Structure Correlation

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1 Structure Correlation Volume 2 Edited by Hans-Beat Bürgi and Jack D. Dunitz \Tg^ww TlTr^ V^U Xi Weinheim New York Basel Cambridge Tokyo

2 Part I Basics 1 Molecular Structure and Coordinate Systems Molecules and Molecular Fragments Positional Coordinates Crystal Coordinates ' Linear Transformations Symmetry Transformations Molecule or Fragment Centered Coordinate Systems Invariants of Molecular or Fragment Structure Internal Coordinates Distance Geometry External or Internal Coordinates? Superposition of Molecules Configuration Space Deformation Coordinates and Reference Structures Linear Transformations in Configuration Space 20 2 Symmetry Aspects of Structure Correlation Introduction Permutation Groups and Point Group Symmetries Symmetry Coordinates, a Simple Example and some Generalizations Related to Point Group Symmetry Symmetry Aspects of Specific Types of Molecule Tetrahedral MX 4, Molecules and Degenerate Irreducible Representations MX 5 Molecules MX 6 Molecules Out-of-Plane Deformations of Five-Membered Rings Out-of-Plane Deformations of Six-Membered Rings 44

3 VI Contents 2.5 Configuration Spaces for Molecules with Several Symmetrical Reference Structures Internal Rotation in Non-Rigid Molecules Ethane, One Internal Rotational Degree of Freedom Simplified Symmetry Analysis of Conformationally Flexible Molecules Two Internal Rotational Degrees of Freedom Three Internal Rotational Degrees of Freedom Four Internal Degrees of Freedom: Tetraphenylmethane and Cognate Molecules Summary 68 3 Crystallographic Databases: Search and Retrieval of Information from the Cambridge Structural Database Introduction Crystallographic Databases Overview The Metals Crystallographic Data File (MCDF) The Inorganic Crystal Structure Database (ICSD) The Cambridge Structural Database (CSD) The Protein Data Bank (PDB) Areas of Structural Overlap Data Acquisition and Data Integrity Overview of the Cambridge Structural Database (CSD) Coverage The Reference Code System Information Content Checking and Evaluation Registration and Archiving Database Statistics The CSD Software Systems Bibliographie, Numerical, and Chemical Searching The Query Language Numerical Information Items Text Information Items Molecular Formula Information Items D Chemical Connectivity Information Bit-encoded Information Items Chemical Similarity Searching Interactive Menu-driven Graphics D Searching and Geometry Tabulations Overview of the GSTAT Program 94

4 VII Location of Fragments in GSTAT Calculation of Fragment Geometry Fragment Selection: the 3D Search Process Tabulation of Fragment Geometry The CSD Version 5 Upgrade Special Considerations in Using the CSD System The Reference Code System Searches Using the SCREEN Command Compound Name Searching Chemical Connectivity Searching Bond-Type Assignments Treatment of Hydrogen Atoms The Crystallographic Data Accuracy and Precision Disorder Hydrogen Atoms Geometrie Searching Bond Length Constraints Torsion Angle Constraints: Stereochemical Searching Conclusion Statistical and Numerical Methods of Data Analysis Introduction and Objectives Choice of Parameters for Statistical Analysis The Coordinate Basis Internal Coordinate Axes Internal Coordinates and Chemical Fragments Internal Coordinates and Types of Analysis Bond Length Studies Studies of Coordination Geometry at Atomic Centres Conformational Studies Studies of Hydrogen Bonding Sources of Variation in Crystallographic Structural Data Mean Values and Other Simple Descriptive Statistics Characteristics of Distributions Means of Normal or Near-Normal Distributions Dispersion Departures from Normality Estimates of Central Tendency for Non-Normal Distributions Comparison of Distributions Introduction Significance of Differences between Means 129

