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Using the Cambridge Structural Database for Teaching

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USING THE CAMBRIDGE STRUCTURAL DATABASE FOR TEACHING Copyright © 2008 The Cambridge Crystallographic Data Centre Registered Charity No 800579 CSDS Teaching Modules 2 CSDS Teaching Modules Conditions of Use The Cambridge Structural Database System (CSD System) comprising all or some of the following: ConQuest, Quest, PreQuest, Mercury, (Mercury CSD and Materials Module of Mercury), VISTA, Mogul, IsoStar, SuperStar, web accessible CSD tools and services, WebCSD, CSD Java sketcher, CSD data file, CSD-UNITY, CSD-MDL, CSD-SDfile, CSD data updates, sub files derived from the foregoing data files, documentation and command procedures (each individually a Component) is a database and copyright work belonging to the Cambridge Crystallographic Data Centre (CCDC) and its licensors and all rights are protected. Use of the CSD System is permitted solely in accordance with a valid Licence of Access Agreement and all Components included are proprietary. When a Component is supplied independently of the CSD System its use is subject to the conditions of the separate licence. All persons accessing the CSD System or its Components should make themselves aware of the conditions contained in the Licence of Access Agreement or the relevant licence. In particular: • The CSD System and its Components are licensed subject to a time limit for use by a specified organisation at a specified location. • The CSD System and its Components are to be treated as confidential and may NOT be disclosed or re- distributed in any form, in whole or in part, to any third party. • Software or data derived from or developed using the CSD System may not be distributed without prior written approval of the CCDC. Such prior approval is also needed for joint projects between academic and for-profit organisations involving use of the CSD System. • The CSD System and its Components may be used for scientific research, including the design of novel compounds. Results may be published in the scientific literature, but each such publication must include an appropriate citation as indicated in the Schedule to the Licence of Access Agreement and on the CCDC website. • No representations, warranties, or liabilities are expressed or implied in the supply of the CSD System or its Components by CCDC, its servants or agents, except where such exclusion or limitation is prohibited, void or unenforceable under governing law. Licences may be obtained from: Cambridge Crystallographic Data Centre 12 Union Road Cambridge CB2 1EZ United Kingdom Web: http://www.ccdc.cam.ac.uk Telephone: +44-1223-336408 Email: [email protected] (UNITY is a product of Tripos, L.P. and MDL is a registered trademark of Elsevier MDL) 1 INTRODUCTION This booklet contains a series of step-by-step exercises that utilise the Cambridge Structural Database to assist and enhance the teaching of many of the concepts encountered in a typical undergraduate chemistry curriculum. Crystal structure analyses are remarkable for the richness of structural information they provide. Both the 3D geometric structures of molecules and also the nature and geometry of their interactions with other molecules and ions are characterised. Integrate the use of crystal structure data into your course, visualise and manipulate molecules in 3D, and expose students to real experimental data. • Non-subscribers : A number of the exercises presented here draw exclusively from a free 500- structure teaching subset of the Cambridge Structural Database, and thus do not require a CSD licence, see TEACHING SUBSET OF THE CSD (see page 6). • CSD licence holders : Providing your institution holds at least one CSDS licence then you can install as many copies of Classroom ConQuest as you require for group teaching purposes. This will allow your students to fully utilise the search and analyses capabilities of the CSD, see: CLASSROOM CONQUEST (see page 7). This booklet is also present in the top level of the UNIX , Windows, and MacOSX software DVD- ROMs as both HTML and PDF files should you require additional copies. teaching_examples.html teaching_examples.pdf Alternatively, these and other CSD System teaching examples can be accessed via the CCDC website at the following address: http://www.ccdc.cam.ac.uk/free_services/teaching/ CSDS Teaching Modules 2 TEACHING SUBSET OF THE CSD A free 500-structure teaching subset of the Cambridge Structural Database is available as a download from the following URL: http://www.ccdc.cam.ac.uk/free_services/teaching/ The subset has been specifically designed to provide a wide diversity of chemical content and includes many of the key molecules typically used to exemplify the chemical concepts taught in undergraduate courses. The subset is provided in CSD-database format and can be viewed using our free crystal structure visualisation program Mercury, see: http://www.ccdc.cam.ac.uk/free_services/ mercury/ A number of the teaching exercise presented here draw exclusively from the teaching subset and thus do not require a CSDS licence, whilst others will require access to the full database and associated search tools. For further information, see TEACHING MODULES (see page 8). The free 500-structure subset is based upon work supported by the United States National Science Foundation under Grant No. 0725294. 