Front Matter
 1 Numeric Analysis
  1.1 Linear Algebraic Equations and Matrix.
   1.1.1 Square Matrix
   1.1.2 Elementary Operations on Matrices
   1.1.3 Inverse Matrices
  1.2 Di®erential Equations
   1.2.1 Cauchy Problem
   1.2.2 Discrete One-Step Methods for Equations of First Order Principles
   1.2.3 Discrete Methods with Multiple Steps for Di®erential Equations of Order
  Problems
 2 Minimization
  2.1 One-dimensional Minimization
   2.1.1 Golden Section Search
   2.1.2 Parabolic Interpolation: Brent's Method
  2.2 Multidimensional Minimization
   2.2.1 Downhill Simplex (Nelder et Mead, 1965)
   2.2.2 Direction Set Method (Powell's Method)
   2.2.3 Conjugate Directions
   2.2.4 Powell's Quadratically Convergent Method: Find N Conjugate Directions
   2.2.5 Gradient and the Steepest Descent Method.
   2.2.6 Newton-Raphson Method
  Problems
 3 Ab Initio
  3.1 SchrÄodinger Equation
  3.2 Hartree-Fock Theory
  3.3 Post-SCF Methods
   3.3.1 Con¯guration Interaction
   3.3.2 Moller-Plesset Perturbation Theory
  3.4 Gaussian
   3.4.1 Capabilities
   3.4.2 Overview of Geometry Optimizations
   3.4.3 Model Chemistries
   3.4.4 Basis Sets
   3.4.5 Limitations
  3.5 Example of Applications
  Problem
 4 Density Functional Theory and Applications
  4.1 Theoretical Aspects
   4.1.1 Hohenberg-Kohn Theorems
   4.1.2 Kohn-Sham Theory
   4.1.3 Exchange-Correlation Functionals
  4.2 Comparison with Traditional Ab Initio Methods
  4.3 Applications
   4.3.1 Atoms
   4.3.2 Clusters.
   4.3.3 Carbonyl Complexes
   4.3.4 Other Applications.
  Problems
 5 Semi-Empirical Models
  5.1 Extended HÄuckel Theory (EHT)
  5.2 CNDO Method
  5.3 INDO Method
  5.4 MINDO Method
  5.5 MNDO Method
  5.6 AM1 and PM3 Methods
  5.7 Example of Applications
   5.7.1 Proposed Problem
   5.7.2 Calculations
   5.7.3 Conclusion
 6 Molecular Mechanics
  6.1 Stereochemistry
   6.1.1 Constitution Isomers and Tautomers
   6.1.2 Stereoisomers
  6.2 Principle of Molecular Mechanics
  6.3 Mathematical Expressions of Energy Terms
   6.3.1 Bond Stretching Energy
   6.3.2 Angle Bending Energy
   6.3.3 Torsion Energy
   6.3.4 Improper Torsions and Out-of-plane Bending Motions
   6.3.5 Cross Terms: Class 1, 2 and 3 Force Fields
   6.3.6 Energy of Non-binding Interactions
  6.4 Force Fields
   6.4.1 Parameterization Methods
   6.4.2 SYBYL and TRIPOS Force Field
   6.4.3 KOLLMAN Force Field
   6.4.4 JUMNA and FLEX Force Field
  6.5 Application Example
   6.5.1 Problem to be Solved
  Problems
 7 Molecular Dynamics
  7.1 Molecular Dynamics with Simple Models
  7.2 Molecular Dynamics with Continuous Potentials
  7.3 Verlet Algorithm.
  7.4 Variations of Verlet Algorithm
  7.5 Predictor-Corrector Integration Methods
  7.6 Choosing the Time Step
  7.7 Multiple Time Step Dynamics
  7.8 Constraint Dynamics
  7.9 Steps of Molecular Dynamics Simulation
  7.10 Time-dependent Properties
  7.11 Example of Applications
  Problems
 8 Monte Carlo and Conformational Analysis
  8.1 Monte Carlo
   8.1.1 Calculations of Properties
   8.1.2 Theory of Metropolis MC(MMC)
   8.1.3 Implementation of MMC.
   8.1.4 Simulation of Molecules
  8.2 Conformational Analysis
   8.2.1 Conformational Search
   8.2.2 Model-building Approaches
   8.2.3 Random Search Methods.
   8.2.4 Distance Geometry
   8.2.5 Other Approaches
  Problems
 9 Molecular Graph and Presentation
  9.1 Generality in Molecular Graph
  9.2 Molecular Description
   9.2.1 Computer Representation of Two-dimensional Chemical Structures
   9.2.2 Connection Table
  9.3 Sub-Structures and FREL
   9.3.1 Extraction of FREL
   9.3.2 Correlation of FREL with Properties
  9.4 Canonical Numbering
  9.5 Three-dimensional Representation of Molecular Structures
  9.6 XML Representation
   9.6.1 Principles of XML
   9.6.2 XML for Structuring the Information
  Problem
 10 Ring Perception
  10.1 Graphs and Searching Methods
   10.1.1 Graphs and Molecular Graphs
   10.1.2 Depth-First Search
   10.1.3 Breadth-First Search
  10.2 Complete Ring Systems
   10.2.1 De¯ned Terms
   10.2.2 Number of Rings in SSSR
  10.3 Zamora's Algorithm
  10.4 Elimination Technique
  Problems
 11 Constitutional Equivalence
  11.1 Morgan Algorithm
  11.2 Munk Algorithm
  11.3 RÄucker Algorithm
  11.4 Varmuza Algorithm