5 4.5.3 Covariance, Correlation, and Regression Comparison of Ratios Multivariate Statistics Introduction Fragment Symmetry and Chirality Principal Component Analysis (PCA) An Asymmetrical Example: /M'-Aminoribofuranosides A Symmetrical Example: Conformations of Six-Membered Rings Symmetrical Examples: Coordinate Geometries at Metal Centres Methods Based on Dissimilarity Matrices Introduction Measures of Dissimilarity Multidimensional Scaling Cluster Analysis Cluster Analysis of Symmetrical Fragments Symmetry-Modified Clustering: An Example Mean Geometries for Complete Fragments Least-Squares Superposition Methods Averaging Clusters: The Most Representative Fragment Miscellaneous Graphical Methods Statistical Software Conclusion Structure Correlation, the Chemical Point of View Introduction Structural Probes of Reactivity, Non-Bonded Distances Conceptual Framework: Energy Surfaces Energy Minima, Force Constants and Structure Correlation Energy Minima, Symmetry Force Constants and Structure Correlation Reaction Profiles and Structure Correlation The Principle of Structure-(Structure) Correlation Structure-Energy Correlation Equilibria in Crystals Transition-State Theory and Free-Energy Relationships Structural Reorganization in Degenerate Reactions Structural Reorganization in Nondegenerate Reactions. Determination of Transition-State Structure The Principle of Structure-Energy Correlation Conclusions 201

6 Part II Molecular Structure and Reactivity Contents IX 6 Organic Addition and Elimination Reactions; Transformation Paths of Carbonyl Derivatives Introduction Reaction Pathway for sp 2 *=* sp 3 Transformations of Carbonyls Initial Stages of Nucleophilic Addition to a Carbonyl Correlation of Partial Pyramidalization and the Incipient Bond Distance Distribution of the Nu..,C = 0 Angle in Intra- and Intermolecular Contacts Initial Stages of Spontaneous Hydrolysis of Acetals Distortions from C 2v Symmetry in Acetals: Correlation of the Antisymmetric Stretching and Bending Displacement Coordinates Structural Expression of the Anomeric Effect in Acetals; Correlation of the O-C-O Angle and Ad Inorganic Models Ligand Addition to the B0 3 Group: Correlation of Partial Pyramidalization and the Incipient Bond Distance Ligand Elimination from the Tetrahedral XY 4 Species: Bond Length and Valence Angle Correlations Reaction Pathway for sp 2 <=* sp Transformations of Carbonyls Initial Stages of Nucleophilic Addition to sp Centers Initial Stages of Spontaneous Cleavage of Ketene Acetal-Like Fragments Bond Length and Valence Angle Correlations in Sydnones and Enamines Bond Length and Valence Angle Correlations in Ester Enolates Initial Stages of Spontaneous Cleavage of Carbonyl Derivatives to Acylium Ion Valence Angle Correlations in Lactones and Lactams Bond Length and Valence Angle Correlations in RC( = 0)X Derivatives Reaction Path for Elimination Computational Investigations of Reaction Pathways for Carbonyl Additions and Eliminations and Related Reactions Formaldehyde Anionic Nucleophiles Neutral Nucleophiles Metal Hydrides and Organometallics Acetaldehyde and Homologs Acetone and Homologs Carboxylic Acid Derivatives Solvent Effects 261

