DOCSLIB.ORG

Using the Cambridge Structural Database for Teaching

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Using the Cambridge Structural Database for Teaching 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.
Load more

Recommended publications
  • Clusters – Contemporary Insight in Structure and Bonding 174 Structure and Bonding
    Structure and Bonding 174 Series Editor: D.M.P. Mingos Stefanie Dehnen Editor Clusters – Contemporary Insight in Structure and Bonding 174 Structure and Bonding Series Editor: D.M.P. Mingos, Oxford, United Kingdom Editorial Board: X. Duan, Beijing, China L.H. Gade, Heidelberg, Germany Y. Lu, Urbana, IL, USA F. Neese, Mulheim€ an der Ruhr, Germany J.P. Pariente, Madrid, Spain S. Schneider, Gottingen,€ Germany D. Stalke, Go¨ttingen, Germany Aims and Scope Structure and Bonding is a publication which uniquely bridges the journal and book format. Organized into topical volumes, the series publishes in depth and critical reviews on all topics concerning structure and bonding. With over 50 years of history, the series has developed from covering theoretical methods for simple molecules to more complex systems. Topics addressed in the series now include the design and engineering of molecular solids such as molecular machines, surfaces, two dimensional materials, metal clusters and supramolecular species based either on complementary hydrogen bonding networks or metal coordination centers in metal-organic framework mate- rials (MOFs). Also of interest is the study of reaction coordinates of organometallic transformations and catalytic processes, and the electronic properties of metal ions involved in important biochemical enzymatic reactions. Volumes on physical and spectroscopic techniques used to provide insights into structural and bonding problems, as well as experimental studies associated with the development of bonding models, reactivity pathways and rates of chemical processes are also relevant for the series. Structure and Bonding is able to contribute to the challenges of communicating the enormous amount of data now produced in contemporary research by producing volumes which summarize important developments in selected areas of current interest and provide the conceptual framework necessary to use and interpret mega- databases.
    [Show full text]
  • Planar Cyclopenten‐4‐Yl Cations: Highly Delocalized Π Aromatics
    Angewandte Research Articles Chemie How to cite: Angew.Chem. Int. Ed. 2020, 59,18809–18815 Carbocations International Edition: doi.org/10.1002/anie.202009644 German Edition: doi.org/10.1002/ange.202009644 Planar Cyclopenten-4-yl Cations:Highly Delocalized p Aromatics Stabilized by Hyperconjugation Samuel Nees,Thomas Kupfer,Alexander Hofmann, and Holger Braunschweig* 1 B Abstract: Theoretical studies predicted the planar cyclopenten- being energetically favored by 18.8 kcalmolÀ over 1 (MP3/ 4-yl cation to be aclassical carbocation, and the highest-energy 6-31G**).[11–13] Thebishomoaromatic structure 1B itself is + 1 isomer of C5H7 .Hence,its existence has not been verified about 6–14 kcalmolÀ lower in energy (depending on the level experimentally so far.Wewere now able to isolate two stable of theory) than the classical planar structure 1C,making the derivatives of the cyclopenten-4-yl cation by reaction of bulky cyclopenten-4-yl cation (1C)the least favorable isomer.Early R alanes Cp AlBr2 with AlBr3.Elucidation of their (electronic) solvolysis studies are consistent with these findings,with structures by X-raydiffraction and quantum chemistry studies allylic 1A being the only observable isomer, notwithstanding revealed planar geometries and strong hyperconjugation the nature of the studied cyclopenteneprecursor.[14–18] Thus, interactions primarily from the C Al s bonds to the empty p attempts to generate isomer 1C,orits homoaromatic analog À orbital of the cationic sp2 carbon center.Aclose inspection of 1B,bysolvolysis of 4-Br/OTs-cyclopentene
    [Show full text]
  • NBO Applications, 2020
