Crystallographic Databases: Using the Knowledge Available. Amy Sarjeant CCCW-16, Saint Mary s University, Halifax NS

Transcription

1 Crystallographic Databases: Using the Knowledge Available Amy Sarjeant CCCW-16, Saint Mary s University, Halifax NS 1

2 What is a crystallographic database? A structured collection of data about crystals and crystal structures Generally includes at least (but not limited to) the chemical composition, position of atoms, unit cell dimensions, space group, experimental parameters and bibliographic details May contain a lot more information about structures if relevant to the scientific area The term database also implies some level of quality control each of the major database curators applies some level of processing & validation to the structures 2

3 Primary comprehensive databases 119,137 entries: polypeptides, nucleotides & saccharides 833,163 structures: organics and organometallics PDB Protein Data Bank CSD Cambridge Structural Database ICSD Inorganic Crystal Structure Database CrystMet Metals, Intermetallics & Minerals ~185,000 entries: inorganics (no entries with C-H AND C-C bonds) 161,332 entries: metals, alloys, intermetallics & minerals Data correct as of 1 June

4 Other Databases Pearson s Crystal Data Crystallography Open Data Powder Diffraction File (International Center for Diffraction Data) American Mineralogist Crystal Structure Database 4

5 ICSD (Inorganics) Produced by FIZ Karlsruhe & NIST collaboratively Contains inorganics Accessible through a web interface or desktop application 5

6 CrystMet (Metals) Produced by Toth Information Systems Contains metals, alloys and intermetallics Available through desktop software 6

7 PDB (Proteins/Macromolecules) Produced by wwpdb group Contains macromolecules Available from any of PDBe, PDBj, RCSB & BMRB Accessed through web interfaces 7

8 CSD (Organics/Organometallics) The CSD is the most relevant to chemical crystallographers as it contains all available structures of organics & organometallics The Cambridge Crystallographic Data Centre (CCDC) has been compiling the CSD since 1965 A not-for-profit, charitable institution Community funded and governed A University of Cambridge Partner Institute Around 60 members of staff in UK and US 8

9 The Cambridge Structural Database 833,163 TUWMOP a di-copper paddle wheel the 800,000 th structure in the CSD EFEMUX Lamotrigine CSD Growth CSD Growth

10 June 1 st Sgt. Pepper Advances in AIDS Testing FABVAF01 Capsaicin WUTSUB W.I.F.David, K.Shankland, N.Shankland, Chem.Commun. (1998), 931, doi: /a800855h C.Fandaruff, L.Chelazzi, D.Braga, S.L.Cuffini, M.A.S.Silva, J.A.L.C.Resende, E.Dichiarante, F.Grepioni, Cryst.Growth Des. (2015), 15, 5233, doi: /acs.cgd.5b

11 Nova Scotia BIKINI NUNFUY SEACON HXFAVC DODROE02 11

12 Importance of data quality The ability of a database search to answer a question is limited by the quality of the data Not just the quality of the diffraction experiment & the refinement, but also the CIF & data included! 12

13 Importance of data completeness Alongside the coordinates, cell parameters, experimental parameters etc. you can include many additional text/numeric fields in a CIF e.g. compound name, melting point, colour, habit, re-crystallisation solvent, source of the compound, sensitivity (to heat, light, air, etc.) Details may not be particularly crucial for your specific structure, but they may well be important in someone else s data mining study! The CSD was established in 1965 to fulfil a dream of Olga Kennard and J. D. Bernal s the passionate belief that that the collective use of data would lead to the discovery of new knowledge which transcends the results of individual experiments 13

14 Text, 2D and 3D Search CSD System Visualisation and Analysis ConQuest Mercury PreQuest CSD WebCSD Molecular Geometry Mogul IsoStar Molecular Interactions 14

15 CSD deposition and access services 15

16 CIF Data File CSD-Community CSD-System CIF data files are deposited with the CCDC prior to publication Available to reviewers pre-publication and to everyone post-publication Structures are enriched and validated post-publication by the CCDC Included in the Cambridge Structural Database (CSD) Over 800,000 CSD Entries 16

17 CSD-Community Deposition, dissemination and preservation of the structure of record no charge to deposit or retrieve no charge for referee and publisher services Free software tools Targeted teaching subsets Mercury - structure visualisation encifer - CIF syntax validation CellCheckCSD - reduced cell searching 17

