Pages/CellCheckCSD.aspx

TMy name is Sebastian Suarez, as a Ph. D.Student from the University of Buenos Aires, Ihave attended to the 2013 ACA Meeting, inHawaii, on July 20 -24th.

The first day, I had the pleasure of attending tothe workshop of the Cambridge StructuralDatabase System. The course was given byPeter Wood and Colin Groom and started withan introduction to the CCDC and the CSDSystem. The first task was ConQuest, Mercuryand data analysis tools. These are programsthat I normally use, so allowed me to learnsome new tips. In a second stage, the programsMogul and IsoStar were shown. In this part thehands-on session was very helpful, plus allowedme to learn and solve simple problems.

Finally, there was an introduction to WebCSD,the online search interface to the CSD. This wassomething that was out of my knowledge, andis a perfect complement to the traditionaldatabase. We have a license from the CCDCsince 2004 to the present, until 2012 providedby the Spanish Research Council (CSIC) as free-of-charge. WebCSD really has been very helpfulsince my return from the conference, not onlyfor me but for the entire research group.

In 2007 a grant was obtained by our university(ANPCyT, PME-2006-01113), which resulted inthe purchase of a single crystal diffractometerXRD, Oxford Diffraction Gemini E. It wasinstalled in 2009 in our facilities under the

Helping crystallographersof the future!

Sebastian with his poster at the ACA

The Honolulu waterfront

supervision of Dr. Fabio Doctorovich.Furthermore, another interesting and efficientupgrade has been the CrysAlisPro interface toCellCheckCSD, which performs crystal structurereduced cell checks against the CSD allowing faststructure identification for a new measurement.Sebastian Suarez Ph.D. StudentUniversity of Buenos Aires, Argentina

www.ccdc.cam.ac.uk

Date Conference, meeting or event Venue Activity

10 Nov 2013 9th German Conference on Chemoinformatics Fulda, Germany Poster

12 Nov 2013 BCA Industrial Group Autumn Meeting Diamond Light Source, UK Attendance

27 Nov 2013 Autumn School of Chemoinformatics Tokyo, Japan Talk

29 Nov 2013 Young Modeller’s Forum London, UK Attendance

7 Dec 2013 AsCA Hong Kong, China Talk, Exhibition

8 Jan 2014 ASE 2014 Birmingham, UK Workshop

16 Mar 2014 Spring ACS Dallas, TX, USA Talk

7 Apr 2014 BCA Spring Meeting Loughborough, UK Talk, Exhibition

Events Over the coming months you can come and meet us at various meetings and events around the world.

The CCDC’s User Services TeamIndustrial sales operations are handled by Steveand by Tracy Allgood, with academic saleslooked after by Sarah Amery in conjunctionwith members of the Centre’s financial team.Susan Henderson and Dave Bardwell carry outscientific and technical support of all of theCCDC’s products, with the help of the Centre’sapplication scientists. Juliette Pradon has aspecial role, working with Research Partners(the CCDC’s key industrial users). And Susanand Steve look after the CCDC’s marketingoperations, such as website and social media

presence, conference participation, andliterature provision.

As the CCDC’s user base grows, the team’swork will expand accordingly, and so will theteam! So, the above assignment of names maychange as things develop over time. All of theteam’s members are very much looking forwardto continuing to work with you to make youruse of the CSD System and other products asfruitful as possible.

The CCDC’s sales, marketing and supportactivities have recently been reorganised andplaced under the umbrella of the newly formedUser Services Team. Under the direction of theCCDC’s Business Director Paul Davie, andmanaged by Steve Maginn, who has returned tothe CCDC after more than 11 years awayworking with Chemical Computing Group(CCG), the team sits together on the first floorat the CCDC, and is the first and ongoing pointof contact for academic or industrial users ofthe CSD System and other CCDC products.

The CCDC’s User Services Team pictured in the CCDC building. From left to right: Susan Henderson, Steve Maginn, Sarah Amery, Dave Bardwell, Juliette Pradon and Tracy Allgood.

on DASHSpotlight

www.ccdc.cam.ac.uk

My molecule is very complex: will DASHbe able to solve its structure?