    NBO Bibliography 2020 2531 publications – Revised and compiled by Ariel Andrea on Aug. 9, 2021 Aarabi, M.; Gholami, S.; Grabowski, S. J. S-H ... O and O-H ... O Hydrogen Bonds-Comparison of Dimers of Thiocarboxylic and Carboxylic Acids Chemphyschem, (21): 1653-1664 2020. 10.1002/cphc.202000131 Aarthi, K. V.; Rajagopal, H.; Muthu, S.; Jayanthi, V.; Girija, R. Quantum chemical calculations, spectroscopic investigation and molecular docking analysis of 4-chloro- N-methylpyridine-2-carboxamide Journal of Molecular Structure, (1210) 2020. 10.1016/j.molstruc.2020.128053 Abad, N.; Lgaz, H.; Atioglu, Z.; Akkurt, M.; Mague, J. T.; Ali, I. H.; Chung, I. M.; Salghi, R.; Essassi, E.; Ramli, Y. Synthesis, crystal structure, hirshfeld surface analysis, DFT computations and molecular dynamics study of 2-(benzyloxy)-3-phenylquinoxaline Journal of Molecular Structure, (1221) 2020. 10.1016/j.molstruc.2020.128727 Abbenseth, J.; Wtjen, F.; Finger, M.; Schneider, S. The Metaphosphite (PO2-) Anion as a Ligand Angewandte Chemie-International Edition, (59): 23574-23578 2020. 10.1002/anie.202011750 Abbenseth, J.; Goicoechea, J. M. Recent developments in the chemistry of non-trigonal pnictogen pincer compounds: from bonding to catalysis Chemical Science, (11): 9728-9740 2020. 10.1039/d0sc03819a Abbenseth, J.; Schneider, S. A Terminal Chlorophosphinidene Complex Zeitschrift Fur Anorganische Und Allgemeine Chemie, (646): 565-569 2020. 10.1002/zaac.202000010 Abbiche, K.; Acharjee, N.; Salah, M.; Hilali, M.; Laknifli, A.; Komiha, N.; Marakchi, K. Unveiling the mechanism and selectivity of 3+2 cycloaddition reactions of benzonitrile oxide to ethyl trans-cinnamate, ethyl crotonate and trans-2-penten-1-ol through DFT analysis Journal of Molecular Modeling, (26) 2020.
    [Show full text]
  • An Analysis of Electrophilic Aromatic Substitution: a “Complex Approach” PCCP
    Volume 23 Number 9 7 March 2021 Pages 5033–5682 PCCP Physical Chemistry Chemical Physics rsc.li/pccp ISSN 1463-9076 PERSPECTIVE Janez Cerkovnik et al . An analysis of electrophilic aromatic substitution: a “complex approach” PCCP View Article Online PERSPECTIVE View Journal | View Issue An analysis of electrophilic aromatic substitution: a ‘‘complex approach’’† Cite this: Phys. Chem. Chem. Phys., a a b 2021, 23, 5051 Nikola Stamenkovic´, Natasˇa Poklar Ulrih and Janez Cerkovnik * Electrophilic aromatic substitution (EAS) is one of the most widely researched transforms in synthetic organic chemistry. Numerous studies have been carried out to provide an understanding of the nature of its reactivity pattern. There is now a need for a concise and general, but detailed and up-to-date, overview. The basic principles behind EAS are essential to our understanding of what the mechanisms underlying EAS are. To date, textbook overviews of EAS have provided little information about the Received 5th October 2020, mechanistic pathways and chemical species involved. In this review, the aim is to gather and present the Accepted 21st December 2020 up-to-date information relating to reactivity in EAS, with the implication that some of the key concepts DOI: 10.1039/d0cp05245k will be discussed in a scientifically concise manner. In addition, the information presented herein suggests certain new possibilities to advance EAS theory, with particular emphasis on the role of modern Creative Commons Attribution-NonCommercial 3.0 Unported Licence. rsc.li/pccp
    [Show full text]
  • Introduction to Aromaticity
    Introduction to Aromaticity Historical Timeline:1 Spotlight on Benzene:2 th • Early 19 century chemists derive benzene formula (C6H6) and molecular mass (78). • Carbon to hydrogen ratio of 1:1 suggests high reactivity and instability. • However, benzene is fairly inert and fails to undergo reactions that characterize normal alkenes. - Benzene remains inert at room temperature. - Benzene is more resistant to catalytic hydrogenation than other alkenes. Possible (but wrong) benzene structures:3 Dewar benzene Prismane Fulvene 2,4- Hexadiyne - Rearranges to benzene at - Rearranges to - Undergoes catalytic - Undergoes catalytic room temperature. Faraday’s benzene. hydrogenation easily. hydrogenation easily - Lots of ring strain. - Lots of ring strain. - Lots of ring strain. 1 Timeline is computer-generated, compiled with information from pg. 594 of Bruice, Organic Chemistry, 4th Edition, Ch. 15.2, and from Chemistry 14C Thinkbook by Dr. Steven Hardinger, Version 4, p. 26 2 Chemistry 14C Thinkbook, p. 26 3 Images of Dewar benzene, prismane, fulvene, and 2,4-Hexadiyne taken from Chemistry 14C Thinkbook, p. 26. Kekulé’s solution: - “snake bites its own tail” (4) Problems with Kekulé’s solution: • If Kekulé’s structure were to have two chloride substituents replacing two hydrogen atoms, there should be a pair of 1,2-dichlorobenzene isomers: one isomer with single bonds separating the Cl atoms, and another with double bonds separating the Cl atoms. • These isomers were never isolated or detected. • Rapid equilibrium proposed, where isomers interconvert so quickly that they cannot be isolated or detected. • Regardless, Kekulé’s structure has C=C’s and normal alkene reactions are still expected. - But the unusual stability of benzene still unexplained.
