
Structure Correlation
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Contributions by F.H. Allen, T.L. Blundell, I.D. Brown, H.B. Bürgi, J.D. Dunitz, L. Leiserowitz and others, authoritatively discuss the structure correlation method as well as illustrative results in detail, covering such apparently unrelated subjects as * Bond strength relations in soldis
* Crystal structure prediction
* Reaction pathways of organic molecules
* Ligand/receptor interactions and enzyme mechanisms
This book will be useful to the academic and industrial reader alike. It offers both fundamental aspects and diverse applications of what will surely become a powerful branch of structural chemistry.
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Content
- Structure Correlation
- Contents
- Part I Basics
- 1 Molecular Structure and Coordinate Systems
- 1.1 Molecules and Molecular Fragments
- 1.2 Positional Coordinates
- 1.2.1 Crystal Coordinates
- 1.2.2 Linear Transformations
- 1.2.3 Symmetry Transformations
- 1.2.4 Molecule or Fragment Centered Coordinate Systems
- 1.3 Invariants of Molecular or Fragment Structure
- 1.3.1 Internal Coordinates
- 1.3.2 Distance Geometry
- 1.4 External or Internal Coordinates?
- 1.4.1 Superposition of Molecules
- 1.4.2 Configuration Space
- 1.4.3 Deformation Coordinates and Reference Structures
- 1.4.4 Linear Transformations in Configuration Space
- 2 Symmetry Aspects of Structure Correlation
- 2.1 Introduction
- 2.2 Permutation Groups and Point Group Symmetries
- 2.3 Symmetry Coordinates, a Simple Example and some Generalizations Related to Point Group Symmetry
- 2.4 Symmetry Aspects of Specific Types of Molecule
- 2.4.1 Tetrahedral MX4, Molecules and Degenerate Irreducible Representations
- 2.4.2 MX5 Molecules
- 2.4.3 MX6 Molecules
- 2.4.4 Out-of-Plane Deformations of Five-Membered Rings
- 2.4.5 Out-of-Plane Deformations of Six-Membered Rings
- 2.5 Configuration Spaces for Molecules with Several Symmetrical Reference Structures
- 2.6 Internal Rotation in Non-Rigid Molecules
- 2.6.1 Ethane, One Internal Rotational Degree of Freedom
- 2.6.2 Simplified Symmetry Analysis of Conformationally Flexible Molecules
- 2.6.3 Two Internal Rotational Degrees of Freedom
- 2.6.4 Three Internal Rotational Degrees of Freedom
- 2.6.5 Four Internal Degrees of Freedom: Tetraphenylmethane and Cognate Molecules
- 2.7 Summary
- 3 Crystallographic Databases: Search and Retrieval of Information from the Cambridge Structural Database
- 3.1 Introduction
- 3.2 Crystallographic Databases
- 3.2.1 Overview
- 3.2.2 The Metals Crystallographic Data File (MCDF)
- 3.2.3 The Inorganic Crystal Structure Database (ICSD)
- 3.2.4 The Cambridge Structural Database (CSD)
- 3.2.5 The Protein Data Bank (PDB)
- 3.2.6 Areas of Structural Overlap
- 3.2.7 Data Acquisition and Data Integrity
- 3.3 Overview of the Cambridge Structural Database (CSD)
- 3.3.1 Coverage
- 3.3.2 The Reference Code System
- 3.3.3 Information Content
- 3.3.4 Checking and Evaluation