7 Reaction Pathways and Chemistry of Carbonyls Theoretical Elaborations of the "Rearside" Attack Model: Baldwin's and Liotta-Burgess' Trajectory Analyses Consequences of Directionality of Nucleophilic Addition to Carbonyls Directionality and Regioselection in Nucleophilic Addition to Dicarbonyl Compounds Directionality and Diastereofacial Selection in Nucleophilic Addition to Aldehydes and Ketones Directionality and Rate of Intramolecular Reactions of Nucleophilic Addition to Carbonyls Ground State Geometry of Carbonyl and Related Compounds and Reactivity Valence Angle vs. Bond Length Correlations and Reactivity of Acyl Derivatives towards Elimination Ground-State Structure and Reactivity of Acetals: Empirical Potential Energy Surface and Determination of Transition-State Structure for the Spontaneous Hydrolysis of Axial Tetrahydropyranyl Acetals Partial Pyramidalization and Intrinsic Face Preference in Diastereofacial Selection 288 Concluding Remarks 292 Reaction Paths for Nucleophilic Substitution (S N 2) Reactions 303 Introduction 303 The XCdS 3 Y Fragment 304 Tin Compounds with Coordination Numbers Four to Six The XSnC 3 Y Fragment The X 2 SnC 2 Y 2 Fragment Analogies with Pb(IV) 311 Silicon Compounds with Coordination Numbers Four and Five The OSiC 3 X Fragment Influence of Peripheral Substituents Analogies between Si and Ge, the XGeR 3 Y Fragment Silatranes, the NSi0 3 X Fragment Germatranes, the NGe0 3 X Fragment Inversion versus Retention of Configuration at Si 325 Nucleophilic Substitution at First Row Atoms An Alatrane and a Boratrane Carbon, the XCR 3 Y Fragment 328 Conclusions 332

8 XI 8 Ligand Rearrangement and Substitution Reactions of Transition Metal Complexes Introduction Reaction Paths of ML Coordination Complexes ML 3 Complexes ML 4 Complexes Polyhedral Isomerization Conformational Interconversions in Metal-Phosphine Complexes ML 5 Complexes Associative Ligand Substitution Reactions and the Berry Rearrangement More Sophisticated Methods of Analysis Comparison of Structural Results with a Point-Charge Model Retrospective Comments ML 6 Complexes ML Complexes, n> Discriminating Between Reaction Mechanisms: Metal Cluster Rearrangements Reactions of Organometallic Compounds Ring-Whizzing Reactions Agostic Interactions as Precursors to H-Transfer Reactions Carbonyl Transfer Reactions Substitution Reactions at Sn(IV) Beyond Geometry: Empirical Potential Energy Surfaces? The Case of Cu(II) Complexes: Problems and Possibilities Cu(II)L 5 Complexes Cu(II)L 6 Complexes "Pseudorotation" in Co(ethylenediamine) Chelate Rings Ring Inversion in Metallacyclopentenes Concluding Remarks Conformational Analysis Conformational Analysis Introduction Description of Local Conformations Conformational Analysis of Single Molecules Is the Conformation of Tetraalkyldiphosphines Caused by Stereoelectronic Influence? Conformation and Chemical Reactivity Chair-Boat Interconversion of Six-Membered Rings in the Solid Conformational Analysis of Multiple Molecular Fragments 377

9 9.3.1 Low Energy Conformations of Macrocyclic Ring Systems Conformational Analysis of Carboxylic Esters and Amides Conformational Studies of the Methoxyphenyl Group Conformation and Pseudorotation of Five-Membered Rings Conformational Analysis of Cyclopentenones Space Groups as a Tool to Visualize Conformational Variation Two Torsion Angles Three Torsion Angles Four and More Torsion Angles 400 Part III Crystal Packing 10 Bond-Length - Bond-Valence Relationships in Inorganic Solids Introduction Bond-Length - Bond-Valence Correlations The Correlation between Bond Length and Bond Valence The Distortion Theorem Applications of the Bond-Length - Bond-Valence Correlations Bond Networks and the Network Theorems The Bond Network as a Directed Bipartite Graph The Network Equations Non-Bipartite Graphs The Physical Significance of Bond Valences Bonding between Fragments - Principles of Structure Organization Influence of the Environment on the Structure of a Fragment The Decomposition of an Inorganic Structure into Fragments External Bonding of Fragments Internal Structure of Fragments Failure of the Network Equations Distortions Caused by Electronic Effects Distortions Caused by Spatial Constraints Conclusion 426 Appendix Refcodes Used 427 Appendix Symbols Used The Role of Hydrogen Bonding in Molecular Assemblies Introduction and Scope What Shall We Call a Hydrogen Bond? Electron Density Mapping of Hydrogen-Bonded Molecules 434

