计算机化学与分子设计

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 Differential 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 Differential
Equations of Order 1
Problems
2 Minimization
2.1 One-dimensional Minimization
2.1.1 Golden Section Search
2.1.2 Parabolic Interpolation： Brents Method
2.2 Multidimensional Minimization
2.2.1 Downhill Simplex （Nelder et Mead, 1965）
2.2.2 Direction Set Method （Powells Method）
2.2.3 Conjugate Directions
2.2.4 Powells 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 SchrSdinger Equation
3.2 Haxtree-Fock Theory
3.3 Post-SCF Methods
3.3.1 Configuration 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 Hiickel 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 Defined Terms
10.2.2 Number of Rings in SSSR
10.3 Zamoras Algorithm
10.4 Elimination Technique
Problems
11 Constitutional Equivalence
11.1 Morgan Algorithm
11.2 Munk Algorithm
11.3 Riicker Algorithm
11.4 Varmuza Algorithm
11.5 Fans Method
11.6 Application to Canonical Numbering
Problem
12 Molecular Relative Symmetry
12.1 Relative Symmetry
12.2 Determination of Dissimilarity
12.3 Calculations
12.4 Examples
12.5 Application Examples： Empirical Rules
Problem
13 Isomorphism and 3D CSS Searches
13.1 Ullmans Algorithm
13.2 Crandell and Smiths Algorithm
13.3 Clique-Detection Algorithm
13.4 Lesks Algorithm
13.5 Set-Reduction Algorithm
Problems
14 Chemical Information Management and Exploration
14.1 Concept
14.2 Source of Chemical Information
14.3 Management of Chemical Information
14.4 Data Mining and Spectral Simulation
Problems
15 Molecular Similarity and Diversity
15.1 Approaches on Molecular Similarity and Diversity
15.2 Selection, Classification and Validation Methods
15.3 Comparative Analysis of Approaches/Descriptors-Models Comparison
15.4 Applications in Chemo- and Bio- Informatics
Problems
16 Artificial 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
17.2 Back-Propagation Learning Algorithm
17.3 Radial Basis Function Networks
Problems
18 Hopfield Network
18.1 Modeling
18.2 Application to Optimization Procedures
18.3 Boltzmann Machine
Problems
19 Kohonen Network
19.1 Structure of SOM
19.2 The Learning Process
19.3 Examples and Applications
Problem
20 Genetic Algorithms and Their Applications in Chemistry
20.1 Optimization and Techniques
20.2 Simple Genetic Algorithm
20.3 Mathematical Fundamental
20.4 Application of SGA to QSAR Problem
20.5 Other Application of GA to Chemistry Problems
Problems
21 Support Vector Machine （SVM）
21.1 SVM in Classification
21.2 Regression SVM
21.3 Applications
Problems