- 3.3.5 Registration and Archiving
- 3.3.6 Database Statistics
- 3.4 The CSD Software Systems
- 3.5 Bibliographic, Numerical, and Chemical Searching
- 3.5.1 The Query Language
- 3.5.2 Numerical Information Items
- 3.5.3 Text Information Items
- 3.5.4 Molecular Formula Information Items
- 3.5.5 2D Chemical Connectivity Information
- 3.5.6 Bit-encoded Information Items
- 3.5.7 Chemical Similarity Searching
- 3.5.8 Interactive Menu-driven Graphics
- 3.6 3D Searching and Geometry Tabulations
- 3.6.1 Overview of the GSTAT Program
- 3.6.2 Location of Fragments in GSTAT
- 3.6.3 Calculation of Fragment Geometry
- 3.6.4 Fragment Selection: the 3D Search Process
- 3.6.5 Tabulation of Fragment Geometry
- 3.6.6 The CSD Version 5 Upgrade
- 3.7 Special Considerations in Using the CSD System
- 3.7.1 The Reference Code System
- 3.7.2 Searches Using the SCREEN Command
- 3.7.3 Compound Name Searching
- 3.7.4 Chemical Connectivity Searching
- 3.7.4.1 Bond-Type Assignments
- 3.7.4.2 Treatment of Hydrogen Atoms
- 3.7.5 The Crystallographic Data
- 3.7.5.1 Accuracy and Precision
- 3.7.5.2 Disorder
- 3.7.5.3 Hydrogen Atoms
- 3.7.6 Geometric Searching
- 3.7.6.1 Bond Length Constraints
- 3.7.6.2 Torsion Angle Constraints: Stereochemical Searching
- 3.8 Conclusion
- 4 Statistical and Numerical Methods of Data Analysis
- 4.1 Introduction and Objectives
- 4.2 Choice of Parameters for Statistical Analysis
- 4.2.1 The Coordinate Basis
- 4.2.2 Internal Coordinate Axes
- 4.2.3 Internal Coordinates and Chemical Fragments
- 4.2.4 Internal Coordinates and Types of Analysis
- 4.2.4.1 Bond Length Studies
- 4.2.4.2 Studies of Coordination Geometry at Atomic Centres
- 4.2.4.3 Conformational Studies
- 4.2.4.4 Studies of Hydrogen Bonding
- 4.3 Sources of Variation in Crystallographic Structural Data
- 4.4 Mean Values and Other Simple Descriptive Statistics
- 4.4.1 Characteristics of Distributions
- 4.4.2 Means of Normal or Near-Normal Distributions
- 4.4.3 Dispersion
- 4.4.4 Departures from Normality
- 4.4.5 Estimates of Central Tendency for Non-Normal Distributions
- 4.5 Comparison of Distributions
- 4.5.1 Introduction
- 4.5.2 Significance of Differences between Means
- 4.5.3 Covariance, Correlation, and Regression
- 4.5.4 Comparison of Ratios
- 4.6 Multivariate Statistics
- 4.6.1 Introduction
- 4.6.2 Fragment Symmetry and Chirality
- 4.6.3 Principal Component Analysis (PCA)
- 4.6.3.1 An Asymmetrical Example: B-1'-Aminoribofuranosides
- 4.6.3.2 A Symmetrical Example: Conformations of Six-Membered Rings
- 4.6.3.3 Symmetrical Examples: Coordinate Geometries at Metal Centres
- 4.6.4 Methods Based on Dissimilarity Matrices
- 4.6.4.1 Introduction
- 4.6.4.2 Measures of Dissimilarity
- 4.6.4.3 Multidimensional Scaling
- 4.6.4.4 Cluster Analysis
- 4.6.4.5 Cluster Analysis of Symmetrical Fragments
- 4.6.4.6 Symmetry-Modified Clustering: An Example
- 4.6.5 Mean Geometries for Complete Fragments
- 4.6.5.1 Least-Squares Superposition Methods
- 4.6.5.2 Averaging Clusters: The Most Representative Fragment