10 XIII 11.4 Role Played by C-H...0 and C-H...N Interactions in Molecular Packing Introduction C(sp)-H...O Interactions C(sp 2 )-H...O Interactions C(sp 3 )-H...O Contacts Miscellaneous and Summary Proton Disorder in Hydrogen-Bonded Systems Ice and Other Structures with Disordered Hydrogen Bonds Order-Disorder (O/D) of the Carboxyl Dimer and Proton Transfer Prediction and Generation of Crystal Structures Characterizing the Geometry and Patterns of Hydrogen Bonds Packing Motifs of Commonly Occurring Hydrogen-Bonding Groups Hydrogen-Bonding Arrangements of Molecules ROH Carboxylic Acids The Catemer Motif The Carboxylic Acid Cyclic Dimer Motif Lone-Pair Directionality of O-H...O (Carboxyl) Bonds Primary and Secondary Amides Secondary Amides The Glide or Twofold Screw Relation The Translation Motif Hydrogen Bonding between Molecular Chams Primary Amides Stacking of Amide Cyclic Dimers a-amino Acids Hydrogen Bonding in Phospholipids Acids and Amides with Attached Hydrogen-Bonding Groups Co-Crystals Introduction Selection and Complementarity in the Formation of Co-Crystals Hydrates Purines and Pyrimidines Co-Crystals of Carboxylic Acids and Amides Host/Guest Hydrogen-Bonded Complexes Crystals Based on Intrinsic Hydrogen-Bonding Characteristics (Lacking Preorganization) Co-Crystals as Agents for Materials Design The Role of Hydrogen-Bonding at Crystal Interfaces Growth of Crystals in the Presence of Taylor-Made Auxiliaries The Effect of Solvent on Crystal Growth 499

11 XIV Contents Taylor-Made Auxiliaries as Crystal Growth Promoters Concluding Remarks Molecular Packing and Correlations between Molecular and Crystal Properties Introduction Representation and Properties of a Molecule Atomic Designators Hydrogen Atoms Derived Molecular Properties Size Stoichiometry Electron Distribution Molecular Shape Representation and Properties of a Crystal Data Retrieval and Geometrical Model Crystal Energy Definitions The Packing Energy and its Interpretation Energy Partitioning Energy and the Molecular Coordination Sphere Libration Energy Profiles Physical Properties of the Crystal Correlation between Molecular and Crystal Properties Databases for Non-Hydrogen Bonded Crystals Hydrocarbons (Satured and Unsaturated) Aromatic Hydrocarbons Oxygen or Nitrogen Substitution Mutual Orientation of Carbonyl Dipoles or Benzene Rings Directional Forces Other than H-Bonds Distances between Molecules and Molecular Coordination Sphere Joint Results from the three Databases From Molecular to Crystal Structure Distribution over Space Groups Generation of Crystal Structures Method Choosing the Right Structure Polymorphism Conclusion and Outlook 538 Appendix Formulas and Transformations 538 Appendix Summary of Symbols 541

12 XV Part IV Proteins and Nucleic Acids 13 Structure Correlation and Ligand/Receptor Interactions Factors Determining the Mutual Recognition and the Energetic Aspects of Ligand/Receptor Binding Structural Complementarity and Energy Balance in Ligand/Receptor Binding Enthalpie Contributions Entropie Contributions Structural Systematics in Ligand/Protein Interaction and Mapping the Environmental Characteristics of Functional Groups Structure Correlation to Analyze and Predict Biologically Active Conformations of Small Molecule Ligands The Binding of Retinol to Retinol-Binding Protein The Binding of Citric Acid to Citrate Synthase Conformation of Guanosine and Adenosine Phosphates in Small- Molecule and Ligand/Protein Crystal Structures The Binding of Creatine to Creatinase Conclusions and Predictions Structure Correlation to Describe Elementary Steps in Enzyme Reactions and Differences in Ligand Binding Geometry Nucleophilic Addition and Amide Bond Fission in Creatinase Nucleophilic Substitution at Phosphorus in Ribonuclease Expansion of Coordination and Change of Electronic State at Iron in Cytochrome P-450 cam Conclusion and Outlook Steroid Molecular Structure, Protein Interaction and Biological Function Introduction Steroid Conformation Analysis The 17 ß Side Chain A-Ring Conformation in 4-ene-3-one Derivatives Steroid Structure, Receptor Binding and Hormone Action Estrogen Receptor Binding and Activity Progesterone Receptor Binding and Activity Corticoid Receptor Binding and Activity Androgen Receptor Binding and Activity Steroid-Protein Interactions and Binding Steroid-Binding Enzymes Steroid-Binding Proteins 625