    [Show full text]
  • On the Harmonic Oscillator Model of Electron Delocalization (HOMED) Index and Its Application to Heteroatomic Π-Electron Systems
    Symmetry 2010, 2, 1485-1509; doi:10.3390/sym2031485 OPEN ACCESS symmetry ISSN 2073-8994 www.mdpi.com/journal/symmetry Article On the Harmonic Oscillator Model of Electron Delocalization (HOMED) Index and its Application to Heteroatomic π-Electron Systems Ewa D. Raczyñska 1, *, Małgorzata Hallman 1, Katarzyna Kolczyñska 2 and Tomasz M. Stêpniewski 2 1 Department of Chemistry, Warsaw University of Life Sciences (SGGW), ul. Nowoursynowska 159c, 02-776 Warszawa, Poland 2 Interdisciplinary Department of Biotechnology, Warsaw University of Life Sciences (SGGW), ul. Nowoursynowska 166, 02-776 Warszawa, Poland * Author to whom correspondence should be addressed; E-Mail: [email protected]; Tel.: +48-22-59-37623; Fax: +49-22-59-37635. Received: 23 April 2010; in revised form: 19 May 2010 / Accepted: 7 July 2010 / Published: 12 July 2010 Abstract: The HOMA (Harmonic Oscillator Model of Aromaticity) index, reformulated in 1993, has been very often applied to describe π-electron delocalization for mono- and polycyclic π-electron systems. However, different measures of π-electron delocalization were employed for the CC, CX, and XY bonds, and this index seems to be inappropriate for compounds containing heteroatoms. In order to describe properly various resonance effects (σ-π hyperconjugation, n-π conjugation, π-π conjugation, and aromaticity) possible for heteroatomic π-electron systems, some modifications, based on the original HOMA idea, were proposed and tested for simple DFT structures containing C, N, and O atoms. An abbreviation HOMED was used for the modified index. Keywords: geometry-based index; π -electron delocalization; σ - π hyperconjugation; n-π conjugation; π-π conjugation; aromaticity; heteroatomic compounds; DFT 1.
    [Show full text]
  • Proton-Coupled Reduction of N2 Facilitated by Molecular Fe Complexes
    Proton-Coupled Reduction of N2 Facilitated by Molecular Fe Complexes Thesis by Jonathan Rittle In Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy CALIFORNIA INSTITUTE OF TECHNOLOGY Pasadena, California 2016 (Defended November 9, 2015) ii 2016 Jonathan Rittle All Rights Reserved iii ACKNOWLEDGEMENTS My epochal experience in graduate school has been marked by hard work, intellectual growth, and no shortage of deadlines. These facts leave little opportunity for an acknowledgement of those whose efforts were indispensable to my progress and perseverance, and are therefore disclosed here. First and foremost, I would like to thank my advisor, Jonas Peters, for his tireless efforts in molding me into the scientist that I am today. His scientific rigor has constantly challenged me to strive for excellence and I am grateful for the knowledge and guidance he has provided. Jonas has given me the freedom to pursue scientific research of my choosing and shown a remarkable degree of patience while dealing with my belligerent tendencies. Perhaps equally important, Jonas has built a research group that is perpetually filled with the best students and postdoctoral scholars. Their contributions to my graduate experience are immeasurable and I wish them all the best of luck in their future activities. In particular, John Anderson, Dan Suess, and Ayumi Takaoka were senior graduate students who took me under their wings when I joined the lab as a naïve first-year graduate student. I am grateful for the time and effort that they collectively spent in teaching me the art of chemical synthesis and for our unforgettable experiences outside of lab.