6 CSDS Teaching Modules 3 CLASSROOM CONQUEST Classroom ConQuest is a version of ConQuest which has been designed for group teaching activities. • Anyone with at least one normal ConQuest licence can install as many copies of Classroom ConQuest as they require. • It has all the functionality of normal ConQuest with the limitation that searches can only be done on a subset of entries. • The subset of entries can either be the default selection supplied with Classroom ConQuest or one derived by the user from the main CSD. In order to install Classroom ConQuest you must first obtain a Classroom ConQuest Validation Number from the CCDC. Please contact the CCDC with your Site Code and Confirmation Code using: Email: [email protected] Note : Classroom ConQuest licences do not allow access to Mogul or Mercury CSD. CSDS Teaching Modules 4 TEACHING MODULES AROMATICITY (see page 9) SHAPES OF MOLECULES: VSEPR MODEL (see page 18) METAL CARBONYL BACK-BONDING (see page 28) * DETERMINING MOLECULAR DIMENSIONS (see page 39) * ANALYSING 4-COORDINATE METAL GEOMETRY (see page 47) * REACTION INTERMEDIATES: HALONIUM IONS (see page 60) * HAPTICITY (see page 67) CONFORMATIONS OF RINGS (see page 77) STEREOCHEMISTRY (see page 89) Other teaching exercises and resources are available from: http://www.ccdc.cam.ac.uk/free_services/teaching/ * these exercises require full access to the Cambridge Structural Database System 8 CSDS Teaching Modules 5 AROMATICITY 5.1 INTRODUCTION • The word aromatic can be used to describe fragrant substances such as benzaldehyde (from cherries, almonds), and toluene (from Tolu balsam). • However, in the early nineteenth century such substances were discovered to behave in a different chemical manner from other organic compounds. Thus, in chemistry, the term aromatic is now used to refer to benzene and it’s structural relatives. • The Cambridge Structural Database can be used to explore the structural requirements for aromaticity. By investigating the structure of such compounds we can explain their special stability. 5.2 OBJECTIVES • To investigate the concept of aromaticity by analysing experimental crystal structure data. • To determine the structural requirements for aromaticity by examining a series of benzene and cyclooctatetraene derivatives. • To understand the reason for the observed stability of benzene in terms of its molecular orbital description. • To use your findings to predict whether or not certain given compounds are aromatic. 5.3 GETTING STARTED • If you do not subscribe to the Cambridge Structural Database (CSD) System: • Open free Mercury (the free version of Mercury can be downloaded from http:// www.ccdc.cam.ac.uk/free_services/mercury/ ) • Open the free teaching subset of the CSD (downloadable from http://www.ccdc.cam.ac.uk/ free_services/teaching/downloads ) by selecting File from the top-level menu, followed by Open in the resulting menu, and then selecting the database file teaching_subset.ind • Database reference codes ( refcodes ) of the structures in the teaching database will appear in a list on the right hand side of the main Mercury window. To view a structure select the corresponding refcode in the list. • Once the teaching database has been loaded Mercury can then read text files containing lists of database reference codes ( refcodes ). To read in a file containing just those structures required for this tutorial hit File in the top-level menu, followed by Open , then select the file aromaticity.gcd. • If you subscribe to the Cambridge Structural Database (CSD) System: • Open MercuryCSD. • The full database should be detected and opened within the Structure Navigator on the right hand side of the main Mercury window. CSDS Teaching Modules • Once a database has been loaded Mercury can then read text files containing lists of database reference codes ( refcodes ). To read in a file containing just those structures required for this tutorial hit File in the top-level menu, followed by Open , then select the file vsepr.gcd. • Within the Structure Navigator loaded crystal structures are presented in a hierarchical tree organised first by file type ( Databases , Structures , Refcode Lists , ConQuest Hits , or Mercury Files ) and subsequently by filename and then by individual refcode . The file aromaticity.gcd can be found under Refcode Lists . To view a structure select the corresponding refcode . 5.4 STEPS REQUIRED 5.4.1 Examine the structure of benzene • Benzene (a) is unusually stable for an alkene. Normal alkenes readily react with bromine to give dibromoalkane addition products [1]. However, benzene reacts only in the presence of a Lewis acid catalyst and the product is a monosubstituted benzene not an addition product [2]. Why does benzene not behave like other alkenes? Br Br2 [1] Br Br Br 2/AlCl 3 [2] (a) • Display the structure of benzene by clicking on the identifier BENZEN02 from the Structure Navigator on the right hand side of the main Mercury window.
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