18 EnCIFer CIF syntax checker Freely available through CSD-Community Enables validation and preparation of CIFs for deposition with journals & databases Allows CIF editing without corrupting syntax Data entry wizards enables addition of: Publication details chemical, physical & crystallographic properties Visualises structures in a CIF 18

19 EnCIFer to CSD deposition 19

20 When to deposit data = pre-publication Deposition of data pre-publication By the crystallographer When you are most engaged with your structure When you can benefit most from deposition checks Automated workflows with publishers Guidelines for authors require pre-deposition Data accessible to publishers and referees during the peerreview process Data accessible from article Dealing with pre-publication data Embargo period in place Reduced from 3 years to 1 year in 2014 Easy for depositor to extend embargo CSD-Deposition provides an easy way to revise pre-publication data 21

21 CSD-Community Deposition and checkcif Deposition to CCDC now includes Generation of checkcif reports Available to depositor during submission Stored at CCDC at submission Available to publishers and referees during peer review process An easy way to embed validation responses into CIF Retrieval of edited CIFs and checkcif reports Launched July 2015 Level A Level B Level C Level G Most likely a serious problem - resolve or explain A potentially serious problem, consider carefully Check. Ensure it is not caused by an omission or oversight General information/check it is not something unexpected 22

22 CSD-Community Deposit Easy upload of data Integrated CIF correction tools Enhanced data to the CSD Large files accepted 3D visualisations Streamlined publication addition Validation Integrated integrity checks Structure factor alert Fast route to share data 23

23 CCDC number confirmation 24

24 Creating the CSD 25

25 After deposition publication Generally guidelines for authors require pre-deposition of data to CCDC Data accessible to publishers and referees during the peer-review process Workflows in place with publishers to automatically add your data with corresponding publication details to the CSD We take care of updating publication details associated with your data You are not required to update us about change of journals or publication details What you are requested to do: Provide us with a probable author list at deposition Include CCDC numbers in your manuscript Use CSD refcodes if you are referencing data already in the CSD Example of publisher instructions for authors 26

26 CSD Communications A free mechanism to share your data Quick to do during CSD-Deposit CheckCIF integrity checks available during the process Accessible through the CSD within seconds of deposition Result in a fully curated CSD entry check by expert scientific editors Results in an associated citable data DOI Discoverable in third party repositories Increases your chances of having the millionth CSD entry! Ensures your data is accessible for scientific research All structures are accepted even if they are redeterminations Rise in CSD Communications CIMETD

27 Access Structures Synthesis, Structure, and Catalytic Studies of Palladium and Platinum Bis-Sulfoxide Complexes E. Postgrad, A.Crystallographer and R. Supervisor Abstract DOI: /om The bis-sulfoxide ligand p-tolyl-binaso and its derivatives can be used to synthesize neutral and cationic palladium and platinum complexes. [ ] The nature of the bonding in the synthesized compounds was studied through analysis of their IR and NMR spectra and X-ray crystal structures. [ ] Jsmol visulaliser Curated 2D diagram Supporting Information Cross platform Visualiser options CCDC citation Cross platform Publication details Download deposited data 28

28 Linking articles and data Links are in place for ACS, RSC, Elsevier, Wiley and IUCr journals 29

29 Linking articles to data 30

30 Accessing data through the peer review process From: The Journal of Interesting Crystal Structures Sent: 09/02/2016 Subject : Crystal Data for Review - MAN123456_V1 Dear Referee, In view of your expertise I would be very grateful if you could review the following the data for the following manuscript MANUSCRIPT ID: MAN123456_V1 TITLE: The crystal structure of XXXXXX AUTHORS: Ayesha Jacobs, Francoise M. Amombo Noa CCDC deposition number(s): I would therefore be grateful if you could review the crystallographic aspects of the above manuscript. To do this please use the link below to access the CIF data, reflection data and checkcif report for this manuscript directly from the CCDC: &ccdc= &authors=jacobs 31

31 Retaining the provenance and attribution CSD DOIs Information added to structure of record Dataset Dataset Publication publication CCDC : Experimental Crystal Structure Determination. A. Crystallographer, Cambridge Crystallographic Data Centre (2013) 32