- 4.6.6 Miscellaneous Graphical Methods
- 4.7 Statistical Software
- 4.8 Conclusion
- 5 Structure Correlation
- the Chemical Point of View
- 5.1 Introduction
- 5.2 Structural Probes of Reactivity, Non-Bonded Distances
- 5.3 Conceptual Framework: Energy Surfaces
- 5.3.1 Energy Minima, Force Constants and Structure Correlation
- 5.3.2 Energy Minima, Symmetry Force Constants and Structure Correlation
- 5.3.3 Reaction Profiles and Structure Correlation
- 5.4 The Principle of Structure-(Structure) Correlation
- 5.5 Structure-Energy Correlation
- 5.5.1 Equilibria in Crystals
- 5.5.2 Transition-State Theory and Free-Energy Relationships
- 5.5.3 Structural Reorganization in Degenerate Reactions
- 5.5.4 Structural Reorganization in Nondegenerate Reactions. Determination of Transition-State Structure
- 5.6 The Principle of Structure-Energy Correlation
- 5.7 Conclusions
- Part II Molecular Structure and Reactivity
- 6 Organic Addition and Elimination Reactions
- Transformation Paths of Carbonyl Derivatives
- 6.1 Introduction
- 6.2 Reaction Pathway for sp2 =sp3 Transformations of Carbonyls
- 6.2.1 Initial Stages of Nucleophilic Addition to a Carbonyl
- 6.2.1.1 Correlation of Partial Pyramidalization and the Incipient Bond Distance
- 6.2.1.2 Distribution of the Nu ... C = O Angle in Intra- and Intermolecular Contacts
- 6.2.2 Initial Stages of Spontaneous Hydrolysis of Acetals
- 6.2.2.1 Distortions from C2v Symmetry in Acetals: Correlation of the Antisymmetric Stretching and Bending Displacement Coordinates
- 6.2.2.2 Structural Expression of the Anomeric Effect in Acetals
- Correlation of the O-C-O Angle and Dd
- 6.2.2.3 Inorganic Models
- 6.2.2.3.1 Ligand Addition to the BO3 Group: Correlation of Partial Pyramidalization and the Incipient Bond Distance
- 6.2.2.3.2 Ligand Elimination from the Tetrahedral XY4 Species: Bond Length and Valence Angle Correlations
- 6.3 Reaction Pathway for sp2 = sp Transformations of Carbonyls
- 6.3.1 Initial Stages of Nucleophilic Addition to sp Centers
- 6.3.2 Initial Stages of Spontaneous Cleavage of Ketene Acetal-Like Fragments
- 6.3.2.1 Bond Length and Valence Angle Correlations in Sydnones and Enamines
- 6.3.2.2 Bond Length and Valence Angle Correlations in Ester Enolates
- 6.3.3 Initial Stages of Spontaneous Cleavage of Carbonyl Derivatives to Acylium Ion
- 6.3.3.1 Valence Angle Correlations in Lactones and Lactams
- 6.3.3.2 Bond Length and Valence Angle Correlations in RC(=O)X Derivatives
- 6.3.4 Reaction Path for Elimination
- 6.4 Computational Investigations of Reaction Pathways for Carbonyl Additions and Eliminations and Related Reactions
- 6.4.1 Formaldehyde
- 6.4.1.1 Anionic Nucleophiles
- 6.4.1.2 Neutral Nucleophiles
- 6.4.1.3 Metal Hydrides and Organometallics
- 6.4.2 Acetaldehyde and Homologs
- 6.4.3 Acetone and Homologs
- 6.4.4 Carboxylic Acid Derivatives
- 6.4.5 Solvent Effects
- 6.5 Reaction Pathways and Chemistry of Carbonyls
- 6.5.1 Theoretical Elaborations of the "Rearside" Attack Model: Baldwin's and Liotta-Burgess' Trajectory Analyses