13 XVI Contents Receptor Structure and Steroid Function Summary Structural Patterns in Globular Proteins Introduction Atomic Interactions Backbone Patterns Helices ß Strands ß Turns Additional Loop Patterns Motifs Helical Motifs Accessibility Lost on Complex Formation Motifs where the Helices are Perpendicular Tertiary Motifs A-Sheet Motifs Two-Stranded Motifs Three-Stranded Motifs Four-Stranded Motifs Tertiary /?-Sheet Structures Conclusion Structural Correlations in Families of Homologous Proteins Introduction Techniques for Comparison of Protein Structures Comparative Analyses of Homologue Structures Sequence Substitution Tables The Solvent Inaccessible Core and Main-Chain Conformation The Role of Side-Chain Hydrogen Bonds Conclusions On the Correlation of Protein Structure with Local Sequence Patterns Introduction Protein Sequences and Structures Protein Folding Small Peptides and Protein Structure Database of Short Peptides Derived from Protein Structures Classification of Hexapeptide Folds 691

14 XVII Predictability of Hexapeptide Folds Conclusion Structural Patterns in Nucleic Acids Introduction Right-Handed and Left-Handed Double Helices Variations in the Duplex Geometry The Correlations between Backbone Torsion Angle ö and Glycosidic Torsion Angle x in A-, B-, and Z-DNA Influence of the Sequence on the Conformation of B-DNA Other Correlations Variations in the Conformation of Z-DNA Structure of DNA Duplexes with Mismatched Base Pairs Binding of Drug Molecules to the Minor Groove of B-DNA DNA Intercalation Conformational Changes in the Sugar-Phosphate Backbone Parallel and Perpendicular Intercalators, DNA Unwinding, and Sequence Specificity of Intercalation Interactions between Nucleic Acids and Proteins Sequence-Specific Recognition of Double Helical Nucleic Acids Architecture of DNA-binding Domains in Proteins Protein-RNA Interactions Conclusions and Future Prospects 743 Appendices Appendix A 751 Typical Interatomic Distances in Organic Compounds and Organometallic Compounds and Coordination Complexes of the d- and f-block metals A.l Introduction 751 A.2 Methodology 752 A.2.1 Classification of Bonds 754 A.2.2 Statistics 755 A.3 Contents and Arrangement of Tables of Interatomic Distances A.3.1 The "Bond" Column 759 A.3.2 Definition of "Substructure" 760 A.3.3 Use of the "Note" Column 763

15 XVIII Contents A.3.4 Locating an Entry in Table A A.4 Discussion 764 Appendix B 859 Short Format References to Crystal Structures Cited in this Book Appendix C 867 Tables of the Common Amino Acids, Purine and Pyrimidine Bases Illustration Acknowledgements 871 Index 875

ORGANIC CHEMISTRY. Fifth Edition. Stanley H. Pine

ORGANIC CHEMISTRY. Fifth Edition. Stanley H. Pine ORGANIC CHEMISTRY Fifth Edition Stanley H. Pine Professor of Chemistry California State University, Los Angeles McGraw-Hill, Inc. New York St. Louis San Francisco Auckland Bogota Caracas Lisbon London