Shape in chemistry : an introduction to molecular shape and topology

'Shape in Chemistry' looks at molecular shape from a unique perspective: It introduces the reader to the topological concepts and methods of precise shape characterization that are applicable for direct, non-visual description and analysis of general molecular shapes. The author provides a pictorial introduction to all the topological tools necessary for the subjects discussed. Mathematical description is also provided at an easily comprehensible level. New concepts are introduced beginning at the familiar level of stereochemistry and lead on to more advanced topological shape analysis methods. The structure of the book reflects the author's desire to bring the reader to an early appreciation of the power of topology in chemistry. After a brief review of the quantum chemical concept, the author compares the merits of visual, computer graphics methods and nonvisual, algorithmic shape analysis methods. The book ends with the concepts of approximate symmetry and various generalizations of symmetry. 'Shape in Chemistry' is surely destined to become standard reading in the field. It presents a valuable addition to the literature on shape and modeling of molecules for non-specialists organic, physical and medical chemists, researchers in various aspects of QSAR and pharmacological drug design and advanced undergraduate and graduate students. 1. The Intuitive Concept Of Molecular Shape. 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. 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. 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. 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. 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. 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. 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. 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. Paul G. Mezey. Includes Bibliographical References (p. 203-218) And Index. This textbook contains developments in computational chemistry and molecular modelling on computers. Special attention is given to topological methods suitable for the study of both the highly detailed and the crude, large-scale shape features of molecular systems.