- 6.5.2 Consequences of Directionality of Nucleophilic Addition to Carbonyls
- 6.5.2.1 Directionality and Regioselection in Nucleophilic Addition to Dicarbonyl Compounds
- 6.5.2.2 Directionality and Diastereofacial Selection in Nucleophilic Addition to Aldehydes and Ketones
- 6.5.2.3 Directionality and Rate of Intramolecular Reactions of Nucleophilic Addition to Carbonyls
- 6.5.3 Ground State Geometry of Carbonyl and Related Compounds and Reactivity
- 6.5.3.1 Valence Angle vs. Bond Length Correlations and Reactivity of Acyl Derivatives towards Elimination
- 6.5.3.2 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
- 6.5.3.3 Partial Pyramidalization and Intrinsic Face Preference in Diastereofacial Selection
- 6.6 Concluding Remarks
- 7 Reaction Paths for Nucleophilic Substitution(SN2)Reactions
- 7.1 Introduction
- 7.2 The XCdS3Y-Fragment
- 7.3 Tin Compounds with Coordination Numbers Four to Six
- 7.3.1 The XSnC3Y Fragment
- 7.3.2 The X2SnC2Y2 Fragment
- 7.3.3 Analogies with Pb(IV)
- 7.4 Silicon Compounds with Coordination Numbers Four and Five
- 7.4.1 The OSiC3X Fragment
- 7.4.2 Influence of Peripheral Substituents
- 7.4.3 Analogies between Si and Ge, the XGeR3Y Fragment
- 7.4.4 Silatranes, the NSiO3X Fragment
- 7.4.5 Germatranes, the NGeO3X Fragment
- 7.4.6 Inversion versus Retention of Configuration at Si
- 7.5 Nucleophilic Substitution at First Row Atoms
- 7.5.1 An Alatrane and a Boratrane
- 7.5.2 Carbon, the XCR3Y Fragment
- 7.6 Conclusions
- 8 Ligand Rearrangement and Substitution Reactions of Transition Metal Complexes
- 8.1 Introduction
- 8.2 Reaction Paths of MLn Coordination Complexes
- 8.2.1 ML3 Complexes
- 8.2.2 ML4 Complexes
- 8.2.2.1 Polyhedral Isomerization
- 8.2.2.2 Conformational Interconversions in Metal-Phosphine Complexes
- 8.2.3 ML5 Complexes
- 8.2.3.1 Associative Ligand Substitution Reactions and the Berry Rearrangement
- 8.2.3.2 More Sophisticated Methods of Analysis
- 8.2.3.3 Comparison of Structural Results with a Point-Charge Model
- 8.2.3.4 Retrospective Comments
- 8.2.4 ML6 Complexes
- 8.2.5 MLn Complexes, n&6
- 8.3 Discriminating Between Reaction Mechanisms: Metal Cluster Rearrangements
- 8.4 Reactions of Organometallic Compounds
- 8.4.1 Ring-Whizzing Reactions
- 8.4.2 Agostic Interactions as Precursors to H-Transfer Reactions
- 8.4.3 Carbonyl Transfer Reactions
- 8.4.4 Substitution Reactions at Sn(IV)
- 8.5 Beyond Geometry: Empirical Potential Energy Surfaces?
- 8.5.1 The Case of Cu(II) Complexes: Problems and Possibilities
- 8.5.1.1 Cu(II)L5 Complexes
- 8.5.1.2 Cu(II)L6 Complexes
- 8.5.2 "Pseudorotation" in Co(ethylenediamine) Chelate Rings
- 8.5.3 Ring Inversion in Metallacyclopentenes
- 8.6 Concluding Remarks
- 9 Conformational Analysis
- 9.1 Conformational Analysis
- 9.1.1 Introduction
- 9.1.2 Description of Local Conformations
- 9.2 Conformational Analysis of Single Molecules
- 9.2.1 Is the Conformation of Tetraalkyldiphosphines Caused by Stereoelectronic Influence?