    [Show full text]
  • Aromaticity Sem- Ii
    AROMATICITY SEM- II In 1931, German chemist and physicist Sir Erich Hückel proposed a theory to help determine if a planar ring molecule would have aromatic properties .This is a very popular and useful rule to identify aromaticity in monocyclic conjugated compound. According to which a planar monocyclic conjugated system having ( 4n +2) delocalised (where, n = 0, 1, 2, .....) electrons are known as aromatic compound . For example: Benzene, Naphthalene, Furan, Pyrrole etc. Criteria for Aromaticity 1) The molecule is cyclic (a ring of atoms) 2) The molecule is planar (all atoms in the molecule lie in the same plane) 3) The molecule is fully conjugated (p orbitals at every atom in the ring) 4) The molecule has 4n+2 π electrons (n=0 or any positive integer Why 4n+2π Electrons? According to Hückel's Molecular Orbital Theory, a compound is particularly stable if all of its bonding molecular orbitals are filled with paired electrons. - This is true of aromatic compounds, meaning they are quite stable. - With aromatic compounds, 2 electrons fill the lowest energy molecular orbital, and 4 electrons fill each subsequent energy level (the number of subsequent energy levels is denoted by n), leaving all bonding orbitals filled and no anti-bonding orbitals occupied. This gives a total of 4n+2π electrons. - As for example: Benzene has 6π electrons. Its first 2π electrons fill the lowest energy orbital, and it has 4π electrons remaining. These 4 fill in the orbitals of the succeeding energy level. The criteria for Antiaromaticity are as follows: 1) The molecule must be cyclic and completely conjugated 2) The molecule must be planar.
    [Show full text]
  • FAROOK COLLEGE (Autonomous)
    FAROOK COLLEGE (Autonomous) M.Sc. DEGREE PROGRAMME IN CHEMISTRY CHOICE BASED CREDIT AND SEMESTER SYSTEM-PG (FCCBCSSPG-2019) SCHEME AND SYLLABI 2019 ADMISSION ONWARDS 1 CERTIFICATE I hereby certify that the documents attached are the bona fide copies of the syllabus of M.Sc. Chemistry Programme to be effective from the academic year 2019-20 onwards. Date: Place: P R I N C I P A L 2 FAROOK COLLEGE (AUTONOMOUS) MSc. CHEMISTRY (CSS PATTERN) Regulations and Syllabus with effect from 2019 admission Pattern of the Programme a. The name of the programme shall be M.Sc. Chemistry under CSS pattern. b. The programme shall be offered in four semesters within a period of two academic years. c. Eligibility for admission will be as per the rules laid down by the College from time to time. d. Details of the courses offered for the programme are given in Table 1. The programme shall be conducted in accordance with the programme pattern, scheme of examination and syllabus prescribed. Of the 25 hours per week, 13 hours shall be allotted for theory and 12 hours for practical; 1 theory hour per week during even semesters shall be allotted for seminar. Theory Courses In the first three semesters, there will be four theory courses; and in the fourth semester, three theory courses. All the theory courses in the first and second semesters are core courses. In the third semester there will be three core theory courses and one elective theory course. College can choose any one of the elective courses given in Table 1.
    [Show full text]
  • Organometrallic Chemistry
    CHE 425: ORGANOMETALLIC CHEMISTRY SOURCE: OPEN ACCESS FROM INTERNET; Striver and Atkins Inorganic Chemistry Lecturer: Prof. O. G. Adeyemi ORGANOMETALLIC CHEMISTRY Definitions: Organometallic compounds are compounds that possess one or more metal-carbon bond. The bond must be “ionic or covalent, localized or delocalized between one or more carbon atoms of an organic group or molecule and a transition, lanthanide, actinide, or main group metal atom.” Organometallic chemistry is often described as a bridge between organic and inorganic chemistry. Organometallic compounds are very important in the chemical industry, as a number of them are used as industrial catalysts and as a route to synthesizing drugs that would not have been possible using purely organic synthetic routes. Coordinative unsaturation is a term used to describe a complex that has one or more open coordination sites where another ligand can be accommodated. Coordinative unsaturation is a very important concept in organotrasition metal chemistry. Hapticity of a ligand is the number of atoms that are directly bonded to the metal centre. Hapticity is denoted with a Greek letter η (eta) and the number of bonds a ligand has with a metal centre is indicated as a superscript, thus η1, η2, η3, ηn for hapticity 1, 2, 3, and n respectively. Bridging ligands are normally preceded by μ, with a subscript to indicate the number of metal centres it bridges, e.g. μ2–CO for a CO that bridges two metal centres. Ambidentate ligands are polydentate ligands that can coordinate to the metal centre through one or more atoms. – – – For example CN can coordinate via C or N; SCN via S or N; NO2 via N or N.
