Shape in Chemistry: An Introduction to Molecular Shape and Topology Book

	Introduction	1
1	The Intuitive Concept of Molecular Shape	10
1.1	Shape in Stereochemistry
1.2	Chirality and Molecular Shape
1.3	Point Symmetry Groups and Framework Groups
1.4	Dynamic Shape Properties: Conformational Freedom and Electronic Excitation
2	The Quantum Chemical Concept of Molecular Shape	21
2.1	Electron Distributions and Nuclear Distributions: The Heisenberg Uncertainty Relation and Molecular Shape
2.2	The Concept of Topological Shape of Molecules
2.3	Molecular Isodensity Contours (MIDCO's)
2.4	The Density Domain Approach (DDA) to Chemical Bonding
2.5	Functional Groups and their Shapes as Quantum Chemical Concepts: A Density Domain Criterion for Functional Groups
3	Applied Topology: The Mathematics of the Essential	49
3.1	Topology as "Rubber Geometry"
3.2	Some Basic Concepts of Topology
3.3	Some Relevant Aspects of Knot Theory
3.4	Geometrical Shape and Topological Shape
4	Molecular Bodies, Molecular Surfaces, and Their Topological Representations	82
4.1	Geometrical and Topological Models for Molecular Bodies and Contour Surfaces
4.2	Charge Density and Electrostatic Potential
4.3	Van der Waals Surfaces and Solvent Accessible Surfaces
4.4	Macromolecular Shape and Protein Folding
5	Topological Shape Groups, Shape Codes, Shape Graphs, Shape Matrices, and Shape Globes	96
5.1	Shape Domains of Contour Surfaces
5.2	The Shape Group Method (SGM) for the Analysis of Molecular Shapes
5.3	Shape Codes, Shape Graphs, and Shape Matrices
5.4	Shape Globe Invariance Maps (SGIM)
5.5	Shape Analysis of Fused Sphere Van der Waals Surfaces and Other Locally Nondifferentiable Molecular Surfaces
5.6	Dynamic Shape Analysis: Topological Principles
5.7	Chain Molecule Shape Graphs and Shape Polynomials
6	Molecular Similarity Measures and Molecular Complementary Measures; The Quantification of Molecular Similarity and Complementarity	137
6.1	Absolute and Relative Shape Analysis
6.2	Visual, Computer Graphics Methods for Similarity Assessment by Inspection
6.3	The Principles of Nonvisual, Algorithmic Similarity Analysis: Automated Similarity Assessment by Computer
6.4	The GSTE Principle: Geometrical Similarity as Topological Equivalence
6.5	Whispered Messages and Similarity Sequences
6.6	The Fundamentals of Resolution Based Similarity Measures (RBSM)
6.7	Molecular Similarity Measures and Chirality Measures Based on Resolution and Fuzzy Set Theory
6.8	Semi-Similarity Measures and Scaling-Nesting Similarity Measures (SNSM)
6.9	Molecular Similarity Measures Based on Shape Codes
6.10	Local Shape Codes and Local Similarity Measures
6.11	Molecular Shape Complementarity Measures
7	QShAR (Quantitative Shape-Activity Relations) in Drug Design and Molecular Engineering	175
7.1	Computer Screening of Molecular Sequences by Shape Code Comparison
7.2	Integrated Main and Side Effect Analysis by Shape Correlations
7.3	Shape-Driven Molecular Design and Molecular Engineering
7.4	A Summary of the Main Components of the QShAR Approach
8	Special Topics: Symmetry and Approximate Symmetry, Symmetry Deficiency Measures, Syntopy, and Symmorphy	188
8.1	Symmetry and Imperfect Symmetry
8.2	The Quantification of Approximate Symmetry: Symmetry Deficiency Measures
8.3	Syntopy and Syntopy Groups
8.4	Symmorphy and Symmorphy Groups
	Closing Remarks	202
	References	203
	Index	219