- 9.2.2 Conformation and Chemical Reactivity
- 9.2.3 Chair-Boat Interconversion of Six-Membered Rings in the Solid
- 9.3 Conformational Analysis of Multiple Molecular Fragments
- 9.3.1 Low Energy Conformations of Macrocyclic Ring Systems
- 9.3.2 Conformational Analysis of Carboxylic Esters and Amides
- 9.3.3 Conformational Studies of the Methoxyphenyl Group
- 9.3.4 Conformation and Pseudorotation of Five-Membered Rings
- 9.3.5 Conformational Analysis of Cyclopentenones
- 9.4 Space Groups as a Tool to Visualize Conformational Variation
- 9.4.1 Two Torsion Angles
- 9.4.2 Three Torsion Angles
- 9.4.3 Four and More Torsion Angles
- Part III Crystal Packing
- 10 Bond-Length - Bond-Valence Relationships in Inorganic Solids
- 10.1 Introduction
- 10.2 Bond-Length - Bond-Valence Correlations
- 10.2.1 The Correlation between Bond Length and Bond Valence
- 10.2.2 The Distortion Theorem
- 10.2.3 Applications of the Bond-Length - Bond-Valence Correlations
- 10.3 Bond Networks and the Network Theorems
- 10.3.1 The Bond Network as a Directed Bipartite Graph
- 10.3.2 The Network Equations
- 10.3.3 Non-Bipartite Graphs
- 10.3.4 The Physical Significance of Bond Valences
- 10.4 Bonding between Fragments - Principles of Structure Organization
- 10.5 Influence of the Environment on the Structure of a Fragment
- 10.5.1 The Decomposition of an Inorganic Structure into Fragments
- 10.5.2 External Bonding of Fragments
- 10.5.3 Internal Structure of Fragments
- 10.6 Failure of the Network Equations
- 10.6.1 Distortions Caused by Electronic Effects
- 10.6.2 Distortions Caused by Spatial Constraints
- 10.7 Conclusion
- Appendix 10I . Refcodes Used
- Appendix 10II . Symbols Used
- 11 The Role of Hydrogen Bonding in Molecular Assemblies
- 11.1 Introduction and Scope
- 11.2 What Shall We Call a Hydrogen Bond?
- 11.3 Electron Density Mapping of Hydrogen-Bonded Molecules
- 11.4 Role Played by C-H ... O and C- H ... N Interactions in Molecular Packing
- 11.4.1 Introduction
- 11.4.2 C(sp) - H ... O Interactions
- 11.4.3 C(sp)2 - H ... O Interactions
- 11.4.4 C(sp)3 - H ... O Contacts
- 11.4.5 Miscellaneous and Summary
- 11.5 Proton Disorder in Hydrogen-Bonded Systems
- 11.5.1 Ice and Other Structures with Disordered Hydrogen Bonds
- 11.5.2 Order-Disorder (O/D) of the Carboxyl Dimer and Proton Transfer
- 11.6 Prediction and Generation of Crystal Structures
- 11.7 Characterizing the Geometry and Patterns of Hydrogen Bonds
- 11.8 Packing Motifs of Commonly Occurring Hydrogen-Bonding Groups
- 11.8.1 Hydrogen-Bonding Arrangements of Molecules ROH
- 11.8.2 Carboxylic Acids
- 11.8.2.1 The Catemer Motif
- 11.8.2.2 The Carboxylic Acid Cyclic Dimer Motif
- 11.8.2.3 Lone-Pair Directionality of O - H ... O (Carboxyl) Bonds
- 11.8.3 Primary and Secondary Amides
- 11.8.3.1 Secondary Amides
- 11.8.3.2 The Glide or Twofold Screw Relation
- 11.8.3.3 The Translation Motif
- 11.8.3.4 Hydrogen Bonding between Molecular Chains
- 11.8.3.5 Primary Amides
- 11.8.3.6 Stacking of Amide Cyclic Dimers
- 11.8.4 a-Amino Acids
- 11.8.5 Hydrogen Bonding in Phospholipids
- 11.8.6 Acids and Amides with Attached Hydrogen-Bonding Groups
- 11.9 Co-Crystals
- 11.9.1 Introduction
- 11.9.2 Selection and Complementarity in the Formation of Co-Crystals
- 11.9.3 Hydrates
- 11.9.4 Purines and Pyrimidines
- 11.9.5 Co-Crystals of Carboxylic Acids and Amides
- 11.9.6 Host/Guest Hydrogen-Bonded Complexes
