Durham E-Theses Systematic structural studies in metal complex chemistry Yao, Jing Wen How to cite: Yao, Jing Wen (1998) Systematic structural studies in metal complex chemistry, Durham theses, Durham University. Available at Durham E-Theses Online: http://etheses.dur.ac.uk/5055/ Use policy The full-text may be used and/or reproduced, and given to third parties in any format or medium, without prior permission or charge, for personal research or study, educational, or not-for-prot purposes provided that: • a full bibliographic reference is made to the original source • a link is made to the metadata record in Durham E-Theses • the full-text is not changed in any way The full-text must not be sold in any format or medium without the formal permission of the copyright holders. Please consult the full Durham E-Theses policy for further details. Academic Support Oce, Durham University, University Oce, Old Elvet, Durham DH1 3HP e-mail: [email protected] Tel: +44 0191 334 6107 http://etheses.dur.ac.uk Systematic Structural Studies Metal Complex Chemistry by Jing Wen Yao The copyright of this thesis rests with the author. No quotation from it should be published without the written consent of the author and information derived from it should be acknowledged. A thesis submitted for the degree of Doctor of Philosophy Department of Chemistry- University of Durham November, 1998 16 Contents List of Figures iv List of Tables viii Acknowledgements x Declaration xi Abstract xii Chapter 1. Introduction 1 Chapter 2. Structural Systematics: the Cambridge Structural Database 3 2.1 From X-ray Structures to Database Research 3 2.2 Cambridge Structural Database 6 2.2.1 Information Content of the CSD 6 2.2.2 Software Systems of the CSD 9 2.3 An Overview on the Application of Cambridge Structural Database 10 2.3.1 Correlation Between the Specified Structure Parameters 13 2.3.2 Relationships Between Conformation and Stability 15 2.3.3 Reaction Pathways 20 2.3.4 Intermolecular Interactions in Small Molecule System 24 2.3.5 Structural Correlation to Analyze and Predict Biological Activity ....29 References 31 Chapter 3. A General Method for Identifying and Classifying Metal Coordination Sphere Geometry 34 3.1 Introduction 34 3.2 The General Geometric Descriptions of Metal Coordination Sphere ML„ 35 3.2.1 Two, Three, Four and Five-Coordination 36 3.2.2 Seven-Coordination 38 3.2.3 Eight and Nine-Coordination 39 3.3 Application of Symmetry Deformation Coordinates 41 3.3.1 Symmetry Considerations 41 3.3.2 Symmetry Deformation Coordinates 42 3.4 Atomic Permutation 43 3.5 Multivariate Analysis in the MLn Coordination System 45 3.5.1 Principal Component Analysis (PCA) 46 3.5.2 Factor Analysis (FA) 49 3.5.3 Cluster Analysis 50 3.6 A Discrepancy Index Method for Higher Coordination Number ML„ 52 3.6.1 Rang(x) Index 52 3.6.2 A Program for Calculation of Rang(x) Values 53 3.6.3 The Standard Angles for the Idealized Polyhedra in Seven- Coordination 57 3.6.4 The Standard Angles for the Idealized Polyhedra in Eight- Coordination 59 3.6.5 The Standard Angles for the Idealized Polyhedra in Nine- Coordination 61 References 63 Chapter 4. Systematic Studies of Geometry of Metal Coordination Sphere ML„ Using Crystallographic Data 64 4.1 Introduction 64 4.2 Transition Metal Seven-Coordination 64 4.2.1 Database Retrieval 66 4.2.2 Basic Geometrical Identification and Classification of Seven- Coordination Complexes by Rang(x) Values 67 4.2.3 Comparison with the Potential-Energy surface results 80 4.2.4 Vertex Index VR^x) 85 4.2.5 Multivariate Analysis in ML7 90 4.2.5.1 Symmetry in ML7 91 4.2.5.2 Symmetry Coordinates 93 4.2.5.3 PCAandFA 104 4.3 Eight-Coordination 123 4.3.1 Geometry of Coordination Sphere by Rang(x) Calculations 123 4.3.2 Interconversion Between the DOD and SQUP 129 4.3.3 PCA and FA in 8-Coordination Sphere 133 4.4 Nine-Coordination Sphere 142 4.4.1 Geometry Identified by Rang(x) Values 142 4.4.2 Further Criteria in the Identification of Geometry for Chelate Ligand Complexes 151 4.4.3 Symmetry Coordinates 158 4.5 Geometrical Preferences and Coordination Environments 162 4.6 Rang(x) Index Applied to Lower Coordination MLn System (n = 3, 4, 5 and 6) 166 4.6.1 2D Rang(x) Plots 166 4.6.2 Rang(x) spectra. 