Obviously this will depend on the quality ofthe powder data, but you may be interested toknow that DASH can handle up to 300 atomsin a structure and has been used to solve thecrystal structures of molecules with up to 16flexible torsions and more than 40 non-hydrogen atoms. It has been used to solve thestructures of a diverse array of structure typesincluding pharmaceutical compounds (e.g.naltrexone hydrochloride), salts (e.g.amodiaquinium dichloride dehydrate), solvates(e.g. chlorothiazide N,N-dimethylformamidesolvate), semiconductors (e.g. lithium1,8,15,22-tetraphenoxyphthalocyanine) andexplosives (e.g. silver azide). DASH is alsoroutinely applied to the solution oforganometallic crystal structures, and has beenused to solve inorganic crystal structures.

The structure of verapamil hydrochloride, a salt complex with 13 torsional degrees of freedom, was solved by DASH

The CCDC team frequently publish resultsof their research, which is often the workof collaboration with industrial oracademic scientists. You can find the fulllist of our publications atwww.ccdc.cam.ac.uk/publications.

Here are our most recent titles, publishedsince 1st May 2013.--

Hydrogen bond landscapes, geometry andenergetics of squaric acid and its mono- and di-anions: a Cambridge Structural Database,IsoStar and computational study F. H. Allen, A. J. Cruz-Cabeza, P. A. Wood, D. A.

Bardwell, Acta Cryst. B (2013) 69, 514-523.10.1107/S2052519213020277

The role of chloroform and dichloromethanesolvent molecules in crystal packing: aninteraction propensity study F. H. Allen, P. A. Wood, P. T. A. Galek, Acta Cryst.,B (2013) 69, 379-388,10.1107/S2052519213015078

The versatile role of the ethynyl group incrystal packing: an interaction propensity studyF. H. Allen, P. A. Wood, P. T. A. Galek, Acta Cryst.B (2013) 69, 281-287, 10.1021/ci2005934

Application of hydrogen bond propensity

calculations to an indomethacin-nicotinamide(1:1) co-crystal M. Majumder, G. Buckton, C. Rawlinson-Malone,A. C. Williams, M. J. Spillman, E. Pidcock, K.Shankland, CrystEngComm (2013), 15, 4041-4044, 10.1039/C3CE40367J

Bohr-Sommerfeld quantization condition forDirac states derived from an Ermakov-typeinvariantK.-E. Thylwe, P. McCabe, J. Math. Phys. (2013)54, 052301, 10.1063/1.4803030

CCDC Publications May 2012 to Oct 2013

How long will it take for DASH to solvemy structure?

This is a difficult question to answer, but we dohave a choice of ways in which a structuresolution can be speeded up. For example DASHcan be run in batch mode, either on a singlecomputer, multi-core processor or a GRIDnetwork. Cambridge Structural Database (CSD)System subscribers can take advantage of a linkto our library of intramolecular geometry,Mogul. Preferred values of rotatable torsionscan be imported from Mogul and used to limitthe search space used by DASH during thestructure solution step.

How do I get DASH?

If you work at an academic organisation thenaccess to DASH is provided through theCambridge Structural Database (CSD) System.Industrial organisations should contactadmin@ccdc.cam.ac.uk for further details.

The intuitive DASH interface enables easy monitoring of thestructure solution process

What is DASH?

DASH is a program for solving structures frompowder X-ray diffraction data. The CCDC andthe CCLRC (the UK Council for the CentralLaboratory of the Research Councils) arecollaborating to develop and distribute DASH,which was originally written by KennethShankland and Bill David. First released in 1998,DASH has a long and excellent pedigree.

I’m new to powder X-ray diffraction so byno means an expert…is this a problem?!

Not at all. DASH has been written to help guideusers through each step of its structuresolution process and as such has an intuitivegraphical user interface with an easy to usewizard. It is fully documented and comes withseveral illustrative tutorials.

Which input file formats can DASH handle?

DASH accepts both synchrotron andmonochromatic laboratory X-ray powderdiffraction data in a variety of file formatsincluding .raw (Bruker and STOE), .asc (Rigaku),.xye, .rd and .sd (Philips), as well as many others.