- 11.9.7 Crystals Based on Intrinsic Hydrogen-Bonding Characteristics (Lacking Preorganization)
- 11.9.8 Co-Crystals as Agents for Materials Design
- 11.10 The Role of Hydrogen-Bonding at Crystal Interfaces
- 11.10.1 Growth of Crystals in the Presence of Taylor-Made Auxiliaries
- 11.10.2 The Effect of Solvent on Crystal Growth
- 11.10.3 Taylor-Made Auxiliaries as Crystal Growth Promoters
- 11.11 Concluding Remarks
- 12 Molecular Packing and Correlations between Molecular and Crystal Properties
- 12.1 Introduction
- 12.2 Representation and Properties of a Molecule
- 12.2.1 Atomic Designators
- 12.2.2 Hydrogen Atoms
- 12.2.3 Derived Molecular Properties
- 12.2.3.1 Size
- 12.2.3.2 Stoichiometry
- 12.2.3.3 Electron Distribution
- 12.2.3.4 Molecular Shape
- 12.3 Representation and Properties of a Crystal
- 12.3.1 Data Retrieval and Geometrical Model
- 12.3.2 Crystal Energy
- 12.3.2.1 Definitions
- 12.3.2.2 The Packing Energy and its Interpretation
- 12.3.2.3 Energy Partitioning
- 12.3.2.4 Energy and the Molecular Coordination Sphere
- 12.3.3 Libration Energy Profiles
- 12.3.4 Physical Properties of the Crystal
- 12.4 Correlation between Molecular and Crystal Properties
- 12.4.1 Databases for Non-Hydrogen Bonded Crystals
- 12.4.2 Hydrocarbons (Satured and Unsaturated)
- 12.4.2.1 Aromatic Hydrocarbons
- 12.4.2.2 Oxygen or Nitrogen Substitution
- 12.4.2.3 Mutual Orientation of Carbonyl Dipoles or Benzene Rings
- 12.4.2.4 Directional Forces Other than H-Bonds
- 12.4.3 Distances between Molecules and Molecular Coordination Sphere
- 12.4.4 Joint Results from the three Databases
- 12.5 From Molecular to Crystal Structure
- 12.5.1 Distribution over Space Groups
- 12.5.2 Generation of Crystal Structures
- 12.5.2.1 Method
- 12.5.2.2 Choosing the Right Structure
- 12.5.3 Polymorphism
- 12.6 Conclusion and Outlook
- Appendix 12-I Formulas and Transformations
- Appendix 12-II Summary of Symbols
- Part IV Proteins and Nucleic Acids
- 13 Structure Correlation and Ligand/Receptor Interactions
- 13.1 Factors Determining the Mutual Recognition and the Energetic Aspects of Ligand/Receptor Binding
- 13.1.1 Structural Complementarity and Energy Balance in Ligand/Receptor Binding
- 13.1.2 Enthalpic Contributions
- 13.1.3 Entropic Contributions
- 13.1.4 Structural Systematics in Ligand/Protein Interaction and Mapping the Environmental Characteristics of Functional Groups
- 13.2 Structure Correlation to Analyze and Predict Biologically Active Conformations of Small Molecule Ligands
- 13.2.1 The Binding of Retinol to Retinol-Binding Protein
- 13.2.2 The Binding of Citric Acid to Citrate Synthase
- 13.2.3 Conformation of Guanosine and Adenosine Phosphates in Small- Molecule and Ligand/Protein Crystal Structures
- 13.2.4 The Binding of Creatine to Creatinase
- 13.2.5 Conclusions and Predictions
- 13.3 Structure Correlation to Describe Elementary Steps in Enzyme Reactions and Differences in Ligand Binding Geometry
- 13.3.1 Nucleophilic Addition and Amide Bond Fission in Creatinase
- 13.3.2 Nucleophilic Substitution at Phosphorus in Ribonuclease
- 13.3.3 Expansion of Coordination and Change of Electronic State at Iron in Cytochrome P45Ocam
- 13.4 Conclusion and Outlook
- 14 Steroid Molecular Structure, Protein Interaction and Biological Function
- 14.1 Introduction
- 14.2 Steroid Conformation Analysis