169 4.7 Concluding Remarks 176 References 180 Chapter 5. A Database Study of Transition Metal Alkyne and Alkene Complexes 184 5.1 Introduction 184 5.2 Database Retrieval 188 5.3 Data Analysis 191 5.3.1 Bend Back Angles and C-C Bond Lengths 192 5.3.2 Interactions Between Metal and C-C Bond 195 5.3.3 Influences of Substituents 200 5.3.4 From Triple Bond to Double Bond and to Single Bond 205 5.4 Conclusion 211 References 213 Chapter 6. Crystal Structures of the Metal Complexes 215 6.1 A Brief Summary of Crystal Structure Determination by X-ray Diffraction ii Techniques 215 6.1.1 X-ray Diffraction by Crystals 215 6.1.2 Data Collection 217 6.1.3 Structure Determination 222 6.1.4 Structure Refinements 224 6.2 Determined Structures 226 References 249 Chapter 7. Further Work 251 7.1 Geometry in Higher Coordination Number Spheres 251 7.2 Study in Reaction Pathways 253 Appendix I. Atomic Coordinates 256 Appendix II. Symmetry Isomers and Coordinates for 8-Coordination Sphere in Point Groups D2d (DOD) and D4d (SQAP) 265 Appendix III. Symmetry Isomers for 9-Coordination Sphere in Point Groups D3h (TTP) and C4v (CSA) 271 Appendix IV. Parameters Used to Link to NAG Fortran Library for PCA (G03AAF) and FA (G03CAF, G03CCF) Calculations 273 Appendix V. Publications, Attended Conferences, Seminars and Courses 280 iii List of Figures Figure 2.1 ab initio calculation of energy AE on the torsion angle x and the frequency of appearance N0bs with this torsion angle in the CSD (Allen etal, 1996) 5 Figure 2.2 The Cambridge Structural Database System information fields (reproduced by kind permission of the CCDC) 7 Figure 2.3 Conformational variability of chloroethanoic acid. (a) a diagram shows a single molecule (CLACET01) (b) a line drawing of twelve superimposed fragments from the CSD 11 Figure 2.4 (a) Potential energy versus conformation torsion angle x° (Glusker et al, 1984) for 1,2-substituented ethane and (b) frequency of appearance Nobs in the CSD versus this torsion angle 16 Figure 2.5 Definition of geometric parameters for L3MY species related to Pauling's formula 21 Figure 2.6 Bimolecular nucleophilic substitution reaction for a four-coordinate atom 22 Figure 2.7 Geometry conversions from F to I substitution in lactam derivatives 23 Figure 2.8 The network structure of compound [HMBPT]2[Si8Oi8(OH)2]-41H20 25 Figure 2.9 Definitions of geometric parameters for (a) S(sp2) and (b) S(sp3) 27 Figure 3.1 Geometrical description in 3-coordination 37 Figure 3.2 Geometrical description in 7-coordination 38 Figure 3.3 Geometrical description in 8-coordination 40 Figure 3.4 Geometrical description in 9-coordination 40 Figure 3.5 Definition of valence angles in C11L4. 48 Figure 3.6 PC\ versus PC2 from 24-fold expansion of CwZ/unidetate) 48 Figure 3.7 Connectivity diagram of the coordination sphere in CEHZEU 55 Figure 3.8 Flow chart of the procedure 56 Figure 3.9 The PBP0COC0CTP interconversion pathway: atomic movements in 7-coordination 57 Figure 4.1 Energy level diagram for the d orbitals in 7-coordination field compared with an octahedral field in 6-coordination 65 Figure 4.2 Connectivity diagram of the coordination sphere in hit HABLEB from the CSD 68 Figure 4.3 Rang value(%) vs. angle change(%) from ideal PBP to CTP geometry 72 Figure 4.4 ^-histograms for PBP (a) and CTP (b) 79 Figure 4.5 Comparision of plot of potential energy surface(a) with the plots in complex structures (b) (c) (d) 82 Figure 4.5 contd. (c) and (d) 83 Figure 4.6 (a) Structures from the CSD for Fe3+ complexes 87 Figure 4.6 (b) Structures from the CSD for Mo2+ complexes 88 Figure 4.7 VRmg (%) on each ligand 89 Figure 4.8 (a) Symmetry operations in C2V 91 Figure 4.8 (b) Symmetry operations in Dsh 92 Figure 4.9 Symmetry in C2V 94 iv Figure 4.10 S3 vs s2 for (a) Unidentate,(b)Fe and (c)all seven-coordinate complexes 96 Figure 4.11 Graphical representations of the 18 symmetry coordinates in C2V 102 Figure 4.12 Graphical representations of S6 and S7 in Dsh means larger coefficient on corresponding angles) 104 Figure 4.13 Flow chart for adding PC A or FA to the program D/S*: Correlation/Covariance matrix as input data 105 Figure 4.14 Scatterplots of (a) PC (b) symmetry coordinates for all unidentate ligand complexes 107 Figure 4.14 contd. (c) PC3-PC4 (d) Sna-Siib 108 Figure 4.15 Angle loadings in PC 1 -PC5 110 Figure 4.16 PC scatterplots for all 7-coordinated complexes (a) PCi vs. PC2; 111 Figure 4.16 contd. (b) PC3 vs. PC4; (c) PC5 vs. PC4 ' 112 Figure 4.17 Scatterplots of PCs in C2v symmetry(a) PCi vs. PC2 115 Figure 4.17 contd (b) Histogram of PC3 (c) PC3 vs. PC, 116 Figure 4.18 Angle loadings in FAC's in D5h- PC loadings are also given (in black) for comparison 118 Figure 4.19 Scattergrams of factors in D5h 120 Figure 4.19 conted.