    [Show full text]
  • AROMATIC COMPOUNDS Aromaticity
    AROMATICITY AROMATIC COMPOUNDS Aromaticity Benzene - C6H6 H H H H H H H H H H H H Kekulé and the Structure of Benzene Kekule benzene: two forms are in rapid equilibrium 154 pm 134 pm • All bonds are 140 pm (intermediate between C-C and C=C) • C–C–C bond angles are 120° • Structure is planar, hexagonal A Resonance Picture of Bonding in Benzene resonance hybrid 6 -electron delocalized over 6 carbon atoms The Stability of Benzene Aromaticity: cyclic conjugated organic compounds such as benzene, exhibit special stability due to resonance delocalization of -electrons. Heats of hydrogenation + H2 + 120 KJ/mol + 2 H2 + 230 KJ/mol calc'd value= 240 KJ/mol 10 KJ/mol added stability + 3 H 2 + 208 KJ/mol calc'd value= 360 KJ/mol 152 KJ/mol added stability + 3 H2 + 337 KJ/mol 1,3,5-Hexatriene - conjugated but not cyclic Resonance energy of benzene is 129 - 152 KJ/mol An Orbital Hybridization View of Bonding in Benzene • Benzene is a planar, hexagonal cyclic hydrocarbon • The C–C–C bond angles are 120° = sp2 hybridized • Each carbon possesses an unhybridized p-orbital, which makes up the conjugated -system. • The six -electrons are delocalized through the -system The Molecular Orbitals of Benzene - the aromatic system of benzene consists of six p-orbitals (atomic orbitals). Benzene must have six molecular orbitals. Y6 Y4 Y5 six p-orbitals Y2 Y3 Y1 Degenerate orbitals: Y : zero nodes orbitals that have the 1 Bonding same energy Y2 and Y3: one node Y and Y : two nodes 4 5 Anti-bonding Y6: three node Substituted Derivatives of Benzene and Their Nomenclature
    [Show full text]
  • Bond Distances and Bond Orders in Binuclear Metal Complexes of the First Row Transition Metals Titanium Through Zinc
    Metal-Metal (MM) Bond Distances and Bond Orders in Binuclear Metal Complexes of the First Row Transition Metals Titanium Through Zinc Richard H. Duncan Lyngdoh*,a, Henry F. Schaefer III*,b and R. Bruce King*,b a Department of Chemistry, North-Eastern Hill University, Shillong 793022, India B Centre for Computational Quantum Chemistry, University of Georgia, Athens GA 30602 ABSTRACT: This survey of metal-metal (MM) bond distances in binuclear complexes of the first row 3d-block elements reviews experimental and computational research on a wide range of such systems. The metals surveyed are titanium, vanadium, chromium, manganese, iron, cobalt, nickel, copper, and zinc, representing the only comprehensive presentation of such results to date. Factors impacting MM bond lengths that are discussed here include (a) n+ the formal MM bond order, (b) size of the metal ion present in the bimetallic core (M2) , (c) the metal oxidation state, (d) effects of ligand basicity, coordination mode and number, and (e) steric effects of bulky ligands. Correlations between experimental and computational findings are examined wherever possible, often yielding good agreement for MM bond lengths. The formal bond order provides a key basis for assessing experimental and computationally derived MM bond lengths. The effects of change in the metal upon MM bond length ranges in binuclear complexes suggest trends for single, double, triple, and quadruple MM bonds which are related to the available information on metal atomic radii. It emerges that while specific factors for a limited range of complexes are found to have their expected impact in many cases, the assessment of the net effect of these factors is challenging.
    [Show full text]