- 14.2.1 The 17 B Side Chain
- 14.2.2 A-Ring Conformation in 4-ene-3-one Derivatives
- 14.3 Steroid Structure, Receptor Binding and Hormone Action
- 14.3.1 Estrogen Receptor Binding and Activity
- 14.3.2 Progesterone Receptor Binding and Activity
- 14.3.3 Corticoid Receptor Binding and Activity
- 14.3.4 Androgen Receptor Binding and Activity
- 14.4 Steroid-Protein Interactions and Binding
- 14.4.1 Steroid-Binding Enzymes
- 14.4.2 Steroid-Binding Proteins
- 14.4.3 Receptor Structure and Steroid Function
- 14.5 Summary
- 15 Structural Patterns in Globular Proteins
- 15.1 Introduction
- 15.2 Atomic Interactions
- 15.3 Backbone Patterns
- 15.3.1 Helices
- 15.3.2 B Strands
- 15.3.3 B Turns
- 15.3.4 Additional Loop Patterns
- 15.4 Motifs
- 15.4.1 Helical Motifs
- 15.4.1.1 Accessibility Lost on Complex Formation
- 15.4.1.2 Motifs where the Helices are Perpendicular
- 15.4.1.3 Tertiary Motifs
- 15.4.2 B-Sheet Motifs
- 15.4.2.1 Two-Stranded Motifs
- 15.4.2.2 Three-Stranded Motifs
- 15.4.2.3 Four-Stranded Motifs
- 15.4.2.4 Tertiary B-Sheet Structures
- 15.5 Conclusion
- 16 Structural Correlations in Families of Homologous Proteins
- 16.1 Introduction
- 16.2 Techniques for Comparison of Protein Structures
- 16.3 Comparative Analyses of Homologue Structures
- 16.4 Sequence Substitution Tables
- 16.4.1 The Solvent Inaccessible Core and Main-Chain Conformation
- 16.4.2 The Role of Side-Chain Hydrogen Bonds
- 16.5 Conclusions
- 17 On the Correlation of Protein Structure with Local Sequence Patterns
- 17.1 Introduction
- 17.1.1 Protein Sequences and Structures
- 17.1.2 Protein Folding
- 17.2 Small Peptides and Protein Structure
- 17.2.1 Database of Short Peptides Derived from Protein Structures
- 17.2.2 Classification of Hexapeptide Folds
- 17.2.3 Predictability of Hexapeptide Folds
- 17.3 Conclusion
- 18 Structural Patterns in Nucleic Acids
- 18.1 Introduction
- 18.2 Right-Handed and Left-Handed Double Helices
- 18.3 Variations in the Duplex Geometry
- 18.3.1 The Correlations between Backbone Torsion Angle d and Glycosidic Torsion Angle ? in A-, B, and Z-DNA
- 18.3.2 Influence of the Sequence on the Conformation of B-DNA
- 18.3.3 Other Correlations
- 18.3.4 Variations in the Conformation of Z-DNA
- 18.3.5 Structure of DNA Duplexes with Mismatched Base Pairs
- 18.4 Binding of Drug Molecules to the Minor Groove of B-DNA
- 18.5 DNA Intercalation
- 18.5.1 Conformational Changes in the Sugar-Phosphate Backbone
- 18.5.2 Parallel and Perpendicular Intercalators, DNA Unwinding. and Sequence Specificity of Intercalation
- 18.6 Interactions between Nucleic Acids and Proteins
- 18.6.1 Sequence-Specific Recognition of Double Helical Nucleic Acids
- 18.6.2 Architecture of DNA-binding Domains in Proteins
- 18.6.3 Protein-RNA Interactions
- 18.7 Conclusions and Future Prospects
- Appendices
- Appendix A
- A.1 Introduction
- A.2 Methodology
- A.2.1 Classification of Bonds
- A.2.2 Statistics
- A.3 Contents and Arrangement of Tables of Interatomic Distances
- A.3.1 The "Bond" Column
- A.3.2 Definition of "Substructure"
- A.3.3 Use of the "Note" Column
- A.3.4 Locating an Entry in Table A.2
- A.4 Discussion
- Appendix B Short Format References to Crystal Structures Cited in this Book
- Appendix C Tables of the Common Amino Acids, Purine and Pyrimidine Bases
- Illustration Acknowledgements
- Index
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