  11.5 Fan's Method
  11.6 Application to Canonical Numbering
  Problem
 12 Molecular Relative Symmetry
  12.1 Relative Symmetry
  12.2 Determination of Dissimilarity
   12.2.1 Atom Focus
   12.2.2 Bond Focus
  12.3 Calculations
  12.4 Examples
  12.5 Application Examples: Empirical Rules
   12.5.1 Empirical Rules for Gem Methyl Groups Adjacent to a sp2 Carbon Site
   12.5.2 Empirical Rules for Gem Methyl Groups Borne by a sp3 Atom
  Problem
 13 Isomorphism and 3D CSS Searches
  13.1 Ullman's Algorithm
  13.2 Crandell and Smith's Algorithm
  13.3 Clique-Detection Algorithm
  13.4 Lesk's Algorithm
  13.5 Set-Reduction Algorithm
  Problems
 14 Chemical Information Management and Exploration
  14.1 Concept
  14.2 Source of Chemical Information
   14.2.1 Chemical Abstracts (CA) File
   14.2.2 SCI Search
   14.2.3 Chinese Scienti¯c Citation Database (CSCD).
   14.2.4 Science China Database (SCD)
   14.2.5 SpecInfo
   14.2.6 CrossFire
   14.2.7 Cambridge Structural Database (CSD)
  14.3 Management of Chemical Information
   14.3.1 Principle
   14.3.2 Representation of Chemical Structure
   14.3.3 Chemical Structure Searching
   14.3.4 Examples
  14.4 Data Mining and Spectral Simulation
   14.4.1 Data Mining
   14.4.2 Application: IR/Raman Simulation
   14.4.3 Application: Mass Spectra Simulation
  Problems
 15 Molecular Similarity and Diversity
  15.1 Approaches on Molecular Similarity and Diversity
   15.1.1 Components of the Molecular Similarity
   15.1.2 The Similarity Paradox
   15.1.3 Similarity/Diversity Approaches in Chemoinformatics
  15.2 Selection, Classi¯cation and Validation Methods.
   15.2.1 Classi¯cation Methods
   15.2.2 Selection Methods
   15.2.3 Validation Methods
  15.3 Comparative Analysis of Approaches/Descriptors-Models Comparison
   15.3.1 Comparison of Similarity Coe±cients
   15.3.2 Choice of Descriptors
   15.3.3 Comparison and Selection of Descriptors
  15.4 Applications in Chemo- and Bio- Informatics
   15.4.1 Combinatorial Chemistry, Chemical Libraries
   15.4.2 Drug Design and Medicinal Chemistry
   15.4.3 Synthesis Chemistry, Organic Chemistry and Catalyst
   15.4.4 Bioinformatics
  Problems
 16 Arti¯cial Neural Networks: Biological Fundamental and Modeling
  16.1 Introduction
  16.2 Biological Fundamental
  16.3 Modeling.
  16.4 Structure of Connections
  Problems
 17 Layered Network
  17.1 Mono-Layered Associative Network.
   17.1.1 Perceptron
   17.1.2 Linear Separation
   17.1.3 Limitations
   17.1.4 Widrow-Ho® Rule
  17.2 Back-Propagation Learning Algorithm.
   17.2.1 Example: Prediction of 13C-NMR Shifts for Methyl Substituted Cyclohexanes
  17.3 Radial Basis Function Networks
   17.3.1 Theory
   17.3.2 Training Algorithms
   17.3.3 Algorithms for the Radial Basis Functions Selection
   17.3.4 Design of Training Data Set for the Calibration
   Problem
   17.3.5 Example of Applications
  Problems
 18 Hop¯eld Network
  18.1 Modeling.
   18.1.1 Network Completely Connected
   18.1.2 Leaning Process in a Hop¯eld Network
   18.1.3 Stability of States
  18.2 Application to Optimization Procedures
   18.2.1 Energy of Hop¯eld Network
   18.2.2 Traveling Salesman Problem (TSP)
   18.2.3 3D Structural Recognition
  18.3 Boltzmann Machine
  Problems
 19 Kohonen Network
  19.1 Structure of SOM
  19.2 The Learning Process
   19.2.1 Initialization
   19.2.2 Training
   19.2.3 Variants
  19.3 Examples and Applications
   19.3.1 Mapping the 3D Sphere Surface onto a SOM Plane
   19.3.2 Application to Visual Classi¯cation of Gas Chromatographic Liquid Phase
  Problem
 20 Genetic Algorithms and Their Applications in Chemistry
  20.1 Optimization and Techniques
  20.2 Simple Genetic Algorithm
   20.2.1 Population and Coding
   20.2.2 Fitness Function
   20.2.3 Operators
  20.3 Mathematical Fundamental
  20.4 Application of SGA to QSAR Problem
  20.5 Other Application of GA to Chemistry Problems
   20.5.1 Conformational Searching
   20.5.2 Other Applications
  Problems
 21 Support Vector Machine (SVM)
  21.1 SVM in Classi¯cation
   21.1.1 Basic Principle
   21.1.2 Some Applications
  21.2 Regression SVM
   21.2.1 Basic Principle
   21.2.2 Further Developments
  21.3 Applications
  Problems
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