CAS ONLINEB Available on STN Internationalm The Scientific & Technical Information Network SEARCHING COORDINATION COMPOUNDS December 1986 Chemical Abstracts Service A Division of the American Chemical Society 2540 Olentangy River Road P.O. Box 3012 Columbus, OH 43210 Copyright O 1986 American Chemical Society Quoting or copying of material from this publication for educational purposes is encouraged. providing acknowledgment is made of the source of such material. SEARCHING COORDINATION COMPOUNDS prepared by Adrienne W. Kozlowski Professor of Chemistry Central Connecticut State University while on sabbatical leave as a Visiting Educator, Chemical Abstracts Service Table of Contents Topic PKEFACE ............................s.~........................ 1 CHAPTER 1: INTRODUCTION TO SEARCHING IN CAS ONLINE ............... 1 What is Substructure Searching? ............................... 1 The Basic Commands .............................................. 2 CHAPTEK 2: INTKOOUCTION TO COORDINATION COPPOUNDS ................ 5 Definitions and Terminology ..................................... 5 Ligand Characteristics.......................................... 6 Metal Characteristics .................................... ... 8 CHAPTEK 3: STKUCTUKING AND REGISTKATION POLICIES FOR COORDINATION COMPOUNDS .............................................11 Policies for Structuring Coordination Compounds ................. Ligands .................................................... Ligand Structures........................................... Metal-Ligand Bonds ........................................... Pi.Donors ...............eo.o.................a............... Hydrogens ....................................o.................. Hydride Ions ................o.oo...................e....e.... Charges ..................................so................... Counter Ions ................................................ Ligands with Negative Charges ............................... The Central Metal Atom ...................................... Structuring Assumptions ....................................... Metal-Metal Bonds ............................................... Carboxylates..............................o.......s..e..ao... Incomplete Structures. ...................................... Policies for Assigning Registry Numbers ......................... 18 Counter Ions .................................................. 19 Geometric Ions ................................................ 19 Optical Isomers .............................................. 20 Different Oxidation States .................................... 20 Isotopes ............................................... 20 Ionized Ligands ........................................... 21 Component Registration.................................. 21 Polymers ...................................................... 21 CHAPTER 4: BUILDING STHUCTUKES - THE BASICS...................... 23 The GRAPH Command............................................... 23 The NODE Comand................................................ The BOND Comand................................................ Examples Using the CKAPIL, NODE, and BOND Commands............... Creating a 6-Coordinate Structure............................. Creating Chelate Riag~.....................................,., Creating Fused Rings as Ligands............................... Creating Clusters............................................. Creating Cyclopentadienyl Ligands............................. Creating Macrocyclic Ligands.................................. The RECALL Command - Using Models to Build Structures........... Recall a Registry Number...................................... Recall and Modify a Structure from the Fragment File.......... Variability in Structures....................................... Variable Donor Atoms and Variable Chelate Backbone............ Defining a Central Metal...................................... Defining Ligand Atolns......................................... CHAPTER 5: ADDING ATTKTHUTES TO STRUCTURES....................... The HCOUNT Comand.............................................. The RSPEC Comand............................................... The CONNECT Command............................................. Using CONNECT to Retrieve Metallocenes........................ Using CONNECT in Ligand Structures............................ Metal llydrides................................................ The NSPEC Comand............................................... Effect of aond Type on Node Specification..................... Effect of Bond Type and Node Specification..,................. System Defaults............................................. Ring or Chain Bonds......................................... Chain Bonds and Ring or Chain Nodes......................... All Bonds in Rings.......................................... One Chelate Ring............................................ One Tridentate Ligand....................................... Ring or Chain Node............................................ Bidentate or Tetradentate Ligands........................... CHAPTER 6: ADL)ING SCREENS TO REFINE YOUR SEARCH .................. 61 Screens That Are Often Useful ................................... 64 Adding Metal Screens When Structure Contains the M Node Symbol 64 Adding Screens that Specify Minimum Numbers of Ring or Chain Bonds ......................................................... 65 Hydrogen Augmented Atom Screens for Ligands ................... 69 Type of Ring Screens ......................................... 71 Pi-Bonding Ligands. Organometallics ......................... 72 Screens Not to Use ......................................... 73 BATCH Searching ................................................. 74 Dividing a Search that Will Not Complete in One Search .......... 74 CIWTER 7: SUMMARY OF GENERAL SEARCH TECHNIQUES .................. 75 Using Ring OK Chain Bond Types .................................. 75 LIsing Single Exact Bond Values .................................. 75 Using Ring or Chain Node Specification .......................... 75 Ring Isolation ............................................... 76 Using Gk Nodes ................................................. 76 Tautomers .......................................................76 Using A (Any Atom) Nodes ........................................ 76 Using the CONNECT Attribute ..................................... 77 Determining the Coordination Number ............................. 77 Using Hydrogen Counts for Hydrides .............................. 77 Attributes and the Gk Node ...................................... 77 Using Charges ................................................. 77 Using Screens ................................................... 78 Interpreting SAMPLE Searches .................................... 78 CASE STUDY 1: TAILORING THE COORDINATION SPHERE .................. 79 All Octahedral Dichloro Complexes of Cobalt ..................... 79 Dichloro Cobalt Complexes of Lower Coordination Number .......... 81 Two Different Halide Ligands ................................. 82 Bridging Halides .............................................. 84 Simple Halides and Halo Comp1.exes of Rhenium .................... 88 CASE STUDY 2: ORGANOMETALLZCS .................................... 93 Metallocenes ............................................... 94 Substituted Cyclopentadienyl Ligands ............................ 96 Noncyclic Polyenes .............................................. 97 Ethylene ...................................................... 98 Pentadiene ...................................................99 Partial Coordination of the Pi System ........................... 100 CASE STUDY 3: CAKBOXYLIC ACIDS ...................................103 Comprehensive Searching......................................... 104 .4l 1 Substances with the Ligand Bonded to the Metal .............. 107 Carboxylate Complexes as Salts - No Bond to Metal ............... 109 Specific Structures .N. 0 Chelates ..............................111 Structures with an Uncoordinated Carboxylate Group .............. 1.13 Structures with an Uncoordinated Pyridine Group ................. 115 CASE STUDY 4: UNSPECIFI!dD DEKXVATZVES ............................ 117 Substances without Registry Numbers .............................117 Manually Registered Compounds ............................... 120 CASE STUDY 5: CHELATES AND MACKOCYCLES ........................... 123 Tridentate Che,,ates............................................. 12'3 Tetradentate Macrocycles with Both Sulfur and Nitrogen Donors ... 127 Macrocyclic Complexes with Varying Numbers of Donor Sites ....... 129 CASE STUDY 6: LIYDRIDES ........................................... 133 CASE STUDY 7: XETAL CLUSTERS .....................................139 Gold Clusters with Phosphine Ligands ........................... 139 Iron Carbonyl Clusters .......................................... 142 Terminal Carbonyl Groups .................................. 142 Bridging Carbonyls ....................................... 147 Clusters of Specific Size..................................... 150 CASE STUDY 8: STEREOCHEMISTKY ....................................155 Geometry ........................................................159 Ligand Stereochemistry ..........................................162 Cis or Trans Iso~ners............................................ 165 CASE STUDY 9: NANE AND FOMULA SEARCrlZNG ........................