32 Getting credit for your data Depositing data at the CCDC conforms with all funding mandates Automated linking helps ensure the discoverability of your data Facilitates formal citation AND interoperability. Currently adding indication of full citation and compound name to metadata. Coverage of CCDC data by resources such as the Thomson Reuters Data Citation Index achieved via the DataCite metadata store. 33

33 Summary You can get answers to many important questions... but be careful when constructing your queries Do ask me questions and give us feedback we are community-driven, so your input is needed & valued! 34

34 ConQuest Enables search and retrieval of information from the CSD and in-house databases Provides full range of text/numeric database search options More complex search functionality includes: Chemical substructure searching 3D Geometrical searching Intermolecular non-bonded contact searching 35

35 ConQuest Large range of filtering options based on experimental or chemical considerations (e.g. R-factor, temperature, only organics) Combine searches using various Boolean options and manage hitlists post-search Export results to Mercury for visualisation and advanced numerical analysis & plotting 36

36 ConQuest 37

37 Data Analysis in Mercury 38

38 Hands on Session Introduction to ConQuest Tutorial Example 1: Searching for Similar Molecules Example 2: More Searching in ConQuest Example 3: Intermolecular Interactions with ConQuest Depending on your previous experience you may want to work on advanced exercises (provided) or your own queries. Ask me if you have questions or need help. 39

39 Making Mercury Work for You Visualizations Full Interaction Maps Mogul Geometry Check 40

40 Visualizations 41

41 Mercury: Visualisation Molecular structures and crystal packing Extended networks of H-bonds and other contacts Least squares & Miller planes Reads.cif,.res,.mol2, etc Free download version: 42

42 Mercury: Advanced visualisation Graph sets POV-Ray Symmetry elements Displacement ellipsoids etc. 3D Printing 43

43 Full Interactions Maps 44

44 Full Interaction Mapping Provides your molecule s interaction preferences, in the context of the crystal structure, at the click of a button Based on validated experimental structural knowledge Interactions visualised simply in 3D within Mercury Wood et al.; CrystEngComm, 2013, 15, DOI: /C2CE25849H 45

45 IsoStar A knowledge base of intermolecular interactions for individual functional group pairs Experimental data taken from: Cambridge Structural Database Protein Data Bank (protein-ligand complexes only) Interaction distributions displayed as scatterplots or contour surfaces Bruno et al.; J. Comput.-Aided Mol. Des. 1997, 11, DOI: /A:

46 IsoStar Methodology central group: -CONH 2 contact group: NH Search for structures containing desired contact Superimpose hits and display as scatterplots 47

47 Combining plots into Full Interaction Maps Molecule is broken down into fragments IsoStar maps for each fragment in the molecule & for multiple probe types are combined together to produce Full Interaction Maps 48

48 Full Interaction Maps similar acceptor propensity weaker donor propensity weak acceptor only 49

49 Full Interaction Maps Full Interaction Mapping in Mercury ideal for studying interaction preferences in the context of a crystal structure Overview of interactions for full molecule at once Many interaction types assessed in a single picture Excellent focal point for discussion & investigation of solid form-related questions in a clear and visual context such as Polymorphism Solvation (& hydration) behaviour Co-crystallisation Crystallisability 51

50 Mogul 52

51 Mogul Incorporates pre-computed libraries of bond lengths, valence angles, torsion angles and ring conformations derived entirely from the CSD Validate complete geometry: retrieve distributions, and figures of merit for all bonds, angles, torsions and rings in the molecule Fragment Generalisation: If fragment specified is rare, Mogul will include CSD results from the most similar fragments Hyperlinking to the CSD: View CSD entries in specific areas of histogram Integration with other software: Instruction file permits other programs to interact with Mogul Bruno et al., J. Chem. Inf. Comput. Sci., 44, ,

52 Mogul 54

53 Mogul 55

54 Hands on Session Mercury Tutorials Example 1: Using Full Interaction Maps to assess polymorph stability Example 2: Investigating the potential for co-crystallization Example 3: Investigating a series of halogenated molecules DOI: /acs.cgd.5b00478 Example 4: Using Mogul to assess intramolecular geometry Example 5: Using Mogul to predict geometry of a fragment Example 6: Using Mogul to explain activity data Ask me if you have questions or need help. 56

55 Thank you!!! 57